diff --git a/CalculateTPLikePropsFromSweep.html b/CalculateTPLikePropsFromSweep.html new file mode 100644 index 0000000000..c46305eed3 --- /dev/null +++ b/CalculateTPLikePropsFromSweep.html @@ -0,0 +1,369 @@ + + + + + + + + CalculateTPLikePropsFromSweep Algorithm — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+
+
+

CalculateTPLikePropsFromSweep Algorithm

+
+

Description

+

The CalculateTPLikePropsFromSweep() calculates square pulse properties +from a given sweep. It retrieves the associated setting values for the sweep and +returns the voltage difference, current difference and resistance for each +head stage. The function only works for current clamp mode.

+

The function is split into several parts:

+
+
+
+
+

Principle

+

The goal of the algorithm is to determine the steady state resistance of a +square pulse response. The available sweep data contains the excitation pulse as +well as the response pulse. The excitation pulse is in units of current and the +response is measured in voltage. The actual data consists of discrete points of +digital to analog output (excitation) and analog to digital input (response). +For simplicity this will be neglected in the following.

+

The square pulse DA data is used to find the leading and trailing edge of +the pulse. Therefore a level of 10% of the amplitude of the square pulse is defined +to find the location of signal crossing.

+
+\[level = minimum + (maximum - minimum) * 0.1\]
+

Using a edge finding algorithm the location of firstEdge and secondEdge +is retrieved.

+

For determination of the base line level in front of the pulse a +range is defined to average the points of the square pulse response. The full base +line fraction in front of a square pulse starts after the onSetDelay and ends +at firstEdge. The length of the range is defined as 10% of this distance. The +reference point is the end of this range and it is set close to firstEdge.

+
+\[\begin{split}right &= firstEdge - const \\ +left &= right - (firstEdge - onSetDelay) * 0.1\end{split}\]
+

The base line level is then determined by averaging over the data points p between +left and right.

+
+\[baselinelevel = \frac{1}{N} \sum^{right}_{n=left} p_n\]
+

For determination of the elevated level at the end of the active pulse a +range is defined to average the points of the square pulse response. The active +pulse starts after firstEdge and ends with secondEdge. The length of the +range is defined as 10% of this distance. The reference point is the end of this +range and it is set close to secondEdge.

+
+\[\begin{split}right &= secondEdge - const \\ +left &= right - (secondEdge - firstEdge) * 0.1\end{split}\]
+

The elevated level is then determined by averaging over the data points p between +left and right.

+
+\[elevatedlevel = \frac{1}{N} \sum^{right}_{n=left} p_n\]
+

The difference between elevated level and base line level is the voltage response +for the steady state.

+
+\[\Delta U = elevatedlevel - baselinelevel\]
+

To get the steady state resistance the current from the excitation amplitude of +the square pulse is required. It is retrieved the same way from the square pulse +excitation data as the voltage response from the square pulse response data. +The difference from the square pulse excitation data yields:

+
+\[\Delta I = elevatedlevel - baselinelevel\]
+

The steady state resistance is then:

+
+\[R_{SS} = \frac{\Delta U}{\Delta I}\]
+
+
+

Retrieving settings

+

The sweep number is retrieved, that allows to get the setting for this sweep. +Also the configuration wave for the sweep is retrieved, that is required to +extract the actual ADC and DAC data from the sweep.

+

The totalOnsetDelay is independent of the head stage and the sum of the auto and +user onset delay. The number of the ADC channel that are used per head stage +is read to wave ADCs. The same is done for the number of the DAC channel to the wave DACs. +The units per head stage are read from the saved settings to wave ADunit and +wave DAunit. If a head stage was active is read to the wave wave statusHS.

+
sweepNo     = ExtractSweepNumber(NameofWave(sweep))
+WAVE config = GetConfigWave(sweep)
+
+totalOnsetDelay = GetLastSettingIndep(numericalValues, sweepNo, "Delay onset auto", DATA_ACQUISITION_MODE) + \
+          GetLastSettingIndep(numericalValues, sweepNo, "Delay onset user", DATA_ACQUISITION_MODE)
+
+WAVE ADCs = GetLastSetting(numericalValues, sweepNo, "ADC", DATA_ACQUISITION_MODE)
+WAVE DACs = GetLastSetting(numericalValues, sweepNo, "DAC", DATA_ACQUISITION_MODE)
+
+WAVE/T ADunit = GetLastSetting(textualValues, sweepNo, "AD Unit", DATA_ACQUISITION_MODE)
+WAVE/T DAunit = GetLastSetting(textualValues, sweepNo, "DA Unit", DATA_ACQUISITION_MODE)
+
+WAVE statusHS = GetLastSetting(numericalValues, sweepNo, "Headstage Active", DATA_ACQUISITION_MODE)
+
+
+
+
+

Finding square pulse

+

The following is done for each head stage up to NUM_HEADSTAGES (default = 8):

+
+

If the head stage was not active, continue with next head stage.

+
if(!statusHS[i])
+  continue
+endif
+
+
+

With the number of the DAC channel of this head stage the column in the sweep +with the actual data read with AFH_GetDAQDataColumn() to DAcol. The +same is done for the column with the AD data to ADcol. With the columns the +actual data is read to wave DA and AD respectively with +ExtractOneDimDataFromSweep(). The coordinate in points of +totalOnsetDelay on the scale of DA is saved to onsetDelayPoint.

+
DAcol = AFH_GetDAQDataColumn(config, DACs[i], XOP_CHANNEL_TYPE_DAC)
+ADcol = AFH_GetDAQDataColumn(config, ADCs[i], XOP_CHANNEL_TYPE_ADC)
+
+WAVE DA = ExtractOneDimDataFromSweep(config, sweep, DACol)
+WAVE AD = ExtractOneDimDataFromSweep(config, sweep, ADcol)
+
+onsetDelayPoint = (totalOnsetDelay - DimOffset(DA, ROWS)) / DimDelta(DA, ROWS)
+
+
+

The scaled x coordinates of the full square pulse range including base line are +defined from totalOnsetDelay to the end of the DA wave and saved in +first and last.

+

A signal level is defined for finding the edges in the sent square pulse +(DA channel). The level is 10 % from the difference of maximum - minimum of the +DA data above the minimum level. With FindLevels up to two signal crossings +at the level are searched between first and last in wave DA and +their x position in points is saved to wave levels. The search runs from +lower to higher x coordinates. +An assertion checks if two (or more) signal crossings were found.

+
first = totalOnsetDelay
+last  = IndexToScale(DA, DimSize(DA, ROWS) - 1, ROWS)
+
+low  = WaveMin(DA, first, last)
+high = WaveMax(DA, first, last)
+
+level = low + 0.1 * (high - low)
+
+Make/FREE/D levels
+FindLevels/Q/P/DEST=levels/R=(first, last)/N=2 DA, level
+ASSERT(V_LevelsFound >= 2, "Could not find enough levels")
+
+
+

The first found location is saved to firstEdge and the second to +secondEdge. By default DA contains a pulse so the linear interpolation +between the points done by FindLevels results that firstEdge is found +at last_baseline_point + 0.1 and secondEdge at last_pulse_point + 0.9. The values +are truncated to integers to equal the last baseline point as well as the last +pulse point.

+
firstEdge   = trunc(levels[0])
+secondEdge  = trunc(levels[1])
+
+
+
+
+
+

Extraction of levels

+

The following is done for each head stage:

+
+

For determination of the base line the range is defined as 10 % of the +firstEdge location to totalOnsetDelay. The end point of the range is +firstEdge - 1. The baseline level is then defined as the average of all +AD points in this range.

+
high = firstEdge - 1
+low  = high - (firstEdge - onsetDelayPoint) * 0.1
+
+baseline = mean(AD, IndexToScale(AD, low, ROWS), IndexToScale(AD, high, ROWS))
+
+
+

The elevated range (steady state) is defined by 10 % of the firstEdge +location to secondEdge. The elevated level is then defined as the +average of all AD points in this range.

+
high = secondEdge - 1
+low  = high - (secondEdge - firstEdge) * 0.1
+
+elevated = mean(AD, IndexToScale(AD, low, ROWS), IndexToScale(AD, high, ROWS))
+
+
+

An assertion checks if the ADunit of this head stage is “mV” as this function +only works for I-clamp mode.

+
ASSERT(!cmpstr(ADunit[i], "mV"), "Unexpected AD Unit")
+
+
+

The voltage difference of elevated - baseline from this head stages AD +wave is stored in wave deltaV and scaled by 0.001 to convert to Volts.

+
deltaV[i] = (elevated - baseline) * 1e-3
+
+
+

The baseline level and the elevated level of the DA wave are determined +with the identical calculation as for the AD wave described above.

+
high = firstEdge - 1
+low  = high - (firstEdge - onsetDelayPoint) * 0.1
+
+baseline = mean(DA, IndexToScale(DA, low, ROWS), IndexToScale(DA, high, ROWS))
+
+high = secondEdge - 1
+low  = high - (secondEdge - firstEdge) * 0.1
+
+elevated = mean(DA, IndexToScale(DA, low, ROWS), IndexToScale(DA, high, ROWS))
+
+
+

An assertion checks if the DAunit of this head stage is “pA” as this function +only works for I-clamp mode.

+
ASSERT(!cmpstr(DAunit[i], "pA"), "Unexpected DA Unit")
+
+
+

The current difference of elevated - baseline from this head stages DA +wave is stored in wave deltaI and scaled by 1E-12 to convert to Ampere.

+
deltaI[i] = (elevated - baseline) * 1e-12
+
+
+
+
+
+

Calculation

+

The following is done for each head stage:

+
+

The resistance for the current head stage is calculated by the formula +R = U / I from deltaV / deltaI.

+
resistance[i] = deltaV[i] / deltaI[i]
+
+
+
+

Then the loop continues to the next head stage of this sweep with +Finding square pulse

+
+_images/CalculateTPLikePropsFromSweep.svg
+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/IPNWB/doc/nwb1.html b/IPNWB/doc/nwb1.html new file mode 100644 index 0000000000..e0fd124994 --- /dev/null +++ b/IPNWB/doc/nwb1.html @@ -0,0 +1,264 @@ + + + + + + + + NWB version 1 — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

NWB version 1

+

The File Organization (version 1.0.5) is loosely described in the +archived repository for the NWBv1 schema specification

+

The following tree describes the NWB layout version 1

+
#  specifications:
+#  - version : 1.0.5 beta
+#    url : https://htmlpreview.github.io/?https://raw.githubusercontent.com/NeurodataWithoutBorders/specification_nwbn_1_0_x/master/version_1.0.5_beta/nwb_file_format_specification_1.0.5_beta.html#File_organization
+
+acquisition:
+  timeseries: # empty if no acquired data is saved
+  - data_XXXXX_ADY:
+      stimulus_description : name of the stimset # custom entry
+      data                 : 1D dataset with attributes unit, conversion and resolution
+      electrode_name       : Name of the electrode headstage, more info in /general/intracellular_ephys/electrode_name
+      gain                 : scaling factor
+      num_samples          : Number of rows in data
+      starting_time        : relative to /session_start_time with attributes rate and unit
+
+      # For Voltage Clamp (Missing entries are mentioned in missing_fields):
+      capacitance_fast :
+      capacitance_slow :
+      resistance_comp_bandwidth :
+      resistance_comp_correction :
+      resistance_comp_prediction :
+      whole_cell_capacitance_comp :
+      whole_cell_series_resistance_comp :
+
+      # For Current Clamp (Missing entries are mentioned in missing_fields):
+      bias_current :
+      bridge_balance :
+      capacitance_compensation :
+
+      description    : Unused
+      source         : Human readable description of the source of the data
+      comment        : User comment for the sweep
+      missing_fields : Entries missing for voltage clamp/current clamp data
+      ancestry       : Class hierarchy defined by NWB spec, important members are
+                       CurrentClampSeries, IZeroClampSeries and VoltageClampSeries
+      neurodata_type : TimeSeries
+
+stimulus:
+  presentation: # empty if no acquired data is saved
+  - data_XXXXX_DAY: # DA data as sent to the neuron, including delays, scaling, initial TP, etc.
+      data           : 1D dataset
+      electrode_name : Name of the electrode headstage, more info in /general/intracellular_ephys/electrode_name
+      gain           :
+      num_samples    : Number of rows in data
+      starting_time  : relative to /session_start_time with attributes rate and unit
+      description    : Unused
+      source         : Human readable description of the source of the data
+      ancestry       : Class hierarchy defined by NWB spec, important members are
+                       CurrentClampStimulusSeries and VoltageClampStimulusSeries
+      neurodata_type : TimeSeries
+  template: unused
+
+general:
+  file_create_date    : text array with UTC modification timestamps
+  identifier          : SHA256 hash, ensured to be unique
+  nwb_version         : NWB specification version
+  session_description : unused
+  session_start_time  : ISO8601 timestamp in UTC timezone with sub-second precision defining when the recording session started
+  generated_by: # custom entry
+                Nx2 text data array describing the system which created the data. First column is the key, second the value.
+  history: # custom entry
+           Full Igor Pro history since measurement start (useful for debugging)
+
+  # The following attributes are only available if explicitly set by the user:
+  data_collection :
+  experiment_description :
+  experimenter :
+  institution :
+  lab :
+  notes :
+  pharmacology :
+  protocol :
+  related_publications :
+  session_id :
+  slices :
+  stimulus :
+  age :
+  description :
+  genotype :
+  sex :
+  species :
+  subject_id :
+  weight :
+  surgery :
+  virus :
+
+  devices: # empty if no acquired data is saved
+  - device_XXX: # Name of the DA_ephys device, something like "Harvard Bioscience ITC 18USB"
+      intracellular_ephys:
+        electrode_XXX: # XXX can be set by the user via writing into GetCellElectrodeNames()
+        description : Holds the description of the electrode, something like "Headstage 1".
+        device      : Device used to record the data
+  labnotebook: # custom entry
+  - XXXX: # Name of the device
+      numericalKeys   : Numerical labnotebook
+      numericalValues : Keys for numerical labnotebook
+      textualKeys     : Keys for textual labnotebook
+      textualValues   : Textual labnotebook
+  testpulse: # custom entry
+    - XXXX: # Name of the device
+      TPStorage/TPStorage_X: testpulse property waves
+      StoredTestPulses: Raw testpulses as 1D datasets
+  user_comment:
+  - XXXX: # Name of the device
+      userComment: All user comments from this session
+  stimsets: # custom entry
+    XXXXXX_[DA/TTL]_Y_[SegWvType/WP/WPT]: The Wavebuilder parameter waves. These waves will not be available for
+                                          "third party stimsets" created outside of MIES.
+    XXXXXX_[DA/TTL]_Y: Name of the stimset, referenced from
+                       stimulus_description if acquired data is present. Only present if
+                       not all parameter waves could be found.
+    referenced: All referenced custom waves are stored here in a file-system like group-structure.
+                /general/stimsets/referenced/ relates to root in the igor Experiment.
+  epochs:
+    tags: unused
+
+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/IPNWB/doc/nwb2.html b/IPNWB/doc/nwb2.html new file mode 100644 index 0000000000..59295de8fd --- /dev/null +++ b/IPNWB/doc/nwb2.html @@ -0,0 +1,523 @@ + + + + + + + + NWB version 2 — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

NWB version 2

+

Recent NWB (version 2) schema specifications are tracked in a separate +repository. The +schema is implemented in version 2.2.0 +(62c73400565afc28f67ede4f2e86023c33167cf8).

+

The complete schema tree is described in a hdmf compatible format and +replicated in this repository under namespace/{schema}/{yaml,json}/*. The +JSON files are stored in the nwb file upon storage. A build script exists to +generate the JSON files from their YAML files: update_specifications.sh.

+

The following deviations from NWB schema 2.2.0 were +recorded:

+
 991ab801aae626710a8ec710869bb1b4508e91b7 ndx-MIES (heads/first-steps)
+ 24fba6174ddbad171ee5bb824edfa31f86b1b16d specifications (2.2.4)
+
+# diff namespace core upstream vs IPNWB specifications for nwb.base
+# diff namespace core upstream vs IPNWB specifications for nwb.behavior
+# diff namespace core upstream vs IPNWB specifications for nwb.device
+# diff namespace core upstream vs IPNWB specifications for nwb.ecephys
+# diff namespace core upstream vs IPNWB specifications for nwb.epoch
+# diff namespace core upstream vs IPNWB specifications for nwb.file
+# diff namespace core upstream vs IPNWB specifications for nwb.icephys
+# diff namespace core upstream vs IPNWB specifications for nwb.image
+# diff namespace core upstream vs IPNWB specifications for nwb.misc
+# diff namespace core upstream vs IPNWB specifications for nwb.namespace
+2,4c2
+< - name: core
+<   doc: NWB namespace
+<   author:
+---
+> - author:
+17a16
+>   doc: NWB namespace
+18a18
+>   name: core
+23c23
+<     source: nwb.base.yaml
+---
+>     source: nwb.base
+26c26
+<     source: nwb.device.yaml
+---
+>     source: nwb.device
+29c29
+<     source: nwb.epoch.yaml
+---
+>     source: nwb.epoch
+32c32
+<     source: nwb.image.yaml
+---
+>     source: nwb.image
+35c35
+<     source: nwb.file.yaml
+---
+>     source: nwb.file
+38c38
+<     source: nwb.misc.yaml
+---
+>     source: nwb.misc
+41c41
+<     source: nwb.behavior.yaml
+---
+>     source: nwb.behavior
+45c45
+<     source: nwb.ecephys.yaml
+---
+>     source: nwb.ecephys
+49c49
+<     source: nwb.icephys.yaml
+---
+>     source: nwb.icephys
+52c52
+<     source: nwb.ogen.yaml
+---
+>     source: nwb.ogen
+55c55
+<     source: nwb.ophys.yaml
+---
+>     source: nwb.ophys
+58c58
+<     source: nwb.retinotopy.yaml
+---
+>     source: nwb.retinotopy
+# diff namespace core upstream vs IPNWB specifications for nwb.ogen
+# diff namespace core upstream vs IPNWB specifications for nwb.ophys
+# diff namespace core upstream vs IPNWB specifications for nwb.retinotopy
+# diff namespace hdmf-common upstream vs IPNWB specifications for namespace
+2,4c2
+< - name: hdmf-common
+<   doc: Common data structures provided by HDMF
+<   author:
+---
+> - author:
+13a12
+>   doc: Common data structures provided by HDMF
+14a14
+>   name: hdmf-common
+17c17
+<     source: table.yaml
+---
+>     source: table
+20c20
+<     source: sparse.yaml
+---
+>     source: sparse
+# diff namespace hdmf-common upstream vs IPNWB specifications for sparse
+# diff namespace hdmf-common upstream vs IPNWB specifications for table
+# diff namespace ndx-mies upstream vs IPNWB specifications for namespace
+# diff namespace ndx-mies upstream vs IPNWB specifications for ndx-mies.extensions
+
+
+

The most important core properties are for intracellular ephys.

+
groups:
+- neurodata_type_def: PatchClampSeries
+  neurodata_type_inc: TimeSeries
+  doc: An abstract base class for patch-clamp data - stimulus or response,
+    current or voltage.
+  attributes:
+  - name: stimulus_description
+    dtype: text
+    doc: Protocol/stimulus name for this patch-clamp dataset.
+  - name: sweep_number
+    dtype: uint32
+    doc: Sweep number, allows to group different PatchClampSeries together.
+    required: false
+  datasets:
+  - name: data
+    dtype: numeric
+    dims:
+    - num_times
+    shape:
+    - null
+    doc: Recorded voltage or current.
+    attributes:
+    - name: unit
+      dtype: text
+      doc: Base unit of measurement for working with the data. Actual stored values are
+        not necessarily stored in these units. To access the data in these units,
+        multiply 'data' by 'conversion'.
+  - name: gain
+    dtype: float32
+    doc: Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).
+    quantity: '?'
+  links:
+  - name: electrode
+    target_type: IntracellularElectrode
+    doc: Link to IntracellularElectrode object that describes the electrode that was
+      used to apply or record this data.
+
+- neurodata_type_def: CurrentClampSeries
+  neurodata_type_inc: PatchClampSeries
+  doc: Voltage data from an intracellular current-clamp recording. A
+    corresponding CurrentClampStimulusSeries (stored separately as a stimulus) is
+    used to store the current injected.
+  datasets:
+  - name: data
+    doc: Recorded voltage.
+    attributes:
+    - name: unit
+      dtype: text
+      value: volts
+      doc: Base unit of measurement for working with the data. which is fixed to 'volts'.
+        Actual stored values are not necessarily stored in these units. To access the data in these units,
+        multiply 'data' by 'conversion'.
+  - name: bias_current
+    dtype: float32
+    doc: Bias current, in amps.
+    quantity: '?'
+  - name: bridge_balance
+    dtype: float32
+    doc: Bridge balance, in ohms.
+    quantity: '?'
+  - name: capacitance_compensation
+    dtype: float32
+    doc: Capacitance compensation, in farads.
+    quantity: '?'
+
+- neurodata_type_def: IZeroClampSeries
+  neurodata_type_inc: CurrentClampSeries
+  doc: Voltage data from an intracellular recording when all current
+    and amplifier settings are off (i.e., CurrentClampSeries fields will be zero).
+    There is no CurrentClampStimulusSeries associated with an IZero series because
+    the amplifier is disconnected and no stimulus can reach the cell.
+  datasets:
+  - name: bias_current
+    dtype: float32
+    value: 0.0
+    doc: Bias current, in amps, fixed to 0.0.
+  - name: bridge_balance
+    dtype: float32
+    value: 0.0
+    doc: Bridge balance, in ohms, fixed to 0.0.
+  - name: capacitance_compensation
+    dtype: float32
+    value: 0.0
+    doc: Capacitance compensation, in farads, fixed to 0.0.
+
+- neurodata_type_def: CurrentClampStimulusSeries
+  neurodata_type_inc: PatchClampSeries
+  doc: Stimulus current applied during current clamp recording.
+  datasets:
+  - name: data
+    doc: Stimulus current applied.
+    attributes:
+    - name: unit
+      dtype: text
+      value: amperes
+      doc: Base unit of measurement for working with the data. which is fixed to 'amperes'.
+        Actual stored values are not necessarily stored in these units. To access the data in these units,
+        multiply 'data' by 'conversion'.
+
+- neurodata_type_def: VoltageClampSeries
+  neurodata_type_inc: PatchClampSeries
+  doc: Current data from an intracellular voltage-clamp recording. A
+    corresponding VoltageClampStimulusSeries (stored separately as a stimulus) is
+    used to store the voltage injected.
+  datasets:
+  - name: data
+    doc: Recorded current.
+    attributes:
+    - name: unit
+      dtype: text
+      value: amperes
+      doc: Base unit of measurement for working with the data. which is fixed to 'amperes'.
+        Actual stored values are not necessarily stored in these units. To access the data in these units,
+        multiply 'data' by 'conversion'.
+  - name: capacitance_fast
+    dtype: float32
+    doc: Fast capacitance, in farads.
+    quantity: '?'
+    attributes:
+    - name: unit
+      dtype: text
+      value: farads
+      doc: Unit of measurement for capacitance_fast, which is fixed to 'farads'.
+  - name: capacitance_slow
+    dtype: float32
+    doc: Slow capacitance, in farads.
+    quantity: '?'
+    attributes:
+    - name: unit
+      dtype: text
+      value: farads
+      doc: Unit of measurement for capacitance_fast, which is fixed to 'farads'.
+  - name: resistance_comp_bandwidth
+    dtype: float32
+    doc: Resistance compensation bandwidth, in hertz.
+    quantity: '?'
+    attributes:
+    - name: unit
+      dtype: text
+      value: hertz
+      doc: Unit of measurement for resistance_comp_bandwidth, which is fixed to 'hertz'.
+  - name: resistance_comp_correction
+    dtype: float32
+    doc: Resistance compensation correction, in percent.
+    quantity: '?'
+    attributes:
+    - name: unit
+      dtype: text
+      value: percent
+      doc: Unit of measurement for resistance_comp_correction, which is fixed to 'percent'.
+  - name: resistance_comp_prediction
+    dtype: float32
+    doc: Resistance compensation prediction, in percent.
+    quantity: '?'
+    attributes:
+    - name: unit
+      dtype: text
+      value: percent
+      doc: Unit of measurement for resistance_comp_prediction, which is fixed to 'percent'.
+  - name: whole_cell_capacitance_comp
+    dtype: float32
+    doc: Whole cell capacitance compensation, in farads.
+    quantity: '?'
+    attributes:
+    - name: unit
+      dtype: text
+      value: farads
+      doc: Unit of measurement for whole_cell_capacitance_comp, which is fixed to 'farads'.
+  - name: whole_cell_series_resistance_comp
+    dtype: float32
+    doc: Whole cell series resistance compensation, in ohms.
+    quantity: '?'
+    attributes:
+    - name: unit
+      dtype: text
+      value: ohms
+      doc: Unit of measurement for whole_cell_series_resistance_comp, which is fixed to 'ohms'.
+
+- neurodata_type_def: VoltageClampStimulusSeries
+  neurodata_type_inc: PatchClampSeries
+  doc: Stimulus voltage applied during a voltage clamp recording.
+  datasets:
+  - name: data
+    doc: Stimulus voltage applied.
+    attributes:
+    - name: unit
+      dtype: text
+      value: volts
+      doc: Base unit of measurement for working with the data. which is fixed to 'volts'.
+        Actual stored values are not necessarily stored in these units. To access the data in these units,
+        multiply 'data' by 'conversion'.
+
+- neurodata_type_def: IntracellularElectrode
+  neurodata_type_inc: NWBContainer
+  doc: An intracellular electrode and its metadata.
+  datasets:
+  - name: description
+    dtype: text
+    doc: Description of electrode (e.g.,  whole-cell, sharp, etc.).
+  - name: filtering
+    dtype: text
+    doc: Electrode specific filtering.
+    quantity: '?'
+  - name: initial_access_resistance
+    dtype: text
+    doc: Initial access resistance.
+    quantity: '?'
+  - name: location
+    dtype: text
+    doc: Location of the electrode. Specify the area, layer, comments on estimation
+      of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas
+      names for anatomical regions when possible.
+    quantity: '?'
+  - name: resistance
+    dtype: text
+    doc: Electrode resistance, in ohms.
+    quantity: '?'
+  - name: seal
+    dtype: text
+    doc: Information about seal used for recording.
+    quantity: '?'
+  - name: slice
+    dtype: text
+    doc: Information about slice used for recording.
+    quantity: '?'
+  links:
+  - name: device
+    target_type: Device
+    doc: Device that was used to record from this electrode.
+
+- neurodata_type_def: SweepTable
+  neurodata_type_inc: DynamicTable
+  doc: The table which groups different PatchClampSeries together.
+  datasets:
+  - name: sweep_number
+    neurodata_type_inc: VectorData
+    dtype: uint32
+    doc: Sweep number of the PatchClampSeries in that row.
+  - name: series
+    neurodata_type_inc: VectorData
+    dtype:
+      target_type: PatchClampSeries
+      reftype: object
+    doc: The PatchClampSeries with the sweep number in that row.
+  - name: series_index
+    neurodata_type_inc: VectorIndex
+    doc: Index for series.
+
+
+

The includes a Dynamic Table at /general/intracellular_ephys/sweep_table to +store the sweep numbers of a list of data sets. The table is column centric +and consists of the two columns sweep_number and series. Series contains +links to datasets. The sweep_number for a dataset is stored under the same +row index, specified either by the Dataset id (zero-based indices) or by +series_index (one-based indices). The sweep_table is intended to easily find +datasets that belong to a given sweep number. A sweep table is loaded by +LoadSweepTable and created using AppendToSweepTable

+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/IPNWB/index.html b/IPNWB/index.html new file mode 100644 index 0000000000..0310f638b8 --- /dev/null +++ b/IPNWB/index.html @@ -0,0 +1,390 @@ + + + + + + + + Igor Pro module for reading and writing NeurodataWithoutBorder files — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Igor Pro module for reading and writing NeurodataWithoutBorder files

+

This modules allows to easily write and read valid NeurodataWithoutBorder style HDF5 files. It encapsulates the most commonly used +parts of the specification in easy to use functions.

+
+

Main features

+ +
+
+

Installation

+
    +

  • Quit Igor Pro

    • +

  • Install the HDF5 XOP and the HDF5 Browser as described in DisplayHelpTopic +"Installing The HDF5 Package"

    • +

  • Create the following shortcut in +C:\Users\$username\Documents\WaveMetrics\Igor Pro [78] User Files

    +
      +

    • In “Igor Procedures” a shortcut pointing to the basefolder of the IPNWB +package

      • +
    +
    • +

  • Restart Igor Pro

    • +
+
+
+

Examples

+

The following examples show how to read and write into NWB version 1.0.5

+
+

writing into NWB

+
#pragma TextEncoding = "UTF-8"
+
+#define IPNWB_DEFINE_IM
+#include "IPNWB_include"
+
+Function NWBWriterExample()
+
+	variable fileID
+	string contents, device
+	variable version = 1
+
+	// Open a dialog for selecting an HDF5 file name
+	HDF5CreateFile fileID as ""
+
+	// fill gi/ti/si with appropriate data for your lab and experiment
+	// if you don't care about that info just pass the initialized structures
+	STRUCT IPNWB#GeneralInfo gi
+	STRUCT IPNWB#ToplevelInfo ti
+	STRUCT IPNWB#SubjectInfo si
+
+	// takes care of initializing
+	IPNWB#InitToplevelInfo(ti, version)
+	IPNWB#InitGeneralInfo(gi)
+	IPNWB#InitSubjectInfo(si)
+
+	IPNWB#CreateCommonGroups(fileID, toplevelInfo=ti, generalInfo=gi, subjectInfo=si)
+
+	// If you open an existing NWB file to append to, use the following command
+	// to add an modification time entry, is implicitly called in IPNWB#CreateCommonGroups
+	// IPNWB#AddModificationTimeEntry(locationID)
+
+	// 1D waves from your measurement program
+	// we use fake data here
+	Make/FREE/N=1000 AD = (sin(p) + cos(p/10)) * enoise(0.1)
+	SetScale/P x, 0, 5e-6, "s"
+
+	// write AD data to the file
+	STRUCT IPNWB#WriteChannelParams params
+	IPNWB#InitWriteChannelParams(params)
+
+	params.device          = "My Hardware"
+	params.clampMode       = 0 // 0 for V_CLAMP_MODE, 1 for I_CLAMP_MODE
+	params.channelSuffix   = ""
+	params.sweep           = 123
+	params.electrodeNumber = 1
+	params.electrodeName   = "Nose of the mouse"
+	params.stimset         = "My fancy sine curve"
+	params.channelType     = 0 // @see IPNWBChannelTypes
+	WAVE params.data       = AD
+
+	device = "My selfbuilt DAC"
+
+	IPNWB#CreateIntraCellularEphys(fileID)
+	sprintf contents, "Electrode %d", params.ElectrodeNumber
+	IPNWB#AddElectrode(fileID, params.electrodeName, version, contents, device)
+
+	// calculate the timepoint of the first wave point relative to the session_start_time
+	// last time the wave was modified (UTC)
+	params.startingTime  = NumberByKeY("MODTIME", WaveInfo(AD, 0)) - date2secs(-1, -1, -1)
+	params.startingTime -= ti.session_start_time // relative to the start of the session
+	// we want the timestamp of the beginning of the measurement
+	params.startingTime -= IndexToScale(AD, DimSize(AD, 0) - 1, 0)
+
+	IPNWB#AddDevice(fileID, "Device name", version, "My hardware specs")
+
+	STRUCT IPNWB#TimeSeriesProperties tsp
+	IPNWB#InitTimeSeriesProperties(tsp, params.channelType, params.clampMode)
+
+	// all values not added are written into the missing_fields dataset
+	IPNWB#AddProperty(tsp, "capacitance_fast", 1.0)
+	IPNWB#AddProperty(tsp, "capacitance_slow", 1.0)
+
+	// setting chunkedLayout to zero makes writing faster but increases the final filesize
+	IPNWB#WriteSingleChannel(fileID, "/acquisition/timeseries", version, params, tsp)
+
+	// write DA, stimulus presentation and stimulus template accordingly
+	// ...
+
+	// close file
+	IPNWB#H5_CloseFile(fileID)
+End
+
+
+
+
+

reading from NWB

+
#pragma TextEncoding = "UTF-8"
+
+#define IPNWB_DEFINE_IM
+#include "IPNWB_include"
+
+Function NWBReaderExample()
+
+	variable fileID, groupID, integrityCheck, numChannels, i, version
+	string contents, device, listOfDevices, elem, list
+	STRUCT IPNWB#TimeSeriesProperties tsp
+
+	// Open a dialog for selecting an HDF5 file name
+	fileID = IPNWB#H5_OpenFile("c:\\NWB-Sample-20160216.nwb")
+	version = IPNWB#GetNWBMajorVersion(IPNWB#ReadNWBVersion(fileID))
+
+	integrityCheck = IPNWB#CheckIntegrity(fileID)
+	printf "NWB integrity check: %s\r", SelectString(integrityCheck, "failed", "passed")
+
+	listOfDevices = IPNWB#ReadDevices(fileID, version)
+	printf "List of devices: %s\r", listOfDevices
+
+	list    = IPNWB#ReadAcquisition(fileID, version)
+	groupID = IPNWB#OpenAcquisition(fileID, version)
+
+	numChannels = ItemsInList(list)
+
+	printf "\rLoading acquired data (%d)\r", numChannels
+
+	for(i = 0; i < numChannels; i += 1)
+		elem = StringFromList(i, list)
+
+		printf "sweep number: %d\r", IPNWB#LoadSweepNumber(groupID, elem, version)
+
+		WAVE wv = IPNWB#LoadDataWave(groupID, elem)
+		Duplicate/O wv, $elem
+
+		IPNWB#ReadTimeSeriesProperties(groupID, elem, tsp)
+		print tsp
+	endfor
+
+	HDF5CloseGroup groupID
+
+	list    = IPNWB#ReadStimulus(fileID)
+	groupID = IPNWB#OpenStimulus(fileID)
+
+	numChannels = ItemsInList(list)
+
+	printf "\rLoading presentation data (%d)\r", numChannels
+
+	for(i = 0; i < numChannels; i += 1)
+		elem = StringFromList(i, list)
+
+		printf "sweep number: %d\r", IPNWB#LoadSweepNumber(groupID, elem, version)
+
+		WAVE wv = IPNWB#LoadDataWave(groupID, elem)
+		Duplicate/O wv, $elem
+
+		IPNWB#ReadTimeSeriesProperties(groupID, elem, tsp)
+		print tsp
+	endfor
+
+	HDF5CloseGroup groupID
+
+	STRUCT IPNWB#ToplevelInfo toplevelInfo
+	IPNWB#ReadTopLevelInfo(fileID, toplevelInfo)
+	print toplevelInfo
+	print toplevelInfo.file_create_date
+
+	STRUCT IPNWB#GeneralInfo generalInfo
+	IPNWB#ReadGeneralInfo(fileID, generalInfo)
+	print generalInfo
+
+	STRUCT IPNWB#SubjectInfo subjectInfo
+	IPNWB#ReadSubjectInfo(fileID, subjectInfo)
+	print subjectInfo
+
+	// close file
+	HDF5CloseFile fileID
+End
+
+
+
+
+
+

NWB file format description

+
    +

  • Datasets which originate from Igor Pro waves have the special attributes +IGORWaveScaling, IGORWaveType, IGORWaveUnits, IGORWaveNote. These attributes +allow easy and convenient loading of the data into Igor Pro back.

    • +

  • For AD/DA/TTL groups the naming scheme is data_XXXXX_[AD/DA/TTL] +suffix where XXXXX is a running number and suffix the channel +number. For some hardware types the suffix includes the TTL line as +well. It is important to note that the number of digits in XXXXX is +variable und subject to change, and that XXXXX is not the sweep number.

    • +

  • In NWB v1, the sweep number is accessible from the source attribute only. +Example source contents: +Device=ITC18USB_Dev_0;Sweep=0;AD=0;ElectrodeNumber=0;ElectrodeName=0

    • +

  • For I=0 clamp mode neither the DA data nor the stimset is saved.

    • +

  • Some entries in the following tree are specific to MIES, these are marked as +custom entries. Users running MIES are encouraged to use the same NWB layout +and extensions.

    • +
+
+

NWB File Organization

+

The current major version of the file format is 2. Version 1 is considered +supported but deprecated.

+
+ +
+
+
+

Online Resources

+ +
+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/SweepFormula.html b/SweepFormula.html new file mode 100644 index 0000000000..a7c6441025 --- /dev/null +++ b/SweepFormula.html @@ -0,0 +1,1886 @@ + + + + + + + + The Sweep Formula Module — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

The Sweep Formula Module

+

The Sweep Formula Module in MIES_Sweepformula.ipf is intended to be used from +the SF tab in the BrowserSettingsPanel (BSP). It is useful for analyzing a +range of sweeps using pre-defined functions. The backend parses a formula into +a JSON logic like pattern which in turn is analyzed +to return a wave for plotting.

+
+

Preprocessing

+

The entered code in the notebook is preprocessed. The preprocessor +removes comments before testing the code for the ` vs ` operator after which +it is passed to the formula parser. +Comments start with a # character and end at the end of the current line.

+
+
+

Formula Parser

+

In order for a formula to get executed, it has to be analyzed. This assures +that the correct order of calculations is used. The approach for solving this +is using a token based state machine. We virtually insert one character at a +time from left to right into the state machine. Usually, a character is +collected into a buffer. At some special characters like a + sign, the state +changes from collect to addition. If a state changes, a new evaluation group is +created which is represented with a JSON object who’s (single) member is the +operation. The member name is the operation and the value is an ordered array +of the operands. To ensure that multiplication is executed before addition to +get 1+2*3=7 and not 1+2*3=9 the states have a priority. Higher order states +cause the operation order to switch. The old operation becomes part of the new +operation. In this context, when the first array or function argument separator , +is parsed on a level, it is treated as higher order operations because it creates +a new array.

+
{
+  "+": [
+    1,
+    {
+      "*": [
+        2,
+        3
+      ]
+    }
+  ]
+}
+
+
+

Arrays start with a square bracket [ and end with a ]. Subsequent array elements are +separated by a ,. In a series of arrays like [1, 2], [3, 4], [5, 6] the , after +the ] is enforced by the parser. Arrays can be part of arrays. Since at its core very +formula input is an array the series of arrays [1, 2], [3, 4], [5, 6] is implicitly +a 2-dimensional array: [[1, 2], [3, 4], [5, 6]]. The same applies for simple inputs like +1, which is implicitly treated as 1-dimensional array: [1]. The input [[1]] instead +is treated as 1x1 2-dimensional array. +Arrays are special as +also function arguments contain array elements. Therefore, an array can also +simply be created by omitting the array brackets and only using element +separators similar as in functions. The function max(1,2) is therefore +treated the same as max([1,2]). Arrays can represent data and functions +evaluate to arrays. Arrays can be of arbitrary size and can also be +concatenated as in max(0,min(1,2),1).

+
{
+  "max": [
+    0,
+    {
+      "min": [
+        1,
+        2
+      ]
+    },
+    1
+  ]
+}
+
+
+

A number can be entered as 1000, 1e3, or 10.0e2. It is always stored as a +numeric value and not as string. The formula parser treats everything that is +not parsable but matches alphanumeric characters (excluding operations) to a +string as in a_string. White spaces are ignored throughout the +formula which means that strings do not need to get enclosed by “. In fact, +a “ is an disallowed character.

+
[
+  1000,
+  "a_string"
+]
+
+
+

A function is defined as a string that is directly followed by an opening +parenthesis. The parenthesis token causes to force a collect state until all +parentheses are closed.

+

Everything that is collected in a buffer is sent back to the function via +recursive execution. The formula parser only handles elements inside one +recursion call that are linearly combinable like 1*2+3*4. If same operations +follow each other, they are concatenated into the same array level as for +1+2+3+4.

+
{
+  "+": [
+    1,
+    2,
+    3,
+    4
+  ]
+}
+
+
+
{
+  "+": [
+    {
+      "*": [
+        1,
+        2
+      ]
+    },
+    {
+      "*": [
+        3,
+        4
+      ]
+    }
+  ]
+}
+
+
+

The formula is sent to a preparser that checks for the correct +amount of brackets and converts multi-character operations to their multi-character +UTF-8 representations like … to …. It should be noted that an +operation consists of one UTF-8 character. Functions on the other hand can +consist of an arbitrary length of alphanumeric characters. The corresponding +function for the above operation is range().

+
+
+

Formula Executor

+

The formula executor receives a JSON id. It can only evaluate a specific +structure of a formula which means for usual cases that it should start with an +object that contains one operation. Operations are evaluated via recursive +calls to the formula executor at different paths. This ensures that the formula +is evaluated from the last element to the first element. The formula in the +above example 1*2+3*4 is therefore parsed to

+
{
+  "+": [
+    {
+      "*": [
+        1,
+        2
+      ]
+    },
+    {
+      "*": [
+        3,
+        4
+      ]
+    }
+  ]
+}
+
+
+

The execution follows these steps:

+
    +

  1. evaluate / to + operation, call +

    2. +

  2. called from + operation -> evaluate /+ array to array with two elements

    3. +

  3. evaluate /+/0 to * operation with an array argument with two elements 1, 2

    4. +

  4. called from * operation -> evaluate /+/0/* array to wave {1, 2}

    5. +

  5. * operation is applied to wave {1, 2}, returning wave {2}

    6. +

  6. insert wave {2} as first element of array from step 2

    7. +

  7. evaluate /+/1 to * operation with an array argument with two elements 3, 4

    8. +

  8. called from * operation -> evaluate /+/0/* array to wave {3, 4}

    9. +

  9. * operation is applied to wave {3, 4}, returning wave {12}

    10. +

  10. insert wave {12} as second element of array from step 2

    11. +

  11. + operation is applied to wave {2, 12} returning wave {14}

    12. +
+

At the time of an evaluation, the maximum depth of an array is +four dimensions as Igor Pro supports only four dimensions. This implies that on +recursive evaluation of multi dimensional arrays the sub arrays can be +three dimensional at best.

+
+

Array Evaluation

+

The array evaluation supports numeric and text data. The interpretation of the JSON arrays as +text data is preferred. This means that [“NaN”] returns a one element text wave {“NaN”}, +whereas [1, “NaN”] returns a two element numeric wave {1, NaN}. If one element can not be +parsed as string then it is assumed that the array contains numeric data. +The JSON null element is only allowed for the topmost array as the parser inserts it for +operation with no argument like e.g. select(). For sub arrays null elements [null] +are invalid and result in an error.

+

If the topmost array is empty [] an empty numeric wave with zero size is returned. +When checked in operation code the wave size should be checked before the wave type.

+

If the current array evaluated is of size one, then +the wave note is transferred from the subArray to the current array. This is important for the case where the element of +the current array is an JSON object, thus an operation, and the operation result is a single value with meta data in the wave.

+
+
+

Formula Executor Limitations

+

Mixed data types in arrays are not supported as this JSON property is hard to translate to Igor Pro data +storage in waves.

+
+
+
+

Internal Data Layout

+

The data is stored internally in persistant wave reference waves in a data folder, e.g. +root:MIES:HardwareDevices:Dev1:Databrowser:FormulaData:. The reason is that operation like data(…) +should be able to return multiple independent sweep data waves. These can be returned through a +wave reference wave. Each wave referenced contains numeric or text data. +The formula executor works on the JSON data that was created by the formula parser only. +This data is by definition either an object (operation), numeric or a textual. +If an operation like data(…) returns sweep data of multiple sweeps in a persistent wave reference wave +for the formula executor a single element text wave is created. +This text wave encodes a marker and the path to the wave reference wave in the first element. +The wave reference wave is resolved by wrapper functions when calling the formula executor, +such that the formula executor works only with the data wave(s).

+

Wrapper functions are:

+
    +

  • SF_GetArgument: retrieves an operation argument, returns a wave reference wave. If in the JSON from the parser the argument consists of ‘direct’ data like an array then it is automatically converted to a wave reference wave with one element that refers to the data wave.

    • +

  • SF_GetArgumentSingle: retrieves an operation argument expecting only a single data wave. Returns the data wave.

    • +

  • SF_GetArgumentTop: retrieves all operation arguments as an array, returns a wave reference wave.

    • +

  • SF_GetOutputForExecutor: Takes a wave reference wave as input and creates a single element text wave for returning further to the formula executor.

    • +

  • SF_GetOutputForExecutorSingle: Takes a data wave as input, creates a single element wave reference wave referring to the data wave and creates text wave for returning further to the formula executor.

    • +
+

The wrapper function imply that the formula executor is never called directly from operation code. +Also directly parsing the JSON is not allowed in operation code because every argument could be another operation or multi dimensional array etc.

+
+
+

Debugging Formula Execution

+

By default only the currently used wave reference waves are persistent. For debugging the execution the SWEEPFORMULA_DEBUG define can be set: +#define SWEEPFORMULA_DEBUG. +When set all data waves and wave reference waves are stored persistently in the sweepformula working data folder that are created during the execution. +The naming scheme is as follows: “source_pointOfCreation” with

+
+
source

typically the name of the operation or “ExecutorSubArrayEvaluation”

+
+
+

pointOfCreation:

+
+
output

wave reference wave output of operation

+
+
dataInput

data wave of direct data from JSON

+
+
refFromuserInput

wave reference wave automatically created to for data wave of direct data from JSON

+
+
return_argX_

data wave(s) returned by an operation, X counts the data waves aka index in the associated wave reference wave

+
+
argTop

prefix for the upper tags, added when data was parsed from the top level, used e.g. by integrate(1, 2)

+
+
+

The final wave name might be suffixed by a number guaranteeing unique wave names when multiple times the same operation was called.

+
+
+

Operations

+

In the context of the formula executor, different operations and functions are +defined. Some of them are MIES specific, some of them are wrappers to Igor +Pro operations or functions, some borrowed from other languages and there are +also the simple, trivial operations. This section should give a list of the +available operations and give a look into how they are meant to be used

+

The trivial operations are +, -, *, /. They are defined for all +available dimensions and evaluate column based.

+

They can be used for evaluating

+
    +

  1. scalars with 1d waves as in 1 + [1, 2] = [1, 1] + [1, 2] = [2, 3]

    2. +

  2. 1d waves with 1d waves as in [1, 2] + [3, 4] = [4, 6]

    3. +

  3. 1d waves with 2d waves as in [1, 2] + [[3, 4], [5, 6]] = [[1 + 3, 2 + 5], [NaN + 4, NaN + 6]] = [[4, 7], [NaN, NaN]]

    4. +

  4. 2d waves with 2d waves as in [[1, 2], [3, 4]] + [[5, 6], [7, 8]] = [[6, 8], [10, 12]]

    5. +
+

The size in each dimension is expanded to match the maximum array size. The maximum array size is determined by the required maximum dimensions of the elements in the topmost array. +An array element can be a number, a string, an array or an operation. A number or string a scalar. An sub array or operaton result is scalar if it returns a single element. +The expansion is filled with for numeric waves with NaN or for textual waves with “”. +In the special case of a scalar element, the value is expanded to the full size and dimensions of the expanded arrays size. +This means that in our first example, 1 is scalar and is internally expanded to an array of size 2 because the second operand determines the maximum size of 2: +1 + [1, 2] == [1, 1] + [1, 2]. +On the other hand in the third example above the first arrays size is expanded but not its value as it is not a scalar. +The array size expansion and scalar elements expansion is applied recursively for more dimensions. +Note that operations in array elements may return multi dimensional sub arrays that lead to an overall array expansion that is greater as the formula input suggests.

+
+
+

Statistical Operations

+
+

min and max

+

min and max return the minimum and maximum of an array. +The operation takes 1 to N arguments. The input data must be 1d or 2d, numeric and have at least one data point. +The operations work column based, such that for each column e.g. the maximum of all row values is determined. An 2d input array of size MxN is returned as 1d array of the size N. +When called with a single argument the operation accepts multiple data waves. +For this case the operation is applied on each input data wave independently and returns the same number of data waves. +The returned data type is SF_DATATYPE_MIN or SF_DATATYPE_MAX. +If input data type is SF_DATATYPE_SWEEP from the data operation the sweep meta data is transferred to the returned data waves. +The default suggested x-axis values for the formula plotter are sweep numbers.

+
min([[1, 2],[3, 4]]) = [1, 2]
+
+max(min([[1, 2],[3, 4]])) = [2]
+
+min(2) == [2]
+
+
+
+
+

avg and mean

+
avg(array data[, string mode])
+
+
+

avg and mean are synonyms for the same operation. +They calculate the arithmetic average \(\frac{1}{n}\sum_i{x_i}\).

+

data: input data wave(s)

+
+
mode: optional parameter that defines in which direction the average is applied.
    +

  • in default, applies the average over each input data wave. In this mode the operation returns the same number of waves as input waves were specified. Each output wave contains a single data point. If input data type is SF_DATATYPE_SWEEP from the data operation the sweep meta data is transferred to the returned data waves. The default suggested x-axis values for the formula plotter are sweep numbers.

    • +

  • over averages over all input data waves. In this mode the operation returns a single wave. NaN values in input waves are ignored in the average calculation. A trace generated from the returned wave will be shown as topmost trace in the default color for averaged data.

    • +
+
+
+

The returned data type is SF_DATATYPE_AVG.

+
avg([1, 2, 3]) == [2]
+
+avg(data(ST, select(channels(AD), sweeps(), all)), over)
+
+avg(data(ST, select()), in)
+
+
+
+
+

root mean square

+

rms calculates the root mean square \(\sqrt{\frac{1}{n}\sum_i{x_i^2}}\) of a row if the wave is 1d. It calculates column based if the wave is 2d. +The operation takes 1 to N arguments. The input data must be 1d or 2d, numeric and have at least one data point. +The operations works column based, such that for each column e.g. the average of all row values is determined. An 2d input array of size MxN is returned as 1d array of the size N. +When called with a single argument the operation accepts multiple data waves. +For this case the operation is applied on each input data wave independently and returns the same number of data waves. +The returned data type is SF_DATATYPE_RMS. +If input data type is SF_DATATYPE_SWEEP from the data operation the sweep meta data is transferred to the returned data waves. +The default suggested x-axis values for the formula plotter are sweep numbers.

+
rms(1, 2, 3) == [2.160246899469287]
+
+rms([1, 2, 3],[2, 3, 4],[3, 4, 5]) == [2.160246899469287, 3.109126351029605, 4.08248290463863]
+
+
+
+
+

variance

+

variance calculates the variance of a row if the wave is 1d. It calculates column based if the wave is 2d. +Note that compared to the Igor Pro function variance() the operation does not ignore NaN or Inf. +The operation takes 1 to N arguments. The input data must be 1d or 2d, numeric and have at least one data point. +The operations works column based, such that for each column e.g. the average of all row values is determined. An 2d input array of size MxN is returned as 1d array of the size N. +When called with a single argument the operation accepts multiple data waves. +For this case the operation is applied on each input data wave independently and returns the same number of data waves. +The returned data type is SF_DATATYPE_VARIANCE. +If input data type is SF_DATATYPE_SWEEP from the data operation the sweep meta data is transferred to the returned data waves. +The default suggested x-axis values for the formula plotter are sweep numbers.

+
variance(1, 2, 4) == [2.33333]
+
+variance([1, 2, 4],[2, 3, 2],[4, 2, 1]) == [2.33333, 0.33333, 2.33333]
+
+
+
+
+

stdev

+

stdev calculates the variance of a row if the wave is 1d. It calculates column based if the wave is 2d. +The operation does not ignore NaN or Inf. +The operation takes 1 to N arguments. The input data must be 1d or 2d, numeric and have at least one data point. +The operations works column based, such that for each column e.g. the average of all row values is determined. An 2d input array of size MxN is returned as 1d array of the size N. +When called with a single argument the operation accepts multiple data waves. +For this case the operation is applied on each input data wave independently and returns the same number of data waves. +The returned data type is SF_DATATYPE_STDEV. +If input data type is SF_DATATYPE_SWEEP from the data operation the sweep meta data is transferred to the returned data waves. +The default suggested x-axis values for the formula plotter are sweep numbers.

+
stdev(1, 2, 4) == [1.52753]
+
+stdev([1, 2, 4],[2, 3, 2],[4, 2, 1]) == [1.52753, 0.57735, 1.52753]
+
+
+
+
+
+

Igor Pro Wrappers

+
+

area

+

Use area to calculate the area below a 1D array using trapezoidal integration.

+
area(array data[, variable zero])
+
+
+

The first argument is the data, the second argument specifies if the data is zeroed. Zeroing refers to an additional differentiation and integration of the data prior the +area calculation. If the zero argument is set to 0 then zeroing is disabled. By default zeroing is enabled. +If zeroing is enabled the input data must have at least 3 points. If zeroing is disabled the input data must have at least one point. +The operation ignores NaN in the data. +The operations works column based, such that for each column e.g. the area of all row values is determined. An 2d input array of size MxN is returned as 1d array of the size N. +An 3d input array of size MxNxO is returned as 2d array of the size NxO. +The operation accepts multiple data waves for the data argument. +For this case the operation is applied on each input data wave independently and returns the same number of data waves. +The returned data type is SF_DATATYPE_AREA. +If input data type is SF_DATATYPE_SWEEP from the data operation the sweep meta data is transferred to the returned data waves. +The default suggested x-axis values for the formula plotter are sweep numbers.

+
area([0, 1, 2, 3, 4], 0) == [8]
+
+area([0, 1, 2, 3, 4], 1) == [4]
+
+
+
+
+

derivative

+

Use derivative to differentiate along rows for 1- and 2-dimensional data.

+
derivative(array data)
+
+
+

Central differences are used. The same amount of points as the input is returned. +The input data must have at least one point. +The operation ignores NaN in the data. +The operation accepts multiple data waves for the data argument. +For this case the operation is applied on each input data wave independently and returns the same number of data waves. +The returned data type is SF_DATATYPE_DERIVATIVE.

+
derivative(1, 2, 4) == [1, 1.5, 2]
+
+derivative([1, 2, 4],[2, 3, 2],[4, 2, 1]) == [1, 1, -2],[1.5, 0, -1.5],[2, -1, -1]
+
+
+
+
+

integrate

+

Use integrate to apply trapezoidal integration along rows. The operation returns the same number of points as the input wave(s).

+
integrate(array data)
+
+
+

Note that due to the end point problem it is not the counter-part of derivative. +The input data must have at least one point. +The operation ignores NaN in the data. +The operation accepts multiple data waves for the data argument. +For this case the operation is applied on each input data wave independently and returns the same number of data waves. +The returned data type is SF_DATATYPE_INTEGRATE.

+
integrate(1, 2, 4) == [0, 1.5, 4.5]
+
+integrate([1, 2, 4],[2, 3, 2],[4, 2, 1]) == [0, 0, 0],[1.5, 2.5, 3],[4.5, 5, 4.5]
+
+
+
+
+

butterworth

+

The operation butterworth applies a butterworth filter on the given data +using FilterIIR from Igor Pro. The operation calculates along rows. It takes +four arguments:

+
butterworth(array data, variable lowPassCutoffInHz, variable highPassCutoffInHz, variable order)
+
+
+

The first parameter data is intended to be used with the data() operation but +can be an arbitrary numeric array. The parameters lowPassCutoffInHz and +highPassCutoffInHz must be given in Hz. The maximum value for order is 100. +The operation accepts multiple data waves for the data argument. +For this case the operation is applied on each input data wave independently and returns the same number of data waves. +The returned data type is SF_DATATYPE_BUTTERWORTH.

+
butterworth([0,1,0,1,0,1,0,1], 90E3, 100E3, 2) == [0, 0.863871, 0.235196, 0.692709, 0.359758, 0.60206, 0.425727, 0.554052]
+
+
+
+
+

xvalues and time

+

The function xvalues or time are synonyms for the same function. +The function returns a wave containing the x-scaling of the +input data.

+
xvalues(array data)
+
+
+

The output data wave has the same dimension as the input data. The x-scaling values are filled in the rows for all dimensions. +The operation accepts multiple data waves for the data argument. +For this case the operation is applied on each input data wave independently and returns the same number of data waves.

+
xvalues(10, 20, 30, 40, 50) == [0, 1, 2, 3, 4]
+
+// The sweeps in this example were sampled at 250 kHz.
+// For each data point in the sweep the time is returned.
+time(data([0, 1000], channels(AD), sweeps())) == [0, 0.004, 0.008, 0.012, ...]
+
+
+
+
+

setscale

+

setscale sets a new wave scaling to an input wave. It accepts 2 to 5 arguments.

+
setscale(array data, string dim[, variable dimOffset[, variable dimDelta[, string unit]]])
+
+
+
+
data

input data wave

+
+
dim

dimension where the scale should be set, either d, x, y, z or t.

+
+
dimOffset

optional, the scale offset for the first data point. If not specified, 0 is used as default.

+
+
dimDelta

optional, the scale delta for the data point distance. If not specified, 1 is used as default.

+
+
unit

optional, the scale unit for the data points. If not specified, “” is used as default.

+
+
+

If d is used for dim, then in analogy to Igor Pros SetScale operation the dimOffset and dimDelta argument set the nominal minimum and nominal maximum data values of the wave.

+

If x, y, z or t is used for dim and dimDelta is 0 then the default dimDelta 1 is used.

+

The operation accepts multiple data waves for the data argument. +For this case the operation is applied on each input data wave independently and returns the same number of data waves.

+
xvalues(setscale([0, 1, 2, 3, 4], x, 0, 0.2, firkin)) == [0, 0.2, 0.4, 0.6, 0.8]
+
+
+
+
+

channels

+

channels([str name]+) converts named channels from strings to numbers.

+

The function accepts an arbitrary amount of channel names like AD, DA or +TTL with a combination of numbers AD1 or channel numbers alone like 2. +The maximum allowed channel number is NUM_MAX_CHANNELS (16). For all channel +types the channel numbers as given on the DAEphys panel are accepted. +The operation returns a numeric array of [[channelType+], [channelNumber+]] that has as +row dimension the number of the input strings. +When called without argument all channel types / channel numbers are set by setting the +returned value for type and number to NaN.

+

channels is intended to be used with the select() operation.

+
channels([AD0,AD1, DA0, DA1]) == [[0, 0, 1, 1], [0, 1, 0, 1]]
+
+// Internally NaN is evaluated as joker for all channel types and all channel numbers
+channels() == [[NaN], [NaN]]
+
+
+
+
+

sweeps

+

The operation sweeps return an 1d-array with the sweep numbers of all sweeps. The operation takes no arguments. +If there are no sweeps a null wave is returned.

+
// For this example two sweeps were acquired
+sweeps() == [0, 1]
+
+
+
+
+

cursors

+

The cursors operation returns the x-values of the named cursor(s).

+
cursors([A-J]+)
+
+
+

The cursors operation takes any number of arguments. If no argument is given +it defaults to cursors(A, B). When cursors is used as argument for a range specification, e.g. for data +two arguments for cursors should be used to have a compatible output. +Valid cursor names are A-J. The operation returns a numeric 1d-wave containing the x-values of the named cursor(s). +If a named cursor is not present, then NaN is returned as position.

+
cursors(A,B) vs A,B
+
+cursors() vs A,B // same as above
+
+cursors(B,A,D,J,I,G,G) // returns a 7 element array with the x-values of the named cursors
+
+
+
+
+

wave

+

The wave operation returns the content of the referenced wave.

+
wave(string pathToWave)
+
+
+

If no wave can be resolved at the given path a null wave is returned. The further handling depends how the operations receiving such null wave handles this special case. +The formula plotter skips null waves.

+
wave(root:mywave)
+
+
+
+
+

text

+

The operation text converts the given numeric data to a text data.

+
text(array data)
+
+
+

This can be used to force, for example, a category plot. +text requires numeric input data. The output data has the same dimension as the input data. The output precision for the text are 7 digits after the dot. +The operation accepts multiple data waves for the data argument. +For this case the operation is applied on each input data wave independently and returns the same number of data waves.

+
range(5) vs text(range(5))
+
+
+
+
+

data

+

The data operation is the core of the SweepFormula library. It returns sweep data from MIES. +It can be called in two variants:

+
data(array range[, array selectData])
+
+data(string epochShortName[, array selectData])
+
+
+

The range can be either supplied explicitly using [100, 300] which would +select 100 ms to 300 ms or by using cursors that also returns a range +specification. Use [0, inf] to extract the full x-range. A numerical range +applies to all sweeps.

+

Instead of a numerical range also the short names of epochs can be given including wildcard expressions. Then the range +is determined from the epoch information of each sweep/channel/epoch data iterates over. If a specified epoch does not exist in a sweep +that sweep data is not included in the sweep data returned. If the same epoch is resolved multiple times from wildcard expressions or +multiple epoch names then it is included only once per sweep.

+

A given range as numbers or epoch extracts a subrange of data points from the sweep. The start and end time is converted to +closest integer indices, where the included points range from startIndex to endIndex - 1. This matches the general handling +of epochs in MIES, where the data point at the end time of an epoch is not part of the epoch range.

+

selectData is retrieved through the select operation. It selects for which sweeps and channels sweep data is returned. +select also allows to choose currently displayed sweeps or all existing sweeps as data source. +When the optional selectData argument is omitted, select() is used as default that includes all displayed sweeps and channels.

+

For each selected sweep/channel combination data returns a data wave. The data wave contains the sweep data for the specified range/epoch. +If no sweep/channel was selected then the number of returned data waves is zero. Each data wave gets meta data about the originating sweep/channel added. +The returned data type is SF_DATATYPE_SWEEP.

+
// Shows the AD channels of all displayed sweeps with the range 0 - 1s
+data([0, 1000], select(channels(AD), sweeps()))
+
+// Shows epoch "E1" range of the AD channels of all displayed sweeps
+data("E1", select(channels(AD), sweeps()))
+
+// Shows epoch "E1" range with the start offsetted by 10ms of the AD channels of all displayed sweeps
+sel = select(channels(AD), sweeps())
+data(epochs("E1", $sel) + [10, 0], $sel)
+
+// Shows sweep data from all epochs starting with "E" of the AD channels of all displayed sweeps
+data("E*", select(channels(AD), sweeps()))
+
+// Shows sweep data from all epochs starting with "E"  and "TP" of the AD channels of all displayed sweeps
+data(["E*","TP*"], select(channels(AD), sweeps()))
+
+// Shows sweep data from all epochs that do not start with "E"  and that do start with "TP" of the AD channels of all displayed sweeps
+data(["!E*","TP*"], select(channels(AD), sweeps()))
+
+// No double resolve of the same epoch name: Shows sweep data from epoch "TP" of the AD channels of all displayed sweeps.
+data(["TP","TP"], select(channels(AD), sweeps()))
+
+// extract the first pulse from TTL1 as epoch and extract the AD data
+// in that range
+ep = epochs(E0_PT_P0, select(channels(TTL1),sweeps()))
+data($ep,select(channels(AD),sweeps()))
+
+
+
+
+

labnotebook

+
labnotebook(string key[, array selectData [, string entrySourceType]])
+
+
+

The labnotebook function returns the (case insensitive) key entry from the +labnotebook for the selected channel and sweep combination(s). The optional +entrySourceType can be one of the constants DataAcqModes for data +acquisition modes as defined in ../MIES/MIES_Constants.ipf. If the +entrySourceType is omitted it defaults to DATA_ACQUISITION_MODE.

+

When the optional select argument is omitted, select() is used as default that includes all displayed sweeps and channels.

+

The labnotebook operation returns a data wave for each selected sweep/channel combination. Each data wave contains a single element, that is depending on the +requested labnotebook entry numeric or textual.

+

The returned data type is SF_DATATYPE_LABNOTEBOOK. +If input data type is SF_DATATYPE_SWEEP from the data operation the sweep meta data is transferred to the returned data waves. +The default suggested x-axis values for the formula plotter are sweep numbers. +The suggested y-axis label is the labnotebook key.

+
max(
+   data(
+      cursors(A, B)
+      channels(AD),
+      sweeps()
+   )
+)
+vs
+labnotebook(
+   "set cycle count",
+   select(channels(AD), sweeps()),
+   DATA_ACQUISITION_MODE
+)
+
+
+

The function searches for numeric entries in the labnotebook first and then for +text entries. It returns a null wave if no match was found.

+
+
+

findlevel

+

The operation findlevel returns the x-position of the first transition to the given level.

+
findlevel(array data, variable level[, variable edge])
+
+
+
+
data

one or multiple data waves. If multiple data waves are given then the same number of data waves is returned. The operation is applied for each data wave separately.

+
+
level

level value to find

+
+
edge

defines which transition is to be found. Valid values are rising and falling 0, rising 1 or falling 2. The default for edge is rising and falling 0.

+
+
+

The returned data type is SF_DATATYPE_FINDLEVEL. +If input data type is SF_DATATYPE_SWEEP from the data operation the sweep meta data is transferred to the returned data waves.

+
findlevel([1, 2, 3], 1.5) == [0.5]
+
+
+
+
+

apfrequency

+

The apfrequency operation returns the action potential frequency using the given method.

+
apfrequency(array data[, variable method[, variable level[, string resultType[, string normalize,[string xAxisType]]]]])
+
+
+
+
data

one or multiple data waves. If multiple data waves are given then the same number of data waves is returned. The operation is applied for each data wave separately.

+
+
method

the method can be either

+
    +

  • 0 for “full”

    • +

  • 1 for “instantaneous”

    • +

  • 2 for apcount

    • +

  • 3 for “instantaneous pair”

    • +
+

The default method is 0.

+
+
level

level threshold for peak detection. The level refers to the amplitude of the sweep(s). level is a numeric value and defaults to 0.

+
+
resultType

the result type defines what result(s) the apfrequency operation returns if the method 3 (instantaneous pair) is set.

+
    +

  • time returns time intervals

    • +

  • freq returns frequencies.

    • +
+
+
normalize

sets the way the results get normalized

+
    +

  • nonorm: no normalzation is applied (default)

    • +

  • normoversweepsmin: normalizes over all sweeps based on the minimum result value in all sweeps based on the current method

    • +

  • normoversweepsmax: normalizes over all sweeps based on the maximum result value in all sweeps based on he current method

    • +

  • normoversweepsavg: normalizes over all sweeps based on the average result value in all sweeps based on the current method

    • +

  • norminsweepsmin: normalizes each sweep based on the minimum result value in the specific sweep based on the current method

    • +

  • norminsweepsmax: normalizes each sweep based on the maximum result value in the specific sweep based on the current method

    • +

  • norminsweepsavg: normalizes each sweep based on the average result value in the specific sweep based on the current method

    • +
+
+
xAxisType

if the method 3 (instantaneous pair) is set then xAxisType defines the x-axis of the data display.

+
    +

  • time: the x-axis shows the occurence in time of the first peak of the pair(s), default

    • +

  • count: the x-axis counts the pair(s)

    • +
+
+
+

The basic calculation for these methods are done using the below formulas where +\(l\) denotes the number of found levels, \(t_{i}\) the timepoint in +seconds of the level and \(T\) the total x range of the data in seconds.

+
+\[\begin{split}f_{\text{full}} &= \frac{l}{T} \\ +f_{\text{instantaneous}} &= \frac{1}{\frac{\sum_{i = 0}^{i = l - 1} \left( t_{i + 1} - t_{i} \right)}{l}} \\ +f_{\text{apcount}} &= l \\ +f_{\text{instantaneous_pair}} &= \frac{1}{\left( t_{i + 1} - t_{i} \right)}\end{split}\]
+

The method 2 (instantaneous) and 3 (instantaneous pair) treat the peaks as interleaved pairs of peaks and returns results only if there are two or more peaks found.

+

The returned data type is SF_DATATYPE_APFREQUENCY. If input data type is +SF_DATATYPE_SWEEP from the data operation the sweep meta data is transferred +to the returned data waves. There is no input data verification, so it is left +to the user to select a reasonable range or epoch.

+
apfrequency([10, 20, 30], 1, 15)
+
+apfrequency(data(ST, select(channels(AD), sweeps(), all)), 3, 100, freq, normoversweepsavg, count)
+
+apfrequency(data(ST, select(channels(AD), sweeps(), all)), 3, 42, time, norminsweepsmin, time)
+
+
+
+
+

powerspectrum

+

The powerspectrum operation returns the power spectrum of the input data

+
powerspectrum(array data[, string unit[, string average[, variable ratioFrequency[, variable cutOffFrequency[, string windowFunction]]]]])
+
+
+
+
data

one or multiple data waves.

+
+
unit

the unit can be either default, dB for decibel or normalized for the spectrum normalized by its total energy. The default method is default. +default means e.g. if the signal unit is V then the y-axis unit of the power spectrum is V^2.

+
+
average

this argument allows to enable averaging over all sweeps of the same channel/channeltype combination. Possible values are avg and noavg. +The default average setting is noavg. If data waves do not originate from a sweep, then it is averaged over all of these data waves. +e.g. if there are two data waves from sweep 0,1 AD1, two data waves from sweep 0,1 AD2 and two data waves not from a sweep then +there will be three averaged waves: over all sweeps for channel combination AD1, over all sweeps for channel combination AD2 and over all data waves not from a sweep.

+
+
ratioFrequency

this argument allows to specify a frequency where the ratio between base line and signal is determined through a gaussian fit with a linear base. +A typical use is to look for line noise at 50 Hz or 60 Hz. If a non zero ratioFrequency is set then the result is a single data point per power spectrum wave. +The returned ratio is (amplitude + baseline_level) / baseline_level. The default ratioFrequency is 0, that disables the ratio determination.

+
+
cutOffFrequency

The cutOffFrequency allows to limit the maximum displayed frequency of the powerspectrum. The default cutOffFrequncy is 1000 Hz. +The maximum cutOffFrequency is half of the sample frequency. This argument is ignored if a ratioFrequency > 0 is set.

+
+
windowFunction

allows to specify the window function applied for the FFT. The default windowFunction is Hanning. +Possible options are none to disable the application of a window function and the window functions known to Igor Pro 9. See DisplayHelpTopic “FFT”.

+
+
+

The gaussian fit for the power ratio calculation uses the following constraints:

+
    +

  • The peak position must be between ratioFrequency ± 0.25 Hz

    • +

  • The maximum FWHM are 5 Hz

    • +

  • The amplitude must be >= 0

    • +

  • The base of the peak must be > 0

    • +
+

If the fit fails a ratio of 0 is returned.

+

The returned data type is SF_DATATYPE_POWERSPECTRUM. +If input data type is SF_DATATYPE_SWEEP from the data operation and non-averaged power spectrum is calculated the sweep meta data is transferred to the returned data waves.

+
powerspectrum(data(ST,select(channels(AD),sweeps(),all)))
+
+powerspectrum(data(ST,select(channels(AD),sweeps(),all)),dB,avg,0,100,HFT248D) // db units, averaging on, display up to 100 Hz, use HFT248D window
+
+powerspectrum(data(ST,select(channels(AD),sweeps(),all)),dB,avg,60) // db units, averaging on, determine power ratio at 60 Hz
+
+
+
+
+

psx

+

The psx operation allows to classify miniature PSC/PSP’s interactively.

+
psx(id, [psxKernel(), numSDs, filterLow, filterHigh, maxTauFactor, psxRiseTime(), psxDeconvFilter()])
+
+
+

The function accepts one to seven arguments.

+
+
id

identifier string, must adhere to strict igor object names. +Used for identifying the data to store/query the results wave

+
+
psxKernel

result from the psxKernel operation

+
+
numSDs

Number of standard deviations for the gaussian fit of the all points histogram, defaults to 2.5

+
+
filterLow

low threshold for the bandpass filter, defaults to 550 Hz

+
+
filterHigh

high threshold for the bandpass filter, defaults to 0 Hz

+
+
maxTauFactor

maximum tau factor, the decay tau from fitting the event must be smaller than the fit range +times maxTauFactor, defaults to 10

+
+
psxRiseTime

results from the psxRiseTime operation

+
+
psxDeconvFilter

results from the psxDeconvFilter operation

+
+
+

The plotting is implemented in a custom way. Due to that multiple psx +operations can only be separated by with and not and.

+
psx(myID)
+psx(psxkernel(), 3, 400, 100)
+
+
+

See SweepFormula PSC/PSP classification for an in-depth explanation of the available user +interface for acceptance/rejectance.

+
+

psxkernel

+

Helper operation for psx which allows to create a custom kernel and choose +the subset of data to work on.

+
psxkernel([array range, array selectData, riseTau, decayTau, amp])
+
+
+

The function accepts zero to five arguments.

+
+
range

either an explicit array in milliseconds, cursors or a text array with one +or multiple epoch names, see also data, defaults to the full range.

+
+
select

sweep and channels to operate on from the select operation

+
+
riseTau

Time constant for kernel, defaults to 1

+
+
decayTau

Time constant for kernel, defaults to 15

+
+
amp

Amplitude for kernel, defaults to -5

+
+
+
psxkernel([100, 200])
+psxkernel([E0, E1]) # list of epoch names
+psxkernel(ST, select(channels(AD10), [49, 50], all), 2, 13, 2)
+
+
+
+
+
+

psxPrep

+

The psxPrep operation outputs the peak threshold to be used for psx event searching.

+
+

psxPrep(psx(), [numberOfSDs])

+
+

The function accepts one to two arguments.

+
+
psx

results of the psx operation

+
+
numberOfSDs

Number of standard deviations of the gaussian fit to return as threshold

+
+
+
psxPrep(psx(psxKernel(E0, select()), 0.2, 400, 100, 12))
+
+
+
+
+

psxRiseTime

+

The psxRiseTime operation is a helper operation for psx to manage the lower and upper thresholds for the rise time calculation.

+
+

psxRiseTime([lowerThreshold, upperThreshold])

+
+

The function accepts zero to two arguments.

+
+
lowerThreshold

defaults to 20%

+
+
upperThreshold

defaults to 80%

+
+
+
psxRiseTime(0.5)
+psxRiseTime(0.5, 0.9)
+
+
+
+
+

psxDeconvFilter

+

The psxDeconvFilter operation is a helper operation for psx to manage the deconvolution filter settings.

+
+

psxDeconvFilter([lowFreq, highFreq, order])

+
+

The function accepts zero to three arguments.

+
+
lowFreq [Hz]

defaults to NaN

+
+
highFreq [Hz]

defaults to NaN

+
+
order

defaults to NaN

+
+
+

The default values of NaN are replaced inside psx. For the order this is +101, for the frequencies this is a normalized frequency which depends on the +sampling interval of the data. Here lowFreq is the end of the passband and +highFreq the start of the reject band see also the description of /LO from +FilterFIR.

+
psxDeconvFilter(500, 1000)
+psxDeconvFilter(400, 600, 91)
+
+
+
+
+

psxstats

+

Plot properties of the result waves of a miniature PSC/PSP classification. The +operation combines the data from all input sweeps.

+

The operation allows to visualize psx data from the results wave or locally, +i.e. from an psx operation from another formula separated by and. The +local results are prefered over the results wave.

+

The traces are colored using the common headstage colors. The markers are the +same as used for visualizing the event state in psx (accepted -> circle, +rejected -> triangle, undetermined -> square).

+
psxstats(id, array range, array selectData, prop, state, [postproc])
+
+
+

The function accepts five or six arguments.

+
+
id

identifier string, must adhere to strict igor object names. +Used for identifying the data to query, also from the results wave

+
+
range

either an explicit array in milliseconds, cursors or a text array with one +or multiple epoch names, see also data

+
+
select

sweep and channels to operate on from the select operation

+
+
prop

column of the psx event results waves to plot. +Choices are: amp, xpos, xinterval, tau, estate, fstate, fitresult, risetime

+
+
state

QC state to select the events. +Choices are: accept/reject/undetermined/all/every

+

The used QC state depends on prop:

+
    +

  • Event state QC -> amp/xpos/xinterval/estate/risetime

    • +

  • Fit state QC -> tau/fstate/fitresult

    • +
+

The difference between all and every is that all plots the events from +all possible states in one trace whereas every creates multiple +traces, one for each state.

+
+
postproc

post process the results, defaults to nothing +Choices are: nothing, stats, nonfinite, count, hist, log10

+
+
nothing

no post processing

+
+
stats

calculate various statistical properties of the data

+
+
nonfinite

selects non-finite values (-inf/NaN/inf)

+
+
count

count the number of data elements

+
+
hist

create a histogram from the data

+
+
log10

apply the decadic logarithm (base 10) to each data point

+
+
+
+
+
psxstats(myID, [100, 200], select(channels(AD10), [49, 50], all), amp, accept)
+psxstats(otherID, [E0], select(channels(AD7), 40...60, all), xpos, every, log10)
+
+
+
+
+

fit

+

The fit operation allows to perform a CurveFit on the given x and y data and +accepts exactly three parameters.

+
fit(arrays xdata, arrays ydata, fitOp)
+
+
+
+
xdata, ydata

one or multiple arrays with data

+
+
fitOp

helper operation with fit type and possible constrained parameters, +currently only fitline is available.

+
+
+

xdata and ydata all need to be 1D, but multiple can be given. The +number of points in the corresponding x and y waves must be the same.

+

Example:

+
# we look at four sweeps
+sweeps = [5, 7, 8, 10]
+
+# grab the DA data from channel 0 and epoch E1
+selDA = select(channels(DA0), $sweeps)
+dDA   = data("E1", $selDA)
+
+# E2 from AD channel 2
+selAD = select(channels(AD2), $sweeps)
+dAD   = data("E2", $selAD)
+
+# calculate minimum for the data in each sweep,
+# but merge the data into one wave for the fit
+setX = merge(min($dDA))
+
+# and average for AD
+setY = merge(avg($dAD))
+
+# plot the extracted data
+$dDA
+
+and
+
+$dAD
+
+and
+
+# and the input data
+$setY vs $setX
+
+with
+
+# and do the fit
+fit($setX, $setY, fitline())
+
+
+
+
+

fitline

+

The fitline operation allows to select a straight line for the fit and +accepts zero or one argument.

+
fitline([textarray constraints])
+
+
+
+
constraints

text array with constrain definitions like K0=5

+
+
+
fit($xData, $yData, fitline())
+
+# holds the second fit parameter at 3
+fit($xData, $yData, fitline(["K1=3"]))
+
+
+
+
+
+

Utility Functions

+
+

select

+

The select operation allows to choose a selection of sweep data from a given list of sweeps and channels. +It is intended to be used with operations like data, labnotebook, epochs and tp.

+
select([array channels, array sweeps[, string mode[, string clampMode]]])
+
+
+

The function accepts none, two, three or four arguments.

+
+
channels

array with channel specification from channels operation. When channels is not specified, it defaults to channels(). The input channel numbers are treated as GUI channel numbers.

+
+
sweeps

array with sweep number, typically from sweeps operation. When sweeps is not specified, it defaults to sweeps().

+
+
mode

string specifying which sweeps are selected. Possible strings are displayed and all that refer to the currently displayed sweeps or all acquired sweeps. When mode is not specified it defaults to displayed.

+
+
clampMode

string specifying which clamp mode is selected. Possible strings are all, vc, ic and izero. When clampMode is not specified it defaults to all. The clampMode selection is only applied for associated AD/DA channels.

+
+
+

To retrieve a correct array of channels the channels function must be used.

+

If a given channel/sweep combination does not exist it is omitted in the output.

+

The output is a N x 3 array where the columns are sweep number, channel type, GUI channel number.

+

The output is sorted. The order is sweep -> channel type -> channel number. +e.g. for two sweeps numbered 0, 1 that have channels AD0, AD1, DA6, DA7: +{{0, 0, 0, 0, 1, 1, 1, 1}, {0, 0, 1, 1, 0, 0, 1, 1}, {0, 1, 6, 7, 0, 1, 6, 7}}.

+

If the mode is displayed and no traces are displayed then a null wave is returned. +If sweeps or channels is a null wave then select returns a null wave. +If there are no matching sweeps found a null wave is returned.

+
select()
+select(channels(AD), sweeps(), all)
+select(channels(AD4, DA), [1, 5]], all)
+select(channels(AD2, DA5, AD0, DA6), [0, 1, 3, 7], all)
+select(channels(AD2, DA5, AD0, DA6), [0, 1, 3, 7], all, ic)
+
+
+
+
+

range

+

The range function is borrowed from python. It expands +values into a new array.

+

This function can also be used as an operation with the “…” operator which is +the Unicode Character ‘HORIZONTAL ELLIPSIS’ (U+2026). Writing “…” is automatically converted to “…”.

+
range(variable start[, variable stop[, variable step]])
+
+start...stop
+
+start…stop
+
+
+

The function generally accepts 1 to 3 arguments. The operation is intended to be +used with two arguments.

+

The operation accepts also multiple data waves as first argument. Each data wave content must follow the operation argument order and size in that case. +For this case the operation is applied on each input data wave independently and returns the same number of data waves. +The returned data type is SF_DATATYPE_RANGE.

+
range(1, 5, 0.7) == [1, 1.7, 2.4, 3.1, 3.8, 4.5]
+
+
+
+
+

epochs

+

The epochs operation returns information from epochs.

+
epochs(array names[, array selectData[, string type]])
+
+
+
+
name

the name(s) of the epoch. The names can contain wildcard * and !.

+
+
selectData

the second argument is a selection of sweeps and channels where the epoch information is retrieved from. It must be specified through the select operation. When the optional second argument is omitted, select() is used as default that includes all displayed sweeps and channels.

+
+
type

sets what information is returned. Valid types are: range, name or treelevel. If type is not specified then range is used as default.

+
+
+

The operation returns for each selected sweep times matching epoch a data wave. The sweep meta data is transferred to the output data waves. +If there was nothing selected the number of returned data waves is zero. +If the selection contains channels that do not have epoch information stored, e.g. AD, these selections are skipped in the evaluation. +For example if select() is used for the selectData argument then all channels are selected, but only for DA channels epoch information is stored in the labnotebook. +Thus, there are data waves only returned for the DA channels. +If a selection has epoch information stored in the labnotebook and the specified epoch does not exist it is skipped and thus, not included in the output waves.

+

The output data varies depending on the requested type. Multiple epochs for one +sweep always result in additional columns.

+

range: +Each output data wave is numeric and has the start/end times in the rows [ms].

+

name: +Each output data wave is textual and contains name of the epoch.

+

treelevel: +Each output data wave is numeric and has the tree level of the epoch.

+

The returned data type is SF_DATATYPE_EPOCHS. +The default suggested x-axis values for the formula plotter are sweep numbers. The suggested y-axis label is the combination of the requested type (name, tree level, range) and the epoch name wildcards.

+
// get stimset range (epoch ST) from all displayed sweeps and channels
+epochs(ST)
+
+// two sweeps acquired with two headstages set with PulseTrain_100Hz_DA_0 and PulseTrain_150Hz_DA_0 from _2017_09_01_192934-compressed.nwb
+epochs(ST, select(channels(AD), sweeps()), range) == [[20, 1376.01], [20, 1342.67], [20, 1376.01], [20, 1342.67]]
+
+// get stimset range from epochs starting with TP_ and epochs starting with E from all displayed sweeps and channels
+epochs(["TP_*", "E*"], select(channels(AD), sweeps()))
+
+// get stimset range from specified epochs from all displayed sweeps and channels
+epochs(["TP_B?", "E?_*"], select(channels(AD), sweeps()))
+
+// get ranges for epochs TP_B0/TP_B1 where the start is offsetted by 5/10 ms
+epochs(["TP_B0", "TP_B1"], select(channels(AD), sweeps())) + [[5, 10], [0, 0]]
+
+
+
+
+

tp

+

The tp operation returns analysis values for test pulses that are part of selected sweeps.

+
tp(operation mode[, array selectData[, array ignoreTPs]])
+
+
+

The mode argument sets what test pulse analysis is run. +The following tp analysis modes are supported:

+

tpbase() Returns the baseline level in pA or mV depending on the clamp mode.

+

tpinst() Returns the instantaneous resistance values in MΩ.

+

tpss() Returns the steady state resistance values in MΩ.

+

tpfit(string fitFunc, string retValue[, variable maxTrail]) Returns results from fitting the test pulse range.

+

See specific subsections for more details.

+

The second argument is a selection of sweeps and channels where the test pulse information is retrieved from. +It must be specified through the select operation. +When the optional second argument is omitted, select() is used as default that includes all displayed sweeps and channels. +The tp operation pre-filters the selected sweeps, only sweeps with channel type AD are used.

+

The optional argument ignoreTPs allows to ignore some of the found test-pulses. The indices are zero-based and identify the +test-pulses by ascending starting time.

+

If a single sweep contains multiple test pulses then the data from the test +pulses is averaged before analysis. The included test pulses in a single sweep must have the same duration.

+

The operation returns multiple data waves. There is one data wave returned for each sweep/channel selected through selectData. +The sweep and channel meta data is included in each data wave.

+

The returned data type is SF_DATATYPE_TP. +The default suggested x-axis values for the formula plotter are sweep numbers. The suggested y-axis label is the unit of the analysis value (pA, mV, MΩ).

+

Test pulses that are part of sweeps are identified through their respective epoch short name, that starts with “TP” or “U_TP”. +If in selectData nothing is selected the number of returned data waves is zero. +If a selected sweep does not contain any test pulse then for that data wave a null wave is returned.

+
// Get steady state resistance from all displayed sweeps and channels
+tp(tpss())
+
+// Get steady state resistance from all displayed sweeps and AD channels
+tp(tpss(), select(channels(AD), sweeps()))
+
+// Get base line level from all displayed sweeps and DA1 channel
+tp(tpbase(), select(channels(DA1), sweeps()))
+
+// Get base line level from all displayed sweeps and channels ignoring test pulse 0 and 1
+tp(tpbase(), select(), [0, 1])
+
+// Fit the test pulse from all displayed sweeps and channels exponentially and show the amplitude.
+tp(tpfit(exp, amp))
+
+// Fit the test pulse from all displayed sweeps and channels double-exponentially and show the smaller tau from the two exponentials.
+// The fitting range is changed from the default maximum of 250 ms to 500 ms if the next epoch is sufficiently long.
+tp(tpfit(doubleexp, tausmall, 500))
+
+
+
+

tpbase

+

The tpbase operation specifies an operation mode for the tp operation. +In that mode the tp operation returns the baseline level in pA or mV depending on the clamp mode. +tpbase uses a fixed algorithm and takes no arguments.

+
+
+

tpss

+

The tpss operation specifies an operation mode for the tp operation. +In that mode the tp operation returns the steady state resistance values in MΩ. +tpss uses a fixed algorithm and takes no arguments.

+
+
+

tpinst

+

The tpinst operation specifies an operation mode for the tp operation. +In that mode the tp operation returns the instantaneous resistance values in MΩ. +tpinst uses a fixed algorithm and takes no arguments.

+
+
+

tpfit

+

The tpfit operation specifies an operation mode for the tp operation. +In that mode the tp operation fits data from test pulses with the specified fit function template and returns the specified fit result value. +By default the fit range includes the epoch that follows after the test pulse limited up to 250 ms. Whichever ends first. The default time limit can be overwritten with +the third argument.

+
tpfit(string fitFunc, string retValue[, variable maxTrail])
+
+
+

The first argument is the name of a fit function, valid fit functions are exp and doubleexp. +The fit function exp applies the fit: \(y = K_0+K_1*e^{-\frac{x-x_0}{K_2}}\). +The fit function doubleexp applies the fit: \(y = K_0+K_1*e^{-\frac{x-x_0}{K_2}}+K_3*e^{-\frac{x-x_0}{K_4}}\).

+

The second argument specifies the value returned from the fit function. Options are tau, tausmall, amp, minabsamp and fitq. +The option tau returns for the fit function exp the coefficient \(K_2\), for doubleexp it returns \(max(K_2, K_4)\). +The option tausmall returns for the fit function exp the coefficient \(K_2\), for doubleexp it returns \(min(K_2, K_4)\). +The option amp returns for the fit function exp the coefficient \(K_1\), for doubleexp it returns \(K_1\) if \(max(|K_1|, |K_3|) = |K_1|\), \(K_3\) otherwise. +The option minabsamp returns for the fit function exp the coefficient \(K_1\), for doubleexp it returns \(K_1\) if \(min(|K_1|, |K_3|) = |K_1|\), \(K_3\) otherwise. +The option fitq returns the fit quality defined as \(\sum_0^n{(y_i-y_{fit})^2}/(x_n-x_0)\).

+

The optional third argument specifies the time in [ms] after the test pulse that is included in the input data for the fit. +The trail starts at the begin of the TP_B1 epoch. A maxTrail value of zero refers to the end of the TP_B1 epoch. +The value of maxTrail can be negative up to the begin of TP_B1. +If maxTrail is not set then the trail range ends at the beginning of the next epoch on tree level 1 or 250 ms after the end of TP_B1, whichever occurs first.

+
+
+
+

log

+

The log operation prints the first element of input wave to the command line but +passes the wave transparently to the next operation. It is useful for debugging +inside large formulas.

+

The operation accepts also multiple data waves as first argument. +For this case the operation is applied on each input data wave independently and returns the same number of data waves.

+

If the input wave is empty, then log prints nothing and the number of data waves returned is zero.

+
// outputs "1" to the history area
+log(1, 10, 100) == [1, 10, 100]
+
+
+
+
+

log10

+

The log10 operation applies the decadic (base 10) logarithm to its input.

+

The operation accepts also multiple data waves as first argument. +For this case the operation is applied on each input data wave independently and returns the same number of data waves.

+
log10(1, 10, 100) == [0,1,2]
+
+
+
+
+

store

+

The store operation stores data in the labnotebook.

+
store(string name, array data)
+
+
+
+
name

name suffix for the labnotebook entry. The full entry name is “Sweep Formula store [name]” without brackets.

+
+
data

a data wave.

+
+
+

The entries are written to the textual results wave for documentation purposes and +later querying. The second parameter which can be any numerical/textual array, +or output from other operations, is serialized and stored under the given name.

+

The operation returns the data argument unchanged.

+
store("fancy feature", [10, 100])
+
+
+

adds the entry “Sweep Formula store [fancy feature]” with a serialized version +of given array. The serialization format is JSON as described in the +preliminary specification.

+
+
+

merge

+

The merge operation combines multiple single-point waves into a single wave +and accepts one to infinite arguments.

+
merge(array data1, array data2, ...)
+
+
+
+
data1, data2, …

data waves (numeric and text) with only one point.

+
+
+

Especially useful for fitting data from operations like apfrequency which +return the data from different sweeps in separate waves.

+

The operation currently throws away all metadata.

+
merge(4, 7, 8) == [4, 7, 8]
+
+
+
+
+

dataset

+

The dataset operation allows to create arbitrary datasets with any content +and accepts zero to infinite arguments.

+
dataset(array data1, array data2, ...)
+
+
+
+
data1, data2, …

data waves (numeric and text)

+
+
+

Useful for testing SweepFormula itself mainly.

+
dataset(1, [2, 3], "abcd") == [1], [2, 3], ["abcd]
+
+
+
+
+
+

Plotting

+

When clicking the Display button in the SF tab the formula gets parsed, executed and +the result plotted. Evaluating the JSON object from the Formula Parser through the Formula Executor +gives a resulting wave. +For each data wave, the data from the rows is plotted as traces and the columns and layers +are evaluated as an array of traces. Thus, a single plotted trace is created by the following input: +1, 2, 3, 4, 5. Two traces with 5 data points each are created by this input: +[1, 3], [2, 4], [3, 5], [4, 6], [5, 7]. Whereas the input 0…10, 20…30 creates +ten traces with two data points each, starting with the first trace X = 0, Y = 0; X = 1, Y = 20.

+

In typical use cases instead of explicitly writing static data in the formula the data +operation is utilized that returns data in the correct layout.

+

The plotter parses the meta data from data waves as well. For suitable data types +trace colors and legend annotations are associated automatically. Operations can suggest x-values and x-axis labels to the plotter. +If the user has not specified a formula for the x-values then the plotter uses the suggested x-values instead.

+

If the formula results returns a null wave as wave reference wave an error is generated by the formula plotter. +If the formula results contains data waves that are null waves they are skipped by the formula plotter.

+
+

Plotting Text Waves

+

The formula plotter supports that the y-data or the x-data can be a 1d-text-wave. The other wave must be numeric. +2d-text-waves are not supported for plotting.

+
+
+

Separate X-values

+

Sometimes it is useful to explicitly specify X values for a series of data values. +Therefore, two formulas can be plotted against each other by using the vs operator.

+
0...10 vs range(10, 100, 10)
+
+
+

gives

+
+_images/sweepFormulaPlot.svg
+

Note that in this example there are 10 Y-values and only 9 X-values returned by the +respective formula part. The resulting graph shows 9 data points and thus does not show +data points where either an X or Y value for the X, Y value pair is missing.

+
min(data(TP,select(channels(AD0), 4...11,all)))
+vs
+1...8
+
+
+

In the example the select operation selects channel AD0 from sweep 4, 5, 6, 7, 8, 9, 10 and 11. Thus, the data operation returns exactly 8 data waves with sweep data. +Therefore, the min operation returns 8 data waves with exactly one data point. With the specified X-wave that also contains 8 points +the first data wave from min gets the first value of the X-wave paired, the second data wave from min gets the second value of the X-wave paired a.s.o.

+
+
+

Multiple graphs

+

Several graphs can generated with a single input by separating the formulas +with and. The and must be on an own line.

+
0...10 vs range(10, 100, 10)
+and
+10...20 vs range(10, 100, 10)
+and
+20...30
+
+
+

The above code creates a panel with three separate graphs arranged vertically evenly spaced.

+
+_images/sweepFormulaPlot4.png +
+
+
+

Multiple Y-Formulas

+

Several y-formulas can be plotted with the keyword with. The with must be +on an own line between the y-formulas. If the y-data contains different data +units the y-axis will show all data units separated by /. The vs allows to +set a custom x-formula for the single y-formula left to it. Variables, see +next section, can be used to reuse x-formulas for multiple statements without +code duplication.

+
xdata = range(10, 100, 10)
+
+0...10
+with
+20...30 vs $xdata
+and
+30...40
+with
+40...50 vs $xdata
+
+
+
+
+
+

Variables

+

Variables store results of expressions. In formulas variables are included as strings prefixed by $. +They are specified in the lines before the formula expression. The format of a variable definition is +variableName = expression. The variable name must start with a letter. Further allowed letters are alphanumeric and _. +The variable names are treated case-insensitive.

+
c = cursors(A,B)
+s = select(channels(AD), sweeps(), all)
+
+data($c, $s)
+
+
+

The section containing the variable definition can contain empty lines. The first line that is not fulfilling the format for a variable definition is treated as the first line +of the formula expression(s) section. Variable definitions can use variables that were defined in a preceding line.

+
c = cursors(A,B)
+s = select(channels(AD), sweeps(), all)
+d = data($c, $s)
+
+$d
+
+
+

Previous variable content is discarded when the formula notebook is executed.

+
+
Limitations of the current variable definition concept:
    +

  • The expression for a variable definition is resolved to a single wave reference wave

    • +

  • A single variable can not replace multiple arguments of an operation as operation arguments are processed one-at-a-time.

    • +
+
+
+
# This does NOT work
+c = cursors(A,B)
+s = select(channels(AD), sweeps(), all)
+p = $c, $s # p is resolved to a single numerical array
+
+data($p) # the data operation sees a single argument
+
+
+

As a general rule of thumb the result of an operation is a single wave reference wave and thus valid for a variable assignment.

+

Variables are stored in the Data/SweepBrowsers data folder in the variableStorage wave.

+
+
+

Getting Quick Help

+

In the Sweep Formula notebook it is possible to get a quick help for operation and keywords like vs and and. +Mark the operation in question with the mouse and hover over it, a tooltip appears that shows the help for this operation. +Alternatively hold shift and right-click to jump to the Help tab that shows the help for the marked operation.

+
+
+

Writing Operations

+

The following sketches some templates to write an operation.

+

Generally the JSON must not be parsed by the operation itself, but the wrapper functions have to be used.

+

Steps:

+
    +

  • Get and check the number of arguments.

    • +

  • Retrieve and check all mandatory arguments. Use SF_GetArgument for arguments that can consist of multiple data waves and SF_GetArgumentSingle for arguments that are expected to return only a single data wave.

    • +

  • Retrieve all optional arguments from last to first and set for each a default value of not present. (see also operation code for setscale)

    • +

  • Create a output waveRef wave with SF_CreateSFRefWave of the correct size.

    • +

  • Execute the operation calculation, typically for each input data wave independently.

    • +

  • Be aware that a data wave might be a null wave, check sanity of input data wave, tranfer scales from input to calculation result if possible

    • +

  • Handle the Meta data, set a data type and transfer the wave notes on demand.

    • +

  • Return the operation result(s) through SF_GetOutputForExecutor or SF_GetOutputForExecutorSingle if the operation has only a single data wave as result.

    • +

  • Add the data type handling in SF_GetTraceColor and SF_GetMetaDataAnnotationText for proper trace colors and legend annotations in the formula plotter.

    • +
+

Example code for a typical operation taking three arguments, the first argument is some kind of input data.

+
static Function/WAVE SF_OperationTemplate(variable jsonId, string jsonPath, string graph)
+
+       variable numArgs
+       string inDataType
+
+       numArgs = SF_GetNumberOfArguments(jsonID, jsonPath) // Get number of arguments 0 to N
+       SF_ASSERT(numArgs <=3, "Operation has 3 arguments at most.") // Check if number of arguments is correct
+       SF_ASSERT(numArgs > 1, "Operation needs at least two arguments.")
+
+  WAVE/WAVE arg0 = SF_GetArgument(jsonID, jsonPath, graph, SF_OP_OPSHORTNAME, 0) // Get first argument, this getter allows multiple data waves in the argument
+  // For easy operation arguments it is good to have only a single argument with multiple data waves
+
+       WAVE arg1 = SF_GetArgumentSingle(jsonID, jsonPath, graph, SF_OP_OPSHORTNAME, 1, checkExist=1) // Get second argument, only a single data wave is expected that must exist
+       SF_ASSERT(DimSize(arg1, ROWS) == 1, "Too many input values for argument two") // Sanity checks for second argument
+       SF_ASSERT(IsNumericWave(arg1), "opName argument two must be numeric")
+
+  // Parse optional arguments from last to first
+       if(numArgs == 3)
+               WAVE arg2 = SF_GetArgumentSingle(jsonID, jsonPath, graph, SF_OP_OPSHORTNAME, 2, checkExist=1)
+               SF_ASSERT(DimSize(arg2, ROWS) == 1, "Too many input values for parameter edge")
+               SF_ASSERT(IsNumericWave(arg2), "edge parameter must be numeric")
+       else
+     // Set default value for optional argument if not existing
+               Make/FREE edge = {FINDLEVEL_EDGE_BOTH}
+       endif
+
+  // Create output wave
+       WAVE/WAVE output = SF_CreateSFRefWave(graph, SF_OP_OPSHORTNAME, DimSize(arg0, ROWS))
+       output = OperationCalculation(arg0[p], arg1[0], arg2[0])
+
+  // Handle meta data
+  // Set data type and transfer sweep information if input data was of the correct type
+
+       SetStringInJSONWaveNote(results, SF_META_DATATYPE, SF_DATATYPE_THISOP)
+       inDataType = GetStringFromJSONWaveNote(dataRef, SF_META_DATATYPE)
+       if(!CmpStr(inDataType, SF_DATATYPE_SWEEP))
+               SF_TransferFormulaDataWaveNote(arg0, output, "Sweeps", SF_META_SWEEPNO)
+       endif
+
+  // Return multiple data waves to executor, the function will wrap the wave ref wave to a one element text wave
+       return SF_GetOutputForExecutor(results, graph, SF_OP_OPSHORTNAME)
+End
+
+static Function/WAVE OperationCalculation(WAVE/Z input, variable arg1, variable arg2)
+
+       if(!WaveExists(input))
+               return $""
+       endif
+
+  // Sanity checks on input data waves
+       SF_ASSERT(IsNumericWave(input), "opname requires numeric data as input")
+       SF_ASSERT(WaveDims(input) <= 2, "opname accepts only upto 2d data")
+       SF_ASSERT(DimSize(input, ROWS) > 0, "opname requires at least one data point")
+       // Do the actual calculation
+  MatrixOP/FREE out = sqrt(averageCols(magsqr(input)))^t
+  // Transfer the scaling if possible
+       SF_FormulaWaveScaleTransfer(input, out, COLS, ROWS)
+
+       return out
+End
+
+
+

Example code for an operation taking the top array as input data. The specific difference here is that we use a convention that if there +is only a single argument then we parse it as it could possibly an argument with multiple data waves. If it is just regular data then it is converted +to a single data wave with one element and thus, stays compatible with the SF_GetArgumentTop parsing, if that would have encountered a single element. +This allows to put output from e.g. data directly in such an operation as first argument. The operation works then on each data wave separately.

+
 static Function/WAVE SF_OperationTemplate(variable jsonId, string jsonPath, string graph)
+
+        variable numArgs
+
+        numArgs = SF_GetNumberOfArguments(jsonId, jsonPath)
+        if(numArgs > 1)
+                WAVE/WAVE input = SF_GetArgumentTop(jsonId, jsonPath, graph, SF_OP_OPSHORTNAME)
+        else
+                WAVE/WAVE input = SF_GetArgument(jsonId, jsonPath, graph, SF_OP_OPSHORTNAME, 0)
+        endif
+        WAVE/WAVE output = SF_CreateSFRefWave(graph, SF_OP_OPSHORTNAME, DimSize(input, ROWS))
+
+        output[] = OperationCalculation(input[p])
+
+        SFH_TransferFormulaDataWaveNoteAndMeta(input, output, SF_OP_OPSHORTNAME, SF_DATATYPE_OP)
+
+        return SF_GetOutputForExecutor(output, graph, SF_OP_OPSHORTNAME, clear=input)
+End
+
+static Function/WAVE OperationCalculation(WAVE/Z input)
+
+  // data waves can be null
+       if(!WaveExists(input))
+              return $""
+       endif
+
+       SF_ASSERT(IsNumericWave(input), "opName requires numeric input data.")
+       SF_ASSERT(DimSize(input, ROWS) > 0, "opName input must have at least one data point")
+  // Do actual calculation
+       WAVE out = NewFreeWave(IGOR_TYPE_64BIT_FLOAT, 0)
+       Integrate/METH=1/DIM=(ROWS) input/D=out
+  // Transfer scales and adapt
+       CopyScales input, out
+       SetScale/P x, DimOffset(input, ROWS), DimDelta(input, ROWS), "dx", out
+
+       return out
+End
+
+
+

The function SFH_TransferFormulaDataWaveNoteAndMeta transfers the meta information and wave notes of the reference and data waves. +It also updates the operation stack information. There are two cases where SFH_TransferFormulaDataWaveNoteAndMeta can not be used:

+
    +

  • The operation does not take an input reference wave

    • +

  • The operation returns data through SF_GetOutputForExecutorSingle that creates the reference wave.

    • +
+

For operation that do not take an input reference wave that is calculated to an output reference wave the approach is to update the operation stack +meta information directly through JWN_SetStringInWaveNote(output, SF_META_OPSTACK, AddListItem(SF_OP_OPSHORT, “”)). +If SF_GetOutputForExecutorSingle is called then the optional parameter opStack should be set to the previous operation stack. For operations like +sweeps() there is no previous operation, thus the parameter would be opStack=””.

+

It should be noted that there is a difference for parsing a single first argument through SF_GetArgument or SF_GetArgumentTop. +SF_GetArgument starts execution for argument 0 specifically at the /0 JSON path location, whereas SF_GetArgumentTop starts execution at /. +Set the case that the first argument is wave(pathToWave) with a 1d-wave containing a single element with value 17. +SF_GetArgument executes the wave operation first, whereas SF_GetArgumentTop executes the array [wave(pathToWave)] first. +Thus, SF_GetArgument sees with the resolved wave operation [17], whereas SF_GetArgumentTop sees [[17]]. Therefore the first returns a +{17} wave and the latter a {{17}} wave.

+

More complex operation such as data build the output wave reference wave dynamically. See SF_GetSweepsForFormula how the output wave is build depending on selectData and the found sweeps.

+
+

Meta Data Handling

+

Operation as well as the formula plotter can evaluate returned meta data from the result wave(s). Generally meta data is set through JSON wave notes. +Data wave independent meta data is set in the wave ref wave, whereas data wave dependent data is set as note of the data wave(s) itself. +Currently certain key constants for meta data fields are defined.

+

For the wave ref wave:

+
    +

  • SF_META_DATATYPE: string, data type of operation result (some operations are transparent for that)

    • +

  • SF_META_XAXISLABEL: string, suggested label for the x-axis for the plotter, typically combined with x-value meta data in the data wave(s)

    • +

  • SF_META_YAXISLABEL: string, suggested label for the y-axis for the plotter

    • +

  • SF_META_OPSTACK: string, tracks the operation stack

    • +
+

For the data wave(s):

+
    +

  • SF_META_SWEEPNO: number, number of the sweep that provided the source data

    • +

  • SF_META_CHANNELTYPE: number, channel type from the sweep that provided the source data

    • +

  • SF_META_CHANNELNUMBER: number, channel number from the sweep that provided the source data

    • +

  • SF_META_XVALUES: wave, suggested x-wave for the plotter to display this data wave

    • +
+

See also SF_OperationLabnotebookImpl, where such meta data is set.

+

The function SFH_TransferFormulaDataWaveNoteAndMeta transfers meta data from one operation to the next. +If the following conditions are met then a suggested X-values are set in the meta data:

+
    +

  • The input data type is SF_DATATYPE_SWEEP and all output data waves have no wave units for x set and all output data waves have only one data point -> sweep number is set as X-value and “Sweeps” as x label

    • +

  • For any not above specified input data type: if all output data wave have one data point and all output data waves have no wave units for x set and the input data wave has a sweep number value set in the meta data -> sweep number is set as X-value and “Sweeps” as x label

    • +
+
min(
+  butterworth(
+    integrate(
+      derivative(
+        data(TP,select(channels(AD0), 4...11,all))
+      )
+    )
+  ,4,100,4)
+)
+
+
+

In the above example the data operation sets sweep number as meta data. The SFH_TransferFormulaDataWaveNoteAndMeta function transfers that meta data also to the results of the outer operations. +The data waves returned from the min operation contain only a single data point and the result complies with the second set of conditions mentioned above. Thus, the results are +displayed in the plotter with sweep numbers on the x-axis and “Sweeps” as x-label.

+
+
+

Operation Stack

+

The operation stack meta data is updated in the called operation, typically through SFH_TransferFormulaDataWaveNoteAndMeta. +It is a semicolon separated list of operations called for a single formula, where the most recent operation is at the front of the list. +Operations where data from several sources is joined, like plus discard the previous operation stack. Thus, the operation stack contains +only operations that were relevant for the strands of data that reaches ultimately the formula plotter. +The operation stack information is used to create the trace legend(s) in the graph(s) as well as for the trace names. +Also the trace color is determined through evaluation of the operation stack. For example, only if the operation stack indicates that the most recent data +originated from a data() operation without intermediate operations that break this data strand, such as +, then the meta iformation about sweep data is taken to +determine the traces color.

+
+
+

Argument Setup Stack

+

The idea of the argument setup stack is to store the arguments of each operation to be able determine differences between formulas +in the end. This information can be used to change the trace style for differently setup formulas when plotted in the same graph with the +with keyword. Also in the legend it can be shown what was setup differently. +Operations can prepare argument setup information through a key/value style text wave with two columns. The wave is created with +SFH_GetNewArgSetupWave and is filled then by the operation e.g.:

+
WAVE/T argSetup = SFH_GetNewArgSetupWave(5)
+
+argSetup[0][%KEY] = "Method"
+argSetup[0][%VALUE] = SF_OperationApFrequencyMethodToString(method)
+argSetup[1][%KEY] = "Level"
+argSetup[1][%VALUE] = num2str(level)
+argSetup[2][%KEY] = "ResultType"
+argSetup[2][%VALUE] = timeFreq
+argSetup[3][%KEY] = "Normalize"
+argSetup[3][%VALUE] = normalize
+argSetup[4][%KEY] = "XAxisType"
+argSetup[4][%VALUE] = xAxisType
+
+
+

This information is stored when SFH_TransferFormulaDataWaveNoteAndMeta is called with the optional argSetup argument. +If not setup by the operation, by default the only argSetup entry is the operation short name. Thus, the information content +without setting it up is the same as in the operation stack.

+

The information is evaluated in the Formula Plotter to determine if traces from different formulas specified through the with keyword +need to be shown with a different marker or line style. It also adapts the legend to show details about differences in arguments in formulas.

+
apfrequency(data(ST, select(channels(AD), sweeps(), all)), 3, 100, freq, normoversweepsavg, count)
+with
+apfrequency(data(ST, select(channels(AD), sweeps(), all)), 3, 100, time, norminsweepsavg, count)
+
+
+
+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/SweepFormula_PSX.html b/SweepFormula_PSX.html new file mode 100644 index 0000000000..bb03315f5b --- /dev/null +++ b/SweepFormula_PSX.html @@ -0,0 +1,319 @@ + + + + + + + + SweepFormula PSC/PSP classification — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

SweepFormula PSC/PSP classification

+

When using the psx SweepFormula operation the normal graphing is +enhanced by various additional graphs and user interface options. +The following graph shows the layout for a psx and psxStats operation with +real acquired data.

+
+_images/SweepFormula-PSX-GUI.png +
+

SweepFormula PSX GUI

+
+
+

The main panel SweepFormula plot from <Browser> has a left vertical column +with UI controls, the psx graph at the top and a psxstats graph at the bottom.

+

Above the main panel are again some UI controls on the very left, the all event +graph and then the single event graph at the very right.

+
+
+

Main panel

+
+

Left UI controls

+
    +

  • Store: Store the event properties including the classification results +(Event State and Fit State) in the results waves using the +id as key and JSON as serialization format.

    • +

  • Load: Load the event properties from the results wave using the currently +active id

    • +

  • Jump: Jump to the next event having event state undetermined, also +changes the combination if required.

    • +

  • Suppress Update: Avoid updating the top all and single event graphs on +event/fit state and/or cursor changes.

    • +

  • ListBox: The combinations listbox has an entry for every combination of +range and select where psx found at least one event. The psx +graph only ever plots one combination, and therefore one can choose the +to-be-plotted combination here.

    • +

  • i: Button to copy the psx/psxkernel/psxRiseTime input parameters to +the clipboard

    • +

  • UI: Hover over this element with the mouse to learn about the keyboard shortcuts

    • +
+
+

psx

+

The psx graph represents the results of the event search and is split +vertically into two graphs. The top one shows the filtered and offsetted sweep +data, the lower one in addition the deconvolution with the input from psxkernel.

+

All found events are marked initially as undetermined for the Event/Fit state.

+

The Event state is visualized by colorized markers: a grey square for +undetermined, a green circle for accept and a red triangle for reject.

+

With the A cursor a single event can be selected, properties of that event are +displayed in the single event graph (top right).

+

The following options exist to set the event and fit state of a single or multiple events:

+
+
Mouse Control
+
    +

  • Toggle the state of a single event by pressing CTRL and clicking on it +with the left mouse button

    • +

  • Draw a marquee and select one of following custom menu entries:

    +
      +

    • PSX: Accept Event & Fit

      • +

    • PSX: Reject Event & Fit

      • +

    • PSX: Accept Fit

      • +

    • PSX: Reject Fit

      • +
    +

    which operate on all events inside the marquee and perform the obvious thing.

    +

    The PSX: Jump to Events entry is only useful inside the psxstats graph as +it brings the events inside the marquee into view in the psx plot.

    +
    • +
+
+
+
Keyboard Control
+

The following keyboard shortcuts work for either the psx or the psxstats +graphs. All of them require that the cursor A is located on an event, which +is by default the case for the psx graph. The current direction for automatic +advancement defaults to left-to-right.

+
    +

  • ↑ (up): Accept the current event, changing both event and fit state to +accept, and advance the cursor to the next event in the current direction

    • +

  • ↓ (down): Reject the current event, changing both event and fit state to +reject, and advance the cursor to the next event in the current direction

    • +

  • → (right): Move the cursor to the next event on the right

    • +

  • ← (left): Move the cursor to the previous event on the left

    • +

  • (space): Toggle the event and fit state of the current event without any movement

    • +

  • r: Reverse the current direction

    • +

  • c: Center the x-axis around the current event

    • +

  • e: Toggle the event state

    • +

  • f: Toggle the fit state

    • +

  • z: Accept the event state but reject the fit state

    • +
+
+
+
+

psxstats

+

Visualizes properties of the given combinations. The marquee and the keyboard +control options from the psx graph are also available.

+
+
+
+
+

Top Panel

+
+

Left UI controls

+

The combination to select the drawn single events and their averages from are +determined by the state of the Current combo checkbox. The state to use for +the selection, either fit or event state, is determined by the popup menu.

+
    +

  • Accept: Show all accepted events

    • +

  • Reject: Show all rejected events

    • +

  • Undetermined: Show all undetermined events

    • +

  • Average:

    +
      +

    • Accept: Show all the average of all accepted events

      • +

    • Reject: Show all the average of all rejected events

      • +

    • Undetermined: Show the average of all undetermined events

      • +

    • All: Show the average of all events regardless of the state

      • +
    • +
      Fit: Show the fit of the averaged events, the fit coefficients are also
      +

      stored in the results wave

      +
      +
        +

      • i: Hover over this element with the mouse to view the average fit +coefficients

        • +
      +
      +
      +
      • +
    +
    • +

  • Current combo: Restrict the event selection to the currently selected +combination (checked) or use all of them (unchecked)

    • +

  • Fit State/Event State: Select the state to use as basis for selection

    • +

  • dblexp_peak/dblexp_XOffset: Select the fit curve for the average fit

    • +

  • Onset/peak: Select the event property to offset the events in the all +events graph to

    • +

  • Block size [%]: Percentage to select what part of the events are +displayed in the all events graph. This can help with reducing the number of +plotted events so that the interactive event classification in the all event +graph is easier.

    • +

  • Block: Block number to display in the all events graph in case a block +size smaller than 100% was selected.

    • +
+
+

All event graph

+

The top left graph shows events and average selected by the UI controls to its +left. The state can be changed by hovering the mouse over an event trace and +pressing the keyboard shortcuts available for the psx graph.

+
+
+

Single event graph

+

The top right graph shows a single event including its fit (greyish line) which might +not be present as well. The shown event is selected by cursor A in the psx +graph. The textbox has various properties of the shown event.

+

No UI options are available for this graph.

+
+
+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/TPAnalysis_algorithm.html b/TPAnalysis_algorithm.html new file mode 100644 index 0000000000..2bd2a9f229 --- /dev/null +++ b/TPAnalysis_algorithm.html @@ -0,0 +1,584 @@ + + + + + + + + Testpulse Analysis Algorithm — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+
+
+

Testpulse Analysis Algorithm

+

This algorithm has been moved as simpler code to TP_TSAnalysis() and TP_ROAnalysis().

+
+

Description

+

The algorithm analyses the measured test pulse response to determine the instantaneous resistance, +the steady state resistance and the baseline steady state.

+

The TP_Delta() function is called after data is available for each device. +This data can contain test pulse responses from several head stages from multiple ADC channels.

+

The function is split into several parts:

+
+
+
+
+
+

Principles

+

The goal of the algorithm is to determine the base line level, +steady state resistance and instantaneous resistance of a test pulse response. +The available data contains the response pulse as +well as information about the excitation amplitude and length. +The excitation pulse is in units of current or voltage depending on the used +clamp mode. The actual data consists of discrete points of analog to digital +input (response). +For simplicity this will be neglected in the following.

+

The resistance is calculated by

+
+\[R = \frac{U}{I}\]
+

Where depending on voltage- or current clamp mode the response test pulse is either +a current or voltage. The response is the difference between base line live and +steady state / instantaneous level. For determining the levels in the response data +ranges are defined where the data points get averaged.

+

The known ranges are

+
+\[\begin{split}baselinefraction &= fullTPrange * baselinefrac \\ +duration &= activeTPtime\end{split}\]
+

Where baselinefrac is the part relative to the full test pulse range in the +front of the test pulse where the excitation signal was at its base line level. +The time duration is the length of the active portion of the exciting test pulse.

+

The range for averaging for the base line level is defined minimum of:

+
+\[baselineAvgRange = Min( 5 ms, 0.2 * duration, 0.2 * baselinefraction)\]
+

The reference point for the end of the range is defined to be close to the start +of the active test pulse:

+
+\[\begin{split}end &= baselinefraction - const \\ +begin &= end - baselineAvgRange\end{split}\]
+

The base line level is determined by averaging over all discrete data points +p in this range:

+
+\[baselinelevel = \frac{1}{N} \sum^{end}_{n=begin} p_n\]
+

The range for averaging for the steady state level is defined to be equal to the +base line averaging length. The reference point for the end of the range is +defined to be close to the end of the active test pulse:

+
+\[\begin{split}end &= (1 - baselinefrac) * fullTPrange - const \\ +begin &= end - baselineAvgRange\end{split}\]
+

The steady state level is determined by averaging over all discrete data points +p in this range:

+
+
+\[steadystatelevel = \frac{1}{N} \sum^{end}_{n=begin} p_n\]
+
+

The range for averaging for the instantaneous level is 0.25 ms. The reference +point for the start of the range is defined to be close after the start of the +active test pulse:

+
+
+\[\begin{split}end &= baselinefraction + const \\ +begin &= end - 0.25 ms\end{split}\]
+
+

In this partial range P I of all points p the discrete location of the +point with maximum value is determined.

+
+
+\[locMax = MaxLocation(P_I); P_I = P[begin, end]\]
+
+

The instantaneous level is determined by the data point p at +locMax:

+
+
+\[instantaneouslevel = p_{locMax}\]
+
+

Note that the constant const for the reference point offset is the same for +all three ranges.

+

The current/voltage amplitudes for are the differences of the levels to the base +line level:

+
+\[\begin{split}steadstateAmp &= steadystatelevel - baselinelevel \\ +instantaneousAmp &= instantaneouslevel - baselinelevel\end{split}\]
+

With the amplitudes and the known clamp amplitudes the resistances are:

+
+\[\begin{split}R_{SS} &= \frac{steadystateAmp}{currentClampAmp} \\ +R_{Inst} &= \frac{instantaneoueAmp}{currentClampAmp}\end{split}\]
+

Respectively for voltage clamp:

+
+\[\begin{split}R_{SS} &= \frac{voltageClampAmp}{steadystateAmp} \\ +R_{Inst} &= \frac{voltageClampAmp}{instantaneoueAmp}\end{split}\]
+

The function returns the resistances as well as the base line level.

+
+
+

Miscellaneous at startup

+

To log the function execution time the current time is retrieved by

+
referenceTime = DEBUG_TIMER_START()
+
+
+

The test pulse response is saved if the GUI checkbox was enabled by TP_StoreFullWave():

+
WAVE GUIState = GetDA_EphysGuiStateNum(device)
+
+if(GUIState[0][%check_Settings_TP_SaveTP])
+  TP_StoreFullWave(device)
+endif
+
+
+
+
+

Retrieving input data

+

The device specific data folder for the test pulse is retrieved. The current and +voltage clamp parameters are retrieved from it. It is used as well to put the +calculated BaselineSSAvg, SSResistance and InstResistance back to the +devices test pulse data folder.

+
DFREF dfr = GetDeviceTestPulse(device)
+
+
+

The actual test pulse data is retrieved from OscilloscopeData, where the data +points are stored in rows and the columns count the DAC, ADC and TTL channels +(in this order).

+
WAVE OscilloscopeData = GetOscilloscopeWave(device)
+
+
+

Retrieve device specific Current Clamp and Voltage Clamp amplitudes. The values +are in pA and mV and can be set on the front panel in the tab +“Data Acquisition”. Default: -50 pA / 10 mV.

+

Retrieve the column of the first ADC channel in OscilloscopeData wave, +due to the DAC, ADC, TTL order it is 1 for one enabled head stage, +2 for two enabled head stages a.s.o.

+
NVAR ADChannelToMonitor = $GetADChannelToMonitor(device)
+
+
+

Retrieve head stage properties, where rows count the active head stages and +columns enumerate the properties. It is used later to decide if a certain head +stage operates in current clamp or voltage clamp mode.

+
WAVE activeHSProp = GetActiveHSProperties(device)
+
+
+

The test pulse is centered on a baseline, the baselineFrac is a number < 1, that +defines the fraction in front and after the test pulse. Example: With a typical +value of 0.25 for baselineFrac, the whole test pulse consists of parts of +0.25_baseline + 0.5_testpulse + 0.25_baseline.

+

Length of the buffer that stores previous results of BaselineSSAvg, +SSResistance and InstResistance for a running average. The running +average is later applied by TP_CalculateAverage() if the size is > 1. +The size is set on the front panel in the Settings tab.

+

The later resistance calculation is based on R = U / I. Since R is always +positive, the sign of the local clamp current/voltage variables is removed.

+
amplitudeIC = abs(amplitudeICGlobal)
+amplitudeVC = abs(amplitudeVCGlobal)
+
+
+
+
+

Extraction of ranges

+

The duration of the test pulse is converted to time by using the scale delta of +the OscilloscopeData waves rows, which is the sample interval.

+
durationInTime = duration * DimDelta(OscilloscopeData, ROWS)
+
+
+

The length in time of the base line fraction is calculated by the fraction of the +full test pulse length multiplied by the scale delta of the OscilloscopeData +waves rows, which is the sample interval.

+
baselineInTime = baseLineFrac * lengthTPInPoints * DimDelta(OscilloscopeData, ROWS)
+
+
+

For the determination of the baseline level and the steady state level a small +range of points is taken into account. The range the lowest value of either

+
+
    +

  • 5 ms

    • +

  • 20% of the test pulse duration

    • +

  • 20% of the base line duration

    • +
+
+

The range is converted to points by dividing through the sample interval.

+
evalRangeInPoints = min(5, 0.2 * min(durationInTime, baselineInTime)) / DimDelta(OscilloscopeData, ROWS)
+
+
+

The reference point for the base line determination is defined by the base line +fraction multiplied by the length of the test pulse in points, which gives the +onset point of the active test pulse.

+
evalOffsetPointsCorrected = (TP_EVAL_POINT_OFFSET / sampleInt) * HARDWARE_ITC_MIN_SAMPINT
+refPoint = baselineFrac * lengthTPInPoints - evalOffsetPointsCorrected
+
+
+

The base line range in points is defined from the reference point minus the +evalRangeInPoints to the reference point.

+
BaselineSSStartPoint = refPoint - evalRangeInPoints
+BaselineSSEndPoint   = refPoint
+
+
+

The reference point for the steady state level determination is defined by +1 - base line fraction multiplied by the length of the test pulse, which gives +the end point of the active test pulse.

+
refPoint = (1 - baselineFrac) * lengthTPInPoints - evalOffsetPointsCorrected
+
+
+

The steady state range in points is defined from the reference point minus the +evalRangeInPoints to the reference point.

+
TPSSStartPoint = refPoint - evalRangeInPoints
+TPSSEndPoint   = refPoint
+
+
+

The range for the points to calculate the instantaneous resistance is a fixed range +of 0.25 ms. It is converted to points by dividing the sample interval.

+
evalRangeInPoints = 0.25 / DimDelta(OscilloscopeData, ROWS)
+
+
+

The reference point is defined by the base line +fraction multiplied by the length of the test pulse in points, which gives the +onset point of the active test pulse.

+
refPoint = baselineFrac * lengthTPInPoints + evalOffsetPointsCorrected
+
+
+

The range of points for the instantaneous resistance calculation is defined from +the reference point to the reference point plus 0.25 ms in points.

+
TPInstantaneousOnsetPoint = refPoint
+TPInstantaneousEndPoint   = refPoint + evalRangeInPoints
+
+
+
+
The calculated ranges are used to create free waves BaselineSS, TPSS and

Instantaneous that store the specific row range of the OscilloscopeData +wave. This includes all columns.

+
+
+
Duplicate/FREE/R=[BaselineSSStartPoint, BaselineSSEndPoint][] OscilloscopeData, BaselineSS
+Duplicate/FREE/R=[TPSSStartPoint, TPSSEndPoint][] OscilloscopeData, TPSS
+Duplicate/FREE/R=[TPInstantaneousOnsetPoint, TPInstantaneousEndPoint][] OscilloscopeData, Instantaneous
+
+
+
+_images/testPulse-visualization_new.svg
+
+
+

Calculation

+

The steady state ranges are summed by columns (n x m to 1 x m wave) and divided +the number of rows (i.e. number of points) to get the average per channel. The +resulting wave is AvgTPSS (1 x m) holding the steady state averages.

+
MatrixOP /free /NTHR = 0 AvgTPSS = sumCols(TPSS)
+avgTPSS /= dimsize(TPSS, ROWS)
+
+
+

The base line ranges are summed by columns (n x m to 1 x m wave) and divided +by the number of rows (equals number of points per channel) to get the average +per channel. The resulting wave is AvgBaselineSS (1 x m) holding the base +line averages.

+
MatrixOp /FREE /NTHR = 0   AvgBaselineSS = sumCols(BaselineSS)
+AvgBaselineSS /= dimsize(BaselineSS, ROWS)
+
+
+

The base line average wave is duplicated to a reduced wave containing only the +active ADC channels and is put back into the test pulse folder. A reference to +the reduced wave is kept as BaselineSSAvg. The current number of AD channels +is used to skip the DAC channels. The full remaining range is duplicated, requiring +that no TTL channels are active (original column order from OscilloscopeData +wave with DAC, ADC, TTL)

+
Duplicate/O/R=[][ADChannelToMonitor, dimsize(BaselineSS,1) - 1] AvgBaselineSS dfr:BaselineSSAvg/Wave=BaselineSSAvg
+
+
+

The absolute difference of the steady state level and the base line level is +calculated by abs(AvgTPSS - AvgBaselineSS) per AD channel and stored in +AvgDeltaSS.

+
Duplicate/FREE AvgTPSS, AvgDeltaSS
+AvgDeltaSS -= AvgBaselineSS
+AvgDeltaSS = abs(AvgDeltaSS)
+
+
+

A free wave InstAvg (1 x col) for calculating the instantaneous average is +created, where col is the column number of OscilloscopeData, but at least 1.

+
columnsInWave = dimsize(Instantaneous, 1)
+if(columnsInWave == 0)
+  columnsInWave = 1
+endif
+
+Make/FREE/N=(1, columnsInWave) InstAvg
+
+
+

For each active AD channel:

+
+

The column of Instantaneous is extracted to a 1d +free wave Instantaneous1d. WaveStats is applied to retrieve the point location +of the minimum and maximum value V_minRowLoc and V_maxRowLoc in Instantaneous1d. +The base line level average for the current AD channel is read from AvgBaselineSS +to the variable OndDBaseline, which is not further used. +Depending on the set clamp mode of the current AD channel from activeHSProp +and the sign of V/I-clamp amplitude of the current device the maximum or minimum +region is averaged:

+
+
    +

  • V-clamp mode and positive amplitude -> maximum region

    • +

  • V-clamp mode and negative amplitude -> minimum region

    • +

  • I-clamp mode and positive amplitude -> maximum region

    • +

  • I-clamp mode and negative amplitude -> minimum region

    • +
+
+

The average is calculated by using the mean function that averages from scaled +location x1 to x2. x1 is the scaled location for the point at V_maxRowLoc - 1 +and x2 is the scaled location for the point at V_maxRowLoc + 1. This effectively +calculated the mean from three consecutive points in Instantaneous1d and +puts it into the first row of InstAvg at the unreduced column position of +the active AD channel.

+

The same averaging is done when the minimum region is targeted with V_minRowLoc.

+

The MultiThread directive is questionable here as it is a single value assignment.

+
+
do
+  matrixOp /Free Instantaneous1d = col(Instantaneous, i + ADChannelToMonitor)
+  WaveStats/Q/M=1 Instantaneous1d
+  OndDBaseline = AvgBaselineSS[0][i + ADChannelToMonitor]
+  if((activeHSProp[i][%ClampMode] == V_CLAMP_MODE ? sign(amplitudeVCGlobal) : sign(amplitudeICGlobal)) == 1) // handles positive or negative TPs
+    Multithread InstAvg[0][i + ADChannelToMonitor] = mean(Instantaneous1d, pnt2x(Instantaneous1d, V_maxRowLoc - 1), pnt2x(Instantaneous1d, V_maxRowLoc + 1))
+  else
+    Multithread InstAvg[0][i + ADChannelToMonitor] = mean(Instantaneous1d, pnt2x(Instantaneous1d, V_minRowLoc - 1), pnt2x(Instantaneous1d, V_minRowLoc + 1))
+  endif
+  i += 1
+while(i < (columnsInWave - ADChannelToMonitor))
+
+
+

Afterwards the absolute difference to the base line averages from +AvgBaselineSS is calculated and put back to InstAvg. Also here the +MultiThread is questionable as the wave is (1 x m) with m the number of channels.

+
Multithread InstAvg -= AvgBaselineSS
+Multithread InstAvg = abs(InstAvg)
+
+
+

The steady state delta wave is duplicated to a reduced wave containing only the +active AD channels and is put back into the test pulse folder. A reference to +the reduced wave is kept as SSResistance. The current number of AD channels +is used to skip the DAC channels. The full remaining range is duplicated, requiring +that no TTL channels are active (original column order from OscilloscopeData +wave with DAC, ADC, TTL)

+

The x scale of the SSResistance wave is set to the time where the +TPSSEndPoint is located. As SSResistance is a (1 x m) wave, this sets the +time point for the averaged data.

+
Duplicate/O/R=[][ADChannelToMonitor, dimsize(TPSS,1) - 1] AvgDeltaSS dfr:SSResistance/Wave=SSResistance
+SetScale/P x IndexToScale(OscilloscopeData, TPSSEndPoint, ROWS),1,"ms", SSResistance // this line determines where the value sit on the bottom axis of the oscilloscope
+
+
+

The instantaneous average wave is duplicated to a reduced wave containing only the +active AD channels and is put back into the test pulse folder. A reference to +the reduced wave is kept as InstResistance. The current number of AD channels +is used to skip the DAC channels. The full remaining range is duplicated, requiring +that no TTL channels are active (original column order from OscilloscopeData +wave with DAC, ADC, TTL)

+

The x scale of the InstResistance wave is set to the time where the +TPInstantaneousOnsetPoint is located. As InstResistance is a (1 x m) wave, +this sets the time point for the averaged data.

+
Duplicate/O/R=[][(ADChannelToMonitor), (dimsize(TPSS,1) - 1)] InstAvg dfr:InstResistance/Wave=InstResistance
+SetScale/P x IndexToScale(OscilloscopeData, TPInstantaneousOnsetPoint, ROWS),1,"ms", InstResistance
+
+
+

For each active AD channel: The actual resistance is calculated by the formula R = U / I for +SSResistance and InstResistance.

+

For I-clamp mode of the current channel:

+
+
    +

  • SSResistance = AvgDeltaSS / amplitudeIC * 1000

    • +

  • InstResistance = InstAvg / amplitudeIC * 1000

    • +
+
+

For V-clamp mode of the current channel:

+
+
    +

  • SSResistance = amplitudeVC / AvgDeltaSS * 1000

    • +

  • InstResistance = amplitudeVC / InstAvg * 1000

    • +
+
+

AvgDeltaSS contains the absolute difference of the steady state level and the base line level. +InstAvg contains the absolute difference of the instantaneous level and the base line level. +By default the current values are in pA and the voltage values in mV, thus the resulting resistance values are +in MΩ.

+
i = 0
+do
+  if(activeHSProp[i][%ClampMode] == I_CLAMP_MODE)
+    // R = V / I
+    Multithread SSResistance[0][i] = (AvgDeltaSS[0][i + ADChannelToMonitor] / (amplitudeIC)) * 1000
+    Multithread InstResistance[0][i] =  (InstAvg[0][i + ADChannelToMonitor] / (amplitudeIC)) * 1000
+  else
+    Multithread SSResistance[0][i] = ((amplitudeVC) / AvgDeltaSS[0][i + ADChannelToMonitor]) * 1000
+    Multithread InstResistance[0][i] = ((amplitudeVC) / InstAvg[0][i + ADChannelToMonitor]) * 1000
+  endif
+  i += 1
+while(i < (dimsize(AvgDeltaSS, 1) - ADChannelToMonitor))
+
+
+

columns is set that holds the number of active AD channels, but at least 1. +It is later used to set the number of ADCs for calling TP_RecordTP().

+
columns = DimSize(TPSS, 1) - ADChannelToMonitor
+if(!columns)
+  columns = 1
+endif
+
+
+
+_images/testPulse-averaging.svg
+
+
+

Running Average of results

+

A running average is applied if tpBufferSize is greater than one. +TPBaselineBuffer, TPInstBuffer and TPSSBuffer are the waves holding +the values for the running average and are at maximum (tpBufferSize x m) in size. +TP_CalculateAverage() takes the new value from the second parameter and puts the +averaged value back therein.

+
 if(tpBufferSize > 1)
+   // the first row will hold the value of the most recent TP,
+   // the waves will be averaged and the value will be passed into what was storing the data for the most recent TP
+   WAVE/SDFR=dfr TPBaselineBuffer, TPInstBuffer, TPSSBuffer
+
+  TP_CalculateAverage(TPBaselineBuffer, BaselineSSAvg)
+  TP_CalculateAverage(TPInstBuffer, InstResistance)
+  TP_CalculateAverage(TPSSBuffer, SSResistance)
+endif
+
+
+
+
+

Final Calls

+

numADCs is set to the value of columns and TP_RecordTP() is called to +set the TPStorage wave with the given averages. All the input waves are reduced +waves holding only AD channels. DQ_ApplyAutoBias() is called with the +current values of BaselineSSAvg and SSResistance. +Finally the elapsed time since function start is printed to the debug output.

+
variable numADCs = columns
+TP_RecordTP(device, BaselineSSAvg, InstResistance, SSResistance, numADCs)
+DQ_ApplyAutoBias(device, BaselineSSAvg, SSResistance)
+
+DEBUGPRINT_ELAPSED(referenceTime)
+
+
+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/_downloads/67f59d897c12b62a94a4795fb94a9ccb/0001-WIP-fast-sphinx-rst-update-cycle.patch b/_downloads/67f59d897c12b62a94a4795fb94a9ccb/0001-WIP-fast-sphinx-rst-update-cycle.patch new file mode 100644 index 0000000000..b9b0527282 --- /dev/null +++ b/_downloads/67f59d897c12b62a94a4795fb94a9ccb/0001-WIP-fast-sphinx-rst-update-cycle.patch @@ -0,0 +1,78 @@ +From 442b099da06bd393b5ae53211ae2c8026dcef869 Mon Sep 17 00:00:00 2001 +From: Thomas Braun +Date: Wed, 29 Mar 2023 18:18:04 +0200 +Subject: [PATCH 1/1] WIP: fast sphinx compilation without breathe + +--- + Packages/doc/conf.py | 6 +++--- + tools/build-documentation.sh | 27 --------------------------- + 2 files changed, 3 insertions(+), 30 deletions(-) + +diff --git a/Packages/doc/conf.py b/Packages/doc/conf.py +index ad61b69d90..13385ff369 100644 +--- a/Packages/doc/conf.py ++++ b/Packages/doc/conf.py +@@ -16,11 +16,11 @@ def get_version(): + return "({branch}) {version}".format(branch=branchString.decode('ascii'), version=revString.decode('ascii')) + + # sphinx config +-extensions = ['sphinx.ext.mathjax', 'sphinx.ext.todo', 'breathe', \ ++extensions = ['sphinx.ext.mathjax', 'sphinx.ext.todo', \ + 'sphinxcontrib.fulltoc', 'sphinxcontrib.images', \ + 'sphinxcontrib.youtube'] + +-master_doc = "index" ++master_doc = "user" + project= "MIES Igor" + + html_static_path = ['_static'] +@@ -28,7 +28,7 @@ html_static_path = ['_static'] + html_copy_source = False + html_show_sourcelink = False + +-exclude_patterns = [ 'releasenotes_template.rst', 'IPNWB/specifications'] ++exclude_patterns = [ 'releasenotes_template.rst', 'IPNWB/specifications', 'index.rst'] + + cpp_id_attributes = [ 'threadsafe' ] + +diff --git a/tools/build-documentation.sh b/tools/build-documentation.sh +index 1375d65a07..f709100c55 100755 +--- a/tools/build-documentation.sh ++++ b/tools/build-documentation.sh +@@ -91,33 +91,6 @@ trap "rm -rf ${top_level}/Packages/doc/IPNWB" EXIT + # workaround https://github.com/sphinx-contrib/images/pull/31 + mkdir _video_thumbnail + +-if hash breathe-apidoc 2>/dev/null; then +- echo "Start breathe-apidoc" +- +- breathe-apidoc -f -o . xml +- +-else +- echo "Errors building the documentation" 1>&2 +- echo "breathe-apidoc could not be found" 1>&2 +- exit 1 +-fi +- +-# Add labels to each group and each file +-# can be referenced via :ref:`Group LabnotebookQueryFunctions` +-# or :ref:`File MIES_Utilities.ipf` +- +-for i in `ls group/group_*.rst` +-do +- name=$(sed -e '$!d' -e 's/.*doxygengroup:: \(.*\)$/\1/' $i) +- sed -i "1s/^/.. _Group ${name}:\n\n/" $i +-done +- +-for i in `ls file/*.rst` +-do +- name=$(sed -e '$!d' -e 's/.*doxygenfile:: \(.*\)$/\1/' $i) +- sed -i "1s/^/.. _File ${name}:\n\n/" $i +-done +- + # create rst substitutions for up-to-date IP nightly links + grep "IgorPro[0-9]Nightly" $top_level/Packages/MIES_Include.ipf \ + | sed -e "s/^\/\/ //" \ +-- +2.42.0.rc0.windows.1 + diff --git a/_downloads/94e6e1968a7e69c4ef61a5bb51aad2a2/public-key.cer b/_downloads/94e6e1968a7e69c4ef61a5bb51aad2a2/public-key.cer new file mode 100644 index 0000000000..6f5c81d392 Binary files /dev/null and b/_downloads/94e6e1968a7e69c4ef61a5bb51aad2a2/public-key.cer differ diff --git a/_images/AnalysisBrowser.png b/_images/AnalysisBrowser.png new file mode 100644 index 0000000000..b23c7e88b7 Binary files /dev/null and b/_images/AnalysisBrowser.png differ diff --git a/_images/Browser-SettingsHistory.png b/_images/Browser-SettingsHistory.png new file mode 100644 index 0000000000..e34f2e2696 Binary files /dev/null and b/_images/Browser-SettingsHistory.png differ diff --git a/_images/Browser-SweepControl.png b/_images/Browser-SweepControl.png new file mode 100644 index 0000000000..6e4bb7ec81 Binary files /dev/null and b/_images/Browser-SweepControl.png differ diff --git a/_images/Browser-all.png b/_images/Browser-all.png new file mode 100644 index 0000000000..61635fd071 Binary files /dev/null and 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a/_images/BrowserSettingsPanel-Overlay-Sweeps.png b/_images/BrowserSettingsPanel-Overlay-Sweeps.png new file mode 100644 index 0000000000..a9739b437d Binary files /dev/null and b/_images/BrowserSettingsPanel-Overlay-Sweeps.png differ diff --git a/_images/BrowserSettingsPanel-PA-plot.png b/_images/BrowserSettingsPanel-PA-plot.png new file mode 100644 index 0000000000..654f5d0ae6 Binary files /dev/null and b/_images/BrowserSettingsPanel-PA-plot.png differ diff --git a/_images/BrowserSettingsPanel-Settings.png b/_images/BrowserSettingsPanel-Settings.png new file mode 100644 index 0000000000..c5163be89c Binary files /dev/null and b/_images/BrowserSettingsPanel-Settings.png differ diff --git a/_images/BrowserSettingsPanel-Sweepformula.png b/_images/BrowserSettingsPanel-Sweepformula.png new file mode 100644 index 0000000000..86fa17cb92 Binary files /dev/null and b/_images/BrowserSettingsPanel-Sweepformula.png differ diff --git a/_images/CalculateTPLikePropsFromSweep.svg b/_images/CalculateTPLikePropsFromSweep.svg new file mode 100644 index 0000000000..43b8a76c6e --- /dev/null +++ b/_images/CalculateTPLikePropsFromSweep.svg @@ -0,0 +1,1578 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CalculateTPLikePropsFromSweep + + + + Qt SVG Document + + Generated with Qt + + + + + + + + + + 20 + + + + + + 15 + + + + + + 10 + + + + + + 5 + + + + + + 0 + ms + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + totalOnsetDelay + + + + + + base line fraction(firstEdge - totalOnsetDelay) + + + + + + active test pulse time(secondEdge - firstEdge) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Edge Finderruns on DA waveedge finder threshold(from DA wave)0.1 * (Max – Min) + Minfinds firstEdge / secondEdge positionthat are then used on AD wave + + + + + + + + + + + + + reference point: trunc(firstEdge) - 1 + + + + + + + + + + + + + secondEdge + + + + + + + + + + + + + firstEdge + + + + + + + + + + + + + reference point:trunc(secondEdge) - 1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10 % of base line fraction + + + + + + + + + + + + + 10 % of active test pulse time + + + + + + + + + + + + + Base line level = mean of points in rangeElevated level = mean of points in rangeDU = (Elevated level – Base line level)Same method of level determinationon DA wave to get current amplitude:DI = (Elevated level – Base line level)Resistance calculation: + + + + + + + + + + + + R + = + Δ + U + + Δ 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E0_PT_P10_B + + + + OD0 + ODx + E0_PT_Px_P + E0_PT_Px_B + + + + + + + E0_PT_Px + + + + + + + + + poisson distributed pulse train + square pulse + square pulsewith amplitude 0 + delay from oodDAQ shift + joined pulses + + + poisson distributed pulse train + baseline trail + TP + TP + + + + flipped stimset + flipped stimset + diff --git a/_images/epoch-visualization3.svg b/_images/epoch-visualization3.svg new file mode 100644 index 0000000000..c966dbf9ee --- /dev/null +++ b/_images/epoch-visualization3.svg @@ -0,0 +1,14282 @@ + + + + Qt SVG Document + Generated with Qt + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 8 + + + + + + + + + + + + + + 4 + + + + + + + + + + + + + + 0 + + + + + + + + + + DA0 + + + + (mV) + + + + + + + + + + + + + + 3000 + + + + + + + + + + 2500 + + + + + + + + + + 2000 + + + + + + + + + + 1500 + + + + + + + + + + 1000 + + + + + + + + + + 500 + + + + + + + + + + 0 + + + + + + ms + + + + + + + + + + + + + + + + + + 8 + + + + + + + + + + + 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E0_TG_C2_H0 + + + E0_TG_C2_H1 + + E1_TG_C0 + E1_TG_C1 + E0_TG_C1 + E0_TG_C2 + E0_TG_C0_H0 + E0_TG_C0_H1 + E1_TG_C0_H0 + E2_TG_C0_H0 + E2_TG_C0_H1 + E2_TG_C1_H0 + E2_TG_C1_H1 + E1_TG_C0_H1 + E1_TG_C1_H0 + E1_TG_C1_H1 + E0_TG_C1_H0 + + E0_TG_C1_H1 + + E0_TG_C2_H0 + + E0_TG_C2_H1 + + E0_TG_C1 + E0_TG_C2 + + E0_TG_I1 + + E1_TG_I0 + E2_TG_C0 + E2_TG_C1 + E3_TG_I0 + E4_TG_I0 + E1_TG_I1 + + E1_TG_C0 + + E1_TG_C1 + + + TP_B0 + TP_B1 + E0 + E1 + E2 + E3 + E4 + E1 + E2 + E3 + E4 + stimset with trigonometric wave epochs + flipped stimset with trigonometric wave epochs + + TP_P + + + + + TP_B0 + TP_B1 + + TP_P + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/_images/multi-patch-seq-dascale1.svg b/_images/multi-patch-seq-dascale1.svg new file mode 100644 index 0000000000..bff43a32a3 --- /dev/null +++ b/_images/multi-patch-seq-dascale1.svg @@ -0,0 +1,397 @@ + + + + + + +G + + + +Start DAQ/RA (only call for last active headstage) + +Start DAQ/RA (only call for last active headstage) + + + +Post DAQ Event + +Post DAQ Event + + + +Start DAQ/RA (only call for last active headstage)->Post DAQ Event + + + + + +Prepare DAQ + +Prepare DAQ + + + +Start DAQ/RA (only call for last active headstage)->Prepare DAQ + + + + + +Pre Set Event + +Pre Set Event + + + +Start DAQ/RA (only call for last active headstage)->Pre Set Event + + + + + +Post Sweep Event + +Post Sweep Event + + + +Start DAQ/RA (only call for last active headstage)->Post Sweep Event + + + + + +Post Set Event + +Post Set Event + + + +Start DAQ/RA (only call for last active headstage)->Post Set Event + + + + + +n38 + +Update Dashboard + + + +Post DAQ Event->n38 + + + + + +Enable "Multidevice DAQ" + +Enable "Multidevice DAQ" + + + +Prepare DAQ->Enable "Multidevice DAQ" + + + + + +Enable "Autobias" + +Enable "Autobias" + + + +Pre Set Event->Enable "Autobias" + + + + + +Set next DAScale value,\nuse the analysis parameter values as offset\nonto the earlier FastRheoEstimate guess + +Set next DAScale value, +use the analysis parameter values as offset +onto the earlier FastRheoEstimate guess + + + +Pre Set Event->Set next DAScale value,\nuse the analysis parameter values as offset\nonto the earlier FastRheoEstimate guess + + + + + +Post Sweep Event->Set next DAScale value,\nuse the analysis parameter values as offset\nonto the earlier FastRheoEstimate guess + + + + + +Mark all active headstages as passed + +Mark all active headstages as passed + + + +Post Sweep Event->Mark all active headstages as passed + + + + + +Read active headstages from labnotebook\nand turn them all on again + +Read active headstages from labnotebook +and turn them all on again + + + +Post Set Event->Read active headstages from labnotebook\nand turn them all on again + + + + + +Enable "Repeated Acquisition" + +Enable "Repeated Acquisition" + + + +Enable "Multidevice DAQ"->Enable "Repeated Acquisition" + + + + + +Enable "Insert TP" + +Enable "Insert TP" + + + +Enable "Autobias"->Enable "Insert TP" + + + + + +Mark Sweep as passed + +Mark Sweep as passed + + + +Mark all active headstages as passed->Mark Sweep as passed + + + + + +Mark set as passed + +Mark set as passed + + + +Read active headstages from labnotebook\nand turn them all on again->Mark set as passed + + + + + +n29 + +"Unlocked Indexing" is active + + + +Enable "Repeated Acquisition"->n29 + + + + + +Enable "TP during ITI" + +Enable "TP during ITI" + + + +Enable "Insert TP"->Enable "TP during ITI" + + + + + +Force Sampling Multiplier to 1 + +Force Sampling Multiplier to 1 + + + +Enable "Insert TP"->Force Sampling Multiplier to 1 + + + + + +Update Dashboard + +Update Dashboard + + + +Mark set as passed->Update Dashboard + + + + + +Abort + +Abort + + + +n29->Abort + + +Yes + + + +Valid Autobias voltage (finite and non-zero) + +Valid Autobias voltage (finite and non-zero) + + + +Enable "TP during ITI"->Valid Autobias voltage (finite and non-zero) + + + + + +Check if no TTL channels are active + +Check if no TTL channels are active + + + +Force Sampling Multiplier to 1->Check if no TTL channels are active + + + + + +Enable "dDAQ" + +Enable "oodDAQ" + + + +Valid Autobias voltage (finite and non-zero)->Enable "dDAQ" + + + + + +Store active headstages in labnotebook + +Store active headstages in labnotebook + + + +Check if no TTL channels are active->Store active headstages in labnotebook + + + + + +Look for an existing and passing FastRheoEstimate sweep\n within a passing set and\n a pulse duration of more than 500ms + +Look for an existing and passing FastRheoEstimate sweep + within a passing set and + a pulse duration of more than 500ms + + + +Enable "dDAQ"->Look for an existing and passing FastRheoEstimate sweep\n within a passing set and\n a pulse duration of more than 500ms + + + + + +Turn off active non-IC headstages\nor headstages which have not passed FastRheoEstimate + +Turn off active non-IC headstages +or headstages which have not passed FastRheoEstimate + + + +Store active headstages in labnotebook->Turn off active non-IC headstages\nor headstages which have not passed FastRheoEstimate + + + + + +Look for an existing and passing FastRheoEstimate sweep\n within a passing set and\n a pulse duration of more than 500ms->Abort + + +Not found + + + +Use the DAScale value of that sweep\n as offset to the DAScale values from the analysis parameters + +Use the DAScale value of that sweep + as offset to the DAScale values from the analysis parameters + + + +Look for an existing and passing FastRheoEstimate sweep\n within a passing set and\n a pulse duration of more than 500ms->Use the DAScale value of that sweep\n as offset to the DAScale values from the analysis parameters + + +Found + + + +Check if there is at least\none active IC headstage + +Check if there is at least +one active IC headstage + + + +Turn off active non-IC headstages\nor headstages which have not passed FastRheoEstimate->Check if there is at least\none active IC headstage + + + + + +All checks passed + +All checks passed + + + +Check if there is at least\none active IC headstage->All checks passed + + + + + +All checks passed->Abort + + +No + + + diff --git a/_images/multi-patch-seq-fast-rheo-estimate1.svg b/_images/multi-patch-seq-fast-rheo-estimate1.svg new file mode 100644 index 0000000000..3063dbadda --- /dev/null +++ b/_images/multi-patch-seq-fast-rheo-estimate1.svg @@ -0,0 +1,782 @@ + + + + + + +G + + + +Prepare DAQ/Pre Set Event + +Pre Set Event + + + +Check if there is at least\none active IC headstage + +Check if there is at least +one active IC headstage + + + +Prepare DAQ/Pre Set Event->Check if there is at least\none active IC headstage + + + + + +Check if no TTL channels are active + +Check if no TTL channels are active + + + +Check if there is at least\none active IC headstage->Check if no TTL channels are active + + + + + +All required analysis parameters present? + +All required analysis parameters present? + + + +Check if no TTL channels are active->All required analysis parameters present? + + + + + +Check if all active IC\n headstages have the same stimset + +Check if all active IC + headstages have the same stimset + + + +All required analysis parameters present?->Check if all active IC\n headstages have the same stimset + + + + + +All checks passed + +All checks passed + + + +Check if all active IC\n headstages have the same stimset->All checks passed + + + + + +Abort + +Abort + + + +All checks passed->Abort + + +No + + + +Set DAScale to 100pA\nfor all active IC headstages + +Set DAScale to 100pA +for all active IC headstages + + + +All checks passed->Set DAScale to 100pA\nfor all active IC headstages + + +Yes + + + +Write initial stepsize of 100pA into\nlabnotebook for all active IC headstages + +Write initial stepsize of 100pA into +labnotebook for all active IC headstages + + + +Set DAScale to 100pA\nfor all active IC headstages->Write initial stepsize of 100pA into\nlabnotebook for all active IC headstages + + + + + +Set "DAScale exceeded" labnotebook entry\nto false for all active IC headstages + +Set "DAScale exceeded" labnotebook entry +to false for all active IC headstages + + + +Write initial stepsize of 100pA into\nlabnotebook for all active IC headstages->Set "DAScale exceeded" labnotebook entry\nto false for all active IC headstages + + + + + +Store active headstages in labnotebook + +Store active headstages in labnotebook + + + +Set "DAScale exceeded" labnotebook entry\nto false for all active IC headstages->Store active headstages in labnotebook + + + + + +Turn off active non-IC headstages + +Turn off active non-IC headstages + + + +Store active headstages in labnotebook->Turn off active non-IC headstages + + + + + +Set "User onset delay" to 0ms + +Set "User onset delay" to 0ms + + + +Turn off active non-IC headstages->Set "User onset delay" to 0ms + + + + + +Start DAQ/RA (only call for last active headstage) + +Start DAQ/RA (only call for last active headstage) + + + +Start DAQ/RA (only call for last active headstage)->Prepare DAQ/Pre Set Event + + + + + +Post Sweep Event + +Post Sweep Event + + + +Start DAQ/RA (only call for last active headstage)->Post Sweep Event + + + + + +Post DAQ Event + +Post DAQ Event + + + +Start DAQ/RA (only call for last active headstage)->Post DAQ Event + + + + + +Post Set Event + +Post Set Event + + + +Start DAQ/RA (only call for last active headstage)->Post Set Event + + + + + +n60 + +Pre DAQ Event + + + +Start DAQ/RA (only call for last active headstage)->n60 + + + + + +Iterate over all active headstages + +Iterate over all active headstages + + + +Post Sweep Event->Iterate over all active headstages + + + + + +Store pulse duration in labnotebook + +Store pulse duration in labnotebook + + + +Post Sweep Event->Store pulse duration in labnotebook + + + + + +Update Dashboard + +Update Dashboard + + + +Post DAQ Event->Update Dashboard + + + + + +Mark set as passed if 1 sweep passed,\nas failure otherwise + +Mark set as passed if 1 sweep passed, +as failure otherwise + + + +Post Set Event->Mark set as passed if 1 sweep passed,\nas failure otherwise + + + + + +Set "TP during ITI" to enabled + +Set "TP during ITI" to enabled + + + +Post Set Event->Set "TP during ITI" to enabled + + + + + +Enable "Multidevice DAQ" + +Enable "Multidevice DAQ" + + + +n60->Enable "Multidevice DAQ" + + + + + +Active headstages left? + +Active headstages left? + + + +Iterate over all active headstages->Active headstages left? + + + + + +Analysis parameter "PostDAQSetDAScale" is true + +Analysis parameter "PostDAQSetDAScale" is true + + + +Mark set as passed if 1 sweep passed,\nas failure otherwise->Analysis parameter "PostDAQSetDAScale" is true + + + + + +Set "TP inserting" to enabled + +Set "TP inserting" to enabled + + + +Set "TP during ITI" to enabled->Set "TP inserting" to enabled + + + + + +Enable "Repeated Acquisition" + +Enable "Repeated Acquisition" + + + +Enable "Multidevice DAQ"->Enable "Repeated Acquisition" + + + + + +Have all headstages passed in one sweep\nof their stimset cycle? + +Have all headstages passed in one sweep +of their stimset cycle? + + + +Active headstages left?->Have all headstages passed in one sweep\nof their stimset cycle? + + +No + + + +Headstage passed? + +Headstage passed? + + + +Active headstages left?->Headstage passed? + + +Yes + + + +Set DAScale to the stored LBN value taking into account\nthe analysis parameter "PostDAQDAScaleFactor"\nand "PostDAQDAScaleMinOffset".\nSet it to "PostDAQDAScaleForFailedHS" for failed headstages. + +Set DAScale to the stored LBN value taking into account +the analysis parameter "PostDAQDAScaleFactor" +and "PostDAQDAScaleMinOffset". +Set it to "PostDAQDAScaleForFailedHS" for failed headstages. + + + +Analysis parameter "PostDAQSetDAScale" is true->Set DAScale to the stored LBN value taking into account\nthe analysis parameter "PostDAQDAScaleFactor"\nand "PostDAQDAScaleMinOffset".\nSet it to "PostDAQDAScaleForFailedHS" for failed headstages. + + + + + +n61 + +Is "Unlocked indexing" active + + + +Enable "Repeated Acquisition"->n61 + + + + + +Mark sweep as failed + +Mark sweep as failed + + + +Have all headstages passed in one sweep\nof their stimset cycle?->Mark sweep as failed + + +No + + + +Mark sweep as passed + +Mark sweep as passed + + + +Have all headstages passed in one sweep\nof their stimset cycle?->Mark sweep as passed + + +Yes + + + +Headstage exceeded DAScale\n according to labnotebook entry? + +Headstage exceeded DAScale + according to labnotebook entry? + + + +Headstage passed?->Headstage exceeded DAScale\n according to labnotebook entry? + + +No + + + +Read active headstages from labnotebook\nand turn them all on again + +Read active headstages from labnotebook +and turn them all on again + + + +Set DAScale to the stored LBN value taking into account\nthe analysis parameter "PostDAQDAScaleFactor"\nand "PostDAQDAScaleMinOffset".\nSet it to "PostDAQDAScaleForFailedHS" for failed headstages.->Read active headstages from labnotebook\nand turn them all on again + + + + + +n61->Abort + + +Yes + + + +Have all active headstages an DAScale exceeded\n labnotebook entry? + +Have all active headstages an DAScale exceeded + labnotebook entry? + + + +Mark sweep as failed->Have all active headstages an DAScale exceeded\n labnotebook entry? + + + + + +Skip to end of active set + +Skip to end of active set + + + +Mark sweep as passed->Skip to end of active set + + + + + +Spike detected?\n(x range: pulse onset to end of sweep\ny condition: max above 0.01mV)\nStore result in labnotebook + +Spike detected? +(x range: pulse onset to end of sweep +y condition: max above 0.01mV) +Store result in labnotebook + + + +Headstage exceeded DAScale\n according to labnotebook entry?->Spike detected?\n(x range: pulse onset to end of sweep\ny condition: max above 0.01mV)\nStore result in labnotebook + + +No + + + +Have all active headstages an DAScale exceeded\n labnotebook entry?->Skip to end of active set + + +Yes + + + +Step size from labnotebook? (1) + +Step size from labnotebook? (1) + + + +Spike detected?\n(x range: pulse onset to end of sweep\ny condition: max above 0.01mV)\nStore result in labnotebook->Step size from labnotebook? (1) + + +Yes + + + +Step size from labnotebook? (2) + +Step size from labnotebook? (2) + + + +Spike detected?\n(x range: pulse onset to end of sweep\ny condition: max above 0.01mV)\nStore result in labnotebook->Step size from labnotebook? (2) + + +No + + + +Store DAScale in labnotebook + +Store DAScale in labnotebook + + + +Step size from labnotebook? (1)->Store DAScale in labnotebook + + ++10pA + + + +Offset DAScale by -50pA + +Offset DAScale by -50pA + + + +Step size from labnotebook? (1)->Offset DAScale by -50pA + + +-50pA + + + +Write step size of -50pA to labnotebook + +Write step size of -50pA to labnotebook + + + +Step size from labnotebook? (1)->Write step size of -50pA to labnotebook + + ++100pA + + + +Write step size of +10pA to labnotebook + +Write step size of +10pA to labnotebook + + + +Step size from labnotebook? (2)->Write step size of +10pA to labnotebook + + +-50pA + + + +Offset DAScale by +10pA + +Offset DAScale by +10pA + + + +Step size from labnotebook? (2)->Offset DAScale by +10pA + + ++10pA + + + +Offset DAScale by +100pA + +Offset DAScale by +100pA + + + +Step size from labnotebook? (2)->Offset DAScale by +100pA + + ++100pA + + + +Mark headstage as passed + +Mark headstage as passed + + + +Store DAScale in labnotebook->Mark headstage as passed + + + + + +Mark headstage as failed + +Mark headstage as failed + + + +Offset DAScale by -50pA->Mark headstage as failed + + + + + +Write step size of -50pA to labnotebook->Offset DAScale by -50pA + + + + + +Write step size of +10pA to labnotebook->Offset DAScale by +10pA + + + + + +Offset DAScale by +10pA->Mark headstage as failed + + + + + +Offset DAScale by +100pA->Mark headstage as failed + + + + + +Set DAScale to zero + +Set DAScale to zero + + + +Mark headstage as passed->Set DAScale to zero + + + + + +"MaximumDAScale" analysis parameter is not NaN? + +"MaximumDAScale" analysis parameter is not NaN? + + + +Mark headstage as failed->"MaximumDAScale" analysis parameter is not NaN? + + + + + +DAScale is larger than "MaximumDAScale"? + +DAScale is larger than "MaximumDAScale"? + + + +"MaximumDAScale" analysis parameter is not NaN?->DAScale is larger than "MaximumDAScale"? + + +Yes + + + +Mark headstage as "DAScale exceeded"\nin labnotebook + +Mark headstage as "DAScale exceeded" +in labnotebook + + + +DAScale is larger than "MaximumDAScale"?->Mark headstage as "DAScale exceeded"\nin labnotebook + + +Yes + + + +Set "Termination delay" to 0 ms + +Set "Termination delay" to 0 ms + + + +Set "User onset delay" to 0ms->Set "Termination delay" to 0 ms + + + + + +Mark headstage as "DAScale exceeded"\nin labnotebook->Set DAScale to zero + + + + + +Disable "dDAQ"/"oodDAQ" + +Disable "dDAQ"/"oodDAQ" + + + +Set "TP during ITI" to disabled + +Set "TP during ITI" to disabled + + + +Disable "dDAQ"/"oodDAQ"->Set "TP during ITI" to disabled + + + + + +Set "ITI" to 100ms + +Set "ITI" to 100ms + + + +Set "TP during ITI" to disabled->Set "ITI" to 100ms + + + + + +Set "TP inserting" to disabled + +Set "TP inserting" to disabled + + + +Set "ITI" to 100ms->Set "TP inserting" to disabled + + + + + +Set "Termination delay" to 0 ms->Disable "dDAQ"/"oodDAQ" + + + + + diff --git a/_images/multi-patch-seq-spike-control1.svg b/_images/multi-patch-seq-spike-control1.svg new file mode 100644 index 0000000000..e30f86adbf --- /dev/null +++ b/_images/multi-patch-seq-spike-control1.svg @@ -0,0 +1,977 @@ + + + + + + +G + + + +Start DAQ/RA (only call for last active headstage) + +Start DAQ/RA (only call for last active headstage) + + + +Post DAQ Event + +Post DAQ Event + + + +Start DAQ/RA (only call for last active headstage)->Post DAQ Event + + + + + +Prepare DAQ + +Pre DAQ Event + + + +Start DAQ/RA (only call for last active headstage)->Prepare DAQ + + + + + +Pre Set Event + +Pre Set Event + + + +Start DAQ/RA (only call for last active headstage)->Pre Set Event + + + + + +Post Sweep Event + +Post Sweep Event + + + +Start DAQ/RA (only call for last active headstage)->Post Sweep Event + + + + + +Update Dashboard + +Update Dashboard + + + +Post DAQ Event->Update Dashboard + + + + + +n45 + +Enable "Multidevice DAQ" + + + +Prepare DAQ->n45 + + + + + +n36 + +Check if TTL channels + are present + + + +Pre Set Event->n36 + + + + + +n39 + +Check if all IC headstages + have the same stimset + + + +Pre Set Event->n39 + + + + + +n44 + +Adjust several other controls + as done with SetControlInEvent normally + + + +Pre Set Event->n44 + + + + + +n80 + +Gather all pulses from each active IC headstage + + + +Post Sweep Event->n80 + + + + + +n46 + +Enable "Repeated Acquisition" + + + +n45->n46 + + + + + +All checks passed + +All checks passed + + + +n36->All checks passed + + + + + +n39->All checks passed + + + + + +n34 + +Open Databrowser (if not yet open) + and link to current device + + + +n44->n34 + + + + + +n84 + +From each pulse read out the number of + spikes and the spike positions + + + +n80->n84 + + + + + +n47 + +Is "Unlocked indexing" active + + + +n46->n47 + + + + + +Abort + +Abort + + + +All checks passed->Abort + + +No + + + +n35 + +Enable "Search failed pulses" + in PA tab + + + +n34->n35 + + + + + +n86 + +Store the number of spikes + in the textual labnotebook + + + +n84->n86 + + + + + +n47->Abort + + +Yes + + + +n38 + +Set "Ideal Number of Spikes" from + analysis parameter in PA plotb store in labnotebook + + + +n35->n38 + + + + + +n87 + +Convert the spike positions to + "Pulse active coordinate system" + and store them in the textual labnotebook. + + + +n86->n87 + + + + + +n69 + +"Failed Pulse Level" +analysis parameter present? + + + +n38->n69 + + + + + +n85 + +Set oodDAQ regions to NaN from the AD data +and check if the maximum + is below the "Failed Pulse Level" + + + +n87->n85 + + + + + +n78 + +Read "Ideal number of spikes" from labnotebook + + + +n87->n78 + + + + + +n92 + +For all spikes of a pulse + calculate the average spike position + + + +n87->n92 + + + + + +n71 + +Read "Failed Pulse Level" from PA plot + + + +n69->n71 + + +No + + + +n72 + +Set "Failed Pulse Level" in PA plot + + + +n69->n72 + + +Yes + + + +n61 + +Set "Spontaneous spike check" + as passed in labnotebook. + + + +n85->n61 + + +Yes + + + +n64 + +Set "Spontaneous spike check" + as failed in labnotebook. + + + +n85->n64 + + +No + + + +n93 + +Compare the "Ideal number of spikes" + with the actual number of spikes + in each pulse for all + pulses for a headstage + + + +n78->n93 + + + + + +n89 + +Check if the average is larger than + the analysis parameter "Minimum Spike Position". + + + +n92->n89 + + + + + +n60 + +Add "Failed Pulse Level" into labnotebook + + + +n71->n60 + + + + + +n72->n60 + + + + + +n99 + +Spontaneous spike QC + + + +n61->n99 + + + + + +n64->n99 + + + + + +n97 + +Add "Spike counts state" with + "Good/Too few/Too many/Mixed" to + textual labnotebook. + "Mixed" happens when it is + "Too Few" on some pulses + and "Too Many" on others. + + + +n93->n97 + + + + + +n91 + +Set "Spike position QC" + as failed in labnotebook + + + +n89->n91 + + +No + + + +n98 + +Set "Spike position QC" + as passed in labnotebook + + + +n89->n98 + + +Yes + + + +n40 + +Enable PA plot + + + +n60->n40 + + + + + +n100 + +Mark headstage as failed + + + +n99->n100 + + +Failed + + + +n101 + +Spike counts state + + + +n99->n101 + + +Passed + + + +n97->n99 + + + + + +n42 + +Enable OVS + + + +n40->n42 + + + + + +n58 + +Determine the number of trials + for the current set sweep count. + + + +n100->n58 + + + + + +n101->n100 + + + + + +n103 + +Mark headstage as passed + + + +n101->n103 + + +Good + + + +n43 + +Enable "Clear on new SCI" + + + +n42->n43 + + + + + +n59 + +Add "Rerun Trials" into numerical + labnotebook + + + +n58->n59 + + + + + +n73 + +Iterate over all active IC headstages + + + +n58->n73 + + + + + +n103->n58 + + + + + +n41 + +Enable "Display last sweep acquired" + + + +n43->n41 + + + + + +n51 + +Check if all IC headstages passed + with the current set sweep count. + + + +n59->n51 + + + + + +n88 + +Headstage passed? + + + +n73->n88 + + + + + +Enable "Multidevice DAQ" + +Enable "Multidevice DAQ" + + + +n41->Enable "Multidevice DAQ" + + + + + +n52 + +Mark sweep as passed + + + +n51->n52 + + +True + + + +n53 + +Mark sweep as failed + + + +n51->n53 + + +False + + + +n74 + +Was spontaneous spiking detected? + + + +n88->n74 + + +Failed + + + +n79 + +Spike Count state? + + + +n88->n79 + + +Failed + + + +n94 + +Spike position passed? + + + +n88->n94 + + +Passed + + + +n63 + +Mark set as passed if all IC headstages + passed with all set sweep counts. + + + +n52->n63 + + + + + +n54 + +Analysis parameter "Max Trials" present? + + + +n53->n54 + + + + + +n70 + +Set passed? + + + +n63->n70 + + + + + +n55 + +Check if the current trial count +of the current set sweep count + exceeds "Max Trials" + + + +n54->n55 + + +Yes + + + +n56 + +Skip back one sweep + + + +n54->n56 + + +No + + + +n65 + +Analysis parameter "Max Trials" present? [2] + + + +n70->n65 + + +No + + + +n68 + +Skip to end of active set + + + +n70->n68 + + +Yes + + + +n55->n56 + + +No + + + +n57 + +Add "Rerun Trials Exceeded" + into numerical labnotebook + + + +n55->n57 + + +Yes + + + +n56->n63 + + + + + +n66 + +Was it reached on all IC headstages? + + + +n65->n66 + + +Yes + + + +n67 + +Mark set as failed + + + +n66->n67 + + + + + +n67->n68 + + + + + +n75 + +Add "Auto bias baseline modifier" analysis parameter + value to autobias target voltage + + + +n74->n75 + + +Yes + + + +n81 + +Decrease DA Scale according to analysis parameters + "DaScaleTooManySpikesModifier" and "DaScaleTooManySpikesOperator" + + + +n79->n81 + + +Too Many + + + +n82 + +Warn user in history once +during this RA cycle + + + +n79->n82 + + +Mixed + + + +n83 + +Increase DA scale according to analysis parameters + "DAScaleModifier" + and "DAScaleOperator" + + + +n79->n83 + + +Too Few + + + +n77 + +Increase DA scale according to analysis parameters + "DAScaleSpikePositionModifier" + and "DAScaleSpikePositionOperator" + + + +n94->n77 + + +Failed + + + +n62 + +Increase DA scale according to analysis parameters + "DAScaleModifier" and "DAScaleOperator" + + + +n82->n62 + + + + + diff --git a/_images/normal-delays.svg b/_images/normal-delays.svg new file mode 100644 index 0000000000..26c039daad --- /dev/null +++ b/_images/normal-delays.svg @@ -0,0 +1,1000 @@ + + +Qt SVG Document +Generated with Qt + + + + + + + + + + + + + + + + + + + + + + +50 + + + + + + + + + + + + + +40 + + + + + + + + + + + + + +30 + + + + + + + + + + + + + +20 + + + + + + + + + + + + + +10 + + + + + + + + + + + + + +0 + + + + + + + + + + + + + + + + + + + + +900 + + + + + + + + + + + + + +800 + + + + + + + + + + + + + +700 + + + + + + + + + + + + + +600 + + + + + + + + + + + + + +500 + + + + + + + + + + + + + +400 + + + + + + + + + + + + + +300 + + + + + + + + + + + + + +200 + + + + + + + + + + + + + +100 + + + + + + + + + + + + + +0 + + + + + + +ms + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Onset delay due to inserted TP + + + +TP duration: 50ms ->100ms delay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Onset delay user: 100ms + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Stimset with 500ms duration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Termination delay: 200ms + + + + + + diff --git a/_images/oodDAQ-delays.svg b/_images/oodDAQ-delays.svg new file mode 100644 index 0000000000..4c0f235ddc --- /dev/null +++ b/_images/oodDAQ-delays.svg @@ -0,0 +1,1487 @@ + + +Qt SVG Document +Generated with Qt + + + + + + + + + + + + + + + + + + + + + + +500 + + + + + + + + + + + + + +400 + + + + + + + + + + + + + +300 + + + + + + + + + + + + + +200 + + + + + + + + + + + + + +100 + + + + + + +AD0 + + + +(pA) + + + + + + + + + + + + + + + + + + + + +1000 + + + + + + + + + + + + + +800 + + + + + + + + + + + + + +600 + + + + + + + + + + + + + +400 + + + + + + + + + + + + + +200 + + + + + + + + + + + + + +0 + + + + + + +ms + + + + + + + + + + + + + + + + + + + + +500 + + + + + + + + + + + + + +400 + + + + + + + + + + + + + +300 + + + + + + + + + + + + + +200 + + + + + + + + + + + + + +100 + + + + + + +AD1 + + + +(pA) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +oodDAQ + + + +pre-feature delay: 150ms + + + +post-feature delay: 50ms + + + +Total delay: 150ms + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Total delay: At least 150ms + + + + + + + + + + + + + + + + + + + + +oodDAQ post-feature delay: 50ms + + + + + + diff --git a/_images/patch-seq-access-resistance-smoke1.svg b/_images/patch-seq-access-resistance-smoke1.svg new file mode 100644 index 0000000000..db263be2d9 --- /dev/null +++ b/_images/patch-seq-access-resistance-smoke1.svg @@ -0,0 +1,826 @@ + + + + + + +G + + + +n3 + +Start DAQ/RA + + + +n5 + +Pre Sweep Config Event + + + +n3->n5 + + + + + +n6 + +Pre DAQ Event + + + +n3->n6 + + + + + +n7 + +Post Set Event + + + +n3->n7 + + + + + +n8 + +Pre Set Event + + + +n3->n8 + + + + + +n9 + +Post Sweep Event + + + +n3->n9 + + + + + +n10 + +Post DAQ Event + + + +n3->n10 + + + + + +n51 + +Mid Sweep Event + + + +n3->n51 + + + + + +n91 + + +Standard AsyncQCChannels handling + + + + + +n5->n91 + + + + + +n73 + +Check that the length of epoch 0 + matches "BaselineChunkLength" + analysis parameter + + + +n5->n73 + + + + + +n29 + +Check that only one headstage is active + + + +n6->n29 + + + + + +n22 + +Turn multi device support on + + + +n6->n22 + + + + + +n11 + +Update dashboard + + + +n7->n11 + + + + + +n15 + +Do we have PSQ_AR_NUM_SWEEPS_PASS + passing  sweeps? + + + +n7->n15 + + + + + +n19 + +Set analysis function version + + + +n8->n19 + + + + + +n92 + + +Standard AsyncQCChannels handling + + + + + +n9->n92 + + + + + +n55 + +Check used sampling frequency + and store result in labnotebook + + + +n9->n55 + + + + + +n49 + +Read BL QC from labnotebook + + + +n9->n49 + + + + + +n57 + +Enable SweepFormula + + + +n9->n57 + + + + + +n10->n11 + + + + + +n48 + +Read Set QC from labnotebook + + + +n10->n48 + + + + + +n54 + +BL QC passed? + + + +n51->n54 + + + + + +n61 + +Abort + + + +n73->n61 + + +Failure + + + +n74 + +Check that we have enough epochs for + "NumberOfTestpulses"  TPs + + + +n73->n74 + + + + + +n76 + +Add baseline chunk selection user epoch + for epoch 0 + + + +n73->n76 + + + + + +n29->n61 + + +Failure + + + +n30 + +Check that no TTL channels are active + + + +n29->n30 + + + + + +n23 + +Turn repeated acquisition on + + + +n22->n23 + + + + + +n16 + +Mark Set QC as failed + + + +n15->n16 + + +No + + + +n17 + +Mark Set QC as passed + + + +n15->n17 + + +Yes + + + +n20 + +Set sampling rate multiplier + analysis parameter and check it + + + +n19->n20 + + + + + +n56 + +Are all five QC labnotebook + entries passing? + + + +n55->n56 + + + + + +n49->n56 + + + + + +n58 + +Set formula for getting the peak and access resistance + of all TPs in the stimset + + + +n57->n58 + + + + + +n85 + +Read optional "NextStimsetName" analysis parameter + and set that as next stimulus set + + + +n48->n85 + + +Passed + + + +n47 + +Iterate over all baseline QC + selection user epochs + + + +n54->n47 + + +No + + + +n74->n61 + + +Failure + + + +n75 + +Check amplitude of epochs for TPs + baseline zero, pulse non-zero + + + +n74->n75 + + + + + +n30->n61 + + +Failure + + + +n31 + +Check that the active headstage + is in voltage clamp + + + +n30->n31 + + + + + +n24 + +Turn off oodDAQ + + + +n23->n24 + + + + + +n18 + +Publish results via ZeroMQ + + + +n16->n18 + + + + + +n17->n18 + + + + + +n59 + +Mark Sweep QC as failed + + + +n56->n59 + + +No + + + +n60 + +Mark Sweep QC as passed + + + +n56->n60 + + +Yes + + + +n62 + +Run it + + + +n58->n62 + + + + + +n86 + +Read optional "NextIndexingEndStimsetName" analysis parameter + and set that as indexing end stimulus set + + + +n85->n86 + + + + + +n72 + +Check RMS short + + + +n47->n72 + + + + + +n77 + +Create TP-like epochs + + + +n75->n77 + + + + + +n31->n61 + + +Failure + + + +n25 + +Turn off dDAQ + + + +n24->n25 + + + + + +n52 + +Usual checks for early abort possibilities + + + +n59->n52 + + + + + +n53 + +Jump to end of set + + + +n60->n53 + + + + + +n63 + +Store both resistances + in the labnotebook + + + +n62->n63 + + + + + +n78 + +Check RMS long + + + +n72->n78 + + +Passed + + + +n80 + +Add BL chunk QC failed + labnotebook entry + + + +n72->n80 + + +Failed + + + +n26 + +Turn on inserted Testpulse + + + +n25->n26 + + + + + +n64 + +Is Access Resistance / Steady State Resistance + smaller than the "MaxAccessToSteadyStateResistanceRatio" + analysis parameter? + + + +n63->n64 + + + + + +n65 + +Is the access resistance smaller + than the "MaxAccessResistance" analysis parameter? + + + +n63->n65 + + + + + +n78->n80 + + +Failed + + + +n79 + +Check maximum leak current + + + +n78->n79 + + +Passed + + + +n82 + +Add BL QC failed + labnotebook entry + + + +n80->n82 + + + + + +n79->n80 + + +Failed + + + +n81 + +Add BL chunk QC passed + labnotebook entry + + + +n79->n81 + + +Passed + + + +n84 + +Early sweep stop + + + +n82->n84 + + + + + +n83 + +Add BL QC passed + labnotebook entry + + + +n81->n83 + + + + + +n67 + +Store result in labnotebook + + + +n64->n67 + + + + + +n66 + +Store result in labnotebook + + + +n65->n66 + + + + + +n67->n56 + + + + + +n66->n56 + + + + + diff --git a/_images/patch-seq-chirp-bounds-state-action1.png b/_images/patch-seq-chirp-bounds-state-action1.png new file mode 100644 index 0000000000..ec7e673fe4 Binary files /dev/null and b/_images/patch-seq-chirp-bounds-state-action1.png differ diff --git a/_images/patch-seq-chirp1.svg b/_images/patch-seq-chirp1.svg new file mode 100644 index 0000000000..d3b7e16725 --- /dev/null +++ b/_images/patch-seq-chirp1.svg @@ -0,0 +1,1375 @@ + + + + + + +G + + + +Start DAQ/RA + +Start DAQ/RA + + + +Mid Sweep Event + +Mid Sweep Event + + + +Start DAQ/RA->Mid Sweep Event + + + + + +Pre Sweep Config Event + +Pre Sweep Config Event + + + +Start DAQ/RA->Pre Sweep Config Event + + + + + +Post DAQ Event + +Post DAQ Event + + + +Start DAQ/RA->Post DAQ Event + + + + + +Post Set Event + +Post Set Event + + + +Start DAQ/RA->Post Set Event + + + + + +Post Sweep Event + +Post Sweep Event + + + +Start DAQ/RA->Post Sweep Event + + + + + +Prepare DAQ/Pre Set Event + +Prepare DAQ/Pre Set Event + + + +Start DAQ/RA->Prepare DAQ/Pre Set Event + + + + + +BL QC passed? + +BL QC passed? + + + +Mid Sweep Event->BL QC passed? + + + + + +"Inside Bounds" labnotebook\n entry present? + +"Inside Bounds" labnotebook + entry present? + + + +Mid Sweep Event->"Inside Bounds" labnotebook\n entry present? + + + + + +n63 + +Is "SpikeCheck" enabled? + (Given by optional analysis parameter + "SpikeCheck" defaulting to 1) + + + +Mid Sweep Event->n63 + + + + + +n91 + + +Standard AsyncQCChannels handling + + + + + +Pre Sweep Config Event->n91 + + + + + +Update Dashboard + +Update Dashboard + + + +Post DAQ Event->Update Dashboard + + + + + +Post Set Event->Update Dashboard + + + + + +Has three passing sweeps in set\n with the same DAScale value? [1] + +Has three passing sweeps in set + with the same DAScale value? [1] + + + +Post Set Event->Has three passing sweeps in set\n with the same DAScale value? [1] + + + + + +n84 + +Set "Delay onset user" back from labnotebook entry + + + +Post Set Event->n84 + + + + + +n97 + +Read analysis parameter + "AmpBesselFilterRestore", + defaulting to true. + + + +Post Set Event->n97 + + + + + +n92 + + +Standard AsyncQCChannels handling + + + + + +Post Sweep Event->n92 + + + + + +Enable "Autobias" + +Enable "Autobias" + + + +Prepare DAQ/Pre Set Event->Enable "Autobias" + + + + + +Valid Autobias voltage (finite and non-zero) + +Valid Autobias voltage (finite and non-zero) + + + +Prepare DAQ/Pre Set Event->Valid Autobias voltage (finite and non-zero) + + + + + +n95 + +Store amplifier setting + LPF primary output in labnotebook + + + +Prepare DAQ/Pre Set Event->n95 + + + + + +Grab next completely acquired chunk\n(500ms) of stimset baseline + +Grab next completely acquired chunk +(500ms) of stimset baseline + + + +BL QC passed?->Grab next completely acquired chunk\n(500ms) of stimset baseline + + +No + + + +Calculate number of cycles\n in chirp, store in labnotebook + +Add stimset QC entry +which denotes if the stimset is suitable + + + +"Inside Bounds" labnotebook\n entry present?->Calculate number of cycles\n in chirp, store in labnotebook + + +No + + + +n64 + +Store Spike check in labnotebook + + + +n63->n64 + + + + + +n65 + +Spike QC labnotebook entry found? + + + +n63->n65 + + + + + +Mark set as failed\n in labnotebook + +Mark set as failed + in labnotebook + + + +Has three passing sweeps in set\n with the same DAScale value? [1]->Mark set as failed\n in labnotebook + + +No + + + +Mark set as passed\n in labnotebook + +Mark set as passed + in labnotebook + + + +Has three passing sweeps in set\n with the same DAScale value? [1]->Mark set as passed\n in labnotebook + + +Yes + + + +n98 + +Set amplifier setting + LPF primary output + from labnotebook entry + + + +n97->n98 + + +True + + + +n73 + +"Spike Check" labnotebook entry is true? + + + +n92->n73 + + + + + +Enable "TP during ITI" + +Enable "TP during ITI" + + + +Enable "Autobias"->Enable "TP during ITI" + + + + + +Check if no TTL channels are active + +Check if no TTL channels are active + + + +Valid Autobias voltage (finite and non-zero)->Check if no TTL channels are active + + + + + +n96 + +Use "AmpBesselFilter" analysis parameter + (defaulting to 10e3 if not present) + as LPF primary output + + + +n95->n96 + + + + + +Chunk already evaluated? + +Chunk already evaluated? + + + +Grab next completely acquired chunk\n(500ms) of stimset baseline->Chunk already evaluated? + + +Have one + + + +Last chunk? + +Last chunk? + + + +Grab next completely acquired chunk\n(500ms) of stimset baseline->Last chunk? + + +None left + + + +n99 + +Early sweep stop +and jump to end of set + + + +Calculate number of cycles\n in chirp, store in labnotebook->n99 + + +Failed + + + +n100 + +n100 + + + +Calculate number of cycles\n in chirp, store in labnotebook->n100 + + +Passed + + + +n66 + +Has acquired data in chirp region? + + + +n65->n66 + + +No + + + +n87 + +Read analysis parameter "UseTrueRestingMembranePotentialVoltage", + defaulting to true. + + + +Mark set as passed\n in labnotebook->n87 + + + + + +Has BL QC and "Inside Bounds"\n entries being true in labnotebook? + +Has BL QC and "Inside Bounds" + entries being true in labnotebook? + + + +n73->Has BL QC and "Inside Bounds"\n entries being true in labnotebook? + + +No + + + +n74 + +Spike QC passed? + + + +n73->n74 + + +Yes + + + +Enable "Multidevice DAQ" + +Enable "Multidevice DAQ" + + + +Enable "TP during ITI"->Enable "Multidevice DAQ" + + + + + +Stimset is large enough + +Stimset is large enough + + + +Check if no TTL channels are active->Stimset is large enough + + + + + +Chunk already evaluated?->Grab next completely acquired chunk\n(500ms) of stimset baseline + + +Yes + + + +Baseline chunk type + +Baseline chunk type + + + +Chunk already evaluated?->Baseline chunk type + + +No + + + +Mark Sweep as failed + +Mark Sweep as failed + + + +Last chunk?->Mark Sweep as failed + + +Yes + + + +Acquired requested number of cycles?\n(Given by optional analysis parameter\n"NumberOfChirpCycles" defaulting to 1.) + +Acquired requested number of cycles? +(Given by optional analysis parameter +"NumberOfChirpCycles" defaulting to 1.) + + + +n100->Acquired requested number of cycles?\n(Given by optional analysis parameter\n"NumberOfChirpCycles" defaulting to 1.) + + + + + +n68 + +Has spike in AD data of acquired chirp region? +Uses "FailedLevel" analysis parameter for spike search. + + + +n66->n68 + + +Yes + + + +n80 + +Is the analysis parameter "AutobiasTargetVAtSetEnd" present? + If yes, set the autobias target voltage to it. + + + +n87->n80 + + +False + + + +n88 + +Find passing set with PSQ_TrueRestingMembranePotential + analysis function + + + +n87->n88 + + +True + + + +Mark sweep as failed\n in labnotebook + +Mark sweep as failed + in labnotebook + + + +Has BL QC and "Inside Bounds"\n entries being true in labnotebook?->Mark sweep as failed\n in labnotebook + + +No + + + +n76 + +Read "SamplingFrequency" analysis parameter + (defaulting to 50kHz) if not present + + + +Has BL QC and "Inside Bounds"\n entries being true in labnotebook?->n76 + + +Yes + + + +n74->Has BL QC and "Inside Bounds"\n entries being true in labnotebook? + + +Yes + + + +n74->Mark sweep as failed\n in labnotebook + + +No + + + +Disable "dDAQ"/"oodDAQ" + +Disable "dDAQ"/"oodDAQ" + + + +Enable "Multidevice DAQ"->Disable "dDAQ"/"oodDAQ" + + + + + +Check if mode is IC + +Check if mode is IC + + + +Stimset is large enough->Check if mode is IC + + + + + +Check RMS short + +Check RMS short + + + +Baseline chunk type->Check RMS short + + +pre pulse + + + +Check target voltage [2] + +Check target voltage [2] + + + +Baseline chunk type->Check target voltage [2] + + +post pulse + + + +Calculate min/max of AD data during these cycles + +Calculate min/max of AD data during these cycles + + + +Acquired requested number of cycles?\n(Given by optional analysis parameter\n"NumberOfChirpCycles" defaulting to 1.)->Calculate min/max of AD data during these cycles + + +Yes + + + +Determine bounds state and action\n from min/max values and table\n store in labnotebook + +Determine bounds state and action + from min/max values and table + store in labnotebook + + + +Calculate min/max of AD data during these cycles->Determine bounds state and action\n from min/max values and table\n store in labnotebook + + + + + +n69 + +Add Spike QC failed labnotebook entry + + + +n68->n69 + + +Yes + + + +n71 + +Has acquired past the end of chirp? + + + +n68->n71 + + +No + + + +n88->n80 + + +None + + + +n90 + +Read full average voltage from labnotebook + from that sweep and set it as autobias target voltage. + + + +n88->n90 + + +Found + + + +Has three passing sweeps in set\n with the same DAScale value? [2] + +Has three passing sweeps in set + with the same DAScale value? [2] + + + +Mark sweep as failed\n in labnotebook->Has three passing sweeps in set\n with the same DAScale value? [2] + + + + + +n85 + +Check if the acquired data + has that sampling interval + + + +n76->n85 + + + + + +Skip to end of set + +Skip to end of set + + + +Has three passing sweeps in set\n with the same DAScale value? [2]->Skip to end of set + + +Yes + + + +Read analysis parameter "NumberOfFailedSweeps",\n if not present use 3.\n Have that many sweeps failed? + +Read analysis parameter "NumberOfFailedSweeps", + if not present use 3. + Have that many sweeps failed? + + + +Has three passing sweeps in set\n with the same DAScale value? [2]->Read analysis parameter "NumberOfFailedSweeps",\n if not present use 3.\n Have that many sweeps failed? + + +No + + + +n85->Mark sweep as failed\n in labnotebook + + +No + + + +Skip to end of DAQ + +Skip to end of DAQ + + + +n85->Skip to end of DAQ + + +No + + + +n93 + +Has Async Channels QC + labnotebook entry passed? + + + +n85->n93 + + +Yes + + + +Enable "Repeated Acquisition" + +Enable "Repeated Acquisition" + + + +Disable "dDAQ"/"oodDAQ"->Enable "Repeated Acquisition" + + + + + +Check if only one headstage is active + +Check if only one headstage is active + + + +Check if mode is IC->Check if only one headstage is active + + + + + +Check RMS long + +Check RMS long + + + +Check RMS short->Check RMS long + + +Passed + + + +Add BL QC failed labnotebook entry + +Add BL QC failed labnotebook entry + + + +Check RMS short->Add BL QC failed labnotebook entry + + +Failed + + + +Mark chunk as passed/failed [2] + +Mark chunk as passed/failed [2] + + + +Check target voltage [2]->Mark chunk as passed/failed [2] + + + + + +Store "Inside Bounds" as true in labnotebook + +Store "Inside Bounds" as true in labnotebook + + + +Determine bounds state and action\n from min/max values and table\n store in labnotebook->Store "Inside Bounds" as true in labnotebook + + +PASS + + + +Store "Inside Bounds" as false in labnotebook + +Store "Inside Bounds" as false in labnotebook + + + +Determine bounds state and action\n from min/max values and table\n store in labnotebook->Store "Inside Bounds" as false in labnotebook + + +RERUN + + + +Determine bounds state and action\n from min/max values and table\n store in labnotebook->Store "Inside Bounds" as false in labnotebook + + +INCREASE + + + +Determine bounds state and action\n from min/max values and table\n store in labnotebook->Store "Inside Bounds" as false in labnotebook + + +DECREASE + + + +Abort Sweep + +Abort Sweep + + + +Determine bounds state and action\n from min/max values and table\n store in labnotebook->Abort Sweep + + +RERUN + + + +Calculate scaling factor\n to be inside the bounds + +Calculate scaling factor + to be inside the bounds + + + +Determine bounds state and action\n from min/max values and table\n store in labnotebook->Calculate scaling factor\n to be inside the bounds + + +INCREASE + + + +Determine bounds state and action\n from min/max values and table\n store in labnotebook->Calculate scaling factor\n to be inside the bounds + + +DECREASE + + + +n67 + +Increase DA scale according to analysis parameters + "DAScaleModifier" and "DAScaleOperator" + + + +n69->n67 + + + + + +n72 + +Add Spike QC passed labnotebook entry + + + +n71->n72 + + +Yes + + + +Read analysis parameter "NumberOfFailedSweeps",\n if not present use 3.\n Have that many sweeps failed?->Skip to end of DAQ + + +Yes + + + +Set can still pass? + +Set can still pass? + + + +Read analysis parameter "NumberOfFailedSweeps",\n if not present use 3.\n Have that many sweeps failed?->Set can still pass? + + +No + + + +n93->Mark sweep as failed\n in labnotebook + + +No + + + +Mark sweep as passed\n in labnotebook + +Mark sweep as passed + in labnotebook + + + +n93->Mark sweep as passed\n in labnotebook + + +Yes + + + +Enable "Insert TP" + +Enable "Insert TP" + + + +Enable "Repeated Acquisition"->Enable "Insert TP" + + + + + +All checks passed + +All checks passed + + + +Check if only one headstage is active->All checks passed + + + + + +Check RMS long->Add BL QC failed labnotebook entry + + +Failed + + + +Check target voltage [1] + +Check target voltage [1] + + + +Check RMS long->Check target voltage [1] + + +Passed + + + +Early Sweep stop + +Early Sweep stop + + + +Add BL QC failed labnotebook entry->Early Sweep stop + + + + + +Mark chunk as passed/failed [2]->Grab next completely acquired chunk\n(500ms) of stimset baseline + + +Failed + + + +Add BL QC passed labnotebook entry + +Add BL QC passed labnotebook entry + + + +Mark chunk as passed/failed [2]->Add BL QC passed labnotebook entry + + +Passed + + + +Adjust DAScale (rounded to full pA)\n according to scaling factor + +Adjust DAScale (rounded to full pA) + according to scaling factor + + + +Calculate scaling factor\n to be inside the bounds->Adjust DAScale (rounded to full pA)\n according to scaling factor + + + + + +n75 + +Abort sweep + + + +n67->n75 + + + + + +Set can still pass?->Skip to end of DAQ + + +No + + + +Mark sweep as passed\n in labnotebook->Has three passing sweeps in set\n with the same DAScale value? [2] + + + + + +n89 + +Use "SamplingMultiplier" analysis parameter + (defaulting to 4 if not present) and set it. + + + +Enable "Insert TP"->n89 + + + + + +Abort + +Abort + + + +All checks passed->Abort + + +No + + + +Look for an existing and passing PSQ_DAScale sweep\n in subthreshold mode + +Look for an existing and passing PSQ_DAScale sweep + in subthreshold mode + + + +All checks passed->Look for an existing and passing PSQ_DAScale sweep\n in subthreshold mode + + +Yes + + + +Mark chunk as passed/failed [1] + +Mark chunk as passed/failed [1] + + + +Check target voltage [1]->Mark chunk as passed/failed [1] + + + + + +Add BL QC passed labnotebook entry->Early Sweep stop + + + + + +Adjust DAScale (rounded to full pA)\n according to scaling factor->Abort Sweep + + + + + +n78 + +Is the analysis parameter "AutobiasTargetV" present? + If yes, set the autobias target voltage to it. + + + +n89->n78 + + + + + +Look for an existing and passing PSQ_DAScale sweep\n in subthreshold mode->Abort + + +Not found + + + +Get DeltaI/DeltaV from labnotebook + +Get DeltaI/DeltaV from labnotebook + + + +Look for an existing and passing PSQ_DAScale sweep\n in subthreshold mode->Get DeltaI/DeltaV from labnotebook + + +Found + + + +Mark chunk as passed/failed [1]->Grab next completely acquired chunk\n(500ms) of stimset baseline + + +Passed + + + +Early sweep stop, repurpose ITI and add 10s to ITI + +Early sweep stop, repurpose ITI and add 10s to ITI + + + +Mark chunk as passed/failed [1]->Early sweep stop, repurpose ITI and add 10s to ITI + + +Failed + + + +n82 + +Store "Delay onset user" in labnotebook + + + +n78->n82 + + + + + +Calculate Resistance from it\n store in labnotebook + +Calculate Resistance from it + store in labnotebook + + + +Get DeltaI/DeltaV from labnotebook->Calculate Resistance from it\n store in labnotebook + + + + + +n83 + + Is the analysis parameter "UserOnsetDelay" present? + If yes, set it. + + + +n82->n83 + + + + + +Calculate initial DAScale\n store in labnotebook + +Calculate initial DAScale + store in labnotebook + + + +Calculate Resistance from it\n store in labnotebook->Calculate initial DAScale\n store in labnotebook + + + + + +n83->All checks passed + + + + + +Set DAScale + +Set DAScale + + + +Calculate initial DAScale\n store in labnotebook->Set DAScale + + + + + diff --git a/_images/patch-seq-dascale1.svg b/_images/patch-seq-dascale1.svg new file mode 100644 index 0000000000..fe9dd9a160 --- /dev/null +++ b/_images/patch-seq-dascale1.svg @@ -0,0 +1,1784 @@ + + + + + + +G + + + +Start DAQ/RA + +Start DAQ/RA + + + +Mid Sweep Event + +Mid Sweep Event + + + +Start DAQ/RA->Mid Sweep Event + + + + + +Post DAQ Event + +Post DAQ Event + + + +Start DAQ/RA->Post DAQ Event + + + + + +Post Set Event + +Post Set Event + + + +Start DAQ/RA->Post Set Event + + + + + +Post Sweep Event + +Post Sweep Event + + + +Start DAQ/RA->Post Sweep Event + + + + + +Pre Sweep Config Event + +Pre Sweep Config Event + + + +Start DAQ/RA->Pre Sweep Config Event + + + + + +Prepare DAQ/Pre Set Event + +Prepare DAQ/Pre Set Event + + + +Start DAQ/RA->Prepare DAQ/Pre Set Event + + + + + +BL QC passed? + +BL QC passed? + + + +Mid Sweep Event->BL QC passed? + + + + + +Update Dashboard + +Update Dashboard + + + +Post DAQ Event->Update Dashboard + + + + + +Post Set Event->Update Dashboard + + + + + +Get OperationMode [2] + +Get OperationMode [2] + + + +Post Set Event->Get OperationMode [2] + + + + + +n91 + + +Standard AsyncQCChannels handling + + + + + +Post Sweep Event->n91 + + + + + +Get OperationMode [3] + +Get OperationMode [3] + + + +Post Sweep Event->Get OperationMode [3] + + + + + +n92 + + +Standard AsyncQCChannels handling + + + + + +Pre Sweep Config Event->n92 + + + + + +Enable "Autobias" + +Enable "Autobias" + + + +Prepare DAQ/Pre Set Event->Enable "Autobias" + + + + + +Valid Autobias voltage (finite and non-zero) + +Valid Autobias voltage (finite and non-zero) + + + +Prepare DAQ/Pre Set Event->Valid Autobias voltage (finite and non-zero) + + + + + +Grab next completely acquired chunk\n(500ms) of stimset baseline + +Grab next completely acquired chunk +(500ms) of stimset baseline + + + +BL QC passed?->Grab next completely acquired chunk\n(500ms) of stimset baseline + + +No + + + +Mark set as passed if $NUM_DA_SCALES\nsweeps passed, as failure otherwise + +Mark set as passed if $NUM_DA_SCALES +sweeps passed, as failure otherwise + + + +Get OperationMode [2]->Mark set as passed if $NUM_DA_SCALES\nsweeps passed, as failure otherwise + + +Sub + + + +Labnotebook has fI-Slope reached entry? + +Labnotebook has fI-Slope reached entry? + + + +Get OperationMode [2]->Labnotebook has fI-Slope reached entry? + + +Supra + + + +n79 + +Do we have measured all + required DAScales? + + + +Get OperationMode [2]->n79 + + +Adaptive Supra + + + +Last Sweep passed? + +BL QC passed? [2] + + + +Get OperationMode [3]->Last Sweep passed? + + + + + +n130 + +Passing baseline QC? + + + +Get OperationMode [3]->n130 + + +Adaptive Supra + + + +Enable "TP during ITI" + +Enable "TP during ITI" + + + +Enable "Autobias"->Enable "TP during ITI" + + + + + +Check if no TTL channels are active + +Check if no TTL channels are active + + + +Valid Autobias voltage (finite and non-zero)->Check if no TTL channels are active + + + + + +Chunk already evaluated? + +Chunk already evaluated? + + + +Grab next completely acquired chunk\n(500ms) of stimset baseline->Chunk already evaluated? + + +Have one + + + +Last chunk? + +Last chunk? + + + +Grab next completely acquired chunk\n(500ms) of stimset baseline->Last chunk? + + +None left + + + +Labnotebook has fI-Slope reached entry?->Mark set as passed if $NUM_DA_SCALES\nsweeps passed, as failure otherwise + + +No + + + +Reached? + +Reached? + + + +Labnotebook has fI-Slope reached entry?->Reached? + + +Yes + + + +Mark set as failed + +Mark set as failed + + + +n79->Mark set as failed + + +No + + + +n80 + +Was the fit slope from RhSuAd sweep + evaluation valid? + + + +n79->n80 + + +Yes + + + +n72 + +Mark sweep as failed + + + +Last Sweep passed?->n72 + + +No + + + +n75 + +Read "SamplingFrequency" analysis parameter + (defaulting to 50kHz) if not present + + + +Last Sweep passed?->n75 + + +Yes + + + +n87 + +Use SweepFormula to gather the AP frequency + and DAScale value + of the sweep + + + +n130->n87 + + +Yes + + + +n90 + +Fetch the AP frequency and DAScale data + from RhSuAd sweeps + + + +n130->n90 + + +No + + + +Enable "Multidevice DAQ" + +Enable "Multidevice DAQ" + + + +Enable "TP during ITI"->Enable "Multidevice DAQ" + + + + + +Stimset is large enough + +Stimset is large enough + + + +Check if no TTL channels are active->Stimset is large enough + + + + + +Chunk already evaluated?->Grab next completely acquired chunk\n(500ms) of stimset baseline + + +Yes + + + +Baseline chunk type + +Baseline chunk type + + + +Chunk already evaluated?->Baseline chunk type + + +No + + + +Mark Sweep as failed + +Mark Sweep as failed + + + +Last chunk?->Mark Sweep as failed + + +Yes + + + +Reached?->Mark set as passed if $NUM_DA_SCALES\nsweeps passed, as failure otherwise + + +Yes + + + +Reached?->Mark set as failed + + +No + + + +n81 + +Mark set as passed + + + +n80->n81 + + +No + + + +n132 + +Do we have at least NumSweepsWithSaturation + sweeps which are adjacent, ignoring sweeps with failed sweep QC, + and have sweep QC and f-I slope QC passing? + + + +n80->n132 + + +Yes + + + +Check if the Set can still pass + +Check if the Set can still pass + + + +n72->Check if the Set can still pass + + + + + +n76 + +Check if the acquired data + has that sampling interval + + + +n75->n76 + + + + + +n87->n90 + + +Failure + + + +n88 + +Write the AP frequency to the labnotebook + + + +n87->n88 + + +Sucess + + + +n93 + +Fetch AP frequency and DAScale data + from passing sweeps of this SCI + + + +n90->n93 + + + + + +Disable "dDAQ"/"oodDAQ" + +Disable "dDAQ"/"oodDAQ" + + + +Enable "Multidevice DAQ"->Disable "dDAQ"/"oodDAQ" + + + + + +Check if mode is IC + +Check if mode is IC + + + +Stimset is large enough->Check if mode is IC + + + + + +Check RMS short + +Check RMS short + + + +Baseline chunk type->Check RMS short + + +pre pulse + + + +Check target voltage [2] + +Check target voltage [2] + + + +Baseline chunk type->Check target voltage [2] + + +post pulse + + + +n132->Mark set as failed + + +No + + + +n132->n81 + + +Yes + + + +Skip to end + +Skip to end + + + +Check if the Set can still pass->Skip to end + + +No + + + +n76->n72 + + +No + + + +n76->Skip to end + + +No + + + +n77 + +Has Async Channels QC + labnotebook entry passed? + + + +n76->n77 + + +Yes + + + +n77->n72 + + +No + + + +n86 + +Mark sweep as passed + + + +n77->n86 + + + + + +Enable "Repeated Acquisition" + +Enable "Repeated Acquisition" + + + +Disable "dDAQ"/"oodDAQ"->Enable "Repeated Acquisition" + + + + + +Check if only one headstage is active + +Check if only one headstage is active + + + +Check if mode is IC->Check if only one headstage is active + + + + + +Check RMS long + +Check RMS long + + + +Check RMS short->Check RMS long + + +Passed + + + +Add BL QC failed labnotebook entry + +Add BL QC failed labnotebook entry + + + +Check RMS short->Add BL QC failed labnotebook entry + + +Failed + + + +Mark chunk as passed/failed [2] + +Mark chunk as passed/failed [2] + + + +Check target voltage [2]->Mark chunk as passed/failed [2] + + + + + +Calculate TP-like properties\nand store them in the\nlabnotebook + +Calculate TP-like properties +and store them in the +labnotebook + + + +n86->Calculate TP-like properties\nand store them in the\nlabnotebook + + +Supra + + + +Search for spikes\n(x range: pulse onset to end of pulse\ny condition: max above 0.01mV) + +Search for spikes +(x range: pulse onset to end of pulse +y condition: max above 0.01mV) + + + +n86->Search for spikes\n(x range: pulse onset to end of pulse\ny condition: max above 0.01mV) + + +Sub + + + +Enable "Insert TP" + +Enable "Insert TP" + + + +Enable "Repeated Acquisition"->Enable "Insert TP" + + + + + +All checks passed + +All checks passed + + + +Check if only one headstage is active->All checks passed + + + + + +Check RMS long->Add BL QC failed labnotebook entry + + +Failed + + + +Check target voltage [1] + +Check target voltage [1] + + + +Check RMS long->Check target voltage [1] + + +Passed + + + +Early Sweep stop + +Early Sweep stop + + + +Add BL QC failed labnotebook entry->Early Sweep stop + + + + + +Mark chunk as passed/failed [2]->Grab next completely acquired chunk\n(500ms) of stimset baseline + + +Failed + + + +Add BL QC passed labnotebook entry + +Add BL QC passed labnotebook entry + + + +Mark chunk as passed/failed [2]->Add BL QC passed labnotebook entry + + +Passed + + + +Check if $NUM_DA_SCALES\nsweeps passed from RA cycle + +Check if $NUM_DA_SCALES +sweeps passed from RA cycle + + + +Calculate TP-like properties\nand store them in the\nlabnotebook->Check if $NUM_DA_SCALES\nsweeps passed from RA cycle + + + + + +Optional parameter ShowPlot\nis true or missing + +Optional parameter ShowPlot +is true or missing + + + +Calculate TP-like properties\nand store them in the\nlabnotebook->Optional parameter ShowPlot\nis true or missing + + + + + +Write number of spikes\ninto labnotebook + +Write number of spikes +into labnotebook + + + +Search for spikes\n(x range: pulse onset to end of pulse\ny condition: max above 0.01mV)->Write number of spikes\ninto labnotebook + + + + + +n68 + +Use "SamplingMultiplier" analysis parameter + (defaulting to 4 if not present) and set it. + + + +Enable "Insert TP"->n68 + + + + + +Abort + +Abort + + + +All checks passed->Abort + + +No + + + +Get OperationMode + +Get OperationMode + + + +All checks passed->Get OperationMode + + +Yes + + + +Mark chunk as passed/failed [1] + +Mark chunk as passed/failed [1] + + + +Check target voltage [1]->Mark chunk as passed/failed [1] + + + + + +Add BL QC passed labnotebook entry->Early Sweep stop + + + + + +Skip to end of active set + +Skip to end of active set + + + +Check if $NUM_DA_SCALES\nsweeps passed from RA cycle->Skip to end of active set + + +Yes + + + +Use next DAScale value + +Use next DAScale value + + + +Check if $NUM_DA_SCALES\nsweeps passed from RA cycle->Use next DAScale value + + +No + + + +Plot the resistance (Sub)\nor fI (Supra) + +Plot the resistance (Sub) +or fI (Supra) + + + +Optional parameter ShowPlot\nis true or missing->Plot the resistance (Sub)\nor fI (Supra) + + +Yes + + + +Analysis parameters MinimumSpikeCount,\n MaximumSpikeCount,\n DAScaleModifier\n present? + +Analysis parameters MinimumSpikeCount, + MaximumSpikeCount, + DAScaleModifier + present? + + + +Write number of spikes\ninto labnotebook->Analysis parameters MinimumSpikeCount,\n MaximumSpikeCount,\n DAScaleModifier\n present? + + + + + +Determine pulse duration\nand write it into the labnotebook + +Determine pulse duration +and write it into the labnotebook + + + +Write number of spikes\ninto labnotebook->Determine pulse duration\nand write it into the labnotebook + + + + + +Look for a rheobase sweep with passing set QC,\n pulse duration longer than 500ms\n and having spiked + +Look for a rheobase sweep with passing set QC, + pulse duration longer than 500ms + and having spiked + + + +Get OperationMode->Look for a rheobase sweep with passing set QC,\n pulse duration longer than 500ms\n and having spiked + + +Supra + + + +Use the DAScale values\nfrom the analysis parameters + +Use the DAScale values +from the analysis parameters + + + +Get OperationMode->Use the DAScale values\nfrom the analysis parameters + + +Sub + + + +n110 + +Look for a supra SCI with passing set QC + and a long rheobase SCI with passing set QC + + + +Get OperationMode->n110 + + +Adaptive Supra + + + +Mark chunk as passed/failed [1]->Grab next completely acquired chunk\n(500ms) of stimset baseline + + +Passed + + + +Early sweep stop, repurpose ITI and add 10s to ITI + +Early sweep stop, repurpose ITI and add 10s to ITI + + + +Mark chunk as passed/failed [1]->Early sweep stop, repurpose ITI and add 10s to ITI + + +Failed + + + +n88->n90 + + + + + +n94 + +Do overshoot correction: + This means we want to ensure that all acquired AP frequency DAScale data + has a stepwidth of smaller than MaxFrequencyChangePercent. + If this is not the case we add DAScale values to the future DAScale list + + + +n93->n94 + + +Do we have passing sweeps in this SCI? + + + +n104 + +Determine if we have more than two + points to fit and write the result into the labnotebook + + + +n93->n104 + + + + + +Look for a rheobase sweep with passing set QC,\n pulse duration longer than 500ms\n and having spiked->Abort + + +Not found + + + +Use the DAScale value of that sweep\n as offset to the DAScale values from the analysis parameters + +Use the DAScale value of that sweep + as offset to the DAScale values from the analysis parameters + + + +Look for a rheobase sweep with passing set QC,\n pulse duration longer than 500ms\n and having spiked->Use the DAScale value of that sweep\n as offset to the DAScale values from the analysis parameters + + +Found + + + +Use first DAScale value + +Use first DAScale value + + + +Use the DAScale values\nfrom the analysis parameters->Use first DAScale value + + + + + +n110->Abort + + +Not found + + + +n133 + +Add all passing sweeps from the previous SCI + if all of the following conditions are met: +- DAScale adaptive suprathreshold was run +- failing set QC +-all analysis parameters are the same +- same targetV autobias value + + + +n110->n133 + + +Found + + + +Analysis parameters MinimumSpikeCount,\n MaximumSpikeCount,\n DAScaleModifier\n present?->Use next DAScale value + + +No + + + +Spike count relative to\nMin and Max? + +Spike count relative to +Min and Max? + + + +Analysis parameters MinimumSpikeCount,\n MaximumSpikeCount,\n DAScaleModifier\n present?->Spike count relative to\nMin and Max? + + +Yes + + + +Create spike frequency vs DAScale (fI) data\nand peform linear regression + +Create spike frequency vs DAScale (fI) data +and peform linear regression + + + +Determine pulse duration\nand write it into the labnotebook->Create spike frequency vs DAScale (fI) data\nand peform linear regression + + + + + +Spike count relative to\nMin and Max?->Use next DAScale value + + +In-between + + + +Adapt DAScale\n by a factor of 1 - Modifier + +Adapt DAScale + by a factor of 1 - Modifier + + + +Spike count relative to\nMin and Max?->Adapt DAScale\n by a factor of 1 - Modifier + + +Above + + + +Adapt DAScale\n by a factor of 1 + Modifier + +Adapt DAScale + by a factor of 1 + Modifier + + + +Spike count relative to\nMin and Max?->Adapt DAScale\n by a factor of 1 + Modifier + + +Below + + + +Create spike frequency vs DAScale (fI) data\nand peform linear regression->Optional parameter ShowPlot\nis true or missing + + + + + +Write fI-Slope into labnotebook + +Write fI-Slope into labnotebook + + + +Create spike frequency vs DAScale (fI) data\nand peform linear regression->Write fI-Slope into labnotebook + + + + + +Use the DAScale value of that sweep\n as offset to the DAScale values from the analysis parameters->Use first DAScale value + + + + + +n134 + +Store list of passing RhSuAd sweeps + in the labnotebook + + + +n133->n134 + + + + + +Adapt DAScale\n by a factor of 1 - Modifier->Use next DAScale value + + + + + +Adapt DAScale\n by a factor of 1 + Modifier->Use next DAScale value + + + + + +Optional FinalSlopePercent\nparameter present? + +Optional FinalSlopePercent +parameter present? + + + +Write fI-Slope into labnotebook->Optional FinalSlopePercent\nparameter present? + + + + + +Add labnotebook entry if the\ndesired fI-Slope was reached or not + +Add labnotebook entry if the +desired fI-Slope was reached or not + + + +Optional FinalSlopePercent\nparameter present?->Add labnotebook entry if the\ndesired fI-Slope was reached or not + + +Yes + + + +n114 + +Gather AP frequency and DAScale data + from all RhSuAd sweeps + but using the adaptive E1 epoch length for evaluations + + + +n116 + +Store frequency and DAScale data + in the labnotebook + + + +n114->n116 + + + + + +n117 + +Fit the AP frequency and DAScale data + ignoring entries with the same AP frequency + as their right neighbour + + + +n116->n117 + + + + + +n134->n114 + + + + + +n94->n104 + + + + + +n95 + +Fit the last two AP frequency + and DAScale data from RhSuAd plus this SCI + ignoring entries with the same AP frequency + as their right neighbour + + + +n104->n95 + + +Yes + + + +n97 + +Write fit slope and offset to the labnotebook + + + +n95->n97 + + +Sucess? + + + +n98 + +Mark the fit slope as invalid in the labnotebook + + + +n95->n98 + + +Failure? + + + +n101 + +Determine if the fit slope is valid + and store the result in the labnotebook + + + +n97->n101 + + + + + +n99 + +Calculate the maximum slope in this SCI + and store it in the labnotebook + + + +n98->n99 + + + + + +n101->n99 + + + + + +n102 + +Does the current f-I slope fullfill + all of the following conditions: +- finite +-SlopePercentage smaller than the max slope +- acquired with a larger DAScale value than the maxSlope + + + +n99->n102 + + + + + +n105 + +Mark sweep as passed if all of the following checks passed + - baseline QC + - sampling interval QC + - async QC + - valid fit QC + - enough points for fit + + + +n102->n105 + + + + + +n107 + +Determine if we measured all future DAScale values + and store that value in the labnotebook + + + +n105->n107 + + + + + +n138 + +Plot AP frequency and f-I slope both versus DAScale + + + +n107->n138 + + + + + +n139 + +Do we have at least NumSweepsWithSaturation + sweeps which are adjacent, ignoring sweeps with failed sweep QC, + and have sweep QC and f-I slope QC passing? + + + +n138->n139 + + + + + +n112 + +Mark set as passed + + + +n139->n112 + + +Yes + + + +n109 + +Check if the set can still pass + + + +n139->n109 + + +No + + + +n113 + +Skip to end of active set + + + +n112->n113 + + + + + +n111 + +Skip to end + + + +n109->n111 + + +No + + + +n100 + +Has the sweep passed? + + + +n109->n100 + + +Yes + + + +n103 + +Measured all future DAScale values? + + + +n100->n103 + + +Yes + + + +n106 + +Calculate new DAScale value by + extrapolating fit slope and offset + and using MaximumChangePercent - 2 as frequency distance. + Uses the fit slopes and offsets from the + passing sweep with the highest DAScale searching from the back. + + + +n103->n106 + + +Yes + + + +n108 + +Use the next DAScale value + + + +n103->n108 + + +No + + + +n106->n108 + + + + + +n117->Abort + + +Failure + + + +n118 + +Store the fit slope and offset + in the labnotebook + + + +n117->n118 + + +Success + + + +n119 + +Calculate the maximum fit slope + and store it in the labnotebook + + + +n118->n119 + + + + + +n128 + +Calculate the normalized minimum and maximum + DAScale step witdths and store them in the labnotebook + + + +n119->n128 + + + + + +n131 + +Plot AP frequency and f-I slope both versus DAScale + + + +n128->n131 + + + + + +n120 + +Do overshoot correction + + + +n131->n120 + + + + + +n121 + +Determine if the fit slopes are valid + and store that in the labnotebook + + + +n120->n121 + + +Needed + + + +n135 + +Do we have at least NumSweepsWithSaturation + sweeps which are adjacent, ignoring sweeps with failed sweep QC, + and have sweep QC and f-I slope QC passing? + + + +n120->n135 + + +Not Needed + + + +n121->n106 + + +Success + + + +n136 + +Skip to end of active set + + + +n135->n136 + + +Yes + + + +n137 + +Reuse already set DAScale value + + + +n136->n137 + + + + + diff --git a/_images/patch-seq-pipette-bath1.svg b/_images/patch-seq-pipette-bath1.svg new file mode 100644 index 0000000000..062092aea7 --- /dev/null +++ b/_images/patch-seq-pipette-bath1.svg @@ -0,0 +1,812 @@ + + + + + + +G + + + +Start DAQ/RA + +Start DAQ/RA + + + +Mid Sweep Event + +Mid Sweep Event + + + +Start DAQ/RA->Mid Sweep Event + + + + + +Post DAQ Event + +Post DAQ Event + + + +Start DAQ/RA->Post DAQ Event + + + + + +Post Set Event + +Post Set Event + + + +Start DAQ/RA->Post Set Event + + + + + +Pre Sweep Config Event + +Pre Sweep Config Event + + + +Start DAQ/RA->Pre Sweep Config Event + + + + + +Post Sweep Event + +Post Sweep Event + + + +Start DAQ/RA->Post Sweep Event + + + + + +Prepare DAQ/Pre Set Event + +Pre DAQ Event + + + +Start DAQ/RA->Prepare DAQ/Pre Set Event + + + + + +n83 + +Pre Sweep Config Event + + + +Start DAQ/RA->n83 + + + + + +n85 + +Pre Set Event + + + +Start DAQ/RA->n85 + + + + + +BL QC passed? + +BL QC passed? + + + +Mid Sweep Event->BL QC passed? + + + + + +Update Dashboard + +Update Dashboard + + + +Post DAQ Event->Update Dashboard + + + + + +n81 + +Has passing set QC + labnotebook entry + + + +Post DAQ Event->n81 + + + + + +Post Set Event->Update Dashboard + + + + + +Has three passing sweeps in set\n with the same DAScale value? [1] + +Has one passing sweep? + + + +Post Set Event->Has three passing sweeps in set\n with the same DAScale value? [1] + + + + + +n55 + +Publish results via ZeroMQ message + + + +Post Set Event->n55 + + + + + +n106 + + +Standard AsyncQCChannels handling + + + + + +Pre Sweep Config Event->n106 + + + + + +n105 + + +Standard AsyncQCChannels handling + + + + + +Post Sweep Event->n105 + + + + + +Enable "TP during ITI" + +Disable "Indexing" + + + +Prepare DAQ/Pre Set Event->Enable "TP during ITI" + + + + + +Check if no TTL channels are active + +Check if no TTL channels are active + + + +Prepare DAQ/Pre Set Event->Check if no TTL channels are active + + + + + +n84 + +Check that the number of testpulses + from the analysis parameter "NumberOfTestpulses" + matches the number of actually present test pulses + + + +n83->n84 + + + + + +n86 + +Set analysis function version + in labnotebook + + + +n85->n86 + + + + + +Grab next completely acquired chunk\n(500ms) of stimset baseline + +Grab next completely acquired chunk +(500ms) of stimset baseline + + + +BL QC passed?->Grab next completely acquired chunk\n(500ms) of stimset baseline + + +No + + + +n89 + +Read optional "NextStimsetName" analysis parameter + and set that as next stimulus set + + + +n81->n89 + + +Yes + + + +Mark set as failed\n in labnotebook + +Mark set as failed + in labnotebook + + + +Has three passing sweeps in set\n with the same DAScale value? [1]->Mark set as failed\n in labnotebook + + +No + + + +Mark set as passed\n in labnotebook + +Mark set as passed + in labnotebook + + + +Has three passing sweeps in set\n with the same DAScale value? [1]->Mark set as passed\n in labnotebook + + +Yes + + + +n87 + +Check sampling frequency + and store the QC state in the labnotebook + + + +n105->n87 + + + + + +Enable "Multidevice DAQ" + +Enable "Multidevice DAQ" + + + +Enable "TP during ITI"->Enable "Multidevice DAQ" + + + + + +Check if mode is IC + +Check if mode is VC + + + +Check if no TTL channels are active->Check if mode is IC + + + + + +Abort + +Abort + + + +n84->Abort + + +Yes + + + +Chunk already evaluated? + +Chunk already evaluated? + + + +Grab next completely acquired chunk\n(500ms) of stimset baseline->Chunk already evaluated? + + +Have one + + + +n56 + +Read optional "NextIndexingEndStimsetName" analysis parameter + and set that as indexing end stimulus set + + + +n89->n56 + + + + + +n93 + +Read the "Steady State Resistance" + from the SweepFormula results + labnotebook entry + + + +n87->n93 + + + + + +n94 + +Is the value between the + "MinPipetteResistance" and "MaxPipetteResitance" + analysis parameters? + + + +n93->n94 + + + + + +n95 + +Store it in the labnotebook + + + +n93->n95 + + + + + +Disable "dDAQ"/"oodDAQ" + +Disable "dDAQ"/"oodDAQ" + + + +Enable "Multidevice DAQ"->Disable "dDAQ"/"oodDAQ" + + + + + +Check if only one headstage is active + +Check if only one headstage is active + + + +Check if mode is IC->Check if only one headstage is active + + + + + +Chunk already evaluated?->Grab next completely acquired chunk\n(500ms) of stimset baseline + + +Yes + + + +Baseline chunk type + +Baseline chunk type + + + +Chunk already evaluated?->Baseline chunk type + + +No + + + +n57 + +Enable Indexing + + + +n56->n57 + + + + + +n96 + +Store it in the labnotebook + + + +n94->n96 + + + + + +Enable "Repeated Acquisition" + +Enable "Repeated Acquisition" + + + +Disable "dDAQ"/"oodDAQ"->Enable "Repeated Acquisition" + + + + + +All checks passed + +All checks passed + + + +Check if only one headstage is active->All checks passed + + + + + +Check RMS short + +Check RMS short + + + +Baseline chunk type->Check RMS short + + +pre pulse + + + +n98 + +Does the labnotebook has passing + baseline QC +async channels QC +pipette resistance QC + and sampling frequency QC entries? + + + +n96->n98 + + + + + +n88 + +Open Databrowser + and attach to the current device + + + +Enable "Repeated Acquisition"->n88 + + + + + +n91 + +Apply auto pipette offset + + + +Enable "Repeated Acquisition"->n91 + + + + + +All checks passed->Abort + + +No + + + +Check RMS long + +Check RMS long + + + +Check RMS short->Check RMS long + + +Passed + + + +Add BL QC failed labnotebook entry + +Add BL chunk QC failed + labnotebook entry + + + +Check RMS short->Add BL QC failed labnotebook entry + + +Failed + + + +n99 + +Mark sweep as passed + + + +n98->n99 + + +Yes + + + +n100 + +Mark sweep as failed + + + +n98->n100 + + + + + +n90 + +Enable "Sweep Formula" in the databrowser + + + +n88->n90 + + + + + +Check RMS long->Add BL QC failed labnotebook entry + + +Failed + + + +Check target voltage [1] + +Check leak current + + + +Check RMS long->Check target voltage [1] + + +Passed + + + +n79 + +Add BL QC failed + labnotebook entry + + + +Add BL QC failed labnotebook entry->n79 + + + + + +n101 + +Skip to end of Set + + + +n99->n101 + + + + + +n102 + +Is the number of failed sweeps + larger than the "NumberofFailedSweeps" analysis parameter? + + + +n100->n102 + + + + + +n104 + +Has the sampling frequency QC check failed? + + + +n100->n104 + + + + + +n92 + +Set SweepFormula code for calculating + testpulse properties from testpulse like epochs in the sweep + + + +n90->n92 + + + + + +Mark chunk as passed/failed [1] + +Add BL chunk QC passed + labnotebook entry + + + +Check target voltage [1]->Mark chunk as passed/failed [1] + + +Passed + + + +n78 + +Apply auto pipette offset + + + +Check target voltage [1]->n78 + + +Failed + + + +Early Sweep stop + +Early Sweep stop + + + +n79->Early Sweep stop + + + + + +n80 + +Add BL QC passed + labnotebook entry + + + +Mark chunk as passed/failed [1]->n80 + + + + + +n78->Add BL QC failed labnotebook entry + + + + + +n103 + +Skip to end of DAQ + + + +n102->n103 + + + + + +n104->n103 + + +Yes + + + diff --git a/_images/patch-seq-ramp1.svg b/_images/patch-seq-ramp1.svg new file mode 100644 index 0000000000..345e877921 --- /dev/null +++ b/_images/patch-seq-ramp1.svg @@ -0,0 +1,893 @@ + + + + + + +G + + + +Start DAQ/RA + +Start DAQ/RA + + + +Mid Sweep Event + +Mid Sweep Event + + + +Start DAQ/RA->Mid Sweep Event + + + + + +Post Set Event + +Post Set Event + + + +Start DAQ/RA->Post Set Event + + + + + +Pre Sweep Config Event + +Pre Sweep Config Event + + + +Start DAQ/RA->Pre Sweep Config Event + + + + + +Post Sweep Event + +Post Sweep Event + + + +Start DAQ/RA->Post Sweep Event + + + + + +Post DAQ Event + +Post DAQ Event + + + +Start DAQ/RA->Post DAQ Event + + + + + +Prepare DAQ/Pre Set Event + +Prepare DAQ/Pre Set Event + + + +Start DAQ/RA->Prepare DAQ/Pre Set Event + + + + + +BL QC passed? + +BL QC passed? + + + +Mid Sweep Event->BL QC passed? + + + + + +Search spike result in labnotebook + +Search spike result in labnotebook + + + +Mid Sweep Event->Search spike result in labnotebook + + + + + +Mark set as passed if 3 sweeps passed, as failure otherwise + +Mark set as passed if 3 sweeps passed, as failure otherwise + + + +Post Set Event->Mark set as passed if 3 sweeps passed, as failure otherwise + + + + + +n92 + + +Standard AsyncQCChannels handling + + + + + +Pre Sweep Config Event->n92 + + + + + +n91 + + +Standard AsyncQCChannels handling + + + + + +Post Sweep Event->n91 + + + + + +Update Dashboard + +Update Dashboard + + + +Post DAQ Event->Update Dashboard + + + + + +Enable "Autobias" + +Enable "Autobias" + + + +Prepare DAQ/Pre Set Event->Enable "Autobias" + + + + + +Valid Autobias voltage (finite and non-zero) + +Valid Autobias voltage (finite and non-zero) + + + +Prepare DAQ/Pre Set Event->Valid Autobias voltage (finite and non-zero) + + + + + +Grab next completely acquired chunk (500ms) of stimset baseline + +Grab next completely acquired chunk (500ms) of stimset baseline + + + +BL QC passed?->Grab next completely acquired chunk (500ms) of stimset baseline + + +No + + + +Get pulse duration from labnotebook (calculate if not present) + +Get pulse duration from labnotebook (calculate if not present) + + + +Search spike result in labnotebook->Get pulse duration from labnotebook (calculate if not present) + + +Not Found + + + +n61 + +Read "SamplingFrequency" analysis parameter + (defaulting to 50kHz) if not present + + + +n91->n61 + + + + + +Enable "Inserted TP" + +Enable "Inserted TP" + + + +Enable "Autobias"->Enable "Inserted TP" + + + + + +Stimset is longer than 1.5s + +Stimset is longer than 1.5s + + + +Valid Autobias voltage (finite and non-zero)->Stimset is longer than 1.5s + + + + + +Chunk already evaluated? + +Chunk already evaluated? + + + +Grab next completely acquired chunk (500ms) of stimset baseline->Chunk already evaluated? + + +Have one + + + +Last chunk? + +Last chunk? + + + +Grab next completely acquired chunk (500ms) of stimset baseline->Last chunk? + + +None left + + + +After pulse onset + +After pulse onset + + + +Get pulse duration from labnotebook (calculate if not present)->After pulse onset + + + + + +n63 + +Check if the acquired data + has that sampling interval + + + +n61->n63 + + + + + +Skip to end + +Skip to end + + + +n63->Skip to end + + +No + + + +n62 + +Mark sweep as failed + + + +n63->n62 + + +No + + + +n65 + +BL QC passed? + + + +n63->n65 + + +Yes + + + +Enable "Multidevice DAQ" + +Enable "Multidevice DAQ" + + + +Enable "Inserted TP"->Enable "Multidevice DAQ" + + + + + +Check if only one headstage is active + +Check if only one headstage is active + + + +Stimset is longer than 1.5s->Check if only one headstage is active + + + + + +Chunk already evaluated?->Grab next completely acquired chunk (500ms) of stimset baseline + + +Yes + + + +Baseline chunk type + +Baseline chunk type + + + +Chunk already evaluated?->Baseline chunk type + + +No + + + +Mark Sweep/BL QC as failed + +Mark BL QC as failed + + + +Last chunk?->Mark Sweep/BL QC as failed + + +Yes + + + +Requested number of spikes detected?\n(x range: pulse onset to end of sweep\ny condition: max above 0.01mV) + +Requested number of spikes detected? +(x range: pulse onset to end of sweep +y condition: max above 0.01mV) + + + +After pulse onset->Requested number of spikes detected?\n(x range: pulse onset to end of sweep\ny condition: max above 0.01mV) + + +Yes + + + +Check if the Set can still pass + +Check if the Set can still pass + + + +n62->Check if the Set can still pass + + + + + +n65->n62 + + +No + + + +n64 + +Has Async Channels QC + labnotebook entry passed? + + + +n65->n64 + + +Yes + + + +Enable "TP during ITI" + +Enable "TP during ITI" + + + +Enable "Multidevice DAQ"->Enable "TP during ITI" + + + + + +Stimset has at least three sweeps + +Stimset has at least three sweeps + + + +Check if only one headstage is active->Stimset has at least three sweeps + + + + + +Check RMS short + +Check RMS short + + + +Baseline chunk type->Check RMS short + + +pre pulse + + + +Check target voltage [2] + +Check target voltage [2] + + + +Baseline chunk type->Check target voltage [2] + + +post pulse + + + +Early Sweep stop + +Early Sweep stop + + + +Mark Sweep/BL QC as failed->Early Sweep stop + + + + + +After pulse + +After pulse + + + +Requested number of spikes detected?\n(x range: pulse onset to end of sweep\ny condition: max above 0.01mV)->After pulse + + +No + + + +Write spike result (true/false) into labnotebook + +Write spike result (true/false) into labnotebook + + + +Requested number of spikes detected?\n(x range: pulse onset to end of sweep\ny condition: max above 0.01mV)->Write spike result (true/false) into labnotebook + + +Yes + + + +Check if the Set can still pass->Skip to end + + +No + + + +n64->n62 + + +No + + + +n68 + +Mark sweep as passed + + + +n64->n68 + + +Yes + + + +Disable "dDAQ"/"oodDAQ" + +Disable "dDAQ"/"oodDAQ" + + + +Enable "TP during ITI"->Disable "dDAQ"/"oodDAQ" + + + + + +Stimset is large enough + +Stimset is large enough + + + +Stimset has at least three sweeps->Stimset is large enough + + + + + +Check RMS short->Mark Sweep/BL QC as failed + + +Failed + + + +Check RMS long + +Check RMS long + + + +Check RMS short->Check RMS long + + +Passed + + + +Mark chunk as passed/failed [2] + +Mark chunk as passed/failed [2] + + + +Check target voltage [2]->Mark chunk as passed/failed [2] + + + + + +Write spike result "failed" into LBN + +Write spike result "failed" into LBN + + + +After pulse->Write spike result "failed" into LBN + + +Yes + + + +Write spike position in ms into labnotebook + +Write spike position in ms into labnotebook + + + +Write spike result (true/false) into labnotebook->Write spike position in ms into labnotebook + + + + + +Check if 3 sweeps passed from RA cycle + +Check if three sweeps + passed from the SCI + + + +n68->Check if 3 sweeps passed from RA cycle + + + + + +Skip to end of active set + +Skip to end of active set + + + +Check if 3 sweeps passed from RA cycle->Skip to end of active set + + +Yes + + + +Set ITI to zero + +Set ITI to zero + + + +Disable "dDAQ"/"oodDAQ"->Set ITI to zero + + + + + +Check if mode is IC + +Check if mode is IC + + + +Stimset is large enough->Check if mode is IC + + + + + +Check RMS long->Mark Sweep/BL QC as failed + + +Failed + + + +Check target voltage [1] + +Check target voltage [1] + + + +Check RMS long->Check target voltage [1] + + +Passed + + + +Mark chunk as passed/failed [2]->Grab next completely acquired chunk (500ms) of stimset baseline + + +Failed + + + +Mark Sweep/BL QC as passed + +Mark BL QC as passed + + + +Mark chunk as passed/failed [2]->Mark Sweep/BL QC as passed + + +Passed + + + +Set DA channel to zero from here to the end\n(implies DAQ restart) + +Set DA channel to zero from here to the end +(implies DAQ restart) + + + +Write spike position in ms into labnotebook->Set DA channel to zero from here to the end\n(implies DAQ restart) + + + + + +Set DAScale to 1pA + +Set DAScale to 1pA + + + +Set ITI to zero->Set DAScale to 1pA + + + + + +Check if no TTL channels are active + +Check if no TTL channels are active + + + +Check if mode is IC->Check if no TTL channels are active + + + + + +Mark chunk as passed/failed [1] + +Mark chunk as passed/failed [1] + + + +Check target voltage [1]->Mark chunk as passed/failed [1] + + + + + +Mark Sweep/BL QC as passed->Early Sweep stop + + + + + +Mark Sweep/BL QC as passed->Mark Sweep/BL QC as passed + + + + + +Set AD channel to zero for the duration of the DAQ restart + +Set AD channel to zero for the duration of the DAQ restart + + + +Set DA channel to zero from here to the end\n(implies DAQ restart)->Set AD channel to zero for the duration of the DAQ restart + + + + + +Enable "Repeated Acquisition" + +Enable "Repeated Acquisition" + + + +Set DAScale to 1pA->Enable "Repeated Acquisition" + + + + + +All checks passed + +All checks passed + + + +Check if no TTL channels are active->All checks passed + + + + + +Mark chunk as passed/failed [1]->Grab next completely acquired chunk (500ms) of stimset baseline + + +Passed + + + +Early sweep stop, repurpose ITI and add 10s to ITI + +Early sweep stop, repurpose ITI and add 10s to ITI + + + +Mark chunk as passed/failed [1]->Early sweep stop, repurpose ITI and add 10s to ITI + + +Failed + + + +Recalculate pulse duration and\nstore in labnotebook + +Recalculate pulse duration and +store in labnotebook + + + +Set AD channel to zero for the duration of the DAQ restart->Recalculate pulse duration and\nstore in labnotebook + + + + + +n58 + +Use "SamplingMultiplier" analysis parameter + (defaulting to 4 if not present) and set it + + + +Enable "Repeated Acquisition"->n58 + + + + + +Abort + +Abort + + + +All checks passed->Abort + + +No + + + diff --git a/_images/patch-seq-rheobase1.svg b/_images/patch-seq-rheobase1.svg new file mode 100644 index 0000000000..3ddba5a00f --- /dev/null +++ b/_images/patch-seq-rheobase1.svg @@ -0,0 +1,928 @@ + + + + + + +G + + + +Start DAQ/RA + +Start DAQ/RA + + + +Mid Sweep Event + +Mid Sweep Event + + + +Start DAQ/RA->Mid Sweep Event + + + + + +Post Set Event + +Post Set Event + + + +Start DAQ/RA->Post Set Event + + + + + +Post Sweep Event + +Post Sweep Event + + + +Start DAQ/RA->Post Sweep Event + + + + + +Pre Sweep Config Event + +Pre Sweep Config Event + + + +Start DAQ/RA->Pre Sweep Config Event + + + + + +Prepare DAQ/Pre Set Event + +Prepare DAQ/Pre Set Event + + + +Start DAQ/RA->Prepare DAQ/Pre Set Event + + + + + +Post DAQ Event + +Post DAQ Event + + + +Start DAQ/RA->Post DAQ Event + + + + + +BL QC passed? [1] + +BL QC passed? [1] + + + +Mid Sweep Event->BL QC passed? [1] + + + + + +Mark set as failed if it has not yet passed + +Mark set as failed if it has not yet passed + + + +Post Set Event->Mark set as failed if it has not yet passed + + + + + +n91 + + +Standard AsyncQCChannels handling + + + + + +Post Sweep Event->n91 + + + + + +n92 + + +Standard AsyncQCChannels handling + + + + + +Pre Sweep Config Event->n92 + + + + + +Stimset is large enough + +Stimset is large enough + + + +Prepare DAQ/Pre Set Event->Stimset is large enough + + + + + +Set "Repeat Sets" to 1 + +Set "Repeat Sets" to 1 + + + +Prepare DAQ/Pre Set Event->Set "Repeat Sets" to 1 + + + + + +Update Dashboard + +Update Dashboard + + + +Post DAQ Event->Update Dashboard + + + + + +Grab next completely acquired chunk\n (500ms) of stimset baseline + +Grab next completely acquired chunk + (500ms) of stimset baseline + + + +BL QC passed? [1]->Grab next completely acquired chunk\n (500ms) of stimset baseline + + +No + + + +Skip to end + +Skip to end + + + +Mark set as failed if it has not yet passed->Skip to end + + +Failure + + + +First Sweep? + +First Sweep? + + + +n91->First Sweep? + + + + + +Check if only one headstage is active + +Check if only one headstage is active + + + +Stimset is large enough->Check if only one headstage is active + + + + + +Enable "Autobias" + +Enable "Autobias" + + + +Set "Repeat Sets" to 1->Enable "Autobias" + + + + + +Chunk already evaluated? + +Chunk already evaluated? + + + +Grab next completely acquired chunk\n (500ms) of stimset baseline->Chunk already evaluated? + + +Have one + + + +Last chunk? + +Last chunk? + + + +Grab next completely acquired chunk\n (500ms) of stimset baseline->Last chunk? + + +None left + + + +Store final DAScale of last sweep\n from previous RAC as initial DAScale + +Store final DAScale of last sweep + from previous RAC as initial DAScale + + + +First Sweep?->Store final DAScale of last sweep\n from previous RAC as initial DAScale + + +Yes + + + +n60 + +Read "SamplingFrequency" analysis parameter + (defaulting to 50kHz) if not present + + + +First Sweep?->n60 + + +No + + + +Store DAScale stepsize of 10pA in LBN + +Store DAScale stepsize of 10pA in LBN + + + +Store final DAScale of last sweep\n from previous RAC as initial DAScale->Store DAScale stepsize of 10pA in LBN + + + + + +n61 + +Check if the acquired data + has that sampling interval + + + +n60->n61 + + + + + +Valid Autobias voltage (finite and non-zero) + +Valid Autobias voltage (finite and non-zero) + + + +Check if only one headstage is active->Valid Autobias voltage (finite and non-zero) + + + + + +Set "TP during ITI" + +Set "TP during ITI" + + + +Enable "Autobias"->Set "TP during ITI" + + + + + +Chunk already evaluated?->Grab next completely acquired chunk\n (500ms) of stimset baseline + + +Yes + + + +Baseline chunk type + +Baseline chunk type + + + +Chunk already evaluated?->Baseline chunk type + + +No + + + +Mark BL QC as failed + +Mark BL QC as failed + + + +Last chunk?->Mark BL QC as failed + + +Yes + + + +Store DAScale stepsize of 10pA in LBN->n60 + + + + + +BL QC passed? [2] + +BL QC passed? [2] + + + +n61->BL QC passed? [2] + + +Yes + + + +Mark set as failed + +Mark set as failed + + + +n61->Mark set as failed + + +No + + + +Check if no TTL channels are active + +Check if no TTL channels are active + + + +Valid Autobias voltage (finite and non-zero)->Check if no TTL channels are active + + + + + +Enable "Multidevice DAQ" + +Enable "Multidevice DAQ" + + + +Set "TP during ITI"->Enable "Multidevice DAQ" + + + + + +Check RMS short + +Check RMS short + + + +Baseline chunk type->Check RMS short + + +pre pulse + + + +Check target voltage [2] + +Check target voltage [2] + + + +Baseline chunk type->Check target voltage [2] + + +post pulse + + + +Early sweep stop + +Early sweep stop + + + +Mark BL QC as failed->Early sweep stop + + + + + +n65 + +Has Async Channels QC + labnotebook entry passed? + + + +BL QC passed? [2]->n65 + + +Yes + + + +Mark set as failed->Skip to end + + + + + +All required analysis parameters present?\nSamplingMultiplier: variable + +All required analysis parameters present? +SamplingMultiplier: variable + + + +Check if no TTL channels are active->All required analysis parameters present?\nSamplingMultiplier: variable + + + + + +Disable "dDAQ"/"oodDAQ" + +Disable "dDAQ"/"oodDAQ" + + + +Enable "Multidevice DAQ"->Disable "dDAQ"/"oodDAQ" + + + + + +Check RMS short->Mark BL QC as failed + + +Failed + + + +Check RMS long + +Check RMS long + + + +Check RMS short->Check RMS long + + +Passed + + + +Mark chunk as passed/failed [2] + +Mark chunk as passed/failed [2] + + + +Check target voltage [2]->Mark chunk as passed/failed [2] + + + + + +Spike detected?\n(x range: pulse onset to end of sweep\ny condition: max above 0.01mV)\nStore result in labnotebook + +Spike detected? +(x range: pulse onset to end of sweep +y condition: max above 0.01mV) +Store result in labnotebook + + + +n65->Spike detected?\n(x range: pulse onset to end of sweep\ny condition: max above 0.01mV)\nStore result in labnotebook + + +Yes + + + +Search for final DAScale in one of the existing sweeps + +Search for final DAScale in one of the existing sweeps + + + +All required analysis parameters present?\nSamplingMultiplier: variable->Search for final DAScale in one of the existing sweeps + + + + + +Enable "Repeated Acquisition" + +Enable "Repeated Acquisition" + + + +Disable "dDAQ"/"oodDAQ"->Enable "Repeated Acquisition" + + + + + +Check RMS long->Mark BL QC as failed + + +Failed + + + +Check target voltage [1] + +Check target voltage [1] + + + +Check RMS long->Check target voltage [1] + + +Passed + + + +Mark chunk as passed/failed [2]->Grab next completely acquired chunk\n (500ms) of stimset baseline + + +Failed + + + +Mark BL QC as passed + +Mark BL QC as passed + + + +Mark chunk as passed/failed [2]->Mark BL QC as passed + + +Passed + + + +Previous sweep has opposite spike result\nand same step size? + +Previous sweep has opposite spike result +and same step size? + + + +Spike detected?\n(x range: pulse onset to end of sweep\ny condition: max above 0.01mV)\nStore result in labnotebook->Previous sweep has opposite spike result\nand same step size? + + + + + +DAScale larger than 50pA\nor stepsize is 2pA + +DAScale larger than 50pA +or stepsize is 2pA + + + +Previous sweep has opposite spike result\nand same step size?->DAScale larger than 50pA\nor stepsize is 2pA + + +Yes + + + +Spike detected? (queried from labnotebook) + +Spike detected? (queried from labnotebook) + + + +Previous sweep has opposite spike result\nand same step size?->Spike detected? (queried from labnotebook) + + +No + + + +All checks passed + +All checks passed + + + +Search for final DAScale in one of the existing sweeps->All checks passed + + + + + +Set "ITI" to 4s + +Set "ITI" to 4s + + + +Enable "Repeated Acquisition"->Set "ITI" to 4s + + + + + +Mark chunk as passed/failed [1] + +Mark chunk as passed/failed [1] + + + +Check target voltage [1]->Mark chunk as passed/failed [1] + + + + + +Mark BL QC as passed->Early sweep stop + + + + + +Mark set as passed + +Mark set as passed + + + +DAScale larger than 50pA\nor stepsize is 2pA->Mark set as passed + + +Yes + + + +Store DAScale stepsize of 2pA in LBN + +Store DAScale stepsize of 2pA in LBN + + + +DAScale larger than 50pA\nor stepsize is 2pA->Store DAScale stepsize of 2pA in LBN + + +No + + + +Offset DAScale by minus\nstepsize from LBN + +Offset DAScale by minus +stepsize from LBN + + + +Spike detected? (queried from labnotebook)->Offset DAScale by minus\nstepsize from LBN + + +Yes + + + +Offset DAScale by plus\nstepsize from LBN + +Offset DAScale by plus +stepsize from LBN + + + +Spike detected? (queried from labnotebook)->Offset DAScale by plus\nstepsize from LBN + + +No + + + +Abort + +Abort + + + +All checks passed->Abort + + +No + + + +n59 + +Use "SamplingMultiplier" analysis parameter + (defaulting to 4 if not present) and set it. + + + +Set "ITI" to 4s->n59 + + + + + +Mark chunk as passed/failed [1]->Grab next completely acquired chunk\n (500ms) of stimset baseline + + +Passed + + + +Early sweep stop, repurpose ITI and add 10s to ITI + +Early sweep stop, repurpose ITI and add 10s to ITI + + + +Mark chunk as passed/failed [1]->Early sweep stop, repurpose ITI and add 10s to ITI + + +Failed + + + +Skip to end of active set + +Skip to end of active set + + + +Mark set as passed->Skip to end of active set + + + + + +Store DAScale stepsize of 2pA in LBN->Spike detected? (queried from labnotebook) + + + + + +DAScale is zero? + +DAScale is zero? + + + +Offset DAScale by minus\nstepsize from LBN->DAScale is zero? + + + + + +Offset DAScale by plus\nstepsize from LBN->DAScale is zero? + + + + + +Stepsize? + +Stepsize? + + + +DAScale is zero?->Stepsize? + + +Yes + + + +Difference to initial DAScale larger than 60pA? + +Difference to initial DAScale larger than 60pA? + + + +DAScale is zero?->Difference to initial DAScale larger than 60pA? + + +No + + + +Set DAScale and stepsize to 2pA + +Set DAScale and stepsize to 2pA + + + +Stepsize?->Set DAScale and stepsize to 2pA + + +10pA + + + +Add "limited resolution"\nlabnotebook entry + +Add "limited resolution" +labnotebook entry + + + +Stepsize?->Add "limited resolution"\nlabnotebook entry + + +2pA + + + +Set "range exceeded" labnotebook\nentry to true for sweep + +Set "range exceeded" labnotebook +entry to true for sweep + + + +Difference to initial DAScale larger than 60pA?->Set "range exceeded" labnotebook\nentry to true for sweep + + +Yes + + + +Add "limited resolution"\nlabnotebook entry->Mark set as failed + + + + + +Set "range exceeded" labnotebook\nentry to true for sweep->Mark set as failed + + + + + diff --git a/_images/patch-seq-seal-evaluation1.svg b/_images/patch-seq-seal-evaluation1.svg new file mode 100644 index 0000000000..7adc019b47 --- /dev/null +++ b/_images/patch-seq-seal-evaluation1.svg @@ -0,0 +1,902 @@ + + + + + + +G + + + +n3 + +Start DAQ/RA + + + +n5 + +Pre Sweep Config Event + + + +n3->n5 + + + + + +n6 + +Pre DAQ Event + + + +n3->n6 + + + + + +n7 + +Post Set Event + + + +n3->n7 + + + + + +n8 + +Pre Set Event + + + +n3->n8 + + + + + +n9 + +Post Sweep Event + + + +n3->n9 + + + + + +n10 + +Post DAQ Event + + + +n3->n10 + + + + + +n91 + + +Standard AsyncQCChannels handling + + + + + +n5->n91 + + + + + +n21 + +Turn indexing off + + + +n6->n21 + + + + + +n29 + +Check that only one headstage is active + + + +n6->n29 + + + + + +n11 + +Update dashboard + + + +n7->n11 + + + + + +n15 + +Do we have PSQ_SE_NUM_SWEEPS_PASS + passing sweeps in the stimset cycle? + + + +n7->n15 + + + + + +n19 + +Set analysis function version + + + +n8->n19 + + + + + +n92 + + +Standard AsyncQCChannels handling + + + + + +n9->n92 + + + + + +n47 + +Iterate over all baseline QC + selection user epochs + + + +n9->n47 + + + + + +n55 + +Check used sampling frequency + and store result in labnotebook + + + +n9->n55 + + + + + +n57 + +Read "TestpulseGroupSelector" analysis  parameter + + + +n9->n57 + + + + + +n10->n11 + + + + + +n12 + +Read Set QC from labnotebook + + + +n10->n12 + + + + + +n36 + +Check that the stimset has + PSQ_SE_REQUIRED_EPOCHS (22) epochs + + + +n91->n36 + + + + + +n22 + +Turn multi device support on + + + +n21->n22 + + + + + +n30 + +Check that no TTL channels are active + + + +n29->n30 + + + + + +n16 + +Mark Set QC as failed + + + +n15->n16 + + +No + + + +n17 + +Mark Set QC as passed + + + +n15->n17 + + +Yes + + + +n20 + +Set sampling rate multiplier + analysis parameter and check it + + + +n19->n20 + + + + + +n56 + +All four QC labnotebook + entries are passing? + + + +n92->n56 + + + + + +n48 + +Read "TestpulseGroupSelector" analysis parameter + + + +n47->n48 + + +Done? + + + +n55->n56 + + + + + +n58 + +Read steady state resistance + from results wave for group B + + + +n57->n58 + + +Second + + + +n63 + +Read steady state resistance + from results wave for group A and group B + + + +n57->n63 + + +Both + + + +n64 + +Read steady state resistance + from results wave for group A + + + +n57->n64 + + +First + + + +n13 + +Read optional "NextStimsetName" analysis parameter + and set that as next stimulus set + + + +n12->n13 + + +Passed? + + + +n37 + +Read "TestPulseGroupSelector" analysis parameter + + + +n36->n37 + + + + + +n38 + +Add user epochs for testpulse group A + + + +n37->n38 + + +First + + + +n39 + +Add user epochs for testpulse group B + + + +n37->n39 + + +Second + + + +n41 + +Add user epochs for testpulse group A and B + + + +n37->n41 + + +Both + + + +n23 + +Turn repeated acquisition on + + + +n22->n23 + + + + + +n31 + +Check that the active headstage + is in voltage clamp + + + +n30->n31 + + + + + +n18 + +Publish results via ZeroMQ + + + +n16->n18 + + + + + +n17->n18 + + + + + +n59 + +Mark Sweep QC as failed + + + +n56->n59 + + +No + + + +n60 + +Mark Sweep QC as passed + + + +n56->n60 + + +Yes + + + +n49 + +Baseline chunk 0 and 1 passed? + + + +n48->n49 + + +Both + + + +n50 + +Baseline chunk 0 passed? + + + +n48->n50 + + +First + + + +n48->n50 + + +Second + + + +n65 + +Store resistances and its maximum + in labnotebook + + + +n58->n65 + + + + + +n67 + +Is greater or equal to the  "SealThreshold" + analysis parameter? + + + +n58->n67 + + + + + +n63->n65 + + + + + +n68 + +Is one of them greater or equal + to the  "SealThreshold" analysis parameter? + + + +n63->n68 + + + + + +n64->n65 + + + + + +n64->n67 + + + + + +n61 + +Read optional "NextIndexingEndStimsetName" analysis parameter + and set that as indexing end stimulus set + + + +n13->n61 + + + + + +n42 + +Add baseline selection user epoch + for stimulus set epoch before testpulse group A + + + +n38->n42 + + + + + +n43 + +Add baseline selection user epoch + for stimulus set epoch before testpulse group B + + + +n39->n43 + + + + + +n44 + +Add baseline selection user epoch + for stimulus set epoch before testpulse group A and B + + + +n41->n44 + + + + + +n24 + +Turn off oodDAQ + + + +n23->n24 + + + + + +n32 + +Abort on failed check + + + +n31->n32 + + + + + +n52 + +Mark baseline QC as passed + + + +n49->n52 + + +Passed + + + +n53 + +Mark baseline QC as failed + + + +n49->n53 + + +Failed + + + +n50->n52 + + +Passed + + + +n50->n53 + + +Failed + + + +n66 + +Mark Seal QC as passed + + + +n67->n66 + + +Yes + + + +n69 + +Mark Seal QC as failed + + + +n67->n69 + + +No + + + +n68->n66 + + + + + +n68->n69 + + + + + +n62 + +Enable Indexing + + + +n61->n62 + + + + + +n45 + +Check that the baseline QC user epochs + have the same length as the + analysis parameter "BaselineChunkLength" + + + +n42->n45 + + + + + +n43->n45 + + + + + +n44->n45 + + + + + +n25 + +Turn off dDAQ + + + +n24->n25 + + + + + +n52->n56 + + + + + +n53->n56 + + + + + +n66->n56 + + + + + +n69->n56 + + + + + +n46 + +Check that each Testpulse has three epochs + and that the pulse has amplitude one. + + + +n45->n46 + + + + + +n26 + +Turn on inserted Testpulse + + + +n25->n26 + + + + + +n27 + +Open and bind databrowser + + + +n26->n27 + + + + + +n28 + +Enable SweepFormula + + + +n27->n28 + + + + + +n35 + +Set SweepFormula respecting + "TestPulseGroupSelector" analysis parameter + + + +n28->n35 + + + + + diff --git a/_images/patch-seq-squarepulse1.svg b/_images/patch-seq-squarepulse1.svg new file mode 100644 index 0000000000..3050fe8a63 --- /dev/null +++ b/_images/patch-seq-squarepulse1.svg @@ -0,0 +1,614 @@ + + + + + + +G + + + +Start DAQ/RA + +Start DAQ/RA + + + +Prepare DAQ/Pre Set Event + +Prepare DAQ/Pre Set Event + + + +Start DAQ/RA->Prepare DAQ/Pre Set Event + + + + + +Post Sweep Event + +Post Sweep Event + + + +Start DAQ/RA->Post Sweep Event + + + + + +Post DAQ Event + +Post DAQ Event + + + +Start DAQ/RA->Post DAQ Event + + + + + +Pre Sweep Config Event + +Pre Sweep Config Event + + + +Start DAQ/RA->Pre Sweep Config Event + + + + + +Post Set Event + +Post Set Event + + + +Start DAQ/RA->Post Set Event + + + + + +Enable "Multidevice DAQ" + +Enable "Multidevice DAQ" + + + +Prepare DAQ/Pre Set Event->Enable "Multidevice DAQ" + + + + + +Check if mode is IC + +Check if mode is IC + + + +Prepare DAQ/Pre Set Event->Check if mode is IC + + + + + +n91 + + +Standard AsyncQCChannels handling + + + + + +Post Sweep Event->n91 + + + + + +Spike detected?\n(x range: pulse onset to end of sweep\ny condition: max above 0.01mV)\nStore result in labnotebook + +Spike detected? +(x range: pulse onset to end of sweep +y condition: max above 0.01mV) +Store result in labnotebook + + + +Post Sweep Event->Spike detected?\n(x range: pulse onset to end of sweep\ny condition: max above 0.01mV)\nStore result in labnotebook + + + + + +Update Dashboard + +Update Dashboard + + + +Post DAQ Event->Update Dashboard + + + + + +n92 + + +Standard AsyncQCChannels handling + + + + + +Pre Sweep Config Event->n92 + + + + + +Mark set as passed if 1 sweep passed,\nas failure otherwise + +Mark set as passed if 1 sweep passed, +as failure otherwise + + + +Post Set Event->Mark set as passed if 1 sweep passed,\nas failure otherwise + + + + + +Disable "dDAQ"/"oodDAQ" + +Disable "dDAQ"/"oodDAQ" + + + +Enable "Multidevice DAQ"->Disable "dDAQ"/"oodDAQ" + + + + + +Check if no TTL channels are active + +Check if no TTL channels are active + + + +Check if mode is IC->Check if no TTL channels are active + + + + + +n37 + +Read "SamplingFrequency" analysis parameter + (defaulting to 50kHz) if not present + + + +n91->n37 + + + + + +n43 + +Has Async Channels QC + labnotebook entry passed? + + + +n91->n43 + + + + + +DAScale is zero + +DAScale is zero + + + +Spike detected?\n(x range: pulse onset to end of sweep\ny condition: max above 0.01mV)\nStore result in labnotebook->DAScale is zero + + +Yes + + + +Step Size from labnotebook? + +Step Size from labnotebook? + + + +Spike detected?\n(x range: pulse onset to end of sweep\ny condition: max above 0.01mV)\nStore result in labnotebook->Step Size from labnotebook? + + +No + + + +Skip to end + +Skip to end + + + +Mark set as passed if 1 sweep passed,\nas failure otherwise->Skip to end + + +Failure + + + +Set "TP inserting" to disabled + +Set "TP inserting" to disabled + + + +Disable "dDAQ"/"oodDAQ"->Set "TP inserting" to disabled + + + + + +Check if only one headstage is active + +Check if only one headstage is active + + + +Check if no TTL channels are active->Check if only one headstage is active + + + + + +n38 + +Check if the acquired data + has that sampling interval + + + +n37->n38 + + + + + +n39 + +Mark Sweep as failure + + + +n43->n39 + + +No + + + +Step size from labnotebook? + +Step size from labnotebook? + + + +DAScale is zero->Step size from labnotebook? + + +No + + + +Add labnotebook entry\ndocumenting this case + +Add labnotebook entry +documenting this case + + + +DAScale is zero->Add labnotebook entry\ndocumenting this case + + +Yes + + + +Write step size of\n+10pA to labnotebook + +Write step size of ++10pA to labnotebook + + + +Step Size from labnotebook?->Write step size of\n+10pA to labnotebook + + +-50pA + + + +Offset DAScale\nby +10pA + +Offset DAScale +by +10pA + + + +Step Size from labnotebook?->Offset DAScale\nby +10pA + + ++10pA + + + +Offset DAScale\nby +100pA + +Offset DAScale +by +100pA + + + +Step Size from labnotebook?->Offset DAScale\nby +100pA + + ++100pA + + + +n38->n39 + + +No + + + +Set "TP during ITI" to disabled + +Set "TP during ITI" to disabled + + + +Set "TP inserting" to disabled->Set "TP during ITI" to disabled + + + + + +All checks passed + +All checks passed + + + +Check if only one headstage is active->All checks passed + + + + + +Store DAScale\nin labnotebook + +Store DAScale +in labnotebook + + + +Step size from labnotebook?->Store DAScale\nin labnotebook + + ++10pA + + + +Offset DAScale\nby -50pA + +Offset DAScale +by -50pA + + + +Step size from labnotebook?->Offset DAScale\nby -50pA + + +-50pA + + + +Write step size of\n-50pA to labnotebook + +Write step size of +-50pA to labnotebook + + + +Step size from labnotebook?->Write step size of\n-50pA to labnotebook + + ++100pA + + + +Mark sweep as failure [2] + +Mark sweep as failure [2] + + + +Add labnotebook entry\ndocumenting this case->Mark sweep as failure [2] + + + + + +Write step size of\n+10pA to labnotebook->Offset DAScale\nby +10pA + + + + + +Mark sweep as failed [1] + +Mark sweep as failed [1] + + + +Offset DAScale\nby +10pA->Mark sweep as failed [1] + + + + + +Offset DAScale\nby +100pA->Mark sweep as failed [1] + + + + + +Skip to end of active set + +Skip to end of active set + + + +n39->Skip to end of active set + + + + + +Set "ITI" to 100ms + +Set "ITI" to 100ms + + + +Set "TP during ITI" to disabled->Set "ITI" to 100ms + + + + + +Set DAScale to 100pA + +Set DAScale to 100pA + + + +All checks passed->Set DAScale to 100pA + + +Yes + + + +Abort + +Abort + + + +All checks passed->Abort + + +No + + + +Mark sweep as passed + +Mark sweep as passed + + + +Store DAScale\nin labnotebook->Mark sweep as passed + + + + + +Offset DAScale\nby -50pA->Mark sweep as failed [1] + + + + + +Write step size of\n-50pA to labnotebook->Offset DAScale\nby -50pA + + + + + +Three sweeps exist with\nthis labnotebook entry? + +Three sweeps exist with +this labnotebook entry? + + + +Mark sweep as failure [2]->Three sweeps exist with\nthis labnotebook entry? + + + + + +Enable "Repeated Acquisition" + +Enable "Repeated Acquisition" + + + +Set "ITI" to 100ms->Enable "Repeated Acquisition" + + + + + +Write initial stepsize of 100pA into labnotebook + +Write initial stepsize of 100pA into labnotebook + + + +Set DAScale to 100pA->Write initial stepsize of 100pA into labnotebook + + + + + +Mark sweep as passed->Skip to end of active set + + + + + +Three sweeps exist with\nthis labnotebook entry?->Skip to end of active set + + +Yes + + + diff --git a/_images/patch-seq-true-resting1.svg b/_images/patch-seq-true-resting1.svg new file mode 100644 index 0000000000..4af4008fe1 --- /dev/null +++ b/_images/patch-seq-true-resting1.svg @@ -0,0 +1,1061 @@ + + + + + + +G + + + +n1 + +Stadrt DAQ/RA + + + +n2 + +Pre DAQ Event + + + +n1->n2 + + + + + +n3 + +Pre Set Event + + + +n1->n3 + + + + + +n4 + +Pre Sweep + Config Event + + + +n1->n4 + + + + + +n5 + +Post Set Event + + + +n1->n5 + + + + + +n6 + +Post DAQ Event + + + +n1->n6 + + + + + +n38 + +Mid Sweep Event + + + +n1->n38 + + + + + +n47 + +Post Sweep Event + + + +n1->n47 + + + + + +n7 + +Enable Indexing + + + +n2->n7 + + + + + +n15 + +Set analysis function version + + + +n3->n15 + + + + + +n91 + + +Standard AsyncQCChannels handling + + + + + +n4->n91 + + + + + +n21 + +Check that we have three + wavebuilder epochs + + + +n4->n21 + + + + + +n26 + +Do we have PSQ_VM_NUM_SWEEPS_PASS passing sweeps? + + + +n5->n26 + + + + + +n29 + +Publish ZeroMQ message + + + +n5->n29 + + + + + +n31 + +Enable Get/Set ITI + + + +n5->n31 + + + + + +n32 + +Update dashboard + + + +n5->n32 + + + + + +n6->n32 + + + + + +n34 + +Read Set QC + from labnotebook + + + +n6->n34 + + + + + +n39 + +Has BL QC passed? + + + +n38->n39 + + + + + +n92 + + +Standard AsyncQCChannels handling + + + + + +n47->n92 + + + + + +n48 + +Read baseline QC + from labnotebook + + + +n47->n48 + + + + + +n50 + +Check sampling frequency + and store in labnotebook + + + +n47->n50 + + + + + +n53 + +Search for spikes in the stimset + using the "FailedLevel" analysis parameter + + + +n47->n53 + + + + + +n8 + +Disable oodDAQ/dDAQ + + + +n7->n8 + + + + + +n16 + +Set sampling multiplier from analysis parameter + + + +n15->n16 + + + + + +n14 + +Abort + + + +n21->n14 + + +Failed + + + +n23 + +Check that epoch 0 and 2 + are at least "BaselineChunkLength" long? + + + +n21->n23 + + + + + +n27 + +Add Set QC failed to labnotebook + + + +n26->n27 + + +No + + + +n28 + +Add Set QC passed to labnotebook + + + +n26->n28 + + +Yes + + + +n35 + +Read optional "NextStimsetName" analysis parameter + and set that as next stimulus set + + + +n34->n35 + + +Passed? + + + +n40 + +Do we have acquired the first + baseline chunk selection epoch? + + + +n39->n40 + + +No + + + +n49 + +All five QC values are passing? + + + +n92->n49 + + + + + +n48->n49 + + +All + + + +n69 + +Enable SweepFormula + + + +n48->n69 + + +Passed + + + +n74 + +Store NaN as average voltages + in labnotebook + + + +n48->n74 + + +Failed + + + +n50->n49 + + + + + +n57 + +Store spike positions + in labnotebook + + + +n53->n57 + + + + + +n9 + +Enable repeated acquisition + + + +n8->n9 + + + + + +n17 + +Disable Autobias + + + +n16->n17 + + + + + +n23->n14 + + +Failed + + + +n25 + +Add baseline selection epochs + for epoch 0 and 2 + + + +n23->n25 + + + + + +n33 + +Set autobias target V + to full average voltage from labnotebook + + + +n28->n33 + + + + + +n36 + +Read "NextIndexingEndStimsetName" analysis parameter + and set that as indexing end stimulus set. + Enable Indexing if present. + + + +n35->n36 + + + + + +n41 + +Check RMS short + + + +n40->n41 + + +Yes + + + +n65 + +Add sweep QC passed +to labnotebook + + + +n49->n65 + + +Yes + + + +n66 + +Add sweep QC failed +to labnotebook + + + +n49->n66 + + +No + + + +n70 + +Execute formula for calculating + the average voltage + of epoch 0 and 2 + + + +n69->n70 + + + + + +n75 + +Calculate the average and relative difference + of both  average voltages + + + +n74->n75 + + + + + +n54 + +Do we have any spikes? + + + +n57->n54 + + + + + +n10 + +Enable "Inserted TP" + + + +n9->n10 + + + + + +n18 + +Disable Holding potential + + + +n17->n18 + + + + + +n37 + +Turn Autobias on + + + +n33->n37 + + + + + +n11 + +Check that we have only one active headstage + + + +n10->n11 + + + + + +n11->n14 + + +Failed + + + +n12 + +Check that we don't have TTL channels + + + +n11->n12 + + + + + +n12->n14 + + +Failed + + + +n13 + +Check that the active headstage is in IC + + + +n12->n13 + + + + + +n13->n14 + + +Failed + + + +n19 + +Enable capacitance compensation + + + +n18->n19 + + + + + +n20 + +Enable bridge balance + + + +n19->n20 + + + + + +n30 + +Enable Get/Set ITI + + + +n20->n30 + + + + + +n79 + +Store average QC result + and'ing both intermediate QC results + + + +n79->n49 + + + + + +n68 + +Jump to the end + of the stimulus set + + + +n65->n68 + + + + + +n67 + +Perform common checks + if an early abort is required. + + + +n66->n67 + + + + + +n42 + +Check RMS long + + + +n41->n42 + + +Passed + + + +n43 + +Add baseline chunk QC + failed to labnotebook + + + +n41->n43 + + +Failed + + + +n42->n43 + + +Failed + + + +n44 + +Add baseline chunk QC + passed to labnotebook + + + +n42->n44 + + +Passed + + + +n45 + +Add baseline QC + failed to labnotebook + + + +n43->n45 + + + + + +n46 + +Add baseline QC + passed to labnotebook + + + +n44->n46 + + + + + +n71 + +Store average voltages + in labnotebook + + + +n70->n71 + + + + + +n76 + +Store in labnotebook + + + +n75->n76 + + + + + +n55 + +Add spike QC passed + to labnotebook + + + +n54->n55 + + +No + + + +n56 + +Add spike QC failed + to labnotebook + + + +n54->n56 + + +Yes + + + +n71->n75 + + + + + +n77 + +Is the absolute voltage difference + smaller than "AbsoluteVoltageDiff". + Store QC result in labnotebook. + + + +n76->n77 + + + + + +n78 + +Is the relative voltage difference + smaller than "RelativeVoltageDiff". + Store QC result in labnotebook. + + + +n76->n78 + + + + + +n58 + +Enable Get/Set ITI + + + +n55->n58 + + + + + +n80 + +Read spike QC + from labnotebook + + + +n55->n80 + + + + + +n56->n80 + + + + + +n59 + +Average the acquired AD data + of the stimset ignoring + "SpikeFailureIgnoredTime" around each found spike + + + +n56->n59 + + + + + +n80->n49 + + + + + +n60 + +Add "UserOffsetTargetVAutobias" onto the average + + + +n59->n60 + + + + + +n61 + +Set that value as autobias target V + + + +n60->n61 + + + + + +n62 + +Turn Autobias on + + + +n61->n62 + + + + + +n63 + +Set ITI to 10s + + + +n62->n63 + + + + + +n64 + +Disable Get/Set ITI + + + +n63->n64 + + + + + +n77->n79 + + + + + +n78->n79 + + + + + diff --git a/_images/sweepFormulaPlot.svg b/_images/sweepFormulaPlot.svg new file mode 100644 index 0000000000..090e2c0ba5 --- /dev/null +++ b/_images/sweepFormulaPlot.svg @@ -0,0 +1,314 @@ + + +Qt SVG Document +Generated with Qt + + + + + + + + + + + + + + + + + + + + + + +8 + + + + + + + + + + + + + +6 + + + + + + + + + + + + + +4 + + + + + + + + + + + + + +2 + + + + + + + + + + + + + +0 + + + + + + + + + + + + + + + + + + + + +80 + + + + + + + + + + + + + +60 + + + + + + + + + + + + + +40 + + + + + + + + + + + + + +20 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/_images/sweepFormulaPlot4.png b/_images/sweepFormulaPlot4.png new file mode 100644 index 0000000000..61e23dc2b6 Binary files /dev/null and b/_images/sweepFormulaPlot4.png differ diff --git a/_images/sweep_table1.png b/_images/sweep_table1.png new file mode 100644 index 0000000000..127ab135fc Binary files /dev/null and b/_images/sweep_table1.png differ diff --git a/_images/testPulse-averaging.svg b/_images/testPulse-averaging.svg new file mode 100644 index 0000000000..2157cdd497 --- /dev/null +++ b/_images/testPulse-averaging.svg @@ -0,0 +1,686 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Qt SVG Document + + Generated with Qt + + + + + + 100 + + 80 + + 60 + + 40 + + 20 + pA + + + 20 + + + 18 + + + 16 + + + 14 + + + 12 + + + 10 + + + 8 + + + 6 + + + 4 + + + 2 + + + 0 + ms + + + + + + + + + + + Duration: 10ms + Baseline fraction: 25% + + The + blue + range is evaluated for steady state + resistance calculation and is defined as + min(5, 20% * min(duration, baseline)) + . + + The + green + range is evaluated for + instantaneous/peak resistance calculation + and is defined as 0.25ms at the very onset. + + + + + + Baseline fraction + 25% of 20ms = 5ms + + + + + + Duration + + + + + + + + + + + + + + + + + Testpulse properties:duration: 10 msbaseline fraction: 0.25 (25 %) + + + + + + + + + + + + + + + + + + + + BaselineSS:average over points + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + TPSS:average over points + + + + + + Instantaneous + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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0000000000..58ee387fe3 --- /dev/null +++ b/_images/testPulse-visualization_new.svg @@ -0,0 +1,807 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Qt SVG Document + + Generated with Qt + + + + + + 100 + + 80 + + 60 + + 40 + + 20 + pA + + + 20 + + + 18 + + + 16 + + + 14 + + + 12 + + + 10 + + + 8 + + + 6 + + + 4 + + + 2 + + + 0 + ms + + + + + + + + + + + Duration: 10ms + Baseline fraction: 25% + + The + blue + range is evaluated for steady state + resistance calculation and is defined as + min(5, 20% * min(duration, baseline)) + . + + The + green + range is evaluated for + instantaneous/peak resistance calculation + and is defined as 0.25ms at the very onset. + + + + + + Baseline fraction + 25% of 20ms = 5ms + + + + + + Duration + + + + + + + + + + + + + + + + + Testpulse properties:duration: 10 msbaseline fraction: 0.25 (25 %) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + base line fraction(time) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + evaluation rangeminimum of- 5 ms- 20 % of duration- 20 % of base line fraction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + duration(time) + + + + + + + + + + + + + + + + + + + + reference pointend of base line fraction – TP_EVAL_POINT_OFFSETdefault: TP_EVAL_POINT_OFFSET = 5 points + + + + + + + + + + + + + + + + + + + + reference pointend of base line fraction + TP_EVAL_POINT_OFFSETdefault: TP_EVAL_POINT_OFFSET = 5 points + + + + + + + + + + + + + reference pointbegin of base line fraction trail - TP_EVAL_POINT_OFFSETdefault: TP_EVAL_POINT_OFFSET = 5 points + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + base line fraction ‘trail’(time)Same length as base line fraction + + + + + + evaluation range0.25 ms in integer points + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/_static/O2WxPzBsEfc.jpg b/_static/O2WxPzBsEfc.jpg new file mode 100644 index 0000000000..9c161fe50b Binary files /dev/null and b/_static/O2WxPzBsEfc.jpg differ diff --git a/_static/Y3I-LDX-R2Q.jpg b/_static/Y3I-LDX-R2Q.jpg new file mode 100644 index 0000000000..09715b5486 Binary files /dev/null and b/_static/Y3I-LDX-R2Q.jpg differ diff --git a/_static/basic.css b/_static/basic.css new file mode 100644 index 0000000000..f316efcb47 --- /dev/null +++ b/_static/basic.css @@ -0,0 +1,925 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/_static/classic.css b/_static/classic.css new file mode 100644 index 0000000000..75e0d691e0 --- /dev/null +++ b/_static/classic.css @@ -0,0 +1,269 @@ +/* + * classic.css_t + * ~~~~~~~~~~~~~ + * + * Sphinx stylesheet -- classic theme. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +@import url("basic.css"); + +/* -- page layout ----------------------------------------------------------- */ + +html { + /* CSS hack for macOS's scrollbar (see #1125) */ + background-color: #FFFFFF; +} + +body { + font-family: Helvetica, Arial, sans-serif; + font-size: 100%; + background-color: #11303d; + color: #000; + margin: 0; + padding: 0; +} + +div.document { + display: flex; + background-color: #1c4e63; +} + +div.documentwrapper { + float: left; + width: 100%; +} + +div.bodywrapper { + margin: 0 0 0 230px; +} + +div.body { + background-color: #ffffff; + color: #000000; + padding: 0 20px 30px 20px; +} + +div.footer { + color: #ffffff; + width: 100%; + padding: 9px 0 9px 0; + text-align: center; + font-size: 75%; +} + +div.footer a { + color: #ffffff; + text-decoration: underline; +} + +div.related { + background-color: #133f52; + line-height: 30px; + color: #ffffff; +} + +div.related a { + color: #ffffff; +} + +div.sphinxsidebar { +} + +div.sphinxsidebar h3 { + font-family: Helvetica, Arial, sans-serif; + color: #ffffff; + font-size: 1.4em; + font-weight: normal; + margin: 0; + padding: 0; +} + +div.sphinxsidebar h3 a { + color: #ffffff; +} + +div.sphinxsidebar h4 { + font-family: Helvetica, Arial, sans-serif; + color: #ffffff; + font-size: 1.3em; + font-weight: normal; + margin: 5px 0 0 0; + padding: 0; +} + +div.sphinxsidebar p { + color: #ffffff; +} + +div.sphinxsidebar p.topless { + margin: 5px 10px 10px 10px; +} + +div.sphinxsidebar ul { + margin: 10px; + padding: 0; + color: #ffffff; +} + +div.sphinxsidebar a { + color: #98dbcc; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + + + +/* -- hyperlink styles ------------------------------------------------------ */ + +a { + color: #355f7c; + text-decoration: none; +} + +a:visited { + color: #551a8b; + text-decoration: none; +} + +a:hover { + text-decoration: underline; +} + + + +/* -- body styles ----------------------------------------------------------- */ + +div.body h1, +div.body h2, +div.body h3, +div.body h4, +div.body h5, +div.body h6 { + font-family: Helvetica, Arial, sans-serif; + background-color: #f2f2f2; + font-weight: normal; + color: #20435c; + border-bottom: 1px solid #ccc; + margin: 20px -20px 10px -20px; + padding: 3px 0 3px 10px; +} + +div.body h1 { margin-top: 0; font-size: 200%; } +div.body h2 { font-size: 160%; } +div.body h3 { font-size: 140%; } +div.body h4 { font-size: 120%; } +div.body h5 { font-size: 110%; } +div.body h6 { font-size: 100%; } + +a.headerlink { + color: #c60f0f; + font-size: 0.8em; + padding: 0 4px 0 4px; + text-decoration: none; +} + +a.headerlink:hover { + background-color: #c60f0f; + color: white; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + text-align: justify; + line-height: 130%; +} + +div.admonition p.admonition-title + p { + display: inline; +} + +div.admonition p { + margin-bottom: 5px; +} + +div.admonition pre { + margin-bottom: 5px; +} + +div.admonition ul, div.admonition ol { + margin-bottom: 5px; +} + +div.note { + background-color: #eee; + border: 1px solid #ccc; +} + +div.seealso { + background-color: #ffc; + border: 1px solid #ff6; +} + +nav.contents, +aside.topic, +div.topic { + background-color: #eee; +} + +div.warning { + background-color: #ffe4e4; + border: 1px solid #f66; +} + +p.admonition-title { + display: inline; +} + +p.admonition-title:after { + content: ":"; +} + +pre { + padding: 5px; + background-color: unset; + color: unset; + line-height: 120%; + border: 1px solid #ac9; + border-left: none; + border-right: none; +} + +code { + background-color: #ecf0f3; + padding: 0 1px 0 1px; + font-size: 0.95em; +} + +th, dl.field-list > dt { + background-color: #ede; +} + +.warning code { + background: #efc2c2; +} + +.note code { + background: #d6d6d6; +} + +.viewcode-back { + font-family: Helvetica, Arial, sans-serif; +} + +div.viewcode-block:target { + background-color: #f4debf; + border-top: 1px solid #ac9; + border-bottom: 1px solid #ac9; +} + +div.code-block-caption { + color: #efefef; + background-color: #1c4e63; +} \ No newline at end of file diff --git a/_static/custom.css b/_static/custom.css new file mode 100644 index 0000000000..8728f415e6 --- /dev/null +++ b/_static/custom.css @@ -0,0 +1,12 @@ +dl.function { +margin-bottom: 50px; +} + +div.body { + max-width: 100%; +} + +.sphinxsidebarwrapper { overflow-y: scroll; } + +/* change the cursor for zoomable images */ +a[data-lightbox] {cursor: zoom-in;} diff --git a/_static/doctools.js b/_static/doctools.js new file mode 100644 index 0000000000..4d67807d17 --- /dev/null +++ b/_static/doctools.js @@ -0,0 +1,156 @@ +/* + * doctools.js + * ~~~~~~~~~~~ + * + * Base JavaScript utilities for all Sphinx HTML documentation. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([ + "TEXTAREA", + "INPUT", + "SELECT", + "BUTTON", +]); + +const _ready = (callback) => { + if (document.readyState !== "loading") { + callback(); + } else { + document.addEventListener("DOMContentLoaded", callback); + } +}; + +/** + * Small JavaScript module for the documentation. + */ +const Documentation = { + init: () => { + Documentation.initDomainIndexTable(); + Documentation.initOnKeyListeners(); + }, + + /** + * i18n support + */ + TRANSLATIONS: {}, + PLURAL_EXPR: (n) => (n === 1 ? 0 : 1), + LOCALE: "unknown", + + // gettext and ngettext don't access this so that the functions + // can safely bound to a different name (_ = Documentation.gettext) + gettext: (string) => { + const translated = Documentation.TRANSLATIONS[string]; + switch (typeof translated) { + case "undefined": + return string; // no translation + case "string": + return translated; // translation exists + default: + return translated[0]; // (singular, plural) translation tuple exists + } + }, + + ngettext: (singular, plural, n) => { + const translated = Documentation.TRANSLATIONS[singular]; + if (typeof translated !== "undefined") + return translated[Documentation.PLURAL_EXPR(n)]; + return n === 1 ? singular : plural; + }, + + addTranslations: (catalog) => { + Object.assign(Documentation.TRANSLATIONS, catalog.messages); + Documentation.PLURAL_EXPR = new Function( + "n", + `return (${catalog.plural_expr})` + ); + Documentation.LOCALE = catalog.locale; + }, + + /** + * helper function to focus on search bar + */ + focusSearchBar: () => { + document.querySelectorAll("input[name=q]")[0]?.focus(); + }, + + /** + * Initialise the domain index toggle buttons + */ + initDomainIndexTable: () => { + const toggler = (el) => { + const idNumber = el.id.substr(7); + const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`); + if (el.src.substr(-9) === "minus.png") { + el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`; + toggledRows.forEach((el) => (el.style.display = "none")); + } else { + el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`; + toggledRows.forEach((el) => (el.style.display = "")); + } + }; + + const togglerElements = document.querySelectorAll("img.toggler"); + togglerElements.forEach((el) => + el.addEventListener("click", (event) => toggler(event.currentTarget)) + ); + togglerElements.forEach((el) => (el.style.display = "")); + if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler); + }, + + initOnKeyListeners: () => { + // only install a listener if it is really needed + if ( + !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS && + !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS + ) + return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.altKey || event.ctrlKey || event.metaKey) return; + + if (!event.shiftKey) { + switch (event.key) { + case "ArrowLeft": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const prevLink = document.querySelector('link[rel="prev"]'); + if (prevLink && prevLink.href) { + window.location.href = prevLink.href; + event.preventDefault(); + } + break; + case "ArrowRight": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const nextLink = document.querySelector('link[rel="next"]'); + if (nextLink && nextLink.href) { + window.location.href = nextLink.href; + event.preventDefault(); + } + break; + } + } + + // some keyboard layouts may need Shift to get / + switch (event.key) { + case "/": + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break; + Documentation.focusSearchBar(); + event.preventDefault(); + } + }); + }, +}; + +// quick alias for translations +const _ = Documentation.gettext; + +_ready(Documentation.init); diff --git a/_static/documentation_options.js b/_static/documentation_options.js new file mode 100644 index 0000000000..95a2e5f2ea --- /dev/null +++ b/_static/documentation_options.js @@ -0,0 +1,13 @@ +const DOCUMENTATION_OPTIONS = { + VERSION: '(main) Release_2.8_20240925-4-g349947f6c', + LANGUAGE: 'en', + COLLAPSE_INDEX: false, + BUILDER: 'html', + FILE_SUFFIX: '.html', + LINK_SUFFIX: '.html', + HAS_SOURCE: false, + SOURCELINK_SUFFIX: '.txt', + NAVIGATION_WITH_KEYS: false, + SHOW_SEARCH_SUMMARY: true, + ENABLE_SEARCH_SHORTCUTS: true, +}; \ No newline at end of file diff --git a/_static/file.png b/_static/file.png new file mode 100644 index 0000000000..a858a410e4 Binary files /dev/null and b/_static/file.png differ diff --git a/_static/images/async-qc-channels.svg b/_static/images/async-qc-channels.svg new file mode 100644 index 0000000000..7d93134885 --- /dev/null +++ b/_static/images/async-qc-channels.svg @@ -0,0 +1,127 @@ + + + + + + +G + + + +Start DAQ/RA + +Start DAQ/RA + + + +Post Sweep Event + +Post Sweep Event + + + +Start DAQ/RA->Post Sweep Event + + + + + +Pre Sweep Config Event + +Pre Sweep Config Event + + + +Start DAQ/RA->Pre Sweep Config Event + + + + + +n9 + +Iterate over all asynchronous channels + given in "AsyncQCChannels" + + + +Post Sweep Event->n9 + + + + + +n5 + +Iterate over all asynchronous channels + given in "AsyncQCChannels" + + + +Pre Sweep Config Event->n5 + + + + + +n10 + +Collect alarm state of all + asynchronous channels and store + the and'ed result in the labnotebook + + + +n9->n10 + + + + + +n6 + +Is it enabled? + + + +n5->n6 + + + + + +n7 + +Is the alarm enabled? + + + +n5->n7 + + + + + +n4 + +Abort + + + +n6->n4 + + +No + + + +n7->n4 + + +No + + + diff --git a/_static/language_data.js b/_static/language_data.js new file mode 100644 index 0000000000..367b8ed81b --- /dev/null +++ b/_static/language_data.js @@ -0,0 +1,199 @@ +/* + * language_data.js + * ~~~~~~~~~~~~~~~~ + * + * This script contains the language-specific data used by searchtools.js, + * namely the list of stopwords, stemmer, scorer and splitter. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; + + +/* Non-minified version is copied as a separate JS file, if available */ + +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; + + var step3list = { + icate: 'ic', + ative: '', + alize: 'al', + iciti: 'ic', + ical: 'ic', + ful: '', + ness: '' + }; + + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + diff --git a/_static/minus.png b/_static/minus.png new file mode 100644 index 0000000000..d96755fdaf Binary files /dev/null and b/_static/minus.png differ diff --git a/_static/plus.png b/_static/plus.png new file mode 100644 index 0000000000..7107cec93a Binary files /dev/null and b/_static/plus.png differ diff --git a/_static/pygments.css b/_static/pygments.css new file mode 100644 index 0000000000..5c913eed41 --- /dev/null +++ b/_static/pygments.css @@ -0,0 +1,39 @@ +pre { line-height: 125%; } +td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +.highlight .hll { background-color: #ffffcc } +.highlight { background: #ffffff; } +.highlight .c { color: #FF0000; font-style: italic } /* Comment */ +.highlight .k { color: #0000FF } /* Keyword */ +.highlight .ch { color: #FF0000; font-style: italic } /* Comment.Hashbang */ +.highlight .cm { color: #FF0000; font-style: italic } /* Comment.Multiline */ +.highlight .cp { color: #FF0000; font-style: italic } /* Comment.Preproc */ +.highlight .cpf { color: #FF0000; font-style: italic } /* Comment.PreprocFile */ +.highlight .c1 { color: #FF0000; font-style: italic } /* Comment.Single */ +.highlight .cs { color: #FF0000; font-style: italic } /* Comment.Special */ +.highlight .kc { color: #0000FF } /* Keyword.Constant */ +.highlight .kd { color: #0000FF } /* Keyword.Declaration */ +.highlight .kn { color: #0000FF } /* Keyword.Namespace */ +.highlight .kp { color: #0000FF } /* Keyword.Pseudo */ +.highlight .kr { color: #0000FF } /* Keyword.Reserved */ +.highlight .kt { color: #0000FF } /* Keyword.Type */ +.highlight .s { color: #009C00 } /* Literal.String */ +.highlight .nc { color: #007575 } /* Name.Class */ +.highlight .nd { color: #CC00A3 } /* Name.Decorator */ +.highlight .nf { color: #C34E00 } /* Name.Function */ +.highlight .sa { color: #009C00 } /* Literal.String.Affix */ +.highlight .sb { color: #009C00 } /* Literal.String.Backtick */ +.highlight .sc { color: #009C00 } /* Literal.String.Char */ +.highlight .dl { color: #009C00 } /* Literal.String.Delimiter */ +.highlight .sd { color: #009C00 } /* Literal.String.Doc */ +.highlight .s2 { color: #009C00 } /* Literal.String.Double */ +.highlight .se { color: #009C00 } /* Literal.String.Escape */ +.highlight .sh { color: #009C00 } /* Literal.String.Heredoc */ +.highlight .si { color: #009C00 } /* Literal.String.Interpol */ +.highlight .sx { color: #009C00 } /* Literal.String.Other */ +.highlight .sr { color: #009C00 } /* Literal.String.Regex */ +.highlight .s1 { color: #009C00 } /* Literal.String.Single */ +.highlight .ss { color: #009C00 } /* Literal.String.Symbol */ +.highlight .fm { color: #C34E00 } /* Name.Function.Magic */ \ No newline at end of file diff --git a/_static/searchtools.js b/_static/searchtools.js new file mode 100644 index 0000000000..92da3f8b22 --- /dev/null +++ b/_static/searchtools.js @@ -0,0 +1,619 @@ +/* + * searchtools.js + * ~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlinks", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/_static/sidebar.js b/_static/sidebar.js new file mode 100644 index 0000000000..f28c206896 --- /dev/null +++ b/_static/sidebar.js @@ -0,0 +1,70 @@ +/* + * sidebar.js + * ~~~~~~~~~~ + * + * This script makes the Sphinx sidebar collapsible. + * + * .sphinxsidebar contains .sphinxsidebarwrapper. This script adds + * in .sphixsidebar, after .sphinxsidebarwrapper, the #sidebarbutton + * used to collapse and expand the sidebar. + * + * When the sidebar is collapsed the .sphinxsidebarwrapper is hidden + * and the width of the sidebar and the margin-left of the document + * are decreased. When the sidebar is expanded the opposite happens. + * This script saves a per-browser/per-session cookie used to + * remember the position of the sidebar among the pages. + * Once the browser is closed the cookie is deleted and the position + * reset to the default (expanded). + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +const initialiseSidebar = () => { + + + + + // global elements used by the functions. + const bodyWrapper = document.getElementsByClassName("bodywrapper")[0] + const sidebar = document.getElementsByClassName("sphinxsidebar")[0] + const sidebarWrapper = document.getElementsByClassName('sphinxsidebarwrapper')[0] + const sidebarButton = document.getElementById("sidebarbutton") + const sidebarArrow = sidebarButton.querySelector('span') + + // for some reason, the document has no sidebar; do not run into errors + if (typeof sidebar === "undefined") return; + + const flipArrow = element => element.innerText = (element.innerText === "»") ? "«" : "»" + + const collapse_sidebar = () => { + bodyWrapper.style.marginLeft = ".8em"; + sidebar.style.width = ".8em" + sidebarWrapper.style.display = "none" + flipArrow(sidebarArrow) + sidebarButton.title = _('Expand sidebar') + window.localStorage.setItem("sidebar", "collapsed") + } + + const expand_sidebar = () => { + bodyWrapper.style.marginLeft = "" + sidebar.style.removeProperty("width") + sidebarWrapper.style.display = "" + flipArrow(sidebarArrow) + sidebarButton.title = _('Collapse sidebar') + window.localStorage.setItem("sidebar", "expanded") + } + + sidebarButton.addEventListener("click", () => { + (sidebarWrapper.style.display === "none") ? expand_sidebar() : collapse_sidebar() + }) + + if (!window.localStorage.getItem("sidebar")) return + const value = window.localStorage.getItem("sidebar") + if (value === "collapsed") collapse_sidebar(); + else if (value === "expanded") expand_sidebar(); +} + +if (document.readyState !== "loading") initialiseSidebar() +else document.addEventListener("DOMContentLoaded", initialiseSidebar) \ No newline at end of file diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js new file mode 100644 index 0000000000..8a96c69a19 --- /dev/null +++ b/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js b/_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js new file mode 100644 index 0000000000..a07e4e1d3b --- /dev/null +++ b/_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js @@ -0,0 +1 @@ + jQuery.noConflict(true); diff --git a/_static/sphinxcontrib-images/LightBox2/lightbox2/dist/css/lightbox.css b/_static/sphinxcontrib-images/LightBox2/lightbox2/dist/css/lightbox.css new file mode 100644 index 0000000000..b3b0beb371 --- /dev/null +++ b/_static/sphinxcontrib-images/LightBox2/lightbox2/dist/css/lightbox.css @@ -0,0 +1,204 @@ +body.lb-disable-scrolling { + overflow: hidden; +} + +.lightboxOverlay { 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+ line-height: 0; +} + +.lb-cancel { + display: block; + width: 32px; + height: 32px; + margin: 0 auto; + background: url(../images/loading.gif) no-repeat; +} + +.lb-nav { + position: absolute; + top: 0; + left: 0; + height: 100%; + width: 100%; + z-index: 10; +} + +.lb-container > .nav { + left: 0; +} + +.lb-nav a { + outline: none; + background-image: url('data:image/gif;base64,R0lGODlhAQABAPAAAP///wAAACH5BAEAAAAALAAAAAABAAEAAAICRAEAOw=='); +} + +.lb-prev, .lb-next { + height: 100%; + cursor: pointer; + display: block; +} + +.lb-nav a.lb-prev { + width: 34%; + left: 0; + float: left; + background: url(../images/prev.png) left 48% no-repeat; + filter: progid:DXImageTransform.Microsoft.Alpha(Opacity=0); + opacity: 0; + -webkit-transition: opacity 0.6s; + -moz-transition: opacity 0.6s; + -o-transition: opacity 0.6s; + transition: opacity 0.6s; +} + +.lb-nav a.lb-prev:hover { + filter: progid:DXImageTransform.Microsoft.Alpha(Opacity=100); + opacity: 1; +} + +.lb-nav a.lb-next { + width: 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+
+
+
+ +
+

Analysis function parameters

+ + +++++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
All parameters of the stock analysis functions

Name

Type

Optionality

Used by

Help

AbsFrequencyMinDistance

variable

optional

DA

Minimum absolute frequency distance for DAScale estimation. Only for “AdaptiveSupra”.

AbsoluteVoltageDiff

variable

required

VM

+
Maximum absolute allowed difference of the baseline membrane potentials [mV].

Set to inf to disable this check.

+
+
+

AmpBesselFilter

variable

optional

CR

+
Applies a bessel filter to the primary output.

Defaults to 10e3 [Hz],pass “100000” to select “Bypass”.

+
+
+

AmpBesselFilterRestore

variable

optional

CR

Restores the previously active bessel filter in POST_SET_EVENT. Defaults to ON.

AsyncQCChannels

wave

required

AR, CR, DA, PB, RA, RB, SE, SP, VM

List of asynchronous channels with alarm enabled, which must not be in alarm state.

AutoBiasBaselineModifier

variable

required

SC

Auto bias modifier value in mV on failing baseline QC.

AutobiasTargetV

variable

optional

CR

Autobias targetV [mV] value set in PRE_SET_EVENT

AutobiasTargetVAtSetEnd

variable

optional

CR

Autobias targetV [mV] value set in POST_SET_EVENT (only set if set QC passes).

BaselineChunkLength

variable

optional

AR, SE, VM

Length of a baseline QC chunk to evaluate (defaults to 500)

BaselineRMSLongThreshold

variable

optional

AR, CR, DA, PB, RA, RB, SE, VM

Threshold value in mV for the long RMS baseline QC check (defaults to 0.5)

BaselineRMSShortThreshold

variable

optional

AR, CR, DA, PB, RA, RB, SE, VM

Threshold value in mV for the short RMS baseline QC check (defaults to 0.07)

BaselineTargetVThreshold

variable

optional

CR, DA, RA, RB

Threshold value in mV for the target V baseline QC check (defaults to 1)

BoundsEvaluationMode

string

required

CR

Select the bounds evaluation mode: Symmetric (Lower and Upper), Depolarized (Upper) or Hyperpolarized (Lower)

DAScaleModifier

variable

mixed

CR, DA, SC

Modifier value to the DA Scale of headstages with spikes during chirp +Percentage how the DAScale value is adapted if it is outside of the MinimumSpikeCount”/”MaximumSpikeCount” band. Only for “Supra”. +Modifier value to the DA Scale of headstages for too few spikes

DAScaleOperator

string

mixed

CR, SC

Set the math operator to use for combining the DAScale and the modifier. Valid strings are “+” (addition) and “*” (multiplication). +Set the math operator to use for combining the DAScale and the too few spikes modifier. Valid strings are “+” (addition) and “*” (multiplication).

DAScaleRangeFactor

variable

optional

DA

Fallback factor to apply to the input DAScale range for calculating the DAScale minimum step width when all previous f-I data from Rheobase/Supra/Adaptive is constant. Only for “AdaptiveSupra”.

DAScales

wave

required

DA, DS

DA Scale Factors in pA

DAScaleSpikePositionModifier

variable

required

SC

Modifier value to the DA Scale of headstages with failing spike positions.

DAScaleSpikePositionOperator

string

required

SC

Set the math operator to use for combining the DAScale and the spike position modifier. Valid strings are “+” (addition) and “*” (multiplication).

DaScaleStepWidthMinMaxRatio

variable

optional

DA

Number of times the maximum DAScale step width is larger than the calculated minimum. Only for “AdaptiveSupra”.

DaScaleTooManySpikesModifier

variable

required

SC

Modifier value to the DA Scale of headstages for too many spikes

DaScaleTooManySpikesOperator

string

required

SC

Set the math operator to use for combining the DAScale and the too many spikes modifier. Valid strings are “+” (addition) and “*” (multiplication).

FailedLevel

variable

mixed

CR, VM

Absolute level for spike search

FailedPulseLevel

variable

optional

SC

[Optional, uses the already set value] Numeric level to use for the failed pulse search in the PA plot tab.

FinalSlopePercent

variable

optional

DA

As additional passing criteria the slope of the f-I plot must be larger than this value. Note: The slope is used in percent. Only for “Supra”.

IdealNumberOfSpikesPerPulse

variable

required

SC

Ideal number of spike which should be present. Overwrites the PA plot GUI value.

InnerRelativeBound

variable

required

CR

Lower bound of a confidence band for the acquired data relative to the pre pulse baseline in mV. Must be positive.

InterTrialInterval

variable

optional

VM

Inter trial interval to set, defaults to 10 [s]

MaxAccessResistance

variable

required

AR

Maximum allowed acccess resistance [MΩ]

MaxAccessToSteadyStateResistanceRatio

variable

required

AR

Maximum allowed ratio of access to steady state resistance [%]

MaxFrequencyChangePercent

variable

optional

DA

The maximum allowed difference for the frequency for two consecutive measurements. In case this value is overshot, we redo the measurement with a fitting DAScale in-between. Only for “AdaptiveSupra”.

MaximumDAScale

variable

required

FR

Maximum allowed DAScale, set to NaN to turn the check off [pA]

MaximumSpikeCount

variable

optional

DA

The upper limit of the number of spikes. Only for “Supra”.

MaxLeakCurrent

variable

required

AR, PB

Maximum current [pA] which is allowed in the pre pulse baseline

MaxPipetteResistance

variable

required

PB

Maximum allowed pipette resistance [MΩ]

MaxTrials

variable

optional

SC

[Optional, defaults to infinity] A sweep is rerun this many times on a failed headstage.

MinimumSpikeCount

variable

optional

DA

The lower limit of the number of spikes. Only for “Supra”.

MinimumSpikePosition

variable

required

SC

Minimum allowed spike positions in pulse active coordinate system (0 - 100).

MinPipetteResistance

variable

required

PB

Minimum allowed pipette resistance [MΩ]

NextIndexingEndStimSetName

string

optional

AR, PB, SE, VM

+
Next indexing end stimulus set which should be set in case of success.

Also enables indexing.

+
+
+

NextStimSetName

string

optional

AR, PB, SE, VM

Next stimulus set which should be set in case of success

NumberOfChirpCycles

variable

optional

CR

Number of acquired chirp cycles before the bounds evaluation starts. Defaults to 1.

NumberOfFailedSweeps

variable

required

AR, CR, PB, SE, VM

Number of failed sweeps which marks the set as failed.

NumberOfSpikes

variable

required

RA

Number of spikes required to be found after the pulse onset in order to label the cell as having “spiked”.

NumberOfTestpulses

variable

required

AR, PB

Expected number of testpulses in the stimset

NumInvalidSlopeSweepsAllowed

variable

optional

DA

Number of allowed sweeps with invalid f-I fit slope. Only for “AdaptiveSupra”.

NumSweepsWithSaturation

variable

optional

DA

Number of required consecutive passing sweeps to have passing sweep QC and f-I slope QC, defaults to 2. Only for “AdaptiveSupra”.

OffsetOperator

string

optional

DA

Set the math operator to use for combining the rheobase DAScale value from the previous run and the DAScales values. Valid strings are “+” (addition) and “*” (multiplication). Only for “Supra” and defaults to “+”.

OperationMode

string

required

DA

Operation mode of the analysis function. Can be either “Sub”/”Supra”/”AdaptiveSupra”.

OuterRelativeBound

variable

required

CR

Upper bound of a confidence band for the acquired data relative to the pre pulse baseline in mV. Must be positive.

PostDAQDAScale

variable

required

FR

If true the found DAScale value will be set at the end of the set

PostDAQDAScaleFactor

variable

required

FR

Scaling factor for setting the DAScale of passed headstages at the end of the set

PostDAQDAScaleForFailedHS

variable

required

FR

Failed headstages will be set to this DAScale value [pA] in the post set event

PostDAQDAScaleMinOffset

variable

required

FR

Mininum absolute offset value applied to the found DAScale [pA]

RelativeVoltageDiff

variable

required

VM

+
Maximum relative allowed difference of the baseline membrane potentials [%].

Set to inf to disable this check.

+
+
+

SamplingFrequency

variable

optional

AR, CR, DA, PB, RA, RB, SE, SP, VM

Required sampling frequency for the acquired data [kHz]. Defaults to ITC:50 NI:50 Sutter:50. +Required sampling frequency for the acquired data [kHz]. Defaults to ITC:200 NI:250 Sutter:50. +Required sampling frequency for the acquired data [kHz]. Defaults to ITC:50 NI:50 Sutter:50. +Required sampling frequency for the acquired data [kHz]. Defaults to ITC:50 NI:50 Sutter:50. +Required sampling frequency for the acquired data [kHz]. Defaults to ITC:200 NI:250 Sutter:50. +Required sampling frequency for the acquired data [kHz]. Defaults to ITC:50 NI:50 Sutter:50. +Required sampling frequency for the acquired data [kHz]. Defaults to ITC:200 NI:250 Sutter:50.

SamplingMultiplier

variable

required

AR, CR, DA, FR, PB, RA, RB, SE, SP, VM

Sampling multiplier, use 1 for no multiplier

SealThreshold

variable

required

SE

Minimum required seal threshold [GΩ]

ShowPlot

variable

optional

DA

Show the resistance (“Sub”) or the f-I (“Supra”) plot, defaults to true.

SlopePercentage

variable

optional

DA

Once the slope of the f-I fit is x percentage smaller compared with the maximum slope, the stimset cycle is stopped. Only for “AdaptiveSupra”.

SpikeCheck

variable

optional

CR

Toggle spike check during the chirp. Defaults to off.

SpikeFailureIgnoredTime

variable

required

VM

+
Time [ms] to ignore around spikes for average calculation.

Half of this value before and after each spike.

+
+
+

TestPulseGroupSelector

string

optional

SE

Group(s) which have their resistance evaluated: One of Both/First/Second, defaults to Both

UserOffsetTargetVAutobias

variable

required

VM

Offset value for the autobias target voltage in case spikes were found

UserOnsetDelay

variable

optional

CR

Will be set as user onset delay in PRE_SET_EVENT, the current value will be set back in POST_SET_EVENT.

UseTrueRestingMembranePotentialVoltage

variable

optional

CR

Use the average voltage of a passing True RMS voltage set as Autobias targetV [mV] instead of “AutobiasTargetVAtSetEnd” in POST_SET_EVENT. Defaults to on.

+ + ++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Abbreviation legend

Abbreviation

Name

AR

PSQ_AccessResistanceSmoke()

CR

PSQ_Chirp()

DA

PSQ_DAScale()

DS

MSQ_DAScale()

FR

MSQ_FastRheoEst()

PB

PSQ_PipetteInBath()

RA

PSQ_Ramp()

RB

PSQ_Rheobase()

SC

SC_SpikeControl()

SE

PSQ_SealEvaluation()

SP

PSQ_SquarePulse()

VM

PSQ_TrueRestingMembranePotential()

+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/analysis-function-writing.html b/analysis-function-writing.html new file mode 100644 index 0000000000..1f44a23b2e --- /dev/null +++ b/analysis-function-writing.html @@ -0,0 +1,214 @@ + + + + + + + + Thirty six hints for writing analysis functions — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Thirty six hints for writing analysis functions

+
    +

  1. Create an issue with the description of the new analysis function. +Also define its name and two letter abbreviation (which must not collide with existing ones).

    2. +

  2. Always track any open items in task lists in the issue or the PR itself.

    3. +

  3. Think about what should happen at each event. As a rule of thumb we want +to do only what is really needed in MID_SWEEP_EVENT (if that is used at +all). The common QC entries are determined in the following events:

    +
      +

    • Sweep QC in POST_SWEEP_EVENT

      • +

    • Set QC in POST_SET_EVENT

      • +

    • Baseline QC in MID_SWEEP_EVENT/POST_SWEEP_EVENT.

      • +
    +
    4. +

  4. Create a list of used labnotebook keys. The question which labnotebook keys +are required can be answered by thinking about how the dashboard will interpret +the analysis function run results. Only if it can decide, by looking at +labnotebook entries, for each possible outcome exactly why the run failed, all +labnotebook keys were thought of.

    5. +

  5. Create a list of used user epochs. User epochs are there to define +interesting stimset x-ranges for the analysis function. This should be used +preferrably over other similiar approaches.

    6. +

  6. Create a list of analysis function parameters including required/optional +state and for the latter also the default values.

    7. +

  7. Units for labnotebook keys should be added if possible. For physical units we +tend to prefer base units without prefix, i.e. Ω instead of GΩ.

    8. +

  8. Decide if the new labnotebook entries should be headstage dependent or not. +The existing entries don’t do a very good job in guiding you here. An +ideal choice is that the DEPEND/INDEP type of a entry would not +have to be changed if the analysis function would need to support more or +fewer headstages.

    9. +

  9. Make a list of additional features and/or changes in common PSQ_/MSQ_ functions you +need.

    10. +

  10. Draw a preliminary flowchart, on paper is fine. This serves as a way to think the behaviour through. +Have a look at existing flowcharts for inspiration.

    11. +

  11. Create a stimulus set for testing. The test stimsets can be loaded via +LoadStimsets and saved via SaveStimsets available in +HardwareTests.pxp.

    12. +

  12. At this point you should have a pretty good idea what needs to be done. +Discuss what you think you need to do with your boss.

    13. +

  13. Add a skeleton analysis function, see here, +and add all analysis parameters, their help messages and check code.

    14. +

  14. Add documentation for labnotebook keys and user epochs to the tables at the +top of MIES_AnalysisFunctions_PatchSeq.ipf/MIES_AnalysisFunctions_MultiPatchSeq.ipf

    15. +

  15. Implement the test override entries in +PSQ_CreateOverrideResults()/MSQ_CreateOverrideResults() with +documentation.

    16. +

  16. Implement the behaviour for each event. Going from easy to difficult has proven to work.

    17. +

  17. Now you should have a first version. Congratulation! Pad yourself on the +back and take a break, because now the real fun starts.

    18. +

  18. Add preliminary dashboard support. We do check for every testcase that +the dashboard works.

    19. +

  19. Create a new test suite and add it to UTF_HardwareAnalysisFunctions.ipf. Be sure to +base it on the test suite of the last added analysis function to avoid copying +deprecated approaches.

    20. +

  20. Add a first test case were all test override entries result in failed QC.

    21. +

  21. As rule of thumb what to check in each test case; be sure to have test +assertions for all added labnotebook entries (except standard baseline +entries) and position checking of user epochs.

    22. +

  22. Make that first test case pass, this takes a surprisingly long time. The +function LBV_PlotAllAnalysisFunctionLBNKeys() helps for debugging.

    23. +

  23. After this first test case passes, reassess the test assertions. Are you testing enough or too much?

    24. +

  24. Writeup a test matrix for determining what needs to be +tested, first version in paper is fine. The columns are the inputs, +usually these are test overrides and analysis parameters.

    +

    See UTF_PatchSeqSealEvaluation.ipf for an example.

    +

    We always have the following three test cases:

    +
    +
      +

    • The first has all QC (except Sampling Interval QC) failing.

      • +

    • The second has all QC passing.

      • +

    • The last one only has Sampling Interval QC failing.

      • +
    +
    +
    25. +

  25. Implement all test cases, fixing bugs in the analysis function on the way.

    26. +

  26. Run all tests for this analysis function with instrumentation.

    27. +

  27. Check the coverage output to see if you still have relevant gaps in testing.

    28. +

  28. Add new test cases for filling coverage gaps.

    29. +

  29. Repeat the last three points until the coverage is good enough.

    30. +

  30. Check if some helper code etc. can/should be fleshed out into its own pull request.

    31. +

  31. Be sure to include documentation and tests if your analysis function +publishes ZeroMQ messages. See CheckPipetteInBathPublishing and +PSQ_PB_Publish() for an example. Add it also in +CheckPublishedMessage.

    32. +

  32. Tell your boss to test the current state.

    33. +

  33. Check and fill any gaps in the documentation:

    +
      +

    • Analysis function comment with ascii art stimulus sets

      • +

    • Labnotebook entries

      • +

    • User epochs

      • +
    +
    34. +

  34. Create digital versions of the test matrix and the flowchart. For the +latter see here.

    35. +

  35. Cleanup commits

    36. +

  36. Your done!

    37. +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/analysisbrowser.html b/analysisbrowser.html new file mode 100644 index 0000000000..dd32ea57f7 --- /dev/null +++ b/analysisbrowser.html @@ -0,0 +1,165 @@ + + + + + + + + AnalysisBrowser — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

AnalysisBrowser

+

The AnalysisBrowser allows browsing and loading acquired data from Igor Experiment files +(pxp and uxp) and NeuroDataWithoutBorders files (NWB, v1 and v2) into one Igor +Experiment. The user can also combine sweeps from multiple experiments in one +SweepBrowser, see DataBrowser, inspect the labnotebook entries of these +sweeps and view the TPStorage data.

+
+_images/AnalysisBrowser.png +
+

AnalysisBrowser panel

+
+
+
+

Known Limitations

+

If the experiment file contains acquisitions from multiple devices, e.g. ITC18 and Dev1 then for NWBv1 and NWBv2 files +an under certain circumstances sweeps can not be loaded. The loading attempt results in an Asssertion where multiple waves with the same name are present in the experiment file. +This is related to issue 978 and +issue 1710. +This limitation does not apply when loading sweeps from Igor Pro experiment files (pxp).

+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/asyncframework.html b/asyncframework.html new file mode 100644 index 0000000000..8fc9aa56bf --- /dev/null +++ b/asyncframework.html @@ -0,0 +1,450 @@ + + + + + + + + Async Framework — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+
+
+

Async Framework

+
+

Description

+

The Async Framework enables the user to execute code in parallel in separated +threads. The API reduces the efforts to accomplish parallel execution greatly +compared to the general approach Igor Pro provides.

+

For a specific job only two functions have to be implemented by the user of the +framework.

+
    +

  • A worker function that will be executed in a separate thread. It receives +input data through a data folder. At the end it returns output data through +another data folder to the main program.

    • +

  • A ReadOut function that receives the output data and puts it back to the main programs data.

    • +
+

The frameworks API helps to setup an input data folder for workers. It also +supports running different jobs at the same time. By default the order of input +data send to a worker is tracked per job type. The associated readout function +is then called in the same order with the output data.

+

Though, if output in the same order as the input is not required there is also +an option to readout data just as worker functions output it.

+
+
+

Quick Guide

+
+

Start and Stop

+

The framework is started by ASYNC_Start() that creates a given number +of threads that run in the background and wait for work.

+
+
ASYNC_Start(numThreads, disableTask)
+
+
+
+

By default a task is started that reads out data from finished workers in the +background. If this is not desired, setting the optional parameter +disableTask=1 prevents creation of the task. The user has to call ASYNC_ThreadReadOut() +themselves to retrieve data from finished workers.

+

In the end the framework can be stopped by ASYNC_Stop() that sends +all threads the request to abort. As there might be still input and/or output +data in the queue ASYNC_Stop() waits a given timeout to finish +processing. If timeout is reached further processing is stopped and the threads +are released.

+
+
ASYNC_Stop(timeout)
+
+
+
+
+
+

Creating of a job

+

The worker function for a job that the user has to implement must have the form

+
+
threadsafe Function/DF MyWorkerFunction(dfr)
+  DFREF dfr
+
+
+
+

Input data is received in the data folder dfr. As prepared by ASYNC_AddParam() +input objects such as variables, strings or waves are named param0, param1, +param2 and so on. The input data folder contains a variable paramCount that +stores the number of available param objects.

+

The function has to return a data folder reference to the data folder containing +the output data. The readout function will receive this data.

+

If no or an invalid data folder reference is returned the readout function +receives an empty data folder. This happens as well, if the worker aborts with a +runtime error.

+

The readout function must have the form

+
+
Function MyReadOutFunction(dfr, err, errmsg)
+  DFREF dfr
+  variable err
+  string errmsg
+
+
+
+

Output data from the associated worker is received in the free data folder dfr. +The readout function should put the result data back to the main threads data.

+

By default err contains the return code of the worker and errmsg is emtpy. If +the worker aborts prematurely with a runtime error, err contains the runtime error +code and errmsg the corresponding error message.

+

By default ASYNC_Start() creates a background task that automatically +calls the users readout function when output data is received from workers.

+
+
+

Preparing and executing a job

+

Input data for the worker is given through a free data folder that is created by

+
+
DFREF threadDF = ASYNC_PrepareDF("WorkerFunction", "ReadOutFunction", "WorkLoadClass", inOrder=flag)
+
+
+
+

The ASYNC_PrepareDF() function returns a reference to a prepared data +folder. WorkerFunction and ReadOutFunction are the function names of worker and +readout this job type. The work load class is a string that registers the work +load in a named group. It allows to keep track of the work loads of this group, +e.g. if all work loads that were pushed to execution are already read out and +thus finished.

+

For a work load class the readout function gets called in the same +order as the work loads were executed by ASYNC_Execute().

+

Setting the optional parameter inOrder=0 allows to process read outs as soon +as output data arrives from the worker function.

+

Input data for the worker is added with ASYNC_AddParam() :

+
+
ASYNC_AddParam(threadDF, w=wave, var=variable, str=string, move=0)
+
+
+
+

Either a variable, string or wave can be added to the data folder per call. The +added data is put in order of addition as param0, param1, param2 and so on into +the data folder.

+

By default waves are duplicated when put into the data folder. Setting the +optional parameter move=1 moves the wave instead. It can only be used with +waves.

+

It is possible to vary the number of input parameters for the same job type. +As the worker function can read paramCount from its input data folder the +user is able to handle different input data setups in the worker.

+

If all desired input data was added the job is started by calling ASYNC_Execute()

+
+
ASYNC_Execute(threadDF)
+
+
+
+

The function takes the prepared data folder as input and puts it into the queue +for the workers. If the work load class given when the threadDF was created was not known to the Async frame work it is registered and +the execution order inOrder is set for this work load class. All following work loads of this class must have the same order set. +The registered worker will receive the input data and execute +in parallel. After the worker finishes its output data is queued to be received +by the registered readout function.

+
+
+

Work class types and execution order

+

The work class type setup on ASYNC_PrepareDF() is also used to attribute jobs +for ordered/unordered execution.

+
+
DFREF threadDF1 = ASYNC_PrepareDF("Worker1", "ReadOut1", "workload1")
+
+// This work load is read out unordered (as it is done executing).
+DFREF threadDF2 = ASYNC_PrepareDF("Worker1", "ReadOut1", "workload2", inOrder=0)
+
+
+
+

Any number of job types can be executed with ASYNC_Execute() . +Their respective worker functions will be executed by the threads in parallel. +All jobs are scheduled in the order they were queued by ASYNC_Execute() +independent of their respective type.

+

By default the Async framework tracks the order of jobs as they are queued by +ASYNC_Execute() per work load class type. The associated readout functions are +called in the same order. If a newer job finishes earlier, the jobs output data +is buffered by the framework until it is the jobs turn to be readout.

+

Execution of different work load classes and in-order or without ordered +readout can be mixed.

+
+
+

Check if jobs are finished

+

With the work load class each job gets attributed to a named group as it is queued +by ASYNC_Execute(). The Async framework keeps track if the queued and read out +jobs of each work load class. By calling ASYNC_IsWorkloadClassDone() +the user can check if for all queued work loads of this class the read out of +their respective results were already called. If the number of sent work loads +and received results match, the work load class is considered “done”. +Optionally the same function allows to remove the registration of the work load class, +if it is done, from the Async framework. It is recommended to remove it, when +it is finished.

+

For the case that the user just wants to wait until work loads are finished the function +ASYNC_WaitForWLCToFinishAndRemove() should be used. It allows to wait for a +given work load class to finish with a time out. When the work loads finish within the time +out they are removed automatically.

+
+
+

Changing execution order of a work load class

+

Generally for a new work load class ASYNC_Execute() registers the order for this class as well. +Afterwards the order is fixed for all subsequent work loads of this class.

+

The order can be changed by finishing and removing the work load class with ASYNC_WaitForWLCToFinishAndRemove(). +Afterwards the work load class is unknown to Async frame work. Thus, ASYNC_Execute() will accept a threadDF +with the same work load class name but a different inOrder setting.

+
+
+

Details on Stopping Threads

+

When calling ASYNC_Stop() all threads are requested to quit after +their current worker finished. The stop process runs through the following +stages:

+
    +

  • quit of thread(s) after worker(s) finish(es) is issued

    • +

  • within timeout time, remaining readouts are processed in main thread

    • +

  • within timeout time, ThreadGroupWait sets the Igor internal abort flag for all threads

    • +

  • previous stages finished or after timeout: ThreadGroupRelease releases all threads

    • +
+

If a worker is still running when the main thread issues ThreadGroupRelease in +Igor Pro 8 the thread is killed including all data in the queue. In Igor Pro 7 +a ‘virtual’ runtime error is injected into the thread. The threading loop for +the workers from the Async framework catches this runtime error and quits the +thread gracefully. This kind of behavior in Igor Pro 7 requires to introduce an +additional rule for worker functions that use try-catch-endtry itself. If a +runtime error is caught in a worker the worker has to check the code without +deleting the error state. If the code is zero the worker has to return to the +threading loop.

+
+
Igor Pro 7 try-catch-endtry worker example
+
try
+  subworker()
+catch
+  if(!getRTError(0))
+    return 0
+  endif
+  // further error handler
+endtry
+
+
+
+
+_images/async_framework.svg
+

Depiction of frameworks working principle.

+
+
+
+

Code example

+
+
Code example
+
Constant NUMBER_OF_JOBS = 200
+
+Function AsyncExample(variable inOrder)
+        variable i
+
+        // Start Async FrameWork
+        ASYNC_Start(ThreadProcessorCount)
+
+        // Some data
+        Make/O/N=(NUMBER_OF_JOBS) data = 31337
+
+        // We want to setup NUMBER_OF_JOBS workers to run
+        for(i = 0;i < NUMBER_OF_JOBS; i += 1)
+
+                // Prepare a thread df
+                DFREF threadDF = ASYNC_PrepareDF("Worker", "ReadOut", "myworkload", inOrder=inOrder)
+
+                // Add parameter
+                ASYNC_AddParam(threadDF, var=i, name = "jobCounter")
+                ASYNC_AddParam(threadDF, w=data, move=0, name = "data")
+                Make/O/N=(NUMBER_OF_JOBS) moreData = 31337
+                ASYNC_AddParam(threadDF, w=moreData, move=1, name = "moreData")
+
+                ASYNC_Execute(threadDF)
+        endfor
+        ASYNC_Stop()
+End
+
+// example worker function
+threadsafe Function/DF Worker(DFREF dfr)
+        variable i, j, wID
+        string s
+
+        // lets assume there happens a runtime error each 50 jobs
+        wID = ASYNC_FetchVariable(dfr, "jobCounter")
+        if(!mod(wID, 50))
+                WAVE w = $""
+                w[0] = 0
+        endif
+
+        // some processing that has a random runtime
+        variable runtime = abs(floor(gnoise(1))) * 10
+        for(i = 0; i < runtime; i += 1)
+                // waste some time
+                for(j = 0; j < 100; j += 1)
+                        s = num2str(i)
+                endfor
+        endfor
+
+        // Get input parameter wave references
+        WAVE data = ASYNC_FetchWave(dfr, "data")
+        WAVE moreData = ASYNC_FetchWave(dfr, "moredata")
+
+        // process wave
+        moreData[wID] += wID
+
+        // create a data folder for output data
+        DFREF dfrOut = NewFreeDataFolder()
+
+        // put counter in output data
+        variable/G dfrOut:counter = wID
+
+        // Move processed wave to output DF
+        MoveWave moreData, dfrOut:outWave
+
+        return dfrOut
+End
+
+// example readout function
+Function ReadOut(DFREF dfr, variable err, string errmsg)
+        variable counter
+
+        if(err)
+                // Insert error handling here
+                print "error caught code: " + num2str(err) + "\r" + errmsg
+        else
+                // do the readout here
+                WAVE outWave = ASYNC_FetchWave(dfr, "outWave")
+                counter = ASYNC_FetchVariable(dfr, "counter")
+
+                if(outWave[counter] != 31337 + counter)
+                        print "Processing by worker yielded unexpected result"
+                endif
+        endif
+End
+
+
+
+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/auto_testpulse_tuning.html b/auto_testpulse_tuning.html new file mode 100644 index 0000000000..6668fc497c --- /dev/null +++ b/auto_testpulse_tuning.html @@ -0,0 +1,178 @@ + + + + + + + + Automatic test pulse tuning — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Automatic test pulse tuning

+

Automatic test pulse (TP) tuning. TP tuning, when activated, automatically +adjusts the frequency (~ % baseline) and the amplitude of the TP. TP tuning +works in C-clamp, not V-clamp. TP tuning does not work during data acquisition, +including TP during ITI.

+

TP tuning will standardize the TP voltage response across experiments and +ensure that the cell membrane potential returns to rest before the next TP.

+

TP tuning is intended for use after switching to current-clamp and before +activating auto-bias (the latter is not critical). It can be applied before +and/or after bridge balance and capacitance compensation.

+

By tuning the TP, errors in auto-bias observed in neurons with long membrane +time constants should now be mitigated.

+

The TP tuning parameters are settable from the TP control on the main tab and +the settings tab of the DA_ephys panel.

+

The TP tuning parameters are:

+
    +

  • Vm = the target TP voltage (main tab)

    • +

  • Vm +/- = the allowable error in TP voltage (main tab)

    • +

  • max i inj = the max current that may be used to achieve the target Vm (main tab)

    • +

  • TP amp % = how big a step in current amplitude is taken relative to the +calculated amplitude (settings tab)

    • +

  • Auto TP interval = how often the auto TP attempts to adjust the TP (settings tab)

    • +
+

Set the starting values of the controls via the experiment configuration (JSON).

+

To activate TP tuning, check the TP tuning checkbox. When TP tuning is active, +the checkbox background turns green. When TP tuning is complete, the checkbox +automatically unchecks, and the background of the checkbox returns to the +default coloring. The background color change is intended to inform users when +TP tuning is running headstages other than the (slider) selected headstage. +When only 1 headstage is in use, the background color and unchecking change +will always coincide.

+

TP tuning can fail if the signal-to-noise ratio (SNR) is poor. SNR depends on +the rig noise and cell noise as well as the target TP voltage. 60Hz noise, for +example, can slow or make TP tuning fail. So might a target TP amplitude of 1 +mV. If tuning fails, try a bigger TP target voltage (or fix the noise).

+

Demonstration:

+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/daephys.html b/daephys.html new file mode 100644 index 0000000000..759acdff04 --- /dev/null +++ b/daephys.html @@ -0,0 +1,191 @@ + + + + + + + + Da_Ephys — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Da_Ephys

+

The DA_Epys panel centralizes control of data acquisition, including multiple +hardware components necessary for performing electrophysiology experiments, +such as the DAC, amplifier, and pressure regulators.

+
+_images/DAEphys-Data_Acquisition.png +
+

Main data acquisition panel

+
+
+

The main data acquisition panel centralizes and simplifies manual control of +the amplifier, pressure control, test-pulse, and data acquisition for up to 8 +headstages. For headstage dependent controls, the slider determines which +headstage to apply user input.

+
+

Distributed DAQ (dDAQ)

+

dDAQ simplifies the acquisition of synaptic responses during paired recordings. +In paired recordings, each cell can be pre- and postsynaptic. dDAQ distributes +the stimulus set sweep in time across headstages. Temporal distribution the +stimulus set sweep ensures that the postsynaptic cell isn’t being stimulated +simultaneously with the presynaptic cell, which would obscure any synaptic +response(e.g., PSP, PSC). dDAQ delay inserts an acquisition time delay between +the stimulus set sweeps on each headstage. dDAQ automatically adapts as +headstages are enabled or disabled during data acquisition.

+
+_images/dDAQ-delay.svg
+
+
+

Optimized overlap distributed DAQ (oodDAQ)

+

oodDAQ simplifies and speeds the acquisition of synaptic responses during +paired recordings. In paired recordings, each cell can be pre- and +postsynaptic. oodDAQ distributes the non-zero epochs of the stimulus set sweep +in time across headstages. Temporal distribution of non-zero regions of the +stimulus set sweep ensures that the postsynaptic cell isn’t being stimulated +simultaneously with the presynaptic cell, which would obscure any synaptic +response(e.g., PSP, PSC). oodDAQ pre- and post-delay extend the region of +non-overlap to include zero regions around the non-zero region. These delays +ensure the synaptic response can complete before the cell is stimulated to +elicit a (presynaptic) action potential. Pre- and post-delay are highly +recommended when the stimulus set sweep contains pulse trains. To maintain +optimal stimulus distribution, oodDAQ automatically adapts if headstages are +enabled or disabled during data acquisition.

+
+_images/oodDAQ-delays.svg
+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/daq-details.html b/daq-details.html new file mode 100644 index 0000000000..a6c27bc149 --- /dev/null +++ b/daq-details.html @@ -0,0 +1,174 @@ + + + + + + + + DAQ details — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

DAQ details

+
+_images/acquisition-repeated-indexing-explained.svg
+

Data acquisition modes

+
+
+
+_images/normal-delays.svg
+

Normal delays

+
+
+
+_images/dDAQ-delay.svg
+

Ddaq delay

+
+
+
+_images/oodDAQ-delays.svg
+

oodDAQ delays

+
+
+
+_images/testPulse-visualization.svg
+

Testpulse visualization

+
+
+
+

Indexing definition

+

MIES has different modes to automate the acquisition of multiple stimulus sets.

+

Indexing mode allows the acquisition of a range of stimulus sets across multiple channels and channel types (DA and TTL).

+

As stimulus sets can have a different number of sweeps, the natural question +arises when to switch to the next stimulus set when acquiring data on multiple +channels simultaneously. Locked indexing advances to the next stimulus set when +the stimulus set with the most sweeps (currently acquiring, not globally) on +all active channels is complete. Unlocked indexing advances to the next +stimulus set on an individual channel when the active set on the same channel +is complete. In both modes, the currently active set may automatically repeat +while acquisition on the channel with the most combined sweeps proceeds to +completion; locked indexing repeats and then indexes, while unlocked indexing +indexes and then repeats.

+

Inner-Set randomization is currently broken with indexing.

+

Set randomization with indexing is not implemented.

+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/databrowser.html b/databrowser.html new file mode 100644 index 0000000000..8aded2a50d --- /dev/null +++ b/databrowser.html @@ -0,0 +1,212 @@ + + + + + + + + DataBrowser — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

DataBrowser

+
+ +
+

The DataBrowser allows the user to view acquired sweeps and metadata during and +after an experiment. It has several display modes that facilitate recording +from multiple headstages simultaneously. Users may also manipulate and analyze +(automatically backed up) data using a built-in custom scripting language that +includes general and specialized electrophysiology functions see The Sweep Formula Module.

+

The following figure shows the DataBrowser with all three subpanels. The main +graph to the top right visualizes the currently selected sweep(s), either via +the controls in Sweep Control or via Overlay Sweeps. The +controls on the left, Settings, tune the display behaviour, and the +remaining tabs allow more fine-grained and specialized control for +visualization and data evaluation. See the corresponding sub-pages at the top +of this page. The bottom most panel, Settings History, allows to +visualize labnotebook entries.

+
+_images/Browser-all.png +
+

DataBrowser with all subwindows

+
+
+

For better readability we have a fixed color scheme for the acquired data, most notably the headstages.

+
+

Relevant Colors

+
+_images/RelevantColors.png + +
+

Color scheme used throughout the DataBrowser and other panels which display +headstage and channel dependent information

+
+
+
+
+

SweepBrowser vs DataBrowser

+

We only speak about the DataBrowser here, but nearly everything also applies to the +SweepBrowser. Exceptions are mentioned explicitly.

+

The DataBrowser is used when viewing sweeps during acquisition and when they +are from the currently open Igor Pro experiment. The SweepBrowser is started from the +AnalysisBrowser and can be used to browse acquired sweeps loaded from +PXP and NWB files.

+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/databrowser_artefactremoval.html b/databrowser_artefactremoval.html new file mode 100644 index 0000000000..fc0421e83c --- /dev/null +++ b/databrowser_artefactremoval.html @@ -0,0 +1,166 @@ + + + + + + + + Artefact Removal — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Artefact Removal

+
+_images/BrowserSettingsPanel-Artefact-Removal.png +
+

Artefact Removal

+
+
+

TODO fill me

+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/databrowser_channelselection.html b/databrowser_channelselection.html new file mode 100644 index 0000000000..91e0aac196 --- /dev/null +++ b/databrowser_channelselection.html @@ -0,0 +1,168 @@ + + + + + + + + Channel Selection — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Channel Selection

+

The CS tab allows selecting the displayed headstages, DA and AD channels. +It applies to all sweeps shown in the databrowser. The All checkbox allows +toggling the display of all in one click.

+
+_images/BrowserSettingsPanel-ChannelSelection.png +
+

Tab for selecting the displayed Headstages and Channels

+
+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/databrowser_dashboard.html b/databrowser_dashboard.html new file mode 100644 index 0000000000..c4182f23af --- /dev/null +++ b/databrowser_dashboard.html @@ -0,0 +1,166 @@ + + + + + + + + Dashboard — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Dashboard

+
+_images/BrowserSettingsPanel-Dashboard.png +
+

Analysis Functions Dashboard

+
+
+

TODO fill me

+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/databrowser_note.html b/databrowser_note.html new file mode 100644 index 0000000000..4a0f35e327 --- /dev/null +++ b/databrowser_note.html @@ -0,0 +1,166 @@ + + + + + + + + Note — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Note

+
+_images/BrowserSettingsPanel-Note.png +
+

Wavenote display

+
+
+

TODO fill me

+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/databrowser_overlaysweeps.html b/databrowser_overlaysweeps.html new file mode 100644 index 0000000000..1fa6eeab32 --- /dev/null +++ b/databrowser_overlaysweeps.html @@ -0,0 +1,199 @@ + + + + + + + + Overlay Sweeps — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Overlay Sweeps

+

The OVS tab allows to overlay multiple sweeps in the same graph. The +selection of the sweeps can be done by criteria like stimsets, clamp mode or +similiar, using a step and offset calculation based on sweep numbers, or by +selecting them from the listbox. Ignoring selected headstages of a specific +sweep when overlaying is supported as well.

+

The following section describe the OVS settings.

+
+_images/BrowserSettingsPanel-Overlay-Sweeps.png +
+

Settings for overlaying sweeps

+
+
+
    +

  • Enable: Toggle the overlay sweeps mode. When turned on, all selected +sweeps in the lower list box are displayed. In the off state, only the sweep +selected in Sweep Control will be shown.

    • +

  • Select: Select multiple sweeps based on criteria like stimulus set (DA +and TTL) and clamp mode. Includes also None for unselecting all of them.

    • +

  • Offset and Step: Select every sweep number \(x\) which satisfies +the condition \(x = o + n \cdot s\) where \(o\) is the Offset, +\(s\) the Step and \(n >= 0\) an integer.

    • +

  • Headstage Removal: Toggle the ignoring of headstages. When an existing +headstage is entered in the second column in the listbox, this headstage will +not be displayed in the Databrowser. Headstages can also be selected +interactively from the context menu in the Databrowser. For this hover over +the trace you want to remove, right-click and select Ignore Headstage in Overlay Sweeps.

    • +

  • Non-commulative update: If you have enabled Display last sweep acquired +in Sweep Control this option will remove the +previous last sweep from the list of overlayed sweeps before adding the newly +acquired sweep.

    • +

  • Clear on new RAC: Clear the list of overlayed sweeps when a new repeated acquisition cycle (RAC) starts.

    • +

  • Clear on new SCI: Same approach but this time based on the stimset cycle (SCI).

    • +

  • Listbox: The listbox allows to select which sweeps to overlay +individually. The first colum has the sweep numbers and the second column +holds the headstages for removal. The Headstages column can only be +edited when Headstage Removal is checked. The headstages to be removed +can be single headstages 0 to 7, list of headstages 0;2;6 or a +range 0-2.

    • +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/databrowser_paplot.html b/databrowser_paplot.html new file mode 100644 index 0000000000..2619613e31 --- /dev/null +++ b/databrowser_paplot.html @@ -0,0 +1,413 @@ + + + + + + + + Pulse Average (PA) plot — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Pulse Average (PA) plot

+

The purpose of the pulse averaging (PA) plot is to identify synaptic +connections by pooling (via time alignment) and averaging the responses within +and across sweeps to pulses (intended to produce action potentials) on a single +headstage. It repeats this process for all headstages with pulses (action +potentials).

+

Although the stimulus set will contain Pulse Train epochs in +most cases, the pulse extraction algorithm works with all epoch types and +special measurement modes like Distributed DAQ (dDAQ) or Optimized overlap distributed DAQ (oodDAQ).

+

The dDAQ slider from the Settings tab is respected as is the Channel Selection.

+

For instructional purposes, assume pulse train acquisition on four different +headstages with oodDAQ (to distribute the pulses in time, across headstages). +The PA plot shows AD data from each headstage and will have 16 (4 rows x 4 +columns) PA sets (either in 16 plots on a single graph or 16 individual graphs; +user-defined).

+

The diagonal entries hold the extracted single pulses for each headstage. In the other rows of each column are the +regions plotted which are extracted from the other headstages at the same time coordinates as the diagonal pulses. +So each row shows different regions from the same headstages, and each column shows the same region but from different +headstages.

+

The following two figures, Trace plot and +Image plot, were created with multiple sweeps +overlayed, see Overlay Sweeps, and time alignment and zeroing turned on.

+
+

Trace plot

+
+_images/PulseAverage_traces.png + +
+

Trace plot

+
+
+

The trace plot displays data in each PA set as voltage or current time-series. +Scale bars, shown in black, are provided for each y axes and for each column’s +shared x (time) axes. PA trace colors match databrowser trace colors and encode +the headstage, see also Relevant Colors.

+
+
+

Image plot

+
+_images/PulseAverage_images.png + +
+
+_images/PulseAverage_images_colorscales.png + +
+

   

The image graph supplements the trace plot Trace plot. It renders more quickly than the +trace plot, especially with many (overlayed) sweeps. Each (horizontal) line of the image plot corresponds to a pulse +(unique time-series) and encodes the voltage or current in color (user-defined color mapping). Deconvolution and average +lines (extra wide) are at the bottom of each set image. Image-space is left blank when data is not shown. The image is +filled from top to bottom where the interleaving between pulses and sweeps depends on the +Sort Order.

+
+

Sort Order

+

The following tables visualizes the display of one image set with two sweeps +overlayed and three pulses using different Sort Order settings. The +ordering is always ascending and from top to bottom. Due to implementation +details the Sweep sort order allows much faster incremental updates +(only relevant during data acqisition).

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Comparing different sort orders

Sweep

Pulse

Pulse 0, Sweep 0

Pulse 0, Sweep 0

Pulse 1, Sweep 0

Pulse 0, Sweep 1

Pulse 2, Sweep 0

Pulse 1, Sweep 1

Pulse 0, Sweep 1

Pulse 1, Sweep 0

Pulse 1, Sweep 1

Pulse 2, Sweep 1

Pulse 2, Sweep 1

Pulse 2, Sweep 0

Average

Average

Deconvolution

Deconvolution

+
+
+

Time Alignment

+

Time alignment removes the pulse to pulse jitter in pulse evoked event (action potential) timing.

+

The algorithm is as follows:

+
    +

  • Get the feature position featurePos (wave maximum) for all pulses which belong to the +same set. Store these feature positions using their sweep number and pulse +index as key.

    • +

  • Now shift all pulses in all sets from the same region by -featurePos +where featurePos is used from the same sweep and pulse index.

    • +
+
+
+

Operation order

+

Data operations occur in the following (fixed) order:

+
    +

  • Gather pulses

    • +

  • Pulse sorting

    • +

  • Failed pulse search

    • +

  • Zeroing

    • +

  • Time alignment

    • +

  • Averaging

    • +
+
+
+

PA plot settings

+

The following sections describe PA settings. Settings are configured on the +data browser PA settings tab (shown below).

+
+_images/BrowserSettingsPanel-PA-plot.png +
+

Settings for the pulse average plot

+
+
+
+
+
+

Pulse Averaging

+
    +
  • +
    enable: Toggle the display of the PA image/trace plots.

    To adjust multiple settings at-a-time, disable the PA plot, adjust settings, and re-enable.

    +
    +
    +
    • +
+
+
+

Image settings

+
    +

  • Enable image plot: Toggle the display of the Image plot

    • +
  • +
    Draw X zero line: Draws vertical line at X == 0 in each column. Requires time alignment

    (see below). Facilitates measurement of event latency.

    +
    +
    +
    • +

  • Popup Menu: Color scheme for image plots

    • +

  • Sort order: Sort order of the displayed pulses. For Sweep the pulses are +first ordered by sweep number and then by pulse index. For Pulse it is +first pulse index and then sweep number. See also +Sort Order.

    • +
+
+
+

Trace settings

+
    +

  • Enable trace plot: Toggle the display of the Trace plot.

    • +

  • Vertical scale bar: Size of the vertical scale bar in y-axis units

    • +
+
+
+

Deconvolution

+
    +

  • Deconvolution: Enables deconvolution [4] of the average pulse. +Deconvolution trace is displayed with the average trace in the trace plot and +immediately above the average line in the image plot.

    • +

  • Tau [ms]: Time constant [5]

    • +

  • Smoothing: Smoothing parameter, use 1 to disable smoothing

    • +

  • Display [ms]: Time range of the average pulse used for the deconvolution, use inf to use the full range

    • +
+
+
+

General

+
    +

  • Zero pulse: Toggle Pulse Zeroing. Zeroing is carried out by +differentiation, followed by the integration of each pulse.

    • +

  • Time alignment: Toggle time alignment of pulses from one column. See +Time Alignment for an in-depth explanation.

    • +

  • Show average: Toggle average pulse display. For the image plot, the +average is the bottom-most row. Failed pulses (see below) are not included +in the average.

    • +

  • Use multiple graphs: Creates a panel for each PA set. Normally, multiple +PA sets are distributed onto a single panel.

    • +

  • Show individual pulses: Enables the display of individual pulses. Turning +that off can increase the display update performance. The average and +deconvolution are still shown if enabled.

    • +
+
+
+

Pulses

+

Select a subset of the pulses from a train of pulses (contained within a sweep).

+
    +

  • Starting pulse: First pulse index to display, 0-based.

    • +

  • Ending pulse: Last pulse index to display, use inf to use the last pulse.

    • +

  • Fixed pulse length: Choose the calculation method of the pulse lengths. +When unchecked the pulse length is calculated as the average pulse length +from the extracted pulses. When checked the Override length is used.

    • +

  • Override length: Pulse length to use when no length can be calculated +[6] or when Fixed pulse length is checked

    • +
+
+
+

Failed Pulses

+

Pulse responses may be filtered by their amplitude.

+
    +

  • Search failed pulses: Toggle the failed pulse search

    • +

  • Hide failed pulses: When a pulse failed, hide instead of highlight.

    • +

  • Level: Level in y-data units to search for failed pulses. Every pulse not +reaching that level is considered failing. As mentioned in +Operation order that search is done before zeroing.

    • +

  • Number of Spikes: Number of required spikes for each pulse. Use NaN for accepting any non-zero spike count as +passing.

    • +
+ +
+\[\tau \cdot \frac{dV}{dt} + V = f\]
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/databrowser_settings.html b/databrowser_settings.html new file mode 100644 index 0000000000..8db02f0baf --- /dev/null +++ b/databrowser_settings.html @@ -0,0 +1,166 @@ + + + + + + + + Settings — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Settings

+
+_images/BrowserSettingsPanel-Settings.png +
+

Generic Settings

+
+
+

TODO fill me

+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/databrowser_settingshistory.html b/databrowser_settingshistory.html new file mode 100644 index 0000000000..7e405d3f48 --- /dev/null +++ b/databrowser_settingshistory.html @@ -0,0 +1,166 @@ + + + + + + + + Settings History — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Settings History

+
+_images/Browser-SettingsHistory.png +
+

Settings History

+
+
+

TODO fill me

+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/databrowser_sweepcontrol.html b/databrowser_sweepcontrol.html new file mode 100644 index 0000000000..3e0b3d3174 --- /dev/null +++ b/databrowser_sweepcontrol.html @@ -0,0 +1,166 @@ + + + + + + + + Sweep Control — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Sweep Control

+
+_images/Browser-SweepControl.png +
+

Sweep Control

+
+
+

TODO fill me

+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/databrowser_sweepformula.html b/databrowser_sweepformula.html new file mode 100644 index 0000000000..b04b068131 --- /dev/null +++ b/databrowser_sweepformula.html @@ -0,0 +1,166 @@ + + + + + + + + SweepFormula — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

SweepFormula

+
+_images/BrowserSettingsPanel-Sweepformula.png +
+

SweepFormula

+
+
+

TODO fill me

+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/deprecated.html b/deprecated.html new file mode 100644 index 0000000000..3ec500d9a8 --- /dev/null +++ b/deprecated.html @@ -0,0 +1,153 @@ + + + + + + + + Deprecations — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Deprecations

+
+
+page deprecated
+

+
+Member AFP_ANALYSIS_FUNC_V1  (string device, variable eventType, wave DAQDataWave, variable headStage)
+

Use AFP_ANALYSIS_FUNC_V3() instead

+
+ +
+
+Member AFP_ANALYSIS_FUNC_V2  (string device, variable eventType, wave DAQDataWave, variable headStage, variable realDataLength)
+

Use AFP_ANALYSIS_FUNC_V3() instead

+
+ +
+
+Member SF_GetArgumentTop  (variable jsonId, string jsonPath, string graph, string opShort)
+

: executing all arguments e.g. as array in the executor poses issues as soon as data types get mixed. e.g. operation(0, A, [1, 2, 3]) fails as [0, A, [1, 2, 3]] can not be converted to an Igor wave. Thus, it is strongly recommended to parse each argument separately.

+
+ +

+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/developers.html b/developers.html new file mode 100644 index 0000000000..80d52fd068 --- /dev/null +++ b/developers.html @@ -0,0 +1,611 @@ + + + + + + + + Developer — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Developer

+
+

Getting MIES

+
+

Latest development version from main branch

+
    +

  • git clone --recurse-submodules https://github.com/AllenInstitute/MIES

    • +

  • ./tools/initial-repo-config.sh (Requires a Git Bash shell, named +Git terminal in SourceTree)

    • +
+
+
+

Building the documentation

+
    +

  • The script tools/build-documentation.sh allows to build the documentation locally

    • +

  • This command also installs the required pip packages, so using a dedicated virtual environment is advised

    • +

  • Linux users might directly execute the docker version in tools/documentation/run.sh

    • +
+
+
+

Updating documentation

+

Due to our excessive use of the breathe sphinx extension which feeds from +doxygen, a full documentation build takes around 10 minutes. It is also not +possible to use the sphinx autobuild feature, as it rebuilds all everything from +scratch due to breathe.

+

For fast read-write-view cycles while writing the user documentation do the following:

+
    +

  • Start with a clean Packages/doc folder

    • +

  • Apply the patch +which temporarily removes breathe via git am ...

    • +

  • Call make autobuild which opens a local webbrowser and rebuilds after +every change. This time incremental updates work.

    • +
+
+
+
+

Updating requirements files

+

All python package requirements.txt files we ship must have package hashes +included for improved security.

+

These files are generated from requirements.in via

+
+
pip-compile --generate-hashes --resolver=backtracking requirements.in
+
+
+
+

Therefore updates should be done directly in requirements.in and then calling pip-compile.

+
+
+

Release Handling

+

If guidelines are not followed, the MIES version will be unknown, and +data acquisition is blocked.

+
+

Cutting a new release

+
    +

  • Checkout a new branch git checkout -b feature/XXXX-release-notes main

    • +

  • Paste the contents of Packages\doc\releasenotes_template.rst to +the top of Packages\doc\releasenotes.rst

    • +

  • Call tools\create-changelog.sh which generate a raw changelog and +fill releasenotes.rst with a cleaned up version of it. +Work from bottom to top.

    • +

  • Propose a pull request and get it merged

    • +

  • Checkout the main branch

    • +

  • Tag the current state with git tag Release_X.Y_*, see git tag +for how the asterisk should look like

    • +

  • Push the tag: git push origin $tag. You can pass --dry-run for +testing out what is getting pushed without pushing anything.

    • +

  • Create the release branches:

    +
      +

    • git checkout -b release/X.Y

      • +

    • git push --no-verify -u origin release/X.Y

      • +
    +
    • +

  • Create a new release on github and check that the Github Actions job +correctly uploads the artifacts

    • +
+
+
+
+

Continuous integration server

+

Our CI server, called +Github Actions, provides the following services for MIES:

+
+

Compilation testing

+

The full MIES installation with and without hardware XOPs are IGOR Pro compile +tested using a Github Actions job. This allows to catch compile time errors +early on.

+

For testing compilation manually perform the following steps:

+
    +

  • Create in User Procedures a shortcut pointing to +Packages\MIES_Include.ipf and Packages\tests

    • +

  • Remove the shortcut Packages\MIES_Include.ipf in +Igor Procedures

    • +

  • Close all Igor Pro instances

    • +

  • Execute tools\autorun-test.sh

    • +

  • Watch the output

    • +
+
+
+

Unit and integration testing

+

A couple of our Github Actions jobs are responsible for executing tests. All +tests are written using the Igor Pro Universal Testing Framework.

+

The folders in Packages\tests follow a common naming scheme. Each folder +holds a separate Igor Experiment with tests. The tests in folders starting with +Hardware requires present hardware, the others don’t. In each folder an Igor +Experiment named like the folder with .pxp-suffix is present which allows +to execute all the tests from that folder.

+

For executing the tests manually perform the followings steps:

+
    +

  • Create in User Procedures a shortcut pointing to +Packages\MIES_Include.ipf and Packages\tests

    • +

  • Remove the shortcut Packages\MIES_Include.ipf in Igor Procedures

    • +

  • Open one of the test experiments in Packages\tests

    • +

  • Call RunWithOpts()

    • +

  • Watch the output

    • +
+

The environment variables CI_INSTRUMENT_TESTS/CI_EXPENSIVE_CHECKS allow +to tweak test execution. By default we do expensive tests in CI and +instrumentation in CI for the main branch. Accepted are all numbers but the +values 0/1 are suggested.

+
+
+

Documentation building

+

The documentation for the main branch is automatically built and uploaded by +this +Github Actions job.

+
+
+

Setting up a continuous integration server (Linux)

+
+

Install required software

+
    +

  • Install Docker

    • +

  • Misc required software: dnf install git rg

    • +
+
+
+

Setup Github Actions runner

+
    +

  • Install the Github Actions runner according to the +instructions

    • +

  • Don’t install the runner as a service but use the local user

    • +

  • Add a fitting label to the agent in the repository settings at +Github (see detailed description <https://docs.github.com/en/actions/hosting-your-own-runners/managing-self-hosted-runners/using-labels-with-self-hosted-runners>)

    • +
+
+
+
+

Setting up a continuous integration runner (Windows, ITC and NI)

+
    +

  • Windows 10 with “Remote Desktop” enabled user

    • +

  • Install the folllowing programs:

    +
      +

    • Git (choose the installer option which will make the Unix tools +available in cmd as well)

      • +

    • Multiclamp Commander

      • +

    • NIDAQ-mx driver package 19.0 or later

      • +

    • NIDAQ-mx XOP from WaveMetrics

      • +

    • HEKA Harware Drivers 2014-03 Windows.zip

      • +

    • Igor Pro (latest required versions), the binary folder needs to be named IgorBinaries_x64_r$revision

      • +

    • Github Actions runner as described above

      • +

    • VC Redistributable package from tools/installer/vc_redist.x64.exe

      • +
    +
    • +

  • Start Igor Pro and open a DA_Ephys panel, lock the device. This will +not work, so follow the posted suggestions to get it working (registry fix and ASLR fix).

    • +

  • Add shortcuts to MC700B.exe into C:\ProgramData\Microsoft\Windows\Start Menu\Programs\StartUp

    • +
+
+
+

Setting up a continuous integration runner (Windows, IgorPro)

+
    +

  • Windows 10 with “Remote Desktop” enabled user

    • +

  • Install the folllowing programs:

    +
      +

    • Git (choose the installer option which will make the Unix tools +available in cmd as well)

      • +

    • Igor Pro (latest required versions), the binary folder needs to be named IgorBinaries_x64_r$revision

      • +

    • Multiclamp Commander (the MCC library is required to run the non-hardware tests, +but the application itself does not have to run)

      • +

    • Github Actions runner as described above

      • +

    • VC Redistributable package from tools/installer/vc_redist.x64.exe

      • +
    +
    • +
+
+
+

Available CI servers

+

Distributing jobs to agents in Github Actions is done via runner labels. A +runner can have more than one label at the same time and the runner capabilities +is described by the sum of its labels.

+

The following labels are in use:

+
    +

  • self-hosted: Always use this label to use our own runners

    • +

  • Linux: Agents run on Linux with

    +
      +

    • Rocky Linux release 8.6 (Green Obsidian)

      • +

    • No Hardware

      • +

    • No Igor Pro

      • +
    +
    • +

  • Docker: Agents can run docker containers

    • +

  • Windows: Agents run on Windows with

    +
      +

    • Windows 10

      • +
    +
    • +

  • Certificate: Agent can sign installer packages

    +
      +

    • EV certificate on USB stick

      • +
    +
    • +

  • IgorPro: Can run Igor Pro

    +
      +

    • Igor Pro (latest required versions)

      • +
    +
    • +

  • ITC: Agent can execute hardware tests with ITC18USB hardware

    +
      +

    • ITC18-USB hardware, 2 AD/DA channels are looped

      • +

    • MCC demo amplifier only

      • +
    +
    • +

  • NI: Agent can execute hardware tests with NI/ITC1600 hardware

    +
      +

    • ITC-1600 hardware with one rack, 2 AD/DA channels are looped

      • +

    • NI PCIe-6343, 2 AD/DA channels are looped

      • +

    • MCC demo amplifier only

      • +
    +
    • +
+
+
+

Setting up/Renewing EV certificate

+

Our installer is signed with an EV (extended validation) certificate. This is done to pass through antivirus software. +These certificates come on USB tokens which are usable for three years.

+

The idea for the automation part is from [here](https://stackoverflow.com/a/54439759). +Remember that you have only three tries with a false password!

+
+
+
+

Renewal process

+
    +

  • Ask Tim to get a new certificate. Takes around 4 weeks due to heavy administration involvement.

    • +

  • Exchange the old USB token with the new one

    • +

  • Physically destroy the old USB token

    • +

  • Install SafeNet on the machine if not yet done

    • +

  • As you can’t see the token when logged in via Remote Desktop (RDP) you need to workaround that:

    • +

  • Install Anydesk

    • +

  • Enable Unattended Access with a strong password +- Disconnect with RDP +- Connect with Anydesk +- Open SafeNet +- Change the password (the initial one came via email, it needs to be strong but at most 15 characters long) +- Don’t try to change the admin password or unlock the token. +- Export the public certificate from the Advanced View -> Tokens -> User certificates and save in tools/installer/public-key.cer +- Get the “Container name” as well +- Store the new password and the new container name in a secure place +- Checkout the MIES branch with the new public key/certificate +- ./tools/create-installer.sh +- ./tools/sign-installer.sh -p ‘[]=name’ (name is the “Container name”) +- You should now get asked for the password in a GUI prompt, enter it. +- Now this should have created a signed installer, if not check the previous steps. +- Try with ./tools/sign-installer.sh -p ‘[{{password}}]=name’ this now includes also the password. +- Now this should have created a signed installer again, but this time without password prompt. +- If the last step worked, update the GHA_MIES_CERTIFICATE_PIN in github and make a PR.

    • +

  • Disable Unattended Access in Anydesk again

    • +

  • Add a calendar entry for expiration date minus 6 weeks for the certificate renewal

    • +
+
+

Branch naming scheme

+

For making code review easier we try to follow a naming scheme for branches behind PRs.

+

Scheme: $prefix/$pr-$text

+

Where $prefix is one of feature/bugfix, $pr is the number of the soon-to-be-created pull request and +$text a user defined descriptive text.

+

Contributers are encouraged to install the pre-push git hook from the tools +directory. This hook handles inserting the correct PR number automatically if +the current branch follows the naming scheme $prefix/XXXX-$text.

+
+
+

Continuous Integration Hints

+

As part of the continuous integration pipeline tests are run. A full test run including the hardware tests +tales several hours. Thus, if a lot of pull requests are updated pending test runs could queue up and +it might take rather long until results are available.

+

Thus, for changes where the commits are in a state where no full test run by the CI makes sense it is +possible to inhibit the automatic tests. Typically this is the case if the developer commits changes +in progress and pushes these for the purpose of a secondary backup or further commit organization. +Inhibiting tests for these cases frees testing resources for other pull requests.

+

To inhibit test runs the key [SKIP CI] has to be added to the commit message.

+

The key can be removed later easily through a rebase with rewording the commit message. +After pushing to the repository the CI queues the tests again for this pull request.

+
+
+

Debugging threadsafe functions

+

The function DisableThreadsafeSupport() allows to turn off threadsafe support globally. This allows to use the +debugger in threadsafe functions. Every MIES features which does not complain via ASSERT() or BUG() is supposed +to work without threadsafe support as well.

+
+
+

Preventing Debugger Popup

+

There exist critical function calls that raise a runtime error. In well-defined circumstances the error condition is evaluated properly afterwards. +When debugger is enabled and options are set to “Debug On Error”, then the Debugger will popup on the line where such functions calls take place. +This is inconvenient for debugging because the error is intended and properly handled. To prevent the debugger to open the coding convention is:

+
AssertOnAndClearRTError()
+CriticalFunction(); err = getRTError(1)
+
+
+

Notable the second part that clears the RTE must be in the same line and can not be moved to an own function. +This coding convention is only valid, if the critical function is expected to raise an runtime error.

+
+
+

Runtime Error / Abort Handling Conventions

+

Here a coding convention for try / catch / endtry constructs is introduced to +prevent common issues like silently clearing unexpected runtime error conditions +by using these.

+

A try / catch / endtry construct catches by specification either

+
    +

  • Runtime errors when AbortOnRTE is encountered between try / catch

    • +

  • Aborts when encountered between try / catch

    • +
+

The code must take into account the possibility of runtime errors generated +by bad code. These unexpected RTEs must not be silently cleared.

+

For the case, where an RTE is expected from CriticalFunction, the common approach is:

+
AssertOnAndClearRTError()
+try
+    CriticalFunction(); AbortOnRTE
+catch
+    err = ClearRTError()
+    ...
+endtry
+
+
+

Here pending RTEs are handled before the try. By convention the AbortOnRTE must be +placed in the same function as the try / catch / endtry construct. +The code between try / catch should only include critical function calls and be +kept minimal. The expected RTE condition should be cleared directly after catch.

+

For the case, where an Abort is expected from CriticalFunction, the common approach is:

+
try
+    CriticalFunction()
+catch
+    ...
+endtry
+
+
+

As Abort does not generate an RTE condition the try / catch / endtry construct +leaves any possible unexpected RTE condition pending and no RTE condition is cleared. +The programmer might consider evaluating V_AbortCode after catch.

+

It is recommended to comment in the code before the try what the construct is +intended to handle (RTE, Abort or both).

+
+
+

Retrieving Headstage / Channel Information from the LBN

+

If you would like to retrieve the settings from the last acquisition then look up function like AFH_GetHeadstageFromDAC. +It retrieves the correct information under the following conditions:

+
    +

  • Data Acquisition is ongoing or

    • +

  • Data Acquisition has finished and DAEphys panel was not changed.

    • +
+

This function returns NaN if the active DAC had no associated headstage. +The same applies for AFH_GetHeadstageFromADC.

+

In contrast the functions AFH_GetDACFromHeadstage and AFH_GetADCFromHeadstage return DAC/ADC numbers only for active headstages.

+

One of the most used functions to retrieve specific information from the LBN is +GetLastSettingChannel. The returned wave has NUM_HEADSTAGES + 1 entries. +The first NUM_HEADSTAGES entries refer to the headstages whereas the last entry contains +all headstage independent data. +This is related to the general layout of the LBN, where the headstage is an index of the wave. +In the numerical LBN (GetLBNumericalValues) there are columns with DAC/ADC channel information identified by their respective dimension label. +For associated DAC <-> ADC channels the number of the DAC and ADC is present in the layers. The first NUM_HEADSTAGES layers refer to the headstages.

+

Thus, if headstage 3 uses DAC channel 5 and ADC channel 1 for a sweep then in the LBN +at index 3 in the DAC column a 3 is present and in the ADC column a 1. +Details of the internal data format of the LBN are not required for correct retrieval +of that information as MIES provides functions for that:

+
WAVE/Z numericalValues = BSP_GetLBNWave(graph, LBN_NUMERICAL_VALUES, sweepNumber = sweep)
+if(!WaveExists(numericalValues))
+   // fitting handling code
+endif
+[WAVE/Z settings, index] = GetLastSettingChannel(numericalValues, $"", sweep, "Indexing", channelNumber, channelType, entrySourceType)
+
+
+

This call specifies a sweep number, a channel type and a channel number and asks for information from the “Indexing” field. +It returns a 1D wave settings and an index, where settings[index] is a Boolean entry telling if indexing was off or on. +The value index itself is the headstage number. The index value can also equal NUM_HEADSTAGES when it refers to a headstage independent value.

+

To find the ADC channel from a DAC channel, the example above can also be setup with channelType = XOP_CHANNEL_TYPE_DAC and LBN entry name “ADC”. +This works the same for finding the DAC channel from a ADC channel.

+

If one just wants the headstage number there is an utility function GetHeadstageForChannel that returns the active headstage for a channel.

+

The LBN entry Headstage Active is a Boolean entry and marks which headstage was active in a sweep. +The Headstage Active can only be set (1) for a headstage that has an associated DAC and ADC channel.

+
+
+

Creating LBN entries for tests

+
Make/FREE/N=(1, 1, LABNOTEBOOK_LAYER_COUNT) valuesHSA, valuesDAC, valuesADC
+Make/T/FREE/N=(1, 1, 1) keys
+
+sweepNo = 0
+
+// HS 0: DAC 2 and ADC 6
+// HS 1: DAC 3 and ADC 7
+// HS 2+: No DAC/ADC set
+valuesDAC[]  = NaN
+valuesDAC[0][0][0] = 2 // The layer refers to the headstage number
+valuesDAC[0][0][1] = 3
+keys[] = "DAC"
+ED_AddEntriesToLabnotebook(valuesDAC, keys, sweepNo, device, DATA_ACQUISITION_MODE)
+
+valuesADC[]  = NaN
+valuesADC[0][0][0] = 6
+valuesADC[0][0][1] = 7
+keys[] = "ADC"
+ED_AddEntriesToLabnotebook(valuesADC, keys, sweepNo, device, DATA_ACQUISITION_MODE)
+
+valuesHSA[]  = 0
+valuesHSA[0][0][0] = 1 // the only valid option here is to set HS 0 and 1 active
+valuesHSA[0][0][1] = 1 // because we did not set ADC/DAC channels for the other HS.
+keys[] = "Headstage Active"
+ED_AddEntriesToLabnotebook(valuesHSA, keys, sweepNo, device, DATA_ACQUISITION_MODE)
+
+
+

The key function here is ED_AddEntriesToLabnotebook. There are no checks applied for this +way of creating LBN entries for tests that guarantee a consistent LBN. e.g. setting headstage 2 to active +in the upper code would violate LBN format schema. +Note that in contrast ED_AddEntryToLabnotebook is used to add specific user entries to the LBN +and is not suited for setting up generic test LBN entries. +More example code can be found in PrepareLBN_IGNORE in UTF_Labnotebook.ipf.

+
+
+

Adding support for new NI hardware

+

Newly added NI hardware must fulfill the following properties:

+
+
    +

  • Allow 500kHz sampling rate for one AI/AO channel

    • +

  • At least one port of each type: AI/AO/DIO

    • +

  • Supported by the NIDAQmx XOP and our use of it

    • +
+
+

To add new hardware:

+
+
+
+
+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/epoch_information.html b/epoch_information.html new file mode 100644 index 0000000000..27bee41c95 --- /dev/null +++ b/epoch_information.html @@ -0,0 +1,514 @@ + + + + + + + + Epoch Information — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Epoch Information

+
+

Description

+

At acquisition time, sweep epoch metadata is generated. +Epochs are contiguous time ranges in the input signal that feature certain signal shapes, such as e.g. pulse trains. +This information is exported with each data acquisition to the lab notebook with the key “Epochs” for each DA channel.

+
+_images/epoch-visualization.svg
+

Epoch visualization with level 0 (top, at -10) to 3 (bottom)

+
+
+
+
+

Retrieving Epoch Information

+
+

MIES labnotebook

+

The epoch information can be retrieved from the lab notebook with

+
+
WAVE/T textualValues  = GetLBTextualValues(device)
+WAVE/T epochLBEntries = GetLastSetting(textualValues, sweepNumber, EPOCHS_ENTRY_KEY, DATA_ACQUISITION_MODE)
+WAVE/T epochHeadstage = EP_EpochStrToWave(epochLBEntries[headstage])
+
+
+
+

The epochHeadstage wave has four columns:

+
    +

  • Column 1: start time

    • +

  • Column 2: end time

    • +

  • Column 3: epoch description - a semi-colon separated list of epoch descriptors. e.g., Epoch=1;Type=Pulse Train;Amplitude=1;Pulse=0;

    • +

  • Column 4: (tree) level. e.g., wavebuilder defined EPOCH tree level = 1, a sub epoch of a wavebuilder defined EPOCH = 2 and so on

    • +
+

Each row is an epoch entry.

+
+
+

NWBv2

+

Epoch information is also exported into NWBv2 files into /intervals/epochs +when doing full exports (it is skipped for per-sweep export). Using +pynwb.epoch.TimeIntervals <https://pynwb.readthedocs.io/en/stable/pynwb.epoch.html#pynwb.epoch.TimeIntervals> +this can be read with:

+
with NWBHDF5IO('file.nwb', mode='r', load_namespaces=True) as io:
+    nwbfile = io.read()
+
+    if nwbfile.epochs and len(nwbfile.epochs) > 0:
+        print(nwbfile.epochs[:, 'start_time'])
+        print(nwbfile.epochs[:, 'stop_time'])
+        print(nwbfile.epochs[:, 'tags'])
+        print(nwbfile.epochs[:, 'treelevel'])
+        print(nwbfile.epochs[:, 'timeseries'])
+
+
+
+
+
+

Format

+

The times are in seconds where 0 is the beginning of the signal input. The reference signal is the DA or TTL output wave. +The epochChannel wave can contain several entries with different levels covering the same time range. +Epochs with a level of zero name the main components of the input signal. +Typical epochs with zero level are ‘Inserted Test Pulse’ and ‘StimSet’.

+

A level of one designates a sub epoch of a zero level epoch and can correspond to, for example, the leading baseline a +‘Inserted Test Pulse’, the pulse component, and the trailing baseline of the pulse. For ‘StimSet’s that are level zero, the associated +Stimset-Epochs, like Ramp, Pulse Train, and so on are level one.

+

Accordingly level two epochs are sub epochs of level one epochs. For example, the level two epoch of a pulse train +contains a single pulse of the pulse train.

+

The start time of a level n epoch equals the start time of the first level n+1 epoch within the level n epochs time interval.

+

All epochs between 0 and end of the input signal are consecutive and without gaps (contiguous). +All level n+1 epochs are contiguous for the associated n epoch.

+

The following table sketches how epochs of different levels could be distributed in the range of the full output data:

+ + + + + + + + + + + + + + + + + + + + + +

output data time series range 0 - 100 [s]

level 0: 0 - 60

level 0: 60 - 100

level 1: 0 - 20

level 1: 20 - 60

level 2: 20 - 30

level 2: 30 - 45

level 2: 45 - 51

level 2: 51 - 60

+

The entries in the wave are sorted by increasing start times and secondary by decreasing end times.

+
+
+

Time specialities

+

The epoch start and end times are stored in seconds with sufficiently large +precision as text. The start time of an epoch refers to the first sample point of the feature that +contains the signal. The end time of an epoch refers to the sample point directly after epoch. +This point is also the start point of the next epoch and the first point of the next epoch. +For a pulse epoch following a base line epoch the sample point at the start time +of the pulse epoch is the first point with an amplitude > 0. Thus, the epoch ranges are sample point +exact. The sample point can be calculated by round(epochTime / samplingInterval).

+

An exception from that are oodDAQ region epochs (ODx) that store times that are not sample point exact. +Details are described in the following section.

+
+
+

optimized overlap distributed data acquisistion (oodDAQ) regions

+

oodDAQ regions are saved as level two epoch named oodDAQRegion. While regular epochs are generated from the +stimset note, oodDAQ regions are generated by the oodDAQ optimizer. Thus the oodDAQRegion epochs are not bound to the +constraints described in the previous section. +The oodDAQ regions are added ‘as is’ to the epochs.

+
+
+

Naming

+

The following table describes the 1:1 relationship between epoch names and MIES feature names:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Level

Level

Level

Level

Tags

Short Name

Origin

0

Type=Baseline

B0_OD

Onset Delay

0

Type=Baseline

B0_TP

Baseline on unassociated DA channels where associated DA channels have an inserted +test pulse if checked

0

Type=Baseline

B0_DD

Onset delay of channel due to distributed DAQ [dDAQ]

0

Type=Baseline

B0_DO

Onset delay of channel due to distributed DAQ optimized overlay [dDAQ OptOv]

0

Type=Inserted Testpulse

TP

Inserted TP

1

Type=Inserted Testpulse;SubType=Baseline

TP_B0

preceding baseline of inserted TP

1

Type=Inserted Testpulse;SubType=Pulse;Amplitude=x

TP_P

pulse time of inserted TP

1

Type=Inserted Testpulse;SubType=Baseline

TP_B1

subsequent baseline of inserted TP

0

Type=Stimset

ST

Stimset

1

Type=Epoch;Epoch=x;EpochType=x;Amplitude=x;Details=x

Ex

Stimset-Epoch (Details is optional)

2

+SubType=Baseline

Ex_PT_Px_BT

Stimset-Epoch baseline before first pulse (example pulse train)

2

+Pulse=x

Ex_PT_Px

Stimset-Epoch component (example pulse train)

3

+SubType=Pulse;Pulse=x

Ex_PT_Px_P

High region of pulse (example pulse train)

3

+SubType=Baseline;Pulse=x

Ex_PT_Px_B

Zero region of pulse (example pulse train)

2

+Cycle=x

Ex_TG_Cx

Trigonometric epoch, one epoch for each full sin/cos cycle

3

+Cycle=x;Half Cycle=x

Ex_TG_Cx_Hx

Two for each cycle, one negative and one positive

2

+Incomplete Cycle=x

Ex_TG_Ix

Everything else except full cycles

2

Type=oodDAQ;oodDAQRegion=x

ODx

oodDAQ region

1

Type=Baseline

ST_B

trailing baseline due to different length stimsets

0

Type=Baseline

B0_TD

Termination Delay

0

Type=Baseline

B0_TR

trailing baseline after stimset plus termination delay as another channel can have +e.g. a longer stimset

0

Type=Unacquired

UA

Planned to be acquired but skipped due to early sweep stop

+

If the name entry begins with + then it is appended to the higher-level name. The x is a place holder where +additional information is included in the names, such as Stimset-Epoch numbering, or amplitudes. Currently only +pulse trains and trigonometric are supported with level two and three detail for Stimset-Epochs. +Depending on the setup of the data acquisition, not every entry listed in the table has to appear in the epochs table.

+

The Details key for the Stimset-Epoch can contain a combination of Mixed frequency or Poisson distribution with +shuffled as originally configured for the Stimset in the waveBuilder.

+

When the sweep is terminated earlier as planned, the epoch Unacquired is added in the planned but not acquired +timespan at the end of the sweep. All other epochs are then also either shortend or dropped so that they don’t extend +into the unacquired epoch.

+
+

Short Names

+

In addition to the long names that are generated as described above also unique short names are created. These short names are saved +in the epoch description field as well as key value pair. The key is ShortName and the separator =. To retrieve a short name +the function EP_GetShortName(string name) should be used.

+

Short names are created in the form of blocks of one to two uppercase letters followed optionally by a signed integer number. +Subsequent blocks are separated by an underscore. Example: E0_PT_P48_B.

+
+
+
+

Pulse Trains

+

Pulse Trains are a type of Stimset-Epochs which is widely used and covered in high detail in the epochs table. For pulse +trains each pulse gets an level two epoch entry. The time interval of a pulse begins when the signal is above base line +level and includes the trailing baseline (that precedes the next pulse) unless it is the last pulse in the pulse train. +An epoch named ‘Baseline’ is inserted if the first pulse in the pulse train has a leading baseline. This is applies for +flipped Stimsets containing Stimset-Epochs with type pulse train.

+
+_images/epoch-visualization2.svg
+

Annotated visualization of epoch from flipped stimsets on two headstages. Each stimset consists of a pulse-train with +poisson distribution and a square pulse stimset epoch. The DA output data on the second headstage is offsetted due to enabled oodDAQ.

+
+
+
+_images/epoch-visualization3.svg
+

Annotated visualization of epoch of a regular and a flipped stimset on two headstages. Each stimset consists of several stimset epochs with +trigonometric functions. The stimset on the second headstage is the flipped version of the stimset on the first headstage.

+
+
+
+
+

User epochs

+

Adding custom epoch information is supported via EP_AddUserEpoch(). This is especially useful for analysis +function writers, who can add their own epochs of interest, see File MIES_AnalysisFunctions.ipf for the +supported events.

+

The tags property of user epochs can be freely set. When a shortName is supplied, this is always prefixed with +U_ so that short names for user epochs don’t collide with builtin epochs. Likewise the tree level for user epochs is +fixed to -1.

+

User epochs will also be limited to the acquired sweep data like builtin epochs. This can result in shorter as expected epochs or even +removed user epochs.

+
+
+
Example
+
 string device = "ITC18USB_DEV_0"
+ variable startTime = 1.5
+ variable endTime   = 2.5
+ variable DAC = 1
+ string tags = "Name=Found Spikes;"
+ string shortName = "FS"
+
+ EP_AddUserEpoch(device, XOP_CHANNEL_TYPE_DAC, DAC, startTime, endTime, tags, shortName = shortName)
+
+
+
+
+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_d_r___m_i_e_s___tango_interact_8ipf.html b/file/_d_r___m_i_e_s___tango_interact_8ipf.html new file mode 100644 index 0000000000..4fbb06a0aa --- /dev/null +++ b/file/_d_r___m_i_e_s___tango_interact_8ipf.html @@ -0,0 +1,276 @@ + + + + + + + + File DR_MIES_TangoInteract.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File DR_MIES_TangoInteract.ipf

+

This file is only provided for backward compatibility and will always be empty.

+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_i_p_n_w_b___constants_8ipf.html b/file/_i_p_n_w_b___constants_8ipf.html new file mode 100644 index 0000000000..3812a8e276 --- /dev/null +++ b/file/_i_p_n_w_b___constants_8ipf.html @@ -0,0 +1,705 @@ + + + + + + + + File IPNWB_Constants.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File IPNWB_Constants.ipf

+

Constants.

+
+

HDF5 file paths

+

+
+
+const string NWB_ROOT = "/"
+
+ +
+
+const string NWB_GENERAL = "/general"
+
+ +
+
+const string NWB_SUBJECT = "/general/subject"
+
+ +
+
+const string NWB_DEVICES = "/general/devices"
+
+ +
+
+const string NWB_STIMULUS = "/general/stimsets"
+
+ +
+
+const string NWB_LABNOTEBOOK = "/general/labnotebook"
+
+ +
+
+const string NWB_RESULTS = "/general/results"
+
+ +
+
+const string NWB_INTRACELLULAR_EPHYS = "/general/intracellular_ephys"
+
+ +
+
+const string NWB_STIMULUS_TEMPLATES = "/stimulus/templates"
+
+ +
+
+const string NWB_STIMULUS_PRESENTATION = "/stimulus/presentation"
+
+ +
+
+const string NWB_IMAGES = "/acquisition/images"
+
+ +
+
+const string NWB_EPOCHS = "/epochs"
+
+ +
+
+const string NWB_PROCESSING = "/processing"
+
+ +
+
+const string NWB_ANALYSIS = "/analysis"
+
+ +
+
+const string NWB_SPECIFICATIONS = "/specifications"
+
+ +
+
+const string NWB_TIME_INTERVALS_EPOCHS = "/intervals/epochs"
+
+ +
+
+const string NWB_TIME_INTERVALS_TIMESERIES_EPOCHS = "/intervals/epochs/timeseries"
+
+ +
+
+

IPNWB naming conventions

+
+
+const string NWB_ELECTRODE_PREFIX = "electrode_"
+
+ +
+
+

Channel constants (inspired by the ITC XOP)

+

+
+
+const double IPNWB_CHANNEL_TYPE_OTHER = -1
+
+ +
+
+const double IPNWB_CHANNEL_TYPE_ADC = 0
+
+ +
+
+const double IPNWB_CHANNEL_TYPE_DAC = 1
+
+ +
+
+const double IPNWB_CHANNEL_TYPE_TTL = 3
+
+ +
+
+

Constants for FunctionInfo and WaveType

+

+
+
+const double IGOR_TYPE_COMPLEX = 0x001
+
+ +
+
+const double IGOR_TYPE_32BIT_FLOAT = 0x002
+
+ +
+
+const double IGOR_TYPE_64BIT_FLOAT = 0x004
+
+ +
+
+const double IGOR_TYPE_8BIT_INT = 0x008
+
+ +
+
+const double IGOR_TYPE_16BIT_INT = 0x010
+
+ +
+
+const double IGOR_TYPE_32BIT_INT = 0x020
+
+ +
+
+const double IGOR_TYPE_UNSIGNED = 0x040
+

Can be combined, using bitwise or, with all integer types.

+
+ +
+
+const double IGOR_TYPE_STRUCT_PARAMETER = 0x200
+
+ +
+
+

Unnamed Group

+
+
+const double ROWS = 0
+

Convenience definition to nicify expressions like DimSize(wv, ROWS) easier to read than DimSize(wv, 0).

+
+ +
+
+const double COLS = 1
+
+ +
+
+const double LAYERS = 2
+
+ +
+
+const double CHUNKS = 3
+
+ +
+
+

Constants for the acquisition modes

+

+
+
+const double V_CLAMP_MODE = 0
+
+ +
+
+const double I_CLAMP_MODE = 1
+
+ +
+
+const double I_EQUAL_ZERO_MODE = 2
+
+ +
+
+

Parameters for gnoise and enoise

+
+
+const double NOISE_GEN_LINEAR_CONGRUENTIAL = 1
+

Don’t use for new code.

+
+ +
+
+const double NOISE_GEN_MERSENNE_TWISTER = 2
+
+ +
+
+

Constants for the compression modes

+

+
+
+const double NO_COMPRESSION = 0x0
+
+ +
+
+const double CHUNKED_COMPRESSION = 0x1
+
+ +
+
+const double SINGLE_CHUNK_COMPRESSION = 0x2
+
+ +
+
+

Constants for the reference modes

+

+
+
+const double NO_REFERENCE = 0x0
+
+ +
+
+const double OBJECT_REFERENCE = 0x1
+
+ +
+
+const double REGION_REFERENCE = 0x2
+
+ +
+
+

Constants for NWB version 2 specifications and base classes

+
+
+const string NWB_SPEC_NAME = "core"
+
+ +
+
+const string NWB_SPEC_VERSION = "2.2.4"
+
+ +
+
+const string NWB_SPEC_LOCATION = "namespace:core:json:"
+
+ +
+
+const string NWB_SPEC_START = "nwb.namespace"
+
+ +
+
+const string NWB_SPEC_INCLUDE = "nwb.base;nwb.behavior;nwb.device;nwb.ecephys;nwb.epoch;nwb.file;nwb.icephys;nwb.image;nwb.misc;nwb.ogen;nwb.ophys;nwb.retinotopy;"
+
+ +
+
+const string HDMF_SPEC_NAME = "hdmf-common"
+
+ +
+
+const string HDMF_SPEC_VERSION = "1.1.3"
+
+ +
+
+const string HDMF_SPEC_LOCATION = "namespace:hdmf-common:json:"
+
+ +
+
+const string HDMF_SPEC_START = "namespace"
+
+ +
+
+const string HDMF_SPEC_INCLUDE = "table;sparse;"
+
+ +
+
+const string NDX_MIES_SPEC_NAME = "ndx-mies"
+
+ +
+
+const string NDX_MIES_SPEC_VERSION = "0.1.0"
+
+ +
+
+const string NDX_MIES_SPEC_LOCATION = "namespace:ndx-mies:json:"
+
+ +
+
+const string NDX_MIES_SPEC_START = "namespace"
+
+ +
+
+const string NDX_MIES_SPEC_INCLUDE = "ndx-mies.extensions"
+
+ +
+
+

Variables

+
+
+const string PLACEHOLDER = "PLACEHOLDER"
+
+ +
+
+const double NWB_VERSION_LATEST = 2
+
+ +
+
+const string CHANNEL_NAMES = "AD;DA;;TTL"
+
+ +
+
+const double MAX_OBJECT_NAME_LENGTH_IN_BYTES = 31
+

Maximum length of a valid name in bytes in Igor Pro.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_i_p_n_w_b___debugging_8ipf.html b/file/_i_p_n_w_b___debugging_8ipf.html new file mode 100644 index 0000000000..1a4628e526 --- /dev/null +++ b/file/_i_p_n_w_b___debugging_8ipf.html @@ -0,0 +1,436 @@ + + + + + + + + File IPNWB_Debugging.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File IPNWB_Debugging.ipf

+

Holds functions for debugging.

+
+

Functions

+
+
+variable ASSERT_TS(variable var, string errorMsg)
+

Low overhead function to check assertions (threadsafe variant)

+

+Example usage: 

ASSERT_TS(DataFolderExistsDFR(dfr), "MyFunc: dfr does not exist")
+do something with dfr
+
+
+

+

Unlike ASSERT() this function does not print a stacktrace or jumps into the debugger. The reasons are Igor Pro limitations. Therefore it is advised to prefix errorMsg with the current function name.

+
+
Parameters:
+
    +

  • var – if zero an error message is printed into the history and procedure execution is aborted, nothing is done otherwise.

    • +

  • errorMsg – error message to output in failure case

    • +
+
+
+
+ +
+
+variable DEBUGPRINTv(variable var, string format = defaultValue)
+

Output debug information and return the parameter var.

+

Debug function especially designed for usage in return statements.

+

For example calling the following function 

Function doStuff()
+ variable var = 1 + 2
+ return DEBUGPRINTv(var)
+End
+
+
+ will output 
DEBUG doStuff(...)#L5: return value 3
+
+
+ to the history.

+
+
Parameters:
+
    +

  • var – numerical argument for debug output

    • +

  • format – optional format string to override the default of “%g”

    • +
+
+
+
+ +
+
+string DEBUGPRINTs(string str, string format = defaultValue)
+

Output debug information and return the parameter str.

+

Debug function especially designed for usage in return statements.

+

For example calling the following function 

Function/s doStuff()
+ variable str= "a" + "b"
+ return DEBUGPRINTs(str)
+End
+
+
+ will output 
DEBUG doStuff(...)#L5: return value ab
+
+
+ to the history.

+
+
Parameters:
+
    +

  • str – string argument for debug output

    • +

  • format – optional format string to override the default of “%s”

    • +
+
+
+
+ +
+
+variable DEBUGPRINT(string msg, variable var = defaultValue, string str = defaultValue, string format = defaultValue)
+

Generic debug output function.

+

Outputs variables and strings with optional format argument.

+

Examples: 

DEBUGPRINT("before a possible crash")
+DEBUGPRINT("some variable", var=myVariable)
+DEBUGPRINT("my string", str=myString)
+DEBUGPRINT("Current state", var=state, format="%.5f")
+
+
+

+
+
Parameters:
+
    +

  • msg – descriptive string for the debug message

    • +

  • var – variable

    • +

  • str – string

    • +

  • format – format string overrides the default of “%g” for variables and “%s” for strings

    • +
+
+
+
+ +
+
+variable DEBUG_TIMER_START()
+

Start a timer for performance measurements.

+

Usage: 

variable referenceTime = DEBUG_TIMER_START()
+// part one to benchmark
+DEBUGPRINT_ELAPSED(referenceTime)
+// part two to benchmark
+DEBUGPRINT_ELAPSED(referenceTime)
+
+
+

+
+ +
+
+variable DEBUGPRINT_ELAPSED(variable referenceTime)
+

Print the elapsed time for performance measurements.

+

+

See also

+

DEBUG_TIMER_START()

+
+

+
+ +
+
+variable EnableDebugMode()
+

Enable debug mode.

+
+ +
+
+variable DisableDebugMode()
+

Disable debug mode.

+
+ +
+
+variable DEBUG_STOREFUNCTION()
+
+ +
+
+

Variables

+
+
+static const string functionReturnMessage = "return value"
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_i_p_n_w_b___h_d_f5_helpers_8ipf.html b/file/_i_p_n_w_b___h_d_f5_helpers_8ipf.html new file mode 100644 index 0000000000..78561ddaba --- /dev/null +++ b/file/_i_p_n_w_b___h_d_f5_helpers_8ipf.html @@ -0,0 +1,774 @@ + + + + + + + + File IPNWB_HDF5Helpers.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File IPNWB_HDF5Helpers.ipf

+

H5 Wrapper functions for convenient use of the HDF5 operations

+
+

Unnamed Group

+
+
+static const double kHDF5DataInfoVersion = 1000
+

Taken from HDF5 Browser.ipf

+

Included here for convenience.

+
+ +
+
+static const double H5S_MAX_RANK = 32
+
+ +
+
+static variable InitHDF5DataInfo(HDF5DataInfo *di)
+
+ +
+
+

Functions

+
+
+variable H5_WriteTextDataset(variable locationID, string name, string str = defaultValue, WaveTextOrNull wvText = defaultValue, variable overwrite = defaultValue, variable compressionMode = defaultValue, variable skipIfExists = defaultValue, variable writeIgorAttr = defaultValue, variable appendData = defaultValue, variable refMode = defaultValue)
+

Write a string or text wave into a HDF5 dataset.

+

+Only one of str or wvText can be given.

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier, can be a file or group

    • +

  • name – Name of the HDF5 dataset

    • +

  • str – Contents to write into the dataset

    • +

  • wvText – Contents to write into the dataset

    • +

  • overwrite – [optional, defaults to false] Should existing datasets be overwritten

    • +

  • compressionMode – [optional, defaults to NO_COMPRESSION] Type of compression to use, one of CompressionMode

    • +

  • skipIfExists – [optional, defaults to false] Do nothing if the dataset already exists

    • +

  • writeIgorAttr – [optional, defaults to false] Add Igor specific attributes to the dataset, see the /IGOR flag of HDF5SaveData

    • +

  • appendData – [optional, defaults to -1] Set the dimension to append to within the given dataset (requires compression)

    • +

  • refMode – [optional, defaults to NO_REFERENCE] Set refMode, one in ReferenceMode (DisplayHelpTopic “Saving Reference Data”)

    • +
+
+
+
+ +
+
+variable H5_WriteDataset(variable locationID, string name, variable var = defaultValue, variable varType = defaultValue, WaveOrNull wv = defaultValue, variable overwrite = defaultValue, variable compressionMode = defaultValue, variable skipIfExists = defaultValue, variable writeIgorAttr = defaultValue, variable appendData = defaultValue)
+

Write a variable or text wave into a HDF5 dataset.

+

+Only one of var or wv can be given.

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier, can be a file or group

    • +

  • name – Name of the HDF5 dataset

    • +

  • var – Contents to write into the dataset

    • +

  • varType – Type of the data, must be given if var is supplied. See IgorTypes

    • +

  • wv – Contents to write into the dataset

    • +

  • overwrite – [optional, defaults to false] Should existing datasets be overwritten

    • +

  • compressionMode – [optional, defaults to NO_COMPRESSION] Type of compression to use, one of CompressionMode

    • +

  • skipIfExists – [optional, defaults to false] Do nothing if the dataset already exists

    • +

  • writeIgorAttr – [optional, defaults to false] Add Igor specific attributes to the dataset, see the /IGOR flag of HDF5SaveData

    • +

  • appendData – [optional, defaults to -1] Set the dimension to append to within the given dataset (requires compression)

    • +
+
+
+
+ +
+
+static wave H5_GetChunkSizes(wave wv, variable compressionMode)
+

Return a wave for the valid chunk sizes of each dimension taking into account the compression mode.

+
+ +
+
+static variable H5_WriteDatasetLowLevel(variable locationID, string name, wave wv, variable overwrite, variable compressionMode, variable skipIfExists, variable writeIgorAttr, variable appendData, variable refMode)
+

+

See also

+

H5_WriteTextDataset or H5_WriteDataset

+
+

+
+ +
+
+variable H5_WriteTextAttribute(variable locationID, string attrName, string path, string list = defaultValue, string str = defaultValue, variable overwrite = defaultValue, variable refMode = defaultValue)
+

Attach a text attribute to the given location.

+

+Only one of str or list can be given.

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier, can be a file, group or dataset

    • +

  • attrName – Name of the attribute

    • +

  • path – Additional path on top of locationID which identifies the object onto which the attribute should be attached.

    • +

  • list – Contents to write into the attribute, list will be always written as 1D-array

    • +

  • str – Contents to write into the attribute

    • +

  • overwrite – [optional, defaults to false] Should existing attributes be overwritten

    • +

  • refMode – [optional, defaults to 0] Set refMode, one in ReferenceMode (DisplayHelpTopic “Saving Reference Data”)

    • +
+
+
+
+ +
+
+variable H5_WriteAttribute(variable locationID, string attrName, string path, variable var, variable varType, variable overwrite = defaultValue)
+

Attach a numerical attribute to the given location.

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier, can be a file, group or dataset

    • +

  • attrName – Name of the attribute

    • +

  • path – Additional path on top of locationID which identifies the object onto which the attribute should be attached.

    • +

  • var – Contents to write into the attribute

    • +

  • varType – Type of the attribute, see IgorTypes

    • +

  • overwrite – [optional, defaults to false] Should existing attributes be overwritten

    • +
+
+
+
+ +
+
+variable H5_CreateSoftLink(variable locationID, string path, string target)
+

Create a link to a group.

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier, can be a file, group or dataset

    • +

  • path – Name of the link

    • +

  • target – The linked destination

    • +
+
+
+
+ +
+
+variable H5_OpenFile(string discLocation, variable write = defaultValue)
+

Open HDF5 file and return ID.

+
+
Parameters:
+
    +

  • discLocation – full path to nwb file

    • +

  • write – open file for writing. default is readonly.

    • +
+
+
Returns:
+

ID for referencing open hdf5 file

+
+
+
+ +
+
+variable H5_CloseFile(variable fileID)
+

Close HDF5 file.

+
+
Parameters:
+

fileID – ID of open hdf5 file

+
+
Returns:
+

open state as true/false

+
+
+
+ +
+
+variable H5_IsFileOpen(variable fileID)
+

Return 1 if the given HDF5 file is already open, 0 otherwise.

+
+
Parameters:
+

fileID – HDF5 locationID from HDF5OpenFile.

+
+
+
+ +
+
+variable H5_DatasetExists(variable locationID, string name)
+

Return 1 if the given HDF5 dataset exists, 0 otherwise.

+
+
Parameters:
+
    +

  • locationID – [in] HDF5 identifier, can be a file or group

    • +

  • name – [in] Additional path on top of locationID which identifies the dataset

    • +
+
+
+
+ +
+
+wave H5_LoadDataset(variable locationID, string name)
+

Load a specified dataset as wave.

+
+
Parameters:
+
    +

  • locationID – [in] HDF5 identifier, can be a file or group

    • +

  • name – [in] path on top of locationID which identifies the dataset

    • +
+
+
Returns:
+

reference to wave containing loaded data

+
+
+
+ +
+
+wave H5_GetDatasetSize(variable locationID, string dataset)
+

Return the dimension sizes of the given dataset.

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier, can be a file or group

    • +

  • dataset – name of the dataset

    • +
+
+
Returns:
+

wave with the dimension sizes or an invalid wave reference

+
+
+
+ +
+
+variable H5_AttributeExists(variable locationID, string path, string attribute, variable *objectType = defaultValue)
+

Check if a given attribute exists.

+
+
Parameters:
+
    +

  • locationID – [in] HDF5 identifier, can be a file or group

    • +

  • path – [in] Additional path on top of locationID which identifies the group or dataset

    • +

  • attribute – [in] Name of the attribute

    • +

  • objectType – [out] [optional] Return the type of the element to which the attribute is attached to. Can be used for subsequent HDF5LoadData calls.

    • +
+
+
+
+ +
+
+wave H5_LoadAttribute(variable locationID, string path, string attribute)
+

Load the given attribute and return its contents.

+
+
Parameters:
+
    +

  • locationID – [in] HDF5 identifier, can be a file or group

    • +

  • path – [in] Additional path on top of locationID which identifies the group or dataset

    • +

  • attribute – [in] Name of the attribute to load

    • +
+
+
+
+ +
+
+variable H5_GroupExists(variable locationID, string path)
+

Return 1 if the given HDF5 group exists, 0 otherwise.

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier, can be a file or group

    • +

  • path – Additional path on top of locationID which identifies the group.

    • +
+
+
+
+ +
+
+variable H5_CreateGroupsRecursively(variable locationID, string fullPath)
+

Create all groups along the given path.

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier, can be a file or group

    • +

  • fullPath – Additional path on top of locationID which identifies the group

    • +
+
+
+
+ +
+
+variable H5_IsValidIdentifier(string name)
+

Return true if name is a valid hdf5 identifier.

+

This is more restrictive than the actual HDF5 library checks. See the BNF Grammar here.

+
+ +
+
+string H5_ListGroupMembers(variable locationID, string path)
+

List all datasets at path (non-recursively)

+
+
Parameters:
+
    +

  • locationID – [in] HDF5 identifier, can be a file or group

    • +

  • path – [in] Additional path on top of locationID which identifies the group

    • +
+
+
+
+ +
+
+string H5_ListGroups(variable fileID, string path)
+

List all groups inside a group (non-recursively)

+
+
Parameters:
+
    +

  • fileID – [in] HDF5 file identifier

    • +

  • path – [in] Full path to the group inside fileID

    • +
+
+
+
+ +
+
+variable H5_OpenGroup(variable locationID, string path)
+

Open the group reachable via locationID and path and return its ID.

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier, can be a file or group

    • +

  • path – Additional path on top of locationID which identifies the group

    • +
+
+
Returns:
+

the groupID of the opened group. Return NaN if the group did not exist.

+
+
+
+ +
+
+variable H5_FlushFile(variable fileID)
+

Flush the file contents to disc.

+
+
Parameters:
+

fileID – HDF5 file identifier

+
+
+
+ +
+
+string H5_GetLinkTarget(string discLocation, string path)
+

+
+Todo:
+

Needs HDF5 XOP support for reading link targets use HDF5LinkInfo

+
+ +

+
+ +
+
+string H5_GetLibraryVersion()
+

Return the HDF5 Library version.

+
+ +
+
+

Variables

+
+
+static const double H5_ATTRIBUTE_SIZE_LIMIT = 60e3
+
+ +
+
+static const double H5_CHUNK_SIZE = 8192
+
+ +
+
+
+struct HDF5DataInfo
+
+

Public Members

+
+
+uint32 version
+
+ +
+
+char structName[16]
+
+ +
+
+double datatype_class
+
+ +
+
+char datatype_class_str[32]
+
+ +
+
+double datatype_size
+
+ +
+
+double datatype_sign
+
+ +
+
+double datatype_order
+
+ +
+
+char datatype_str[64]
+
+ +
+
+double dataspace_type
+
+ +
+
+double ndims
+
+ +
+
+double dims[H5S_MAX_RANK]
+
+ +
+
+double maxdims[H5S_MAX_RANK]
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_i_p_n_w_b___include_8ipf.html b/file/_i_p_n_w_b___include_8ipf.html new file mode 100644 index 0000000000..fe3b2a2737 --- /dev/null +++ b/file/_i_p_n_w_b___include_8ipf.html @@ -0,0 +1,276 @@ + + + + + + + + File IPNWB_Include.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File IPNWB_Include.ipf

+

Main include.

+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_i_p_n_w_b___n_w_b_utils_8ipf.html b/file/_i_p_n_w_b___n_w_b_utils_8ipf.html new file mode 100644 index 0000000000..15f60e1d2b --- /dev/null +++ b/file/_i_p_n_w_b___n_w_b_utils_8ipf.html @@ -0,0 +1,665 @@ + + + + + + + + File IPNWB_NWBUtils.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File IPNWB_NWBUtils.ipf

+

NWB utility functions.

+
+

Unnamed Group

+
+
+variable GetNoCompression()
+

Convenience getters.

+

Igor Pro does not allow cross IM access to constants

+
+ +
+
+variable GetChunkedCompression()
+
+ +
+
+variable GetSingleChunkCompression()
+
+ +
+
+string CompressionModeToString(variable mode)
+
+ +
+
+

Functions

+
+
+string DetermineNamespace(string neurodata_type)
+

Determine the namespace of the given neurodata type.

+

Note: - core specification “2.2.0”

    +

  • hdmf-common “1.1.0”

    • +
+

+
+ +
+
+string GetTimeSeriesMissingFields(variable channelType, variable clampMode)
+

Return the initial values for the missing_fields attribute depending on the channel type, one of IPNWBChannelTypes, and the clamp mode, one in IPNWB_ClampModes.

+
+ +
+
+variable GetChannelTypeFromNeurodataType(string neurodata_type)
+

Derive the channel type, one of IPNWBChannelTypes, from the neurodata_type attribute and return it.

+
+
Parameters:
+

neurodata_type – string with neurodata type specification defined in nwb.icephys.json_

+
+
+
+ +
+
+variable GetClampModeFromNeurodataType(string neurodata_type)
+

Derive the clamp mode from the neurodata_type attribute and return it.

+
+
Parameters:
+

neurodata_type – string with neurodata type specification defined in nwb.icephys.json_

+
+
+
+ +
+
+string DetermineDataTypeFromProperties(variable channelType, variable clampMode)
+

Determine the neurodata type based on channel type and clamp mode.

+

+

See also

+

GetClampModeFromNeurodataType

+
+
+

See also

+

IPNWBChannelTypes

+
+
+

See also

+

IPNWB_ClampModes

+
+

+
+
Parameters:
+
    +

  • channelType – one in

    • +

  • clampMode – one in

    • +
+
+
Returns:
+

neurodata_type string with neurodata type specification defined in nwb.icephys.json_

+
+
+
+ +
+
+string ReadNWBVersion(variable fileID)
+

get the (major) version of the nwb file

+
+
Parameters:
+

fileID – id of open hdf5 file

+
+
Returns:
+

major version e.g. 1 or 2

+
+
+
+ +
+
+variable GetNWBMajorVersion(string version)
+

convert version string to major version

+

+

See also

+

GetNWBVersionString

+
+

+
+ +
+
+variable AnalyzeNWBVersion(string version, variable *version0, variable *version1, variable *version2)
+

convert version string to major and all minor numeric versions

+
+
Parameters:
+
    +

  • version – [in]

    • +

  • version0 – [out] numeric first part of the version string (major Version)

    • +

  • version1 – [out] numeric second part of the version string (minor Version)

    • +

  • version2 – [out] numeric third part of the version string (sub Version)

    • +
+
+
Returns:
+

analyzed numeric versions

+
+
+
+ +
+
+variable EnsureValidNWBVersion(variable version)
+
+ +
+
+string LoadSpecification(string specLoc, string specName)
+

Load the NWB specification from files in the main directory.

+

Note: Open, FbinRead and Close are not threadsafe

+
+
Parameters:
+
    +

  • specLoc – Igor Pro file path to specifications (Path Separator: “:”)

    • +

  • specName – specifications file identifier (without trailing *.json ending)

    • +
+
+
Returns:
+

JSON string

+
+
+
+ +
+
+string SpecificationsDiscLocation()
+

Return Folder of NWB:N specifications.

+

Note: This is typically located at the location of the IPNWB program ipf files. FunctionPath is not threadsafe

+
+ +
+
+string ReadTextAttributeAsList(variable locationID, string path, string name)
+

Read a text attribute as semicolon ; separated list.

+
+
Parameters:
+
    +

  • locationID – [in] HDF5 identifier, can be a file or group

    • +

  • path – [in] Additional path on top of locationID which identifies the group or dataset

    • +

  • name – [in] Name of the attribute to load

    • +
+
+
+
+ +
+
+wave ReadTextAttribute(variable locationID, string path, string name)
+

Read a text attribute as text wave, return a single element wave with PLACEHOLDER if it does not exist.

+
+
Parameters:
+
    +

  • locationID – [in] HDF5 identifier, can be a file or group

    • +

  • path – [in] Additional path on top of locationID which identifies the group or dataset

    • +

  • name – [in] Name of the attribute to load

    • +
+
+
+
+ +
+
+string ReadTextAttributeAsString(variable locationID, string path, string name)
+

Read a text attribute as string, return PLACEHOLDER if it does not exist.

+
+
Parameters:
+
    +

  • locationID – [in] HDF5 identifier, can be a file or group

    • +

  • path – [in] Additional path on top of locationID which identifies the group or dataset

    • +

  • name – [in] Name of the attribute to load

    • +
+
+
+
+ +
+
+variable ReadAttributeAsNumber(variable locationID, string path, string name)
+

Read a text attribute as number, return NaN if it does not exist.

+
+
Parameters:
+
    +

  • locationID – [in] HDF5 identifier, can be a file or group

    • +

  • path – [in] Additional path on top of locationID which identifies the group or dataset

    • +

  • name – [in] Name of the attribute to load

    • +
+
+
+
+ +
+
+wave ReadTextDataSet(variable locationID, string name)
+

Read a text dataset as text wave, return a single element wave with PLACEHOLDER if it does not exist.

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier, can be a file or group

    • +

  • name – Name of the HDF5 dataset

    • +
+
+
+
+ +
+
+string ReadTextDataSetAsString(variable locationID, string name)
+

Read a text dataset as string, return PLACEHOLDER if it does not exist.

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier, can be a file or group

    • +

  • name – Name of the HDF5 dataset

    • +
+
+
+
+ +
+
+variable ReadDataSetAsNumber(variable locationID, string name)
+

Read a text dataset as number, return NaN if it does not exist.

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier, can be a file or group

    • +

  • name – Name of the HDF5 dataset

    • +
+
+
+
+ +
+
+variable WriteTextDatasetIfSet(variable locationID, string name, string str, variable compressionMode = defaultValue)
+

Write a text dataset only if it is not equal to PLACEHOLDER.

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier, can be a file or group

    • +

  • name – Name of the HDF5 dataset

    • +

  • str – Contents to write into the dataset

    • +

  • compressionMode – [optional, defaults to NO_COMPRESSION] Type of compression to use, one of CompressionMode

    • +
+
+
+
+ +
+
+string GetNWBgroupPatchClampSeries(variable version)
+

get location of the patchclamp series acquisition object

+
+
Parameters:
+

version – target NWB version

+
+
Returns:
+

full path to patchclampseries group

+
+
+
+ +
+
+string GetNWBVersionString(variable version)
+

get NWB version for current Igor Pro implementation

+
+
Parameters:
+

version – maior NWB version e.g. 2

+
+
Returns:
+

full version string in the format (?:NWB-)?[1,2]\.[0-9](?:\.[0-9])?[b]?

+
+
+
+ +
+
+variable GetNWBVersion()
+

get latest supported NWB version

+
+
Returns:
+

maior version

+
+
+
+ +
+
+string GetHistoryAndLogFileDatasetName(variable version)
+

Return the name of the history dataset.

+
+ +
+
+

Variables

+
+
+static const string NWB_PATCHCLAMPSERIES_V1 = "/acquisition/timeseries"
+
+ +
+
+static const string NWB_PATCHCLAMPSERIES_V2 = "/acquisition"
+
+ +
+
+static const string NWB_VERSION_V1 = "NWB-1.0.5"
+
+ +
+
+static const string NWB_VERSION_V2 = "2.2.4"
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_i_p_n_w_b___reader_8ipf.html b/file/_i_p_n_w_b___reader_8ipf.html new file mode 100644 index 0000000000..c24402ca24 --- /dev/null +++ b/file/_i_p_n_w_b___reader_8ipf.html @@ -0,0 +1,678 @@ + + + + + + + + File IPNWB_Reader.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File IPNWB_Reader.ipf

+

Generic functions related to import from the NeuroDataWithoutBorders format.

+
+

Functions

+
+
+string ReadDevices(variable fileID, variable version)
+

List devices in given hdf5 file.

+
+
Parameters:
+
    +

  • fileID – identifier of open HDF5 file

    • +

  • version – major NWB version

    • +
+
+
Returns:
+

comma separated list of devices

+
+
+
+ +
+
+string ReadElectrodeName(string discLocation, string seriesPath, variable version)
+

return name of electrode

+

+

See also

+

AddElectrode

+
+

+
+
Parameters:
+
    +

  • discLocation – full path to file in Igor disc path notation

    • +

  • seriesPath – Full Path inside HDF5 structure to TimeSeries group

    • +

  • version – major NWB version

    • +
+
+
Returns:
+

the name of the electrode or “” for unassociated channels

+
+
+
+ +
+
+string ReadLabNoteBooks(variable fileID)
+

List groups inside /general/labnotebook.

+
+
Parameters:
+

fileID – identifier of open HDF5 file

+
+
Returns:
+

list with name of all groups inside /general/labnotebook/*

+
+
+
+ +
+
+string ReadAcquisition(variable fileID, variable version)
+

List all acquisition channels.

+
+
Parameters:
+
    +

  • fileID – identifier of open HDF5 file

    • +

  • version – NWB major version

    • +
+
+
Returns:
+

comma separated list of channels

+
+
+
+ +
+
+string ReadStimulus(variable fileID)
+

List all stimulus channels.

+
+
Parameters:
+

fileID – identifier of open HDF5 file

+
+
Returns:
+

comma separated list of channels

+
+
+
+ +
+
+string ReadStimsets(variable fileID)
+

List all stimsets.

+
+
Parameters:
+

fileID – identifier of open HDF5 file

+
+
Returns:
+

comma separated list of contents of the stimset group

+
+
+
+ +
+
+variable AnalyseChannelName(string channel, ReadChannelParams *p)
+

Try to extract information from channel name string.

+
+
Parameters:
+
    +

  • channel – [in] Input channel name in form data_00000_TTL1_3

    • +

  • p – [out] ReadChannelParams structure to get filled

    • +
+
+
+
+ +
+
+variable LoadSourceAttribute(variable locationID, string channel, ReadChannelParams *p)
+

Read parameters from source attribute.

+

Function is NWBv1 specific

+

See also

+

LoadSweepNumber

+
+

+
+
Parameters:
+
    +

  • locationID – [in] HDF5 group specified channel is a member of

    • +

  • channel – [in] channel to load

    • +

  • p – [out] ReadChannelParams structure to get filled

    • +
+
+
+
+ +
+
+variable LoadSweepNumber(variable locationID, string channel, variable version)
+

Load sweep number from specified channel name.

+
+
Parameters:
+
    +

  • locationID – id of an open hdf5 group containing channel

    • +

  • channel – name of channel for which sweep number is loaded

    • +

  • version – NWB maior version

    • +
+
+
Returns:
+

sweep number

+
+
+
+ +
+
+wave LoadDataWave(variable locationID, string channel, string path = defaultValue)
+

Load data wave from specified path.

+
+
Parameters:
+
    +

  • locationID – id of an open hdf5 group containing channel id can also be of an open nwb file. In this case specify (optional) path.

    • +

  • channel – name of channel for which data attribute is loaded

    • +

  • path – use path to specify group inside hdf5 file where ./channel/data is located.

    • +
+
+
Returns:
+

reference to free wave containing loaded data

+
+
+
+ +
+
+wave LoadTimeseries(variable locationID, string path, variable version)
+

Load single TimeSeries data as a wave from NWB_PATCHCLAMPSERIES_V[12].

+
+
Parameters:
+
    +

  • locationID – id of an open hdf5 group or file

    • +

  • path – name or path of TimeSeries for which data is loaded

    • +

  • version – NWB major version

    • +
+
+
Returns:
+

reference to wave containing loaded data

+
+
+
+ +
+
+wave LoadStimulus(variable locationID, string path)
+

Load single TimeSeries data as a wave from NWB_STIMULUS_PRESENTATION.

+
+
Parameters:
+
    +

  • locationID – id of an open hdf5 group or file

    • +

  • path – name or path of TimeSeries for which data is loaded

    • +
+
+
Returns:
+

reference to wave containing loaded data

+
+
+
+ +
+
+variable OpenAcquisition(variable fileID, variable version)
+

Open hdf5 group containing acquisition channels.

+
+
Parameters:
+
    +

  • fileID – id of an open hdf5 group or file

    • +

  • version – NWB major version

    • +
+
+
Returns:
+

id of hdf5 group

+
+
+
+ +
+
+variable OpenStimulus(variable fileID)
+

Open hdf5 group containing stimulus channels.

+
+
Parameters:
+

fileID – id of an open hdf5 group or file

+
+
Returns:
+

id of hdf5 group

+
+
+
+ +
+
+variable OpenStimset(variable fileID)
+

Open hdf5 group containing stimsets.

+
+
Parameters:
+

fileID – id of an open hdf5 group or file

+
+
Returns:
+

id of hdf5 group

+
+
+
+ +
+
+variable StimsetPathExists(variable fileID)
+

Check if the path to the stimsets exist in the NWB file.

+
+ +
+
+variable ReadTopLevelInfo(variable fileID, ToplevelInfo *toplevelInfo)
+

Read in all NWB datasets from the root group (‘/’)

+
+ +
+
+variable ReadGeneralInfo(variable fileID, GeneralInfo *generalinfo)
+

Read in all standard NWB datasets from the group ‘/general’.

+
+ +
+
+variable ReadSubjectInfo(variable fileID, SubjectInfo *subjectInfo)
+

Read in all NWB datasets from the root group ‘/general/subject’.

+
+ +
+
+variable ReadTimeSeriesProperties(variable locationID, string channel, TimeSeriesProperties *tsp)
+

Read the TimeSeries properties from the given group in locationID.

+
+
Parameters:
+
    +

  • locationID – [in] TimeSeries group ID

    • +

  • channel – [in] TimeSeries group name

    • +

  • tsp – [out] TimeSeriesProperties structure

    • +
+
+
+
+ +
+
+string ReadNeuroDataType(variable fileID, string name)
+

Read nwb data type.

+

+

See also

+

WriteNeuroDataType

+
+

+
+
Parameters:
+
    +

  • fileID – HDF5 identifier of file (not group)

    • +

  • name – Path to element who’s DataType is queried

    • +
+
+
Returns:
+

string with data type (e.g. uint, DynamicTable, SweepTable)

+
+
+
+ +
+
+std::tuple<WaveOrNull, WaveTextOrNull> LoadSweepTable(variable locationID, variable version)
+

Return the two SweepTable data columns sweep_number and series

+

+
+Todo:
+

Allow Executions for files with missing SweepTable entry using LoadSweepNumber

+
+ +

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier

    • +

  • version – major NWB version

    • +
+
+
Returns:
+

sweep_number and path to TimeSeries as waves

+
+
+
+ +
+
+wave LoadEpochTable(string nwbFilePath)
+

Return the epoch table as wave reference wave.

+

Due to IP limitations, the NWB file path of the closed file must be passed.

+

See GetEpochsWaveInternal() for the wave layout.

+
+ +
+
+static wave GetTimeseriesProperties(variable locationID, WaveText timeseries, string name, string attrName = defaultValue)
+

Return timeseries properties which can be a dataset or attribute as wave.

+
+ +
+
+static wave GetEpochsWaveInternal(WaveText timeseries)
+

Return a free wave reference wave.

+

ROWS:

    +

  • One entry for each unique timeseries path, with dimension label

    • +
+

+

Each row will hold a Nx4 wave for the epoch info of each row.

+

+

See also

+

GetEpochsWave()

+
+

+
+ +
+
+static wave ExpandRuggedVector(WaveText data_rugged, wave index, string sep)
+

Expand data from rugged DynamicTable column entry.

+

See also https://github.com/hdmf-dev/hdmf-common-schema/blob/main/common/table.yaml#L4.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_i_p_n_w_b___structures_8ipf.html b/file/_i_p_n_w_b___structures_8ipf.html new file mode 100644 index 0000000000..c51703bee7 --- /dev/null +++ b/file/_i_p_n_w_b___structures_8ipf.html @@ -0,0 +1,918 @@ + + + + + + + + File IPNWB_Structures.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File IPNWB_Structures.ipf

+
+

Functions

+
+
+variable InitWriteChannelParams(WriteChannelParams *p)
+

Initialize WriteChannelParams structure.

+
+ +
+
+variable InitReadChannelParams(ReadChannelParams *p)
+

Initialization routine for InitReadChannelParams.

+
+ +
+
+variable InitGeneralInfo(GeneralInfo *gi)
+

Initialization routine for GeneralInfo.

+
+ +
+
+variable InitSubjectInfo(SubjectInfo *si)
+

Initialization routine for SubjectInfo.

+
+ +
+
+variable InitToplevelInfo(ToplevelInfo *ti, variable version)
+

Initialization routine for ToplevelInfo.

+
+
Parameters:
+
    +

  • ti – TopLevelInfo Structure

    • +

  • version – [optional] defaults to latest version specified in NWB_VERSION_LATEST

    • +
+
+
+
+ +
+
+variable InitTimeSeriesProperties(TimeSeriesProperties *tsp, variable channelType, variable clampMode)
+

Initialization of TimeSeriesProperties.

+
+
Parameters:
+
+
+
+
+ +
+
+variable InitDynamicTable(DynamicTable *dt)
+
+ +
+
+variable InitElementIdentifiers(ElementIdentifiers *eli)
+
+ +
+
+variable InitVectorData(VectorData *vd)
+
+ +
+
+variable InitVectorIndex(VectorIndex *vi)
+
+ +
+
+
+struct WriteChannelParams
+

Helper structure for WriteSingleChannel()

+
+

Public Members

+
+
+string device
+

name of the measure device, e.g. “ITC18USB_Dev_0”

+
+ +
+
+string stimSet
+

name of the template simulus set

+
+ +
+
+string channelSuffix
+

custom channel suffix, in case the channel number is ambiguous

+
+ +
+
+string channelSuffixDesc
+

description of the channel suffix, will be added to the source attribute

+
+ +
+
+variable samplingRate
+

sampling rate in Hz

+
+ +
+
+variable startingTime
+

timestamp since Igor Pro epoch in UTC of the start of this measurement

+
+ +
+
+variable sweep
+

running number for each measurement

+
+ +
+
+variable channelType
+

channel type, one of IPNWBChannelTypes

+
+ +
+
+variable channelNumber
+

running number of the channel

+
+ +
+
+variable electrodeNumber
+

electrode identifier the channel was acquired with

+
+ +
+
+string electrodeName
+

electrode identifier the channel was acquired with (string version)

+
+ +
+
+variable clampMode
+

clamp mode, one of IPNWB_ClampModes

+
+ +
+
+variable groupIndex
+

Should be filled with the result of GetNextFreeGroupIndex(locationID, path) before

+
+ +
+
+WAVE data
+

channel data

+

the first call and must stay constant for all channels for this measurement. If NaN an automatic solution is provided.

+
+ +
+
+WaveText epochs
+

epoch information (optional)

+
+ +
+
+ +
+
+struct ReadChannelParams
+

Loader structure analog to WriteChannelParams.

+
+

Public Members

+
+
+string device
+

name of the measure device, e.g. “ITC18USB_Dev_0”

+
+ +
+
+string channelSuffix
+

custom channel suffix, in case the channel number is ambiguous

+
+ +
+
+variable sweep
+

running number for each measurement

+
+ +
+
+variable channelType
+

channel type, one of IPNWBChannelTypes

+
+ +
+
+variable channelNumber
+

running number of the hardware channel

+
+ +
+
+variable electrodeNumber
+

electrode identifier the channel was acquired with

+
+ +
+
+variable groupIndex
+

constant for all channels in this measurement.

+
+ +
+
+variable ttlBit
+

additional information to make the channel number unambigous, in the range 2^0, …, 2^3

+
+ +
+
+variable samplingRate
+

sampling rate in Hz

+
+ +
+
+ +
+
+struct GeneralInfo
+

Structure to hold all properties of the NWB file directly below /general

+
+

Public Members

+
+
+string session_id
+
+ +
+
+string experimenter
+
+ +
+
+string institution
+
+ +
+
+string lab
+
+ +
+
+string related_publications
+
+ +
+
+string notes
+
+ +
+
+string experiment_description
+
+ +
+
+string data_collection
+
+ +
+
+string stimulus
+
+ +
+
+string pharmacology
+
+ +
+
+string surgery
+
+ +
+
+string protocol
+
+ +
+
+string virus
+
+ +
+
+string slices
+
+ +
+
+ +
+
+struct SubjectInfo
+

Structure to hold all properties of the NWB file directly below /general/subject

+
+

Public Members

+
+
+string age
+
+ +
+
+string date_of_birth
+
+ +
+
+string description
+
+ +
+
+string genotype
+
+ +
+
+string sex
+
+ +
+
+string species
+
+ +
+
+string subject_id
+
+ +
+
+string weight
+
+ +
+
+ +
+
+struct ToplevelInfo
+

Structure to hold all properties of the NWB file directly below /

+
+

Public Members

+
+
+string session_description
+
+ +
+
+variable session_start_time
+

timestamp in seconds since Igor Pro epoch, UTC timezone

+
+ +
+
+string nwb_version
+

NWB specification version.

+
+ +
+
+string identifier
+
+ +
+
+WaveText file_create_date
+
+ +
+
+ +
+
+struct TimeSeriesProperties
+

Holds class specific entries for TimeSeries objects.

+

Usage for writers 

STRUCT TimeSeriesProperties tsp
+InitTimeSeriesProperties(tsp, channelType, clampMode)
+AddProperty(tsp, "gain", 1.23456)
+// more calls tp AddProperty()
+WriteSingleChannel(locationID, path, p, tsp)
+
+
+

+

and for readers 

STRUCT TimeSeriesProperties tsp
+InitTimeSeriesProperties(tsp, channelType, clampMode)
+ReadTimeSeriesProperties(groupID, channel, tsp)
+
+
+

+
+

Public Members

+
+
+WaveText names
+
+ +
+
+WAVE data
+
+ +
+
+WaveText unit
+
+ +
+
+WAVE isCustom
+

NWBv1: 1 if the entry should be marked as NWB custom.

+
+ +
+
+string missing_fields
+

keep track of missing fields while reading

+
+ +
+
+string neurodata_type
+
+ +
+
+ +
+
+struct DynamicTable
+
+

Public Members

+
+
+string colnames
+
+ +
+
+string description
+
+ +
+
+string data_type
+
+ +
+
+ +
+
+struct ElementIdentifiers
+
+

Public Members

+
+
+string data_type
+
+ +
+
+ +
+
+struct VectorData
+
+

Public Members

+
+
+string description
+
+ +
+
+string data_type
+
+ +
+
+string path
+
+ +
+
+ +
+
+struct VectorIndex
+
+

Public Members

+
+
+string data_type
+
+ +
+
+VectorData target
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_i_p_n_w_b___utils_8ipf.html b/file/_i_p_n_w_b___utils_8ipf.html new file mode 100644 index 0000000000..ac984b8fd2 --- /dev/null +++ b/file/_i_p_n_w_b___utils_8ipf.html @@ -0,0 +1,928 @@ + + + + + + + + File IPNWB_Utils.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File IPNWB_Utils.ipf

+

Utility functions.

+
+

Functions

+
+
+variable IsFinite(variable var)
+

Returns 1 if var is a finite/normal number, 0 otherwise.

+
+ +
+
+variable IsNaN(variable var)
+

Returns 1 if var is a NaN, 0 otherwise.

+
+ +
+
+variable isNull(string *str)
+

Returns 1 if str is null, 0 otherwise.

+
+
Parameters:
+

str – must not be a SVAR

+
+
+
+ +
+
+variable isEmpty(string *str)
+

Returns one if str is empty or null, zero otherwise.

+
+
Parameters:
+

str – must not be a SVAR

+
+
+
+ +
+
+variable DateTimeInUTC()
+

Return the seconds since Igor Pro epoch (1/1/1904) in UTC time zone.

+
+ +
+
+variable IsInteger(variable var)
+

Returns one if var is an integer and zero otherwise.

+
+ +
+
+string GetISO8601TimeStamp(variable secondsSinceIgorEpoch = defaultValue, variable numFracSecondsDigits = defaultValue, variable localTimeZone = defaultValue)
+

Return a string in ISO 8601 format with timezone UTC.

+
+
Parameters:
+
    +

  • secondsSinceIgorEpoch – [optional, defaults to number of seconds until now] Seconds since the Igor Pro epoch (1/1/1904) in UTC (or local time zone depending on localTimeZone)

    • +

  • numFracSecondsDigits – [optional, defaults to zero] Number of sub-second digits

    • +

  • localTimeZone – [optional, defaults to false] Use the local time zone instead of UTC

    • +
+
+
+
+ +
+
+variable ParseUnit(string unitWithPrefix, string *prefix, variable *numPrefix, string *unit)
+

Parse a simple unit with prefix into its prefix and unit.

+

Note: The currently allowed units are the SI base units [1] and other common derived units. And in accordance to SI definitions, “kg” is a base unit. “Simple” unit means means one unit with prefix, not e.g. “km/s”.

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name

Symbol

Numerical value

yotta

Y

1e24

zetta

Z

1e21

exa

E

1e18

peta

P

1e15

tera

T

1e12

giga

G

1e9

mega

M

1e6

kilo

k

1e3

hecto

h

1e2

deca

da

1e1

deci

d

1e-1

centi

c

1e-2

milli

m

1e-3

micro

mu

1e-6

nano

n

1e-9

pico

p

1e-12

femto

f

1e-15

atto

a

1e-18

zepto

z

1e-21

yocto

y

1e-24

+

+

[1]: 8th edition of the SI Brochure (2014), http://www.bipm.org/en/publications/si-brochure

+
+
Parameters:
+
    +

  • unitWithPrefix – [in] string to parse, examples are “ms” or “kHz”

    • +

  • prefix – [out] symbol of decimal multipler of the unit, see below or [1] chapter 3 for the full list

    • +

  • numPrefix – [out] numerical value of the decimal multiplier

    • +

  • unit – [out] unit

    • +
+
+
+
+ +
+
+variable GetDecimalMultiplierValue(string prefix)
+

Return the numerical value of a SI decimal multiplier.

+

+

See also

+

ParseUnit

+
+

+
+ +
+
+variable IsTextWave(wave wv)
+

Return 1 if the wave is a text wave, zero otherwise.

+
+ +
+
+variable IsNumericWave(wave wv)
+

Return 1 if the wave is a numeric wave, zero otherwise.

+
+ +
+
+string RemovePrefixFromListItem(string prefix, string list, string listSep = defaultValue)
+

Remove a string prefix from each list item and return the new list.

+
+ +
+
+wave MakeWaveFree(wave wv)
+

Turn a persistent wave into a free wave.

+
+ +
+
+string UniqueWaveName(dfref dfr, string baseName)
+

Returns a wave name not used in the given datafolder.

+

Basically a datafolder aware version of UniqueName for datafolders

+
+
Parameters:
+
    +

  • dfr – datafolder reference where the new datafolder should be created

    • +

  • baseName – first part of the wave name, might be shorted due to Igor Pro limitations

    • +
+
+
+
+ +
+
+variable DataFolderExistsDFR(dfref dfr)
+

Checks if the datafolder referenced by dfr exists.

+

Unlike DataFolderExists() a dfref pointing to an empty (“”) dataFolder is considered non-existing here.

+
+
Returns:
+

one if dfr is valid and references an existing or free datafolder, zero otherwise Taken from http://www.igorexchange.com/node/2055

+
+
+
+ +
+
+string GetBaseName(string filePathWithSuffix, string sep = defaultValue)
+

Return the base name of the file.

+

Given path/file.suffix this gives file.

+
+
Parameters:
+
    +

  • filePathWithSuffix – full path

    • +

  • sep – [optional, defaults to “:”] character separating the path components

    • +
+
+
+
+ +
+
+string GetFileSuffix(string filePathWithSuffix, string sep = defaultValue)
+

Return the file extension (suffix)

+

Given path/file.suffix this gives suffix.

+
+
Parameters:
+
    +

  • filePathWithSuffix – full path

    • +

  • sep – [optional, defaults to “:”] character separating the path components

    • +
+
+
+
+ +
+
+string GetFolder(string filePathWithSuffix, string sep = defaultValue)
+

Return the folder of the file.

+

Given /path/file.suffix this gives path/.

+
+
Parameters:
+
    +

  • filePathWithSuffix – full path

    • +

  • sep – [optional, defaults to “:”] character separating the path components

    • +
+
+
+
+ +
+
+string GetFile(string filePathWithSuffix, string sep = defaultValue)
+

Return the filename with extension.

+

Given path/file.suffix this gives file.suffix.

+
+
Parameters:
+
    +

  • filePathWithSuffix – full path

    • +

  • sep – [optional, defaults to “:”] character separating the path components

    • +
+
+
+
+ +
+
+variable ParseISO8601TimeStamp(string timestamp)
+

Parse a ISO8601 timestamp, e.g. created by GetISO8601TimeStamp(), and returns the number of seconds, including fractional parts, since Igor Pro epoch (1/1/1904) in UTC time zone.

+

Accepts also the following specialities:

    +

  • no UTC timezone specifier (UTC timezone is still used)

    • +

  • /T between date and time

    • +

  • fractional seconds

    • +

  • ,/. as decimal separator

    • +
+

+
+ +
+
+string TextWaveToList(WaveText txtWave, string sep)
+

Convert a text wave to string list.

+
+ +
+
+string ResolveAlias(string path, string pathName = defaultValue)
+

Recursively resolve shortcuts to files/directories.

+
+
Returns:
+

full path or an empty string if the file does not exist or the shortcut points to a non existing file/folder

+
+
+
+ +
+
+variable FileExists(string filepath)
+

Check wether the given path points to an existing file.

+

Resolves shortcuts and symlinks recursively.

+
+ +
+
+variable FolderExists(string folderpath)
+

Check wether the given path points to an existing folder.

+
+ +
+
+string AddPrefixToEachListItem(string prefix, string list)
+

Add a string prefix to each list item and return the new list.

+
+ +
+
+variable NewRandomSeed()
+

Initializes the random number generator with a new seed between (0,1] The time base is assumed to be at least 0.1 microsecond precise, so a new seed is available every 0.1 microsecond.

+

Usage example for the case that one needs n non reproducible random numbers. Whenever the following code block is executed a new seed is set, resulting in a different series of numbers

+

Make/D/N=(n) newRandoms
+NewRandomSeed() // Initialize random number series with a new seed
+newRandoms[] = GetReproducibleRandom() // Get n randoms from the new series
+
+
+

+
+ +
+
+variable GetReproducibleRandom()
+

Return a random value in the range (0,1] which can be used as a seed for SetRandomSeed

+

Return a reproducible random number depending on the RNG seed.

+
+ +
+
+string GenerateRFC4122UUID()
+

Generate a version 4 UUID according to https://tools.ietf.org/html/rfc4122.

+

4.4.  Algorithms for Creating a UUID from Truly Random or
+      Pseudo-Random Numbers
+
+   The version 4 UUID is meant for generating UUIDs from truly-random or
+   pseudo-random numbers.
+
+   The algorithm is as follows:
+
+   o  Set the two most significant bits (bits 6 and 7) of the
+      clock_seq_hi_and_reserved to zero and one, respectively.
+
+   o  Set the four most significant bits (bits 12 through 15) of the
+      time_hi_and_version field to the 4-bit version number from
+      Section 4.1.3.
+
+   o  Set all the other bits to randomly (or pseudo-randomly) chosen
+      values.
+
+See Section 4.5 for a discussion on random numbers.
+
+[...]
+
+ In the absence of explicit application or presentation protocol
+ specification to the contrary, a UUID is encoded as a 128-bit object,
+ as follows:
+
+ The fields are encoded as 16 octets, with the sizes and order of the
+ fields defined above, and with each field encoded with the Most
+ Significant Byte first (known as network byte order).  Note that the
+ field names, particularly for multiplexed fields, follow historical
+ practice.
+
+ 0                   1                   2                   3
+  0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1
+ +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
+ |                          time_low                             |
+ +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
+ |       time_mid                |         time_hi_and_version   |
+ +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
+ |clk_seq_hi_res |  clk_seq_low  |         node (0-1)            |
+ +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
+ |                         node (2-5)                            |
+ +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
+
+[...]
+
+4.1.3.  Version
+
+   The version number is in the most significant 4 bits of the time
+   stamp (bits 4 through 7 of the time_hi_and_version field).
+
+   The following table lists the currently-defined versions for this
+   UUID variant.
+
+   Msb0  Msb1  Msb2  Msb3   Version  Description
+
+    0     0     0     1        1     The time-based version
+                                     specified in this document.
+
+    0     0     1     0        2     DCE Security version, with
+                                     embedded POSIX UIDs.
+
+    0     0     1     1        3     The name-based version
+                                     specified in this document
+                                     that uses MD5 hashing.
+
+    0     1     0     0        4     The randomly or pseudo-
+                                     randomly generated version
+                                     specified in this document.
+
+    0     1     0     1        5     The name-based version
+                                     specified in this document
+                                     that uses SHA-1 hashing.
+
+   The version is more accurately a sub-type; again, we retain the term
+   for compatibility.
+
+
+

+

See also https://www.rfc-editor.org/errata/eid3546 and https://www.rfc-editor.org/errata/eid1957 for some clarifications.

+
+ +
+
+variable HexToNumber(string ch)
+

Convert a hexadecimal character into a number.

+
+ +
+
+string NumberToHex(variable var)
+

Convert a number into hexadecimal.

+
+ +
+
+wave HexToBinary(string str)
+

Convert a string in hex format to an unsigned binary wave.

+

This function works on a byte level so it does not care about endianess.

+
+ +
+
+string num2strHighPrec(variable val, variable precision = defaultValue)
+

Converts a number to a string with specified precision (digits after decimal dot). This function is an extension for the regular num2str that is limited to 5 digits. Input numbers are rounded using the “round-half-to-even” rule to the given precision. The default precision is 5. If val is complex only the real part is converted to a string.

+
+
Parameters:
+
    +

  • val – [in] number that should be converted to a string

    • +

  • precision – [in] [optional, default 5] number of precision digits after the decimal dot using “round-half-to-even” rounding rule. Precision must be in the range 0 to 15.

    • +
+
+
Returns:
+

string with textual number representation

+
+
+
+ +
+
+variable ClearRTError()
+

Helper function for try/catch with AbortOnRTE.

+

Not clearing the RTE before calling AbortOnRTE will always trigger the RTE no matter what you do in that line.

+

Usage: 

try
+   ClearRTError()
+   myFunc(); AbortOnRTE
+catch
+  err = GetRTError(1)
+endtry
+
+
+

+

+
+ +
+
+string NormalizeToEOL(string str, string eol)
+

Normalize the line endings in the given string to either classic Mac OS/Igor Pro EOLs (\r) or Unix EOLs (\n)

+
+ +
+
+string GetStackTrace(string prefix = defaultValue)
+

Return a nicely formatted multiline stacktrace.

+
+ +
+
+string GetExperimentName()
+
+ +
+
+string GetExperimentFileType()
+

Return the experiment file type.

+
+ +
+
+string GetIgorProVersion()
+

Return the Igor Pro version string.

+
+ +
+
+string GetWindowsPath(string path)
+

Return the path converted to a windows style path.

+
+ +
+
+variable SetEpochsDimensionLabels(wave wv)
+
+ +
+
+wave GetUniqueEntries(wave wv, variable caseSensitive = defaultValue)
+

Returns an unsorted free wave with all unique entries from wv neglecting NaN/Inf.

+

uses built-in igor function FindDuplicates. Entries are deleted from left to right.

+
+ +
+
+string GetUniqueTextEntriesFromList(string list, string sep = defaultValue, variable caseSensitive = defaultValue)
+

Convenience wrapper around GetUniqueTextEntries() for string lists.

+
+ +
+
+static wave GetUniqueTextEntries(WaveText wv, variable caseSensitive = defaultValue)
+

Search and Remove Duplicates from Text Wave wv.

+

Duplicates are removed from left to right

+
+
Parameters:
+
    +

  • wv – text wave reference

    • +

  • caseSensitive – [optional] Indicates whether comparison should be case sensitive. defaults to True

    • +
+
+
Returns:
+

free wave with unique entries

+
+
+
+ +
+
+variable SetNumberInWaveNote(wave wv, string key, variable val, string format = defaultValue)
+

Updates the numeric value of key found in the wave note to val

+

+The expected wave note format is: key1:val1;key2:val2;

+
+
Parameters:
+
    +

  • wv – wave

    • +

  • key – key of the Key/Value pair

    • +

  • val – value of the Key/Value pair

    • +

  • format – [optional] printf compatible format string to set the conversion to string for val

    • +
+
+
+
+ +
+
+variable GetNumberFromWaveNote(wave wv, string key)
+

Returns the numeric value of key found in the wave note, returns NaN if it could not be found.

+

The expected wave note format is: key1:val1;key2:val2;

+
+ +
+
+
+struct Uuid
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_i_p_n_w_b___writer_8ipf.html b/file/_i_p_n_w_b___writer_8ipf.html new file mode 100644 index 0000000000..a2edcc920c --- /dev/null +++ b/file/_i_p_n_w_b___writer_8ipf.html @@ -0,0 +1,561 @@ + + + + + + + + File IPNWB_Writer.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File IPNWB_Writer.ipf

+

Generic functions related to export into the NeuroDataWithoutBorders format.

+
+

Functions

+
+
+variable CreateCommonGroups(variable locationID, ToplevelInfo *toplevelInfo, GeneralInfo *generalInfo = defaultValue, string subjectInfo = defaultValue)
+

Create and fill common HDF5 groups and datasets.

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier

    • +

  • toplevelInfo – [optional, see ToplevelInfo() for defaults] datasets directly below /

    • +

  • generalInfo – [optional, see GeneralInfo() for defaults] datasets directly below /general

    • +

  • subjectInfo – [optional, see SubjectInfo() for defaults] datasets below /general/subject

    • +
+
+
+
+ +
+
+variable CreateIntraCellularEphys(variable locationID, string filtering = defaultValue)
+

Create the HDF5 group for intracellular ephys.

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier

    • +

  • filtering – [optional, defaults to PLACEHOLDER] filtering information

    • +
+
+
+
+ +
+
+variable AddDevice(variable locationID, string name, variable version, string description)
+

Add an entry for the device name in the nwb file specified by locationID.

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier

    • +

  • name – name of device to create

    • +

  • version – major NWB version

    • +

  • description – a string describing the created device

    • +
+
+
Returns:
+

1 if a new device was created and 0 if it already existed

+
+
+
+ +
+
+variable AddElectrode(variable locationID, string name, variable version, string data, string device)
+

Add an entry for the electrode name with contents data

+
+ +
+
+variable AddModificationTimeEntry(variable locationID, variable version)
+

Add a modification timestamp to the NWB file.

+
+ +
+
+variable MarkAsCustomEntry(variable locationID, string name)
+

Mark a dataset/group as custom.

+

According to the NWB spec everything not required should be specifically marked. In NWBv2, schema extensions can be used to accomplish this.

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier

    • +

  • name – dataset or group name

    • +
+
+
+
+ +
+
+variable AddTimeSeriesUnitAndRes(variable locationID, string fullAbsPath, string unitWithPrefix, variable resolution = defaultValue, variable overwrite = defaultValue)
+

Add unit and resolution to TimeSeries dataset.

+

+

See also

+

ParseUnit

+
+

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier

    • +

  • fullAbsPath – absolute path to the TimeSeries dataset

    • +

  • unitWithPrefix – unit with optional prefix of the data in the TimeSeries,

    • +

  • resolution – [optional, defaults to NaN for unknown] experimental resolution

    • +

  • overwrite – [optional, defaults to false] should existing attributes be overwritten

    • +
+
+
+
+ +
+
+variable AddProperty(TimeSeriesProperties *tsp, string nwbProp, variable value, string unit = defaultValue)
+

Add a TimeSeries property to the tsp structure.

+
+ +
+
+variable AddCustomProperty(TimeSeriesProperties *tsp, string nwbProp, variable value)
+

Add a custom TimeSeries property to the names and data waves.

+

+

See also

+

MarkAsCustomEntry

+
+

+
+ +
+
+variable GetNextFreeGroupIndex(variable locationID, string path)
+

Return the next free group index of the format data_$NUM

+
+ +
+
+variable WriteSingleChannel(variable locationID, string path, variable version, WriteChannelParams *p, TimeSeriesProperties *tsp, variable compressionMode = defaultValue, string nwbFilePath = defaultValue)
+

Write the data of a single channel to the NWB file.

+
+
Parameters:
+
    +

  • locationID – HDF5 file identifier

    • +

  • path – Absolute path in the HDF5 file where the data should be stored

    • +

  • version – major NWB version

    • +

  • p – Filled WriteChannelParams structure

    • +

  • tsp – Filled TimeSeriesProperties structure

    • +

  • compressionMode – [optional, defaults to NO_COMPRESSION] Type of compression to use, one of CompressionMode

    • +

  • nwbFilePath – [optional, required only for epoch writing] disc location of the NWB file

    • +
+
+
Returns:
+

locationID, this is different from the parameter if epoch information was written

+
+
+
+ +
+
+static variable WriteEpochs(string nwbFilePath, WaveText epochs, string timeseries, variable startingTime, variable samplingRate)
+
+ +
+
+static variable AppendToEpochTable(string nwbFilePath, variable startTime, variable stopTime, WaveText tags, WaveText timeseries, wave startingTime, wave rate, variable treelevel)
+

Append an epoch to the TimeIntervals table.

+

Note: NWBv2 specific function

+
+
Parameters:
+
    +

  • nwbFilePath – HDF5 file path (required for writing the timeseries compound using a custom XOP)

    • +

  • startTime – start time of the epoch in seconds in the global time coordinate system (included in the range)

    • +

  • stopTime – stop time of the epoch in seconds in the global time coordinate system (not included in the range)

    • +

  • tags – text wave with strings for the epoch, format is unspecified

    • +

  • timeseries – absolute paths to existing timeseries groups

    • +

  • startingTime – timeseries starting time in s according to NWBv2 spec

    • +

  • rate – timeseries rate in Hz according to NWBv2 spec

    • +

  • treelevel – Tree level of the epoch

    • +
+
+
+
+ +
+
+static variable CreateDynamicTable(variable locationID, string path, DynamicTable *dt)
+

Create a Dynamic Table group at path.

+

Note: A dynamic table needs at least an id and a vectorData column

+
+
Returns:
+

NaN if the group already exists, 1 otherwise

+
+
+
+ +
+
+static variable AppendToSweepTable(variable locationID, string reference, variable sweepNumber)
+

Append a sweep to the sweep table.

+

Note: NWBv2 specific function

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier

    • +

  • reference – path to dataset where sweep is stored

    • +

  • sweepNumber – sweep number

    • +
+
+
+
+ +
+
+variable WriteSpecifications(variable locationID)
+

write NWB:N specifications that were used for creating this file

+

Note: non threadsafe due to limitations in LoadSpecification

+
+
Parameters:
+

locationID – open HDF5 file identifier

+
+
+
+ +
+
+variable WriteSpecification(variable locationID, string spec_name, string spec_version, string spec_location, string spec_start, string spec_include)
+

write a specifications group to NWB_SPECIFICATIONS and link its location in .specloc

+
+
Parameters:
+
    +

  • locationID – open HDF5 file identifier

    • +

  • spec_name – name of namespace, e.g. “core”

    • +

  • spec_version – version of added namespace as string

    • +

  • spec_location – Igor File Path to location of *.json files in IPNWB repository

    • +

  • spec_start – namespace.json declaration file

    • +

  • spec_include – “;” separated list of include files for defining extensions within the namespace

    • +
+
+
+
+ +
+
+variable WriteNeuroDataType(variable locationID, string path, string neurodata_type)
+

Write a NeuroDataType.

+

+

See also

+

ReadNeuroDataType

+
+

+
+
Parameters:
+
    +

  • locationID – HDF5 identifier

    • +

  • path – Path to element who’s DataType is queried

    • +

  • neurodata_type – String version of the data type that should get written

    • +
+
+
+
+ +
+
+string DetermineDataTypeRefTree(string ancestry)
+

Determine the ancestry tree for the specified neurodata type definition.

+
+
Parameters:
+

ancestry – A list of all previously ancester dataTypes

+
+
Returns:
+

a specified neurodata type definition string json

+
+
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___accelerated_modify_graph_8ipf.html b/file/_m_i_e_s___accelerated_modify_graph_8ipf.html new file mode 100644 index 0000000000..628eb19040 --- /dev/null +++ b/file/_m_i_e_s___accelerated_modify_graph_8ipf.html @@ -0,0 +1,361 @@ + + + + + + + + File MIES_AcceleratedModifyGraph.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_AcceleratedModifyGraph.ipf

+

Functions for very fast ModifyGraph invocations for many (> 1000) traces.

+
+

Functions

+
+
+variable ACC_HideTraces(string graph, WaveText w, variable h, variable s)
+

Accelerated setting of multiple traces in a graph to un/hidden.

+
+
Parameters:
+
    +

  • graph – [in] name of graph window

    • +

  • w – [in] 1D text wave with trace names

    • +

  • h – [in] number of traces in text wave

    • +

  • s – [in] new hidden state

    • +
+
+
+
+ +
+
+variable ACC_HideTracesPerTrace(string graph, WaveText w, variable h, wave s)
+

Accelerated setting of multiple traces in a graph to un/hidden with per trace hide state.

+

See GenerateAcceleratedModifyGraphCase() for how to generate the code between BEGIN/END AUTOMATED CODE.

+
+
Parameters:
+
    +

  • graph – [in] name of graph window

    • +

  • w – [in] 1D text wave with trace names

    • +

  • h – [in] number of traces in text wave

    • +

  • s – [in] new hidden state

    • +
+
+
+
+ +
+
+variable ACC_HideTracesAndColor(string graph, WaveText w, variable h, wave hideState, wave color)
+

Accelerated setting of multiple traces in a graph to un/hidden and the color.

+

The code between BEGIN/END AUTOMATED CODE is generated via GenerateAcceleratedModifyGraphCase(“hideTrace”) and cleanup for whitespace errors.

+
+
Parameters:
+
    +

  • graph – [in] name of graph window

    • +

  • w – [in] 1D text wave with trace names

    • +

  • h – [in] number of traces in text wave

    • +

  • hideState – [in] new hidden state

    • +

  • color – [in] new hidden state

    • +
+
+
+
+ +
+
+variable ACC_ModLineSizeTraces(string graph, WaveText w, variable h, variable l)
+

Accelerated setting of line size of multiple traces in a graph.

+
+
Parameters:
+
    +

  • graph – [in] name of graph window

    • +

  • w – [in] 1D text wave with trace names

    • +

  • h – [in] number of traces in text wave

    • +

  • l – [in] new line size

    • +
+
+
+
+ +
+
+

Variables

+
+
+static const double ACC_MAX = 1024
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___acquisition_state_handling_8ipf.html b/file/_m_i_e_s___acquisition_state_handling_8ipf.html new file mode 100644 index 0000000000..ffd6a84ae9 --- /dev/null +++ b/file/_m_i_e_s___acquisition_state_handling_8ipf.html @@ -0,0 +1,347 @@ + + + + + + + + File MIES_AcquisitionStateHandling.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_AcquisitionStateHandling.ipf

+

AS Acquisition state handling

+
+

Functions

+
+
+string AS_StateToString(variable acqState)
+

Get the acquisition state as string.

+
+ +
+
+variable AS_HandlePossibleTransition(string device, variable newAcqState, variable call = defaultValue)
+

Takes care of (possible) acquisition state transitions.

+

We track the acquisition state so that we can perform actions for state transitions when required.

+
+
Parameters:
+
    +

  • device – device

    • +

  • newAcqState – One of AcquisitionStates

    • +

  • call – [optional, defaults to false] Call analysis function which is connected to the state transition.

    • +
+
+
+
+ +
+
+static variable AS_CheckStateTransition(variable oldAcqState, variable newAcqState)
+

Check the acquisition state transition between old and new.

+

The following graph shows the allowed transitions for all states.

+

+

+
+ +
+
+variable AS_GetSweepNumber(string device, variable allowFallback = defaultValue)
+

Return the sweep number of the currently active sweep.

+

The ITI between sweeps belongs to the earlier sweep. The main use is to add a labnotebook entry during data acquisition. The similiar named function AFH_GetLastSweepAcquired() returns the last acquired sweep in comparison.

+
+ +
+
+static variable AS_RecordStateTransition(variable oldAcqState, variable newAcqState)
+
+ +
+
+wave AS_GenerateEncounteredTransitions()
+

Return a wave with all encountered state transitions.

+

Requires that they were recorded with AS_RecordStateTransition().

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___amplifier_interaction_8ipf.html b/file/_m_i_e_s___amplifier_interaction_8ipf.html new file mode 100644 index 0000000000..7aafd6bf5d --- /dev/null +++ b/file/_m_i_e_s___amplifier_interaction_8ipf.html @@ -0,0 +1,784 @@ + + + + + + + + File MIES_AmplifierInteraction.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_AmplifierInteraction.ipf

+

AI Interface with the Axon/MCC amplifiers

+
+

Functions

+
+
+static variable AI_InitAxonTelegraphStruct(AxonTelegraph_DataStruct *tds)
+
+ +
+
+static variable AI_GetAmpAxonSerial(string device, variable headStage)
+

Returns the serial number of the headstage compatible with Axon* functions,.

+

+

See also

+

GetChanAmpAssign

+
+

+
+ +
+
+static string AI_GetAmpMCCSerial(string device, variable headStage)
+

Returns the serial number of the headstage compatible with MCC* functions,.

+

+

See also

+

GetChanAmpAssign

+
+

+
+ +
+
+static variable AI_GetAmpChannel(string device, variable headStage)
+

Return the channel of the currently selected head stage.

+
+ +
+
+static variable AI_IsValidSerialAndChannel(string mccSerial = defaultValue, variable axonSerial = defaultValue, variable channel = defaultValue)
+
+ +
+
+variable AI_GetMCCScale(variable clampMode, variable func)
+

Return the unit prefixes used by MIES in comparison to the MCC app.

+
+
Parameters:
+
    +

  • clampMode – clamp mode (pass NaN for doesn’t matter)

    • +

  • func – MCC function, one of AI_SendToAmpConstants

    • +
+
+
+
+ +
+
+variable AI_UpdateAmpModel(string device, string ctrl, variable headStage, variable value = defaultValue, variable sendToAll = defaultValue, variable checkBeforeWrite = defaultValue, variable selectAmp = defaultValue)
+

Update the AmpStorageWave entry and send the value to the amplifier.

+

Additionally setting the GUI value if the given headstage is the selected one and a value has been passed.

+
+
Parameters:
+
    +

  • device – device

    • +

  • ctrl – name of the amplifier control

    • +

  • headStage – MIES headstage number, must be in the range [0, NUM_HEADSTAGES]

    • +

  • value – [optional: defaults to the controls value] value to set. values is in MIES units, see AI_SendToAmp() and there the description of usePrefixes.

    • +

  • sendToAll – [optional: defaults to the state of the checkbox] should the value be send to all active headstages (true) or just to the given one (false)

    • +

  • checkBeforeWrite – [optional, defaults to false] (ignored for getter functions) check the current value and do nothing if it is equal within some tolerance to the one written

    • +

  • selectAmp – [optional, defaults to true] Select the amplifier before use, some callers might save time in doing that once themselves.

    • +
+
+
Returns:
+

0 on success, 1 otherwise

+
+
+
+ +
+
+variable AI_SyncAmpStorageToGUI(string device, variable headstage)
+

Convenience wrapper for AI_UpdateAmpView.

+

Disallows setting single controls for outside callers as AI_UpdateAmpModel should be used for that.

+
+ +
+
+variable AI_SyncGUIToAmpStorageAndMCCApp(string device, variable headStage, variable clampMode)
+

Sync the settings from the GUI to the amp storage wave and the MCC application.

+
+ +
+
+static variable AI_UpdateAmpView(string device, variable headStage, string ctrl = defaultValue)
+

Synchronizes the AmpStorageWave to the amplifier GUI control.

+
+
Parameters:
+
    +

  • device – device

    • +

  • headStage – MIES headstage number, must be in the range [0, NUM_HEADSTAGES]

    • +

  • ctrl – [optional, defaults to all controls] name of the control being updated

    • +
+
+
+
+ +
+
+static string AI_AmpStorageControlToRowLabel(string ctrl)
+

Convert amplifier controls to row labels for AmpStorageWave

+
+ +
+
+variable AI_SetMIESHeadstage(string device, variable headstage = defaultValue, variable increment = defaultValue)
+
+ +
+
+variable AI_ZeroAmps(string device, variable headStage = defaultValue)
+

Executes MCC auto zero command if the baseline current exceeds ZERO_TOLERANCE.

+
+
Parameters:
+
    +

  • device – device

    • +

  • headStage – [optional: defaults to all active headstages]

    • +
+
+
+
+ +
+
+static variable AI_MIESAutoPipetteOffset(string device, variable headStage)
+

Auto pipette zeroing Quicker than MCC auto pipette offset.

+
+
Parameters:
+
    +

  • device – device

    • +

  • headStage – MIES headstage number, must be in the range [0, NUM_HEADSTAGES]

    • +
+
+
+
+ +
+
+variable AI_QueryGainsUnitsForClampMode(string device, variable headstage, variable clampMode, variable *DAGain, variable *ADGain, string *DAUnit, string *ADUnit)
+

Query the MCC application for the gains and units of the given clamp mode.

+

Assumes that the correct amplifier is already selected!

+
+ +
+
+variable AI_UpdateChanAmpAssign(string device, variable headStage, variable clampMode, variable DAGain, variable ADGain, string DAUnit, string ADUnit)
+

Update the ChanAmpAssign and ChanAmpAssignUnit waves according to the passed clamp mode with the gains and units.

+
+ +
+
+variable AI_AssertOnInvalidClampMode(variable clampMode)
+

Assert on invalid clamp modes, does nothing otherwise.

+
+ +
+
+variable AI_IsValidClampMode(variable clampMode)
+

Return true if the given clamp mode is valid.

+
+ +
+
+variable AI_OpenMCCs(string ampSerialNumList, string ampTitleList = defaultValue)
+

Opens Multi-clamp commander software.

+
+
Parameters:
+
    +

  • ampSerialNumList – A text list of amplifier serial numbers without leading zeroes Ex. “834001;435003;836059”, “0;” starts the MCC in Demo mode Duplicate serial numbers are ignored as well as amplifier titles for the duplicates. For each unique serial number one MCC is opened.

    • +

  • ampTitleList – [optional, defaults to blank] MCC gui window title

    • +
+
+
Returns:
+

1 if all unique MCCs specified in ampSerialNumList were opened, 0 if one or more MCCs specified in ampSerialNumList were not able to be opened

+
+
+
+ +
+
+static wave AI_GetMCCSerialNumbers()
+

Gets the serial numbers of all open MCCs.

+
+
Returns:
+

a 1D FREE wave containing amplifier serial numbers without leading zeroes

+
+
+
+ +
+
+static string AI_GetMCCWinFilePath()
+

Return a path to the MCC.

+

Hardcoded as Igor does not allow to query that information.

+

Distinguishes between i386 and x64 Igor versions

+
+ +
+
+variable AI_GetHoldingCommand(string device, variable headstage)
+
+ +
+
+variable AI_GetMode(string device, variable headstage)
+
+ +
+
+static variable AI_RetrieveGains(string device, variable headstage, variable clampMode, variable *ADGain, variable *DAGain)
+
+ +
+
+static variable AI_SwitchAxonAmpMode()
+
+ +
+
+variable AI_SelectMultiClamp(string device, variable headStage)
+
+ +
+
+variable AI_SetClampMode(string device, variable headStage, variable mode, variable zeroStep = defaultValue)
+
+ +
+
+variable AI_SendToAmp(string device, variable headStage, variable mode, variable func, variable value, variable checkBeforeWrite = defaultValue, variable usePrefixes = defaultValue, variable selectAmp = defaultValue)
+
+ +
+
+variable AI_EnsureCorrectMode(string device, variable headStage, variable selectAmp = defaultValue)
+
+ +
+
+variable AI_FillAndSendAmpliferSettings(string device, variable sweepNo)
+
+ +
+
+variable AI_QueryGainsFromMCC(string device)
+
+ +
+
+variable AI_FindConnectedAmps()
+
+ +
+
+std::tuple<AxonTelegraph_DataStruct> AI_GetTelegraphStruct(variable axonSerial, variable channel)
+
+ +
+
+

Variables

+
+
+static const double ZERO_TOLERANCE = 100
+
+ +
+
+static const string AMPLIFIER_CONTROLS_VC = "setvar_DataAcq_Hold_VC;check_DataAcq_Amp_Chain;check_DatAcq_HoldEnableVC;setvar_DataAcq_WCC;setvar_DataAcq_WCR;check_DatAcq_WholeCellEnable;setvar_DataAcq_RsCorr;setvar_DataAcq_RsPred;check_DataAcq_Amp_Chain;check_DatAcq_RsCompEnable;setvar_DataAcq_PipetteOffset_VC;button_DataAcq_FastComp_VC;button_DataAcq_SlowComp_VC;button_DataAcq_AutoPipOffset_VC"
+
+ +
+
+static const string AMPLIFIER_CONTROLS_IC = "setvar_DataAcq_Hold_IC;check_DatAcq_HoldEnable;setvar_DataAcq_BB;check_DatAcq_BBEnable;setvar_DataAcq_CN;check_DatAcq_CNEnable;setvar_DataAcq_AutoBiasV;setvar_DataAcq_AutoBiasVrange;setvar_DataAcq_IbiasMax;check_DataAcq_AutoBias;setvar_DataAcq_PipetteOffset_IC;button_DataAcq_AutoBridgeBal_IC"
+
+ +
+
+static const double MAX_PIPETTEOFFSET = 150
+
+ +
+
+static const double MIN_PIPETTEOFFSET = -150
+
+ +
+
+static const double NUM_TRIES_AXON_TELEGRAPH = 10
+
+ +
+
+
+struct AxonTelegraph_DataStruct
+
+

Public Members

+
+
+uint32 Version
+

Structure version. Value should always be 13.

+
+ +
+
+uint32 SerialNum
+
+ +
+
+uint32 ChannelID
+
+ +
+
+uint32 ComPortID
+
+ +
+
+uint32 AxoBusID
+
+ +
+
+uint32 OperatingMode
+
+ +
+
+string OperatingModeString
+
+ +
+
+uint32 ScaledOutSignal
+
+ +
+
+string ScaledOutSignalString
+
+ +
+
+double Alpha
+
+ +
+
+double ScaleFactor
+
+ +
+
+uint32 ScaleFactorUnits
+
+ +
+
+string ScaleFactorUnitsString
+
+ +
+
+double LPFCutoff
+
+ +
+
+double MembraneCap
+
+ +
+
+double ExtCmdSens
+
+ +
+
+uint32 RawOutSignal
+
+ +
+
+string RawOutSignalString
+
+ +
+
+double RawScaleFactor
+
+ +
+
+uint32 RawScaleFactorUnits
+
+ +
+
+string RawScaleFactorUnitsString
+
+ +
+
+uint32 HardwareType
+
+ +
+
+string HardwareTypeString
+
+ +
+
+double SecondaryAlpha
+
+ +
+
+double SecondaryLPFCutoff
+
+ +
+
+double SeriesResistance
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___analysis_browser_8ipf.html b/file/_m_i_e_s___analysis_browser_8ipf.html new file mode 100644 index 0000000000..3224621d20 --- /dev/null +++ b/file/_m_i_e_s___analysis_browser_8ipf.html @@ -0,0 +1,1252 @@ + + + + + + + + File MIES_AnalysisBrowser.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_AnalysisBrowser.ipf

+

AB Analysis browser

+

ABM Analysis browser Macro

+

Has no dependencies on any hardware related functions.

+
+

Functions

+
+
+static variable AB_ResetListBoxWaves()
+
+ +
+
+static variable AB_RemoveEmptyWorkingDF()
+

Remove empty working DF from previous AB sessions.

+
+ +
+
+static variable AB_InitializeAnalysisBrowserWaves()
+

Reset all waves of the main experiment browser.

+
+ +
+
+static variable AB_AddMapEntry(string baseFolder, string discLocation)
+

Create relation (map) between file on disk and datafolder in current experiment.

+
+
Returns:
+

index into mapping wave of the newly added entry or -1 if the file is already in the map

+
+
+
+ +
+
+static variable AB_RemoveMapEntry(variable index)
+
+ +
+
+wave AB_GetMap(string discLocation)
+

Get single matching entry from GetAnalysisBrowserMap.

+
+
Parameters:
+

discLocation – first column. Path to file on disc

+
+
Returns:
+

wave with 4 columns Columns: 0: DiscLocation: Path to Experiment on Disc 1: FileName: Name of File in experiment column in ExperimentBrowser 2: DataFolder Data folder inside current Igor experiment 3: FileType File Type identifier for routing to loader functions, one of AnalysisBrowserFileTypes

+
+
+
+ +
+
+wave AB_SaveDeviceList(string deviceList, string dataFolder)
+

save deviceList to wave

+
+
Returns:
+

created wave.

+
+
+
+ +
+
+static variable AB_AddFile(string discLocation, string sourceEntry)
+

general loader for pxp, uxp and nwb files

+
+
Returns:
+

0 if the file was loaded, or 1 if not (usually due to an error or because it was already loaded)

+
+
+
+ +
+
+string AB_PrefixExtendedStimsetNamesToStimsetNames(string stimsets)
+

from a list of extended stimset names with WP_, WPT_ or SegWvType_ prefix return a boiled down list of unique stimset names without prefix

+

+

See also

+

NWB_SuffixExtendedStimsetNamesToStimsetNames

+
+

+
+ +
+
+static string AB_GetStimsetListFromIgorFile(string fullPath)
+

Returns a list of stimset names from an igor experiment file.

+
+ +
+
+static variable AB_FileHasStimsets(WaveText map)
+

returns 1 if the file has stimsets, 0 otherwise

+
+ +
+
+static variable AB_LoadFile(string discLocation)
+

function tries to load Data From discLocation.

+
+ +
+
+static variable AB_HasCompatibleVersion(string discLocation)
+

Check if the given file has a compatible version which this version of the analysis browser can handle.

+
+
Parameters:
+

discLocation – file to check, parameter to AB_GetMap()

+
+
+
+ +
+
+static string AB_GetSettingNumFiniteVals(wave wv, string device, variable sweepNo, string name)
+
+ +
+
+static variable AB_FillListWave(string diskLocation, string fileName, string device, string dataFolder, string fileType, WaveOrNull sweepNums)
+

Creates list-view for AnalysisBrowser.

+

Depends on LabNoteBook to be loaded prior to call.

+
+
Parameters:
+
    +

  • diskLocation – full file path of Project file

    • +

  • fileName – current Project’s filename

    • +

  • device – current device, if device is empty only the experiment name is added

    • +

  • dataFolder – current Project’s Lab Notebook DataFolder reference

    • +

  • fileType – current Project’s file type, one of AnalysisBrowserFileTypes

    • +

  • sweepNums – Wave containing all sweeps actually present for device

    • +
+
+
+
+ +
+
+static string AB_GetRowHash(WaveText list, variable row)
+
+ +
+
+static variable AB_LoadDataWrapper(dfref tmpDFR, string expFilePath, string datafolderPath, string listOfNames, variable typeFlags = defaultValue, variable recursive = defaultValue)
+

Load waves from a packed/unpacked experiment file.

+

This function is special as it does change the CDF!

+
+
Parameters:
+
    +

  • tmpDFR – Temporary work folder, function returns with that folder as CDF

    • +

  • expFilePath – full path to the experiment file on disc

    • +

  • datafolderPath – igor datafolder to look for the waves inside the experiment

    • +

  • listOfNames – list of names of waves/strings/numbers to load

    • +

  • typeFlags – [optional, defaults to 1 (waves)] data types to load, valid values are the same as for LoadData, see also LoadDataConstants

    • +

  • recursive – [optional, defaults to 1] when set loads data recursive from the experiment file

    • +
+
+
Returns:
+

number of loaded items

+
+
+
+ +
+
+static wave AB_GetSweepsFromLabNotebook(string dataFolder, string device, variable clean = defaultValue)
+

Returns a wave containing all present sweep numbers.

+
+
Parameters:
+
    +

  • dataFolder – DataFolder of HDF5 or Experiment File where LabNoteBook is saved

    • +

  • device – device for which to get sweeps.

    • +

  • clean – Variable indicating if ouput can contain duplicate values

    • +
+
+
+
+ +
+
+static variable AB_GetHighestPossibleSweepNum(string dataFolder, string device)
+

Returns the highest referenced sweep number from the labnotebook.

+
+ +
+
+static variable AB_LoadSweepsFromExperiment(string discLocation, string device)
+

Returns a wave containing all present sweep numbers.

+

Function uses Config Waves from Igor Experiment to determine present sweeps

+
+
Parameters:
+
    +

  • discLocation – location of Experiment File on Disc. ID in AnalysisBrowserMap

    • +

  • device – device for which to get sweeps.

    • +
+
+
+
+ +
+
+static variable AB_LoadSweepsFromNWB(string discLocation, string dataFolder, string device)
+

Analyse data in NWB file and sort as sweeps.

+

+
+Todo:
+

: Update this function for the use with SweepTable

+
+ +

+
+
Parameters:
+
    +

  • discLocation – location of NWB File on Disc. ID in AnalysisBrowserMap

    • +

  • dataFolder – datafolder of the project

    • +

  • device – device for which to get sweeps.

    • +
+
+
+
+ +
+
+static variable AB_StoreChannelsBySweep(variable groupID, variable nwbVersion, string channelList, WaveInteger sweeps, WaveText storage)
+

Store channelList in storage wave according to index in sweeps wave.

+

+
+Todo:
+

Update this function for the use with SweepTable

+
+ +

+
+ +
+
+static variable AB_LoadTPStorageFromIgor(string expFilePath, string expFolder, string device)
+
+ +
+
+variable AB_LoadTPStorageFromNWB(string nwbFilePath, string expFolder, string device)
+
+ +
+
+static variable AB_LoadStoredTestpulsesFromNWB(string nwbFilePath, string expFolder, string device)
+
+ +
+
+static variable AB_LoadResultsFromIgor(string expFilePath, string expFolder)
+
+ +
+
+static variable AB_LoadResultsFromNWB(string nwbFilePath, string expFolder)
+
+ +
+
+static variable AB_LoadUserCommentFromFile(string expFilePath, string expFolder, string device)
+
+ +
+
+static variable AB_LoadUserCommentAndHistoryFromNWB(string nwbFilePath, string expFolder, string device)
+
+ +
+
+static string AB_LoadLabNotebook(string discLocation)
+
+ +
+
+static string AB_LoadLabNotebookFromFile(string discLocation)
+
+ +
+
+static string AB_LoadLabNotebookFromIgor(string discLocation)
+
+ +
+
+static variable AB_LoadLabNotebookFromIgorLow(string discLocation, string path, string device, string *deviceList)
+

Try loading the four labnotebooks from path.

+
+
Parameters:
+
    +

  • discLocation – [in] experiment location on disc

    • +

  • path – [in] datafolder path which holds the labnotebooks (might not exist)

    • +

  • device – [in] name of the device

    • +

  • deviceList – [inout] list of loaded devices, for successful loads we add to that list

    • +
+
+
+
+ +
+
+static string AB_LoadLabNotebookFromNWB(string discLocation)
+
+ +
+
+static variable AB_checkLabNotebook(dfref dfr)
+

function checks if LabNoteBook Waves do exist.

+
+
Parameters:
+

dfr – path to labNoteBook dataFolder reference.

+
+
Returns:
+

0 labNotebook does not exist. 1 labNoteBook exists. also update dimension lables

+
+
+
+ +
+
+static variable AB_updateLabelsInLabNotebook(dfref dfr)
+

add dimension labels in older versions of igor-MIES and hdf5-loaded data overwrite invalid dim labels (labnotebook waves created with versions prior to a8f0f43)

+
+ +
+
+static string AB_TranslatePath(string path, string expFolder)
+
+ +
+
+static variable AB_LoadSweepConfigData(string expFilePath, string expFolder, string device, variable highestSweepNumber)
+

Load all Config_Sweep_* waves from the given experiment file or folder and the given device.

+

The implementation here tries to load LOAD_CONFIG_CHUNK_SIZE number of config sweep waves at a time until there could not be loaded at least one config sweep wave and we have reached highestSweepNumber.

+

The size of LOAD_CONFIG_CHUNK_SIZE is limited by a limitation of LoadData as this operations accepts only a stringlist of waves shorter than 400 characters.

+
+ +
+
+static variable AB_ExpandListColumn(variable col)
+

Expand all tree views in the given column.

+
+ +
+
+static variable AB_CollapseListColumn(variable col)
+

Collapse all tree views in the given column.

+
+ +
+
+static variable AB_SetGUISelBits(wave selBits)
+

Set the selection bits of the experiment browser ListBox selection wave.

+
+
Parameters:
+

selBits – wave returned by AB_ReturnAndClearGUISelBits

+
+
+
+ +
+
+static wave AB_ReturnAndClearGUISelBits()
+

Return the selection bits from the experiment browser ListBox selection wave and clear them.

+
+ +
+
+static variable AB_CollapseListEntry(variable row, variable col)
+

Collapse the given treeview.

+
+ +
+
+static variable AB_ExpandListEntry(variable row, variable col)
+

Expand the given treeview.

+
+ +
+
+static variable AB_GetListRowWithSameHash(WaveText list, string h)
+
+ +
+
+static variable AB_ExpandIfCollapsed(variable row, variable subSectionColumn)
+
+
Returns:
+

0 if the treeview could be expanded, zero otherwise

+
+
+
+ +
+
+static wave AB_GetExpandedIndices()
+

get indizes from AB window while successive expanding all columns

+
+
Returns:
+

valid indizes wave on success

+
+
+
+ +
+
+static variable AB_GUIRowIsStimsetsOnly(variable row)
+
+ +
+
+static variable AB_LoadFromExpandedRange(variable row, variable subSectionColumn, variable loadType, variable overwrite = defaultValue, dfref sweepBrowserDFR = defaultValue, WaveText dfCollect = defaultValue)
+
+
Returns:
+

0 if at least one sweep or stimset could be loaded, 1 otherwise

+
+
+
+ +
+
+static variable AB_GetRowWithNextTreeView(wave selWave, variable startRow, variable col)
+

Return the row with treeview in the column col starting from startRow.

+
+ +
+
+static variable AB_LoadFromFile(variable loadType, dfref sweepBrowserDFR = defaultValue)
+
+ +
+
+variable AB_FreeWorkingDFs(WaveText relativeDFPaths, variable actualSize)
+
+ +
+
+variable AB_AllocWorkingDFs(WaveText relativeDFPaths, variable actualSize)
+
+ +
+
+static variable AB_FreeOrAllocWorkingDF(WaveText relativeDFPaths, variable actualSize, variable free)
+
+ +
+
+variable AB_LoadStimsetForSweep(string device, variable index, variable sweep)
+
+ +
+
+static variable AB_LoadFromFileASSERT(string discLocation, string dataFolder, string fileType, string device, variable sweep, variable overwrite)
+
+ +
+
+static variable AB_LoadSweepFromFile(string discLocation, string dataFolder, string fileType, string device, variable sweep, variable overwrite = defaultValue)
+
+
Returns:
+

0 if the sweeps could be loaded, or already exists, and 1 on error

+
+
+
+ +
+
+static variable AB_LoadStimsetFromFile(string discLocation, string dataFolder, string fileType, string device, variable sweep, variable overwrite = defaultValue)
+
+ +
+
+static variable AB_LoadSweepFromNWB(string discLocation, dfref sweepDFR, string device, variable sweep)
+
+ +
+
+static variable AB_LoadSweepFromNWBgeneric(variable h5_groupID, variable nwbVersion, string channelList, dfref sweepDFR, WaveInteger configSweep)
+
+ +
+
+static variable AB_SortConfigSweeps(WaveInteger config)
+

Sorts the faked Config Sweeps Wave to get correct display order in Sweep Browser.

+

function is oriented at MDSort()

+
+ +
+
+static variable AB_LoadSweepFromIgor(string discLocation, string expFolder, dfref sweepDFR, string device, variable sweep)
+

Load specified device/sweep combination from Igor experiment file to sweepDFR.

+
+
Returns:
+

name of loaded sweep

+
+
+
+ +
+
+static variable AB_LoadStimsetsRAW(string expFilePath, string stimsets, variable overwrite)
+

a failsave alternative for AB_LoadStimsets() to load RAW stimsets

+

If a stimset could not get loaded using AB_LoadStimsets() this function is used in addition to try to load the stimset without its corresponding Parameter Waves. overwrite is not supported

+
+
Parameters:
+
    +

  • expFilePath – Path on disc to igor experiment

    • +

  • stimsets – “;” separated list of all stimsets

    • +

  • overwrite – overwrite flag

    • +
+
+
Returns:
+

1 on error and 0 on success

+
+
+
+ +
+
+static string AB_LoadStimsets(string expFilePath, string stimsets, variable overwrite, string processedStimsets = defaultValue)
+

Load specified stimsets from Igor experiment file.

+

recurses into all dependent stimsets as soon as they have been loaded. the list of stimsets is extended “on the left side”: new items are added left. use numEnd to indicate unto which item the list was already processed. see StimsetRecursion() for a similar structure

+
+
Parameters:
+
    +

  • expFilePath – Path on disc to igor experiment

    • +

  • stimsets – “;” separated list of all stimsets of the current sweep.

    • +

  • processedStimsets – [optional] input a list of already processed stimsets

    • +

  • overwrite – overwrite flag

    • +
+
+
Returns:
+

1 on error and 0 on success

+
+
+
+ +
+
+static variable AB_LoadStimset(string expFilePath, string stimset, variable overwrite)
+

Load specified stimset from Igor experiment file.

+
+
Returns:
+

1 on error and 0 on success

+
+
+
+ +
+
+static variable AB_LoadStimsetRAW(string expFilePath, string stimset, variable overwrite)
+
+ +
+
+static variable AB_LoadStimsetTemplateWaves(string expFilePath, string stimset)
+

Load template waves for a specific stimset from Igor experiment file.

+
+
Returns:
+

1 on error and 0 on success

+
+
+
+ +
+
+static string AB_LoadCustomWaves(string expFilePath, string stimsets, variable overwrite)
+

Load custom waves for specified stimset from Igor experiment file.

+
+
Returns:
+

1 on error and 0 on success

+
+
+
+ +
+
+static variable AB_LoadWave(string expFilePath, string fullPath, variable overwrite)
+

Load specified wave from Igor Experiment file.

+
+
Returns:
+

1 on error and 0 on success

+
+
+
+ +
+
+static variable AB_SplitSweepIntoComponents(string expFolder, string device, variable sweep, wave sweepWave)
+
+ +
+
+static variable AB_RemoveExperimentEntry(string win, string entry)
+
+ +
+
+static wave AB_GetCurrentlyOpenNWBFiles()
+

returns currently open NWB files for data export. If no file is open returns a zero sized text wave.

+
+ +
+
+static variable AB_AddExperimentEntries(string win, WaveText entries)
+
+ +
+
+string AB_GetPanelName()
+
+ +
+
+static variable AB_SetUserData(string key, string value)
+
+ +
+
+static string AB_GetUserData(string key)
+
+ +
+
+string AB_OpenAnalysisBrowser(variable restoreSettings = defaultValue)
+
+ +
+
+static variable AB_CheckPanelVersion(string panel)
+
+ +
+
+variable AB_BrowserStartupSettings()
+
+ +
+
+variable AB_ButtonProc_ExpandAll(WMButtonAction *ba)
+

Button “Expand all”.

+
+ +
+
+variable AB_ButtonProc_CollapseAll(WMButtonAction *ba)
+

Button “Collapse all”.

+
+ +
+
+variable AB_ButtonProc_LoadSweeps(WMButtonAction *ba)
+

Button “Load Sweeps”.

+
+ +
+
+variable AB_ButtonProc_LoadBoth(WMButtonAction *ba)
+

Button “Load Both”.

+
+ +
+
+variable AB_ButtonProc_LoadStimsets(WMButtonAction *ba)
+

Button “Load Stimsets”.

+
+ +
+
+variable AB_ButtonProc_Refresh(WMButtonAction *ba)
+

Button “Refresh”.

+
+ +
+
+variable AB_ButtonProc_OpenFolders(WMButtonAction *ba)
+

Button “Open folder(s)”.

+
+ +
+
+variable AB_ButtonProc_Remove(WMButtonAction *ba)
+

Button “Remove folder(s)”.

+
+ +
+
+variable AB_ButtonProc_AddFolder(WMButtonAction *ba)
+

Button “Add folder” Display dialog box for choosing a folder and call AB_ScanFolder()

+
+ +
+
+variable AB_ButtonProc_AddFiles(WMButtonAction *ba)
+

Button “Add files” Display dialog box for choosing files and call AB_AddFolder()

+
+ +
+
+static variable AB_AddFiles(string win, WaveText selFiles)
+
+ +
+
+variable AB_AddElementToSourceList(string entry)
+
+ +
+
+static variable AB_SaveSourceListInSettings()
+
+ +
+
+variable AB_ButtonProc_SelectStimSets(WMButtonAction *ba)
+

Button “Select same stim set sweeps”.

+
+ +
+
+variable AB_ListBoxProc_ExpBrowser(WMListboxAction *lba)
+

main ListBox list_experiment_contents

+
+ +
+
+static variable AB_UpdateColors()
+
+ +
+
+variable AB_ButtonProc_OpenCommentNB(WMButtonAction *ba)
+

Button “Open comment NB”.

+
+ +
+
+variable AB_ButtonProc_ResaveAsNWB(WMButtonAction *ba)
+
+ +
+
+static variable AB_LoadAllSweepsAndStimsets(string discLocation, string dataFolder, string fileType, string device)
+
+ +
+
+static string AB_ReExportGetNewFullFilePath(string fullFilePath, variable numDevices, string device)
+
+ +
+
+static variable AB_ReExport(variable index, variable overwrite)
+
+ +
+
+static variable BeforeFileOpenHook(variable refNum, string file, string pathName, string type, string creator, variable kind)
+

Load dropped NWB files into the analysis browser.

+
+ +
+
+string AB_GetAllDevicesForExperiment(string dataFolder)
+
+ +
+
+string AB_GetAllExperiments()
+

Return all experiments the analysis browser knows about.

+
+ +
+
+string AB_GetStimsetList(string fileType, string discLocation, string dataFolder, string device, variable sweep)
+

Get stimset list either by analysing dataFolder of loaded sweep or if device is empty, get all stimsets.

+

numericalValues and textualValues are generated from previously loaded data. used in the context of loading from a stored experiment file. on load a sweep is stored in a device/dataFolder hierarchy.

+
+
Returns:
+

list of stimsets

+
+
+
+ +
+
+static string AB_GetStimsetFromSweepGeneric(variable sweep, wave numericalValues, WaveText textualValues)
+

Get related Stimsets by corresponding sweep.

+

input numerical and textual values storage waves for current sweep

+
+
Returns:
+

list of stimsets

+
+
+
+ +
+
+string AB_GetStimsetFromPanel(string device, variable sweep)
+

Get stimsets by analysing currently loaded sweep.

+

numericalValues and textualValues are generated from device

+
+
Returns:
+

list of stimsets

+
+
+
+ +
+
+variable AB_WindowHook(WMWinHookStruct *s)
+
+ +
+
+static variable AB_MemoryFreeMappedDF()
+
+ +
+
+

Variables

+
+
+static const double EXPERIMENT_TREEVIEW_COLUMN = 0
+
+ +
+
+static const double DEVICE_TREEVIEW_COLUMN = 3
+
+ +
+
+static const double AB_LOAD_SWEEP = 0
+
+ +
+
+static const double AB_LOAD_STIMSET = 1
+
+ +
+
+static const string AB_UDATA_WORKINGDF = "datafolder"
+
+ +
+
+static const string AB_WORKFOLDER_NAME = "workFolder"
+
+ +
+
+static const double LOAD_CONFIG_CHUNK_SIZE = 50
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___analysis_browser___macro_8ipf.html b/file/_m_i_e_s___analysis_browser___macro_8ipf.html new file mode 100644 index 0000000000..06e65cf918 --- /dev/null +++ b/file/_m_i_e_s___analysis_browser___macro_8ipf.html @@ -0,0 +1,286 @@ + + + + + + + + File MIES_AnalysisBrowser_Macro.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_AnalysisBrowser_Macro.ipf

+
+

Functions

+
+
+void AnalysisBrowser()
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___analysis_browser___sweep_browser_8ipf.html b/file/_m_i_e_s___analysis_browser___sweep_browser_8ipf.html new file mode 100644 index 0000000000..0e99ceea25 --- /dev/null +++ b/file/_m_i_e_s___analysis_browser___sweep_browser_8ipf.html @@ -0,0 +1,512 @@ + + + + + + + + File MIES_AnalysisBrowser_SweepBrowser.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_AnalysisBrowser_SweepBrowser.ipf

+

SB Visualization of sweep data in the analysis browser

+
+

Functions

+
+
+static wave SB_GetSweepBrowserMapFromGraph(string win)
+
+ +
+
+dfref SB_GetSweepBrowserFolder(string win)
+
+ +
+
+variable SB_TranslateSBMapIndexToABMapIndex(string win, variable sbIndex)
+
+ +
+
+dfref SB_GetSweepDataFolder(WaveText sweepMap, variable sweepNo = defaultValue, variable index = defaultValue)
+

Return the sweep data folder.

+
+ +
+
+static dfref SB_GetSweepDataPathFromIndex(dfref sweepBrowserDFR, variable mapIndex)
+
+ +
+
+variable SB_GetIndexFromSweepDataPath(string win, dfref dataDFR)
+
+ +
+
+static variable SB_SetUserData(string win)
+

set graph userdata similar to DB_SetUserData()

+
+
Parameters:
+

win – name of main window or external subwindow in SweepBrowser

+
+
+
+ +
+
+static wave SB_GetSweepPropertyFromNumLBN(string graph, variable mapIndex, string key)
+

Return numeric labnotebook entries.

+
+
Parameters:
+
    +

  • graph – sweep browser graph

    • +

  • mapIndex – index into the sweep browser map, equal to the index into the popup menu (0-based)

    • +

  • key – labnotebook key

    • +
+
+
Returns:
+

wave with the setting for each headstage or an invalid wave reference if the setting does not exist

+
+
+
+ +
+
+string SB_GetListOfExperiments(string graph)
+

Return a list of experiments from which the sweeps in the sweep browser graph originated from.

+
+
Parameters:
+

graph – sweep browser name

+
+
+
+ +
+
+wave SB_GetChannelInfoFromGraph(string graph, string channel, string experiment = defaultValue)
+

Return a text wave with information about the channel waves of the sweep browser graph of all or a specific experiment.

+

The returned textwave will have multiple columns with different information on each wave.

+

Rows:

    +

  • One entry for each wave

    • +
+

+

Columns:

    +

  • 0: channel number

    • +

  • 1: absolute path to the wave

    • +

  • 2: headstage

    • +
+

+

variable channelNumber, headstage, numWaves, i
+string graph   = "SweepBrowser1" // name of an existing sweep browser graph
+string channel = "DA"
+WAVE/T wv =  SB_GetChannelInfoFromGraph(graph, channel)
+
+numWaves = DimSize(wv, ROWS)
+for(i = 0; i < numWaves; i += 1)
+    WAVE data     = $(wv[i][%path])
+    channelNumber = str2num(wv[i][%channel])
+    headstage     = str2num(wv[i][%headstage])
+
+    printf "Channel %d acquired by headstage %d is stored in %s\r", channelNumber, headstage, NameOfWave(data)
+endfor
+
+
+

+
+
Parameters:
+
    +

  • graph – name of main window or external subwindow in SweepBrowser

    • +

  • channel – type of the channel, one of XOP_CHANNEL_NAMES

    • +

  • experiment – [optional, defaults to all] name of the experiment the channel wave should originate from

    • +
+
+
+
+ +
+
+variable SB_UpdateSweepPlot(string win)
+
+ +
+
+variable SB_AddToSweepBrowser(dfref sweepBrowser, string fileName, string dataFolder, string device, variable sweep)
+
+ +
+
+dfref SB_OpenSweepBrowser(variable mode = defaultValue)
+
+ +
+
+string SB_GetSweepList(string win)
+
+ +
+
+wave SB_GetPlainSweepList(string win)
+

Returns a numeric wave with all sweep numbers.

+

Can contain duplicates!

+
+ +
+
+wave SB_GetSweepsFromDevice(string win, string device)
+

Gets sweep numbers for a given device.

+
+ +
+
+wave SB_GetDeviceList(string win)
+

Gets the unique devices for which data was loaded into the sweepbrowser.

+
+ +
+
+wave SB_GetLogbookWave(string win, variable logbookType, variable logbookWaveType, variable sweepNumber = defaultValue, string dataFolder = defaultValue, string device = defaultValue)
+

Generic getter for the labnotebook waves.

+

LBT_LABNOTEBOOK:

+

Use case 1:

    +

  • No optional parameters given: Returns a wave reference wave with all labnotebook waves from all displayed sweeps, ordered by index

    • +
+

+

Use case 2:

    +

  • sweepNumber given: Return the labnotebook wave of that sweep only

    • +
+

+

Use case 3:

    +

  • dataFolder and device given: Return the labnotebook for the given nwb/pxp data folder and device combination

    • +
+

+

LBT_RESULTS:

+

Use case 1:

    +

  • sweepNumber given: Return one of the four results waves from the sweeps nwb/pxp data folder

    • +
+

+

Use case 2:

    +

  • datafolder given: Return one of the four results waves from the given datafolder sweeps nwb/pxp data folder

    • +
+

+
+
Parameters:
+
    +

  • win – panel

    • +

  • logbookType – one of LogbookTypes

    • +

  • logbookWaveType – one of LabnotebookWaveTypes

    • +

  • sweepNumber – [optional] sweep number

    • +

  • dataFolder – [optional] nwb/pxp data folder (aka experiment)

    • +

  • device – [optional] device of the experiment

    • +
+
+
Returns:
+

valid labnotebook wave or a null wave in case it does not exist

+
+
+
+ +
+
+variable SB_PopupMenuSelectSweep(WMPopupAction *pa)
+
+ +
+
+variable SB_ButtonProc_ExportTraces(WMButtonAction *ba)
+
+ +
+
+variable SB_AddSweepToGraph(string win, variable index)
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___analysis_browser___sweep_browser___export_8ipf.html b/file/_m_i_e_s___analysis_browser___sweep_browser___export_8ipf.html new file mode 100644 index 0000000000..a77e31ab41 --- /dev/null +++ b/file/_m_i_e_s___analysis_browser___sweep_browser___export_8ipf.html @@ -0,0 +1,490 @@ + + + + + + + + File MIES_AnalysisBrowser_SweepBrowser_Export.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_AnalysisBrowser_SweepBrowser_Export.ipf

+

SBE Panel for exporting sweepbrowser traces to new graphs or existing graphs

+
+

Functions

+
+
+static variable SBE_FillExportSettings(string win, SBE_ExportSettings *sett)
+
+ +
+
+string SBE_GetSelectedAxis(string graphPopup, variable axisOrientation)
+

Return a list of possible axes for the export panel.

+
+ +
+
+static variable SBE_AddMissingADTraceInfo(WaveText traceData)
+

Add all available sweep data to traceData.

+

This function can fill in the available data for traces which are not shown.

+
+ +
+
+static wave SBE_GetPulseStartTimesForSel()
+
+ +
+
+variable SBE_ShowExportPanel(string sourceWindow)
+

Display the export panel.

+
+ +
+
+string SBE_ListOfGraphsAndNew()
+

Return a list of possible target graphs for the export panel.

+
+ +
+
+string SBE_ListOfSweepGraphs()
+

Return a list of possible source graphs for the export panel.

+
+ +
+
+string SBE_GetSourceGraphADTraces()
+

Return a list of all AD traces from the selected target graph.

+
+ +
+
+static variable SBE_ExportSweepBrowser(SBE_ExportSettings *sett)
+

Export the sweep browser traces to a user given folder.

+

Creates a new graph from it or appends to an existing one. Only duplicates the main graph without external subwindows

+
+ +
+
+variable SBE_PopMenu_ExportTargetAxis(WMPopupAction *pa)
+
+ +
+
+variable SBE_PopMenu_ExportTargetGraph(WMPopupAction *pa)
+
+ +
+
+variable SBE_ButtonProc_PerformExport(WMButtonAction *ba)
+
+ +
+
+variable SBE_CheckProc_UsePulseForXRange(WMCheckboxAction *cba)
+
+ +
+
+variable SBE_PopMenuProc_PulsesADTrace(WMPopupAction *pa)
+
+ +
+
+

Variables

+
+
+static const string SBE_EXPORT_PANEL = "ExportSettingsPanel"
+
+ +
+
+
+struct SBE_ExportSettings
+
+

Public Members

+
+
+string dataFolder
+
+ +
+
+variable useCursorRange
+
+ +
+
+variable resetWaveZero
+
+ +
+
+variable manualRangeBegin
+
+ +
+
+variable manualRangeEnd
+
+ +
+
+string leftAxis
+
+ +
+
+string bottomAxis
+
+ +
+
+string targetGraph
+
+ +
+
+string sourceGraph
+
+ +
+
+variable axisEqualizing
+
+ +
+
+variable equalYRange
+
+ +
+
+variable usePulses
+
+ +
+
+variable numPulses
+
+ +
+
+variable preFirstPulse
+
+ +
+
+variable postLastPulse
+
+ +
+
+variable ADC
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___analysis_browser___sweep_browser___export___macro_8ipf.html b/file/_m_i_e_s___analysis_browser___sweep_browser___export___macro_8ipf.html new file mode 100644 index 0000000000..ba87eda2c6 --- /dev/null +++ b/file/_m_i_e_s___analysis_browser___sweep_browser___export___macro_8ipf.html @@ -0,0 +1,286 @@ + + + + + + + + File MIES_AnalysisBrowser_SweepBrowser_Export_Macro.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_AnalysisBrowser_SweepBrowser_Export_Macro.ipf

+
+

Functions

+
+
+void ExportSettingsPanel()
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___analysis_function_helpers_8ipf.html b/file/_m_i_e_s___analysis_function_helpers_8ipf.html new file mode 100644 index 0000000000..5f36a83582 --- /dev/null +++ b/file/_m_i_e_s___analysis_function_helpers_8ipf.html @@ -0,0 +1,905 @@ + + + + + + + + File MIES_AnalysisFunctionHelpers.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_AnalysisFunctionHelpers.ipf

+

AFH Helper functions for analysis function writers

+

Additionally the following functions might be useful

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Function

Return value

GetADCListFromConfig()

Free wave with all active AD channels as entries

GetDACListFromConfig()

Free wave with all active DA channels as entries

GetLBNumericalValues()

Wave reference to the labnotebook (numerical version)

GetLBTextualValues()

Wave reference to the labnotebook (textual version)

GetLastSetting()

Last documented value for headstages of a specific setting in the labnotebook for a given sweep number.

GetLastSweepWithSetting()

Last documented numerical value for headstages of a specific setting in the labnotebook and the sweep number it was set last.

GetLastSweepWithSettingText()

Last documented textual value for headstages of a specific setting in the labnotebook and the sweep number it was set last.

ED_AddEntryToLabnotebook()

Add a user entry to the numerical/textual labnotebook

+

+
+

Functions

+
+
+variable AFH_GetHeadstageFromADC(string device, variable AD)
+

Return the headstage the AD channel is assigned to.

+
+
Parameters:
+
    +

  • device – device

    • +

  • AD – AD channel in the range [0,8[ or [0,16[ depending on the hardware

    • +
+
+
Returns:
+

headstage or NaN (for non-associated channels)

+
+
+
+ +
+
+variable AFH_GetHeadstageFromDAC(string device, variable DA)
+

Return the headstage the DA channel is assigned to.

+
+
Parameters:
+
    +

  • device – device

    • +

  • DA – DA channel in the range [0,4[ or [0,8[ depending on the hardware

    • +
+
+
Returns:
+

headstage or NaN (for non-associated channels)

+
+
+
+ +
+
+variable AFH_GetADCFromHeadstage(string device, variable headstage)
+

Return the AD channel assigned to the headstage.

+
+
Parameters:
+
    +

  • device – device

    • +

  • headstage – headstage in the range [0,8[

    • +
+
+
Returns:
+

AD channel or NaN (for non-associated channels)

+
+
+
+ +
+
+variable AFH_GetDACFromHeadstage(string device, variable headstage)
+

Return the DA channel assigned to the headstage.

+
+
Parameters:
+
    +

  • device – device

    • +

  • headstage – headstage in the range [0,8[

    • +
+
+
Returns:
+

DA channel or NaN (for non-associated channels)

+
+
+
+ +
+
+variable AFH_GetDAQDataColumn(wave DAQConfigWave, variable channelNumber, variable channelType)
+

Return the column index into DAQDataWave for the given channel/type combination.

+
+
Parameters:
+
    +

  • DAQConfigWave – DAQ configuration wave, most users need to call GetDAQConfigWave(device) to get that wave.

    • +

  • channelNumber – hardware channel number

    • +

  • channelType – channel type, one of XopChannelConstants

    • +
+
+
+
+ +
+
+wave AFH_GetChannelUnits(wave DAQConfigWave)
+

Return all channel units as free text wave.

+
+
Parameters:
+

DAQConfigWave – DAQ configuration wave, most users need to call GetDAQConfigWave(device) to get that wave.

+
+
+
+ +
+
+string AFH_GetChannelUnit(wave DAQConfigWave, variable channelNumber, variable channelType)
+

Return the channel unit.

+
+
Parameters:
+
    +

  • DAQConfigWave – DAQ configuration wave, most users need to call GetDAQConfigWave(device) to get that wave.

    • +

  • channelNumber – hardware channel number

    • +

  • channelType – channel type, one of XopChannelConstants

    • +
+
+
+
+ +
+
+variable AFH_GetLastSweepAcquired(string device)
+

Return the sweep number of the last acquired sweep.

+
+
Returns:
+

a non-negative integer sweep number or NaN if there is no data

+
+
+
+ +
+
+wave AFH_GetSweeps(string device)
+

Return a numeric wave with all acquired sweep numbers, $”” if there is none.

+
+ +
+
+wave AFH_GetLastSweepWaveAcquired(string device)
+

Return the sweep wave of the last acquired sweep.

+
+
Returns:
+

an existing sweep wave or an invalid wave reference if there is no data

+
+
+
+ +
+
+string AFH_GetStimSetName(string device, variable chanNo, variable channelType)
+

Return the stimset for the given channel.

+
+
Parameters:
+
+
+
Returns:
+

an existing stimulus set name for a DA channel

+
+
+
+ +
+
+string AFH_GetStimSetNameForHeadstage(string device, variable headstage)
+

Convenience wrapper for AFH_GetStimSetName.

+
+ +
+
+static wave AFH_GetSweepsFromSameRACycleNC(wave numericalValues, variable sweepNo)
+

Return a free wave with all sweep numbers (in ascending order) which belong to the same RA cycle. Uncached version, general users should prefer AFH_GetSweepsFromSameRACycle().

+

Return an invalid wave reference if not all required labnotebook entries are available

+
+ +
+
+wave AFH_GetSweepsFromSameRACycle(wave numericalValues, variable sweepNo)
+

Return a free wave with all sweep numbers (in ascending order) which belong to the same RA cycle.

+

Return an invalid wave reference if not all required labnotebook entries are available

+
+ +
+
+wave AFH_GetSweepsFromSameSCI(wave numericalValues, variable sweepNo, variable headstage)
+

Return a free wave with all sweep numbers (in ascending order) which belong to the same stimset cycle.

+

Return an invalid wave reference if not all required labnotebook entries are available

+
+ +
+
+static wave AFH_GetSweepsFromSameSCINC(wave numericalValues, variable sweepNo, variable headstage)
+

Return a free wave with all sweep numbers (in ascending order) which belong to the same stimset cycle id. Uncached version, general users should prefer AFH_GetSweepsFromSameSCI().

+

Return an invalid wave reference if not all required labnotebook entries are available

+
+ +
+
+wave AFH_ExtractOneDimDataFromSweep(string device, wave sweep, variable headstageOrChannelNum, variable channelType, wave config = defaultValue)
+

Return a free 1D wave from the given sweep.

+

Extract the AD channel data from headstage 1:

+

variable sweepNo = 5
+WAVE sweep = GetSweepWave(device, sweepNo)
+variable headstage = 1
+WAVE data = AFH_ExtractOneDimDataFromSweep(device, sweep, headstage, XOP_CHANNEL_TYPE_ADC)
+
+
+

+

Extract the TTL channel 1:

+

variable sweepNo = 6
+WAVE sweep = GetSweepWave(device, sweepNo)
+variable ttlChannel = 1
+WAVE data = AFH_ExtractOneDimDataFromSweep(device, sweep, ttlChannel, XOP_CHANNEL_TYPE_TTL)
+
+
+

+
+
Parameters:
+
    +

  • device – device

    • +

  • sweep – sweep wave

    • +

  • headstageOrChannelNum – headstage [0, NUM_HEADSTAGES[ or channel number for TTL channels [0, NUM_DA_TTL_CHANNELS]

    • +

  • channelType – One of XopChannelConstants

    • +

  • config – [optional, defaults to config wave of the sweep returned by GetConfigWave()] config wave

    • +
+
+
+
+ +
+
+string AFH_GetAnalysisFunctions(variable versionBitMask, variable includeUserFunctions = defaultValue)
+

Get list of possible analysis functions.

+
+
Parameters:
+
    +

  • versionBitMask – bitmask of different analysis function versions which should be returned, one of AnalysisFunctionVersions

    • +

  • includeUserFunctions – include analysis functions defined in “UserAnalysisFunctions.ipf”

    • +
+
+
+
+ +
+
+string AFH_GetListOfAnalysisParams(string func, variable mode)
+

Return the list of required/optional analysis function parameters, possibly including the type, as specified by the function $func_GetParams

+
+
Parameters:
+
    +

  • func – Analysis function V3 which must be valid and existing

    • +

  • mode – Bit mask values from GetListOfParamsModeFlags

    • +
+
+
+
+ +
+
+string AFH_GetHelpForAnalysisParameter(string func, string name)
+

Get help string from optional $func_GetHelp

+
+
Parameters:
+
    +

  • func – Analysis function V3

    • +

  • name – Parameter name

    • +
+
+
+
+ +
+
+string AFH_GetListOfAnalysisParamNames(string params)
+

Return a semicolon separated list of user parameters.

+
+
Parameters:
+

params – serialized parameters, usually just AnalysisFunction_V3.params

+
+
+
+ +
+
+variable AFH_IsParameterPresent(string name, string params)
+

Check if the given analysis parameter is present.

+
+
Parameters:
+
+
+
Returns:
+

one if present, zero otherwise

+
+
+
+ +
+
+string AFH_GetAnalysisParamType(string name, string params, variable typeCheck = defaultValue, string expectedType = defaultValue)
+

Return the type of the user parameter.

+
+
Parameters:
+
+
+
Returns:
+

one of AnalysisFunctionParameterTypes or an empty string

+
+
+
+ +
+
+variable AFH_GetAnalysisParamNumerical(string name, string params, variable defValue = defaultValue)
+

Return a numerical user parameter.

+
+
Parameters:
+
    +

  • name – parameter name

    • +

  • params – serialized parameters, usually just AnalysisFunction_V3.params

    • +

  • defValue – [optional, defaults to NaN] return this value if the parameter could not be found

    • +
+
+
+
+ +
+
+string AFH_GetAnalysisParamTextual(string name, string params, string defValue = defaultValue, variable percentDecoded = defaultValue)
+

Return a textual user parameter.

+
+
Parameters:
+
    +

  • name – parameter name

    • +

  • params – serialized parameters, usually just AnalysisFunction_V3.params

    • +

  • defValue – [optional, defaults to an empty string] return this value if the parameter could not be found

    • +

  • percentDecoded – [optional, defaults to true] if the return value should be percent decoded or not.

    • +
+
+
+
+ +
+
+wave AFH_GetAnalysisParamWave(string name, string params, wave defValue = defaultValue)
+

Return a numerical wave user parameter.

+
+
Parameters:
+
    +

  • name – parameter name

    • +

  • params – serialized parameters, usually just AnalysisFunction_V3.params

    • +

  • defValue – [optional, defaults to an invalid wave ref] return this value if the parameter could not be found

    • +
+
+
Returns:
+

wave reference to free numeric wave, or invalid wave ref in case the parameter could not be found.

+
+
+
+ +
+
+wave AFH_GetAnalysisParamTextWave(string name, string params, WaveText defValue = defaultValue, variable percentDecoded = defaultValue)
+

Return a textual wave user parameter.

+
+
Parameters:
+
    +

  • name – parameter name

    • +

  • params – serialized parameters, usually just AnalysisFunction_V3.params

    • +

  • defValue – [optional, defaults to an invalid wave ref] return this value if the parameter could not be found

    • +

  • percentDecoded – [optional, defaults to true] if the return value should be percent decoded or not.

    • +
+
+
Returns:
+

wave reference to free text wave, or invalid wave ref in case the parameter could not be found.

+
+
+
+ +
+
+variable AFH_IsValidAnalysisParameter(string name)
+

Check if the given name is a valid user parameter name.

+
+ +
+
+variable AFH_IsValidAnalysisParamType(string type)
+

Check if the given type is a valid user parameter type.

+
+ +
+
+string AFH_GetAnalysisParameter(string name, string params, string expectedType = defaultValue)
+

Return an user parameter’s value as string.

+
+
Parameters:
+
+
+
+
+ +
+
+string AFH_RemoveAnalysisParameter(string name, string params)
+

Delete the given user parameter name.

+
+
Parameters:
+
+
+
Returns:
+

serialized parameters with name removed

+
+
+
+ +
+
+string AFH_CheckAnalysisParameter(string genericFunc, CheckParametersStruct *s)
+

Check the analysis parameters.

+

The following checks are made:

    +

  • Valid and matching types

    • +

  • Non-empty waves supplied

    • +

  • All required parameters are present

    • +

  • No additional parameters are present if some are required/optional

    • +

  • Valid names

    • +

  • Check function passes if present

    • +
+

+
+
Parameters:
+
    +

  • genericFunc – Name of an analysis V3 function

    • +

  • s – struct CheckParametersStruct with additional info

    • +
+
+
Returns:
+

multiline error messages, an empty string on success

+
+
+
+ +
+
+variable AFH_AddAnalysisParameter(string setName, string name, variable var = defaultValue, string str = defaultValue, wave wv = defaultValue)
+

Add an analysis function parameter to the given stimset.

+

This function adds the parameter to the WPT wave and checks that it is valid.

+

Exactly one of var/str/wv must be given.

+
+
Parameters:
+
    +

  • setName – stimset name

    • +

  • name – name of the parameter

    • +

  • var – [optional] numeric parameter

    • +

  • str – [optional] string parameter

    • +

  • wv – [optional] wave parameter can be numeric or text

    • +
+
+
+
+ +
+
+string AFH_GetAnalysisParameterAsText(string name, string params)
+

Return a stringified version of the analysis parameter value.

+
+
Parameters:
+
+
+
+
+ +
+
+variable AFH_GetHeadstageFromActiveADC(WaveOrNull statusADC, variable activeADCount)
+

Return the headstage from the given active AD count.

+
+
Parameters:
+
    +

  • statusADC – channel status as returned by GetLastSetting()

    • +

  • activeADCount – running number of active ADC’s, starting at zero

    • +
+
+
Returns:
+

headstage in the range [0, NUM_HEADSTAGES], or NaN if nothing could be found

+
+
+
+ +
+
+wave AFH_GetConfigWave(string device, wave sweepWave)
+

returns the correct config wave depending on the fact if sweepwave is either a scaledDataWave from a currently running acquisition or sweep wave from a finished acquisition

+
+ +
+
+variable AFH_GetFifoInStimsetTime(string device, AnalysisFunction_V3 *s)
+

Some analysis function like PSQ_Ramp and PSQ_EvaluateBaselineChunks need the current acquisition time within the stimset (where the fifo is currently). This function wraps this calculation and returns the time in ms. The stimset begin is the reference point and 0 ms on that time scale.

+
+
Parameters:
+
    +

  • device – device name

    • +

  • s – analysis function structure V3

    • +
+
+
Returns:
+

point in time where the current fifo is within the stimset in ms

+
+
+
+ +
+
+wave AFH_GetChannelFromSweepOrScaledWave(wave sweepOrScaled, variable channelIndex)
+
+ +
+
+std::tuple<variable, variable> AFH_GetSampleIntervalsFromSweep(wave sweep, wave config)
+

Returns the DA and AD sample intervals of the given sweep. The sweep data input can be text sweep wave, 2D numeric sweep wave or waveRef sweep wave (including e.g. scaledDataWave)

+
+ +
+
+string AFH_GetAnaFuncParamsFromLNB(wave numericalValues, WaveText textualValues, variable sweepNo, variable DAC)
+

Returns the analysis function parameters string from the given LNB.

+
+
Parameters:
+
    +

  • numericalValues – numerical labnotebook

    • +

  • textualValues – textual labnotebook

    • +

  • sweepNo – sweep number

    • +

  • DAC – DA channel number

    • +
+
+
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___analysis_function_management_8ipf.html b/file/_m_i_e_s___analysis_function_management_8ipf.html new file mode 100644 index 0000000000..61b420d4d2 --- /dev/null +++ b/file/_m_i_e_s___analysis_function_management_8ipf.html @@ -0,0 +1,301 @@ + + + + + + + + File MIES_AnalysisFunctionManagement.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_AnalysisFunctionManagement.ipf

+

AFM Analysis functions routines

+
+

Functions

+
+
+variable AFM_CallAnalysisFunctions(string device, variable eventType)
+

Call the analysis function associated with the stimset from the wavebuilder.

+
+
Returns:
+

Valid analysis function return types, zero otherwise, see also AnalysisFunctionReturnTypes

+
+
+
+ +
+
+variable AFM_UpdateAnalysisFunctionWave(string device)
+

Update the analysis function storage wave from the stimset waves notes.

+

We are called earlier than DAP_CheckSettings() so we can not rely on anything setup in a sane way.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___analysis_function_prototypes_8ipf.html b/file/_m_i_e_s___analysis_function_prototypes_8ipf.html new file mode 100644 index 0000000000..ae147ac98c --- /dev/null +++ b/file/_m_i_e_s___analysis_function_prototypes_8ipf.html @@ -0,0 +1,384 @@ + + + + + + + + File MIES_AnalysisFunctionPrototypes.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_AnalysisFunctionPrototypes.ipf

+

AFP Analysis functions prototypes to be called during data acquisition

+

+

See also

+

MIES_AnalysisFunctions.ipf

+
+

+
+

Functions

+
+
+variable AFP_ANALYSIS_FUNC_V1(string device, variable eventType, wave DAQDataWave, variable headStage)
+

+
+Deprecated:
+

Use AFP_ANALYSIS_FUNC_V3() instead

+
+ +

+
+
Parameters:
+
    +

  • device – device

    • +

  • eventType – eventType, one of EVENT_TYPE_ANALYSIS_FUNCTIONS, always compare eventType with the constants, never use the current numerical value directly

    • +

  • DAQDataWave – data wave (locked to prevent changes using SetWaveLock)

    • +

  • headStage – active headstage index

    • +
+
+
Returns:
+

ignored

+
+
+
+ +
+
+variable AFP_ANALYSIS_FUNC_V2(string device, variable eventType, wave DAQDataWave, variable headStage, variable realDataLength)
+

+
+Deprecated:
+

Use AFP_ANALYSIS_FUNC_V3() instead

+
+ +

+
+
Parameters:
+
    +

  • device – device

    • +

  • eventType – eventType, one of EVENT_TYPE_ANALYSIS_FUNCTIONS, always compare eventType with the constants, never use the current numerical value directly

    • +

  • DAQDataWave – data wave (locked to prevent changes using SetWaveLock)

    • +

  • headStage – active headstage index

    • +

  • realDataLength – number of rows in DAQDataWave with data, the total number of rows in DAQDataWave might be higher due to alignment requirements of the data acquisition hardware. NaN for PRE_DAQ_EVENT events.

    • +
+
+
Returns:
+

see AnalysisFunction_V3DescriptionTable

+
+
+
+ +
+
+variable AFP_ANALYSIS_FUNC_V3(string device, AnalysisFunction_V3 *s)
+
+
Parameters:
+
    +

  • device – device

    • +

  • s – analysis event structure

    • +
+
+
Returns:
+

see AnalysisFunction_V3DescriptionTable

+
+
+
+ +
+
+string AFP_PARAM_GETTER_V3()
+

Prototype function for the user supplied parameter getter functions.

+
+ +
+
+string AFP_PARAM_HELP_GETTER_V3(string name)
+

Prototype function for the user supplied parameter help functions.

+
+ +
+
+string AFP_PARAM_CHECK_V1(string name, string params)
+

Prototype function for the user supplied parameter check function (legacy signature)

+
+ +
+
+string AFP_PARAM_CHECK_V2(string name, CheckParametersStruct *s)
+

Prototype function for the user supplied parameter check function.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___analysis_functions_8ipf.html b/file/_m_i_e_s___analysis_functions_8ipf.html new file mode 100644 index 0000000000..a91b21ad7e --- /dev/null +++ b/file/_m_i_e_s___analysis_functions_8ipf.html @@ -0,0 +1,807 @@ + + + + + + + + File MIES_AnalysisFunctions.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_AnalysisFunctions.ipf

+

AF Analysis functions to be called during data acquisition

+

+Users can implement functions which are called at certain events for each data acquisition cycle. See TestAnalysisFunction_V3() for an example.

+

See also

+

MIES_AnalysisFunctionPrototypes.ipf

+
+

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Event

Description

Specialities

User epochs

Pre DAQ

Before any DAQ occurs

Called before the settings are validated completely, only the +analysis parameters are validated if present. With Indexing ON, +only the analysis function of the first stimset will receive +that event.

No

Pre Sweep Config

Before the sweep is configured

None

Write

Pre Set

Before a new set starts

None

Write

Mid Sweep

Each time when new data is polled

Available for background DAQ only. +Will always be called at least once and +also with the full stimset acquired.

Write

Post Sweep

After each sweep (before possible ITI pause)

None

Read/Write

Post Set

After a full set has been acquired

This event is not always reached as the user might not acquire +all steps of a set. With indexing, locked and unlocked, only +the post set events for fully acquired stimsets are reached.

Read/Write

Post DAQ

After DAQ has finished and before potential +“TP after DAQ”

None

No

+

User epochs will only be recorded in events which support them, see User epochs for more information about user epochs.

+

+

+

Useful helper functions are defined in MIES_AnalysisFunctionHelpers.ipf.

+

The Post/Pre Sweep/Set/DAQ functions are not executed if a currently running sweep is aborted. Changing the stimset in the Post DAQ event is only possible without indexing active.

+

Analysis function return types

+

Some event types support a range of different return types which let the user decide what should happen next. See also AnalysisFuncReturnTypesConstants. The first analysis function returning with a special value requesting a DAQ stop or preventing it from starting will immediately do so, thus subsequent analysis functions for other active headstage will not run.

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Value

Event Types

Action

NaN

All

Nothing

0

All

Nothing

1

Pre DAQ

DAQ is prevented to start

1

Pre Set

DAQ is stopped

1

Pre Sweep Config

DAQ is stopped

ANALYSIS_FUNC_RET_REPURP_TIME

Mid Sweep

Current sweep is immediately stopped. Left over time is repurposed for ITI.

ANALYSIS_FUNC_RET_EARLY_STOP

Mid Sweep

Current sweep is immediately stopped without honouring the left over time in a special way.

+

+

Analysis function user parameters (V3 only)

+

For some analysis functions it is beneficial to send in additional data depending on the stimset. This is supported by adding parameters and their values via AFH_AddAnalysisParameter() to the stimset, or using the Wavebuilder GUI, and then querying them with the help of Analysis Helper functions for dealing with user parameters. The parameters are stored serialized in the WPT wave, see GetWaveBuilderWaveTextParam() for the exact format. See TestAnalysisFunction_V3() for an example implementation.

+

If you want to propose a list of parameters which should/must be present, define an additional function named like your analysis function but suffixed with _GetParams and return a comma separated list of names. Adding the type is also possible via $name:$type syntax. The list of parameter names and types is then checked before DAQ. The supplied names are taken to be required by default, optional parameters, and their types, must be enclosed with []. The list at ANALYSIS_FUNCTION_PARAMS_TYPES holds all valid types. Case does not matter for the parameter names.

+

The optional function _CheckParam allows you to validate passed parameters. In case of a valid parameter it must return an emtpy string and an error message in case of failure. Parameters which don’t pass can neither be added to stimsets nor can they be used for data acquisition. All required, optional and present parameters are passed into the check function. Passing in the present parameters as well allows for dynamic parameter names not known beforehand.

+

The optional function _GetHelp allows you to create per parameter help text which is shown in the Wavebuilder.

+

Example:

+

Function MyAnalysisFunction(string device, struct AnalysisFunction_V3& s)
+    // ...
+End
+
+Function/S MyAnalysisFunction_GetParams()
+    return "param1:variable,[optParam1:wave]"
+End
+
+Function/S MyAnalysisFunction_CheckParam(string name, struct CheckParametersStruct& s)
+    variable value
+
+    strswitch(name)
+        case "param1":
+            value = AFH_GetAnalysisParamNumerical(name, s.params)
+            if(!IsFinite(value) || !(value >= 0 && value <= 100))
+                return "Needs to be between 0 and 100."
+            endif
+            break
+        case "optParam1":
+            WAVE/Z wv = AFH_GetAnalysisParamWave(name, s.params)
+            if(!WaveExists(wv) || !IsFloatingPointWave(wv))
+                return "Needs to be an existing floating point wave."
+            endif
+            break
+    endswitch
+
+    // default to passing for other parameters
+    return ""
+End
+
+Function/S MyAnalysisFunction_GetHelp(string name)
+
+    strswitch(name)
+        case "param1":
+             return "This parameter helps in finding pink unicorns"
+             break
+        case "optParam1":
+             return "This parameter delivers food right to your door"
+             break
+        default:
+             ASSERT(0, "Unimplemented for parameter " + name)
+             break
+    endswitch
+End
+
+
+

+
+

Initial parameters for stimulation

+
+
+static const string DEFAULT_DEVICE = "ITC18USB_Dev_0"
+

device device

+
+ +
+
+static const string STIM_SET_LOCAL = "PulseTrain_150Hz_DA_0"
+

Initial stimulus set.

+
+ +
+
+static const double VM1_LOCAL = -55
+

Initial holding potential.

+
+ +
+
+static const double VM2_LOCAL = -85
+

Second holding potential to switch to.

+
+ +
+
+static const double SCALE_LOCAL = 70
+

Stimulus amplitude.

+
+ +
+
+static const double NUM_SWEEPS_LOCAL = 6
+

Number of sweeps to acquire.

+
+ +
+
+static const double ITI_LOCAL = 15
+

Inter-trial-interval.

+
+ +
+
+

Initial settings for oodDAQ stimulation

+
+
+static const double POST_DELAY = 150
+

Delay after stimulation event in which no other event can occur in ms.

+
+ +
+
+

Functions

+
+
+variable TestAnalysisFunction_V1(string device, variable eventType, wave DAQDataWave, variable headStage)
+
+ +
+
+variable TestAnalysisFunction_V2(string device, variable eventType, wave DAQDataWave, variable headStage, variable realDataLength)
+
+ +
+
+variable TestAnalysisFunction_V3(string device, AnalysisFunction_V3 *s)
+
+ +
+
+variable MeasureMidSweepTiming_V3(string device, AnalysisFunction_V3 *s)
+

Measure the time between mid sweep calls.

+

Used mainly for debugging.

+
+ +
+
+variable Enforce_VC(string device, variable eventType, wave DAQDataWave, variable headStage, variable realDataLength)
+
+ +
+
+variable Enforce_IC(string device, variable eventType, wave DAQDataWave, variable headStage, variable realDataLength)
+
+ +
+
+variable SetStimConfig_Vclamp(string device, variable eventType, wave DAQDataWave, variable headStage)
+

Force active headstages into voltage clamp.

+
+ +
+
+variable SetStimConfig_Iclamp(string device, variable eventType, wave DAQDataWave, variable headStage)
+

Force active headstages into current clamp.

+
+ +
+
+variable ChangeHoldingPotential(string device, variable eventType, wave DAQDataWave, variable headStage)
+

Change holding potential midway through stim set.

+
+ +
+
+variable LastStimSet(string device, variable eventType, wave DAQDataWave, variable headStage)
+

Print last Stim Set run and headstage mode and holding potential.

+
+ +
+
+variable StimParamGUI()
+

GUI to set initial stimulus parameters using SetStimParam() and begin data acquisition. NOTE: DATA ACQUISITION IS INTIATED AT THE END OF FUNCTION!

+
+ +
+
+variable SetStimParam(string stimSet, variable Vm1, variable Scale, variable Sweeps, variable ITI)
+

Called by StimParamGUI to set initial stimulus parameters.

+
+
Parameters:
+
    +

  • stimSet – Stimulus set to run

    • +

  • Vm1 – Holding potential

    • +

  • Scale – Stimulus amplitude in mV

    • +

  • Sweeps – Number of sweeps

    • +

  • ITI – Inter-trial-interval

    • +
+
+
+
+ +
+
+variable setHolding(variable Vm1)
+

Set holding potential for active headstages.

+
+
Parameters:
+

Vm1 – Holding potential

+
+
+
+ +
+
+variable setVClampMode()
+

Set active headstages into V-clamp.

+
+ +
+
+variable setIClampMode()
+

Set active headstages into I-clamp.

+
+ +
+
+variable switchHolding(variable Vm2)
+

Change holding potential on active headstages to Vm2. Switch occurs after X/2 number of data sweeps. If X!/2 switchSweep = floor(X/2)

+
+
Parameters:
+

Vm2 – Holding potential to switch to

+
+
+
+ +
+
+variable InitoodDAQ()
+

Initialize oodDAQ settings.

+
+ +
+
+variable LastStimSetRun()
+

Print last full stim set aqcuired.

+
+ +
+
+variable TestPrematureSweepStop(string device, variable eventType, wave DAQDataWave, variable headStage, variable realDataLength)
+

Mid sweep analysis function which stops the sweeps and repurposes the left over time at the 20th call.

+

This function needs to be set for Pre DAQ, Mid Sweep and Post Sweep Event.

+
+ +
+
+variable preDAQ_MP_mainConfig(string device, variable eventType, wave DAQDataWave, variable headStage, variable realDataLength)
+
+ +
+
+variable preDAQ_MP_IfMixed(string device, variable eventType, wave DAQDataWave, variable headStage, variable realDataLength)
+
+ +
+
+variable preDAQ_MP_ChirpBlowout(string device, variable eventType, wave DAQDataWave, variable headStage, variable realDataLength)
+
+ +
+
+variable AdjustDAScale(string device, variable eventType, wave DAQDataWave, variable headStage, variable realDataLength)
+

Analysis function to set different “DA Scale” values for a sweep.

+

Prerequisites:

    +

  • Stimset with multiple but identical sweeps and testpulse-like shape. The number of sweeps must be larger than the number of rows in the DAScales wave below.

    • +

  • This stimset must have this analysis function set for the “Pre DAQ” and the “Post Sweep” Event

    • +

  • Does currently nothing for “Mid Sweep” Event

    • +

  • Does not support DA/AD channels not associated with a MIES headstage (aka unassociated DA/AD Channels)

    • +

  • All active headstages must be in “Current Clamp”

    • +
+

+
+ +
+
+variable FitResistance(string device, variable headstage, variable showPlot = defaultValue, variable anaFuncType = defaultValue)
+

Plot the resistance of the sweeps of the same SCI

+

Usually called by PSQ_AdjustDAScale().

+
+ +
+
+variable SetDAScaleModOp(string device, variable headstage, variable modifier, string operator, variable invert = defaultValue, variable roundTopA = defaultValue)
+

Helper for setting the DAScale.

+
+ +
+
+variable SetDAScale(string device, variable headstage, variable absolute = defaultValue, variable relative = defaultValue, variable offset = defaultValue, variable roundTopA = defaultValue)
+

Set the DAScale value of the given headstage.

+
+
Parameters:
+
    +

  • device – device

    • +

  • headstage – MIES headstage

    • +

  • absolute – (optional) DAScale value in A (Amperes)

    • +

  • relative – (optional) relative DAScale modifier

    • +

  • offset – (optional) offset DAScale value

    • +

  • roundTopA – (optional, defaults to false) round the set DAScale to integer pA values

    • +
+
+
+
+ +
+
+string ReachTargetVoltage_GetParams()
+

Return a list of required parameters.

+
+ +
+
+string ReachTargetVoltage_GetHelp(string name)
+
+ +
+
+string ReachTargetVoltage_CheckParam(string name, CheckParametersStruct *s)
+
+ +
+
+variable ReachTargetVoltage(string device, AnalysisFunction_V3 *s)
+

Analysis function to experimentally determine the cell resistance by sweeping through a wave of target voltages.

+

Prerequisites:

    +

  • Stimset with multiple but identical sweeps and testpulse-like shape. The number of sweeps must be larger than the number of rows in the targetVoltages wave below.

    • +

  • Does not support DA/AD channels not associated with a MIES headstage (aka unassociated DA/AD Channels)

    • +

  • All active headstages must be in “Current Clamp”

    • +

  • All active IC headstages must run this analysis function

    • +

  • An inital DAScale of -20pA is used, a fixup value of -100pA is used on the next sweep if the measured resistance is smaller than 20MΩ

    • +
+

+
+ +
+
+string SetControlInEvent_CheckParam(string name, CheckParametersStruct *s)
+
+ +
+
+variable SetControlInEvent(string device, AnalysisFunction_V3 *s)
+

Analysis function to set GUI controls or notebooks in the events.

+

Usage:

    +

  • Add analysis parameters named like the control/notebook

    • +

  • Their value must be a textwave with at least one tuple of event type and data.

    • +

  • Valid number of rows are therefore 2, 4, 6, …

    • +

  • The first tuple element is the event type, one of EVENT_NAME_LIST without “Mid Sweep” and “Generic”, and the second element the value to set

    • +

  • For PopupMenus the passed value is the menu item and not its index

    • +

  • The controls are searched in all open panels and graphs. The notebook can be a toplevel or subwindow notebook.

    • +
+

+

Examples:

+

+ + + + + + + + + + + + + + + + +

Name

Value

setvar_DataAcq_OnsetDelayUser

Pre DAQ;20

Popup_Settings_FixedFreq

Pre Sweep;100;Post Sweep;Maximum

sweepFormula_formula

Pre Set;data(cursors(A,B), select(channels(AD), sweeps()))

+

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___analysis_functions___dashboard_8ipf.html b/file/_m_i_e_s___analysis_functions___dashboard_8ipf.html new file mode 100644 index 0000000000..54a88007ce --- /dev/null +++ b/file/_m_i_e_s___analysis_functions___dashboard_8ipf.html @@ -0,0 +1,490 @@ + + + + + + + + File MIES_AnalysisFunctions_Dashboard.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_AnalysisFunctions_Dashboard.ipf

+

AD Dashboard for pass/fail style analysis functions

+
+

Functions

+
+
+variable AD_UpdateAllDatabrowser()
+

Update the dashboards of all databrowsers.

+
+ +
+
+static variable AD_GetColorForResultMessage(string result)
+
+ +
+
+variable AD_Update(string win)
+

Update the dashboards of the given sweepbrowser/databrowser.

+
+ +
+
+static string AD_GetResultMessage(variable anaFuncType, variable passed, wave numericalValues, WaveText textualValues, variable sweepNo, dfref sweepDFR, variable headstage, variable ongoingDAQ, variable waMode)
+
+ +
+
+static variable AD_FillWaves(string win, WaveText list, WaveText info)
+

Get result list of analysis function runs.

+
+ +
+
+std::tuple<variable, variable> AD_GetAnalysisFunctionType(wave numericalValues, wave anaFuncTypes, variable sweepNo, variable headstage)
+

Return the analysis function type and a bit-mask of possible workarounds for CreateAnaFuncLBNKey()

+
+
Parameters:
+
    +

  • numericalValues – numeric labnotebook

    • +

  • anaFuncTypes – wave with the analysis function types as derived from MapAnaFuncToConstant()

    • +

  • sweepNo – sweep number

    • +

  • headstage – headstage

    • +
+
+
+
+ +
+
+static string AD_FormatListKey(variable stimsetCycleID, variable headstage)
+
+ +
+
+static variable AD_LabnotebookEntryExistsAndIsTrue(WaveOrNull data)
+
+ +
+
+static string AD_GetSquarePulseFailMsg(wave numericalValues, variable sweepNo, variable headstage, variable waMode)
+
+ +
+
+static string AD_GetDAScaleOperationMode(wave numericalValues, WaveText textualValues, variable sweepNo, variable headstage)
+
+ +
+
+static string AD_GetDAScaleFailMsg(wave numericalValues, WaveText textualValues, variable sweepNo, dfref sweepDFR, variable headstage)
+
+ +
+
+static string AD_GetRheobaseFailMsg(wave numericalValues, WaveText textualValues, variable sweepNo, dfref sweepDFR, variable headstage)
+
+ +
+
+static string AD_GetFastRheoEstFailMsg(wave numericalValues, variable sweepNo, variable headstage)
+
+ +
+
+static string AD_GetSpikeControlFailMsg(wave numericalValues, wave textualValues, variable sweepNo, variable headstage)
+
+ +
+
+static string AD_GetChirpFailMsg(wave numericalValues, WaveText textualValues, variable sweepNo, dfref sweepDFR, variable headstage)
+
+ +
+
+static std::tuple<variable, string> AD_GetBaselineFailMsg(variable anaFuncType, wave numericalValues, variable sweepNo, variable headstage)
+

Return an appropriate error message if the baseline QC failed for the given sweep, or an empty string otherwise.

+
+
Parameters:
+
    +

  • anaFuncType – One of PatchSeqAnalysisFunctionTypes

    • +

  • numericalValues – Numerical labnotebook

    • +

  • sweepNo – Sweep number

    • +

  • headstage – Headstage

    • +
+
+
Return values:
+
    +

  • qc – 0/1 for failing or passing, NaN in case it could not be determined

    • +

  • msg – error message for the failure case

    • +
+
+
+
+ +
+
+static string AD_GetBaselineChunkFailMsg(variable anaFuncType, wave numericalValues, variable sweepNo, variable headstage, variable chunk, string subkey, string testname)
+
+ +
+
+static string AD_GetPerSweepFailMessage(variable anaFuncType, wave numericalValues, WaveText textualValues, variable refSweepNo, dfref sweepDFR, variable headstage, variable numRequiredPasses = defaultValue)
+

Gather per sweep failure information for some analysis function types.

+

+

See also

+

AD_GetResultMessage()

+
+

+
+
Parameters:
+
    +

  • anaFuncType – analysis function type

    • +

  • numericalValues – numerical labnotebook

    • +

  • textualValues – textual labnotebook

    • +

  • refSweepNo – reference sweep number

    • +

  • sweepDFR – datafolder reference to the folder holding the sweep data

    • +

  • headstage – headstage

    • +

  • numRequiredPasses – [optional, defaults to off] allows to determine the set failure state by not having reached enough passing sets

    • +
+
+
+
+ +
+
+static string AD_HasAsyncQCFailed(wave numericalValues, WaveText textualValues, variable anaFuncType, variable sweepNo, variable headstage)
+
+ +
+
+static string AD_HasPrematureStopLegacy(wave numericalValues, WaveText textualValues, variable anaFuncType, variable sweepNo, dfref sweepDFR, variable headstage)
+
+ +
+
+static variable AD_SelectResult(string win)
+

Show the sweeps from the selected SCIs in the dashboard.

+
+ +
+
+variable AD_PlotBounds(string browser, variable sweepNo)
+

Plot the inner/outer bounds for PSQ_CHIRP

+

Requires that the sweep is displayed.

+
+ +
+
+variable AD_ListBoxProc(WMListboxAction *lba)
+
+ +
+
+variable AD_CheckProc_PassedSweeps(WMCheckboxAction *cba)
+
+ +
+
+variable AD_CheckProc_FailedSweeps(WMCheckboxAction *cba)
+
+ +
+
+variable AD_CheckProc_Toggle(WMCheckboxAction *cba)
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___analysis_functions___multi_patch_seq_8ipf.html b/file/_m_i_e_s___analysis_functions___multi_patch_seq_8ipf.html new file mode 100644 index 0000000000..a878c3161d --- /dev/null +++ b/file/_m_i_e_s___analysis_functions___multi_patch_seq_8ipf.html @@ -0,0 +1,900 @@ + + + + + + + + File MIES_AnalysisFunctions_MultiPatchSeq.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_AnalysisFunctions_MultiPatchSeq.ipf

+

MSQ Analysis functions for multi patch sequence

+

The Multi Patch Seq analysis functions store various results in the labnotebook.

+

For orientation the following table shows their relation. All labnotebook keys can and should be created via CreateAnaFuncLBNKey().

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Naming constant

Description

Unit

Labnotebook

Analysis +function

Per +chunk?

Headstage +dependent?

List? +(semicolon)

Key-Value pairs? +(colon)

Values are lists? +(comma)

MSQ_FMT_LBN_SPIKE_DETECT

The required number of spikes were detected on the sweep

ms

Numerical

FRE

No

Yes

No

No

No

MSQ_FMT_LBN_STEPSIZE

Current DAScale step size

(none)

Numerical

FRE

No

Yes

No

No

No

MSQ_FMT_LBN_FINAL_SCALE

Final DAScale of the given headstage, only set on success

(none)

Numerical

FRE

No

Yes

No

No

No

MSQ_FMT_LBN_HEADSTAGE_PASS

Pass/fail state of the headstage

On/Off

Numerical

FRE, DS, SC

No

Yes

No

No

No

MSQ_FMT_LBN_SWEEP_PASS

Pass/fail state of the complete sweep

On/Off

Numerical

FRE, DS, SC

No

No

No

No

No

MSQ_FMT_LBN_SET_PASS

Pass/fail state of the complete set

On/Off

Numerical

FRE, DS, SC

No

No

No

No

No

MSQ_FMT_LBN_ACTIVE_HS

Active headstages in pre set event

On/Off

Numerical

FRE, DS

No

Yes

No

No

No

MSQ_FMT_LBN_DASCALE_EXC

Allowed DAScale exceeded given limit

(none)

Numerical

FRE

No

Yes

No

No

No

MSQ_FMT_LBN_PULSE_DUR

Square pulse duration

ms

Numerical

FRE

No

Yes

No

No

No

MSQ_FMT_LBN_SPIKE_POSITIONS

Spike positions with P{1}_R{2}, pulse index ({1}) and +region ({2}), as key and the spike positions as value in pulse +active coordinate system (0 - 100)

(none)

Textual

SC

No

Yes

Yes

Yes

Yes

MSQ_FMT_LBN_SPIKE_COUNTS

Spike count with P{1}_R{2}, pulse index ({1}) and +region ({2}), as key and the spike counts as value

(none)

Textual

SC

No

Yes

Yes

Yes

No

MSQ_FMT_LBN_SPIKE_POSITION_PASS

Pass/fail state of the spike positions

On/Off

Numerical

SC

No

Yes

No

No

No

MSQ_FMT_LBN_SPIKE_COUNTS_STATE

Result of the spike count check: +Too few/Too many/Pass/Mixed

(none)

Textual

SC

No

Yes

No

No

No

MSQ_FMT_LBN_SPONT_SPIKE_PASS

Pass/fail state of the complete baseline

On/Off

Numerical

SC

No

Yes

No

No

No

MSQ_FMT_LBN_IDEAL_SPIKE_COUNTS

Ideal number of spikes (-1 for not present)

(none)

Numerical

SC

No

No

No

No

No

MSQ_FMT_LBN_FAILED_PULSE_LEVEL

Failed pulse level

(none)

Numerical

SC

No

No

No

No

No

MSQ_FMT_LBN_RERUN_TRIAL

Number of repetitions of given stimulus set sweep due to relevant +QC failures (spike count or baseline)

(none)

Numerical

SC

No

Yes

No

No

No

MSQ_FMT_LBN_RERUN_TRIAL_EXC

Number of repetitions was exceeded for that stimulus sweep set count

On/Off

Numerical

SC

No

Yes

No

No

No

FMT_LBN_ANA_FUNC_VERSION

Integer version of the analysis function

(none)

Numerical

All

No

Yes

No

No

No

+

+

Query the standard STIMSET_SCALE_FACTOR_KEY entry from labnotebook for getting the DAScale.

+
+

Functions

+
+
+static variable MSQ_GetPulseSettingsForType(variable type, MSQ_PulseSettings *s)
+

Fills s according to the analysis function type.

+
+ +
+
+static wave MSQ_GetPulseDurations(string device, variable type, variable sweepNo, variable totalOnsetDelay, variable headstage, variable useSCI = defaultValue, variable forceRecalculation = defaultValue)
+

Return the pulse durations from the labnotebook or calculate them before if required. For convenience unused headstages will have 0 instead of NaN in the returned wave.

+
+ +
+
+static wave MSQ_DeterminePulseDuration(string device, variable sweepNo, variable totalOnsetDelay)
+

Determine the pulse duration on each headstage.

+

Returns the labnotebook wave as well.

+
+ +
+
+static variable MSQ_NumAcquiredSweepsInSet(string device, variable sweepNo, variable headstage)
+

Return the number of already acquired sweeps of the given stimset cycle ID.

+
+ +
+
+static variable MSQ_NumPassesInSet(wave numericalValues, variable type, variable sweepNo, variable headstage)
+

Return the number of passed sweeps in all sweeps from the given repeated acquisition cycle.

+
+ +
+
+static variable MSQ_GetDAStimsetLength(string device, variable headstage)
+

Return the DA stimset length in ms of the given headstage.

+
+
Returns:
+

stimset length or -1 on error

+
+
+
+ +
+
+wave MSQ_CreateOverrideResults(string device, variable headstage, variable type)
+

MSQ_PSQ_CreateOverrideResults(“ITC18USB_DEV_0”, 0, $type) where type is one of:

+

MSQ_FAST_RHEO_EST

+

Type:

    +

  • Double wave

    • +
+

+

Value:

    +

  • x position in ms where the spike is in each sweep/step For convenience the values 0 always means no spike and 1 spike detected (at the appropriate position).

    • +
+

+

Rows:

    +

  • Sweeps in set

    • +
+

+

Cols:

    +

  • IC headstages

    • +
+

+

MSQ_DA_SCALE

+

Nothing

+

SC_SPIKE_CONTROL

+

Type:

    +

  • Text wave

    • +
+

+

Value:

    +

  • Key-Valuse pairs in format key1:value1;key2:value2; where value can be a comma separated list

    • +

  • SpontaneousSpikeMax: single value denoting the maximum value for the spontaneous spiking check

    • +

  • SpikePosition_ms: comma separated list with the spike positions in ms. Zero is the start of each pulse

    • +
+

+

Rows:

    +

  • Sweeps in set

    • +
+

+

Cols (NUM_HEADSTAGES):

    +

  • Headstage

    • +
+

+

Layers (10):

    +

  • Pulse index, 0-based

    • +
+

+

Chunks (10):

    +

  • Region, 0-based

    • +
+

+
+ +
+
+static wave MSQ_SearchForSpikes(string device, variable type, wave sweepWave, variable headstage, variable totalOnsetDelay, variable numberOfSpikes = defaultValue, variable defaultValue = defaultValue, wave spikePositions = defaultValue)
+

Search the AD channel of the given headstage for spikes from the pulse onset until the end of the sweep.

+
+
Parameters:
+
    +

  • device – [in] device

    • +

  • type – [in] One of MultiPatchSeqAnalysisFunctionTypes

    • +

  • sweepWave – [in] sweep wave with acquired data

    • +

  • headstage – [in] headstage in the range [0, NUM_HEADSTAGES[

    • +

  • totalOnsetDelay – [in] total delay in ms until the stimset data starts

    • +

  • numberOfSpikes – [in] [optional, defaults to one] number of spikes to look for

    • +

  • spikePositions – [out] [optional] returns the position of the first numberOfSpikes found on success in ms

    • +

  • defaultValue – [in] [optiona, defaults to NaN] the value of the other headstages in the returned wave

    • +
+
+
Returns:
+

labnotebook value wave suitable for ED_AddEntryToLabnotebook()

+
+
+
+ +
+
+static variable MSQ_GetLBNEntryForHSSCIBool(wave numericalValues, variable sweepNo, variable type, string str, variable headstage)
+

Return true if one of the entries is true for the given headstage. False otherwise. Searches in the complete SCI and assumes that the entries are either 0/1/NaN.

+

+
+Todo:
+

merge with LBN functions once these are reworked.

+
+ +

+
+ +
+
+static variable MSQ_GetLBNEntryForHeadstageSCI(wave numericalValues, variable sweepNo, variable type, string str, variable headstage)
+

Return the last entry for a given headstage from the full SCI.

+

This differs from GetLastSettingSCI as specifically the setting for the passed headstage must be valid.

+

+
+Todo:
+

merge with LBN functions once these are reworked.

+
+ +

+
+ +
+
+string MSQ_FastRheoEst_GetParams()
+

Return a list of required parameters for MSQ_FastRheoEst()

+
+ +
+
+string MSQ_FastRheoEst_GetHelp(string name)
+
+ +
+
+string MSQ_FastRheoEst_CheckParam(string name, CheckParametersStruct *s)
+
+ +
+
+variable MSQ_FastRheoEst(string device, AnalysisFunction_V3 *s)
+

Analysis function to find the smallest DAScale where the cell spikes.

+

Prerequisites:

    +

  • Assumes that the stimset has a square pulse

    • +
+

+

Testing: For testing the spike detection logic, the results can be defined in the override wave,

+

Decision logic flowchart:

+
+

See also

+

MSQ_CreateOverrideResults().

+
+

+

+

+
///
+/// Sketch of a stimset with pre pulse baseline (-), square pulse (*), and post pulse baseline (-).
+///
+///    *******
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+/// ---|     |--------------------------------------------
+///
+///
+
+
+
+ +
+
+static wave MSQ_DS_GetDAScaleOffset(string device, variable headstage)
+

Return the DAScale offset [pA] for MSQ_DaScale()

+
+
Returns:
+

wave with LABNOTEBOOK_LAYER_COUNT entries, each holding the final DA Scale entry from the previous fast rheo estimate run.

+
+
+
+ +
+
+static variable MSQ_GetLastPassingLongRHSweep(string device, variable headstage)
+

Return a sweep number of an existing sweep matching the following conditions.

+

    +

  • Acquired with Rheobase analysis function

    • +

  • Sweep set was passing

    • +

  • Pulse duration was longer than 500ms

    • +
+

+

And as usual we want the last matching sweep.

+
+
Returns:
+

existing sweep number or -1 in case no such sweep could be found

+
+
+
+ +
+
+static variable MSQ_ForceSetEvent(string device, variable headstage)
+

Manually force the pre/post set events.

+

Required to do before skipping sweeps.

+
+Todo:
+

this hack must go away.

+
+ +

+
+ +
+
+variable MSQ_CommonPreDAQ(string device, variable headstage, variable clampMode = defaultValue)
+

Common pre DAQ calls for all multipatch analysis functions.

+
+ +
+
+string MSQ_DAScale_GetParams()
+

Require parameters from stimset.

+
+ +
+
+string MSQ_DAScale_GetHelp(string name)
+
+ +
+
+string MSQ_DAScale_CheckParam(string name, CheckParametersStruct *s)
+
+ +
+
+variable MSQ_DAScale(string device, AnalysisFunction_V3 *s)
+

Analysis function to apply a list of DAScale values to a range of sweeps.

+

Decision logic flowchart:

+

+

+
+ +
+
+

Variables

+
+
+static const double MSQ_BL_PRE_PULSE = 0x0
+
+ +
+
+static const double MSQ_BL_POST_PULSE = 0x1
+
+ +
+
+static const double MSQ_RMS_SHORT_TEST = 0x0
+
+ +
+
+static const double MSQ_RMS_LONG_TEST = 0x1
+
+ +
+
+static const double MSQ_TARGETV_TEST = 0x2
+
+ +
+
+
+struct MSQ_PulseSettings
+

Settings structure filled by MSQ_GetPulseSettingsForType()

+
+

Public Members

+
+
+variable prePulseChunkLength
+
+ +
+
+variable pulseDuration
+
+ +
+
+variable postPulseChunkLength
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___analysis_functions___multi_patch_seq___spike_control_8ipf.html b/file/_m_i_e_s___analysis_functions___multi_patch_seq___spike_control_8ipf.html new file mode 100644 index 0000000000..a9f24f2f03 --- /dev/null +++ b/file/_m_i_e_s___analysis_functions___multi_patch_seq___spike_control_8ipf.html @@ -0,0 +1,593 @@ + + + + + + + + File MIES_AnalysisFunctions_MultiPatchSeq_SpikeControl.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_AnalysisFunctions_MultiPatchSeq_SpikeControl.ipf

+

SC Spike Control analysis function for multi patch sequence

+
+

Functions

+
+
+static std::tuple<variable, variable> SC_GetTrials(string device, variable sweepNo, variable headstage)
+

Store the newly calculated rerun trials in the labnotebook and return the minimum and maximum of it.

+
+ +
+
+static wave SC_GetHeadstageQCForSetCount(string device, variable sweepNo)
+

Return a 2D wave with the headstage QC result as a function of the set sweep count.

+

This function does return the result for all active headstages. The headstage argument is needed for fetching all sweeps from the current SCI.

+

Value:

    +

  • Cumulated headstage QC result

    • +
+

+

Rows:

    +

  • Headstage

    • +
+

+

Cols:

    +

  • Stimulus set sweep count

    • +
+

+
+ +
+
+static variable SC_GetSetSweepCount(wave numericalValues, variable sweepNo)
+

Return the stimulus set sweep count for the given sweep.

+
+ +
+
+static variable SC_GetSetPassed(string device, variable sweepNo)
+

Return pass/fail state of the set.

+

This is true iff we have for very stimulus set sweep count a passing headstage

+
+ +
+
+static variable SC_GetSweepPassed(string device, variable sweepNo)
+

Return pass/fail state of the sweep.

+

This is true iff we have for the current stimulus set sweep count a passing headstage

+
+ +
+
+static variable SC_LastSweepInSet(string device, variable sweepNo, variable headstage)
+

Return 1 if we are currently acquiring the last sweep in the stimulus set, 0 otherwise.

+
+ +
+
+static wave SC_FilterPulses(WaveRefWave propertiesWaves, WaveOrNull indizesAll, WaveOrNull indizesSweep)
+

Given a list of pulses by their indizes, this function return only the diagonal ones which are matching the given sweep.

+
+ +
+
+static variable SC_AddPulseRegionLBNEntries(WaveText inputLBN, variable pulseIndex, variable region, variable headstage, WaveOrNull data = defaultValue)
+

Add a new PX_PY:.. entry in to the wave inputLBN

+

The value part after the : is only present if data is passed in

+
+ +
+
+static std::tuple<WAVE, WaveRefWave> SC_GetPulseAveragePropertiesWaves(string device)
+

Return the PA plot waves from the databrowser connected to the given device.

+
+ +
+
+static wave SC_GetPulseIndizes(wave properties, WaveRefWave propertiesWaves, variable sweepNo)
+

Return the diagonal pulses for the given sweep.

+
+ +
+
+static std::tuple<WaveText, WaveText> SC_GetSpikeNumbersAndPositions(string device, variable sweepNo)
+

Return the spike numbers and positions in waves prepared for labnotebook writing.

+
+ +
+
+static variable SC_ProcessPulses(string device, variable sweepNo, variable minimumSpikePosition, variable idealNumberOfSpikes)
+

Fetch the pulses from the PA plot and write the results into the labnotebooks.

+
+ +
+
+static string SC_SpikeCountStateToString(variable countState)
+

Convert a numeric spike counts state to its string.

+

Returns “” for unknown state variables

+
+ +
+
+static variable SC_SpikeCountsCalcDetail(variable minimum, variable maximum, variable idealNumberOfSpikes)
+

Determine the spike counts state.

+

    +

  • Minimum[HS] == Maximum[HS] == idealNumberOfSpikes -> Pass

    • +

  • idealNumberOfSpikes >= Maximum[HS] -> Too few

    • +

  • idealNumberOfSpikes <= Mininum[HS] -> Too many

    • +

  • If nothing else matched -> Mixed

    • +
+

+

We assume:

    +

  • minimum < maximum

    • +

  • idealNumberOfSpikes >= 1

    • +

  • All numbers are integers

    • +
+

+
+ +
+
+static wave SC_SpikeCountsCalc(string device, wave minimum, wave maximum, variable idealNumberOfSpikes)
+

Determine the spike counts state for all headstages.

+
+ +
+
+static wave SC_SpikeCountsQC(string device, WaveText spikeNumbersLBN, variable idealNumberOfSpikes)
+

Check that the we have found the expected number of spikes per pulse.

+
+
Returns:
+

Spike counts state according to SpikeCountsStateConstants stringified

+
+
+
+ +
+
+static variable SC_SpikePositionsCalcDetail(wave spikePositions, variable minimumSpikePosition)
+

Calculate the QC state of a list of spike positions from one pulse.

+

All are in Pulse active coordinate system

+
+
Parameters:
+
    +

  • spikePositions – spike position

    • +

  • minimumSpikePosition – minimum allowed spike position

    • +
+
+
+
+ +
+
+static wave SC_SpikePositionQC(string device, WaveTextOrNull spikePositionsLBN, variable minimumSpikePosition)
+

Calculate the QC state of the spike positions of each pulse.

+

All values are in PA crd, see SC_SpikeControl().

+
+
Parameters:
+
    +

  • device – device

    • +

  • spikePositionsLBN – spike position of each pulse, ordered per headstage, for the current sweep

    • +

  • minimumSpikePosition – minimum allowed spike position

    • +
+
+
+
+ +
+
+static wave SC_RegionBlanked(wave data, variable totalOnsetDelay, WaveText oodDAQRegion)
+

Replace all points inside an oodDAQ region with NaN in the data wave.

+
+ +
+
+static wave SC_SpontaneousSpikingCheckQC(string device, variable sweepNo)
+

Return a wave ready for the labnotebook with the spontaneous spike check QC entries.

+
+ +
+
+static wave SC_HeadstageQC(string device, WaveText spikeCountStateLBN, wave spontaneousSpikingCheckLBN)
+

Determine the headstage QC result.

+
+ +
+
+static variable SC_DetermineQCState(string device, variable sweepNo, wave spikeNumbersLBN, WaveOrNull spikePositionsLBN, variable minimumSpikePosition, variable idealNumberOfSpikes)
+

Determine and write the QC states to the labnotebook.

+
+ +
+
+static variable SC_CanStillSkip(variable maxTrials, string params)
+

Check if we can still skip sweeps without running more than maxTrials

+
+ +
+
+static variable SC_SkipsExhausted(variable minTrials, string params)
+

Check if we have exhausted the available trials on all headstages.

+
+ +
+
+static variable SC_ReactToQCFailures(string device, variable sweepNo, string params)
+

Perform various actions on QC failures.

+
+ +
+
+string SC_SpikeControl_GetParams()
+
+ +
+
+string SC_SpikeControl_GetHelp(string name)
+
+ +
+
+string SC_SpikeControl_CheckParam(string name, CheckParametersStruct *s)
+
+ +
+
+variable SC_SpikeControl(string device, AnalysisFunction_V3 *s)
+

Analysis function to check sweeps for failed pulses and rerun them if the pulses failed.

+

Decision logic flowchart:

+

+

+

For judging the quality of the spike positions we have introduced a new coordinate system which we call pulse active coordinate system (PA crd).

+

Consider the following pulse on the DA wave and the response spike in the AD wave

+

///
+///        +---------+
+///        |         |
+///        |         |
+///        |         |
+///        |         |
+///        |         |
+///        |         |
+/// -------+         +----------------------
+///
+///                   X
+///                  XXX
+///                 X   XX
+///                X      XX
+///               X         X
+///              X           X
+///             X             X
+///            X               X
+///           X                X
+///          X                  X
+///         X                   X
+/// -------X                    X--------
+///
+///
+
+
+ 
and the let pulse active start at 5ms and end at 15ms. We define the start as 0 and the end as 100.
+Therefore the spike position will be 110 in `PA crd` which is one point after the end of the pulse.
+
+The graphs were made with http://asciiflow.com.
+
+
+

+
+ +
+
+

Variables

+
+
+static const string SC_PULSE_PREFIX_RE = "^[^:]+:"
+

Pulse information in the labnotebook is stored as PX_RY:.... This regular expression can be used to match the prefix in order to remove it with RemovePrefix.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___analysis_functions___patch_seq_8ipf.html b/file/_m_i_e_s___analysis_functions___patch_seq_8ipf.html new file mode 100644 index 0000000000..29a42752db --- /dev/null +++ b/file/_m_i_e_s___analysis_functions___patch_seq_8ipf.html @@ -0,0 +1,3180 @@ + + + + + + + + File MIES_AnalysisFunctions_PatchSeq.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_AnalysisFunctions_PatchSeq.ipf

+

PSQ Analysis functions for patch sequence

+

The stimsets with the analysis functions attached are executed in the following order:

    +

  • PSQ_PipetteInBath PB

    • +

  • PSQ_SealEvaluation SE

    • +

  • PSQ_AccessResistanceSmoke AR

    • +

  • PSQ_TrueRestingMembranePotential VM

    • +

  • PSQ_DaScale (sub threshold) DA (sub)

    • +

  • PSQ_SquarePulse (long pulse) SP

    • +

  • PSQ_Rheobase (long pulse) RB

    • +

  • PSQ_DaScale (supra threshold) DA (supra)

    • +

  • PSQ_DaScale (adaptive threshold) DA (adaptive)

    • +

  • PSQ_SquarePulse (short pulse) SP

    • +

  • PSQ_Rheobase (short pulse) RB

    • +

  • PSQ_Ramp RA

    • +

  • PSQ_Chirp CR

    • +
+

+

See GetAbbreviationForAnalysisFunction() for a generating the abbreviation of each analysis function.

+

The Patch Seq analysis functions store various results in the labnotebook.

+

For orientation the following table shows their relation. All labnotebook keys can and should be created via CreateAnaFuncLBNKey().

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Naming constant

Description

Unit

Labnotebook

Analysis function

Per Chunk?

Headstage dependent?

PSQ_FMT_LBN_SPIKE_DETECT

The required number of spikes were detected on the sweep

On/Off

Numerical

SP, RB, RA, DA (Supra)

No

Yes

PSQ_FMT_LBN_SPIKE_POSITIONS

Spike positions

ms

Numerical

RA, VM

No

Yes

PSQ_FMT_LBN_SPIKE_COUNT

Spike count

(none)

Numerical

DA (Supra)

No

Yes

PSQ_FMT_LBN_STEPSIZE

Current DAScale step size

(none)

Numerical

SP, RB

No

No

PSQ_FMT_LBN_STEPSIZE_FUTURE

Future DAScale step size

(none)

Numerical

RB

No

No

PSQ_FMT_LBN_RB_DASCALE_EXC

Range for valid DAScale values is exceeded

On/Off

Numerical

RB

No

Yes

PSQ_FMT_LBN_RB_LIMITED_RES

Failed due to limited DAScale resolution

On/Off

Numerical

RB

No

Yes

PSQ_FMT_LBN_FINAL_SCALE

Final DAScale of the given headstage, only set on success

(none)

Numerical

SP, RB

No

No

PSQ_FMT_LBN_SPIKE_DASCALE_ZERO

Sweep spiked with DAScale of 0

On/Off

Numerical

SP

No

No

PSQ_FMT_LBN_INITIAL_SCALE

Initial DAScale

(none)

Numerical

RB, CR

No

No

PSQ_FMT_LBN_RMS_SHORT_PASS

Short RMS baseline QC result

On/Off

Numerical

DA, RB, RA, CR, SE, VM, AR

Yes

Yes

PSQ_FMT_LBN_RMS_SHORT_THRESHOLD

Short RMS baseline threshold

V

Numerical

DA, RB, RA, CR, SE, VM, AR

No

Yes

PSQ_FMT_LBN_RMS_LONG_PASS

Long RMS baseline QC result

On/Off

Numerical

DA, RB, RA, CR, SE, VM, AR

Yes

Yes

PSQ_FMT_LBN_RMS_LONG_THRESHOLD

Long RMS baseline threshold

V

Numerical

DA, RB, RA, CR, SE, VM, AR

No

Yes

PSQ_FMT_LBN_TARGETV

Target voltage baseline

Volt

Numerical

DA, RB, RA, CR

Yes

Yes

PSQ_FMT_LBN_TARGETV_PASS

Target voltage baseline QC result

On/Off

Numerical

DA, RB, RA, CR

Yes

Yes

PSQ_FMT_LBN_TARGETV_THRESHOLD

Target voltage threshold

V

Numerical

DA, RB, RA, CR

No

Yes

PSQ_FMT_LBN_LEAKCUR

Leak current

Amperes

Numerical

PB, VM, AR

Yes

Yes

PSQ_FMT_LBN_LEAKCUR_PASS

Leak current QC result

On/Off

Numerical

PB, VM, AR

Yes

Yes

PSQ_FMT_LBN_AVERAGEV

Average voltage

Volt

Numerical

VM

Yes

Yes

PSQ_FMT_LBN_CHUNK_PASS

Which chunk passed/failed baseline QC

On/Off

Numerical

DA, RB, RA, CR, PB, SE, VM, AR

Yes

Yes

PSQ_FMT_LBN_BL_QC_PASS

Pass/fail state of the complete baseline

On/Off

Numerical

DA, RB, RA, CR, PB, SE, VM, AR

No

Yes

PSQ_FMT_LBN_SWEEP_PASS

Pass/fail state of the complete sweep

On/Off

Numerical

DA, SP, RA, CR, PB, SE, VM, AR

No

No

PSQ_FMT_LBN_SET_PASS

Pass/fail state of the complete set

On/Off

Numerical

DA, RB, RA, SP, CR, PB, SE, VM, AR

No

No

PSQ_FMT_LBN_SAMPLING_PASS

Pass/fail state of the sampling interval check

On/Off

Numerical

DA, RB, RA, SP, CR, PB, SE, VM, AR

No

No

PSQ_FMT_LBN_PULSE_DUR

Pulse duration as determined experimentally

ms

Numerical

RB, DA, CR

No

Yes

PSQ_FMT_LBN_SPIKE_PASS

Pass/fail state of the spike search (No spikes → Pass)

On/Off

Numerical

CR, VM

No

Yes

PSQ_FMT_LBN_DA_fI_SLOPE

Fitted slope in the f-I plot

% Hz/pA

Numerical

DA (Supra, Adapt)

No

Yes

PSQ_FMT_LBN_DA_fI_SLOPE_REACHED_PASS

Fitted slope in the f-I plot exceeds target value

On/Off

Numerical

DA (Supra, Adapt)

No

No

PSQ_FMT_LBN_DA_AT_FI_OFFSET

Fitted offset in the f-I plot

Hz

Numerical

DA (Adapt)

No

Yes

PSQ_FMT_LBN_DA_AT_FREQ

AP frequency

Hz

Numerical

DA (Adapt)

No

Yes

PSQ_FMT_LBN_DA_AT_RSA_FREQ

AP frequencies from previous sweep reevaluation

Hz

Textual

DA (Adapt)

No

Yes

PSQ_FMT_LBN_DA_AT_RSA_DASCALE

DAScale values from previous sweep reevaluation

(none)

Textual

DA (Adapt)

No

Yes

PSQ_FMT_LBN_DA_AT_RSA_FI_SLOPES

Slopes in the f-I plot from previous sweep reevaluation

% Hz/pA

Textual

DA (Adapt)

No

Yes

PSQ_FMT_LBN_DA_AT_RSA_FI_SLOPES_PASS

Slope QCs in the f-I plot from previous sweep reevaluation

On/Off

Textual

DA (Adapt)

No

No

PSQ_FMT_LBN_DA_AT_RSA_VALID_SLOPE_PASS

Valid slope from f-I plot QC of supra sweep reevaluation

On/Off

Numerical

DA (Adapt)

No

Yes

PSQ_FMT_LBN_SWEEP_PASS

Pass/fail state from previous sweep reevaluation

On/Off

Numerical

DA (Adapt)

No

No

PSQ_FMT_LBN_DA_AT_MAX_SLOPE

Maximum encountered f-I plot slope in the SCI

% Hz/pA

Numerical

DA (Adapt)

No

Yes

PSQ_FMT_LBN_DA_AT_VALID_SLOPE_PASS

Valid slope from f-I plot QC

On/Off

Numerical

DA (Adapt)

No

Yes

PSQ_FMT_LBN_DA_AT_ENOUGH_FI_POINTS_PASS

Enough f-I pairs for line fit QC

On/Off

Numerical

DA (Adapt)

No

No

PSQ_FMT_LBN_DA_AT_FUTURE_DASCALES

DAScale values left to acquire

(none)

Textual

DA (Adapt)

No

Yes

PSQ_FMT_LBN_DA_AT_FUTURE_DASCALES_PASS

Measured all DAScale values

On/Off

Numerical

DA (Adapt)

No

No

PSQ_FMT_LBN_DA_AT_MIN_DASCALE_NORM

Minimum DAScale step width (normalized)

(none)

Numerical

DA (Adapt)

No

No

PSQ_FMT_LBN_DA_AT_MAX_DASCALE_NORM

Maximum DAScale step width (normalized)

(none)

Numerical

DA (Adapt)

No

No

PSQ_FMT_LBN_DA_OPMODE

Operation Mode: One of PSQ_DS_SUB/PSQ_DS_SUPRA/PSQ_DS_ADAPT

(none)

Textual

DA

No

No

PSQ_FMT_LBN_CR_INSIDE_BOUNDS

AD response is inside the given bands

On/Off

Numerical

CR

No

No

PSQ_FMT_LBN_CR_RESISTANCE

Calculated resistance from DAScale sub threshold

Ohm

Numerical

CR

No

No

PSQ_FMT_LBN_CR_BOUNDS_ACTION

Action according to min/max positions

(none)

Numerical

CR

No

No

PSQ_FMT_LBN_CR_BOUNDS_STATE

Upper and Lower bounds state according to min/max pos.

(none)

Textual

CR

No

No

PSQ_FMT_LBN_CR_SPIKE_CHECK

Spike check was enabled/disabled

(none)

Numerical

CR

No

No

PSQ_FMT_LBN_CR_INIT_UOD

Initial user onset delay

ms

Numerical

CR

No

No

PSQ_FMT_LBN_CR_INIT_LPF

Initial MCC low pass filter

Hz

Numerical

CR

No

No

PSQ_FMT_LBN_CR_STIMSET_QC

Stimset valid/invalid QC state

On/Off

Numerical

CR

No

No

FMT_LBN_ANA_FUNC_VERSION

Integer version of the analysis function

(none)

Numerical

All

No

Yes

PSQ_FMT_LBN_PB_RESISTANCE

Pipette Resistance

Ohm

Numerical

PB

No

No

PSQ_FMT_LBN_PB_RESISTANCE_PASS

Pipette Resistance QC

On/Off

Numerical

PB

No

No

PSQ_FMT_LBN_SE_TP_GROUP_SEL

Selected Testpulse groups: One of Both/First/Second

(none)

Textual

SE

No

No

PSQ_FMT_LBN_SE_RESISTANCE_A

Seal Resistance of TPs in group A

Ω

Numerical

SE

No

No

PSQ_FMT_LBN_SE_RESISTANCE_B

Seal Resistance of TPs in group B

Ω

Numerical

SE

No

No

PSQ_FMT_LBN_SE_RESISTANCE_MAX

Maximum Seal Resistance of TPs in both groups

Ω

Numerical

SE

No

No

PSQ_FMT_LBN_SE_RESISTANCE_PASS

Seal Resistance QC

On/Off

Numerical

SE

No

No

PSQ_FMT_LBN_VM_FULL_AVG

Average voltage of all baseline chunks

Volt

Numerical

VM

No

No

PSQ_FMT_LBN_VM_FULL_AVG_ADIFF

Average voltage absolute difference

Volt

Numerical

VM

No

No

PSQ_FMT_LBN_VM_FULL_AVG_ADIFF_PASS

Average voltage absolute difference QC

On/Off

Numerical

VM

No

No

PSQ_FMT_LBN_VM_FULL_AVG_RDIFF

Average voltage relative difference

(none)

Numerical

VM

No

No

PSQ_FMT_LBN_VM_FULL_AVG_RDIFF_PASS

Average voltage relative difference QC

On/Off

Numerical

VM

No

No

PSQ_FMT_LBN_VM_FULL_AVG_PASS

Full average voltage QC result

On/Off

Numerical

VM

No

No

PSQ_FMT_LBN_AR_ACCESS_RESISTANCE

Access resistance of all TPs in the stimset

Ω

Numerical

AR

No

No

PSQ_FMT_LBN_AR_ACCESS_RESISTANCE_PASS

Access resistance QC

On/Off

Numerical

AR

No

No

PSQ_FMT_LBN_AR_STEADY_STATE_RESISTANCE

Steady state resistance of all TPs in the stimset

Ω

Numerical

AR

No

No

PSQ_FMT_LBN_AR_RESISTANCE_RATIO

Ratio of access resistance to steady state

(none)

Numerical

AR

No

No

PSQ_FMT_LBN_AR_RESISTANCE_RATIO_PASS

Ratio of access resistance to steady state QC

On/Off

Numerical

AR

No

No

PSQ_FMT_LBN_ASYNC_PASS

Combined alarm state of all async channels

On/Off

Numerical

All

No

No

LBN_DELTA_I

Delta current in pulse

Amperes

Numerical

RV, AD, DA (Sub)

No

Yes

LBN_DELTA_V

Delta voltage in pulse

Volts

Numerical

RV, AD, DA (Sub)

No

Yes

LBN_RESISTANCE_FIT

Fitted resistance from pulse

Ohm

Numerical

RV, AD, DA (Sub)

No

Yes

LBN_RESISTANCE_FIT_ERR

Error of fitted resistance from pulse

Ohm

Numerical

RV, AD, DA (Sub)

No

Yes

LBN_AUTOBIAS_TARGET_DIAG

Autobias target voltage from dialog

mV

Numerical

RV

No

Yes

+

Query the standard STIMSET_SCALE_FACTOR_KEY entry from labnotebook for getting the DAScale.

+

+

The following table lists the user epochs which are added during data acquisition:

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Tags

Short Name

Analysis function

Description

Level

Name=Baseline Chunk;Index=x

U_BLCx

DA, RB, RA, CR, SE, VM, AR

Baseline QC evaluation chunks

-1

Name=Baseline Chunk QC Selection;Index=x

U_BLSx

SE, VM, AR

Selects the chunk for Baseline QC evaluation

-1

Name=DA Suppression

U_RA_DS

RA

DA was suppressed in this time interval

-1

Name=Unacquired DA data

U_RA_UD

RA

Interval of unacquired data

-1

Type=Testpulse Like;Index=x

U_TPx

PB, SE, AR

Testpulse like region in stimset

-1

Type=Testpulse Like;SubType=Baseline;Index=x

U_TPx_B0

PB, SE, AR

Pre pulse baseline of testpulse

-1

Type=Testpulse Like;SubType=Pulse;Amplitude=y;Index=x

U_TPx_P

PB, SE, AR

Pulse of testpulse

-1

Type=Testpulse Like;SubType=Baseline;Index=x

U_TPx_B1

PB, SE, AR

Post pulse baseline of testpulse

-1

Type=Chirp Cycle Evaluation

U_CR_CE

CR

Evaluation chunk for bounds state

-1

Type=Chirp Spike Evaluation

U_CR_SE

CR

Evaluation chunk for spike check

-1

+

The tag entry Index=x is a zero-based index, which tracks how often the specific type of user epoch appears. So for different +epoch types duplicated index entries are to be expected.

+

See also Time specialities.

+

+

Textual results entries stored by the sweep formula store operation with the names Sweep Formula store [XXX]:

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name

Analysis function

Steady state resistance

PB

Steady state resistance (group A)

PB

Steady state resistance (group B)

PB

Average U_BLS0

VM

Average U_BLS1

VM

Steady state resistance

AR

Peak resistance

AR

+

+
+

Type constants for PSQ_DS_GetLabnotebookData

+

+
+
+static const double PSQ_DS_FI_SLOPE = 0x1
+
+ +
+
+static const double PSQ_DS_FI_SLOPE_REACHED_PASS = 0x2
+
+ +
+
+static const double PSQ_DS_FI_OFFSET = 0x3
+
+ +
+
+static const double PSQ_DS_SWEEP_PASS = 0x4
+
+ +
+
+static const double PSQ_DS_SWEEP = 0x5
+
+ +
+
+static const double PSQ_DS_APFREQ = 0x6
+
+ +
+
+static const double PSQ_DS_DASCALE = 0x7
+
+ +
+
+

Functions

+
+
+variable PSQ_GetPulseSettingsForType(variable type, PSQ_PulseSettings *s)
+

Fills s according to the analysis function type.

+
+ +
+
+static wave PSQ_GetPulseDurations(string device, variable type, variable sweepNo, variable totalOnsetDelay, variable forceRecalculation = defaultValue)
+

Return the pulse durations from the labnotebook or calculate them before if required in ms. For convenience unused headstages will have 0 instead of NaN in the returned wave.

+

We recalculate the durations on every sweep again as we can not assume that it is constant for the whole stimulus set.

+
+ +
+
+static wave PSQ_DeterminePulseDuration(string device, variable sweepNo, variable type, variable totalOnsetDelay)
+

Determine the pulse duration on each headstage.

+

Returns the labnotebook wave as well.

+
+ +
+
+wave PSQ_DeterminePulseDurationFinder(wave statusHS, WaveRefWave allSingleDA, variable type, variable totalOnsetDelay)
+
+ +
+
+static std::tuple<variable, variable, variable> PSQ_GetBaselineThresholds(string params)
+

Return the baseline RMS short/long and target V thresholds in mV.

+
+ +
+
+static variable PSQ_StoreThresholdsInLabnotebook(string device, variable type, variable sweepNo, variable headstage, variable rmsShortThreshold, variable rmsLongThreshold, variable targetVThreshold)
+
+ +
+
+static variable PSQ_EvaluateBaselinePassed(string device, variable type, variable sweepNo, variable headstage, variable chunk, variable ret)
+
+ +
+
+static std::tuple<variable, variable> PSQ_EvaluateBaselineChunks(string device, variable type, AnalysisFunction_V3 *s)
+
+ +
+
+std::tuple<variable, variable> PSQ_GetBaselineChunkTimes(variable chunk, PSQ_PulseSettings *ps, variable totalOnsetDelayMS, WaveOrNull durations)
+

Calculates the baseline chunk times.

+
+ +
+
+static variable PSQ_EvaluateBaselineProperties(string device, AnalysisFunction_V3 *s, variable type, variable chunk, variable fifoInStimsetTime, variable totalOnsetDelay)
+

Evaluate one chunk of the baseline.

+
+
Parameters:
+
    +

  • device – device

    • +

  • s – AnalysisFunction_V3 struct

    • +

  • type – analysis function type, one of PatchSeqAnalysisFunctionTypes

    • +

  • chunk – chunk number, chunk == 0 -> Pre pulse baseline chunk, chunk >= 1 -> Post pulse baseline for traditional baseline evaluation if PSQ_PulseSettings::usesBaselineChunkEpochs is false.

    • +

  • fifoInStimsetTime – Fifo position in ms relative to the start of the stimset (therefore ignoring the totalOnsetDelay)

    • +

  • totalOnsetDelay – total onset delay in ms

    • +
+
+
Returns:
+

pre pulse baseline: 0 if the chunk passes, one of the possible AnalysisFuncReturnTypesConstants values otherwise post pulse baseline: 0 if the chunk passes, PSQ_BL_FAILED if it does not pass generic baseline: 0 if the chunk passes, PSQ_BL_FAILED if it does not pass

+
+
+
+ +
+
+variable PSQ_AddBaselineEpoch(wave epochWave, variable DAC, variable chunk, variable chunkStartTimeMax, variable chunkLengthTime)
+

Add base line epoch to user epochs.

+
+
Parameters:
+
    +

  • epochWave – 4D epochs wave

    • +

  • DAC – DAC channel number

    • +

  • chunk – number of evaluated chunk

    • +

  • chunkStartTimeMax – start time of chunk in ms

    • +

  • chunkLengthTime – time length of chunk in ms

    • +
+
+
+
+ +
+
+static variable PSQ_GetNumberOfChunks(string device, variable sweepNo, variable headstage, variable type, variable sampleIntervalAD)
+

Return the number of chunks.

+

A chunk is PSQ_BL_EVAL_RANGE [ms] of baseline.

+

For calculating the number of chunks we ignore the one chunk after the pulse which we don’t evaluate!

+
+ +
+
+static variable PSQ_Calculate(wave wv, variable column, variable startTime, variable rangeTime, variable method)
+
+ +
+
+static variable PSQ_NumAcquiredSweepsInSet(string device, variable sweepNo, variable headstage)
+

Return the number of already acquired sweeps from the given stimset cycle.

+
+ +
+
+variable PSQ_NumPassesInSet(wave numericalValues, variable type, variable sweepNo, variable headstage)
+

Return the number of passed sweeps in all sweeps from the given stimset cycle.

+
+ +
+
+static variable PSQ_GetDAStimsetLength(string device, variable headstage)
+

Return the DA stimset length in ms of the given headstage.

+
+
Returns:
+

stimset length or -1 on error

+
+
+
+ +
+
+wave PSQ_CreateOverrideResults(string device, variable headstage, variable type, string opMode = defaultValue)
+

Create the overrides results wave for CI testing.

+

PSQ_SQUARE_PULSE:

+

Rows:

    +

  • Only one

    • +
+

+

Cols:

    +

  • sweeps/steps

    • +
+

+

Layers:

    +

  • 0: x position in ms where the spike is in each sweep/step For convenience the values 0 always means no spike and 1 spike detected (at the appropriate position).

    • +

  • 1: async channel QC

    • +
+

+

PSQ_RHEOBASE/PSQ_RAMP:

+

Rows:

    +

  • chunk indizes

    • +
+

+

Cols:

    +

  • sweeps/steps

    • +
+

+

Layers:

    +

  • 0: 1 if the chunk has passing baseline QC or not

    • +

  • 1: x position in ms where the spike is in each sweep/step For convenience the values 0 always means no spike and 1 spike detected (at the appropriate position).

    • +

  • 2: async channel QC

    • +
+

+

Chunks (only for layer 0):

    +

  • 0: RMS short baseline QC

    • +

  • 1: RMS long baseline QC

    • +

  • 2: target voltage baseline QC

    • +

  • 3: leak current baseline QC

    • +
+

+

PSQ_DA_SCALE (Sub and Supra):

+

Rows:

    +

  • chunk indizes

    • +
+

+

Cols:

    +

  • sweeps/steps

    • +
+

+

Layers:

    +

  • 0: 1 if the chunk has passing baseline QC or not

    • +

  • 1: x position in ms where the spike is in each sweep/step For convenience the values 0 always means no spike and 1 spike detected (at the appropriate position).

    • +

  • 2: Number of spikes

    • +

  • 3: Async channel QC

    • +
+

+

Chunks (only for layer 0):

    +

  • 0: RMS short baseline QC

    • +

  • 1: RMS long baseline QC

    • +

  • 2: target voltage baseline QC

    • +

  • 3: leak current baseline QC

    • +
+

+

PSQ_DA_SCALE (Adaptive):

+

Rows:

    +

  • chunk indizes

    • +
+

+

Cols:

    +

  • sweeps/steps

    • +
+

+

Layers:

    +

  • 0: 1 if the chunk has passing baseline QC or not

    • +

  • 1: APFrequency

    • +

  • 2: Async channel QC

    • +
+

+

Chunks (only for layer 0):

    +

  • 0: RMS short baseline QC

    • +

  • 1: RMS long baseline QC

    • +

  • 2: target voltage baseline QC

    • +

  • 3: leak current baseline QC

    • +
+

+

JSON-Wavenote:

    +

  • ”APFrequenciesRhSuAd”: List of frequencies from the previous passing rheobase/supra/adaptive SCI

    • +

  • ”DAScalesRhSuAd”: List of DAScale values from previous passing rheobase/supra/adaptive SCI

    • +

  • ”PassingSupraSweep”: Sweep with passing supra set QC

    • +

  • ”PassingRheobaseSweep”: Sweep with passing rheobase set QC

    • +

  • ”PassingRhSuAdSweeps”: List of passing rheobase/supra/adaptive SCI sweeps

    • +

  • ”FailingAdaptiveSweep”: Failing adaptive sweep, the very last one, of the previous SCI (written by PSQ_DaScale)

    • +
+

+

PSQ_CHIRP:

+

Rows:

    +

  • chunk indizes

    • +
+

+

Cols:

    +

  • sweeps/steps

    • +
+

+

Layers:

    +

  • 0: 1 if the chunk has passing baseline QC or not

    • +

  • 1: maximum of AD data in chirp region [first row only, others are ignored], use NaN to use the real values

    • +

  • 2: minimum of AD data in chirp region [first row only, others are ignored], use NaN to use the real values

    • +

  • 3: passing spike check in chirp region or not [first row only, others are ignored]

    • +

  • 4: async channel QC

    • +
+

+

Chunks (only for layer 0):

    +

  • 0: RMS short baseline QC

    • +

  • 1: RMS long baseline QC

    • +

  • 2: target voltage baseline QC

    • +

  • 3: leak current baseline QC

    • +
+

+

PSQ_PIPETTE_BATH:

+

Rows:

    +

  • chunk indizes

    • +
+

+

Cols:

    +

  • sweeps/steps

    • +
+

+

Layers:

    +

  • 0: 1 if the chunk has passing baseline QC or not

    • +

  • 1: averaged steady state resistance [MΩ]

    • +

  • 2: async channel QC

    • +
+

+

Chunks (only for layer 0):

    +

  • 0: RMS short baseline QC

    • +

  • 1: RMS long baseline QC

    • +

  • 2: target voltage baseline QC

    • +

  • 3: leak current baseline QC

    • +
+

+

PSQ_SEAL_EVALUATION:

+

Rows:

    +

  • chunk indizes (only selected chunks via user epoch, sorted by ascending chunk start time)

    • +
+

+

Cols:

    +

  • sweeps/steps

    • +
+

+

Layers:

    +

  • 0: 1 if the chunk has passing baseline QC or not

    • +

  • 1: Resistance A [MΩ]

    • +

  • 2: Resistance B [MΩ]

    • +

  • 3: Async Channel QC

    • +
+

+

Chunks (only for layer 0):

    +

  • 0: RMS short baseline QC

    • +

  • 1: RMS long baseline QC

    • +

  • 2: target voltage baseline QC

    • +

  • 3: leak current baseline QC

    • +
+

+

PSQ_TRUE_REST_VM:

+

Rows:

    +

  • chunk indizes (only selected chunks via user epoch, sorted by ascending chunk start time)

    • +
+

+

Cols:

    +

  • sweeps/steps

    • +
+

+

Layers:

    +

  • 0: 1 if the chunk has passing baseline QC or not

    • +

  • 1: number of spikes (QC passes with 0)

    • +

  • 2: average voltage [mV]

    • +

  • 3: async channel QC

    • +
+

+

Chunks (only for row/layer 0):

    +

  • 0: RMS short baseline QC

    • +

  • 1: RMS long baseline QC

    • +

  • 2: target voltage baseline QC (unused)

    • +

  • 3: leak current baseline QC (unused)

    • +
+

+

PSQ_ACC_RES_SMOKE:

+

Rows:

    +

  • chunk indizes (only selected chunks via user epoch, sorted by ascending chunk start time)

    • +
+

+

Cols:

    +

  • sweeps/steps

    • +
+

+

Layers:

    +

  • 0: 1 if the chunk has passing baseline QC or not

    • +

  • 1: Access Resistance [MΩ]

    • +

  • 2: Steady State Resistance [MΩ]

    • +

  • 3: Async Channel QC

    • +
+

+

Chunks (only for layer 0):

    +

  • 0: RMS short baseline QC

    • +

  • 1: RMS long baseline QC

    • +

  • 2: target voltage baseline QC

    • +

  • 3: leak current baseline QC

    • +
+

+
+ +
+
+static variable PSQ_StoreStepSizeInLBN(string device, variable type, variable sweepNo, variable stepsize, variable future = defaultValue)
+

Store the step size in the labnotebook.

+
+ +
+
+static wave PSQ_SearchForSpikes(string device, variable type, wave sweepWave, variable headstage, variable offset, variable level, variable searchEnd = defaultValue, variable numberOfSpikesReq = defaultValue, wave spikePositions = defaultValue, variable *numberOfSpikesFound = defaultValue)
+

Search the AD channel of the given headstage for spikes from the pulse onset until the end of the sweep or searchEnd if given.

+
+
Parameters:
+
    +

  • device – [in] device

    • +

  • type – [in] One of PatchSeqAnalysisFunctionTypes

    • +

  • sweepWave – [in] sweep wave with acquired data

    • +

  • headstage – [in] headstage in the range [0, NUM_HEADSTAGES[

    • +

  • offset – [in] offset in ms where the spike search should start, commonly the totalOnsetDelay

    • +

  • level – [in] set the level for the spike search

    • +

  • searchEnd – [in] [optional, defaults to inf] total length in ms of the spike search, relative to sweepWave start

    • +

  • numberOfSpikesReq – [in] [optional, defaults to one] number of spikes to look for Positive finite value: Return value is 1 iff at least numberOfSpikes were found Inf: Return value is 1 if at least 1 spike was found

    • +

  • spikePositions – [out] [optional] returns the position of the first numberOfSpikes found on success in ms

    • +

  • numberOfSpikesFound – [out] [optional] returns the number of spikes found

    • +
+
+
Returns:
+

labnotebook value wave suitable for ED_AddEntryToLabnotebook()

+
+
+
+ +
+
+static variable PSQ_GetLastPassingLongRHSweep(string device, variable headstage, variable duration)
+

Return a sweep number of an existing sweep matching the following conditions.

+

    +

  • Acquired with Rheobase analysis function

    • +

  • Set QC passed for this SCI

    • +

  • Pulse duration was longer than duration

    • +

  • Spiked

    • +
+

+

And as usual we want the last matching sweep.

+
+
Returns:
+

existing sweep number or INVALID_SWEEP_NUMBER in case no such sweep could be found

+
+
+
+ +
+
+static variable PSQ_GetPreviousSetQCFailingAdaptive(string device, variable headstage, string params)
+

Return the previously acquired sweep number.

+

But only when it fullfills all of the following conditions:

    +

  • DAScale supra adaptive analysis function was run

    • +

  • failing set QC

    • +

  • all analysis parameters are the same

    • +

  • used same targetV autobias value

    • +
+

+
+ +
+
+variable PSQ_DS_IsValidMode(string str)
+

Return the truth that str is a valid PSQ_DAScale operation mode.

+
+ +
+
+static variable PSQ_GetLastPassingDAScale(string device, variable headstage, string opMode)
+

Return the sweep number of the last sweep using the PSQ_DaScale() analysis function, where the set passes and was in the given mode.

+
+ +
+
+static variable PSQ_GetLastPassingTrueRMP(string device, variable headstage)
+

Return the sweep number of the last sweep using the PSQ_TrueRestingMembranePotential() analysis function.

+
+ +
+
+static variable PSQ_DS_GetDAScaleOffset(string device, variable headstage, string opMode)
+

Return the DAScale offset for PSQ_DaScale()

+
+
Returns:
+

DAScale value in pA or NaN on error

+
+
+
+ +
+
+static variable PSQ_FoundAtLeastOneSpike(string device, variable sweepNo)
+

Check if the given sweep has at least one “spike detected” entry in the labnotebook.

+
+
Returns:
+

1 if found at least one, zero if none and NaN if no such entry could be found

+
+
+
+ +
+
+static variable PSQ_GetDefaultSamplingFrequency(string device, variable type)
+
+ +
+
+variable PSQ_GetDefaultSamplingFrequencyForSingleHeadstage(string device)
+

Returns the sampling frequency in kHz of our supported NI and ITC hardware for one active headstage and no TTL channels.

+
+ +
+
+static variable PSQ_CheckADSamplingFrequencyAndStoreInLabnotebook(string device, variable type, AnalysisFunction_V3 *s)
+

Return the QC state of the sampling interval/frequency check and store it also in the labnotebook.

+
+ +
+
+static variable PSQ_DS_GatherEpochDuration(string setName, variable epochIndex)
+

Return the duration of the given epoch in the stimulus set.

+

Does not require epoch info, and also supports combine epochs which don’t have a “Duration” parameter.

+
+ +
+
+static std::tuple<variable, variable> PSQ_DS_GetFrequencyEvalRangeForRhSuAd(string device, variable headstage, variable sweepNo)
+
+ +
+
+static std::tuple<variable, variable> PSQ_DS_GetFrequencyEvalRange(string device, variable headstage, variable sweepNo)
+
+ +
+
+static std::tuple<WAVE, WAVE> PSQ_DS_GatherFrequencyCurrentData(string device, variable sweepNo, variable headstage, wave sweeps, variable fromRhSuAd = defaultValue)
+

Use SweepFormula to gather the AP frequency and DAScale data from the given sweeps.

+
+
Parameters:
+
    +

  • device – DAC hardware device

    • +

  • sweepNo – current sweep

    • +

  • headstage – headstage

    • +

  • sweeps – wave of sweep numbers to gather the data from

    • +

  • fromRhSuAd – [optional, defaults to off] called for rheobase/supra/previous adaptive data (on) or adaptive data (off)

    • +
+
+
Return values:
+
    +

  • apfreq – AP frequency data

    • +

  • DAScale – DAScale data

    • +
+
+
+
+ +
+
+static std::tuple<WAVE, WAVE, WAVE, variable> PSQ_DS_FilterFrequencyCurrentData(wave apfreq, wave DAScales)
+

Filter duplicated AP frequencies out.

+
+
Parameters:
+
    +

  • apfreq – AP frequencies

    • +

  • DAScales – DA scale values

    • +
+
+
Return values:
+
    +

  • apfreqFiltered – AP frequencies with neighbouring duplicates removed

    • +

  • DAScalesFiltered – DScales values with intact indices

    • +

  • deletedIndizes – Possibly non-existing wave with the removed indizes

    • +

  • numPoints – Number of points in the apfreq/DAScales waves after filtering

    • +
+
+
+
+ +
+
+static std::tuple<WaveDouble, WaveDouble, string> PSQ_DS_FitFrequencyCurrentData(string device, variable sweepNo, WaveOrNull apfreq, WaveOrNull DAScales, variable singleFit = defaultValue)
+

Fit the AP frequency and DAScale data with a line fit and return the fit results (offsets and slopes)

+
+
Parameters:
+
    +

  • device – DAC hardware device

    • +

  • sweepNo – current sweep

    • +

  • apfreq – AP frequency data

    • +

  • DAScales – DAScale data

    • +

  • singleFit – [optional, defaults to false] if only a single fit should be done

    • +
+
+
Return values:
+
    +

  • fitOffset – offsets of all line fits

    • +

  • fitSlope – slopes of all line fits

    • +

  • errMsg – error message if both fitOffset and fitSlope are null

    • +
+
+
+
+ +
+
+static variable PSQ_DS_CreateSurveyPlotForUser(string device, variable sweepNo, variable headstage, variable fromRhSuAd = defaultValue)
+
+ +
+
+static variable PSQ_DS_AreFitResultsValid(string device, variable sweepNo, variable headstage, WaveOrNull fitOffset, WaveOrNull fitSlope, variable fromRhSuAd = defaultValue)
+

Check if the fit results from PSQ_DS_FitFrequencyCurrentData are valid.

+
+
Parameters:
+
    +

  • device – DAC hardware device

    • +

  • sweepNo – current sweep

    • +

  • headstage – headstage

    • +

  • fitOffset – fit offsets

    • +

  • fitSlope – fit slopes

    • +

  • fromRhSuAd – [optional, defaults to false] if the fit offset/slope data is from the rheobase/supra threshold sweeps or not

    • +
+
+
+
+ +
+
+std::tuple<variable, variable> PSQ_DS_GetDAScaleStepsNorm(string device, variable sweepNo, variable headstage)
+
+ +
+
+static wave PSQ_DS_GatherOvershootCorrection(PSQ_DS_DAScaleParams *cdp, wave apfreqParam, wave DAScalesParam, WaveOrNull futureDAScalesHistoric)
+

Calculate a list of DAScale values which need to be acquired in addition so that the AP frequency differences between consecutive points is smaller than maxFrequencyChangePercent.

+
+ +
+
+static variable PSQ_DS_CalculateDAScale(PSQ_DS_DAScaleParams *cdp, variable a, variable m, variable x, variable y)
+

Calculate the new DAScale value for adaptive threshold using linear extrapolation.

+
+
Parameters:
+
    +

  • cdp – calculation parameters

    • +

  • a – offset of the f-I straight line fit [Hz]

    • +

  • m – its slope [% Hz/pA]

    • +

  • x – DAScale of last acquired sweep [pA]

    • +

  • y – frequency value of last acquired sweep [Hz]

    • +
+
+
Returns:
+

new DAScale value [pA]

+
+
+
+ +
+
+static variable PSQ_DS_GatherAndWriteFrequencyToLabnotebook(string device, variable sweepNo, variable headstage)
+
+ +
+
+static std::tuple<variable, WAVE, WAVE> PSQ_DS_CalculateMaxSlopeAndWriteToLabnotebook(string device, variable sweepNo, variable headstage, variable fitSlope)
+
+ +
+
+static variable PSQ_DS_CalculateReachedFinalSlope(variable validFit, wave fitSlopes, wave DAScales, variable fitSlope, variable maxSlope, variable slopePercentage)
+

Determine the f-I slope QC.

+

For a passing we need all of the following to be true:

    +

  • valid fit

    • +

  • finite slope and not PSQ_DS_SKIPPED_FI_SLOPE

    • +

  • slope must be slopePercentage smaller than the maximum slope

    • +

  • slope must be acquired with a larger DAScale value than maximum slope

    • +
+

+
+ +
+
+static variable PSQ_DS_CalculateReachedFinalSlopeAndWriteToLabnotebook(string device, variable sweepNo, wave fitSlopes, wave DAScales, variable fitSlope, variable maxSlope, variable slopePercentage, variable validFit)
+
+ +
+
+static variable PSQ_DS_IsValidFitSlopePosition(wave fitSlopes, wave DAScales, variable fitSlope, variable maxSlope)
+

Check if the given fitSlope is a suitable candidate for maxSlope.

+

The condition is that the fitSlope is not acquired earlier than maxSlope as we want to find the case there it drops off and not where it starts to rise. We do use the DAScales values for this to ensure that measurements from overshoot correction (aka fill-in) don’t have a chance of interfering.

+
+ +
+
+static std::tuple<WAVE> PSQ_DS_EvaluateAdaptiveThresholdSweep(string device, variable sweepNo, variable headstage, PSQ_DS_DAScaleParams *cdp)
+

Evaluate the complete adaptive supra threshold sweep.

+

    +

  • Gather AP frequency and DAscale data

    • +

  • Fetch the same data from the passing rheobase/supra sweeps and previous adaptive sweeps from the same SCI

    • +

  • Create a new line fit for the last two points with differing AP frequency

    • +

  • Check if the resulting fit slope is smaller than slopePercentage

    • +
+

+

+

See also

+

PSQ_DS_GatherFutureDAScalesAndFrequency

+
+

+
+
Return values:
+

futureDAScales – future DAScale values including the historic ones,

+
+
+
+ +
+
+static variable PSQ_DS_AdaptiveDetermineSweepQCResults(string device, variable sweepNo, variable headstage, variable numInvalidSlopeSweepsAllowed, variable numSweepsWithSaturation)
+

Determine from the POST_SWEEP_EVENT if the set is already finished.

+

We don’t check here for passing/failing set QC but only if we need to continue acquisition.

+
+ +
+
+static std::tuple<string, string, variable> PSQ_DS_GetLabnotebookKeyConstants(variable type)
+

Helper function for PSQ_DS_GetLabnotebookData.

+
+
Parameters:
+

type – One of PSQDAScaleAdaptiveLBNTypeConstants

+
+
Return values:
+
    +

  • currentSCI – labnotebook string (PSQ_FMT_XXX or stock entry) for data from the current SCI

    • +

  • RhSuAd – labnotebook PSQ_FMT_XXX string for RhSuAd data

    • +

  • headstageContingencyMode – One of HCM_INDEP/HCM_DEPEND

    • +
+
+
+
+ +
+
+static std::tuple<WAVE, variable> PSQ_DS_GetLabnotebookData(wave numericalValues, wave textualValues, variable sweepNo, variable headstage, variable type, variable filterPassing = defaultValue, variable beforeSweepQCResult = defaultValue, variable fromRhSuAd = defaultValue)
+

Return some labnotebook entries for all passing sweeps from RhSuAd and the current SCI.

+
+ +
+
+static variable PSQ_DS_AdaptiveIsFinished(string device, variable sweepNo, variable headstage, variable numSweepsWithSaturation, variable fromRhSuAd = defaultValue)
+
+ +
+
+static std::tuple<WAVE, WAVE, WAVE> PSQ_DS_GatherFutureDAScalesAndFrequency(string device, variable sweepNo, variable headstage, PSQ_DS_DAScaleParams *cdp)
+
+ +
+
+static variable PSQ_DS_CalcFutureDAScalesAndStoreInLBN(string device, variable sweepNo, variable headstage, wave futureDAScales)
+
+ +
+
+static wave PSQ_DS_FilterPassingData(WaveOrNull data, WaveOrNull booleanQC, variable inBetween = defaultValue)
+

Return the entries of data which have passing state in booleanQC.

+

Both data and booleanQC are usually from the full SCI.

+
+ +
+
+static wave PSQ_DS_GetPassingDAScaleSweeps(wave numericalValues, variable passingSweep, variable headstage)
+
+ +
+
+static wave PSQ_DS_GetPassingRheobaseSweeps(wave numericalValues, variable passingRheobaseSweep, variable headstage)
+
+ +
+
+static wave PSQ_DS_GetPassingRhSuAdSweepsAndStoreInLBN(string device, variable sweepNo, variable headstage, string params)
+
+ +
+
+static std::tuple<variable, variable> PSQ_DS_CalculateAndStoreDAScaleStepWidths(string device, variable sweepNo, wave apfreqRhSuAd, wave DAScalesRhSuAd, variable maxFrequencyChangePercent, variable dascaleStepWidthMinMaxRatio, variable fallbackDAScaleRangeFac)
+

Calculate the minimum and maximum step widths for DAScale normalized.

+

Stored in the labnotebook.

+

Multiply by AP Frequency to get scaled values.

+
+ +
+
+static std::tuple<variable, variable, variable, variable> PSQ_DS_GetValuesOfLargestDAScale(wave numericalValues, WaveText textualValues, variable sweepNo, variable headstage)
+
+ +
+
+static variable PSQ_DS_DAScaleParamsAreFinite(PSQ_DS_DAScaleParams *cdp)
+
+ +
+
+static variable PSQ_DS_InitDAScaleParams(PSQ_DS_DAScaleParams *cdp)
+
+ +
+
+static string PSQ_GetHelpCommon(variable type, string name)
+

Help strings for common parameters.

+

Not every analysis function uses every parameter though.

+
+ +
+
+static string PSQ_CheckParamCommon(string name, CheckParametersStruct *s, variable maxThreshold = defaultValue)
+
+ +
+
+string PSQ_DAScale_GetParams()
+

Require parameters from stimset.

+
+ +
+
+string PSQ_DAScale_GetHelp(string name)
+
+ +
+
+string PSQ_DAScale_CheckParam(string name, CheckParametersStruct *s)
+
+ +
+
+variable PSQ_DAScale(string device, AnalysisFunction_V3 *s)
+

Patch Seq Analysis function to find a suitable DAScale.

+

Prerequisites:

    +

  • Does only work for one headstage

    • +

  • Assumes that the stimset has 500ms of pre pulse baseline, a non-zero pulse and at least 1000ms post pulse baseline.

    • +

  • Each 500ms (PSQ_BL_EVAL_RANGE) of the baseline is a chunk

    • +
+

+

Testing: For testing the spike detection logic, the results can be defined in the override wave,

+

Reading the results from the labnotebook:

+
+

See also

+

PSQ_CreateOverrideResults().

+
+

+

WAVE numericalValues = GetLBNumericalValues(device)
+
+// set properties
+
+key = CreateAnaFuncLBNKey(PSQ_DA_SCALE, PSQ_FMT_LBN_SET_PASS, query = 1)
+setPassed = GetLastSettingIndepSCI(numericalValues, sweepNo, key, headstage, UNKNOWN_MODE)
+
+if(setPassed)
+  // set passed
+else
+  // set did not pass
+endif
+
+// single sweep properties
+key = CreateAnaFuncLBNKey(PSQ_DA_SCALE, PSQ_FMT_LBN_SWEEP_PASS, query = 1)
+sweepPassed = GetLastSettingIndep(numericalValues, sweepNo, key, UNKNOWN_MODE)
+
+// chunk (500ms portions of the baseline) properties
+key = CreateAnaFuncLBNKey(PSQ_DA_SCALE, PSQ_FMT_LBN_CHUNK_PASS, chunk = chunk, query = 1)
+chunkPassed = GetLastSettingIndep(numericalValues, sweepNo, key, UNKNOWN_MODE)
+
+// single test properties
+key = CreateAnaFuncLBNKey(PSQ_DA_SCALE, PSQ_FMT_LBN_RMS_SHORT_PASS, chunk = chunk, query = 1)
+rmsShortPassed = GetLastSettingIndep(numericalValues, sweepNo, key, UNKNOWN_MODE)
+key = CreateAnaFuncLBNKey(PSQ_DA_SCALE, PSQ_FMT_LBN_RMS_LONG_PASS, chunk = chunk, query = 1)
+rmsLongPassed  = GetLastSettingIndep(numericalValues, sweepNo, key, UNKNOWN_MODE)
+key = CreateAnaFuncLBNKey(PSQ_DA_SCALE, PSQ_FMT_LBN_TARGETV_PASS, chunk = chunk, query = 1)
+targetVPassed  = GetLastSettingIndep(numericalValues, sweepNo, key, UNKNOWN_MODE)
+
+// get fitted resistance from last passing sweep
+// resistance for the first headstage can be found in resistanceFitted[0]
+WAVE/Z resistanceFitted = GetLastSettingSCI(numericalValues, sweepNo, LABNOTEBOOK_USER_PREFIX + LBN_RESISTANCE_FIT, headstage, UNKNOWN_MODE)
+
+
+

+

Decision logic flowchart:

+

+

+
///
+/// Sketch of a stimset with inserted TP, pre pulse baseline (-), pulse (*), and post pulse baseline (-).
+///
+///  |-|                 ***********************************
+///  | |                 |                                 |
+///  | |                 |                      \WWW/      |
+///  | |                 |                      /   \      |
+///  | |                 |                     /wwwww\     |
+///  | |                 |                   _|  o_o  |_   |
+///  | |                 |      \WWWWWWW/   (_   / \   _)  |
+///  | |                 |    _/`  o_o  `\_   |  \_/  |    |
+///  | |                 |   (_    (_)    _)  : ~~~~~ :    |
+///  | |                 |     \ '-...-' /     \_____/     |
+///  | |                 |     (`'-----'`)     [     ]     |
+///  | |                 |      `"""""""`      `"""""`     |
+///  | |                 |                                 |
+/// -| |-----------------|                                 |--------------------------------------------
+///
+/// ascii art image from: http://ascii.co.uk/art/erniebert
+///
+///
+
+
+
+ +
+
+string PSQ_SquarePulse_GetParams()
+

Return a list of required parameters.

+
+ +
+
+string PSQ_SquarePulse_GetHelp(string name)
+
+ +
+
+string PSQ_SquarePulse_CheckParam(string name, CheckParametersStruct *s)
+
+ +
+
+variable PSQ_SquarePulse(string device, AnalysisFunction_V3 *s)
+

Analysis function to find the smallest DAScale where the cell spikes.

+

Prerequisites:

    +

  • Does only work for one headstage

    • +

  • Assumes that the stimset has a pulse

    • +
+

+

Testing: For testing the spike detection logic, the results can be defined in the override wave,

+

Decision logic flowchart:

+
+

See also

+

PSQ_CreateOverrideResults().

+
+

+

+

+
///
+/// Sketch of a stimset with pre pulse baseline (-), pulse (*), and post pulse baseline (-).
+///
+///    *******
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+/// ---|     |--------------------------------------------
+///
+///
+
+
+
+ +
+
+string PSQ_Rheobase_GetParams()
+

Return a list of required parameters.

+
+ +
+
+string PSQ_Rheobase_GetHelp(string name)
+
+ +
+
+string PSQ_Rheobase_CheckParam(string name, CheckParametersStruct *s)
+
+ +
+
+variable PSQ_Rheobase(string device, AnalysisFunction_V3 *s)
+

Analysis function for finding the exact DAScale value between spiking and non-spiking.

+

Prerequisites:

    +

  • Does only work for one headstage

    • +

  • Assumes that the stimset has a pulse of non-zero and arbitrary length

    • +

  • Pre pulse baseline length is PSQ_BL_EVAL_RANGE

    • +

  • Post pulse baseline length a multiple of PSQ_BL_EVAL_RANGE

    • +
+

+

Testing: For testing the spike detection logic, the results can be defined in the override wave,

+

Decision logic flowchart:

+
+

See also

+

PSQ_CreateOverrideResults().

+
+

+

+

+
///
+/// Sketch of a stimset with pre pulse baseline (-), pulse (*), and post pulse baseline (-).
+///
+///    *******
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+///    |     |
+/// ---|     |--------------------------------------------
+///
+///
+
+
+
+ +
+
+variable PSQ_GetFinalDAScaleFake()
+
+ +
+
+string PSQ_Ramp_GetParams()
+

Return a list of required parameters.

+
+ +
+
+string PSQ_Ramp_GetHelp(string name)
+
+ +
+
+string PSQ_Ramp_CheckParam(string name, CheckParametersStruct *s)
+
+ +
+
+variable PSQ_Ramp(string device, AnalysisFunction_V3 *s)
+

Analysis function for applying a ramp stim set and finding the position were it spikes.

+

Prerequisites:

    +

  • Does only work for one headstage

    • +

  • Assumes that the stimset has a ramp of non-zero and arbitrary length

    • +

  • Pre pulse baseline length is PSQ_BL_EVAL_RANGE

    • +

  • Post pulse baseline length is at least two times PSQ_BL_EVAL_RANGE

    • +
+

+

Testing: For testing the spike detection logic, the results can be defined in the override wave,

+

Decision logic flowchart:

+
+

See also

+

PSQ_CreateOverrideResults().

+
+

+

+

+
///
+/// Sketch of a stimset with pre pulse baseline (-), ramp (/|), and post pulse baseline (-).
+///
+///                 /|
+///                / |
+///               /  |
+///              /   |
+///             /    |
+///            /     |
+///           /      |
+///          /       |
+///         /        |
+///        /         |
+///       /          |
+///      /           |
+///     /            |
+/// ---/             |--------------------------------------------
+///
+///
+
+
+
+ +
+
+static variable PSQ_Ramp_AddEpoch(string device, variable headstage, wave wv, string tags, string shortName, variable first, variable last)
+
+ +
+
+variable PSQ_Ramp_AddEpochImpl(WaveText epochWave, wave wv, variable DAC, string tags, string shortName, variable first, variable last)
+

device independent implementation of PSQ_Ramp_AddEpoch

+
+ +
+
+std::tuple<variable, variable> PSQ_CR_SetHasPassed(wave numericalValues, variable sweepNo, variable headstage)
+

Determine if we have three passing sweeps with the same DAScale value.

+
+
Returns:
+

result set passing state (0/1)

+
+
Returns:
+

maxOccurences maximum number of passing sets with the same DASCale value

+
+
+
+ +
+
+static std::tuple<ChirpBoundsInfo> PSQ_CR_DetermineBoundsState(variable baseline, variable minimum, variable maximum, variable value)
+

Returns the two letter states “AA”, “BB” and “BA” for the value and the scaling factors to reach min/center/max.

+

We need the real baseline value (measured), whereas the center between minimum/maximum would be targetV, which the user entered together with an allowed ± range.

+
+ +
+
+string PSQ_CR_BoundsActionToString(variable boundsAction)
+
+ +
+
+static variable PSQ_CR_DetermineBoundsActionHelper(wave wv, string state, variable action)
+
+ +
+
+static variable PSQ_CR_DetermineBoundsActionFromState(string upperState, string lowerState)
+

Returns an action depending on the upper and lower states, see ChirpBoundsAction.

+
+ +
+
+static variable PSQ_CR_DetermineScalingFactor(ChirpBoundsInfo *lowerInfo, ChirpBoundsInfo *upperInfo, variable boundsEvaluationMode)
+

Determine the scaling factor for DAScale which is required for being inside the bounds.

+
+ +
+
+static std::tuple<variable, variable> PSQ_CR_DetermineBoundsAction(string device, wave scaledDACWave, variable headstage, variable sweepNo, variable chirpStart, variable cycleEnd, variable innerRelativeBound, variable outerRelativeBound, variable boundsEvaluationMode)
+

Determine the bounds action given the requested chirp slice.

+
+
Parameters:
+
    +

  • device – device

    • +

  • scaledDACWave – DAQ data wave with correct units and scaling

    • +

  • headstage – headstage

    • +

  • sweepNo – sweep number

    • +

  • chirpStart – x-position relative to stimset start where the chirp starts

    • +

  • cycleEnd – x-position relative to stimset start where the requested number of cycles finish

    • +

  • innerRelativeBound – analysis parameter

    • +

  • outerRelativeBound – analysis parameter

    • +

  • boundsEvaluationMode – bounds evaluation mode, one of PSQChirpBoundsEvaluationMode

    • +
+
+
Returns:
+

boundsAction, one of ChirpBoundsAction

+
+
Returns:
+

scalingFactorDAScale, scaling factor to be inside the bounds for actions PSQ_CR_INCREASE/PSQ_CR_DECREASE

+
+
+
+ +
+
+static string PSQ_CR_BoundsEvaluationModeToString(variable val)
+
+ +
+
+static variable PSQ_CR_ParseBoundsEvaluationModeString(string str)
+
+ +
+
+static variable PSQ_SetAutobiasTargetVIfPresent(string device, variable headstage, string params, string name)
+
+ +
+
+static variable PSQ_SetAutobiasTargetV(string device, variable headstage, variable value)
+
+ +
+
+static variable PSQ_CR_SetAutobiasTargetVFromTrueRMP(string device, variable headstage, string params)
+

Set autobias target V from the average voltage of a passing PSQ_TrueRestingMembranePotential() sweep.

+
+
Returns:
+

0 on success, 1 otherwise

+
+
+
+ +
+
+string PSQ_Chirp_GetHelp(string name)
+
+ +
+
+string PSQ_Chirp_CheckParam(string name, CheckParametersStruct *s)
+
+ +
+
+string PSQ_Chirp_GetParams()
+

Return a list of required analysis functions for PSQ_Chirp()

+
+ +
+
+variable PSQ_Chirp(string device, AnalysisFunction_V3 *s)
+

Analysis function for determining the impedance of the cell using a sine chirp stim set.

+

Prerequisites:

    +

  • Does only work for one headstage

    • +

  • Assumes that the stimset has a chirp of non-zero and arbitrary length

    • +

  • Pre pulse baseline length is PSQ_BL_EVAL_RANGE

    • +

  • Post pulse baseline length is at least two times PSQ_BL_EVAL_RANGE

    • +
+

+

Testing: For testing the range detection logic, the results can be defined in the wave root:overrideResults.

+

Decision logic flowchart:

+
+

See also

+

PSQ_CreateOverrideResults()

+
+

+

+

+

The bounds action for Symmetric (Upper and Lower) is derived from the state according to the following sketch:

+

+

Depolarized (Upper only):

+ + + + + + + + + + + + + + + + + +

State

Action

BA

Pass

AA

Decrease

BB

Increase

+

Hyperpolarized (Lower only):

+ + + + + + + + + + + + + + + + + +

State

Action

BA

Pass

AA

Increase

BB

Decrease

+

+
///
+/// Sketch of a stimset with pre pulse baseline (-), sine chirp (~), and post pulse baseline (-).
+///
+///
+///
+///                     ~               ~
+///                   ~  ~             ~ ~
+///                  ~    ~           ~   ~
+///                 ~      ~         ~     ~
+/// ---------------~        ~       ~       ~--------------------------------
+///                          ~     ~
+///                           ~   ~
+///                             ~
+///
+///
+
+
+
+ +
+
+static variable PSQ_CR_FindDependentAnalysisParameter(string device, string name, string params)
+
+ +
+
+static std::tuple<variable, variable> PSQ_CR_GetSpikeEvaluationRange(string device, variable sweepNo, variable headstage)
+

Return the begin/start [ms] of the spike bounds evaluation range.

+

Zero is the DA/AD wave zero.

+
+ +
+
+std::tuple<variable, variable> PSQ_CR_AddSpikeEvaluationEpoch(WaveText epochsWave, variable DAC, variable headstage, wave durations, variable totalOnsetDelayMS)
+

Adds PSQ_Chirp spike evaluation epoch.

+
+
Parameters:
+
    +

  • epochsWave – 4d epochs wave

    • +

  • DAC – DAC number

    • +

  • headstage – headstage number

    • +

  • durations – pulse duration wave

    • +

  • totalOnsetDelayMS – totalOnsetDelay in ms

    • +
+
+
Return values:
+
    +

  • epBegin – epoch begin in s

    • +

  • epEnd – epoch end in s

    • +
+
+
+
+ +
+
+static std::tuple<variable, variable> PSQ_CR_GetChirpEvaluationRange(string device, variable sweepNo, variable headstage, variable requestedCycles)
+

Return the begin/start [ms] of the chirp bounds evaluation range.

+

Zero is the DA/AD wave zero.

+
+ +
+
+std::tuple<variable, variable> PSQ_CR_AddCycleEvaluationEpoch(WaveText epochsWave, WaveText fullCycleEpochs, variable DAC)
+

Add PSQ_Chirp cycle evaluation epoch.

+
+
Parameters:
+
    +

  • epochsWave – 4d epoch wave

    • +

  • fullCycleEpochs – 2d epoch wave with epochs of full cycles (sorted)

    • +

  • DAC – DAC number

    • +
+
+
Return values:
+
    +

  • epBegin – epoch begin in s

    • +

  • epEnd – epoch end in s

    • +
+
+
+
+ +
+
+wave PSQ_CR_GetFullCycleEpochs(wave numericalValues, WaveText textualValues, variable DAC, WaveText epochsWave, variable requestedCycles)
+
+ +
+
+static variable PSQ_ForceSetEvent(string device, variable headstage)
+

Manually force the pre/post set events.

+

Required to do before skipping sweeps.

+
+Todo:
+

this hack must go away.

+
+ +

+
+ +
+
+static string PSQ_ExecuteSweepFormula(string device, string code)
+

Execute code in the SweepFormula notebook.

+
+ +
+
+static variable PSQ_SetSamplingIntervalMultiplier(string device, variable multiplier)
+
+ +
+
+static variable PSQ_SetStimulusSets(string device, variable headstage, string params)
+
+ +
+
+string PSQ_PipetteInBath_CheckParam(string name, CheckParametersStruct *s)
+
+ +
+
+string PSQ_PipetteInBath_GetHelp(string name)
+
+ +
+
+string PSQ_PipetteInBath_GetParams()
+
+ +
+
+variable PSQ_PipetteInBath_GetNumberOfTestpulses(string params)
+
+ +
+
+variable PSQ_PipetteInBath(string device, AnalysisFunction_V3 *s)
+

Analysis function for determining the pipette resistance while that is located in the bath.

+

Prerequisites:

    +

  • Does only work for one headstage

    • +

  • We expect three epochs per test pulse in the stimset, plus one epoch before all TPs, and at the very end

    • +

  • Assumes that the stimset has NumberOfTestpulses test pulses

    • +

  • Pre pulse baseline length is PSQ_BL_EVAL_RANGE

    • +

  • Post pulse baseline is not evaluated

    • +
+

+

Testing: For testing the range detection logic, the results can be defined in the wave root:overrideResults.

+

Decision logic flowchart:

+
+

See also

+

PSQ_CreateOverrideResults()

+
+

+

+

+
///
+/// Sketch of a stimset with three test pulse like epochs
+///
+///                    +-----+       +-----+       +-----+
+///                    |     |       |     |       |     |
+///                    |     |       |     |       |     |
+///                    |     |       |     |       |     |
+/// -------------------+     +-------+     +-------+     +------------------------
+///
+/// Epoch borders
+/// -------------
+///
+///       0        | 1 |  2  | 3 | 4 |  5  | 6 | 7 |  8  | 9 |     10
+///
+///
+
+
+
+ +
+
+static wave PSQ_GetSweepFormulaResultWave(WaveText textualResultsValues, string key)
+

Return entries from the textual result wave written using store with the given key

+

Note: This function always returns the last entry, so this needs to be called directly after PSQ_ExecuteSweepFormula without giving control back to Igor Pro.

+
+ +
+
+static variable PSQ_GetSweepFormulaResult(WaveText textualResultsValues, string key)
+
+ +
+
+static variable PSQ_PB_GetPrePulseBaselineDuration(string device, variable headstage)
+
+ +
+
+static variable PSQ_CreateTestpulseEpochs(string device, variable headstage, variable numTestPulses)
+

Create user epochs for the testpulse like shapes in the stimset.

+

Assumes that all sweeps in the stimset are the same.

+
+
Returns:
+

0 on success, 1 on failure

+
+
+
+ +
+
+variable PSQ_CreateTestpulseEpochsImpl(WaveText epochWave, variable DAC, string setName, variable totalOnsetDelay, variable DAScale, variable numTestPulses)
+

Device independent implementation function for PSQ_CreateTestpulseEpochs.

+

Assumes that all sweeps in the stimset are the same.

+
+
Returns:
+

0 on success, 1 on failure

+
+
+
+ +
+
+static variable PSQ_CreateTestpulseLikeEpoch(WaveText epochWave, variable DAC, string setName, variable DAScale, variable start, variable epochIndex, variable tpIndex)
+
+ +
+
+string PSQ_SealEvaluation_CheckParam(string name, CheckParametersStruct *s)
+
+ +
+
+string PSQ_SealEvaluation_GetHelp(string name)
+
+ +
+
+string PSQ_SealEvaluation_GetParams()
+
+ +
+
+variable PSQ_SealEvaluation(string device, AnalysisFunction_V3 *s)
+

Analysis function for checking the seal resistance.

+

Prerequisites:

    +

  • Does only work for one headstage

    • +

  • See below for the stimset layout

    • +

  • The dedicated baseline epochs before each testpulse group (epoch 0 and 11) and must be at least as large as the given BaselineChunkLength analysis parameter

    • +
+

+

Testing: For testing the range detection logic, the results can be defined in the wave root:overrideResults.

+

Decision logic flowchart:

+
+

See also

+

PSQ_CreateOverrideResults()

+
+

+

+

+
///
+/// Sketch of the stimset
+///
+///                    +-----+       +-----+       +-----+                                    +-----+       +-----+       +-----+
+///                    |     |       |     |       |     |                                    |     |       |     |       |     |
+///                    |     |       |     |       |     |                                    |     |       |     |       |     |
+///                    |     |       |     |       |     |                                    |     |       |     |       |     |
+/// -------------------+     +-------+     +-------+     +------------------------------------+     +-------+     +-------+     +------------
+///
+/// Epoch borders
+/// -------------
+///
+///       0        | 1 |  2  | 3 | 4 |  5  | 6 | 7 |  8  | 9 |             10    |     11 | 12| 13  | 14| 15| 16  | 17|18 | 19  | 20 |  21  |
+///
+/// We always expect PSQ_SE_REQUIRED_EPOCHS (22) epochs even if the user only chose `First` or `Second` on testpulse selection.
+///
+///    BEGIN group A
+/// 0: baselineQC chunk with length `BaselineChunkLength` or longer before group A
+/// 1-3: 1. TP
+/// 4-6: 2. TP
+/// 7-9: 3. TP
+///    END group A
+/// 10: empty space, can be zero points long, but is always present
+///    BEGIN group B
+/// 11: baselineQC chunk with length `BaselineChunkLength` or longer before group B
+/// 12-14: 1. TP
+/// 15-17: 2. TP
+/// 18-20: 3. TP
+///    END group B
+/// 21: trailing empty space
+///
+///
+
+
+
+ +
+
+static variable PSQ_SE_CreateEpochs(string device, variable headstage, string params)
+

Create user epochs.

+

Assumes that all sweeps in the stimset are the same.

+
+
Returns:
+

0 on success, 1 on failure

+
+
+
+ +
+
+variable PSQ_SE_CreateEpochsImpl(WaveText epochWave, variable DAC, variable totalOnsetDelayMS, string setName, variable testpulseGroupSel, variable DAScale, variable numEpochs, variable chunkLength)
+
+ +
+
+variable PSQ_SE_GetTestpulseGroupSelection(string params)
+
+ +
+
+static variable PSQ_SE_ParseTestpulseGroupSelection(string str)
+
+ +
+
+string PSQ_TrueRestingMembranePotential_CheckParam(string name, CheckParametersStruct *s)
+
+ +
+
+string PSQ_TrueRestingMembranePotential_GetHelp(string name)
+
+ +
+
+string PSQ_TrueRestingMembranePotential_GetParams()
+
+ +
+
+variable PSQ_TrueRestingMembranePotential(string device, AnalysisFunction_V3 *s)
+

Analysis function for determining the mean potential of a stimset.

+

Prerequisites:

    +

  • Does only work for one headstage

    • +

  • See below for the stimset layout

    • +
+

+

Testing: For testing the range detection logic, the results can be defined in the wave root:overrideResults.

+

Decision logic flowchart:

+
+

See also

+

PSQ_CreateOverrideResults()

+
+

+

+

+
///
+/// Sketch of the stimset
+///
+/// --------------------------------------------
+///
+/// Epoch borders
+/// -------------
+///
+/// |         0          | 1 |        2        |
+///
+/// We always expect PSQ_VM_REQUIRED_EPOCHS (3) epochs.
+///
+/// 0: baselineQC chunk with length `BaselineChunkLength` or larger
+/// 1: empty space, can be zero points long, but is always present
+/// 2: baselineQC chunk with length `BaselineChunkLength` or larger
+///
+///
+
+
+
+ +
+
+static std::tuple<string, string> PSQ_CreateBaselineChunkSelectionStrings(variable index)
+
+ +
+
+static variable PSQ_CreateBaselineChunkSelectionEpochs(string device, variable headstage, string params, wave epochIndizes, variable numRequiredEpochs = defaultValue)
+

Create baseline selection epochs.

+

Assumes that all sweeps in the stimset are the same.

+
+
Parameters:
+
    +

  • device – device

    • +

  • headstage – headstage

    • +

  • params – analysis function parameters

    • +

  • epochIndizes – indizes of stimset epochs for which we should create BLS epochs

    • +

  • numRequiredEpochs – number of required epochs in the stimset, use

    • +
+
+
Returns:
+

0 on success, 1 on failure

+
+
+
+ +
+
+variable PSQ_CreateBaselineChunkSelectionEpochs_AddEpochs(WaveText epochWave, variable DAC, variable totalOnsetDelayMS, string setName, wave epochIndizes, variable numEpochs, variable chunkLength)
+
+ +
+
+static variable PSQ_DetermineSweepQCResults(string device, variable type, variable sweepNo, variable headstage, variable requiredPassesInSet, variable numSweepsFailedAllowed)
+

Check if we need to act on the now available sweep QC state.

+
+
Parameters:
+
    +

  • device – device

    • +

  • type – analysis function type

    • +

  • sweepNo – sweep number

    • +

  • headstage – headstage

    • +

  • requiredPassesInSet – number of passes in set which makes the set pass

    • +

  • numSweepsFailedAllowed – number of failures in set which makes the set fail

    • +
+
+
Returns:
+

One of DetermineSweepQCReturns

+
+
+
+ +
+
+static variable PSQ_VM_EvaluateAverageVoltage(string device, variable sweepNo, variable headstage, string params, variable baselineQCPassed)
+
+ +
+
+static std::tuple<variable, WAVE> PSQ_VM_CheckForSpikes(string device, variable sweepNo, variable headstage, wave scaledDACWave, variable level)
+
+ +
+
+static variable PSQ_VM_HandleFailingSpikeQC(string device, AnalysisFunction_V3 *s, wave spikePositions)
+
+ +
+
+static variable PSQ_CheckThatAlarmIsEnabled(string device, wave asyncChannels)
+
+ +
+
+static variable PSQ_CheckAsyncAlarmStateAndStoreInLabnotebook(string device, variable type, variable sweepNo, wave asyncChannels)
+
+ +
+
+string PSQ_AccessResistanceSmoke_CheckParam(string name, CheckParametersStruct *s)
+
+ +
+
+string PSQ_AccessResistanceSmoke_GetHelp(string name)
+
+ +
+
+string PSQ_AccessResistanceSmoke_GetParams()
+
+ +
+
+variable PSQ_AccessResistanceSmoke_GetNumberOfTestpulses(string params)
+
+ +
+
+variable PSQ_AccessResistanceSmoke(string device, AnalysisFunction_V3 *s)
+

Analysis function for determining the TP resistances and their ratio.

+

Prerequisites:

    +

  • Does only work for one headstage

    • +

  • We expect three epochs per test pulse in the stimset, plus one epoch before all TPs, and at the very end

    • +

  • Assumes that the stimset has NumberOfTestpulses test pulses

    • +

  • Pre pulse baseline length is given by BaselineChunkLength

    • +

  • Post pulse baseline is not evaluated

    • +
+

+

Testing: For testing the range detection logic, the results can be defined in the wave root:overrideResults.

+

Decision logic flowchart:

+
+

See also

+

PSQ_CreateOverrideResults()

+
+

+

+

+
///
+/// Sketch of a stimset with three test pulse like epochs
+///
+///                    +-----+       +-----+       +-----+
+///                    |     |       |     |       |     |
+///                    |     |       |     |       |     |
+///                    |     |       |     |       |     |
+/// -------------------+     +-------+     +-------+     +------------------------
+///
+/// Epoch borders
+/// -------------
+///
+///        0       | 1 |  2  | 3 | 4 |  5  | 6 | 7 |  8  | 9 |      10
+///
+/// So for this stimset we have two epochs at the very beginning and end, plus
+/// three epochs per test pulse and three test pulses, which gives eleven in
+/// total.
+///
+///
+
+
+
+ +
+
+

Variables

+
+
+static const double PSQ_BL_PRE_PULSE = 0x0
+
+ +
+
+static const double PSQ_BL_POST_PULSE = 0x1
+
+ +
+
+static const double PSQ_BL_GENERIC = 0x2
+
+ +
+
+static const double PSQ_RMS_SHORT_TEST = 0x0
+
+ +
+
+static const double PSQ_RMS_LONG_TEST = 0x1
+
+ +
+
+static const double PSQ_TARGETV_TEST = 0x2
+
+ +
+
+static const double PSQ_LEAKCUR_TEST = 0x3
+
+ +
+
+static const double PSQ_DEFAULT_SAMPLING_MULTIPLIER = 4
+
+ +
+
+static const double PSQ_RHEOBASE_DURATION = 500
+
+ +
+
+static const double PSQ_DA_FALLBACK_DASCALE_RANGE_FAC = 1.5
+
+ +
+
+
+struct PSQ_DS_DAScaleParams
+
+

Public Members

+
+
+variable absFrequencyMinDistance
+
+ +
+
+variable maxFrequencyChangePercent
+
+ +
+
+variable daScaleStepMinNorm
+
+ +
+
+variable daScaleStepMaxNorm
+
+ +
+
+variable slopePercentage
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___artefact_removal_8ipf.html b/file/_m_i_e_s___artefact_removal_8ipf.html new file mode 100644 index 0000000000..faae6ada58 --- /dev/null +++ b/file/_m_i_e_s___artefact_removal_8ipf.html @@ -0,0 +1,402 @@ + + + + + + + + File MIES_ArtefactRemoval.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_ArtefactRemoval.ipf

+

AR Functions related to artefact removal

+
+

Functions

+
+
+static wave AR_ComputeRanges(dfref sweepDFR, variable sweepNo, wave numericalValues)
+

Return a free 2D wave with artefact positions and the corresponding DA channel from which it originated.

+

Columns:

    +

  • Artefact position [ms]

    • +

  • DAC

    • +

  • ADC

    • +

  • Headstage

    • +
+

+
+ +
+
+static variable AR_UpdatePanel(string device, wave ranges, dfref sweepDFR)
+
+ +
+
+static variable AR_UpdateListBoxWave(string device)
+
+ +
+
+static variable AR_RemoveTraces(string graph)
+

Remove the traces used for highlightning the to-be-removed ranges.

+
+ +
+
+static string AR_GetHighlightTraces(string graph)
+

Return a list of the traces used for highlightning the to-be-removed ranges.

+
+ +
+
+variable AR_HighlightArtefactsEntry(string graph)
+
+ +
+
+static variable AR_HandleRanges(string graph, variable removeRange = defaultValue)
+
+ +
+
+static dfref AR_GetFolder(string device)
+

Return the datafolder reference to the folder storing the listbox wave and the artefact data wave.

+

Requires the user data PANEL_FOLDER of the external artefact removal panel.

+
+ +
+
+static dfref AR_GetSweepFolder(string device)
+

Return the datafolder reference to the folder storing the single 1D sweep waves.

+

Requires the user data AR_SWEEPFOLDER of the external artefact removal panel.

+
+ +
+
+static variable AR_SetSweepFolder(string device, dfref sweepDFR)
+

Updates the AR_SWEEPFOLDER user data of the artefact removal panel.

+
+ +
+
+variable AR_MainListBoxProc(WMListboxAction *lba)
+
+ +
+
+variable AR_SetVarProcCutoffLength(WMSetVariableAction *sva)
+
+ +
+
+variable AR_ButtonProc_RemoveRanges(WMButtonAction *ba)
+
+ +
+
+variable AR_UpdateTracesIfReq(string graph, dfref sweepFolder, variable sweepNo)
+
+ +
+
+variable AR_CheckProc_Update(WMCheckboxAction *cba)
+
+ +
+
+variable AR_IsActive(string win)
+

checks if AR is active.

+
+ +
+
+

Variables

+
+
+static const double AR_MIN_RANGE_FACTOR = 0.1
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___async_8ipf.html b/file/_m_i_e_s___async_8ipf.html new file mode 100644 index 0000000000..350a54a0cd --- /dev/null +++ b/file/_m_i_e_s___async_8ipf.html @@ -0,0 +1,597 @@ + + + + + + + + File MIES_Async.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Async.ipf

+

ASYNC This file holds the asynchronous execution framework

+

See Async Framework for the full documentation.

+
+

Variable names for free data folder structure

+
+
+static const string ASYNC_THREAD_MARKER_STR = "threadDFMarker"
+
+ +
+
+static const string ASYNC_WORKERFUNC_STR = "WorkerFunc"
+
+ +
+
+static const string ASYNC_READOUTFUNC_STR = "ReadOutFunc"
+
+ +
+
+static const string ASYNC_WORKLOADCLASS_STR = "workloadClass"
+
+ +
+
+static const string ASYNC_PARAMCOUNT_STR = "paramCount"
+
+ +
+
+static const string ASYNC_INORDER_STR = "inOrder"
+
+ +
+
+static const string ASYNC_ABORTFLAG_STR = "abortFlag"
+
+ +
+
+static const string ASYNC_RTERROR_STR = "rtErr"
+
+ +
+
+static const string ASYNC_RTERRORMSG_STR = "rtErrMessage"
+
+ +
+
+static const string ASYNC_ABORTCODE_STR = "abortCode"
+
+ +
+
+static const string ASYNC_WLCOUNTER_STR = "workloadClassCounter"
+
+ +
+
+

Functions

+
+
+variable ASYNC_Start(variable numThreads, variable disableTask = defaultValue)
+

Starts the Async Framework with numThreads parallel threads.

+
+
Parameters:
+
    +

  • numThreads – number of threads to setup for processing data, must be >= 1 and <= ASYNC_MAX_THREADS

    • +

  • disableTask – [optional, default = 0] when set to 1 the background task processing readouts is not started

    • +
+
+
Returns:
+

1 if ASYNC framework was started, 0 if ASYNC framework was already running, in this case the number of threads is not changed

+
+
+
+ +
+
+dfref ASYNC_Worker(dfref dfr)
+

Prototype function for an async worker function.

+
+
Parameters:
+

dfr – reference to thread data folder

+
+
Returns:
+

data folder reference to output data folder

+
+
+
+ +
+
+variable ASYNC_ReadOut(ASYNC_ReadOutStruct *ar)
+

Prototype function for an async readout function.

+
+
Parameters:
+

ar – ASYNC readout structure

+
+
+
+ +
+
+static variable ASYNC_Thread()
+

thread function that receives data folders from the thread input queue and calls the setup custom worker function. With :cpp:func:ASYNC_Start numThreads :cpp:func:ASYNC_Thread functions will be started in their own thread. Each will run until the framework is stopped. UTF_NOINSTRUMENTATION

+
+ +
+
+static dfref ASYNC_Run_Worker(dfref dfr)
+
+ +
+
+variable ASYNC_ThreadReadOut()
+

Receives data from finished workloads. Calls the user defined readout function. For in order readouts this function buffers pending result data folders until they can be processed in order.

+
+ +
+
+variable ASYNC_IsWorkloadClassDone(string workloadClass, variable removeClass = defaultValue)
+

Allows to check if all executed work loads of a specific work load class were read out. For that case, the work load class can optionally be removed from Async.

+
+
Parameters:
+
    +

  • workloadClass – [in] work load class string

    • +

  • removeClass – [in] [optional, default = 0] when set the specified work load class is removed from Async The parameter has no effect, if the work loads of the specified class are not done.

    • +
+
+
Returns:
+

1 if work load class finished, 0 if work load class did not finish, NaN if work load class not known to ASYNC

+
+
+
+ +
+
+variable ASYNC_WaitForWLCToFinishAndRemove(string workloadClass, variable timeout)
+

Wait for TP analysis from specific panel to finish and remove it.

+
+
Parameters:
+
    +

  • workloadClass – [in] name of work load class

    • +

  • timeout – [in] time out in seconds

    • +
+
+
Returns:
+

0 if work load class is unknown or has finished and was removed, 1 if timeout was encountered.

+
+
+
+ +
+
+variable ASYNC_BackgroundReadOut(WMBackgroundStruct *s)
+

Background function that reads data folders from the thread output queue and calls the setup custom readout function The function takes care to buffer results if they should be processed in order.

+
+
Parameters:
+

s – default structure for Igor background tasks

+
+
+
+ +
+
+variable ASYNC_AddParam(dfref dfr, wave w = defaultValue, variable var = defaultValue, string str = defaultValue, variable move = defaultValue, string name = defaultValue)
+

Adds one parameter to a data folder for a threaded worker execution.

+

The parameters are globals in the threads data folder and named param0, param1, param2… in order of adding them. Only one parameter can be added per call. move is only allowed in combination with a wave.

+
+
Parameters:
+
    +

  • dfr – data folder reference to thread df, prepared by calling ASYNC_PrepareDF

    • +

  • w – [optional, default = null] wave reference of wave to be added as parameter

    • +

  • var – [optional, default = 0] variable to be added as parameter

    • +

  • str – [optional, default = 0] string to be added as parameter

    • +

  • move – [optional, default = 0] if a wave was given as parameter and move is not zero then the wave is moved to the threads data folder

    • +

  • name – [optional, default = paramXXX] name of the added parameter

    • +
+
+
+
+ +
+
+wave ASYNC_FetchWave(dfref dfr, string name)
+

Fetch a wave from the DFREF in the worker function.

+
+ +
+
+variable ASYNC_FetchVariable(dfref dfr, string name)
+

Fetch a variable from the DFREF in the worker function.

+
+ +
+
+string ASYNC_FetchString(dfref dfr, string name)
+

Fetch a string from the DFREF in the worker function.

+
+ +
+
+variable ASYNC_Stop(variable timeout = defaultValue, variable fromAssert = defaultValue)
+

Stops the Async Framework.

+
+
Parameters:
+
    +

  • timeout – [optional, default = Inf] time in s to wait for running threads, the function waits for pending threads and pending readouts within this time. After a timeout happened the readout processing is stopped and threads are stopped. Any pending data is lost. If the threads have to be stopped forcefully, an assertion is raised. Using a finite timeout is strongly recommended.

    • +

  • fromAssert – [optional, default = 0] specified when called as cleanup function from ASSERT Suppresses further assertions such that all required cleanup routines such as ThreadGroupRelease are executed.

    • +
+
+
Returns:
+

2 if ASYNC framework was not running, 1 if a timeout was encountered, 0 otherwise

+
+
+
+ +
+
+dfref ASYNC_PrepareDF(string WorkerFunc, string ReadOutFunc, string workloadClass, variable inOrder = defaultValue)
+

Prepares a thread data folder for use with the AsyncFramework This function should be called first when setting up a worker with parameters.

+
+
Parameters:
+
    +

  • WorkerFunc – string naming a threadsafe worker function in the form of the ASYNC_Worker template

    • +

  • ReadOutFunc – string naming a readout function in the form of the ASYNC_ReadOut template

    • +

  • workloadClass – string naming a work load class for work load attribution like “TestPulse” The string must follow strict object naming rules.

    • +

  • inOrder – [optional, default = 1] flag that allows to disable in order readout of results

    • +
+
+
Returns:
+

data folder for thread, where parameters can be put to with :cpp:func:ASYNC_AddParam

+
+
+
+ +
+
+variable ASYNC_Execute(dfref dfr)
+

Puts a prepared thread data folder to parallel execution in another thread.

+
+
Parameters:
+

dfr – data folder that is setup for thread and is to be deployed

+
+
+
+ +
+
+static variable ASYNC_IsThreadDF(dfref dfr)
+

test if data folder is marked for thread usage

+

UTF_NOINSTRUMENTATION

+
+ +
+
+static variable ASYNC_IsASYNCRunning()
+

returns 1 if ASYNC framework is running, 0 otherwise

+
+ +
+
+

Variables

+
+
+static const string ASYNC_BACKGROUND = "AsyncFramework"
+
+ +
+
+static const double ASYNC_THREAD_MARKER = 299792458
+
+ +
+
+static const double ASYNC_MAX_THREADS = 64
+
+ +
+
+static const double ASYNC_SLEEP_ON_WAIT = 0.01
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___asynchronous_data_8ipf.html b/file/_m_i_e_s___asynchronous_data_8ipf.html new file mode 100644 index 0000000000..eef23b9923 --- /dev/null +++ b/file/_m_i_e_s___asynchronous_data_8ipf.html @@ -0,0 +1,295 @@ + + + + + + + + File MIES_AsynchronousData.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_AsynchronousData.ipf

+

ASD Support functions for the asynchronous channels

+
+

Functions

+
+
+variable ASD_CheckAsynAlarmState(string device, variable value, variable minValue, variable maxValue)
+

Check if the given asynchronous channel is in alarm state.

+
+ +
+
+variable ASD_ReadChannel(string device, variable channel)
+

Read the given asynchronous channel and return the scaled value It is only valid to call for ITC and SUTTER when there is no acquisition running.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___background_watchdog_8ipf.html b/file/_m_i_e_s___background_watchdog_8ipf.html new file mode 100644 index 0000000000..d71687a839 --- /dev/null +++ b/file/_m_i_e_s___background_watchdog_8ipf.html @@ -0,0 +1,431 @@ + + + + + + + + File MIES_BackgroundWatchdog.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_BackgroundWatchdog.ipf

+

BW Panel for inspecting the state of the MIES DAQ/TP background functions

+
+
+namespace BkgWatcher
+
+

Functions

+
+
+static variable ASSERT(variable var, string errorMsg)
+
+ +
+
+static variable SetValDisplay(string win, string control, variable var = defaultValue, string str = defaultValue, string format = defaultValue)
+
+ +
+
+static string GetValDisplayAsString(string win, string control)
+
+ +
+
+static variable IsBackgroundTaskRunning(string task)
+
+ +
+
+variable BW_StartPanel()
+
+ +
+
+variable BW_CreatePanel()
+
+ +
+
+variable BW_StartTask()
+
+ +
+
+variable BW_StopTask()
+
+ +
+
+variable BW_PanelUpdate()
+
+ +
+
+variable BW_BackgroundWatchdog(WMBackgroundStruct *s)
+

Helper background task for debugging.

+
+ +
+
+variable BW_ButtonProc_ShowTask(WMButtonAction *ba)
+
+ +
+
+variable BW_ButtonProc_QuitTask(WMButtonAction *ba)
+
+ +
+
+variable BW_WindowHook(WMWinHookStruct *s)
+
+ +
+
+variable BW_ButtonProc_StartTask(WMButtonAction *ba)
+
+ +
+
+variable BW_ButtonProc_StopTask(WMButtonAction *ba)
+
+ +
+
+

Variables

+
+
+static const string PANEL = "BW_MiesBackgroundWatchPanel"
+
+ +
+
+static const string TASK = "BW_BackgroundWatchdog"
+
+ +
+
+static const string CONTROL_PREFIX = "bckrdw"
+
+ +
+
+static const double INVALIDATE_STATE = -1
+
+ +
+
+static const double XGRID = 20
+
+ +
+
+static const double XOFFS = 240
+
+ +
+
+static const double YGRID = 20
+
+ +
+
+static const double CONTROL_TYPE_VALDISPLAY = 4
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___blowout_8ipf.html b/file/_m_i_e_s___blowout_8ipf.html new file mode 100644 index 0000000000..aa52b45cfa --- /dev/null +++ b/file/_m_i_e_s___blowout_8ipf.html @@ -0,0 +1,403 @@ + + + + + + + + File MIES_Blowout.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Blowout.ipf

+

BWO Automates amplifier configuration and acquisition of the sweep used to measure drift in the zero calibration of the amplifer.

+
+

Functions

+
+
+variable BWO_SelectDevice()
+

Initiates blowout protocol on single locked device.

+
+ +
+
+variable BWO_Go(string device)
+

Executes blowout protocol.

+
+ +
+
+static variable BWO_CheckGlobalSettings(string device)
+

Checks that MIES is correctly configured for automated blowout protocol.

+
+
Returns:
+

one if settings are valid, zero otherwise

+
+
+
+ +
+
+static variable BWO_ConfigureTP(string device)
+

Initates test pulse.

+
+ +
+
+static variable BWO_SetMIESSettings(string device)
+

Configures data acquisition settings for blowout.

+
+ +
+
+static variable BWO_InitParaPipetteClear(string device)
+

Applies a pressure pulse to all headstages with valid pressure settings.

+
+ +
+
+static variable BWO_CheckAndClearPipettes(string device)
+

Attempts to clear pipettes that have a resistance larger than MAX_RESISTANCE.

+
+ +
+
+static variable BWO_AllMCCCtrlsOFF(string device)
+

Turns OFF all relevant MCC amplifier controls in I- and V-clamp modes.

+
+ +
+
+static variable BWO_SetClampModeAll(string device, variable mode)
+

Wrapper function for setting the clamp mode on all headstages (T̶h̶o̶m̶a̶s̶ ̶p̶r̶o̶b̶a̶b̶l̶y̶ ̶w̶o̶n̶’̶t̶ ̶l̶i̶k̶e̶ ̶i̶t̶ He liked it!! :/ ).

+
+ +
+
+static variable BWO_DisableMCCIClampCtrls(string device)
+

Turns OFF I-clamp controls.

+
+ +
+
+static variable BWO_DisableMCCVClampCtrls(string device)
+

Turns OFF V-clamp controls.

+
+ +
+
+static variable BWO_AcquireSweep(string device)
+

Acquires blowout sweep.

+
+ +
+
+

Variables

+
+
+static const double BWO_MAX_RESISTANCE = 10
+
+ +
+
+static const double BWO_INIT_PRESSURE = 5
+
+ +
+
+static const double BWO_PRESSURE_INCREMENT = 1
+
+ +
+
+static const double TWO_SECONDS = 120
+
+ +
+
+static const double FIFTEEN_SECONDS = 900
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___browser___plotter_8ipf.html b/file/_m_i_e_s___browser___plotter_8ipf.html new file mode 100644 index 0000000000..ed50eb406a --- /dev/null +++ b/file/_m_i_e_s___browser___plotter_8ipf.html @@ -0,0 +1,470 @@ + + + + + + + + File MIES_Browser_Plotter.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Browser_Plotter.ipf

+

Functions for plotting DataBrowser/Sweepbrowser Graphs.

+
+

Functions

+
+
+static std::tuple<string, variable> GetOodDAQFullRange(TiledGraphSettings *tgs, WaveText oodDAQRegions)
+

Get all selected oodDAQ regions and the total X range in ms.

+
+ +
+
+variable CreateTiledChannelGraph(string graph, wave config, variable sweepNo, wave numericalValues, WaveText textualValues, TiledGraphSettings *tgs, dfref sweepDFR, WaveText axisLabelCache, variable *traceIndex, string experiment, wave channelSelWave, BufferedDrawInfo *bdi = defaultValue)
+

Create a vertically tiled graph for displaying AD and DA channels.

+

For preservering the axis scaling callers should do the following: 

WAVE ranges = GetAxesRanges(graph)
+
+CreateTiledChannelGraph()
+
+    SetAxesRanges(graph, ranges)
+
+
+

+

+

+

See also

+

OVS_EndIncrementalUpdate

+
+

+
+
Parameters:
+
    +

  • graph – window

    • +

  • config – DAQ config wave

    • +

  • sweepNo – number of the sweep

    • +

  • numericalValues – numerical labnotebook wave

    • +

  • textualValues – textual labnotebook wave

    • +

  • tgs – settings for tuning the display, see TiledGraphSettings

    • +

  • sweepDFR – top datafolder to splitted 1D sweep waves

    • +

  • axisLabelCache – store existing vertical axis labels

    • +

  • traceIndex – [internal use only] set to zero on the first call in a row of successive calls

    • +

  • experiment – name of the experiment the sweep stems from

    • +

  • channelSelWave – channel selection wave

    • +

  • bdi – [optional, default = n/a] initialized BufferedDrawInfo structure, when given draw calls are buffered instead for later execution

    • +
+
+
+
+ +
+
+variable TiledGraphAccelerateDraw(BufferedDrawInfo *bdi)
+

Runs through all graph groups in the json and appends them to the graph.

+
+ +
+
+static variable TiledGraphAccelerateAppendTracesImpl(string w, string v, string h, variable r, variable g, variable b, wave y, WaveText t, WaveRefWave d)
+

Appends a group of traces to a graph, properties w to b must be constant for the group.

+
+
Parameters:
+
    +

  • w – [in] name of graph window

    • +

  • v – [in] name of vertical axis

    • +

  • h – [in] name of horizontal axis

    • +

  • r – [in] red color component

    • +

  • g – [in] green color component

    • +

  • b – [in] blue color component

    • +

  • y – [in] 1D wave with indices into wave d for the actual plot data

    • +

  • t – [in] 1D wave with trace names, same size as y

    • +

  • d – [in] wave reference wave with plot data

    • +
+
+
+
+ +
+
+variable PostPlotTransformations(string win, variable mode, WaveOrNull additionalData = defaultValue)
+

Perform common transformations on the graphs traces.

+

Keeps track of all internal details wrt. to the order of the operations, backups, etc.

+

Needs to be called after adding/removing/updating sweeps via AddSweepToGraph(), RemoveSweepFromGraph(), UpdateSweepInGraph().

+
+
Parameters:
+
    +

  • win – graph with sweep traces

    • +

  • mode – update mode, one of PostPlotUpdateModes

    • +

  • additionalData – [optional, defaults to invalid wave reference] additional data for subsequent users. Currently supported:

      +

    • POST_PLOT_REMOVED_SWEEPS -> OVS indizes of the removed sweep

      • +

    • POST_PLOT_ADDED_SWEEPS -> OVS indizes of the added sweep Use OVS_GetSweepAndExperiment() to convert an index into a sweep/experiment pair.

      • +
    +

    • +
+
+
+
+ +
+
+static variable InitPostPlotSettings(string win, PostPlotSettings *pps)
+
+ +
+
+static variable AverageWavesFromSameYAxisIfReq(string graph, variable averagingEnabled, dfref averageDataFolder, variable hideSweep)
+

Average traces in the graph from the same y-axis and append them to the graph.

+
+
Parameters:
+
    +

  • graph – graph with traces create by CreateTiledChannelGraph

    • +

  • averagingEnabled – switch if averaging is enabled or not

    • +

  • averageDataFolder – permanent datafolder where the average waves can be stored

    • +

  • hideSweep – are normal channel traces hidden or not

    • +
+
+
+
+ +
+
+static variable ZeroTracesIfReq(string graph, WaveTextOrNull traces, variable zeroTraces)
+

Zero all given traces.

+
+ +
+
+static variable LayoutGraph(string win, TiledGraphSettings *tgs)
+

Layout the DataBrowser/SweepBrowser graph.

+

Takes also care of adding free axis for the headstage display.

+

Concept:

    +

  • Block [#]: One axis with surrounded GRAPH_DIV_SPACING space

    • +

  • Slot [#]: Unit of vertical space, a block can occupy multiple slots

    • +

  • We have 100% space for all axes

    • +

  • AD axes should occupy four times the space of DA/TTL channels

    • +

  • So DA/TTL occupy one slot, AD occupy four slots

    • +

  • Between each axes we want GRAPH_DIV_SPACING clear space

    • +

  • Count the number of vertical blocks and slots to be used

    • +

  • Derive the space per slot

    • +

  • For overlay channels we reserve only one slot times slot multiplier per channel

    • +
+

+

The display order from top to bottom:

    +

  • Associated channels (above: DA, below: AD) with increasing headstage number

    • +

  • Unassociated channels (above: DA, below: AD)

    • +

  • TTL channels

    • +
+

+

For overlayed channels we have up to three blocks (DA, AD, TTL) in that order.

+
+ +
+
+static variable TweakAxes(string graph, TiledGraphSettings *tgs, WaveText allVerticalAxes, WaveText allHorizontalAxes)
+
+ +
+
+static variable EnableAxis(string graph, WaveText axes, variable spacePerSlot, variable *first, variable *last)
+

Helper function for LayoutGraph()

+

Enables the given axis between [last - spacePerSlot, last] and updates both on return. Expects last to be 1.0 on the first call.

+
+ +
+
+

Variables

+
+
+static const double NUM_CHANNEL_TYPES = 3
+
+ +
+
+static const double ADC_SLOT_MULTIPLIER = 4
+
+ +
+
+static const double EPOCH_SLOT_MULTIPLIER = 3
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___browser_settings_panel_8ipf.html b/file/_m_i_e_s___browser_settings_panel_8ipf.html new file mode 100644 index 0000000000..e7c4560e9d --- /dev/null +++ b/file/_m_i_e_s___browser_settings_panel_8ipf.html @@ -0,0 +1,1136 @@ + + + + + + + + File MIES_BrowserSettingsPanel.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_BrowserSettingsPanel.ipf

+

BSP Panel for DB and AB (SweepBrowser) that combines different settings in a tabcontrol.

+
+

Functions

+
+
+string BSP_GetPanel(string mainPanel)
+

return the name of the external panel depending on main window name

+
+
Parameters:
+

mainPanel – mainWindow panel name

+
+
+
+ +
+
+string BSP_GetNotebookSubWindow(string win)
+

return the name of the WaveNote Display inside BSP

+
+ +
+
+string BSP_GetSweepControlsPanel(string mainPanel)
+

return the name of the bottom Panel

+
+
Parameters:
+

mainPanel – mainWindow panel name

+
+
+
+ +
+
+string BSP_GetSFFormula(string mainPanel)
+
+ +
+
+string BSP_GetSFJSON(string mainPanel)
+
+ +
+
+string BSP_GetSFHELP(string mainPanel)
+
+ +
+
+variable BSP_InitPanel(string mainPanel)
+

Inits controls of BrowserSettings side Panel.

+
+
Parameters:
+

mainPanel – mainWindow panel name

+
+
+
+ +
+
+static variable BSP_UnHidePanel(string mainPanel)
+

UnHides BrowserSettings side Panel.

+
+
Parameters:
+

mainPanel – mainWindow panel name

+
+
+
+ +
+
+static variable BSP_UnHideSettingsPanel(string mainPanel)
+
+ +
+
+static variable BSP_UnHideSweepControls(string mainPanel)
+

open bottom Panel

+
+
Parameters:
+

mainPanel – mainWindow panel name

+
+
+
+ +
+
+static variable BSP_DynamicSweepControls(string mainPanel)
+

dynamic settings for bottom panel at initialization

+
+
Parameters:
+

mainPanel – mainWindow panel name

+
+
+
+ +
+
+static variable BSP_AddWindowHooks(string win)
+

Add default window hooks.

+
+ +
+
+variable BSP_RemoveWindowHooks(string win)
+

Remove all window hooks from the window and its subwindows.

+
+ +
+
+variable BSP_DynamicStartupSettings(string mainPanel)
+

dynamic settings for panel initialization

+
+
Parameters:
+

mainPanel – mainWindow panel name

+
+
+
+ +
+
+variable BSP_SweepFormulaHook(WMWinHookStruct *s)
+

Hook function for the Sweep Formula Notebook.

+
+ +
+
+variable BSP_UnsetDynamicStartupSettings(string mainPanel)
+

Unsets all control properties that are set in BSP_DynamicStartupSettings for DataBrowser type.

+
+
Parameters:
+

mainPanel – mainWindow panel name

+
+
+
+ +
+
+variable BSP_BindListBoxWaves(string win)
+
+ +
+
+wave BSP_GetChannelSelectionWave(string win)
+

Get the channel selection wave.

+
+
Parameters:
+

win – name of external panel or main window

+
+
Returns:
+

channel selection wave

+
+
+
+ +
+
+dfref BSP_GetFolder(string win, string folderType, variable versionCheck = defaultValue)
+

get a FOLDER property from the specified panel

+
+
Parameters:
+
    +

  • win – name of external panel or main window

    • +

  • folderType – see the FOLDER constants in this file

    • +

  • versionCheck – [optional, defaults to true] abort on outdated window version

    • +
+
+
Returns:
+

DFR to specified folder. No check for invalid folders

+
+
+
+ +
+
+variable BSP_SetFolder(string win, dfref dfr, string folderType)
+

set a FOLDER property at the specified panel

+
+
Parameters:
+
    +

  • win – name of external panel or main window

    • +

  • dfr – DataFolder Reference to the folder

    • +

  • folderType – see the FOLDER constants in this file

    • +
+
+
+
+ +
+
+string BSP_GetDevice(string win)
+

get the assigned DEVICE property from the main panel

+
+
Parameters:
+

win – name of external panel or main window

+
+
Returns:
+

device as string

+
+
+
+ +
+
+string BSP_SetDevice(string win, string device)
+

set DEVICE property to the userdata of the main panel

+
+
Parameters:
+
    +

  • win – name of external panel or main window

    • +

  • device – bound device as string

    • +
+
+
+
+ +
+
+string BSP_GetBrowserType(string win)
+

get the MIES Browser Type

+
+
Parameters:
+

win – name of external panel or main window

+
+
Returns:
+

D for DataBrowser or S for SweepBrowser

+
+
+
+ +
+
+static string BSP_SetBrowserType(string win, string type, variable mode)
+

set DEVICE property to the userdata of the main panel

+
+
Parameters:
+
+
+
+
+ +
+
+static variable BSP_ParseBrowserMode(string mode)
+
+ +
+
+static string BSP_SerializeBrowserMode(variable mode)
+
+ +
+
+variable BSP_GetBrowserMode(string win)
+
+ +
+
+variable BSP_SetDataBrowser(string win, variable mode)
+

wrapper function for external calls

+
+ +
+
+variable BSP_SetSweepBrowser(string win, variable mode)
+

wrapper function for external calls

+
+ +
+
+variable BSP_IsSweepBrowser(string win)
+

wrapper function for external calls

+
+ +
+
+variable BSP_IsDataBrowser(string win)
+

wrapper function for external calls

+
+ +
+
+variable BSP_HasBoundDevice(string win)
+

check if the DEVICE property has a not nullstring property

+
+
Parameters:
+

win – name of external panel or main window

+
+
Returns:
+

1 if device is assigned and 0 otherwise. does not check if device is valid.

+
+
+
+ +
+
+static variable BSP_InitMainCheckboxes(string win)
+

set the initial state of the enable/disable buttons

+
+
Parameters:
+

win – name of external panel or main window

+
+
+
+ +
+
+variable BSP_SetOVSControlStatus(string win)
+

enable/disable the OVS buttons

+
+
Parameters:
+

win – specify mainPanel or bsPanel with OVS controls

+
+
+
+ +
+
+variable BSP_SetARControlStatus(string win)
+

enable/disable the AR buttons

+
+
Parameters:
+

win – specify mainPanel or bsPanel with OVS controls

+
+
+
+ +
+
+variable BSP_SetSFControlStatus(string win)
+

enable/disable the SF buttons

+
+
Parameters:
+

win – specify mainPanel or bsPanel with OVS controls

+
+
+
+ +
+
+variable BSP_SetControlStatus(string win, string controlList, variable status)
+

enable/disable a list of controls

+
+
Parameters:
+
    +

  • win – specify mainPanel or bsPanel with OVS controls

    • +

  • controlList – list of controls

    • +

  • status – 1: enable; 0: disable

    • +
+
+
+
+ +
+
+static variable BSP_MainPanelButtonToggle(string mainPanel, variable visible)
+

action for button in mainPanel

+
+
Parameters:
+
    +

  • mainPanel – main Panel window

    • +

  • visible – set status of external Panel (opened: visible = 1)

    • +
+
+
+
+ +
+
+static variable BSP_HidePanel(string win)
+
+ +
+
+variable BSP_ClosePanelHook(WMWinHookStruct *s)
+

panel close hook for side panel

+
+ +
+
+variable BSP_SweepsAndMouseWheel(WMWinHookStruct *s)
+
+ +
+
+variable BSP_CheckBoxProc_ArtRemoval(WMCheckBoxAction *cba)
+

enable/disable checkbox control for side panel

+
+ +
+
+variable BSP_CheckBoxProc_PerPulseAver(WMCheckBoxAction *cba)
+

enable/disable checkbox control for side panel

+
+ +
+
+variable BSP_CheckBoxProc_SweepFormula(WMCheckBoxAction *cba)
+

enable/disable checkbox control for side panel

+
+ +
+
+variable BSP_ButtonProc_Panel(WMButtonAction *ba)
+

procedure for the open button of the side panel

+
+ +
+
+variable BSP_SliderProc_ChangedSetting(WMSliderAction *spa)
+
+ +
+
+variable BSP_TimeAlignmentProc(WMCheckBoxAction *cba)
+
+ +
+
+variable BSP_TimeAlignmentPopup(WMPopupAction *pa)
+
+ +
+
+variable BSP_TimeAlignmentLevel(WMSetVariableAction *sva)
+
+ +
+
+variable BSP_DoTimeAlignment(WMButtonAction *ba)
+
+ +
+
+variable BSP_CheckProc_ScaleAxes(WMCheckboxAction *cba)
+
+ +
+
+variable BSP_AxisScalingLevelCross(WMSetVariableAction *sva)
+
+ +
+
+static variable BSP_UpdateSweepControls(string win, string ctrl, variable firstSweepOrIndex, variable lastSweepOrIndex)
+

update controls in scPanel and change to new sweep

+
+
Parameters:
+
    +

  • win – name of external panel or main window

    • +

  • ctrl – name of the button that was pressed and is initiating the update

    • +

  • firstSweepOrIndex – first available sweep(DB) or index(SB)

    • +

  • lastSweepOrIndex – last available sweep(DB) or index(SB)

    • +
+
+
Returns:
+

the new sweep number in case of DB or the index for SB

+
+
+
+ +
+
+variable BSP_IsActive(string win, variable elementID)
+

check if the specified setting is activated

+
+
Parameters:
+
    +

  • win – name of external panel or main window

    • +

  • elementID – one of MIES_BSP_* constants like MIES_BSP_PA

    • +
+
+
Returns:
+

1 if setting was activated, 0 otherwise

+
+
+
+ +
+
+variable BSP_UpdateHelpNotebook(string helpNotebook)
+

Fill the SweepFormula help notebook with the contents of the stored file.

+
+ +
+
+string BSP_GetFormulaGraph(string win)
+

Return a sweep formula graph name unique for that sweepbrowser/databrowser.

+
+ +
+
+string BSP_GetFormulaGraphTitle(string win)
+
+ +
+
+variable BSP_ParseChannelSelectionControl(string ctrl, string *channelType, variable *channelNum)
+

Parse a control name for the “Channel Selection Panel” and return its channel type and number. The number will be NaN for the ALL control.

+
+ +
+
+variable BSP_ChannelSelectionWaveToGUI(string panel, wave channelSel)
+

Set the channel selection dialog controls according to the channel selection wave.

+
+ +
+
+variable BSP_GUIToChannelSelectionWave(string win, string ctrl, variable checked)
+

Set the channel selection wave acccording to the channel selection controls.

+
+ +
+
+variable BSP_RemoveDisabledChannels(wave channelSel, wave ADCs, wave DACs, wave statusHS, wave numericalValues, variable sweepNo)
+

Removes the disabled channels and headstages from ADCs, DACs and statusHS

+

channelSel will be the result from BSP_FetchSelectedChannels() which is a copy of the permanent channel selection wave.

+
+ +
+
+variable BSP_ScaleAxes(string win)
+
+ +
+
+std::tuple<TiledGraphSettings> BSP_GatherTiledGraphSettings(string win)
+
+ +
+
+variable BSP_CheckProc_ChangedSetting(WMCheckBoxAction *cba)
+
+ +
+
+variable BSP_ButtonProc_RestoreData(WMButtonAction *ba)
+
+ +
+
+variable BSP_CheckProc_OverlaySweeps(WMCheckBoxAction *cba)
+
+ +
+
+wave BSP_GetLogbookWave(string win, variable logbookType, variable logbookWaveType, variable sweepNumber = defaultValue, variable selectedExpDevice = defaultValue)
+

Generic getter for logbook waves.

+

Works with Databrowser/Sweepbrowser.

+

For the Sweepbrowser this returns the stored logbooks. If you want to fetch the global results wave use GetLogbookWaves().

+
+
Parameters:
+
    +

  • win – panel

    • +

  • logbookType – one of LogbookTypes

    • +

  • logbookWaveType – one of LabnotebookWaveTypes

    • +

  • sweepNumber – [optional] sweep number

    • +

  • selectedExpDevice – [optional, defaults to off] return the labnotebook for the selected experiment/device combination

    • +
+
+
Returns:
+

returns the specified logbook wave or a null wave

+
+
+
+ +
+
+wave BSP_FetchSelectedChannels(string graph, variable index = defaultValue, variable sweepNo = defaultValue)
+

Return the wave with the selected channels respecting the overlay sweeps headstage ignore list. The wave has the same layout as BSP_GetChannelSelectionWave.

+
+ +
+
+std::tuple<variable, variable> BSP_FirstAndLastSweepAcquired(string win)
+

Return the last and first sweep numbers.

+
+ +
+
+variable BSP_ButtonProc_ChangeSweep(WMButtonAction *ba)
+
+ +
+
+variable BSP_MainTabControlFinal(WMTabControlAction *tca)
+
+ +
+
+variable BSP_UpdateSweepNote(string win)
+
+ +
+
+static variable BSP_UnHideSettingsHistory(string win)
+
+ +
+
+static variable BSP_RemoveTraces(string graph)
+
+ +
+
+variable BSP_AddTracesForEpochs(string win)
+

Debug function to add traces with epoch information.

+
+ +
+
+variable BSP_EpochGraphToolTip(WMTooltipHookStruct *s)
+
+ +
+
+variable BSP_SFHelpWindowHook(WMWinHookStruct *s)
+
+ +
+
+static string BSP_GetHelpOperationHeadline(string op)
+
+ +
+
+static string BSP_GetHelpKeywordHeadline(string keyWord)
+
+ +
+
+static variable BSP_SFFormulaColoring(string sfWin)
+
+ +
+
+variable BSP_TTHookSFFormulaNB(WMTooltipHookStruct *s)
+
+ +
+
+static string BSP_RetrieveSFHelpTextImpl(string win, string hlpStart, string hlpEnd)
+
+ +
+
+variable BSP_WindowHook(WMWinHookStruct *s)
+
+ +
+
+string BSP_RenameAndSetTitle(string win, string newName)
+

Renames the browser window and sets an informative title.

+
+
Parameters:
+
    +

  • win – name of the existing window

    • +

  • newName – suggested new name, will be adapted to be unique

    • +
+
+
+
+ +
+
+static variable BSP_MemoryFreeMappedDF(string win)
+
+ +
+
+dfref BSP_GetSweepDF(string win, variable sweepNo)
+

Gets sweep browser data folder from sweep- or data browser window name and sweep number.

+
+
Parameters:
+
    +

  • win – [in] sweep- or data browser window

    • +

  • sweepNo – [in] sweep number

    • +
+
+
Returns:
+

sweep data folder reference, null reference if requirements not met

+
+
+
+ +
+
+

Variables

+
+
+static const string EXT_PANEL_SUBWINDOW = "BrowserSettingsPanel"
+
+ +
+
+static const string EXT_PANEL_SWEEPCONTROL = "SweepControl"
+
+ +
+
+static const string EXT_PANEL_SF_FORMULA = "sweepFormula_formula"
+
+ +
+
+static const string EXT_PANEL_SF_JSON = "sweepFormula_json"
+
+ +
+
+static const string EXT_PANEL_SF_HELP = "sweepFormula_help"
+
+ +
+
+static const string BROWSERTYPE_DATABROWSER = "D"
+
+ +
+
+static const string BROWSERTYPE_SWEEPBROWSER = "S"
+
+ +
+
+static const string BROWSERSETTINGS_CONTROLS_DATABROWSER = "popup_DB_lockedDevices;"
+

exclusive controls that are enabled/disabled for the specific browser window type

+
+ +
+
+static const string BROWSERSETTINGS_AXES_SCALING_CHECKBOXES = "check_Display_VisibleXrange;check_Display_EqualYrange;check_Display_EqualYignore"
+
+ +
+
+static const string SWEEPCONTROL_CONTROLS_DATABROWSER = "check_SweepControl_AutoUpdate;setvar_SweepControl_SweepNo;"
+

exclusive controls that are enabled/disabled for the specific browser window type

+
+ +
+
+static const string SWEEPCONTROL_CONTROLS_SWEEPBROWSER = "popup_SweepControl_Selector;"
+
+ +
+
+static const string BSP_USER_DATA_SF_CONTENT_CRC = "SweepFormulaContentCRC"
+
+ +
+
+static const double BSP_EPOCH_LEVELS = 5
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___cache_8ipf.html b/file/_m_i_e_s___cache_8ipf.html new file mode 100644 index 0000000000..8ef2ad8a2d --- /dev/null +++ b/file/_m_i_e_s___cache_8ipf.html @@ -0,0 +1,641 @@ + + + + + + + + File MIES_Cache.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Cache.ipf

+

CA This file holds functions related to caching of waves.

+

The cache allows to store waves using a unique key for later retrieval. The stored waves are kept until they are explicitly removed.

+

Usage:

    +

  • Write a key generator function returning a string The parameters to CA_GenKey() must completely determine the wave you will later store. The appended version string to the key allows you to invalidate old keys if the algorithm creating the wave changes, but all input stays the same.

    • +
+

+

Function/S CA_GenKey(input)
+    variable input
+
+    return stringCRC(0, num2str(input)) + "Version 1"
+End
+
+
+

+

    +

  • Write your main function as in the following example. The first time MyFancyCalculation(input) is called you get a cache miss and result has to be created from scratch, but all subsequent calls are fast as the entry is fetched from the cache.

    • +
+

+

Function/WAVE MyFancyCalculation(input)
+    variable input
+
+    string key = CA_GenKey(input)
+
+    WAVE/Z result = CA_TryFetchingEntryFromCache(key)
+
+    if(WaveExists(result))
+        return result
+    endif
+
+    // create result from scratch
+    // ...
+
+    CA_StoreEntryIntoCache(key, result)
+
+    return result
+End
+
+
+

+

    +

  • Deleting cache entries has to be done manually via CA_DeleteCacheEntry(). The cache is also stored in a packed experiment.

    • +

  • The entries in the cache are stored as free wave copies of what you feed into CA_StoreEntryIntoCache(). Similiary you get a free wave copy from CA_TryFetchingEntryFromCache().

    • +

  • Storing 1D wave reference waves is supported, they are by default deep copied.

    • +
+

+
+

Cache key generators

+

+
+
+string CA_KeyRecreatedEpochs(wave numericalValues, WaveText textualValues, dfref sweepDFR, variable sweepNo)
+

Cache key generator for recreated epochs wave.

+
+ +
+
+string CA_DistDAQCreateCacheKey(OOdDAQParams *params)
+

Cache key generator for oodDAQ offset waves.

+
+ +
+
+string CA_PulseTimes(wave wv, string fullPath, variable channelNumber, variable totalOnsetDelay)
+

Cache key generator for FindLevel in PA_CalculatePulseTimes()

+
+ +
+
+string CA_SmoothDeconv(wave wv, variable smoothingFactor, variable range_pnts)
+

Cache key generator for PA_SmoothDeconv()

+
+
Parameters:
+
    +

  • wv – input wave (average)

    • +

  • smoothingFactor – smoothing factor

    • +

  • range_pnts – number of points (p) the smoothing was performed

    • +
+
+
+
+ +
+
+string CA_Deconv(wave wv, variable tau)
+

Cache key generator for PA_Deconvolution()

+
+
Parameters:
+
    +

  • wv – input wave (smoothed average)

    • +

  • tau – convolution time

    • +
+
+
+
+ +
+
+string CA_GenKeyGetActiveChannels(wave numericalValues, wave textualValues, variable sweepNo, variable channelType, variable TTLmode)
+

Cache key generator for GetActiveChannels.

+
+ +
+
+string CA_GenKeyLogbookSortedKeys(wave keys)
+

Cache key generator for Logbook sortedKeyWave.

+
+ +
+
+string CA_ArtefactRemovalRangesKey(dfref singleSweepDFR, variable sweepNo)
+

Cache key generator for artefact removal ranges.

+
+ +
+
+string CA_AveragingKey(WaveRefWave waveRefs)
+

Cache key generator for averaging.

+
+ +
+
+string CA_AveragingWaveModKey(wave wv)
+

Cache key generator for averaging info from non-free waves.

+
+ +
+
+static variable CA_RecursiveWavemodCRC(WaveOrNull wv, variable prevCRC = defaultValue)
+

Calculated a CRC from non wave reference waves using modification data, wave modification count and wave location. If the given wave is a wave reference wave, then the CRC is calculated recursively from all non wave reference waves and null wave references found.

+
+ +
+
+static variable CA_GetWaveModCRC(wave wv, variable crc)
+
+ +
+
+static variable CA_WaveScalingCRC(variable crc, wave wv, variable dimension = defaultValue)
+

Calculate the CRC of all metadata of all or the given dimension.

+
+ +
+
+static string CA_WaveCRCs(WaveRefWave waveRefs, variable crcMode = defaultValue, variable includeWaveScalingAndUnits = defaultValue, variable dims = defaultValue)
+

Calculate all CRC values of the waves referenced in waveRefs.

+
+
Parameters:
+
    +

  • waveRefs – wave reference wave

    • +

  • crcMode – [optional] parameter to WaveCRC

    • +

  • includeWaveScalingAndUnits – [optional] include the wave scaling and units of filled dimensions

    • +

  • dims – [optional] number of dimensions to include wave scaling and units in crc

    • +
+
+
+
+ +
+
+string CA_SamplingIntervalKey(wave lut, ActiveChannels *s)
+

Calculate the cache key for SI_FindMatchingTableEntry.

+

We are deliberatly not using a WaveCRC here as know that the wave is not changed in IP once loaded. Therefore using its name and ModDate is enough.

+
+ +
+
+string CA_TemporaryWaveKey(wave dims)
+

Generic key generator for storing throw away waves used for Multithread assignments.

+

Only the size is relevant, the rest is undefined.

+
+ +
+
+string CA_HWDeviceInfoKey(string device, variable hardwareType, variable deviceID)
+

Calculate the cache key for the hardware device info wave.

+
+ +
+
+string CA_HardwareDataTPKey(HardwareDataTPInput *s)
+

Generate a key for the DAQDataWave in TEST_PULSE_MODE.

+

Properties which influence the Testpulse:

    +

  • hardwareType

    • +

  • numDA (filled columns)

    • +

  • numActiveChannels (number of columns)

    • +

  • number of rows, return from DC_CalculateDAQDataWaveLength(device, TEST_PULSE_MODE)

    • +

  • samplingInterval

    • +

  • DAGain

    • +

  • DACAmp[][TPAmp] column

    • +

  • testPulseLength, baselineFrac

    • +
+

+
+ +
+
+string CA_PSXKernelOperationKey(variable riseTau, variable decayTau, variable amp, variable numPoints, variable dt, wave range)
+
+ +
+
+static string CA_PSXBaseKey(string comboKey, string psxParameters)
+
+ +
+
+string CA_PSXEventsKey(string comboKey, string psxParameters)
+

Generate the key for the cache and the results wave for psxEvent data of the psx SweepFormula operation.

+
+
Parameters:
+
    +

  • comboKey – combination key, see PSX_GenerateComboKey()

    • +

  • psxParameters – JSON dump of the psx/psxKernel operation parameters

    • +
+
+
+
+ +
+
+string CA_PSXOperationKey(string comboKey, string psxParameters)
+
+ +
+
+string CA_PSXRiseTimeKey(string comboKey, string psxParameters)
+
+ +
+
+string CA_PSXAnalyzePeaks(string comboKey, string psxParameters)
+
+ +
+
+string CA_IgorInfoKey(variable selector)
+

Return the key for the igor info entries.

+
+ +
+
+string CA_GetLabnotebookNamesKey(WaveTextOrNull textualValues, WaveTextOrNull numericalValues)
+

Return the key for the filled labnotebook parameter names.

+
+ +
+
+

Functions

+
+
+static variable CA_MakeSpaceForNewEntry()
+

Make space for one new entry in the cache waves.

+
+
Returns:
+

index into cache waves

+
+
+
+ +
+
+variable CA_StoreEntryIntoCache(string key, wave val, variable options = defaultValue)
+

Add a new entry into the cache.

+

+Existing entries with the same key are overwritten.

+
+
Parameters:
+
    +

  • key – string which uniquely identifies the cached wave

    • +

  • val – wave to store

    • +

  • options – [optional, defaults to none] One or multiple constants from CacheFetchOptions

    • +
+
+
+
+ +
+
+static variable CA_GetCacheIndex(wave keys, string key)
+

Return the index of the entry key

+

+UTF_NOINSTRUMENTATION

+
+
Returns:
+

non-negative number or NaN if it could not be found.

+
+
+
+ +
+
+wave CA_TryFetchingEntryFromCache(string key, variable options = defaultValue)
+

Try to fetch the wave stored under key from the cache.

+
+
Parameters:
+
    +

  • key – string which uniquely identifies the cached wave

    • +

  • options – [optional, defaults to none] One or multiple constants from CacheFetchOptions

    • +
+
+
Returns:
+

A wave reference with the stored data or a invalid wave reference if nothing could be found.

+
+
+
+ +
+
+variable CA_DeleteCacheEntry(string key)
+

Try to delete a cache entry.

+
+
Returns:
+

One if it could be found and deleted, zero otherwise

+
+
+
+ +
+
+variable CA_FlushCache()
+

Remove all entries from the wave cache.

+
+ +
+
+variable CA_OutputCacheStatistics()
+

Output cache statistics.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___check_installation_8ipf.html b/file/_m_i_e_s___check_installation_8ipf.html new file mode 100644 index 0000000000..b52c42038d --- /dev/null +++ b/file/_m_i_e_s___check_installation_8ipf.html @@ -0,0 +1,382 @@ + + + + + + + + File MIES_CheckInstallation.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_CheckInstallation.ipf

+

CHI Routines for checking the health of the MIES installation

+
+

Functions

+
+
+static variable CHI_InitInstallationState(CHI_InstallationState *state)
+
+ +
+
+static variable CHI_CheckJSONXOPVersion(CHI_InstallationState *state)
+
+ +
+
+static variable CHI_CheckTUFXOPVersion(CHI_InstallationState *state)
+
+ +
+
+static variable CHI_OutputVersionCheckResult(CHI_InstallationState *state, string xopName, string expectedVersion, string foundVersion)
+
+ +
+
+static variable CHI_CheckITCXOPVersion(CHI_InstallationState *state)
+
+ +
+
+static variable CHI_CheckXOP(string *list, string *item, string *name, CHI_InstallationState *state, string expectedHash = defaultValue)
+

Search list for matches of item and print the results.

+
+ +
+
+variable CHI_CheckInstallation()
+

Check the installation and print the results to the history.

+

Currently checks that all expected/optional XOPs are installed.

+
+
Returns:
+

number of errors

+
+
+
+ +
+
+

Variables

+
+
+static const string CHI_NIDAQ_XOP_64_HASH = "b13267a080053c07b80302212b7f73ac199e1f001d9a1b4303e2d7dce1aeb39e"
+
+ +
+
+static const string CHI_JSON_XOP_VERSION = "version-892-g9251933"
+
+ +
+
+static const string CHI_TUF_XOP_VERSION = "version-163-g686effb"
+
+ +
+
+static const string CHI_ITC_XOP_VERSION = "latest-174-gb9915a9"
+
+ +
+
+
+struct CHI_InstallationState
+

Collection of counters used for installation checking.

+
+

Public Members

+
+
+variable numErrors
+
+ +
+
+variable numTries
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___configuration_8ipf.html b/file/_m_i_e_s___configuration_8ipf.html new file mode 100644 index 0000000000..4ef17cbaf1 --- /dev/null +++ b/file/_m_i_e_s___configuration_8ipf.html @@ -0,0 +1,1671 @@ + + + + + + + + File MIES_Configuration.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Configuration.ipf

+

CONF Import user settings to configure paramters for Ephys experiments

+

Module brief description

+

The Configuration module allows to save and load the GUI state of complete windows including its subwindows

+

The main functions are CONF_SaveWindow and CONF_RestoreWindow. CONF_SaveWindow automatically detects if the current window is a DA_Ephys panel and uses the DA_Ephys GUI state savig configuration settings and saves additional information. CONF_RestoreWindow also detects if the current window is of DA_Ephys type and handles that specific for this case. CONF_RestoreDAEphys can be called directly as well if there is no panel open. It will open a new DA_Ephys panel automatically if no other viable candidate panel was found.

+

The GUI state is saved in a text file in json format. In the basic structure of the file the main blocks are the windows and subwindows and within are the control blocks. For notebook windows the content of the notebook is saved as plain text and restored as plain text. A bitmask parameter allows to configure which control information is saved. See WindowControlSavingMask Currently supported is Value, Position/Size, Userdata, Disabled state and Type of a control. Not implemented is e.g. Color/Background Color As Value only the V_Value and/or S_Value and/or S_DataFolder is saved. Special control properties for e.g. ListBox like V_SelCol are currently not implemented.

+

How GUI controls are handled can be controlled through userdata settings of each control. The following userdata settings are supported:

    +

  • Config_NiceName: sets a human readable name of the control used in the configuration file This name may not be a duplicate of another controls name or ControlArray name. Also suffixing with “ ControlGroup” is not allowed.

    • +

  • Config_GroupPath: Sets a group path in which the control appears in the configuration file. If not set then “Generic” is used. The group path elements can not contain the ‘/’ character. Several levels can be separated by “;”, e.g. “level1;level2;”. In the configuration file the group path elements are suffixed by “ ControlGroup” which identifies them as path compared to actual control names.

    • +

  • Config_DontSave: When set to 1 the control is ignored on saving the window.

    • +

  • Config_DontRestore: When set to 1 the control is ignored on restoring the window.

    • +

  • Config_PushButtonOnRestore: Only valid with Button controls. When the button is restored a button press is issued.

    • +

  • Config_RestorePriority: Sets a double precision number that defines the order in which controls get restored. Lower numbers correspond to earlier restore. If not set a priority of Inf is used. If multiple controls have the same priority the order of restore is not defined.

    • +

  • Config_RadioCouplingFunc: A function name of a function that returns a text wave with lists of coupled CheckBoxes (aka RadioButtons). It is assumed that only one CheckBox of the group is in enabled state at the same time. See DAP_GetRadioButtonCoupling for example.

    • +

  • ControlArray: Stores a name of a group of controls. All controls with the same ControlArray name are saved as group with that name in the configuration file. ControlArrays save only values and nothing is saved if the configured WindowControlSavingMask does not include values.

    • +

  • ControlArrayIndex: Only valid if also ControlArray is set. Stores the index number of the control in its ControlArray. All member of the same ControlArray must have different indices. Currently not more than 100 controls are allowed for each ControlArray.

    • +
+

+

The function WindowtoJSON allows to give optional a list of control types that should be excluded.

+

If the type of the control was saved, it is checked against the GUI controls type on restore.

+

CheckBoxes are saved with true/false values.

+

For the DA_Ephys panel: The function CONF_DefaultSettings sets default values for parameters not present in the GUI.

+

Special mask flags:

    +

  • EXPCONFIG_SAVE_ONLY_RELEVANT: Saves only most relevant value data of a control. It is configured in EXPCONFIG_GUI_PREFERRED

    • +

  • EXPCONFIG_SAVE_POPUPMENU_AS_STRING_ONLY: Saves value for PopupMenu only as string

    • +

  • EXPCONFIG_SAVE_POPUPMENU_AS_INDEX_ONLY: Saves value for PopupMenu only as index value

    • +

  • EXPCONFIG_MINIMIZE_ON_RESTORE: Minimize window while restoring it.

    • +

  • EXPCONFIG_SAVE_BUTTONS_ONLY_PRESSED: Saves Buttons only when its userdata Config_PushButtonOnRestore is “1”

    • +
+

+

Handling of window names on restore: The currently selected windows main window is used as reference. The main window name in the configuration file is internally replaced with the current main window. This allows to save from “DataBrowser” and load to “DataBrowser2”.

+

Handling of errors in input data: If input data is of unexpected format an ASSERTion or RTE is issued. The wrapping function converts the RTE to an ASSERT. The panel restore is aborted and the panel stays in its state. It gets unhided.

+

Default configuration for generic windows: By default only the Value property is saved and controls from EXPCONFIG_EXCLUDE_CTRLTYPES excluded.

+

Default configuration for DA_Ephys panel:

    +

  • By default only the Value property is saved

    • +

  • Controls from DAEPHYS_EXCLUDE_CTRLTYPES are excluded.

    • +

  • The window is minimized while restoring

    • +

  • PopupMenu values are saved as string only

    • +

  • Buttons are only saved if its userdata Config_PushButtonOnRestore is “1”

    • +

  • Only most relevant data of a control is saved.

    • +
+

+

*_rig.json configuration files store settings that are specific to a rig. When restoring a DAEphys panel the settings from the rig file are joined with the settings in the DAEphys configuration file. Having entries for the same setting in both files is invalid and an assertion will be thrown.

+

Saving a DAEphys panel that was originally restored from a configuration file:

    +

  • entries from the “Common configuration data” block are updated with the values from the previous configuration, if they already existed. New entries are set at default values.

    • +

  • entries defined in an associated rig file are removed from the DAEphys panel configuration because they would appear in both files

    • +

  • the previously used rig file is copied to the new location

    • +

  • By default for both files (DAEphys configuration and rig file) new file names are generated. If the new files already exist a save dialog is opened to allow the user to modify the path/name.

    • +
+

+
+

Unnamed Group

+
+
+static const double CONF_AUTO_LOADER_GLOBAL = 0x0
+

Parameters for CONF_GetSettingsPath()

+
+ +
+
+static const double CONF_AUTO_LOADER_USER = 0x1
+
+ +
+
+

Functions

+
+
+static variable CONF_DefaultSettings()
+

Creates a json with default experiment configuration block.

+
+
Returns:
+

json with default experiment configuration

+
+
+
+ +
+
+variable CONF_OpenConfigInNotebook()
+

Open all configuration files in plain text notebooks.

+

Existing notebooks with the files are brought to the front.

+
+ +
+
+static wave CONF_GetConfigFiles(string customIPath = defaultValue)
+

Return a text wave with absolute paths to the JSON configuration files.

+
+ +
+
+variable CONF_AutoLoader(string customIPath = defaultValue)
+

Automatically loads all *.json files from MIES Settings folder and opens and restores the corresponding windows Files are restored in case-insensitive alphanumeric order. Associated *_rig.json files are taken into account.

+
+ +
+
+static string CONF_GetSettingsPath(variable type)
+

Returns a symbolic path to the settings folder.

+
+
Parameters:
+

type – One of CONF_AUTO_LOADER_GLOBAL or CONF_AUTO_LOADER_USER

+
+
Returns:
+

name of an igor symbolic path to the settings folder

+
+
+
+ +
+
+variable CONF_SaveWindow(string fName)
+

Saves the GUI state of a window and all of its subwindows to a configuration file.

+
+
Parameters:
+

fName – file name of configuration file to save configuration

+
+
+
+ +
+
+variable CONF_RestoreWindow(string fName, string rigFile = defaultValue)
+

Restores the GUI state of window and all of its subwindows from a configuration file. If the configuration file contains a panel type string then a new window of that type is opened and restored.

+
+
Parameters:
+
    +

  • fName – file name of configuration file to read configuration

    • +

  • rigFile – [optional, default = “”] name of secondary rig configuration file with complementary data. This parameter is valid when loading for a DA_Ephys panel

    • +
+
+
+
+ +
+
+static variable CONF_SaveDAEphys(string fName)
+

Saves the GUI state of a DA_Ephys panel to a configuration file.

+
+
Parameters:
+

fName – file name of configuration file to store DA_Ephys configuration

+
+
+
+ +
+
+variable CONF_PrimeDeviceLists(string device)
+
+ +
+
+string CONF_RestoreDAEphys(variable jsonID, string fullFilePath, variable middleOfExperiment = defaultValue, variable forceNewPanel = defaultValue)
+

Restores the GUI state of a DA_Ephys panel from a configuration file.

+
+
Parameters:
+
    +

  • jsonID – json ID of json object to restore DA_Ephys panel from

    • +

  • fullFilePath – full file path of the file where the json object was parsed from

    • +

  • middleOfExperiment – [optional, default = 0] Allows MIES config in the middle of experiment. Instead of setting MCC parameters they are pulled from actively recording MCCs to configure MIES]

    • +

  • forceNewPanel – [optional, default = 0] When set opens always a fresh DA_Ephys panel, otherwise follows this priority order:

      +

    • Reuses locked DA_Ephys panel with same device as saved in configuration

      • +

    • Uses open unlocked DA_Ephys panel

      • +

    • Opens new DA_Ephys panel

      • +
    +

    • +
+
+
Returns:
+

name of the created DAEphys panel

+
+
+
+ +
+
+static variable CONF_AddConfigFileUserData(string win, string fullFilePath, string rigFile)
+

Add the config file paths and SHA-256 hashes to the panel as user data.

+
+ +
+
+static variable CONF_ParseJSON(string str)
+

Parses a json formatted string to a json object. This function shows a helpful error message if the parse fails.

+
+
Parameters:
+

str – [in] string in json format

+
+
Returns:
+

jsonID of the json object

+
+
+
+ +
+
+static string CONF_GetDAEphysActiveHeadstages(variable jsonID)
+

Retrieves list of active headstages saved in a DA_Ephys configuration file.

+
+
Parameters:
+

jsonID – ID of existing json

+
+
Returns:
+

List of active head stages

+
+
+
+ +
+
+static variable CONF_RequireConfigBlockExists(variable jsonID)
+

Checks if EXPCONFIG_RESERVED_DATABLOCK exists in json; ASSERTion is thrown if not found.

+
+
Parameters:
+

jsonID – ID of existing json

+
+
+
+ +
+
+static string CONF_GetStringFromSettings(variable jsonID, string keyName)
+

Retrieves a string value from a setting.

+
+
Parameters:
+
    +

  • jsonID – ID of existing json

    • +

  • keyName – key name of setting

    • +
+
+
Returns:
+

string from member with keyname in the EXPCONFIG_RESERVED_DATABLOCK

+
+
+
+ +
+
+static variable CONF_GetVariableFromSettings(variable jsonID, string keyName, variable defaultValue = defaultValue)
+

Retrieves a variable/boolean/null value from a saved control note: boolean control property values are also saved in the EXPCONFIG_FIELD_CTRLVVALUE field.

+
+
Parameters:
+
    +

  • jsonID – ID of existing json

    • +

  • keyName – key name of setting

    • +

  • defaultValue – [optional, defaults to off] allows to query optional entries, if the value could not be found this is returned instead

    • +
+
+
Returns:
+

value of the EXPCONFIG_FIELD_CTRLVVALUE field of the control

+
+
+
+ +
+
+static string CONF_FindControl(variable jsonID, string niceName)
+

Returns the path to the first control named nicename found in the json in all saved windows This might as well be a ControlArray.

+
+
Parameters:
+
    +

  • jsonID – ID of existing json

    • +

  • niceName – nice name of control

    • +
+
+
Returns:
+

Path to control in json, empty string if not found

+
+
+
+ +
+
+static string CONF_TraversalFinder(variable jsonID, string basePath, string niceName)
+

Returns the path to the first control named nicename found traversing the json starting at basePath This might as well be a ControlArray. This function runs recursively.

+
+
Parameters:
+
    +

  • jsonID – ID of existing json

    • +

  • basePath – root of traversal start

    • +

  • niceName – nice name of control

    • +
+
+
Returns:
+

Path to control in json, empty string if not found

+
+
+
+ +
+
+static wave CONF_GetWaveFromSavedControlArray(variable jsonID, string arrayName)
+

Retrieves a wave from a saved ControlArray It is REQUIRED that ALL ELEMENTS of the ControlArray are of NUMERIC type.

+
+
Parameters:
+
    +

  • jsonID – ID of existing json

    • +

  • arrayName – name of ControlArray

    • +
+
+
Returns:
+

text wave with data from ControlArray

+
+
+
+ +
+
+static string CONF_GetStringFromSavedControl(variable jsonID, string niceName)
+

Retrieves a string value from a saved control.

+
+
Parameters:
+
    +

  • jsonID – ID of existing json

    • +

  • niceName – nice name of control

    • +
+
+
Returns:
+

value of the EXPCONFIG_FIELD_CTRLSVALUE field of the control

+
+
+
+ +
+
+static variable CONF_GetVariableFromSavedControl(variable jsonID, string niceName)
+

Retrieves a variable value from a saved control.

+
+
Parameters:
+
    +

  • jsonID – ID of existing json

    • +

  • niceName – nice name of control

    • +
+
+
Returns:
+

value of the EXPCONFIG_FIELD_CTRLVVALUE field of the control

+
+
+
+ +
+
+static wave CONF_GetWindowNames(variable jsonID)
+

Returns a wave with all configuration sections ( aka control groups). This equals the top level keys without the EXPCONFIG_RESERVED_DATABLOCK key.

+
+
Parameters:
+

jsonID – [in] ID of existing json

+
+
Returns:
+

Text wave with all named configuration sections

+
+
+
+ +
+
+static wave CONF_GetControlArrayList(string wName)
+

Returns a two column free wave with ControlArrayName and associated control list from a window.

+
+
Parameters:
+

wName – [in] Name of window

+
+
Returns:
+

Text wave with two columns and in each row ControlArray name (column ARRAYNAME) and control list (column CTRLNAMELIST)

+
+
+
+ +
+
+static variable CONF_GatherControlsFromJSON(WaveText ctrlData, variable jsonID, string basePath)
+

Gathers recursively all control nice names and control paths from a configuration json by traversing all sub objects.

+
+
Parameters:
+
    +

  • ctrlData – [in] ctrlData wave, 2d four column text wave as created in CONF_JSONToWindow(). This wave is updated by this function.

    • +

  • jsonID – [in] json object to traverse

    • +

  • basePath – [in] root path for traversal

    • +
+
+
+
+ +
+
+string CONF_JSONToWindow(string wName, variable restoreMask, variable jsonID)
+

Restores GUI state of a window from a json The following userdata properties are considered: EXPCONFIG_UDATA_EXCLUDE_RESTORE, EXPCONFIG_UDATA_RESTORE_PRIORITY It is supported that the current main reference window in the GUI changes its name. It is not supported that a not yet restored subwindow of it changes its name.

+
+
Parameters:
+
    +

  • wName – main reference window name in GUI

    • +

  • restoreMask – Bit mask which properties are restored from WindowControlSavingMask constants

    • +

  • jsonID – ID of existing json

    • +
+
+
Returns:
+

name of main window after restore

+
+
+
+ +
+
+static variable CONF_RestoreNotebookWindow(string wName, string srcWin, variable jsonID)
+

Restores a notebook window content.

+
+
Parameters:
+
    +

  • wName – Name of notebook window in Igor

    • +

  • srcWin – Name of window in JSON

    • +

  • jsonID – Id of JSON

    • +
+
+
+
+ +
+
+static string CONF_FindWindow(string winHandle, string uKey = defaultValue)
+

Returns the window with the set window handle.

+
+
Parameters:
+
    +

  • winHandle – window handle

    • +

  • uKey – [optional, default = EXPCONFIG_UDATA_WINHANDLE] userdata key that stores the handle value

    • +
+
+
Returns:
+

Window name of the window with the given handle; empty string if not found.

+
+
+
+ +
+
+static variable CONF_RestoreControl(string wName, variable restoreMask, variable jsonID, string ctrlName, string jsonPath = defaultValue)
+

Restores properties of a control from a json The following control userdata properties are considered: EXPCONFIG_UDATA_EXCLUDE_RESTORE; EXPCONFIG_UDATA_BUTTONPRESS (for Buttons)

+
+
Parameters:
+
    +

  • wName – Window name

    • +

  • restoreMask – Bit mask which properties are restored from WindowControlSavingMask constants

    • +

  • jsonID – ID of existing json

    • +

  • ctrlName – Control name

    • +

  • jsonPath – [optional, default = n/a] When given: the control is expected to be a named json object (with the control nice name) If not given: the jsons second level (assuming default format) is searched for the associated object. This is slower.

    • +
+
+
+
+ +
+
+variable CONF_AllWindowsToJSON(string wName, variable saveMask, string excCtrlTypes = defaultValue)
+

Serializes all controls of a window and its subwindows into a json object.

+

+

See also

+

WindowControlSavingMask

+
+

+
+
Parameters:
+
    +

  • wName – [in] name of main window

    • +

  • saveMask – [in] bit pattern based configuration setting for saving

    • +

  • excCtrlTypes – [in] [optional, default = “”], list of control type codes for excluded control types for saving e.g. “1;6;” to exclude all buttons and charts

    • +
+
+
Returns:
+

json ID of object where all controls where serialized into

+
+
+
+ +
+
+wave CONF_GetRadioButtonCouplingProtoFunc()
+
+ +
+
+variable CONF_WindowToJSON(string wName, variable saveMask, string excCtrlTypes = defaultValue)
+

Saves complete GUI state of a window in a json For coupled CheckBoxes aka (radio buttons) the enabled radio button is saved, the disabled is not saved. For three or more coupled CheckBoxes the first enabled radio button is saved, the disabled are not saved. For three or more coupled CheckBoxes an assertion is thrown if no CheckBox is set.

+
+
Parameters:
+
    +

  • wName – Window name

    • +

  • saveMask – Bit mask which properties are saved from WindowControlSavingMask constants

    • +

  • excCtrlTypes – [optional, default = “”] List of excluded control types that are ignored

    • +
+
+
Returns:
+

jsonID ID of json containing the serialized GUI data

+
+
+
+ +
+
+static string CONF_GetCompleteJSONCtrlPath(string path)
+
+ +
+
+static variable CONF_NotebookToJSON(string wName, variable jsonID)
+

Adds a notebook window including content to a json.

+
+
Parameters:
+
    +

  • wName – Window name

    • +

  • jsonID – ID of existing json

    • +
+
+
+
+ +
+
+static variable CONF_ControlToJSON(string wName, string ctrlName, variable saveMask, variable jsonID, string excCtrlTypes, string excUserKeys)
+

Adds properties of a control to a json.

+
+
Parameters:
+
    +

  • wName – Window name

    • +

  • ctrlName – Control name

    • +

  • saveMask – Bit mask which properties are saved from WindowControlSavingMask constants

    • +

  • jsonID – ID of existing json

    • +

  • excCtrlTypes – List of excluded control types that are ignored

    • +

  • excUserKeys – List of excluded keys of userdata fields that are ignored

    • +
+
+
+
+ +
+
+static variable CONF_RestoreHeadstageAssociation(string device, variable jsonID, variable midExp)
+

Opens MCCs and restores Headstage Association from configuration data to DA_Ephys panel.

+
+
Parameters:
+
    +

  • device – [in] panel title of DA_Ephys panel

    • +

  • jsonID – [in] ID of json object with configuration data

    • +

  • midExp – [in] middle of experiment - uploads MCC relevant settings from panel to MCC instead

    • +
+
+
+
+ +
+
+static variable CONF_OnExistSetAndActivateControlVar(string win, string ctrl, variable jsonId, string jsonPath)
+
+ +
+
+static variable CONF_OnExistSetAndActivateControlStr(string win, string ctrl, variable jsonId, string jsonPath)
+
+ +
+
+static variable CONF_SetDAEPhysChannelPopup(string device, string ctrl, variable jsonId, string jsonPath)
+
+ +
+
+static variable CONF_GetUserPressure(string device)
+

Retrieves current User Pressure settings to json.

+
+
Parameters:
+

device – [in] panel title of DA_Ephys panel

+
+
Returns:
+

jsonID ID of json object with user pressure configuration data

+
+
+
+ +
+
+static variable CONF_RestoreUserPressure(string device, variable jsonID)
+

Restore User Pressure settings.

+
+
Parameters:
+
    +

  • device – [in] panel title of DA_Ephys panel

    • +

  • jsonID – [in] ID of json object with configuration data

    • +
+
+
+
+ +
+
+static variable CONF_GetAmplifierSettings(string device)
+

Retrieves current amplifier and pressure settings to json.

+
+
Parameters:
+

device – [in] device

+
+
Returns:
+

jsonID ID of json object with user pressure configuration data

+
+
+
+ +
+
+static variable CONF_RestoreAmplifierSettings(string device, variable headStage, variable jsonID, string basePath)
+

Restore the per headstage amplifier settings.

+
+
Parameters:
+
    +

  • device – [in] device

    • +

  • headStage – [in] MIES headstage number, must be in the range [0, NUM_HEADSTAGES]

    • +

  • jsonID – [in] ID of json object with configuration data

    • +

  • basePath – [in] absolute path in the json file to search the entries

    • +
+
+
+
+ +
+
+static variable CONF_FindAmpInList(variable ampSerialRef, variable ampChannelIDRef)
+

Find the list index of a connected amplifier serial number.

+
+
Parameters:
+
    +

  • ampSerialRef – Amplifier Serial Number to search for

    • +

  • ampChannelIDRef – Headstage reference number

    • +
+
+
+
+ +
+
+static variable CONF_MCC_MidExp(string device, variable headStage, variable jsonID)
+
+ +
+
+variable CONF_Position_MCC_Win(string serialNum, string winTitle, string winPosition)
+

Position MCC windows to upper right monitor using nircmd.exe.

+
+
Parameters:
+
    +

  • serialNum – Serial number of MCC

    • +

  • winTitle – Name of MCC window

    • +

  • winPosition – One of 4 monitors to position MCCs in

    • +
+
+
+
+ +
+
+static variable CONF_JoinRigFile(variable jsonID, string rigFileName)
+

Loads, parses and joins a *_rig.json file to a main configuration file.

+
+
Parameters:
+
    +

  • jsonID – [in] jsonID of main configuration

    • +

  • rigFileName – [in] full file path of rig file

    • +
+
+
+
+ +
+
+static std::tuple<variable, string> CONF_LoadConfigUsedForDAEphysPanel(string wName, variable loadRigFile = defaultValue)
+

Retrieves the JSON original used to restore the DAEphys panel from the disk.

+
+
Parameters:
+
    +

  • wName – [in] name of DAEphys panel

    • +

  • loadRigFile – [in] [optional, default 0] when set, load the rig file instead

    • +
+
+
Returns:
+

jsonId or NaN if data was not present

+
+
+
+ +
+
+static variable CONF_TransferPreviousDAEphysJson(variable jsonId, variable prevJsonId)
+
+ +
+
+static variable CONF_RemoveRigElementsFromDAEphysJson(variable jsonId, variable rigJsonId, string jsonPath = defaultValue)
+
+ +
+
+static string CONF_GetDAEphysConfigurationFileNameSuggestion(string wName)
+
+ +
+
+variable CONF_UpdatePackageSettingsFromConfigFiles(variable jsonIdPkg)
+

Loads through all config json files and synchronizes global package settings in config files (if present) to user package settings with overwrite.

+
+ +
+
+

Variables

+
+
+static const string EXPCONFIG_FIELD_CTRLTYPE = "Type"
+
+ +
+
+static const string EXPCONFIG_FIELD_CTRLVVALUE = "NumValue"
+
+ +
+
+static const string EXPCONFIG_FIELD_CTRLSVALUE = "StrValue"
+
+ +
+
+static const string EXPCONFIG_FIELD_CTRLSDF = "DataSource"
+
+ +
+
+static const string EXPCONFIG_FIELD_CTRLDISABLED = "Disabled"
+
+ +
+
+static const string EXPCONFIG_FIELD_CTRLPOSHEIGHT = "Height"
+
+ +
+
+static const string EXPCONFIG_FIELD_CTRLPOSWIDTH = "Width"
+
+ +
+
+static const string EXPCONFIG_FIELD_CTRLPOSTOP = "Top"
+
+ +
+
+static const string EXPCONFIG_FIELD_CTRLPOSLEFT = "Left"
+
+ +
+
+static const string EXPCONFIG_FIELD_CTRLPOSRIGHT = "Right"
+
+ +
+
+static const string EXPCONFIG_FIELD_CTRLPOSPOS = "Pos"
+
+ +
+
+static const string EXPCONFIG_FIELD_CTRLPOSALIGN = "Align"
+
+ +
+
+static const string EXPCONFIG_FIELD_CTRLUSERDATA = "Userdata"
+
+ +
+
+static const string EXPCONFIG_FIELD_BASE64PREFIX = "Base64 "
+
+ +
+
+static const string EXPCONFIG_FIELD_CTRLARRAYVALUES = "Values"
+
+ +
+
+static const string EXPCONFIG_FIELD_NOTEBOOKTEXT = "NotebookText"
+
+ +
+
+static const string EXPCONFIG_UDATA_NICENAME = "Config_NiceName"
+
+ +
+
+static const string EXPCONFIG_UDATA_JSONPATH = "Config_GroupPath"
+
+ +
+
+static const string EXPCONFIG_UDATA_BUTTONPRESS = "Config_PushButtonOnRestore"
+
+ +
+
+static const string EXPCONFIG_UDATA_RESTORE_PRIORITY = "Config_RestorePriority"
+
+ +
+
+static const string EXPCONFIG_UDATA_WINHANDLE = "Config_WindowHandle"
+
+ +
+
+static const string EXPCONFIG_UDATA_RADIOCOUPLING = "Config_RadioCouplingFunc"
+
+ +
+
+static const string EXPCONFIG_UDATA_CTRLARRAY = "ControlArray"
+
+ +
+
+static const string EXPCONFIG_UDATA_CTRLARRAYINDEX = "ControlArrayIndex"
+
+ +
+
+static const double EXPCONFIG_UDATA_MAXCTRLARRAYINDEX = 100
+
+ +
+
+static const double EXPCONFIG_JSON_INDENT = 4
+
+ +
+
+static const string EXPCONFIG_FILEFILTER = "Configuration Files (*.json):.json;All Files:.*;"
+
+ +
+
+static const string EXPCONFIG_CTRLGROUP_SUFFIX = " ControlGroup"
+
+ +
+
+static const string EXPCONFIG_SETTINGS_FOLDER = "Settings"
+
+ +
+
+static const string DAEPHYS_UDATA_WINHANDLE = "DAEphys_WindowHandle"
+
+ +
+
+static const string DAEPHYS_HEADSTAGECTRLARRAYPREFIX = "Check_DataAcqHS"
+
+ +
+
+static const string DAEPHYS_EXCLUDE_CTRLTYPES = "12;9;10;4;"
+
+ +
+
+static const string EXPCONFIG_DEFAULT_CTRL_JSONPATH = "Generic"
+
+ +
+
+static const string EXPCONFIG_RESERVED_DATABLOCK = "Common configuration data"
+
+ +
+
+static const string EXPCONFIG_RESERVED_TAGENTRY = "Target Window Type"
+
+ +
+
+static const string EXPCONFIG_EXCLUDE_USERDATA = "ResizeControlsInfo;"
+
+ +
+
+static const string EXPCONFIG_EXCLUDE_CTRLTYPES = "12;9;10;"
+
+ +
+
+static const string EXPCONFIG_SETTINGS_AMPTITLE = "0,1;2,3;4,5;6,7"
+
+ +
+
+static const string EXPCONFIG_JSON_GLOBALPACKAGESETTINGBLOCK = "Global Package Settings"
+
+ +
+
+static const string EXPCONFIG_JSON_HSASSOCBLOCK = "Headstage Association"
+
+ +
+
+static const string EXPCONFIG_JSON_AMPBLOCK = "Amplifier"
+
+ +
+
+static const string EXPCONFIG_JSON_ICBLOCK = "IC"
+
+ +
+
+static const string EXPCONFIG_JSON_VCBLOCK = "VC"
+
+ +
+
+static const string EXPCONFIG_JSON_PRESSUREBLOCK = "Pressure"
+
+ +
+
+static const string EXPCONFIG_JSON_AMPSERIAL = "Serial"
+
+ +
+
+static const string EXPCONFIG_JSON_AMPTITLE = "Title"
+
+ +
+
+static const string EXPCONFIG_JSON_AMPCHANNEL = "Channel"
+
+ +
+
+static const string EXPCONFIG_JSON_AMPVCDA = "DA"
+
+ +
+
+static const string EXPCONFIG_JSON_AMPVCDAGAIN = "DA gain"
+
+ +
+
+static const string EXPCONFIG_JSON_AMPVCDAUNIT = "DA unit"
+
+ +
+
+static const string EXPCONFIG_JSON_AMPVCAD = "AD"
+
+ +
+
+static const string EXPCONFIG_JSON_AMPVCADGAIN = "AD gain"
+
+ +
+
+static const string EXPCONFIG_JSON_AMPVCADUNIT = "AD unit"
+
+ +
+
+static const string EXPCONFIG_JSON_AMPICDA = "DA"
+
+ +
+
+static const string EXPCONFIG_JSON_AMPICDAGAIN = "DA gain"
+
+ +
+
+static const string EXPCONFIG_JSON_AMPICDAUNIT = "DA unit"
+
+ +
+
+static const string EXPCONFIG_JSON_AMPICAD = "AD"
+
+ +
+
+static const string EXPCONFIG_JSON_AMPICADGAIN = "AD gain"
+
+ +
+
+static const string EXPCONFIG_JSON_AMPICADUNIT = "AD unit"
+
+ +
+
+static const string EXPCONFIG_JSON_PRESSDEV = "Device"
+
+ +
+
+static const string EXPCONFIG_JSON_PRESSDA = "DA"
+
+ +
+
+static const string EXPCONFIG_JSON_PRESSAD = "AD"
+
+ +
+
+static const string EXPCONFIG_JSON_PRESSDAGAIN = "DA Gain"
+
+ +
+
+static const string EXPCONFIG_JSON_PRESSADGAIN = "AD Gain"
+
+ +
+
+static const string EXPCONFIG_JSON_PRESSDAUNIT = "DA Unit"
+
+ +
+
+static const string EXPCONFIG_JSON_PRESSADUNIT = "AD Unit"
+
+ +
+
+static const string EXPCONFIG_JSON_PRESSTTLA = "TTLA"
+
+ +
+
+static const string EXPCONFIG_JSON_PRESSTTLB = "TTLB"
+
+ +
+
+static const string EXPCONFIG_JSON_PRESSCONSTNEG = "const double Negative"
+
+ +
+
+static const string EXPCONFIG_JSON_PRESSCONSTPOS = "const double Positive"
+
+ +
+
+static const string EXPCONFIG_JSON_SAVE_PATH = "Save data to"
+
+ +
+
+static const string EXPCONFIG_JSON_STIMSET_NAME = "Stim set file name"
+
+ +
+
+static const string EXPCONFIG_JSON_POSITION_MCC = "Position MCCs"
+
+ +
+
+static const string EXPCONFIG_JSON_LOGFILE_UPLOAD = "Automatic logfile upload"
+
+ +
+
+static const double EXPCONFIG_JSON_LOGFILE_UPLOAD_DEFAULT = 0
+
+ +
+
+static const string EXPCONFIG_JSON_USERPRESSBLOCK = "User Pressure Devices"
+
+ +
+
+static const string EXPCONFIG_JSON_USERPRESSDEV = "DAC Device"
+
+ +
+
+static const string EXPCONFIG_JSON_USERPRESSDA = "DA"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_HOLD_VC = "Holding"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_HOLD_ENABLE_VC = "Holding Enable"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_LPF = "LPF primary output"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_GAIN = "Gain primary output"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_PIPETTE_OFFSET_VC = "Pipette Offset"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_WHOLE_CELL_CAPACITANCE = "Whole Cell Capacitance"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_WHOLE_CELL_RESISTANCE = "Whole Cell Resistance"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_WHOLE_CELL_ENABLE = "Whole Cell Enable"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_RS_COMP_CORRECTION = "RS Compensation Correction"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_RS_COMP_PREDICTION = "RS Compensation Prediction"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_RS_COMP_ENABLE = "RS Compensation Enable"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_COMP_CHAIN = "RS Compensation Chain"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_HOLD_IC = "Holding"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_HOLD_ENABLE_IC = "Holding Enable"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_BRIDGE_BALANCE = "Bridge Balance"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_BRIDGE_BALANCE_ENABLE = "Bridge Balance Enable"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_CAP_NEUTRALIZATION = "Capacitance Neutralization"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_CAP_NEUTRALIZATION_ENABLE = "Capacitance Neutralization Enable"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_AUTOBIAS_V = "Autobias Voltage"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_AUTOBIAS_V_RANGE = "Autobias Voltage Range"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_AUTOBIAS_I_BIAS_MAX = "Autobias Current Max"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_AUTOBIAS = "Autobias Enable"
+
+ +
+
+static const string EXPCONFIG_JSON_AMP_PIPETTE_OFFSET_IC = "Pipette Offset"
+
+ +
+
+static const string EXPCONFIG_RIGFILESUFFIX = "_rig.json"
+
+ +
+
+static const double EXPCONFIG_MIDDLEEXP_OFF = 0
+
+ +
+
+static const double EXPCONFIG_MIDDLEEXP_ON = 1
+
+ +
+
+static const string CONF_AUTO_LOADER_USER_PATH = "C:ProgramData:AllenInstitute:MIES:Settings"
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___constants_8ipf.html b/file/_m_i_e_s___constants_8ipf.html new file mode 100644 index 0000000000..f64cf41f35 --- /dev/null +++ b/file/_m_i_e_s___constants_8ipf.html @@ -0,0 +1,8154 @@ + + + + + + + + File MIES_Constants.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Constants.ipf

+

Global constants.

+
+

Version constants

+

+
+
+const double DAQ_CONFIG_WAVE_VERSION = 3
+
+ +
+
+const double DA_EPHYS_PANEL_VERSION = 64
+

Used to upgrade the GuiStateWave as well as the DA Ephys panel.

+
+ +
+
+const double DATA_SWEEP_BROWSER_PANEL_VERSION = 50
+
+ +
+
+const double WAVEBUILDER_PANEL_VERSION = 14
+
+ +
+
+const double ANALYSISBROWSER_PANEL_VERSION = 5
+
+ +
+
+const double STIMSET_NOTE_VERSION = 11
+

Version of the stimset wave note.

+
+ +
+
+const double SWEEP_EPOCH_VERSION = 9
+

Version of the epoch information for DA+TTL data.

+
+ +
+
+const double LABNOTEBOOK_VERSION = 76
+

Version of the labnotebooks and results (numerical and textual) waves

+

Has to be increased on the following occasions:

    +

  • New/Removed entries

    • +

  • Changed names of entries

    • +

  • Changed units or meaning of entries

    • +

  • New/Changed layers of entries

    • +
+

+
+ +
+
+const double RESULTS_VERSION = 3
+
+ +
+
+

Analysis function versions

+
+
+const double PSQ_PIPETTE_BATH_VERSION = 4
+
+ +
+
+const double PSQ_ACC_RES_SMOKE_VERSION = 2
+
+ +
+
+const double PSQ_CHIRP_VERSION = 13
+
+ +
+
+const double PSQ_DA_SCALE_VERSION = 11
+
+ +
+
+const double PSQ_RAMP_VERSION = 6
+
+ +
+
+const double PSQ_RHEOBASE_VERSION = 5
+
+ +
+
+const double PSQ_SQUARE_PULSE_VERSION = 4
+
+ +
+
+const double PSQ_SEAL_EVALUATION_VERSION = 3
+
+ +
+
+const double PSQ_TRUE_REST_VM_VERSION = 2
+
+ +
+
+const double MSQ_FAST_RHEO_EST_VERSION = 1
+
+ +
+
+const double MSQ_DA_SCALE_VERSION = 1
+
+ +
+
+const double SC_SPIKE_CONTROL_VERSION = 2
+
+ +
+
+

Constans for the number of channels

+

+
+
+const double NUM_DA_TTL_CHANNELS = 8
+
+ +
+
+const double NUM_HEADSTAGES = 8
+
+ +
+
+const double NUM_AD_CHANNELS = 16
+
+ +
+
+const double NUM_ASYNC_CHANNELS = 8
+
+ +
+
+const double NUM_ITC_TTL_BITS_PER_RACK = 4
+
+ +
+
+

Task names

+

+
+
+const string TASKNAME_TP = "Testpulse"
+
+ +
+
+const string TASKNAME_TPMD = "TestpulseMD"
+
+ +
+
+const string TASKNAME_TIMER = "Timer"
+
+ +
+
+const string TASKNAME_TIMERMD = "TimerMD"
+
+ +
+
+const string TASKNAME_FIFOMON = "FIFOMonitor"
+
+ +
+
+const string TASKNAME_FIFOMONMD = "FIFOMonitorMD"
+
+ +
+
+const string TASKNAMES = "Testpulse;TestpulseMD;Timer;TimerMD;FIFOMonitor;FIFOMonitorMD;"
+
+ +
+
+

Various mies specific regular expressions

+

+
+
+const string DATA_SWEEP_REGEXP = "(?i)^Sweep_[[:digit:]]+$"
+
+ +
+
+const string DATA_CONFIG_REGEXP = "(?i)^Config_Sweep_[[:digit:]]+$"
+
+ +
+
+const string TP_STORAGE_REGEXP = "(?i)^TPStorage(_[[:digit:]]+)?$"
+
+ +
+
+const string STORED_TESTPULSES_REGEXP = "(?i)^StoredTestPulses_([[:digit:]]+)$"
+
+ +
+
+const string DATA_SWEEP_REGEXP_BAK = "(?i)^Sweep_[[:digit:]]+_bak$"
+
+ +
+
+const string DATA_CONFIG_REGEXP_BAK = "(?i)^Config_Sweep_[[:digit:]]+_bak$"
+
+ +
+
+

Pressure Control constants

+

Max and min pressure regulator pressure in psi

+
+
+const double MAX_REGULATOR_PRESSURE = 9.9
+
+ +
+
+const double MIN_REGULATOR_PRESSURE = -9.9
+
+ +
+
+

Channel constants shared with the ITC XOP.

+

Due to historic reasons these are now also used for other hardware types

+
+
+const double XOP_CHANNEL_TYPE_ADC = 0
+
+ +
+
+const double XOP_CHANNEL_TYPE_DAC = 1
+
+ +
+
+const double XOP_CHANNEL_TYPE_TTL = 3
+
+ +
+
+const double XOP_CHANNEL_TYPE_COUNT = 4
+
+ +
+
+

DAQ Channel Type constants used in DAQConfigWave

+

+
+
+const double DAQ_CHANNEL_TYPE_UNKOWN = -1
+
+ +
+
+const double DAQ_CHANNEL_TYPE_DAQ = 1
+
+ +
+
+const double DAQ_CHANNEL_TYPE_TP = 2
+
+ +
+
+

When all DAQ Channels are set to TestPulse the output runs for TIME_TP_ONLY_ON_DAQ seconds

+

+
+
+const double TIME_TP_ONLY_ON_DAQ = 1
+
+ +
+
+

Flags for GetActiveChannels

+

+
+
+const double TTL_HARDWARE_CHANNEL = 0x0
+
+ +
+
+const double TTL_DAEPHYS_CHANNEL = 0x1
+
+ +
+
+const double TTL_GUITOHW_CHANNEL = 0x2
+
+ +
+
+const double TTL_HWTOGUI_CHANNEL = 0x3
+
+ +
+
+

Wave dimension constants

+

Convenience definition to nicify expressions like DimSize(wv, ROWS) easier to read than DimSize(wv, 0).

+
+
+const double DATADIMENSION = -1
+
+ +
+
+const double ROWS = 0
+
+ +
+
+const double COLS = 1
+
+ +
+
+const double LAYERS = 2
+
+ +
+
+const double CHUNKS = 3
+
+ +
+
+

append userData constants

+

Convenience definition. easier to read than ModifyGraph userData(trace)={name, 0, value}

+
+
+const double USERDATA_MODIFYGRAPH_REPLACE = 0
+
+ +
+
+const double USERDATA_MODIFYGRAPH_APPEND = 1
+
+ +
+
+

Constants used by Downsample

+
+
+const double DECIMATION_BY_OMISSION = 1
+
+ +
+
+const double DECIMATION_BY_SMOOTHING = 2
+
+ +
+
+const double DECIMATION_BY_AVERAGING = 4
+
+ +
+
+

WMWinHookStruct eventCode field constants

+

+
+
+const double EVENT_WINDOW_HOOK_ACTIVATE = 0
+
+ +
+
+const double EVENT_WINDOW_HOOK_DEACTIVATE = 1
+
+ +
+
+const double EVENT_WINDOW_HOOK_KILL = 2
+
+ +
+
+const double EVENT_WINDOW_HOOK_MOUSEDOWN = 3
+
+ +
+
+const double EVENT_WINDOW_HOOK_MOUSEMOVED = 4
+
+ +
+
+const double EVENT_WINDOW_HOOK_MOUSEUP = 5
+
+ +
+
+const double EVENT_WINDOW_HOOK_RESIZE = 6
+
+ +
+
+const double EVENT_WINDOW_HOOK_CURSORMOVED = 7
+
+ +
+
+const double EVENT_WINDOW_HOOK_MODIFIED = 8
+
+ +
+
+const double EVENT_WINDOW_HOOK_ENABLEMENU = 9
+
+ +
+
+const double EVENT_WINDOW_HOOK_MENU = 10
+
+ +
+
+const double EVENT_WINDOW_HOOK_KEYBOARD = 11
+
+ +
+
+const double EVENT_WINDOW_HOOK_MOVED = 12
+
+ +
+
+const double EVENT_WINDOW_HOOK_RENAMED = 13
+
+ +
+
+const double EVENT_WINDOW_HOOK_SUBWINDOWKILL = 14
+
+ +
+
+const double EVENT_WINDOW_HOOK_HIDE = 15
+
+ +
+
+const double EVENT_WINDOW_HOOK_SHOW = 16
+
+ +
+
+const double EVENT_WINDOW_HOOK_KILLVOTE = 17
+
+ +
+
+const double EVENT_WINDOW_HOOK_SHOWTOOLS = 18
+
+ +
+
+const double EVENT_WINDOW_HOOK_HIDETOOLS = 19
+
+ +
+
+const double EVENT_WINDOW_HOOK_SHOWINFO = 20
+
+ +
+
+const double EVENT_WINDOW_HOOK_HIDEINFO = 21
+
+ +
+
+const double EVENT_WINDOW_HOOK_MOUSEWHEEL = 22
+
+ +
+
+const double EVENT_WINDOW_HOOK_SPINUPDATE = 23
+
+ +
+
+const double EVENT_WINDOW_HOOK_TABLEENTRYACCEPTED = 24
+
+ +
+
+const double EVENT_WINDOW_HOOK_TABLEENTRYCANCELLED = 25
+
+ +
+
+const double EVENT_WINDOW_HOOK_EARLYKEYBOARD = 26
+
+ +
+
+

Trace Display Types

+

+
+
+const double TRACE_DISPLAY_MODE_LINES = 0
+
+ +
+
+const double TRACE_DISPLAY_MODE_STICKS = 1
+
+ +
+
+const double TRACE_DISPLAY_MODE_DOTS = 2
+
+ +
+
+const double TRACE_DISPLAY_MODE_MARKERS = 3
+
+ +
+
+const double TRACE_DISPLAY_MODE_LINES_MARKERS = 4
+
+ +
+
+const double TRACE_DISPLAY_MODE_BARS = 5
+
+ +
+
+const double TRACE_DISPLAY_MODE_CITY = 6
+
+ +
+
+const double TRACE_DISPLAY_MODE_FILL = 7
+
+ +
+
+const double TRACE_DISPLAY_MODE_STICKS_MARKERS = 8
+
+ +
+
+const double TRACE_DISPLAY_MODE_LAST_VALID = 8
+
+ +
+
+

CountObjects, CountObjectsDFR, GetIndexedObjName, GetIndexedObjNameDFR constants

+

+
+
+const double COUNTOBJECTS_WAVES = 1
+
+ +
+
+const double COUNTOBJECTS_VAR = 2
+
+ +
+
+const double COUNTOBJECTS_STR = 3
+
+ +
+
+const double COUNTOBJECTS_DATAFOLDER = 4
+
+ +
+
+

Control types from ControlInfo

+

+
+
+const double CONTROL_TYPE_BUTTON = 1
+
+ +
+
+const double CONTROL_TYPE_CHECKBOX = 2
+
+ +
+
+const double CONTROL_TYPE_POPUPMENU = 3
+
+ +
+
+const double CONTROL_TYPE_VALDISPLAY = 4
+
+ +
+
+const double CONTROL_TYPE_SETVARIABLE = 5
+
+ +
+
+const double CONTROL_TYPE_CHART = 6
+
+ +
+
+const double CONTROL_TYPE_SLIDER = 7
+
+ +
+
+const double CONTROL_TYPE_TAB = 8
+
+ +
+
+const double CONTROL_TYPE_GROUPBOX = 9
+
+ +
+
+const double CONTROL_TYPE_TITLEBOX = 10
+
+ +
+
+const double CONTROL_TYPE_LISTBOX = 11
+
+ +
+
+const double CONTROL_TYPE_CUSTOMCONTROL = 12
+
+ +
+
+

Modifier flags from the eventMod field of the WMWinHookStruct

+

+
+
+const double WINDOW_HOOK_EMOD_MBUTTONDOWN = 1
+
+ +
+
+const double WINDOW_HOOK_EMOD_SHIFTKEYDOWN = 2
+
+ +
+
+const double WINDOW_HOOK_EMOD_ALTKEYDOWN = 4
+
+ +
+
+const double WINDOW_HOOK_EMOD_CTRLKEYDOWN = 8
+
+ +
+
+const double WINDOW_HOOK_EMOD_RIGHTCLICK = 16
+
+ +
+
+

Parameters for FindIndizes

+

+
+
+const double PROP_NOT = 0x01
+

Inverts the matching.

+
+ +
+
+const double PROP_EMPTY = 0x02
+

Wave entry is NaN or “”.

+
+ +
+
+const double PROP_MATCHES_VAR_BIT_MASK = 0x04
+

Wave entry matches the bitmask given in var.

+
+ +
+
+const double PROP_GREP = 0x08
+

Wave entry matches the regular expression given in str.

+
+ +
+
+const double PROP_WILDCARD = 0x10
+

Wave entry matches the wildcard expression given in str.

+
+ +
+
+

Parameters for GetPanelControl and IDX_GetSetsInRange, GetSetFolder, GetSetParamFolder and GetChanneListFromITCConfig

+

+
+
+const double CHANNEL_TYPE_DAC = 0x000
+
+ +
+
+const double CHANNEL_TYPE_TTL = 0x001
+
+ +
+
+const double CHANNEL_TYPE_ADC = 0x002
+
+ +
+
+const double CHANNEL_CONTROL_WAVE = 0x004
+
+ +
+
+const double CHANNEL_CONTROL_INDEX_END = 0x008
+
+ +
+
+const double CHANNEL_CONTROL_UNIT = 0x010
+
+ +
+
+const double CHANNEL_CONTROL_GAIN = 0x020
+
+ +
+
+const double CHANNEL_CONTROL_SCALE = 0x030
+
+ +
+
+const double CHANNEL_CONTROL_CHECK = 0x040
+
+ +
+
+const double CHANNEL_TYPE_HEADSTAGE = 0x080
+
+ +
+
+const double CHANNEL_TYPE_ASYNC = 0x100
+
+ +
+
+const double CHANNEL_TYPE_ALARM = 0x110
+
+ +
+
+const double CHANNEL_CONTROL_ALARM_MIN = 0x120
+
+ +
+
+const double CHANNEL_CONTROL_ALARM_MAX = 0x130
+
+ +
+
+const double CHANNEL_CONTROL_SEARCH = 0x140
+
+ +
+
+const double CHANNEL_TYPE_UNKNOWN = 0x150
+
+ +
+
+const double CHANNEL_CONTROL_TITLE = 0x160
+
+ +
+
+

Controls for multiple channels have negative channel indizes

+

+
+
+const double CHANNEL_INDEX_ALL = -1
+
+ +
+
+const double CHANNEL_INDEX_ALL_V_CLAMP = -2
+
+ +
+
+const double CHANNEL_INDEX_ALL_I_CLAMP = -3
+
+ +
+
+const double CHANNEL_INDEX_ALL_I_ZERO = -4
+
+ +
+
+

Constants for the bitmask entries stored in the selection wave

+

of a ListBox

+
+
+const double LISTBOX_SELECTED = 0x01
+
+ +
+
+const double LISTBOX_CELL_EDITABLE = 0x02
+
+ +
+
+const double LISTBOX_CELL_DOUBLECLICK_EDIT = 0x04
+
+ +
+
+const double LISTBOX_SHIFT_SELECTION = 0x08
+
+ +
+
+const double LISTBOX_CHECKBOX_SELECTED = 0x10
+
+ +
+
+const double LISTBOX_CHECKBOX = 0x20
+
+ +
+
+const double LISTBOX_TREEVIEW_EXPANDED = 0x10
+

Convenience definition, equal to LISTBOX_CHECKBOX_SELECTED.

+
+ +
+
+const double LISTBOX_TREEVIEW = 0x40
+
+ +
+
+

Constants for the note of the wave returned by GetTPStorage

+
+
+const string AUTOBIAS_LAST_INVOCATION_KEY = "AutoBiasLastInvocation"
+
+ +
+
+const string DIMENSION_SCALING_LAST_INVOC = "DimensionScalingLastInvocation"
+
+ +
+
+const string PRESSURE_CTRL_LAST_INVOC = "PressureControlLastInvocation"
+
+ +
+
+const string INDEX_ON_TP_START = "IndexOnTestPulseStart"
+
+ +
+
+const string AUTOTP_LAST_INVOCATION_KEY = "AutoTPLastInvocation"
+
+ +
+
+

Modes for SaveExperimentSpecial

+

+
+
+const double SAVE_AND_CLEAR = 0x01
+
+ +
+
+const double SAVE_AND_SPLIT = 0x02
+
+ +
+
+

Constants for data acquisition modes

+

+
+
+const double UNKNOWN_MODE = NaN
+
+ +
+
+const double DATA_ACQUISITION_MODE = 0
+
+ +
+
+const double TEST_PULSE_MODE = 1
+
+ +
+
+const double SWEEP_FORMULA_RESULT = 2
+
+ +
+
+const double SWEEP_FORMULA_PSX = 3
+
+ +
+
+

Constants for three Amplifier modes

+

+
+
+const double V_CLAMP_MODE = 0
+
+ +
+
+const double I_CLAMP_MODE = 1
+
+ +
+
+const double I_EQUAL_ZERO_MODE = 2
+
+ +
+
+

Possible values for the function parameter of AI_SendToAmp

+

+
+
+const double MCC_BEGIN_INVALID_FUNC = 10000
+
+ +
+
+const double MCC_SETHOLDING_FUNC = 10001
+
+ +
+
+const double MCC_GETHOLDING_FUNC = 10002
+
+ +
+
+const double MCC_SETHOLDINGENABLE_FUNC = 10003
+
+ +
+
+const double MCC_GETHOLDINGENABLE_FUNC = 10004
+
+ +
+
+const double MCC_SETBRIDGEBALENABLE_FUNC = 10005
+
+ +
+
+const double MCC_GETBRIDGEBALENABLE_FUNC = 10006
+
+ +
+
+const double MCC_SETBRIDGEBALRESIST_FUNC = 10007
+
+ +
+
+const double MCC_GETBRIDGEBALRESIST_FUNC = 10008
+
+ +
+
+const double MCC_AUTOBRIDGEBALANCE_FUNC = 10009
+
+ +
+
+const double MCC_SETNEUTRALIZATIONENABL_FUNC = 10010
+
+ +
+
+const double MCC_GETNEUTRALIZATIONENABL_FUNC = 10011
+
+ +
+
+const double MCC_SETNEUTRALIZATIONCAP_FUNC = 10012
+
+ +
+
+const double MCC_GETNEUTRALIZATIONCAP_FUNC = 10013
+
+ +
+
+const double MCC_SETWHOLECELLCOMPENABLE_FUNC = 10014
+
+ +
+
+const double MCC_GETWHOLECELLCOMPENABLE_FUNC = 10015
+
+ +
+
+const double MCC_SETWHOLECELLCOMPCAP_FUNC = 10016
+
+ +
+
+const double MCC_GETWHOLECELLCOMPCAP_FUNC = 10017
+
+ +
+
+const double MCC_SETWHOLECELLCOMPRESIST_FUNC = 10018
+
+ +
+
+const double MCC_GETWHOLECELLCOMPRESIST_FUNC = 10019
+
+ +
+
+const double MCC_AUTOWHOLECELLCOMP_FUNC = 10020
+
+ +
+
+const double MCC_SETRSCOMPENABLE_FUNC = 10021
+
+ +
+
+const double MCC_GETRSCOMPENABLE_FUNC = 10022
+
+ +
+
+const double MCC_SETRSCOMPBANDWIDTH_FUNC = 10023
+
+ +
+
+const double MCC_GETRSCOMPBANDWIDTH_FUNC = 10024
+
+ +
+
+const double MCC_SETRSCOMPCORRECTION_FUNC = 10025
+
+ +
+
+const double MCC_GETRSCOMPCORRECTION_FUNC = 10026
+
+ +
+
+const double MCC_SETRSCOMPPREDICTION_FUNC = 10027
+
+ +
+
+const double MCC_GETRSCOMPPREDICTION_FUNC = 10028
+
+ +
+
+const double MCC_SETOSCKILLERENABLE_FUNC = 10029
+
+ +
+
+const double MCC_GETOSCKILLERENABLE_FUNC = 10030
+
+ +
+
+const double MCC_AUTOPIPETTEOFFSET_FUNC = 10031
+
+ +
+
+const double MCC_SETPIPETTEOFFSET_FUNC = 10032
+
+ +
+
+const double MCC_GETPIPETTEOFFSET_FUNC = 10033
+
+ +
+
+const double MCC_SETFASTCOMPCAP_FUNC = 10034
+
+ +
+
+const double MCC_GETFASTCOMPCAP_FUNC = 10035
+
+ +
+
+const double MCC_SETSLOWCOMPCAP_FUNC = 10036
+
+ +
+
+const double MCC_GETSLOWCOMPCAP_FUNC = 10037
+
+ +
+
+const double MCC_SETFASTCOMPTAU_FUNC = 10038
+
+ +
+
+const double MCC_GETFASTCOMPTAU_FUNC = 10039
+
+ +
+
+const double MCC_SETSLOWCOMPTAU_FUNC = 10040
+
+ +
+
+const double MCC_GETSLOWCOMPTAU_FUNC = 10041
+
+ +
+
+const double MCC_SETSLOWCOMPTAUX20ENAB_FUNC = 10042
+
+ +
+
+const double MCC_GETSLOWCOMPTAUX20ENAB_FUNC = 10043
+
+ +
+
+const double MCC_AUTOFASTCOMP_FUNC = 10044
+
+ +
+
+const double MCC_AUTOSLOWCOMP_FUNC = 10045
+
+ +
+
+const double MCC_SETSLOWCURRENTINJENABL_FUNC = 10046
+
+ +
+
+const double MCC_GETSLOWCURRENTINJENABL_FUNC = 10047
+
+ +
+
+const double MCC_SETSLOWCURRENTINJLEVEL_FUNC = 10048
+
+ +
+
+const double MCC_GETSLOWCURRENTINJLEVEL_FUNC = 10049
+
+ +
+
+const double MCC_SETSLOWCURRENTINJSETLT_FUNC = 10050
+
+ +
+
+const double MCC_GETSLOWCURRENTINJSETLT_FUNC = 10051
+
+ +
+
+const double MCC_SETPRIMARYSIGNALGAIN_FUNC = 10052
+
+ +
+
+const double MCC_GETPRIMARYSIGNALGAIN_FUNC = 10053
+
+ +
+
+const double MCC_SETSECONDARYSIGNALGAIN_FUNC = 10054
+
+ +
+
+const double MCC_GETSECONDARYSIGNALGAIN_FUNC = 10055
+
+ +
+
+const double MCC_SETPRIMARYSIGNALHPF_FUNC = 10056
+
+ +
+
+const double MCC_GETPRIMARYSIGNALHPF_FUNC = 10057
+
+ +
+
+const double MCC_SETPRIMARYSIGNALLPF_FUNC = 10058
+
+ +
+
+const double MCC_GETPRIMARYSIGNALLPF_FUNC = 10059
+
+ +
+
+const double MCC_SETSECONDARYSIGNALLPF_FUNC = 10060
+
+ +
+
+const double MCC_GETSECONDARYSIGNALLPF_FUNC = 10061
+
+ +
+
+const double MCC_END_INVALID_FUNC = 10062
+
+ +
+
+

Constants for FunctionInfo and WaveType

+

+
+
+const double IGOR_TYPE_COMPLEX = 0x001
+
+ +
+
+const double IGOR_TYPE_32BIT_FLOAT = 0x002
+
+ +
+
+const double IGOR_TYPE_64BIT_FLOAT = 0x004
+
+ +
+
+const double IGOR_TYPE_8BIT_INT = 0x008
+
+ +
+
+const double IGOR_TYPE_16BIT_INT = 0x010
+
+ +
+
+const double IGOR_TYPE_32BIT_INT = 0x020
+
+ +
+
+const double IGOR_TYPE_64BIT_INT = 0x080
+
+ +
+
+const double IGOR_TYPE_UNSIGNED = 0x040
+

Can be combined, using bitwise or, with all integer types.

+
+ +
+
+const double IGOR_TYPE_STRUCT_PARAMETER = 0x200
+
+ +
+
+const double IGOR_TYPE_NULL_WAVE = 0x000
+
+ +
+
+const double IGOR_TYPE_NUMERIC_WAVE = 0x001
+
+ +
+
+const double IGOR_TYPE_TEXT_WAVE = 0x002
+
+ +
+
+const double IGOR_TYPE_DFREF_WAVE = 0x003
+
+ +
+
+const double IGOR_TYPE_WAVEREF_WAVE = 0x004
+
+ +
+
+const double IGOR_TYPE_GLOBAL_WAVE = 0x001
+
+ +
+
+const double IGOR_TYPE_FREE_WAVE = 0x002
+
+ +
+
+const double IGOR_TYPE_FREEDF_WAVE = 0x002
+
+ +
+
+

TabControl values in Browser Settings Panel

+
+
+const double MIES_BSP_OVS = 1
+
+ +
+
+const double MIES_BSP_CS = 2
+
+ +
+
+const double MIES_BSP_AR = 3
+
+ +
+
+const double MIES_BSP_PA = 4
+
+ +
+
+const double MIES_BSP_SF = 5
+
+ +
+
+const double MIES_BSP_DS = 7
+
+ +
+
+

values for UserData in BrowserSettings and derived windows

+
+
+const string MIES_BSP_BROWSER = "BROWSER"
+
+ +
+
+const string MIES_BSP_BROWSER_MODE = "BROWSERMODE"
+
+ +
+
+const string MIES_BSP_DEVICE = "DEVICE"
+
+ +
+
+const string MIES_BSP_PANEL_FOLDER = "PANEL_FOLDER"
+
+ +
+
+const string MIES_BSP_AR_SWEEPFOLDER = "AR_SWEEPFOLDER"
+
+ +
+
+const string MIES_BSP_PA_MAINPANEL = "HOSTWINDOW"
+
+ +
+
+

Constants for the type flag of <tt>LoadData</tt>

+

+
+
+const double LOAD_DATA_TYPE_WAVES = 1
+
+ +
+
+const double LOAD_DATA_TYPE_NUMBERS = 2
+
+ +
+
+const double LOAD_DATA_TYPE_STRING = 4
+
+ +
+
+

Constants for the time alignment mode of TimeAlignmentIfReq

+

+
+
+const double TIME_ALIGNMENT_NONE = -1
+
+ +
+
+const double TIME_ALIGNMENT_LEVEL_RISING = 0
+
+ +
+
+const double TIME_ALIGNMENT_LEVEL_FALLING = 1
+
+ +
+
+const double TIME_ALIGNMENT_MIN = 2
+
+ +
+
+const double TIME_ALIGNMENT_MAX = 3
+
+ +
+
+

Test pulse modes

+

+
+
+const double TEST_PULSE_NOT_RUNNING = 0x000
+
+ +
+
+const double TEST_PULSE_BG_SINGLE_DEVICE = 0x001
+
+ +
+
+const double TEST_PULSE_BG_MULTI_DEVICE = 0x002
+
+ +
+
+const double TEST_PULSE_FG_SINGLE_DEVICE = 0x004
+
+ +
+
+const double TEST_PULSE_DURING_RA_MOD = 0x100
+

Or’ed with the testpulse mode. Special casing for testpulse during DAQ/RA/ITI.

+
+ +
+
+

Data acquisition modes

+

+
+
+const double DAQ_NOT_RUNNING = 0x000
+
+ +
+
+const double DAQ_BG_SINGLE_DEVICE = 0x001
+
+ +
+
+const double DAQ_BG_MULTI_DEVICE = 0x002
+
+ +
+
+const double DAQ_FG_SINGLE_DEVICE = 0x004
+
+ +
+
+

Reserved Stim set name for TP while DAQ

+

+
+
+const string STIMSET_TP_WHILE_DAQ = "TestPulse"
+
+ +
+
+

Constants for GetAxisOrientation

+

+
+
+const double AXIS_ORIENTATION_HORIZ = 0x01
+
+ +
+
+const double AXIS_ORIENTATION_BOTTOM = 0x05
+
+ +
+
+const double AXIS_ORIENTATION_TOP = 0x09
+
+ +
+
+const double AXIS_ORIENTATION_VERT = 0x02
+
+ +
+
+const double AXIS_ORIENTATION_LEFT = 0x12
+
+ +
+
+const double AXIS_ORIENTATION_RIGHT = 0x22
+
+ +
+
+

Constants for Set/GetAxesRanges modes, use binary pattern

+

+
+
+const double AXIS_RANGE_DEFAULT = 0x00
+
+ +
+
+const double AXIS_RANGE_USE_MINMAX = 0x01
+
+ +
+
+const double AXIS_RANGE_INC_AUTOSCALED = 0x02
+
+ +
+
+

Constants for Axis name template

+

+
+
+const string AXIS_SCOPE_AD = "AD"
+
+ +
+
+const string AXIS_SCOPE_AD_REGEXP = "AD[0123456789]+"
+
+ +
+
+const string AXIS_SCOPE_TP_TIME = "top"
+
+ +
+
+

Constants for DAP_ToggleAcquisitionButton

+

+
+
+const double DATA_ACQ_BUTTON_TO_STOP = 0x01
+
+ +
+
+const double DATA_ACQ_BUTTON_TO_DAQ = 0x02
+
+ +
+
+

Constants for DAP_ToggleTestpulseButton

+

+
+
+const double TESTPULSE_BUTTON_TO_STOP = 0x01
+
+ +
+
+const double TESTPULSE_BUTTON_TO_START = 0x02
+
+ +
+
+

Constants for functions using rack number parameters

+

+
+
+const double RACK_ZERO = 0x00
+
+ +
+
+const double RACK_ONE = 0x01
+
+ +
+
+

Return types of @ref GetInternalSetVariableType

+

+
+
+const double SET_VARIABLE_BUILTIN_NUM = 0x01
+
+ +
+
+const double SET_VARIABLE_BUILTIN_STR = 0x02
+
+ +
+
+const double SET_VARIABLE_GLOBAL = 0x04
+
+ +
+
+

Acquisition states

+

+
+Todo:
+

extend these with PRE_SET_EVENT and POST_SET_EVENT once this is reworked, see https://github.com/AllenInstitute/MIES/issues/658 and https://github.com/AllenInstitute/MIES/issues/39.

+
+ +

+

The state values are serialized to the labnotebooks, so they must never change.

+
+
+const double AS_INACTIVE = 0
+
+ +
+
+const double AS_EARLY_CHECK = 1
+
+ +
+
+const double AS_PRE_DAQ = 2
+
+ +
+
+const double AS_PRE_SWEEP = 3
+
+ +
+
+const double AS_MID_SWEEP = 4
+
+ +
+
+const double AS_POST_SWEEP = 5
+
+ +
+
+const double AS_ITI = 6
+
+ +
+
+const double AS_POST_DAQ = 7
+
+ +
+
+const double AS_PRE_SWEEP_CONFIG = 8
+
+ +
+
+const double AS_NUM_STATES = 9
+
+ +
+
+

Event types for analysis functions

+

+
+
+const double PRE_DAQ_EVENT = 0
+
+ +
+
+const double MID_SWEEP_EVENT = 1
+
+ +
+
+const double POST_SWEEP_EVENT = 2
+
+ +
+
+const double POST_SET_EVENT = 3
+
+ +
+
+const double POST_DAQ_EVENT = 4
+
+ +
+
+const double PRE_SWEEP_CONFIG_EVENT = 5
+
+ +
+
+const double PRE_SET_EVENT = 7
+
+ +
+
+

Special return values for analysis functions. See also @ref

+

AnalysisFunctionReturnTypes.

+

+
+
+const double ANALYSIS_FUNC_RET_REPURP_TIME = -100
+
+ +
+
+const double ANALYSIS_FUNC_RET_EARLY_STOP = -101
+
+ +
+
+

Constants for differentiating between different analysis function versions

+

+
+
+const double ANALYSIS_FUNCTION_VERSION_V1 = 0x0001
+
+ +
+
+const double ANALYSIS_FUNCTION_VERSION_V2 = 0x0002
+
+ +
+
+const double ANALYSIS_FUNCTION_VERSION_V3 = 0x0004
+
+ +
+
+const double ANALYSIS_FUNCTION_VERSION_ALL = 0xFFFF
+
+ +
+
+

Unnamed Group

+
+
+const double LEFT_KEY = 28
+

Window hook key constants

+
+ +
+
+const double RIGHT_KEY = 29
+
+ +
+
+const double UP_KEY = 30
+
+ +
+
+const double DOWN_KEY = 31
+
+ +
+
+const double SPACE_KEY = 32
+
+ +
+
+const double C_KEY = 99
+
+ +
+
+const double E_KEY = 101
+
+ +
+
+const double F_KEY = 102
+
+ +
+
+const double R_KEY = 114
+
+ +
+
+const double Z_KEY = 122
+
+ +
+
+

Trigger modes

+

External trigger is used for yoking multiple ITC 1600 devices (not supported anymore)

+
+
+const double HARDWARE_DAC_DEFAULT_TRIGGER = 0x0
+
+ +
+
+const double HARDWARE_DAC_EXTERNAL_TRIGGER = 0x1
+
+ +
+
+

The channel numbers for the different ITC devices used for accesssing

+

the TTLs

+
+
+const double HARDWARE_ITC_TTL_DEF_RACK_ZERO = 1
+
+ +
+
+const double HARDWARE_ITC_TTL_1600_RACK_ZERO = 0
+
+ +
+
+const double HARDWARE_ITC_TTL_1600_RACK_ONE = 3
+
+ +
+
+

Flags for all hardware interaction functions from MIES_DAC-Hardware.ipf

+

+
+
+const double HARDWARE_ABORT_ON_ERROR = 0x01
+
+ +
+
+const double HARDWARE_PREVENT_ERROR_MESSAGE = 0x04
+
+ +
+
+

Indizes into HARDWARE_DAC_TYPES

+

+
+
+const double HARDWARE_ITC_DAC = 0
+
+ +
+
+const double HARDWARE_NI_DAC = 1
+
+ +
+
+const double HARDWARE_SUTTER_DAC = 2
+
+ +
+
+const double HARDWARE_UNSUPPORTED_DAC = 1000
+
+ +
+
+

Name of NI_DAC FIFO

+

FIFO Name

+
+
+const string HARDWARE_NI_ADC_FIFO = "NI_AnalogIn"
+
+ +
+
+

Minimum possible sampling intervals in milliseconds (1e-3s)

+
+
+const double HARDWARE_NI_DAC_MIN_SAMPINT = 0.002
+

NI 6343 and other devices, so it is 4E-3 ms for 2 channels, 6E-3 ms for 3 a.s.o.

+
+ +
+
+const double HARDWARE_ITC_MIN_SAMPINT = 0.005
+

ITC DACs.

+
+ +
+
+const double HARDWARE_NI_6001_MIN_SAMPINT = 0.2
+

NI 6001 USB.

+
+ +
+
+const double HARDWARE_SU_MIN_SAMPINT_DAC = 0.1
+
+ +
+
+const double HARDWARE_SU_MIN_SAMPINT_ADC = 0.02
+

Sutter output -> 10 kHz.

+
+ +
+
+

Constants for the return value of AI_SelectMultiClamp()

+

+
+
+const double AMPLIFIER_CONNECTION_SUCCESS = 0
+

success

+
+ +
+
+const double AMPLIFIER_CONNECTION_INVAL_SER = 1
+

stored amplifier serials are invalid

+
+ +
+
+const double AMPLIFIER_CONNECTION_MCC_FAILED = 2
+

calling MCC_SelectMultiClamp700B failed

+
+ +
+
+

Constants for the options parameter of DAP_ChangeHeadStageMode()

+

+
+
+const double DO_MCC_MIES_SYNCING = 0x0
+

Default mode with all bells and whistles.

+
+ +
+
+const double NO_SLIDER_MOVEMENT = 0x2
+

Does not move the headstage slider.

+
+ +
+
+const double MCC_SKIP_UPDATES = 0x4
+

Skips all unnecessary updates. Intereseting for temporarily switching the clamp mode, e.g. for an auto MCC amplifier function. Using that option requires to switch the clamp mode back to its original value.

+
+ +
+
+

Constants for AnalysisBrowserMap (Text Wave)

+

+
+
+const string ANALYSISBROWSER_FILE_TYPE_IGOR = "Igor"
+
+ +
+
+const string ANALYSISBROWSER_FILE_TYPE_NWBv1 = "NWBv1"
+
+ +
+
+const string ANALYSISBROWSER_FILE_TYPE_NWBV2 = "NWBv2"
+
+ +
+
+

Available pressure modes for P_SetPressureMode()

+

See P_PressureMethodToString() for getting a string representation.

+

+
+
+const double PRESSURE_METHOD_ATM = -1
+
+ +
+
+const double PRESSURE_METHOD_APPROACH = 0
+
+ +
+
+const double PRESSURE_METHOD_SEAL = 1
+
+ +
+
+const double PRESSURE_METHOD_BREAKIN = 2
+
+ +
+
+const double PRESSURE_METHOD_CLEAR = 3
+
+ +
+
+const double PRESSURE_METHOD_MANUAL = 4
+
+ +
+
+

Different pressure types of each headstage

+

+
+
+const double PRESSURE_TYPE_ATM = -1
+
+ +
+
+const double PRESSURE_TYPE_AUTO = 0
+
+ +
+
+const double PRESSURE_TYPE_MANUAL = 1
+
+ +
+
+const double PRESSURE_TYPE_USER = 2
+
+ +
+
+

Constants for different WaveBuilder epochs

+

Numbers are stored in the SegWvType waves, so they are part of our “API”.

+
+
+const double EPOCH_TYPE_SQUARE_PULSE = 0
+
+ +
+
+const double EPOCH_TYPE_RAMP = 1
+
+ +
+
+const double EPOCH_TYPE_NOISE = 2
+
+ +
+
+const double EPOCH_TYPE_SIN_COS = 3
+
+ +
+
+const double EPOCH_TYPE_SAW_TOOTH = 4
+
+ +
+
+const double EPOCH_TYPE_PULSE_TRAIN = 5
+
+ +
+
+const double EPOCH_TYPE_PSC = 6
+
+ +
+
+const double EPOCH_TYPE_CUSTOM = 7
+
+ +
+
+const double EPOCH_TYPE_COMBINE = 8
+
+ +
+
+const double EPOCH_TYPES_TOTAL_NUMBER = 9
+
+ +
+
+

Parameters for gnoise and enoise

+
+
+const double NOISE_GEN_LINEAR_CONGRUENTIAL = 1
+

Don’t use for new code.

+
+ +
+
+const double NOISE_GEN_MERSENNE_TWISTER = 2
+

Don’t use for new code.

+
+ +
+
+const double NOISE_GEN_XOSHIRO = 3
+
+ +
+
+

Different types of noise epochs

+

+
+
+const double NOISE_TYPE_WHITE = 0
+
+ +
+
+const double NOISE_TYPE_PINK = 1
+
+ +
+
+const double NOISE_TYPE_BROWN = 2
+
+ +
+
+

Unnamed Group

+
+
+const string NOTE_KEY_PULSE_HAS_FAILED = "PulseHasFailed"
+

Only present for diagonal pulses

+
+ +
+
+const string NOTE_KEY_PULSE_FOUND_SPIKES = "NumberOfFoundSpikes"
+
+ +
+
+const string NOTE_KEY_PULSE_SPIKE_POSITIONS = "SpikePositions"
+
+ +
+
+

Parameters for GetAllDevicesWithContent()

+

+
+
+const double CONTENT_TYPE_SWEEP = 0x01
+
+ +
+
+const double CONTENT_TYPE_TPSTORAGE = 0x02
+
+ +
+
+const double CONTENT_TYPE_COMMENT = 0x04
+
+ +
+
+const double CONTENT_TYPE_ALL = 0xFF
+
+ +
+
+

Parameter type flags for WB_GetParameterWaveName

+

+
+
+const double STIMSET_PARAM_WP = 0
+
+ +
+
+const double STIMSET_PARAM_WPT = 1
+
+ +
+
+const double STIMSET_PARAM_SEGWVTYPE = 2
+
+ +
+
+

Ranges for different integer wave types

+

+
+
+const double SIGNED_INT_16BIT_MIN = -32768
+
+ +
+
+const double SIGNED_INT_16BIT_MAX = 32767
+
+ +
+
+

Ranges for NIDAQ analog output in volts

+

+
+
+const double NI_DAC_MIN = -10
+
+ +
+
+const double NI_DAC_MAX = 10
+
+ +
+
+const double NI_ADC_MIN = -10
+
+ +
+
+const double NI_ADC_MAX = 10
+
+ +
+
+const double NI_TTL_MIN = 0
+
+ +
+
+const double NI_TTL_MAX = 1
+
+ +
+
+

Ranges for Sutter DAQ analog output in volts

+

+
+
+const double SU_HS_IN_V_MIN = -1
+
+ +
+
+const double SU_HS_IN_V_MAX = 1
+
+ +
+
+const double SU_HS_IN_I_MIN = -20E-9
+
+ +
+
+const double SU_HS_IN_I_MAX = 20E-9
+
+ +
+
+const double SU_DAC_MIN = -10
+
+ +
+
+const double SU_DAC_MAX = 10
+
+ +
+
+const double SU_ADC_MIN = -10
+
+ +
+
+const double SU_ADC_MAX = 10
+
+ +
+
+const double SU_HS_OUT_MIN = -1
+
+ +
+
+const double SU_HS_OUT_MAX = 1
+
+ +
+
+const double SU_TTL_MIN = 0
+
+ +
+
+const double SU_TTL_MAX = 1
+
+ +
+
+

Update flags for DAP_UpdateDAQControls()

+

+
+
+const double REASON_STIMSET_CHANGE = 0x01
+
+ +
+
+const double REASON_HEADSTAGE_CHANGE = 0x02
+
+ +
+
+const double REASON_STIMSET_CHANGE_DUR_DAQ = 0x04
+
+ +
+
+

Mode parameters for OVS_GetSelectedSweeps()

+
+
+const double OVS_SWEEP_SELECTION_INDEX = 0x0
+
+ +
+
+const double OVS_SWEEP_SELECTION_SWEEPNO = 0x1
+
+ +
+
+const double OVS_SWEEP_ALL_SWEEPNO = 0x2
+
+ +
+
+

Export type parameters for NWB_ExportWithDialog()

+
+
+const double NWB_EXPORT_DATA = 0x1
+
+ +
+
+const double NWB_EXPORT_STIMSETS = 0x2
+
+ +
+
+

PatchSeq various constants

+
+
+const double PSQ_BL_EVAL_RANGE = 500
+
+ +
+
+const double PSQ_DS_SPIKE_LEVEL = -20
+
+ +
+
+const string PSQ_CR_BEM = "Symmetric;Depolarized;Hyperpolarized"
+
+ +
+
+

Different bounds evaluation modes

+

+
+
+const double PSQ_CR_BEM_SYMMETRIC = 0x0
+
+ +
+
+const double PSQ_CR_BEM_DEPOLARIZED = 0x1
+
+ +
+
+const double PSQ_CR_BEM_HYPERPOLARIZED = 0x2
+
+ +
+
+

PatchSeq labnotebook constants

+

Use with CreateAnaFuncLBNKey() only.

+

The longest key must be tested in CheckLength().

+

+
+
+const string PSQ_FMT_LBN_RB_DASCALE_EXC = "%s DAScale exceeded"
+
+ +
+
+const string PSQ_FMT_LBN_STEPSIZE = "%s step size"
+
+ +
+
+const string PSQ_FMT_LBN_STEPSIZE_FUTURE = "%s step size (fut.)"
+
+ +
+
+const string PSQ_FMT_LBN_SPIKE_DETECT = "%s spike detected"
+
+ +
+
+const string PSQ_FMT_LBN_SPIKE_POSITIONS = "%s spike positions"
+
+ +
+
+const string PSQ_FMT_LBN_SPIKE_COUNT = "%s spike count"
+
+ +
+
+const string PSQ_FMT_LBN_FINAL_SCALE = "%s final DAScale"
+
+ +
+
+const string PSQ_FMT_LBN_INITIAL_SCALE = "%s initial DAScale"
+
+ +
+
+const string PSQ_FMT_LBN_RMS_SHORT_PASS = "%s Chk%d S-RMS QC"
+
+ +
+
+const string PSQ_FMT_LBN_RMS_SHORT_THRESHOLD = "%s S-RMS Threshold"
+
+ +
+
+const string PSQ_FMT_LBN_RMS_LONG_PASS = "%s Chk%d L-RMS QC"
+
+ +
+
+const string PSQ_FMT_LBN_RMS_LONG_THRESHOLD = "%s L-RMS Threshold"
+
+ +
+
+const string PSQ_FMT_LBN_TARGETV = "%s Chk%d T-V BL"
+
+ +
+
+const string PSQ_FMT_LBN_TARGETV_THRESHOLD = "%s T-V Threshold"
+
+ +
+
+const string PSQ_FMT_LBN_TARGETV_PASS = "%s Chk%d T-V BL QC"
+
+ +
+
+const string PSQ_FMT_LBN_LEAKCUR = "%s Chk%d Leak Current BL"
+
+ +
+
+const string PSQ_FMT_LBN_LEAKCUR_PASS = "%s Chk%d Leak Current BL QC"
+
+ +
+
+const string PSQ_FMT_LBN_CHUNK_PASS = "%s Chk%d BL QC"
+
+ +
+
+const string PSQ_FMT_LBN_BL_QC_PASS = "%s BL QC"
+
+ +
+
+const string PSQ_FMT_LBN_SWEEP_PASS = "%s Sweep QC"
+
+ +
+
+const string PSQ_FMT_LBN_SET_PASS = "%s Set QC"
+
+ +
+
+const string PSQ_FMT_LBN_SAMPLING_PASS = "%s Sampling interval QC"
+
+ +
+
+const string PSQ_FMT_LBN_PULSE_DUR = "%s Pulse duration"
+
+ +
+
+const string PSQ_FMT_LBN_SPIKE_DASCALE_ZERO = "%s spike with zero"
+
+ +
+
+const string PSQ_FMT_LBN_RB_LIMITED_RES = "%s limited resolut."
+
+ +
+
+const string PSQ_FMT_LBN_DA_FI_SLOPE = "%s f-I slope"
+
+ +
+
+const string PSQ_FMT_LBN_DA_AT_FI_OFFSET = "%s f-I offset"
+
+ +
+
+const string PSQ_FMT_LBN_DA_FI_SLOPE_REACHED_PASS = "%s f-I slope QC"
+
+ +
+
+const string PSQ_FMT_LBN_DA_OPMODE = "%s operation mode"
+
+ +
+
+const string PSQ_FMT_LBN_DA_AT_ENOUGH_FI_POINTS_PASS = "%s enough f-I pairs for line fit QC"
+
+ +
+
+const string PSQ_FMT_LBN_DA_AT_FREQ = "%s AP frequency"
+
+ +
+
+const string PSQ_FMT_LBN_DA_AT_FUTURE_DASCALES = "%s DAScale values left"
+
+ +
+
+const string PSQ_FMT_LBN_DA_AT_FUTURE_DASCALES_PASS = "%s DAScale values left QC"
+
+ +
+
+const string PSQ_FMT_LBN_DA_AT_MAX_DASCALE_NORM = "%s Max. norm. DAScale step"
+
+ +
+
+const string PSQ_FMT_LBN_DA_AT_MAX_SLOPE = "%s f-I maximum slope"
+
+ +
+
+const string PSQ_FMT_LBN_DA_AT_MIN_DASCALE_NORM = "%s Min. norm. DAScale step"
+
+ +
+
+const string PSQ_FMT_LBN_DA_AT_RSA_DASCALE = "%s DAScale from rheobase, supra, adaptive"
+
+ +
+
+const string PSQ_FMT_LBN_DA_AT_RSA_FI_OFFSETS = "%s f-I offsets from rheobase, supra, adaptive"
+
+ +
+
+const string PSQ_FMT_LBN_DA_AT_RSA_FI_SLOPES = "%s f-I slopes from rheobase, supra, adaptive"
+
+ +
+
+const string PSQ_FMT_LBN_DA_AT_RSA_FI_SLOPES_PASS = "%s f-I slope QCs from rheobase, supra, adaptive"
+
+ +
+
+const string PSQ_FMT_LBN_DA_AT_RSA_FREQ = "%s AP frequency from rheobase, supra, adaptive"
+
+ +
+
+const string PSQ_FMT_LBN_DA_AT_RSA_SWEEPS = "%s passing sweep numbers from rheobase, supra, adaptive"
+
+ +
+
+const string PSQ_FMT_LBN_DA_AT_RSA_VALID_SLOPE_PASS = "%s f-I initial slope valid from rheobase, supra, adaptive QC"
+
+ +
+
+const string PSQ_FMT_LBN_DA_AT_VALID_SLOPE_PASS = "%s f-I slope valid QC"
+
+ +
+
+const string PSQ_FMT_LBN_CR_RESISTANCE = "%s input resistance"
+
+ +
+
+const string PSQ_FMT_LBN_CR_INSIDE_BOUNDS = "%s inside bounds"
+
+ +
+
+const string PSQ_FMT_LBN_CR_BOUNDS_ACTION = "%s bounds action"
+
+ +
+
+const string PSQ_FMT_LBN_CR_CYCLES = "%s cycle x values"
+
+ +
+
+const string PSQ_FMT_LBN_CR_BOUNDS_STATE = "%s bounds state"
+
+ +
+
+const string PSQ_FMT_LBN_CR_SPIKE_CHECK = "%s spike check"
+
+ +
+
+const string PSQ_FMT_LBN_CR_INIT_UOD = "%s initial user onset delay"
+
+ +
+
+const string PSQ_FMT_LBN_CR_INIT_LPF = "%s initial low pass filter"
+
+ +
+
+const string PSQ_FMT_LBN_CR_STIMSET_QC = "%s stimset QC"
+
+ +
+
+const string PSQ_FMT_LBN_SPIKE_PASS = "%s spike QC"
+
+ +
+
+const string PSQ_FMT_LBN_PB_RESISTANCE = "%s pipette resistance"
+
+ +
+
+const string PSQ_FMT_LBN_PB_RESISTANCE_PASS = "%s pipette resistance QC"
+
+ +
+
+const string PSQ_FMT_LBN_SE_RESISTANCE_A = "%s seal resistance A"
+
+ +
+
+const string PSQ_FMT_LBN_SE_RESISTANCE_B = "%s seal resistance B"
+
+ +
+
+const string PSQ_FMT_LBN_SE_RESISTANCE_MAX = "%s seal resistance max"
+
+ +
+
+const string PSQ_FMT_LBN_SE_RESISTANCE_PASS = "%s seal resistance QC"
+
+ +
+
+const string PSQ_FMT_LBN_SE_TESTPULSE_GROUP = "%s test pulse group"
+
+ +
+
+const string PSQ_FMT_LBN_AVERAGEV = "%s Chk%d Average"
+
+ +
+
+const string PSQ_FMT_LBN_VM_FULL_AVG = "%s Full Average"
+
+ +
+
+const string PSQ_FMT_LBN_VM_FULL_AVG_ADIFF = "%s Full Average absolute difference"
+
+ +
+
+const string PSQ_FMT_LBN_VM_FULL_AVG_ADIFF_PASS = "%s Full Average absolute difference QC"
+
+ +
+
+const string PSQ_FMT_LBN_VM_FULL_AVG_RDIFF = "%s Full Average relative difference"
+
+ +
+
+const string PSQ_FMT_LBN_VM_FULL_AVG_RDIFF_PASS = "%s Full Average relative difference QC"
+
+ +
+
+const string PSQ_FMT_LBN_VM_FULL_AVG_PASS = "%s Full Average QC"
+
+ +
+
+const string PSQ_FMT_LBN_AR_ACCESS_RESISTANCE = "%s access resistance"
+
+ +
+
+const string PSQ_FMT_LBN_AR_ACCESS_RESISTANCE_PASS = "%s access resistance QC"
+
+ +
+
+const string PSQ_FMT_LBN_AR_STEADY_STATE_RESISTANCE = "%s steady state resistance"
+
+ +
+
+const string PSQ_FMT_LBN_AR_RESISTANCE_RATIO = "%s access vs steady state ratio"
+
+ +
+
+const string PSQ_FMT_LBN_AR_RESISTANCE_RATIO_PASS = "%s access vs steady state ratio QC"
+
+ +
+
+const string PSQ_FMT_LBN_ASYNC_PASS = "%s async QC"
+
+ +
+
+

PatchSeq and MultiPatchSeq types of analysis functions

+

Constant values must not overlap between PSQ_XXX and MSQ_YYY.

+
+
+const double INVALID_ANALYSIS_FUNCTION = 0xFFFF
+
+ +
+
+const double TEST_ANALYSIS_FUNCTION = 0x10000
+
+ +
+
+const double ADJUST_DA_SCALE = 0x1000
+

Legacy analysis functions

+
+ +
+
+const double REACH_TARGET_VOLTAGE = 0x2000
+
+ +
+
+

Unnamed Group

+
+
+const string LBN_DELTA_I = "Delta I"
+

Legacy analysis functions labnotebook entries

+

These are without analysis function prefixes.

+
+ +
+
+const string LBN_DELTA_V = "Delta V"
+
+ +
+
+const string LBN_RESISTANCE_FIT = "ResistanceFromFit"
+
+ +
+
+const string LBN_RESISTANCE_FIT_ERR = "ResistanceFromFit_Err"
+
+ +
+
+const string LBN_AUTOBIAS_TARGET_DIAG = "Autobias target voltage from dialog"
+
+ +
+
+

Unnamed Group

+
+
+const double PSQ_DA_SCALE = 0x001
+

+
+ +
+
+const double PSQ_SQUARE_PULSE = 0x002
+
+ +
+
+const double PSQ_RHEOBASE = 0x004
+
+ +
+
+const double PSQ_RAMP = 0x008
+
+ +
+
+const double PSQ_CHIRP = 0x080
+
+ +
+
+const double PSQ_PIPETTE_BATH = 0x100
+
+ +
+
+const double PSQ_SEAL_EVALUATION = 0x200
+
+ +
+
+const double PSQ_TRUE_REST_VM = 0x400
+
+ +
+
+const double PSQ_ACC_RES_SMOKE = 0x800
+
+ +
+
+

Unnamed Group

+
+
+const double MSQ_FAST_RHEO_EST = 0x010
+

+
+ +
+
+const double MSQ_DA_SCALE = 0x020
+
+ +
+
+const double SC_SPIKE_CONTROL = 0x040
+
+ +
+
+

PatchSeq SquarePulse

+
+
+const double PSQ_SP_INIT_AMP_m50 = -50e-12
+
+ +
+
+const double PSQ_SP_INIT_AMP_p100 = +100e-12
+
+ +
+
+const double PSQ_SP_INIT_AMP_p10 = +10e-12
+
+ +
+
+const double PSQ_SP_MAX_DASCALE_ZERO = 3
+
+ +
+
+const double PSQ_SP_NUM_SWEEPS_PASS = 1
+
+ +
+
+

PatchSeq Rheobase

+
+
+const double PSQ_RB_MAX_DASCALE_DIFF = 60e-12
+
+ +
+
+const double PSQ_RB_DASCALE_SMALL_BORDER = 50e-12
+
+ +
+
+const double PSQ_RB_DASCALE_STEP_LARGE = 10e-12
+
+ +
+
+const double PSQ_RB_DASCALE_STEP_SMALL = 2e-12
+
+ +
+
+const string PSQ_RB_FINALSCALE_FAKE_KEY = "PSQRheobaseFinalDAScaleFake"
+
+ +
+
+

PatchSeq DAScale

+
+
+const double PSQ_DS_OFFSETSCALE_FAKE = 23
+
+ +
+
+const string PSQ_DS_SUB = "Sub"
+
+ +
+
+const string PSQ_DS_SUPRA = "Supra"
+
+ +
+
+const string PSQ_DS_ADAPT = "AdaptiveSupra"
+
+ +
+
+const double PSQ_DS_MAX_FREQ_OFFSET = 2
+
+ +
+
+const double PSQ_DS_SKIPPED_FI_SLOPE = -Inf
+
+ +
+
+const double PSQ_DA_ABS_FREQUENCY_MIN_DISTANCE = 15
+
+ +
+
+const double PSQ_DA_SLOPE_PERCENTAGE_DEFAULT = 10
+
+ +
+
+const double PSQ_DA_NUM_POINTS_LINE_FIT = 2
+
+ +
+
+const double PSQ_DA_NUM_SWEEPS_SATURATION = 2
+
+ +
+
+const double PSQ_DA_NUM_INVALID_SLOPE_SWEEPS_ALLOWED = 3
+
+ +
+
+const double PSQ_DA_MAX_FREQUENCY_CHANGE_PERCENT = 20
+
+ +
+
+const double PSQ_DA_DASCALE_STEP_WITH_MIN_MAX_FACTOR = 3
+
+ +
+
+

PatchSeq Ramp

+
+
+const double PSQ_RA_DASCALE_DEFAULT = 1
+
+ +
+
+const double PSQ_RA_NUM_SWEEPS_PASS = 3
+
+ +
+
+

PatchSeq Chirp

+
+
+const double PSQ_CR_NUM_SWEEPS_PASS = 3
+
+ +
+
+const double PSQ_CR_RESISTANCE_FAKE = 1
+
+ +
+
+const double PSQ_CR_BASELINE_V_FAKE = 1
+
+ +
+
+const double PSQ_CR_LIMIT_BAND_LOW = 1
+
+ +
+
+const double PSQ_CR_LIMIT_BAND_HIGH = 100
+
+ +
+
+const double PSQ_CR_USE_TRUE_RMP_DEF = 1
+
+ +
+
+const double PSQ_CR_DEFAULT_LPF = 10e3
+
+ +
+
+

PatchSeq Pipette

+
+
+const double PSQ_PB_NUM_SWEEPS_PASS = 1
+
+ +
+
+

PatchSeq SealCheck

+
+
+const double PSQ_SE_NUM_SWEEPS_PASS = 1
+
+ +
+
+const double PSQ_SE_REQUIRED_EPOCHS = 22
+
+ +
+
+

Testpulse Group Selector values, see also PSQ_SE_ParseTestpulseGroupSelection()

+
+
+const double PSQ_SE_TGS_FIRST = 0x1
+
+ +
+
+const double PSQ_SE_TGS_SECOND = 0x2
+
+ +
+
+const double PSQ_SE_TGS_BOTH = 0x3
+
+ +
+
+

PatchSeq True Resting Membrane Potential

+
+
+const double PSQ_VM_NUM_SWEEPS_PASS = 1
+
+ +
+
+const double PSQ_VM_REQUIRED_EPOCHS = 3
+
+ +
+
+

Bounds action values, see also PSQ_CR_BoundsActionToString()

+

+
+
+const double PSQ_CR_PASS = 0x1
+
+ +
+
+const double PSQ_CR_DECREASE = 0x2
+
+ +
+
+const double PSQ_CR_INCREASE = 0x4
+
+ +
+
+const double PSQ_CR_RERUN = 0x8
+
+ +
+
+

PatchSeq AccessResistance

+
+
+const double PSQ_AR_NUM_SWEEPS_PASS = 1
+
+ +
+
+

MultiPatchSeq various constants

+
+
+const double MSQ_FRE_INIT_AMP_m50 = -50e-12
+
+ +
+
+const double MSQ_FRE_INIT_AMP_p100 = +100e-12
+
+ +
+
+const double MSQ_FRE_INIT_AMP_p10 = +10e-12
+
+ +
+
+const double MSQ_DS_PULSE_DUR = 1000
+
+ +
+
+const double MSQ_DS_OFFSETSCALE_FAKE = 23
+
+ +
+
+const double MSQ_DS_SWEEP_FAKE = 42
+
+ +
+
+const double MSQ_SPIKE_LEVEL = -10.0
+
+ +
+
+const double MSQ_RMS_SHORT_THRESHOLD = 0.07
+
+ +
+
+const double MSQ_RMS_LONG_THRESHOLD = 0.5
+
+ +
+
+const double MSQ_TARGETV_THRESHOLD = 1
+
+ +
+
+

Spike Counts state constants

+

+
+
+const double SC_SPIKE_COUNT_NUM_GOOD = 0x0
+
+ +
+
+const double SC_SPIKE_COUNT_NUM_TOO_FEW = 0x1
+
+ +
+
+const double SC_SPIKE_COUNT_NUM_TOO_MANY = 0x2
+
+ +
+
+const double SC_SPIKE_COUNT_NUM_MIXED = 0x4
+
+ +
+
+const string SC_SPIKE_COUNT_STATE_STR_GOOD = "Good"
+
+ +
+
+const string SC_SPIKE_COUNT_STATE_STR_TOO_FEW = "Too few"
+
+ +
+
+const string SC_SPIKE_COUNT_STATE_STR_TOO_MANY = "Too many"
+
+ +
+
+const string SC_SPIKE_COUNT_STATE_STR_MIXED = "Mixed"
+
+ +
+
+

Unnamed Group

+
+
+const string MSQ_FMT_LBN_DASCALE_EXC = "%s DAScale exceeded"
+

+
+ +
+
+const string MSQ_FMT_LBN_STEPSIZE = "%s step size"
+
+ +
+
+const string MSQ_FMT_LBN_SPIKE_DETECT = "%s spike detected"
+
+ +
+
+const string MSQ_FMT_LBN_SPIKE_POSITIONS = "%s Spike positions"
+
+ +
+
+const string MSQ_FMT_LBN_SPIKE_COUNTS = "%s Spike counts"
+
+ +
+
+const string MSQ_FMT_LBN_FINAL_SCALE = "%s final DAScale"
+
+ +
+
+const string MSQ_FMT_LBN_INITIAL_SCALE = "%s initial DAScale"
+
+ +
+
+const string MSQ_FMT_LBN_RMS_SHORT_PASS = "%s Chk%d S-RMS QC"
+
+ +
+
+const string MSQ_FMT_LBN_RMS_LONG_PASS = "%s Chk%d L-RMS QC"
+
+ +
+
+const string MSQ_FMT_LBN_TARGETV_PASS = "%s Chk%d T-V BL QC"
+
+ +
+
+const string MSQ_FMT_LBN_CHUNK_PASS = "%s Chk%d BL QC"
+
+ +
+
+const string MSQ_FMT_LBN_SPONT_SPIKE_PASS = "%s Spontaneous Spiking QC"
+
+ +
+
+const string MSQ_FMT_LBN_HEADSTAGE_PASS = "%s Headstage QC"
+
+ +
+
+const string MSQ_FMT_LBN_SWEEP_PASS = "%s Sweep QC"
+
+ +
+
+const string MSQ_FMT_LBN_SET_PASS = "%s Set QC"
+
+ +
+
+const string MSQ_FMT_LBN_PULSE_DUR = "%s Pulse duration"
+
+ +
+
+const string MSQ_FMT_LBN_ACTIVE_HS = "%s Active Headstage"
+
+ +
+
+const string MSQ_FMT_LBN_FAILED_PULSE_LEVEL = "%s Failed Pulse Level"
+
+ +
+
+const string MSQ_FMT_LBN_SPIKE_POSITION_PASS = "%s Spike positions QC"
+
+ +
+
+const string MSQ_FMT_LBN_SPIKE_COUNTS_STATE = "%s Spike counts state"
+
+ +
+
+const string MSQ_FMT_LBN_IDEAL_SPIKE_COUNTS = "%s Ideal spike counts"
+
+ +
+
+const string MSQ_FMT_LBN_RERUN_TRIAL = "%s Rerun Trials"
+
+ +
+
+const string MSQ_FMT_LBN_RERUN_TRIAL_EXC = "%s Rerun Trials exceeded"
+
+ +
+
+

Workaround flags for CreateAnaFuncLBNKey()

+

+
+
+const double PSQ_LBN_WA_NONE = 0x0
+
+ +
+
+const double PSQ_LBN_WA_SP_SE = 0x1
+
+ +
+
+

Constants for the wave cache

+
+
+const double CA_OPTS_NO_DUPLICATE = 0x1
+

Don’t return a duplicate of the cached wave, but return the wave itself. Useful if you use the wave cache as an alternative storage.

+
+ +
+
+

Constants for the different delta operation modes in the Wavebuilder

+

+
+
+const double DELTA_OPERATION_DEFAULT = 0
+
+ +
+
+const double DELTA_OPERATION_FACTOR = 1
+
+ +
+
+const double DELTA_OPERATION_LOG = 2
+
+ +
+
+const double DELTA_OPERATION_SQUARED = 3
+
+ +
+
+const double DELTA_OPERATION_POWER = 4
+
+ +
+
+const double DELTA_OPERATION_ALTERNATE = 5
+
+ +
+
+const double DELTA_OPERATION_EXPLICIT = 6
+
+ +
+
+

Stimset wave note entry types for WB_GetWaveNoteEntry()

+

+
+
+const double VERSION_ENTRY = 0x1
+
+ +
+
+const double SWEEP_ENTRY = 0x2
+
+ +
+
+const double EPOCH_ENTRY = 0x4
+
+ +
+
+const double STIMSET_ENTRY = 0x8
+
+ +
+
+

Mode flag for AFH_GetListOfAnalysisParams()

+

+
+
+const double REQUIRED_PARAMS = 0x1
+
+ +
+
+const double OPTIONAL_PARAMS = 0x2
+
+ +
+
+

GUI settings oscilloscopy Y scale update modes

+

+
+
+const double GUI_SETTING_OSCI_SCALE_AUTO = 0
+
+ +
+
+const double GUI_SETTING_OSCI_SCALE_FIXED = 1
+
+ +
+
+const double GUI_SETTING_OSCI_SCALE_INTERVAL = 2
+
+ +
+
+

Match expression types for GetListOfObjects

+

+
+
+const double MATCH_REGEXP = 0x1
+
+ +
+
+const double MATCH_WILDCARD = 0x2
+
+ +
+
+

Options for SplitTTLWaveIntoComponents() and SplitSweepIntoComponents()

+

+
+
+const double TTL_RESCALE_OFF = 0x0
+
+ +
+
+const double TTL_RESCALE_ON = 0x1
+
+ +
+
+

Epoch key constants

+

+
+
+const string EPOCH_OODDAQ_REGION_KEY = "oodDAQRegion"
+
+ +
+
+const string EPOCH_BASELINE_REGION_KEY = "Baseline"
+
+ +
+
+

Time parameter for SWS_GetChannelGains()

+

+
+
+const double GAIN_BEFORE_DAQ = 0x1
+
+ +
+
+const double GAIN_AFTER_DAQ = 0x2
+
+ +
+
+

Find level edge types

+

+
+
+const double FINDLEVEL_EDGE_INCREASING = 1
+
+ +
+
+const double FINDLEVEL_EDGE_DECREASING = 2
+
+ +
+
+const double FINDLEVEL_EDGE_BOTH = 0
+
+ +
+
+

Find level modes

+

+
+
+const double FINDLEVEL_MODE_SINGLE = 1
+
+ +
+
+const double FINDLEVEL_MODE_MULTI = 2
+
+ +
+
+

Return codes of the Igor exists function

+

+
+
+const double EXISTS_NAME_NOT_USED = 0
+
+ +
+
+const double EXISTS_AS_WAVE = 1
+
+ +
+
+const double EXISTS_AS_VAR_OR_STR = 2
+
+ +
+
+const double EXISTS_AS_FUNCTION = 3
+
+ +
+
+const double EXISTS_AS_OPERATION = 4
+
+ +
+
+const double EXISTS_AS_MACRO = 5
+
+ +
+
+const double EXISTS_AS_USERFUNCTION = 6
+
+ +
+
+

Return codes of the Igor WinType function

+

+
+
+const double WINTYPE_NOWINDOW = 0
+
+ +
+
+const double WINTYPE_GRAPH = 1
+
+ +
+
+const double WINTYPE_TABLE = 2
+
+ +
+
+const double WINTYPE_LAYOUT = 3
+
+ +
+
+const double WINTYPE_NOTEBOOK = 5
+
+ +
+
+const double WINTYPE_PANEL = 7
+
+ +
+
+const double WINTYPE_XOP = 13
+
+ +
+
+const double WINTYPE_CAMERA = 15
+
+ +
+
+const double WINTYPE_GIZMO = 17
+
+ +
+
+

Panel tag codes to identify panel types, set in creation macro as main window userdata($EXPCONFIG_UDATA_PANELTYPE)

+

+
+
+const string EXPCONFIG_UDATA_PANELTYPE = "Config_PanelType"
+
+ +
+
+const string PANELTAG_DAEPHYS = "DA_Ephys"
+
+ +
+
+const string PANELTAG_DATABROWSER = "DataBrowser"
+
+ +
+
+const string PANELTAG_WAVEBUILDER = "WaveBuilder"
+
+ +
+
+const string PANELTAG_ANALYSISBROWSER = "AnalysisBrowser"
+
+ +
+
+const string PANELTAG_IVSCCP = "IVSCControlPanel"
+
+ +
+
+

Bit mask constants for properties for window control saving/restore

+

+
+
+const double EXPCONFIG_SAVE_VALUE = 1
+
+ +
+
+const double EXPCONFIG_SAVE_POSITION = 2
+
+ +
+
+const double EXPCONFIG_SAVE_USERDATA = 4
+
+ +
+
+const double EXPCONFIG_SAVE_DISABLED = 8
+
+ +
+
+const double EXPCONFIG_SAVE_CTRLTYPE = 16
+
+ +
+
+const double EXPCONFIG_SAVE_POPUPMENU_AS_STRING_ONLY = 32
+
+ +
+
+const double EXPCONFIG_SAVE_POPUPMENU_AS_INDEX_ONLY = 64
+
+ +
+
+const double EXPCONFIG_MINIMIZE_ON_RESTORE = 128
+
+ +
+
+const double EXPCONFIG_SAVE_BUTTONS_ONLY_PRESSED = 256
+
+ +
+
+const double EXPCONFIG_SAVE_ONLY_RELEVANT = 512
+
+ +
+
+

Correlated control name/type/valuetype list for use with e.g. ControlInfo

+

+
+
+const string EXPCONFIG_GUI_CTRLLIST = "Button;Chart;CheckBox;CustomControl;GroupBox;ListBox;PopupMenu;SetVariable;Slider;TabControl;TitleBox;ValDisplay;"
+
+ +
+
+const string EXPCONFIG_GUI_CTRLTYPES = "1;6;2;12;9;11;3;5;7;8;10;4;"
+
+ +
+
+const string EXPCONFIG_GUI_VVALUE = "1;1;1;1;0;1;1;1;1;1;0;1;"
+
+ +
+
+const string EXPCONFIG_GUI_SVALUE = "0;1;0;0;1;1;1;1;1;1;0;1;"
+
+ +
+
+const string EXPCONFIG_GUI_SDATAFOLDER = "0;0;0;0;0;1;0;1;1;0;1;0;"
+
+ +
+
+const string EXPCONFIG_GUI_PREFERRED = "0;2;0;0;0;3;2;0;1;1;0;1;"
+

0 does not apply, 1 V_Value, 2 S_Value, 3 S_DataFolder for EXPCONFIG_SAVE_ONLY_RELEVANT

+
+ +
+
+const string EXPCONFIG_GUI_SUSERDATA = "1;0;1;1;0;1;1;1;1;1;0;0;"
+
+ +
+
+

PopupMenu extension keys for userdata definition of procedures

+

+
+
+const string PEXT_UDATA_ITEMGETTER = "Items"
+
+ +
+
+const string PEXT_UDATA_POPUPPROC = "popupProc"
+
+ +
+
+

PopupMenu extension sub menu splitting methods

+

+
+
+const double PEXT_SUBSPLIT_DEFAULT = 0
+
+ +
+
+const double PEXT_SUBSPLIT_ALPHA = 1
+
+ +
+
+

PopupMenu extension sub menu name generation methods

+

+
+
+const double PEXT_SUBNAMEGEN_DEFAULT = 0
+
+ +
+
+

Incremental update modes for PostPlotTransformations()

+

+
+
+const double POST_PLOT_ADDED_SWEEPS = 0x1
+

The only change: Some sweeps were added.

+
+ +
+
+const double POST_PLOT_REMOVED_SWEEPS = 0x2
+

The only change: Some sweeps were removed.

+
+ +
+
+const double POST_PLOT_CONSTANT_SWEEPS = 0x4
+

The displayed data in the databrowser stayed constant but some settings changed.

+
+ +
+
+const double POST_PLOT_FULL_UPDATE = 0x8
+

Forces a complete update from scratch, use that if nothing else fits.

+
+ +
+
+

Work Load Class names used in ASYNC frame work

+

+
+
+const string WORKLOADCLASS_TP = "TestPulse"
+
+ +
+
+const string WORKLOADCLASS_NWB = "nwb_writing"
+
+ +
+
+

Column numbers of epoch information

+

+
+
+const double EPOCH_COL_STARTTIME = 0
+
+ +
+
+const double EPOCH_COL_ENDTIME = 1
+
+ +
+
+const double EPOCH_COL_TAGS = 2
+
+ +
+
+const double EPOCH_COL_TREELEVEL = 3
+
+ +
+
+

Modes for what PA_GetSetWaves returns

+

+
+
+const double PA_GETSETWAVES_ALL = 0x01
+
+ +
+
+const double PA_GETSETWAVES_OLD = 0x02
+
+ +
+
+const double PA_GETSETWAVES_NEW = 0x04
+
+ +
+
+

Indices into PA properties wave

+

+
+
+const double PA_PROPERTIES_INDEX_SWEEP = 0
+
+ +
+
+const double PA_PROPERTIES_INDEX_CHANNELNUMBER = 1
+
+ +
+
+const double PA_PROPERTIES_INDEX_REGION = 2
+
+ +
+
+const double PA_PROPERTIES_INDEX_HEADSTAGE = 3
+
+ +
+
+const double PA_PROPERTIES_INDEX_PULSE = 4
+
+ +
+
+const double PA_PROPERTIES_INDEX_PULSEHASFAILED = 5
+
+ +
+
+const double PA_PROPERTIES_INDEX_LASTSWEEP = 6
+
+ +
+
+const double PA_PROPERTIES_INDEX_CLAMPMODE = 7
+
+ +
+
+

Indices into PA propertiesWaves wave

+

+
+
+const double PA_PROPERTIESWAVES_INDEX_PULSE = 0
+
+ +
+
+const double PA_PROPERTIESWAVES_INDEX_PULSENOTE = 1
+
+ +
+
+

Header labels for draw groups within the json of a BufferedDrawInfo structure

+

Currently this method is only used in

+

See also

+

CreateTiledChannelGraph

+
+

+
+
+const string BUFFEREDDRAWAPPEND = "AppendToGraph"
+
+ +
+
+const string BUFFEREDDRAWLABEL = "Label"
+
+ +
+
+const string BUFFEREDDRAWHIDDENTRACES = "HiddenTraces"
+
+ +
+
+const string BUFFEREDDRAWDDAQAXES = "dDAQAxes"
+
+ +
+
+

National Instruments input configuration

+

+
+
+const double HW_NI_CONFIG_RSE = 1
+
+ +
+
+const double HW_NI_CONFIG_NRSE = 2
+
+ +
+
+const double HW_NI_CONFIG_DIFFERENTIAL = 4
+
+ +
+
+const double HW_NI_CONFIG_PSEUDO_DIFFERENTIAL = 8
+
+ +
+
+

Flags for stopping DAQ

+

+
+
+const double DQ_STOP_REASON_DAQ_BUTTON = 0x0001
+
+ +
+
+const double DQ_STOP_REASON_CONFIG_FAILED = 0x0002
+
+ +
+
+const double DQ_STOP_REASON_FINISHED = 0x0004
+
+ +
+
+const double DQ_STOP_REASON_UNCOMPILED = 0x0008
+
+ +
+
+const double DQ_STOP_REASON_HW_ERROR = 0x0010
+
+ +
+
+const double DQ_STOP_REASON_ESCAPE_KEY = 0x0020
+
+ +
+
+const double DQ_STOP_REASON_TP_STARTED = 0x0040
+
+ +
+
+const double DQ_STOP_REASON_STIMSET_SELECTION = 0x0080
+
+ +
+
+const double DQ_STOP_REASON_UNLOCKED_DEVICE = 0x0100
+
+ +
+
+const double DQ_STOP_REASON_OUT_OF_MEMORY = 0x0200
+
+ +
+
+const double DQ_STOP_REASON_FIFO_TIMEOUT = 0x0400
+
+ +
+
+const double DQ_STOP_REASON_STUCK_FIFO = 0x0800
+
+ +
+
+const double DQ_STOP_REASON_INVALID = 0xFFFF
+
+ +
+
+

Mode flags for ID_AskUserForSettings()

+

+
+
+const double ID_HEADSTAGE_SETTINGS = 0x1
+
+ +
+
+const double ID_POPUPMENU_SETTINGS = 0x2
+
+ +
+
+

Popup menu list types

+

+
+
+const double POPUPMENULIST_TYPE_BUILTIN = 0x1
+
+ +
+
+const double POPUPMENULIST_TYPE_OTHER = 0x2
+
+ +
+
+

Possible log book types

+

+
+
+const double LBT_LABNOTEBOOK = 0x1
+
+ +
+
+const double LBT_TPSTORAGE = 0x2
+
+ +
+
+const double LBT_RESULTS = 0x4
+
+ +
+
+

Possible labnotebook wave types

+

+
+
+const double LBN_NUMERICAL_KEYS = 0x1
+
+ +
+
+const double LBN_NUMERICAL_VALUES = 0x2
+
+ +
+
+const double LBN_TEXTUAL_KEYS = 0x4
+
+ +
+
+const double LBN_TEXTUAL_VALUES = 0x8
+
+ +
+
+

Labnotebook wave names

+

+
+
+const string LBN_NUMERICAL_VALUES_NAME = "numericalValues"
+
+ +
+
+const string LBN_NUMERICAL_KEYS_NAME = "numericalKeys"
+
+ +
+
+const string LBN_TEXTUAL_VALUES_NAME = "textualValues"
+
+ +
+
+const string LBN_TEXTUAL_KEYS_NAME = "textualKeys"
+
+ +
+
+const string LBN_NUMERICALRESULT_VALUES_NAME = "numericalResultsValues"
+
+ +
+
+const string LBN_NUMERICALRESULT_KEYS_NAME = "numericalResultsKeys"
+
+ +
+
+const string LBN_TEXTUALRESULT_VALUES_NAME = "textualResultsValues"
+
+ +
+
+const string LBN_TEXTUALRESULT_KEYS_NAME = "textualResultsKeys"
+
+ +
+
+

All available ZeroMQ message filters

+

+
+
+const string IVS_PUB_FILTER = "ivscc"
+
+ +
+
+const string PRESSURE_STATE_FILTER = "pressure:state"
+
+ +
+
+const string PRESSURE_SEALED_FILTER = "pressure:sealed"
+
+ +
+
+const string PRESSURE_BREAKIN_FILTER = "pressure:break in"
+
+ +
+
+const string AUTO_TP_FILTER = "testpulse:autotune result"
+
+ +
+
+const string AMPLIFIER_CLAMP_MODE_FILTER = "amplifier:clamp mode"
+
+ +
+
+const string AMPLIFIER_AUTO_BRIDGE_BALANCE = "amplifier:auto bridge balance"
+
+ +
+
+const string ANALYSIS_FUNCTION_PB = "analysis function:pipette in bath"
+
+ +
+
+const string ANALYSIS_FUNCTION_SE = "analysis function:seal evaluation"
+
+ +
+
+const string ANALYSIS_FUNCTION_VM = "analysis function:true resting membrane potential"
+
+ +
+
+const string DAQ_TP_STATE_CHANGE_FILTER = "data acquisition:state change"
+
+ +
+
+const string ANALYSIS_FUNCTION_AR = "analysis function:access resistance smoke"
+
+ +
+
+

Possible cell state values

+

+
+
+const double TPSTORAGE_SEALED = 0x1
+
+ +
+
+

SweepFormula display modes

+

+
+
+const double SF_DM_NORMAL = 1
+
+ +
+
+const double SF_DM_SUBWINDOWS = 2
+
+ +
+
+

Parameters for GetTTLLabnotebookEntry()

+

+
+
+const string LABNOTEBOOK_TTL_STIMSETS = "stim sets"
+
+ +
+
+const string LABNOTEBOOK_TTL_SETSWEEPCOUNTS = "set sweep counts"
+
+ +
+
+const string LABNOTEBOOK_TTL_SETCYCLECOUNTS = "set cycle counts"
+
+ +
+
+

Unnamed Group

+
+
+const double PGC_MODE_ASSERT_ON_DISABLED = 0
+

Mode flags for PGC_SetAndActivateControl .

+
+ +
+
+const double PGC_MODE_FORCE_ON_DISABLED = 1
+
+ +
+
+const double PGC_MODE_SKIP_ON_DISABLED = 2
+
+ +
+
+

Unnamed Group

+
+
+const double TP_BASELINE_FIT_RESULT_OK = 0
+

Possible result values for TP_AutoFitBaseline

+
+ +
+
+const double TP_BASELINE_FIT_RESULT_ERROR = 1
+
+ +
+
+const double TP_BASELINE_FIT_RESULT_TOO_NOISY = 32
+
+ +
+
+

Unnamed Group

+
+
+const double TP_GETVALUES_DEFAULT = 0x0
+

Possible option values for TP_GetValuesFromTPStorage

+
+ +
+
+const double TP_GETVALUES_LATEST_AUTOTPCYCLE = 0x1
+
+ +
+
+

Unnamed Group

+
+
+const string TSDS_BUGCOUNT = "BugCount"
+

Possible names for TSDS_Read*/TSDS_Write

+
+ +
+
+

Unnamed Group

+
+
+const double HCM_EMPTY = 0x00
+

Headstage contingency modes

+

+
+ +
+
+const double HCM_DEPEND = 0x01
+
+ +
+
+const double HCM_INDEP = 0x02
+
+ +
+
+

Decimation methods

+

+
+
+const double DECIMATION_NONE = 0x0
+
+ +
+
+const double DECIMATION_MINMAX = 0x1
+
+ +
+
+

Possible return values for PSQ_DetermineSweepQCResults()

+

+
+
+const double PSQ_RESULTS_DONE = 0x1
+
+ +
+
+const double PSQ_RESULTS_CONT = 0x2
+
+ +
+
+

Possible mode parameters for AdaptDependentControls

+

+
+
+const double DEP_CTRLS_SAME = 0x1
+
+ +
+
+const double DEP_CTRLS_INVERT = 0x2
+
+ +
+
+

Returned bits of DataFolderRefStatus

+

+
+
+const double DFREF_VALID = 0x1
+
+ +
+
+const double DFREF_FREE = 0x2
+
+ +
+
+

Called once names

+

+
+
+const string CO_EMPTY_DAC_LIST = "emptyDACList"
+
+ +
+
+const string CO_SF_TOO_MANY_TRACES = "SF_tooManyTraces"
+
+ +
+
+const string CO_PSX_CLIPPED_STATS = "psx_clippedStats"
+
+ +
+
+const string CO_ARCHIVE_ONCE = "ArchiveLogs"
+
+ +
+
+

Constants for SweepFormula Meta data in JSON format

+

+
+
+const string SF_META_DATATYPE = "/DataType"
+
+ +
+
+const string SF_META_SWEEPNO = "/SweepNumber"
+
+ +
+
+const string SF_META_RANGE = "/Range"
+
+ +
+
+const string SF_META_CHANNELTYPE = "/ChannelType"
+
+ +
+
+const string SF_META_CHANNELNUMBER = "/ChannelNumber"
+
+ +
+
+const string SF_META_ISAVERAGED = "/IsAveraged"
+
+ +
+
+const string SF_META_AVERAGED_FIRST_SWEEP = "/AveragedFirstSweep"
+
+ +
+
+const string SF_META_XVALUES = "/XValues"
+
+ +
+
+const string SF_META_XTICKLABELS = "/XTickLabels"
+
+ +
+
+const string SF_META_XTICKPOSITIONS = "/XTickPositions"
+
+ +
+
+const string SF_META_XAXISLABEL = "/XAxisLabel"
+
+ +
+
+const string SF_META_YAXISLABEL = "/YAxisLabel"
+
+ +
+
+const string SF_META_LEGEND_LINE_PREFIX = "/LegendLinePrefix"
+
+ +
+
+const string SF_META_OPSTACK = "/OperationStack"
+
+ +
+
+const string SF_META_MOD_MARKER = "/Marker"
+
+ +
+
+const string SF_META_SHOW_LEGEND = "/ShowLegend"
+
+ +
+
+const string SF_META_CUSTOM_LEGEND = "/CustomLegend"
+
+ +
+
+const string SF_META_ARGSETUPSTACK = "/ArgSetupStack"
+
+ +
+
+const string SF_META_TRACECOLOR = "/TraceColor"
+
+ +
+
+const string SF_META_LINESTYLE = "/LineStyle"
+
+ +
+
+const string SF_META_TRACE_MODE = "/TraceMode"
+
+ +
+
+const string SF_META_TRACETOFRONT = "/TraceToFront"
+
+ +
+
+const string SF_META_USER_GROUP = "/User/"
+
+ +
+
+const string SF_META_FIT_COEFF = "FitCoefficients"
+
+ +
+
+const string SF_META_FIT_SIGMA = "FitSigma"
+
+ +
+
+const string SF_META_FIT_PARAMETER = "FitParameter"
+
+ +
+
+const string SF_DATATYPE_SWEEP = "SweepData"
+
+ +
+
+const string SF_DATATYPE_FINDLEVEL = "FindLevel"
+
+ +
+
+const string SF_DATATYPE_APFREQUENCY = "ApFrequency"
+
+ +
+
+const string SF_DATATYPE_LABNOTEBOOK = "LabNotebook"
+
+ +
+
+const string SF_DATATYPE_BUTTERWORTH = "Butterworth"
+
+ +
+
+const string SF_DATATYPE_AREA = "Area"
+
+ +
+
+const string SF_DATATYPE_INTEGRATE = "Integrate"
+
+ +
+
+const string SF_DATATYPE_DERIVATIVE = "Derivative"
+
+ +
+
+const string SF_DATATYPE_STDEV = "StDev"
+
+ +
+
+const string SF_DATATYPE_VARIANCE = "Variance"
+
+ +
+
+const string SF_DATATYPE_RMS = "RMS"
+
+ +
+
+const string SF_DATATYPE_AVG = "Average"
+
+ +
+
+const string SF_DATATYPE_MAX = "Max"
+
+ +
+
+const string SF_DATATYPE_MIN = "Min"
+
+ +
+
+const string SF_DATATYPE_RANGE = "Range"
+
+ +
+
+const string SF_DATATYPE_EPOCHS = "Epochs"
+
+ +
+
+const string SF_DATATYPE_TP = "TestPulse"
+
+ +
+
+const string SF_DATATYPE_TPSS = "TestPulseMode_SteadyState"
+
+ +
+
+const string SF_DATATYPE_TPINST = "TestPulseMode_Instantaneous"
+
+ +
+
+const string SF_DATATYPE_TPBASE = "TestPulseMode_Baseline"
+
+ +
+
+const string SF_DATATYPE_TPFIT = "TestPulseMode_Fit"
+
+ +
+
+const string SF_DATATYPE_POWERSPECTRUM = "Powerspectrum"
+
+ +
+
+const string SF_DATATYPE_PSX = "PSX"
+
+ +
+
+const string SF_WREF_MARKER = "\"WREF@\":"
+
+ +
+
+const string SF_VARIABLE_MARKER = "/SF_IsVariable"
+
+ +
+
+

Available source options for RA_SkipSweeps()

+

+
+
+const double SWEEP_SKIP_USER = 0x1
+
+ +
+
+const double SWEEP_SKIP_AUTO = 0x2
+
+ +
+
+

Public constants from MIES_Configuration

+

+
+
+const string EXPCONFIG_UDATA_EXCLUDE_SAVE = "Config_DontSave"
+
+ +
+
+const string EXPCONFIG_UDATA_EXCLUDE_RESTORE = "Config_DontRestore"
+
+ +
+
+

FFT Window Functions

+

+
+
+const string FFT_WINF = "Bartlet;Bartlett;Blackman367;Blackman361;Blackman492;Blackman474;Cos1;Cos2;Cos3;Cos4;Hamming;Hanning;KaiserBessel20;KaiserBessel25;KaiserBessel30;Parzen;Poisson2;Poisson3;Poisson4;Riemann;SFT3F;SFT3M;FTNI;SFT4F;SFT5F;SFT4M;FTHP;HFT70;FTSRS;SFT5M;HFT90D;HFT95;HFT116D;HFT144D;HFT169D;HFT196D;HFT223D;HFT248D;"
+
+ +
+
+const string FFT_WINF_DEFAULT = "Hanning"
+
+ +
+
+

Types for DB_GetBoundDataBrowser

+

+
+
+const double BROWSER_MODE_USER = 0x01
+
+ +
+
+const double BROWSER_MODE_AUTOMATION = 0x02
+
+ +
+
+const double BROWSER_MODE_ALL = 0xFF
+
+ +
+
+

Available result types for SFH_CreateResultsWaveWithCode()

+

+
+
+const double SFH_RESULT_TYPE_STORE = 0x01
+
+ +
+
+const double SFH_RESULT_TYPE_PSX_EVENTS = 0x02
+
+ +
+
+const double SFH_RESULT_TYPE_PSX_MISC = 0x04
+
+ +
+
+

Constants used in the wave note JSON support

+

+
+
+const string WAVE_NOTE_EMPTY_JSON = "{}"
+
+ +
+
+const string WAVE_NOTE_JSON_SEPARATOR = "\rJSON_BEGIN\r"
+
+ +
+
+

Different log modes for ModifyGraph/Axes

+

+
+
+const double MODIFY_GRAPH_LOG_MODE_NORMAL = 0
+
+ +
+
+const double MODIFY_GRAPH_LOG_MODE_LOG10 = 1
+
+ +
+
+const double MODIFY_GRAPH_LOG_MODE_LOG2 = 2
+
+ +
+
+

Constants for EqualWaves mode

+

+
+
+const double EQWAVES_DATA = 1
+
+ +
+
+const double EQWAVES_DATATYPE = 2
+
+ +
+
+const double EQWAVES_SCALING = 4
+
+ +
+
+const double EQWAVES_DATAUNITS = 8
+
+ +
+
+const double EQWAVES_DIMUNITS = 16
+
+ +
+
+const double EQWAVES_DIMLABELS = 32
+
+ +
+
+const double EQWAVES_WAVENOTE = 64
+
+ +
+
+const double EQWAVES_LOCKSTATE = 128
+
+ +
+
+const double EQWAVES_DATAFULLSCALE = 256
+
+ +
+
+const double EQWAVES_DIMSIZE = 512
+
+ +
+
+const double EQWAVES_ALL = -1
+
+ +
+
+

Igor reserved layer dim labels for ListBox GUI control

+

+
+
+const string LISTBOX_LAYER_FOREGROUND = "foreColors"
+
+ +
+
+const string LISTBOX_LAYER_BACKGROUND = "backColors"
+
+ +
+
+

MIES Settings paths

+

+
+
+const string SETTINGS_AB_FOLDER = "/analysisbrowser/directory"
+
+ +
+
+const string SETTINGS_AB_FOLDER_OLD_DEFAULT = "C:"
+
+ +
+
+

Constants for Hash/WaveHash

+

+
+
+const double HASH_SHA2_256 = 1
+
+ +
+
+

Igor Pro week days

+

+
+
+const double SUNDAY = 1
+
+ +
+
+const double MONDAY = 2
+
+ +
+
+const double TUESDAY = 3
+
+ +
+
+const double WEDNESDAY = 4
+
+ +
+
+const double THURSDAY = 5
+
+ +
+
+const double FRIDAY = 6
+
+ +
+
+const double SATURDAY = 7
+
+ +
+
+

DataBrowser visualisation constants

+

+
+
+const string DB_AXIS_PART_EPOCHS = "_EP"
+
+ +
+
+

Available PSX states

+

+
+
+const double PSX_ACCEPT = 0x01
+
+ +
+
+const double PSX_REJECT = 0x02
+
+ +
+
+const double PSX_UNDET = 0x04
+
+ +
+
+const double PSX_LAST = 0x04
+
+ +
+
+const double PSX_ALL = 0x07
+
+ +
+
+

Available PSX state types

+

+
+
+const double PSX_STATE_EVENT = 0x1
+
+ +
+
+const double PSX_STATE_FIT = 0x2
+
+ +
+
+const double PSX_STATE_BOTH = 0x3
+
+ +
+
+

Custom error codes for PSX_FitEventDecay()

+

+
+
+const double PSX_DECAY_FIT_ERROR = -10000
+
+ +
+
+

Horizontal offset modes in all event graph

+

Corresponds to zero-based indizes of popup_event_offset

+

+
+
+const double PSX_HORIZ_OFFSET_ONSET = 0
+
+ +
+
+const double PSX_HORIZ_OFFSET_PEAK = 1
+
+ +
+
+

Igor Internal Abort Codes

+

+
+
+const double ABORTCODE_ABORTONRTE = -4
+
+ +
+
+const double ABORTCODE_ABORT = -3
+
+ +
+
+const double ABORTCODE_STACKOVERFLOW = -2
+
+ +
+
+const double ABORTCODE_USERABORT = -1
+
+ +
+
+

Variables

+
+
+const double EXPERIMENT_VERSION = 3
+

Especially interesting for PXP consumers like the analysis browser.

+
+ +
+
+const double ANALYSIS_BROWSER_SUPP_VERSION = 3
+

All experiment versions up to the given value are supported.

+
+ +
+
+const double PA_SETTINGS_STRUCT_VERSION = 6
+
+ +
+
+const double NUM_MAX_CHANNELS = 16
+

Maximum values of NUM_CHANNELS_CONSTANTS.

+
+ +
+
+const string ITC_DEVICE_REGEXP = "^ITC.*"
+
+ +
+
+const string DEVICE_TYPES_ITC = "ITC16;ITC18;ITC1600;ITC00;ITC16USB;ITC18USB"
+
+ +
+
+const string DEVICE_NUMBERS = "0;1;2;3;4;5;6;7;8;9;10"
+
+ +
+
+const string DEVICE_NAME_NICE_SUTTER = "Sutter Instrument Integrated Patch Amplifier"
+
+ +
+
+const string DEVICE_SUTTER_NAME_START_CLEAN = "IPA_E_"
+
+ +
+
+const double SUTTER_AI_PER_AMP = 4
+
+ +
+
+const double SUTTER_AO_PER_AMP = 2
+
+ +
+
+const double SUTTER_DIO_PER_AMP = 8
+
+ +
+
+const string BASE_WINDOW_NAME = "DA_Ephys"
+
+ +
+
+const string DATABROWSER_WINDOW_NAME = "DataBrowser"
+
+ +
+
+const string SWEEPBROWSER_WINDOW_NAME = "SweepBrowser"
+
+ +
+
+const string EXT_PANEL_SETTINGSHISTORY = "SettingsHistoryPanel"
+
+ +
+
+const string UNTITLED_EXPERIMENT = "Untitled"
+
+ +
+
+const string PACKED_FILE_EXPERIMENT_SUFFIX = ".pxp"
+
+ +
+
+const double FREE_MEMORY_LOWER_LIMIT = 0.75
+

Amount of free memory required to perform data aquisition in GB.

+
+ +
+
+const string XOP_CHANNEL_NAMES = "AD;DA;;TTL"
+

The indizies correspond to the values from XopChannelConstants.

+
+ +
+
+const double MINIMUM_WAVE_SIZE = 64
+
+ +
+
+const double MINIMUM_WAVE_SIZE_LARGE = 2048
+
+ +
+
+const double MAXIMUM_WAVE_SIZE = 16384
+
+ +
+
+const double MAX_DIMENSION_COUNT = 4
+
+ +
+
+const double DEFAULT_DECIMATION_FACTOR = -1
+
+ +
+
+const string NONE = "- none -"
+

Common string to denote an invalid entry in a popupmenu.

+
+ +
+
+const double CONTROL_PANEL_TYPE = 9
+

Used by CheckName and UniqueName.

+
+ +
+
+const string CURSOR_NAMES = "A;B;C;D;E;F;G;H;I;J"
+
+ +
+
+const double TICKS_TO_SECONDS = 0.0166666666666667
+
+ +
+
+const string TRASH_FOLDER_PREFIX = "trash"
+
+ +
+
+const string SIBLING_FILENAME_SUFFIX = "sibling"
+
+ +
+
+const string NOTE_INDEX = "Index"
+
+ +
+
+const double INITIAL_KEY_WAVE_COL_COUNT = 5
+
+ +
+
+const string LABNOTEBOOK_KEYS_INITIAL = "SweepNum;TimeStamp;TimeStampSinceIgorEpochUTC;EntrySourceType;AcquisitionState"
+
+ +
+
+const double NUMBER_OF_LBN_DAQ_MODES = 4
+
+ +
+
+const double NUM_CLAMP_MODES = 3
+
+ +
+
+const double LPF_BYPASS = 100e3
+

Magic value for selecting “Bypass” in the bessel filter for the primary output.

+
+ +
+
+const double CHECKBOX_SELECTED = 1
+
+ +
+
+const double CHECKBOX_UNSELECTED = 0
+
+ +
+
+const string NUMERALS = "First;Second;Third;Fourth;Fifth;Sixth;Seventh;Eighth"
+
+ +
+
+const string VERT_AXIS_BASE_NAME = "row"
+

Generic axis name for graphs using split axis.

+
+ +
+
+const string HORIZ_AXIS_BASE_NAME = "col"
+
+ +
+
+const double SAMPLING_INTERVAL_FALLBACK = 0.050
+

Fallback value for the sampling interval in milliseconds (1e-3) used by SI_CalculateMinSampInterval if the lookup table could not be found on disk.

+
+ +
+
+const string WAVE_BACKUP_SUFFIX = "_bak"
+
+ +
+
+const string STIM_WAVE_NAME_KEY = "Stim Wave Name"
+
+ +
+
+const double WB_TOTAL_NUMBER_OF_EPOCHS = 94
+

Last valid row index for storing epoch types in GetSegmentTypeWave.

+
+ +
+
+const double MINIMUM_ITCDATAWAVE_EXPONENT = 20
+

Minimum logarithm to base two for the DAQDataWave size for ITC hardware.

+
+ +
+
+const double MINIMUM_TP_BASELINE_PERCENTAGE = 25
+

Minimum value for the baseline fraction of the Testpulse in percent.

+
+ +
+
+const double DISABLE_CONTROL_BIT = 2
+
+ +
+
+const double HIDDEN_CONTROL_BIT = 1
+
+ +
+
+const double GENERIC_EVENT = 6
+

Only used for internal bookkeeping. Never

+
+ +
+
+const double TOTAL_NUM_EVENTS = 8
+

send to analysis functions.

+

Number of EVENT_TYPE_ANALYSIS_FUNCTIONS

+
+ +
+
+const double ANALYSIS_FUNCTION_PARAMS = 8
+

Column for GetAnalysisFunctionStorage(). Same value as TOTAL_NUM_EVENTS but more readable.

+
+ +
+
+const string ANALYSIS_FUNCTION_PARAMS_LBN = "Function params (encoded)"
+
+ +
+
+const string ANALYSIS_FUNCTION_PARAMS_STIMSET = "Function params (encoded)"
+
+ +
+
+const string EVENT_NAME_LIST = "Pre DAQ;Mid Sweep;Post Sweep;Post Set;Post DAQ;Pre Sweep Config;Generic;Pre Set"
+

Human readable names for EVENT_TYPE_ANALYSIS_FUNCTIONS.

+
+ +
+
+const string EVENT_NAME_LIST_LBN = "Pre DAQ function;Mid Sweep function;Post Sweep function;Post Set function;Post DAQ function;Pre Sweep Config function;Generic function;Pre Set function"
+

Labnotebook entries.

+
+ +
+
+const string ANALYSIS_FUNCTION_PARAMS_TYPES = "variable;string;wave;textwave"
+

List of valid analysis function types

+
+ +
+
+const double LABNOTEBOOK_LAYER_COUNT = 9
+

Number of layers in the labnotebook.

+
+ +
+
+const double INDEP_HEADSTAGE = 8
+

Index for storing headstage independent data into the labnotebook.

+
+ +
+
+const string UNKNOWN_MIES_VERSION = "unknown version"
+
+ +
+
+const double COMMON_CONTROL_GROUP_COUNT_NUM = 19
+

Number of common control groups in the DA_EPHYS panel.

+
+ +
+
+const double COMMON_CONTROL_GROUP_COUNT_TXT = 10
+
+ +
+
+const double ESCAPE_KEY = 32
+

Equals 2^5 from GetKeyState

+
+ +
+
+const double MAX_COMMANDLINE_LENGTH = 2500
+
+ +
+
+const string WAVEBUILDER_COMBINE_FORMULA_VER = "1"
+
+ +
+
+const double HARDWARE_ITC_BITS_PER_VOLT = 3200
+

Conversion factor between volts and bits for the AD/DA channels The ITC 16 bit range is +-10.24 V such that a value of 32000 represents exactly 10 V, thus 3200 -> 1 V.

+
+ +
+
+const string HARDWARE_DAC_TYPES = "ITC;NI;SUTTER;"
+

List of different DAC hardware types.

+
+ +
+
+const double HARDWARE_NI_TTL_PORT = 0
+

We always use this DIO port for NI hardware.

+
+ +
+
+const double HARDWARE_MAX_DEVICES = 10
+
+ +
+
+const double WAVEBUILDER_MIN_SAMPINT = 0.005
+

Sutter input -> 50 kHz.

+

[ms]

+
+ +
+
+const double WAVEBUILDER_MIN_SAMPINT_HZ = 200e3
+

Stimulus sets are created with that frequency.

+
+ +
+
+const string CHANNEL_DA_SEARCH_STRING = "*DA*"
+
+ +
+
+const string CHANNEL_TTL_SEARCH_STRING = "*TTL*"
+
+ +
+
+const string NWB_SOURCE_TTL_BIT = "TTLBit"
+

Additional entry in the NWB source attribute for TTL data.

+
+ +
+
+const string IPNWB_PLACEHOLDER = "PLACEHOLDER"
+
+ +
+
+const double ZEROMQ_NUM_BIND_TRIALS = 32
+

Number of trials to find a suitable port for binding a ZeroMQ service.

+
+ +
+
+const double ZEROMQ_BIND_REP_PORT = 5670
+
+ +
+
+const double ZEROMQ_BIND_PUB_PORT = 5770
+
+ +
+
+const double MAIN_THREAD = 0
+

Convenience definition for functions interacting with threads.

+
+ +
+
+const string POPUPMENU_DIVIDER = "\\M1(-"
+
+ +
+
+const double INDEP_EPOCH_TYPE = 0
+

Used for the textual wavebuilder parameter wave WPT as that stores the set parameters in layer 0. Coincides with EPOCH_TYPE_SQUARE_PULSE.

+
+ +
+
+const string SEGMENTWAVE_SPECTRUM_PREFIX = "segmentWaveSpectrum"
+
+ +
+
+const string NOISE_TYPES_STRINGS = "White;Pink;Brown"
+
+ +
+
+const string PULSE_TYPES_STRINGS = "Square;Triangle"
+
+ +
+
+const string NOTE_KEY_ZEROED = "Zeroed"
+
+ +
+
+const string NOTE_KEY_TIMEALIGN = "TimeAlign"
+
+ +
+
+const string NOTE_KEY_ARTEFACT_REMOVAL = "ArtefactRemoval"
+
+ +
+
+const string NOTE_KEY_SEARCH_FAILED_PULSE = "SearchFailedPulses"
+
+ +
+
+const string NOTE_KEY_FAILED_PULSE_LEVEL = "FailedPulseLevel"
+
+ +
+
+const string NOTE_KEY_NUMBER_OF_SPIKES = "NumberOfSpikes"
+
+ +
+
+const string NOTE_KEY_PULSE_SORT_ORDER = "PulseSortOrder"
+
+ +
+
+const string NOTE_KEY_WAVE_MINIMUM = "WaveMinimum"
+
+ +
+
+const string NOTE_KEY_WAVE_MAXIMUM = "WaveMaximum"
+
+ +
+
+const string NOTE_KEY_PULSE_LENGTH = "PulseLength"
+
+ +
+
+const string NOTE_KEY_TIMEALIGN_FEATURE_POS = "TimeAlignmentFeaturePosition"
+
+ +
+
+const string NOTE_KEY_TIMEALIGN_TOTAL_OFFSET = "TimeAlignmentTotalOffset"
+
+ +
+
+const string NOTE_KEY_IMG_PMIN = "PulsesMinimum"
+
+ +
+
+const string NOTE_KEY_IMG_PMAX = "PulsesMaximum"
+
+ +
+
+const string NOTE_KEY_PULSE_IS_DIAGONAL = "IsDiagonal"
+
+ +
+
+const string NOTE_KEY_PULSE_START = "PulseStart"
+
+ +
+
+const string NOTE_KEY_PULSE_END = "PulseEnd"
+
+ +
+
+const string NOTE_KEY_CLAMP_MODE = "ClampMode"
+
+ +
+
+const double DA_EPHYS_PANEL_DATA_ACQUISITION = 0
+

DA_Ephys Panel Tabs.

+
+ +
+
+const double DA_EPHYS_PANEL_DA = 1
+
+ +
+
+const double DA_EPHYS_PANEL_AD = 2
+
+ +
+
+const double DA_EPHYS_PANEL_TTL = 3
+
+ +
+
+const double DA_EPHYS_PANEL_ASYNCHRONOUS = 4
+
+ +
+
+const double DA_EPHYS_PANEL_SETTINGS = 5
+
+ +
+
+const double DA_EPHYS_PANEL_HARDWARE = 6
+
+ +
+
+const double DA_EPHYS_PANEL_VCLAMP = 0
+
+ +
+
+const double DA_EPHYS_PANEL_ICLAMP = 1
+
+ +
+
+const double DA_EPHYS_PANEL_IEQUALZERO = 2
+
+ +
+
+const double DA_EPHYS_PANEL_PRESSURE_AUTO = 0
+
+ +
+
+const double DA_EPHYS_PANEL_PRESSURE_MANUAL = 1
+
+ +
+
+const double DA_EPHYS_PANEL_PRESSURE_USER = 2
+
+ +
+
+const string PULSE_START_TIMES_KEY = "Pulse Train Pulses"
+
+ +
+
+const string PULSE_TO_PULSE_LENGTH_KEY = "Pulse To Pulse Length"
+
+ +
+
+const string HIGH_PREC_SWEEP_START_KEY = "High precision sweep start"
+
+ +
+
+const string STIMSET_SCALE_FACTOR_KEY = "Stim Scale Factor"
+
+ +
+
+const string STIMSET_WAVE_NOTE_KEY = "Stim Wave Note"
+
+ +
+
+const string EPOCHS_ENTRY_KEY = "Epochs"
+
+ +
+
+const string CLAMPMODE_ENTRY_KEY = "Clamp Mode"
+
+ +
+
+const string TP_AMPLITUDE_VC_ENTRY_KEY = "TP Amplitude VC"
+
+ +
+
+const string TP_AMPLITUDE_IC_ENTRY_KEY = "TP Amplitude IC"
+
+ +
+
+const string PULSE_START_INDICES_KEY = "Pulse Train Pulse Start Indices"
+
+ +
+
+const string PULSE_END_INDICES_KEY = "Pulse Train Pulse End Indices"
+
+ +
+
+const string INFLECTION_POINTS_INDEX_KEY = "Inflection Points Indices"
+
+ +
+
+const string EPOCH_LENGTH_INDEX_KEY = "Epoch Length Indices"
+
+ +
+
+const string STIMSET_SIZE_KEY = "Stimset Size"
+
+ +
+
+const string STIMSET_ERROR_KEY = "Wavebuilder Error"
+
+ +
+
+const string AUTOBIAS_PERC_KEY = "Autobias %"
+
+ +
+
+const double WAVEBUILDER_STATUS_ERROR = 1
+
+ +
+
+const string CONTROLS_DISABLE_DURING_DAQ = "Check_DataAcqHS_All;Radio_ClampMode_AllIClamp;Radio_ClampMode_AllVClamp;Radio_ClampMode_AllIZero;SetVar_Sweep;Check_DataAcq_Indexing;check_DataAcq_IndexRandom;Check_DataAcq1_IndexingLocked;check_DataAcq_RepAcqRandom;Check_DataAcq1_RepeatAcq;Check_Settings_SkipAnalysFuncs;check_Settings_MD"
+

DA_Ephys controls which should be disabled during DAQ.

+
+ +
+
+const string CONTROLS_DISABLE_DURING_IDX = "SetVar_DataAcq_ListRepeats;SetVar_DataAcq_SetRepeats"
+
+ +
+
+const string CONTROLS_DISABLE_DURING_DAQ_TP = "Check_Settings_BkgTP;Check_Settings_BackgrndDataAcq"
+

DA_Ephys controls which should be disabled during DAQ and TP.

+
+ +
+
+const double MAX_OBJECT_NAME_LENGTH_IN_BYTES = 255
+

Maximum length of a valid object name in bytes in Igor Pro >= 8.

+
+ +
+
+const double MAX_OBJECT_NAME_LENGTH_IN_BYTES_SHORT = 31
+

(Deprecated) Maximum length of a valid object name in bytes in Igor Pro < 8

+
+ +
+
+const string LABNOTEBOOK_NO_TOLERANCE = "-"
+
+ +
+
+const string LABNOTEBOOK_BINARY_UNIT = "On/Off"
+
+ +
+
+const string LABNOTEBOOK_NO_UNIT = ""
+
+ +
+
+const string LABNOTEBOOK_USER_PREFIX = "USER_"
+

Key prefix for runtime added labnotebooks by ED_AddEntryToLabnotebook()

+
+ +
+
+const string RA_ACQ_CYCLE_ID_KEY = "Repeated Acq Cycle ID"
+
+ +
+
+const string STIMSET_ACQ_CYCLE_ID_KEY = "Stimset Acq Cycle ID"
+
+ +
+
+const string SKIP_SWEEPS_KEY = "Skip Sweeps"
+
+ +
+
+const string SKIP_SWEEPS_SOURCE_KEY = "Skip Sweeps source"
+
+ +
+
+const double LABNOTEBOOK_GET_RANGE = -1
+

Parameters for GetLastSetting() for using the row caching mechanism.

+
+ +
+
+const double MAX_NUM_MS_TIMERS = 10
+

Maximum number of microsecond timers in Igor Pro.

+
+ +
+
+const double PSQ_SPIKE_LEVEL = 0.01
+
+ +
+
+const double PSQ_RMS_SHORT_THRESHOLD = 0.07
+
+ +
+
+const double PSQ_RMS_LONG_THRESHOLD = 0.5
+
+ +
+
+const double PSQ_TARGETV_THRESHOLD = 1
+
+ +
+
+const double PSQ_CALC_METHOD_AVG = 0x1
+
+ +
+
+const double PSQ_CALC_METHOD_RMS = 0x2
+
+ +
+
+const double PSQ_BL_FAILED = 1
+
+ +
+
+const string PSQ_BASELINE_CHUNK_SHORT_NAME_PREFIX = "BLC"
+
+ +
+
+const string PSQ_BASELINE_CHUNK_SHORT_NAME_RE_MATCHER = "^U_BLC[[:digit:]]+$"
+
+ +
+
+const string PSQ_BASELINE_SELECTION_SHORT_NAME_RE_MATCHER = "^U_BLS[[:digit:]]+$"
+
+ +
+
+const string FMT_LBN_ANA_FUNC_VERSION = "%s version"
+
+ +
+
+const double TP_MD_THREAD_DEAD_MAX_RETRIES = 10
+
+ +
+
+const double DAQ_MD_THREAD_DEAD_MAX_RETRIES = 10
+
+ +
+
+const double NUM_ENTRIES_FOR_MULTITHREAD = 16
+

+
+Todo:
+

: IP8 convert all call sites to use MultiThread/T=

+
+ +

+
+ +
+
+const string DAQ_ALLOWED_FUNCTIONS = "DQ_RestartDAQ;DAP_ButtonProc_TPDAQ;RA_CounterMD"
+

Exclusive list of functions which are allowed to call DQS_StartDAQSingleDevice()/DQM_StartDAQMultiDevice()

+
+ +
+
+const string RESISTANCE_GRAPH = "AnalysisFuncResistanceGraph"
+
+ +
+
+const string SPIKE_FREQ_GRAPH = "SpikeFrequencyGraph"
+
+ +
+
+const string CHANNEL_UNIT_KEY = "ChannelUnit"
+
+ +
+
+const double MAX_SWEEP_DURATION_IN_MS = 1.8e6
+

Maximum length of a sweep in the wavebuilder.

+
+ +
+
+const string REC_MACRO_PROCEDURE = "proc"
+
+ +
+
+const string REC_MACRO_MODE = "mode"
+
+ +
+
+const double LABNOTEBOOK_MISSING_VALUE = -1
+
+ +
+
+const double LABNOTEBOOK_UNCACHED_VALUE = -2
+
+ +
+
+const string LABNOTEBOOK_MOD_COUNT = "Labnotebook modification count"
+
+ +
+
+const double MINIMUM_FREE_DISK_SPACE = 10737418240
+
+ +
+
+const string PRESSURE_CONTROL_LED_DASHBOARD = "valdisp_DataAcq_P_LED_0;valdisp_DataAcq_P_LED_1;valdisp_DataAcq_P_LED_2;valdisp_DataAcq_P_LED_3;valdisp_DataAcq_P_LED_4;valdisp_DataAcq_P_LED_5;valdisp_DataAcq_P_LED_6;valdisp_DataAcq_P_LED_7"
+
+ +
+
+const string USER_DATA_MENU_EXP = "MenuExp"
+

User data on the stimset controls listing all stimsets in range.

+
+ +
+
+const string EXPCONFIG_UDATA_SOURCEFILE_PATH = "Config_FileName"
+
+ +
+
+const string EXPCONFIG_UDATA_SOURCEFILE_HASH = "Config_FileHash"
+
+ +
+
+const string EXPCONFIG_UDATA_STIMSET_NWB_PATH = "Config_StimsetNWBPath"
+
+ +
+
+const string TUD_INDEX_JSON = "INDEX_JSON"
+

Wave note key for the indexing helper JSON document.

+
+ +
+
+const double TRACE_NAME_NUM_DIGITS = 6
+

sprintf field width for trace names

+
+ +
+
+const string NUMBER_UNIT_SPACE = "\u2006"
+

Space used between numbers and their units.

+
+ +
+
+const double PA_IMAGE_SPECIAL_ENTRIES_RANGE = 0.065
+
+ +
+
+const double PA_IMAGE_FAILEDMARKERSTART = 0.9
+
+ +
+
+const string NOTE_NEEDS_UPDATE = "NeedsUpdate"
+
+ +
+
+const double GRAPH_DIV_SPACING = 0.03
+
+ +
+
+const string NOTE_PA_NEW_PULSES_START = "StartIndexOfNewPulses"
+
+ +
+
+const string PULSEWAVE_NOTE_SUFFIX = "_note"
+
+ +
+
+const string PA_AVERAGE_WAVE_PREFIX = "average_"
+
+ +
+
+const string PA_DECONVOLUTION_WAVE_PREFIX = "deconv_"
+
+ +
+
+const string TP_PROPERTIES_HASH = "TestPulsePropertiesHash"
+
+ +
+
+const string DASHBOARD_PASSING_MESSAGE = "Pass"
+
+ +
+
+const string DAQ_STOPPED_EARLY_LEGACY_MSG = "DAQ was stopped early (n.a.)"
+
+ +
+
+const double MAX_DOUBLE_PRECISION = 15
+
+ +
+
+const string PACKAGE_MIES = "MIES"
+
+ +
+
+const string LOGFILE_NWB_MARKER = "### LOGFILE:JSONL ###"
+
+ +
+
+const string PACKAGE_SETTINGS_JSON = "Settings.json"
+
+ +
+
+const string PACKAGE_SETTINGS_USERPING = "userping"
+
+ +
+
+const double PACKAGE_SETTINGS_USERPING_DEFAULT = 1
+
+ +
+
+const string LOGFILE_NAME = "Log.jsonl"
+
+ +
+
+const double PSQ_CR_SPIKE_CHECK_DEFAULT = 1
+
+ +
+
+const string NOT_AVAILABLE = "n/a"
+
+ +
+
+const double DND_STIMSET_DANDI_SET = 107
+
+ +
+
+const string WAVEBUILDER_DELTA_MODES = "None;Multiplier;Log;Squared;Power;Alternate;Explicit"
+
+ +
+
+const string WAVEBUILDER_TRIGGER_TYPES = "Sin;Cos"
+
+ +
+
+const string LOGBOOK_WAVE_TEMP_FOLDER = "Temp"
+
+ +
+
+const double EPOCHTIME_PRECISION = 7
+

which is sufficient to represent each sample point time with a distinctive number up to rates of 10 MHz.

+
+ +
+
+const string EPOCH_LIST_ROW_SEP = ":"
+
+ +
+
+const string EPOCH_LIST_COL_SEP = ","
+
+ +
+
+const string EPOCH_TAG_INVALID_CHARS_REGEXP = "[:,]"
+

These characters are not allowed to be in epoch tags as they are used for serialization.

+
+ +
+
+const double EPOCH_USER_LEVEL = -1
+
+ +
+
+const string EPOCH_SHORTNAME_USER_PREFIX = "U_"
+
+ +
+
+const double TP_BASELINE_FRACTION_LOW = 0.25
+
+ +
+
+const double TP_BASELINE_FRACTION_HIGH = 0.49
+
+ +
+
+const string DAEPHYS_TP_CONTROLS_ALL = "SetVar_DataAcq_TPDuration;SetVar_DataAcq_TPBaselinePerc;SetVar_DataAcq_TPAmplitude;SetVar_DataAcq_TPAmplitudeIC;setvar_Settings_TPBuffer;setvar_Settings_TP_RTolerance;Check_TP_SendToAllHS;check_DataAcq_AutoTP;setvar_DataAcq_IinjMax;setvar_DataAcq_targetVoltage;setvar_DataAcq_targetVoltageRange;setvar_Settings_autoTP_perc;setvar_Settings_autoTP_int"
+
+ +
+
+const string DAEPHYS_TP_CONTROLS_DEPEND = "SetVar_DataAcq_TPAmplitude;SetVar_DataAcq_TPAmplitudeIC;check_DataAcq_AutoTP;setvar_DataAcq_IinjMax;setvar_DataAcq_targetVoltage;setvar_DataAcq_targetVoltageRange"
+
+ +
+
+const string DAEPHYS_TP_CONTROLS_INDEP = "SetVar_DataAcq_TPDuration;SetVar_DataAcq_TPBaselinePerc;setvar_Settings_TPBuffer;setvar_Settings_TP_RTolerance;Check_TP_SendToAllHS;setvar_Settings_autoTP_perc;setvar_Settings_autoTP_int"
+
+ +
+
+const string DAEPHYS_TP_CONTROLS_NO_RESTART = "Check_TP_SendToAllHS;check_DataAcq_AutoTP;setvar_DataAcq_IinjMax;setvar_DataAcq_targetVoltage;setvar_DataAcq_targetVoltageRange;setvar_Settings_autoTP_perc;setvar_Settings_autoTP_int"
+
+ +
+
+const double TP_BASELINE_RATIO_HIGH = 0.285714
+
+ +
+
+const double TP_BASELINE_RATIO_OPT = 0.25
+
+ +
+
+const double TP_BASELINE_RATIO_LOW = 0.222222
+
+ +
+
+const double TP_AUTO_TP_CONSECUTIVE_PASSES = 3
+
+ +
+
+const double TP_AUTO_TP_BASELINE_RANGE_EXCEEDED_FAILS = 3
+
+ +
+
+const double TP_OVERRIDE_RESULTS_AUTO_TP = 0x0
+
+ +
+
+const string DEFAULT_KEY_SEP = ":"
+
+ +
+
+const string DEFAULT_LIST_SEP = ";"
+
+ +
+
+const string PREFIX_SHORT_LIST = ";Y;Z;E;P;T;G;M;k;h;da;d;c;m;mu;n;p;f;a;z;y"
+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name

Symbol

Numerical value

yotta

Y

1e24

zetta

Z

1e21

exa

E

1e18

peta

P

1e15

tera

T

1e12

giga

G

1e9

mega

M

1e6

kilo

k

1e3

hecto

h

1e2

deca

da

1e1

deci

d

1e-1

centi

c

1e-2

milli

m

1e-3

micro

mu

1e-6

nano

n

1e-9

pico

p

1e-12

femto

f

1e-15

atto

a

1e-18

zepto

z

1e-21

yocto

y

1e-24

+

+

From: 9th edition of the SI Brochure (2019), https://www.bipm.org/en/publications/si-brochure

+
+ +
+
+const string PREFIX_LONG_LIST = "one;yotta;zetta;exa;peta;tera;giga;mega;kilo;hecto;deca;deci;centi;milli;micro;nano;pico;femto;atto;zepto;yocto"
+
+ +
+
+const string PREFIX_VALUE_LIST = "1;1e24;1e21;1e18;1e15;1e12;1e9;1e6;1e3;1e2;1e1;1e-1;1e-2;1e-3;1e-6;1e-9;1e-12;1e-15;1e-18;1e-21;1e-24"
+
+ +
+
+const double FIRST_XOP_ERROR = 10000
+

Smaller error codes are from Igor Pro.

+
+ +
+
+const double THREAD_QUEUE_TRIES = 1000
+
+ +
+
+const double HARDWARE_ITC_FIFO_ERROR = -1
+
+ +
+
+const double HARDWARE_ITC_STUCK_FIFO_TICKS = 120
+
+ +
+
+const string SF_PLOT_NAME_TEMPLATE = "SweepFormula plot"
+
+ +
+
+const string SFH_USER_DATA_BROWSER = "browser"
+
+ +
+
+const string FILE_LIST_SEP = "|"
+
+ +
+
+const string ANALYSIS_BROWSER_NAME = "AnalysisBrowser"
+
+ +
+
+const string MEMORY_REFCOUNTER_DF = "MemoryReferenceCounterDF"
+
+ +
+
+const string LOG_ACTION_ASSERT = "assert"
+
+ +
+
+const string LOG_MESSAGE_KEY = "msg"
+
+ +
+
+const string LOG_ACTION_REPORT = "report"
+
+ +
+
+const double SUBWINDOW_MOVE_CORRECTION = 5
+

Poorly understood difference required for vertical direction for MoveSubWindow.

+
+ +
+
+const double LOADWAVE_V_FLAGS_IGNORECOLEND = 0x01
+
+ +
+
+const double LOADWAVE_V_FLAGS_WCOLSPACEBLANK = 0x02
+
+ +
+
+const double LOADWAVE_V_FLAGS_DISABLELINEPRECOUNTING = 0x04
+
+ +
+
+const double LOADWAVE_V_FLAGS_DISABLEUNESCAPEBACKSLASH = 0x08
+
+ +
+
+const double LOADWAVE_V_FLAGS_DISABLESUPPORTQUOTEDSTRINGS = 0x10
+
+ +
+
+const double MEGABYTE = 1048576
+
+ +
+
+const double STRING_MAX_SIZE = 2147483647
+
+ +
+
+const double LOGUPLOAD_PAYLOAD_SPLITSIZE = 104857600
+
+ +
+
+const double LOG_ARCHIVING_SPLITSIZE = 524288000
+
+ +
+
+const double LOG_MAX_LINESIZE = 2097152
+
+ +
+
+const string LOG_FILE_LINE_END = "\n"
+
+ +
+
+const double SECONDS_PER_DAY = 86400
+
+ +
+
+const string SF_OP_PSX = "psx"
+
+ +
+
+const string SF_OP_PSX_KERNEL = "psxKernel"
+
+ +
+
+const string SF_OP_PSX_STATS = "psxStats"
+
+ +
+
+const string SF_OP_PSX_RISETIME = "psxRiseTime"
+
+ +
+
+const string SF_OP_PSX_PREP = "psxPrep"
+
+ +
+
+const string SF_OP_PSX_DECONV_FILTER = "psxDeconvFilter"
+
+ +
+
+const string PSX_EVENTS_COMBO_KEY_WAVE_NOTE = "comboKey"
+
+ +
+
+const double PSX_MARKER_ACCEPT = 19
+
+ +
+
+const double PSX_MARKER_REJECT = 23
+
+ +
+
+const double PSX_MARKER_UNDET = 18
+
+ +
+
+const string PSX_STATS_LABELS = "Average;Median;Average Deviation;Standard deviation;Skewness;Kurtosis"
+
+ +
+
+const double PSX_DECONV_FILTER_DEF_LOW = 0.002
+
+ +
+
+const double PSX_DECONV_FILTER_DEF_HIGH = 0.004
+
+ +
+
+const double PSX_DECONV_FILTER_DEF_ORDER = 101
+
+ +
+
+const string SF_OP_MERGE = "merge"
+
+ +
+
+const string SF_OP_FIT = "fit"
+
+ +
+
+const string SF_OP_FITLINE = "fitline"
+
+ +
+
+const string SF_OP_DATASET = "dataset"
+
+ +
+
+const string SWEEP_NOTE_KEY_ORIGCREATIONTIME_UTC = "OriginalCreationTimeInUTC"
+
+ +
+
+const string DF_NAME_FREE = "freeroot"
+
+ +
+
+const string DF_NAME_MIES = "MIES"
+
+ +
+
+const double SUTTER_MAX_MAX_TP_PULSES = 10000
+
+ +
+
+const double INVALID_SWEEP_NUMBER = -1
+
+ +
+
+const string PERCENT_F_MAX_PREC = "%.15f"
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___conversion_constants_8ipf.html b/file/_m_i_e_s___conversion_constants_8ipf.html new file mode 100644 index 0000000000..c51d7587d6 --- /dev/null +++ b/file/_m_i_e_s___conversion_constants_8ipf.html @@ -0,0 +1,2827 @@ + + + + + + + + File MIES_ConversionConstants.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_ConversionConstants.ipf

+
+

Conversion constants for decimal multiples

+

These must be used only with * to avoid confusion, the inverse exists as well, so this is no limitation.

+

Example:

+

// pA -> A
+value_A = value_pA * PICO_TO_ONE
+
+// V -> mV
+value_mV = value_V * ONE_TO_MILLI
+
+
+

+

+

Generated code from GenerateMultiplierConstants().

+
+
+const double ONE_TO_YOTTA = 1e-24
+
+ +
+
+const double ONE_TO_ZETTA = 1e-21
+
+ +
+
+const double ONE_TO_EXA = 1e-18
+
+ +
+
+const double ONE_TO_PETA = 1e-15
+
+ +
+
+const double ONE_TO_TERA = 1e-12
+
+ +
+
+const double ONE_TO_GIGA = 1e-09
+
+ +
+
+const double ONE_TO_MEGA = 1e-06
+
+ +
+
+const double ONE_TO_KILO = 1e-03
+
+ +
+
+const double ONE_TO_HECTO = 1e-02
+
+ +
+
+const double ONE_TO_DECA = 1e-01
+
+ +
+
+const double ONE_TO_DECI = 1e+01
+
+ +
+
+const double ONE_TO_CENTI = 1e+02
+
+ +
+
+const double ONE_TO_MILLI = 1e+03
+
+ +
+
+const double ONE_TO_MICRO = 1e+06
+
+ +
+
+const double ONE_TO_NANO = 1e+09
+
+ +
+
+const double ONE_TO_PICO = 1e+12
+
+ +
+
+const double ONE_TO_FEMTO = 1e+15
+
+ +
+
+const double ONE_TO_ATTO = 1e+18
+
+ +
+
+const double ONE_TO_ZEPTO = 1e+21
+
+ +
+
+const double ONE_TO_YOCTO = 1e+24
+
+ +
+
+const double YOTTA_TO_ONE = 1e+24
+
+ +
+
+const double YOTTA_TO_ZETTA = 1e+03
+
+ +
+
+const double YOTTA_TO_EXA = 1e+06
+
+ +
+
+const double YOTTA_TO_PETA = 1e+09
+
+ +
+
+const double YOTTA_TO_TERA = 1e+12
+
+ +
+
+const double YOTTA_TO_GIGA = 1e+15
+
+ +
+
+const double YOTTA_TO_MEGA = 1e+18
+
+ +
+
+const double YOTTA_TO_KILO = 1e+21
+
+ +
+
+const double YOTTA_TO_HECTO = 1e+22
+
+ +
+
+const double YOTTA_TO_DECA = 1e+23
+
+ +
+
+const double YOTTA_TO_DECI = 1e+25
+
+ +
+
+const double YOTTA_TO_CENTI = 1e+26
+
+ +
+
+const double YOTTA_TO_MILLI = 1e+27
+
+ +
+
+const double YOTTA_TO_MICRO = 1e+30
+
+ +
+
+const double YOTTA_TO_NANO = 1e+33
+
+ +
+
+const double YOTTA_TO_PICO = 1e+36
+
+ +
+
+const double YOTTA_TO_FEMTO = 1e+39
+
+ +
+
+const double YOTTA_TO_ATTO = 1e+42
+
+ +
+
+const double YOTTA_TO_ZEPTO = 1e+45
+
+ +
+
+const double YOTTA_TO_YOCTO = 1e+48
+
+ +
+
+const double ZETTA_TO_ONE = 1e+21
+
+ +
+
+const double ZETTA_TO_YOTTA = 1e-03
+
+ +
+
+const double ZETTA_TO_EXA = 1e+03
+
+ +
+
+const double ZETTA_TO_PETA = 1e+06
+
+ +
+
+const double ZETTA_TO_TERA = 1e+09
+
+ +
+
+const double ZETTA_TO_GIGA = 1e+12
+
+ +
+
+const double ZETTA_TO_MEGA = 1e+15
+
+ +
+
+const double ZETTA_TO_KILO = 1e+18
+
+ +
+
+const double ZETTA_TO_HECTO = 1e+19
+
+ +
+
+const double ZETTA_TO_DECA = 1e+20
+
+ +
+
+const double ZETTA_TO_DECI = 1e+22
+
+ +
+
+const double ZETTA_TO_CENTI = 1e+23
+
+ +
+
+const double ZETTA_TO_MILLI = 1e+24
+
+ +
+
+const double ZETTA_TO_MICRO = 1e+27
+
+ +
+
+const double ZETTA_TO_NANO = 1e+30
+
+ +
+
+const double ZETTA_TO_PICO = 1e+33
+
+ +
+
+const double ZETTA_TO_FEMTO = 1e+36
+
+ +
+
+const double ZETTA_TO_ATTO = 1e+39
+
+ +
+
+const double ZETTA_TO_ZEPTO = 1e+42
+
+ +
+
+const double ZETTA_TO_YOCTO = 1e+45
+
+ +
+
+const double EXA_TO_ONE = 1e+18
+
+ +
+
+const double EXA_TO_YOTTA = 1e-06
+
+ +
+
+const double EXA_TO_ZETTA = 1e-03
+
+ +
+
+const double EXA_TO_PETA = 1e+03
+
+ +
+
+const double EXA_TO_TERA = 1e+06
+
+ +
+
+const double EXA_TO_GIGA = 1e+09
+
+ +
+
+const double EXA_TO_MEGA = 1e+12
+
+ +
+
+const double EXA_TO_KILO = 1e+15
+
+ +
+
+const double EXA_TO_HECTO = 1e+16
+
+ +
+
+const double EXA_TO_DECA = 1e+17
+
+ +
+
+const double EXA_TO_DECI = 1e+19
+
+ +
+
+const double EXA_TO_CENTI = 1e+20
+
+ +
+
+const double EXA_TO_MILLI = 1e+21
+
+ +
+
+const double EXA_TO_MICRO = 1e+24
+
+ +
+
+const double EXA_TO_NANO = 1e+27
+
+ +
+
+const double EXA_TO_PICO = 1e+30
+
+ +
+
+const double EXA_TO_FEMTO = 1e+33
+
+ +
+
+const double EXA_TO_ATTO = 1e+36
+
+ +
+
+const double EXA_TO_ZEPTO = 1e+39
+
+ +
+
+const double EXA_TO_YOCTO = 1e+42
+
+ +
+
+const double PETA_TO_ONE = 1e+15
+
+ +
+
+const double PETA_TO_YOTTA = 1e-09
+
+ +
+
+const double PETA_TO_ZETTA = 1e-06
+
+ +
+
+const double PETA_TO_EXA = 1e-03
+
+ +
+
+const double PETA_TO_TERA = 1e+03
+
+ +
+
+const double PETA_TO_GIGA = 1e+06
+
+ +
+
+const double PETA_TO_MEGA = 1e+09
+
+ +
+
+const double PETA_TO_KILO = 1e+12
+
+ +
+
+const double PETA_TO_HECTO = 1e+13
+
+ +
+
+const double PETA_TO_DECA = 1e+14
+
+ +
+
+const double PETA_TO_DECI = 1e+16
+
+ +
+
+const double PETA_TO_CENTI = 1e+17
+
+ +
+
+const double PETA_TO_MILLI = 1e+18
+
+ +
+
+const double PETA_TO_MICRO = 1e+21
+
+ +
+
+const double PETA_TO_NANO = 1e+24
+
+ +
+
+const double PETA_TO_PICO = 1e+27
+
+ +
+
+const double PETA_TO_FEMTO = 1e+30
+
+ +
+
+const double PETA_TO_ATTO = 1e+33
+
+ +
+
+const double PETA_TO_ZEPTO = 1e+36
+
+ +
+
+const double PETA_TO_YOCTO = 1e+39
+
+ +
+
+const double TERA_TO_ONE = 1e+12
+
+ +
+
+const double TERA_TO_YOTTA = 1e-12
+
+ +
+
+const double TERA_TO_ZETTA = 1e-09
+
+ +
+
+const double TERA_TO_EXA = 1e-06
+
+ +
+
+const double TERA_TO_PETA = 1e-03
+
+ +
+
+const double TERA_TO_GIGA = 1e+03
+
+ +
+
+const double TERA_TO_MEGA = 1e+06
+
+ +
+
+const double TERA_TO_KILO = 1e+09
+
+ +
+
+const double TERA_TO_HECTO = 1e+10
+
+ +
+
+const double TERA_TO_DECA = 1e+11
+
+ +
+
+const double TERA_TO_DECI = 1e+13
+
+ +
+
+const double TERA_TO_CENTI = 1e+14
+
+ +
+
+const double TERA_TO_MILLI = 1e+15
+
+ +
+
+const double TERA_TO_MICRO = 1e+18
+
+ +
+
+const double TERA_TO_NANO = 1e+21
+
+ +
+
+const double TERA_TO_PICO = 1e+24
+
+ +
+
+const double TERA_TO_FEMTO = 1e+27
+
+ +
+
+const double TERA_TO_ATTO = 1e+30
+
+ +
+
+const double TERA_TO_ZEPTO = 1e+33
+
+ +
+
+const double TERA_TO_YOCTO = 1e+36
+
+ +
+
+const double GIGA_TO_ONE = 1e+09
+
+ +
+
+const double GIGA_TO_YOTTA = 1e-15
+
+ +
+
+const double GIGA_TO_ZETTA = 1e-12
+
+ +
+
+const double GIGA_TO_EXA = 1e-09
+
+ +
+
+const double GIGA_TO_PETA = 1e-06
+
+ +
+
+const double GIGA_TO_TERA = 1e-03
+
+ +
+
+const double GIGA_TO_MEGA = 1e+03
+
+ +
+
+const double GIGA_TO_KILO = 1e+06
+
+ +
+
+const double GIGA_TO_HECTO = 1e+07
+
+ +
+
+const double GIGA_TO_DECA = 1e+08
+
+ +
+
+const double GIGA_TO_DECI = 1e+10
+
+ +
+
+const double GIGA_TO_CENTI = 1e+11
+
+ +
+
+const double GIGA_TO_MILLI = 1e+12
+
+ +
+
+const double GIGA_TO_MICRO = 1e+15
+
+ +
+
+const double GIGA_TO_NANO = 1e+18
+
+ +
+
+const double GIGA_TO_PICO = 1e+21
+
+ +
+
+const double GIGA_TO_FEMTO = 1e+24
+
+ +
+
+const double GIGA_TO_ATTO = 1e+27
+
+ +
+
+const double GIGA_TO_ZEPTO = 1e+30
+
+ +
+
+const double GIGA_TO_YOCTO = 1e+33
+
+ +
+
+const double MEGA_TO_ONE = 1e+06
+
+ +
+
+const double MEGA_TO_YOTTA = 1e-18
+
+ +
+
+const double MEGA_TO_ZETTA = 1e-15
+
+ +
+
+const double MEGA_TO_EXA = 1e-12
+
+ +
+
+const double MEGA_TO_PETA = 1e-09
+
+ +
+
+const double MEGA_TO_TERA = 1e-06
+
+ +
+
+const double MEGA_TO_GIGA = 1e-03
+
+ +
+
+const double MEGA_TO_KILO = 1e+03
+
+ +
+
+const double MEGA_TO_HECTO = 1e+04
+
+ +
+
+const double MEGA_TO_DECA = 1e+05
+
+ +
+
+const double MEGA_TO_DECI = 1e+07
+
+ +
+
+const double MEGA_TO_CENTI = 1e+08
+
+ +
+
+const double MEGA_TO_MILLI = 1e+09
+
+ +
+
+const double MEGA_TO_MICRO = 1e+12
+
+ +
+
+const double MEGA_TO_NANO = 1e+15
+
+ +
+
+const double MEGA_TO_PICO = 1e+18
+
+ +
+
+const double MEGA_TO_FEMTO = 1e+21
+
+ +
+
+const double MEGA_TO_ATTO = 1e+24
+
+ +
+
+const double MEGA_TO_ZEPTO = 1e+27
+
+ +
+
+const double MEGA_TO_YOCTO = 1e+30
+
+ +
+
+const double KILO_TO_ONE = 1e+03
+
+ +
+
+const double KILO_TO_YOTTA = 1e-21
+
+ +
+
+const double KILO_TO_ZETTA = 1e-18
+
+ +
+
+const double KILO_TO_EXA = 1e-15
+
+ +
+
+const double KILO_TO_PETA = 1e-12
+
+ +
+
+const double KILO_TO_TERA = 1e-09
+
+ +
+
+const double KILO_TO_GIGA = 1e-06
+
+ +
+
+const double KILO_TO_MEGA = 1e-03
+
+ +
+
+const double KILO_TO_HECTO = 1e+01
+
+ +
+
+const double KILO_TO_DECA = 1e+02
+
+ +
+
+const double KILO_TO_DECI = 1e+04
+
+ +
+
+const double KILO_TO_CENTI = 1e+05
+
+ +
+
+const double KILO_TO_MILLI = 1e+06
+
+ +
+
+const double KILO_TO_MICRO = 1e+09
+
+ +
+
+const double KILO_TO_NANO = 1e+12
+
+ +
+
+const double KILO_TO_PICO = 1e+15
+
+ +
+
+const double KILO_TO_FEMTO = 1e+18
+
+ +
+
+const double KILO_TO_ATTO = 1e+21
+
+ +
+
+const double KILO_TO_ZEPTO = 1e+24
+
+ +
+
+const double KILO_TO_YOCTO = 1e+27
+
+ +
+
+const double HECTO_TO_ONE = 1e+02
+
+ +
+
+const double HECTO_TO_YOTTA = 1e-22
+
+ +
+
+const double HECTO_TO_ZETTA = 1e-19
+
+ +
+
+const double HECTO_TO_EXA = 1e-16
+
+ +
+
+const double HECTO_TO_PETA = 1e-13
+
+ +
+
+const double HECTO_TO_TERA = 1e-10
+
+ +
+
+const double HECTO_TO_GIGA = 1e-07
+
+ +
+
+const double HECTO_TO_MEGA = 1e-04
+
+ +
+
+const double HECTO_TO_KILO = 1e-01
+
+ +
+
+const double HECTO_TO_DECA = 1e+01
+
+ +
+
+const double HECTO_TO_DECI = 1e+03
+
+ +
+
+const double HECTO_TO_CENTI = 1e+04
+
+ +
+
+const double HECTO_TO_MILLI = 1e+05
+
+ +
+
+const double HECTO_TO_MICRO = 1e+08
+
+ +
+
+const double HECTO_TO_NANO = 1e+11
+
+ +
+
+const double HECTO_TO_PICO = 1e+14
+
+ +
+
+const double HECTO_TO_FEMTO = 1e+17
+
+ +
+
+const double HECTO_TO_ATTO = 1e+20
+
+ +
+
+const double HECTO_TO_ZEPTO = 1e+23
+
+ +
+
+const double HECTO_TO_YOCTO = 1e+26
+
+ +
+
+const double DECA_TO_ONE = 1e+01
+
+ +
+
+const double DECA_TO_YOTTA = 1e-23
+
+ +
+
+const double DECA_TO_ZETTA = 1e-20
+
+ +
+
+const double DECA_TO_EXA = 1e-17
+
+ +
+
+const double DECA_TO_PETA = 1e-14
+
+ +
+
+const double DECA_TO_TERA = 1e-11
+
+ +
+
+const double DECA_TO_GIGA = 1e-08
+
+ +
+
+const double DECA_TO_MEGA = 1e-05
+
+ +
+
+const double DECA_TO_KILO = 1e-02
+
+ +
+
+const double DECA_TO_HECTO = 1e-01
+
+ +
+
+const double DECA_TO_DECI = 1e+02
+
+ +
+
+const double DECA_TO_CENTI = 1e+03
+
+ +
+
+const double DECA_TO_MILLI = 1e+04
+
+ +
+
+const double DECA_TO_MICRO = 1e+07
+
+ +
+
+const double DECA_TO_NANO = 1e+10
+
+ +
+
+const double DECA_TO_PICO = 1e+13
+
+ +
+
+const double DECA_TO_FEMTO = 1e+16
+
+ +
+
+const double DECA_TO_ATTO = 1e+19
+
+ +
+
+const double DECA_TO_ZEPTO = 1e+22
+
+ +
+
+const double DECA_TO_YOCTO = 1e+25
+
+ +
+
+const double DECI_TO_ONE = 1e-01
+
+ +
+
+const double DECI_TO_YOTTA = 1e-25
+
+ +
+
+const double DECI_TO_ZETTA = 1e-22
+
+ +
+
+const double DECI_TO_EXA = 1e-19
+
+ +
+
+const double DECI_TO_PETA = 1e-16
+
+ +
+
+const double DECI_TO_TERA = 1e-13
+
+ +
+
+const double DECI_TO_GIGA = 1e-10
+
+ +
+
+const double DECI_TO_MEGA = 1e-07
+
+ +
+
+const double DECI_TO_KILO = 1e-04
+
+ +
+
+const double DECI_TO_HECTO = 1e-03
+
+ +
+
+const double DECI_TO_DECA = 1e-02
+
+ +
+
+const double DECI_TO_CENTI = 1e+01
+
+ +
+
+const double DECI_TO_MILLI = 1e+02
+
+ +
+
+const double DECI_TO_MICRO = 1e+05
+
+ +
+
+const double DECI_TO_NANO = 1e+08
+
+ +
+
+const double DECI_TO_PICO = 1e+11
+
+ +
+
+const double DECI_TO_FEMTO = 1e+14
+
+ +
+
+const double DECI_TO_ATTO = 1e+17
+
+ +
+
+const double DECI_TO_ZEPTO = 1e+20
+
+ +
+
+const double DECI_TO_YOCTO = 1e+23
+
+ +
+
+const double CENTI_TO_ONE = 1e-02
+
+ +
+
+const double CENTI_TO_YOTTA = 1e-26
+
+ +
+
+const double CENTI_TO_ZETTA = 1e-23
+
+ +
+
+const double CENTI_TO_EXA = 1e-20
+
+ +
+
+const double CENTI_TO_PETA = 1e-17
+
+ +
+
+const double CENTI_TO_TERA = 1e-14
+
+ +
+
+const double CENTI_TO_GIGA = 1e-11
+
+ +
+
+const double CENTI_TO_MEGA = 1e-08
+
+ +
+
+const double CENTI_TO_KILO = 1e-05
+
+ +
+
+const double CENTI_TO_HECTO = 1e-04
+
+ +
+
+const double CENTI_TO_DECA = 1e-03
+
+ +
+
+const double CENTI_TO_DECI = 1e-01
+
+ +
+
+const double CENTI_TO_MILLI = 1e+01
+
+ +
+
+const double CENTI_TO_MICRO = 1e+04
+
+ +
+
+const double CENTI_TO_NANO = 1e+07
+
+ +
+
+const double CENTI_TO_PICO = 1e+10
+
+ +
+
+const double CENTI_TO_FEMTO = 1e+13
+
+ +
+
+const double CENTI_TO_ATTO = 1e+16
+
+ +
+
+const double CENTI_TO_ZEPTO = 1e+19
+
+ +
+
+const double CENTI_TO_YOCTO = 1e+22
+
+ +
+
+const double MILLI_TO_ONE = 1e-03
+
+ +
+
+const double MILLI_TO_YOTTA = 1e-27
+
+ +
+
+const double MILLI_TO_ZETTA = 1e-24
+
+ +
+
+const double MILLI_TO_EXA = 1e-21
+
+ +
+
+const double MILLI_TO_PETA = 1e-18
+
+ +
+
+const double MILLI_TO_TERA = 1e-15
+
+ +
+
+const double MILLI_TO_GIGA = 1e-12
+
+ +
+
+const double MILLI_TO_MEGA = 1e-09
+
+ +
+
+const double MILLI_TO_KILO = 1e-06
+
+ +
+
+const double MILLI_TO_HECTO = 1e-05
+
+ +
+
+const double MILLI_TO_DECA = 1e-04
+
+ +
+
+const double MILLI_TO_DECI = 1e-02
+
+ +
+
+const double MILLI_TO_CENTI = 1e-01
+
+ +
+
+const double MILLI_TO_MICRO = 1e+03
+
+ +
+
+const double MILLI_TO_NANO = 1e+06
+
+ +
+
+const double MILLI_TO_PICO = 1e+09
+
+ +
+
+const double MILLI_TO_FEMTO = 1e+12
+
+ +
+
+const double MILLI_TO_ATTO = 1e+15
+
+ +
+
+const double MILLI_TO_ZEPTO = 1e+18
+
+ +
+
+const double MILLI_TO_YOCTO = 1e+21
+
+ +
+
+const double MICRO_TO_ONE = 1e-06
+
+ +
+
+const double MICRO_TO_YOTTA = 1e-30
+
+ +
+
+const double MICRO_TO_ZETTA = 1e-27
+
+ +
+
+const double MICRO_TO_EXA = 1e-24
+
+ +
+
+const double MICRO_TO_PETA = 1e-21
+
+ +
+
+const double MICRO_TO_TERA = 1e-18
+
+ +
+
+const double MICRO_TO_GIGA = 1e-15
+
+ +
+
+const double MICRO_TO_MEGA = 1e-12
+
+ +
+
+const double MICRO_TO_KILO = 1e-09
+
+ +
+
+const double MICRO_TO_HECTO = 1e-08
+
+ +
+
+const double MICRO_TO_DECA = 1e-07
+
+ +
+
+const double MICRO_TO_DECI = 1e-05
+
+ +
+
+const double MICRO_TO_CENTI = 1e-04
+
+ +
+
+const double MICRO_TO_MILLI = 1e-03
+
+ +
+
+const double MICRO_TO_NANO = 1e+03
+
+ +
+
+const double MICRO_TO_PICO = 1e+06
+
+ +
+
+const double MICRO_TO_FEMTO = 1e+09
+
+ +
+
+const double MICRO_TO_ATTO = 1e+12
+
+ +
+
+const double MICRO_TO_ZEPTO = 1e+15
+
+ +
+
+const double MICRO_TO_YOCTO = 1e+18
+
+ +
+
+const double NANO_TO_ONE = 1e-09
+
+ +
+
+const double NANO_TO_YOTTA = 1e-33
+
+ +
+
+const double NANO_TO_ZETTA = 1e-30
+
+ +
+
+const double NANO_TO_EXA = 1e-27
+
+ +
+
+const double NANO_TO_PETA = 1e-24
+
+ +
+
+const double NANO_TO_TERA = 1e-21
+
+ +
+
+const double NANO_TO_GIGA = 1e-18
+
+ +
+
+const double NANO_TO_MEGA = 1e-15
+
+ +
+
+const double NANO_TO_KILO = 1e-12
+
+ +
+
+const double NANO_TO_HECTO = 1e-11
+
+ +
+
+const double NANO_TO_DECA = 1e-10
+
+ +
+
+const double NANO_TO_DECI = 1e-08
+
+ +
+
+const double NANO_TO_CENTI = 1e-07
+
+ +
+
+const double NANO_TO_MILLI = 1e-06
+
+ +
+
+const double NANO_TO_MICRO = 1e-03
+
+ +
+
+const double NANO_TO_PICO = 1e+03
+
+ +
+
+const double NANO_TO_FEMTO = 1e+06
+
+ +
+
+const double NANO_TO_ATTO = 1e+09
+
+ +
+
+const double NANO_TO_ZEPTO = 1e+12
+
+ +
+
+const double NANO_TO_YOCTO = 1e+15
+
+ +
+
+const double PICO_TO_ONE = 1e-12
+
+ +
+
+const double PICO_TO_YOTTA = 1e-36
+
+ +
+
+const double PICO_TO_ZETTA = 1e-33
+
+ +
+
+const double PICO_TO_EXA = 1e-30
+
+ +
+
+const double PICO_TO_PETA = 1e-27
+
+ +
+
+const double PICO_TO_TERA = 1e-24
+
+ +
+
+const double PICO_TO_GIGA = 1e-21
+
+ +
+
+const double PICO_TO_MEGA = 1e-18
+
+ +
+
+const double PICO_TO_KILO = 1e-15
+
+ +
+
+const double PICO_TO_HECTO = 1e-14
+
+ +
+
+const double PICO_TO_DECA = 1e-13
+
+ +
+
+const double PICO_TO_DECI = 1e-11
+
+ +
+
+const double PICO_TO_CENTI = 1e-10
+
+ +
+
+const double PICO_TO_MILLI = 1e-09
+
+ +
+
+const double PICO_TO_MICRO = 1e-06
+
+ +
+
+const double PICO_TO_NANO = 1e-03
+
+ +
+
+const double PICO_TO_FEMTO = 1e+03
+
+ +
+
+const double PICO_TO_ATTO = 1e+06
+
+ +
+
+const double PICO_TO_ZEPTO = 1e+09
+
+ +
+
+const double PICO_TO_YOCTO = 1e+12
+
+ +
+
+const double FEMTO_TO_ONE = 1e-15
+
+ +
+
+const double FEMTO_TO_YOTTA = 1e-39
+
+ +
+
+const double FEMTO_TO_ZETTA = 1e-36
+
+ +
+
+const double FEMTO_TO_EXA = 1e-33
+
+ +
+
+const double FEMTO_TO_PETA = 1e-30
+
+ +
+
+const double FEMTO_TO_TERA = 1e-27
+
+ +
+
+const double FEMTO_TO_GIGA = 1e-24
+
+ +
+
+const double FEMTO_TO_MEGA = 1e-21
+
+ +
+
+const double FEMTO_TO_KILO = 1e-18
+
+ +
+
+const double FEMTO_TO_HECTO = 1e-17
+
+ +
+
+const double FEMTO_TO_DECA = 1e-16
+
+ +
+
+const double FEMTO_TO_DECI = 1e-14
+
+ +
+
+const double FEMTO_TO_CENTI = 1e-13
+
+ +
+
+const double FEMTO_TO_MILLI = 1e-12
+
+ +
+
+const double FEMTO_TO_MICRO = 1e-09
+
+ +
+
+const double FEMTO_TO_NANO = 1e-06
+
+ +
+
+const double FEMTO_TO_PICO = 1e-03
+
+ +
+
+const double FEMTO_TO_ATTO = 1e+03
+
+ +
+
+const double FEMTO_TO_ZEPTO = 1e+06
+
+ +
+
+const double FEMTO_TO_YOCTO = 1e+09
+
+ +
+
+const double ATTO_TO_ONE = 1e-18
+
+ +
+
+const double ATTO_TO_YOTTA = 1e-42
+
+ +
+
+const double ATTO_TO_ZETTA = 1e-39
+
+ +
+
+const double ATTO_TO_EXA = 1e-36
+
+ +
+
+const double ATTO_TO_PETA = 1e-33
+
+ +
+
+const double ATTO_TO_TERA = 1e-30
+
+ +
+
+const double ATTO_TO_GIGA = 1e-27
+
+ +
+
+const double ATTO_TO_MEGA = 1e-24
+
+ +
+
+const double ATTO_TO_KILO = 1e-21
+
+ +
+
+const double ATTO_TO_HECTO = 1e-20
+
+ +
+
+const double ATTO_TO_DECA = 1e-19
+
+ +
+
+const double ATTO_TO_DECI = 1e-17
+
+ +
+
+const double ATTO_TO_CENTI = 1e-16
+
+ +
+
+const double ATTO_TO_MILLI = 1e-15
+
+ +
+
+const double ATTO_TO_MICRO = 1e-12
+
+ +
+
+const double ATTO_TO_NANO = 1e-09
+
+ +
+
+const double ATTO_TO_PICO = 1e-06
+
+ +
+
+const double ATTO_TO_FEMTO = 1e-03
+
+ +
+
+const double ATTO_TO_ZEPTO = 1e+03
+
+ +
+
+const double ATTO_TO_YOCTO = 1e+06
+
+ +
+
+const double ZEPTO_TO_ONE = 1e-21
+
+ +
+
+const double ZEPTO_TO_YOTTA = 1e-45
+
+ +
+
+const double ZEPTO_TO_ZETTA = 1e-42
+
+ +
+
+const double ZEPTO_TO_EXA = 1e-39
+
+ +
+
+const double ZEPTO_TO_PETA = 1e-36
+
+ +
+
+const double ZEPTO_TO_TERA = 1e-33
+
+ +
+
+const double ZEPTO_TO_GIGA = 1e-30
+
+ +
+
+const double ZEPTO_TO_MEGA = 1e-27
+
+ +
+
+const double ZEPTO_TO_KILO = 1e-24
+
+ +
+
+const double ZEPTO_TO_HECTO = 1e-23
+
+ +
+
+const double ZEPTO_TO_DECA = 1e-22
+
+ +
+
+const double ZEPTO_TO_DECI = 1e-20
+
+ +
+
+const double ZEPTO_TO_CENTI = 1e-19
+
+ +
+
+const double ZEPTO_TO_MILLI = 1e-18
+
+ +
+
+const double ZEPTO_TO_MICRO = 1e-15
+
+ +
+
+const double ZEPTO_TO_NANO = 1e-12
+
+ +
+
+const double ZEPTO_TO_PICO = 1e-09
+
+ +
+
+const double ZEPTO_TO_FEMTO = 1e-06
+
+ +
+
+const double ZEPTO_TO_ATTO = 1e-03
+
+ +
+
+const double ZEPTO_TO_YOCTO = 1e+03
+
+ +
+
+const double YOCTO_TO_ONE = 1e-24
+
+ +
+
+const double YOCTO_TO_YOTTA = 1e-48
+
+ +
+
+const double YOCTO_TO_ZETTA = 1e-45
+
+ +
+
+const double YOCTO_TO_EXA = 1e-42
+
+ +
+
+const double YOCTO_TO_PETA = 1e-39
+
+ +
+
+const double YOCTO_TO_TERA = 1e-36
+
+ +
+
+const double YOCTO_TO_GIGA = 1e-33
+
+ +
+
+const double YOCTO_TO_MEGA = 1e-30
+
+ +
+
+const double YOCTO_TO_KILO = 1e-27
+
+ +
+
+const double YOCTO_TO_HECTO = 1e-26
+
+ +
+
+const double YOCTO_TO_DECA = 1e-25
+
+ +
+
+const double YOCTO_TO_DECI = 1e-23
+
+ +
+
+const double YOCTO_TO_CENTI = 1e-22
+
+ +
+
+const double YOCTO_TO_MILLI = 1e-21
+
+ +
+
+const double YOCTO_TO_MICRO = 1e-18
+
+ +
+
+const double YOCTO_TO_NANO = 1e-15
+
+ +
+
+const double YOCTO_TO_PICO = 1e-12
+
+ +
+
+const double YOCTO_TO_FEMTO = 1e-09
+
+ +
+
+const double YOCTO_TO_ATTO = 1e-06
+
+ +
+
+const double YOCTO_TO_ZEPTO = 1e-03
+
+ +
+
+

Variables

+
+
+const double ONE_TO_PERCENT = 1e+02
+
+ +
+
+const double PERCENT_TO_ONE = 1e-02
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___d_a_c-_hardware_8ipf.html b/file/_m_i_e_s___d_a_c-_hardware_8ipf.html new file mode 100644 index 0000000000..319f66b63a --- /dev/null +++ b/file/_m_i_e_s___d_a_c-_hardware_8ipf.html @@ -0,0 +1,1464 @@ + + + + + + + + File MIES_DAC-Hardware.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_DAC-Hardware.ipf

+

HW Low level hardware configuration and querying functions

+

Naming scheme of the functions is HW_$TYPE_$Suffix where $TYPE is one of ITC or NI.

+
+

Error codes for the ITC XOP2

+

Generic check for NIDAQmx XOP

+

In case newer functions are required which might not be present in all NIDAQmx XOP versions, check for their existance directly

+

+
+
+static const double OLD_IGOR = 10001
+
+ +
+
+static const double UNHANDLED_CPP_EXCEPTION = 10002
+
+ +
+
+static const double SLOT_LOCKED_TO_OTHER_THREAD = 10003
+
+ +
+
+static const double SLOT_EMPTY = 10004
+
+ +
+
+static const double COULDNT_FIND_EMPTY_SLOT = 10005
+
+ +
+
+static const double ITC_DLL_ERROR = 10006
+
+ +
+
+static const double INVALID_DEVICETYPE_NUMERIC = 10007
+
+ +
+
+static const double INVALID_DEVICETYPE_STRING = 10008
+
+ +
+
+static const double DTN_DTS_DISAGREE = 10009
+
+ +
+
+static const double INVALID_CHANNELTYPE_NUMERIC = 10010
+
+ +
+
+static const double INVALID_CHANNELTYPE_STRING = 10011
+
+ +
+
+static const double CHN_CHS_DISAGREE = 10012
+
+ +
+
+static const double MUST_SPECIFY_CHN_OR_CHS = 10013
+
+ +
+
+static const double ITCCONFIGCHANNEL2_BAD_S = 10014
+
+ +
+
+static const double ITCCONFIGCHANNEL2_BAD_M = 10015
+
+ +
+
+static const double ITCCONFIGCHANNEL2_BAD_A = 10016
+
+ +
+
+static const double ITCCONFIGCHANNEL2_BAD_O = 10017
+
+ +
+
+static const double ITCCONFIGCHANNEL2_BAD_U = 10018
+
+ +
+
+static const double NEED_MIN_ROWS = 10019
+
+ +
+
+static const double F_FLAG_REQ_ITC18_18USB_1600 = 10020
+
+ +
+
+static const double D_FLAG_REQUIRES_ITC1600 = 10021
+
+ +
+
+static const double H_FLAG_REQUIRES_ITC1600 = 10022
+
+ +
+
+static const double R_FLAG_REQUIRES_ITC1600 = 10023
+
+ +
+
+static const double THREAD_DEVICE_ID_NOT_SET = 10024
+
+ +
+
+

Wrapper functions redirecting to the correct internal implementations depending on #HARDWARE_DAC_TYPES

+
+
+variable HW_PrepareAcq(variable hardwareType, variable deviceID, variable mode, WaveOrNull data = defaultValue, HW_WAVE_GETTER_PROTOTYPE dataFunc = defaultValue, WaveOrNull config = defaultValue, HW_WAVE_GETTER_PROTOTYPE configFunc = defaultValue, variable flags = defaultValue, variable offset = defaultValue)
+

Prepare for data acquisition.

+
+
Parameters:
+
+
+
+
+ +
+
+variable HW_SelectDevice(variable hardwareType, variable deviceID, variable flags = defaultValue)
+

Select a device.

+

Only used in special cases for ITC hardware as all ITC operations use the /DEV flag nowadays.

+
+
Parameters:
+
+
+
Returns:
+

0 if sucessfull, 1 on error

+
+
+
+ +
+
+variable HW_OpenDevice(string deviceToOpen, variable *hardwareType, variable *flags = defaultValue)
+

Open a device.

+
+
Parameters:
+
+
+
Returns:
+

device identifier

+
+
+
+ +
+
+variable HW_CloseDevice(variable hardwareType, variable deviceID, variable flags = defaultValue)
+

Close a device.

+
+
Parameters:
+
+
+
+
+ +
+
+variable HW_WriteDAC(variable hardwareType, variable deviceID, variable channel, variable value, variable flags = defaultValue)
+

Write a value to a DA/AO channel.

+
+
Parameters:
+
    +

  • hardwareType – One of HardwareDACTypeConstants

    • +

  • deviceID – device identifier

    • +

  • channel – hardware channel number

    • +

  • value – value to write in volts

    • +

  • flags – [optional, default none] One or multiple flags from HardwareInteractionFlags

    • +
+
+
+
+ +
+
+variable HW_ReadADC(variable hardwareType, variable deviceID, variable channel, variable flags = defaultValue)
+

Read a value from an AD/AI channel.

+
+
Parameters:
+
+
+
Returns:
+

value in volts

+
+
+
+ +
+
+variable HW_ReadDigital(variable hardwareType, variable deviceID, variable channel, variable line = defaultValue, variable flags = defaultValue)
+

Read from a digital channel.

+
+
Parameters:
+
    +

  • hardwareType – One of HardwareDACTypeConstants

    • +

  • deviceID – device identifier

    • +

  • channel – The hardware documentation terms this as port(NI). For the ITC we call that ttlBit. Takes care of special rack handling for the ITC 1600. Range depends on hardware and hardware type.

    • +

  • line – bit of TTL line, (only for hardware types which support single TTL writes/read)

    • +

  • flags – [optional, default none] One or multiple flags from HardwareInteractionFlags

    • +
+
+
Returns:
+

bitmask denoting the state of the channel/line

+
+
+
+ +
+
+variable HW_WriteDigital(variable hardwareType, variable deviceID, variable channel, variable value, variable line = defaultValue, variable flags = defaultValue)
+

Write to a digital channel.

+
+
Parameters:
+
    +

  • hardwareType – One of HardwareDACTypeConstants

    • +

  • deviceID – device identifier

    • +

  • channel – The hardware documentation terms this as port(NI). For the ITC we call that ttlBit. Takes care of special rack handling for the ITC 1600. Range depends on hardware and hardware type.

    • +

  • value – bitmask to write

    • +

  • line – bit of TTL line, (only for hardware types which support single TTL writes/read)

    • +

  • flags – [optional, default none] One or multiple flags from HardwareInteractionFlags

    • +
+
+
+
+ +
+
+variable HW_EnableYoking(variable hardwareType, variable deviceID, variable flags = defaultValue)
+

Enable yoking.

+
+
Parameters:
+
+
+
+
+ +
+
+variable HW_DisableYoking(variable hardwareType, variable deviceID, variable flags = defaultValue)
+

Enable yoking.

+
+
Parameters:
+
+
+
+
+ +
+
+variable HW_StopAcq(variable hardwareType, variable deviceID, variable prepareForDAQ = defaultValue, variable zeroDAC = defaultValue, variable flags = defaultValue)
+

Stop data acquisition.

+
+
Parameters:
+
    +

  • hardwareType – One of HardwareDACTypeConstants

    • +

  • deviceID – device identifier

    • +

  • prepareForDAQ – immediately prepare for the next data acquisition after stopping it

    • +

  • zeroDAC – set all used DA channels to zero

    • +

  • flags – [optional, default none] One or multiple flags from HardwareInteractionFlags

    • +
+
+
+
+ +
+
+variable HW_IsRunning(variable hardwareType, variable deviceID, variable flags = defaultValue)
+

Determine if data acquisition is currently active.

+
+
Parameters:
+
+
+
Returns:
+

one if running, zero otherwise

+
+
+
+ +
+
+wave HW_GetDeviceInfo(variable hardwareType, variable deviceID, variable flags = defaultValue)
+

Return hardware specific information from the device.

+
+
Parameters:
+
+
+
Returns:
+

free numeric/text wave with information and dimension labels

+
+
+
+ +
+
+wave HW_GetDeviceInfoUnregistered(variable hardwareType, string device, variable flags = defaultValue)
+

Return hardware specific information from the device.

+

This function does not require the device to be registered compared to HW_GetDeviceInfo().

+
+
Parameters:
+
+
+
+
+ +
+
+variable HW_WriteDeviceInfo(variable hardwareType, string device, wave deviceInfo)
+

Fill the device info wave.

+
+ +
+
+variable HW_StartAcq(variable hardwareType, variable deviceID, variable triggerMode = defaultValue, variable flags = defaultValue, variable repeat = defaultValue)
+

Start data acquisition.

+
+
Parameters:
+
+
+
+
+ +
+
+variable HW_ResetDevice(variable hardwareType, variable deviceID, variable flags = defaultValue)
+

Reset the device.

+
+
Parameters:
+
+
+
+
+ +
+
+variable HW_AssertOnInvalid(variable hardwareType, variable deviceID)
+

Assert on using an invalid value of hardwareType or deviceID

+
+
Parameters:
+
+
+
+
+ +
+
+static variable HW_IsValidHardwareType(variable hardwareType)
+

Check if the given hardware type is valid.

+

Invalid here means that the value is out-of-range.

+
+ +
+
+static variable HW_IsValidDeviceID(variable deviceID)
+

Check if the given device ID is valid.

+

Invalid here means that the value is out-of-range.

+
+ +
+
+variable HW_RegisterDevice(string mainDevice, variable hardwareType, variable deviceID, string pressureDevice = defaultValue)
+

Register an opened device in our device map.

+
+
Parameters:
+
    +

  • mainDevice – Name of the DA_EPhys device

    • +

  • hardwareType – One of HardwareDACTypeConstants

    • +

  • deviceID – device identifier

    • +

  • pressureDevice – required for registering pressure control devices

    • +
+
+
+
+ +
+
+variable HW_DeRegisterDevice(variable hardwareType, variable deviceID, variable flags = defaultValue)
+

Deregister an opened device in our device map.

+
+
Parameters:
+
+
+
+
+ +
+
+string HW_GetMainDeviceName(variable hardwareType, variable deviceID, variable flags = defaultValue)
+

Return the name of the main device given the deviceID and the hardwareType

+

Use this function if you want to derive a storage location from the device name.

+
+
Parameters:
+
+
+
+
+ +
+
+string HW_GetDeviceName(variable hardwareType, variable deviceID, variable flags = defaultValue)
+

Return the name of the device given the deviceID and the hardwareType

+

Prefers the pressure device name if set.

+
+
Parameters:
+
+
+
+
+ +
+
+variable HW_GetEffectiveADCWaveLength(string device, variable dataAcqOrTP)
+

Generic function to retrieve the wave length of ADC channel(s). For ITC this is defined through stopCollectionPoint, for other devices like NI the acquisition wave had the correct size and the value can be retrieved directly from that wave.

+

+

See also

+

DataAcqModes

+
+

+
+
Parameters:
+
    +

  • device – device name

    • +

  • dataAcqOrTP – data acquisition or tp mode

    • +
+
+
Returns:
+

effective size of ADC channel wave (for ITC the actual size is bigger)

+
+
+
+ +
+
+variable HW_GetEffectiveDACWaveLength(string device, variable dataAcqOrTP)
+
+ +
+
+variable HW_GetDAFifoPosition(string device, variable dataAcqOrTP)
+
+ +
+
+std::tuple<variable, variable> HW_GetVoltageRange(variable hardwareType, variable channelType, variable isAssociated)
+

Return the minimum/maximum voltage ranges for the given hardware and channel type.

+
+
Parameters:
+
+
+
+
+ +
+
+

ITC

+
+
+string HW_ITC_BuildDeviceString(string deviceType, string deviceNumber)
+

Build the device string for ITC devices.

+

There is no corresponding function for other hardware types like NI devices because those do not have a two part device name

+
+ +
+
+string HW_ITC_ListOfOpenDevices()
+
+ +
+
+string HW_ITC_ListDevices()
+
+ +
+
+variable HW_ITC_HandleReturnValues(variable flags, variable ITCError, variable ITCXOPError)
+
+ +
+
+static string HW_ITC_GetXOPErrorMessage(variable errCode)
+
+ +
+
+variable HW_ITC_OpenDevice(variable deviceType, variable deviceNumber, variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_CloseAllDevices(variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_CloseDevice(variable deviceID, variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_SelectDevice(variable deviceID, variable flags = defaultValue)
+
+ +
+
+wave HW_ITC_GetDeviceInfo(variable deviceID, variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_EnableYoking(variable deviceID, variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_DisableYoking(variable deviceID, variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_StopAcq_TS(variable deviceID, variable prepareForDAQ = defaultValue, variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_StopAcq(variable deviceID, WaveOrNull config = defaultValue, HW_WAVE_GETTER_PROTOTYPE configFunc = defaultValue, variable prepareForDAQ = defaultValue, variable zeroDAC = defaultValue, variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_GetCurrentDevice(variable flags = defaultValue)
+
+ +
+
+static wave HW_ITC_GetFifoPosFromConfig(wave config_t)
+
+ +
+
+variable HW_ITC_ResetFifo_TS(variable deviceID, wave config, variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_ResetFifo(variable deviceID, WaveOrNull config = defaultValue, HW_WAVE_GETTER_PROTOTYPE configFunc = defaultValue, variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_StartAcq_TS(variable deviceID, variable triggerMode, variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_StartAcq(variable deviceID, variable triggerMode, variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_IsRunning(variable deviceID, variable flags = defaultValue)
+
+ +
+
+wave HW_ITC_GetState(variable deviceID, variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_ReadADC(variable deviceID, variable channel, variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_WriteDAC(variable deviceID, variable channel, variable value, variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_ReadDigital(variable deviceID, variable xopChannel, variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_WriteDigital(variable deviceID, variable xopChannel, variable value, variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_DebugMode_TS(variable state, variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_DebugMode(variable state, variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_PrepareAcq(variable deviceID, variable mode, WaveOrNull data = defaultValue, HW_WAVE_GETTER_PROTOTYPE dataFunc = defaultValue, WaveOrNull config = defaultValue, HW_WAVE_GETTER_PROTOTYPE configFunc = defaultValue, variable flags = defaultValue, variable offset = defaultValue)
+
+ +
+
+variable HW_ITC_MoreData_TS(variable deviceID, variable ADChannelToMonitor, variable stopCollectionPoint, wave config, variable *fifoPos = defaultValue, variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_MoreData(variable deviceID, variable ADChannelToMonitor = defaultValue, variable stopCollectionPoint = defaultValue, WaveOrNull config = defaultValue, HW_WAVE_GETTER_PROTOTYPE configFunc = defaultValue, variable *fifoPos = defaultValue, variable flags = defaultValue)
+
+ +
+
+wave HW_ITC_GetVersionInfo(variable flags = defaultValue)
+
+ +
+
+variable HW_ITC_SetLoggingTemplate(string template, variable flags = defaultValue)
+
+ +
+
+wave HW_WAVE_GETTER_PROTOTYPE(string str)
+
+ +
+
+wave HW_ITC_Transpose(wave wv)
+
+ +
+
+wave HW_ITC_TransposeAndToInt(wave wv)
+
+ +
+
+

Utility functions not interacting with hardware

+
+
+variable HW_ITC_CalculateDevChannelOff(string device)
+

Returns the device channel offset for the given device.

+
+
Returns:
+

16 for ITC1600 and 0 for all other types

+
+
+
+ +
+
+variable HW_ITC_GetRackRange(variable rack, variable *first, variable *last)
+

Return the first and last TTL bits/channels for the given rack

+
+ +
+
+variable HW_ITC_ClipTTLBit(string device, variable ttlBit)
+

Clip the ttlBit to adapt for differences in notation.

+

The DA_Ephys panel e.g. labels the first ttlBit of RACK_ONE as 4, but the ITC XOP treats that as 0.

+
+ +
+
+variable HW_ITC_GetRackForTTLBit(string device, variable ttlBit)
+

Return the rack number for the given ttlBit (the ttlBit is called TTL channel in the DA Ephys panel)

+
+ +
+
+variable HW_ITC_GetITCXOPChannelForRack(string device, variable rack)
+

Return the ITC XOP channel for the given rack.

+

Only the ITC1600 has two racks. The channel numbers differ for the different ITC device types.

+
+ +
+
+variable HW_ITC_GetNumberOfRacks(string device)
+

Get the number of racks for the given device.

+

    +

  • ITC1600 can have 1 or 2 racks

    • +

  • other device types have 1

    • +
+

+
+ +
+
+variable HW_ITC_AssertOnInvalid(string deviceName)
+

Assert on using an invalid ITC device name.

+
+
Parameters:
+

deviceName – ITC device name

+
+
+
+ +
+
+variable HW_ITC_IsValidDeviceName(string deviceName)
+

Check wether the given ITC device name is valid.

+

Currently a device name is valid if it is not empty.

+
+ +
+
+

NI

+
+
+variable HW_NI_AssertOnInvalid(string deviceName)
+

Assert on using an invalid NI device name.

+
+
Parameters:
+

deviceName – NI device name

+
+
+
+ +
+
+variable HW_NI_IsValidDeviceName(string deviceName)
+

Check wether the given NI device name is valid.

+

Currently a device name is valid if it is not empty.

+
+ +
+
+string HW_NI_AnalogInputToString(variable config)
+

Return the analog input configuration bits as string.

+
+
Parameters:
+

config – Bit combination of NIAnalogInputConfigs

+
+
+
+ +
+
+variable HW_NI_StartAcq(variable deviceID, variable triggerMode, variable flags = defaultValue, variable repeat = defaultValue)
+
+ +
+
+variable HW_NI_PrepareAcq(variable deviceID, variable mode, WaveOrNull data = defaultValue, HW_WAVE_GETTER_PROTOTYPE dataFunc = defaultValue, WaveOrNull config = defaultValue, HW_WAVE_GETTER_PROTOTYPE configFunc = defaultValue, variable flags = defaultValue, variable offset = defaultValue)
+
+ +
+
+string HW_NI_GetPropertyListOfDevices(string device)
+
+ +
+
+variable HW_NI_PrintPropertiesOfDevices()
+
+ +
+
+variable HW_NI_ReadDigital(string device, variable DIOPort = defaultValue, variable DIOLine = defaultValue, variable flags = defaultValue)
+
+ +
+
+variable HW_NI_WriteDigital(string device, variable value, variable DIOPort = defaultValue, variable DIOLine = defaultValue, variable flags = defaultValue)
+
+ +
+
+variable HW_NI_WriteAnalogSingleAndSlow(string device, variable channel, variable value, variable flags = defaultValue)
+
+ +
+
+variable HW_NI_ReadAnalogSingleAndSlow(string device, variable channel, variable flags = defaultValue)
+
+ +
+
+variable HW_NI_GetAnalogInputConfig(string device, variable channel, variable flags = defaultValue)
+
+ +
+
+string HW_NI_ListDevices(variable flags = defaultValue)
+
+ +
+
+variable HW_NI_StopAcq(variable deviceID, variable zeroDAC = defaultValue, variable flags = defaultValue)
+
+ +
+
+variable HW_NI_StopDAC(variable deviceID, variable flags = defaultValue)
+
+ +
+
+variable HW_NI_StopADC(variable deviceID, variable flags = defaultValue)
+
+ +
+
+variable HW_NI_StopTTL(variable deviceID, variable flags = defaultValue)
+
+ +
+
+variable HW_NI_ZeroDAC(variable deviceID, variable flags = defaultValue)
+
+ +
+
+static variable HW_NI_ResetDevice(string device, variable flags = defaultValue)
+
+ +
+
+static variable HW_NI_CalibrateDevice(string device, variable force = defaultValue, variable flags = defaultValue)
+
+ +
+
+variable HW_NI_IsRunning(string device, variable flags = defaultValue)
+
+ +
+
+variable HW_NI_OpenDevice(string device, variable flags = defaultValue)
+
+ +
+
+variable HW_NI_CloseDevice(variable deviceID, variable flags = defaultValue)
+
+ +
+
+wave HW_NI_GetDeviceInfo(string device, variable flags = defaultValue)
+
+ +
+
+variable HW_NI_ResetTaskIDs(string device)
+
+ +
+
+variable HW_SU_OpenDevice(variable flags = defaultValue)
+
+ +
+
+string HW_SU_ListDevices(variable flags = defaultValue)
+
+ +
+
+variable HW_SU_CloseDevice(variable deviceId, variable flags = defaultValue)
+
+ +
+
+static variable HW_SU_ResetDevice(variable flags = defaultValue)
+
+ +
+
+variable HW_SU_GetDeviceInfo(WaveText deviceInfo)
+
+ +
+
+static variable HW_SU_IsRunning(string device)
+
+ +
+
+variable HW_SU_StopAcq(variable deviceId, variable zeroDAC = defaultValue, variable flags = defaultValue)
+
+ +
+
+variable HW_SU_PrepareAcq(variable deviceId, variable mode, WaveOrNull data = defaultValue, HW_WAVE_GETTER_PROTOTYPE dataFunc = defaultValue, WaveOrNull config = defaultValue, HW_WAVE_GETTER_PROTOTYPE configFunc = defaultValue, variable flags = defaultValue, variable offset = defaultValue)
+
+ +
+
+variable HW_SU_StartAcq(variable deviceId, variable flags = defaultValue)
+
+ +
+
+variable HW_SU_GetADCSamplePosition()
+
+ +
+
+variable HW_SU_ZeroDAC(variable deviceID, variable flags = defaultValue)
+
+ +
+
+variable HW_SU_ReadADC(variable deviceID, variable channel, variable flags = defaultValue)
+
+ +
+
+variable HW_SU_WriteDAC(variable deviceID, variable channel, variable value, variable flags = defaultValue)
+
+ +
+
+

Variables

+
+
+static const double HW_ITC_RUNNING_STATE = 0x10
+
+ +
+
+static const double HW_ITC_MAX_TIMEOUT = 10
+
+ +
+
+static const double HW_ITC_DSP_TIMEOUT = 0x80303001
+
+ +
+
+static const double SUTTER_CHANNELOFFSET_TTL = 3
+
+ +
+
+static const double SUTTER_ACQUISITION_FOREGROUND = 1
+
+ +
+
+static const double SUTTER_ACQUISITION_BACKGROUND = 2
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___d_a_ephys_8ipf.html b/file/_m_i_e_s___d_a_ephys_8ipf.html new file mode 100644 index 0000000000..78a07c6522 --- /dev/null +++ b/file/_m_i_e_s___d_a_ephys_8ipf.html @@ -0,0 +1,1515 @@ + + + + + + + + File MIES_DAEphys.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_DAEphys.ipf

+

DAP Main data acquisition panel routines

+
+

Unnamed Group

+
+
+variable DAP_EphysPanelStartUpSettings()
+

Restores the base state of the DA_Ephys panel. Useful when adding controls to GUI. Facilitates use of auto generation of GUI code. Useful when template experiment file has been overwritten.

+
+ +
+
+

Functions

+
+
+wave DAP_GetRadioButtonCoupling()
+

Creates meta information about coupled CheckBoxes (Radio Button) controls Used for saving/restoring the GUI state.

+
+
Returns:
+

Free text wave with lists of coupled CheckBox controls

+
+
+
+ +
+
+string DAP_GetNIDeviceList()
+

Returns a list of DAC devices for NI devices.

+
+
Returns:
+

list of NI DAC devices, NONE if there are none

+
+
+
+ +
+
+string DAP_GetITCDeviceList()
+

Returns a list of ITC devices for DAC, NONE if there are none.

+
+ +
+
+string DAP_GetSUDeviceList()
+

Returns a list of SU devices for DAC, NONE if there are none.

+
+ +
+
+string DAP_GetDACDeviceList()
+

Returns a list of available ITC and NI devices.

+
+
Returns:
+

list of DAC devices

+
+
+
+ +
+
+static variable DAP_SuggestIssueForAdditionalNIHardware()
+
+ +
+
+variable DAP_WindowHook(WMWinHookStruct *s)
+
+ +
+
+string DAP_FormatStimSetPopupValue(variable channelType, string searchString = defaultValue)
+

Return a popValue string suitable for stimsets.

+

+
+Todo:
+

rework the code to have a fixed popValue

+
+ +

+
+ +
+
+static variable DAP_UpdateDrawElements(string device, variable tab)
+
+ +
+
+variable DAP_TabControlFinalHook(WMTabControlAction *tca)
+

Called by ACL tab control after the tab is updated. see line 257 of ACL_TabUtilities.ipf.

+
+ +
+
+variable DAP_SetVarProc_Channel_Search(WMSetVariableAction *sva)
+
+ +
+
+variable DAP_DAorTTLCheckProc(WMCheckboxAction *cba)
+
+ +
+
+variable DAP_CheckProc_Channel_All(WMCheckboxAction *cba)
+
+ +
+
+variable DAP_IsAllControl(variable channelIndex)
+

Determines if the control refers to an “All” control.

+
+ +
+
+variable DAP_DACHasExpectedClampMode(string device, variable controlChannelIndex, variable channelNumber, variable channelType)
+

Helper for “All” controls in the DA tab.

+
+
Returns:
+

0 if the given channel is a DA channel and not in the expected clamp mode as determined by controlChannelIndex, 1 otherwise

+
+
+
+ +
+
+variable DAP_CheckProc_AD(WMCheckboxAction *cba)
+
+ +
+
+variable GetHeadstageFromSettings(string device, variable channelType, variable channelNumber, variable clampMode)
+

Get the headstage for the given channel number and type from the amplifier settings.

+

This is different from what GetChannelClampMode holds as we here hold the setup information and GetChannelClampMode holds what is currently active.

+
+ +
+
+static variable DAP_AdaptAssocHeadstageState(string device, string checkboxCtrl)
+

Adapt the state of the associated headstage on DA/AD channel change.

+
+ +
+
+static variable DAP_GetRAAcquisitionCycleID(string device)
+

Return the repeated acquisition cycle ID for the given devide.

+
+ +
+
+variable DAP_OneTimeCallBeforeDAQ(string device, variable runMode)
+

One time initialization before data acquisition.

+
+
Parameters:
+
    +

  • device – device

    • +

  • runMode – One of DAQRunModes except DAQ_NOT_RUNNING

    • +
+
+
+
+ +
+
+static variable DAP_ResetClampModeTitle(string device, string ctrl)
+
+ +
+
+static variable DAP_ResetGUIAfterDAQ(string device)
+

Enable all controls which were disabled before DAQ by DAP_OneTimeCallBeforeDAQ.

+
+ +
+
+variable DAP_OneTimeCallAfterDAQ(string device, variable stopReason, variable forcedStop = defaultValue, variable startTPAfterDAQ = defaultValue)
+

One time cleaning up after data acquisition.

+
+
Parameters:
+
    +

  • device – device

    • +

  • stopReason – One of DAQStoppingFlags

    • +

  • forcedStop – [optional, defaults to false] if DAQ was aborted (true) or stopped by itself (false)

    • +

  • startTPAfterDAQ – [optional, defaults to true] start “TP after DAQ” if enabled at the end

    • +
+
+
+
+ +
+
+static variable DAP_DocumentStopReason(string device, variable stopReason)
+
+ +
+
+variable DAP_CheckProc_IndexingState(WMCheckboxAction *cba)
+
+ +
+
+variable DAP_CheckProc_ShowScopeWin(WMCheckboxAction *cba)
+
+ +
+
+static variable DAP_TurnOffAllChannels(string device, variable channelType)
+
+ +
+
+variable DAP_ButtonProc_AllChanOff(WMButtonAction *ba)
+
+ +
+
+variable DAP_UpdateITIAcrossSets(string device, variable maxITI)
+

Update the ITI for the given device.

+
+ +
+
+variable DAP_PopMenuChkProc_StimSetList(WMPopupAction *pa)
+

Procedure for DA/TTL popupmenus including indexing wave popupmenus.

+
+ +
+
+variable DAP_SetVarProc_DA_Scale(WMSetVariableAction *sva)
+
+ +
+
+static variable DAP_UpdateSweepLimitsAndDisplay(string device)
+
+ +
+
+variable DAP_GetSampInt(string device, variable dataAcqOrTP, variable channelType, variable *valid = defaultValue)
+

Return the sampling interval in μs with taking the mode, the multiplier and the fixed frequency selection into account.

+

+

See also

+

SI_CalculateMinSampInterval()

+
+

+
+
Parameters:
+
    +

  • device – [in] device

    • +

  • dataAcqOrTP – [in] one of DataAcqModes

    • +

  • channelType – [in] channel type, one of XopChannelConstants

    • +

  • valid – [out] [optional] returns if the choosen sampling interval is valid or not (DAQ only)

    • +
+
+
+
+ +
+
+static variable DAP_IsSampleIntervalValid(string device, variable channelType, variable sampInt)
+
+ +
+
+variable DAP_UpdateSweepSetVariables(string device)
+
+ +
+
+variable DAP_SetVarProc_TotSweepCount(WMSetVariableAction *sva)
+
+ +
+
+variable DAP_ButtonCtrlFindConnectedAmps(WMButtonAction *ba)
+
+ +
+
+string DAP_GetNiceAmplifierChannelList()
+

Return a nicely layouted list of amplifier channels.

+
+ +
+
+string DAP_FormatTelegraphServerList(wave telegraphServers)
+
+ +
+
+static string DAP_GetAmplifierDef(variable ampSerial, variable ampChannel)
+
+ +
+
+variable DAP_ParseAmplifierDef(string amplifierDef, variable *ampSerial, variable *ampChannelID)
+

Parse the entries which DAP_GetAmplifierDef() created.

+
+ +
+
+variable DAP_SyncDeviceAssocSettToGUI(string device, variable headStage)
+
+ +
+
+variable DAP_PopMenuProc_Headstage(WMPopupAction *pa)
+
+ +
+
+variable DAP_PopMenuProc_CAA(WMPopupAction *pa)
+
+ +
+
+variable DAP_SetVarProc_CAA(WMSetVariableAction *sva)
+
+ +
+
+variable DAP_ButtonProc_ClearChanCon(WMButtonAction *ba)
+
+ +
+
+static variable DAP_HasAscendingSweepOrdering(string device)
+

Return true if the sweep ordering is ascending, false otherwise.

+
+ +
+
+static variable DAP_CheckSampleInterval(string device, variable mode)
+
+ +
+
+variable DAP_CheckSettings(string device, variable mode)
+

Check if all settings are valid to send a test pulse or acquire data.

+

For invalid settings an informative message is printed into the history area.

+

Callers must ensure to set the acquisition state back to AS_INACTIVE when calling with DATA_ACQUISITION_MODE.

+
+
Parameters:
+
+
+
Returns:
+

0 for valid settings, 1 for invalid settings

+
+
+
+ +
+
+static variable DAP_CheckAsyncSettings(string device)
+
+ +
+
+static variable DAP_CheckPressureSettings(string device)
+
+ +
+
+static variable DAP_CheckHeadStage(string device, variable headStage, variable mode)
+

Returns zero if everything is okay, 1 if a non-recoverable error was found and 2 on recoverable errors.

+
+ +
+
+static variable DAP_CheckChannel(string device, variable channelType, variable channel)
+
+ +
+
+static variable DAP_CheckAnalysisFunctionAndParameter(string device, string setName)
+
+ +
+
+static variable DAP_CheckStimset(string device, variable channelType, variable channel, variable headstage)
+
+ +
+
+static variable DAP_CheckEpochLengthsOfStimset(string device, string setName)
+
+ +
+
+static variable DAP_SyncChanAmpAssignToActiveHS(string device)
+

Synchronizes the contents of ChanAmpAssign and ChanAmpAssignUnit to all active headstages.

+
+ +
+
+static variable DAP_ApplyClmpModeSavdSettngs(string device, variable headStage, variable clampMode)
+

Reads the channel amp waves and inserts that info into the DA_EPHYS panel.

+
+ +
+
+static variable DAP_RemoveClampModeSettings(string device, variable headStage, variable clampMode)
+
+ +
+
+string DAP_GetClampModeControl(variable mode, variable headstage)
+

Returns the name of the checkbox control (radio button) handling the clamp mode of the given headstage or all headstages.

+
+
Parameters:
+
+
+
+
+ +
+
+variable DAP_GetInfoFromControl(string device, string ctrl, variable *mode, variable *headStage)
+

Return information readout from headstage and clamp mode controls.

+

Users interested in the clamp mode of a known headstage should prefer DAG_GetHeadstageMode() instead.

+
+
Parameters:
+
    +

  • device – [in] panel

    • +

  • ctrl – [in] control can be either Radio_ClampMode_* or Check_DataAcqHS_* referring to an existing control

    • +

  • mode – [out] I_CLAMP_MODE, V_CLAMP_MODE or I_EQUAL_ZERO_MODE, the currently active mode for headstage controls and the clamp mode of the control for clamp mode controls

    • +

  • headStage – [out] number of the headstage or one of AllHeadstageModeConstants

    • +
+
+
+
+ +
+
+variable DAP_CheckProc_ClampMode(WMCheckboxAction *cba)
+
+ +
+
+variable DAP_CheckProc_HedstgeChck(WMCheckboxAction *cba)
+
+ +
+
+variable DAP_ChangeHeadStageMode(string device, variable clampMode, variable headstage, variable options)
+

Change the clamp mode of the given headstage.

+
+
Parameters:
+
+
+
+
+ +
+
+static variable DAP_SetAmpModeControls(string device, variable headstage, variable clampMode, variable delayed = defaultValue)
+

Sets the control state of the radio buttons used for setting the clamp mode on the Data Acquisition Tab of the DA_Ephys panel.

+
+
Parameters:
+
    +

  • device – device

    • +

  • headstage – controls associated with headstage are set

    • +

  • clampMode – clamp mode to activate

    • +

  • delayed – indicate on the control that the change is delayed

    • +
+
+
+
+ +
+
+static variable DAP_SetHeadstageChanControls(string device, variable headstage, variable clampMode, variable delayed = defaultValue)
+

Sets the DA and AD channel settings according to the headstage mode.

+
+
Parameters:
+
    +

  • device – Device (used for data acquisition)

    • +

  • headstage – Channels associated with headstage are set

    • +

  • clampMode – Clamp mode to activate

    • +

  • delayed – [optional, defaults to false] Indicate that this is a delayed clamp mode change

    • +
+
+
+
+ +
+
+static variable DAP_UpdateClampmodeTabs(string device, variable headStage, variable clampMode)
+
+ +
+
+static variable DAP_ChangeHeadstageState(string device, string headStageCtrl, variable enabled)
+
+ +
+
+variable DAP_ToggleAcquisitionButton(string device, variable mode)
+

Set the acquisition button text.

+
+
Parameters:
+
+
+
+
+ +
+
+variable DAP_ToggleTestpulseButton(string device, variable mode)
+

Set the testpulse button text.

+
+
Parameters:
+
+
+
+
+ +
+
+variable DAP_ButtonProc_AutoFillGain(WMButtonAction *ba)
+
+ +
+
+variable DAP_SliderProc_MIESHeadStage(WMSliderAction *sc)
+
+ +
+
+variable DAP_SetVarProc_AmpCntrls(WMSetVariableAction *sva)
+
+ +
+
+variable DAP_ButtonProc_AmpCntrls(WMButtonAction *ba)
+
+ +
+
+variable DAP_CheckProc_AmpCntrls(WMCheckboxAction *cba)
+
+ +
+
+variable DAP_CheckProc_MDEnable(WMCheckboxAction *cba)
+

Check box procedure for multiple device (MD) support.

+
+ +
+
+variable DAP_HandleSingleDeviceDependentControls(string device)
+

Enable controls post DAQ/TP in single device mode.

+
+
Parameters:
+

device – device

+
+
+
+ +
+
+variable DAP_CheckProc_InsertTP(WMCheckBoxAction *cba)
+

Controls TP Insertion into set sweeps before the sweep begins.

+
+ +
+
+variable DAP_UpdateOnsetDelay(string device)
+

Update the onset delay due to the Insert TP setting.

+
+ +
+
+variable DAP_SetVarProc_TestPulseSett(WMSetVariableAction *sva)
+
+ +
+
+variable DAP_CheckProc_TestPulseSett(WMCheckboxAction *cba)
+
+ +
+
+variable DAP_AdaptAutoTPColorAndDependent(string device)
+
+ +
+
+variable DAP_UnlockAllDevices()
+
+ +
+
+variable DAP_CheckProc_RepeatedAcq(WMCheckboxAction *cba)
+
+ +
+
+static variable DAP_ToggleCheckBoxes(string win, string ctrl, string list, variable checked)
+

Allows two checkboxes to be treated as a group where only one can be checked at a time.

+

Write into the GUI state wave as well

+
+ +
+
+variable DAP_CheckProc_SyncCtrl(WMCheckboxAction *cba)
+
+ +
+
+variable DAP_SetVarProc_SyncCtrl(WMSetVariableAction *sva)
+
+ +
+
+variable DAP_ButtonProc_TPDAQ(WMButtonAction *ba)
+
+ +
+
+string DAP_GetCommentPanel(string device)
+

Return the comment panel name.

+
+ +
+
+string DAP_GetCommentNotebook(string device)
+

Return the full window path to the comment notebook.

+
+ +
+
+static variable DAP_OpenCommentPanel(string device)
+

Create the comment panel.

+
+ +
+
+variable DAP_ButtonProc_OpenCommentNB(WMButtonAction *ba)
+
+ +
+
+static string DAP_FormatCommentString(string device, string comment, variable sweepNo)
+
+ +
+
+static variable DAP_AddUserComment(string device)
+

Add the current user comment of the previous sweep to the comment notebook and to the labnotebook.

+

The SetVariable for the user comment is also cleared

+
+ +
+
+variable DAP_LockCommentNotebook(string device)
+

Make the comment notebook read-only.

+
+ +
+
+variable DAP_UnlockCommentNotebook(string device)
+

Make the comment notebook writeable.

+
+ +
+
+variable DAP_ClearCommentNotebook(string device)
+

Clear the comment notebook’s content and the serialized string.

+
+ +
+
+variable DAP_SerializeAllCommentNBs()
+

Serialize all comment notebooks.

+
+ +
+
+variable DAP_SerializeCommentNotebook(string device)
+

Copy the contents of the comment notebook to the user comment string.

+
+ +
+
+variable DAP_CommentPanelHook(WMWinHookStruct *s)
+
+ +
+
+string DAP_CreateDAEphysPanel()
+

Create a new DA_Ephys panel.

+
+
Returns:
+

panel name

+
+
+
+ +
+
+variable DAP_CheckProc_LockedLogic(WMCheckboxAction *cba)
+

Sets the locked indexing logic checkbox states.

+
+ +
+
+variable DAP_ParsePanelControl(string ctrl, variable *channelIndex, variable *channelType, variable *controlType)
+

Extracts channelType, controlType and channelIndex from ctrl

+

Counterpart to GetPanelControl()

+

+UTF_NOINSTRUMENTATION

+
+
Returns:
+

0 if the control name could be parsed, one otherwise

+
+
+
+ +
+
+variable DAP_UpdateListOfPressureDevices()
+

Update the list of available pressure devices on all locked device panels.

+
+ +
+
+variable DAP_DeviceIsUnlocked(string device)
+

Query the device lock status.

+
+
Returns:
+

device lock status, 1 if unlocked, 0 if locked

+
+
+
+ +
+
+variable DAP_AbortIfUnlocked(string device)
+
+ +
+
+variable DAP_CheckProc_UpdateGuiState(WMCheckboxAction *cba)
+

GUI procedure which has the only purpose of storing the control state in the GUI state wave.

+
+ +
+
+variable DAP_SetVar_SetScale(WMSetVariableAction *sva)
+
+ +
+
+variable DAP_SetVar_UpdateGuiState(WMSetVariableAction *sva)
+
+ +
+
+variable DAP_CheckProc_Settings_PUser(WMCheckboxAction *cba)
+
+ +
+
+variable DAP_ButtonProc_LockDev(WMButtonAction *ba)
+
+ +
+
+variable DAP_ButProc_Hrdwr_UnlckDev(WMButtonAction *ba)
+
+ +
+
+static variable DAP_UpdateDataFolderDisplay(string device, variable locked)
+
+ +
+
+variable DAP_LockDevice(string win)
+
+ +
+
+static variable DAP_AdaptPanelForDeviceSpecifics(string device, variable forceEnable = defaultValue)
+
+ +
+
+static string DAP_GetControlsForChannelIndex(variable channelIndex, variable channelType)
+
+ +
+
+static variable DAP_LoadBuiltinStimsets()
+
+ +
+
+static variable DAP_ClearWaveIfExists(WaveOrNull wv)
+
+ +
+
+static variable DAP_UnlockDevice(string device)
+
+ +
+
+static variable DAP_UpdateListOfLockedDevices()
+

Update the list of locked devices.

+
+ +
+
+static variable DAP_UpdateChanAmpAssignStorWv(string device)
+
+ +
+
+static variable DAP_UpdateChanAmpAssignPanel(string device)
+
+ +
+
+variable DAP_UpdateDAQControls(string device, variable updateFlag)
+

Helper function to update all DAQ related controls after something changed.

+
+
Parameters:
+
+
+
+
+ +
+
+static variable DAP_AllChanDASettings(string device, variable headStage, variable delayed = defaultValue)
+

Applies user settings for the clamp mode stimulus sets (DA Set and Indexing End Set) on mode switch.

+
+
Parameters:
+
    +

  • device – device

    • +

  • headStage – MIES headstage number, must be in the range [0, NUM_HEADSTAGES]

    • +

  • delayed – [optional, defaults to false] On a delayed clamp mode change the stimulus set is not set.

    • +
+
+
+
+ +
+
+variable DAP_ButtonProc_skipSweep(WMButtonAction *ba)
+
+ +
+
+variable DAP_ButtonProc_skipBack(WMButtonAction *ba)
+
+ +
+
+variable DAP_GetskipAhead(string device)
+
+ +
+
+variable DAP_ResetskipAhead(string device)
+
+ +
+
+variable DAP_getFilteredSkipAhead(string device, variable skipAhead)
+
+ +
+
+variable DAP_setSkipAheadLimit(string device, variable filteredSkipAhead)
+
+ +
+
+variable DAP_SetVarProc_skipAhead(WMSetVariableAction *sva)
+
+ +
+
+variable DAP_CheckProc_RandomRA(WMCheckboxAction *cba)
+
+ +
+
+variable DAP_CheckSkipAhead(string device)
+
+ +
+
+variable DAP_PopMenuProc_UpdateGuiState(WMPopupAction *pa)
+
+ +
+
+string DAP_GetSamplingMultiplier()
+

Return the list of available sampling multipliers.

+

Has no NONE element as 1 means no multiplier.

+
+ +
+
+variable DAP_PopMenuProc_SampMult(WMPopupAction *pa)
+
+ +
+
+variable DAP_CheckProc_RequireAmplifier(WMCheckboxAction *cba)
+
+ +
+
+string DAP_GetSamplingFrequencies()
+

Return the list of available fixed sampling frequencies.

+
+ +
+
+variable DAP_PopMenuProc_FixedSampInt(WMPopupAction *pa)
+
+ +
+
+string DAP_GetOsciUpdModes()
+

Return the list of available Oscilloscope Update Modes.

+
+ +
+
+variable DAP_PopMenuProc_OsciUpdMode(WMPopupAction *pa)
+
+ +
+
+variable DAP_ApplyDelayedClampModeChange(string device)
+
+ +
+
+variable DAP_ClearDelayedClampModeChange(string device)
+
+ +
+
+variable ButtonProc_Hardware_rescan(WMButtonAction *ba)
+
+ +
+
+variable DAP_CheckProc_PowerSpectrum(WMCheckboxAction *cba)
+
+ +
+
+variable DAP_UpdateDaEphysStimulusSetPopups(string device = defaultValue)
+

Update the popup menus and its USER_DATA_MENU_EXP user data after stim set changes.

+
+
Parameters:
+

device – [optional, defaults to all locked devices] device

+
+
+
+ +
+
+static variable DAP_UpdateStimulusSetPopup(string device, string ctrl, string stimsets)
+
+ +
+
+variable DAP_DeleteStimulusSet(string setName, string device = defaultValue)
+

Delete the stimulus set in the given DAEphys.

+

Internal use only, outside callers should use ST_RemoveStimSet()

+
+ +
+
+variable DAP_TPSettingsToWave(string device, wave TPSettings)
+

Write all TP settings from the data acquisition/settings tab to the settings wave.

+
+ +
+
+static string DAP_TPControlToLabel(string ctrl)
+

Convert the control name to a dimension label for GetTPSettings()

+
+ +
+
+static variable DAP_TPGUISettingToWave(string device, string ctrl, variable val)
+

Write a new TP setting value to the wave.

+
+ +
+
+variable DAP_TPSettingsToGUI(string device, string entry = defaultValue)
+

Synchronize the TP settings from the wave into the GUI.

+

Needs to be done when the selected headstage changes or the TPsettings wave contents. This function ignores “Send To All HS” as this does not make sense to respect here.

+
+
Parameters:
+
    +

  • device – device

    • +

  • entry – [optional, defaults to all] Only update one of the entries TPSettings. Accepted strings are the labels from DAP_TPControlToLabel().

    • +
+
+
+
+ +
+
+

Variables

+
+
+static const double DATA_ACQU_TAB_NUM = 0
+
+ +
+
+static const double HARDWARE_TAB_NUM = 6
+
+ +
+
+static const string COMMENT_PANEL = "UserComments"
+
+ +
+
+static const string COMMENT_PANEL_NOTEBOOK = "NB"
+
+ +
+
+static const string AMPLIFIER_DEF_FORMAT = "AmpNo %d Chan %d"
+
+ +
+
+static const string NI_DAC_PATTERNS = "AI:32;AO:4;COUNTER:4;DIOPORTS:3;LINES:32,8,8|AI:32;AO:4;COUNTER:2;DIOPORTS:3;LINES:32,8,8|AI:16;AO:2;COUNTER:4;DIOPORTS:3;LINES:8,8,8|AI:8;AO:2;COUNTER:4;DIOPORTS:3;LINES:8,8,8"
+
+ +
+
+static const double DAP_WAITFORTPANALYSIS_TIMEOUT = 2
+
+ +
+
+static const string SU_DISABLED_CONTROLS = "Popup_Settings_VC_DA;Popup_Settings_VC_AD;Popup_Settings_IC_DA;Popup_Settings_IC_AD;button_Hardware_ClearChanConn;"
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___d_a_ephys___gui_state_8ipf.html b/file/_m_i_e_s___d_a_ephys___gui_state_8ipf.html new file mode 100644 index 0000000000..6e38b99137 --- /dev/null +++ b/file/_m_i_e_s___d_a_ephys___gui_state_8ipf.html @@ -0,0 +1,509 @@ + + + + + + + + File MIES_DAEphys_GuiState.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_DAEphys_GuiState.ipf

+

DAG Routines dealing with the DA_Ephys GUI state waves

+
+

Functions

+
+
+variable DAG_RecordGuiStateNum(string device, wave GUIState = defaultValue)
+

Records the state of the DA_ephys panel into the numerical GUI state wave.

+
+ +
+
+variable DAG_RecordGuiStateTxT(string device, wave GUIState = defaultValue)
+

Records the state of the DA_ephys panel into the textual GUI state wave.

+
+ +
+
+variable DAG_GetNumericalValue(string device, string ctrl, variable index = defaultValue)
+

Query a control value from the numerical gui state wave.

+

This does return the zero-based index for PopupMenues.

+

Convienience wrapper to make the call sites nicer.

+

+UTF_NOINSTRUMENTATION

+
+
Parameters:
+
    +

  • device – device

    • +

  • ctrl – control name

    • +

  • index – [optional, default to NaN] Some control entries have multiple entries per headstage/channel/etc.

    • +
+
+
+
+ +
+
+string DAG_GetTextualValue(string device, string ctrl, variable index = defaultValue)
+

Query a control value from the textual gui state wave.

+

Convienience wrapper to make the call sites nicer.

+
+
Parameters:
+
    +

  • device – device

    • +

  • ctrl – control name

    • +

  • index – [optional, default to NaN] Some control entries have multiple entries per headstage/channel/etc.

    • +
+
+
+
+ +
+
+wave DAG_GetChannelState(string device, variable type)
+

Return a free wave of the status of the checkboxes specified by channelType, uses GetDA_EphysGuiStateNum() instead of GUI queries.

+
+
Parameters:
+
+
+
+
+ +
+
+wave DAG_GetActiveHeadstages(string device, variable clampMode)
+

Return a wave with NUM_HEADSTAGES rows with 1 where the given headstages is active and in the given clamp mode.

+
+ +
+
+variable DAG_HeadstageIsHighestActive(string device, variable headstage, variable clampMode = defaultValue)
+

Return true/false if the given headstage is the highest active.

+
+
Parameters:
+
    +

  • device – device

    • +

  • headstage – headstage to check

    • +

  • clampMode – [optional, defaults to all clamp modes] Restrict to the given clamp mode

    • +
+
+
+
+ +
+
+wave DAG_GetChannelTextual(string device, variable channelType, variable controlType)
+

Return a free wave of the popup menu strings specified by channelType, uses GetDA_EphysGuiStateTxT() instead of GUI queries.

+
+
Parameters:
+
+
+
+
+ +
+
+variable DAG_GetHeadstageState(string device, variable headStage)
+

Returns the headstage State.

+
+ +
+
+variable DAG_GetHeadstageMode(string device, variable headStage)
+
+
Returns:
+

the mode of the headstage defined in the locked DA_ephys panel, can be V_CLAMP_MODE or I_CLAMP_MODE or NC

+
+
+
+ +
+
+variable DAG_Update(string device, string controlName, variable val = defaultValue, string str = defaultValue)
+

Updates the state of a control in the GUIState numeric wave.

+

One or both parameters have to be passed.

+
+
Parameters:
+
    +

  • device – device

    • +

  • controlName – control name

    • +

  • val – [optional] numerical value, 0-based index for popup menues

    • +

  • str – [optional] textual value

    • +
+
+
+
+ +
+
+string DAG_GetUniqueSpecCtrlListNum(string device)
+

Returns a list of unique and type specific controls.

+
+ +
+
+string DAG_GetUniqueSpecCtrlListTxT(string device)
+

Returns a list of unique and type specific controls with textual values.

+
+ +
+
+static wave DAG_ControlStatusWave(string device, variable type)
+

Returns a free wave of the status of the checkboxes specified by channelType.

+

The only caller should be DAG_RecordGuiStateNum().

+
+
Parameters:
+
+
+
+
+ +
+
+static wave DAG_GetAllHSMode(string device)
+

Return the mode of all DA_Ephys panel headstages.

+

All callers, except the ones updating the GUIState wave, should prefer DAG_GetHeadstageMode() instead.

+
+ +
+
+static string DAG_GetUniqueCtrlList(string device)
+

Parses a list of controls in the device and returns a list of unique controls.

+
+ +
+
+static string DAG_GetSpecificCtrlNum(string device, string list)
+

Parses a list of controls and returns numeric checkBox, valDisplay, setVariable, popUpMenu, and slider controls.

+
+ +
+
+static string DAG_GetSpecificCtrlTxT(string device, string list)
+

Parses a list of controls and returns textual valDisplay, setVariable and popUpMenu controls.

+
+ +
+
+static wave GetAllDAEphysSetVarNum(string device, variable channelType, variable controlType)
+

Returns the mode of all setVars in the DA_Ephys panel of a controlType.

+
+ +
+
+static wave GetAllDAEphysSetVarTxT(string device, variable channelType, variable controlType)
+

Returns the mode of all setVars in the DA_Ephys panel of a controlType.

+
+ +
+
+static wave GetAllDAEphysPopMenuIndex(string device, variable channelType, variable controlType)
+

Returns the index of all popupmenus in the DA_Ephys panel of a controlType.

+
+ +
+
+static wave GetAllDAEphysPopMenuString(string device, variable channelType, variable controlType)
+

Returns the string contents of all popupmenus in the DA_Ephys panel of a controlType.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___d_a_ephys___macro_8ipf.html b/file/_m_i_e_s___d_a_ephys___macro_8ipf.html new file mode 100644 index 0000000000..f5cb3bf950 --- /dev/null +++ b/file/_m_i_e_s___d_a_ephys___macro_8ipf.html @@ -0,0 +1,287 @@ + + + + + + + + File MIES_DAEphys_Macro.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_DAEphys_Macro.ipf

+

DA DA_Ephys panel macro

+
+

Functions

+
+
+void DA_Ephys()
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___d_a_n_d_i_8ipf.html b/file/_m_i_e_s___d_a_n_d_i_8ipf.html new file mode 100644 index 0000000000..f1086a4806 --- /dev/null +++ b/file/_m_i_e_s___d_a_n_d_i_8ipf.html @@ -0,0 +1,320 @@ + + + + + + + + File MIES_DANDI.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_DANDI.ipf

+
+

Functions

+
+
+static string DND_GetDestinationIgorPath()
+
+ +
+
+static string DND_ChooseAsset(WaveText props)
+
+ +
+
+static string DND_FetchAsset(variable setNumber, string assetID, string assetPath)
+

Download the given asset from the set.

+

The asset hash is checked before returning.

+
+
Returns:
+

absolute path to the downloaded asset

+
+
+
+ +
+
+static wave DND_ParseSetReponse(string response)
+

Parse the REST API response and fill the DANDI set properties wave.

+

The returned wave will have the format as described at GetDandiSetProperties() and row dimension label with the asset ID.

+

Example: https://api.dandiarchive.org/api/dandisets/000068/versions/draft/assets/

+
+ +
+
+string DND_FetchAssetFromSet(variable setNumber)
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___data_acquisition_8ipf.html b/file/_m_i_e_s___data_acquisition_8ipf.html new file mode 100644 index 0000000000..18065171cb --- /dev/null +++ b/file/_m_i_e_s___data_acquisition_8ipf.html @@ -0,0 +1,366 @@ + + + + + + + + File MIES_DataAcquisition.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_DataAcquisition.ipf

+

DQ Routines for Data acquisition

+
+

Functions

+
+
+variable DQ_StopOngoingDAQAllLocked(variable stopReason)
+

Stop DAQ and TP on all locked devices.

+
+ +
+
+variable DQ_StopOngoingDAQ(string device, variable stopReason, variable startTPAfterDAQ = defaultValue)
+

Stop the DAQ and testpulse.

+

Works with single/multi device mode

+
+
Parameters:
+
    +

  • device – device

    • +

  • stopReason – One of DAQStoppingFlags

    • +

  • startTPAfterDAQ – [optional, defaults to true] start “TP after DAQ” if enabled

    • +
+
+
+
+ +
+
+variable DQ_StartDAQDeviceTimer(string device)
+

Start the per-device timer used for the ITI (inter trial interval)

+

This function and DQ_StopDAQDeviceTimer are used to correct the ITI for the time it took to collect data, and pre and post processing of data. It allows for a real time, start to start, ITI

+
+ +
+
+variable DQ_StopDAQDeviceTimer(string device)
+

Stop the per-device timer associated with a particular device.

+
+
Returns:
+

time in seconds

+
+
+
+ +
+
+variable DQ_StopDAQ(string device, variable stopReason, variable startTPAfterDAQ = defaultValue)
+

Stop any running background DAQ.

+

Assumes that single device and multi device do not run at the same time.

+
+
Returns:
+

One of DAQRunModes

+
+
+
+ +
+
+variable DQ_RestartDAQ(string device, variable dataAcqRunMode)
+
+ +
+
+variable DQ_ApplyAutoBias(string device, wave TPResults)
+

Handle automatic bias current injection.

+
+
Parameters:
+
    +

  • device – Locked panel with test pulse running occasionally

    • +

  • TPResults – Data from TP_ROAnalysis()

    • +
+
+
+
+ +
+
+variable DQ_GetNumDevicesWithDAQRunning()
+

Return the number of devices which have DAQ running.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___data_acquisition___multi_8ipf.html b/file/_m_i_e_s___data_acquisition___multi_8ipf.html new file mode 100644 index 0000000000..0c9aa5dd3d --- /dev/null +++ b/file/_m_i_e_s___data_acquisition___multi_8ipf.html @@ -0,0 +1,406 @@ + + + + + + + + File MIES_DataAcquisition_Multi.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_DataAcquisition_Multi.ipf

+

DQM Routines for Multi Device Data acquisition

+
+

Functions

+
+
+variable DQM_FIFOMonitor(BackgroundStruct *s)
+

Fifo monitor for DAQ Multi Device.

+
+ +
+
+variable DQM_TerminateOngoingDAQHelper(string device)
+

Stop ongoing multi device DAQ.

+
+ +
+
+variable DQM_StartDAQMultiDevice(string device, variable initialSetupReq = defaultValue)
+

Handles function calls for data acquistion.

+

Handles the calls to the data configurator (DC) functions and BackgroundMD it is required because of the special handling syncronous ITC1600s require

+
+
Parameters:
+
    +

  • device – device

    • +

  • initialSetupReq – [optional, defaults to true] performs initialization routines at the very beginning of DAQ, turn off for RA

    • +
+
+
+
+ +
+
+variable DQM_StartBackgroundTimer(string device, variable runTime, string funcList)
+

Start the background timer for the inter trial interval (ITI)

+

Multi device variant

+
+
Parameters:
+
    +

  • device – device

    • +

  • runTime – left over time to wait in seconds

    • +

  • funcList – list of functions to execute at the end of the ITI

    • +
+
+
+
+ +
+
+variable DQM_StopBackgroundTimer(string device)
+

Stop the background timer used for ITI tracking.

+
+ +
+
+variable DQM_Timer(WMBackgroundStruct *s)
+

Background function for tracking ITI.

+
+ +
+
+static variable DQM_StartBckrdFIFOMonitor()
+
+ +
+
+static variable DQM_StopDataAcq(string device, variable deviceID)
+
+ +
+
+static variable DQM_BkrdDataAcq(string device, variable triggerMode = defaultValue)
+
+ +
+
+static variable DQM_RemoveDevice(string device, variable deviceID)
+

Removes a device from the ActiveDeviceList.

+
+
Parameters:
+
    +

  • device – panel title

    • +

  • deviceID – id of the device to be removed

    • +
+
+
+
+ +
+
+variable DQM_GetActiveDeviceRow(variable deviceID)
+

Return the row into ActiveDeviceList for the given deviceID.

+
+ +
+
+static variable DQM_AddDevice(string device)
+

Adds a device to the ActiveDeviceList.

+
+
Parameters:
+

device – panel title

+
+
+
+ +
+
+static variable DQM_MakeOrUpdateTimerParamWave(string device, string listOfFunctions, variable startTime, variable RunTime, variable EndTime, variable addOrRemoveDevice)
+
+ +
+
+static variable DQM_MakeOrUpdtDevTimerTxtWv(string device, string listOfFunctions, variable rowToRemove, variable addOrRemoveDevice)
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___data_acquisition___single_8ipf.html b/file/_m_i_e_s___data_acquisition___single_8ipf.html new file mode 100644 index 0000000000..e8eee7a51f --- /dev/null +++ b/file/_m_i_e_s___data_acquisition___single_8ipf.html @@ -0,0 +1,366 @@ + + + + + + + + File MIES_DataAcquisition_Single.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_DataAcquisition_Single.ipf

+

DQS Routines for Single Device Data acquisition

+
+

Functions

+
+
+variable DQS_StartDAQSingleDevice(string device, variable useBackground = defaultValue)
+

Start data acquisition using single device mode.

+

This is the high level function usable for all external users.

+
+
Parameters:
+
    +

  • device – device

    • +

  • useBackground – [optional, defaults to background checkbox setting in the DA_Ephys panel]

    • +
+
+
+
+ +
+
+variable DQS_DataAcq(string device)
+
+ +
+
+variable DQS_BkrdDataAcq(string device)
+

Fifo monitor for DAQ Single Device.

+
+ +
+
+static variable DQS_StopDataAcq(string device, variable stopReason, variable forcedStop = defaultValue)
+

Stop single device data acquisition.

+
+ +
+
+variable DQS_StartBackgroundFifoMonitor()
+
+ +
+
+variable DQS_FIFOMonitor(WMBackgroundStruct *s)
+

Fifo monitor for DAQ Single Device.

+
+ +
+
+variable DQS_StopBackgroundFifoMonitor()
+
+ +
+
+variable DQS_StartBackgroundTimer(string device, variable runTime, string funcList)
+

Start the background timer for the inter trial interval (ITI)

+
+
Parameters:
+
    +

  • device – device

    • +

  • runTime – left over time to wait in seconds

    • +

  • funcList – list of functions to execute at the end of the ITI

    • +
+
+
+
+ +
+
+variable DQS_StopBackgroundTimer()
+

Stop the background timer used for ITI tracking.

+
+ +
+
+variable DQS_Timer(WMBackgroundStruct *s)
+

Keep track of time during ITI.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___data_browser_8ipf.html b/file/_m_i_e_s___data_browser_8ipf.html new file mode 100644 index 0000000000..a72a5eba73 --- /dev/null +++ b/file/_m_i_e_s___data_browser_8ipf.html @@ -0,0 +1,472 @@ + + + + + + + + File MIES_DataBrowser.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_DataBrowser.ipf

+

DB Panel for browsing acquired data during acquisition

+
+

Functions

+
+
+string DB_OpenDataBrowser(variable mode = defaultValue)
+
+ +
+
+variable DB_ResetAndStoreCurrentDBPanel()
+

Utility function to generate new window recreation macro of DataBrowser (also used for SweepBrowser) after GUI editor adapted controls in development process.

+
+ +
+
+string DB_GetMainGraph(string win)
+
+ +
+
+string DB_ClearAllGraphs()
+
+ +
+
+static string DB_LockToDevice(string win, string device)
+
+ +
+
+static variable DB_SetUserData(string win, string device)
+
+ +
+
+wave DB_GetPlainSweepList(string win)
+
+ +
+
+variable DB_UpdateLastSweepControls(string win, variable first, variable last)
+
+ +
+
+variable DB_UpdateSweepPlot(string win)
+

Update the sweep plotting facility.

+

Only outside callers are generic external panels which must update the graph.

+
+
Parameters:
+

win – locked databrowser

+
+
+
+ +
+
+wave DB_GetLBNWave(string win, variable type)
+

Return the labnotebook waves.

+

The databrowser only knows about one experiment/device at a time so we don’t need to specify what we return further.

+
+
Parameters:
+
+
+
+
+ +
+
+variable DB_UpdateToLastSweep(string databrowser, variable force = defaultValue)
+

Update the databrowser to the last sweep.

+

force is off by default and in this case respects the autoupdate checkbox setting.

+
+ +
+
+static variable DB_UpdateToLastSweepWrapper(string win, variable force)
+
+ +
+
+variable DB_PopMenuProc_LockDBtoDevice(WMPopupAction *pa)
+
+ +
+
+variable DB_SetVarProc_SweepNo(WMSetVariableAction *sva)
+
+ +
+
+string DB_GetAllDevicesWithData()
+
+ +
+
+variable DB_AddSweepToGraph(string win, variable index, BufferedDrawInfo *bdi = defaultValue)
+

Adds traces of a sweep to the databrowser graph.

+
+
Parameters:
+
    +

  • win – Name of the DataBrowser

    • +

  • index – Index of the sweep

    • +

  • bdi – [optional, default = n/a] BufferedDrawInfo structure, when given buffered draw is used.

    • +
+
+
+
+ +
+
+variable DB_SplitSweepsIfReq(string win, variable sweepNo)
+

Split sweeps to single sweep waves if required.

+
+
Parameters:
+
    +

  • win – Databrowser window name

    • +

  • sweepNo – Number of sweep to split

    • +
+
+
Returns:
+

1 on error, 0 on success

+
+
+
+ +
+
+string DB_FindDataBrowser(string device, variable mode = defaultValue)
+

Find a Databrowser which is locked to the given DAEphys panel.

+
+ +
+
+wave DB_FindAllDataBrowser(string device, variable mode = defaultValue)
+

Find all Databrowser which are locked to the given DAEphys panel.

+
+ +
+
+string DB_GetBoundDataBrowser(string device, variable mode = defaultValue)
+

Returns a databrowser bound to the given device

+

+Creates a new one, if none is found nor bound.

+
+
Parameters:
+
+
+
+
+ +
+
+variable DB_SFHelpJumpToLine(string str)
+

Jumps in the SweepFormula help notebook of the current data/sweepbrowser to the first location of the search string from the notebook start. Used for scrolling to operation help.

+

The convention is that the headlines of the operation description in the sweepformula help notebook is operation - <operationName>

+
+
Parameters:
+

str – [in] characters to find, use “” to jump to the notebook start

+
+
Returns:
+

0 if help for operation was found, 1 in case of error

+
+
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___data_browser___macro_8ipf.html b/file/_m_i_e_s___data_browser___macro_8ipf.html new file mode 100644 index 0000000000..5cbdb78ee4 --- /dev/null +++ b/file/_m_i_e_s___data_browser___macro_8ipf.html @@ -0,0 +1,287 @@ + + + + + + + + File MIES_DataBrowser_Macro.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_DataBrowser_Macro.ipf

+

DBM Macro for DataBrowser

+
+

Functions

+
+
+void DataBrowser()
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___data_configuraton_recreation_8ipf.html b/file/_m_i_e_s___data_configuraton_recreation_8ipf.html new file mode 100644 index 0000000000..9045caf650 --- /dev/null +++ b/file/_m_i_e_s___data_configuraton_recreation_8ipf.html @@ -0,0 +1,360 @@ + + + + + + + + File MIES_DataConfiguratonRecreation.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_DataConfiguratonRecreation.ipf

+

DCR Functions for recreating the DataConfigurationResult structure from the labnotebook

+
+

Functions

+
+
+std::tuple<DataConfigurationResult> DCR_RecreateDataConfigurationResultFromLNB(wave numericalValues, WaveText textualValues, dfref sweepDFR, variable sweepNo)
+
+ +
+
+static variable DCR_RecreateDataConfigurationResultFromLNB_TTL(DataConfigurationResult *s, wave numericalValues, WaveText textualValues, variable sweepNo)
+
+ +
+
+static std::tuple<WaveDouble> DCR_RecreateDataConfigurationResultFromLNB_ADC(DataConfigurationResult *s, wave numericalValues, WaveText textualValues, variable sweepNo)
+
+ +
+
+static wave DCR_RecreateDataConfigurationResultFromLNB_DAGains(DataConfigurationResult *s, wave numericalValues, WaveText textualValues, variable sweepNo)
+
+ +
+
+static variable DCR_RecreateDataConfigurationResultFromLNB_DAC(DataConfigurationResult *s, wave numericalValues, WaveText textualValues, variable sweepNo)
+
+ +
+
+static variable DCR_FindStimsetOffset(DataConfigurationResult *s, wave numericalValues, WaveText textualValues, dfref sweepDFR, variable sweepNo)
+
+ +
+
+static variable DCR_FindStimsetOffsetFromTP(DataConfigurationResult *s, wave numericalValues, WaveText textualValues, dfref sweepDFR, variable sweepNo, variable channelIndex)
+

This function requires that the stimset is featureless (zero)

+
+ +
+
+static variable DCR_FindStimsetOffsetForChannel(DataConfigurationResult *s, wave numericalValues, WaveText textualValues, dfref sweepDFR, variable sweepNo, variable channelIndex)
+
+ +
+
+static std::tuple<variable, variable> DCR_FindTestPulse(wave sweep, variable testPulseLength)
+
+ +
+
+static variable DCR_RecreateDataConfigurationResultFromLNB_baselineFrac_Path2(DataConfigurationResult *s, wave numericalValues, WaveText textualValues, dfref sweepDFR, variable sweepNo)
+
+ +
+
+static variable DCR_RecreateDataConfigurationResultFromLNB_SamplingInterval_Path2(DataConfigurationResult *s, wave numericalValues, WaveText textualValues, dfref sweepDFR, variable sweepNo)
+
+ +
+
+static variable DCR_RecreateDataConfigurationResultFromLNB_Indep(DataConfigurationResult *s, wave numericalValues, WaveText textualValues, dfref sweepDFR, variable sweepNo)
+
+ +
+
+static variable DCR_RecreateDataConfigurationResultFromLNB_TP(DataConfigurationResult *s, wave numericalValues, variable sweepNo)
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___data_configurator_8ipf.html b/file/_m_i_e_s___data_configurator_8ipf.html new file mode 100644 index 0000000000..1433328765 --- /dev/null +++ b/file/_m_i_e_s___data_configurator_8ipf.html @@ -0,0 +1,875 @@ + + + + + + + + File MIES_DataConfigurator.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_DataConfigurator.ipf

+

DC Handle preparations before data acquisition or test pulse related to the DAQ data and config waves

+
+

Functions

+
+
+static variable DC_UpdateGlobals(string device, variable dataAcqOrTP)
+

Update global variables used by the Testpulse or DAQ.

+
+ +
+
+variable DC_Configure(string device, variable dataAcqOrTP, variable multiDevice = defaultValue)
+

Prepare test pulse/data acquisition.

+
+
Parameters:
+
    +

  • device – panel title

    • +

  • dataAcqOrTP – one of DATA_ACQUISITION_MODE or TEST_PULSE_MODE

    • +

  • multiDevice – [optional: defaults to false] Fine tune data handling for single device (false) or multi device (true)

    • +
+
+
Throws:
+

Abort – configuration failure

+
+
+
+ +
+
+static variable DC_UpdateHSProperties(string device, wave ADCs)
+
+ +
+
+static variable DC_NoOfChannelsSelected(string device, variable type)
+

Return the number of selected checkboxes for the given type.

+
+ +
+
+static variable DC_ChannelCalcForDAQConfigWave(string device, variable dataAcqOrTP)
+

Returns the total number of combined channel types (DA, AD, and front TTLs) selected in the DA_Ephys Gui.

+
+
Parameters:
+
+
+
+
+ +
+
+static variable DC_AreTTLsInRackChecked(string device, variable rackNo)
+

Returns the ON/OFF status of the front TTLs on a specified rack.

+
+
Parameters:
+
    +

  • device – device

    • +

  • rackNo – Only the ITC1600 can have two racks. For all other ITC devices RackNo = 0.

    • +
+
+
+
+ +
+
+static variable DC_LongestOutputWave(string device, variable dataAcqOrTP, variable channelType)
+

Returns the number of points in the longest stimset.

+
+
Parameters:
+
+
+
+
+ +
+
+static variable DC_CalculateDAQDataWaveLength(string device, variable dataAcqOrTP, variable channelType)
+

Calculate the required length of the DAQDataWave.

+

ITC Hardware:

    +

  • The DAQDataWave length = 2^x where is the first integer large enough to contain the longest output wave plus one. X also has a minimum value of 17 to ensure sufficient time for communication with the ITC device to prevent FIFO overflow or underrun.

    • +
+

+

NI Hardware:

    +

  • Returns stopCollectionPoint

    • +
+

+

+

See also

+

XopChannelConstants

+
+

+
+
Parameters:
+
+
+
+
+ +
+
+variable DC_CalculateDAQDataWaveLengthImpl(variable dataLength, variable hardwareType, variable dataAcqOrTP)
+

device independent implkementation for DC_CalculateDAQDataWaveLength

+
+ +
+
+static variable DC_MakeDAQConfigWave(string device, variable numActiveChannels)
+

Create the DAQConfigWave used to configure the DAQ device.

+
+
Parameters:
+
+
+
+
+ +
+
+static std::tuple<WaveOrNull, WaveRefWave> DC_MakeAndGetDAQDataWave(string device, DataConfigurationResult *s, variable dataAcqOrTP)
+

Creates DAQDataWave; The wave that the device takes DA and TTL data from and passes AD data to for all channels.

+

Config all refers to configuring all the channels at once

+
+
Parameters:
+
+
+
+
+ +
+
+static wave DC_SetDataScaleNISUChannelWave(wave channel, variable type)
+

set a data scale for channel waves, this is not required for operation but allows to keep track of the scales The waves for the hardware that output data and read back data are typically in V because any other unit, like pA in current clamp mode on DAC channels is converted by the gain from pA to voltage and then by the hardware amplifier converted back from V to pA.

+
+ +
+
+static wave DC_MakeNIChannelWave(string device, variable dataAcqOrTP, variable channelType, variable samplingInterval, variable index, variable dataType)
+

Creates a single NIChannel wave.

+

Config all refers to configuring all the channels at once

+

+

See also

+

XopChannelConstants

+
+

+
+
Parameters:
+
    +

  • device – panel title

    • +

  • dataAcqOrTP – one of DATA_ACQUISITION_MODE or TEST_PULSE_MODE

    • +

  • channelType – channel type, one of

    • +

  • samplingInterval – minimum sample intervall in microseconds

    • +

  • index – number of NI channel

    • +

  • dataType – numeric data type of NI channel

    • +
+
+
Returns:
+

Wave Reference to NI Channel wave

+
+
+
+ +
+
+static wave DC_MakeSUTTERChannelWave(string device, variable dataAcqOrTP, variable channelType, variable samplingInterval, variable index, variable dataType)
+

Creates a single SUTTER Channel wave.

+

Config all refers to configuring all the channels at once

+

+

See also

+

XopChannelConstants

+
+

+
+
Parameters:
+
    +

  • device – panel title

    • +

  • dataAcqOrTP – one of DATA_ACQUISITION_MODE or TEST_PULSE_MODE

    • +

  • channelType – channel type, one of

    • +

  • samplingInterval – minimum sample intervall in microseconds

    • +

  • index – number of NI channel

    • +

  • dataType – numeric data type of NI channel

    • +
+
+
Returns:
+

Wave Reference to NI Channel wave

+
+
+
+ +
+
+static variable DC_MakeHelperWaves(string device, variable dataAcqOrTP)
+

Initializes the waves used for displaying DAQ/TP results in the oscilloscope window and the scaled data wave.

+
+
Parameters:
+
+
+
+
+ +
+
+static variable DC_CalculateChannelSizeForScaledData(string device, variable dataAcqOrTP, variable channelIndex = defaultValue)
+

Returns the size of a channel for scaledData wave creation. The DAQDataWave must already be existing at this point. channelIndex must be given for non-ITC hardware in DATA_ACQUISITION_MODE.

+
+ +
+
+static variable DC_InitScaledDataWave(string device, variable dataAcqOrTP)
+

Initialize scaledDataWave, as NI and SUTTER output already properly scaled data, we can prefill output channels. So in in the more time critical SCOPE_xx_UpdateOscilloscope we can optimize by only copying the ADC data over (ADC data from SUTTER and NI is already properly scaled by hardware)

+
+ +
+
+static variable DC_InitOscilloscopeDataWave(wave wv, variable numRows, variable sampleInterval, variable numDACs, variable numADCs, variable numTTLs, variable type = defaultValue, variable isFourierTransform = defaultValue)
+

Initialize OscilloscopeData waves to NaN.

+
+ +
+
+wave DC_GetFilteredChannelState(string device, variable dataAcqOrTP, variable channelType, variable DAQChannelType = defaultValue)
+

Return the list of active channels, filtered for various special cases.

+
+
Parameters:
+
+
+
+
+ +
+
+static variable DC_PlaceDataInDAQConfigWave(string device, variable dataAcqOrTP)
+

Places channel (DA, AD, and TTL) settings data into DAQConfigWave.

+
+
Parameters:
+
+
+
+
+ +
+
+static variable DC_GetDecimationFactor(string device, variable dataAcqOrTP)
+

Get the decimation factor for the current channel configuration.

+

This is the factor between the minimum sampling interval and the real. If the multiplier is taken into account depends on dataAcqOrTP.

+
+
Parameters:
+
+
+
+
+ +
+
+variable DC_GetDecimationFactorCalc(variable samplingInterval)
+

Calculcate decimation factor device independent.

+
+
Parameters:
+

samplingInterval – sampling interval in microseconds

+
+
+
+ +
+
+static variable DC_CalculateLongestSweep(string device, variable dataAcqOrTP, variable channelType)
+

Returns the longest sweep in a stimulus set across the given channel type.

+
+
Parameters:
+
+
+
Returns:
+

number of data points, not time

+
+
+
+ +
+
+variable DC_CalculateStimsetLength(wave stimSet, string device, variable dataAcqOrTP)
+

Get the stimset length for the real sampling interval.

+
+
Parameters:
+
+
+
+
+ +
+
+static variable DC_CalculateGeneratedDataSize(string device, variable dataAcqOrTP, variable genLength)
+

Get the length for the real sampling interval from a generated wave with length.

+
+
Parameters:
+
+
+
+
+ +
+
+variable DC_CalculateGeneratedDataSizeDAQMode(variable genLength, variable decimationFactor)
+
+ +
+
+static variable DC_PlaceDataInDAQDataWave(string device, variable numActiveChannels, variable dataAcqOrTP, variable multiDevice)
+

Places data from appropriate DA and TTL stimulus set(s) into DAQDataWave. Also records certain DA_Ephys GUI settings into sweepDataLNB and sweepDataTxTLNB.

+
+
Parameters:
+
+
+
Throws:
+

Abort – configuration failure

+
+
+
+ +
+
+static variable DC_MakeTTLWave(string device, DataConfigurationResult *s)
+
+ +
+
+static variable DC_WriteTTLIntoDAQDataWave(string device, DataConfigurationResult *s)
+
+ +
+
+static variable DC_PrepareLBNEntries(string device, DataConfigurationResult *s)
+
+ +
+
+static variable DC_FillSetEventFlag(string device, DataConfigurationResult *s)
+
+ +
+
+static variable DC_FillDAQDataWaveForTP(string device, DataConfigurationResult *s)
+
+ +
+
+static variable DC_FillDAQDataWaveForDAQ(string device, DataConfigurationResult *s)
+
+ +
+
+static std::tuple<DataConfigurationResult> DC_GetConfiguration(string device, variable numActiveChannels, variable dataAcqOrTP, variable multiDevice)
+
+ +
+
+variable DC_CalculateInsertStart(DataConfigurationResult *s)
+

Calculate s.insertStart for DATA_ACQUISITION_MODE.

+
+ +
+
+static variable DC_SetupConfigurationTTLstimSets(string device, DataConfigurationResult *s)
+

fills in TTL stimset wave references in DataConfigurationResult structure needs: s.hardwareType, s.numXXXEntries fields

+
+ +
+
+static variable DC_DocumentHardwareProperties(string device, variable hardwareType)
+

Document hardware type/name/serial number into the labnotebook.

+
+ +
+
+static variable DC_GetStimsetAcqCycleID(string device, variable fingerprint, variable DAC)
+

Return the stimset acquisition cycle ID.

+
+
Parameters:
+
+
+
+
+ +
+
+static variable DC_GenerateStimsetFingerprint(variable raCycleID, string setName, variable setCycleCount, variable setChecksum)
+

Generate the stimset fingerprint.

+

This fingerprint is unique for the combination of the following properties:

    +

  • Repeated acquisition cycle ID

    • +

  • stimset name

    • +

  • stimset checksum

    • +

  • set cycle count

    • +
+

+

Always then this fingerprint changes, a new stimset acquisition cycle ID has to be generated.

+
+ +
+
+static std::tuple<variable, variable, variable> DC_CheckIfDataWaveHasBorderVals(string device, variable dataAcqOrTP)
+
+ +
+
+variable DC_DocumentChannelProperty(string device, string entry, variable headstage, variable channelNumber, variable channelType, variable var = defaultValue, string str = defaultValue)
+

Document channel properties of DA and AD channels.

+

Knows about unassociated channels and creates the special key returned by CreateLBNUnassocKey().

+
+
Parameters:
+
    +

  • device – device

    • +

  • entry – name of the property

    • +

  • headstage – number of headstage, must be NaN for unassociated channels

    • +

  • channelNumber – number of the channel

    • +

  • channelType – type of the channel

    • +

  • var – [optional] numeric value

    • +

  • str – [optional] string value

    • +
+
+
+
+ +
+
+static variable DC_ITC_MakeTTLWave(string device, DataConfigurationResult *s)
+

Combines the TTL stimulus sweeps across different TTL channels into a single wave.

+
+
Parameters:
+
+
+
+
+ +
+
+static variable DC_NI_MakeTTLWave(string device, DataConfigurationResult *s)
+
+ +
+
+static std::tuple<variable, variable> DC_CalculateChannelColumnNo(string device, string setName, variable channelNo, variable channelType)
+

Returns column number/step of the stimulus set, independent of the times the set is being cycled through (as defined by SetVar_DataAcq_SetRepeats)

+
+
Parameters:
+
    +

  • device – panel title

    • +

  • setName – name of the stimulus set

    • +

  • channelNo – channel number

    • +

  • channelType – channel type, one of CHANNEL_TYPE_DAC or CHANNEL_TYPE_TTL

    • +
+
+
Return values:
+
    +

  • column – stimset column

    • +

  • setCycleCount – set cycle count

    • +
+
+
+
+ +
+
+static variable DC_ReturnTotalLengthIncrease(DataConfigurationResult *s)
+

Returns the length increase of the DAQDataWave following onset/termination delay insertion and distributed data aquisition. Does not incorporate adaptations for oodDAQ.

+

All returned values are in number of points, not in time.

+
+ +
+
+static variable DC_GetStopCollectionPoint(string device, DataConfigurationResult *s)
+

Calculate the stop collection point, includes all required global adjustments.

+
+ +
+
+variable DC_GotTPChannelWhileDAQ(string device)
+

Returns 1 if a channel is set to TP, the check is through the stimset name from the GUI.

+
+ +
+
+variable DC_GetChannelTypefromHS(string device, variable headstage)
+

Get the channel type of given headstage.

+
+
Parameters:
+
    +

  • device – panel title

    • +

  • headstage – head stage

    • +
+
+
Returns:
+

One of DaqChannelTypeConstants

+
+
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___debug_panel_8ipf.html b/file/_m_i_e_s___debug_panel_8ipf.html new file mode 100644 index 0000000000..c6a1bff779 --- /dev/null +++ b/file/_m_i_e_s___debug_panel_8ipf.html @@ -0,0 +1,332 @@ + + + + + + + + File MIES_DebugPanel.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_DebugPanel.ipf

+

DP Holds the debug panel

+
+

Functions

+
+
+variable DP_DebuggingEnabledForFile(string file)
+
+ +
+
+variable DP_DebuggingEnabledForCaller()
+
+ +
+
+string DP_OpenDebugPanel()
+
+ +
+
+static variable DP_FillDebugPanelWaves()
+
+ +
+
+variable DP_WindowHook(WMWinHookStruct *s)
+
+ +
+
+variable DP_CheckProc_Debug(WMCheckboxAction *cba)
+
+ +
+
+variable DP_PopMenuProc_Selection(WMPopupAction *pa)
+
+ +
+
+

Variables

+
+
+static const string PANEL = "DebugPanel"
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___debug_panel___macro_8ipf.html b/file/_m_i_e_s___debug_panel___macro_8ipf.html new file mode 100644 index 0000000000..6c989d88b5 --- /dev/null +++ b/file/_m_i_e_s___debug_panel___macro_8ipf.html @@ -0,0 +1,286 @@ + + + + + + + + File MIES_DebugPanel_Macro.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_DebugPanel_Macro.ipf

+
+

Functions

+
+
+void DebugPanel()
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___debugging_8ipf.html b/file/_m_i_e_s___debugging_8ipf.html new file mode 100644 index 0000000000..28439a899a --- /dev/null +++ b/file/_m_i_e_s___debugging_8ipf.html @@ -0,0 +1,624 @@ + + + + + + + + File MIES_Debugging.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Debugging.ipf

+

Holds functions for handling debugging information.

+
+

Functions

+
+
+static variable FindFirstOutsideCaller(string *func, string *line, string *file)
+

Return the first function from the stack trace not located in this file.

+
+ +
+
+variable DEBUGPRINTv(variable var, string format = defaultValue)
+

Output debug information and return the parameter var.

+

Debug function especially designed for usage in return statements.

+

For example calling the following function 

Function doStuff()
+    variable var = 1 + 2
+    return DEBUGPRINTv(var)
+End
+
+
+

+

+

will output 

DEBUG doStuff(...)#L5: return value 3
+
+
+ to the history.

+
+
Parameters:
+
    +

  • var – numerical argument for debug output

    • +

  • format – optional format string to override the default of “%g”

    • +
+
+
+
+ +
+
+wave DEBUGPRINTw(WaveOrNull wv, string format = defaultValue)
+

Output debug information and return the wave wv.

+

Debug function especially designed for usage in return statements.

+

For example calling the following function 

Function/WAVE doStuff()
+    Make/D/N=5 data = p
+    return DEBUGPRINTw(data)
+End
+
+
+

+

+

will output 

DEBUG doStuff(...)#L5: return value {0, 1, 2, 3, 4}
+
+
+ to the history.

+
+
Parameters:
+
    +

  • wv – wave argument for debug output

    • +

  • format – optional format string to override the default of “%g”

    • +
+
+
+
+ +
+
+string DEBUGPRINTs(string str, string format = defaultValue)
+

Output debug information and return the parameter str.

+

Debug function especially designed for usage in return statements.

+

For example calling the following function 

Function/s doStuff()
+    variable str= "a" + "b"
+    return DEBUGPRINTs(str)
+End
+
+
+

+ will output 
DEBUG doStuff(...)#L5: return value ab
+
+
+ to the history.

+
+
Parameters:
+
    +

  • str – string argument for debug output

    • +

  • format – optional format string to override the default of “%s”

    • +
+
+
+
+ +
+
+variable DEBUGPRINT(string msg, variable var = defaultValue, string str = defaultValue, WaveOrNull wv = defaultValue, string format = defaultValue)
+

Generic debug output function.

+

Outputs variables and strings with optional format argument.

+

Examples: 

DEBUGPRINT("before a possible crash")
+DEBUGPRINT("some variable", var=myVariable)
+DEBUGPRINT("my string", str=myString)
+DEBUGPRINT("Current state", var=state, format="%.5f")
+
+
+

+

+
+
Parameters:
+
    +

  • msg – descriptive string for the debug message

    • +

  • var – variable

    • +

  • str – string

    • +

  • wv – wave (can be null)

    • +

  • format – format string overrides the default of “%g” for variables and “%s” for strings

    • +
+
+
+
+ +
+
+variable DEBUGPRINT_TS(string msg, variable var = defaultValue, string str = defaultValue, string format = defaultValue)
+

Generic debug output function (threadsafe variant)

+

Outputs variables and strings with optional format argument.

+

Examples: 

DEBUGPRINT("before a possible crash")
+DEBUGPRINT("some variable", var=myVariable)
+DEBUGPRINT("my string", str=myString)
+DEBUGPRINT("Current state", var=state, format="%.5f")
+
+
+

+

+
+
Parameters:
+
    +

  • msg – descriptive string for the debug message

    • +

  • var – variable

    • +

  • str – string

    • +

  • format – format string overrides the default of “%g” for variables and “%s” for strings

    • +
+
+
+
+ +
+
+variable DEBUGPRINTSTACKINFO()
+

Print a nicely formatted stack trace to the history.

+
+ +
+
+static variable CreateHistoryLog()
+

Creates a notebook with the special name “HistoryCarbonCopy” which will hold a copy of the history

+
+ +
+
+static variable SaveHistoryLog()
+

Save the contents of the history notebook on disk in the same folder as this experiment as timestamped file “run_*_*.log”

+
+ +
+
+variable DEBUGPRINT_OR_ABORT(string msg)
+

Prints a message to the command history in debug mode, aborts with dialog in release mode.

+
+ +
+
+variable DEBUG_TIMER_START()
+

Start a timer for performance measurements.

+

Usage: 

variable referenceTime = DEBUG_TIMER_START()
+// part one to benchmark
+DEBUGPRINT_ELAPSED(referenceTime)
+// part two to benchmark
+DEBUGPRINT_ELAPSED(referenceTime)
+
+
+

+

+
+ +
+
+variable DEBUGPRINT_ELAPSED(variable referenceTime)
+

Print the elapsed time for performance measurements in seconds.

+

+

See also

+

DEBUG_TIMER_START()

+
+

+
+ +
+
+variable DEBUGPRINT_ELAPSED_WAVE(variable referenceTime)
+

Print and store the elapsed time for performance measurements.

+

+

See also

+

DEBUG_TIMER_START()

+
+

+
+ +
+
+variable EnableDebugMode()
+

Enable debug mode.

+
+ +
+
+variable DisableDebugMode()
+

Disable debug mode.

+
+ +
+
+variable EnableEvilMode()
+

Enable evil mode.

+
+ +
+
+variable DisableEvilMode()
+

Disable evil mode.

+
+ +
+
+variable DisableThreadsafeSupport()
+

Disable threadsafe support.

+
+ +
+
+variable EnableThreadsafeSupport()
+

Enable threadsafe support again (default on IP startup)

+
+ +
+
+variable DisableWaveCache()
+

Disable wave caching support.

+
+ +
+
+variable EnableWaveCache()
+

Enable wave caching support again.

+
+ +
+
+variable EnableDangerousDebugging()
+

Enable dangerous debugging (allows to call user-defined functions in the debugger)

+
+ +
+
+variable QueryIgorOption(string option)
+
+ +
+
+static variable ReportBugToLogfile(string msg, WaveTextOrNull keys, WaveTextOrNull values)
+
+ +
+
+variable BUG(string msg, WaveText keys = defaultValue, WaveText values = defaultValue)
+

Complain and ask the user to report the error.

+

In nearly all cases ASSERT() is the more appropriate method to use.

+

If a testcase wants to trigger a BUG message and needs to treat that as non-fatal, it needs to set bugCount to NaN before.

+
+ +
+
+variable BUG_TS(string msg, WaveText keys = defaultValue, WaveText values = defaultValue)
+

Threadsafe variant of BUG()

+
+ +
+
+variable GetSizeOfAllWavesInExperiment()
+

Debug helper which creates a textwave which will hold the names of all waves and their size in MiB.

+
+ +
+
+variable CheckAllDimensionLabels()
+

Check that all stored waves (permanent and free) adhere to the liberal naming rules.

+

These are only enforced since IP9 beta9 or later.

+
+
Returns:
+

Number of waves not matching

+
+
+
+ +
+
+static string CheckDimensionLabels(WaveOrNull wv)
+
+ +
+
+variable DEBUG_STOREFUNCTION()
+
+ +
+
+

Variables

+
+
+static const string functionReturnMessage = "return value"
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___downsample_8ipf.html b/file/_m_i_e_s___downsample_8ipf.html new file mode 100644 index 0000000000..efa12e6e68 --- /dev/null +++ b/file/_m_i_e_s___downsample_8ipf.html @@ -0,0 +1,603 @@ + + + + + + + + File MIES_Downsample.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Downsample.ipf

+

Panel for downsampling acquired data.

+

Folders and waves managed by code in this file + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Object type

Name

Purpose

Function

DFREF

$dataPath

location of all the GUI and temporary data

GetDownsampleDataFolder()

Wave

$dataPath:dataRef

Holds wave references to all waves currently displayed in the list box

GetDownsampleDataRefWave()

Wave

$dataPath:rateWave

Holds all rates in kHz for each wave.

GetDownsampleRateWave()

Wave

$dataPath:sweepProperties

Used by the list box to show the properties of each sweep

GetDownsampleListWave()

+

+
+

Functions

+
+
+static dfref GetDownsampleDataFolder()
+
+ +
+
+static wave GetDownsampleDataRefWave()
+
+ +
+
+static wave GetDownsampleRateWave()
+
+ +
+
+static wave GetDownsampleListWave()
+
+ +
+
+string GetPopupMenuDeviceListWithData()
+

Create a list of all devices with acquired data.

+
+
Returns:
+

list of all devices with data in the format ITC18USB_Dev_1;ITC1600_Dev_1

+
+
+
+ +
+
+static variable AppendEntries(WaveText list, WaveRefWave dataRef, wave rate, variable startIndex, string deviceType, string deviceNumber)
+

Searches for sweep waves from all devices.

+
+
Parameters:
+
    +

  • list – ListBox wave, see GetDownsampleListWave() for the format

    • +

  • dataRef – wave with wave references to all data waves

    • +

  • rate – wave with the sampling rates in kHz of all data waves

    • +

  • startIndex – first unused index into the passed waves

    • +

  • deviceType – device type

    • +

  • deviceNumber – device number

    • +
+
+
Returns:
+

index of the last valid entry into the passed waves

+
+
+
+ +
+
+static variable UpdateDataWaves(string deviceType, string deviceNumber)
+

Updates all waves holding acquired data info.

+
+ +
+
+static variable UpdateCurrentSize(string win)
+
+ +
+
+static variable GetTargetRate(string win)
+
+ +
+
+static variable UpdateEstimatedSizeAfterwards(string win)
+
+ +
+
+static variable ApplyConstantRateChanges(string win)
+

Disable the equalize checkbox if all data waves have the same rate.

+
+ +
+
+static string ExpandRateToList(string win, variable var, variable constantRates = defaultValue)
+

Returns a list of values 1/k*var with k = {1..10} or k = {2..10} if constantRates == 1.

+
+
Parameters:
+
    +

  • win – panel name

    • +

  • var – variable to expand

    • +

  • constantRates – boolean switch, defaults to false

    • +
+
+
+
+ +
+
+string GetPopupMenuRates()
+

Returns a list of all possible equalize/downsampling rates.

+
+ +
+
+static variable GetDecimationMethod(string win)
+
+ +
+
+static variable UpdateCheckBoxes(string win, string control, variable state)
+
+ +
+
+static variable UpdatePopupMenuWindowFunction(string win, variable decimationMethod = defaultValue)
+
+ +
+
+variable CreateDownsamplePanel()
+
+ +
+
+variable DownsampleWindowHook(WMWinHookStruct *s)
+
+ +
+
+variable CheckBoxInterpolation(WMCheckboxAction *cba)
+
+ +
+
+variable PopupMenuTargetRate(WMPopupAction *pa)
+
+ +
+
+variable ButtonRestoreBackup(WMButtonAction *ba)
+
+ +
+
+variable ButtonDoIt(WMButtonAction *ba)
+
+ +
+
+static variable UpdatePopupMenuTargetRate(string win)
+
+ +
+
+static variable UpdatePanel(string win, string deviceSelectionString = defaultValue)
+
+ +
+
+variable PopupMenuDeviceSelection(WMPopupAction *pa)
+
+ +
+
+variable PopupMenuDecimationMethod(WMPopupAction *pa)
+
+ +
+
+variable CheckBoxEqualizeDown(WMCheckboxAction *cba)
+
+ +
+
+

Variables

+
+
+static const string checkbox_equalize = "checkbox_equalize_id"
+
+ +
+
+static const string checkbox_downsample = "checkbox_downsample_id"
+
+ +
+
+static const string popup_targetrate = "popup_targetrate_id"
+
+ +
+
+static const string checkbox_interpolation = "checkbox_interpolation_id"
+
+ +
+
+static const string popup_windowfunction = "popup_windowfunction_id"
+
+ +
+
+static const string popup_decimationmethod = "popup_decimationmethod_id"
+
+ +
+
+static const string popup_deviceselection = "popup_deviceselection_id"
+
+ +
+
+static const string checkbox_backupwaves = "checkbox_backupwaves_id"
+
+ +
+
+static const string valdisp_estimatedsize = "valdisp_estimatedsize_id"
+
+ +
+
+static const string valdisp_currentsize = "valdisp_currentsize_id"
+
+ +
+
+static const string listbox_waves = "listbox_waves_id"
+
+ +
+
+static const string button_doit = "button_doit_id"
+
+ +
+
+static const string button_restorebackup = "button_restorebackup_id"
+
+ +
+
+static const string dataPath = "root:MIES:postExperimentProcedures:downsample:"
+
+ +
+
+static const string panel = "Downsampling"
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___enhanced_w_m_routines_8ipf.html b/file/_m_i_e_s___enhanced_w_m_routines_8ipf.html new file mode 100644 index 0000000000..2b0cc9dbe9 --- /dev/null +++ b/file/_m_i_e_s___enhanced_w_m_routines_8ipf.html @@ -0,0 +1,309 @@ + + + + + + + + File MIES_EnhancedWMRoutines.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_EnhancedWMRoutines.ipf

+

Routines packaged with IGOR PRO but enhanced from us.

+

Everthing in this file is copyrighted by WaveMetrics Inc.

+
+

Functions taken from <tt>Waves Average.ipf</tt> from Igor Pro 6.3.6.4

+
+
+wave MIES_fWaveAverage(WaveOrNull yWaves, variable ignoreNaNs, variable averageWaveType, variable getComponents = defaultValue, WaveRefWave prevAvgData = defaultValue)
+

Average the given waves.

+
+
Parameters:
+
    +

  • yWaves – Y waves

    • +

  • ignoreNaNs – Ignoring NaNs means that the average does skip over NaNs.

    • +

  • averageWaveType – wave type of the average wave. Currently supported are IGOR_TYPE_64BIT_FLOAT and IGOR_TYPE_32BIT_FLOAT.

    • +

  • getComponents – [optional, default = 0] Return sum / count components as well

    • +

  • prevAvgData – [optional, default = $””] wave reference wave with data from previous averaging for incremental averaging. first entry refers to the sum per row wave and second to the counts per row wave.

    • +
+
+
Returns:
+

wave ref wave containing three free waves with the average per row, sums per row and counts per row. The latter two are only calculated when getComponents was set to 1. The latter two are undefined when getComponents is 0.

+
+
+
+ +
+
+static variable x2pntWithFrac(wave wv, variable scaledDim)
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___epochs_8ipf.html b/file/_m_i_e_s___epochs_8ipf.html new file mode 100644 index 0000000000..5cb64aae77 --- /dev/null +++ b/file/_m_i_e_s___epochs_8ipf.html @@ -0,0 +1,1419 @@ + + + + + + + + File MIES_Epochs.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Epochs.ipf

+

EP Handle code relating to epoch information

+
+

Functions

+
+
+variable EP_ClearEpochs(string device)
+

Clear the list of epochs.

+
+ +
+
+variable EP_CollectEpochInfo(WaveText epochWave, DataConfigurationResult *s)
+

Fill the epoch wave with epochs before DAQ/TP.

+
+
Parameters:
+
    +

  • epochWave – epochs wave

    • +

  • s – struct holding all input

    • +
+
+
+
+ +
+
+static variable EP_CollectEpochInfoDA(WaveText epochWave, DataConfigurationResult *s)
+
+ +
+
+static variable EP_CollectEpochInfoTTL(WaveText epochWave, DataConfigurationResult *s)
+
+ +
+
+static variable EP_AddEpochsFromTP(EP_EpochCreationData *ec, variable amplitude)
+

Adds four epochs for a test pulse and three sub epochs for test pulse components.

+
+
Parameters:
+
    +

  • ec – [in] EP_EpochCreationData

    • +

  • amplitude – [in] amplitude of the TP in the DA wave without gain

    • +
+
+
+
+ +
+
+static variable EP_AddEpochsFromOodDAQRegions(wave epochWave, variable channel, string oodDAQRegions, variable stimsetBegin, variable stimsetEnd)
+

Adds epochs for oodDAQ regions.

+
+
Parameters:
+
    +

  • epochWave – [in] epoch wave

    • +

  • channel – [in] number of DA channel

    • +

  • oodDAQRegions – [in] string containing list of oodDAQ regions as d-d;…

    • +

  • stimsetBegin – [in] offset time in micro seconds where stim set begins

    • +

  • stimsetEnd – [in] offset time in micro seconds where stim set ends

    • +
+
+
+
+ +
+
+static std::tuple<WaveDouble, WaveDouble> EP_GetStimEpochsOffsetAndLength(EP_EpochCreationData *ec)
+

Calculate stimset epoch offsets and stimset epoch lengths in wavebuilder stimset indices.

+
+ +
+
+static std::tuple<WaveDouble, WaveDouble> EP_GetStimEpochsOffsetTimeAndDuration(EP_EpochCreationData *ec, wave wbStimsetEpochOffset, wave wbStimsetEpochLength)
+

Calculates the offset times in microseconds of stimset epochs relative to the stimset start in the data wave.

+
+
Parameters:
+
    +

  • ec – EP_EpochCreationData

    • +

  • wbStimsetEpochOffset – offsets of the epochs of the stimset in wavebuilder stimset wave indices

    • +

  • wbStimsetEpochLength – length of the epochs of the stimset in wavebuilder stimset wave indices

    • +
+
+
+
+ +
+
+static std::tuple<variable, variable, variable, variable> EP_AddEpochsForStimset(EP_EpochCreationData *ec, wave stimepochDuration)
+

Adds the stimset level 0 epoch, oodDAQ offset epoch level 0, stimset sweep extension from delta method as level 1 epoch.

+
+
Parameters:
+
    +

  • ec – EP_EpochCreationData

    • +

  • stimepochDuration – durations of the stimset epochs in microseconds

    • +
+
+
+
+ +
+
+static variable EP_GetEpochType(string stimNote, variable sweep, variable epochNr)
+

Returns numerical epoch type from a stimset epoch of a sweep WaveBuilderEpochTypes.

+
+
Parameters:
+
    +

  • stimNote – stimset wave note

    • +

  • sweep – stimset sweep number

    • +

  • epochNr – epoch number

    • +
+
+
+
+ +
+
+static string EP_GetStimsetEpochShortName(variable epochNr)
+

Returns epoch short name from stimset epoch number.

+
+
Parameters:
+

epochNr – epoch number

+
+
+
+ +
+
+static std::tuple<variable, variable, string> EP_AddStimsetEpoch(EP_EpochCreationData *ec, variable stimepochOffsetTime, variable stimepochDuration, variable epochNr, variable stimsetBegin, variable stimsetEnd)
+

Adds the epochs of a stimset as level 1 epochs.

+
+
Parameters:
+
    +

  • ec – EP_EpochCreationData

    • +

  • stimepochOffsetTime – stimset epoch offset time in microseconds

    • +

  • stimepochDuration – stimset epoch duration in microseconds

    • +

  • epochNr – epoch number

    • +

  • stimsetBegin – stimset begin time offset in microseconds

    • +

  • stimsetEnd – stimset end time offset in microseconds

    • +
+
+
+
+ +
+
+static std::tuple<WAVE, WAVE> EP_PTGetPulseIndices(EP_EpochCreationData *ec, variable epochNr)
+

Get PulseTrain start and end indices (inclusive), where the pulse is active in the wavebuilder stimset wave.

+
+
Parameters:
+
+
+
Returns:
+

pulse start and end indices where the pulse is active in the wavebuilder stimset wave

+
+
+
+ +
+
+static variable EP_PTCorrectOverlap(wave pulseStartIndices, wave pulseEndIndices)
+

Correction for overlapping pulses from e.g. poisson distribution.

+
+
Parameters:
+
    +

  • pulseStartIndices – pulse active start indices in wavebuilder stimset wave indices

    • +

  • pulseEndIndices – pulse active end indices in wavebuilder stimset wave indices

    • +
+
+
+
+ +
+
+static wave EP_PTGetPulseStartTimes(EP_EpochCreationData *ec, variable wbStimsetEpochOffset, wave pulseStartIndices)
+

Calculates the start times of PulseTrain pulses in the data wave.

+
+
Parameters:
+
    +

  • ec – EP_EpochCreationData

    • +

  • wbStimsetEpochOffset – offset of the stimset epoch in wavebuilder stimset indices

    • +

  • pulseStartIndices – start indices of PulseTrain pulses in the wavebuilder stimset

    • +
+
+
Returns:
+

wave with start times of PulseTrain pulses in the data wave relative to the stimset begin in the data wave in microseconds

+
+
+
+ +
+
+static std::tuple<variable, variable> EP_PTAddPTPEpoch(EP_EpochCreationData *ec, string shortNameEpTypePT, string epSubTags, wave startTimes, variable pulseNr, variable epochBegin, variable epochEnd)
+

Adds the PulseTrain Pulse-To-Pulse level 2 epoch.

+
+
Parameters:
+
    +

  • ec – EP_EpochCreationData

    • +

  • shortNameEpTypePT – short name for the epoch type PulseTrain

    • +

  • epSubTags – tags for the PulseTrain epoch

    • +

  • startTimes – start times in micro seconds of the pulses relative to the start of the data wave (zero)

    • +

  • pulseNr – pulse number

    • +

  • epochBegin – start time of stimset epoch (level 1) in microseconds

    • +

  • epochEnd – end time of stimset epoch (level 1) in microseconds

    • +
+
+
Returns:
+

start and end time of the added Pulse-To-Pulse level 2 epoch in microseconds

+
+
+
+ +
+
+static variable EP_PTAddPTBLTEpoch(EP_EpochCreationData *ec, string shortNameEpTypePT, string epSubTags, variable pulseNr, variable numPulses, variable epochBegin, variable epochEnd, variable subEpochbegin, variable subEpochend)
+

Adds the PulseTrain Pulse-To-Pulse-Baseline-Trail level 2 epoch if present.

+
+
Parameters:
+
    +

  • ec – EP_EpochCreationData

    • +

  • shortNameEpTypePT – short name for the epoch type PulseTrain

    • +

  • epSubTags – tags for the PulseTrain epoch

    • +

  • pulseNr – pulse number

    • +

  • numPulses – number of pulses in PulseTrain

    • +

  • epochBegin – start time of stimset epoch (level 1) in microseconds

    • +

  • epochEnd – end time of stimset epoch (level 1) in microseconds

    • +

  • subEpochbegin – start time of Pulse-To-Pulse epoch (level 2) in microseconds

    • +

  • subEpochend – end time of Pulse-To-Pulse epoch (level 2) in microseconds

    • +
+
+
+
+ +
+
+static variable EP_PTAddPTPActiveAndBaseFlipped(EP_EpochCreationData *ec, string shortNameEpTypePT, string epSubTags, variable stimsetEndIndex, variable wbStimsetEpochOffset, variable pulseNr, variable pulseStartIndexWB, variable pulseEndIndexWB, variable subEpochBegin, variable subEpochEnd)
+

For flipped stimsets: Adds the PulseTrain Pulse-Active level 3 epoch, and Pulse-Baseline level 3 epoch if present.

+
+
Parameters:
+
    +

  • ec – EP_EpochCreationData

    • +

  • shortNameEpTypePT – short name for the epoch type PulseTrain

    • +

  • epSubTags – tags for the PulseTrain epoch

    • +

  • stimsetEndIndex – offset of the stimset epoch in wavebuilder stimset indices

    • +

  • wbStimsetEpochOffset – end index of the stimset in the data wave

    • +

  • pulseNr – pulse number

    • +

  • pulseStartIndexWB – start index of the pulse in wavebuilder stimset indices

    • +

  • pulseEndIndexWB – end index of the pulse in wavebuilder stimset indices

    • +

  • subEpochBegin – start time of Pulse-To-Pulse epoch (level 2) in microseconds

    • +

  • subEpochEnd – end time of Pulse-To-Pulse epoch (level 2) in microseconds

    • +
+
+
+
+ +
+
+static variable EP_PTAddPTPActiveAndBase(EP_EpochCreationData *ec, string shortNameEpTypePT, string epSubTags, variable stimsetEndIndex, variable wbStimsetEpochOffset, variable pulseNr, variable pulseStartIndexWB, variable pulseEndIndexWB, variable subEpochBegin, variable subEpochEnd)
+

For non-flipped stimsets: Adds the PulseTrain Pulse-Active level 3 epoch, and Pulse-Baseline level 3 epoch if present.

+
+
Parameters:
+
    +

  • ec – EP_EpochCreationData

    • +

  • shortNameEpTypePT – short name for the epoch type PulseTrain

    • +

  • epSubTags – tags for the PulseTrain epoch

    • +

  • stimsetEndIndex – offset of the stimset epoch in wavebuilder stimset indices

    • +

  • wbStimsetEpochOffset – end index of the stimset in the data wave

    • +

  • pulseNr – pulse number

    • +

  • pulseStartIndexWB – start index of the pulse in wavebuilder stimset indices

    • +

  • pulseEndIndexWB – end index of the pulse in wavebuilder stimset indices

    • +

  • subEpochBegin – start time of Pulse-To-Pulse epoch (level 2) in microseconds

    • +

  • subEpochEnd – end time of Pulse-To-Pulse epoch (level 2) in microseconds

    • +
+
+
+
+ +
+
+static variable EP_GetFlippingIndex(EP_EpochCreationData *ec)
+
+ +
+
+static std::tuple<variable, variable> EP_AddEpochsFromStimSetNote(EP_EpochCreationData *ec)
+

Adds epochs for a stimset including higher tree level epochs.

+

Hints for epoch calculation:

    +

  • prefer index based calculation over time based

    • +

  • for IndexAfterDecimation(wbStimOffset, decimationFactor) the wbStimOffset must always refer to the same runnign index value as used in the decimation in DC It is usually (e.g. for DA) dwIndex = dwOffset + IndexAfterDecimation(wbStimOffset, decimationFactor) with dwOffset equal to ec.dwStimsetBegin (from s.insertStart)

    • +

  • In contrast to the generated stimset wave the stimset epoch includes only the effective stimset, extensions from oodDAQ shifts get an own epoch.

    • +

  • For DA without oodDAQ the generated and effective stimset are the same

    • +

  • If ITC hardware is used and multiple TTL channels are active where one channel uses a shorter wavebuilder stimset than the other(s) then the shorter stimset is extended to match the size of the largest stimset. The larger size is in DC then decimated to the data wave. Due to decimation effects such stimset can increase in size in the data wave (e.g. with wb stimset size 185000, decimation factor 5 the increase is 2 points in the data wave) relative to the calculated setLength.

    • +
+

+
+
Parameters:
+

ec – EP_EpochCreationData

+
+
Return values:
+
    +

  • err – one if error, zero otherwise

    • +

  • stimsetEndIndex – stimset end index in data wave

    • +
+
+
+
+ +
+
+variable EP_SortEpochs(WaveText epochWave)
+

Sorts all epochs per channel number / channel type in EpochsWave.

+

Removes epochs marked for removal, those with NaN as StartTime and EndTime, as well.

+

Sorting:

    +

  • Ascending starting time

    • +

  • Descending ending time

    • +

  • Ascending tree level

    • +
+

+
+
Parameters:
+

epochWave – [in] epoch wave

+
+
+
+ +
+
+static variable EP_GetEpochCount(WaveText epochWave, variable channel, variable channelType)
+

Returns the number of epoch in the epochsWave for the given channel.

+
+
Parameters:
+
    +

  • epochWave – [in] wave with epoch info

    • +

  • channel – [in] number of DA/TTL channel

    • +

  • channelType – [in] type of channel (DA or TTL)

    • +
+
+
Returns:
+

number of epochs for channel

+
+
+
+ +
+
+variable EP_AddUserEpoch(WaveText epochWave, variable channelType, variable channelNumber, variable epBegin, variable epEnd, string tags, string shortName = defaultValue)
+

Add user epochs.

+

Allows to add user epochs for not yet finished sweeps. The tree level is fixed to EPOCH_USER_LEVEL to not collide with stock entries.

+
+
Parameters:
+
    +

  • epochWave – epoch wave

    • +

  • channelType – channel type, currently only XOP_CHANNEL_TYPE_DAC and XOP_CHANNEL_TYPE_TTL is supported

    • +

  • channelNumber – channel number

    • +

  • epBegin – start time of the epoch in seconds

    • +

  • epEnd – end time of the epoch in seconds

    • +

  • tags – tags for the epoch

    • +

  • shortName – [optional, defaults to auto-generated] user defined short name for the epoch, will be prefixed with EPOCH_SHORTNAME_USER_PREFIX

    • +
+
+
+
+ +
+
+static variable EP_AddEpoch(WaveText epochWave, variable channel, variable channelType, variable epBegin, variable epEnd, string epTags, string epShortName, variable level, variable lowerlimit = defaultValue, variable upperlimit = defaultValue)
+

Adds a epoch to the epochsWave.

+
+
Parameters:
+
    +

  • epochWave – [in] epochs wave

    • +

  • channel – [in] number of DA/TTL channel

    • +

  • channelType – [in] type of channel (either DA or TTL)

    • +

  • epBegin – [in] start time of the epoch in micro seconds

    • +

  • epEnd – [in] end time of the epoch in micro seconds

    • +

  • epTags – [in] tags of the epoch

    • +

  • epShortName – [in] short name of the epoch, should be unique

    • +

  • level – [in] level of epoch

    • +

  • lowerlimit – [in] [optional, default = -Inf] epBegin is limited between lowerlimit and Inf, epEnd must be > this limit

    • +

  • upperlimit – [in] [optional, default = Inf] epEnd is limited between -Inf and upperlimit, epBegin must be < this limit

    • +
+
+
+
+ +
+
+variable EP_WriteEpochInfoIntoSweepSettings(string device, variable sweepNo, variable acquiredTime, variable plannedTime)
+

Write the epoch info into the sweep settings wave.

+
+
Parameters:
+
    +

  • device – device

    • +

  • sweepNo – sweep Number

    • +

  • acquiredTime – if acquisition was stopped early time of last acquired point in AD wave, NaN otherwise

    • +

  • plannedTime – time of one point after the end of the DA wave

    • +
+
+
+
+ +
+
+string EP_EpochWaveToStr(wave epochsWave, variable channel, variable channelType)
+

Convert the epochs wave layer given by channel and channelType to a string suitable for storing the labnotebook.

+
+
Parameters:
+
    +

  • epochsWave – wave with epoch information

    • +

  • channel – DA/TTL channel number

    • +

  • channelType – channel type (DA or TTL)

    • +
+
+
+
+ +
+
+wave EP_EpochStrToWave(string epochStr)
+

Converts a string containing epoch information in the format that is stored in the Labnotebook to a 2D epoch wave.

+

+

See also

+

GetEpochsWave

+
+

+
+
Parameters:
+

epochStr – [in] string with epoch information in the format as stored in the labnotebook

+
+
Returns:
+

2D text wave with epoch information, use EPOCH_COL_ constants for column access

+
+
+
+ +
+
+string EP_GetShortName(string name)
+

Returns the ShortName from a epoch name string, empty string if no ShortName is present.

+
+ +
+
+string EP_RemoveShortNameFromTags(string tags)
+
+ +
+
+static variable EP_AdaptEpochInfo(string device, wave configWave, variable acquiredTime, variable plannedTime)
+

Adapt epoch information.

+

    +

  • Adjust epoch end time to the acquired time

    • +

  • Blanks out which are then too small or lie outside the acquired region

    • +

  • Add an unacquired epoch

    • +
+

+
+
Parameters:
+
    +

  • device – device

    • +

  • configWave – DAQ config wave

    • +

  • acquiredTime – if acquisition was stopped early time of last acquired point in AD wave [s], NaN otherwise

    • +

  • plannedTime – planned acquisition time, time at one point after the end of the DA wave [s]

    • +
+
+
+
+ +
+
+static variable EP_AdaptEpochInfoChannel(string device, variable channelNumber, variable channelType, variable acquiredTime, variable plannedTime)
+
+ +
+
+variable EP_AdaptEpochInfoChannelImpl(WaveText epochWave, variable channelNumber, variable channelType, variable samplingInterval, variable acquiredTime, variable plannedTime)
+

Device independent implementation of EP_AdaptEpochInfoChannel.

+
+
Parameters:
+
    +

  • epochWave – epoch wave (4d)

    • +

  • channelNumber – GUI channel number

    • +

  • channelType – channel type

    • +

  • samplingInterval – sampling interval of channel type

    • +

  • acquiredTime – acquiredTime in [s]

    • +

  • plannedTime – plannedTime in [s]

    • +
+
+
+
+ +
+
+wave EP_GetEpochs(wave numericalValues, wave textualValues, variable sweepNo, variable channelType, variable channelNumber, string shortname, variable treelevel = defaultValue, WaveTextOrNull epochsWave = defaultValue, dfref sweepDFR = defaultValue)
+

Get epochs from the LBN filtered by given parameters.

+

+

See also

+

XopChannelConstants

+
+

+
+
Parameters:
+
    +

  • numericalValues – Numerical values from the labnotebook

    • +

  • textualValues – Textual values from the labnotebook

    • +

  • sweepNo – Number of sweep

    • +

  • channelType – type of channel

    • +

  • channelNumber – GUI channel number

    • +

  • shortname – short name filter, can be a regular expression which is matched caseless. For older tag formats it can be a simple tag entry (or regexp).

    • +

  • treelevel – [optional: default = not set] tree level of epochs, if not set then treelevel is ignored

    • +

  • epochsWave – [optional: defaults to $””] when passed, gathers epoch information from this wave directly. This is required for callers who want to read epochs during MID_SWEEP_EVENT in analysis functions.

    • +

  • sweepDFR – [optional: defaults to $””] when passed, allows to fetch also epoch from recreation

    • +
+
+
Returns:
+

Text wave with epoch information, only rows fitting the input parameters are returned. Can also be a null wave.

+
+
+
+ +
+
+wave EP_FetchEpochs_TS(wave numericalValues, WaveTextOrNull textualValues, variable sweep, variable channelNumber, variable channelType)
+

Return free text wave with the epoch information of the given channel, do not attempt recreation.

+

+

See also

+

XopChannelConstants

+
+

+
+
Parameters:
+
    +

  • numericalValues – Numerical values from the labnotebook

    • +

  • textualValues – Textual values from the labnotebook

    • +

  • sweep – Number of sweep

    • +

  • channelNumber – GUI channel number

    • +

  • channelType – Type of channel

    • +
+
+
Returns:
+

epochs wave, see GetEpochsWave() for the wave layout

+
+
+
+ +
+
+wave EP_FetchEpochs(wave numericalValues, WaveTextOrNull textualValues, variable sweep, dfref singleSweepDFR, variable channelNumber, variable channelType)
+

Return free text wave with the epoch information of the given channel, attempt recreation.

+

+

See also

+

XopChannelConstants

+
+

+
+
Parameters:
+
    +

  • numericalValues – Numerical values from the labnotebook

    • +

  • textualValues – Textual values from the labnotebook

    • +

  • sweep – Number of sweep

    • +

  • singleSweepDFR – sweep DF, e.g. from GetSingleSweepFolder(deviceDFR, sweepNo)

    • +

  • channelNumber – GUI channel number

    • +

  • channelType – Type of channel

    • +
+
+
Returns:
+

epochs wave, see GetEpochsWave() for the wave layout

+
+
+
+ +
+
+static wave EP_FetchEpochsFromRecreation(wave numericalValues, WaveTextOrNull textualValues, variable sweep, dfref singleSweepDFR, variable channelNumber, variable channelType)
+
+ +
+
+static wave EP_FetchEpochsFromLNB(wave numericalValues, WaveTextOrNull textualValues, variable sweep, variable channelNumber, variable channelType)
+
+ +
+
+static variable EP_GetDACFromADCChannel(wave numericalValues, variable sweep, variable channelNumber)
+
+ +
+
+variable EP_CopyLBNEpochsToEpochsWave(string device, variable sweepNo)
+

Append epoch information from the labnotebook to the newly cleared epoch wave.

+
+ +
+
+static wave EP_GetGaps(wave numericalValues, wave textualValues, variable sweepNo, dfref sweepDFR, variable channelType, variable channelNumber)
+

Helper function that returns (unintended) gaps between epochs.

+
+ +
+
+wave EP_GetNextEpoch(wave numericalValues, wave textualValues, variable sweepNo, dfref sweepDFR, variable channelType, variable channelNumber, string shortname, variable treelevel, variable ignoreGaps = defaultValue)
+

Returns the following epoch of a given epoch name in a specified tree level.

+
+ +
+
+variable EP_GetEpochAmplitude(string epochTag)
+

returns the Amplitude value from the epoch tag data

+
+ +
+
+static wave EP_RecreateEpochsFromLoadedData(wave numericalValues, WaveText textualValues, dfref sweepDFR, variable sweepNo)
+

Recreate DA epochs from loaded data. The following must be loaded: LabNotebook, Sweep data of sweepNo, Stimsets used in the sweep User epochs are not recreated !

+
+
Parameters:
+
    +

  • numericalValues – numerical LabNotebook

    • +

  • textualValues – textual LabNotebook

    • +

  • sweepDFR – single sweep folder, e.g. for measurement with a device this wold be DFREF sweepDFR = GetSingleSweepFolder(deviceDFR, sweepNo)

    • +

  • sweepNo – sweep number

    • +
+
+
Returns:
+

recreated 4D epoch wave

+
+
+
+ +
+
+static variable EP_AddRecreatedUserEpochs(wave numericalValues, WaveText textualValues, dfref sweepDFR, variable sweepNo, DataConfigurationResult *s, WaveText epochWave)
+
+ +
+
+static wave EP_AddRecreatedUserEpochs_DetermineDurations(wave numericalValues, WaveText textualValues, dfref sweepDFR, variable type, variable sweepNo, DataConfigurationResult *s)
+
+ +
+
+static variable EP_AddRecreatedUserEpochs_Baseline(wave numericalValues, WaveText textualValues, variable waMode, dfref sweepDFR, variable type, variable sweepNo, DataConfigurationResult *s, WaveText epochWave)
+
+ +
+
+static variable EP_AddRecreatedUserEpochs_AddTPUserEpochs(WaveText epochWave, DataConfigurationResult *s, string params, variable type)
+
+ +
+
+static variable EP_AddRecreatedUserEpochs_PSQ_DaScale(wave numericalValues, WaveText textualValues, variable waMode, dfref sweepDFR, variable sweepNo, DataConfigurationResult *s, WaveText epochWave)
+
+ +
+
+static variable EP_AddRecreatedUserEpochs_PSQ_Rheobase(wave numericalValues, WaveText textualValues, variable waMode, dfref sweepDFR, variable sweepNo, DataConfigurationResult *s, WaveText epochWave)
+
+ +
+
+static variable EP_AddRecreatedUserEpochs_PSQ_Ramp(wave numericalValues, WaveText textualValues, variable waMode, dfref sweepDFR, variable sweepNo, DataConfigurationResult *s, WaveText epochWave)
+
+ +
+
+static variable EP_AddRecreatedUserEpochs_PSQ_PipetteInBath(wave numericalValues, WaveText textualValues, variable waMode, dfref sweepDFR, variable sweepNo, DataConfigurationResult *s, WaveText epochWave)
+
+ +
+
+static variable EP_AddRecreatedUserEpochs_PSQ_SealEvaluation(wave numericalValues, WaveText textualValues, variable waMode, dfref sweepDFR, variable sweepNo, DataConfigurationResult *s, WaveText epochWave)
+
+ +
+
+static variable EP_AddRecreatedUserEpochs_PSQ_TrueRestingMembranePotential(wave numericalValues, WaveText textualValues, variable waMode, dfref sweepDFR, variable sweepNo, DataConfigurationResult *s, WaveText epochWave)
+
+ +
+
+static variable EP_AddRecreatedUserEpochs_PSQ_AccessResistanceSmoke(wave numericalValues, WaveText textualValues, variable waMode, dfref sweepDFR, variable sweepNo, DataConfigurationResult *s, WaveText epochWave)
+
+ +
+
+static variable EP_AddRecreatedUserEpochs_PSQ_Chirp(wave numericalValues, WaveText textualValues, variable waMode, dfref sweepDFR, variable sweepNo, DataConfigurationResult *s, WaveText epochWave)
+
+ +
+
+wave EP_FetchEpochsFromRecreated(wave epochWave, variable channelNumber, variable channelType)
+

Fetches a single epoch channel from a recreated epoch wave. The returned epoch channel wave has the same form as epoch information that was stored in the LNB returned by EP_FetchEpochs.

+
+
Parameters:
+
    +

  • epochWave – 4d epoch wave

    • +

  • channelNumber – GUI channel number

    • +

  • channelType – channel type, one of XopChannelConstants

    • +
+
+
Returns:
+

epoch channel wave (2d)

+
+
+
+ +
+
+

Variables

+
+
+static const string EPOCH_SHORTNAME_KEY = "ShortName"
+
+ +
+
+static const string EPOCH_TYPE_KEY = "Type"
+
+ +
+
+static const string EPOCH_SUBTYPE_KEY = "SubType"
+
+ +
+
+static const string EPOCH_AMPLITUDE_KEY = "Amplitude"
+
+ +
+
+static const string EPOCH_PULSE_KEY = "Pulse"
+
+ +
+
+static const string EPOCH_CYCLE_KEY = "Cycle"
+
+ +
+
+static const string EPOCH_INCOMPLETE_CYCLE_KEY = "Incomplete Cycle"
+
+ +
+
+static const string EPOCH_HALF_CYCLE_KEY = "Half Cycle"
+
+ +
+
+static const string EPOCHNAME_SEP = ";"
+
+ +
+
+static const string STIMSETKEYNAME_SEP = "="
+
+ +
+
+static const string SHORTNAMEKEY_SEP = "="
+
+ +
+
+static const string EPOCH_SN_BL_TOTALONSETDELAY = "B0_TO"
+
+ +
+
+static const string EPOCH_SN_BL_ONSETDELAYUSER = "B0_OD"
+
+ +
+
+static const string EPOCH_SN_BL_DDAQ = "B0_DD"
+
+ +
+
+static const string EPOCH_SN_BL_TERMINATIONDELAY = "B0_TD"
+
+ +
+
+static const string EPOCH_SN_BL_UNASSOC_NOTP_BASELINE = "B0_TP"
+
+ +
+
+static const string EPOCH_SN_BL_DDAQOPT = "B0_DO"
+
+ +
+
+static const string EPOCH_SN_BL_GENERALTRAIL = "B0_TR"
+
+ +
+
+static const string EPOCH_SN_TP = "TP"
+
+ +
+
+static const string EPOCH_SN_TP_PULSE = "TP_P"
+
+ +
+
+static const string EPOCH_SN_TP_BLFRONT = "TP_B0"
+
+ +
+
+static const string EPOCH_SN_TP_BLBACK = "TP_B1"
+
+ +
+
+static const string EPOCH_SN_OODAQ = "OD"
+
+ +
+
+static const string EPOCH_SN_STIMSET = "ST"
+
+ +
+
+static const string EPOCH_SN_STIMSETBLTRAIL = "B"
+
+ +
+
+static const string EPOCH_SN_EPOCH = "E"
+
+ +
+
+static const string EPOCH_SN_PULSETRAIN = "PT"
+
+ +
+
+static const string EPOCH_SN_PULSETRAIN_FULLPULSE = "P"
+
+ +
+
+static const string EPOCH_SN_PULSETRAIN_PULSEAMP = "P"
+
+ +
+
+static const string EPOCH_SN_PULSETRAIN_PULSEBASE = "B"
+
+ +
+
+static const string EPOCH_SN_PULSETRAIN_PULSEBASETRAIL = "BT"
+
+ +
+
+static const string EPOCH_SN_PULSETRAINBASETRAIL = "BT"
+
+ +
+
+static const string EPOCH_SN_TRIG = "TG"
+
+ +
+
+static const string EPOCH_SN_TRIG_CYCLE = "C"
+
+ +
+
+static const string EPOCH_SN_TRIG_CYCLE_INCOMPLETE = "I"
+
+ +
+
+static const string EPOCH_SN_TRIG_HALF_CYCLE = "H"
+
+ +
+
+static const string EPOCH_SN_UNACQUIRED = "UA"
+
+ +
+
+static const double EPOCH_GAPS_WORKAROUND = 0
+
+ +
+
+
+struct EP_EpochCreationData
+

Helper structure for data used in epoch creation.

+

structure variables for index based positions are prefixed: dw* - index in the data wave (e.g. DAChannel) wb* - index in the stimset wave from the wave builder

+
+

Public Members

+
+
+WaveText epochWave
+

Epochs wave.

+
+ +
+
+variable channel
+

GUI channel number.

+
+ +
+
+variable channelType
+

channel type as of XopChannelConstants

+
+ +
+
+variable sweep
+

sweep of stimset

+
+ +
+
+variable decimationFactor
+

decimation factor from stimset to data wave

+
+ +
+
+variable samplingInterval
+

sampling interval of data wave

+
+ +
+
+variable scale
+

DAScale of channel.

+
+ +
+
+string stimNote
+

stimset wave note

+
+ +
+
+variable dwStimsetSize
+

stimset size in data wave

+
+ +
+
+variable reducedStimsetSize
+

For DA: size of stimset wave that was decimated to the data wave the duration of that stimset can be reduced compared to the duration of the original wavebuilder stimset due to oodDAQ end cutoff, typically DimSize of the stimset in DC For TTL: same as dwStimsetSize note: While for DA the stimset size in DC can only be reduced for TTL channels it can be increased, see structure element dwJoinedTTLStimsetSize

+
+ +
+
+variable dwStimsetBegin
+

begin of stimset in indicces of the data wave

+
+ +
+
+variable wbOodDAQOffset
+

offset from oodDAQ shift in wavebuilder stimset wave indices

+
+ +
+
+variable wbStimsetSize
+

size of the original wavebuilder stimset, used as reference point for flipping calculation

+
+ +
+
+variable wbEffectiveStimsetSize
+

sum of all stimset epochs without extension from delta mechanism (multi sweep, different size)

+
+ +
+
+variable dwJoinedTTLStimsetSize
+

for ITC TTL stimsets are joined in DC to a single 2D wave that ROWS size equals the largest single stimset. This value is the data wave length that is used to decimate the from DC modified stimset into the data wave. The stimset is decimated to the data wave until dwJoinedTTLStimsetSize - 1. The related value for DA channels is s.setLength. For DA channels: NaN

+
+ +
+
+variable flipping
+

set to one if the stimset is flipped, zero otherwise

+
+ +
+
+variable tpTotalLengthPoints
+

test pulse properties transferred from DataConfigurationResult structure, originally calculated by TP_GetCreationPropertiesInPoints

+
+ +
+
+variable tpPulseStartPoint
+
+ +
+
+variable tpPulseLengthPoints
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___experiment_documentation_8ipf.html b/file/_m_i_e_s___experiment_documentation_8ipf.html new file mode 100644 index 0000000000..76c8d7b845 --- /dev/null +++ b/file/_m_i_e_s___experiment_documentation_8ipf.html @@ -0,0 +1,496 @@ + + + + + + + + File MIES_ExperimentDocumentation.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_ExperimentDocumentation.ipf

+

ED Writing numerical/textual information to the labnotebook

+
+

Functions

+
+
+variable ED_AddEntriesToLabnotebook(wave vals, WaveText keys, variable sweepNo, string device, variable entrySourceType)
+

Add numerical/textual entries to the labnotebook.

+

+

See also

+

ED_createTextNotes, ED_createWaveNote

+
+

+
+ +
+
+variable ED_AddEntriesToResults(wave vals, WaveText keys, variable entrySourceType)
+

Add numerical/textual entries to results.

+
+ +
+
+static variable ED_CheckValuesAndKeys(wave vals, wave keys)
+
+ +
+
+static variable ED_createTextNotes(WaveText incomingTextualValues, WaveText incomingTextualKeys, variable sweepNo, variable entrySourceType, variable logbookType, string device = defaultValue)
+

Add textual entries to the logbook.

+

The text documentation wave will use layers to report the different headstages.

+

The incoming value wave can have zero to nine (NUM_HEADSTAGES + 1) layers. The first eight layers are for headstage dependent data, the last layer for headstage independent data.

+
+
Parameters:
+
    +

  • incomingTextualValues – incoming Text Documentation Wave sent by the each reporting subsystem

    • +

  • incomingTextualKeys – incoming Text Documentation key wave that is used to reference the incoming settings wave

    • +

  • sweepNo – sweep number

    • +

  • device – [optional for logbookType LBT_RESULTS only] device

    • +

  • entrySourceType – type of reporting subsystem, one of DataAcqModes

    • +

  • logbookType – type of the logbook, one of LogbookTypes

    • +
+
+
+
+ +
+
+static variable ED_ParseHeadstageContigencyMode(string str)
+
+ +
+
+static string ED_HeadstageContigencyModeToString(variable mode)
+
+ +
+
+static variable ED_GetHeadstageContingency(wave values)
+

Return the headstage contigency mode for values.

+
+ +
+
+static variable ED_createWaveNotes(wave incomingNumericalValues, WaveText incomingNumericalKeys, variable sweepNo, variable entrySourceType, variable logbookType, string device = defaultValue)
+

Add numerical entries to the labnotebook.

+

The history wave will use layers to report the different headstages.

+

The incoming value wave can have zero to nine LABNOTEBOOK_LAYER_COUNT layers. The first eight layers are for headstage dependent data, the last layer for headstage independent data.

+
+
Parameters:
+
    +

  • incomingNumericalValues – settingsWave sent by the each reporting subsystem

    • +

  • incomingNumericalKeys – key wave that is used to reference the incoming settings wave

    • +

  • sweepNo – sweep number

    • +

  • device – [optional for logbooktype LBT_RESULTS only] device

    • +

  • entrySourceType – type of reporting subsystem, one of DataAcqModes

    • +

  • logbookType – one of LogbookTypes

    • +
+
+
+
+ +
+
+variable ED_AddEntryToLabnotebook(string device, string key, wave values, string unit = defaultValue, variable tolerance = defaultValue, variable overrideSweepNo = defaultValue)
+

Add custom entries to the numerical/textual labnotebook for the very last sweep acquired.

+

The entries are prefixed with USER_ to distinguish them from stock MIES entries.

+

The index of the entry in values determines the headstage to which the setting applies. You can not set both headstage dependent and independent values at the same time as this does not make sense.

+

Sample invocation: 

WAVE values = LBN_GetNumericWave()
+values[0] = 4711 // setting of the first headstage
+ED_AddEntryToLabnotebook(device, "SomeSetting", values)
+
+
+

+

+

The later on the labnotebook can be queried with: 

WAVE/Z settings = GetLastSetting(values, NaN, LABNOTEBOOK_USER_PREFIX + key, UNKNOWN_MODE)
+
+
+

+

+
+
Parameters:
+
    +

  • device – device

    • +

  • key – name under which to store the entry.

    • +

  • values – entry to add, wave can be numeric (floating point) or text, must have LABNOTEBOOK_LAYER_COUNT rows. It can be all NaN or empty (text), this is useful if you want to make the key known without adding an entry. Use LBN_GetNumericWave() or LBN_GetTextWave() to create them.

    • +

  • unit – [optional, defaults to “”] physical unit of the entry

    • +

  • tolerance – [optional, defaults to LABNOTEBOOK_NO_TOLERANCE] tolerance of the entry, used for judging if a change is “relevant” and should then be written to the sweep wave

    • +

  • overrideSweepNo – [optional, defaults to last acquired sweep] Adds metadata to the given sweep number. Mostly useful for adding labnotebook entries during MID_SWEEP_EVENT for analysis functions.

    • +
+
+
+
+ +
+
+static variable ED_WriteChangedValuesToNote(string device, variable sweepNo)
+

Record changed labnotebook entries compared to the last sweep to the sweep wave note.

+

Honours tolerances defined in the keywave and LABNOTEBOOK_BINARY_UNIT values

+
+ +
+
+static variable ED_WriteChangedValuesToNoteText(string device, variable sweepNo)
+

Record changed labnotebook entries compared to the last sweep to the sweep wave note.

+

Textual version.

+

Honours tolerances defined in the keywave and LABNOTEBOOK_BINARY_UNIT values

+
+ +
+
+static std::tuple<WAVE, variable> ED_FindIndizesAndRedimension(WaveText incomingKey, wave incomingValues, WaveText key, wave values, variable logbookType)
+

Returns the column indizes of each parameter in incomingKey into the key wave.

+

Redimensions key and values waves. Prefills key with incomingKey data if necessary.

+

Ensures that key and values have a matching column size at return.

+
+
Parameters:
+
    +

  • incomingKey – text wave with the keys to add

    • +

  • incomingValues – wave with the values to add

    • +

  • key – key wave of the labnotebook (Rows: 1/3/6, Columns: Same as values, Layers: 1)

    • +

  • values – values/data wave of the labnotebook

    • +

  • logbookType – type of the logbook, one of LogbookTypes

    • +
+
+
Return values:
+
    +

  • colIndizes – column indizes of the entries from incomingKey

    • +

  • rowIndex – returns the row index into values at which the new values should be written

    • +
+
+
+
+ +
+
+variable ED_MarkSweepStart(string device)
+

Remember the “exact” start of the sweep.

+

Should be called immediately after HW_StartAcq().

+
+ +
+
+variable ED_createWaveNoteTags(string device, variable sweepCount)
+

Add sweep specific information to the labnotebook.

+
+ +
+
+variable ED_WriteUserCommentToLabNB(string device, string comment, variable sweepNo)
+

Write the user comment from the DA_Ephys panel to the labnotebook.

+
+ +
+
+static variable ED_createAsyncWaveNoteTags(string device, variable sweepCount)
+

This function is used to create wave notes for the informations found in the Asynchronous tab in the DA_Ephys panel.

+
+ +
+
+variable ED_TPDocumentation(string device)
+

Stores test pulse related data in the labnotebook.

+
+ +
+
+static variable ED_TPSettingsDocumentation(string device, variable sweepNo, variable entrySourceType)
+

Document the settings of the Testpulse.

+

The source type entry is not fixed. We want to document the testpulse settings during ITI and the testpulse settings for plain test pulses.

+
+
Parameters:
+
    +

  • device – device

    • +

  • sweepNo – sweep number

    • +

  • entrySourceType – type of reporting subsystem, one of DataAcqModes

    • +
+
+
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___foreign_function_interface_8ipf.html b/file/_m_i_e_s___foreign_function_interface_8ipf.html new file mode 100644 index 0000000000..ba331c81c2 --- /dev/null +++ b/file/_m_i_e_s___foreign_function_interface_8ipf.html @@ -0,0 +1,360 @@ + + + + + + + + File MIES_ForeignFunctionInterface.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_ForeignFunctionInterface.ipf

+

FFI ACQ4/ZeroMQ accessible functions

+
+

Functions

+
+
+wave FFI_ReturnTPValues()
+

Function to return Peak Resistance, Steady State Resistance to ACQ4 (Neurophysiology Acquisition and Analysis System. See http://acq4.org/ for more details)

+

The function will pull the values (PeakResistance, SteadyStateResistance, and TimeStamp) out of the TP storage wave and put them in a 3x8 wave, in a designated location where ACQ4 can then find them

+
+ +
+
+wave FFI_GetAvailableMessageFilters()
+

Return a text wave with all available message filters for Publisher/Subscriber ZeroMQ sockets.

+

See also ZeroMQMessageFilters.

+

+

See also

+

PUB_GetJSONTemplate

+
+

+
+ +
+
+variable FFI_SetCellElectrodeName(string device, variable headstage, string name)
+

Set the headstage/cell electrode name.

+
+ +
+
+wave FFI_QueryLogbook(string device, variable logbookType, variable sweepNo, string setting, variable entrySourceType)
+

Query logbook entries from devices.

+

This allows to query labnotebook/results entries from associated channels.

+

+

See also

+

GetLockedDevices()

+
+

+
+
Parameters:
+
+
+
Returns:
+

Numerical/Textual wave with LABNOTEBOOK_LAYER_COUNT rows or a null wave reference if nothing could be found

+
+
+
+ +
+
+wave FFI_QueryLogbookUniqueSetting(string device, variable logbookType, string setting)
+

Return all unique logbook entries from devices.

+

+

See also

+

GetLockedDevices()

+
+

+
+
Parameters:
+
    +

  • device – Name of the hardware device panel,

    • +

  • logbookType – One of LBT_LABNOTEBOOK or LBT_RESULTS

    • +

  • setting – Name of the entry

    • +
+
+
Returns:
+

Numerical/Textual 1D wave or a null wave reference if nothing could be found

+
+
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___global_string_and_variable_access_8ipf.html b/file/_m_i_e_s___global_string_and_variable_access_8ipf.html new file mode 100644 index 0000000000..7f903083ca --- /dev/null +++ b/file/_m_i_e_s___global_string_and_variable_access_8ipf.html @@ -0,0 +1,842 @@ + + + + + + + + File MIES_GlobalStringAndVariableAccess.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_GlobalStringAndVariableAccess.ipf

+

Helper functions for accessing global variables and strings.

+

The functions GetNVARAsString() and GetSVARAsString() are static as they should not be used directly.

+

Instead if you have a global variable named iceCreamCounter in root:myfood you would write in this file here a function like

+

Function/S GetIceCreamCounterAsVariable()
+    return GetNVARAsString(createDFWithAllParents("root:myfood"), "iceCreamCounter")
+End
+
+
+

+

and then use it in your code as

+

Function doStuff()
+    NVAR iceCreamCounter = $GetIceCreamCounterAsVariable()
+
+    iceCreamCounter += 1
+End
+
+
+

+

if you want to ensure that you only get read-only access you can use ROVar() as in

+

Function doStuffReadOnly()
+    variable iceCreamCounter = ROVar(GetIceCreamCounterAsVariable())
+
+    iceCreamCounter += 1
+End
+
+
+

+

this avoids accidental changes.

+
+

Functions

+
+
+static string GetNVARAsString(dfref dfr, string globalVarName, variable initialValue = defaultValue)
+

Returns the full path to a global variable.

+
+
Parameters:
+
    +

  • dfr – location of the global variable, must exist

    • +

  • globalVarName – name of the global variable

    • +

  • initialValue – initial value of the variable. Will only be used if it is created. 0 by default.

    • +
+
+
+
+ +
+
+static string GetSVARAsString(dfref dfr, string globalStrName, string initialValue = defaultValue)
+

Returns the full path to a global string.

+
+
Parameters:
+
    +

  • dfr – location of the global string, must exist

    • +

  • globalStrName – name of the global string

    • +

  • initialValue – initial value of the string. Will only be used if it is created. null by default.

    • +
+
+
+
+ +
+
+variable ROVar(string path)
+

Helper function to get read-only access to a global variable.

+
+
Parameters:
+

path – absolute path to a global variable

+
+
+
+ +
+
+string ROStr(string path)
+

Helper function to get read-only access to a global string.

+
+
Parameters:
+

path – absolute path to a global string

+
+
+
+ +
+
+string GetMiesVersion()
+

Returns the full path to the mies-igor version string. Creating it when necessary.

+

Never ever write this string!

+
+ +
+
+wave GetPossiblePathsToGit()
+

Return a text wave with absolute paths to git binaries with HFS : separators.

+

The paths may not exist.

+
+ +
+
+static string CreateMiesVersion()
+

Return the version string for the mies-igor project.

+

The mies version looks like

+

/// Release_1.4_20170929-16-g497e7aa8
+/// Date and time of last commit: 2018-05-08T14:42:50+02:00
+/// Submodule status:
+/// 160000 6c47163858d99986b27c70f6226e8fca894ed5f7 0   Packages/IPNWB
+/// 160000 ed7e824a6e065e383ae31bb304383e13d7c7ccb5 0   Packages/ITCXOP2
+/// 160000 2bd259940cb332339ed3c82b74632f06c9b68a15 0   Packages/ZeroMQ
+/// 160000 657e9e8abdc92aa299301796d710a0a717da4ef8 0   Packages/unit-testing
+///
+
+
+ 
or #UNKNOWN_MIES_VERSION on error
+
+@returns the mies version
+
+
+

+
+ +
+
+string GetDataAcqRunMode(string device)
+

Returns the absolute path to the variable runMode

+

The variable holds one of DAQRunModes.

+
+ +
+
+string GetDAQDeviceID(string device)
+

Returns the absolute path to the device ID.

+
+ +
+
+string GetCount(string device)
+

Returns the absolute path to the global variable count storing the number of data acquisition cycles performed.

+

Count equals zero on the first sweep.

+
+ +
+
+string GetLockedDevices()
+

Returns the list of locked devices.

+
+ +
+
+string GetUserComment(string device)
+

Return the absolute path to the user comment string.

+
+ +
+
+string GetStopCollectionPoint(string device)
+

Return the stop collection point, this is a length in points. The StopCollectionPoint is the effective length of the DAC data. While for NI and SUTTER hardware this equals the length of the DAC output wave, for ITC the DAC output wave is longer, see DC_CalculateDAQDataWaveLengthImpl.

+

Also for SUTTER hardware the ADC input wave length is different from the DAC output wave. StopCollectionPoint CAN NOT be used to determine the length of the ADC input wave.

+

+

See also

+

GetFifoPosition()

+
+

+
+ +
+
+string GetADChannelToMonitor(string device)
+

Return the ADC to monitor.

+

This is the first actice AD channel in DAQDataWave and DAQConfigWave.

+
+ +
+
+string GetRunningSingleDevice()
+

Return global device for background tasks.

+

+
+Todo:
+

remove and use background struct members for the deviceID and GetDeviceMapping instead

+
+ +

+
+ +
+
+string GetActiveSetCount(string device)
+

Return the active set count.

+

Active set count keeps track of how many steps of the largest currently selected set on all active channels still have to be done. Not counting the currently acquiring sweep.

+
+ +
+
+string GetInteractiveMode()
+

Return the interactive mode.

+

By default MIES operates in interactive mode (1) in the main thread and in non-interactive mode in preemptive threads. The user can change that to non-interactive mode where all dialog/popups etc. are avoided and replaced with sensible defaults.

+
+ +
+
+string GetTestpulseRunMode(string device)
+

Returns the absolute path to the testpulse running modes, holds one of TestPulseRunModes.

+
+ +
+
+string GetSUDeviceList()
+

Returns SU device list.

+

Internal use only, prefer DAP_GetSUDeviceList() instead.

+

The initial value "" is different from NONE which denotes no matches.

+
+ +
+
+string GetNIDeviceList()
+

Returns NI device list.

+

Internal use only, prefer DAP_GetNIDeviceList() instead.

+

The initial value "" is different from NONE which denotes no matches.

+
+ +
+
+string GetITCDeviceList()
+

Returns ITC device list.

+

Internal use only, prefer DAP_GetITCDeviceList() instead.

+

The initial value "" is different from NONE which denotes no matches.

+
+ +
+
+string GetLastAcqHookCallTimeStamp(string device)
+

Returns the last time stamp HW_NI_RepeatAcqHook was called.

+
+ +
+
+string GetFIFOFileRef(string device)
+

Returns FIFO file reference.

+
+ +
+
+string GetNITestPulseCounter(string device)
+

Returns TestPulse Counter for Background Task.

+
+ +
+
+string GetNI_AISetup(string device)
+

Returns the current NI setup string for analog in through DAQmx_Scan.

+
+ +
+
+string GetNI_ADCTaskID(string device)
+

Returns the ADC task ID set after DAQmx_Scan in HW_NI_StartAcq.

+
+ +
+
+string GetNI_DACTaskID(string device)
+

Returns the DAC task ID set after DAQmx_WaveFormGen in HW_NI_PrepareAcq.

+
+ +
+
+string GetSU_IsAcquisitionRunning(string device)
+

Returns if the Sutter hardware is acquiring.

+
+ +
+
+string GetSU_AcquisitionError(string device)
+

Returns if the Sutter hardware had an acquisition error.

+
+ +
+
+string GetNI_TTLTaskID(string device)
+

Returns the TTL task ID set by DAQmx_DIO_Config in HW_NI_PrepareAcq.

+
+ +
+
+string GetSessionStartTime()
+

Return the experiment session start time in NWB-speech.

+

This is the time when the last device was locked.

+
+ +
+
+string GetNWBFileIDExport(string device)
+

Return the HDF5 file identifier for the NWB export.

+
+ +
+
+string GetNWBFilePathExport(string device)
+

Return the absolute path to the file for NWB export.

+
+ +
+
+string GetSessionStartTimeReadBack(string device)
+

Return the experiment session start time in NWB-speech as read back from the NWB file.

+
+ +
+
+string GetThreadGroupIDFIFO(string device)
+

Return the thread group ID for the FIFO monitor/resetting daemon.

+
+ +
+
+string GetTemporaryString()
+

Return the absolute path to the temporary global string.

+

Callers should always assume that this string contains garbage.

+
+ +
+
+string GetTemporaryVar()
+

Return the absolute path to the temporary global variable.

+

Callers should always assume that this variable contains garbage.

+
+ +
+
+string GetRNGSeed(string device)
+

Return the absolute path to the RNG seed value.

+

This seed value can be used for deriving device dependent random numbers.

+

Typical sequence:

+

NVAR rngSeed = $GetRNGSeed(device)
+SetRandomSeed/BETR=1 rngSeed
+rngSeed += 1
+variable val = GetReproducibleRandonNumber()
+
+
+

+
+ +
+
+string GetRepeatedAcquisitionCycleID(string device)
+

Return the absolute path to the repeated acquisition cycle ID.

+
+ +
+
+string GetRepurposedSweepTime(string device)
+

Return the absolute path to the repurposed sweep time global variable.

+

Units are seconds.

+

This value is added on top of the left over sweep time. Use a negative value to have a shorter ITI than what is left over in the sweep.

+

+

See also

+

LeftOverSweepTime()

+
+

+
+ +
+
+string GetRepeatedAcquisitionFuncList()
+

Return the list of functions to be executed after ITI in repeated acquisition.

+
+ +
+
+string GetRepeatedAcquisitionStart()
+

Return the start time, in ticks, of the ITI cycle.

+
+ +
+
+string GetRepeatedAcquisitionDuration()
+

Return the duration, in ticks, of the ITI cycle.

+
+ +
+
+string GetFifoPosition(string device)
+

Return the current fifo position (a length)

+

Only valid if called during DAQ with DATA_ACQUISITION_MODE. This value is relative to first row of the rawDACWave, so an possible offset is already included in it.

+
+ +
+
+string GetAnalysisFuncErrorCounter(string device)
+

Return the error counter for the analysis function management.

+

Mainly used during testing to ensure that no RTE was thrown.

+
+ +
+
+string GetMaxIntertrialInterval(string device)
+

Return the maximum ITI of all active sets.

+

Only meaningful after preparing DAQ in DC_Configure()

+
+ +
+
+string GetPxPVersion()
+

Return the version number of the Igor experiment.

+
+ +
+
+string GetPxPVersionForAB(dfref dfr)
+

Return the version number of the Igor experiment loaded into the analysis browser.

+

+

See also

+

GetAnalysisExpFolder()

+
+

+
+
Parameters:
+

dfr – experiment folder,

+
+
+
+ +
+
+string GetSweepFormulaJSONid(dfref dfr)
+

Return the JSON ID for the sweep formula.

+
+ +
+
+string GetSweepFormulaParseErrorMessage()
+

Return the formula error message for the sweep formula.

+
+ +
+
+string GetSettingsJSONid()
+

Return the JSON id of the settings file.

+

Loads the stored settings on disc if required.

+
+ +
+
+string GetAcquisitionState(string device)
+

Return the path to the acquisition state.

+

Holds one of AcquisitionStates

+
+ +
+
+string GetBugCount()
+

Return the global bug count, incremented by Bug()

+

Mostly used for testing.

+
+ +
+
+string GetNWBOverrideHistoryAndLogFile()
+

Temporary storage for IP history and logfile.

+

Used for reexporting from NWBv1 into NWBv2, see AB_ReExport()

+
+ +
+
+string GetTestpulseCycleID(string device)
+

Return the absolute path to the test pulse cycle ID.

+
+ +
+
+string GetCalledOnceVariable(string name)
+

Returns the path to the “called once” variable of the given name.

+
+ +
+
+string GetThreadGroupID()
+

Returns string path to the thread group id.

+
+ +
+
+string GetNumThreads()
+

Returns string path to the number of threads.

+
+ +
+
+string GetTaskDisableStatus()
+

Returns string path to flag if background task was disabled.

+
+ +
+
+string GetLastSweepFormulaCode(dfref dfr)
+

Returns the string path to the last successfully executed SweepFormula code.

+
+ +
+
+string GetDFReferenceCount(dfref dfr)
+

Returns the reference count variable of the given DF.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___gui_popup_menu_ext_8ipf.html b/file/_m_i_e_s___gui_popup_menu_ext_8ipf.html new file mode 100644 index 0000000000..2cc597c953 --- /dev/null +++ b/file/_m_i_e_s___gui_popup_menu_ext_8ipf.html @@ -0,0 +1,522 @@ + + + + + + + + File MIES_GuiPopupMenuExt.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_GuiPopupMenuExt.ipf

+

Helper functions related to GUI controls.

+

These procedures provide a way to replace popup menus with many entries with context menus. Context menus can provide submenus, that allow better organization of menu entries.

+

Example:

+

Function SetupPopupMenuExt()
+    KillWindow/Z panel0
+    NewPanel/N=$"panel0"/K=1
+    Button popupext_menu1, pos={3.00, 20.00}, size={200,20},proc=PEXT_ButtonProc,title="DropDownMenu1 ▼", userdata($PEXT_UDATA_POPUPPROC)="DemoProc", userdata($PEXT_UDATA_ITEMGETTER)="GetMenuList1"
+    Button popupext_menu2, pos={3.00, 55.00}, size={200,20},proc=PEXT_ButtonProc,title="DropDownMenu2 ▼", userdata($PEXT_UDATA_POPUPPROC)="DemoProc", userdata($PEXT_UDATA_ITEMGETTER)="GetMenuList2"
+    Button popupext_menu3, pos={3.00, 90.00}, size={200,20},proc=PEXT_ButtonProc,title="DropDownMenu3 ▼", userdata($PEXT_UDATA_POPUPPROC)="DemoProc", userdata($PEXT_UDATA_ITEMGETTER)="GetMenuList3"
+End
+
+Function DemoProc(pa) : PopupMenuControl
+    STRUCT WMPopupAction &pa
+
+    print "EventCode/Win/Selected/ctrlName: ", pa.eventCode, pa.win, pa.popStr, pa.ctrlName
+End
+
+Function/S GetMenuList1()
+
+    Make/FREE/T/N=300 testItems = num2char(97 + mod(p, 26)) + "_" + num2str(p)
+    return TextWaveToList(testItems, ";")
+End
+
+Function/WAVE GetMenuList2(device)
+    string device
+
+    Make/FREE/T/N=(2) menus
+    menus[0] = "Kriemhild;Brünhild"
+    menus[1] = "Siegfried;Gunther"
+    SetDimLabel ROWS, 0, $"Women", menus
+    SetDimLabel ROWS, 1, $"Men", menus
+
+    return menus
+End
+
+Function/WAVE GetMenuList3(device)
+    string device
+
+    Make/FREE/T menus = {"Kriemhild", "Brünhild", "Siegfried", "Gunther"}
+    WAVE/T splitMenu = PEXT_SplitToSubMenus(menus, method = PEXT_SUBSPLIT_ALPHA)
+    PEXT_GenerateSubMenuNames(splitMenu)
+    return splitMenu
+End
+
+
+

+

The original popupmenu has to be replaced by a button with the PEXT_ButtonProc as procedure. The userdata of the button stores as list with key value pairs a function that returns the menu item list and a function that is the PopupMenuControl procecure of the former popupmenu. The function for the menu item list corresponds to the function given for a popupmenu as e.g. value=GetMenuList1() that returns a string with semicolon separated list of menu items. The names for the submenus are generated automatically in that case. If one wants to disable the menu, return “” as menu item list. Then a disabled “_none_” is shown that can not be selected.

+

The constants PEXT_UDATA_ITEMGETTER and PEXT_UDATA_POPUPPROC were defined for the keys in the userdata string.

+

When a user selects an entry in the context menu the PopupMenuControl control defined through PEXT_UDATA_POPUPPROC is called. So the proc of the previous popupmenu can be used without further adaptations.

+

User defined sub menus:

+

User defined submenus can be created as well. Therefore an extension was added to the function that returns the menu items. Instead of a string as described before a function can be defined that returns a 1D text wave, e.g. GetMenuList2() in the example. Each element contains a semicolon separated list of menu items. Each rows DimLabel is used as submenu name, where the elements menu items are put. The DimLabels must not be empty. The wave can have up to MAX_SUBMENUS elements. The button popupext_menu2 shows this extension in the example.

+

Half automatic generation:

+

Example 3 from Button popupext_menu3 shows how a menu is created by defining a wave with menu items first. Then the menu items are split to sub menus with PEXT_SplitToSubMenus using the method PEXT_SUBSPLIT_ALPHA. In the second step the sub menu named are generated with the default algorithm by calling PEXT_GenerateSubMenuNames.

+

Method Description

+

PEXT_SUBSPLIT_DEFAULT

+

In each sub menu up to NUM_SUBENTRIES menu items are placed. If MAX_SUBMENUS number of sub menus are reached then the remaining menu items are placed in the last sub menu.

+

PEXT_SUBSPLIT_ALPHA

+

In each sub menu up to NUM_SUBENTRIES menu items are placed. If the beginning letter of the last menu item in the sub menu differs from the beginning letter of the first menu item then the menu items in the sub menu get reduced. All menu item beginning with the letter of the last menu item are moved to the next sub menu. If the beginning letters match then no menu items get moved. If MAX_SUBMENUS number of sub menus are reached then the remaining menu items are placed in the last sub menu.

+

PEXT_SUBNAMEGEN_DEFAULT

+

In a sub menu from the first and last menu item the number of letters from the beginning is counted until the letters do not match. This part of the menu item is used and taken as a sub menu name in a range notation: Alfons, Aluminium -> Alf .. Alu This is also applied between different sub menus, so the last menu item and the first menu item of the next sub menu. If in the previous sub menu the number of letters determined for the last menu item is higher then for the first name component the higher amount is taken: e.g. Balalaika, Cembalo -> B .. C -> Bal .. C (because Alu were three letters)

+
+

Functions

+
+
+string PEXT_SubMenuName(variable subMenuNr)
+

Menu definition templates for up to MAX_SUBMENUS sub menus. The constant MAX_SUBMENUS stores the number of these definitions and must be updated if more definitions are added.

+

Returns sub menu names for all PEXT sub menus This is called on each menu click/compilation for all dynamic defined Menus where PEXT_SubMenuName is used.

+
+
Parameters:
+

subMenuNr – number of current sub menu

+
+
+
+ +
+
+string PEXT_PopupMenuItems(variable subMenuNr)
+

Returns menu items for all PEXT menus This is called on each menu click/compilation for all dynamic defined Menus where PEXT_PopupMenuItems is used.

+

Callled very often (MAX_SUBMENUS^2/2).

+
+
Parameters:
+

subMenuNr – number of current sub menu

+
+
+
+ +
+
+variable PEXT_Callback(string popupStr, string text, variable itemNum)
+

This callback is executed when the user selected a PEXT dynamic menu item. It is not called if the user aborted the menu by clicking somewhere else.

+
+
Parameters:
+
    +

  • popupStr – popup string

    • +

  • text – selected menu item text

    • +

  • itemNum – selected item index in submenu

    • +
+
+
+
+ +
+
+string PEXT_ITEMGETTER_LIST_PROTO()
+

Prototype for the menu item getter that allows user defined sub menu attribution of menu items.

+
+ +
+
+wave PEXT_ITEMGETTER_WAVE_PROTO(string device)
+

Prototype for the menu item getter that is compatible with the former popupmenu value=procedure definition.

+
+ +
+
+variable PEXT_POPUPACTION_PROTO(WMPopupAction *pa)
+

Prototype for the former popupaction procedure, that is only called virtually now through the PopupContextualMenu callback.

+
+
Parameters:
+

pa – WMPopupAction structure

+
+
+
+ +
+
+variable PEXT_ButtonProc(WMButtonAction *ba)
+

Generic procedure for button actions from popup extension controls Fills the global popupExtMenuInfo wave with current menu setup information retrieved from the function defined in the buttons userdata through PEXT_UDATA_ITEMGETTER key. This getter function can either return a string or 1D text wave.

+
+
Parameters:
+

ba – WMButtonAction structure

+
+
+
+ +
+
+static variable PEXT_VerifyAndSetMenuWave(WaveTextOrNull menuWave)
+

Verifies menu data input wave and transfers it to global.

+
+ +
+
+static variable PEXT_SetDisabledMenu()
+

Sets the menu to show a non selectable “_none_” entry.

+
+ +
+
+wave PEXT_SplitToSubMenus(WaveTextOrNull menuList, variable method = defaultValue)
+

Automatically splits a 1D text wave with menu items to submenus This function does not name submenus.

+

+

See also

+

PEXT_SubMenuSplitting

+
+

+
+
Parameters:
+
    +

  • menuList – [in] 1d text wave with menu items

    • +

  • method – [in] [optional, default = PEXT_SUBSPLIT_DEFAULT] sets how the menu items are split to sub menus

    • +
+
+
Returns:
+

1d text wave where each element contains a list of menu items. Each element represents a sub menu.

+
+
+
+ +
+
+variable PEXT_GenerateSubMenuNames(WaveTextOrNull splitMenu, variable method = defaultValue)
+

Automatically generates submenu names and applies them on the given wave.

+

+

See also

+

PEXT_SubMenuNameGeneration

+
+

+
+
Parameters:
+
    +

  • splitMenu – [in] 1d text wave with menu item lists for sub menus as returned by PEXT_SplitToSubMenus()

    • +

  • method – [in] [optional, default = PEXT_SUBNAMEGEN_DEFAULT] sets how the sub menu names are generated

    • +
+
+
+
+ +
+
+

Variables

+
+
+static const double MAX_SUBMENUS = 12
+
+ +
+
+static const string WAVE_NOTE_PROCNAME = "PROC"
+
+ +
+
+static const string WAVE_NOTE_WINDOWNAME = "WINNAME"
+
+ +
+
+static const string WAVE_NOTE_CTRLNAME = "CTRLNAME"
+
+ +
+
+static const string MENUNAME_UNUSED = "*** bug, report to dev ***"
+
+ +
+
+static const string MENU_DISABLE_SPECIAL = "\\M0"
+
+ +
+
+static const string LSEP = ";"
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___gui_utilities_8ipf.html b/file/_m_i_e_s___gui_utilities_8ipf.html new file mode 100644 index 0000000000..a693229ea7 --- /dev/null +++ b/file/_m_i_e_s___gui_utilities_8ipf.html @@ -0,0 +1,1480 @@ + + + + + + + + File MIES_GuiUtilities.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_GuiUtilities.ipf

+

Helper functions related to GUI controls.

+
+

Unnamed Group

+
+
+variable PointsToPixel(variable var)
+

Conversion between pixel <-> points.

+
+ +
+
+variable PixelToPoints(variable var)
+
+ +
+
+

Functions

+
+
+variable ShowControl(string win, string control)
+

Show a GUI control in the given window.

+
+ +
+
+variable ShowControls(string win, string controlList)
+

Show a list of GUI controls in the given window.

+
+ +
+
+variable HideControl(string win, string control)
+

Hide a GUI control in the given window.

+
+ +
+
+variable HideControls(string win, string controlList)
+

Hide a list of GUI controls in the given window.

+
+ +
+
+variable EnableControl(string win, string control)
+

Enable a GUI control in the given window.

+
+ +
+
+variable EnableControls(string win, string controlList)
+

Enable a list of GUI controls in the given window.

+
+ +
+
+variable DisableControl(string win, string control)
+

Disable a GUI control in the given window.

+
+ +
+
+variable DisableControls(string win, string controlList)
+

Disable a list of GUI controls in the given window.

+
+ +
+
+variable SetControlTitles(string win, string controlList, string controlTitleList)
+

Set the title of a list of controls.

+
+ +
+
+variable SetControlTitle(string win, string controlName, string newTitle)
+

Set the title of a control.

+
+ +
+
+variable SetControlProcedures(string win, string controlList, string newProcedure)
+

Set the procedure of a list of controls.

+
+ +
+
+variable SetControlProcedure(string win, string controlName, string newProcedure)
+

Set the procedure of a control.

+
+ +
+
+string GetTitle(string recMacro, variable supress = defaultValue)
+

Return the title of a control.

+
+
Parameters:
+
    +

  • recMacro – recreation macro for ctrl

    • +

  • supress – supress assertion that ctrl must have a title

    • +
+
+
Returns:
+

Returns the title or an empty string

+
+
+
+ +
+
+variable SetControlTitleColors(string win, string controlList, variable R, variable G, variable B)
+

Change color of the title of mulitple controls.

+
+ +
+
+variable SetControlTitleColor(string win, string controlName, variable R, variable G, variable B)
+

Change color of a control.

+
+ +
+
+variable ChangeControlColor(string win, string controlName, variable R, variable G, variable B)
+

Change color of a control.

+
+ +
+
+variable ChangeControlValueColor(string win, string controlName, variable R, variable G, variable B)
+

Change the font color of a control.

+
+ +
+
+variable ChangeControlValueColors(string win, string controlList, variable R, variable G, variable B)
+

Change the font color of a list of controls.

+
+ +
+
+variable SetControlBckgColor(string win, string controlName, variable R, variable G, variable B, variable Alpha = defaultValue)
+

Changes the background color of a control.

+
+
Parameters:
+
    +

  • win – panel

    • +

  • controlName – GUI control name

    • +

  • R – red

    • +

  • G – green

    • +

  • B – blue

    • +

  • Alpha – defaults to opaque if not provided

    • +
+
+
+
+ +
+
+variable ChangeControlBckgColors(string win, string controlList, variable R, variable G, variable B)
+

Change the background color of a list of controls.

+
+ +
+
+variable GetCheckBoxState(string win, string control)
+

Returns one if the checkbox is selected or zero if it is unselected.

+
+ +
+
+variable SetSetVariable(string win, string Control, variable newValue, variable respectLimits = defaultValue)
+

Set the internal number in a setvariable control.

+
+ +
+
+variable SetSetVariableString(string win, string control, string str, variable setHelp = defaultValue)
+

Set the SetVariable contents as string.

+
+
Parameters:
+
    +

  • win – window

    • +

  • control – control of type SetVariable

    • +

  • str – string to set

    • +

  • setHelp – [optional, defaults to false] set the help string as well. Allows to work around long text in small controls.

    • +
+
+
+
+ +
+
+variable SetCheckBoxState(string win, string control, variable state)
+

Set the state of the checkbox.

+
+ +
+
+variable SetSetVariableLimits(string win, string Control, variable low, variable high, variable increment)
+

Set the input limits for a setVariable control.

+
+ +
+
+variable GetSetVariable(string win, string control)
+

Returns the contents of a SetVariable.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetSetVariableString(string win, string control)
+

Returns the contents of a SetVariable with an internal string.

+
+ +
+
+string GetPopupMenuString(string win, string control)
+

Returns the current PopupMenu item as string.

+
+ +
+
+variable GetPopupMenuIndex(string win, string control)
+

Returns the zero-based index of a PopupMenu.

+
+ +
+
+variable SetPopupMenuIndex(string win, string control, variable index)
+

Sets the zero-based index of the PopupMenu.

+
+ +
+
+variable SetPopupMenuVal(string win, string control, string list = defaultValue, string func = defaultValue)
+

Sets the popupmenu value.

+
+ +
+
+string SetPopupMenuString(string win, string control, string str)
+

Sets the popupmenu string.

+
+
Parameters:
+
    +

  • win – target window

    • +

  • control – target control

    • +

  • str – popupmenu string to select. Supports wildcard character(*)

    • +
+
+
Returns:
+

set string with wildcard expanded

+
+
+
+ +
+
+string GetValDisplayAsString(string win, string control)
+

Returns the contents of a ValDisplay.

+
+ +
+
+variable GetValDisplayAsNum(string win, string control)
+

Returns the contents of a ValDisplay as a number.

+
+ +
+
+variable GetSliderPositionIndex(string win, string control)
+

Returns the slider position.

+
+ +
+
+variable SetSliderPositionIndex(string win, string control, variable index)
+

Sets the slider position.

+
+ +
+
+variable SetValDisplay(string win, string control, variable var = defaultValue, string str = defaultValue, string format = defaultValue)
+

Set a ValDisplay.

+

+The following parameter combinations are valid:

    +

  • var

    • +

  • var and format

    • +

  • str

    • +
+

+
+
Parameters:
+
    +

  • win – panel

    • +

  • control – GUI control

    • +

  • var – numeric variable to set

    • +

  • format – format string referencing the numeric variable var

    • +

  • str – path to global variable or wave element

    • +
+
+
+
+ +
+
+variable ControlExists(string win, string control)
+

Check if a given control exists.

+
+ +
+
+string FindControl(string control)
+

Return the full subwindow path to the windows the control belongs to.

+
+ +
+
+string FindNotebook(string nb)
+

Return the full subwindow path to the given notebook.

+
+ +
+
+variable GetTabID(string win, string ctrl)
+

Returns the number of the current tab.

+
+
Parameters:
+
    +

  • win – window name

    • +

  • ctrl – name of the control

    • +
+
+
+
+ +
+
+variable SetControlUserData(string win, string control, string key, string value)
+

Set value as the user data named key.

+
+
Parameters:
+
    +

  • win – window name

    • +

  • control – name of the control

    • +

  • key – user data identifier

    • +

  • value – user data value

    • +
+
+
+
+ +
+
+std::tuple<RGBColor> GetTraceColor(variable index)
+

Get distinctive trace colors for a given index.

+

Holds 21 different trace colors, code originally from http://www.igorexchange.com/node/6532 but completely rewritten and bug-fixed.

+

The colors are “Twenty two colors of maximum contrast” by L. Kelly, see http://www.iscc.org/pdf/PC54_1724_001.pdf, where the color white has been removed.

+
+ +
+
+std::tuple<RGBColor> GetTraceColorForAverage()
+

Returns the trace color used for avergae type traces.

+
+ +
+
+std::tuple<RGBColor> GetTraceColorAlternative(variable index)
+

Get colors from alternative color scheme.

+

Uses 8 colors with maximum contrast for colorblind people, see https://www.wavemetrics.com/code-snippet/distinguishable-color-index and https:// jfly.iam.u-tokyo.ac.jp/color/

+

+

See also

+

GetTraceColor

+
+

+
+ +
+
+std::tuple<variable, variable> GetAxisRange(string graph, string axis, variable mode = defaultValue)
+

Query the axis minimum and maximum values.

+

For none existing graph or axis NaN is returned for minimum and high.

+

The return value for autoscale axis depends on the mode flag: AXIS_RANGE_INC_AUTOSCALED -> [0, 0] AXIS_RANGE_DEFAULT -> [NaN, NaN]

+
+
Parameters:
+
+
+
Returns:
+

minimum and maximum value of the axis range

+
+
+
+ +
+
+static std::tuple<variable, variable> GetAxisRangeFromInfo(string graph, string info, string axis, variable mode)
+
+ +
+
+variable GetAxisOrientation(string graph, string axes)
+

Return the orientation of the axis as numeric value.

+
+
Returns:
+

one of AxisOrientationConstants

+
+
+
+ +
+
+static string GetAxisRecreationMacro(string info)
+

Return the recreation macro for an axis.

+
+ +
+
+variable GetAxisLogMode(string graph, string axis)
+

Return the logmode of the axis.

+
+
Returns:
+

One of ModifyGraphLogModes

+
+
+
+ +
+
+static variable GetAxisLogModeFromInfo(string info)
+
+ +
+
+wave GetAxesProperties(string graph, string axesRegexp = defaultValue, variable orientation = defaultValue, variable mode = defaultValue)
+

Returns a wave with the minimum and maximum values of each axis.

+

Use SetAxesRanges to set the minimum and maximum values

+

See also

+

GetAxisRange

+
+

+
+
Parameters:
+
    +

  • graph – [in] Name of graph

    • +

  • axesRegexp – [in] [optional: default not set] filter axes names list by this optional regular expression

    • +

  • orientation – [in] [optional: default not set] filter orientation of axes see AxisOrientationConstants

    • +

  • mode – [in] [optional: default AXIS_RANGE_DEFAULT] filter returned axis information by mode see AxisPropModeConstants

    • +
+
+
Returns:
+

free wave with rows = axes, cols = axes info, dimlabel of rows is axis name

+
+
+
+ +
+
+variable SetAxesProperties(string graph, wave props, string axesRegexp = defaultValue, variable orientation = defaultValue, variable mode = defaultValue)
+

Set the properties of all axes as stored by GetAxesProperties.

+

Includes a heuristic if the name of the axis changed after GetAxesProperties. The axis range is also restored if its index in the sorted axis list and its orientation is the same.

+

+

See also

+

GetAxisProps

+
+

+
+
Parameters:
+
    +

  • graph – [in] Name of graph

    • +

  • props – [in] wave with graph props as set in GetAxesProperties

    • +

  • axesRegexp – [in] [optional: default not set] filter axes names list by this optional regular expression

    • +

  • orientation – [in] [optional: default not set] filter orientation of axes see AxisOrientationConstants

    • +

  • mode – [in] [optional: default 0] axis set mode see AxisPropModeConstants

    • +
+
+
+
+ +
+
+string GetNextFreeAxisName(string graph, string axesBaseName)
+

Returns the next axis name in a row of consecutive and already existing axis names.

+
+ +
+
+string GetUniqueAxisName(string graph, string axesBaseName)
+

Return a unique axis name.

+
+ +
+
+variable SetGuiControlValue(string win, string control, string value)
+

Generic wrapper for setting a control’s value pass in the value as a string, and then decide whether to change to a number based on the type of control.

+
+ +
+
+string GetGuiControlValue(string win, string control)
+

Generic wrapper for getting a control’s value.

+
+ +
+
+string GetGuiControlState(string win, string control)
+

Generic wrapper for getting a controls state (enabled, hidden, disabled)

+
+ +
+
+variable SetGuiControlState(string win, string control, string controlState)
+

Generic wrapper for setting a controls state (enabled, hidden, disabled)

+
+ +
+
+variable IsControlDisabled(string win, string control)
+

Return one if the given control is disabled, zero otherwise.

+
+ +
+
+variable IsControlHidden(string win, string control)
+

Return one if the given control is hidden, zero otherwise.

+
+ +
+
+string GetMainWindow(string subwindow)
+

Return the main window name from a full subwindow specification.

+

+UTF_NOINSTRUMENTATION

+
+
Parameters:
+

subwindow – window name including subwindows, e.g. panel#subWin1#subWin2

+
+
+
+ +
+
+string GetCurrentWindow()
+

Return the currently active window.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+wave GetCursorInfos(string graph)
+

Return a 1D text wave with all infos about the cursors.

+

Returns an invalid wave reference when no cursors are present. Counterpart to RestoreCursors().

+

The data is sorted like CURSOR_NAMES.

+
+ +
+
+variable RestoreCursors(string graph, WaveTextOrNull cursorInfos)
+

Restore the cursors from the info of GetCursorInfos().

+
+ +
+
+wave GetAnnotationInfo(string graph)
+

Return the infos for all annotations on the graph.

+
+ +
+
+variable RestoreAnnotationPositions(string graph, WaveText annoInfo)
+

Restore annotation positions.

+
+ +
+
+variable AutoscaleVertAxisVisXRange(string graph)
+

Autoscale all vertical axes in the visible x range.

+
+ +
+
+variable GetInternalSetVariableType(string recMacro)
+

Return the type of the variable of the SetVariable control.

+
+
Returns:
+

one of GetInternalSetVariableTypeReturnTypes

+
+
+
+ +
+
+variable ExtractLimitsFromRecMacro(string recMacro, variable *minVal, variable *maxVal, variable *incVal)
+
+ +
+
+variable ExtractLimits(string win, string control, variable *minVal, variable *maxVal, variable *incVal)
+

Extract the limits specification of the control and return it in minVal, maxVal and incVal

+

+

See also

+

ExtractLimitsFromRecMacro for a faster way if you already have the recreation macro

+
+

+
+
Returns:
+

0 on success, 1 if no specification could be found

+
+
+
+ +
+
+variable CheckIfValueIsInsideLimits(string win, string control, variable val)
+

Check if the given value is inside the limits defined by the control.

+
+
Returns:
+

- 0: outside limits

    +

  • 1: inside limits, i.e. val lies in the range [min, max]

    • +

  • NaN: no limits could be found

    • +
+

+
+
+
+ +
+
+variable GetLimitConstrainedSetVar(string recMacro, variable val)
+

Returns a value that is constrained by the limits defined by the control.

+
+
Returns:
+

val <= control max and val >= contorl min

+
+
+
+ +
+
+variable GetFunctionParameterType(string func, variable paramIndex)
+

Return the parameter type a function parameter.

+
+
Parameters:
+
    +

  • func – name of the function

    • +

  • paramIndex – index of the parameter

    • +
+
+
+
+ +
+
+string GetValueFromRecMacro(string key, string recMacro)
+

Return an entry from the given recreation macro.

+

The recreation macro of a single GUI control looks like: 

PopupMenu popup_ctrl,pos={1.00,1.00},size={55.00,19.00},proc=PGCT_PopMenuProc
+PopupMenu popup_ctrl,mode=1,popvalue="Entry1",value= #"\"Entry1;Entry2;Entry3\""
+
+
+

+

+

This function allows to extract key/value pairs from it.

+
+
Parameters:
+
    +

  • key – non-empty string (must be followed by = in the recreation macro)

    • +

  • recMacro – GUI control recreation macro as returned by ControlInfo

    • +
+
+
+
+ +
+
+variable SearchForInvalidControlProcs(string win, variable warnOnEmpty = defaultValue)
+

Search for invalid control procedures in the given panel or graph.

+

Searches recursively in all subwindows.

+
+
Parameters:
+
    +

  • win – panel or graph

    • +

  • warnOnEmpty – [optional, default to false] print out controls which don’t have a control procedure but can have one.

    • +
+
+
Returns:
+

1 on error, 0 if everything is fine.

+
+
+
+ +
+
+variable GetNumericSubType(string subType)
+

Convert the function subType names for GUI control procedures to a numeric value as used by ControlInfo

+
+ +
+
+variable GetControlType(string win, string control)
+

Return the numeric control type.

+
+
Returns:
+

one of GUIControlTypes

+
+
+
+ +
+
+variable DoesControlHaveInternalString(string recMacro)
+

Determines if control stores numeric or text data.

+
+ +
+
+variable GetCheckBoxMode(string win, string checkBoxName)
+

Returns checkbox mode.

+
+ +
+
+variable GetListBoxSelRow(string win, string ctrl)
+

Returns the selected row of the ListBox for some modes without selection waves.

+
+ +
+
+variable SetListBoxSelection(string win, string ctrl, variable val, variable row, variable col = defaultValue)
+

Set the listbox selection.

+
+
Parameters:
+
    +

  • win – panel

    • +

  • ctrl – control

    • +

  • val – One of ListBoxSelectionWaveFlags

    • +

  • row – row index

    • +

  • col – [optional, defaults to all columns] column index

    • +
+
+
+
+ +
+
+variable IsInsideRect(Point *loc, RectF *r)
+

Check if the location loc is inside the rectangle r

+
+ +
+
+variable GetControlCoordinates(string win, string ctrl, RectF *s)
+

Return the coordinates of the control borders relative to the top left corner in pixels.

+
+ +
+
+string GetNotebookText(string win, variable mode = defaultValue)
+

Get the text (plain or formatted) from the notebook.

+
+ +
+
+variable ReplaceNotebookText(string win, string text)
+

Replace the contents of the notebook.

+
+ +
+
+variable AppendToNotebookText(string win, string text)
+

Append to a notebook.

+
+ +
+
+variable NotebookSelectionAtEnd(string win)
+

Select the end in the given notebook.

+

The selection is the place where the user would naïvely enter new text.

+
+ +
+
+wave GetUserdataKeys(string recMacro)
+

Retrieves named userdata keys from a recreation macro string.

+
+
Parameters:
+

recMacro – recreation macro string

+
+
Returns:
+

Textwave with all unqiue entries or $"" if nothing could be found.

+
+
+
+ +
+
+string ControlTypeToName(variable ctrlType)
+

Converts an Igor control type number to control name.

+
+
Parameters:
+

ctrlType – ctrl type of Igor control

+
+
Returns:
+

Igor name of control type

+
+
+
+ +
+
+variable Name2ControlType(string ctrlName)
+

Converts an Igor control name to control type number.

+
+
Parameters:
+

ctrlName – Name of Igor control

+
+
Returns:
+

Igor control type number

+
+
+
+ +
+
+variable WindowTypeCanHaveChildren(string wName)
+

Checks if a certain window can act as valid host for subwindows developer note: The only integrated Igor function that does this is ChildWindowList. Though, ChildWindowList generates an RTE for non-valid windows, where this check function does not.

+
+
Parameters:
+

wName – window name that should be checked to be a valid host for subwindows

+
+
Returns:
+

1 if window is a valid host, 0 otherwise

+
+
+
+ +
+
+string GetAllWindows(string wName)
+

Recursively build a list of windows, including all child windows, starting with wName.

+
+
Parameters:
+

wName – parent window name to start with

+
+
Returns:
+

A string containing names of windows. This list is a semicolon separated list. It will include the window wName and all of its children and children of children, etc.

+
+
+
+ +
+
+static variable GetAllWindowsImpl(string wName, string *windowList)
+
+ +
+
+variable IsSubwindow(string win)
+
+ +
+
+variable PanelIsType(string device, string typeTag)
+

Checks if a window is tagged as certain type.

+

+

See also

+

panelTags returns 1 if window is a DA_Ephys panel

+
+

+
+
Parameters:
+
    +

  • device – [in] Window name to check

    • +

  • typeTag – [in] one of PANELTAG_* constants

    • +
+
+
+
+ +
+
+variable ShowSetVariableLimitsSelectionPopup(WMSetVariableAction *sva)
+

Show a contextual popup menu which allows the user to change the set variable limit’s increment.

+

    +

  • Expects the ctrl to have the named user data “DefaultIncrement”

    • +

  • Works only on right mouse click on the title or the value field, not the up/down arrow buttons

    • +
+

+
+ +
+
+variable DrawScaleBar(string graph, variable x0, variable y0, variable x1, variable y1, string unit = defaultValue, variable drawLength = defaultValue, variable labelOffset = defaultValue, variable newlineBeforeUnit = defaultValue)
+

Draw a scale bar on a graph.

+
+
Parameters:
+
    +

  • graph – graph

    • +

  • x0 – horizontal coordinate of first point

    • +

  • y0 – vertical coordinate of first point

    • +

  • x1 – horizontal coordinate of second point

    • +

  • y1 – vertical coordinate of second point

    • +

  • unit – [optional] data unit when drawing the label

    • +

  • drawLength – [optional, defaults to false] true/false for outputting the label

    • +

  • labelOffset – [optional] offset in current coordinates of the label

    • +

  • newlineBeforeUnit – [optional] Use a newline before the unit instead of a space

    • +
+
+
+
+ +
+
+std::tuple<string, variable> ParsePopupMenuValue(string recMacro)
+

Return the value and type of the popupmenu list.

+
+
Return values:
+
    +

  • value – extracted string with the contents of value from the recreation macro

    • +

  • type – popup menu list type, one of PopupMenuListTypes

    • +
+
+
+
+ +
+
+string GetPopupMenuList(string value, variable type)
+

Return the popupmenu list entries.

+
+
Parameters:
+
    +

  • value – String with a list or function (what you enter with PopupMenu value=#XXX)

    • +

  • type – One of PopupMenuListTypes

    • +
+
+
+
+ +
+
+variable ShowTraceInfoTags()
+

Enable show trace info tags globally.

+
+ +
+
+std::tuple<string, variable> GetRecreationMacroAndType(string win, string control)
+

Return the recreation macro and the type of the given control.

+
+ +
+
+variable GetControlSettingVar(string recMacro, string setting, variable defValue = defaultValue)
+

Query a numeric GUI control property.

+
+ +
+
+string GetControlSettingStr(string recMacro, string setting, string defValue = defaultValue)
+

Query a string GUI control property.

+
+ +
+
+static std::tuple<string, variable> GetControlSettingImpl(string recMacro, string setting)
+
+ +
+
+variable AdaptDependentControls(string win, string controls, variable restoreOnState, variable newMainState, variable mode)
+

Dependent on a control state set the state of a list of checkboxes.

+

newMainState: state of the main control after the user interaction, in an event handler typically the cba.checked value restoreOnState: If the newMainState is different from the restoreOnState then the states of the dependent checkboxes is saved. If the newMainState is the same as the restoreOnState then the states of the dependent checkboxes are restored mode: DEP_CTRLS_SAME or DEP_CTRLS_INVERT, defines if the dependent checkbox state follows the newMainState or the inverted newMainState

+

When the dependent checkboxes are in the dependent state they are disabled. Example: if checkbox A is on, then checkbox B must be on as well and if checkbox A is off, then any state of checkbox B is valid and if checkbox A is changed to off then the state of checkbox B when A was in the off state before should be restored. results in: newMainState -> CHECKBOX_SELECTED (when A is switched on, then B is also switched according to mode and gets disabled, as a dependent checkbox) mode -> DEP_CTRLS_SAME (A -> on then B -> on) restoreOnState -> CHECKBOX_UNSELECTED (A -> off then B gets independent and restored, A -> on then B gets dependent and B’s state saved)

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Restore on State

Main new

Mode

Action on dependent checkboxes

ON

OFF

DEP_CTRLS_SAME

state saved, unchecked, disabled

ON

OFF

DEP_CTRLS_INVERT

state saved, checked, disabled

ON

ON

ignored

state restored, enabled

OFF

ON

DEP_CTRLS_SAME

state saved, checked, disabled

OFF

ON

DEP_CTRLS_INVERT

state saved, unchecked, disabled

OFF

OFF

ignored

state restored, enabled

+

+
+ +
+
+variable ReflowNotebookText(string win)
+

Adjust the “Normal” ruler in the notebook so that all text is visible.

+
+ +
+
+variable ColorNotebookKeywords(string win, string keyWord, variable r, variable g, variable b)
+

In a formatted notebook sets a location where keyWord appear to the given color.

+
+ +
+
+std::tuple<variable, variable> GetMarqueeHelper(string axisName, variable kill = defaultValue, variable doAssert = defaultValue, variable horiz = defaultValue, variable vert = defaultValue, string *win = defaultValue)
+

Marquee helper.

+
+
Parameters:
+
    +

  • axisName – [in] coordinate system to use for returned values

    • +

  • kill – [in] [optional, defaults to false] should the marquee be killed afterwards

    • +

  • doAssert – [in] [optional, defaults to true] ASSERT out if nothing can be returned

    • +

  • horiz – [in] [optional] direction to return, exactly one of horiz/vert must be defined

    • +

  • vert – [in] [optional] direction to return, exactly one of horiz/vert must be defined

    • +

  • win – [out] [optional] allows to query the window as returned by GetMarquee

    • +
+
+
Return values:
+
    +

  • first – start of the range

    • +

  • last – end of the range

    • +
+
+
+
+ +
+
+variable ResizeControlsSafe(WMWinHookStruct *s)
+

Wrapper for ResizeControlsHook which handles a free datafolder as CDF.

+

+
+Todo:
+

reported as #5100 to WM

+
+ +

+
+ +
+
+

Variables

+
+
+static const string USERDATA_PREFIX = "userdata("
+
+ +
+
+static const string USERDATA_SUFFIX = ")"
+
+ +
+
+static const double AXIS_MODE_NO_LOG = 0
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___h_d_f5_ops_8ipf.html b/file/_m_i_e_s___h_d_f5_ops_8ipf.html new file mode 100644 index 0000000000..2148cbcd46 --- /dev/null +++ b/file/_m_i_e_s___h_d_f5_ops_8ipf.html @@ -0,0 +1,276 @@ + + + + + + + + File MIES_HDF5Ops.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_HDF5Ops.ipf

+

This file is only provided for backward compatibility and will always be empty.

+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___i_v_s_c_c_8ipf.html b/file/_m_i_e_s___i_v_s_c_c_8ipf.html new file mode 100644 index 0000000000..e58ac050b7 --- /dev/null +++ b/file/_m_i_e_s___i_v_s_c_c_8ipf.html @@ -0,0 +1,438 @@ + + + + + + + + File MIES_IVSCC.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_IVSCC.ipf

+

IVS Routines for IVSCC/PatchSeq automation

+

ZeroMQ Infos:

    +

  • Listening port for the REP/ROUTER socket starts at ZEROMQ_BIND_REP_PORT.

    • +

  • Listening port for the PUBLISHER socket starts at ZEROMQ_BIND_PUB_PORT

    • +

  • If one of those ports is already in use, the next larger port is tried.

    • +

  • The publisher socket does include an automatic heartbeat message every 5 seconds. Subscribe to ZeroMQ_HEARTBEAT if you want to receive that.

    • +

  • All available message filters can be queried via FFI_GetAvailableMessageFilters().

    • +

  • More information regarding the ZeroMQ-XOP is located here

    • +

  • See IVS_PublishQCState() for more infos about the published messages

    • +
+

+
+

Functions

+
+
+variable IVS_ConfigureMCC()
+
+ +
+
+variable IVS_runBaselineCheckQC()
+

Run the baseline QC check.

+

+

See also

+

PSQ_PipetteInBath

+
+

+
+ +
+
+variable IVS_runInitAccessResisQC()
+

Run the initial access resistance smoke from the WSE.

+
+ +
+
+variable IVS_RunGigOhmSealQC()
+

Run PSQ_SealEvaluation()

+
+ +
+
+variable IVS_Load_StimSet(string stim_filename)
+

Loads a single stimulus for the user when using the ZMQ Proxy.

+
+ +
+
+variable IVS_ExportAllData(string filePath)
+
+ +
+
+string IVS_ReturnNWBFileLocation()
+
+ +
+
+variable IVS_SaveExperiment(string filename)
+
+ +
+
+variable IVS_runStimWave(string stimWaveName, variable scaleFactor)
+

Run a designated stim wave.

+
+
Parameters:
+
    +

  • stimWaveName – stimWaveName to be used

    • +

  • scaleFactor – scale factor to run the stim wave at

    • +
+
+
+
+ +
+
+variable IVS_ButtonProc_Setup(WMButtonAction *ba)
+
+ +
+
+variable IVS_ButtonProc_BaselineQC(WMButtonAction *ba)
+
+ +
+
+variable IVS_ButtonProc_AccessResist(WMButtonAction *ba)
+
+ +
+
+variable IVS_ButtonProc_GOhmSeal(WMButtonAction *ba)
+
+ +
+
+variable IVS_CreatePanel()
+
+ +
+
+variable IVS_GetSetQCForSweep(string device, variable sweepNo)
+

Return the Set QC passed/failed state for the given sweep.

+
+
Returns:
+

1 if passed, 0 if not (or not yet) and asserts out on all other errors.

+
+
+
+ +
+
+variable IVS_EnableStoringEveryTP(string device)
+
+ +
+
+variable IVS_DisableStoringEveryTP(string device)
+
+ +
+
+

Variables

+
+
+static const double IVS_DEFAULT_NWBVERSION = 2
+
+ +
+
+static const double IVS_DEFAULT_HEADSTAGE = 0
+
+ +
+
+static const string IVS_DEFAULT_DEVICE = "ITC18USB_Dev_0"
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___i_v_s_c_c___macro_8ipf.html b/file/_m_i_e_s___i_v_s_c_c___macro_8ipf.html new file mode 100644 index 0000000000..5a3add8f22 --- /dev/null +++ b/file/_m_i_e_s___i_v_s_c_c___macro_8ipf.html @@ -0,0 +1,286 @@ + + + + + + + + File MIES_IVSCC_Macro.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_IVSCC_Macro.ipf

+
+

Functions

+
+
+void IVSCCControlPanel()
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___igor_hooks_8ipf.html b/file/_m_i_e_s___igor_hooks_8ipf.html new file mode 100644 index 0000000000..2a1dfc85e7 --- /dev/null +++ b/file/_m_i_e_s___igor_hooks_8ipf.html @@ -0,0 +1,375 @@ + + + + + + + + File MIES_IgorHooks.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_IgorHooks.ipf

+

IH Various hooks which influence the behaviour at certain global events

+
+

Functions

+
+
+static variable IH_KillTemporaries()
+

Remove all strings/variables/waves which should not survive experiment reload/quit/saving.

+

Mainly useful for temporaries which you want to recreate on initialization

+
+ +
+
+variable IH_RemoveAmplifierConnWaves()
+

Remove the amplifier connection waves.

+
+ +
+
+static variable IH_KillStimSets()
+

Delete all wavebuilder stim sets to save memory.

+
+ +
+
+static variable IH_SerializeSettings()
+

Write the current JSON settings to disc.

+

We also invalidate the stored json ID, so that on the next access it is read again.

+
+ +
+
+static variable BeforeExperimentSaveHook(variable rN, string fileName, string path, string type, string creator, variable kind)
+
+ +
+
+static variable IH_Cleanup()
+

Cleanup before closing or starting a new experiment.

+

Takes care of unlocking the hardware, removing any data which is stale on reload anyway (amplifier connection details) and removes temporary waves.

+
+ +
+
+static variable IgorBeforeQuitHook(variable unsavedExp, variable unsavedNotebooks, variable unsavedProcedures)
+
+ +
+
+static variable ShowQuitMessage()
+
+ +
+
+static variable IgorQuitHook(string igorApplicationNameStr)
+
+ +
+
+static variable IgorBeforeNewHook(string igorApplicationNameStr)
+

Called before a new experiment is opened, in response to the New Experiment, Revert Experiment, or Open Experiment menu items in the File menu.

+
+ +
+
+static variable IgorStartOrNewHook(string igorApplicationNameStr)
+

Called when Igor is first launched and then whenever a new experiment is being created.

+
+ +
+
+static variable BeforeUncompiledHook(variable changeCode, string procedureWindowTitleStr, string textChangeStr)
+
+ +
+
+static variable AfterCompiledHook()
+
+ +
+
+variable IH_ResetScaling(WMWinHookStruct *s)
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___include_8ipf.html b/file/_m_i_e_s___include_8ipf.html new file mode 100644 index 0000000000..da560414b0 --- /dev/null +++ b/file/_m_i_e_s___include_8ipf.html @@ -0,0 +1,340 @@ + + + + + + + + File MIES_Include.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Include.ipf

+

Main include.

+

Developer instructions for raising the required nightly versions:

+

    +

  • Update the revision numbers for IP9 below in the expression involving BUILD, and also CI_IGOR_REVISION in .github/workflows/test-igor-workflow.yml

    • +

  • Upload the nightly zip packages to the FTP (Thomas’ job). Don’t delete the old zip packages, we still need them.

    • +

  • Update the below URLs

    • +

  • Update Igor Pro on the CI boxes (Thomas’ job).

    • +

  • Remove old workarounds marked with @todo

    • +
+

+
+

Defines

+
+
+TOO_OLD_IGOR
+
+ +
+
+

Functions

+
+
+void OpenPanelWithDocumentationLink()
+
+ +
+
+variable ButtonProc_OpenMiesDocuUpdateNightly(WMButtonAction *ba)
+
+ +
+
+static string GetDownloadLink()
+
+ +
+
+static string GetFileNameFromURL(string url)
+
+ +
+
+static string GetDestinationIgorPath()
+
+ +
+
+variable ButtonProc_DownloadNightly(WMButtonAction *ba)
+
+ +
+
+static variable AfterCompiledHook()
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___indexing_8ipf.html b/file/_m_i_e_s___indexing_8ipf.html new file mode 100644 index 0000000000..a5e78084eb --- /dev/null +++ b/file/_m_i_e_s___indexing_8ipf.html @@ -0,0 +1,457 @@ + + + + + + + + File MIES_Indexing.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Indexing.ipf

+

IDX Indexing related functionality

+
+

Functions

+
+
+variable IDX_StoreStartFinishForIndexing(string device)
+
+ +
+
+variable IDX_ResetStartFinishForIndexing(string device)
+

Resets the selected set popupmenus stored by IDX_StoreStartFinishForIndexing.

+
+ +
+
+static variable IDX_IndexingDoIt(string device)
+

Locked indexing, indexes all active channels at once.

+
+ +
+
+static variable IDX_IndexSingleChannel(string device, variable channelType, variable channel)
+

Indexes a single channel - used when indexing is unlocked.

+

Callers need to call DAP_UpdateDAQControls() with REASON_STIMSET_CHANGE_DUR_DAQ.

+
+ +
+
+variable IDX_MaxSweepsLockedIndexing(string device)
+

Sum of the largest sets for each indexing step.

+
+ +
+
+static variable IDX_StepsInSetWithMaxSweeps(string device, variable IndexNo, variable channelType)
+

Return the number of steps in the largest set for a particular index number.

+
+ +
+
+static std::tuple<variable, variable> IDX_GetCurrentSets(string device, variable channelType, variable channelNumber)
+

Return the 0-based popup menu indizes of the current WAVE/INDEX_END stimsets.

+
+ +
+
+static variable IDX_MaxSets(string device, variable channelType)
+

Return the number of sets on the active channel with the most sets.

+
+ +
+
+variable IDX_MaxNoOfSweeps(string device, variable IndexOverRide)
+

determine the max number of sweeps in the largest start set on active (checked) DA or TTL channels works for unlocked (independent) indexing

+
+
Parameters:
+
    +

  • device – device

    • +

  • IndexOverRide – index override is the same as indexing off. some Functions that call this function only want the max number of steps in the start (active) set, when indexing is on. 1 = over ride ON

    • +
+
+
+
+ +
+
+variable IDX_MinNoOfSweeps(string device)
+

Returns the number of sweeps in the stimulus set with the smallest number of sweeps (across all active stimulus sets).

+
+
Parameters:
+

device – device

+
+
+
+ +
+
+wave IDX_GetSetsInRange(string device, variable channel, variable channelType, variable lockedIndexing)
+

Returns a 1D textwave of selected set names.

+

+Constants are defined at ChannelTypeAndControlConstants

+
+
Parameters:
+
    +

  • device – panel

    • +

  • channel – channel

    • +

  • channelType – CHANNEL_TYPE_DAC or CHANNEL_TYPE_TTL

    • +

  • lockedIndexing – defaults to false, true returns just the DAC/TTL setname

    • +
+
+
+
+ +
+
+static variable IDX_NumberOfSweepsAcrossSets(string device, variable channel, variable channelType, variable lockedIndexing)
+

Determine the number of sweeps for a DA or TTL channel.

+
+ +
+
+variable IDX_NumberOfSweepsInSet(string setName)
+

Return the number of sweeps.

+
+ +
+
+static variable IDX_ApplyUnLockedIndexing(string device, variable count)
+
+ +
+
+static variable IDX_TotalIndexingListSteps(string device, variable channelNumber, variable channelType)
+
+ +
+
+variable IDX_UnlockedIndexingStepNo(string device, variable channelNumber, variable channelType, variable count)
+
+ +
+
+static variable IDX_DetIfCountIsAtSetBorder(string device, variable count, variable channelNumber, variable channelType)
+
+ +
+
+variable IDX_CalculcateActiveSetCount(string device)
+

Calculate the active set count.

+
+ +
+
+static wave IDX_GetStimsets(string device, variable channelIdx, variable channelType)
+

Extract the list of stimsets from the control user data.

+
+ +
+
+static string IDX_GetSingleStimset(WaveText listWave, variable idx, variable allowNone = defaultValue)
+

Return the stimset from the list of stimsets returned by IDX_GetStimsets()

+
+
Parameters:
+
    +

  • listWave – list of stim sets returned by IDX_GetStimsets()

    • +

  • idx – 0-based index

    • +

  • allowNone – [optional, defaults to false] Return the NONE stimset for idx 0. Not allowed during DAQ.

    • +
+
+
+
+ +
+
+variable IDX_HandleIndexing(string device)
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___input_dialog_8ipf.html b/file/_m_i_e_s___input_dialog_8ipf.html new file mode 100644 index 0000000000..7544ff36e3 --- /dev/null +++ b/file/_m_i_e_s___input_dialog_8ipf.html @@ -0,0 +1,350 @@ + + + + + + + + File MIES_InputDialog.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_InputDialog.ipf

+

ID Input dialog handling for numeric entries

+
+

Functions

+
+
+variable ID_AskUserForSettings(variable mode, string title, wave data, wave mock)
+

Shows a dialog and queries numeric values from the user.

+

We currently ask for NUM_HEADSTAGES headstage dependent entries and one independent value when mode = ID_HEADSTAGE_SETTINGS. All values must be numeric. For ID_POPUPMENU_SETTINGS the row dimension labels of data fill the popup menu, and on return data will have a 1 at the selected entry.

+
+
Parameters:
+
    +

  • mode – One of AskUserSettingsModeFlag

    • +

  • title – dialog title

    • +

  • data – 1D numeric wave, which must be permanent and in an otherwise empty folder

    • +

  • mock – This is mock data for testing which is written into data when GetInteractiveMode() is false

    • +
+
+
Returns:
+

0 on success, 1 if the user cancelled the dialog

+
+
+
+ +
+
+static variable ID_SetTitle(string win, string title)
+
+ +
+
+static string ID_GetControl(variable index)
+
+ +
+
+static dfref ID_GetFolder(string win)
+
+ +
+
+static wave ID_GetWave(string win)
+
+ +
+
+variable ID_ButtonProc(WMButtonAction *ba)
+
+ +
+
+variable ID_SetVarProc(WMSetVariableAction *sva)
+
+ +
+
+variable ID_PopMenuProc(WMPopupAction *pa)
+
+ +
+
+string ID_GetPopupEntries()
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___input_dialog___macro_8ipf.html b/file/_m_i_e_s___input_dialog___macro_8ipf.html new file mode 100644 index 0000000000..03248cd964 --- /dev/null +++ b/file/_m_i_e_s___input_dialog___macro_8ipf.html @@ -0,0 +1,292 @@ + + + + + + + + File MIES_InputDialog_Macro.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_InputDialog_Macro.ipf

+
+

Functions

+
+
+void IDM_Headstage_Panel()
+
+ +
+
+void IDM_Popup_Panel()
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___j_s_o_n_wave_notes_8ipf.html b/file/_m_i_e_s___j_s_o_n_wave_notes_8ipf.html new file mode 100644 index 0000000000..48800f6b42 --- /dev/null +++ b/file/_m_i_e_s___j_s_o_n_wave_notes_8ipf.html @@ -0,0 +1,504 @@ + + + + + + + + File MIES_JSONWaveNotes.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_JSONWaveNotes.ipf

+
+

Functions

+
+
+string JWN_GetWaveNoteAsString(wave wv)
+

Gets the JSON wave note part as string.

+
+ +
+
+variable JWN_GetWaveNoteAsJSON(wave wv)
+

Gets the JSON wave note part as JSON object The caller is responsible to release the returned jsonId after use.

+
+ +
+
+variable JWN_SetWaveNoteFromJSON(wave wv, variable jsonID, variable release = defaultValue)
+

Set the JSON json document as JSON wave note. Releases json if release is true (default).

+
+ +
+
+variable JWN_GetNumberFromWaveNote(wave wv, string jsonPath)
+

Return the numerical value at jsonPath found in the wave note.

+
+
Parameters:
+
    +

  • wv – wave reference where the WaveNote is taken from

    • +

  • jsonPath – path to string

    • +
+
+
Returns:
+

the value on success. NaN is returned if it could not be found

+
+
+
+ +
+
+wave JWN_GetNumericWaveFromWaveNote(wave wv, string jsonPath)
+

Return the numeric wave value at jsonPath found in the wave note Note that for numeric waves the data type of the returned wave is double precision.

+
+
Parameters:
+
    +

  • wv – wave reference where the WaveNote is taken from

    • +

  • jsonPath – path to string

    • +
+
+
Returns:
+

the wave on success. null wave is returned if it could not be found or the referenced entry contains non-numeric data

+
+
+
+ +
+
+wave JWN_GetTextWaveFromWaveNote(wave wv, string jsonPath)
+

Return the text wave value at jsonPath found in the wave note.

+
+
Parameters:
+
    +

  • wv – wave reference where the WaveNote is taken from

    • +

  • jsonPath – path to string

    • +
+
+
Returns:
+

the wave on success. null wave is returned if it could not be found

+
+
+
+ +
+
+wave JWN_GetWaveRefNumericFromWaveNote(wave wv, string jsonPath)
+

Return the wave reference wave at jsonPath found in the wave note.

+

All contained waves must be numeric.

+
+
Parameters:
+
    +

  • wv – wave reference where the WaveNote is taken from

    • +

  • jsonPath – path to array

    • +
+
+
Returns:
+

the wave on success. null wave is returned if it could not be found

+
+
+
+ +
+
+wave JWN_GetWaveRefTextFromWaveNote(wave wv, string jsonPath)
+

Return the wave reference wave at jsonPath found in the wave note.

+

All contained waves must be text.

+
+
Parameters:
+
    +

  • wv – wave reference where the WaveNote is taken from

    • +

  • jsonPath – path to array

    • +
+
+
Returns:
+

the wave on success. null wave is returned if it could not be found

+
+
+
+ +
+
+static wave JWN_GetWaveRefFromWaveNote_Impl(wave wv, string jsonPath, variable type)
+
+ +
+
+string JWN_GetStringFromWaveNote(wave wv, string jsonPath)
+

Return the string value at jsonPath found in the wave note.

+
+
Parameters:
+
    +

  • wv – wave reference where the WaveNote is taken from

    • +

  • jsonPath – path to string

    • +
+
+
Returns:
+

the value on success. An empty string is returned if it could not be found

+
+
+
+ +
+
+string JWN_GetWaveNoteHeader(WaveOrNull wv)
+

Gets the non-JSON wave note part.

+
+ +
+
+static variable JWN_WriteWaveNote(wave wv, string header, variable jsonID, variable release = defaultValue)
+

Writes a wave note from header string and json back. Releases json if release is true (default).

+
+ +
+
+variable JWN_SetNumberInWaveNote(wave wv, string jsonPath, variable val)
+

Updates the numeric value of key found in the wave note as jsonPath.

+
+
Parameters:
+
    +

  • wv – wave

    • +

  • jsonPath – path in json

    • +

  • val – new numerical value

    • +
+
+
+
+ +
+
+variable JWN_SetStringInWaveNote(wave wv, string jsonPath, string str)
+

Update the string value at jsonPath found in the wave note at jsonPath.

+
+
Parameters:
+
    +

  • wv – wave

    • +

  • jsonPath – path in json

    • +

  • str – new string value

    • +
+
+
+
+ +
+
+variable JWN_SetWaveInWaveNote(wave wv, string jsonPath, wave noteWave)
+

Update the wave value at jsonPath found in the wave note at jsonPath Note that only wave data and dimensions are stored.

+
+
Parameters:
+
    +

  • wv – wave

    • +

  • jsonPath – path in json

    • +

  • noteWave – new wave value

    • +
+
+
+
+ +
+
+wave JWN_CreatePath(wave wv, string jsonPath)
+

Create a JSON object at the specified path.

+

Non-existing path elements are recursively created.

+
+
Parameters:
+
    +

  • wv – wave reference where the WaveNote is taken from

    • +

  • jsonPath – path to create as object

    • +
+
+
+
+ +
+
+

Variables

+
+
+static const double JWN_DEFAULT_RELEASE = 1
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___labnotebook_8ipf.html b/file/_m_i_e_s___labnotebook_8ipf.html new file mode 100644 index 0000000000..f62d97741d --- /dev/null +++ b/file/_m_i_e_s___labnotebook_8ipf.html @@ -0,0 +1,337 @@ + + + + + + + + File MIES_Labnotebook.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Labnotebook.ipf

+
+

Functions

+
+
+variable LBN_SetDimensionLabels(WaveText keys, wave values, variable start = defaultValue)
+

Set column dimension labels from the first row of the key wave.

+
+ +
+
+std::tuple<variable, string, variable> LBN_GetEntryProperties(WaveTextOrNull keyWave, string key)
+

Queries the unit and column from the key wave.

+
+
Parameters:
+
    +

  • keyWave – labnotebook key wave

    • +

  • key – key to look for

    • +
+
+
Return values:
+
    +

  • result – one on error, zero otherwise

    • +

  • unit – unit of the result [empty if not found]

    • +

  • col – column of the result into the keyWave [NaN if not found]

    • +
+
+
+
+ +
+
+wave LBN_GetNumericWave(variable defValue = defaultValue)
+

Return a wave suitable for consumption by ED_AddEntryToLabnotebook()

+
+ +
+
+wave LBN_GetTextWave(string defValue = defaultValue)
+

Return a wave suitable for consumption by ED_AddEntryToLabnotebook()

+
+ +
+
+wave LBV_GetFilledLabnotebookEntries(WaveOrNull values)
+

Return all labnotebook entries which are at least written once.

+
+ +
+
+static string LBV_IsLabnotebookColumnFilled(wave values, variable col)
+

Return the name of the given labnotebook column if it was written into at least once, an empty string otherwise.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___logbook_viewer_8ipf.html b/file/_m_i_e_s___logbook_viewer_8ipf.html new file mode 100644 index 0000000000..96b09a16a8 --- /dev/null +++ b/file/_m_i_e_s___logbook_viewer_8ipf.html @@ -0,0 +1,611 @@ + + + + + + + + File MIES_LogbookViewer.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_LogbookViewer.ipf

+

LBV Panel for browsing the labnotebook and TPStorage waves

+
+

Functions

+
+
+string LBV_GetSettingsHistoryPanel(string win)
+
+ +
+
+string LBV_GetLabNoteBookGraph(string win)
+
+ +
+
+string LBV_GetDescriptionNotebook(string win)
+
+ +
+
+static wave LBV_PopupExtFormatEntries(WaveTextOrNull entries)
+
+ +
+
+wave LBV_PopupExtGetTPStorageKeys(string win)
+

Returns the list of TPStorage keys.

+
+ +
+
+wave LBV_PopupExtGetLBKeys(string win)
+

Returns the list of LNB keys for the settings history window menu.

+
+ +
+
+wave LBV_PopupExtGetResultsKeys(string win)
+

Returns the list of results keys for the settings history window menu.

+
+ +
+
+wave LBV_GetAllLogbookParamNames(WaveTextOrNull textualValues, WaveTextOrNull numericalValues)
+

Returns the combined parameter names (non-empty) from the numerical and textual MD key loogbook waves as 1D text wave.

+
+ +
+
+static wave LBV_GetAllLogbookParamNames_NoCache(WaveTextOrNull textualValues, WaveTextOrNull numericalValues)
+
+ +
+
+static wave LBV_CleanLogbookParamNames(WaveTextOrNull names)
+
+ +
+
+wave LBV_GetTPStorageEntries(dfref dfr)
+

Return a text wave with all entries from all TPStorage waves which are candidates for plotting.

+
+ +
+
+static dfref LBV_GetTPStorageLocation(string win)
+

Return the datafolder reference where TPStorage waves can be found.

+
+ +
+
+variable LBV_ButtonProc_ClearGraph(WMButtonAction *ba)
+
+ +
+
+variable LBV_ButtonProc_SwitchXAxis(WMButtonAction *ba)
+
+ +
+
+variable LBV_PopMenuProc_LabNotebookAndResults(WMPopupAction *pa)
+
+ +
+
+std::tuple<WAVE, WAVE> LBV_GetLogbookWavesForEntry(string win, string key)
+

Return the keys/values logbook pair for the given key.

+
+
Returns:
+

valid waves or null if it can not be found.

+
+
+
+ +
+
+variable LBV_PopMenuProc_TPStorage(WMPopupAction *pa)
+
+ +
+
+string LBV_GetExperiments(string win)
+
+ +
+
+string LBV_GetAllDevicesForExperiment(string win)
+
+ +
+
+variable LBV_ClearGraph(string win)
+
+ +
+
+static variable LBV_UpdateLBGraphLegend(string graph, string traceList = defaultValue)
+

Update the legend in the labnotebook graph.

+

Passing traceList is required if you just added traces to the graph as these can not be immediately queried using TraceNameList as that would require an DoUpdate call before.

+

Assumes that the traceList displays information from the labnotebook. All entries with indizes equal or higher than NUM_HEADSTAGES will be labeled as all denoting that the information is headstage independent and therefore valid for all headstages.

+
+
Parameters:
+
    +

  • graph – name of the graph

    • +

  • traceList – list of traces in the graph

    • +
+
+
+
+ +
+
+static wave LBV_GetTraceUserDataNames()
+
+ +
+
+static string LBV_MakeTraceNameUnique(string graph, string trace)
+
+ +
+
+static variable LBV_AddTraceToLBGraph(string graph, wave keys, wave values, string key)
+

Add a trace to the labnotebook graph.

+
+
Parameters:
+
    +

  • graph – name of the graph

    • +

  • keys – labnotebook keys wave (numerical or text)

    • +

  • values – labnotebook values wave (numerical or text)

    • +

  • key – name of the key to add

    • +
+
+
+
+ +
+
+variable LBV_Update(string win)
+
+ +
+
+variable LBV_UpdateTagsForTextualLBNEntries(string win, variable sweepNo)
+
+ +
+
+static variable LBV_AddTraceToLBGraphTPStorage(string graph, dfref dfr, string key, variable isTimeAxis = defaultValue)
+
+ +
+
+static std::tuple<WaveTextOrNull, string, string, variable> LBV_GetPropertiesForLabnotebookEntry(WaveText keys, string key)
+
+ +
+
+static std::tuple<WaveText, string> LBV_GenerateTraceNames(string name, variable count)
+
+ +
+
+static variable LBV_AddTagsForTextualLBNEntries(string graph, WaveText keys, WaveText values, string key, variable firstSweep = defaultValue)
+
+ +
+
+static variable LBV_SwitchLBGraphXAxis(string graph)
+

Switch the labnotebook graph x axis type (time <-> sweep numbers)

+
+ +
+
+static variable LBV_CheckIfXAxisIsTime(string graph, variable logbookType = defaultValue)
+

Check if the x wave belonging to the first trace in the graph has a date/time scale.

+
+ +
+
+static variable LBV_SetLabNotebookBottomLabel(string graph, variable isTimeAxis)
+

Set the appropriate label for the bottom axis of the graph created by CreateTiledChannelGraph.

+

Assumes that wave data units are equal for all traces

+
+ +
+
+variable LBV_SelectExperimentAndDevice(string win)
+
+ +
+
+static string LBV_FormatDescription(WaveTextOrNull keys, string name)
+
+ +
+
+variable LBV_EntryDescription(WMWinHookStruct *s)
+
+ +
+
+variable LBV_PlotAllAnalysisFunctionLBNKeys(string browser, variable anaFuncType)
+
+ +
+
+static variable LBV_LimitXRangeToSelected(string browser)
+

Limit the bottom axis of the settings history graph to the selected/displayed sweeps.

+
+ +
+
+variable LBV_CheckProc_XRangeSelected(WMCheckboxAction *cba)
+
+ +
+
+

Variables

+
+
+static const string LABNOTEBOOK_BOTTOM_AXIS_DELTA_TIME = "Relative time [s]"
+
+ +
+
+static const string LABNOTEBOOK_BOTTOM_AXIS_TIME = "Timestamp (a. u.)"
+
+ +
+
+static const string LABNOTEBOOK_BOTTOM_AXIS_SWEEP = "Sweep Number (a. u.)"
+
+ +
+
+static const string LBV_UD_VALUES_WAVE = "values"
+
+ +
+
+static const string LBV_UD_KEYS_WAVE = "keys"
+
+ +
+
+static const string LBV_UD_HEADSTAGE = "headstage"
+
+ +
+
+static const string LBV_UD_KEY = "key"
+
+ +
+
+static const string LBV_UD_ISTEXT = "text"
+
+ +
+
+static const string LBV_UD_YAXIS = "yaxis"
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___logging_8ipf.html b/file/_m_i_e_s___logging_8ipf.html new file mode 100644 index 0000000000..b6da572c44 --- /dev/null +++ b/file/_m_i_e_s___logging_8ipf.html @@ -0,0 +1,366 @@ + + + + + + + + File MIES_Logging.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Logging.ipf

+
+

Functions

+
+
+string LOG_GetFile(string package)
+

Get the absolute path to the log file.

+
+ +
+
+static variable LOG_HasRequiredKeys(variable JSONid)
+

Check that the given JSON document has the required top level keys.

+

Currently we require:

    +

  • source: Source of the log entry, usually the function issuing the add entry

    • +

  • exp: Name of the Igor Pro experiment

    • +

  • id: Igor Pro instance identifier, see also GetIgorInstanceID()

    • +
+

+
+ +
+
+variable LOG_GenerateEntryTemplate(string source)
+

Generate a JSON text with all required entries.

+

Caller is responsible for the JSON text memory.

+
+ +
+
+variable LOG_MarkSessionStart(string package)
+

Adds a special entry to the logfile to mark the start of a session.

+

Should be called from IgorBeforeNewHook().

+
+ +
+
+static variable LOG_AddEntryWithoutChecks(string package, variable JSONid)
+

Adds the JSONid text to the logfile without any checks.

+
+ +
+
+variable LOG_AddEntry(string package, string action, variable stacktrace = defaultValue, WaveTextOrNull keys = defaultValue, WaveTextOrNull values = defaultValue)
+

Add entry for the current function into the log file.

+

Before LOG_AddEntry can be used the symbolic path must have been initialized via PS_Initialize or PS_FixPackageLocation. This is best done from the AfterCompiledHook().

+

Usage: 

Function DoWork()
+
+    LOG_AddEntry("my package", "start")
+
+    // ...
+
+    LOG_AddEntry("my package", "end")
+End
+
+
+

+

+

Result: 

{"action":"start","exp":"HardwareTests","source":"DoWork","ts":"2021-03-09T17:20:10.252+01:00"}
+{"action":"end","exp":"HardwareTests","source":"DoWork","ts":"2021-03-09T17:20:10.298+01:00"}
+
+
+

+

+
+
Parameters:
+
    +

  • package – package name, this determines the log file

    • +

  • action – additional string, can be something like start or end

    • +

  • stacktrace – [optional, defaults to false] add the stacktrace to the log

    • +

  • keys – [optional, defaults to $””] Additional key-value pairs to be written into the log file. Same size as values. Either both keys and values are present or none.

    • +

  • values – [optional, defaults to $””] Additional key-value pairs to be written into the log file. Same size as keys. Either both keys and values are present or none.

    • +
+
+
+
+ +
+
+static variable LOG_AddStackTrace(variable JSONid)
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___mass_experiment_processing_8ipf.html b/file/_m_i_e_s___mass_experiment_processing_8ipf.html new file mode 100644 index 0000000000..f442671082 --- /dev/null +++ b/file/_m_i_e_s___mass_experiment_processing_8ipf.html @@ -0,0 +1,437 @@ + + + + + + + + File MIES_MassExperimentProcessing.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_MassExperimentProcessing.ipf

+

MEP Process multiple MIES pxps to convert data into NWBv2

+

Installation:

    +

  • Stop Igor Pro

    • +

  • Install MIES from the installer

    • +

  • Create a shortcut to this file and place it in the Igor Procedures folder

    • +

  • Ensure that only MIES is installed and no other Igor Pro packages

    • +

  • In the MIES installation folder (All Users: C:\Program Files\MIES, User: C:\Users\$User\Documents\MIES) create an empty file named UserConfig.txt.

    • +
+

+

Running:

    +

  • Start Igor Pro

    • +

  • Select “Macros” -> “Mass convert PXPs to NWBv2”

    • +

  • Enter an input and output folder for the conversion

    • +

  • Wait until it’s done

    • +
+

+

In the output folder there will be a conversion.json file with results of the conversion process. Search for the error key for failed conversions.

+
+

Functions

+
+
+static variable LoadPackagePrefs(MultiExperimentProcessPrefs *prefs)
+
+ +
+
+static variable SavePackagePrefs(MultiExperimentProcessPrefs *prefs)
+
+ +
+
+static variable ProcessCurrentExperiment(MultiExperimentProcessPrefs *prefs)
+
+ +
+
+static variable PerformMiesTasks(string outputFilePath)
+
+ +
+
+static variable IsAppropriateExperiment()
+
+ +
+
+static string FindNextExperiment(MultiExperimentProcessPrefs *prefs)
+
+ +
+
+static variable GetJSON(MultiExperimentProcessPrefs *prefs)
+
+ +
+
+static variable StoreJSON(MultiExperimentProcessPrefs *prefs, variable jsonID)
+
+ +
+
+static variable PostLoadNextExperiment(string nextExperimentFullPath)
+
+ +
+
+static variable AfterFileOpenHook(variable refNum, string file, string pathName, string type, string creator, variable kind)
+
+ +
+
+variable StartMultiExperimentProcess()
+
+ +
+
+variable StartMultiExperimentProcessWrapper()
+
+ +
+
+

Variables

+
+
+static const string INPUT_FOLDER = ""
+
+ +
+
+static const string OUTPUT_FOLDER = ""
+
+ +
+
+static const string kPackageName = "MIES PXP to NWBv2"
+
+ +
+
+static const string kPreferencesFileName = "ProcessPrefsMIESNWBv2.bin"
+
+ +
+
+static const double kPrefsRecordID = 0
+
+ +
+
+static const double kPrefsVersionNumber = 102
+
+ +
+
+
+struct MultiExperimentProcessPrefs
+
+

Public Members

+
+
+uint32 version
+
+ +
+
+uint32 processRunning
+
+ +
+
+char settingsFile[256]
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___menu_8ipf.html b/file/_m_i_e_s___menu_8ipf.html new file mode 100644 index 0000000000..71d630b69f --- /dev/null +++ b/file/_m_i_e_s___menu_8ipf.html @@ -0,0 +1,364 @@ + + + + + + + + File MIES_Menu.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Menu.ipf

+

MEN Definition of the menu items

+
+

Functions

+
+
+variable MEN_CloseMies()
+
+ +
+
+variable MEN_OpenAboutDialog()
+
+ +
+
+variable MEN_OpenBackgroundWatcherPanel()
+
+ +
+
+variable MEN_CreateIssueOnGithub()
+

Custom notebook action for the “About MIES” dialog.

+

Opens a prefilled new issue on github.

+
+ +
+
+variable MEN_ClearPackageSettings()
+
+ +
+
+variable MEN_OpenPackageSettingsAsNotebook()
+
+ +
+
+string MEN_GetUserPingMenuString()
+
+ +
+
+static variable MEN_OpenLogFile(string path, string name)
+

Generic routine for displaying a logfile in a notebook.

+
+
Parameters:
+
    +

  • path – full path to the file on disc

    • +

  • name – notebook name

    • +
+
+
+
+ +
+
+variable MEN_OpenMIESLogFile()
+
+ +
+
+variable MEN_OpenZeroMQXOPLogFile()
+
+ +
+
+variable MEN_OpenITCXOP2LogFile()
+
+ +
+
+variable MEN_DownloadStimsets()
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___mies_utilities___algorithm_8ipf.html b/file/_m_i_e_s___mies_utilities___algorithm_8ipf.html new file mode 100644 index 0000000000..14e12f0706 --- /dev/null +++ b/file/_m_i_e_s___mies_utilities___algorithm_8ipf.html @@ -0,0 +1,407 @@ + + + + + + + + File MIES_MiesUtilities_Algorithm.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_MiesUtilities_Algorithm.ipf

+

This file holds MIES utility functions implementing various algorithms.

+
+

Functions

+
+
+wave CalculateAverage(WaveRefWave waveRefs, dfref averageDataFolder, string averageWaveName, variable skipCRC = defaultValue, variable writeSourcePaths = defaultValue, wave inputAverage = defaultValue)
+

Calculate the average of a list of waves, wrapper for MIES_fWaveAverage().

+

For performance enhancements:

    +

  • The average waves are cached

    • +

  • References to existing average waves are returned in case they already exist

    • +
+

+
+
Parameters:
+
    +

  • waveRefs – waves to average in a wave reference wave

    • +

  • averageDataFolder – folder where the data is to be stored

    • +

  • averageWaveName – base name of the averaged data

    • +

  • skipCRC – [optional, defaults to false] Add the average wave CRC as suffix to its name

    • +

  • writeSourcePaths – [optional, defaults to true] Write the full paths of the source waves into the average wave note

    • +

  • inputAverage – [optional, defaults to invalid wave ref] Override the average calculation and use the given wave as result. This is relevant for callers which want to leverage MultiThread statements together with MIES_fWaveAverage.

    • +
+
+
Returns:
+

wave reference to the average wave

+
+
+
+ +
+
+variable CalculateTPLikePropsFromSweep(wave numericalValues, wave textualValues, wave sweep, wave deltaI, wave deltaV, wave resistance)
+

Calculate deltaI/deltaV from a testpulse like stimset in “Current Clamp” mode.

+

+
+Todo:
+

unify with TP_Delta code

+

add support for evaluating “inserted TP” only

+
+ +

See CalculateTPLikePropsFromSweep Algorithm for the full documentation.

+

+
+ +
+
+variable DecimateWithMethod(wave input, wave output, variable decimationFactor, variable method, variable firstRowInp = defaultValue, variable lastRowInp = defaultValue, variable firstColInp = defaultValue, variable lastColInp = defaultValue, variable firstColOut = defaultValue, variable lastColOut = defaultValue, WaveOrNull factor = defaultValue)
+

Decimate the the given input wave.

+

This allows to decimate a given input row range into output rows using the given method. The columns of input/output can be different. The input row coordinates can be used to do a chunked conversion, e.g. when receiving data from hardware. Incomplete chunks will be redone when necessary.

+

Algorithm visualized:

+

Input (16 entries): [ | | | | | | | | | | | | | | | ]
+Decimation factor: 4
+Method: MinMax
+Output (4 entries): [ min(input[0, 7]) | max(input[0, 7]) | min(input[8, 15]) | max(input[8, 15]) ]
+
+
+

+
+
Parameters:
+
    +

  • input – wave to decimate

    • +

  • output – target wave which will be around decimationFactor smaller than input

    • +

  • decimationFactor – decimation factor, must be an integer and larger than 1

    • +

  • method – one of DecimationMethods

    • +

  • firstRowInp – [optional, defaults to 0] first row input coordinates

    • +

  • lastRowInp – [optional, defaults to last element] last row in input coordinates

    • +

  • firstColInp – [optional, defaults to 0] first col in input coordinates

    • +

  • lastColInp – [optional, defaults to last element] last col in input coordinates

    • +

  • firstColOut – [optional, defaults to firstColInp] first col in output coordinates

    • +

  • lastColOut – [optional, defaults to lastColInp] last col in output coordinates

    • +

  • factor – [optional, defaults to none] factor which is applied to all input columns and written into the output columns

    • +
+
+
+
+ +
+
+static variable DecimateMinMax(wave input, wave output, variable idx, variable firstRowInp, variable lastRowInp, variable colInp, variable colOut, variable decimationFactor)
+

Threadsafe helper function for DecimateWithMethod.

+
+
Parameters:
+
    +

  • input – input wave

    • +

  • output – output wave

    • +

  • idx – output pair index

    • +

  • firstRowInp – first row in input coordinates

    • +

  • lastRowInp – last row in input coordinates

    • +

  • colInp – column in input coordinates

    • +

  • colOut – column in output coordinates

    • +

  • decimationFactor – decimation factor

    • +
+
+
+
+ +
+
+wave FindIndizes(wave numericOrTextWave, variable col = defaultValue, string colLabel = defaultValue, variable var = defaultValue, string str = defaultValue, variable prop = defaultValue, variable startRow = defaultValue, variable endRow = defaultValue, variable startLayer = defaultValue, variable endLayer = defaultValue)
+

Extended version of FindValue

+

Allows to search only the specified column for a value and returns all matching row indizes in a wave. By defaults only looks into the first layer for backward compatibility reasons. When multiple layers are searched startLayer/endLayer the result contains matches from all layers, and this also means the resulting wave is still 1D.

+

Exactly one of var/str/prop has to be given except for prop == PROP_MATCHES_VAR_BIT_MASK which requires a var/str parameter as well. prop == PROP_GREP requires str. prop == PROP_WILDCARD requires str. PROP_NOT can be set by logical ORing it to one of the other PROP_* constants prop == PROP_NOT can also be set solely to invert the matching of the default behavior

+

Exactly one of col/colLabel has to be given.

+
+
Parameters:
+
    +

  • numericOrTextWave – wave to search in

    • +

  • col – [optional, default=0] column to search in only

    • +

  • colLabel – [optional] column label to search in only

    • +

  • var – [optional] numeric value to search

    • +

  • str – [optional] string value to search

    • +

  • prop – [optional] property to search, see FindIndizesProps

    • +

  • startRow – [optional] starting row to restrict the search to

    • +

  • endRow – [optional] ending row to restrict the search to

    • +

  • startLayer – [optional, defaults to zero] starting layer to restrict search to

    • +

  • endLayer – [optional, defaults to zero] ending layer to restrict search to

    • +
+
+
Returns:
+

A wave with the row indizes of the found values. An invalid wave reference if the value could not be found.

+
+
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___mies_utilities___backup_waves_8ipf.html b/file/_m_i_e_s___mies_utilities___backup_waves_8ipf.html new file mode 100644 index 0000000000..fc1cb5bf96 --- /dev/null +++ b/file/_m_i_e_s___mies_utilities___backup_waves_8ipf.html @@ -0,0 +1,348 @@ + + + + + + + + File MIES_MiesUtilities_BackupWaves.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_MiesUtilities_BackupWaves.ipf

+

This file holds MIES utility functions for wave backup.

+
+

Functions

+
+
+variable RestoreFromBackupWavesForAll(dfref dfr)
+

Looks for backup waves in the datafolder and recreates the original waves from them. The original waves do not need to be present. If present they are overwritten. This is different to RestoreFromBackupWavesForAll, where the original waves need to be existing.

+
+ +
+
+variable CreateBackupWavesForAll(dfref dfr)
+

Create backup waves for all waves in the datafolder.

+
+ +
+
+static string GetBackupNameOfWave(wave wv)
+
+ +
+
+wave GetBackupWave_TS(wave wv)
+
+ +
+
+wave CreateBackupWave(wave wv, variable forceCreation = defaultValue)
+

Create a backup of the wave wv if it does not already exist or if forceCreation is true.

+

The backup wave will be located in the same data folder and its name will be the original name with WAVE_BACKUP_SUFFIX appended. If the backup wave exists and the main type of the backup wave can be overridden by Duplicate/O then the wave reference of the backup wave is kept. Otherwise the main type is changed and the wave reference is not kept (e.g. backup wave is numerical, original wave is text)

+
+ +
+
+wave GetBackupWave(wave wv)
+

Return a wave reference to the possibly not existing backup wave.

+
+ +
+
+variable ReplaceWaveWithBackupForAll(dfref dfr)
+

Replace all waves from the datafolder with their backup.

+
+ +
+
+wave ReplaceWaveWithBackup(wave wv, variable nonExistingBackupIsFatal = defaultValue, variable keepBackup = defaultValue)
+

Replace the wave wv with its backup. If possible the backup wave will be killed afterwards. If the backup wave exists then the wave reference of the restored wave stays the same. Thus the returned wave reference equals the wv wave reference.

+
+
Parameters:
+
    +

  • wv – wave to replace by its backup

    • +

  • nonExistingBackupIsFatal – [optional, defaults to true] behaviour for the case that there is no backup. Passing a non-zero value will abort if the backup wave does not exist, with zero it will just do nothing.

    • +

  • keepBackup – [optional, defaults to false] don’t delete the backup after restoring from it

    • +
+
+
Returns:
+

wave reference to the restored data, in case of no backup an invalid wave reference

+
+
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___mies_utilities___channels_8ipf.html b/file/_m_i_e_s___mies_utilities___channels_8ipf.html new file mode 100644 index 0000000000..55e9163c18 --- /dev/null +++ b/file/_m_i_e_s___mies_utilities___channels_8ipf.html @@ -0,0 +1,546 @@ + + + + + + + + File MIES_MiesUtilities_Channels.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_MiesUtilities_Channels.ipf

+

This file holds MIES utility functions for Channels.

+
+

Functions

+
+
+wave GetADCListFromConfig(wave config)
+

Return a list of the AD channels from the DAQ config.

+
+ +
+
+wave GetDACListFromConfig(wave config)
+

Return a list of the DA channels from the DAQ config.

+
+ +
+
+wave GetTTLListFromConfig(wave config)
+

Return a list of the TTL channels from the DAQ config.

+
+ +
+
+static wave GetChanneListFromDAQConfigWave(wave config, variable channelType)
+

Return a wave with all active channels.

+

+
+Todo:
+

change to return a 0/1 wave with constant size a la DAG_GetChannelState

+
+ +

+
+
Parameters:
+
+
+
+
+ +
+
+variable GetNrOfTypedChannels(wave chanTypes, variable type)
+

Returns the number of given mode channels from channelType wave.

+
+
Parameters:
+
+
+
Returns:
+

number of types present in chanTypes

+
+
+
+ +
+
+wave GetTTLTypesFromConfig(wave config)
+

Return a types of the AD channels from the ITC config.

+
+ +
+
+wave GetADCTypesFromConfig(wave config)
+

Return a types of the AD channels from the ITC config.

+
+ +
+
+wave GetDACTypesFromConfig(wave config)
+

Return a types of the DA channels from the ITC config.

+
+ +
+
+static wave GetTypeListFromITCConfig(wave config, variable channelType)
+

Return a wave with all active channels.

+

+
+Todo:
+

change to return a 0/1 wave with constant size a la DAG_GetChannelState

+
+ +

+
+
Parameters:
+
+
+
+
+ +
+
+variable GotTPChannelsOnADCs(string device)
+

Checks if a channel of TP type exists on ADCs.

+
+
Parameters:
+

device – device

+
+
Returns:
+

1 if TP type present, 0 otherwise

+
+
+
+ +
+
+variable GetTTLBits(wave numericalValues, variable sweep, variable channel)
+

Get the TTL bit mask from the labnotebook.

+
+
Parameters:
+
    +

  • numericalValues – Numerical labnotebook values

    • +

  • sweep – Sweep number

    • +

  • channel – TTL hardware channel

    • +
+
+
+
+ +
+
+variable GetUsedHWDACFromLNB(wave numericalValues, variable sweep)
+

Returns the used hardware DAC type from the LNB.

+

+

See also

+

HardwareDACTypeConstants

+
+

+
+
Parameters:
+
    +

  • numericalValues – Numerical labnotebook values

    • +

  • sweep – Sweep number

    • +
+
+
Returns:
+

used hardware dac type

+
+
+
+ +
+
+static wave GetActiveChannelsTTL(wave numericalValues, wave textualValues, variable sweep, variable TTLmode)
+

Return a wave with the requested TTL channel information defined by TTLmode.

+
+
Parameters:
+
    +

  • numericalValues – Numerical labnotebook values

    • +

  • textualValues – Text labnotebook values

    • +

  • sweep – Sweep number

    • +

  • TTLmode – One of ActiveChannelsTTLMode.

    • +
+
+
+
+ +
+
+wave GetActiveChannels(wave numericalValues, wave textualValues, variable sweepNo, variable channelType, variable TTLmode = defaultValue)
+

Return a fixed size wave with the the active channels for the given channel type.

+

The function takes into account unassociated DA/AD channels as well. It returns fixed size waves with the active entries having the same value as their index. This allows users to either remove unused entries and use the wave as active entries list or use the whole wave where not being NaN is active.

+

With the following DAEphys setup (only the first four channels are shown)

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Nr

DA

AD

TTL

0

    +
  • +
+

1

    +
  • +
+

2

    +
  • +
+

3

    +
  • +
+
+

this function returns the following:

+
    +

  • DA: {NaN,  1, NaN, NaN, ...}

    • +

  • AD: {0, NaN, NaN, NaN, ...}

    • +

  • TTL:

    +
      +

    • NI hardware (regardless of TTLmode): {NaN, NaN, 2, 3, ...}

      • +

    • ITC hardware with TTLmode, example for two active racks:

      +
        +

      • TTL_DAEPHYS_CHANNEL: {NaN, NaN, 2, 3, NaN, 5, NaN, NaN}

        • +

      • TTL_HARDWARE_CHANNEL: {0, NaN, NaN, 3, NaN, NaN, Nan, NaN}

        • +

      • TTL_GUITOHW_CHANNEL: returns a 2D wave that allows to index by GUI channel (row) and retrieve hardware channel number and ttlbit number. +The columns are %HWCHANNEL and %TTLBITNR. The %TTLBITNR column is only valid for ITC hardware.

        • +

      • TTL_HWTOGUI_CHANNEL: returns a 2D wave that allows to index by hardware channel number and TTL bit number and retrieve the GUI channel number. +The hardware channel is indexed in the row and the TTL bit number in the column dimension. For NI hardware the TTL bit index should be zero. +Inactive hardware channel/ttlbit combinations return NaN.

        • +
      +
      • +
    +
    • +
+

+

+

See also

+

HW_ITC_GetITCXOPChannelForRack

+
+

+
+
Parameters:
+
+
+
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___mies_utilities___checks_8ipf.html b/file/_m_i_e_s___mies_utilities___checks_8ipf.html new file mode 100644 index 0000000000..4c9c25fe79 --- /dev/null +++ b/file/_m_i_e_s___mies_utilities___checks_8ipf.html @@ -0,0 +1,320 @@ + + + + + + + + File MIES_MiesUtilities_Checks.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_MiesUtilities_Checks.ipf

+

This file holds MIES utility functions for checks.

+
+

Functions

+
+
+variable IsValidEpochNumber(variable epochNo)
+

Check if the given epoch number is valid.

+
+ +
+
+variable IsValidSweepAndConfig(WaveOrNull sweep, WaveOrNull config, variable configVersion = defaultValue)
+

Check if the two waves are valid and compatible.

+
+
Parameters:
+
    +

  • sweep – sweep wave

    • +

  • config – config wave

    • +

  • configVersion – [optional, defaults to DAQ_CONFIG_WAVE_VERSION] minimum required version of the config wave

    • +
+
+
+
+ +
+
+variable IsValidSamplingMultiplier(variable multiplier)
+

Check if the given multiplier is a valid sampling interval multiplier.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+variable IsValidHeadstage(variable headstage)
+

Check if the given headstage index is valid.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___mies_utilities___config_8ipf.html b/file/_m_i_e_s___mies_utilities___config_8ipf.html new file mode 100644 index 0000000000..bf1575a952 --- /dev/null +++ b/file/_m_i_e_s___mies_utilities___config_8ipf.html @@ -0,0 +1,349 @@ + + + + + + + + File MIES_MiesUtilities_Config.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_MiesUtilities_Config.ipf

+

This file holds MIES utility functions for the config wave.

+
+

Functions

+
+
+variable GetSamplingInterval(wave config, variable channelType)
+

Returns the sampling interval of the sweep in microseconds (1e-6s)

+
+ +
+
+variable GetDataOffset(wave config)
+

Returns the data offset of the sweep in points.

+
+ +
+
+variable UpdateSweepConfig(wave config, variable samplingInterval = defaultValue)
+

Write the given property to the config wave.

+
+

Note

+

Please add new properties as required

+
+
+
Parameters:
+
    +

  • config – configuration wave

    • +

  • samplingInterval – sampling interval in microseconds (1e-6s)

    • +
+
+
+
+ +
+
+string GetDefaultElectrodeName(variable headstage)
+

Return the default name of a electrode.

+
+ +
+
+std::tuple<variable, variable> GetConfigWaveDims(wave config)
+
+ +
+
+variable IsValidConfigWave(WaveOrNull config, variable version = defaultValue)
+

Check if the given wave is a valid ITCConfigWave.

+

The optional version parameter allows to check if the wave is at least comaptible with this version. The function assumes that higher versions are compatible with lower versions which is for most callers true. For a special case see AFH_GetChannelUnits.

+
+
Parameters:
+
    +

  • config – wave reference to a ITCConfigWave

    • +

  • version – [optional, default=DAQ_CONFIG_WAVE_VERSION], check against a specific version current versions known are 0 (equals NaN), 1, 2, 3

    • +
+
+
+
+ +
+
+variable GetFirstADCChannelIndex(wave config)
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___mies_utilities___conversion_8ipf.html b/file/_m_i_e_s___mies_utilities___conversion_8ipf.html new file mode 100644 index 0000000000..4051783994 --- /dev/null +++ b/file/_m_i_e_s___mies_utilities___conversion_8ipf.html @@ -0,0 +1,369 @@ + + + + + + + + File MIES_MiesUtilities_Conversion.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_MiesUtilities_Conversion.ipf

+

This file holds MIES utility functions for conversions.

+
+

Functions

+
+
+string ChannelTypeToString(variable channelType)
+

Convert a channel type constant from ChannelTypeAndControlConstants to a string.

+
+ +
+
+variable ParseChannelTypeFromString(string channelType, variable allowFail = defaultValue)
+

Convert a channel type string from ChannelTypeToString to one of the constants from ChannelTypeAndControlConstants.

+

+UTF_NOINSTRUMENTATION

+
+
Parameters:
+
    +

  • channelType – channel type

    • +

  • allowFail – [optional, defaults to false] return NaN on unknown channel types (true) or assert (false)

    • +
+
+
+
+ +
+
+variable GetNumberFromType(variable var = defaultValue, string str = defaultValue, variable xopVar = defaultValue)
+

Return the maximum count of the given type.

+
+
Parameters:
+
    +

  • var – numeric channel types

    • +

  • str – string channel types

    • +

  • xopVar – numeric XOP channel types

    • +
+
+
+
+ +
+
+string GetWaveBuilderParameterTypeName(variable type)
+

Return the name short String of the Parameter Wave used in the WaveBuilder.

+
+
Parameters:
+

type – One of ParameterWaveTypes

+
+
Returns:
+

name as string

+
+
+
+ +
+
+string ConvertAmplifierModeShortStr(variable mode)
+

Stringified short version of the clamp mode.

+
+ +
+
+string ConvertAmplifierModeToString(variable mode)
+

Stringified version of the clamp mode.

+
+ +
+
+string GetAbbreviationForAnalysisFunction(string anaFunc)
+

Return the short/abbreviated analysis function name used in the tables.

+
+ +
+
+variable MapAnaFuncToConstant(string anaFunc)
+

Map from analysis function name to numeric constant.

+
+
Returns:
+

One of SpecialAnalysisFunctionTypes which includes INVALID_ANALYSIS_FUNCTION and for CI testing TEST_ANALYSIS_FUNCTION

+
+
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___mies_utilities___data_management_8ipf.html b/file/_m_i_e_s___mies_utilities___data_management_8ipf.html new file mode 100644 index 0000000000..3f82f76d5a --- /dev/null +++ b/file/_m_i_e_s___mies_utilities___data_management_8ipf.html @@ -0,0 +1,313 @@ + + + + + + + + File MIES_MiesUtilities_DataManagement.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_MiesUtilities_DataManagement.ipf

+

This file holds MIES utility functions for data handling.

+
+

Functions

+
+
+variable KillOrMoveToTrash(WaveOrNull wv = defaultValue, dfref dfr = defaultValue)
+

Convenience wrapper for KillOrMoveToTrashPath()

+
+ +
+
+variable KillOrMoveToTrashPath(string path)
+

Delete a datafolder or wave. If this is not possible, because Igor has locked the file, the wave or datafolder is moved into a trash folder named root:mies:trash_$digit.

+

The trash folders will be removed, if possible, from KillTemporaries().

+
+
Parameters:
+

path – absolute path to a datafolder or wave

+
+
+
+ +
+
+variable MoveToTrash(WaveOrNull wv = defaultValue, dfref dfr = defaultValue)
+
+ +
+
+variable KillTrashFolders()
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___mies_utilities___device_8ipf.html b/file/_m_i_e_s___mies_utilities___device_8ipf.html new file mode 100644 index 0000000000..6961f2b218 --- /dev/null +++ b/file/_m_i_e_s___mies_utilities___device_8ipf.html @@ -0,0 +1,390 @@ + + + + + + + + File MIES_MiesUtilities_Device.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_MiesUtilities_Device.ipf

+

This file holds MIES utility functions for Device handling.

+
+

Functions

+
+
+string GetAllDevices()
+

Returns a list of all devices, e.g. “ITC18USB_Dev_0;…” which were locked at some point.

+
+ +
+
+static variable DeviceHasUserComments(string device)
+
+ +
+
+string GetAllDevicesWithContent(variable contentType = defaultValue)
+

Returns a list of all devices, e.g. “ITC18USB_Dev_0;”, which have content.

+
+
Parameters:
+

contentType – [optional, defaults to CONTENT_TYPE_SWEEP] type of content to look for, one of CONTENT_TYPES

+
+
+
+ +
+
+variable GetHardwareType(string device)
+

Return the hardware type of the device.

+

+UTF_NOINSTRUMENTATION

+
+
Returns:
+

One of HardwareDACTypeConstants

+
+
+
+ +
+
+variable IsDeviceNameFromSutter(string device)
+
+ +
+
+variable ParseDeviceString(string device, string *deviceType, string *deviceNumber)
+

Parse a device string: for ITC devices of the form X_DEV_Y, where X is from DEVICE_TYPES_ITC and Y from DEVICE_NUMBERS. for NI devices of the form X, where X is from DAP_GetNIDeviceList() for Sutter devices of the form IPA_E_Xxxxxx, where X must be present.

+

Returns the result in deviceType and deviceNumber. Currently the parsing is successfull if for ITC devices X and Y are non-empty. for NI devices X is non-empty. for Sutter devices if the name starts with IPA_E_ and is at least 7 characters long deviceNumber is empty for NI devices as it does not apply

+

UTF_NOINSTRUMENTATION

+

+
+
Parameters:
+
    +

  • device – [in] input device string X_DEV_Y

    • +

  • deviceType – [out] returns the device type X

    • +

  • deviceNumber – [out] returns the device number Y

    • +
+
+
Returns:
+

one on successfull parsing, zero on error

+
+
+
+ +
+
+string GetListOfUnlockedDevices()
+

Return the list of unlocked DA_Ephys panels.

+
+ +
+
+string GetListOfLockedDevices()
+

Return the list of locked devices.

+
+ +
+
+string GetListOfLockedITC1600Devices()
+

Return the list of locked ITC1600 devices.

+
+ +
+
+variable IsITC1600(string device)
+

Check that the device is of type ITC1600.

+
+ +
+
+variable IsDeviceActiveWithBGTask(string device, string task)
+

Check wether the given background task is running and that the device is active in multi device mode.

+
+ +
+
+variable GetNextRandomNumberForDevice(string device)
+

Return the next random number using the device specific RNG seed.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___mies_utilities___g_u_i_8ipf.html b/file/_m_i_e_s___mies_utilities___g_u_i_8ipf.html new file mode 100644 index 0000000000..27c461e0ff --- /dev/null +++ b/file/_m_i_e_s___mies_utilities___g_u_i_8ipf.html @@ -0,0 +1,542 @@ + + + + + + + + File MIES_MiesUtilities_GUI.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_MiesUtilities_GUI.ipf

+

This file holds MIES utility functions for GUI.

+
+

Functions

+
+
+string GetSpecialControlLabel(variable channelType, variable controlType)
+

Return the dimension label for the special, aka non-unique, controls.

+
+ +
+
+string GetPanelControl(variable channelIndex, variable channelType, variable controlType)
+

Returns the name of a control from the DA_EPHYS panel.

+

Constants are defined at ChannelTypeAndControlConstants

+
+ +
+
+variable GetNextTraceIndex(string graph)
+

Helper function for CreateTiledChannelGraph and friends.

+

Return the next trace index for a graph which uses our trace data storage wave.

+
+ +
+
+string GetTraceNamePrefix(variable traceIndex)
+

Return a trace name prefix suitable for GetNextTraceIndex()

+
+ +
+
+std::tuple<RGBColor> GetHeadstageColor(variable headstage, variable channelType = defaultValue, variable channelNumber = defaultValue, variable isSplitted = defaultValue)
+

Return the color of the given headstage.

+
+
Parameters:
+
    +

  • headstage – Headstage, Use “NaN” for non-associated channels

    • +

  • channelType – [optional, empty by default] The channel type for non-associated channels, currently only XOP_CHANNEL_TYPE_TTL is evaluated

    • +

  • channelNumber – [optional, empty by default] For plotting “TTL” channels only, GUI channel number

    • +

  • isSplitted – [optional, default 1] For plotting “TTL” channels only, Flag if the color for a splitted or unsplitted channel should be returned

    • +
+
+
+
+ +
+
+variable TimeAlignMainWindow(string graph, PostPlotSettings *pps)
+

Time Alignment for the BrowserSettingsPanel.

+

This function should work for any given reference trace in pps.timeAlignRefTrace in the popup menu. (DB and SB)

+
+
Parameters:
+
    +

  • graph – graph with sweep traces

    • +

  • pps – settings

    • +
+
+
+
+ +
+
+string TimeAlignGetAllTraces(string graph)
+

return a list of all traces relevant for TimeAlignment

+
+ +
+
+variable TimeAlignHandleCursorDisplay(string win)
+

Adds or removes the cursors from the graphs depending on the panel settings.

+
+
Parameters:
+

win – main DB/SB graph or any subwindow panel.

+
+
+
+ +
+
+variable TimeAlignUpdateControls(string win)
+

Enable/Disable TimeAlignment Controls and Cursors.

+
+ +
+
+variable TimeAlignCursorMovedHook(WMWinHookStruct *s)
+
+ +
+
+wave GetAllSweepTraces(string graphs, variable region = defaultValue, variable channelType = defaultValue, variable prefixTraces = defaultValue)
+

Get a textwave of all traces from a list of graphs.

+
+
Parameters:
+
    +

  • graphs – semicolon separated list of graph names

    • +

  • region – [optional] return only traces with the specified region userdata entry

    • +

  • channelType – [optional] return only the traces with the given channel type

    • +

  • prefixTraces – [optional, defaults to true] prefix the traces names with the graph name and a #

    • +
+
+
Returns:
+

graph::trace named patterns

+
+
+
+ +
+
+wave GetSweepUserData(string graph, string key, variable channelType = defaultValue, variable region = defaultValue)
+
+ +
+
+static variable CalculateFeatureLoc(wave wv, variable mode, variable level, variable first, variable last)
+

Find the given feature in the given wave range first and last are in x coordinates and clipped to valid values.

+
+ +
+
+variable TimeAlignmentIfReq(string graphtrace, variable mode, variable level, variable pos1x, variable pos2x, variable force = defaultValue)
+

Perform time alignment of features in the sweep traces.

+

+

See also

+

CalculateFeatureLoc

+
+

+
+
Parameters:
+
    +

  • graphtrace – reference trace in the form of graph::trace

    • +

  • mode – time alignment mode

    • +

  • level – level input to the FindLevel operation in

    • +

  • pos1x – specify start range for feature position

    • +

  • pos2x – specify end range for feature position

    • +

  • force – [optional, defaults to false] redo time aligment regardless of wave note

    • +
+
+
+
+ +
+
+variable EqualizeVerticalAxesRanges(string graph, variable ignoreAxesWithLevelCrossing = defaultValue, variable level = defaultValue, variable rangePerClampMode = defaultValue)
+

Equalize all vertical axes ranges so that they cover the same range.

+
+
Parameters:
+
    +

  • graph – graph

    • +

  • ignoreAxesWithLevelCrossing – [optional, defaults to false] ignore all vertical axis which cross the given level in the visible range

    • +

  • level – [optional, defaults to zero] level to be used for ignoreAxesWithLevelCrossing=1

    • +

  • rangePerClampMode – [optional, defaults to false] use separate Y ranges per clamp mode

    • +
+
+
+
+ +
+
+variable UpdateSweepPlot(string win)
+
+ +
+
+variable UpdateSettingsPanel(string win)
+

update of panel elements and related displayed graphs in BSP

+
+ +
+
+wave GetPlainSweepList(string win)
+
+ +
+
+wave GetTraceInfos(string graph, WaveText addFilterKeys = defaultValue, WaveText addFilterValues = defaultValue)
+

Return the graph user data as 2D text wave.

+

Only returns infos for sweep traces without duplicates. Duplicates are present with oodDAQ display mode.

+
+
Parameters:
+
    +

  • graph – [in] Name of graph

    • +

  • addFilterKeys – [in] [optional, default = $””] additional keys for filtering

    • +

  • addFilterValues – [in] [optional, default = $””] additional values for filtering, must have same size as keys

    • +
+
+
+
+ +
+
+variable RemoveSweepFromGraph(string win, variable index)
+

Remove the given sweep from the Databrowser/Sweepbrowser.

+

Needs a manual call to PostPlotTransformations() afterwards.

+
+
Parameters:
+
    +

  • win – graph

    • +

  • index – overlay sweeps listbox index

    • +
+
+
+
+ +
+
+variable AddSweepToGraph(string win, variable index, BufferedDrawInfo *bdi = defaultValue)
+

Add the given sweep to the Databrowser/Sweepbrowser.

+

Needs a manual call to PostPlotTransformations() afterwards.

+
+
Parameters:
+
    +

  • win – graph

    • +

  • index – overlay sweeps listbox index

    • +

  • bdi – [optional, default = n/a] BufferedDrawInfo structure, when given buffered draw is used.

    • +
+
+
+
+ +
+
+variable UpdateSweepInGraph(string win, variable index)
+

Update the given sweep in the Databrowser/Sweepbrowser plot.

+

Needs a manual call to PostPlotTransformations() afterwards.

+
+
Parameters:
+
    +

  • win – graph

    • +

  • index – overlay sweeps listbox index

    • +
+
+
+
+ +
+
+variable StoreWindowCoordinatesHook(WMWinHookStruct *s)
+

Generic window hooks for storing the window coordinates in the JSON settings file.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___mies_utilities___getter_8ipf.html b/file/_m_i_e_s___mies_utilities___getter_8ipf.html new file mode 100644 index 0000000000..6c387b5cbc --- /dev/null +++ b/file/_m_i_e_s___mies_utilities___getter_8ipf.html @@ -0,0 +1,346 @@ + + + + + + + + File MIES_MiesUtilities_Getter.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_MiesUtilities_Getter.ipf

+

This file holds MIES utility functions that get names/objects.

+
+

Functions

+
+
+wave GetConfigWave(wave sweepWave)
+

Returns the config wave for a given sweep wave.

+
+ +
+
+wave GetSweepWave(string device, variable sweepNo)
+

Returns the, possibly non existing, sweep data wave for the given sweep number There are two persistent formats how sweep data is stored.

+

The current format is: The sweep wave is a 1D text wave. Each entry contains the relative path to a single channel wave, including the wave name. The reference data folder for the relative path is the data folder where the sweep wave is located. The number of rows of the sweep wave equals the number of columns of the config wave and indexes the channels. Thus, the sweep wave can not be a free wave.

+

The deprecated format is: A 2D numeric wave, where the rows are the sample points and the columns the sweep channels. In that format all channels have the same number of points and the same sample interval. The sample interval is saved a ROW DimDelta. The number of columns equals the number of columns of the config waves and indexes the channels.

+

Intermediate sweep wave format: Intermediate sweep format is used in some parts of MIES, e.g. NWB saving as it is easier to handle. The sweep wave is a wave reference wave, where each element refers to a channel. It can be a free wave. The number of rows of the sweep wave equals the number of columns of the config wave and indexes the channels. To convert a text sweep wave to a waveRef sweep wave use TextSweepToWaveRef The programmer has to consider if pure references to channels are good enough (TextSweepToWaveRef) or if the channels should be duplicated.

+
+ +
+
+string GetConfigWaveName(variable sweepNo)
+

Return the config wave name.

+
+ +
+
+string GetSweepWaveName(variable sweepNo)
+

Return the sweep wave name.

+
+ +
+
+string GetNIFIFOName(variable deviceID)
+

constructs a fifo name for NI device ADC operations from the deviceID

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetMIESVersionAsString()
+

Return the MIES version with canonical EOLs.

+
+ +
+
+variable GetAnalysisFunctionVersion(variable type)
+

Return the current version of the analysis functions.

+
+ +
+
+std::tuple<WAVE, WAVE> GetSweepAndConfigWaveFromDevice(string device, variable sweepNo)
+
+ +
+
+string GetWorkLoadName(string workload, string device)
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___mies_utilities___logbook_8ipf.html b/file/_m_i_e_s___mies_utilities___logbook_8ipf.html new file mode 100644 index 0000000000..4b3a5ea73b --- /dev/null +++ b/file/_m_i_e_s___mies_utilities___logbook_8ipf.html @@ -0,0 +1,1079 @@ + + + + + + + + File MIES_MiesUtilities_Logbook.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_MiesUtilities_Logbook.ipf

+

This file holds MIES utility functions for working with the various Logbooks.

+
+

Functions

+
+
+variable GetLogbookType(wave wv)
+

Return the logbook type, one of LogbookTypes.

+
+ +
+
+wave GetLogbookWaves(variable logbookType, variable logbookWaveType, string device = defaultValue)
+

Return the logbook waves.

+
+
Parameters:
+
+
+
+
+ +
+
+wave ExtractLogbookSliceTimeStamp(wave logbook)
+

Extract a date/time slice of the logbook wave.

+
+ +
+
+wave ExtractLogbookSliceDeltaTime(wave logbook)
+

Extract the delta time slice of the logbook wave.

+
+ +
+
+wave ExtractLogbookSliceSweep(wave values)
+

Extract the sweep number slice of the labnotebook values wave.

+
+ +
+
+wave ExtractLogbookSliceEmpty(wave values)
+

Extract a slice of the logbook wave and makes it empty.

+
+ +
+
+static wave ExtractLogbookSlice(wave logbook, variable logbookType, variable colOrLayer, string suffix)
+

Extract a single column/layer of the labnotebook/TPStorage values wave.

+

This is useful if you want to plot values against e.g time and let Igor do the formatting of the date/time values. Always returns a numerical wave.

+

The slice is returned as-is if it exists already. Callers which modify the logbook are responsible to resize the slice as well.

+
+ +
+
+variable GetLastSettingIndep(wave numericalValues, variable sweepNo, string setting, variable entrySourceType, variable defValue = defaultValue)
+

Return a headstage independent setting from the numerical labnotebook.

+

+

See also

+

GetLastSetting()

+
+

+
+
Returns:
+

the headstage independent setting or defValue

+
+
+
+ +
+
+string GetLastSettingTextIndep(WaveText textualValues, variable sweepNo, string setting, variable entrySourceType, string defValue = defaultValue)
+

Return a headstage independent setting from the textual labnotebook.

+

+

See also

+

GetLastSetting()

+
+

+
+
Returns:
+

the headstage independent setting or defValue

+
+
+
+ +
+
+variable GetLastSettingIndepRAC(wave numericalValues, variable sweepNo, string setting, variable entrySourceType, variable defValue = defaultValue)
+

Return a headstage independent setting from the numerical labnotebook of the sweeps in the same RA cycle.

+

+

See also

+

GetLastSetting()

+
+

+
+
Returns:
+

the headstage independent setting or defValue

+
+
+
+ +
+
+variable GetLastSettingIndepSCI(wave numericalValues, variable sweepNo, string setting, variable headstage, variable entrySourceType, variable defValue = defaultValue)
+

Return a headstage independent setting from the numerical labnotebook of the sweeps in the same SCI cycle.

+

+

See also

+

GetLastSetting()

+
+

+
+
Returns:
+

the headstage independent setting or defValue

+
+
+
+ +
+
+string GetLastSettingTextIndepSCI(wave numericalValues, WaveText textualValues, variable sweepNo, string setting, variable headstage, variable entrySourceType, string defValue = defaultValue)
+

Return a headstage independent setting from the textual labnotebook of the sweeps in the same SCI cycle.

+

+

See also

+

GetLastSetting()

+
+

+
+
Returns:
+

the headstage independent setting or defValue

+
+
+
+ +
+
+string GetLastSettingTextIndepRAC(wave numericalValues, WaveText textualValues, variable sweepNo, string setting, variable entrySourceType, string defValue = defaultValue)
+

Return a headstage independent setting from the numerical labnotebook of the sweeps in the same RA cycle.

+
+
Returns:
+

the headstage independent setting or defValue

+
+
+
+ +
+
+std::tuple<WaveOrNull, variable> GetLastSettingChannel(wave numericalValues, WaveTextOrNull textualValues, variable sweepNo, string setting, variable channelNumber, variable channelType, variable entrySourceType)
+

Return a numerical or text setting for the given channel.

+

It also returns headstage independent entries when the given channel refers to an active channel.

+

+

See also

+

GetLastSettingChannelInternal()

+
+

+
+
Returns:
+

the wave containing the setting and the index into it.

+
+
+
+ +
+
+static std::tuple<WaveOrNull, variable> GetLastSettingChannelInternal(wave numericalValues, wave values, variable sweepNo, string setting, variable channelNumber, variable channelType, variable entrySourceType)
+

Return a numerical/textual setting for the given channel.

+

The function takes care of associated/unassociated channel properties and all other internals.

+

+

See also

+

GetLastSettingChannel

+
+

+
+
Parameters:
+
    +

  • numericalValues – numerical labnotebook

    • +

  • values – labnotebook to read data from, either numerical or textual

    • +

  • sweepNo – sweep number

    • +

  • setting – name of the labnotebook entry to search

    • +

  • channelNumber – channel number

    • +

  • channelType – channel type, one of XopChannelConstants

    • +

  • entrySourceType – type of the labnotebook entry, one of DataAcqModes. If you don’t care about the entry source type pass UNKNOWN_MODE.

    • +
+
+
Returns:
+

A tuple of the result wave and the index into it.

+
+
+
+ +
+
+static variable GetLogbookSettingsColumn(wave values, string key)
+
+ +
+
+static variable GetLogbookSettingsColumnFromSorted(WaveText sortedKeys, wave indices, string key)
+
+ +
+
+wave GetLastSetting(wave values, variable sweepNo, string setting, variable entrySourceType)
+

Return a numeric/textual wave with the latest value of a setting from the numerical/labnotebook labnotebook for the given sweep number.

+
+
Parameters:
+
    +

  • values – numerical/textual labnotebook

    • +

  • sweepNo – sweep number

    • +

  • setting – name of the setting to query

    • +

  • entrySourceType – type of the labnotebook entry, one of DataAcqModes. If you don’t care about the entry source type pass UNKNOWN_MODE.

    • +
+
+
Returns:
+

a free wave with LABNOTEBOOK_LAYER_COUNT rows. In case the setting could not be found an invalid wave reference is returned.

+
+
+
+ +
+
+wave GetLastSettingNoCache(wave values, variable sweepNo, string setting, variable entrySourceType, variable *first = defaultValue, variable *last = defaultValue, variable *rowIndex = defaultValue, variable settingCol = defaultValue)
+

Return a wave with the latest value of a setting from the numerical/textual labnotebook for the given sweep number. Uncached version, general users should prefer GetLastSetting().

+
+
Parameters:
+
    +

  • values – numerical/textual labnotebook

    • +

  • sweepNo – sweep number

    • +

  • setting – name of the setting to query

    • +

  • entrySourceType – type of the labnotebook entry, one of DataAcqModes

    • +

  • first – [inout] [optional] Can be used to query and return the labnotebook row range. Useful for routines which must make a lot of queries to the same sweep and want to avoid the overhead of calculating first and last. Passing LABNOTEBOOK_GET_RANGE will set the calculated values of first and last after the function returns. Passing a value greater or equal zero will use these values instead.

    • +

  • last – [inout] [optional] see first

    • +

  • rowIndex – [out] [optional] return the row where the setting could be found, otherwise it is set to LABNOTEBOOK_MISSING_VALUE

    • +

  • settingCol – [optional, default: determined by function] if the caller has already determined the setting column, it can set this argument then GetLastSettingNoCache saves the find

    • +
+
+
Returns:
+

a free wave with LABNOTEBOOK_LAYER_COUNT rows. In case the setting could not be found an invalid wave reference is returned.

+
+
+
+ +
+
+wave GetLastSettingTextRAC(wave numericalValues, WaveText textualValues, variable sweepNo, string setting, variable entrySourceType)
+

Return the last textual value of the sweeps in the same RA cycle.

+

+

See also

+

GetLastSetting()

+
+

+
+ +
+
+wave GetLastSettingRAC(wave numericalValues, variable sweepNo, string setting, variable entrySourceType)
+

Return the last numerical value of the sweeps in the same RA cycle.

+

+

See also

+

GetLastSetting()

+
+

+
+ +
+
+wave GetLastSettingIndepEachRAC(wave numericalValues, variable sweepNo, string setting, variable entrySourceType, variable defValue = defaultValue)
+

Return the last numerical value for the given setting of each sweep in the same RA cycle.

+

The returned wave will have NaN for sweeps which do not have that entry. This is done in order to keep the indizes intact.

+

+

See also

+

GetLastSetting()

+
+

+
+ +
+
+wave GetLastSettingTextIndepEachRAC(wave numericalValues, WaveText textualValues, variable sweepNo, string setting, variable entrySourceType, string defValue = defaultValue)
+

Return the last textual value for the given setting of each sweep in the same RA cycle.

+

The returned wave will have NaN for sweeps which do not have that entry. This is done in order to keep the indizes intact.

+

+

See also

+

GetLastSetting()

+
+

+
+ +
+
+wave GetLastSettingEachRAC(wave numericalValues, variable sweepNo, string setting, variable headstage, variable entrySourceType)
+

Return the last numerical value for the given setting of each sweep for a given headstage in the same RA cycle.

+

The returned wave will have NaN for sweeps which do not have that entry. This is done in order to keep the indizes intact.

+

+

See also

+

GetLastSetting

+
+

+
+ +
+
+wave GetLastSettingTextEachRAC(wave numericalValues, WaveText textualValues, variable sweepNo, string setting, variable headstage, variable entrySourceType)
+

Return the last textual value for the given setting of each sweep for a given headstage in the same RA cycle.

+

The returned wave will have NaN for sweeps which do not have that entry. This is done in order to keep the indizes intact.

+

+

See also

+

GetLastSetting()

+
+

+
+ +
+
+wave GetLastSettingTextSCI(wave numericalValues, WaveText textualValues, variable sweepNo, string setting, variable headstage, variable entrySourceType)
+

Return the last textual value of the sweeps in the same stimset cycle.

+

+

See also

+

GetLastSetting()

+
+

+
+ +
+
+wave GetLastSettingSCI(wave numericalValues, variable sweepNo, string setting, variable headstage, variable entrySourceType)
+

Return the last numerical value of the sweeps in the same stimset cycle.

+

+

See also

+

GetLastSetting()

+
+

+
+ +
+
+wave GetLastSettingIndepEachSCI(wave numericalValues, variable sweepNo, string setting, variable headstage, variable entrySourceType, variable defValue = defaultValue)
+

Return the last numerical value for the given setting of each sweep in the same stimset cycle.

+

The returned wave will have NaN for sweeps which do not have that entry. This is done in order to keep the indizes intact.

+

+

See also

+

GetLastSetting()

+
+

+
+ +
+
+wave GetLastSettingTextIndepEachSCI(wave numericalValues, WaveText textualValues, variable sweepNo, variable headstage, string setting, variable entrySourceType, string defValue = defaultValue)
+

Return the last textual value for the given setting of each sweep in the same stimset cycle.

+

The returned wave will have NaN for sweeps which do not have that entry. This is done in order to keep the indizes intact.

+

+

See also

+

GetLastSetting()

+
+

+
+ +
+
+wave GetLastSettingEachSCI(wave numericalValues, variable sweepNo, string setting, variable headstage, variable entrySourceType)
+

Return the last numerical value for the given setting of each sweep for a given headstage in the same stimset cycle.

+

The returned wave will have NaN for sweeps which do not have that entry. This is done in order to keep the indizes intact.

+

+

See also

+

GetLastSetting

+
+

+
+ +
+
+wave GetLastSettingTextEachSCI(wave numericalValues, WaveText textualValues, variable sweepNo, string setting, variable headstage, variable entrySourceType)
+

Return the last textual value for the given setting of each sweep for a given headstage in the same stimset cycle.

+

The returned wave will have NaN for sweeps which do not have that entry. This is done in order to keep the indizes intact.

+

+

See also

+

GetLastSetting()

+
+

+
+ +
+
+std::tuple<WAVE, variable> GetNonEmptyLBNRows(wave labnotebookValues, string setting)
+

Return a wave with all labnotebook rows which have a non-empty entry for setting.

+
+ +
+
+static variable EnforceIndependentSetting(wave settings)
+

Test helper to enforce that every query done for an INDEP_HEADSTAGE setting does not search an entry which is HEADSTAGE dependent. The additional check that not all entries are the same is for really old legacy entries which are INDEP but set for all headstages.

+

Does nothing outside of CI.

+
+ +
+
+static variable FindRange(wave wv, variable col, variable val, variable entrySourceType, variable *first, variable *last)
+

Find the first and last point index of a consecutive range of values in the labnotebook, searches the range from the back.

+
+
Parameters:
+
    +

  • wv – [in] wave to search

    • +

  • col – [in] column to look for

    • +

  • val – [in] value to search

    • +

  • entrySourceType – [in] type of the labnotebook entry, one of DataAcqModes

    • +

  • first – [out] point index of the beginning of the range

    • +

  • last – [out] point index of the end of the range

    • +
+
+
+
+ +
+
+variable GetSweepColumn(wave labnotebookValues)
+

Returns the numerical index for the sweep number column in the settings history waves (numeric and text)

+
+ +
+
+wave GetSweepsWithSetting(wave labnotebookValues, string setting)
+

Return a wave with all sweep numbers which have a non-empty entry for setting.

+
+
Parameters:
+
    +

  • labnotebookValues – numerical/textual labnotebook

    • +

  • setting – name of the value to search

    • +
+
+
Returns:
+

a 1D free wave with the matching sweep numbers. In case the setting could not be found an invalid wave reference is returned.

+
+
+
+ +
+
+wave GetUniqueSettings(wave values, string setting)
+

Return a unique list of labnotebook entries of the given setting.

+
+
Parameters:
+
    +

  • values – numerical logbook wave

    • +

  • setting – name of the value to search

    • +
+
+
+
+ +
+
+wave GetLastSweepWithSetting(wave numericalValues, string setting, variable *sweepNo)
+

Return the last numerical value of a setting from the labnotebook and the sweep it was set.

+
+
Parameters:
+
    +

  • numericalValues – [in] numerical labnotebook

    • +

  • setting – [in] name of the value to search

    • +

  • sweepNo – [out] sweep number the value was last set

    • +
+
+
Returns:
+

a free wave with LABNOTEBOOK_LAYER_COUNT rows. In case the setting could not be found an invalid wave reference is returned.

+
+
+
+ +
+
+variable GetLastSweepWithSettingIndep(wave numericalValues, string setting, variable *sweepNo, variable defValue = defaultValue)
+

Return the last numerical value of a headstage independent setting from the labnotebook and the sweep it was set.

+
+
Parameters:
+
    +

  • numericalValues – [in] numerical labnotebook

    • +

  • setting – [in] name of the value to search

    • +

  • sweepNo – [out] sweep number the value was last set

    • +

  • defValue – [in] [optional, defaults to NaN] value to return in case nothing could be found

    • +
+
+
+
+ +
+
+wave GetLastSweepWithSettingText(WaveText textualValues, string setting, variable *sweepNo)
+

Return the last textual value of a setting from the labnotebook and the sweep it was set.

+
+
Parameters:
+
    +

  • textualValues – [in] textual labnotebook

    • +

  • setting – [in] name of the value to search

    • +

  • sweepNo – [out] sweep number the value was last set

    • +
+
+
Returns:
+

a free wave with LABNOTEBOOK_LAYER_COUNT rows. In case the setting could not be found an invalid wave reference is returned.

+
+
+
+ +
+
+string GetLastSweepWithSettingTextI(wave numericalValues, string setting, variable *sweepNo, string defValue = defaultValue)
+

Return the last textual value of a headstage independent setting from the labnotebook and the sweep it was set.

+
+
Parameters:
+
    +

  • numericalValues – [in] numerical labnotebook

    • +

  • setting – [in] name of the value to search

    • +

  • sweepNo – [out] sweep number the value was last set

    • +

  • defValue – [in] [optional, defaults to an empty string] value to return in case nothing could be found

    • +
+
+
+
+ +
+
+variable GetIndexForHeadstageIndepData(wave values)
+

Return the index for headstage independent data.

+

Before dfe2d862 (Make the function AB_SplitTTLWaveIntoComponents available for all, 2015-10-07) we stored headstage independent data in either all entries or only the first one. Since that commit we store the data in INDEP_HEADSTAGE.

+
+ +
+
+string CreateLBNUnassocKey(string setting, variable channelNumber, variable channelType)
+

Create a labnotebook key for unassociated channels.

+

We support two types of unassociated keys. Old style, prior to 403c8ec2 (Merge pull request #370 from AllenInstitute/feature/sweepformula_enable, 2019-11-13) but after its introduction in ad8dc8ec (Allow AD/DA channels not associated with a headstage again, 2015-10-22) are written as “$Name UNASSOC_$ChannelNumber”.

+

New style have the format “$Name u_(AD|DA)$ChannelNumber”, these include the channel type to make them more self explaining.

+
+ +
+
+string CreateTTLChannelLBNKey(string entry, variable channelNumber)
+

Create a LBN key for TTL channels.

+
+ +
+
+variable IsUnassocLBNKey(string name)
+

Check if the given labnotebook entry is from an unassociated DA/AD channel.

+
+ +
+
+string RemoveUnassocLBNKeySuffix(string name)
+

Remove the unassociated, old and new, prefix of the given labnotebook entry name.

+

+

See also

+

CreateLBNUnassocKey()

+
+

+
+ +
+
+variable EntrySourceTypeMapper(variable entrySourceType)
+

Maps the labnotebook entry source type, one of DataAcqModes, to a valid wave index.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+variable ReverseEntrySourceTypeMapper(variable mapped)
+

Rerverse the effect of EntrySourceTypeMapper()

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string CreateAnaFuncLBNKey(variable type, string formatString, variable chunk = defaultValue, variable query = defaultValue, variable waMode = defaultValue)
+

Return labnotebook keys for patch seq analysis functions.

+
+
Parameters:
+
+
+
+
+ +
+
+variable SetAnalysisFunctionVersion(string device, variable type, variable headstage, variable sweepNo)
+

Add a labnotebook entry denoting the analysis function version.

+
+ +
+
+variable GetHeadstageForChannel(wave numericalValues, variable sweep, variable channelType, variable channelNumber, variable entrySourceType)
+

Returns the active headstage for a given sweep, channelType, channelNumber from the LBN.

+
+
Parameters:
+
    +

  • numericalValues – LBN wave with numerical values

    • +

  • sweep – sweep number

    • +

  • channelType – channel type number

    • +

  • channelNumber – channel number

    • +

  • entrySourceType – type of the labnotebook entry, one of DataAcqModes

    • +
+
+
Returns:
+

headstage number or NaN if no headstage was found

+
+
+
+ +
+
+wave GetTTLLabnotebookEntry(WaveText textualValues, string name, variable sweep)
+

Return a list of TTL stimsets which are indexed by DAEphys TTL channels.

+

The indexing here is hardware independent. For ITC hardware the assertion “log(ttlBit)/log(2) == DAEphys TTL channel” holds.

+
+
Parameters:
+
    +

  • textualValues – Text labnotebook values

    • +

  • name – One of LabnotebookTTLNames

    • +

  • sweep – Sweep number

    • +
+
+
+
+ +
+
+variable GetTotalOnsetDelayFromDevice(string device)
+

Return the total onset delay from the given device during DAQ.

+

+UTF_NOINSTRUMENTATION

+

See also

+

GetTotalOnsetDelay

+
+

+
+ +
+
+

Variables

+
+
+static const double GET_LB_MODE_NONE = 0
+
+ +
+
+static const double GET_LB_MODE_READ = 1
+
+ +
+
+static const double GET_LB_MODE_WRITE = 2
+
+ +
+
+static const string LBN_UNASSOC_REGEXP_LEGACY = "^(.*) UNASSOC_[[:digit:]]+$"
+
+ +
+
+static const string LBN_UNASSOC_REGEXP = "^(.*) u_(AD|DA)[[:digit:]]+$"
+
+ +
+
+static const string PSQ_PB_LBN_PREFIX = "Pipette in Bath"
+
+ +
+
+static const string PSQ_CR_LBN_PREFIX = "Chirp"
+
+ +
+
+static const string PSQ_SP_LBN_PREFIX = "Squ. Pul."
+
+ +
+
+static const string PSQ_DS_LBN_PREFIX = "DA Scale"
+
+ +
+
+static const string PSQ_RB_LBN_PREFIX = "Rheobase"
+
+ +
+
+static const string PSQ_RA_LBN_PREFIX = "Ramp"
+
+ +
+
+static const string PSQ_SE_LBN_PREFIX = "Seal evaluation"
+
+ +
+
+static const string PSQ_VM_LBN_PREFIX = "True Rest Memb."
+
+ +
+
+static const string PSQ_AR_LBN_PREFIX = "Access Res. Smoke"
+
+ +
+
+static const string MSQ_FRE_LBN_PREFIX = "F Rheo E"
+
+ +
+
+static const string MSQ_DS_LBN_PREFIX = "Da Scale"
+
+ +
+
+static const string MSQ_SC_LBN_PREFIX = "Spike Control"
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___mies_utilities___logging_8ipf.html b/file/_m_i_e_s___mies_utilities___logging_8ipf.html new file mode 100644 index 0000000000..07ed0dd2f9 --- /dev/null +++ b/file/_m_i_e_s___mies_utilities___logging_8ipf.html @@ -0,0 +1,383 @@ + + + + + + + + File MIES_MiesUtilities_Logging.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_MiesUtilities_Logging.ipf

+

This file holds MIES utility functions for logging.

+
+

Functions

+
+
+string GetZeroMQXOPLogfile()
+

Return the disc location of the (possibly non-existing) ZeroMQ-XOP logfile.

+
+ +
+
+string GetITCXOP2Logfile()
+

Return the disc location of the (possibly non-existing) ITCXOP2 logfile.

+
+ +
+
+std::tuple<WaveText, variable> FilterByDate(WaveText entries, variable first, variable last)
+

Filters log file entries by data, returns a null wave if no entries were found.

+
+ +
+
+static variable FindFirstLogEntryElementByDate(WaveText entries, variable timeStamp)
+

Find the index of the first log file line that is from a time greater or equal than timeStamp The algorithm is a binary search that requires ascending order of time stamps of the log file entries. entries is a text wave where each line contains a log file entry as JSON. This JSON can contain a timestamp but can also contain no or an invalid timestamp. If the binary search hits an invalid timestamp the current search index is moved by a linear search to lower indices until a valid timestamp or the lower boundary is reached.

+
+
Parameters:
+
    +

  • entries – text wave where each line contains a log file entry as serialized JSON with ascending order of time stamps

    • +

  • timeStamp – time stamp that is searched

    • +
+
+
Returns:
+

index + 1 of the last entry with a time stamp lower than timeStamp

+
+
+
+ +
+
+static variable FindLastLogEntryElementByDate(WaveText entries, variable timeStamp)
+

Find the index of the last log file line that is from a time smaller or equal than timeStamp The algorithm is a binary search that requires ascending order of time stamps of the log file entries. entries is a text wave where each line contains a log file entry as JSON. This JSON can contain a timestamp but can also contain no or an invalid timestamp. If the binary search hits an invalid timestamp the current search index is moved by a linear search to higher indices until a valid timestamp or the higher boundary is reached.

+
+
Parameters:
+
    +

  • entries – text wave where each line contains a log file entry as serialized JSON with ascending order of time stamps

    • +

  • timeStamp – time stamp that is searched

    • +
+
+
Returns:
+

index - 1 of the first entry with a time stamp greater than timeStamp

+
+
+
+ +
+
+variable ArchiveLogFilesOnceAndKeepMonth()
+
+ +
+
+static string GetDateOfLogEntry(string entry)
+
+ +
+
+static variable ArchiveLogFile(WaveText logData, string fullFilePath, variable index)
+
+ +
+
+static variable SaveRemainingLog(WaveText logData, variable index, string fullFilePath)
+
+ +
+
+static string LastArchivedLogFile(string fullFilePath)
+
+ +
+
+

Variables

+
+
+static const double ARCHIVE_SIZETHRESHOLD = 52428800
+
+ +
+
+static const string ARCHIVEDLOG_SUFFIX = "_old_"
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___mies_utilities___recreation_8ipf.html b/file/_m_i_e_s___mies_utilities___recreation_8ipf.html new file mode 100644 index 0000000000..12a372e07a --- /dev/null +++ b/file/_m_i_e_s___mies_utilities___recreation_8ipf.html @@ -0,0 +1,383 @@ + + + + + + + + File MIES_MiesUtilities_Recreation.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_MiesUtilities_Recreation.ipf

+

This file holds MIES utility functions for sweep and config wave recreation.

+
+

Functions

+
+
+variable RecreateMissingSweepAndConfigWaves(string device, dfref deviceDataDFR)
+

Tries to find deleted sweep and config waves which are still present due to 1D waves from databrowser backups or labnotebook entries.

+

The result is placed in root:reconstructed which is overwritten.

+

For reconstructing single sweep or config waves, see RecreateSweepWaveFromBackupAndLBN() and RecreateConfigWaveFromLBN().

+

Example invocation:

    +

  • RecreateMissingSweepAndConfigWaves(“ITC18USB_DEV_0”, root:MIES:HardwareDevices:ITC18USB:Device0:Data:)

    • +

  • Inspect the results in root:reconstructed

    • +

  • If you are satisfied, move the waves from root:reconstructed into e.g. root:MIES:HardwareDevices:ITC18USB:Device0:Data:

    • +

  • Proceed with the data as usual

    • +
+

+

In case the routine throws an assertion, please open an issue so that we can investigate.

+
+ +
+
+wave RecreateSweepWaveFromBackupAndLBN(wave numericalValues, WaveText textualValues, variable sweepNo, dfref deviceDataDFR)
+

Try recreating a WaveRef sweep wave from its databrowser backup. For a text sweep wave, call SplitSweepIntoComponents afterwards with a target DF.

+
+
Returns:
+

$”” if reconstruction failed or a free wave with the sweep data and correct metadata

+
+
+
+ +
+
+wave RecreateConfigWaveFromLBN(string device, wave numericalValues, wave textualValues, variable sweepNo)
+

Try recreating the DAQ config wave from labnotebook entries.

+
+
Returns:
+

$"" if recreation failed or a free wave on success.

+
+
+
+ +
+
+static std::tuple<WAVE, WaveRefWave> GetSingleSweepWaves(dfref singleSweepFolder, variable channelType)
+

Return waves with the channel numbers and references to 1D waves from the X_XXXX folders.

+
+ +
+
+static variable AddToSweepWave(WaveRefWave channelWaves, wave channelNumbers, WaveRefWave sweepWave, variable indexOffset)
+

Add the returned 1D waves from GetSingleSweepWaves() into sweepWave. sweepWave must be WaveRef wave. The size of sweepWave is increased if required.

+
+
Returns:
+

index of last row filled

+
+
+
+ +
+
+static variable AddChannelPropertiesFromLBN(wave numericalValues, wave textualValues, variable sweepNo, wave configWave, variable channelType)
+

Set ChannelNumber and ChannelType in configWave.

+
+ +
+
+static variable GetSamplingIntervalFromLBN(wave numericalValues, variable sweepNo, variable channelType)
+

Return the sampling interval [ms] rounded to microseconds.

+
+ +
+
+static variable AddDAQChannelTypeFromLBN(wave numericalValues, wave textualValues, variable sweepNo, wave configWave)
+

Set DAQChannelType in configWave.

+
+ +
+
+static variable AddHeadstageFromLBN(wave numericalValues, variable sweepNo, wave configWave)
+

Set Headstage in configWave.

+
+ +
+
+static variable AddClampModeFromLBN(wave numericalValues, variable sweepNo, wave configWave)
+

Set ClampMode in configWave.

+
+ +
+
+static variable AddChannelUnitFromLBN(wave numericalValues, WaveText textualValues, variable sweepNo, wave configWave)
+

Add wave note entry CHANNEL_UNIT_KEY for the used channel units.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___mies_utilities___settings_8ipf.html b/file/_m_i_e_s___mies_utilities___settings_8ipf.html new file mode 100644 index 0000000000..7754d2bcc1 --- /dev/null +++ b/file/_m_i_e_s___mies_utilities___settings_8ipf.html @@ -0,0 +1,353 @@ + + + + + + + + File MIES_MiesUtilities_Settings.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_MiesUtilities_Settings.ipf

+

This file holds MIES utility functions for settings management.

+
+

Functions

+
+
+variable GenerateSettingsDefaults()
+

Generate a default settings file in JSON format.

+

{
+  "diagnostics": {
+    "last upload": "2020-03-05T13:43:32Z"
+  },
+  "version": 1
+}
+
+
+

+

Explanation:

+

Window coordinates are stored as

+


+
+
+

{“coordinates” : {“left” : 123, “top” : 456, “bottom” 789, “right” : 101112}}

+

+

Entries:

+

    +

  • “version”: Major version number to track breaking changes

    • +

  • ”diagnostics”: Groups settings related to diagnostics and crash dump handling

    • +

  • ”diagnostics/last upload”: ISO8601 timestamp when the last successfull upload of crash dumps was tried. This is also set when no crash dumps have been uploadad.

    • +

  • ”analysisbrowser”: Groups settings related to the Analysisbrowser

    • +

  • ”analysisbrowser/directory”: The directory initially opened for browsing existing NWB/PXP files

    • +

  • ”logfiles”: Groups settings related to log files

    • +

  • ”logfiles/last upload”: ISO8601 timestamp when the last successfull upload of log files was tried. This is also set when no log files have been uploadad.

    • +

  • ”*[/*]/coordinates”: window coordinates

    • +
+

+

+Caller is responsible for releasing the document.

+
+
Returns:
+

JSONid

+
+
+
+ +
+
+variable UpgradeSettings(variable JSONid)
+
+ +
+
+variable ToggleUserPingSetting()
+
+ +
+
+variable GetUserPingEnabled()
+
+ +
+
+string GetUserPingTimestamp()
+
+ +
+
+variable SetUserPingTimestamp(variable timeStamp)
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___mies_utilities___sweep_8ipf.html b/file/_m_i_e_s___mies_utilities___sweep_8ipf.html new file mode 100644 index 0000000000..610f15e210 --- /dev/null +++ b/file/_m_i_e_s___mies_utilities___sweep_8ipf.html @@ -0,0 +1,532 @@ + + + + + + + + File MIES_MiesUtilities_Sweep.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_MiesUtilities_Sweep.ipf

+

This file holds MIES utility functions for working with sweeps.

+
+

Functions

+
+
+wave GetDAQDataSingleColumnWaves(dfref sweepDFR, variable channelType)
+

Return a wave reference wave with all single column waves of the given channel type.

+

Holds invalid wave refs for non-existing entries.

+

+

See also

+

GetDAQDataSingleColumnWave() or SplitSweepIntoComponents()

+
+

+
+
Parameters:
+
    +

  • sweepDFR – datafolder reference with 1D sweep data

    • +

  • channelType – One of XopChannelConstants

    • +
+
+
+
+ +
+
+wave GetDAQDataSingleColumnWaveNG(wave numericalValues, WaveText textualValues, variable sweepNo, dfref sweepDFR, variable channelType, variable GUIchannelNumber)
+

Return a 1D sweep data wave previously created by SplitSweepIntoComponents()

+

Returned wave reference can be null.

+
+
Parameters:
+
    +

  • numericalValues – numerical labnotebook

    • +

  • textualValues – textual labnotebook

    • +

  • sweepNo – sweep number

    • +

  • sweepDFR – datafolder holding 1D waves

    • +

  • channelType – One of XopChannelConstants

    • +

  • GUIchannelNumber – GUI channel number

    • +
+
+
+
+ +
+
+wave GetDAQDataSingleColumnWave(dfref sweepDFR, variable channelType, variable channelNumber, variable splitTTLBits = defaultValue, variable ttlBit = defaultValue)
+

Return a 1D data wave previously created by SplitSweepIntoComponents()

+

Returned wave reference can be invalid.

+
+
Parameters:
+
    +

  • sweepDFR – datafolder holding 1D waves

    • +

  • channelType – One of XopChannelConstants

    • +

  • channelNumber – hardware channel number

    • +

  • splitTTLBits – [optional, defaults to false] return a single bit of the TTL wave

    • +

  • ttlBit – [optional] number specifying the TTL bit

    • +
+
+
+
+ +
+
+variable IsValidSweepNumber(variable sweepNo)
+

Check if the given sweep number is valid.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+wave ExtractOneDimDataFromSweep(wave config, wave sweep, variable index)
+

Extract an one dimensional wave from the given sweep/hardware data wave and column.

+
+
Parameters:
+
    +

  • config – config wave

    • +

  • sweep – sweep wave or hardware data wave from all hardware types

    • +

  • index – index into sweep, can be queried with AFH_GetDAQDataColumn

    • +
+
+
Returns:
+

a reference to a free wave with the single channel data

+
+
+
+ +
+
+wave CopySweepToWRef(wave sweep, wave config)
+

Creates a copy of the sweep data and returns it in wRef format.

+
+ +
+
+variable SplitAndUpgradeSweep(wave numericalValues, variable sweep, wave sweepWave, wave configWave, variable rescale, variable doUpgrade, dfref targetDFR = defaultValue, variable createBackup = defaultValue)
+

Split a sweep wave into one 1D-wave per channel/ttlBit and convert the sweep wave to the current text sweep format. Sweeps already in text format are not split (because that already part of their format). When attempted to split, already existing single channel waves are preserved. The old 2D sweep format is converted automatically to the current text sweep format. If targetDFR is a free DF then only splitting is done. The sweepWave can get invalid and must be reobtained after calling. See GetSweepWave for detailed documentation of the sweep format.

+
+
Parameters:
+
    +

  • numericalValues – numerical labnotebook

    • +

  • sweep – sweep number

    • +

  • sweepWave – sweep wave, either old 2D numerical sweep wave, wave ref wave or text sweep wave

    • +

  • configWave – config wave

    • +

  • rescale – One of TTLRescalingOptions

    • +

  • doUpgrade – When this flag is set, then the sweep wave is upgraded to the latest format. When set, createBackup must be set and targetDFR must not be a free DF.

    • +

  • targetDFR – [optional, defaults to the sweep wave DFR] datafolder where to put the waves, can be a free datafolder

    • +

  • createBackup – [optional, defaults 1] flag to enable/disable backup creation of single channel sweep waves

    • +
+
+
+
+ +
+
+static dfref GetParentDFR(dfref dfr)
+
+ +
+
+static variable AreAllSingleSweepWavesPresent(dfref targetDFR, WaveText componentNames, variable backupMustExist = defaultValue)
+
+ +
+
+static variable SplitSweepWave(wave numericalValues, variable sweep, wave sweepWave, wave configWave, variable rescale, dfref targetDFR, WaveText componentNames, variable createBackup)
+
+ +
+
+static variable UpgradeSweepWave(wave sweepWave, WaveText componentNames, dfref targetDFR)
+
+ +
+
+static variable SplitTTLWaveIntoComponents(wave data, variable ttlBits, dfref targetDFR, string wavePrefix, variable rescale, variable createBackup)
+

Split TTL data into a single wave for each bit.

+

This function is only for data from ITC hardware.

+

+The created waves will be named TTL_3_3 so the final suffix is the running TTL Bit.

+
+
Parameters:
+
    +

  • data – 1D channel data extracted by ExtractOneDimDataFromSweep

    • +

  • ttlBits – bit mask of the active TTL channels form e.g. GetTTLBits

    • +

  • targetDFR – datafolder where to put the waves, can be a free datafolder

    • +

  • wavePrefix – prefix of the created wave names

    • +

  • rescale – One of TTLRescalingOptions. Rescales the data to be in the range [0, 1] when on, does no rescaling when off.

    • +

  • createBackup – when set then backups are created

    • +
+
+
+
+ +
+
+wave ResolveSweepChannel(WaveText sweepWave, variable index, variable allowFail = defaultValue)
+

Resolves a single channel of a text sweep wave and returns a reference to it.

+
+
Parameters:
+
    +

  • sweepWave – text sweep wave

    • +

  • index – index of the channel

    • +

  • allowFail – [optional: default = 0] when set a null wave ref is returned if the channel could not be resolved, e.g. through a missing single channel wave. On default the function checks for a valid wave and asserts if none was found.

    • +
+
+
+
+ +
+
+std::tuple<string, string> SplitTextSweepElement(string element)
+

Splits a text sweep wave element into the DF and wave name part.

+
+ +
+
+string GetSweepComponentWaveName(wave config, variable channelIndex)
+

Returns a wave name for a single channel sweep wave. The wave name is based on the channel type and channel number and is built from the XOP_CHANNEL_NAMES in the form DA_0, DA_1, AD_0, AD_1, TTL_0 and so on.

+
+
Parameters:
+
    +

  • config – config wave

    • +

  • channelIndex – index in config wave

    • +
+
+
Returns:
+

string with a constructed wave name

+
+
+
+ +
+
+variable UpdateLeftOverSweepTime(string device, variable fifoPos)
+

Update the repurposed sweep time global variable.

+

Currently only useful for handling mid sweep analysis functions.

+
+ +
+
+variable LeftOverSweepTime(string device, variable fifoPos)
+
+ +
+
+variable IsValidSweepWave(WaveOrNull sweep)
+

Check if the given wave is a valid DAQDataWave.

+
+ +
+
+variable GetTotalOnsetDelay(wave numericalValues, variable sweepNo)
+

Return the total onset delay of the given sweep from the labnotebook.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+variable SplitAndUpgradeSweepGlobal(string device, variable sweepNo)
+
+ +
+
+wave TextSweepToWaveRef(wave sweepWave)
+

Converts a text sweep wave to a free waveRef sweep wave. The waveRef sweep wave contains references to the channels from the text sweep wave, that are local or global waves. See also GetSweepWave docu on “intermediate sweep format”. Generally waveRef waves are easier to handle. It is currently used for NWB saving where the sweep channel data needs to be available in a preemptive thread.

+
+ +
+
+variable ExtractSweepNumber(string str)
+

Extract the sweep number from a $something_* string.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___mies_utilities___system_8ipf.html b/file/_m_i_e_s___mies_utilities___system_8ipf.html new file mode 100644 index 0000000000..6963fbf3b2 --- /dev/null +++ b/file/_m_i_e_s___mies_utilities___system_8ipf.html @@ -0,0 +1,337 @@ + + + + + + + + File MIES_MiesUtilities_System.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_MiesUtilities_System.ipf

+

This file holds MIES utility functions related to the system.

+
+

Functions

+
+
+variable SetupBackgroundTasks()
+
+ +
+
+variable SaveExperimentSpecial(variable mode)
+

Save the current experiment under a new name and clear all/some data.

+
+
Parameters:
+

mode – mode for generating the experiment name, one of SaveExperimentModes

+
+
+
+ +
+
+variable SaveExperimentWrapper(string path, string filename, variable overrideInteractiveMode = defaultValue)
+

Returns 1 if the user cancelled, zero if SaveExperiment was called.

+

It is currently not possible to check if SaveExperiment was successfull (E-Mail from Howard Rodstein WaveMetrics, 30 Jan 2015)

+
+
Parameters:
+
    +

  • path – Igor symbolic path where the experiment should be stored

    • +

  • filename – filename of the experiment including suffix, usually PACKED_FILE_EXPERIMENT_SUFFIX

    • +

  • overrideInteractiveMode – [optional, defaults to GetInteractiveMode()] Overrides the current setting of the interactive mode

    • +
+
+
+
+ +
+
+variable NewExperiment()
+

Starts with a new experiment.

+

You have to manually save before, see SaveExperimentWrapper()

+
+ +
+
+variable TestOverrideActive()
+

Return if the function results are overriden for testing purposes.

+
+ +
+
+variable HandleOutOfMemory(string device, string name)
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___mies_utilities___uploads_8ipf.html b/file/_m_i_e_s___mies_utilities___uploads_8ipf.html new file mode 100644 index 0000000000..36f6e639ea --- /dev/null +++ b/file/_m_i_e_s___mies_utilities___uploads_8ipf.html @@ -0,0 +1,367 @@ + + + + + + + + File MIES_MiesUtilities_Uploads.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_MiesUtilities_Uploads.ipf

+

This file holds MIES utility functions for data upload.

+
+

Functions

+
+
+variable UploadCrashDumpsDaily()
+

Call UploadCrashDumps() if we haven’t called it since at least a day.

+
+ +
+
+variable UploadLogFilesDaily()
+

Call UploadLogFiles() if we haven’t called it since at least a day.

+
+ +
+
+variable UploadPingPeriodically()
+
+ +
+
+static variable UploadPing()
+
+ +
+
+variable GenerateJSONTemplateForUpload(string timeStamp = defaultValue)
+

Return JSON text with default entries for upload.

+

Caller is responsible for releasing JSON text.

+
+ +
+
+variable UploadCrashDumps()
+

Convert the Igor Pro crash dumps and the report file to JSON and upload them.

+

Does nothing if none of these files exists.

+

The uploaded files are moved out of the way afterwards.

+

See tools/http-upload/upload-json-payload-v1.php for the JSON format description.

+
+
Returns:
+

1 if crash dumps had been uploaded, 0 otherwise

+
+
+
+ +
+
+variable UploadLogFiles(variable verbose = defaultValue, variable firstDate = defaultValue, variable lastDate = defaultValue)
+

Upload the MIES and ZeroMQ logfiles.

+
+
Parameters:
+
    +

  • verbose – [optional, defaults to true] Only in verbose mode the ticket ID is output to the history

    • +

  • firstDate – [optional, defaults to false] Allows to filter the logfiles to include entries within the given dates. Both firstDate and lastDate must be present for filtering. The timestamps are in seconds since Igor Pro epoch.

    • +

  • lastDate – [optional, defaults to false] See firstDate

    • +
+
+
+
+ +
+
+static variable UploadLogFilesPrint(string str, variable verbose)
+
+ +
+
+

Variables

+
+
+static const string EXPCONFIG_JSON_HWDEVBLOCK = "DAQHardwareDevices"
+
+ +
+
+static const string UPLOAD_BLOCK_USERPING = "UserPing"
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___mies_utilities___zero_m_q_8ipf.html b/file/_m_i_e_s___mies_utilities___zero_m_q_8ipf.html new file mode 100644 index 0000000000..431c13d93e --- /dev/null +++ b/file/_m_i_e_s___mies_utilities___zero_m_q_8ipf.html @@ -0,0 +1,307 @@ + + + + + + + + File MIES_MiesUtilities_ZeroMQ.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_MiesUtilities_ZeroMQ.ipf

+

This file holds MIES utility functions for ZeroMQ.

+
+

Functions

+
+
+variable GetZeroMQXOPFlags()
+
+ +
+
+variable StartZeroMQSockets(variable forceRestart = defaultValue)
+

Start the ZeroMQ sockets and the message handler.

+

Debug note: Tracking the connection state can be done via netstat | grep $port. The binded port only shows up after a successfull connection with zeromq_client_connect() is established.

+
+
Returns:
+

NaN if already running, otherwise it returns the number of trials it had to iterate for an unused port.

+
+
+
+ +
+
+variable UpdateXOPLoggingTemplate()
+

Update the logging template used by the ZeroMQ-XOP and ITCXOP2.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___neuro_data_without_borders_8ipf.html b/file/_m_i_e_s___neuro_data_without_borders_8ipf.html new file mode 100644 index 0000000000..936e536a7f --- /dev/null +++ b/file/_m_i_e_s___neuro_data_without_borders_8ipf.html @@ -0,0 +1,816 @@ + + + + + + + + File MIES_NeuroDataWithoutBorders.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_NeuroDataWithoutBorders.ipf

+

NWB Functions related to MIES data export into the NeuroDataWithoutBorders format

+

For writing a full NWB file the following functions are used:

+

+

For exporting sweep-by-sweep:

+

+
+

Functions

+
+
+static variable NWB_GetStartTimeOfSweep(WaveText textualValues, variable sweepNo, wave sweepWave)
+

Return the starting time, in fractional seconds since Igor Pro epoch in UTC, of the given sweep.

+

For existing sweeps with HIGH_PREC_SWEEP_START_KEY labnotebook entries we use the sweep wave’s modification time. The sweep wave can be either an DAQDataWave or a Sweep_$num wave. Passing the DAQDataWave is more accurate.

+
+ +
+
+static variable NWB_FirstStartTimeOfAllSweeps()
+

Return the creation time, in seconds since Igor Pro epoch in UTC, of the oldest sweep wave for all devices.

+

Return NaN if no sweeps could be found

+
+ +
+
+static string NWB_GetFileNameSuffixDevice(string device)
+
+ +
+
+static string NWB_GetFileNamePrefix()
+
+ +
+
+static std::tuple<variable, variable> NWB_GetFileForExport(variable nwbVersion, string device, string overrideFullFilePath = defaultValue)
+

Return the HDF5 file identifier referring to an open NWB file for export.

+

Create one if it does not exist yet.

+
+
Parameters:
+
    +

  • nwbVersion – Set NWB version if new file is created

    • +

  • device – device name

    • +

  • overrideFullFilePath – [optional] file path for new files to override the internal generation algorithm

    • +
+
+
Return values:
+
    +

  • fileID – HDF5 file identifier or NaN on user abort

    • +

  • createdNewNWBFile – new NWB file was created (1) or an existing opened (0)

    • +
+
+
+
+ +
+
+static variable NWB_AddGeneratorString(variable fileID, variable nwbVersion)
+
+ +
+
+static variable NWB_AddSpecifications(variable fileID, variable nwbVersion)
+
+ +
+
+static variable NWB_ReadSessionStartTime(variable fileID)
+
+ +
+
+static variable NWB_AddDevice(NWBAsyncParameters *s)
+
+ +
+
+static string NWB_GenerateDeviceDescription(string device, wave numericalValues, WaveText textualValues)
+
+ +
+
+dfref NWB_ASYNC_Worker(dfref dfr)
+
+ +
+
+variable NWB_ASYNC_Readout(ASYNC_ReadOutStruct *ar)
+
+ +
+
+static variable NWB_WriteLabnoteBooksAndComments(NWBAsyncParameters *s)
+
+ +
+
+static variable NWB_WriteResultsWaves(NWBAsyncParameters *s)
+
+ +
+
+static variable NWB_AddDeviceSpecificData(NWBAsyncParameters *s, variable writeStoredTestPulses)
+
+ +
+
+variable NWB_WriteTestpulseData(NWBAsyncParameters *s, variable writeStoredTestPulses)
+
+ +
+
+static variable NWB_HandleFileOverwrite(string fullFilePath, variable overwrite, variable verbose, string device = defaultValue)
+

Handle a NWB file handling for overwite flag.

+
+
Parameters:
+
    +

  • fullFilePath – full file path

    • +

  • overwrite – flag that indicates if overwrite is enabled or not

    • +

  • verbose – flag that indicates if verbose status messgaes are enabled

    • +

  • device – [optiona, default auto-determined] device name that uses the given file

    • +
+
+
Returns:
+

returns 1 if error occured

+
+
+
+ +
+
+variable NWB_ExportAllData(variable nwbVersion, string device = defaultValue, string overrideFullFilePath = defaultValue, string overrideFileTemplate = defaultValue, variable writeStoredTestPulses = defaultValue, variable writeIgorHistory = defaultValue, variable compressionMode = defaultValue, variable keepFileOpen = defaultValue, variable overwrite = defaultValue, variable verbose = defaultValue)
+

Programmatically export all acquired data from all devices into a NWB file.

+

Use NWB_ExportWithDialog() for interactive export.

+
+
Parameters:
+
    +

  • nwbVersion – major NWB format version, one of 1 or 2 (aka NWB_VERSION_LATEST)

    • +

  • device – [optional, defaults to all devices] when set, only data for the given single device is exported

    • +

  • overrideFullFilePath – [optional, defaults to auto-gen] use this full file path instead of an internally derived one, only valid when single device has data

    • +

  • overrideFileTemplate – [optional, defaults to auto-gen] use this template file path instead of an internally derived one

    • +

  • writeStoredTestPulses – [optional, defaults to false] store the raw test pulse data

    • +

  • writeIgorHistory – [optional, defaults to true] store the Igor Pro history and the log file

    • +

  • compressionMode – [optional, defaults to chunked compression] One of CompressionMode

    • +

  • keepFileOpen – [optional, defaults to false] keep the NWB file open after return, or close it

    • +

  • overwrite – [optional, defaults to false] overwrite any existing NWB file with the same name, only used when overrideFilePath is passed

    • +

  • verbose – [optional, defaults to true] get diagnostic output to the command line

    • +
+
+
Returns:
+

0 on success, non-zero on failure

+
+
+
+ +
+
+static wave NWB_GetSweepWave(string device, variable sweep)
+
+ +
+
+variable NWB_ASYNC_FinishWriting(string device)
+

Wait for ASYNC nwb writing to finish.

+

Currently wait up to 10min (NWB_ASYNC_WRITING_TIMEOUT * NWB_ASYNC_MAX_ITERATIONS), everything above 5s is considered a bug.

+
+ +
+
+variable NWB_CheckForMissingSweeps(string device, WaveText sweepNames)
+
+ +
+
+static variable NWB_GetExportedFileSize(string device)
+

Return the file size in MiB of the currently written into NWB file.

+

This is only approximately correct as the file is open in HDF5 and thus not everything is flushed.

+
+ +
+
+static variable NWB_ExportAllStimsets(variable nwbVersion, string overrideFullFilePath)
+

Export all stimsets into NWB.

+

NWB file is closed after the function returns.

+
+ +
+
+variable NWB_ExportWithDialog(variable exportType, variable nwbVersion = defaultValue)
+

Export all data into NWB using compression.

+

Ask the file location from the user

+
+
Parameters:
+
    +

  • exportType – Export all data and referenced stimsets (NWB_EXPORT_DATA) or all stimsets (NWB_EXPORT_STIMSETS)

    • +

  • nwbVersion – [optional, defaults to latest version] major NWB version

    • +
+
+
+
+ +
+
+static variable NWB_AppendStoredTestPulses(string device, variable nwbVersion, variable locationID, variable compressionMode)
+

Write the stored test pulses to the NWB file.

+
+ +
+
+static variable NWB_AppendStimset(variable nwbVersion, variable locationID, string stimsets, variable compressionMode)
+

Export given stimsets to NWB file.

+
+
Parameters:
+
    +

  • nwbVersion – major NWB version

    • +

  • locationID – Identifier of open hdf5 group or file

    • +

  • stimsets – Single stimset as string or list of stimsets sparated by ;

    • +

  • compressionMode – Type of compression to use, one of CompressionMode

    • +
+
+
+
+ +
+
+variable NWB_PrepareExport(variable nwbVersion, string device)
+

Prepare everything for sweep-by-sweep NWB export.

+
+ +
+
+variable NWB_AppendSweepDuringDAQ(string device, wave DAQDataWave, wave DAQConfigWave, variable sweep, variable nwbVersion)
+
+ +
+
+static variable NWB_AppendSweepLowLevel(NWBAsyncParameters *s)
+
+ +
+
+static variable NWB_ClearWriteChannelParams(WriteChannelParams *s)
+

Clear all entries which are channel specific.

+
+ +
+
+static variable NWB_WriteStimsetCustomWave(variable nwbVersion, variable locationID, wave custom_wave, variable compressionMode)
+

Save Custom Wave (from stimset) in NWB file.

+
+
Parameters:
+
    +

  • nwbVersion – major NWB version

    • +

  • locationID – Open HDF5 group or file identifier

    • +

  • custom_wave – Wave reference to the wave that is to be saved

    • +

  • compressionMode – [optional, defaults to NO_COMPRESSION] Type of compression to use, one of CompressionMode

    • +
+
+
+
+ +
+
+static variable NWB_WriteStimsetTemplateWaves(variable nwbVersion, variable locationID, string stimSet, WaveRefWave customWaves, variable compressionMode)
+
+ +
+
+static variable NWB_LoadStimset(variable locationID, string stimset, variable overwrite, variable verbose = defaultValue)
+

Load specified stimset from Stimset Group.

+
+
Parameters:
+
    +

  • locationID – id of an open hdf5 group containing the stimsets

    • +

  • stimset – string of stimset

    • +

  • verbose – [optional] set to get more output to the command line

    • +

  • overwrite – indicate whether the stored stimsets should be deleted if they exist

    • +
+
+
Returns:
+

1 on error

+
+
+
+ +
+
+variable NWB_LoadCustomWave(variable locationID, string fullPath, variable overwrite)
+

Load a custom wave from NWB file.

+

loads waves that were saved by NWB_WriteStimsetCustomWave

+
+
Parameters:
+
    +

  • locationID – open file or group from nwb file

    • +

  • fullPath – full Path in igor notation to custom wave

    • +

  • overwrite – indicate whether the stored custom wave should be deleted if it exists

    • +
+
+
Returns:
+

1 on error and 0 on success

+
+
+
+ +
+
+static string NWB_SuffixExtendedStimsetNamesToStimsetNames(string stimsets)
+

from a list of extended stimset names with _WP, _WPT or _SegWvType suffix return a boiled down list of unique stimset names without suffix

+
+ +
+
+string NWB_ReadStimSetList(string fullPath)
+
+ +
+
+variable NWB_LoadAllStimsets(variable overwrite = defaultValue, string fileName = defaultValue, variable loadOnlyBuiltins = defaultValue)
+

Load all stimsets from specified HDF5 file.

+
+
Parameters:
+
    +

  • fileName – [optional, shows a dialog on default] provide full file name/path for loading stimset

    • +

  • overwrite – [optional, defaults to false] indicate if the stored stimset should be deleted before the load.

    • +

  • loadOnlyBuiltins – [optional, defaults to false] load only builtin stimsets

    • +
+
+
Returns:
+

1 on error and 0 on success

+
+
+
+ +
+
+variable NWB_LoadStimsets(variable groupID, string stimsets, variable overwrite, string processedStimsets = defaultValue)
+

Load specified stimsets and their dependencies from NWB file.

+

see AB_LoadStimsets() for similar structure

+
+
Parameters:
+
    +

  • groupID – Open Stimset Group of HDF5 File. See OpenStimset()

    • +

  • stimsets – “;” separated list of all stimsets of the current sweep.

    • +

  • processedStimsets – [optional] the list indicates which stimsets were already loaded. on recursion this parameter avoids duplicate circular references.

    • +

  • overwrite – indicate whether the stored stimsets should be deleted if they exist

    • +
+
+
Returns:
+

1 on error and 0 on success

+
+
+
+ +
+
+variable NWB_LoadCustomWaves(variable groupID, string stimsets, variable overwrite)
+

Load custom waves for specified stimset from Igor experiment file.

+

see AB_LoadCustomWaves() for similar structure

+
+
Returns:
+

1 on error and 0 on success

+
+
+
+ +
+
+static variable NWB_GetTimeSeriesProperties(variable nwbVersion, WaveText numericalKeys, wave numericalValues, WriteChannelParams *p, TimeSeriesProperties *tsp)
+
+ +
+
+static variable NWB_AddSweepDataSets(WaveText numericalKeys, wave numericalValues, variable sweep, string settingsProp, string nwbProp, variable headstage, TimeSeriesProperties *tsp, variable factor = defaultValue, string enabledProp = defaultValue)
+
+ +
+
+variable NWB_LoadLabNoteBook(variable locationID, string notebook, dfref dfr)
+

function saves contents of specified notebook to data folder

+
+
Parameters:
+
    +

  • locationID – id of nwb file or notebooks folder

    • +

  • notebook – name of notebook to be loaded

    • +

  • dfr – igor data folder where data should be loaded into

    • +
+
+
+
+ +
+
+variable NWB_Flush(variable locationID)
+

Flushes the contents of the NWB file to disc.

+
+ +
+
+static variable NWB_AppendLogFileToString(string path, string *str)
+
+ +
+
+static variable NWB_AppendIgorHistoryAndLogFile(variable nwbVersion, variable locationID)
+
+ +
+
+variable NWB_ConvertToStandardTTLBit(variable value)
+

Convert between 2^x, this is what we store as channelSuffix for TTL data in NWB, to x what we call TTL bit in MIES.

+
+ +
+
+variable NWB_ConvertTTLBitToChannelSuffix(variable value)
+

Reverse direction of NWB_ConvertToStandardTTLBit()

+
+ +
+
+variable NWB_CloseAllNWBFiles()
+

Closes all possibly open export-into-NWB files.

+
+ +
+
+variable NWB_CloseNWBFile(string device)
+

Close a possibly open export-into-NWB file.

+
+ +
+
+

Variables

+
+
+static const double NWB_ASYNC_WRITING_TIMEOUT = 5
+
+ +
+
+static const double NWB_ASYNC_MAX_ITERATIONS = 120
+
+ +
+
+static const string NWB_OPEN_FILTER = "NWB files (*.nwb):.nwb;"
+
+ +
+
+static const string NWB_FILE_SUFFIX = ".nwb"
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___optimzed_overlap_distributed_acquisition_8ipf.html b/file/_m_i_e_s___optimzed_overlap_distributed_acquisition_8ipf.html new file mode 100644 index 0000000000..0e58e089d1 --- /dev/null +++ b/file/_m_i_e_s___optimzed_overlap_distributed_acquisition_8ipf.html @@ -0,0 +1,479 @@ + + + + + + + + File MIES_OptimzedOverlapDistributedAcquisition.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_OptimzedOverlapDistributedAcquisition.ipf

+

OOD This file holds functions related to oodDAQ.

+
+

Functions

+
+
+static variable OOD_GetThresholdLevel(wave stimset)
+

returns the threshold level for ood region detection from a single column stimset

+
+
Parameters:
+

stimset – [in] 1d wave containing stimset data

+
+
Returns:
+

threshold level defining signal above baseline

+
+
+
+ +
+
+static wave OOD_GetRegionsFromStimset(wave stimset, variable prePoints, variable postPoints)
+

retrieves regions with signal from a 1D data wave, used for stimsets

+
+
Parameters:
+
    +

  • stimset – [in] 1D wave containing stimset data

    • +

  • prePoints – [in] oodDAQ pre delay in points the regions get expanded at the rising edge

    • +

  • postPoints – [in] oodDAQ post delay in points the regions get expanded at the falling edge

    • +
+
+
Returns:
+

2D wave with region information

+
+
+
+ +
+
+static wave OOD_CompactRegions(wave regions)
+

Reduces a 2D region wave by joining overlapping regions to one.

+
+
Parameters:
+

regions – [in] 2D wave containing region data

+
+
Returns:
+

2D wave with compacted regions

+
+
+
+ +
+
+static wave OOD_GetRegionsFromStimsets(OOdDAQParams *params)
+

generates regions data waves from stimsets taking the pre and post delay into account

+
+
Parameters:
+

params – [in] OOdDAQParams structure

+
+
Returns:
+

wave reference wave holding the 2D region waves for each stimset

+
+
+
+ +
+
+static wave OOD_GetFeatureRegions(WaveRefWave setRegions, wave offsets)
+

returns a 1D wave with regions as lists from the input regions waves, is used for the LNB

+
+
Parameters:
+
    +

  • setRegions – [in] wave reference wave of 2D region waves

    • +

  • offsets – [in] offset wave storing the offsets per stimset

    • +
+
+
Returns:
+

1D text wave with lists of regions

+
+
+
+ +
+
+static wave OOD_CalculateOffsetsImpl(WaveRefWave setRegions)
+

Calculates offsets for each stimset for OOD.

+
+
Parameters:
+

setRegions – wave reference wave of 2D region waves for each stimset

+
+
Returns:
+

1D wave with offsets for each stimset in points

+
+
+
+ +
+
+static variable OOD_CalculateOffsets(string device, OOdDAQParams *params)
+

Calculated the offsets for normal acquisition.

+
+
Parameters:
+
    +

  • device – [in] title of the device panel

    • +

  • params – [in] OOdDAQParams structure with oodDAQ setup data

    • +
+
+
+
+ +
+
+static string OOD_AddToRegionList(variable first, variable last, string list)
+

Return a list with $first-$last added at the end with ; as separator.

+
+
Parameters:
+
    +

  • first – [in] sample point number in wavebuilder scale with start of region

    • +

  • last – [in] sample point number in wavebuilder scale with end of region

    • +

  • list – [in] list string where the element is added

    • +
+
+
Returns:
+

list string with added element

+
+
+
+ +
+
+static variable OOD_Debugging(OOdDAQParams *params)
+

Prints various internals useful for oodDAQ debugging, called when DEBUGGING_ENABLED is set.

+
+
Parameters:
+

params – [in] OOdDAQParams structure with oodDAQ internals

+
+
+
+ +
+
+wave OOD_GetResultWaves(string device, OOdDAQParams *params)
+

Return the oodDAQ optimized stimsets.

+

The offsets and the regions are returned in params and all results are cached.

+
+
Parameters:
+
    +

  • device – [in] title of the device panel

    • +

  • params – [in] OOdDAQParams structure with the initial settings

    • +
+
+
Returns:
+

one dimensional numberic wave with the offsets in points for each stimset

+
+
+
+ +
+
+static wave OOD_CreateStimSet(OOdDAQParams *params)
+

Generate a stimset for “overlapped dDAQ” from the calculated offsets by OOD_CalculateOffsets().

+
+
Parameters:
+

params – [in] OOdDAQParams structure with the stimsets and offset information

+
+
Returns:
+

stimsets with offsets, one wave per offset

+
+
+
+ +
+
+wave OOD_OffsetStimSetColAndCutoff(wave stimSet, variable column, variable offset, variable postFeaturePoints)
+

Here the trailing baseline is of the stimset column removed (postFeatureTime) The last feature amplitude should stay as DA signal until the whole stimset (all columns) ends.

+
+ +
+
+

Variables

+
+
+static const double OOD_SIGNAL_THRESHOLD = 0.1
+

Signal threshold level in parts of dynamic range above minimum

+

See also

+

OOD_GetThresholdLevel()

+
+

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___oscilloscope_8ipf.html b/file/_m_i_e_s___oscilloscope_8ipf.html new file mode 100644 index 0000000000..cd2393e854 --- /dev/null +++ b/file/_m_i_e_s___oscilloscope_8ipf.html @@ -0,0 +1,428 @@ + + + + + + + + File MIES_Oscilloscope.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Oscilloscope.ipf

+

SCOPE Scope window handling for data acquisition and testpulse results

+
+

Functions

+
+
+string SCOPE_GetGraph(string device)
+
+ +
+
+string SCOPE_GetPanel(string device)
+
+ +
+
+variable SCOPE_OpenScopeWindow(string device)
+
+ +
+
+variable SCOPE_KillScopeWindowIfRequest(string device)
+
+ +
+
+variable SCOPE_GetTPTopAxisStart(string device, variable *axisMin)
+
+ +
+
+variable SCOPE_UpdateGraph(string device, variable dataAcqOrTP)
+
+ +
+
+static std::tuple<variable, variable, variable> SCOPE_GetCheckBoxesForAddons(string device, variable dataAcqOrTP)
+
+ +
+
+variable SCOPE_CreateGraph(string device, variable dataAcqOrTP)
+
+ +
+
+variable SCOPE_SetADAxisLabel(string device, variable dataAcqOrTP, variable activeHeadStage)
+
+ +
+
+static variable SCOPE_UpdatePowerSpectrum(string device, wave columns, wave osci = defaultValue)
+
+ +
+
+variable SCOPE_UpdateOscilloscopeData(string device, variable dataAcqOrTP, variable chunk = defaultValue, variable fifoPos = defaultValue, variable deviceID = defaultValue)
+

Prepares a subset/copy of DAQDataWave for displaying it in the oscilloscope panel.

+
+
Parameters:
+
    +

  • device – panel title

    • +

  • dataAcqOrTP – One of DATA_ACQUISITION_MODE or TEST_PULSE_MODE

    • +

  • chunk – Only for TEST_PULSE_MODE and multi device mode; Selects the testpulse to extract

    • +

  • fifoPos – Position of the hardware DAQ fifo to keep track of the position which will be written next

    • +

  • deviceID – device ID

    • +
+
+
+
+ +
+
+static variable SCOPE_SU_UpdateOscilloscope(string device, variable dataAcqOrTP, variable chunk, variable fifoPos)
+
+ +
+
+static variable SCOPE_NI_UpdateOscilloscope(string device, variable dataAcqOrTP, variable deviceiD, variable fifoPos)
+
+ +
+
+static variable SCOPE_ITC_UpdateOscilloscope(string device, variable dataAcqOrTP, variable chunk, variable fifoPos)
+
+ +
+
+static variable SCOPE_ITC_AdjustFIFOPos(string device, variable fifopos)
+

Adjusts the fifo position when using ITC.

+
+
Parameters:
+
    +

  • device – device

    • +

  • fifopos – fifo position

    • +
+
+
Returns:
+

adjusted fifo position

+
+
+
+ +
+
+

Variables

+
+
+static const double SCOPE_TIMEAXIS_RESISTANCE_RANGE = 120
+
+ +
+
+static const double SCOPE_GREEN = 26122
+
+ +
+
+static const double SCOPE_BLUE = 39168
+
+ +
+
+static const string RES_FORMAT_STR = "\\[1\\K(%d, %d, %d)\\{\"%%s\", FloatWithMinSigDigits(%s[%%%s][%d], numMinSignDigits = 2)}\\]1\\K(0, 0, 0)"
+
+ +
+
+static const double PRESSURE_SPECTRUM_PERCENT = 0.05
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___overlay_sweeps_8ipf.html b/file/_m_i_e_s___overlay_sweeps_8ipf.html new file mode 100644 index 0000000000..95a2fcc2b7 --- /dev/null +++ b/file/_m_i_e_s___overlay_sweeps_8ipf.html @@ -0,0 +1,526 @@ + + + + + + + + File MIES_OverlaySweeps.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_OverlaySweeps.ipf

+
+

Functions

+
+
+variable OVS_IgnoreHeadstageInOverlay()
+

This user trace menu function allows the user to select a trace in overlay sweeps mode which should be ignored.

+
+ +
+
+string OVS_GetSweepSelectionChoices(string win)
+

Return a list of choices for the sweep selection popup.

+

Includes a unique list of the DA stimsets of all available sweeps

+
+ +
+
+static variable OVS_RemoveLowCountEntries(WaveText stimsets, WaveText setSweepCounts, WaveText dupsRemovedSetSweepCounts, WaveText dupsRemovedSetCycleCounts)
+

Remove all stimsets which were only acquired once, disregaring RAC/SCI, this means we just look at all sweeps.

+
+ +
+
+dfref OVS_GetFolder(string win)
+

Return the datafolder reference to the folder storing the listbox and selection wave.

+

Requires the user data PANEL_FOLDER of the BrowserSettings panel

+
+
Returns:
+

a valid DFREF or an invalid one in case the external panel could not be found

+
+
+
+ +
+
+variable OVS_UpdatePanel(string win, variable fullUpdate = defaultValue)
+

Update the overlay sweep waves.

+

+Must be called after the sweeps changed.

+
+
Parameters:
+
    +

  • win – databrowser panel or graph

    • +

  • fullUpdate – [optional, defaults to false] Performs a full update instead of an incremental one. Selects the first sweep if nothing is selected as well.

    • +
+
+
+
+ +
+
+variable OVS_UpdateSweepSelectionChoices(string win, WaveText sweepSelectionChoices)
+

Update the sweep selection choices for the popup menu.

+

This function is expensive as it iterates over all sweeps.

+
+ +
+
+wave OVS_GetSelectedSweeps(string win, variable mode)
+

Return the selected sweeps (either indizes or the real sweep numbers)

+
+
Parameters:
+
+
+
Returns:
+

invalid wave reference in case nothing is selected or numeric indizes/sweep numbers depending on mode parameter

+
+
+
+ +
+
+variable OVS_ChangeSweepSelectionState(string win, variable newState, variable sweepNo = defaultValue, variable index = defaultValue, WaveOrNull sweeps = defaultValue, variable invertOthers = defaultValue)
+

Change the selection state of the the given sweep in the listbox wave.

+

Triggers a update for the affected sweep.

+

+One of sweepNo/index is required.

+
+
Parameters:
+
    +

  • win – panel

    • +

  • sweepNo – [optional] sweep number

    • +

  • sweeps – [optional] sweeps to change, can be $""

    • +

  • index – [optional] index into the listbox wave

    • +

  • newState – new checkbox state of the given sweeps

    • +

  • invertOthers – [optional, default to false] set the other sweeps to !newState if true

    • +
+
+
+
+ +
+
+variable OVS_IsActive(string win)
+

checks if OVS is active.

+
+ +
+
+static variable OVS_AddToIgnoreList(string win, variable headstage, variable sweepNo = defaultValue, variable index = defaultValue)
+

Add headstage to the ignore list of the given sweepNo/index

+
+ +
+
+static variable OVS_UpdateHeadstageRemoval(string win, variable index)
+

Update the OVS headstage removal wave from the listbox entry.

+
+ +
+
+wave OVS_GetHeadstageRemoval(string win, variable sweepNo = defaultValue, variable index = defaultValue)
+
+ +
+
+static wave OVS_ParseIgnoreList(string ignoreList, variable sweepNo)
+

Parse the headstage removal list.

+

The expected format of the list entries is a semicolon (“;”) separated list of subranges (without the possibility of denoting the step size).

+

Examples:

    +

  • 0 (ignore HS 0)

    • +

  • 1,3;0 (ignore HS 0 to 3)

    • +

  • * (ignore all headstages)

    • +
+

+
+
Parameters:
+
    +

  • ignoreList – list of entries to parse

    • +

  • sweepNo – sweep number

    • +
+
+
Returns:
+

free wave of size NUM_HEADSTAGES denoting with 0/1 the active state of the headstage

+
+
+
+ +
+
+variable OVS_CheckBoxProc_HS_Select(WMCheckboxAction *cba)
+
+ +
+
+static variable OVS_HighlightSweep(string win, variable index)
+
+ +
+
+std::tuple<variable, string> OVS_GetSweepAndExperiment(string win, variable index)
+

Return the sweep number and experiment name for the given list index.

+
+ +
+
+static variable OVS_ChangeSweepSelection(string win, string choiceString)
+

Change the selected sweep according to one of the popup menu options.

+
+ +
+
+static wave OVS_BeginIncrementalUpdate(string win, variable fullUpdate = defaultValue)
+

Incremental sweep plot updates for overlay sweeps.

+

When modifying the listbox selection and contents wave this function can be called before doing so. After the modifications OVS_EndIncrementalUpdate() will take care of updating all sweeps which got changed.

+

The returned wave should be considered an opaque handle and not modified.

+

Usage:

+

WAVE updateHandle = OVS_BeginIncrementalUpdate(win)
+
+// modify list waves
+// ...
+
+OVS_EndIncrementalUpdate(win, updateHandle)
+
+
+

+

By setting fullUpdate to true a conventional full, that means non-incremental, update will be performed.

+
+
Parameters:
+
    +

  • win – graph

    • +

  • fullUpdate – [optional, defaults to true when OVS is off, false otherwise] allows to force a full update in OVS_EndIncrementalUpdate()

    • +
+
+
+
+ +
+
+static variable OVS_EndIncrementalUpdate(string win, WaveRefWave updateHandle)
+

Perform the update of all changed sweeps.

+

Counterpart to OVS_BeginIncrementalUpdate().

+
+ +
+
+variable OVS_MainListBoxProc(WMListboxAction *lba)
+
+ +
+
+variable OVS_PopMenuProc_Select(WMPopupAction *pa)
+
+ +
+
+variable OVS_SetVarProc_SelectionRange(WMSetVariableAction *sva)
+
+ +
+
+

Variables

+
+
+static const string OVS_FULL_UPDATE_NOTE = "FullUpdate"
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___package_settings_8ipf.html b/file/_m_i_e_s___package_settings_8ipf.html new file mode 100644 index 0000000000..86fd97d54c --- /dev/null +++ b/file/_m_i_e_s___package_settings_8ipf.html @@ -0,0 +1,454 @@ + + + + + + + + File MIES_PackageSettings.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_PackageSettings.ipf

+

LOG Routines for dealing with JSON log files

+

PS Routines for dealing with JSON settings

+

See https://jsonlines.org and Line-delimited JSON for background.

+

In short the log will contain a complete JSON document in each line. The lines are separated by \n.

+
+

Functions

+
+
+variable PS_Initialize(string package)
+

Initialize the PackageFolder symbolic path.

+
+ +
+
+variable PS_GenerateSettingsDefaults()
+

This functions should return a JSON ID with the default settings.

+
+ +
+
+variable PS_ReadSettings(string package, PS_GenerateSettingsDefaults generateDefaults)
+

Return a JSON ID with an opened JSON settings file.

+

Caller is responsible for releasing the document.

+
+ +
+
+variable PS_WriteSettings(string package, variable JSONid)
+

Write the settings from JSONid for package to disc.

+

Call this function in BeforeExperimentSaveHook to write the settings to disc

+
+ +
+
+string PS_GetSettingsFolder_TS(string package)
+

Return the absolute path to the settings folder for package

+
   Threadsafe variant which requires the symbolic path `PackageFolder` created by
+   PS_Initialize() to exist.
+
+   The returned folder location includes a trailing colon (":")
+
+
+
+ +
+
+string PS_GetSettingsFolder(string package)
+

Return the absolute path to the settings folder for package creating it when necessary.

+

The returned folder location includes a trailing colon (“:”)

+
+ +
+
+static string PS_GetSettingsFile(string package)
+

Return the absolute path to the JSON settings file for package

+
+ +
+
+static variable PS_ApplyStoredWindowCoordinate(variable JSONid, string win)
+

Move the window to the stored location.

+
+ +
+
+static variable PS_RegisterForCoordinateSaving(string win, string name)
+

Add user data to mark the window as using coordinate saving.

+
+ +
+
+variable PS_RemoveCoordinateSaving(string win)
+

Remove user data related to coordinate saving.

+
+ +
+
+static variable PS_StoreWindowCoordinates(variable JSONid)
+

Store the coordinates of all registered windows in the JSON settings file.

+

The windows must have been registered beforehand with PS_InitCoordinates().

+
+ +
+
+variable PS_StoreWindowCoordinate(variable JSONid, string win)
+

Store the window coordinates of win in the JSON settings file.

+

The window must have been registered beforehand with PS_InitCoordinates().

+
+ +
+
+variable PS_InitCoordinates(variable JSONid, string win, string name, variable addHook = defaultValue)
+

Add support for window coordinate storing and loading.

+

Takes care of:

    +

  • Marking the window as using it with the given name

    • +

  • Adding a hook to store the coordinates on window killing

    • +

  • Read the current coordinates from the JSON settings file and applying them

    • +
+

+
+
Parameters:
+
    +

  • JSONid – JSON document with settings

    • +

  • win – window name

    • +

  • name – name to store the window under (especially useful for windows which are renamed to their locked device)

    • +

  • addHook – [optional, defaults to true] Add a window hook to store the coordinates on window killing. Users with their own kill event handling must pass addHook=0.

    • +
+
+
+
+ +
+
+variable PS_SerializeSettings(string package, variable JSONid)
+

Write the current JSON settings to disc.

+

Caller must invalidate JSONid after return.

+
+ +
+
+variable PS_OpenNotebook(string package, variable JSONid)
+

Caller must invalidate JSONid after return.

+
+ +
+
+variable PS_FixPackageLocation(string package)
+

Fixup the settings and log file location for Igor Pro prior to 0855279d (Fix package folder location on disk, 2021-04-01).

+

Package JSON:

    +

  • Incorrect is moved to the correct location

    • +
+

+

JSONL logfile:

    +

  • Incorrect is moved to the correct location only if the correct does not exists

    • +

  • If the correct does exist as well, the incorrect is read and appened to to the correct one

    • +
+

+
+ +
+
+

Variables

+
+
+static const string PS_STORE_COORDINATES = "JSONSettings_StoreCoordinates"
+
+ +
+
+static const string PS_WINDOW_NAME = "JSONSettings_WindowName"
+
+ +
+
+static const string PS_COORDINATE_SAVING_HOOK = "windowCoordinateSaving"
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___pictures_8ipf.html b/file/_m_i_e_s___pictures_8ipf.html new file mode 100644 index 0000000000..00bc6c723c --- /dev/null +++ b/file/_m_i_e_s___pictures_8ipf.html @@ -0,0 +1,300 @@ + + + + + + + + File MIES_Pictures.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Pictures.ipf

+

Common place to store Igor Pro specific proc pictures.

+

All proc pictures should have a corresponding xcf file in Packages/Artwork.

+
+

Functions

+
+
+void HardwareScanButton()
+
+ +
+
+void SynPhys()
+
+ +
+
+void CellTypes()
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___pressure_control_8ipf.html b/file/_m_i_e_s___pressure_control_8ipf.html new file mode 100644 index 0000000000..7910f7fcd6 --- /dev/null +++ b/file/_m_i_e_s___pressure_control_8ipf.html @@ -0,0 +1,1176 @@ + + + + + + + + File MIES_PressureControl.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_PressureControl.ipf

+

P Supports use of analog pressure regulators controlled via a ITC device for automated pressure control during approach, seal, break in, and clearing of pipette.

+

+
+Todo:
+

TPbackground can crash while operating pressure regulators if called in the middle of a TP. Need to call P_Pressure control from TP functions that occur between TPs to prevent this from happening

+
+ +

+
+

Constants used by pressure control

+

+
+
+static const string PRESSURE_CONTROLS_BUTTON_LIST = "button_DataAcq_Approach;button_DataAcq_Seal;button_DataAcq_BreakIn;button_DataAcq_Clear;button_DataAcq_SSSetPressureMan"
+
+ +
+
+static const string PRESSURE_CONTROL_TITLE_LIST = "Approach;Seal;Break In;Clear;Apply"
+
+ +
+
+static const string PRESSURE_CONTROL_CHECKBOX_LIST = "check_DatAcq_ApproachAll;check_DatAcq_SealAll;check_DatAcq_BreakInAll;check_DatAcq_ClearEnable;check_DataAcq_ManPressureAll"
+
+ +
+
+static const string PRESSURE_CONTROL_PRESSURE_DISP = "valdisp_DataAcq_P_0;valdisp_DataAcq_P_1;valdisp_DataAcq_P_2;valdisp_DataAcq_P_3;valdisp_DataAcq_P_4;valdisp_DataAcq_P_5;valdisp_DataAcq_P_6;valdisp_DataAcq_P_7"
+
+ +
+
+static const string PRESSURE_CONTROL_LED_MODE_USER = "valdisp_DataAcq_P_LED_Approach;valdisp_DataAcq_P_LED_Seal;valdisp_DataAcq_P_LED_BreakIn;valdisp_DataAcq_P_LED_Clear"
+
+ +
+
+static const string PRESSURE_CONTROL_USER_CHECBOXES = "check_Settings_UserP_Approach;check_Settings_UserP_Seal;check_Settings_UserP_BreakIn;check_Settings_UserP_Clear"
+
+ +
+
+static const string LOW_COLOR_HILITE = "0;0;0"
+
+ +
+
+static const string ZERO_COLOR_HILITE = "0;0;65535"
+
+ +
+
+static const string HIGH_COLOR_HILITE = "65278;0;0"
+
+ +
+
+static const string LOW_COLOR = "65535;65535;65535"
+
+ +
+
+static const string ZERO_COLOR = "49151;53155;65535"
+
+ +
+
+static const string HIGH_COLOR = "65535;49000;49000"
+
+ +
+
+static const double NEG_PRESSURE_PULSE_INCREMENT = 0.2
+
+ +
+
+static const double POS_PRESSURE_PULSE_INCREMENT = 0.1
+
+ +
+
+static const double PRESSURE_PULSE_ENDpt = 70000
+
+ +
+
+static const double PRESSURE_TTL_HIGH_START = 20000
+
+ +
+
+static const double GIGA_SEAL = 1000
+
+ +
+
+static const double PRESSURE_OFFSET = 5
+
+ +
+
+static const double MIN_NEG_PRESSURE_PULSE = -2
+
+ +
+
+static const double MAX_POS_PRESSURE_PULSE = 0.1
+
+ +
+
+static const double ATMOSPHERIC_PRESSURE = 0
+
+ +
+
+static const double PRESSURE_CHANGE = 1
+
+ +
+
+static const double P_NEGATIVE_PULSE = 0x0
+
+ +
+
+static const double P_POSITIVE_PULSE = 0x1
+
+ +
+
+static const double P_MANUAL_PULSE = 0x2
+
+ +
+
+static const double SEAL_POTENTIAL = -70
+
+ +
+
+static const double SEAL_RESISTANCE_THRESHOLD = 100
+
+ +
+
+static const double ACCESS_ATM = 0
+
+ +
+
+static const double ACCESS_REGULATOR = 1
+
+ +
+
+static const double ACCESS_USER = 2
+
+ +
+
+

Functions

+
+
+variable P_PressureControl(string device)
+

Applies pressure methods based on data in PressureDataWv.

+

This function gets called by TP_RecordTP. It also gets called when the approach button is pushed. A key point is that data acquisition used to run pressure pulses cannot be active if the TP is inactive.

+
+ +
+
+static variable P_RecordUserPressure(string device)
+
+ +
+
+static variable P_UpdateTPStorage(string device, variable headStage)
+

Record pressure in TPStorage wave.

+
+ +
+
+static variable P_FindLastSetEntry(wave wv, variable row, variable col, string name)
+

Return the last non-NaN entry from the wave’s column col and layer name starting from the row row going to 0.

+
+ +
+
+static variable P_AddSealedEntryToTPStorage(string device, variable headstage)
+
+ +
+
+static variable P_MethodAtmospheric(string device, variable headstage)
+

Sets the pressure to atmospheric.

+
+ +
+
+static variable P_MethodApproach(string device, variable headStage)
+

Applies approach pressures.

+
+ +
+
+static variable P_MethodSeal(string device, variable headStage)
+

Applies seal methods.

+
+ +
+
+static variable P_MethodBreakIn(string device, variable headStage)
+

Applies break-in method.

+
+ +
+
+static variable P_MethodClear(string device, variable headStage)
+

Applies pipette clearing method.

+
+ +
+
+static variable P_ApplyNegV(string device, variable headStage)
+

Applies updates the command voltage to the SEAL_POTENTIAL when SEAL_RESISTANCE_THRESHOLD is crossed.

+
+ +
+
+static variable P_UpdateVcom(string device, variable vCom, variable headStage)
+

Updates the command voltage.

+
+ +
+
+static variable P_CloseDevice(string device)
+

Determines which devices to close. Ensures all DA_Ephys panels using a particular device for pressure regulation are updated correctly.

+
+ +
+
+static variable P_OpenDevice(string mainDevice, string pressureDevice)
+

Open device used for pressure regulation.

+
+ +
+
+static variable P_PrepareITCWaves(string mainDevice, string pressureDevice, variable deviceID)
+

Adapt the ITC DAQ waves for hardware specialities.

+
+ +
+
+static variable P_CloseDeviceLowLevel(string device, string deviceToClose, variable refHeadstage)
+

Used to close the device used for pressure regulation.

+
+ +
+
+static string P_HeadstageUsingDevice(string device, string pressureDevice)
+

Returns a list of rows that contain a particular string.

+
+ +
+
+static string P_GetListOfPressureCtrlDevices(string device)
+

Returns a list of ITC/NI devices to open.

+

Pulls a non repeating list of ITC/NI devices to open from the device specific pressure data wave.

+
+ +
+
+variable P_SetAndGetPressure(string device, variable headStage, variable psi)
+

Sets the pressure on a headStage.

+
+ +
+
+variable P_GetUserAccess(string device, variable headStage, variable pressureMode)
+

Returns pressure access defined in PRESSURE_CONSTANTS of the headstage.

+
+
Parameters:
+
    +

  • device – The DAQ device for which user access is being queried

    • +

  • headStage – MIES headstage number, must be in the range [0, NUM_HEADSTAGES]

    • +

  • pressureMode – One of the pressure modes defined in PRESSURE_CONSTANTS

    • +
+
+
+
+ +
+
+variable P_SetPressureValves(string device, variable headStage, variable Access)
+

Maps the access (defined in PRESSURE_CONSTANTS) to the TTL settings.

+
+ +
+
+variable P_UpdateTTLstate(string device, variable headStage, variable ONorOFFA, variable ONorOFFB)
+

Updates the TTL channel associated with headStage while maintaining existing channel states.

+

When setting TTLs, all channels are set at once. To keep existing TTL state on some channels, active state must be known. This function queries the hardware to determine the active state.

+

ITC hardware: This requires the TTL out to be looped back to the TTL in on the ITC DAC.

+

NI hardware: There are no dedicated input or output channels for DIO. The last written value is read according to documentation.

+
+ +
+
+static variable P_UpdateSSRSlopeAndSSR(string device)
+

Updates resistance slope and the resistance in PressureDataWv from TPStorageWave param.

+
+ +
+
+variable P_UpdatePressureDataStorageWv(string device)
+

Updates the pressure state (approach, seal, break in, or clear) from DA_Ephys panel to the pressureData wave.

+
+ +
+
+variable P_UpdatePressureControls(string device, variable headStageNo)
+

Retrieves the parameters stored in the PressureData wave and passes them to the GUI controls.

+
+ +
+
+static variable P_UpdatePopupDevices(string device, variable headStageNo)
+

Updates the popupmenu popup_Settings_Pressure_dev.

+
+ +
+
+static variable P_ManPressurePulse(string device, variable headStage)
+

Initiates a pressure pulse who’s settings are are controlled in the manual tab of the pressure regulation controls.

+
+ +
+
+static variable P_NegPressurePulse(string device, variable headStage)
+

Sends a negative pressure pulse to the pressure regulator. Gates the TTLs apropriately to maintain the exisiting TTL state while opening the TTL on the channel with the pressure pulse.

+
+ +
+
+static variable P_PosPressurePulse(string device, variable headStage)
+

Initiates a positive pressure pulse to the pressure regulator. Gates the TTLs apropriately to maintain the exisiting TTL state while opening the TTL on the channel with the pressure pulse.

+
+ +
+
+static variable P_ITC_SetChannels(string device, variable headstage)
+
+ +
+
+variable P_DeviceIsUsedForPressureCtrl(string device, string pressureDevice)
+

Check wether the given device is used as pressure device already.

+
+ +
+
+static variable P_DataAcq(string device, variable headStage)
+

Perform an acquisition cycle on the pressure device for pressure control.

+
+ +
+
+variable P_ITC_FIFOMonitorProc(WMBackgroundStruct *s)
+

Monitor the device FIFO and terminates acquisition when sufficient data has been collected.

+
+ +
+
+variable P_NI_StopDAQ(string device, variable headStage)
+
+ +
+
+static variable P_FindDeviceExecutingPP(string *device, variable *deviceID, variable *headStage)
+

Returns the device of the device associated with device conducting a pressure pulse.

+
+ +
+
+static variable P_GetPressureForDA(string device, variable headStage, variable pressureMode, P_PressureDA *p)
+

Fill the passed structure with pressure details for the DA wave.

+
+
Parameters:
+
+
+
+
+ +
+
+static wave P_NI_GetDAWave(string device, variable headStage)
+
+ +
+
+static wave P_NI_GetADWave(string device, variable headStage)
+
+ +
+
+static variable P_FillDAQWaves(string device, variable headStage, P_PressureDA *p)
+
+ +
+
+static variable P_DAforNegPpulse(string device, variable headStage)
+

Updates the DA data used for ITC controlled pressure devices for a negative pressure pulse.

+
+ +
+
+static variable P_GetPulseAmp(string device, variable headStage)
+

Returns the negative pressure pulse amplitude.

+
+ +
+
+static variable P_LastPulseCount(variable pulseAmp)
+

Returns the pulse count.

+
+ +
+
+static variable P_DAforPosPpulse(string device, variable headstage)
+

Updates the DA data used for ITC controlled pressure devices for a positive pressure pulse.

+
+ +
+
+static variable P_DAforManPpulse(string device, variable Headstage)
+

Updates the DA data used for ITC controlled pressure devices for a manual pressure pulse.

+
+ +
+
+static variable P_TTLforPpulse(string device, variable headStage)
+

Updates the rack 0 and rack 1 TTL waves used for ITC controlled pressure devices.

+
+ +
+
+static variable P_UpdateTTLdecimal(string pressureDevice, variable dec, variable ttlBit, variable ONorOFF)
+

returns the new TTL state based on the starting TTL state.

+
+ +
+
+variable P_UpdatePressureMode(string device, variable pressureMode, string pressureControlName, variable checkALL)
+

Updates the pressure mode button state in the DA_Ephys Data Acq tab.

+
+ +
+
+static variable P_ResetPressureData(string device, variable headStageNo = defaultValue)
+

Resets pressure data to base state.

+
+ +
+
+static variable P_CheckAll(string device, variable pressureMode, variable SavedPressureMode)
+

Applies pressure mode to all headstages with valid pressure settings.

+
+ +
+
+variable P_SetPressureOffset(string device, variable headstage, variable userOffset)
+
+ +
+
+variable P_InitBeforeTP(string device)
+
+ +
+
+variable P_LoadPressureButtonState(string device)
+

Colors and changes the title of the pressure buttons based on the saved pressure mode.

+
+ +
+
+static variable SetPressureButtonsToBaseState(string device)
+

Sets the pressure toggle buttons to disabled, default color, default title.

+
+ +
+
+static variable P_EnableButtonsIfValid(string device, variable headStageNo)
+

Checks if the Approach button can be enabled or all pressure mode buttons can be enabled. Enables buttons that pass checks.

+
+ +
+
+variable P_UpdatePressureModeTabs(string device, variable headStage)
+

updates the tablabels for the pressure tabControl according to the pressure mode

+
+ +
+
+variable P_ValidatePressureSetHeadstage(string device, variable headStageNo)
+

Checks if all the pressure settings for a headStage are valid.

+
+
Returns:
+

1 if all settings are valid, 0 otherwise

+
+
+
+ +
+
+static variable P_DACIsCollectingData(string device, variable headStage)
+

Determines if device is active (i.e. collecting data)

+

used to determine if pressure pulse has completed.

+
+ +
+
+static variable P_PressureMethodPossible(string device, variable headstage)
+

Return true if pressure methods can be used on that headstage now.

+

Does not check if the headstage has valid settings, see P_ValidatePressureSetHeadstage(), or that no pressure pulse is currently ongoing, see P_DACIsCollectingData().

+
+ +
+
+static variable P_IsHSActiveAndInVClamp(string device, variable headStage)
+

Determines headStage is on and in V-Clamp mode.

+
+ +
+
+static variable P_ResetAll_P_ButtonsToBaseState(string device)
+

Returns the four pressure buttons to the base state (gray color; removes “Stop” string from button title)

+
+ +
+
+variable P_PressureDisplayHighlite(string device, variable hilite)
+
+ +
+
+static std::tuple<variable, string> P_CheckDeviceAndChannelSelection(string device)
+
+ +
+
+static variable P_Enable()
+

Enables devices for all locked DA_Ephys panels. Sets the correct pressure button state for all locked DA_Ephys panels.

+
+ +
+
+variable P_Disable()
+

Disables devices for all locked DA_Ephys panels. Sets the correct pressure button state for all locked DA_Ephys panels.

+
+ +
+
+static wave P_DecToBinary(variable dec)
+

Decimal to binary in 8bit wave.

+

Wave is always 4 rows long so that each TTL channel on the front of the ITC DAC gets “encoded”

+
+ +
+
+static variable P_ManSetPressure(string device, variable headStage, variable manPressureAll)
+

Manual pressure control.

+
+ +
+
+variable P_SaveUserSelectedHeadstage(string device, variable headStage)
+

Saves user seleted headstage in pressureData wave.

+
+ +
+
+variable P_SetAllHStoAtmospheric(string device)
+

Sets all headstage to atmospheric pressure.

+
+ +
+
+variable P_GetPressureMode(string device, variable headStage)
+

Gets the pressure mode for a headstage.

+
+ +
+
+variable P_SetPressureMode(string device, variable headStage, variable pressureMode, variable pressure = defaultValue)
+

Sets the pressure mode.

+

Intended for use by other processes

+
+
Parameters:
+
    +

  • device – device

    • +

  • headStage – MIES headstage number, must be in the range [0, NUM_HEADSTAGES]

    • +

  • pressureMode – One of the pressure modes defined in PressureModeConstants

    • +

  • pressure – [optional, ignored by default. Sets pressure of manual mode]

    • +
+
+
+
+ +
+
+variable ButtonProc_Approach(WMButtonAction *ba)
+

Approach button.

+
+ +
+
+variable P_SetApproach(string device, string cntrlName)
+

Sets approach state.

+

Handles the TP depency of the approach pressure application

+
+ +
+
+variable ButtonProc_Seal(WMButtonAction *ba)
+

Seal button.

+
+ +
+
+variable ButtonProc_BreakIn(WMButtonAction *ba)
+

Break in button.

+
+ +
+
+variable ButtonProc_Clear(WMButtonAction *ba)
+

Clear button.

+
+ +
+
+static variable P_SetManual(string device, string cntrlName)
+

Handles the TP depency of the Manual pressure application.

+
+ +
+
+variable CheckProc_ClearEnable(WMCheckboxAction *cba)
+

Clear all check box.

+
+ +
+
+variable ButtonProc_Hrdwr_P_UpdtDAClist(WMButtonAction *ba)
+

Update DAC list button.

+
+ +
+
+variable P_ButtonProc_Enable(WMButtonAction *ba)
+

Pressure control device Enable button in Hardware tab of DA_Ephys panel.

+
+ +
+
+variable P_ButtonProc_Disable(WMButtonAction *ba)
+

Pressure control device Disable button in Hardware tab of DA_Ephys panel.

+
+ +
+
+variable ButtonProc_DataAcq_ManPressSet(WMButtonAction *ba)
+

Set pressure button.

+
+ +
+
+variable ButtonProc_ManPP(WMButtonAction *ba)
+

Manual pressure pulse button.

+
+ +
+
+variable P_Check_ApproachNear(WMCheckboxAction *cba)
+
+ +
+
+variable P_Check_SealAtm(WMCheckboxAction *cba)
+
+ +
+
+variable P_ButtonProc_UserPressure(WMButtonAction *ba)
+
+ +
+
+variable P_RunP_ControlIfTPOFF(string device)
+

Runs P_PressureControl if the TP is OFF.

+
+ +
+
+variable P_GetAutoUserOff(string device)
+

If auto-user-OFF is checked, then user access is turned off this function is run by the active headstage slider control.

+
+ +
+
+static variable P_SetLEDValueAssoc(string device)
+

Sets the value of the headstage LED valDisplays to the correct cell in pressureType wave.

+
+ +
+
+variable P_UpdatePressureType(string device)
+

Encodes the pressure type for each headstage.

+

See also PressureTypeConstants

+
+ +
+
+string P_PressureMethodToString(variable method)
+
+ +
+
+
+struct P_PressureDA
+

Filled by P_GetPressureForDA()

+
+

Public Members

+
+
+variable calPressure
+
+ +
+
+variable calPressureOffset
+

preconditioned for the DAC hardware

+
+ +
+
+variable pressure
+

[psi]

+
+ +
+
+variable first
+
+ +
+
+variable last
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___programmatic_g_u_i_control_8ipf.html b/file/_m_i_e_s___programmatic_g_u_i_control_8ipf.html new file mode 100644 index 0000000000..d729501c83 --- /dev/null +++ b/file/_m_i_e_s___programmatic_g_u_i_control_8ipf.html @@ -0,0 +1,398 @@ + + + + + + + + File MIES_ProgrammaticGUIControl.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_ProgrammaticGUIControl.ipf

+

PGC Control GUI controls from code

+
+

Prototype functions for #PGC_SetAndActivateControl

+

+
+
+variable PGC_ButtonControlProcedure(WMButtonAction *ba)
+
+ +
+
+variable PGC_PopupActionControlProcedure(WMPopupAction *pa)
+
+ +
+
+variable PGC_CheckboxControlProcedure(WMCheckBoxAction *cba)
+
+ +
+
+variable PGC_TabControlProcedure(WMTabControlAction *tca)
+
+ +
+
+variable PGC_SetVariableControlProcedure(WMSetVariableAction *tca)
+
+ +
+
+variable PGC_SliderControlProcedure(WMSliderAction *sla)
+
+ +
+
+variable PGC_ListBoxControlProcedure(WMListBoxAction *lba)
+
+ +
+
+

Functions

+
+
+static variable PGC_ShowControlInTab(string win, string control)
+

Bring all tabs which hold the control to the front (recursively).

+

Requires that these are managed by ACL_TabUtilities.ipf.

+
+ +
+
+static string PGC_GetProcAndCheckParamType(string recMacro)
+
+ +
+
+variable PGC_SetAndActivateControlStr(string win, string control, string str)
+

Wrapper for PGC_SetAndActivateControl()

+
+ +
+
+variable PGC_SetAndActivateControlVar(string win, string control, variable var)
+

Wrapper for PGC_SetAndActivateControl()

+
+ +
+
+variable PGC_SetAndActivateControl(string win, string control, variable val = defaultValue, string str = defaultValue, variable switchTab = defaultValue, variable mode = defaultValue)
+

Set the control’s value and execute the control procedure of the given control.

+

The function tries to mimick interactive operation as closely as possible. Therefore interacting with disabled controls results in an assertion. See mode for a way to avoid that.

+

+PopupMenus:

    +

  • Only one of val or str can be supplied

    • +

  • val is 0-based

    • +

  • str must be the name of an entry, can include * using wildcard syntax.

    • +
+

+

ValDisp:

    +

  • Setting this control always changes its mode from ‘internal number’ to ‘global expression’

    • +
+

+

SetVariable:

    +

  • Both str and val are accepted and converted to the target type. Read-only controls can only be set with mode = PGC_MODE_FORCE_ON_DISABLED.

    • +
+

+

ListBox:

    +

  • Setting the column is not supported

    • +

  • Simulated event code is 3 (double click)

    • +
+

+
+
Parameters:
+
    +

  • win – window name or path, when referring to subwindows in a window hierarchy a full subwindow specification with # is required

    • +

  • control – GUI control

    • +

  • val – [optionality depends on control type] Numeric value to set

    • +

  • str – [optionality depends on control type] String value to set

    • +

  • switchTab – [optional, defaults to false] Switches tabs so that the control is shown

    • +

  • mode – [optional, defaults to PGC_MODE_ASSERT_ON_DISABLED] One of PGC_MODES. Allows to fine tune the behaviour for disabled controls.

    • +
+
+
Returns:
+

1 if the numeric value was modified by control limits, 0 if not (only relevant for SetVariable controls)

+
+
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___publish_8ipf.html b/file/_m_i_e_s___publish_8ipf.html new file mode 100644 index 0000000000..2606713870 --- /dev/null +++ b/file/_m_i_e_s___publish_8ipf.html @@ -0,0 +1,632 @@ + + + + + + + + File MIES_Publish.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Publish.ipf

+
+

Functions

+
+
+static variable PUB_GetJSONTemplate(string device, variable headstage)
+

Get a template for publishing messages.

+

Publishers in MIES should in general supply additional information like device/sweep number/timestamp. This function allows to autofill these entries.

+
+ +
+
+static variable PUB_Publish(variable jsonID, string messageFilter)
+

Publish the given message as given by the JSON and the filter.

+
+ +
+
+static variable PUB_AddLabnotebookEntriesToJSON(variable jsonID, wave values, wave keys, variable sweepNo, string key, variable headstage, variable labnotebookLayer)
+
+ +
+
+variable PUB_AutoBridgeBalance(string device, variable headstage, variable resistance)
+

Filter: AMPLIFIER_AUTO_BRIDGE_BALANCE

+

Example:

+

{
+  "bridge balance resistance": {
+    "unit": "Ohm",
+    "value": 4711
+  },
+  "device": "my_device",
+  "headstage": 0,
+  "sweep number": "NaN",
+  "timestamp": "2022-05-13T18:56:39Z"
+}
+
+
+

+
+ +
+
+variable PUB_PipetteInBath(string device, variable sweepNo, variable headstage)
+

Published message in POST_SET_EVENT for the analysis function PSQ_PipetteInBath()

+

Keys under /results are labnotebook keys. The arrays under /results/XXX/values are the values for each sweep in the stimset cycle. This array has currently always one entry as PSQ_PB_NUM_SWEEPS_PASS is one. The encoding is UTF-8.

+

Example:

+

{
+ "device": "my_device",
+ "headstage": 0,
+ "results": {
+   "USER_Pipette in Bath Chk0 Leak Current BL": {
+     "unit": "Amperes",
+     "value": [
+       123.0
+     ]
+   },
+   "USER_Pipette in Bath Chk0 Leak Current BL QC": {
+     "unit": "On/Off",
+     "value": [
+       0.0
+     ]
+   },
+   "USER_Pipette in Bath Set QC": {
+     "unit": "On/Off",
+     "value": [
+       1.0
+     ]
+   },
+   "USER_Pipette in Bath pipette resistance": {
+     "unit": "Ω",
+     "value": [
+       456.0
+     ]
+   },
+   "USER_Pipette in Bath pipette resistance QC": {
+     "unit": "On/Off",
+     "value": [
+       1.0
+     ]
+   }
+ },
+ "sweep number": "NaN",
+ "timestamp": "2022-02-10T20:48:22Z"
+}
+
+
+

+
+ +
+
+variable PUB_SealEvaluation(string device, variable sweepNo, variable headstage)
+

Published message in POST_SET_EVENT for the analysis function PSQ_SealEvaluation()

+

Keys under /results are labnotebook keys. The arrays under /results/XXX/values are the values for each sweep in the stimset cycle. This array has currently always one entry as PSQ_SE_NUM_SWEEPS_PASS is one. The encoding is UTF-8.

+

Example:

+

{
+  "device": "my_device",
+  "headstage": 0,
+  "results": {
+    "USER_Seal evaluation Set QC": {
+    "unit": "On/Off",
+    "value": [
+     1.0
+      ]
+     },
+     "USER_Seal evaluation seal resistance max": {
+       "unit": "Ω",
+       "value": [
+         123.0
+       ]
+     }
+  },
+  "sweep number": "NaN",
+  "timestamp": "2022-02-22T12:27:07Z"
+}
+
+
+

+
+ +
+
+variable PUB_TrueRestingMembranePotential(string device, variable sweepNo, variable headstage)
+

Published message in POST_SET_EVENT for the analysis function PSQ_TrueRestingMembranePotential()

+

Keys under /results are labnotebook keys. The arrays under /results/XXX/values are the values for each sweep in the stimset cycle. This array has currently always one entry as PSQ_VM_NUM_SWEEPS_PASS is one. The encoding is UTF-8.

+

Example:

+

{
+  "device": "my_device",
+  "headstage": 0,
+  "results": {
+    "USER_True Rest Memb. Full Average": {
+      "unit": "Volt",
+      "value": [
+        123.0
+      ]
+    },
+    "USER_True Rest Memb. Set QC": {
+      "unit": "On/Off",
+      "value": [
+        1.0
+      ]
+    }
+  },
+  "sweep number": "NaN",
+  "timestamp": "2022-04-27T16:52:28Z"
+}
+
+
+

+
+ +
+
+variable PUB_ClampModeChange(string device, variable headstage, variable oldClampMode, variable newClampMode)
+

Filter: AMPLIFIER_CLAMP_MODE_FILTER

+

Example:

+

{
+  "clamp mode": {
+    "new": "V_CLAMP_MODE",
+    "old": "I_CLAMP_MODE"
+  },
+  "device": "my_device",
+  "headstage": 0,
+  "sweep number": "NaN",
+  "timestamp": "2022-05-13T18:54:39Z"
+}
+
+
+

+
+ +
+
+variable PUB_PressureMethodChange(string device, variable headstage, variable oldMethod, variable newMethod)
+

Filter: PRESSURE_STATE_FILTER

+

Example:

+

{
+  "device": "my_device",
+  "headstage": 0,
+  "pressure method": {
+    "new": "Approach",
+    "old": "Atmosphere"
+  },
+  "sweep number": "NaN",
+  "timestamp": "2022-05-13T18:45:38Z"
+}
+
+
+

+
+ +
+
+variable PUB_PressureSealedState(string device, variable headstage)
+

Filter: PRESSURE_SEALED_FILTER

+

Example:

+

{
+  "device": "my_device",
+  "headstage": 0,
+  "sealed": true,
+  "sweep number": "NaN",
+  "timestamp": "2022-05-13T18:52:14Z"
+}
+
+
+

+
+ +
+
+variable PUB_PressureBreakin(string device, variable headstage)
+

Filter: PRESSURE_BREAKIN_FILTER

+

Example:

+

{
+  "break in": true,
+  "device": "my_device",
+  "headstage": 0,
+  "sweep number": "NaN",
+  "timestamp": "2022-05-13T18:58:04Z"
+}
+
+
+

+
+ +
+
+variable PUB_AutoTPResult(string device, variable headstage, variable result)
+

Filter: AUTO_TP_FILTER

+

Example:

+

{
+  "device": "my_device",
+  "headstage": 0,
+  "results": {
+    "QC": true,
+    "amplitude IC": {
+      "unit": "pA",
+      "value": 456
+    },
+    "amplitude VC": {
+      "unit": "mV",
+      "value": 789
+    },
+    "baseline": {
+      "unit": "%",
+      "value": 123
+    },
+    "delta V": {
+      "unit": "mV",
+      "value": 0.5
+    }
+  },
+  "sweep number": "NaN",
+  "timestamp": "2022-05-13T18:59:44Z"
+}
+
+
+

+
+ +
+
+variable PUB_DAQStateChange(string device, variable mode, variable oldState, variable newState)
+

Filter: DAQ_TP_STATE_CHANGE_FILTER

+

DAQ:

+

{
+  "daq": "starting",
+  "device": "my_device",
+  "headstage": "NaN",
+  "sweep number": "NaN",
+  "timestamp": "2022-05-16T17:12:24Z",
+  "tp": null
+}
+
+
+

+

TP:

+

{
+  "daq": null,
+  "device": "my_device",
+  "headstage": "NaN",
+  "sweep number": "NaN",
+  "timestamp": "2022-05-16T17:12:29Z",
+  "tp": "stopping"
+}
+
+
+

+

The strings for daq/tp are either starting or stopping.

+
+ +
+
+variable PUB_AccessResistanceSmoke(string device, variable sweepNo, variable headstage)
+

Published message in POST_SET_EVENT for the analysis function PSQ_AccessResistanceSmoke()

+

Keys under /results are labnotebook keys. The arrays under /results/XXX/values are the values for each sweep in the stimset cycle. This array has currently always one entry as PSQ_AR_NUM_SWEEPS_PASS is one. The encoding is UTF-8.

+

Example:

+

{
+  "device": "my_device",
+  "headstage": 0,
+  "results": {
+    "USER_Access Res. Smoke Set QC": {
+      "unit": "On/Off",
+      "value": [
+        1.0
+      ]
+    },
+    "USER_Access Res. Smoke access resistance": {
+      "unit": "Ω",
+      "value": [
+        123.0
+      ]
+    },
+    "USER_Access Res. Smoke access resistance QC": {
+      "unit": "On/Off",
+      "value": [
+        0.0
+      ]
+    },
+    "USER_Access Res. Smoke access vs steady state ratio": {
+      "unit": "",
+      "value": [
+        0.5
+      ]
+    },
+    "USER_Access Res. Smoke access vs steady state ratio QC": {
+      "unit": "On/Off",
+      "value": [
+        1.0
+      ]
+    }
+  },
+  "sweep number": "NaN",
+  "timestamp": "2022-05-07T13:59:39Z"
+}
+
+
+

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___pulse_averaging_8ipf.html b/file/_m_i_e_s___pulse_averaging_8ipf.html new file mode 100644 index 0000000000..608fefd2a9 --- /dev/null +++ b/file/_m_i_e_s___pulse_averaging_8ipf.html @@ -0,0 +1,1382 @@ + + + + + + + + File MIES_PulseAveraging.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_PulseAveraging.ipf

+

PA Routines for dealing with pulse averaging.

+

    +

  • Averaging is done for all pulses in a set

    • +

  • Zeroing is done for all pulses

    • +

  • Deconvolution is done for the average wave only

    • +

  • See also PA_AutomaticTimeAlignment

    • +
+

+

Drawing layers:

    +

  • ProgAxes: X=0 line for images

    • +

  • ProgFront: Scale bars

    • +

  • ProgBack: Failed pulses triangles

    • +
+

+
+

Unnamed Group

+
+
+static const string PA_DRAWLAYER_XZEROLINE = "ProgAxes"
+
+ +
+
+static const string PA_DRAWLAYER_SCALEBAR = "ProgFront"
+
+ +
+
+static const string PA_DRAWLAYER_FAILED_PULSES = "ProgBack"
+
+ +
+
+

Pulse sort order

+

Popupmenu indizes for the PA plot controls

+
+
+static const double PA_PULSE_SORTING_ORDER_SWEEP = 0x0
+
+ +
+
+static const double PA_PULSE_SORTING_ORDER_PULSE = 0x1
+
+ +
+
+

Defines

+
+
+PA_HIDE_AXIS
+
+ +
+
+PA_HIDE_EXECUTION_TIME
+
+ +
+
+

Functions

+
+
+static string PA_GetGraphs(string win, variable displayMode)
+

Return a list of all graphs.

+
+ +
+
+static string PA_GetGraphName(string win, PulseAverageSettings *pa, variable displayMode, variable channelNumber, variable activeRegionCount)
+
+ +
+
+static string PA_GetGraphPrefix(string win, variable displayMode)
+
+ +
+
+string PA_GetColorScalePanel(string win)
+

Return the subwindow path to the panel which holds the graphs with the color scales.

+

Only present for PA_DISPLAYMODE_IMAGES graphs.

+
+ +
+
+string PA_GetColorScaleGraph(string win)
+

Return the subwindow path to the graph which holds the color scales.

+

Only present for PA_DISPLAYMODE_IMAGES graphs.

+
+ +
+
+static string PA_GetGraph(string mainWin, PulseAverageSettings *pa, variable displayMode, variable channelNumber, variable region, variable activeRegionCount, variable activeChanCount, variable numRegions)
+

Return the name of the pulse average graph.

+

This function takes care of creating a graph if it does not exist, and laying it out correctly

+

Layout scheme for multiple graphs turned on:

    +

  • Positions the graphs right to mainWin in matrix form

    • +

  • Columns: Regions (aka headstages with pulse starting time information respecting region selection in GUI)

    • +

  • Rows: Active unique channels

    • +
+

+
+ +
+
+static wave PA_GetAxes(PulseAverageSettings *pa, variable channel, variable region)
+

Return the names of the vertical and horizontal axes.

+
+ +
+
+static wave PA_CalculatePulseInfos(wave DA, string fullPath, variable channelNumber, variable totalOnsetDelay)
+

Derive the pulse infos from a DA wave.

+

Uses plain FindLevels after the onset delay using 10% of the full range above the minimum as threshold

+
+
Returns:
+

pulse info wave or if nothing could be found, an invalid wave reference

+
+
+
+ +
+
+static wave PA_GetUniqueHeadstages(WaveText traceData)
+

Return a wave with headstage numbers, duplicates replaced with NaN so that the indizes still correspond the ones in traceData.

+
+ +
+
+wave PA_GetPulseInfos(WaveText traceData, variable idx, variable region, string channelTypeStr)
+

Return pulse infos.

+
+
Parameters:
+
    +

  • traceData – 2D wave with trace information, from GetTraceInfos()

    • +

  • idx – Index into traceData, used for determining sweep numbers, labnotebooks, etc.

    • +

  • region – Region (headstage) to get pulse starting times for

    • +

  • channelTypeStr – Type of the channel, one of XOP_CHANNEL_NAMES

    • +
+
+
Returns:
+

invalid wave reference if no pulses could be found or 2D wave see GetPulseInfoWave()

+
+
+
+ +
+
+static variable PA_DiffPulseInfos(wave numericalValues, variable sweepNo, WaveOrNull pulseInfosEpochs, WaveOrNull pulseInfosCalc)
+

Compare epoch and calculated pulse infos.

+
+ +
+
+static wave PA_RetrievePulseInfosFromEpochs(string epochInfo)
+

Extracts the pulse info from the lab notebook and returns them as wave.

+
+
Parameters:
+

epochInfo – [in] epoch data to extract pulse starting times

+
+
Returns:
+

pulse info, see GetPulseInfoWave() or an invalid wave reference on error

+
+
+
+ +
+
+static variable PA_GetPulseLength(wave pulseInfos, variable pulseIndex, variable overridePulseLength, variable fixedPulseLength)
+
+ +
+
+static std::tuple<WAVE, WAVE> PA_CreateAndFillPulseWaveIfReq(WaveOrNull wv, dfref singleSweepFolder, variable channelType, variable channelNumber, variable clampMode, variable region, variable pulseIndex, variable first, variable length, wave pulseInfos)
+

Single pulse wave creator.

+

The wave note for the pulse waves is stored in a separate empty wave. This speeds up the caching logic for the pulse waves a lot.

+

The wave note is used for documenting the applied operations:

    +

  • $NOTE_KEY_FAILED_PULSE_LEVEL: Level used for failed pulse search

    • +

  • $NOTE_KEY_NUMBER_OF_SPIKES: Number of spikes used for failed pulse search

    • +

  • $NOTE_KEY_PULSE_LENGTH: Length in points of the pulse wave (before any operations)

    • +

  • $NOTE_KEY_SEARCH_FAILED_PULSE: Checkbox state of “Search failed pulses”

    • +

  • $NOTE_KEY_TIMEALIGN: Time alignment was active and applied

    • +

  • $NOTE_KEY_TIMEALIGN_TOTAL_OFFSET: Calculated offset from time alignment

    • +

  • $NOTE_KEY_ZEROED: Zeroing was active and applied

    • +

  • $NOTE_KEY_WAVE_MINIMUM: Minimum value of the data

    • +

  • $NOTE_KEY_WAVE_MAXIMUM: Maximum value of the data

    • +

  • $NOTE_KEY_TIMEALIGN_FEATURE_POS: Position where the feature for time alignment was found

    • +

  • $NOTE_KEY_PULSE_IS_DIAGONAL: Stores if pulse is shown in the diagonal of the output layout

    • +

  • $PA_SOURCE_WAVE_TIMESTAMP: Last modification time of the pulse wave before creation.

    • +

  • $NOTE_KEY_PULSE_START: ms coordinates where the pulse starts

    • +

  • $NOTE_KEY_PULSE_END: ms coordinates where the pulse ends

    • +

  • $NOTE_KEY_PULSE_CLAMPMODE: Clamp mode of the pulse data, one of AmplifierClampModes

    • +
+

+

Diagonal pulses only with failed pulse search enabled:

    +

  • $NOTE_KEY_PULSE_HAS_FAILED: Pulse has failed

    • +

  • $NOTE_KEY_PULSE_SPIKE_POSITIONS: Comma separated list of spike positions in ms. 0 is the start of the pulse.

    • +
+

+
+ +
+
+static variable PA_UpdateMinAndMax(wave wv, wave noteWave)
+
+ +
+
+static string PA_GenerateFailedPulseKey(variable sweep, variable region, variable pulse)
+

Generate a key for a pulse.

+

All pulses with that key are either failing or passing.

+
+ +
+
+static std::tuple<WaveDouble, WaveText> PA_GetSweepsAndExperimentsFromIndices(string win, WaveOrNull additionalData)
+
+ +
+
+static std::tuple<PulseAverageSetIndices> PA_GenerateAllPulseWaves(string win, PulseAverageSettings *pa, variable mode, WaveOrNull additionalData)
+

Create all single pulse waves.

+

This function needs to be called when ever traces in the databrowser/sweepbrowser are removed or added.

+

Idea:

    +

  • Gather all AD sweep traces in the databrowser/sweepbrowser (skipping duplicates from oodDAQ)

    • +

  • Iterate over all regions (there are as many regions as unique headstages)

    • +

  • Now gather the pulse starting time from the region and create single pulse waves for all of them

    • +
+

+

The result is feed into GetPulseAverageProperties() and GetPulseAveragepropertiesWaves() for further consumption.

+

Fast path for incremental update:

    +

  • The previous list of regions/channels is saved

    • +

  • We get the indizes of the new sweep (from additionalData)

    • +

  • Only these indizes are added to the properties wave, as well as the setIndice waves at the end

    • +

  • information is stored where the new data begins

    • +

  • The region/channels of the new Sweep(s) are merged with the old ones.

    • +

  • In case the layout changed compared to the old regions/channels it is calculated again.

    • +
+

+
+ +
+
+static variable PA_SetDiagonalityNote(wave indices, variable startIndex, variable numEntries, WaveRefWave propertiesWaves, variable isDiagonal)
+
+ +
+
+static std::tuple<PulseAverageSetIndices> PA_InitPASIInParts(PulseAverageSettings *pa, variable part, variable disableIncremental)
+

This function fills a structure with information we need in most further processing functions, e.g. PA DFs, references to properties, setIndice waves, regions, channels, axes, a.s.o. Since not every information might be available at the time this structure is filled there are two steps defined, that are enabled by setting ‘part’ with PA_PASIINIT_BASE and/or PA_PASIINIT_INDICEMETA.

+
+
Parameters:
+
    +

  • pa – PulseAverageSettings structure

    • +

  • part – filling step for the returned structure, set depending on available data

    • +

  • disableIncremental – When set then the meta information for incremental updates is just initialized with zero.

    • +
+
+
+
+ +
+
+static variable PA_CopySetIndiceSizeDispRestart(WaveRefWave setIndices)
+

For incremental display update copy current size of of setIndices to new display start.

+
+ +
+
+static std::tuple<WaveRefWave, WAVE, WAVE, WAVE> PA_GetSetIndicesHelper(dfref pulseAverageHelperDFR, variable prevIndices)
+

Retrieve setIndices, channels and regions of the current or the previous layout, as is saved in the properties wave wave note.

+
+
Parameters:
+
    +

  • pulseAverageHelperDFR – [in] Reference to pulse average helper DF

    • +

  • prevIndices – [in] When set then the indices, channels and regions of the previous layout are returned, otherwise the current layout is returned. Note that only the layout is considered, the returned indices always contain the current indices for each channel/region at the time of calling this function.

    • +
+
+
+
+ +
+
+static variable PA_UpdateIndiceNotes(wave currentDisplayMapping, wave prevDisplayMapping, PulseAverageSetIndices *pasi, variable layoutChanged)
+

Updates the setIndices notes with information about the layout and layout changes. Therefore the function compares the previous display mapping and the current display mapping for each region/channel in the layout and determines if the setIndices at this region/channel are added as new/moved/stayed at the same position or were removed. In the setIndices wave note the following keys are set: ‘$PA_SETINDICES_KEY_DISPCHANGE’: change in the layout for this set ‘$PA_SETINDICES_KEY_ACTIVEREGIONCOUNT’: grid location on the vertical where this set is displayed ‘$PA_SETINDICES_KEY_ACTIVECHANCOUNT’: grid location on the horizontal where this set is displayed (this data is currently not used, but created for further PA plot extension)

+
+
Parameters:
+
    +

  • currentDisplayMapping – [in] 3D wave, rows and columns map the region/channels, in the two layers the associated activeRegion and activeChannel are stored. The layer information is the position in the grid of the layout.

    • +

  • prevDisplayMapping – [in] Technically the same wave as currentDisplayMapping, but it stores the information about the previous layout.

    • +

  • pasi – [in] Pulse Average structure storing PA information

    • +

  • layoutChanged – [in] when set then the layout has changed compared to the previous one displayed. This is directly related to a region/channel change.

    • +
+
+
+
+ +
+
+static variable PA_UpdateIndiceNotesImpl(wave indices, wave currentMap, wave oldMap, variable channel, variable region, variable layoutChanged, variable indiceType)
+

Evaluate the previous and current mapping and set the display change in the wave note of the indice sets as well as activeChanCount, activeRegionCount. IMPORTANT: To have a consistent state for the case the layout changed the function must be called with the current and the previous indices. Otherwise removed sets wont be flagged properly.

+
+ +
+
+static variable PA_ApplyPulseSortingOrder(wave setIndices, variable channelNumber, variable region, wave properties, PulseAverageSettings *pa)
+
+ +
+
+static variable PA_GatherSettings(string win, PulseAverageSettings *s)
+

Populates pps.pulseAverSett with the user selection from the panel.

+
+ +
+
+static variable PA_DeconvGatherSettings(string win, PulseAverageDeconvSettings *deconvolution)
+

gather deconvolution settings from PA section in BSP

+
+ +
+
+variable PA_Update(string win, variable mode, WaveOrNull additionalData = defaultValue)
+

Update the PA plot to accomodate changed settings.

+
+ +
+
+static wave PA_GetSetWaves(dfref dfr, variable channelNumber, variable region, variable removeFailedPulses = defaultValue)
+

Returns the two column setWave with pulse/pulsenote.

+
+ +
+
+static wave PA_GetSetWaves_TS(wave properties, WaveRefWave propertiesWaves, wave setIndizes, variable getMode, variable removeFailedPulses)
+

Returns a 1D wave ref wave containing the refs to the setwave2 refs of {all, new, old} sets, depending on the mode constant given in getModes. For mode constants.

+

+

See also

+

PAGetSetWavesModes, they can be combined by ORing the bits. Each setWave2 component wave entry in the returned wave is a 2D wave ref wave that refrences the pulse data in col 0, and the pulse note in col 1. The rows count the pulses.

+
+

+
+ +
+
+static variable PA_MarkFailedPulses(PulseAverageSettings *pa, PulseAverageSetIndices *pasi)
+

Handle marking pulses as failed/passed if required.

+
+ +
+
+static variable PA_TagSearchedPulses(PulseAverageSettings *pa, wave wv)
+
+ +
+
+static variable PA_GetTraceCountFromGraphData(string graph, variable clear = defaultValue)
+

This function returns data from the light-weight data storage for PA graph data.

+
+
Parameters:
+
    +

  • graph – [in] name of PA graph

    • +

  • clear – [in] [optional, default = 0] when set reinitializes the data for the given graph

    • +
+
+
Returns:
+

row index of the wave where the graph data is stored

+
+
+
+ +
+
+static string PA_ShowPulses(string win, PulseAverageSettings *pa, PA_ConstantSettings *cs, PulseAverageSetIndices *pasi, variable mode)
+
+ +
+
+static variable PA_ClearGraphs(string graphs)
+

Remove all traces, image and annotations from the graph and clears its trace user data.

+
+ +
+
+static std::tuple<PA_ConstantSettings> PA_DetermineConstantSettings(PulseAverageSettings *pa, PulseAverageSettings *paOld, variable mode)
+

Returns a filled structure PA_ConstantSettings which has 1 for all constant entries of the given category.

+
+ +
+
+static std::tuple<PulseAverageSetIndices, variable> PA_PreProcessPulses(string win, PulseAverageSettings *pa, PA_ConstantSettings *cs, variable mode, WaveOrNull additionalData)
+

Gather and pre-process the single pulses for display.

+

This function is display-type agnostic and only does preparational steps. No graphs are created or killed.

+

The work with pulses is done in the following order:

    +

  • Gather pulses

    • +

  • Sort pulses (in setIndizes)

    • +

  • Reset pulses to backup

    • +

  • Failed pulse marking

    • +

  • Zeroing

    • +

  • Time alignment

    • +

  • Averaging

    • +
+

+
+
Return values:
+
    +

  • pasi – structure keeping references to current PA data set

    • +

  • needsPlotting – dest boolean denoting if there are pulses to plot

    • +
+
+
+
+ +
+
+static variable PA_CalculateAllAverages(PulseAverageSettings *pa, PulseAverageSetIndices *pasi, variable mode)
+
+ +
+
+static variable PA_TAAdaptAverageWave(WaveOrNull avg, WaveRefWave set)
+
+ +
+
+static variable PA_MakeAverageWavePermanent(dfref dfr, WaveOrNull avg, variable channel, variable region)
+
+ +
+
+static wave PA_ExtractPulseSetFromSetWaves2(WaveRefWaveOrNull setWave2)
+
+ +
+
+static variable PA_StoreMaxAndUnitsInWaveNote(WaveOrNull w, WaveOrNull unitSource)
+

Stores the WaveMaximum in the wave note of the given wave and sets the wave unit to the same as from unitSource.

+
+
Parameters:
+
    +

  • w – [in] Wave where the maximum is determined and written to the wave note, the wave unit determiend from unitSource is also set for w

    • +

  • unitSource – [in] a source wave for wave unit information for w

    • +
+
+
+
+ +
+
+static wave PA_ExtractSumsCountsOnly(WaveRefWave w)
+
+ +
+
+variable PA_UpdateScaleBars(string win, variable resetToUserLength)
+

Update the scale bars of the passed plot.

+

+This functions is non-statc as it is called from the operation queue. This is necessary as the window hooks listen to the mouse wheel event, and we want to update only after the mouse wheel triggered the axis range change. And that is only possible with the operation queue.

+
+
Parameters:
+
    +

  • win – PA trace or image plot

    • +

  • resetToUserLength – Reset the scale bars to the user upplied values

    • +
+
+
+
+ +
+
+static variable PA_DrawScaleBars(string win, PulseAverageSettings *pa, PulseAverageSetIndices *pasi, variable displayMode, variable axisMode, variable resetToUserLength = defaultValue)
+
+ +
+
+static std::tuple<variable, variable, variable, variable> PA_GetMinAndMax(WaveRefWave setWaves2)
+
+ +
+
+static std::tuple<variable, variable> PA_NeedsForcedScaleBar(string win, string userDataName, variable physicalLength, variable axisMinimum, variable axisMaximum, variable userLength = defaultValue, string userLengthName = defaultValue, variable resetToUserLength = defaultValue)
+

Determine if we need a scale bar label.

+

Without any optional parameters we always need a label if we have a stored entry userDataName and that differs from physicalLength.

+

With the optional parameters we prioritize userLength if it has changed compared to the stored value userLengthName or if it needs resetting on a new plot. Otherwise we use the same approach as above.

+
+ +
+
+static variable PA_DrawScaleBarsHelper(string win, variable axisMode, variable displayMode, WaveRefWave setWaves2, string vertAxis, string horizAxis, variable ylength, string xUnit, string yUnit, variable activeChanCount, variable activeRegionCount, variable numActive, variable resetToUserLength)
+
+ +
+
+wave PA_SpikePositionsForNonVC(wave wv, variable failedPulsesLevel)
+

Calculate the number of spikes in the given wave for IC and I=0 data.

+
+ +
+
+static variable PA_PulseHasFailed(wave pulseWave, wave noteWave, PulseAverageSettings *s)
+
+ +
+
+string PA_GeneratePulseWaveName(variable channelType, variable channelNumber, variable region, variable pulseIndex)
+

Generate the wave name for a single pulse.

+
+ +
+
+string PA_BaseName(variable channelNumber, variable headStage)
+

Generate a static base name for objects in the current averaging folder.

+
+ +
+
+static variable PA_ZeroPulses(WaveOrNull setWave2)
+

Zero single pulses using ZeroWave.

+
+ +
+
+static variable PA_ZeroWave(wave wv, wave noteWave)
+

Zero the wave using differentiation and integration.

+

Overwrites the input wave Preserves the WaveNote and adds the entry NOTE_KEY_ZEROED

+

2D waves are zeroed along each row

+
+ +
+
+static wave PA_SmoothDeconv(wave input, PulseAverageDeconvSettings *deconvolution)
+
+ +
+
+static wave PA_Deconvolution(wave average, dfref outputDFR, string outputWaveName, PulseAverageDeconvSettings *deconvolution)
+
+ +
+
+variable PA_CheckProc_Common(WMCheckboxAction *cba)
+
+ +
+
+variable PA_SetVarProc_Common(WMSetVariableAction *sva)
+
+ +
+
+variable PA_PopMenuProc_ColorScale(WMPopupAction *pa)
+
+ +
+
+variable PA_PopMenuProc_Common(WMPopupAction *pa)
+
+ +
+
+static variable PA_AutomaticTimeAlignment(PulseAverageSetIndices *pasi)
+

Time alignment for PA single pulses.

+

See Time Alignment for an explanation of the algorithm.

+
+ +
+
+static variable PA_GetFeaturePosition(wave wv, wave noteWave)
+
+ +
+
+static variable PA_SetFeaturePosition(wave wv, wave noteWave, variable featurePos)
+
+ +
+
+static variable PA_ResetWavesIfRequired(WaveOrNull setWave2, PulseAverageSettings *pa, variable mode)
+

Reset All pulse and pulse note waves from a set to its original state if they are outdated.

+
+ +
+
+static variable PA_LayoutGraphs(string win, PulseAverageSettings *pa, PulseAverageSetIndices *pasi, variable displayMode)
+
+ +
+
+static variable PA_GetSetXAxisUserData(string graph, string horizAxis)
+
+ +
+
+static variable PA_AddColorScales(string win, PulseAverageSettings *pa, PulseAverageSetIndices *pasi)
+
+ +
+
+static variable PA_AddColorScale(string graph, string colorScaleGraph, string name, string text, variable index, variable numSlots, string traceName)
+
+ +
+
+static variable PA_SerializeSettings(string win, PulseAverageSettings *pa)
+

Write the PA settings pa to the panel user data and return a JSON id with the settings.

+
+
Returns:
+

Valid JSON id, caller must release memory.

+
+
+
+ +
+
+static variable PA_DeserializeSettings(string win, PulseAverageSettings *pa)
+

Read the PA settings from the panel user data into pa and return a JSON id with the settings.

+
+
Returns:
+

Valid JSON id, caller must release memory, or NaN on error/incompatible struct

+
+
+
+ +
+
+static string PA_ShowImage(string win, PulseAverageSettings *pa, PA_ConstantSettings *cs, PulseAverageSetIndices *pasi, variable mode, WaveOrNull additionalData)
+
+ +
+
+static variable PA_HighligthFailedPulsesInImage(string graph, PulseAverageSettings *pa, string vertAxis, string horizAxis, wave img, wave properties, wave setIndizes, variable numPulses)
+
+ +
+
+static variable PA_SetColorScale(string win, string colScale)
+

Apply the given color scale to all PA plot images.

+
+ +
+
+static variable PA_ResizeColorScalePanel(string imageGraph)
+

Adjust the size of the panel with the color scale graph.

+
+ +
+
+variable PA_TraceWindowHook(WMWinHookStruct *s)
+
+ +
+
+variable PA_ImageWindowHook(WMWinHookStruct *s)
+
+ +
+
+static variable PA_IsDataOnSubPlot(PulseAverageSettings *pa, PulseAverageSetIndices *pasi, variable xLoc, variable yLoc, variable displayMode)
+

Returns 1 if data is displayed on the given layout grid location. When data is displayed in PA_ShowPulses and PA_ShowImage then in PulseAverageSetIndices this is tagged.

+
+
Parameters:
+
    +

  • pa – [in] Pulse Average Setting information

    • +

  • pasi – [in] Pulse Average Set Indices information

    • +

  • xLoc – [in] x location on display grid, typically the channel index

    • +

  • yLoc – [in] y location on display grid, typically the region index

    • +

  • displayMode – [in] Return data for either trace plot (PA_DISPLAYMODE_TRACES) or image plot (PA_DISPLAYMODE_IMAGES)

    • +
+
+
Returns:
+

1 if data is displayed on this grid location, 0 if no data is displayed

+
+
+
+ +
+
+static variable PA_DrawXZeroLines(string win, PulseAverageSettings *pa, PulseAverageSetIndices *pasi, variable displayMode)
+
+ +
+
+static variable PA_AccelerateAppendTraces(variable jsonID, WaveRefWave plotWaves)
+

Runs through all graph groups in the json and appends them to the graph.

+
+ +
+
+static variable PA_AccelerateAppendTracesImpl(string w, string v, string h, variable r, variable g, variable b, variable a, variable s, wave y, WaveText t, WaveRefWave d)
+

Appends a group of traces to a graph, properties v to s must be constant for the group.

+
+
Parameters:
+
    +

  • w – [in] name of graph window

    • +

  • v – [in] name of vertical axis

    • +

  • h – [in] name of horizontal axis

    • +

  • r – [in] red color component

    • +

  • g – [in] green color component

    • +

  • b – [in] blue color component

    • +

  • a – [in] alpha component

    • +

  • s – [in] step width of graph display

    • +

  • y – [in] 1D wave with indices into wave d for the actual plot data

    • +

  • t – [in] 1D wave with trace names, same size as y

    • +

  • d – [in] wave reference wave with plot data

    • +
+
+
+
+ +
+
+

Variables

+
+
+static const string PA_GRAPH_PREFIX = "PulseAverage"
+
+ +
+
+static const string PA_SOURCE_WAVE_TIMESTAMP = "SOURCE_WAVE_TS"
+
+ +
+
+static const string PA_SETTINGS = "PulseAverageSettings"
+
+ +
+
+static const string PA_USER_DATA_X_START_RELATIVE_PREFIX = "XAxisStartPlotRelative_"
+
+ +
+
+static const string PA_USER_DATA_CALC_XLENGTH = "CalculatedXBarLength"
+
+ +
+
+static const string PA_USER_DATA_CALC_YLENGTH = "CalculatedYBarLength"
+
+ +
+
+static const string PA_USER_DATA_USER_YLENGTH = "UserYBarLength"
+
+ +
+
+static const double PA_USE_WAVE_SCALES = 0x01
+
+ +
+
+static const double PA_USE_AXIS_SCALES = 0x02
+
+ +
+
+static const double PA_X_AXIS_OFFSET = 0.01
+
+ +
+
+static const double PA_PLOT_STEPPING = 16
+
+ +
+
+static const double PA_DISPLAYMODE_TRACES = 0x01
+
+ +
+
+static const double PA_DISPLAYMODE_IMAGES = 0x02
+
+ +
+
+static const double PA_DISPLAYMODE_ALL = 0xFF
+
+ +
+
+static const double PA_COLORSCALE_PANEL_WIDTH = 150
+
+ +
+
+static const double PA_PEAK_BOX_AVERAGE = 5
+
+ +
+
+static const double PA_AVGERAGE_PLOT_LSIZE = 1.5
+
+ +
+
+static const double PA_DECONVOLUTION_PLOT_LSIZE = 2
+
+ +
+
+static const string PA_PROPERTIES_KEY_REGIONS = "Regions"
+
+ +
+
+static const string PA_PROPERTIES_KEY_CHANNELS = "Channels"
+
+ +
+
+static const string PA_PROPERTIES_KEY_PREVREGIONS = "PreviousRegions"
+
+ +
+
+static const string PA_PROPERTIES_KEY_PREVCHANNELS = "PreviousChannels"
+
+ +
+
+static const string PA_PROPERTIES_KEY_SWEEPS = "Sweeps"
+
+ +
+
+static const string PA_PROPERTIES_KEY_LAYOUTCHANGE = "LayoutChanged"
+
+ +
+
+static const string PA_PROPERTIES_STRLIST_SEP = ","
+
+ +
+
+static const string PA_SETINDICES_KEY_ACTIVECHANCOUNT = "ActiveChanCount"
+
+ +
+
+static const string PA_SETINDICES_KEY_ACTIVEREGIONCOUNT = "ActiveRegionCount"
+
+ +
+
+static const string PA_SETINDICES_KEY_DISPCHANGE = "DisplayChange"
+
+ +
+
+static const string PA_SETINDICES_KEY_DISPSTART = "DisplayStart"
+
+ +
+
+static const double PA_UPDATEINDICES_TYPE_PREV = 1
+
+ +
+
+static const double PA_UPDATEINDICES_TYPE_CURR = 2
+
+ +
+
+static const double PA_INDICESCHANGE_NONE = 0
+
+ +
+
+static const double PA_INDICESCHANGE_MOVED = 1
+
+ +
+
+static const double PA_INDICESCHANGE_REMOVED = 2
+
+ +
+
+static const double PA_INDICESCHANGE_ADDED = 3
+
+ +
+
+static const double PA_PASIINIT_BASE = 0x01
+
+ +
+
+static const double PA_PASIINIT_INDICEMETA = 0x02
+
+ +
+
+static const double PA_MINIMUM_SPIKE_WIDTH = 0.2
+
+ +
+
+
+struct PA_ConstantSettings
+

Helper structure to store the constantness of various categories of settings.

+
+

Public Members

+
+
+variable singlePulse
+
+ +
+
+variable traces
+
+ +
+
+variable images
+
+ +
+
+variable failedPulses
+
+ +
+
+variable dontResetWaves
+
+ +
+
+variable multipleGraphs
+
+ +
+
+variable showAverage
+
+ +
+
+variable deconvolution
+
+ +
+
+variable hideFailedPulses
+
+ +
+
+variable showIndividualPulses
+
+ +
+
+variable showTraces
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___repeated_acquisition_8ipf.html b/file/_m_i_e_s___repeated_acquisition_8ipf.html new file mode 100644 index 0000000000..89dbcbc166 --- /dev/null +++ b/file/_m_i_e_s___repeated_acquisition_8ipf.html @@ -0,0 +1,443 @@ + + + + + + + + File MIES_RepeatedAcquisition.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_RepeatedAcquisition.ipf

+

comment in to enable repeated acquisition performance measurement code

+

RA Repated acquisition functionality

+
+

Functions

+
+
+static variable RA_RecalculateITI(string device)
+

Recalculate the Inter trial interval (ITI) for the given device.

+
+ +
+
+static variable RA_HandleITI_MD(string device)
+
+ +
+
+static variable RA_WaitUntiIITIDone(string device, variable elapsedTime)
+
+ +
+
+static variable RA_HandleITI(string device)
+
+ +
+
+static variable RA_GetTotalNumberOfSweeps(string device)
+

Calculate the total number of sweeps for repeated acquisition.

+
+ +
+
+variable RA_StepSweepsRemaining(string device)
+

Update the “Sweeps remaining” control.

+
+ +
+
+static variable RA_Start(string device)
+

Function gets called after the first sweep is already acquired and if repeated acquisition is on.

+
+ +
+
+variable RA_Counter(string device)
+
+ +
+
+static variable RA_FinishAcquisition(string device)
+
+ +
+
+static variable RA_BckgTPwithCallToRACounter(string device)
+
+ +
+
+static variable RA_StartMD(string device)
+
+ +
+
+variable RA_CounterMD(string device)
+
+ +
+
+static variable RA_BckgTPwithCallToRACounterMD(string device)
+
+ +
+
+variable RA_IsFirstSweep(string device)
+

Return one if we are acquiring currently the very first sweep of a possible repeated acquisition cycle. Zero means that we acquire a later sweep than the first one in a repeated acquisition cycle.

+
+ +
+
+variable RA_SkipSweeps(string device, variable skipCount, variable source, variable limitToSetBorder = defaultValue)
+

Allows skipping forward or backwards the sweep count during data acquistion.

+
+
Parameters:
+
    +

  • device – device

    • +

  • skipCount – The number of sweeps to skip (forward or backwards) during repeated acquisition

    • +

  • source – One of SkipSweepOptions

    • +

  • limitToSetBorder – [optional, defaults to false] Limits skipCount so that we don’t skip further than after the last sweep of the stimset with the most number of sweeps.

    • +
+
+
+
+ +
+
+static variable RA_DocumentSweepSkipping(string device, variable skipCount, variable source)
+

Document the number of skipped sweeps.

+
+ +
+
+static variable RA_SkipSweepCalc(string device, variable skipCount)
+

Returns valid count after adding skipCount.

+
+
Parameters:
+
    +

  • device – device

    • +

  • skipCount – The number of sweeps to skip (forward or backwards) during repeated acquisition.

    • +
+
+
+
+ +
+
+static variable RA_PerfInitialize(string device)
+
+ +
+
+static variable RA_PerfAddMark(string device, variable idx)
+
+ +
+
+static variable RA_PerfFinish(string device)
+
+ +
+
+variable RA_ContinueOrStop(string device, variable multiDevice = defaultValue)
+

Continue DAQ if requested or stop it.

+
+
Parameters:
+
    +

  • device – device

    • +

  • multiDevice – [optional, defaults to false] DAQ mode

    • +
+
+
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___sampling_interval_8ipf.html b/file/_m_i_e_s___sampling_interval_8ipf.html new file mode 100644 index 0000000000..e64001cfa9 --- /dev/null +++ b/file/_m_i_e_s___sampling_interval_8ipf.html @@ -0,0 +1,441 @@ + + + + + + + + File MIES_SamplingInterval.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_SamplingInterval.ipf

+

SI Routines for calculating and handling the minimum sampling interval

+
+

Functions

+
+
+static variable SI_FillITCConfig(wave wv, wave results, variable idx, variable totalNumDA, variable totalNumAD, variable totalNumTTL)
+

Fill the passed wave to be used as DAQConfigWave.

+
+ +
+
+static variable SI_FillITCConfigWithPerms(wave wv, variable start, variable value, variable channelType)
+

Fill the passed wave to be used as DAQConfigWave for the exhaustive search.

+
+ +
+
+static variable SI_CompressWave(wave wv)
+

Removes invalid and duplicated entries from the generated table from SI_CreateLookupWave.

+
+ +
+
+static variable SI_SortWave(wave wv)
+

Sort the lookup wave.

+
+ +
+
+static variable SI_FindMatchingTableEntry(wave wv, ActiveChannels *ac)
+

Search the given active channel combination in the lookup wave.

+
+ +
+
+static wave SI_LoadMinSampIntFromDisk(string deviceType)
+

Try to load the lookup wave for the minimum sampling interval from disk for the given deviceType.

+
+
Returns:
+

a lookup wave or an invalid wave ref if it could not be loaded from disk

+
+
+
+ +
+
+wave SI_StoreMinSampIntOnDisk(wave wv, string deviceType)
+

Store the lookup wave on disc.

+
+ +
+
+static variable SI_FillActiveChannelsStruct(string device, ActiveChannels *ac)
+

Query the DA_EPhys panel for the active channels and fill it in the passed structure.

+
+
Returns:
+

number of active channels

+
+
+
+ +
+
+variable SI_CreateLookupWave(string device, variable ignoreChannelOrder = defaultValue)
+
+ +
+
+static variable SI_TestSampInt(string device)
+
+ +
+
+variable SI_CalculateMinSampInterval(string device, variable dataAcqOrTP, variable channelType)
+

Calculate the minimum sampling interval.

+

+

See also

+

XopChannelConstants

+
+

+
+
Parameters:
+
+
+
Returns:
+

sampling interval in microseconds (1e-6)

+
+
+
+ +
+
+static variable SI_NI_CalculateMinSampInterval(string device)
+

Calculate the minimum sampling interval for NI hardware.

+

+

See also

+

SI_CalculateMinSampInterval

+
+

+
+
Returns:
+

sampling interval in microseconds (1e-6)

+
+
+
+ +
+
+static variable SI_ITC_CalculateMinSampInterval(string device, variable dataAcqOrTP)
+

Calculate the minimum sampling interval for ITC hardware using the lookup waves on disk.

+

+

See also

+

SI_CalculateMinSampInterval

+
+

+
+
Parameters:
+
+
+
Returns:
+

sampling interval in microseconds (1e-6)

+
+
+
+ +
+
+static wave SI_GetMinSampIntWave(string device)
+

Return a wave ref with the lookup wave for the sampling interval.

+

This functions tries to load the wave from disk on the first call so this function might take a while to execute.

+
+ +
+
+

Variables

+
+
+static const double MIN_CONSECUTIVE_SAMPINT = 6
+

The consecutive check in SI_TestSampInt enforces not only one sucessfull sampling interval but also the multiples 2^x where x ranges from 1 to MIN_CONSECUTIVE_SAMPINT Set to 0 to deactivate

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___stimset_a_p_i_8ipf.html b/file/_m_i_e_s___stimset_a_p_i_8ipf.html new file mode 100644 index 0000000000..b402afb034 --- /dev/null +++ b/file/_m_i_e_s___stimset_a_p_i_8ipf.html @@ -0,0 +1,384 @@ + + + + + + + + File MIES_StimsetAPI.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_StimsetAPI.ipf

+

ST Stimulus set API

+
+

Functions for manipulating stimulus sets

+
+
+string ST_GetStimsetList(variable channelType = defaultValue, string searchString = defaultValue, string *WBstimSetList = defaultValue, string *thirdPartyStimSetList = defaultValue)
+

Return a sorted list of all DA/TTL stim set waves.

+
+
Parameters:
+
    +

  • channelType – [in] [optional, defaults to all] CHANNEL_TYPE_DAC or CHANNEL_TYPE_TTL

    • +

  • searchString – [in] [optional, defaults to “*”] search string in wildcard syntax

    • +

  • WBstimSetList – [out] [optional] returns the list of stim sets built with the wavebuilder

    • +

  • thirdPartyStimSetList – [out] [optional] returns the list of third party stim sets not built with the wavebuilder

    • +
+
+
+
+ +
+
+string ST_CreateStimSet(string baseName, variable stimulusType, variable setNumber = defaultValue, variable saveAsBuiltin = defaultValue)
+

Create a new stimset with one square pulse epoch with 1ms duration.

+
+
Parameters:
+
    +

  • baseName – user choosable part of the stimset name

    • +

  • stimulusType – one of CHANNEL_TYPE_DAC or CHANNEL_TYPE_TTL

    • +

  • setNumber – [optional, defaults to 0] stimset number, allows for convenient alphabetic increasing names used in indexing

    • +

  • saveAsBuiltin – [optional, defaults to false] allows to create builtin stimsets when enabled

    • +
+
+
+
+ +
+
+variable ST_RemoveStimSet(string setName)
+

Remove the given stimulus set and update all relevant GUIs.

+
+ +
+
+wave ST_GetStimsetParameters(string setName, variable epochType = defaultValue)
+

Returns the available stimsets parameters.

+

Return the epoch-independent parameters when epochType is not present.

+
+ +
+
+variable ST_GetStimsetParameterAsVariable(string setName, string entry, variable epochIndex = defaultValue)
+

Return the given stimset numeric parameter.

+
+
Parameters:
+
    +

  • setName – name of the stimset

    • +

  • entry – name of the parameter, can be global or epoch

    • +

  • epochIndex – [optional, when not given this sets global parameters] epoch index (0-based)

    • +
+
+
+
+ +
+
+string ST_GetStimsetParameterAsString(string setName, string entry, variable epochIndex = defaultValue)
+

Return the given stimset string parameter.

+
+
Parameters:
+
    +

  • setName – name of the stimset

    • +

  • entry – name of the parameter, can be global or epoch

    • +

  • epochIndex – [optional, when not given this sets global parameters] epoch index (0-based)

    • +
+
+
+
+ +
+
+variable ST_SetStimsetParameter(string setName, string entry, variable epochIndex = defaultValue, variable var = defaultValue, string str = defaultValue)
+

Set the given stimset parameter.

+

If you use this function in analysis functions be sure to use an event which happens before the stimset is read, for example PRE_DAQ_EVENT, PRE_SET_EVENT or PRE_SWEEP_CONFIG_EVENT. The last one is always called for each sweep before it is configured.

+
+
Parameters:
+
    +

  • setName – name of the stimset

    • +

  • entry – name of the parameter, can be global or epoch

    • +

  • epochIndex – [optional, when not given this sets global parameters] epoch index (0-based)

    • +

  • var – [optional, one of var/str must be present] numeric parameter to set

    • +

  • str – [optional, one of var/str must be present] string parameter to set

    • +
+
+
Returns:
+

0 on success, 1 on error

+
+
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___structures_8ipf.html b/file/_m_i_e_s___structures_8ipf.html new file mode 100644 index 0000000000..3881cbf920 --- /dev/null +++ b/file/_m_i_e_s___structures_8ipf.html @@ -0,0 +1,2095 @@ + + + + + + + + File MIES_Structures.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Structures.ipf

+

All non-static structures together with their initialization routines are defined here.

+
+

Functions

+
+
+variable InitPulseAverageSettings(PulseAverageSettings *pa)
+
+ +
+
+variable InitFormulaProperties(FormulaProperties *fp)
+
+ +
+
+variable InitOOdDAQParams(OOdDAQParams *params, WaveRefWave stimSets, wave setColumns, variable preFeatureTime, variable postFeatureTime)
+
+ +
+
+variable InitDeltaControlNames(DeltaControlNames *s)
+
+ +
+
+variable InitRectD(RectD *s)
+
+ +
+
+variable InitBufferedDrawInfo(BufferedDrawInfo *s)
+

initializes a BufferedDrawInfo structure The json path for AppendTracesToGraph and Labels is set empty by default

+

+

See also

+

TiledGraphAccelerateDraw

+
+

+
+ +
+
+variable NWB_ASYNC_SerializeStruct(NWBAsyncParameters *s, dfref threadDFR)
+
+ +
+
+std::tuple<NWBAsyncParameters> NWB_ASYNC_DeserializeStruct(dfref threadDFR)
+
+ +
+
+
+struct BackgroundStruct
+
+

Public Members

+
+
+WMBackgroundStruct wmbs
+
+ +
+
+int32 count
+

Number of invocations of background function.

+
+ +
+
+int32 threadDeadCount
+

DAQ/TP-MD with ITC hardware only: Number of successive tries to get data from the thread.

+
+ +
+
+variable tickslastReceivedFifoPos
+

DAQ-MD with ITC hardware only: ticks count when the fifo position was last updated.

+
+ +
+
+variable lastReceivedFifoPos
+

DAQ-MD with ITC hardware only: last received fifo position.

+
+ +
+
+ +
+
+struct PostPlotSettings
+
+

Trace averaging settings

+
+
+variable averageTraces
+
+ +
+
+DFREF averageDataFolder
+
+ +
+
+

Time alignment settings

+
+
+variable timeAlignment
+
+ +
+
+variable timeAlignMode
+
+ +
+
+string timeAlignRefTrace
+
+ +
+
+variable timeAlignLevel
+
+ +
+
+

Public Members

+
+
+variable hideSweep
+
+ +
+
+variable zeroTraces
+

Zero traces settings.

+
+ +
+
+variable visualizeEpochs
+
+ +
+
+PulseAverageSettings pulseAverSett
+
+ +
+
+ +
+
+struct PulseAverageSettings
+
+

Time alignment settings

+
+
+variable startingPulse
+

These settings influence the extracted single pulse waves, see also PA_GenerateAllPulseWaves().

+
+ +
+
+variable endingPulse
+
+ +
+
+variable overridePulseLength
+
+ +
+
+variable fixedPulseLength
+
+ +
+
+

Public Members

+
+
+variable showIndividualPulses
+
+ +
+
+variable showAverage
+
+ +
+
+variable regionSlider
+
+ +
+
+variable multipleGraphs
+
+ +
+
+variable zeroPulses
+
+ +
+
+variable autoTimeAlignment
+
+ +
+
+variable enabled
+
+ +
+
+variable hideFailedPulses
+
+ +
+
+variable searchFailedPulses
+
+ +
+
+variable failedPulsesLevel
+
+ +
+
+variable failedNumberOfSpikes
+
+ +
+
+variable yScaleBarLength
+
+ +
+
+variable showImages
+
+ +
+
+variable showTraces
+
+ +
+
+variable drawXZeroLine
+
+ +
+
+variable pulseSortOrder
+
+ +
+
+string imageColorScale
+
+ +
+
+DFREF dfr
+
+ +
+
+PulseAverageDeconvSettings deconvolution
+
+ +
+
+ +
+
+struct PulseAverageDeconvSettings
+
+

Public Members

+
+
+variable enable
+
+ +
+
+variable smth
+
+ +
+
+variable tau
+
+ +
+
+variable range
+
+ +
+
+ +
+
+struct PulseAverageSetIndices
+
+

Public Members

+
+
+WaveRefWave setIndices
+
+ +
+
+WaveRefWave setIndicesUnsorted
+
+ +
+
+WaveRefWave setWaves2Unsorted
+
+ +
+
+WAVE properties
+
+ +
+
+WaveRefWave propertiesWaves
+
+ +
+
+WaveRefWave axesNames
+
+ +
+
+WAVE ovlTracesAvg
+
+ +
+
+WAVE ovlTracesDeconv
+
+ +
+
+WAVE imageAvgDataPresent
+
+ +
+
+WAVE imageDeconvDataPresent
+
+ +
+
+DFREF pulseAverageHelperDFR
+
+ +
+
+DFREF pulseAverageDFR
+
+ +
+
+WAVE channels
+
+ +
+
+WAVE regions
+
+ +
+
+WAVE numEntries
+
+ +
+
+WAVE startEntry
+
+ +
+
+WAVE indexHelper
+
+ +
+
+ +
+
+struct TiledGraphSettings
+

Parameter to CreateTiledChannelGraph.

+
+

Public Members

+
+
+int16 displayDAC
+
+ +
+
+int16 displayADC
+
+ +
+
+int16 displayTTL
+
+ +
+
+int16 splitTTLBits
+
+ +
+
+int16 overlaySweep
+
+ +
+
+int16 overlayChannels
+
+ +
+
+int16 dDAQDisplayMode
+
+ +
+
+int16 dDAQHeadstageRegions
+
+ +
+
+int16 hideSweep
+
+ +
+
+int16 visualizeEpochs
+
+ +
+
+ +
+
+struct FormulaProperties
+

Helper structure for formula parsing of the Wavebuilder combine epoch.

+
+

Public Members

+
+
+string formula
+
+ +
+
+string stimsetList
+
+ +
+
+variable numRows
+
+ +
+
+variable numCols
+
+ +
+
+ +
+
+struct WaveLocationMod
+

Helper structure for UpgradeWaveLocationAndGetIt()

+
+

Public Members

+
+
+DFREF dfr
+

former location of the wave

+
+ +
+
+DFREF newDFR
+

new location of the wave (can be invalid)

+
+ +
+
+string name
+

former name of the wave

+
+ +
+
+string newName
+

new name of the wave (can be null/empty)

+
+ +
+
+ +
+
+struct OOdDAQParams
+

Helper structure for Optimized overlap distributed acquisition (oodDAQ) functions.

+
+

Input

+
+
+WaveRefWave stimSets
+

Wave ref wave with different stimsets.

+
+ +
+
+WAVE setColumns
+

Set (aka column) to use for each stimset.

+
+ +
+
+variable preFeaturePoints
+

Time in points which should be kept signal-free before features.

+
+ +
+
+variable postFeaturePoints
+

Time in points which should be kept signal-free after features.

+
+ +
+
+

Output

+

+
+
+WAVE offsets
+

Result of the optimization in points.

+
+ +
+
+WaveText regions
+

the smeared regions in units of time of the DAQDataWave.

+

List of the form begin-end;... which denotes the x-coordinates of

+

See also

+

OOD_GetFeatureRegions()

+
+

+
+ +
+
+ +
+
+struct AnalysisFunction_V3
+

The structure passed into V3 and later analysis functions.

+
+

Public Members

+
+
+variable eventType
+

one of EVENT_TYPE_ANALYSIS_FUNCTIONS

+
+ +
+
+WaveRefWave scaledDACWave
+

scaled and undecimated data from the DAC hardware, wave ref wave where each element is a channel wave. Channels are in the same order as the config wave rows.

+
+ +
+
+variable headStage
+

active headstage index, [0, NUM_HEADSTAGES[

+
+ +
+
+variable sweepNo
+

Potential future number of the sweep. Once the sweep is finished it will be saved with this number. Use GetSweepWave() to query the sweep itself.

+
+ +
+
+variable sweepsInSet
+

Number of sweeps in the currently acquired stimset of the passed headstage.

+
+ +
+
+string params
+

Analysis function parameters set in the stimset’s textual parameter wave. Settable via AFH_AddAnalysisParameter().

+
+ +
+
+variable lastValidRowIndexDA
+

last valid row index for DA channels in rawDAQWave which will be filled with data at the end of DAQ. If the acquisition was aborted, the remaining samples beyond lastValidRowIndexDA are NaN. The total number of rows in rawDAQWave might be higher due to alignment requirements of the data acquisition hardware (e.g. ITC).

+

Always NaN for PRE_DAQ_EVENT/PRE_SET_EVENT events.

+
+ +
+
+variable lastValidRowIndexAD
+

last valid row index for AD/TTL channels in rawDAQWave which will be filled with data at the end of DAQ. The total number of rows in rawDAQWave might be higher due to alignment requirements of the data acquisition hardware (e.g. ITC).

+

Always NaN for PRE_DAQ_EVENT/PRE_SET_EVENT events.

+
+ +
+
+variable lastKnownRowIndexDA
+

last written row index in rawDAQWave/scaledDACWaves DA channel(s) with already acquired data

+

Always NaN for PRE_DAQ_EVENT/PRE_SET_EVENT/PRE_SWEEP_CONFIG_EVENT.

+
+ +
+
+variable lastKnownRowIndexAD
+

last written row index in rawDAQWave/scaledDACWaves AD/TTL channel(s) with already acquired data

+

Always NaN for PRE_DAQ_EVENT/PRE_SET_EVENT/PRE_SWEEP_CONFIG_EVENT.

+
+ +
+
+variable sampleIntervalDA
+

sample interval of DA channel(s) in ms

+
+ +
+
+variable sampleIntervalAD
+

sample interval of AD channel(s) in ms

+
+ +
+
+ +
+
+struct DeltaControlNames
+

Helper structure for WB_GetDeltaDimLabel()

+
+

Public Members

+
+
+string main
+
+ +
+
+string delta
+
+ +
+
+string dme
+
+ +
+
+string op
+
+ +
+
+string ldelta
+
+ +
+
+ +
+
+struct TPAnalysisInput
+

Helper structure for TP data transfer to analysis.

+
+

Public Members

+
+
+WAVE data
+
+ +
+
+variable clampAmp
+
+ +
+
+variable clampMode
+
+ +
+
+variable duration
+
+ +
+
+variable baselineFrac
+
+ +
+
+variable tpLengthPoints
+
+ +
+
+variable readTimeStamp
+
+ +
+
+variable hsIndex
+
+ +
+
+string device
+
+ +
+
+variable measurementMarker
+
+ +
+
+variable activeADCs
+
+ +
+
+ +
+
+struct RectD
+

Helper structure for GetPlotArea()

+
+

Public Members

+
+
+double top
+
+ +
+
+double left
+
+ +
+
+double bottom
+
+ +
+
+double right
+
+ +
+
+ +
+
+struct HardwareDataTPInput
+

Helper structure for CA_HardwareDataTPKey()

+
+

Public Members

+
+
+variable hardwareType
+
+ +
+
+variable numDACs
+
+ +
+
+variable numActiveChannels
+
+ +
+
+variable numberOfRows
+
+ +
+
+variable samplingInterval
+
+ +
+
+WAVE gains
+
+ +
+
+WAVE DACAmpTP
+
+ +
+
+variable testPulseLength
+
+ +
+
+variable baselineFrac
+
+ +
+
+ +
+
+struct BufferedDrawInfo
+

Stores information for buffered draw jsonID - stores information about traces and labels to draw/setup traceWaves - wave ref wave with references to the trace waves (which are always non-free)

+
+

Public Members

+
+
+variable jsonID
+
+ +
+
+WaveRefWave traceWaves
+
+ +
+
+ +
+
+struct ChirpBoundsInfo
+

Helper strucuture for PSQ_CR_DetermineBoundsState()

+
+

Public Members

+
+
+variable minimumFac
+
+ +
+
+variable centerFac
+
+ +
+
+variable maximumFac
+
+ +
+
+string state
+
+ +
+
+ +
+
+struct NWBAsyncParameters
+

Helper structure for the ASYNC NWB writing during DAQ.

+

+

See also

+

NWB_ASYNC_SerializeStruct() and NWB_ASYNC_DeserializeStruct()

+
+

+
+

Public Members

+
+
+string device
+
+ +
+
+string userComment
+
+ +
+
+string nwbFilePath
+
+ +
+
+variable sweep
+
+ +
+
+variable compressionMode
+
+ +
+
+variable session_start_time
+
+ +
+
+variable locationID
+
+ +
+
+variable nwbVersion
+
+ +
+
+WAVE DAQDataWave
+
+ +
+
+WAVE DAQConfigWave
+
+ +
+
+WAVE numericalValues
+
+ +
+
+WaveText numericalKeys
+
+ +
+
+WaveText textualValues
+
+ +
+
+WaveText textualKeys
+
+ +
+
+WAVE numericalResultsValues
+
+ +
+
+WaveText numericalResultsKeys
+
+ +
+
+WaveText textualResultsValues
+
+ +
+
+WaveText textualResultsKeys
+
+ +
+
+ +
+
+struct DataConfigurationResult
+

Structure to hold the result of data configuration from DC_GetConfiguration()

+
+

Unnamed Group

+
+
+variable globalTPInsert
+

Various GUI settings

+
+ +
+
+variable scalingZero
+
+ +
+
+variable indexingLocked
+
+ +
+
+variable indexing
+
+ +
+
+variable distributedDAQ
+
+ +
+
+variable distributedDAQOptOv
+
+ +
+
+variable distributedDAQOptPre
+
+ +
+
+variable distributedDAQOptPost
+
+ +
+
+variable multiDevice
+
+ +
+
+variable powerSpectrum
+
+ +
+
+WAVE statusHS
+
+ +
+
+

Various delays in points of the DA data wave

+
+
+variable onsetDelayUser
+
+ +
+
+variable onsetDelayAuto
+
+ +
+
+variable onsetDelay
+

Sum of onsetDelayUser and onsetDelayAuto.

+
+ +
+
+variable distributedDAQDelay
+
+ +
+
+variable terminationDelay
+
+ +
+
+

Unnamed Group

+
+
+WAVE offsets
+

[ms]

+

oodDAQ optimization results, see OOdDAQParams_Output

+
+ +
+
+WaveText regions
+
+ +
+
+

Unnamed Group

+
+
+WAVE DACList
+

List of active channels per type

+
+ +
+
+WAVE ADCList
+
+ +
+
+WAVE TTLList
+
+ +
+
+

Unnamed Group

+
+
+WaveDouble DACAmp
+

All waves here use active channel indexing like DataConfigurationResult::DACList and can thus be all indexed together.

+

+

See also

+

GetDACAmplitudes()

+
+

+
+ +
+
+WaveText setName
+

Stimulus set name.

+
+ +
+
+WaveText TTLsetName
+
+ +
+
+WaveRefWave stimSet
+

Stimulus set wave (2D)

+
+ +
+
+WaveRefWave TTLstimSet
+
+ +
+
+WaveDouble setLength
+

+

See also

+

DC_CalculateStimsetLength()

+
+

+
+ +
+
+WaveDouble TTLsetLength
+
+ +
+
+WaveDouble headstageDAC
+

Headstage of DAC if associated, NaN iff unassociated.

+
+ +
+
+WaveDouble setColumn
+

+

See also

+

DC_CalculateChannelColumnNo()

+
+

+
+ +
+
+WaveDouble TTLsetColumn
+
+ +
+
+WaveDouble setCycleCount
+
+ +
+
+WaveDouble TTLcycleCount
+
+ +
+
+

Public Members

+
+
+variable dataAcqOrTP
+

What type of operation is done. Either DAQ(DATA_ACQUISITION_MODE) or TP(TEST_PULSE_MODE)

+
+ +
+
+variable baselineFrac
+

+

See also

+

GetTestpulseBaselineFraction()

+
+

+
+ +
+
+variable decimationFactor
+

+

See also

+

DC_GetDecimationFactor()

+
+

+
+ +
+
+variable numDACEntries
+

Number of DAC’s, always larger than 0.

+
+ +
+
+variable numADCEntries
+

Number of ADC’s, always larger than 0.

+
+ +
+
+variable numTTLEntries
+

Number of TTLs, can be zero.

+
+ +
+
+variable numActiveChannels
+

Sum of numDACEntries/numADCEntries/numTTLEntries.

+
+ +
+
+variable hardwareType
+

One of HardwareDACTypeConstants.

+
+ +
+
+variable samplingIntervalDA
+

Sampling interval for DA channels in μs,.

+

+

See also

+

DAP_GetSampInt()

+
+

+
+ +
+
+variable samplingIntervalAD
+

Sampling interval for AD channels in μs,.

+

+

See also

+

DAP_GetSampInt()

+
+

+
+ +
+
+variable samplingIntervalTTL
+

Sampling interval for TTL channels in μs,.

+

+

See also

+

DAP_GetSampInt()

+
+

+
+ +
+
+WAVE testPulse
+

+

See also

+

GetTestPulse()

+
+

+
+ +
+
+variable testPulseLength
+

Length of the DataConfigurationResult::testPulse wave in points test pulse properties from TP_GetCreationPropertiesInPoints

+
+ +
+
+variable tpPulseStartPoint
+
+ +
+
+variable tpPulseLengthPoints
+
+ +
+
+WAVE gains
+

+

See also

+

SWS_GetChannelGains() with GAIN_BEFORE_DAQ

+
+

+
+ +
+
+WaveDouble insertStart
+

Offset in points where the stimulus set starts in the DAQ data wave.

+
+ +
+
+WaveDouble headstageADC
+

Headstage of ADC if associated, NaN iff unassociated Uses active channel indexing like DataConfigurationResult::ADCList

+
+ +
+
+variable skipAhead
+

Number of sweeps to skip over on start of data acquisition.

+
+ +
+
+variable stopCollectionPoint
+

Maximum number of samples that can be acquired to the data wave For ITC can be higher that planned samples to be acquired (no automatic stop, only programmatic)

+
+ +
+
+variable joinedTTLStimsetSize
+

for ITC, TTL stimset size in DC after TTL stimsets were bit-combined to a joined wave fixing https://github.com/AllenInstitute/MIES/issues/2007 should remove the need for this

+
+ +
+
+WAVE statusTTLFiltered
+

wave indexing GUI TTL channels, 1 - activated, 0 deactivated

+
+ +
+
+ +
+
+struct ActiveChannels
+

Helper struct for storing the number of active channels per rack.

+
+

Public Members

+
+
+int32 numDARack1
+
+ +
+
+int32 numADRack1
+
+ +
+
+int32 numTTLRack1
+
+ +
+
+int32 numDARack2
+
+ +
+
+int32 numADRack2
+
+ +
+
+int32 numTTLRack2
+
+ +
+
+ +
+
+struct PSQ_PulseSettings
+

Settings structure filled by PSQ_GetPulseSettingsForType()

+
+

Public Members

+
+
+variable prePulseChunkLength
+
+ +
+
+variable pulseDuration
+
+ +
+
+variable postPulseChunkLength
+
+ +
+
+variable usesBaselineChunkEpochs
+

Allows to define the baseline chunks by user epochs with shortname U_BLSd other members are ignored with this option. The baseline chunks should be added in PRE_SWEEP_CONFIG_EVENT.

+
+ +
+
+ +
+
+struct CheckParametersStruct
+
+

Public Members

+
+
+string params
+
+ +
+
+string setName
+
+ +
+
+ +
+
+struct SF_PlotMetaData
+

Helper struct for data gathered by SF formula plotter in SF_GatherFormulaResults.

+
+

Public Members

+
+
+string dataType
+
+ +
+
+string opStack
+
+ +
+
+string argSetupStack
+
+ +
+
+string xAxisLabel
+
+ +
+
+string yAxisLabel
+
+ +
+
+ +
+
+struct ASYNC_ReadOutStruct
+

ReadOut Structure for ASYNC.

+
+

Public Members

+
+
+DFREF dfr
+
+ +
+
+variable rtErr
+
+ +
+
+string rtErrMsg
+
+ +
+
+variable abortCode
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___sweep_formula_8ipf.html b/file/_m_i_e_s___sweep_formula_8ipf.html new file mode 100644 index 0000000000..9260ed9eb5 --- /dev/null +++ b/file/_m_i_e_s___sweep_formula_8ipf.html @@ -0,0 +1,2209 @@ + + + + + + + + File MIES_SweepFormula.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_SweepFormula.ipf

+

SF Sweep formula allows to do analysis on sweeps with a dedicated formula language

+
+

Functions

+
+
+variable SF_BringBrowserToFront()
+
+ +
+
+wave SF_GetNamedOperations()
+
+ +
+
+wave SF_GetFormulaKeywords()
+
+ +
+
+static string SF_StringifyState(variable state)
+
+ +
+
+static string SF_StringifyAction(variable action)
+
+ +
+
+static variable SF_FormulaParser(string formula, variable *createdArray = defaultValue, variable indentLevel = defaultValue)
+

serialize a string formula into JSON

+
+
Parameters:
+
    +

  • formula – string formula

    • +

  • createdArray – [optional, default 0] set on recursive calls, returns boolean if parser created a JSON array

    • +

  • indentLevel – [internal use only] recursive call level, used for debug output

    • +
+
+
Returns:
+

a JSONid representation

+
+
+
+ +
+
+static variable SF_ParserHandleRemainingBuffer(variable jsonId, string jsonPath, string formula, string buffer)
+
+ +
+
+static std::tuple<variable, string, variable, variable, variable> SF_ParserModifyJSON(variable action, variable lastAction, variable state, string buffer, string token, variable indentLevel)
+
+ +
+
+static std::tuple<variable, variable, variable> SF_ParserGetActionFromState(variable jsonId, variable state, variable lastCalculation, variable bufferIsEmpty)
+
+ +
+
+static std::tuple<variable, variable, variable> SF_ParserGetStateFromToken(string token, variable jsonId, string buffer)
+
+ +
+
+static std::tuple<string, string> SF_ParserEvaluatePossibleSign(variable jsonId, variable indentLevel)
+
+ +
+
+static variable SF_ParserAddJSON(variable jsonId, string jsonPath, string formula, variable indentLevel)
+
+ +
+
+static string SF_ParserInsertNegation(variable jsonId, string jsonPath, variable indentLevel)
+
+ +
+
+static string SF_ParserAdaptSubPath(variable jsonId, string jsonPath, string subPath)
+
+ +
+
+static variable SF_FPPutInArrayAtPath(variable subId, string jsonPath)
+

Create a new empty array object, add mainId into it at path and return created json, release subId.

+
+ +
+
+static variable SF_FPAddArray(variable mainId, string jsonPath, variable subId, variable arrayWasCreated)
+

Adds subId to mainId, if necessary puts subId into an array, release subId.

+
+ +
+
+static string SF_EscapeJsonPath(string str)
+

add escape characters to a path element

+
+ +
+
+static variable SF_PlaceSubArrayAt(WaveOrNull out, WaveOrNull subArray, variable index)
+
+ +
+
+static wave SF_FormulaExecutorStringOrVariable(string graph, variable jsonId, string jsonPath)
+
+ +
+
+static std::tuple<WaveRefWave, SF_PlotMetaData> SF_GatherFormulaResults(string xFormula, string yFormula, string graph)
+
+ +
+
+static string SF_GetAnnotationPrefix(string dataType)
+
+ +
+
+static string SF_GetTraceAnnotationText(SF_PlotMetaData *plotMetaData, wave data)
+
+ +
+
+static string SF_GetMetaDataAnnotationText(SF_PlotMetaData *plotMetaData, wave data, string traceName)
+
+ +
+
+std::tuple<RGBColor> SF_GetTraceColor(string graph, string opStack, wave data)
+
+ +
+
+static std::tuple<WaveText, variable> SF_CreateTraceNames(variable numTraces, variable dataNum, SF_PlotMetaData *plotMetaData, wave data)
+

Generate numTraces trace names for the given input.

+

Generates the trace names required for a single formula in the plotter and therefore the trace names range from traceCnt to traceCnt + numTraces - 1.

+
+
Return values:
+
    +

  • traces – generated trace names

    • +

  • traceCnt – total count of all traces (input and output)

    • +
+
+
+
+ +
+
+static string SF_ShrinkLegend(string annotation)
+

Reduces a multi line legend to a single line if only the sweep number changes. Returns the original annotation if more changes or the legend text does not follow the exected format

+
+ +
+
+static std::tuple<WaveText, WaveRefWave> SF_PreparePlotter(string winNameTemplate, string graph, variable winDisplayMode, variable numGraphs)
+
+ +
+
+static variable SF_CommonWindowSetup(string win, string graph)
+
+ +
+
+static wave SF_GatherYUnits(WaveRefWave formulaResults, string explicitLbl, WaveTextOrNull yUnits)
+
+ +
+
+static string SF_CombineYUnits(WaveText units)
+
+ +
+
+static variable SF_CheckNumTraces(string graph, variable numTraces)
+
+ +
+
+static variable SF_CleanUpPlotWindowsOnFail(WaveText plotGraphs)
+
+ +
+
+static variable SF_KillWorkingDF(string graph)
+
+ +
+
+static variable SF_FormulaPlotter(string graph, string formula, variable dmMode = defaultValue)
+

Plot the formula using the data from graph.

+
+
Parameters:
+
    +

  • graph – graph to pass to SF_FormulaExecutor

    • +

  • formula – formula to plot

    • +

  • dmMode – [optional, default DM_SUBWINDOWS] display mode that defines how multiple sweepformula graphs are arranged

    • +
+
+
+
+ +
+
+static variable SF_DeriveTraceDisplayMode(WaveOrNull wvX, wave wvY)
+
+ +
+
+static variable SF_GetShowLegend(wave wv)
+
+ +
+
+static variable SF_SplitPlotting(wave wv, variable dim, variable i, variable split)
+

utility function for SF_FormulaPlotter

+

split dimension dim of wave wv into slices of size split and get the starting index i

+
+ +
+
+static variable SF_FormulaWaveScaleTransfer(wave source, wave dest, variable dimSource, variable dimDest)
+

transfer the wave scaling from one wave to another

+

Note: wave scale transfer requires wave units for the first wave or second wave

+
+
Parameters:
+
    +

  • source – Wave whos scaling should get transferred

    • +

  • dest – Wave that accepts the new scaling

    • +

  • dimSource – dimension of the source wave, if SF_TRANSFER_ALL_DIMS is used then all scales and units are transferred on the same dimensions, dimDest is ignored in that case, no unit check is applied in that case

    • +

  • dimDest – dimension of the destination wave

    • +
+
+
+
+ +
+
+static wave SF_GetActiveChannelNumbersForSweeps(string graph, WaveOrNull channels, WaveOrNull sweeps, variable fromDisplayed, variable clampMode)
+

Use the labnotebook information to return the active channel numbers for a given set of sweeps.

+
+
Parameters:
+
    +

  • graph – DataBrowser or SweepBrowser reference graph

    • +

  • channels – SF_FormulaExecutor style channels() wave

    • +

  • sweeps – SF_FormulaExecutor style sweeps() wave

    • +

  • fromDisplayed – boolean variable, if set the selectdata is determined from the displayed sweeps

    • +

  • clampMode – numerical variable, sets the clamp mode considered

    • +
+
+
Returns:
+

a selectData style wave with three columns containing sweepNumber, channelType and channelNumber

+
+
+
+ +
+
+static wave SF_SortSelectData(wave selectData)
+
+ +
+
+static string SF_PreprocessInput(string formula)
+

Pre process code entered into the notebook.

+

    +

  • unify line endings to CR

    • +

  • remove comments at line ending

    • +

  • cut off last CR from back conversion with TextWaveToList

    • +
+

+
+ +
+
+static variable SF_SetStatusDisplay(string bsPanel, string errMsg, variable errState)
+
+ +
+
+variable SF_button_sweepFormula_check(WMButtonAction *ba)
+
+ +
+
+static variable SF_CheckInputCode(string code, string graph)
+

Checks input code, sets globals for jsonId and error string.

+
+ +
+
+static variable SF_ParseFormulaToJSON(string formula)
+
+ +
+
+variable SF_Update(string graph)
+
+ +
+
+variable SF_IsActive(string win)
+

checks if SweepFormula (SF) is active.

+
+ +
+
+std::tuple<string, string> SF_GetCode(string win)
+

Return the sweep formula code in raw and with all necessary preprocesssing.

+
+ +
+
+variable SF_button_sweepFormula_display(WMButtonAction *ba)
+
+ +
+
+variable SF_TabProc_Formula(WMTabControlAction *tca)
+
+ +
+
+static wave SF_FilterEpochs(WaveOrNull epochs, WaveOrNull ignoreTPs)
+
+ +
+
+static wave SF_OperationTPSS(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationTPInst(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationTPBase(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationTPFit(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationTP(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static variable SF_GetTPFitQuality(wave residuals, wave sweepData, variable beginTrail, variable endTrail)
+
+ +
+
+static wave SF_OperationTPImpl(string graph, WaveRefWave mode, WaveOrNull selectDataPreFilter, WaveOrNull ignoreTPs, string opShort)
+
+ +
+
+static wave SF_OperationEpochs(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationEpochsImpl(string graph, WaveText epochPatterns, WaveOrNull selectData, variable epType, string opShort)
+
+ +
+
+static variable SF_AssertOnMismatchedWaves(wave data0, wave data1, string opShort)
+
+ +
+
+static wave SF_OperationMinus(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationMinusImplDataSets(WaveOrNull data0, WaveOrNull data1)
+
+ +
+
+static wave SF_OperationPlus(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationPlusImplDataSets(WaveOrNull data0, WaveOrNull data1)
+
+ +
+
+static wave SF_IndexOverDataSetsForPrimitiveOperation(variable jsonId, string jsonPath, string graph, string opShort)
+
+ +
+
+static wave SF_OperationDiv(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationDivImplDataSets(WaveOrNull data0, WaveOrNull data1)
+
+ +
+
+static wave SF_OperationMult(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationMultImplDataSets(WaveOrNull data0, WaveOrNull data1)
+
+ +
+
+static wave SF_OperationRange(variable jsonId, string jsonPath, string graph)
+

range (start[, stop[, step]])

+
+ +
+
+static wave SF_OperationMin(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationMinImpl(WaveOrNull input)
+
+ +
+
+static wave SF_OperationMax(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationMaxImpl(WaveOrNull input)
+
+ +
+
+static wave SF_OperationAvg(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationAvgImplOver(WaveRefWave input, string graph, string opShort)
+
+ +
+
+static wave SF_OperationAvgImplIn(WaveOrNull input)
+
+ +
+
+static wave SF_OperationRMS(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationRMSImpl(WaveOrNull input)
+
+ +
+
+static wave SF_OperationVariance(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationVarianceImpl(WaveOrNull input)
+
+ +
+
+static wave SF_OperationStdev(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationStdevImpl(WaveOrNull input)
+
+ +
+
+static wave SF_OperationDerivative(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationDerivativeImpl(WaveOrNull input)
+
+ +
+
+static wave SF_OperationIntegrate(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationIntegrateImpl(WaveOrNull input)
+
+ +
+
+static wave SF_OperationArea(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationAreaImpl(WaveOrNull input, variable zero)
+
+ +
+
+static wave SF_OperationButterworth(variable jsonId, string jsonPath, string graph)
+

butterworth(data, lowPassCutoff, highPassCutoff, order)

+
+ +
+
+static wave SF_OperationButterworthImpl(WaveOrNull input, variable lowPassCutoff, variable highPassCutoff, variable order)
+
+ +
+
+static wave SF_OperationXValues(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationXValuesImpl(WaveOrNull input)
+
+ +
+
+static wave SF_OperationText(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationTextImpl(WaveOrNull input)
+
+ +
+
+static wave SF_OperationSetScale(variable jsonId, string jsonPath, string graph)
+

setscale(data, dim, [dimOffset, [dimDelta[, unit]]])

+
+ +
+
+static wave SF_OperationSetScaleImpl(WaveOrNull input, string dim, variable offset, variable delta, string unit)
+
+ +
+
+static wave SF_OperationWave(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationChannels(variable jsonId, string jsonPath, string graph)
+

channels([str name]+) converts a named channel from string to numbers.

+

returns [[channelName, channelNumber]+]

+
+ +
+
+static wave SF_OperationSweeps(variable jsonId, string jsonPath, string graph)
+

sweeps() returns all possible sweeps as 1d array

+
+ +
+
+static wave SF_OperationPowerSpectrum(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_PowerSpectrumRatio(WaveOrNull input, variable ratioFreq, variable deltaHz, wave fitData = defaultValue)
+
+ +
+
+variable SF_LineNoiseFit(wave w, variable x)
+
+ +
+
+static wave SF_OperationPowerSpectrumImpl(WaveOrNull input, string unit, variable cutoff, string winFunc)
+
+ +
+
+static wave SF_OperationSelect(variable jsonId, string jsonPath, string graph)
+

select([array channels, array sweeps, [string mode, [string clamp]]])

+

returns n x 3 with columns [sweepNr][channelType][channelNr]

+
+ +
+
+static wave SF_OperationData(variable jsonId, string jsonPath, string graph)
+

data(array range[, array selectData])

+

returns [sweepData][sweeps][channelTypeNumber] for all sweeps selected by selectData

+
+ +
+
+static wave SF_OperationLabnotebook(variable jsonId, string jsonPath, string graph)
+

labnotebook(string key[, array selectData [, string entrySourceType]])

+

return lab notebook key for all sweeps that belong to the channels channels

+
+ +
+
+static wave SF_OperationLabnotebookImpl(string graph, string lbnKey, WaveOrNull selectData, variable mode, string opShort)
+
+ +
+
+static wave SF_OperationLog(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static variable SF_OperationLogImpl(WaveOrNull input)
+
+ +
+
+static wave SF_OperationLog10(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationLog10Impl(WaveOrNull input)
+
+ +
+
+static wave SF_OperationCursors(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationFindLevel(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_OperationApFrequency(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static variable SF_OperationApFrequencyNormalizeOverSweeps(WaveRefWave output, variable normValue)
+
+ +
+
+static variable SF_OperationApFrequencyNormalizeOverSweepsImpl(WaveOrNull data, variable normValue)
+
+ +
+
+static wave SF_OperationApFrequencyImpl(WaveOrNull data, variable level, variable method, string yStr, string normStr, string xAxisTypeStr, variable *normOSValue, wave normMean)
+
+ +
+
+static string SF_OperationApFrequencyMethodToString(variable method)
+
+ +
+
+static variable SF_ApFrequencyInstantaneous(wave peaksAt)
+
+ +
+
+static wave SF_ApFrequencyInstantaneousPairs(wave peaksAt, variable yModeTime, variable xAxisIsCounts)
+
+ +
+
+static wave SF_OperationStore(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static wave SF_SplitCodeToGraphs(string code)
+
+ +
+
+static std::tuple<string, string> SF_SplitGraphsToFormula(string graphCode)
+
+ +
+
+static string SF_GetFormulaWinNameTemplate(string mainWindow)
+
+ +
+
+variable SF_button_sweepFormula_tofront(WMButtonAction *ba)
+
+ +
+
+static wave SF_NewChannelsWave(variable size)
+
+ +
+
+static wave SF_AverageTPFromSweep(WaveText epochMatches, wave sweepData)
+
+ +
+
+static variable SF_AverageTPFromSweepImpl(wave tpData, wave tpStart, wave sweepData, variable i)
+
+ +
+
+wave SF_GetAllOldCodeForGUI(string win)
+
+ +
+
+static wave SF_GetAllOldCode()
+
+ +
+
+variable SF_PopMenuProc_OldCode(WMPopupAction *pa)
+
+ +
+
+variable SF_SetFormula(string databrowser, string formula)
+
+ +
+
+wave SF_ExecuteFormula(string formula, string graph, variable singleResult = defaultValue, variable checkExist = defaultValue, variable useVariables = defaultValue)
+

Executes a given formula without changing the current SweepFormula notebook supports by default variable assignments does not support “with” and “and” keywords.

+
+
Parameters:
+
    +

  • formula – formula string to execute

    • +

  • graph – name of databrowser window

    • +

  • singleResult – [optional, default 0], if set then the first dataSet is retrieved from the waveRef wave and returned, the waveRef wave is disposed

    • +

  • checkExist – [optional, default 0], only valid if singleResult=1, if set then the data wave in the single dataSet retrieved must exist

    • +

  • useVariables – [optional, default 1], when not set, hint the function that the formula string contains only an expression and no variable definitions

    • +
+
+
+
+ +
+
+static variable SF_ConvertAllReturnDataToPermanent(WaveRefWave output, string win, string opShort)
+
+ +
+
+static wave SF_GetArgumentTop(variable jsonId, string jsonPath, string graph, string opShort)
+

Executes the complete arguments of the JSON and parses the resulting data to a waveRef type.

+

+
+Deprecated:
+

: executing all arguments e.g. as array in the executor poses issues as soon as data types get mixed. e.g. operation(0, A, [1, 2, 3]) fails as [0, A, [1, 2, 3]] can not be converted to an Igor wave. Thus, it is strongly recommended to parse each argument separately.

+
+ +

+
+ +
+
+static wave SFH_GetNumericVarArgs(variable jsonId, string jsonPath, string graph, string opShort)
+
+ +
+
+static wave SF_AverageDataOverSweeps(WaveRefWave input)
+
+ +
+
+static wave SF_SweepAverageHelper(WaveRefWave group)
+
+ +
+
+static variable SF_RemoveEndOfSweepNaNs(WaveOrNull input)
+
+ +
+
+static wave SF_CreatePlotFormulaDataWave()
+
+ +
+
+static variable SF_CollectTraceData(variable *index, WaveRefWave graphData, string traceName, WaveOrNull wx, wave wy)
+
+ +
+
+static std::tuple<string, string> SF_SplitVariableAssignment(string line)
+
+ +
+
+static std::tuple<WaveText, string> SF_GetVariableAssignments(string preProcCode)
+
+ +
+
+static string SF_CheckVariableAssignments(string preProcCode, variable jsonId)
+
+ +
+
+static string SF_ExecuteVariableAssignments(string graph, string preProcCode)
+
+ +
+
+dfref SF_GetBrowserDF(string graph)
+
+ +
+
+wave SF_ResolveDatasetFromJSON(variable jsonId, string jsonPath, string graph, variable argNum)
+

Executes the part of the argument part of the JSON and parses the resulting data to a waveRef type.

+
+ +
+
+static wave SF_ResolveDataset(wave input)
+
+ +
+
+string SF_GetDefaultFormula()
+
+ +
+
+wave SF_OperationMerge(variable jsonId, string jsonPath, string graph)
+
+ +
+
+wave SF_OperationDataset(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static std::tuple<WaveDouble, WaveDouble> SF_ParseFitConstraints(WaveTextOrNull constraints, variable numParameters)
+
+ +
+
+wave SF_OperationFitLine(variable jsonId, string jsonPath, string graph)
+
+ +
+
+wave SF_OperationFit(variable jsonId, string jsonPath, string graph)
+
+ +
+
+wave SF_OperationFitImpl(wave xData, wave yData, string fitFunc, wave holdWave, wave initialValues)
+
+ +
+
+static wave SF_ConvertNonFiniteElements(WaveText subArray)
+
+ +
+
+static variable SF_ConvertNonFiniteElementsImpl(string element)
+
+ +
+
+static std::tuple<WAVE, WaveText> SF_ExecutorCreateOrCheckNumeric(WaveDoubleOrNull out, WaveTextOrNull outT, variable size0, variable size1, variable size2, variable size3)
+
+ +
+
+static std::tuple<WAVE, WaveText> SF_ExecutorCreateOrCheckTextual(WaveOrNull out, WaveTextOrNull outT, variable size0, variable size1, variable size2, variable size3)
+
+ +
+
+static variable SF_FormulaPlotterExtendResultsIfCompatible(WaveRefWave formulaResults)
+

This function extends formulaResults if possible. For each result from a Y formula it is attempted to move datasets from inside an array outside in the form [dataset(1, 2), dataset(3, 4)] -> dataset([1, 3], [3, 4]) because the plotter can iterate over datasets only at the outermost occurrence. As result the inside elements may be plottable after this transformation. algorithm details: Each Y formula result is ‘repackaged’ in an array and attempted to be transformed Case 1: On a failed transformation the initial array is returned. Case 2: On a successful transformation a dataset with one or more elements is returned Regarding the plotter the array of case 1 is treated as a single dataset. All the results from case 1 and case 2 are gathered in a waveref wave collectY. The X formula results are associated multiple times for case 2 if multiple datasets were returned and are gathered in a waveref wave collectX that grows identical to collectY. The formulaResults wave gets modified to store the new transformed results.

+
+ +
+
+

Variables

+
+
+static const double SF_STATE_UNINITIALIZED = -1
+
+ +
+
+static const double SF_STATE_COLLECT = 1
+
+ +
+
+static const double SF_STATE_ADDITION = 2
+
+ +
+
+static const double SF_STATE_SUBTRACTION = 3
+
+ +
+
+static const double SF_STATE_MULTIPLICATION = 4
+
+ +
+
+static const double SF_STATE_PARENTHESIS = 6
+
+ +
+
+static const double SF_STATE_FUNCTION = 7
+
+ +
+
+static const double SF_STATE_ARRAY = 8
+
+ +
+
+static const double SF_STATE_ARRAYELEMENT = 9
+
+ +
+
+static const double SF_STATE_WHITESPACE = 10
+
+ +
+
+static const double SF_STATE_NEWLINE = 12
+
+ +
+
+static const double SF_STATE_DIVISION = 13
+
+ +
+
+static const double SF_STATE_STRING = 14
+
+ +
+
+static const double SF_STATE_STRINGTERMINATOR = 15
+
+ +
+
+static const double SF_ACTION_UNINITIALIZED = -1
+
+ +
+
+static const double SF_ACTION_SKIP = 0
+
+ +
+
+static const double SF_ACTION_COLLECT = 1
+
+ +
+
+static const double SF_ACTION_LOWERORDER = 2
+
+ +
+
+static const double SF_ACTION_HIGHERORDER = 3
+
+ +
+
+static const double SF_ACTION_ARRAYELEMENT = 4
+
+ +
+
+static const double SF_ACTION_PARENTHESIS = 5
+
+ +
+
+static const double SF_ACTION_FUNCTION = 6
+
+ +
+
+static const double SF_ACTION_ARRAY = 7
+
+ +
+
+static const string SF_PARSER_REGEX_SIGNED_NUMBER = "^(?i)[+-]?[0-9]+(?:\.[0-9]+)?(?:[\+-]?E[0-9]+)?$"
+
+ +
+
+static const string SF_PARSER_REGEX_QUOTED_STRING = "^\".*\"$"
+
+ +
+
+static const string SF_PARSER_REGEX_SIGNED_PARENTHESIS = "^(?i)[+-]?\\([\s\S]*$"
+
+ +
+
+static const string SF_PARSER_REGEX_SIGNED_FUNCTION = "^(?i)[+-]?[A-Za-z]+"
+
+ +
+
+static const string SF_PARSER_REGEX_OTHER_VALID_CHARS = "[A-Za-z0-9_\.:;=!$]"
+
+ +
+
+static const string SF_SWEEPFORMULA_REGEXP = "^(.+?)(?:\\bvs\\b(.+))?$"
+

Regular expression which extracts both formulas from $a vs $b

+
+ +
+
+static const string SF_SWEEPFORMULA_GRAPHS_REGEXP = "^(.+?)(?:\\r[ \t]*and[ \t]*\\r(.*))?$"
+

Regular expression which extracts formulas pairs from $a vs $b\rand\r$c vs $d\rand\r...

+
+ +
+
+static const string SF_SWEEPFORMULA_WITH_REGEXP = "^(.+?)(?:\\r[ \t]*with[ \t]*\\r(.*))?$"
+

Regular expression which extracts y-formulas from $a\rwith\r$b\rwith\r$c\r...

+
+ +
+
+static const double SF_MAX_NUMPOINTS_FOR_MARKERS = 1000
+
+ +
+
+static const double SF_APFREQUENCY_FULL = 0x0
+
+ +
+
+static const double SF_APFREQUENCY_INSTANTANEOUS = 0x1
+
+ +
+
+static const double SF_APFREQUENCY_APCOUNT = 0x2
+
+ +
+
+static const double SF_APFREQUENCY_INSTANTANEOUS_PAIR = 0x3
+
+ +
+
+static const string SF_OP_MINUS = "-"
+
+ +
+
+static const string SF_OP_PLUS = "+"
+
+ +
+
+static const string SF_OP_MULT = "*"
+
+ +
+
+static const string SF_OP_DIV = "~1"
+
+ +
+
+static const string SF_OP_RANGE = "range"
+
+ +
+
+static const string SF_OP_RANGESHORT = "…"
+
+ +
+
+static const string SF_OP_MIN = "min"
+
+ +
+
+static const string SF_OP_MAX = "max"
+
+ +
+
+static const string SF_OP_AVG = "avg"
+
+ +
+
+static const string SF_OP_MEAN = "mean"
+
+ +
+
+static const string SF_OP_RMS = "rms"
+
+ +
+
+static const string SF_OP_VARIANCE = "variance"
+
+ +
+
+static const string SF_OP_STDEV = "stdev"
+
+ +
+
+static const string SF_OP_DERIVATIVE = "derivative"
+
+ +
+
+static const string SF_OP_INTEGRATE = "integrate"
+
+ +
+
+static const string SF_OP_TIME = "time"
+
+ +
+
+static const string SF_OP_XVALUES = "xvalues"
+
+ +
+
+static const string SF_OP_TEXT = "text"
+
+ +
+
+static const string SF_OP_LOG = "log"
+
+ +
+
+static const string SF_OP_LOG10 = "log10"
+
+ +
+
+static const string SF_OP_APFREQUENCY = "apfrequency"
+
+ +
+
+static const string SF_OP_CURSORS = "cursors"
+
+ +
+
+static const string SF_OP_SWEEPS = "sweeps"
+
+ +
+
+static const string SF_OP_AREA = "area"
+
+ +
+
+static const string SF_OP_SETSCALE = "setscale"
+
+ +
+
+static const string SF_OP_BUTTERWORTH = "butterworth"
+
+ +
+
+static const string SF_OP_CHANNELS = "channels"
+
+ +
+
+static const string SF_OP_DATA = "data"
+
+ +
+
+static const string SF_OP_LABNOTEBOOK = "labnotebook"
+
+ +
+
+static const string SF_OP_WAVE = "wave"
+
+ +
+
+static const string SF_OP_FINDLEVEL = "findlevel"
+
+ +
+
+static const string SF_OP_EPOCHS = "epochs"
+
+ +
+
+static const string SF_OP_TP = "tp"
+
+ +
+
+static const string SF_OP_STORE = "store"
+
+ +
+
+static const string SF_OP_SELECT = "select"
+
+ +
+
+static const string SF_OP_POWERSPECTRUM = "powerspectrum"
+
+ +
+
+static const string SF_OP_TPSS = "tpss"
+
+ +
+
+static const string SF_OP_TPINST = "tpinst"
+
+ +
+
+static const string SF_OP_TPBASE = "tpbase"
+
+ +
+
+static const string SF_OP_TPFIT = "tpfit"
+
+ +
+
+static const string SF_OPSHORT_MINUS = "minus"
+
+ +
+
+static const string SF_OPSHORT_PLUS = "plus"
+
+ +
+
+static const string SF_OPSHORT_MULT = "mult"
+
+ +
+
+static const string SF_OPSHORT_DIV = "div"
+
+ +
+
+static const string SF_OP_EPOCHS_TYPE_RANGE = "range"
+
+ +
+
+static const string SF_OP_EPOCHS_TYPE_NAME = "name"
+
+ +
+
+static const string SF_OP_EPOCHS_TYPE_TREELEVEL = "treelevel"
+
+ +
+
+static const string SF_OP_TP_TYPE_BASELINE = "base"
+
+ +
+
+static const string SF_OP_TP_TYPE_INSTANT = "inst"
+
+ +
+
+static const string SF_OP_TP_TYPE_STATIC = "ss"
+
+ +
+
+static const string SF_OP_SELECT_CLAMPMODE_ALL = "all"
+
+ +
+
+static const string SF_OP_SELECT_CLAMPMODE_IC = "ic"
+
+ +
+
+static const string SF_OP_SELECT_CLAMPMODE_VC = "vc"
+
+ +
+
+static const string SF_OP_SELECT_CLAMPMODE_IZERO = "izero"
+
+ +
+
+static const double SF_OP_SELECT_CLAMPCODE_ALL = -1
+
+ +
+
+static const string SF_OP_TPFIT_FUNC_EXP = "exp"
+
+ +
+
+static const string SF_OP_TPFIT_FUNC_DEXP = "doubleexp"
+
+ +
+
+static const string SF_OP_TPFIT_RET_TAULARGE = "tau"
+
+ +
+
+static const string SF_OP_TPFIT_RET_TAUSMALL = "tausmall"
+
+ +
+
+static const string SF_OP_TPFIT_RET_AMP = "amp"
+
+ +
+
+static const string SF_OP_TPFIT_RET_MINAMP = "minabsamp"
+
+ +
+
+static const string SF_OP_TPFIT_RET_FITQUALITY = "fitq"
+
+ +
+
+static const string SF_OP_APFREQUENCY_Y_TIME = "time"
+
+ +
+
+static const string SF_OP_APFREQUENCY_Y_FREQ = "freq"
+
+ +
+
+static const string SF_OP_APFREQUENCY_NORMOVERSWEEPSMIN = "normoversweepsmin"
+
+ +
+
+static const string SF_OP_APFREQUENCY_NORMOVERSWEEPSMAX = "normoversweepsmax"
+
+ +
+
+static const string SF_OP_APFREQUENCY_NORMOVERSWEEPSAVG = "normoversweepsavg"
+
+ +
+
+static const string SF_OP_APFREQUENCY_NORMWITHINSWEEPMIN = "norminsweepsmin"
+
+ +
+
+static const string SF_OP_APFREQUENCY_NORMWITHINSWEEPMAX = "norminsweepsmax"
+
+ +
+
+static const string SF_OP_APFREQUENCY_NORMWITHINSWEEPAVG = "norminsweepsavg"
+
+ +
+
+static const string SF_OP_APFREQUENCY_NONORM = "nonorm"
+
+ +
+
+static const string SF_OP_APFREQUENCY_X_COUNT = "count"
+
+ +
+
+static const string SF_OP_APFREQUENCY_X_TIME = "time"
+
+ +
+
+static const string SF_OP_AVG_INSWEEPS = "in"
+
+ +
+
+static const string SF_OP_AVG_OVERSWEEPS = "over"
+
+ +
+
+static const double EPOCHS_TYPE_INVALID = -1
+
+ +
+
+static const double EPOCHS_TYPE_RANGE = 0
+
+ +
+
+static const double EPOCHS_TYPE_NAME = 1
+
+ +
+
+static const double EPOCHS_TYPE_TREELEVEL = 2
+
+ +
+
+static const string SF_CHAR_COMMENT = "#"
+
+ +
+
+static const string SF_CHAR_CR = "\r"
+
+ +
+
+static const string SF_CHAR_NEWLINE = "\n"
+
+ +
+
+static const double SF_TRANSFER_ALL_DIMS = -1
+
+ +
+
+static const string SF_PLOTTER_GUIDENAME = "HOR"
+
+ +
+
+static const string SF_XLABEL_USER = ""
+
+ +
+
+static const double SF_MSG_OK = 1
+
+ +
+
+static const double SF_MSG_ERROR = 0
+
+ +
+
+static const double SF_MSG_WARN = -1
+
+ +
+
+static const double SF_NUMTRACES_ERROR_THRESHOLD = 10000
+
+ +
+
+static const double SF_NUMTRACES_WARN_THRESHOLD = 1000
+
+ +
+
+static const string SF_AVERAGING_NONSWEEPDATA_LBL = "NOSWEEPDATA"
+
+ +
+
+static const string SF_POWERSPECTRUM_UNIT_DEFAULT = "default"
+
+ +
+
+static const string SF_POWERSPECTRUM_UNIT_DB = "db"
+
+ +
+
+static const string SF_POWERSPECTRUM_UNIT_NORMALIZED = "normalized"
+
+ +
+
+static const string SF_POWERSPECTRUM_AVG_ON = "avg"
+
+ +
+
+static const string SF_POWERSPECTRUM_AVG_OFF = "noavg"
+
+ +
+
+static const string SF_POWERSPECTRUM_WINFUNC_NONE = "none"
+
+ +
+
+static const double SF_POWERSPECTRUM_RATIO_DELTAHZ = 10
+
+ +
+
+static const double SF_POWERSPECTRUM_RATIO_EPSILONHZ = 0.25
+
+ +
+
+static const double SF_POWERSPECTRUM_RATIO_EPSILONPOSFIT = 1E-3
+
+ +
+
+static const double SF_POWERSPECTRUM_RATIO_MAXFWHM = 5
+
+ +
+
+static const double SF_POWERSPECTRUM_RATIO_GAUSS_SIGMA2FWHM = 2.35482004503
+
+ +
+
+static const double SF_POWERSPECTRUM_RATIO_GAUSS_NUMCOEFS = 4
+
+ +
+
+static const double SF_VARIABLE_PREFIX = 36
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___sweep_formula___helpers_8ipf.html b/file/_m_i_e_s___sweep_formula___helpers_8ipf.html new file mode 100644 index 0000000000..ea2a27be24 --- /dev/null +++ b/file/_m_i_e_s___sweep_formula___helpers_8ipf.html @@ -0,0 +1,782 @@ + + + + + + + + File MIES_SweepFormula_Helpers.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_SweepFormula_Helpers.ipf

+

SFH Sweep formula related helper code

+
+

Functions

+
+
+variable SFH_StringChecker_Prototype(string str)
+
+ +
+
+variable SFH_NumericChecker_Prototype(variable var)
+
+ +
+
+variable SFH_GetArgumentAsNumeric(variable jsonId, string jsonPath, string graph, string opShort, variable argNum, variable defValue = defaultValue, WaveOrNull allowedValues = defaultValue, SFH_NumericChecker_Prototype checkFunc = defaultValue, variable checkDefault = defaultValue)
+

Convenience helper function to get a numeric SweepFormula operation argument.

+

Given the operation fetchBeer(variable numBottles, [variable size]) one can fetch both parameters via:

+

opShort    = "fetchBeer"
+numBottles = SFH_GetArgumentAsNumeric(jsonId, jsonPath, graph, opShort, 0)
+size       = SFH_GetArgumentAsNumeric(jsonId, jsonPath, graph, opShort, 1, defValue = 0.5, allowedValues = {0.33, 0.5, 1.0})
+
+
+

+

Here numBottles is argument number 0 and mandatory as defValue is not present.

+

The second argument size is optional with 0.5 as default and also defines a list of valid values.

+
+ +
+
+string SFH_GetArgumentAsText(variable jsonId, string jsonPath, string graph, string opShort, variable argNum, string defValue = defaultValue, WaveTextOrNull allowedValues = defaultValue, SFH_StringChecker_Prototype checkFunc = defaultValue, variable checkDefault = defaultValue)
+

Convenience helper function to get a textual SweepFormula operation argument.

+

Given the operation getTrainTable(string date, [string type]) one can fetch both parameters via:

+

opShort = "getTrainTable"
+date    = SFH_GetArgumentAsText(jsonId, jsonPath, graph, opShort, 0)
+type    = SFH_GetArgumentAsText(jsonId, jsonPath, graph, opShort, 1, defValue = "steam train", allowedValues = {"steam train", "light rail"})
+
+
+

+

Here date is argument number 0 and mandatory as defValue is not present.

+

The second argument type is optional with steam train as default and a list of allowed values.

+

The text argument can be abbreviated as long as it is unique, the unabbreviated result is returned in all cases.

+
+ +
+
+wave SFH_GetArgumentAsWave(variable jsonId, string jsonPath, string graph, string opShort, variable argNum, string defOp = defaultValue, WaveOrNull defWave = defaultValue, variable singleResult = defaultValue, variable expectedWaveType = defaultValue)
+

Convenience helper function to get a wave SweepFormula operation argument.

+

Given the operation countBirds(array birds, [birdTypes()]) one can fetch both parameters via:

+

opShort      = "countBirds"
+WAVE/D birds = SFH_GetArgumentAsWave(jsonId, jsonPath, graph, opShort, 0, singleResult = 1)
+WAVE/T types = SFH_GetArgumentAsWave(jsonId, jsonPath, graph, opShort, 1, defOp = "birdTypes()", singleResult = 1, expectedWaveType = IGOR_TYPE_TEXT_WAVE)
+
+
+

+

Here birds is argument number 0 and mandatory as defOp is not present. Passing singleResult == 1 already unpacks the outer wave reference wave container. It should always be passed if you only expect one wave to be returned.

+

The second argument birdTypes is optional, if not present the operation birdTypes() is called and its result returned. Alternatively defWave can be supplied which is then returned if the argument is not present.

+
+ +
+
+variable SFH_ASSERT(variable condition, string message, variable jsonId = defaultValue)
+

Assertion for sweep formula.

+

This assertion does not indicate a general programmer error but a sweep formula user error.

+

All programmer error checks must still use ASSERT().

+

UTF_NOINSTRUMENTATION

+
+ +
+
+wave SFH_GetEmptyRange()
+
+ +
+
+variable SFH_IsEmptyRange(wave range)
+
+ +
+
+wave SFH_GetFullRange()
+
+ +
+
+variable SFH_IsFullRange(wave range)
+
+ +
+
+wave SFH_AsDataSet(wave data)
+
+ +
+
+static variable SFH_ExtendIncompleteRanges(wave ranges)
+

Formula “cursors(A,B)” can return NaNs if no cursor(s) are set.

+
+ +
+
+wave SFH_EvaluateRange(variable jsonId, string jsonPath, string graph, string opShort, variable argNum)
+

Evaluate range parameter.

+

Range is read as dataset(s), it can be per dataset:

    +

  • numerical 1D: [start,end]

    • +

  • numerical 2D with multiple ranges: [[start1,start2,start3],[end1,end2,end3]]

      +

    • implicit: cursors(A, B) or [cursors(A, B), cursors(C, D)]

      • +

    • implicit: epochs([E0, TP])

      • +

    • implicit with offset calculcation: epochs(E0) + [1, -1]

      • +
    +

    • +

  • named epoch: E0 or a as wildcard expression E* or multiple

    • +
+

+

If one dataset is returned, numRows == 1, all ranges will be used for all sweeps in the selection.

+

When multiple datasets are returned, numRows > 1, the i-th sweep will use all ranges from the i-th dataset. The number of sweeps and datasets also has to match.

+
+
Returns:
+

One or multiple datasets

+
+
+
+ +
+
+wave SFH_GetRangeFromEpoch(string graph, string epochName, variable sweep, variable chanType, variable channel)
+

Returns a range from a epochName.

+
+
Parameters:
+
    +

  • graph – name of databrowser graph

    • +

  • epochName – name epoch

    • +

  • sweep – number of sweep

    • +

  • chanType – type of channel

    • +

  • channel – number of DA channel

    • +
+
+
Returns:
+

a 1D wave with two elements, [startTime, endTime] in ms, if no epoch could be resolved [NaN, NaN] is returned

+
+
+
+ +
+
+wave SFH_GetSweepsForFormula(string graph, WaveRefWave range, WaveOrNull selectData, string opShort)
+

Return a wave reference wave with the requested sweep data. The argument range can contain multiple datasets, if it is a single dataset the range(s) are extracted from each selection, if there are multiple datasets then the number of datasets must equal the number of selections, for that case range datasets and selections are indexed the same. This is usually only senseful if the same select arguments are used for e.g. data to retrieve sweeps and epochs to retrieve ranges.

+

All wave input parameters are treated as const and are thus not modified.

+
+
Parameters:
+
    +

  • graph – name of databrowser graph

    • +

  • range – wave ref wave with range specification defining the x-range of the extracted data, see also SFH_EvaluateRange(), range specification per dataset can be numerical or text

    • +

  • selectData – channel/sweep selection, see also SFH_GetArgumentSelect()

    • +

  • opShort – operation name (short)

    • +
+
+
+
+ +
+
+variable SFH_GetNumberOfArguments(variable jsonId, string jsonPath)
+
+ +
+
+dfref SFH_GetWorkingDF(string win)
+
+ +
+
+wave SFH_CreateSFRefWave(string win, string opShort, variable size)
+
+ +
+
+variable SFH_CleanUpInput(wave input)
+
+ +
+
+variable SFH_AddOpToOpStack(wave w, string oldStack, string opShort)
+
+ +
+
+variable SFH_AddToArgSetupStack(wave output, WaveOrNull input, string argSetupStr, variable resetStack = defaultValue)
+
+ +
+
+wave SFH_GetOutputForExecutorSingle(WaveOrNull data, string graph, string opShort, variable discardOpStack = defaultValue, wave clear = defaultValue, string dataType = defaultValue)
+
+ +
+
+wave SFH_GetOutputForExecutor(wave output, string win, string opShort, wave clear = defaultValue)
+
+ +
+
+static variable SFH_ConvertAllReturnDataToPermanent(WaveRefWave output, string win, string opShort)
+
+ +
+
+wave SFH_ResolveDatasetElementFromJSON(variable jsonId, string jsonPath, string graph, string opShort, variable argNum, variable checkExist = defaultValue)
+

Retrieves from an argument the first dataset and disposes the argument.

+
+ +
+
+variable SFH_TransferFormulaDataWaveNoteAndMeta(WaveRefWave input, WaveRefWave output, string opShort, string newDataType, WaveText argSetup = defaultValue, variable keepX = defaultValue)
+

Transfer wavenote from input data sets to output data sets set a label for a x-axis and x-value(s) for data waves.

+

+

See also

+

SFH_GetNewArgSetupWave

+
+

+
+
Parameters:
+
    +

  • input – Input wave reference wave

    • +

  • output – Output wave reference wave

    • +

  • opShort – operation short name

    • +

  • newDataType – data type of output

    • +

  • argSetup – [optional, default=$””] 2d text wave with argument setup of operation

    • +

  • keepX – [optional, default=0] When set then xvalues and xlabel of output are kept.

    • +
+
+
+
+ +
+
+wave SFH_GetArgumentSelect(variable jsonId, string jsonPath, string graph, string opShort, variable argNum)
+
+ +
+
+wave SFH_GetEpochNamesFromInfo(WaveText epochInfo)
+
+ +
+
+wave SFH_GetEpochIndicesByWildcardPatterns(WaveText epochNames, WaveText patterns)
+
+ +
+
+string SFH_ResultTypeToString(variable resultType)
+
+ +
+
+string SFH_FormatResultsKey(variable resultType, string name)
+
+ +
+
+std::tuple<WaveText, WaveText> SFH_CreateResultsWaveWithCode(string graph, string code, wave data = defaultValue, string name = defaultValue, variable resultType = defaultValue)
+
+ +
+
+string SFH_GetBrowserForFormulaGraph(string win)
+

Return the SweepBrowser/DataBrowser from which the given SweepFormula plot window originated from.

+
+ +
+
+string SFH_GetFormulaGraphForBrowser(string browser)
+

Return the SweepFormula plot created by the given SweepBrowser/DataBrowser.

+
+ +
+
+wave SFH_GetFormulaGraphs()
+

Return a text wave with all formula graph windows.

+
+ +
+
+wave SFH_NewSelectDataWave(variable numSweeps, variable numChannels)
+

Create a new selectData wave The row counts the selected combinations of sweep, channel type, channel number The three columns per row store the sweep number, channel type, channel number.

+
+ +
+
+std::tuple<WAVE, WAVE> SFH_ParseToSelectDataWaveAndRange(wave sweepData)
+

Recreate a single select data wave and range stored in the JSON wavenote from SFH_GetSweepsForFormula()

+
+ +
+
+wave SFH_GetNewArgSetupWave(variable size)
+
+ +
+
+static string SFH_SerializeArgSetup(WaveText argSetup)
+
+ +
+
+wave SFH_DeSerializeArgSetup(variable jsonId, string jsonPath)
+
+ +
+
+variable SFH_ResetArgSetupStack(wave output, string opShort)
+
+ +
+
+static string SFH_GetArgSetupValueByKey(WaveText argSetup, string key)
+
+ +
+
+static string SFH_GetEmptyArgSetup()
+
+ +
+
+variable SFH_EnrichAnnotations(WaveText annotations, WaveText formulaArgSetup)
+

Based on the argument setup modifies the annotations per formula with additional information from the different arguments.

+
+
Returns:
+

1 of difference was found, 0 otherwise

+
+
+
+ +
+
+static variable SFH_EnrichAnnotationsRelease(wave formulaIDs)
+
+ +
+
+variable SFH_GetPlotMarkerCodeSelection(variable count)
+
+ +
+
+variable SFH_GetPlotLineCodeSelection(variable count)
+
+ +
+
+wave SFH_FilterSelect(WaveOrNull selectData, variable keepChanType)
+

filters data from select, currently supports only one option:

+

    +

  • specify a channel type to keep

    • +
+

+
+ +
+
+variable SFH_CheckArgumentCount(variable jsonId, string jsonPath, string opShort, variable minArgs, variable maxArgs = defaultValue)
+

checks the argument count and returns the number of arguments

+
+ +
+
+wave SFH_GetStimsetRange(string graph, wave data, wave selectData)
+

Return a SF range in ms with the stimset range.

+

Prefers the ST epoch if present, otherwise it tries to deduce the equivalent from labnotebook entries.

+
+ +
+
+std::tuple<WAVE, WaveText> SFH_GetNumericRangeFromEpoch(string graph, wave numericalValues, wave textualValues, wave range, variable sweepNo, variable chanType, variable chanNr)
+

From a single numeric/textual range wave we return a 2xN numeric range.

+

Supports numeric ranges, epochs, and epochs with wildcards.

+

+

See also

+

SFH_EvaluateRange

+
+

+
+
Parameters:
+
    +

  • graph – name of graph window

    • +

  • numericalValues – numeric labnotebok

    • +

  • textualValues – textual labnotebok

    • +

  • range – one numerical or one/multiple epoch ranges with optional wildcard,

    • +

  • sweepNo – sweep number

    • +

  • chanType – channel type

    • +

  • chanNr – channel number

    • +
+
+
Return values:
+
    +

  • adaptedRange – 2xN numeric wave with the start/stop ranges [ms]

    • +

  • epochRangeNames – epoch names (wildcard expanded) in case range was textual, a null wave ref otherwise

    • +
+
+
+
+ +
+
+wave SFH_AttemptDatasetResolve(string element)
+

Attempt a resolution of a dataset based on a string input, returns null wave if not resolvable.

+
+ +
+
+variable SFH_IsArray(wave data)
+

Check if data wave refers to an array Note: The check is rather weak, another option would be tagging in the wavenote by the executor?

+
+ +
+
+wave SFH_MoveDatasetHigherIfCompatible(WaveRefWave data)
+

Moves datasets from array elements to higher level e.g. [dataset(1, 2), dataset(3, 4)] -> dataset([1, 3], [3, 4]) e.g. [dataset(1, 2, 3), dataset(4, 5, 6)] -> dataset([1, 4], [2, 5], [3, 6]) e.g. [dataset(1, 2), dataset(4, 5), dataset(6, 7)] -> dataset([1, 4, 6], [2, 5, 7]) Requirements that this is possible are:

+

    +

  • all initial array elements must resolve to datasets

    • +

  • all dataset waves of the initial array elements must be non-null, have the same size and must be 1d

    • +

  • all elements of these datasets must be non-null, have the same type and the same size and must be max 3d

    • +

  • only numeric and text is supported as type, thus the datasets may not contain datasets themselves If none of the requirements are met the input data is returned.

    • +
+

+
+ +
+
+

Variables

+
+
+static const string SFH_WORKING_DF = "FormulaData"
+
+ +
+
+static const string SFH_ARGSETUP_OPERATION_KEY = "Operation"
+
+ +
+
+static const string SFH_ARGSETUP_EMPTY_OPERATION_VALUE = "NOOP"
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___sweep_formula___p_s_x_8ipf.html b/file/_m_i_e_s___sweep_formula___p_s_x_8ipf.html new file mode 100644 index 0000000000..1d734998ac --- /dev/null +++ b/file/_m_i_e_s___sweep_formula___p_s_x_8ipf.html @@ -0,0 +1,1883 @@ + + + + + + + + File MIES_SweepFormula_PSX.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_SweepFormula_PSX.ipf

+

PSX Sweep formula related code for PSP/PSC (-> PSX) detection and classification

+

GUI layout

+

///
+/// +---+-----------+-----------+
+/// |   | All event | Single    |
+/// |   | graph     | event     |
+/// |   |           | graph     |
+/// |   |           |           |
+/// +------+-------------------------------+
+/// |      |  PSX graph                    |
+/// |      |                               |
+/// |      |-------------------------------|
+/// |      |  PSX stats graph              |
+/// |      |                               |
+/// |      |-------------------------------|
+/// |      | ...                           |
+/// +------+-------------------------------+
+///
+///
+
+
+ 
Related functions:
+- PSX_GetSpecialPanel()
+- PSX_GetAllEventGraph()
+- PSX_GetSingleEventGraph()
+- PSX_GetPSXGraph()
+
+To find the sweep/data browser use SFH_GetBrowserForFormulaGraph() and for the reverse direction use SFH_GetFormulaGraphForBrowser.
+
+
+

+
+

State types

+

+
+
+static const string PSX_TUD_FIT_STATE_KEY = "Fit State"
+
+ +
+
+static const string PSX_TUD_EVENT_STATE_KEY = "Event State"
+
+ +
+
+

Trace types

+

+
+
+static const string PSX_TUD_TYPE_SINGLE = "single"
+
+ +
+
+static const string PSX_TUD_TYPE_AVERAGE = "average"
+
+ +
+
+

Different ways to derive cache key from the parameters JSON

+

+
+
+static const double PSX_CACHE_KEY_EVENTS = 0x1
+
+ +
+
+static const double PSX_CACHE_KEY_RISETIME = 0x2
+
+ +
+
+static const double PSX_CACHE_KEY_ANALYZE_PEAKS = 0x3
+
+ +
+
+

Functions

+
+
+static string PSX_GetUserDataForWorkingFolder()
+
+ +
+
+static dfref PSX_GetWorkingFolder(string win)
+

Return the working folder for the psx operation.

+

Can be null in case the operation was not executed in this sweep formula panel

+
+ +
+
+static string PSX_GetSpecialPanel(string win)
+
+ +
+
+static string PSX_GetSingleEventGraph(string win)
+
+ +
+
+static string PSX_GetAllEventGraph(string win)
+
+ +
+
+static wave PSX_GetCheckboxStatesFromSpecialPanel(string win, string traceType)
+

Return a wave with the checkbox states, single or average, of the special event panel.

+

Can be indexed with the state as dimension label.

+
+
Parameters:
+
+
+
+
+ +
+
+static string PSX_GetStateTypeFromSpecialPanel(string win)
+

Return the state type (fit or event) state from the special event panel.

+

One of SpecialEventPanelEventTypes

+
+ +
+
+static variable PSX_GetRestrictEventsToCurrentCombo(string win)
+
+ +
+
+static wave PSX_FilterSweepData(wave sweepData, variable low, variable high)
+

Filter the sweep data.

+
+
Parameters:
+
    +

  • sweepData – data from a single sweep and channel without inserted TP

    • +

  • high – high cutoff [Hz]

    • +

  • low – low cutoff [Hz]

    • +
+
+
+
+ +
+
+static wave PSX_CreateHistogram(wave sweepData, variable bin_start = defaultValue, variable bin_end = defaultValue, variable bin_width = defaultValue)
+

Create a histogram of the sweep data.

+
+
Parameters:
+
    +

  • sweepData – data from a single sweep and channel without inserted TP

    • +

  • bin_start – [optional, defaults to data’s minimum] first histogram bin

    • +

  • bin_end – [optional, defaults to data’s maximum] last histogram bin

    • +

  • bin_width – [optional, defaults to 0.1] width of a histogram bin

    • +
+
+
+
+ +
+
+static std::tuple<WAVE, variable> PSX_OffsetSweepData(wave sweepData)
+

Offset sweepData by X.

+

X is calculated as the x coordinate of histogram’s maximum taken of sweepData.

+

The result is that the histogram maximum of the offsetted trace is at zero.

+
+ +
+
+static wave PSX_DeconvoluteSweepData(wave sweepData, WaveComplex psxKernelFFT, wave deconvFilter)
+

Return the deconvoluted sweep data.

+
+
Parameters:
+
    +

  • sweepData – data from a single sweep and channel without inserted TP

    • +

  • psxKernelFFT – FFT’ed kernel from PSX_CreatePSXKernel()

    • +

  • deconvFilter – deconvolution filter settings

    • +
+
+
+
+ +
+
+static wave PSX_CreateHistogramOfDeconvSweepData(wave deconvSweepData)
+

Creates a histogram of the deconvoluted sweep data.

+
+ +
+
+static std::tuple<WAVE, WAVE> PSX_FitHistogram(wave input)
+

Fit the given wave with a gaussian where K0, y offset, is fixed at zero.

+
+ +
+
+static std::tuple<WAVE, WAVE> PSX_Analysis(wave sweepData, wave psxKernelFFT, variable sweepFilterLow, variable sweepFilterHigh, wave deconvFilter)
+

Full analysis cycle:

    +

  • filtering

    • +

  • offsetting

    • +

  • deconvolution

    • +

  • histogram of deconvolution

    • +

  • gaussian fit of histogram

    • +
+

+
+ +
+
+static std::tuple<WaveDouble, WaveDouble> PSX_FindPeaks(wave sweepDataFiltOffDeconv, variable threshold, variable numPeaksMax = defaultValue, variable start = defaultValue, variable stop = defaultValue)
+

Searches for peaks in sweepData

+
+
Parameters:
+
    +

  • sweepDataFiltOffDeconv – 1D wave

    • +

  • threshold – FindPeak parameter

    • +

  • numPeaksMax – maximum number of peaks to search

    • +

  • start – [optional, defaults first point] start x value

    • +

  • stop – [optional, defaults last point] end x value

    • +
+
+
Return values:
+
    +

  • peakX – x-coordinates of peaks

    • +

  • peakY – y-coordinates of peaks

    • +
+
+
+
+ +
+
+static variable PSX_AnalyzePeaks(wave sweepDataFiltOffDeconv, wave sweepDataFiltOff, wave peakX, wave peakY, variable maxTauFactor, variable kernelAmp, wave psxEvent, wave eventFit)
+

Analyze the peaks.

+
+ +
+
+static std::tuple<variable, variable> PSX_GetSingleEventRange(wave psxEvent, variable index)
+

Return the x-axis range useful for displaying and extracting a single event.

+
+ +
+
+static std::tuple<variable, variable> PSX_GetEventFitRange(wave sweepDataFiltOff, wave psxEvent, variable eventIndex)
+

Return the x-axis range for single event fitting.

+

x-zero is taken from sweepData

+
+ +
+
+static variable PSX_FitEventDecay(wave sweepDataFiltOff, wave psxEvent, variable maxTauFactor, WaveRefWave eventFit, variable eventIndex)
+

Return the decay coefficient tau by fitting the filtered and offsetted sweep data with an offsetted exponential.

+

exp_XOffset: \(y = K0 + K1 \cdot exp(-(x - x0)/K2)\)

+
+ +
+
+static wave PSX_CreateOverrideResults(variable numEvents, WaveText combos)
+

Create the override results 2D wave.

+

ROWS:

    +

  • event number

    • +
+

+

COLS:

    +

  • combination

    • +
+

+

LAYERS:

    +

  • 0: Fit result, see GetPSXEventWaveAsFree

    • +

  • 1: Replacement tau, the default of NaN means don’t use

    • +
+

+
+ +
+
+static variable PSX_OperationSweepGathering(string graph, WaveRefWave psxKernelDataset, variable parameterJsonID, variable sweepFilterLow, variable sweepFilterHigh, wave deconvFilter, variable index, WaveRefWave output)
+
+ +
+
+static variable PSX_OperationImpl(string graph, variable parameterJSONID, string id, variable peakThresh, variable maxTauFactor, wave riseTimeParams, variable kernelAmp, variable index, WaveRefWave output)
+

Implementation of psx operation.

+
+
Returns:
+

0 on success, 1 on failure

+
+
+
+ +
+
+static string PSX_GenerateKey(string name, variable index)
+

Generate the dimension label for the output wave reference waves.

+

Used for psx and psxKernel as both hold #PSX_KERNEL_OUTPUTWAVES_PER_ENTRY and #PSX_OPERATION_OUTPUT_WAVES_PER_ENTRY entries per input range/sweep combination.

+
+ +
+
+static wave PSX_GetPSXKernel(variable riseTau, variable decayTau, variable amp, variable numPoints, variable dt, wave range)
+

Return the PSX kernel from the cache or create it.

+
+ +
+
+static std::tuple<WAVE, WAVE> PSX_CreatePSXKernel(variable riseTau, variable decayTau, variable amp, variable numPoints, variable dt)
+

Create the psx_kernel waves

+

+from Ken Burke’s deconvolution code

+

The time units are abitrary but fixed for all three components.

+
+
Parameters:
+
    +

  • riseTau – time constant

    • +

  • decayTau – time constant

    • +

  • amp – amplitude [no unit]

    • +

  • numPoints – number of data points

    • +

  • dt – time constant for normalisation

    • +
+
+
+
+ +
+
+static std::tuple<WaveDouble, WAVE, WAVE, WaveText> PSX_GetStatsResults(WaveRefWave allEvents, variable state, string prop)
+

Return the data/index/marker/comboKeys of the events matching the given state and property.

+
+ +
+
+static string PSX_BuildSweepEquivKey(variable chanType, variable chanNr)
+

Build the dimension label used for the sweep equivalence wave.

+
+ +
+
+static std::tuple<variable, variable, variable> PSX_GetSweepEquivKeyAndSweep(wave sweepEquiv, variable channelNumberType, variable sweepIndex)
+

Return the triplett channel number, channel type and sweep number from the sweep equivalence wave located in the given channelNumberType and sweepIndex coordinates.

+
+ +
+
+static wave PSX_GenerateSweepEquiv(wave selectData)
+

Generate the equivalence classes of selectData.

+

All selections which have the same channel number and type are in one equivalence class.

+

The returned 2D wave has row labels from PSX_BuildSweepEquivKey() for the channel type/number and the sweep numbers in the columns.

+
+ +
+
+variable PSX_CollectResolvedRanges(string graph, wave range, wave singleSelectData, wave allResolvedRanges, WaveText allSelectHashes)
+

Collect all resolved ranges in allResolvedRanges together with a hash of the select data.

+
+ +
+
+static variable PSX_CheckResolvedRanges(wave allResolvedRanges, WaveText allSelectHashes)
+

Check that the 2xN wave allResolvedRanges has only non-intersecting ranges for the same select data hash.

+
+ +
+
+static wave PSX_OperationStatsImpl(string graph, string id, WaveRefWave rangeParam, wave selectData, string prop, string stateAsStr, string postProc)
+

Helper function of the psxStats operation.

+
+ +
+
+static wave PSX_CalculateRiseTime(wave psxEvent, wave sweepDataFiltOff, variable parameterJsonID, variable kernelAmp, variable lowerThreshold, variable upperThreshold)
+
+ +
+
+static variable PSX_CalculateRiseTimeImpl(wave psxEvent, wave sweepDataFiltOff, variable kernelAmp, variable index, variable lowerThreshold, variable upperThreshold)
+
+ +
+
+static wave PSX_GetStates(variable withAllState = defaultValue)
+

Return all possible fit/event states.

+
+
Parameters:
+

withAllState – [optional, defaults to false] choose to include PSX_ALL (true) or not (false)

+
+
+
+ +
+
+static variable PSX_ParseState(string state)
+
+ +
+
+string PSX_StateToString(variable state)
+
+ +
+
+string PSX_FitResultToString(variable fitResult)
+
+ +
+
+static variable PSX_UpdateAllEventGraph(string win, variable forceSingleEventUpdate = defaultValue, variable forceAverageUpdate = defaultValue, variable forceBlockIndexUpdate = defaultValue, variable forceSingleEventOffsetUpdate = defaultValue)
+
+ +
+
+static variable PSX_UpdateSingleEventGraph(string win, variable index)
+

Update the single event graph.

+

The passed event index is from the current combo.

+
+ +
+
+static variable PSX_UpdateDisplayedFit(dfref comboDFR, variable index)
+

Update the displayed fit in the single event graph.

+
+ +
+
+static variable PSX_UpdateOffsetInAllEventGraph(string win)
+
+ +
+
+static variable PSX_AdaptColorsInAllEventGraph(string win, variable forceAverageUpdate = defaultValue, variable forceSingleEventUpdate = defaultValue)
+

Update trace colors in all event graph.

+

This needs to be done every time an event changes its state.

+
+
Parameters:
+
    +

  • win – window

    • +

  • forceAverageUpdate – [optional, defaults to false] perform an average wave update regardless if required or not.

    • +

  • forceSingleEventUpdate – [optional, defaults to false] update every single event trace regardless of its old state

    • +
+
+
+
+ +
+
+static variable PSX_UpdateAverageTraces(string win, WaveText eventIndexFromTraces, WaveText comboIndizesFromTraces, wave stateNew, wave indexMapper, WaveDoublef comboFolders)
+

Update the contents of the average waves for the all event graph.

+
+ +
+
+static variable PSX_UpdateAverageWave(WaveRefWave sourceWaves, variable numFilledSourceWaves, dfref averageDFR, variable state)
+

Helper function to update the average waves for the all event graph.

+
+ +
+
+static dfref PSX_GetAverageFolder(string win)
+
+ +
+
+static variable PSX_FitAcceptAverage(string win, dfref averageDFR, wave eventStartTime, wave eventStopTime)
+
+ +
+
+static variable PSX_StoreIntoResultsWave(string browser, variable resultType, wave data, string name)
+
+ +
+
+static string PSX_GetPSXParameters(variable jsonID, variable cacheKeyType)
+
+ +
+
+static variable PSX_StoreEventsIntoCache(wave psxEvent)
+
+ +
+
+static wave PSX_LoadEventsFromCache(string comboKey, string psxParameters)
+
+ +
+
+static std::tuple<WaveText, WaveText> PSX_GetTraceSelectionWaves(string win, string traceType, variable respectBlock = defaultValue)
+

Return the trace user data keys/values wave for the given trace type.

+
+
Parameters:
+
    +

  • win – Window

    • +

  • traceType – One of AllEventGraphTraceType

    • +

  • respectBlock – [optional, defaults to true] Restrict the traces to the currently selected block

    • +
+
+
+
+ +
+
+static variable PSX_UpdateHideStateInAllEventGraph(string win)
+

Update the hide state of all traces in the all event graph.

+
+ +
+
+static variable PSX_UpdateHideStateInAllEventGraphImpl(string win, string traceType)
+
+ +
+
+static variable PSX_UpdateBlockIndizes(string win)
+
+ +
+
+static variable PSX_WriteBlockNumberAsUserData(string win, variable numBlocks)
+
+ +
+
+static variable PSX_CalculateNumberOfBlocks(string win)
+
+ +
+
+string PSX_GetAllEventBlockNumbers(string win)
+
+ +
+
+static variable PSX_GetStateMatchPattern(wave active)
+

Return a bit pattern to match fit/event state.

+
+
Parameters:
+

active – Wave with at least 3 entries denoting which states are active

+
+
+
+ +
+
+static variable PSX_AppendTracesToAllEventGraph(string win)
+

Add the total number of required traces to the all event graph.

+

The number of average waves is 4 due to the number of different states, see PSXStates.

+

    +

  • Single event traces for all combinations

    • +

  • 4 average waves for each combination

    • +

  • 4 average waves for the global average across all combinations

    • +
+

+
+ +
+
+static string PSX_GetAverageTraceName(variable idx, string basename, variable comboIndex, string traceSuffix)
+
+ +
+
+static variable PSX_AppendAverageTraces(string extAllGraph, dfref averageDFR, string traceSuffix, variable idx, string comboKey, variable comboIndex, wave traceUserDataKeys, wave states, wave acceptColors, wave rejectColors, wave undetColors)
+

Helper function to append the average traces to the all event graph.

+
+ +
+
+static variable PSX_GetCurrentEventIndex(string win)
+

Return the event index where cursor A is currently placed in the psx plot.

+
+
Returns:
+

event index of the current combination or NaN if there is no psx plot or valid cursor position

+
+
+
+ +
+
+static variable PSX_UpdateSingleEventTextbox(string win, variable eventIndex = defaultValue)
+

Update the textbox in the single event graph.

+
+ +
+
+static string PSX_GetCursorInfo(string psxGraph)
+

Return the cursor info of cursor A from the psxGraph.

+

Checks also that the cursor is on the expected trace

+
+ +
+
+static variable PSX_CenterCursor(string win, variable leftIndex, variable constantWidth, variable rightIndex = defaultValue)
+

Adjust the axis ranges of the psx graph so that the cursor is visible.

+
+
Parameters:
+
    +

  • win – window

    • +

  • leftIndex – event index to bring in axis range

    • +

  • constantWidth – determine if the covered x-axis range should stay constant or not

    • +

  • rightIndex – [optional, defaults to none] additional event index to bring in x-axis range

    • +
+
+
+
+ +
+
+static variable PSX_MoveCursor(string win, string trace, variable index, variable direction)
+

Move the cursor A to the event index + direction

+

The window win can either be the psx graph or one of the psxStats graphs. The function wraps around on both ends and selects the previous/next combo if required.

+
+
Returns:
+

event index (clipped)

+
+
+
+ +
+
+variable PSX_MoveCursorHelper(string win, string trace, variable index)
+
+ +
+
+static variable PSX_MoveAndCenterCursor(string win, variable index, variable direction = defaultValue, variable constantWidth = defaultValue)
+

Move and center cursor.

+

+

See also

+

PSX_MoveCursor

+
+
+

See also

+

PSX_CenterCursor

+
+

+
+ +
+
+static variable PSX_GetKeyboardDirection(string psxGraph)
+

Get the keyboard direction stored in user data in the psx graph.

+
+ +
+
+static variable PSX_SetKeyboardDirection(string psxGraph, variable direction)
+

Set the keyboard direction in user data in the psx graph.

+
+ +
+
+static variable PSX_GetMoveDirection(string psxGraph)
+

Get the move direction as +/- 1 from the keyboard direction.

+
+ +
+
+static wave PSX_SelectColor(variable state, wave acceptColors, wave rejectColors, wave undetColors)
+

Return the appropriate color wave for the given fit/event state.

+
+ +
+
+static variable PSX_SelectMarker(variable state)
+

Return a marker for the given fit/event state.

+
+ +
+
+static variable PSX_UpdateEventWaves(string win, variable val = defaultValue, variable index = defaultValue, variable toggle = defaultValue, WaveOrNull indizes = defaultValue, variable writeState = defaultValue, variable stateType = defaultValue, variable comboIndex = defaultValue)
+

Update all event related waves.

+

One of val or toggle has to be supplied.

+

If neither index nor indizes is supplied all event indizes are set.

+
+
Parameters:
+
    +

  • win – window

    • +

  • val – [optional] new state, one of PSXStates

    • +

  • index – [optional] event index to set

    • +

  • toggle – [optional] switch event state from accepted <-> rejected

    • +

  • indizes – [optional] event indizes to set

    • +

  • writeState – [optional, defaults to true] set the event state itself

    • +

  • stateType – [optional, defaults to PSX_STATE_EVENT] one of PSXStateTypes

    • +

  • comboIndex – [optional, defaults to listbox selection] select/range combination to update the events for

    • +
+
+
+
+ +
+
+static std::tuple<WAVE, WAVE, WAVE> PSX_GetEventColors()
+

Return RGBA waves with the colors for the three event states.

+
+ +
+
+static string PSX_GenerateComboKey(string graph, wave selectData, wave range)
+

Generate the unique combination key made up from selectData and range

+

This is used in the results wave, the listbox for selection and is attached to the wave note of psxEvent.

+
+ +
+
+static wave PSX_GetAllCombinationFolders(dfref workDFR)
+

Return a datafolder reference wave with all psx combination folders.

+
+ +
+
+static wave PSX_GetEventContainer(string graph, string requestID = defaultValue)
+

Return the psxEvent container wave for the given graph.

+
+ +
+
+static wave PSX_GetEventContainerFromResults(string id)
+

Return the psxEvent container from the results wave for the given id.

+
+ +
+
+static wave PSX_FilterEventContainer(WaveRefWaveOrNull eventContainer, string refComboKey)
+
+ +
+
+static string PSX_GetPSXGraph(string win)
+

Return the psx graph.

+

Searches all subwindows of win.

+
+ +
+
+static string PSX_GetPSXStatsGraph(string win)
+

Return the name of the possibly non-existing stats subwindow.

+
+ +
+
+static wave PSX_GetEventsInsideAxisRange(string win, string traceName, variable first, variable last, wave xCrds)
+
+ +
+
+static string PSX_GetComboKeyFromDFR(dfref comboDFR)
+

Return the combo key from the combo datafolder.

+
+ +
+
+static string PSX_GetIDFromDFR(dfref comboDFR)
+

Return the ID from the combo datafolder.

+
+ +
+
+static wave PSX_GetSpecialEventPanelCheckboxes(string specialEventPanel)
+
+ +
+
+static wave PSX_GetSpecialEventPanelPopups(string specialEventPanel)
+
+ +
+
+static variable PSX_StoreGuiState(string win, string browser)
+

Store the PSX panel GUI state in the window user data of browser

+
+ +
+
+static variable PSX_RestoreGuiState(string win)
+

Restore the PSX panel GUI state from the window user data of browser

+
+ +
+
+static dfref PSX_GetCurrentComboFolder(string win)
+

Return the currently in the listbox selected combination folder.

+
+ +
+
+static variable PSX_GetCurrentComboIndex(string win)
+

Return the current combo index as selected in the listbox.

+
+ +
+
+static variable PSX_GetComboIndexForComboKey(string win, string comboKey)
+

Return the combo index for the given comboKey.

+
+ +
+
+static variable PSX_GetComboIndexFromDFR(dfref comboDFR)
+

Return the combo index from the given comboDFR.

+

The combo folder is created by GetPSXFolderForCombo()

+
+ +
+
+static variable PSX_MoveWavesToDataFolders(dfref workDFR, WaveRefWaveOrNull results, variable offset, variable numCombos)
+

Write all psx data from results in the combination folders.

+

Takes care of existing combination data due to other psx calls in the same code.

+
+
Returns:
+

Number of combinations without event data

+
+
+
+ +
+
+static string PSX_CheckForUniqueIDs(dfref workDFR)
+
+ +
+
+static variable PSX_CreateSingleEventWaves(dfref comboDFR, wave psxEvent, wave sweepDataFiltOff)
+

Extract a single wave for each event from sweepDataFiltOff.

+
+ +
+
+static string PSX_FormatSingleEventWaveName(variable i)
+

Generate a wave name for single event waves.

+
+ +
+
+static variable PSX_EventGraphSuppressUpdate(string win)
+
+ +
+
+string PSX_GetEventStateNames()
+
+ +
+
+string PSX_GetAverageFitAcceptNames()
+
+ +
+
+static string PSX_GetUIControlHelp()
+
+ +
+
+static variable PSX_CreatePSXGraphAndSubwindows(string win, string graph, SF_PlotMetaData *plotMetaData)
+

Create the PSX graph together with all subwindows (all event graph, single event graph)

+

This is only called for the very first psx operation output, subsequent psx operation outputs are just added as additional combos.

+
+ +
+
+static variable PSX_MarkGraphForPSX(string win)
+

Mark win as being an psx graph.

+
+ +
+
+static variable PSX_ApplySpecialPlotProperties(string win, wave eventLocationTicks, wave eventLocationLabels)
+

Apply plot properties which have to be reapplied on every combo index change.

+
+ +
+
+static variable PSX_AddLegend(string win, WaveRefWave results)
+

Read the user JWN from results and create a legend from all operation parameters.

+
+ +
+
+static std::tuple<variable, variable, variable> PSX_GetEventIndexAndComboIndex(string win, variable direction = defaultValue)
+

Return the event, wave and combo index.

+

Direction is taken into account.

+
+
Parameters:
+
    +

  • win – window, can be an psx/psxStats graph

    • +

  • direction – [optional, defaults to 0] offset from the current position

    • +
+
+
Return values:
+
    +

  • eventIndex – event index

    • +

  • waveIndex – index into the y wave of the cursor

    • +

  • comboIndex – combination index

    • +
+
+
+
+ +
+
+variable PSX_PlotInteractionHook(WMWinHookStruct *s)
+

Window hook responsible for keyboard and mouse support.

+

Works with psx and psxStats graphs.

+
+ +
+
+variable PSX_AllEventGraphHook(WMWinHookStruct *s)
+
+ +
+
+static variable PSX_GetDirectionFromKeyCode(string psxGraph, variable keyCode)
+
+ +
+
+static variable PSX_MoveMouseForKeyPress(string win, variable keyCode, variable comboIndex, variable eventIndex)
+
+ +
+
+static variable PSX_ReactToKeyPressWithoutMouse(string win, variable keyCode, variable comboIndex, variable eventIndex)
+
+ +
+
+wave PSX_CreateCombinationsListBoxWaveAsFree(dfref workDFR)
+

Return a free text wave with all combo keys.

+
+ +
+
+static variable PSX_GetNumberOfCombinations(WaveRefWave results)
+
+ +
+
+variable PSX_Plot(string win, string graph, WaveRefWaveOrNull results, SF_PlotMetaData *plotMetaData)
+

High-level function responsible for psx data and plot management.

+
+ +
+
+variable PSX_PostPlot(string win)
+

Init the psx plot after filling it with data.

+
+ +
+
+wave PSX_Operation(variable jsonId, string jsonPath, string graph)
+

Implementation of the psx operation.

+
+ +
+
+wave PSX_OperationKernel(variable jsonId, string jsonPath, string graph)
+

Implementation of the psxKernel operation.

+
+ +
+
+wave PSX_OperationRiseTime(variable jsonId, string jsonPath, string graph)
+
+ +
+
+wave PSX_OperationDeconvFilter(variable jsonId, string jsonPath, string graph)
+
+ +
+
+wave PSX_OperationStats(variable jsonId, string jsonPath, string graph)
+
+ +
+
+wave PSX_OperationPrep(variable jsonId, string jsonPath, string graph)
+
+ +
+
+static std::tuple<WAVE, WAVE, variable, string> PSX_CalculatePeakThreshold(WaveRefWave results, variable numCombos, variable numSDs)
+
+ +
+
+variable PSX_MouseEventSelection(variable newState, variable stateType)
+

Menu item for selecting event inside a marquee and changing their state.

+
+
Parameters:
+
+
+
+
+ +
+
+static variable PSX_GetIndexOrientation(string axisLbl)
+
+ +
+
+static wave PSX_GetEventsInsideMarqueeForStatsPlot(string win, variable indexOrient, variable left, variable top, variable right, variable bottom)
+

Returns a 2D wave reference wave with event indices/comboKey entries in each column.

+

ROWS:

    +

  • Result for each trace

    • +
+

+

COLUMNS:

    +

  • 0 (eventIndizes): Indizes of events which are in range

    • +

  • 1 (comboIndex) Combo index for the events in column 0 Always only one element!

    • +
+

+
+ +
+
+variable PSX_JumpToEvents()
+

Make the events inside the marquee visible in the psx plot.

+
+ +
+
+static variable PSX_SetCombo(string win, variable comboIndex)
+

Change the current combination to comboIndex

+
+ +
+
+static string PSX_GetID(string graph)
+
+ +
+
+variable PSX_ButtonProc_StoreEvents(WMButtonAction *ba)
+
+ +
+
+variable PSX_ButtonProc_LoadEvents(WMButtonAction *ba)
+
+ +
+
+static wave PSX_GetPSXEventForComboKey(WaveRefWave eventContainer, string refComboKey)
+
+ +
+
+variable PSX_ButtonProcJumpFirstUndet(WMButtonAction *ba)
+
+ +
+
+variable PSX_ListBoxSelectCombo(WMListBoxAction *lba)
+
+ +
+
+variable PSX_CopyHelpToClipboard(WMButtonAction *ba)
+
+ +
+
+variable PSX_CheckboxProcSuppressUpdate(WMCheckboxAction *cba)
+
+ +
+
+variable PSX_PopupMenuState(WMPopupAction *cba)
+
+ +
+
+variable PSX_CheckboxProcAllEventPlotUpdate(WMCheckboxAction *cba)
+
+ +
+
+variable PSX_CheckboxProcChangeRestrictCurrentCombo(WMCheckboxAction *cba)
+
+ +
+
+variable PSX_CheckboxProcFitAcceptAverage(WMCheckboxAction *cba)
+
+ +
+
+variable PSX_PopupMenuBlockNumber(WMPopupAction *cba)
+
+ +
+
+variable PSX_SetVarBlockSize(WMSetVariableAction *sva)
+
+ +
+
+variable PSX_PopupFitAcceptAverageFunc(WMPopupAction *cba)
+
+ +
+
+variable PSX_PlotStartupSettings()
+
+ +
+
+variable PSX_ApplyMacroToExistingPanel(string win, string mac)
+

Apply the macro mac onto the panel win

+
+ +
+
+

Variables

+
+
+static const double PSX_DEFAULT_FILTER_HIGH = 0
+
+ +
+
+static const double PSX_DEFAULT_FILTER_LOW = 550
+
+ +
+
+static const double PSX_COLOR_ACCEPT_R = 0
+
+ +
+
+static const double PSX_COLOR_ACCEPT_G = 65535
+
+ +
+
+static const double PSX_COLOR_ACCEPT_B = 0
+
+ +
+
+static const double PSX_COLOR_REJECT_R = 65535
+
+ +
+
+static const double PSX_COLOR_REJECT_G = 0
+
+ +
+
+static const double PSX_COLOR_REJECT_B = 0
+
+ +
+
+static const double PSX_COLOR_UNDET_R = 48059
+
+ +
+
+static const double PSX_COLOR_UNDET_G = 48059
+
+ +
+
+static const double PSX_COLOR_UNDET_B = 48059
+
+ +
+
+static const double PSX_KEYBOARD_DIR_RL = 0
+
+ +
+
+static const double PSX_KEYBOARD_DIR_LR = 1
+
+ +
+
+static const double PSX_NUMBER_OF_SDS_DEFAULT = 2.5
+
+ +
+
+static const double PSX_NUM_PEAKS_MAX = 2000
+
+ +
+
+static const double PSX_PLOT_DEFAULT_X_RANGE = 200
+
+ +
+
+static const double PSX_DEFAULT_X_START_OFFSET = 2
+
+ +
+
+static const string USER_DATA_KEYBOARD_DIR = "keyboard_direction"
+
+ +
+
+static const string PSX_USER_DATA_WORKING_FOLDER = "psxFolder"
+
+ +
+
+static const string PSX_X_DATA_UNIT = "X_DATA_UNIT"
+
+ +
+
+static const string PSX_Y_DATA_UNIT = "Y_DATA_UNIT"
+
+ +
+
+static const string PSX_EVENT_DIMENSION_LABELS = "sweepData;sweepDataFiltOff;sweepDataFiltOffDeconv;peakX;peakY;psxEvent;eventFit"
+
+ +
+
+static const double PSX_KERNEL_OUTPUTWAVES_PER_ENTRY = 3
+
+ +
+
+static const double PSX_OPERATION_OUTPUT_WAVES_PER_ENTRY = 7
+
+ +
+
+static const string PSX_SPECIAL_EVENT_PANEL = "SpecialEventPanel"
+
+ +
+
+static const string PSX_SINGLE_EVENT_SUB_GRAPH = "Single"
+
+ +
+
+static const string PSX_ALL_EVENT_SUB_GRAPH = "All"
+
+ +
+
+static const string PSX_CURSOR_TRACE = "peakY"
+
+ +
+
+static const string PSX_USER_DATA_TYPE = "type"
+
+ +
+
+static const string PSX_USER_DATA_PSX = "PSX"
+
+ +
+
+static const string PSX_JWN_COMBO_KEYS_NAME = "ComboKeys"
+
+ +
+
+static const string PSX_JWN_PARAMETERS = "Parameters"
+
+ +
+
+static const string PSX_JWN_STATS_POST_PROC = "PostProcessing"
+
+ +
+
+static const string PSX_TUD_EVENT_INDEX_KEY = "eventIndex"
+
+ +
+
+static const string PSX_UD_NUM_BLOCKS = "NumberOfBlocks"
+
+ +
+
+static const string PSX_TUD_TRACE_HIDDEN_KEY = "traceHidden"
+
+ +
+
+static const string PSX_TUD_TYPE_KEY = "type"
+
+ +
+
+static const string PSX_TUD_COMBO_KEY = "comboKey"
+
+ +
+
+static const string PSX_TUD_COMBO_INDEX = "comboIndex"
+
+ +
+
+static const string PSX_TUD_BLOCK_INDEX = "blockIndex"
+
+ +
+
+static const double PSX_GUI_SETTINGS_VERSION = 1
+
+ +
+
+static const string PSX_GUI_SETTINGS_PSX = "GuiSettingsPSX"
+
+ +
+
+static const double PSX_MAX_NUM_EVENTS = 1e6
+
+ +
+
+static const string PSX_GLOBAL_AVERAGE_SUFFIX = "_global"
+
+ +
+
+static const string PSX_TUD_AVERAGE_ALL_COMBO_KEY = "allCombos"
+
+ +
+
+static const double PSX_TUD_AVERAGE_ALL_COMBO_INDEX = NaN
+
+ +
+
+static const string PSX_AVERAGE_FIT_RESULT_DEFAULT_HELP = "No fit results available for average accept"
+
+ +
+
+static const double PSX_DEFAULT_PEAK_SEARCH_RANGE_MS = 5
+
+ +
+
+static const double PSX_STATS_TAU_FACTOR = 10
+
+ +
+
+static const double PSX_STATS_AMP_FACTOR = 100
+
+ +
+
+static const double PSX_DEFAULT_MAX_TAU_FACTOR = 10
+
+ +
+
+static const string PSX_PANEL_MACRO = "PSXPanel"
+
+ +
+
+static const double EVENT_INDEX_HORIZONTAL = 0x1
+
+ +
+
+static const double EVENT_INDEX_VERTICAL = 0x2
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___sweep_formula___p_s_x___macro_8ipf.html b/file/_m_i_e_s___sweep_formula___p_s_x___macro_8ipf.html new file mode 100644 index 0000000000..c8d5863ffa --- /dev/null +++ b/file/_m_i_e_s___sweep_formula___p_s_x___macro_8ipf.html @@ -0,0 +1,286 @@ + + + + + + + + File MIES_SweepFormula_PSX_Macro.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_SweepFormula_PSX_Macro.ipf

+
+

Functions

+
+
+void PSXPanel()
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___sweep_saving_8ipf.html b/file/_m_i_e_s___sweep_saving_8ipf.html new file mode 100644 index 0000000000..934733b1b9 --- /dev/null +++ b/file/_m_i_e_s___sweep_saving_8ipf.html @@ -0,0 +1,457 @@ + + + + + + + + File MIES_SweepSaving.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_SweepSaving.ipf

+

SWS Scale and store acquired data

+
+

Functions

+
+
+variable SWS_SaveAcquiredData(string device, variable forcedStop = defaultValue)
+

Save the acquired sweep permanently.

+
+
Parameters:
+
    +

  • device – device

    • +

  • forcedStop – [optional, defaults to false] if DAQ was aborted (true) or stopped by itself (false)

    • +
+
+
+
+ +
+
+static std::tuple<variable, variable> SWS_ProcessDATTLChannelsOnEarlyAcqStop(string device, WaveRefWave scaledDataWave, wave config)
+

Determine actual acquisition times and if acquisition was stopped early, change the remaining data points in DA/TTL with NaN. DA/TTL data was prefilled in.

+

+

See also

+

DC_InitScaledDataWave with no early acquisition stop as default

+
+

+
+
Parameters:
+
    +

  • device – device name

    • +

  • scaledDataWave – scaled data wave

    • +

  • config – config wave

    • +
+
+
Return values:
+
    +

  • plannedTime – planned acquisition time, time at one point after the end of the DA wave [s]

    • +

  • acquiredTime – if acquisition was aborted early, time of last acquired point in AD wave [s], NaN otherwise

    • +
+
+
+
+ +
+
+static variable SWS_SetUnacquiredTimeInADCToNaN(wave config, WaveRefWave scaledDataWave, variable acquiredTime)
+

Sets the data points in the AD channels of the unacquired time interval to NaN.

+
+ +
+
+std::tuple<variable, variable> SWS_DeterminePlannedAndAcquiredTime(wave channelDA, wave channelAD, variable adSize, variable lastFifoPos)
+

Determines the acquired and planned time.

+
+
Parameters:
+
    +

  • channelDA – DA channel, as all DA channels run synchroneously, the first DA channel is good enough

    • +

  • channelAD – AD channel, as all AD channels run synchroneously, the first AD channel is good enough

    • +

  • adSize – effective size of the AD channel, where data was sampled (for ITC the AD wave can be longer)

    • +

  • lastFifoPos – at this index - 1 was the last data point sampled

    • +
+
+
+
+ +
+
+static variable SWS_SweepSettingsEpochInfoToLBN(string device, variable sweepNo)
+
+ +
+
+static variable SWS_AfterSweepDataChangeHook(string device)
+

General hook function which gets always executed after sweep data was added or removed.

+
+
Parameters:
+

device – device name

+
+
+
+ +
+
+wave SWS_GetChannelGains(string device, variable timing = defaultValue)
+

Return a free wave with all channel gains.

+

Rows:

    +

  • Active channels only (same as DAQConfigWave)

    • +
+

+

Different hardware has different requirements how the DA, AD and TLL channels are scaled. As general rule use data * SWS_GetChannelGains for GAIN_BEFORE_DAQ and data / SWS_GetChannelGains for GAIN_AFTER_DAQ, i.e. before_gain * data(before_DAQ) == after_gain * data(after_DAQ).

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Hardware

Channel

Specialities

ITC

DA

None

ITC

AD

None

ITC

TTL

Multiple TTL bits are combined. See SplitTTLWaveIntoComponents() for details.

NI

DA

None

NI

AD

Scaled directly on acquisition.

NI

TTL

One channel per TTL bit.

SU

DA

None

SU

AD

Scaled directly on acquisition.

SU

TTL

One channel per TTL bit.

+

+

With GAIN_BEFORE_DAQ the function returns the gain factor for all channels. With GAIN_AFTER_DAC the gain factor for ADC channels is returned as 1. Gain handling for NI: In dataconfigurator setup DAC_values = data(before_DAQ) * gain_factor(DAC_channel)

+

See also

+

DC_FillDAQDataWaveForDAQ at acquisition time done by hardware ADC_values = data(acquired_by_ADC) * gain_factor(ADC_channel)

+
+
+

See also

+

HW_NI_PrepareAcq at acquisition time on readout: oscilloscopeValues = DAC_values scaledValues = DAC_values / gain_factor(DAC_channel) ADC_values are NOT changed, thus a gain factor of 1 is used when calculation indexes over all DAC, ADC, TTL channels.

+
+
+

See also

+

SCOPE_NI_UpdateOscilloscope

+
+
+

See also

+

GetDAQDataWave()

+
+

+
+
Parameters:
+
+
+
+
+ +
+
+variable SWS_GetRawDataFPType(string device)
+

Return the floating point type for storing the raw data.

+

The returned values are the same as for WaveType

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___tango_interact_8ipf.html b/file/_m_i_e_s___tango_interact_8ipf.html new file mode 100644 index 0000000000..ee8d8c4f4c --- /dev/null +++ b/file/_m_i_e_s___tango_interact_8ipf.html @@ -0,0 +1,276 @@ + + + + + + + + File MIES_TangoInteract.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_TangoInteract.ipf

+

This file is only provided for backward compatibility and will always be empty.

+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___test_pulse_8ipf.html b/file/_m_i_e_s___test_pulse_8ipf.html new file mode 100644 index 0000000000..f56dc57740 --- /dev/null +++ b/file/_m_i_e_s___test_pulse_8ipf.html @@ -0,0 +1,839 @@ + + + + + + + + File MIES_TestPulse.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_TestPulse.ipf

+

TP Basic Testpulse related functionality

+
+

Functions

+
+
+variable TP_IsValidBaselineFraction(variable value)
+

Check if the value is a valid baseline fraction.

+

Comment in for debugging of TP_TSAnalysis

+

For visualising the evaluation ranges from the returned DFREF:

+

Duplicate/O dfr:data, root:data
+Duplicate/O dfr:colors, root:colors
+
+ModifyGraph zColor(data)={colors,*,*,Rainbow,1}
+
+
+

+
+ +
+
+static variable TP_CalculateTestPulseLength(variable pulseDuration, variable baselineFrac)
+

Return the total length of a single testpulse with baseline.

+

Static on purpose as all users during DAQ/TP should prefer GetTPSettingsCalculated()

+
+
Parameters:
+
    +

  • pulseDuration – duration of the high portion of the testpulse in points or time

    • +

  • baselineFrac – fraction, not percentage, of the baseline

    • +
+
+
+
+ +
+
+variable TP_CalculateBaselineFraction(variable pulseDuration, variable totalLength)
+

Inverse function of TP_CalculateTestPulseLength.

+

Can be used when reconstructing the baseline fraction from epoch information.

+
+ +
+
+variable TP_StoreTP(string device, wave TPWave, variable tpMarker, string hsList)
+

Stores the given TP wave.

+

+The stored test pulse waves will have column dimension labels in the format HS_X.

+
+
Parameters:
+
    +

  • device – device

    • +

  • TPWave – reference to wave holding the TP data, see GetOscilloscopeWave()

    • +

  • tpMarker – unique number for this set of TPs from all TP channels

    • +

  • hsList – list of headstage numbers in the same order as the columns of TPWave

    • +
+
+
+
+ +
+
+wave TP_GetStoredTPs(string device, variable tpMarker, variable number)
+

Return a number of consecutive test pulses ending with the TP identified by tpMarker.

+

The wave reference wave will have as many columns as active headstages were used.

+
+ +
+
+variable TP_SplitStoredTestPulseWave(string device)
+

Split the stored testpulse wave reference wave into single waves for easier handling.

+
+ +
+
+variable TP_ROAnalysis(ASYNC_ReadOutStruct *ar)
+

Receives data from the async function TP_TSAnalysis(), buffers partial results and puts complete results back to main thread, results are base line level, steady state resistance, instantaneous resistance and their positions collected results for all channels of a measurement are send to TP_RecordTP(), DQ_ApplyAutoBias() when complete.

+
+
Parameters:
+

ar – ASYNC_ReadOutStruct structure with dfr with input data

+
+
+
+ +
+
+static wave TP_CreateOverrideResults(string device, variable type)
+
+ +
+
+static wave TP_GetTPWaveForAutoTP(string device, variable marker)
+

Return a 2D wave with two testpulses concatenated.

+

Rows:

    +

  • TPs

    • +
+

+

Columns:

    +

  • Active headstages

    • +
+

+
+ +
+
+static variable TP_AutoBaseline(string device, variable headstage, wave TPResults, wave TPs)
+
+ +
+
+static std::tuple<variable, variable, variable> TP_AutoFitBaseline(wave data, variable pulseLengthMS)
+

Fit the tail of the first TP with an expontential and return it’s time constant.

+

///
+///        +----+        +----+
+///        |    |        |    |
+///        |    |        |    |
+///        |    |        |    |
+///        |    |        |    |
+///    ----+    +--------+    +----
+///
+///             <-------->
+///            Fitting range
+///
+///    <------------>
+///        One TP
+///
+///        <---->
+///        Pulse
+///
+///
+
+
+ 
@param data          input data
+@param pulseLengthMS length of the pulse (high part) of the testpulse [ms]
+
+@retval result       One of @ref TPBaselineFitResults
+@retval tau          time constant of the decay [ms]
+@retval baseline     baseline length of one pulse (same as the fitting range) [ms]
+
+
+

+
+ +
+
+static variable TP_AutoAmplitudeAndBaseline(string device, wave TPResults, variable marker)
+

Automatically tune the Testpulse amplitude and baseline.

+

Decision logic flowchart:

+

+

+
+ +
+
+variable TP_AutoTPActive(string device)
+
+ +
+
+static variable TP_AutoTPTurnOff(string device, wave autoTPEnable, variable headstage, variable QC)
+
+ +
+
+static variable TP_AutoDisableIfFinished(string device, wave TPStorage)
+

Disable Auto TP if it passed TP_AUTO_TP_CONSECUTIVE_PASSES times in a row.

+
+ +
+
+variable TP_AutoTPGenerateNewCycleID(string device, variable headstage = defaultValue, variable first = defaultValue, variable last = defaultValue)
+

Generate new auto TP cycle IDs.

+

This is required everytime we lock a device or toggle Auto TP for a headstage

+
+
Parameters:
+
    +

  • device – device

    • +

  • headstage – [optional, default to all headstages] only update it for a specific headstage

    • +

  • first – [optional, default to all headstages] only update the range [first, last]

    • +

  • last – [optional, default to all headstages] only update the range [first, last]

    • +
+
+
+
+ +
+
+wave TP_GetValuesFromTPStorage(wave TPStorage, variable headstage, string entry, variable numReqEntries, variable options = defaultValue)
+

Return the last numReqEntries non-NaN values from layer entry of headstage

+
+
Parameters:
+
    +

  • TPStorage – TP results wave, see GetTPStorage()

    • +

  • headstage – Headstage

    • +

  • entry – Name of the value to search

    • +

  • numReqEntries – Number of entries to return, supports integer values and inf

    • +

  • options – [optional, default to nothing] One of TPStorageQueryingOptions

    • +
+
+
+
+ +
+
+dfref TP_TSAnalysis(dfref dfrInp)
+

This function analyses a TP data set. It is called by the ASYNC frame work in an own thread. currently six properties are determined.

+
+
Parameters:
+

dfrInp – input data folder from the ASYNC framework, parameter input order therein follows the setup in TP_SendToAnalysis()

+
+
+
+ +
+
+static variable TP_CalculateAverage(wave TPResultsBuffer, wave TPResults)
+

Calculates running average [box average] for all entries and all headstages.

+
+ +
+
+static variable TP_RecordTP(string device, wave TPResults, variable now, variable tpMarker)
+

Records values from TPResults into TPStorage at defined intervals.

+

Used for analysis of TP over time.

+
+ +
+
+static variable TP_FitResistance(wave TPStorage, variable startRow, variable endRow, variable headstage)
+

Threadsafe wrapper for performing CurveFits on the TPStorage wave.

+
+ +
+
+static variable TP_AnalyzeTP(string device, WaveOrNull TPStorage, variable endRow)
+

Determine the slope of the steady state resistance over a user defined window (in seconds)

+
+
Parameters:
+
    +

  • device – locked device string

    • +

  • TPStorage – test pulse storage wave

    • +

  • endRow – last valid row index in TPStorage

    • +
+
+
+
+ +
+
+variable TP_StopTestPulseOnAllDevices()
+

Stop running background testpulse on all locked devices.

+
+ +
+
+variable TP_StopTestPulseFast(string device)
+

+

See also

+

TP_StopTestPulseWrapper

+
+

+
+ +
+
+variable TP_StopTestPulse(string device)
+

+

See also

+

TP_StopTestPulseWrapper

+
+

+
+ +
+
+static variable TP_StopTestPulseWrapper(string device, variable fast = defaultValue)
+

Stop any running background test pulses.

+
+
Parameters:
+
    +

  • device – device

    • +

  • fast – [optional, defaults to false] Performs only the totally necessary steps for tear down.

    • +
+
+
Returns:
+

One of TestPulseRunModes

+
+
+
+ +
+
+variable TP_RestartTestPulse(string device, variable testPulseMode, variable fast = defaultValue)
+

Restarts a test pulse previously stopped with TP_StopTestPulse.

+
+ +
+
+variable TP_Setup(string device, variable runMode, variable fast = defaultValue)
+

Prepare device for TestPulse.

+
+
Parameters:
+
    +

  • device – device

    • +

  • runMode – Testpulse running mode, one of TestPulseRunModes

    • +

  • fast – [optional, defaults to false] Performs only the totally necessary steps for setup

    • +
+
+
+
+ +
+
+variable TP_SetupCommon(string device)
+

Common setup calls for TP and TP during DAQ.

+
+ +
+
+variable TP_Teardown(string device, variable fast = defaultValue)
+

Perform common actions after the testpulse.

+
+ +
+
+variable TP_TeardownCommon(string device)
+

Common teardown calls for TP and TP during DAQ.

+
+ +
+
+variable TP_GetNumDevicesWithTPRunning()
+

Return the number of devices which have TP running.

+
+ +
+
+variable TP_CheckIfTestpulseIsRunning(string device)
+

Check if the testpulse is running.

+

Can not be used to check for foreground TP as during foreground TP/DAQ nothing else runs.

+
+ +
+
+variable TP_TestPulseHasCycled(string device, variable cycles)
+

See if the testpulse has run enough times to create valid measurements.

+
+
Parameters:
+
    +

  • device – DA_Ephys panel name

    • +

  • cycles – number of cycles that test pulse must run

    • +
+
+
+
+ +
+
+variable TP_UpdateHoldCmdInTPStorage(string device, variable headStage)
+

Save the amplifier holding command in the TPStorage wave.

+
+ +
+
+variable TP_CreateTestPulseWave(string device, variable dataAcqOrTP)
+

Create the testpulse wave with the current settings.

+
+ +
+
+variable TP_CreateTestPulseWaveImpl(wave tp, variable totalLength, variable pulseStart, variable pulseLength)
+

device independent test pulse wave creation

+
+ +
+
+std::tuple<variable, variable, variable> TP_GetCreationPropertiesInPoints(wave TPSettingsCalc, variable dataAcqOrTP)
+
+ +
+
+dfref TP_PrepareAnalysisDF(string device, TPAnalysisInput *tpInput)
+

Prepares a TP data set data folder to the asynchroneous analysis function TP_TSAnalysis.

+
+
Parameters:
+
    +

  • device – [in] title of panel that ran this test pulse

    • +

  • tpInput – holds the parameters send to analysis

    • +
+
+
Returns:
+

data folder that can be pushed for execution by the async frame work

+
+
+
+ +
+
+variable TP_SendToAnalysis(string device, TPAnalysisInput *tpInput)
+

Send a TP data set to the asynchroneous analysis function TP_TSAnalysis.

+
+
Parameters:
+
    +

  • device – [in] title of panel that ran this test pulse

    • +

  • tpInput – holds the parameters send to analysis

    • +
+
+
+
+ +
+
+variable TP_UpdateTPSettingsCalculated(string device)
+
+ +
+
+variable TP_UpdateTPSettingsCalculatedImpl(wave TPSettings, wave samplingIntervals, wave tpCalculated)
+

Device and globals independent calculcation of TPSettingsCalculated.

+
+ +
+
+string TP_AutoTPLabelToLabnotebookName(string lbl)
+

Convert from row names of GetTPSettings()/GetTPSettingsCalculated() to GetTPSettingsLBN() column names.

+
+ +
+
+variable TP_UpdateTPLBNSettings(string device)
+

Update the Testpulse labnotebook wave.

+

DAQ:

    +

  • TPSettings holds the current GUI values

    • +

  • TPSettingsLabnotebook holds the settings which were active when the sweep started

    • +
+

+

TP:

    +

  • TPSettings holds the current GUI values

    • +

  • TPSettingsLabnotebook is cleared when TP is started and filled from TPSettings when TP is stopped This means we only have the latest values for the TP settings which don’t restart TP. For entries which do restart TP we always have the current values. See also the DAEPHYS_TP_CONTROLS_XXX constants.

    • +
+

+

+

See also

+

DAP_TPGUISettingToWave() for the special auto TP entry handling.

+
+

+
+ +
+
+static variable TP_GetTPCycleID(string device)
+

Return the TP cycle ID for the given device.

+
+ +
+
+variable TP_GetPowerSpectrumLength(variable tpLength)
+

Return the length in points of the power spectrum generated via FFT.

+
+ +
+
+

Variables

+
+
+static const double TP_MAX_VALID_RESISTANCE = 3000
+

Units MΩ

+
+ +
+
+static const double TP_TPSTORAGE_EVAL_INTERVAL = 0.18
+
+ +
+
+static const double TP_FIT_POINTS = 5
+
+ +
+
+static const double TP_PRESSURE_INTERVAL = 0.090
+

[s]

+
+ +
+
+static const double TP_EVAL_POINT_OFFSET = 5
+
+ +
+
+static const double TP_BASELINE_FITTING_INSET = 0.3
+
+ +
+
+static const double TP_SET_PRECISION = 2
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___test_pulse___multi_8ipf.html b/file/_m_i_e_s___test_pulse___multi_8ipf.html new file mode 100644 index 0000000000..ffa2975918 --- /dev/null +++ b/file/_m_i_e_s___test_pulse___multi_8ipf.html @@ -0,0 +1,352 @@ + + + + + + + + File MIES_TestPulse_Multi.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_TestPulse_Multi.ipf

+

TPM Multi device background test pulse functionality

+
+

Functions

+
+
+variable TPM_StartTPMultiDeviceLow(string device, variable runModifier = defaultValue, variable fast = defaultValue)
+

Start the test pulse when MD support is activated.

+
+ +
+
+variable TPM_StartTestPulseMultiDevice(string device, variable fast = defaultValue)
+

Start a multi device test pulse, always done in background mode.

+
+ +
+
+static variable TPM_BkrdTPMD(string device)
+
+ +
+
+variable TPM_BkrdTPFuncMD(BackgroundStruct *s)
+

Background TP Multi Device.

+
+ +
+
+variable TPM_StopTestPulseMultiDevice(string device, variable fast = defaultValue)
+
+ +
+
+static variable TPM_HasActiveDevices()
+
+ +
+
+static variable TPM_RemoveDevice(string device)
+
+ +
+
+static variable TPM_AddDevice(string device)
+
+ +
+
+

Variables

+
+
+static const double TPM_NI_TASKTIMEOUT = 0.5
+

After this time in s the background task reading data from the ADC device.

+

will not read multiple TP data sets subsequently to keep up if late

+

it will however still update once per device

+

so the gui thread can update at least every ~0.5 seconds (default value here)

+

however the fifo may run full if the timeout is hit too often

+
+ +
+
+static const double TPM_NI_FIFO_THRESHOLD_SIZE = 1073741824
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___test_pulse___single_8ipf.html b/file/_m_i_e_s___test_pulse___single_8ipf.html new file mode 100644 index 0000000000..23f5d933d9 --- /dev/null +++ b/file/_m_i_e_s___test_pulse___single_8ipf.html @@ -0,0 +1,333 @@ + + + + + + + + File MIES_TestPulse_Single.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_TestPulse_Single.ipf

+

TPS Single device background test pulse functionality

+
+

Functions

+
+
+variable TPS_StartBackgroundTestPulse(string device)
+
+ +
+
+variable TPS_StopTestPulseSingleDevice(string device, variable fast = defaultValue)
+
+ +
+
+variable TPS_TestPulseFunc(BackgroundStruct *s)
+

Background TP Single Device.

+
+ +
+
+variable TPS_StartTestPulseSingleDevice(string device, variable fast = defaultValue)
+

Start a single device test pulse, either in background or in foreground mode depending on the settings.

+
+
Parameters:
+
    +

  • device – device

    • +

  • fast – [optional, defaults to false] Starts TP without any checks or setup. Can be called after stopping it with TP_StopTestPulseFast().

    • +
+
+
+
+ +
+
+variable TPS_StartTestPulseForeground(string device, variable elapsedTime = defaultValue)
+

Start the single device foreground test pulse.

+
+
Parameters:
+
    +

  • device – device

    • +

  • elapsedTime – [defaults to infinity] allow to run the testpulse for the given amount of seconds only.

    • +
+
+
Returns:
+

zero if time elapsed, one if the Testpulse was manually stopped

+
+
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___threaded_f_i_f_o_handling_8ipf.html b/file/_m_i_e_s___threaded_f_i_f_o_handling_8ipf.html new file mode 100644 index 0000000000..581075f6a3 --- /dev/null +++ b/file/_m_i_e_s___threaded_f_i_f_o_handling_8ipf.html @@ -0,0 +1,359 @@ + + + + + + + + File MIES_ThreadedFIFOHandling.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_ThreadedFIFOHandling.ipf

+

TFH Functions related to threadsafe FIFO monitor and stop daemons

+
+

Unnamed Group

+
+
+static const double TFH_RESTART_ACQ = 0x1
+

Mode constants.

+

DAQ restarting for TP MP

+
+ +
+
+static const double TFH_STOP_ACQ = 0x2
+

DAQ stopping.

+
+ +
+
+

Functions

+
+
+variable TFH_StartFIFOResetDeamon(variable hwType, variable deviceID)
+

Start the FIFO reset daemon used for TP MD.

+
+ +
+
+variable TFH_StartFIFOStopDaemon(variable hwType, variable deviceID)
+

Start the FIFO stop daemon used for DAQ MD.

+
+ +
+
+static variable TFH_StartFIFODeamonInternal(variable hwType, variable deviceID, variable mode)
+

Start the FIFO reset daemon used for TP MD.

+

We create one thread group for each device.

+
+ +
+
+variable TFH_StopFIFODaemon(variable hwType, variable deviceID)
+

Stop the FIFO daemon if required.

+

Sets the global threadGroupIDFifo to NaN afterwards.

+
+ +
+
+static variable TFH_FifoLoop(wave config, variable deviceID, variable stopCollectionPoint, variable ADChannelToMonitor, variable mode)
+

Worker function used for monitoring the FIFO position of the given device.

+

Actions depend on mode:

+

+

Stops in the following cases:

    +

  • An error during ITC operation calls

    • +

  • The input queue is not empty

    • +
+

+

Pushes the following entries into the thread queue:

    +

  • fifoPos: fifo position (relative to offset)

    • +
+

+
+ +
+
+

Variables

+
+
+static const double TIMEOUT_IN_MS = 50
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___threadsafe_data_sharing_8ipf.html b/file/_m_i_e_s___threadsafe_data_sharing_8ipf.html new file mode 100644 index 0000000000..95efc0b347 --- /dev/null +++ b/file/_m_i_e_s___threadsafe_data_sharing_8ipf.html @@ -0,0 +1,329 @@ + + + + + + + + File MIES_ThreadsafeDataSharing.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_ThreadsafeDataSharing.ipf

+

Helper functions for accessing global objects from all threads.

+
+

Functions

+
+
+static variable TSDS_Create(string name, variable var)
+

Creates/Overwrites a threadstorage and puts a numerical value in.

+
+ +
+
+variable TSDS_ReadVar(string name, variable defValue = defaultValue, variable create = defaultValue)
+

Reads a numerical value from a threadstorage.

+
+
Parameters:
+
    +

  • name – name of threadstorage

    • +

  • defValue – [optional: default NaN] default value used when storage is created, create flag must be set

    • +

  • create – [optional: default 0] when set the threadstorage is created if it did not exist or had an incompatible format, defValue must be given

    • +
+
+
+
+ +
+
+static wave TSDS_Read(string name)
+

Reads a single wave ref wave from a named threadstorage.

+
+ +
+
+variable TSDS_WriteVar(string name, variable var)
+

Writes a numerical value to a threadstorage, if the threadstorage does not exist it is automatically created.

+
+
Parameters:
+
    +

  • name – name of threadstorage

    • +

  • var – numerical value that should be written

    • +
+
+
Returns:
+

0 if write was successful, 1 if write was not successful

+
+
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___threadsafe_utilities_8ipf.html b/file/_m_i_e_s___threadsafe_utilities_8ipf.html new file mode 100644 index 0000000000..24743a0d6d --- /dev/null +++ b/file/_m_i_e_s___threadsafe_utilities_8ipf.html @@ -0,0 +1,352 @@ + + + + + + + + File MIES_ThreadsafeUtilities.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_ThreadsafeUtilities.ipf

+

TS Helper functions for threadsafe code and main/worker function interactions.

+
+

Functions

+
+
+variable TS_GetNewestFromThreadQueue(variable tgID, string varName, variable timeout_default = defaultValue, variable timeout_tries = defaultValue)
+

Return the newest variable named varName from the thread queue.

+

Return NaN if the thread is not running anymore.

+

Throws away anything else in the datafolder from the thread queue.

+
+ +
+
+wave TS_GetNewestFromThreadQueueMult(variable tgID, WaveText varNames, variable timeout_default = defaultValue, variable timeout_tries = defaultValue)
+

Return the newest variables from the thread queue.

+

The function returns if it received at least one variable from the thread queue. Return an invalid wave reference if the thread is not running anymore.

+

Throws away anything else in the datafolder from the thread queue.

+
+ +
+
+variable TS_ThreadGroupGetVariable(variable tgID, string varName)
+

Return the variable named varName from the thread queue or NaN if there is none.

+

Throws away anything else in the datafolder from the thread queue.

+
+ +
+
+variable TS_ThreadGroupPutVariable(variable tgID, string varName, variable varValue)
+

Push a single variable named varName with value varValue to the thread queue.

+
+ +
+
+variable TS_ThreadGroupPutDFR(variable tgID, dfref dfr)
+

Push a datafolder to the thread queue.

+

Works on a duplicate of the input DF to remove all references. dfr can be a free DF

+
+ +
+
+variable TS_ThreadGroupFinished(variable tgID)
+

Returns 1 if all worker threads have finished.

+
+ +
+
+variable TS_StopThreadGroup(variable tgID)
+

Stop the given thread group.

+

Assumes that the running worker functions finish on getting the abort variable sent.

+
+ +
+
+

Variables

+
+
+static const double TS_GET_REPEAT_TIMEOUT_IN_MS = 1
+
+ +
+
+static const double TS_ERROR_INVALID_TGID = 980
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___trace_user_data_8ipf.html b/file/_m_i_e_s___trace_user_data_8ipf.html new file mode 100644 index 0000000000..4f8e03d3b9 --- /dev/null +++ b/file/_m_i_e_s___trace_user_data_8ipf.html @@ -0,0 +1,415 @@ + + + + + + + + File MIES_TraceUserData.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_TraceUserData.ipf

+

This file holds helper functions to work with our own trace user data handling.

+

It works by storing the trace user data in one wave per graph. It is cleaned up when the graph is killed. For subwindows the window hook responsible for cleaning up is attached to the top-most parent as only that is receiving window hook events.

+
+

Functions

+
+
+variable TUD_RemoveUserDataWave(WMWinHookStruct *s)
+

Window hook for clearing the user data of the attached graph.

+
+ +
+
+variable TUD_Clear(string graph, variable recursive = defaultValue)
+

Clear the user data wave and release the indexing JSON document.

+

Works recursively on all child windows and calls TUD_ClearImpl on each graph.

+
+ +
+
+static variable TUD_ClearImpl(string graph)
+
+ +
+
+string TUD_GetUserData(string graph, string trace, string key)
+

Return the user data given by the graph and trace named key

+
+ +
+
+wave TUD_GetAllUserData(string graph, string trace)
+

Return all the user data from trace of graph

+
+ +
+
+wave TUD_GetUserDataAsWave(string graph, string key, WaveText keys = defaultValue, WaveText values = defaultValue, variable returnIndizes = defaultValue)
+

Return the user data for key of all traces in graph in a 1D text wave.

+
+
Parameters:
+
    +

  • graph – existing graph

    • +

  • key – key value to gather data for

    • +

  • keys – [optional] Either both keys and values are present or none of them. These allow to further restrict the returned result to traces having all of the additional key/value pairs

    • +

  • values – [optional] See key

    • +

  • returnIndizes – [optional, default to false] Return the indizes of the matches instead of the values

    • +
+
+
+
+ +
+
+variable TUD_SetUserData(string graph, string trace, string key, string value)
+

Set the given user data for the trace of the graph.

+
+ +
+
+variable TUD_SetUserDataFromWaves(string graph, string trace, WaveText keys, WaveText values)
+

Set the given user data for the trace of the graph.

+

The keys/values must span a consecutive range.

+
+ +
+
+static variable TUD_GraphIsManaged(string graph)
+
+ +
+
+variable TUD_GetTraceCount(string graph)
+

Return the number of traces in the user data.

+
+ +
+
+variable TUD_RemoveUserData(string graph, string trace)
+

Remove all user data from the given trace.

+
+ +
+
+variable TUD_TraceIsOnGraph(string graph, string trace)
+

Check if the given trace is displayed on the graph.

+
+ +
+
+variable TUD_Init(string graph)
+

Initialize the graph for our user trace data handling.

+

This is done implicitly after the user data wave is created. Once that is cleared with TUD_Clear() and the window is gone, this function can be used to reattach the cleanup hook to the newly created graph.

+
+ +
+
+static variable TUD_AddTrace(variable jsonID, WaveText graphUserData, string trace)
+
+ +
+
+static variable TUD_RemoveTrace(WaveText graphUserData, string trace)
+
+ +
+
+static variable TUD_ConvertTraceNameToRowIndex(WaveText graphUserData, string trace, variable create = defaultValue, variable allowMissing = defaultValue)
+
+ +
+
+static variable TUD_GetIndexJSON(WaveText graphUserData)
+
+ +
+
+static variable TUD_RegenerateJSONIndex(variable jsonID, WaveText graphUserData)
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___utilities___algorithm_8ipf.html b/file/_m_i_e_s___utilities___algorithm_8ipf.html new file mode 100644 index 0000000000..80afb7223f --- /dev/null +++ b/file/_m_i_e_s___utilities___algorithm_8ipf.html @@ -0,0 +1,651 @@ + + + + + + + + File MIES_Utilities_Algorithm.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Utilities_Algorithm.ipf

+

utility functions for common algorithms

+
+

Functions

+
+
+variable Downsample(WaveOrNull wv, variable downsampleFactor, variable upsampleFactor, variable mode, string winFunction = defaultValue)
+

Downsample data.

+

Downsampling is performed on each column of the input wave. Edge-points of the output wave are by default set to zero.

+
+
Parameters:
+
    +

  • wv – numeric wave, its row must hold more points than downsampleFactor. Will hold the downsampled data on successfull return, in the error case the contents are undetermined

    • +

  • downsampleFactor – positive non-zero integer by which the wave should be downsampled

    • +

  • upsampleFactor – positive non-zero integer by which the wave should be upsampled

    • +

  • mode – decimation mode, one of DECIMATION_BY_OMISSION, DECIMATION_BY_AVERAGING or DECIMATION_BY_SMOOTHING.

    • +

  • winFunction – Windowing function for DECIMATION_BY_SMOOTHING mode, must be one of FFT_WINF.

    • +
+
+
Returns:
+

One on error, zero otherwise

+
+
+
+ +
+
+variable CalculateLCMOfWave(wave wv)
+

Compute the least common multiplier of all entries in the 1D-wave.

+
+ +
+
+wave GetUniqueEntries(wave wv, variable caseSensitive = defaultValue, variable dontDuplicate = defaultValue)
+

Returns an unsorted free wave with all unique entries from wv If dontDuplicate is set, then for a single element input wave no new free wave is created but the input wave is returned.

+

uses built-in igor function FindDuplicates. Entries are deleted from left to right.

+
+
Parameters:
+
    +

  • wv – wave reference, can be numeric or text

    • +

  • caseSensitive – [optional, default = 1] Indicates whether comparison should be case sensitive. Applies only if the input wave is a text wave

    • +

  • dontDuplicate – [optional, default = 0] for a single element input wave no new free wave is created but the input wave is returned.

    • +
+
+
+
+ +
+
+string GetUniqueTextEntriesFromList(string list, string sep = defaultValue, variable caseSensitive = defaultValue)
+

Convenience wrapper around GetUniqueTextEntries() for string lists.

+
+ +
+
+static wave GetUniqueTextEntries(WaveText wv, variable caseSensitive = defaultValue, variable dontDuplicate = defaultValue)
+

Search and Remove Duplicates from Text Wave wv.

+

Duplicates are removed from left to right

+
+
Parameters:
+
    +

  • wv – text wave reference

    • +

  • caseSensitive – [optional, default = 1] Indicates whether comparison should be case sensitive.

    • +

  • dontDuplicate – [optional, default = 0] for a single element input wave no new free wave is created but the input wave is returned.

    • +
+
+
Returns:
+

free wave with unique entries

+
+
+
+ +
+
+variable CALL_FUNCTION_LIST_PROTOTYPE(string str)
+

Function prototype for use with CallFunctionForEachListItem.

+
+ +
+
+variable CALL_FUNCTION_LIST_PROTOTYPE_TS(string str)
+

Function prototype for use with CallFunctionForEachListItem.

+
+ +
+
+variable CallFunctionForEachListItem(CALL_FUNCTION_LIST_PROTOTYPE f, string list, string sep = defaultValue)
+

Convenience function to call the function f with each list item.

+

The function’s type must be CALL_FUNCTION_LIST_PROTOTYPE where the return type is ignored.

+
+ +
+
+variable CallFunctionForEachListItem_TS(CALL_FUNCTION_LIST_PROTOTYPE_TS f, string list, string sep = defaultValue)
+

Compatibility wrapper for threadsafe functions f

+

+

See also

+

CallFunctionForEachListItem()

+
+

+
+ +
+
+variable GetRowIndex(wave wv, variable val = defaultValue, string str = defaultValue, WaveOrNull refWave = defaultValue, variable reverseSearch = defaultValue)
+

Return the row index of the given value, string converted to a variable, or wv.

+

Assumes wv being one dimensional and does not use any tolerance for numerical values.

+
+ +
+
+string GetListDifference(string list1, string list2, variable caseSensitive = defaultValue)
+

calculates the relative complement of list2 in list1

+

Every list item of list2 must be in list1.

+

also called the set-theoretic difference of list1 and list2

+
+
Returns:
+

difference as list

+
+
+
+ +
+
+variable InPlaceRandomShuffle(wave inwave, variable noiseGenMode = defaultValue)
+

Random shuffle of the wave contents.

+

Function was taken from: http://www.igorexchange.com/node/1614 author s.r.chinn

+
+
Parameters:
+
    +

  • inwave – The wave that will have its rows shuffled.

    • +

  • noiseGenMode – [optional, defaults to NOISE_GEN_XOSHIRO] type of RNG to use

    • +
+
+
+
+ +
+
+wave ExtractFromSubrange(string listOfRanges, variable dim)
+

Extract the values of a list of subrange specifications See also DisplayHelpTopic “Subrange Display”.

+

Example invocations:

+

WAVE ranges = ExtractFromSubrange("[3,4]_[*]_[1, *;4]_[]_[5][]", 0)
+
+
+

+
+
Parameters:
+
    +

  • listOfRanges – list of subrange specifications separated by **_**

    • +

  • dim – dimension to extract

    • +
+
+
Returns:
+

2-dim wave with the start, stop, step as columns and rows as number of elements. Returns -1 instead of * or (empty). An invalid wave reference is returned on parsing errors.

+
+
+
+ +
+
+wave GetSetUnion(wave wave1, wave wave2)
+

Return a wave of the union of all entries from both waves with duplicates removed.

+

Given {1, 2, 10} and {2, 5, 11} this will return {1, 2, 5, 10, 11}. The order of the returned entries is not defined.

+
+ +
+
+wave GetSetDifference(wave wave1, wave wave2, variable getIndices = defaultValue)
+

Return a wave were all elements which are in both wave1 and wave2 have been removed from wave1.

+

   The text comparison is case insensitive.
+   wave1 must be 1d, the returned wave is 1d.
+   Waves can be text or numeric, both waves must have the same type
+
+
+
+

See also

+

GetListDifference for string lists

+
+

+
+
Parameters:
+
    +

  • wave1 – first wave

    • +

  • wave2 – second wave

    • +

  • getIndices – [optional, default 0] when this flag is set instead of the values the indices in wave1 are returned

    • +
+
+
Returns:
+

Wave with partial values from wave1 or numeric wave with indices of elements in wave1

+
+
+
+ +
+
+static std::tuple<WAVE, variable> GetSetDifferenceNumeric(wave wave1, wave wave2, variable getIndices)
+
+ +
+
+static std::tuple<WAVE, variable> GetSetDifferenceText(WaveText wave1, WaveText wave2, variable getIndices)
+
+ +
+
+wave GetSetIntersection(wave wave1, wave wave2, variable getIndices = defaultValue)
+

Return a wave with the set theory style intersection of wave1 and wave2.

+

Given {1, 2, 4, 10} and {2, 5, 11} this will return {2}. Given {10, 2, 4, 2, 1} and {11, 5, 2} with getIndices = 1 this will return {1, 3}.

+

Inspired by http://www.igorexchange.com/node/366 but adapted to modern Igor Pro It does work with text waves as well, there it performs case sensitive comparisons

+

For wave1 and wave2 numerical and text waves are allowed, wave1 and wave2 must have the same type.

+
+
Parameters:
+
    +

  • wave1 – first wave

    • +

  • wave2 – second wave

    • +

  • getIndices – [optional, default 0] when this flag is set then the index positions of the intersecting elements in the first wave are returned.

    • +
+
+
Returns:
+

free wave with the set intersection or an null wave reference if the intersection is an empty set

+
+
+
+ +
+
+static variable FindLevelSingle(wave data, variable level, variable edge, variable first, variable last)
+
+ +
+
+static wave FindLevelsMult(wave data, variable level, variable edge, variable first, variable last, variable maxNumLevels)
+
+ +
+
+wave FindLevelWrapper(wave data, variable level, variable edge, variable mode, variable maxNumLevels = defaultValue)
+

FindLevel wrapper which handles 2D data without copying data.

+

+The returned levels are in the wave’s row units.

+

FINDLEVEL_MODE_SINGLE:

    +

  • Return a 1D wave with as many rows as columns in the input data

    • +

  • Contents are the x values of the first level or NaN if none could be found

    • +
+

+

FINDLEVEL_MODE_MULTI:

    +

  • Returns a 2D WAVE rows being the number of columns in the input data and columns holding all found x values of the levels per data column.

    • +
+

+

In both cases the dimension label of the each column holds the number of found levels in each data colum. This will be always 1 for FINDLEVEL_MODE_SINGLE.

+
+
Parameters:
+
    +

  • data – input data, can be either 1D or 2D

    • +

  • level – level to search

    • +

  • edge – type of the edge, one of FindLevelEdgeTypes

    • +

  • mode – mode, one of FindLevelModes

    • +

  • maxNumLevels – [optional, defaults to number of points/rows] maximum number of levels to find

    • +
+
+
+
+ +
+
+wave GrepWave(WaveText wv, string regex)
+

Wrapper for Grep which uses a textwave for input and ouput.

+
+ +
+
+wave GrepTextWave(WaveText in, string regexp, variable invert = defaultValue)
+

Grep the given regular expression in the text wave.

+
+ +
+
+std::tuple<WaveDouble, WaveDouble> DistributeElements(variable numElements, variable offset = defaultValue)
+

Distribute N elements over a range from 0.0 to 1.0 with spacing.

+
+ +
+
+variable CalculateNiceLength(variable range, variable multiple)
+

Calculate a nice length which is an integer number of multiple long.

+

For small values \( 10^{-x} \) times multiple are returned

+
+ +
+
+variable BinarySearchText(WaveText theWave, string theText, variable caseSensitive = defaultValue, variable startPos = defaultValue, variable endPos = defaultValue)
+

Finds the first occurrence of a text within a range of points in a SORTED text wave.

+

From https://www.wavemetrics.com/code-snippet/binary-search-pre-sorted-text-waves by Jamie Boyd Completely reworked, fixed and removed unused features

+
+ +
+
+variable DoPowerSpectrum(wave input, wave output, variable col)
+

Calculate PowerSpectrum on a per column basis on each input[][col] and write the result into output[][col]. The result is capped to the output rows. No window function is applied.

+
+ +
+
+wave DoFFT(wave input, string winFunc = defaultValue, variable padSize = defaultValue)
+

Perform FFT on input with optionally given window function.

+
+
Parameters:
+
    +

  • input – Wave to perform FFT on

    • +

  • winFunc – [optional, defaults to NONE] FFT window function

    • +

  • padSize – [optional, defaults to the next power of 2 of the input wave row size] Target size used for padding

    • +
+
+
+
+ +
+
+string CompressNumericalList(string list, string sepChar)
+

Convert a numerical integer list seperated by sepChar to a list including a range sign (“-”) e. g. 1,2,3,4 -> 1-4 1,2,4,5,6 -> 1-2,4-6 1,1,1,2 -> 1-2 the input list does not have to be sorted.

+
+ +
+
+wave SplitLogDataBySize(WaveText logData, string sep, variable lim, variable lastIndex = defaultValue, variable firstPartSize = defaultValue)
+

Splits a text wave (with e.g. log entries) into parts. The parts are limited by a size in bytes such that each part contains only complete lines and is smaller than the given size limit. A possible separator for line endings is considered in the size calculation.

+
+
Parameters:
+
    +

  • logData – text wave

    • +

  • sep – separator string that is considered in the length calculation. This is useful if the resulting waves are later converted to strings with TextWaveToList, where the size grows by lines * separatorLength.

    • +

  • lim – size limit for each part in bytes

    • +

  • lastIndex – [optional, default DimSize(logData, ROWS) - 1] When set, only elements in logData from index 0 to lastIndex are considered. lastIndex is included. lastIndex is limited between 0 and DimSize(logData, ROWS) - 1.

    • +

  • firstPartSize – [optional, default lim] When set then the first parts size limit is firstPartSize instead of lim

    • +
+
+
Returns:
+

wave reference wave containing text waves that are consecutive and sequential parts of logdata

+
+
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___utilities___checks_8ipf.html b/file/_m_i_e_s___utilities___checks_8ipf.html new file mode 100644 index 0000000000..5574ee6b19 --- /dev/null +++ b/file/_m_i_e_s___utilities___checks_8ipf.html @@ -0,0 +1,614 @@ + + + + + + + + File MIES_Utilities_Checks.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Utilities_Checks.ipf

+

Utility functions that check for certain properties and return either 1 (TRUE) or 0 (FALSE)

+
+

Functions

+
+
+variable IsFinite(variable var)
+

Returns 1 if var is a finite/normal number, 0 otherwise.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+variable IsNaN(variable var)
+

Returns 1 if var is a NaN, 0 otherwise.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+variable IsInf(variable var)
+

Returns 1 if var is +/- inf, 0 otherwise.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+variable IsNull(string *str)
+

Returns 1 if str is null, 0 otherwise.

+

+UTF_NOINSTRUMENTATION

+
+
Parameters:
+

str – must not be a SVAR

+
+
+
+ +
+
+variable IsEmpty(string str)
+

Returns one if str is empty, zero otherwise.

+

+UTF_NOINSTRUMENTATION

+
+
Parameters:
+

str – any non-null string variable or text wave element

+
+
+
+ +
+
+variable WindowExists(string win)
+

Checks if the given name exists as window.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+variable ValueCanBeWritten(WaveOrNull wv, variable value)
+

Check that the given value can be stored in the wave.

+

Does currently ignore floating point precision and ranges for integer waves

+
+ +
+
+variable IsInteger(variable var)
+

Returns one if var is an integer and zero otherwise UTF_NOINSTRUMENTATION.

+
+ +
+
+variable IsEven(variable var)
+

UTF_NOINSTRUMENTATION.

+
+ +
+
+variable IsOdd(variable var)
+

UTF_NOINSTRUMENTATION.

+
+ +
+
+variable FuncRefIsAssigned(string funcInfo)
+

Check wether the function reference points to the prototype function or to an assigned function.

+

Due to Igor Pro limitations you need to pass the function info from FuncRefInfo and not the function reference itself.

+

+UTF_NOINSTRUMENTATION

+
+
Returns:
+

1 if pointing to prototype function, 0 otherwise

+
+
+
+ +
+
+variable CheckIfClose(variable var1, variable var2, variable tol = defaultValue, variable strong_or_weak = defaultValue)
+

Compare two variables and determines if they are close.

+

Based on the implementation of “Floating-point comparison algorithms” in the C++ Boost unit testing framework.

+

Literature:

+

The art of computer programming (Vol II). Donald. E. Knuth. 0-201-89684-2. Addison-Wesley Professional; 3 edition, page 234 equation (34) and (35).

+

+

+UTF_NOINSTRUMENTATION

+
+
Parameters:
+
    +

  • var1 – first variable

    • +

  • var2 – second variable

    • +

  • tol – [optional, defaults to 1e-8] tolerance

    • +

  • strong_or_weak – [optional, defaults to strong] type of condition, can be zero for weak or 1 for strong

    • +
+
+
+
+ +
+
+variable CheckIfSmall(variable var, variable tol = defaultValue)
+

Test if a variable is small using the inequality \( | var | < | tol | \).

+
+
Parameters:
+
    +

  • var – variable

    • +

  • tol – [optional, defaults to 1e-8] tolerance

    • +
+
+
+
+ +
+
+variable IsTextWave(wave wv)
+

Return 1 if the wave is a text wave, zero otherwise UTF_NOINSTRUMENTATION.

+
+ +
+
+variable IsNumericWave(wave wv)
+

Return 1 if the wave is a numeric wave, zero otherwise UTF_NOINSTRUMENTATION.

+
+ +
+
+variable IsWaveRefWave(wave wv)
+

Return 1 if the wave is a wave reference wave, zero otherwise UTF_NOINSTRUMENTATION.

+
+ +
+
+variable IsFloatingPointWave(wave wv)
+

Return 1 if the wave is a floating point wave UTF_NOINSTRUMENTATION.

+
+ +
+
+variable IsDoubleFloatingPointWave(wave wv)
+

Return 1 if the wave is a double (64bit) precision floating point wave.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+variable IsSingleFloatingPointWave(wave wv)
+

Return 1 if the wave is a single (32bit) precision floating point wave.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+variable IsGlobalWave(wave wv)
+

Return 1 if the wave is a global wave (not a null wave and not a free wave)

+
+ +
+
+variable IsComplexWave(wave wv)
+

Return 1 if the wave is a complex wave.

+
+ +
+
+variable IsFreeWave(wave wv)
+

Return true if wv is a free wave, false otherwise.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+variable HasOneValidEntry(wave wv)
+

Return true if not all wave entries are NaN, false otherwise.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+variable HasOneFiniteEntry(wave wv)
+

Return true if wave has one finite entry (not Inf, -Inf or NaN)

+
+ +
+
+variable HasOneNonFiniteEntry(wave wv)
+

Return true if wave has one infinite entry (Inf, -Inf or NaN)

+
+ +
+
+variable StringEndsWith(string str, string suffix)
+

Checks if a string ends with a specific suffix. The check is case-insensitive.

+
+
Parameters:
+
    +

  • str – [in] string to check for suffix

    • +

  • suffix – [in] to check for

    • +
+
+
Returns:
+

1 if str ends with suffix, 0 otherwise. If str and/or suffix are empty or null 0 is returned.

+
+
+
+ +
+
+variable EqualValuesOrBothNaN(variable left, variable right)
+

Check wether val1 and val2 are equal or both NaN.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+variable IsConstant(wave wv, variable val, variable ignoreNaN = defaultValue)
+

Checks wether wv is constant and has the value val

+

+UTF_NOINSTRUMENTATION

+
+
Parameters:
+
    +

  • wv – wave to check

    • +

  • val – value to check

    • +

  • ignoreNaN – [optional, defaults to true] ignore NaN in wv

    • +
+
+
+
+ +
+
+variable IsValidRegexp(string regexp)
+

Return true if the passed regular expression is well-formed.

+
+ +
+
+static variable AreIntervalsIntersectingImpl(variable index, wave intervals)
+
+ +
+
+variable AreIntervalsIntersecting(wave intervalsParam)
+

Return the truth if any of the given intervals ]A, B[ intersect.

+
+
Parameters:
+

intervalsParam – Nx2 wave with the intervals

+
+
+
+ +
+
+variable HasWildcardSyntax(string str)
+

Return true if str is in wildcard syntax, false if not.

+
+ +
+
+variable MatchAgainstWildCardPatterns(WaveText patterns, string matchThis)
+

Attempts matching against a number of wildcard patterns.

+
+
Parameters:
+
    +

  • patterns – text wave with wildcard patterns to match against

    • +

  • matchThis – string that is matched

    • +
+
+
Returns:
+

Returns 1 if matchThis was successfully matches, 0 otherwise

+
+
+
+ +
+
+variable ListHasOnlyOneUniqueEntry(string list, string sep = defaultValue)
+

Check if all elements of the string list are the same.

+

Returns true for lists with less than one element

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___utilities___conversions_8ipf.html b/file/_m_i_e_s___utilities___conversions_8ipf.html new file mode 100644 index 0000000000..d487d460cf --- /dev/null +++ b/file/_m_i_e_s___utilities___conversions_8ipf.html @@ -0,0 +1,610 @@ + + + + + + + + File MIES_Utilities_Conversions.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Utilities_Conversions.ipf

+

Utility functions for conversions.

+
+

Functions

+
+
+variable ConvertFromBytesToMiB(variable var)
+

Convert Bytes to MiBs, a mebibyte being 2^20.

+
+ +
+
+variable ConvertSamplingIntervalToRate(variable val)
+

Convert the sampling interval in microseconds (1e-6s) to the rate in kHz.

+
+ +
+
+variable ConvertRateToSamplingInterval(variable val)
+

Convert the rate in kHz to the sampling interval in microseconds (1e-6s)

+
+ +
+
+string TextWaveToList(WaveTextOrNull txtWave, string rowSep, string colSep = defaultValue, string layerSep = defaultValue, string chunkSep = defaultValue, variable stopOnEmpty = defaultValue, variable maxElements = defaultValue, variable trailSep = defaultValue)
+

Convert a text wave to string list.

+

+Counterpart

+

See also

+

ConvertListToTextWave

+
+
+

See also

+

NumericWaveToList

+
+

+
+
Parameters:
+
    +

  • txtWave – input text wave

    • +

  • rowSep – separator for row entries

    • +

  • colSep – [optional, default = “,”] separator for column entries

    • +

  • layerSep – [optional, default = “:”] separator for layer entries

    • +

  • chunkSep – [optional, default = “/”] separator for chunk entries

    • +

  • stopOnEmpty – [optional, default = 0] when 1 stops generating the list when an empty string entry in txtWave is encountered

    • +

  • maxElements – [optional, defaults to inf] output only the first maxElements entries

    • +

  • trailSep – [optional, defaults to true] add trailing separators at the very end

    • +
+
+
Returns:
+

string with wave entries separated as list using given separators

+
+
+
+ +
+
+wave ListToTextWaveMD(string list, variable dims, string rowSep = defaultValue, string colSep = defaultValue, string laySep = defaultValue, string chuSep = defaultValue)
+

Converts a list to a multi dimensional text wave, treating it row major order The output wave does not contain unused dimensions, so if dims = 4 is specified but no chunk separator is found then the returned wave is 3 dimensional. An empty list results in a zero dimensional wave.

+

+The following call ListToTextWaveMD(“1/5/6/:8/:,;2/:,;3/7/:,;4/:,;”, 4, rowSep=”;”, colSep=”,”,laySep=”:”, chuSep=”/”) returns ‘free’[0][0][0][0]= {“1”,”2”,”3”,”4”} ‘free’[0][0][1][0]= {“8”,””,””,””} ‘free’[0][0][0][1]= {“5”,””,”7”,””} ‘free’[0][0][1][1]= {“”,””,””,””} ‘free’[0][0][0][2]= {“6”,””,””,””} ‘free’[0][0][1][2]= {“”,””,””,””}

+
+
Parameters:
+
    +

  • list – [in] input string with list

    • +

  • dims – [in] number of dimensions the output text wave should have

    • +

  • rowSep – [in] [optional, default = “;”] row separator

    • +

  • colSep – [in] [optional, default = “,”] column separator

    • +

  • laySep – [in] [optional, default = “:”] layer separator

    • +

  • chuSep – [in] [optional, default = “/”] chunk separator

    • +
+
+
Returns:
+

text wave with at least dims dimensions

+
+
+
+ +
+
+string NumericWaveToList(WaveOrNull wv, string sep, string format = defaultValue, string colSep = defaultValue, variable trailSep = defaultValue)
+

Convert a 1D or 2D numeric wave to string list.

+

Counterpart

+

See also

+

ListToNumericWave

+
+
+

See also

+

TextWaveToList

+
+

+
+
Parameters:
+
    +

  • wv – numeric wave

    • +

  • sep – separator

    • +

  • colSep – [optional, default = ,] separator for column entries

    • +

  • format – [optional, defaults to g] sprintf conversion specifier

    • +

  • trailSep – [optional, defaults to false] don’t add a row separator after the last row

    • +
+
+
+
+ +
+
+static string WaveToListFast(wave wv, string format, string sep, string colSep, variable trailSep)
+
+ +
+
+wave ListToNumericWave(string list, string sep, variable type = defaultValue, variable ignoreErr = defaultValue)
+

Convert a list to a numeric wave.

+

Counterpart

+

See also

+

NumericWaveToList().

+
+
+

See also

+

TextWaveToList

+
+

+
+
Parameters:
+
    +

  • list – list with numeric entries

    • +

  • sep – separator

    • +

  • type – [optional, defaults to double precision float (IGOR_TYPE_64BIT_FLOAT)] type of the created numeric wave

    • +

  • ignoreErr – [optional, defaults 0] when this flag is set conversion errors are ignored, the value placed is NaN (-9223372036854775808 for int type)

    • +
+
+
+
+ +
+
+variable str2numSafe(string str)
+

str2num variant with no runtime error on invalid conversions

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string FloatWithMinSigDigits(variable var, variable numMinSignDigits = defaultValue)
+

Return a floating point value as string rounded to the given number of minimum significant digits.

+

This allows to specify the minimum number of significant digits. The normal printf/sprintf specifier only allows the maximum number of significant digits for g.

+
+ +
+
+string ToPassFail(variable passedOrFailed)
+
+ +
+
+string ToTrueFalse(variable var)
+
+ +
+
+string ToOnOff(variable var)
+
+ +
+
+string DAQRunModeToString(variable runMode)
+

Convert the DAQ run mode to a string.

+
+
Parameters:
+

runMode – One of DAQRunModes

+
+
+
+ +
+
+string TestPulseRunModeToString(variable runMode)
+

Convert the Testpulse run mode to a string.

+
+
Parameters:
+

runMode – One of TestPulseRunModes

+
+
+
+ +
+
+string num2strHighPrec(variable val, variable precision = defaultValue, variable shorten = defaultValue)
+

Converts a number to a string with specified precision (digits after decimal dot). This function is an extension for the regular num2str that is limited to 5 digits. Input numbers are rounded using the “round-half-to-even” rule to the given precision. The default precision is 5. If val is complex only the real part is converted to a string.

+
+
Parameters:
+
    +

  • val – [in] number that should be converted to a string

    • +

  • precision – [in] [optional, default 5] number of precision digits after the decimal dot using “round-half-to-even” rounding rule. Precision must be in the range 0 to MAX_DOUBLE_PRECISION.

    • +

  • shorten – [in] [optional, defaults to false] Remove trailing zeros and optionally the decimal dot to get a minimum length string

    • +
+
+
Returns:
+

string with textual number representation

+
+
+
+ +
+
+variable ScaleToIndexWrapper(wave wv, variable scale, variable dim)
+

wrapper to ScaleToIndex

+

ScaleToIndex treats input inf to scale always as the last point in a wave. -inf on the other hand is undefined. This wrapper function respects the scaled point wave. -inf refers to the negative end of the scaled wave and +inf is the positive end of the scaled wave. This means that this wrapper function also respects the DimDelta direction of the wave scaling. and always returns the closest matching (existing) point in the wave. This also means that the returned values cannot be negative or larger than the numer of points in the wave.

+
+
Returns:
+

an existing index in wv between 0 and DimSize(wv, dim) - 1

+
+
+
+ +
+
+variable HexToNumber(string ch)
+

Convert a hexadecimal character into a number.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string NumberToHex(variable var)
+

Convert a number into hexadecimal.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+wave HexToBinary(string str)
+

Convert a string in hex format to an unsigned binary wave.

+

This function works on a byte level so it does not care about endianess.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string ConvertListToRegexpWithAlternations(string list, variable literal = defaultValue, string sep = defaultValue)
+

Turn a list of entries into a regular expression with alternations.

+

Can be used for GetListOfObjects() if you know in advance which entries to filter out.

+
+
Parameters:
+
    +

  • list – semicolon separated list of strings to match

    • +

  • literal – [optional, default = 1] when this flag is cleared the string elements of the list are treated as regular expressions

    • +

  • sep – [optional, default = “;”] separator for list

    • +
+
+
+
+ +
+
+wave ConvertToUniqueNumber(WaveText wv, variable doZapNaNs = defaultValue, variable doSort = defaultValue)
+

Convert a text wave to a double wave with optional support for removing NaNs and sorting.

+
+ +
+
+string GetCodeForWaveContents(WaveText wv)
+

Prepare wave for inline definition.

+

Outputs a wave in a format so that it can be initialized with these contents in an Igor Pro procedure file.

+
+ +
+
+variable WaveTypeStringToNumber(string type)
+

Returns the wave type as constant.

+

Same constant as WaveType with selector zero (default) and Redimension/Y.

+
+ +
+
+string WaveToJSON(WaveOrNull wv)
+

Serialize a wave as JSON and return it as string.

+

The format is documented here.

+
+ +
+
+wave JSONToWave(string str, string path = defaultValue)
+

Deserialize a JSON document generated by WaveToJSON()

+

Supports only a currently used subset.

+

+

See also

+

WaveToJSON

+
+

+
+
Parameters:
+
    +

  • str – serialized JSON document

    • +

  • path – [optional, defaults to “”] json path with the serialized wave info

    • +
+
+
+
+ +
+
+wave UTF8StringToTextWave(string str)
+

Converts a string in UTF8 encoding to a text wave where each wave element contains one UTF8 characters.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___utilities___data_folder_8ipf.html b/file/_m_i_e_s___utilities___data_folder_8ipf.html new file mode 100644 index 0000000000..aae00ab82b --- /dev/null +++ b/file/_m_i_e_s___utilities___data_folder_8ipf.html @@ -0,0 +1,453 @@ + + + + + + + + File MIES_Utilities_DataFolder.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Utilities_DataFolder.ipf

+

utility functions for datafolder handling

+
+

Functions

+
+
+string GetListOfObjects(dfref dfr, string matchExpr, variable typeFlag = defaultValue, variable fullPath = defaultValue, variable recursive = defaultValue, variable exprType = defaultValue)
+

Alternative implementation for WaveList/VariableList/etc. which honours a dfref and thus does not require SetDataFolder calls.

+
+
Parameters:
+
    +

  • dfr – datafolder reference to search for the objects

    • +

  • matchExpr – expression matching the objects, either a regular (exprType == MATCH_REGEXP) or wildcard (exprType == MATCH_WILDCARD) expression

    • +

  • typeFlag – [optional, default: COUNTOBJECTS_WAVES] One of TypeFlags

    • +

  • fullPath – [optional, default: false] should only the object name or the absolute path of the object be returned

    • +

  • recursive – [optional, default: false] descent into all subfolders recursively

    • +

  • exprType – [optional, defaults: MATCH_REGEXP] convention used for matchExpr, one of MatchExpressions

    • +
+
+
Returns:
+

list of object names matching matchExpr

+
+
+
+ +
+
+static string GetAllObjects(dfref dfr, variable typeFlag)
+

Return a list of all objects of the given type from dfr.

+
+ +
+
+variable DataFolderExistsDFR(dfref dfr)
+

Checks if the datafolder referenced by dfr exists.

+
+
Parameters:
+

dfr – [in] data folder to test

+
+
Returns:
+

one if dfr is valid and references an existing or free datafolder, zero otherwise UTF_NOINSTRUMENTATION

+
+
+
+ +
+
+variable IsGlobalDataFolder(dfref dfr)
+

Check if the passed datafolder reference is a global/permanent datafolder.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+variable IsFreeDatafolder(dfref dfr)
+

Returns 1 if dfr is a valid free datafolder, 0 otherwise.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref createDFWithAllParents(string dataFolder)
+

Create a datafolder and all its parents,.

+

Includes fast handling of the common case that the datafolder exists.

+
+
Returns:
+

reference to the datafolder UTF_NOINSTRUMENTATION

+
+
+
+ +
+
+variable RemoveEmptyDataFolder(dfref dfr)
+

Removes the datafolder reference if there are no objects in it anymore.

+
+
Parameters:
+

dfr – data folder reference to kill

+
+
Returns:
+

1 in case the folder was removed and 0 in all other cases

+
+
+
+ +
+
+variable IsDataFolderEmpty(dfref dfr)
+

Return 1 if the datafolder is empty, zero if not.

+
+ +
+
+variable RemoveAllEmptyDataFolders(dfref sourceDFR)
+

Remove all empty datafolders in the passed datafolder reference recursively including sourceDFR.

+
+ +
+
+dfref UniqueDataFolder(dfref dfr, string baseName)
+

Returns a reference to a newly created datafolder.

+

Basically a datafolder aware version of UniqueName for datafolders

+
+
Parameters:
+
    +

  • dfr – datafolder reference where the new datafolder should be created

    • +

  • baseName – first part of the datafolder, might be shortend due to Igor Pro limitations

    • +
+
+
+
+ +
+
+string UniqueDataFolderName(dfref dfr, string baseName)
+

Return an absolute unique data folder name which does not exist in dfr.

+
+
Parameters:
+
    +

  • dfr – datafolder to search

    • +

  • baseName – first part of the datafolder

    • +
+
+
+
+ +
+
+variable RenameDataFolderToUniqueName(string path, string suffix)
+

Rename the given datafolder path to a unique name.

+

With path root:a:b:c and suffix _old the datafolder is renamed to root:a:b:c_old or if that exists root:a:b:c_old_1 and so on.

+
+ +
+
+variable RefCounterDFIncrease(dfref dfr)
+

For DF memory management, increase reference count.

+
+
Parameters:
+

dfr – data folder reference of the target df

+
+
+
+ +
+
+variable RefCounterDFDecrease(dfref dfr)
+

For DF memory management, decrease reference count and kill DF if zero is reached.

+
+
Parameters:
+

dfr – data folder reference of the target df

+
+
+
+ +
+
+variable DFREFClear(dfref *dfr)
+

Clear the given datafolder reference.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___utilities___debugger_8ipf.html b/file/_m_i_e_s___utilities___debugger_8ipf.html new file mode 100644 index 0000000000..59b40c9dda --- /dev/null +++ b/file/_m_i_e_s___utilities___debugger_8ipf.html @@ -0,0 +1,353 @@ + + + + + + + + File MIES_Utilities_Debugger.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Utilities_Debugger.ipf

+

utility functions for debugger

+
+

Debugger state constants for DisableDebugger and ResetDebuggerState

+
+
+static const double DEBUGGER_ENABLED = 0x01
+
+ +
+
+static const double DEBUGGER_DEBUG_ON_ERROR = 0x02
+
+ +
+
+static const double DEBUGGER_NVAR_CHECKING = 0x04
+
+ +
+
+

Functions

+
+
+variable DisableDebugger()
+

Disable the debugger.

+
+
Returns:
+

the full debugger state binary encoded. first bit: on/off, second bit: debugOnError on/off, third bit: nvar/svar/wave checking on/off

+
+
+
+ +
+
+variable ResetDebuggerState(variable debuggerState)
+

Reset the debugger to the given state.

+

Useful in conjunction with DisableDebugger() to temporarily disable the debugger 

variable debuggerState = DisableDebugger()
+// code which might trigger the debugger, e.g. CurveFit
+ResetDebuggerState(debuggerState)
+// now the debugger is in the same state as before
+
+
+

+

+
+ +
+
+variable DisableDebugOnError()
+

Disable Debug on Error.

+
+
Returns:
+

1 if it was enabled, 0 if not, pass this value to ResetDebugOnError()

+
+
+
+ +
+
+variable ResetDebugOnError(variable debugOnError)
+

Reset Debug on Error state.

+
+
Parameters:
+

debugOnError – state before, usually the same value as DisableDebugOnError() returned

+
+
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___utilities___file_8ipf.html b/file/_m_i_e_s___utilities___file_8ipf.html new file mode 100644 index 0000000000..d21f23e285 --- /dev/null +++ b/file/_m_i_e_s___utilities___file_8ipf.html @@ -0,0 +1,664 @@ + + + + + + + + File MIES_Utilities_File.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Utilities_File.ipf

+

utility functions for file handling

+
+

Functions

+
+
+string UniqueFileOrFolder(string symbPath, string baseName, string suffix = defaultValue)
+

Returns a unique and non-existing file or folder name.

+
+

Warning

+

This function must not be used for security relevant purposes, as for that the check-and-file-creation must be an atomic operation.

+
+
+
Parameters:
+
    +

  • symbPath – symbolic path

    • +

  • baseName – base name of the file, must not be empty

    • +

  • suffix – file/folder suffix

    • +
+
+
+
+ +
+
+variable IsDriveValid(string absPath)
+

Return true if the given absolute path refers to an existing drive letter.

+
+ +
+
+string GetDrive(string path)
+

Return the drive letter of the given path (Windows) or the volume name (Macintosh)

+
+ +
+
+variable CreateFolderOnDisk(string absPath)
+

Create a folder recursively on disk given an absolute path.

+

If you pass windows style paths using backslashes remember to always double them.

+
+ +
+
+string GetBaseName(string filePathWithSuffix, string sep = defaultValue)
+

Return the base name of the file.

+

Given path/file.suffix this gives file.

+
+
Parameters:
+
    +

  • filePathWithSuffix – full path

    • +

  • sep – [optional, defaults to “:”] character separating the path components

    • +
+
+
+
+ +
+
+string GetFileSuffix(string filePathWithSuffix, string sep = defaultValue)
+

Return the file extension (suffix)

+

Given path/file.suffix this gives suffix.

+
+
Parameters:
+
    +

  • filePathWithSuffix – full path

    • +

  • sep – [optional, defaults to “:”] character separating the path components

    • +
+
+
+
+ +
+
+string GetFolder(string filePathWithSuffix, string sep = defaultValue)
+

Return the folder of the file.

+

Given path/file.suffix this gives path. The returned result has a trailing separator.

+
+
Parameters:
+
    +

  • filePathWithSuffix – full path

    • +

  • sep – [optional, defaults to “:”] character separating the path components

    • +
+
+
+
+ +
+
+string GetFile(string filePathWithSuffix, string sep = defaultValue)
+

Return the filename with extension.

+

Given path/file.suffix this gives file.suffix.

+
+
Parameters:
+
    +

  • filePathWithSuffix – full path

    • +

  • sep – [optional, defaults to “:”] character separating the path components

    • +
+
+
+
+ +
+
+string GetWindowsPath(string path)
+

Return the path converted to a windows style path.

+
+ +
+
+string GetHFSPath(string path)
+

Return the path converted to a HFS style (aka “:” separated) path.

+
+ +
+
+string ResolveAlias(string path, string pathName = defaultValue)
+

Recursively resolve shortcuts to files/directories.

+
+
Returns:
+

full path or an empty string if the file does not exist or the shortcut points to a non existing file/folder

+
+
+
+ +
+
+string GetUniqueSymbolicPath(string prefix = defaultValue)
+

Return a unique symbolic path name.

+

string symbPath = GetUniqueSymbolicPath()
+NewPath/Q/O $symbPath, "C:"
+
+
+

+
+ +
+
+string GetAllFilesRecursivelyFromPath(string pathName, string extension = defaultValue)
+

Return a list of all files from the given symbolic path and its subfolders. The list is pipe (FILE_LIST_SEP) separated as the semicolon (;) is a valid character in filenames.

+

Note: This function does not work on MacOSX as there filenames are allowed to have pipe symbols in them.

+
+
Parameters:
+
    +

  • pathName – igor symbolic path to search recursively

    • +

  • extension – [optional, defaults to all files] file suffixes to search for

    • +
+
+
+
+ +
+
+string AskUserForExistingFolder(string baseFolder)
+

Open a folder selection dialog.

+
+
Returns:
+

a string denoting the selected folder, or an empty string if nothing was supplied.

+
+
+
+ +
+
+variable HasEnoughDiskspaceFree(string diskPath, variable requiredFreeSpace)
+

Check that the given path on disk has enough free space.

+
+
Parameters:
+
    +

  • diskPath – path on disk to check

    • +

  • requiredFreeSpace – required free space in GB

    • +
+
+
+
+ +
+
+variable GetOpenZFlag()
+

Return a /Z flag value for the Open operation which works with automated testing.

+
+ +
+
+variable SaveTextFile(string *data, string *fileName, string *fileFilter = defaultValue, string *message = defaultValue, string *savedFileName = defaultValue, variable showDialogOnOverwrite = defaultValue)
+

Saves string data to a file.

+
+
Parameters:
+
    +

  • data – [in] string containing data to save

    • +

  • fileName – [in] fileName to use. If the fileName is empty or invalid a file save dialog will be shown.

    • +

  • fileFilter – [in] [optional, default = “Plain Text Files (*.txt):.txt;All Files:.*;”] file filter string in Igor specific notation.

    • +

  • message – [in] [optional, default = “Create file”] window title of the save file dialog.

    • +

  • savedFileName – [out] [optional, default = “”] file name of the saved file

    • +

  • showDialogOnOverwrite – [in] [optional, default = 0] opens save file dialog, if the current fileName would cause an overwrite, to allow user to change fileName

    • +
+
+
Returns:
+

NaN if file open dialog was aborted or an error was encountered, 0 otherwise

+
+
+
+ +
+
+std::tuple<string, string> LoadTextFile(string fileName, string fileFilter = defaultValue, string message = defaultValue)
+

Load data from file to a string. The file size must be < 2GB.

+
+
Parameters:
+
    +

  • fileName – [in] fileName to use. If the fileName is empty or invalid a file load dialog will be shown.

    • +

  • fileFilter – [in] [optional, default = “Plain Text Files (*.txt):.txt;All Files:.*;”] file filter string in Igor specific notation.

    • +

  • message – [in] [optional, default = “Select file”] window title of the save file dialog.

    • +
+
+
Returns:
+

loaded string data and full path fileName

+
+
+
+ +
+
+wave LoadTextFileToWave(string fullFilePath, string sep)
+

Load data from a file to a text wave.

+
+
Parameters:
+
    +

  • fullFilePath – [in] full path to the file to be loaded

    • +

  • sep – [in] separator string that splits the file data to the wave cells, typically the line ending

    • +
+
+
Returns:
+

free text wave with the data, a null wave if the file could not be found or there was a problem reading the file

+
+
+
+ +
+
+variable FileExists(string filepath)
+

Check wether the given path points to an existing file.

+

Resolves shortcuts and symlinks recursively.

+
+ +
+
+variable FolderExists(string folderpath)
+

Check wether the given path points to an existing folder.

+
+ +
+
+string GetFileVersion(string filepath)
+

Return the file version.

+
+ +
+
+variable GetFileSize(string filepath)
+

Return the file size in bytes.

+
+ +
+
+string HFSPathToPosix(string path)
+

Convert a HFS path (:) to a POSIX path (/)

+

The path must exist.

+
+ +
+
+string HFSPathToWindows(string path)
+

Convert a HFS path (:) to a Windows path (\\)

+
+ +
+
+string HFSPathToNative(string path)
+

Convert HFS path (:) to OS native path (\\ or /)

+
+ +
+
+string GetSymbolicPathForDiagnosticsDirectory()
+

Return the name of a symbolic path which points to the crash dump directory on windows.

+
+ +
+
+variable ShowDiagnosticsDirectory()
+
+ +
+
+string SanitizeFilename(string name)
+

Sanitize the given name so that it is a nice file name.

+
+ +
+
+wave LoadWaveFromDisk(string name)
+

Load the wave $name.itx from the folder of this procedure file and store it in the static data folder.

+
+ +
+
+variable StoreWaveOnDisk(wave wv, string name)
+

Store the given wave as $name.itx in the same folder as this procedure file on disk.

+
+ +
+
+string GetUserDocumentsFolderPath()
+

Returns the path to the users documents folder.

+
+ +
+
+string CleanupExperimentName(string expName)
+

Cleanup the experiment name.

+
+ +
+
+string CalcHashForFile(string path, variable method = defaultValue)
+

Calculate a cryptographic hash for the file contents of path.

+
+
Parameters:
+
    +

  • path – absolute path to a file

    • +

  • method – [optional, defaults to HASH_SHA2_256] Type of cryptographic hash function, one of HASH_SHA2_256

    • +
+
+
+
+ +
+
+variable CheckIfPathsRefIdenticalFiles(string list)
+

Check if the file paths referenced in list are pointing to identical files.

+
+ +
+
+string GetProgramFilesFolder()
+

Return a path to the program folder with trailing dir separator.

+

Hardcoded as Igor does not allow to query that information.

+

Distinguishes between i386 and x64 Igor versions

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___utilities___g_u_i_8ipf.html b/file/_m_i_e_s___utilities___g_u_i_8ipf.html new file mode 100644 index 0000000000..fabfbf77fc --- /dev/null +++ b/file/_m_i_e_s___utilities___g_u_i_8ipf.html @@ -0,0 +1,657 @@ + + + + + + + + File MIES_Utilities_GUI.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Utilities_GUI.ipf

+

utility functions for GUI

+
+

Functions

+
+
+variable IsWaveDisplayedOnGraph(string win, WaveOrNull wv = defaultValue, dfref dfr = defaultValue)
+

Check if a given wave, or at least one wave from the dfr, is displayed on a graph.

+
+
Returns:
+

one if one is displayed, zero otherwise

+
+
+
+ +
+
+variable KillCursorInGraphs(string graphs, string cursorName)
+

Kill all cursors in a given list of graphs.

+
+
Parameters:
+
    +

  • graphs – semicolon separated list of graph names

    • +

  • cursorName – name of cursor as string

    • +
+
+
+
+ +
+
+string FindCursorInGraphs(string graphs, string cursorName)
+

Find the first match for a given cursor in a list of graph names.

+
+
Parameters:
+
    +

  • graphs – semicolon separated list of graph names

    • +

  • cursorName – name of cursor as string

    • +
+
+
Returns:
+

graph where cursor was found

+
+
+
+ +
+
+variable GetCursorXPositionAB(string graph, variable *csrAx, variable *csrBx)
+

get the x value of the cursors A and B

+

+
+Todo:
+

make this a generic cursor getter function and merge with cursors() in

+
+ +
+

See also

+

SF_FormulaExecutor

+
+

+
+
Parameters:
+
    +

  • graph – [in] where the cursor are

    • +

  • csrAx – [out] Position of cursor A

    • +

  • csrBx – [out] Position of cursor B

    • +
+
+
+
+ +
+
+variable RemoveAnnotationsFromGraph(string graph)
+

Removes all annotations from the graph.

+
+ +
+
+string UniqueTraceName(string graph, string baseName)
+

Return a unique trace name in the graph.

+

Remember that it might be necessary to call DoUpdate if you added possibly colliding trace names in the current function run.

+
+
Parameters:
+
    +

  • graph – existing graph

    • +

  • baseName – base name of the trace, must not be empty

    • +
+
+
+
+ +
+
+variable GetMarkerSkip(variable numPoints, variable numMarkers)
+

Calculate the value for mskip of ModifyGraph

+
+
Parameters:
+
    +

  • numPoints – number of points shown

    • +

  • numMarkers – desired number of markers

    • +
+
+
+
+ +
+
+variable KillWindows(string list)
+

Kill all passed windows.

+

Silently ignore errors.

+
+ +
+
+string GetAllAxesWithOrientation(string graph, variable axisOrientation)
+

Return all axes with the given orientation.

+
+
Parameters:
+
+
+
+
+ +
+
+variable GetNumFromModifyStr(string info, string key, string listChar, variable item)
+

Polished version of GetNumFromModifyStr from Readback ModifyStr.ipf

+
+
Parameters:
+
    +

  • info – string as returned by AxisInfo or TraceInfo

    • +

  • key – keyword

    • +

  • listChar – empty, { or ( depending on keyword style

    • +

  • item – return the given element from the extracted list

    • +
+
+
+
+ +
+
+string SortAxisList(string graph, string list)
+

Return the list of axis sorted from highest to lowest starting value of the axisEnab keyword.

+

list must be from one orientation, usually something returned by GetAllAxesWithOrientation()

+
+ +
+
+variable GetPlotArea(string win, RectD *s)
+
+ +
+
+std::tuple<RGBAColor> ParseColorSpec(string str)
+

Parse a color specification as used by ModifyGraph having an optionl translucency part.

+
+ +
+
+variable StoreCurrentPanelsResizeInfo(string panel)
+

If the layout of an panel was changed, this function calls the ResizeControlsPanel module functions of the Igor Pro native package to store the changed resize info. The originally intended way to do this was through the Packages GUI, which is clunky for some workflows.

+
+ +
+
+variable GetNotebookCRC(string win)
+

Return the CRC of the contents of the plain/formatted notebook.

+

Takes into account formatting but ignores selection.

+
+ +
+
+string FormatTextWaveForLegend(WaveText input)
+

Format the 2D text wave into a string usable for a legend.

+
+ +
+
+variable IsValidTraceLineStyle(variable lineStyleCode)
+

Checks if given lineStyle code is valid (as of Igor Pro 9)

+
+
Parameters:
+

lineStyleCode – line style code value for a trace

+
+
Returns:
+

1 if valid, 0 otherwise

+
+
+
+ +
+
+variable IsValidTraceDisplayMode(variable traceDisplayCode)
+

Checks if given trace display code is valid (as of Igor Pro 9)

+
+
Parameters:
+

traceDisplayCode – line style code value for a trace

+
+
Returns:
+

1 if valid, 0 otherwise

+
+
+
+ +
+
+variable UpdateInfoButtonHelp(string win, string ctrl, string content)
+

Update the help and user data of a button used as info/copy button.

+
+ +
+
+variable HorizExpandWithVisX()
+

Custom graph marquee.

+

Requires an existing marquee and a graph as current top window

+
+ +
+
+variable EquallySpaceAxis(string graph, string axisRegExp = defaultValue, variable axisOffset = defaultValue, variable axisOrientation = defaultValue, variable sortOrder = defaultValue, string listForBegin = defaultValue, string listForEnd = defaultValue)
+

Space the matching axis in an equal manner.

+
+
Parameters:
+
    +

  • graph – graph

    • +

  • axisRegExp – [optional, defaults to “.*”] regular expression matching the axes names

    • +

  • axisOffset – [optional, defaults to 0] offset of first axis in parts of total width

    • +

  • axisOrientation – [optional, defaults to all] allows to apply equalization to all axis of one orientation

    • +

  • sortOrder – [optional, defaults to no sorting (NaN)] apply different sorting schemes to list of axes, see sortingOrder parameter of SortList

    • +

  • listForBegin – [optional, defaults to an empty list] list of axes to move to the front of the sorted axis list

    • +

  • listForEnd – [optional, defaults to an empty list] list of axes to move to the end of the sorted axis list

    • +
+
+
+
+ +
+
+variable EquallySpaceAxisPA(string graph, string allAxes, string distAxes, variable axisOffset = defaultValue)
+

This is a light weight adapted version of.

+

+

See also

+

EquallySpaceAxis It allows to give a list of distAxes that do not require to exist. Non-existing axes are taken into account on the distribution, but are skipped when the graph is accessed. Also removing images from a graph does not update AxisList until the graph is updated, so we can not rely on Axislist here as we do the Layout after pending changes So with allAxes = “1;2;3;4;” and distAxes = “2;3;” axis 2 and 3 are set at 25% to 50% and 50% to 75% respectively.

+
+

+
+
Parameters:
+
    +

  • graph – [in] Name of graph where axes from distAxes list exist

    • +

  • allAxes – [in] List of all axes, that should be distributed. May include non-existing axes.

    • +

  • distAxes – [in] List of axes that are distributed. Only axes that appear in allAxes as well are modified.

    • +

  • axisOffset – [in] [optional, default = 0] offset between 0 and 1 where distribution starts.

    • +
+
+
+
+ +
+
+variable RemoveFreeAxisFromGraph(string graph)
+

Remove all free axis from the given graph.

+
+ +
+
+variable RemoveDrawLayers(string graph)
+

Remove all draw layers from the graph.

+
+ +
+
+variable RemoveTracesFromGraph(string graph, string trace = defaultValue, WaveOrNull wv = defaultValue, dfref dfr = defaultValue)
+

Remove traces from a graph.

+

+Only one of trace/wv/dfr may be supplied.

+
+
Parameters:
+
    +

  • graph – graph

    • +

  • trace – [optional, default: all] remove the given trace only

    • +

  • wv – [optional, default: ignored] remove all traces which stem from the given wave

    • +

  • dfr – [optional, default: ignored] remove all traces which stem from one of the waves in dfr

    • +
+
+
+
+ +
+
+variable AddVersionToPanel(string win, variable version)
+

Add user data “panelVersion” to the panel.

+
+ +
+
+variable HasPanelLatestVersion(string win, variable expectedVersion)
+

Return 1 if the panel is up to date, zero otherwise.

+
+ +
+
+variable GetPanelVersion(string win)
+

Get the user data “panelVersion”.

+
+
Parameters:
+

win – panel window as string

+
+
Returns:
+

numeric panel version greater 0 and -1 if no version is present or -2 if the windows does not exist

+
+
+
+ +
+
+variable ToggleCheckBoxes(string win, string checkBoxIn, string checkBoxPartner, variable checkBoxInState)
+

Places paired checkboxes in opposite state.

+
+
Parameters:
+
    +

  • win – window name

    • +

  • checkBoxIn – ctrl checkbox ex. cba.ctrlName

    • +

  • checkBoxPartner – checkbox that will be placed in opposite state

    • +

  • checkBoxInState – state of the ctrl checkbox

    • +
+
+
+
+ +
+
+variable EqualizeCheckBoxes(string win, string checkBoxIn, string checkBoxPartner, variable checkBoxInState)
+

Placed paired checkboxes in same state.

+
+
Parameters:
+
    +

  • win – window name

    • +

  • checkBoxIn – ctrl checkbox ex. cba.ctrlName

    • +

  • checkBoxPartner – checkbox that will be placed in the same state

    • +

  • checkBoxInState – state of the ctrl checkbox

    • +
+
+
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___utilities___generators_8ipf.html b/file/_m_i_e_s___utilities___generators_8ipf.html new file mode 100644 index 0000000000..84ec7258d1 --- /dev/null +++ b/file/_m_i_e_s___utilities___generators_8ipf.html @@ -0,0 +1,287 @@ + + + + + + + + File MIES_Utilities_Generators.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Utilities_Generators.ipf

+

utility functions that generate code

+
+

Functions

+
+
+variable GenerateMultiplierConstants()
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___utilities___j_s_o_n_8ipf.html b/file/_m_i_e_s___utilities___j_s_o_n_8ipf.html new file mode 100644 index 0000000000..065bef27f2 --- /dev/null +++ b/file/_m_i_e_s___utilities___j_s_o_n_8ipf.html @@ -0,0 +1,297 @@ + + + + + + + + File MIES_Utilities_JSON.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Utilities_JSON.ipf

+

utility functions for json

+
+

Functions

+
+
+variable AddPayloadEntriesFromFiles(variable jsonID, WaveText paths, variable isBinary = defaultValue)
+

Helper function for UploadCrashDumps.

+

Fill payload array with content from files

+
+ +
+
+variable AddPayloadEntries(variable jsonID, WaveText keys, WaveText values, variable isBinary = defaultValue)
+

Helper function for UploadCrashDumps.

+

Fill payload array

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___utilities___list_8ipf.html b/file/_m_i_e_s___utilities___list_8ipf.html new file mode 100644 index 0000000000..141d94575b --- /dev/null +++ b/file/_m_i_e_s___utilities___list_8ipf.html @@ -0,0 +1,369 @@ + + + + + + + + File MIES_Utilities_List.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Utilities_List.ipf

+

utility functions for lists

+
+

Functions

+
+
+string ListMatchesExpr(string list, string matchExpr, variable exprType)
+

Matches list against the expression matchExpr using the given convention in exprType

+
+ +
+
+string ListFromList(string list, variable itemBegin, variable itemEnd, string listSep = defaultValue)
+

return a subset of the input list

+
+
Parameters:
+
    +

  • list – input list

    • +

  • itemBegin – first item

    • +

  • itemEnd – last item

    • +

  • listSep – [optional] list Separation character. default is “;”

    • +
+
+
Returns:
+

a list with elements ranging from itemBegin to itemEnd of the input list

+
+
+
+ +
+
+string BuildList(string format, variable start, variable step, variable stop)
+

Create a list of strings using the given format in the given range.

+
+
Parameters:
+
    +

  • format – formatting string, must have exactly one specifier which accepts a number

    • +

  • start – first point of the range

    • +

  • step – step size for iterating over the range

    • +

  • stop – last point of the range

    • +
+
+
+
+ +
+
+variable WaveListHasSameWaveNames(string listOfWaves, string *baseName)
+

Checks wether the wave names of all waves in the list are equal Returns 1 if true, 0 if false and NaN for empty lists.

+
+
Parameters:
+
    +

  • listOfWaves – list of waves with full path

    • +

  • baseName – [out] Returns the common baseName if the list has one, otherwise this will be an empty string.

    • +
+
+
+
+ +
+
+string AddPrefixToEachListItem(string prefix, string list, string sep = defaultValue)
+

Add a string prefix to each list item and return the new list.

+
+ +
+
+string AddSuffixToEachListItem(string suffix, string list, string sep = defaultValue)
+

Add a string suffix to each list item and return the new list.

+
+ +
+
+string RemovePrefixFromListItem(string prefix, string list, string listSep = defaultValue, variable regExp = defaultValue)
+

Remove a string prefix from each list item and return the new list.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string MergeLists(string l1, string l2, string sep = defaultValue)
+

Merges list l1 into l2. Double entries in l2 are kept. “a;b;c;” with “a;d;d;f;” -> “a;d;d;f;b;c;”.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___utilities___numeric_8ipf.html b/file/_m_i_e_s___utilities___numeric_8ipf.html new file mode 100644 index 0000000000..ba3fc87d27 --- /dev/null +++ b/file/_m_i_e_s___utilities___numeric_8ipf.html @@ -0,0 +1,595 @@ + + + + + + + + File MIES_Utilities_Numeric.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Utilities_Numeric.ipf

+

utility functions for numerical operations

+
+

Functions

+
+
+variable NewRandomSeed()
+

Initializes the random number generator with a new seed between (0,1] The time base is assumed to be at least 0.1 microsecond precise, so a new seed is available every 0.1 microsecond.

+

Usage example for the case that one needs n non reproducible random numbers. Whenever the following code block is executed a new seed is set, resulting in a different series of numbers

+

Make/D/N=(n) newRandoms
+NewRandomSeed() // Initialize random number series with a new seed
+newRandoms[] = GetReproducibleRandom() // Get n randoms from the new series
+
+
+

+
+ +
+
+variable GetReproducibleRandom(variable noiseGenMode = defaultValue)
+

Return a random value in the range (0,1] which can be used as a seed for SetRandomSeed

+

Return a reproducible random number depending on the RNG seed.

+
+ +
+
+variable GetUniqueInteger()
+

Return a unique integer.

+

The returned values can not be used for statistical purposes as the distribution is not uniform anymore.

+
+ +
+
+variable SetBit(variable var, variable bit)
+

Set the given bit mask in var.

+
+ +
+
+variable ClearBit(variable var, variable bit)
+

Clear the given bit mask in var.

+
+ +
+
+variable PopCount(uint64 value)
+

Count the number of ones in value Note: if the argument given is not an unsigned int64 then it will be implicitly converted to an uint64. This mean e.g. for a double precision argument that the maximum number of bits for positive numbers is 53 from 2^53 - 1 and for negative numbers the result is always >= 11.

+
+
Parameters:
+

value – will be truncated to an 64 bit unsigned integer value

+
+
+
+ +
+
+std::tuple<variable, variable> MinMax(variable a, variable b)
+

Return the minimum and maximum of both values.

+
+ +
+
+variable FindNextPower(variable a, variable p)
+

Find an integer x which is larger than a but the smallest possible power of p.

+

\( x > a \) where \( x = c^p \) holds and \( x \) is the smallest possible value.

+
+ +
+
+variable FindPreviousPower(variable a, variable p)
+

Find an integer x which is smaller than a but the largest possible power of p.

+

\( x < a \) where \( x = c^p \) holds and \( x \) is the largest possible value.

+
+ +
+
+variable GetAlignment(variable val)
+

Return the alignment of the decimal number (usually a 32bit/64bit pointer)

+
+ +
+
+variable CalculateLCM(variable a, variable b)
+

Compute the least common multiplier of two variables.

+
+ +
+
+variable RoundNumber(variable val, variable precision)
+

Round the given number to the given number of decimal digits.

+
+ +
+
+string GenerateRFC4122UUID()
+

Generate a version 4 UUID according to https://tools.ietf.org/html/rfc4122.

+

4.4.  Algorithms for Creating a UUID from Truly Random or
+      Pseudo-Random Numbers
+
+   The version 4 UUID is meant for generating UUIDs from truly-random or
+   pseudo-random numbers.
+
+   The algorithm is as follows:
+
+   o  Set the two most significant bits (bits 6 and 7) of the
+      clock_seq_hi_and_reserved to zero and one, respectively.
+
+   o  Set the four most significant bits (bits 12 through 15) of the
+      time_hi_and_version field to the 4-bit version number from
+      Section 4.1.3.
+
+   o  Set all the other bits to randomly (or pseudo-randomly) chosen
+      values.
+
+See Section 4.5 for a discussion on random numbers.
+
+[...]
+
+ In the absence of explicit application or presentation protocol
+ specification to the contrary, a UUID is encoded as a 128-bit object,
+ as follows:
+
+ The fields are encoded as 16 octets, with the sizes and order of the
+ fields defined above, and with each field encoded with the Most
+ Significant Byte first (known as network byte order).  Note that the
+ field names, particularly for multiplexed fields, follow historical
+ practice.
+
+ 0                   1                   2                   3
+  0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1
+ +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
+ |                          time_low                             |
+ +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
+ |       time_mid                |         time_hi_and_version   |
+ +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
+ |clk_seq_hi_res |  clk_seq_low  |         node (0-1)            |
+ +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
+ |                         node (2-5)                            |
+ +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
+
+[...]
+
+4.1.3.  Version
+
+   The version number is in the most significant 4 bits of the time
+   stamp (bits 4 through 7 of the time_hi_and_version field).
+
+   The following table lists the currently-defined versions for this
+   UUID variant.
+
+   Msb0  Msb1  Msb2  Msb3   Version  Description
+
+    0     0     0     1        1     The time-based version
+                                     specified in this document.
+
+    0     0     1     0        2     DCE Security version, with
+                                     embedded POSIX UIDs.
+
+    0     0     1     1        3     The name-based version
+                                     specified in this document
+                                     that uses MD5 hashing.
+
+    0     1     0     0        4     The randomly or pseudo-
+                                     randomly generated version
+                                     specified in this document.
+
+    0     1     0     1        5     The name-based version
+                                     specified in this document
+                                     that uses SHA-1 hashing.
+
+   The version is more accurately a sub-type; again, we retain the term
+   for compatibility.
+
+
+

+

See also https://www.rfc-editor.org/errata/eid3546 and https://www.rfc-editor.org/errata/eid1957 for some clarifications.

+
+ +
+
+std::tuple<variable, variable> SymmetrizeRangeAroundZero(variable minimum, variable maximum)
+

Given a range [a, b] this returns a symmetric range around zero including both elements.

+
+ +
+
+variable LimitWithReplace(variable val, variable low, variable high, variable replacement)
+

Acts like the limit builtin but replaces values outside the valid range instead of clipping them.

+
+ +
+
+variable Base64EncodeSize(variable unencodedSize)
+

Calculated the size of Base64 encoded data from the unencoded size.

+
+
Parameters:
+

unencodedSize – unencoded size

+
+
Returns:
+

encoded size

+
+
+
+ +
+
+variable FindRightMostHighBit(uint64 value)
+

Find the right most high bit.

+
+
Parameters:
+

value – integer value in the range [0, 2^64]

+
+
Returns:
+

right most high bit or NaN in case nothing could be found

+
+
+
+ +
+
+std::tuple<variable, variable> RoundAndDelta(variable val)
+

Returns the integer result and the difference of it to the original value.

+
+ +
+
+std::tuple<variable, variable> CeilAndDelta(variable val)
+

Returns the integer result and the difference of it to the original value.

+
+ +
+
+std::tuple<variable, variable> FloorAndDelta(variable val)
+

Returns the integer result and the difference of it to the original value.

+
+ +
+
+variable IndexAfterDecimation(variable sourceIndex, variable decimationFactor)
+

Returns the target index closer to zero of a given source index for a decimation in the form target[] = source[round(p * decimationFactor)] Note: For a decimationFactor < 1 a point in source may be decimated to multiple points in target, thus a resulting index in target of sourceIndex + 1 may be equal to the index retrieved for sourceindex. For a decimationFactor > 1 points in source may be skipped on decimation, thus a resulting index in target of sourceIndex + 1 may increase the result by more than 1.

+
+ +
+
+
+struct Uuid
+

Helper structure for GenerateRFC4122UUID()

+
+

Public Members

+
+
+uint32 time_low
+
+ +
+
+uint16 time_mid
+
+ +
+
+uint16 time_hi_and_version
+
+ +
+
+uint16 clock_seq
+
+ +
+
+uint16 node0
+
+ +
+
+uint16 node1
+
+ +
+
+uint16 node2
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___utilities___program_flow_8ipf.html b/file/_m_i_e_s___utilities___program_flow_8ipf.html new file mode 100644 index 0000000000..f6b984a285 --- /dev/null +++ b/file/_m_i_e_s___utilities___program_flow_8ipf.html @@ -0,0 +1,402 @@ + + + + + + + + File MIES_Utilities_ProgramFlow.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Utilities_ProgramFlow.ipf

+

utility functions for program flow

+
+

Functions

+
+
+variable AssertOnAndClearRTError()
+

Helper function to ensure that there is no pending RTE before entering a critical section. If there is a pending RTE then a BUG message is output (which is a CI error).

+

Not catching any pending RTE would clear this condition silently and valid errors would be suppressed. This is dangerous in regards of data consistency.

+

Not clearing the RTE before calling AbortOnRTE will always trigger the RTE no matter what you do in that line. Any call to GetRTErrMessage() must be done prior to clearing the runtime error in the catch block.

+

Usage: 

AssertOnAndClearRTError()
+  try
+    CriticalFunc(); AbortOnRTE
+  catch
+    msg = GetRTErrMessage()
+    err = ClearRTError()
+  endtry
+
+
+

+

+

UTF_NOINSTRUMENTATION

+
+ +
+
+variable ClearRTError()
+

Helper function to unconditionally clear a RTE condition It is generally strongly recommended to use.

+

+UTF_NOINSTRUMENTATION

+

See also

+

AssertOnAndClearRTError before critical code sections. For detailed description of the implications

+
+
+

See also

+

AssertOnAndClearRTError

+
+

+
+ +
+
+variable IsFunctionCalledRecursively()
+

Return true if the calling function is called recursively, i.e. it is present multiple times in the call stack.

+
+ +
+
+variable DoAbortNow(string msg)
+

Wrapper function for Abort which honours our interactive mode setting.

+
+ +
+
+string GetStackTrace(string prefix = defaultValue)
+

Return a nicely formatted multiline stacktrace.

+
+ +
+
+variable ASSERT(variable var, string errorMsg, variable extendedOutput = defaultValue)
+

Low overhead function to check assertions.

+

+Example usage: 

ControlInfo/W = $device popup_MoreSettings_DeviceType
+ASSERT(V_flag > 0, "Non-existing control or window")
+do something with S_value
+
+
+

+

+

UTF_NOINSTRUMENTATION

+
+
Parameters:
+
    +

  • var – if zero an error message is printed into the history and procedure execution is aborted, nothing is done otherwise. If the debugger is enabled, it also steps into it.

    • +

  • errorMsg – error message to output in failure case

    • +

  • extendedOutput – [optional, defaults to true] Output additional information on failure

    • +
+
+
+
+ +
+
+variable ASSERT_TS(variable var, string errorMsg, variable extendedOutput = defaultValue)
+

Low overhead function to check assertions (threadsafe variant)

+

+Example usage: 

ASSERT_TS(DataFolderExistsDFR(dfr), "dfr does not exist")
+do something with dfr
+
+
+

+

+

Unlike ASSERT() this function does not jump into the debugger (Igor Pro limitation).

+

UTF_NOINSTRUMENTATION

+
+
Parameters:
+
    +

  • var – if zero an error message is printed into the history and procedure execution is aborted, nothing is done otherwise.

    • +

  • errorMsg – error message to output in failure case

    • +

  • extendedOutput – [optional, defaults to true] Output additional information on failure

    • +
+
+
+
+ +
+
+variable AlreadyCalledOnce(string name)
+

Return 1 if the function was already called with that argument, and 0 otherwise As named use or create a constant in.

+

+

See also

+

CalledOnceNames

+
+

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___utilities___s_f_h_checkers_8ipf.html b/file/_m_i_e_s___utilities___s_f_h_checkers_8ipf.html new file mode 100644 index 0000000000..3c3dba90f2 --- /dev/null +++ b/file/_m_i_e_s___utilities___s_f_h_checkers_8ipf.html @@ -0,0 +1,360 @@ + + + + + + + + File MIES_Utilities_SFHCheckers.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Utilities_SFHCheckers.ipf

+

Threadsafe check functions which comply with either SFH_NumericChecker_Prototype or SFH_StringChecker_Prototype.

+
+

Functions

+
+
+variable IsValidObjectName(string name)
+

Check if a name for an object adheres to the strict naming rules.

+

+UTF_NOINSTRUMENTATION

+

See also

+

DisplayHelpTopic "Standard Object Names"

+
+

+
+ +
+
+variable IsValidLiberalObjectName(string name)
+

Check if a name for an object adheres to the liberal naming rules.

+

+UTF_NOINSTRUMENTATION

+

See also

+

DisplayHelpTopic "Liberal Object Names"

+
+

+
+ +
+
+static variable NameChecker(string name, variable liberal)
+

UTF_NOINSTRUMENTATION.

+
+ +
+
+variable IsStrictlyPositiveAndFinite(variable var)
+

UTF_NOINSTRUMENTATION.

+
+ +
+
+variable IsNullOrPositiveAndFinite(variable var)
+

UTF_NOINSTRUMENTATION.

+
+ +
+
+variable BetweenZeroAndOneExc(variable val)
+

Return the truth if val is in the range ]0, 1[

+

UTF_NOINSTRUMENTATION

+
+ +
+
+variable BetweenZeroAndOne(variable val)
+

Return the truth if val is in the range [0, 1]

+

UTF_NOINSTRUMENTATION

+
+ +
+
+variable BetweenZeroAndOneHoundredExc(variable val)
+

Return the truth if val is in the range ]0, 100[

+

UTF_NOINSTRUMENTATION

+
+ +
+
+variable BetweenZeroAndOneHoundred(variable val)
+

Return the truth if val is in the range [0, 100]

+

UTF_NOINSTRUMENTATION

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___utilities___strings_8ipf.html b/file/_m_i_e_s___utilities___strings_8ipf.html new file mode 100644 index 0000000000..61de5cd89d --- /dev/null +++ b/file/_m_i_e_s___utilities___strings_8ipf.html @@ -0,0 +1,500 @@ + + + + + + + + File MIES_Utilities_Strings.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Utilities_Strings.ipf

+

utility functions for string handling

+
+

Functions

+
+
+string ExtractStringFromPair(string str, string key, string keySep = defaultValue, string listSep = defaultValue)
+

Same functionality as GetStringFromWaveNote() but accepts a string.

+

+

See also

+

GetStringFromWaveNote()

+
+

+
+ +
+
+string PossiblyUnquoteName(string name, string quote)
+

Remove the surrounding quotes from the string if they are present.

+
+ +
+
+string LineBreakingIntoPar(string str, variable minimumWidth = defaultValue)
+

Break a string into multiple lines.

+

All spaces and tabs which are not followed by numbers are replace by carriage returns (\r) if the minimum width was reached.

+

A generic solution would either implement the real deal

+

Knuth, Donald E.; Plass, Michael F. (1981), Breaking paragraphs into lines Software: Practice and Experience 11 (11): 1119-1184, doi:10.1002/spe.4380111102.

+

or translate 1 from C++ to Igor Pro.

+
+
Parameters:
+
    +

  • str – string to break into lines

    • +

  • minimumWidth – [optional, defaults to zero] Each line, except the last one, will have at least this length

    • +
+
+
+
+ +
+
+string RemovePrefix(string str, string start = defaultValue, variable regExp = defaultValue)
+

Remove a prefix from a string.

+

Same semantics as the RemoveEnding builtin for regExp == 0.

+

+UTF_NOINSTRUMENTATION

+
+
Parameters:
+
    +

  • str – string to potentially remove something from its beginning

    • +

  • start – [optional, defaults to the first character] Remove this from the begin of str

    • +

  • regExp – [optional, defaults to false] If start is a simple string (false) or a regular expression (true)

    • +
+
+
+
+ +
+
+string RemoveEndingRegExp(string str, string endingRegExp)
+

Remove the given reguluar expression from the end of the string.

+

In case the regular expression does not match, the string is returned unaltered.

+

See also DisplayHelpTopic "Regular Expressions".

+
+ +
+
+variable SearchWordInString(string str, string word, string *prefix = defaultValue, string *suffix = defaultValue)
+

Search for a Word inside a String.

+

+example of the usage of SearchStringBase (basically the same as WM GrepString()) 

Function SearchString(str, substring)
+    string str, substring
+
+    ASSERT(!IsEmpty(substring), "supplied substring is empty")
+    WAVE/Z/T wv = SearchStringBase(str, "(.*)\\Q" + substring + "\\E(.*)")
+
+    return WaveExists(wv)
+End
+
+
+

+

+
+
Parameters:
+
    +

  • str – [in] input text in which word should be searched

    • +

  • word – [in] searchpattern (non-regex-sensitive)

    • +

  • prefix – [out] (optional) string preceding word. (”” for unmatched pattern)

    • +

  • suffix – [out] (optional) string succeeding word.

    • +
+
+
Returns:
+

1 if word was found in str and word was not “”. 0 if not.

+
+
+
+ +
+
+static std::tuple<variable, string, string> SearchRegexInString(string str, string regex)
+
+ +
+
+wave SearchStringBase(string str, string regex)
+

More advanced version of SplitString.

+

supports 6 subpatterns, specified by curly brackets in regex

+
+
Returns:
+

text wave containing subpatterns of regex call

+
+
+
+ +
+
+variable CountSubstrings(string str, string pattern)
+

Search for the occurence of pattern in string.

+
+
Returns:
+

number of occurences

+
+
+
+ +
+
+variable ParseUnit(string unitWithPrefix, string *prefix, variable *numPrefix, string *unit)
+

Parses a simple unit with prefix into its prefix and unit.

+

Note: The currently allowed units are the SI base units [1] and other common derived units. And in accordance to SI definitions, “kg” is a base unit.

+
+
Parameters:
+
    +

  • unitWithPrefix – [in] string to parse, examples are “ms” or “kHz”

    • +

  • prefix – [out] symbol of decimal multipler of the unit, see below or [1] chapter 3 for the full list

    • +

  • numPrefix – [out] numerical value of the decimal multiplier

    • +

  • unit – [out] unit

    • +
+
+
+
+ +
+
+variable GetDecimalMultiplierValue(string prefix)
+

Return the numerical value of a SI decimal multiplier.

+

+

See also

+

ParseUnit

+
+

+
+ +
+
+string ReplaceWordInString(string word, string str, string replacement)
+
+ +
+
+string ReplaceRegexInString(string regex, string str, string replacement)
+

Replaces all occurences of the regular expression regex in str with replacement

+
+ +
+
+string NormalizeToEOL(string str, string eol)
+

Normalize the line endings in the given string to either classic Mac OS/Igor Pro EOLs (\r) or Unix EOLs (\n)

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string ElideText(string str, variable returnLength)
+

Elide the given string to the requested length.

+
+ +
+
+variable NumBytesInUTF8Character(string str, variable byteOffset)
+

Returns the number of bytes in the UTF-8 character that starts byteOffset bytes from the start of str. NOTE: If byteOffset is invalid this routine returns 0. Also, if str is not valid UTF-8 text, this routine return 1.

+

From DisplayHelpTopic “Character-by-Character Operations”

+
+ +
+
+variable UTF8CharactersInString(string str)
+

Returns the number of UTF8 characters in a string.

+

From DisplayHelpTopic “Character-by-Character Operations”

+
+ +
+
+string UTF8CharacterAtPosition(string str, variable charPos)
+

Returns the UTF8 characters in a string at position charPos.

+

From DisplayHelpTopic “Character-by-Character Operations”

+
+ +
+
+string UpperCaseFirstChar(string str)
+

Upper case the first character in an ASCII string.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___utilities___system_8ipf.html b/file/_m_i_e_s___utilities___system_8ipf.html new file mode 100644 index 0000000000..e39afb2aa7 --- /dev/null +++ b/file/_m_i_e_s___utilities___system_8ipf.html @@ -0,0 +1,512 @@ + + + + + + + + File MIES_Utilities_System.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Utilities_System.ipf

+

utility functions for system operations

+
+

Functions

+
+
+string GetExperimentName()
+

Return the name of the experiment without the file suffix.

+
+ +
+
+string GetExperimentFileType()
+

Return the experiment file type.

+
+ +
+
+variable GetFreeMemory()
+

Return the amount of free memory in GB.

+

Due to memory fragmentation you can not assume that you can still create a wave occupying as much space as returned.

+
+ +
+
+variable IsBackgroundTaskRunning(string task)
+

Check wether the given background task is currently running.

+

Note: Background functions which are currently waiting for their period to be reached are also running.

+
+
Parameters:
+

task – Named background task identifier, this is not the function set with proc=

+
+
+
+ +
+
+variable QuerySetIgorOption(string name, variable globalSymbol = defaultValue)
+

Query a numeric option settable with SetIgorOption

+
+
Parameters:
+
    +

  • name – name of the keyword/setting

    • +

  • globalSymbol – [optional, defaults to false] name refers to a global symbol set via poundDefine

    • +
+
+
+
+ +
+
+variable ForceRecompile()
+

Force recompilation of all procedure files.

+

Uses the “Operation Queue”.

+
+ +
+
+string GetIgorExtensionFolderName()
+

Return the disc folder name where the XOPs are located.

+

Distinguishes between i386 and x64 Igor versions

+
+ +
+
+string GetIgorExecutable()
+

Return an Igor-style path to the Igor Pro executable.

+
+ +
+
+variable GetArchitectureBits()
+

Return the number of bits of the architecture Igor Pro was built for.

+
+ +
+
+string GetIgorInfo(variable selector)
+

Return the given IgorInfo (cached)

+

This is faster than calling IgorInfo everytime.

+
+ +
+
+string GetIgorProVersion()
+

Return the Igor Pro version string.

+
+ +
+
+variable GetIgorProMajorVersion()
+

Return the major Igor Pro version.

+
+ +
+
+string GetIgorProBuildVersion()
+

Return the Igor Pro build version string.

+

This allows to distinguish different builds from the same major/minor version.

+
+ +
+
+string GetSystemUserName()
+

Return the user name of the running user.

+
+ +
+
+variable ControlWindowToFront()
+

Bring the control window (the window with the command line) to the front of the desktop.

+
+ +
+
+variable ExecuteListOfFunctions(string funcList)
+

Execute a list of functions via the Operation Queue.

+

Special purpose function. Not intended for normal use.

+
+ +
+
+variable SleepHighPrecision(variable var)
+

High precision version of the builtin Sleep command.

+
+
Parameters:
+

var – time in seconds to busy-sleep (current precision is around 0.1ms)

+
+
+
+ +
+
+variable GetMachineEpsilon(variable type)
+

Return the machine epsilon for the given wave type.

+

Experimentally determined with Igor Pro 7.08

+
+ +
+
+variable CreateHistoryNotebook()
+

Create the special Notebook “HistoryCarbonCopy” which will hold a readable copy of the history starting from the time of the notebook creation.

+
+ +
+
+string GetHistoryNotebookText()
+

Return the text of the history notebook.

+
+ +
+
+variable GetASLREnabledState()
+

Return the per application setting of ASLR for the Igor Pro executable.

+

See https://docs.microsoft.com/en-us/windows/security/threat-protection/windows-defender-exploit-guard/enable-exploit-protection for the powershell cmdlet documentation.

+
+
Returns:
+

0 or 1

+
+
+
+ +
+
+variable TurnOffASLR()
+

Turn off ASLR.

+

Requires administrative privileges via UAC. Only required once for ITC hardware.

+
+ +
+
+variable IsWindows10Or11()
+

Check if we are running on Windows 10/11.

+
+ +
+
+variable UploadJSONPayload(variable jsonID)
+

Upload the given JSON document.

+

See tools/http-upload/upload-json-payload-v1.php for the JSON format description.

+
+ +
+
+string GetIgorInstanceID()
+

Returns a hex string which is unique for the given Igor Pro session.

+

It allows to distinguish multiple Igor instances, but is not globally unique.

+
+ +
+
+variable CleanupOperationQueueResult()
+

Allows to remove V_flag which will be present after using the operation queue with /Z

+

Example usage: 

Execute/P/Q/Z "SomeFunction()"
+CleanupOperationQueueResult()
+
+
+

+

+
+ +
+
+variable ConvertXOPErrorCode(variable err)
+

Remove the volatile part of the XOP error code.

+

The result is constant and can therefore be compared with constants.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___utilities___time_8ipf.html b/file/_m_i_e_s___utilities___time_8ipf.html new file mode 100644 index 0000000000..3ba3b75998 --- /dev/null +++ b/file/_m_i_e_s___utilities___time_8ipf.html @@ -0,0 +1,394 @@ + + + + + + + + File MIES_Utilities_Time.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Utilities_Time.ipf

+

utility functions for time/date related operations

+
+

Functions

+
+
+string GetTimeStamp(variable secondsSinceIgorEpoch = defaultValue, variable humanReadable = defaultValue)
+

Return a formatted timestamp of the form YY_MM_DD_HHMMSS

+

Uses the local time zone and not UTC.

+
+
Parameters:
+
    +

  • humanReadable – [optional, default to false] Return a format viable for display in a GUI

    • +

  • secondsSinceIgorEpoch – [optional, defaults to number of seconds until now] Seconds since the Igor Pro epoch (1/1/1904)

    • +
+
+
+
+ +
+
+variable DateTimeInUTC()
+

Return the seconds, including fractional part, since Igor Pro epoch (1/1/1904) in UTC time zone.

+
+ +
+
+string GetISO8601TimeStamp(variable secondsSinceIgorEpoch = defaultValue, variable numFracSecondsDigits = defaultValue, variable localTimeZone = defaultValue)
+

Return a string in ISO 8601 format with timezone UTC.

+
+
Parameters:
+
    +

  • secondsSinceIgorEpoch – [optional, defaults to number of seconds until now] Seconds since the Igor Pro epoch (1/1/1904) in UTC (or local time zone depending on localTimeZone)

    • +

  • numFracSecondsDigits – [optional, defaults to zero] Number of sub-second digits

    • +

  • localTimeZone – [optional, defaults to false] Use the local time zone instead of UTC

    • +
+
+
+
+ +
+
+variable ParseISO8601TimeStamp(string timestamp)
+

Parse a ISO8601 timestamp, e.g. created by GetISO8601TimeStamp(), and returns the number of seconds, including fractional parts, since Igor Pro epoch (1/1/1904) in UTC time zone.

+

Accepts also the following specialities:

    +

  • no UTC timezone specifier (UTC timezone is still used)

    • +

  • /T between date and time

    • +

  • fractional seconds

    • +

  • ,/. as decimal separator

    • +
+

+
+ +
+
+std::tuple<variable, string, string, string, string, string, string, string, string, string, string> ParseISO8601TimeStampToComponents(string timestamp)
+

Parses a ISO8601 timestamp to its components, year, month, day, hour, minute are required and the remaining components are optional and can be returned as empty strings.

+
+ +
+
+variable StopAllMSTimers()
+

Stop all millisecond Igor Pro timers.

+
+ +
+
+variable RelativeNowHighPrec()
+

Return a time in seconds with high precision, microsecond resolution, using an arbitrary zero point.

+
+ +
+
+variable GetReferenceTime()
+

Start a timer for performance measurements.

+

Usage: 

variable referenceTime = GetReferenceTime()
+// part one to benchmark
+print GetReferenceTime(referenceTime)
+// part two to benchmark
+print GetReferenceTime(referenceTime)
+// you can also store all times via
+StoreElapsedTime(referenceTime)
+
+
+

+

+
+ +
+
+variable GetElapsedTime(variable referenceTime)
+

Get the elapsed time in seconds.

+
+ +
+
+variable StoreElapsedTime(variable referenceTime)
+

Store the elapsed time in a wave.

+
+ +
+
+variable GetDayOfWeek(variable seconds)
+

Returns the day of the week, where 1 == Sunday, 2 == Monday … 7 == Saturday.

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___utilities___wave_handling_8ipf.html b/file/_m_i_e_s___utilities___wave_handling_8ipf.html new file mode 100644 index 0000000000..abd0a55987 --- /dev/null +++ b/file/_m_i_e_s___utilities___wave_handling_8ipf.html @@ -0,0 +1,918 @@ + + + + + + + + File MIES_Utilities_WaveHandling.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_Utilities_WaveHandling.ipf

+

utility functions for wave handling

+
+

Functions

+
+
+variable EnsureLargeEnoughWave(wave wv, variable indexShouldExist = defaultValue, variable dimension = defaultValue, variable initialValue = defaultValue, variable checkFreeMemory = defaultValue)
+

Redimension the wave to at least the given size.

+

The redimensioning is only done if it is required.

+

Can be used to fill a wave one at a time with the minimum number of redimensions. In the following example NOTE_INDEX is the index of the next free row and the total number of rows filled with data.

+

Make/FREE/N=(MINIMUM_WAVE_SIZE) data
+SetNumberInWaveNote(data, NOTE_INDEX, 0)
+// ...
+for(...)
+    index = GetNumberFromWaveNote(data, NOTE_INDEX)
+    // ...
+    EnsureLargeEnoughWave(data, dimension = ROWS, indexShouldExist = index)
+    data[index] = ...
+    // ...
+    SetNumberInWaveNote(data, NOTE_INDEX, ++index)
+endfor
+
+
+

+
+
Parameters:
+
    +

  • wv – wave to redimension

    • +

  • indexShouldExist – [optional, default is implementation defined] the minimum size of the wave. The actual size of the wave after the function returns might be larger.

    • +

  • dimension – [optional, defaults to ROWS] dimension to resize, all other dimensions are left untouched.

    • +

  • initialValue – [optional, defaults to zero] initialValue of the new wave points

    • +

  • checkFreeMemory – [optional, defaults to false] check if the free memory is enough for increasing the size

    • +
+
+
Returns:
+

0 on success, (only for checkFreeMemory = True) 1 if increasing the wave’s size would fail due to out of memory

+
+
+
+ +
+
+variable EnsureSmallEnoughWave(wave wv, variable maximumSize = defaultValue)
+

Resize the number of rows to maximumSize if it is larger than that.

+
+
Parameters:
+
    +

  • wv – wave to redimension

    • +

  • maximumSize – maximum number of the rows, defaults to MAXIMUM_SIZE

    • +
+
+
+
+ +
+
+wave GetWaveDimensions(wave wv)
+

Return a wave with MAX_DIMENSION_COUNT entries with the size of each dimension.

+
+ +
+
+static variable GetWaveSizeImplementation(wave wv)
+

Returns the size of the wave in bytes.

+
+ +
+
+variable GetSizeOfType(wave wv)
+

Return the size in bytes of a given type.

+

Inspired by http://www.igorexchange.com/node/1845

+
+ +
+
+variable GetWaveSize(WaveOrNull wv, variable recursive = defaultValue)
+

Returns the size of the wave in bytes.

+
+ +
+
+variable GetLockState(wave wv)
+

Return the lock state of the passed wave.

+
+ +
+
+variable GetNumberFromWaveNote(wave wv, string key)
+

Returns the numeric value of key found in the wave note, returns NaN if it could not be found.

+

The expected wave note format is: key1:val1;key2:val2; UTF_NOINSTRUMENTATION

+
+ +
+
+variable SetNumberInWaveNote(wave wv, string key, variable val, string format = defaultValue)
+

Updates the numeric value of key found in the wave note to val

+

+The expected wave note format is: key1:val1;key2:val2;

+
+
Parameters:
+
    +

  • wv – wave

    • +

  • key – key of the Key/Value pair

    • +

  • val – value of the Key/Value pair

    • +

  • format – [optional] printf compatible format string to set the conversion to string for val

    • +
+
+
+
+ +
+
+string GetStringFromWaveNote(wave wv, string key, string keySep = defaultValue, string listSep = defaultValue, variable recursive = defaultValue)
+

Return the string value of key found in the wave note default expected wave note format: key1:val1;key2:str2; counterpart of AddEntryIntoWaveNoteAsList when supplied with keySep = “=”.

+
+
Parameters:
+
    +

  • wv – wave reference where the WaveNote is taken from

    • +

  • key – search for the value at key:value;

    • +

  • keySep – [optional, defaults to DEFAULT_KEY_SEP] separation character for (key, value) pairs

    • +

  • listSep – [optional, defaults to DEFAULT_LIST_SEP] list separation character

    • +

  • recursive – [optional, defaults to false] checks all wave notes in referenced waves from wave reference waves

    • +
+
+
Returns:
+

the value on success. An empty string is returned if it could not be found

+
+
+
+ +
+
+variable SetStringInWaveNote(wave wv, string key, string str, variable recursive = defaultValue, string keySep = defaultValue, string listSep = defaultValue)
+

Update the string value of key found in the wave note to str

+

The expected wave note format is: key1:val1;key2:str2;

+
+ +
+
+variable AddEntryIntoWaveNoteAsList(wave wv, string key, variable var = defaultValue, string str = defaultValue, variable appendCR = defaultValue, variable replaceEntry = defaultValue, string format = defaultValue)
+

Structured writing of numerical values with names into wave notes.

+

The general layout is key1 = var;key2 = str; and the note is never prefixed with a carriage return (“\r”).

+
+
Parameters:
+
    +

  • wv – wave to add the wave note to

    • +

  • key – string identifier

    • +

  • var – variable to output

    • +

  • str – string to output

    • +

  • appendCR – 0 (default) or 1, should a carriage return (“\r”) be appended to the note

    • +

  • replaceEntry – 0 (default) or 1, should existing keys named key be replaced (does only work reliable in wave note lists without carriage returns).

    • +

  • format – [optional, defaults to g] format string used for converting var to str

    • +
+
+
+
+ +
+
+variable HasEntryInWaveNoteList(wave wv, string key, string value)
+

Checks if key = value; can be found in the wave note.

+

Ignores spaces around the equal (“=”) sign.

+

+

See also

+

AddEntryIntoWaveNoteAsList()

+
+

+
+ +
+
+string UniqueWaveName(dfref dfr, string baseName)
+

Returns a wave name not used in the given datafolder.

+

Basically a datafolder aware version of UniqueName for datafolders

+
+
Parameters:
+
    +

  • dfr – datafolder reference where the new datafolder should be created

    • +

  • baseName – first part of the wave name

    • +
+
+
+
+ +
+
+wave DuplicateSubRange(wave wv, variable first, variable last)
+

Return a new wave from the subrange of the given 1D wave.

+
+ +
+
+variable GetRowWithSameContent(WaveText refWave, WaveText sourceWave, variable row)
+

Search the row in refWave which has the same contents as the given row in the sourceWave.

+
+ +
+
+wave GetColfromWavewithDimLabel(wave wv, string dimLabel)
+

Returns the column from a multidimensional wave using the dimlabel.

+
+ +
+
+wave MakeWaveFree(WaveOrNull wv)
+

Turn a persistent wave into a free wave.

+
+ +
+
+variable SetDimensionLabels(wave wv, string list, variable dim, variable startPos = defaultValue)
+

Sets the dimension labels of a wave.

+
+
Parameters:
+
    +

  • wv – Wave to add dim labels

    • +

  • list – List of dimension labels, semicolon separated.

    • +

  • dim – Wave dimension, see, WaveDimensions

    • +

  • startPos – [optional, defaults to 0] First dimLabel index

    • +
+
+
+
+ +
+
+wave DeepCopyWaveRefWave(WaveRefWave src, variable dimension = defaultValue, variable index = defaultValue, wave indexWave = defaultValue)
+

Return a wave with deep copies of all referenced waves.

+

The deep copied waves will be free waves. Does not allow invalid wave references in src.

+
+
Parameters:
+
    +

  • src – wave reference wave

    • +

  • dimension – [optional] copy only a single dimension, requires index or indexWave as well

    • +

  • index – [optional] specifies the index into dimension, index is not checked

    • +

  • indexWave – [optional] specifies the indizes into dimension, allows for differing indizes per src entry, indices are not checked

    • +
+
+
+
+ +
+
+variable ReduceWaveDimensionality(WaveOrNull wv, variable minDimension = defaultValue)
+

Shrinks a waves dimensionality if higher dimensions have size 1.

+
+
Parameters:
+
    +

  • wv – Wave that should be shrinked

    • +

  • minDimension – [optional, default COLS] shrinks a wave only up to this dimension, e.g. with minDimension = LAYERS a wave of size (1,1,1,1) is shrinked to (1,1,1,0).

    • +
+
+
+
+ +
+
+variable RemoveAllDimLabels(WaveOrNull wv)
+

Remove the dimlabels of all dimensions with data.

+

Due to no better solutions the dim labels are actually overwritten with an empty string

+
+ +
+
+variable WaveModCountWrapper(wave wv)
+

Return the modification count of the (permanent) wave.

+

Returns NaN when running in a preemptive thread

+

UTF_NOINSTRUMENTATION

+
+ +
+
+wave MergeTwoWaves(wave wv1, wave wv2)
+

Merge two floating point waves labnotebook waves.

+

The result will hold the finite row entry of either wv1 or wv2.

+
+ +
+
+variable ChangeWaveLock(WaveRefWave wv, variable val)
+

Adapt the wave lock status on the wave and its contained waves.

+
+ +
+
+variable DeleteWavePoint(wave wv, variable dim, variable index = defaultValue, wave indices = defaultValue)
+

Deletes one row, column, layer or chunk from a wave Advantages over DeletePoints: Keeps the dimensionality of the wave when deleting the last row, column, layer or chunk in a wave Implements range check Advantages over DeletePoints + KillWaves: The wave reference stays valid.

+
+
Parameters:
+
    +

  • wv – wave where the row, column, layer or chunk should be deleted

    • +

  • dim – dimension 0 - rows, 1 - column, 2 - layer, 3 - chunk

    • +

  • index – [optional, default n/a] index where one point in the given dimension is deleted

    • +

  • indices – [optional, default n/a] 1d numerical wave with indices of points to delete

    • +
+
+
+
+ +
+
+variable RemoveTextWaveEntry1D(WaveText w, string entry, variable options = defaultValue, variable all = defaultValue)
+

Removes found entry from a text wave.

+
+
Parameters:
+
    +

  • w – text wave

    • +

  • entry – element content to compare

    • +

  • options – [optional, defaults to “whole wave element”] FindValue/TXOP options

    • +

  • all – [optional, defaults to false] removes all entries

    • +
+
+
Returns:
+

0 if at least one entry was found, 1 otherwise

+
+
+
+ +
+
+std::tuple<WaveText, WaveText> SplitTextWaveBySuffix(WaveText source, string suffix)
+

Splits a 1d text wave into two waves. The first contains elements with a suffix, the second elements without.

+
+
Parameters:
+
    +

  • source – [in] 1d text wave

    • +

  • suffix – [in] string suffix to distinguish elements

    • +
+
+
Returns:
+

two 1d text waves, the first contains all elements with the suffix, the second all elements without

+
+
+
+ +
+
+wave WaveRef(WaveOrNull w, variable row = defaultValue, variable col = defaultValue, variable layer = defaultValue, variable chunk = defaultValue)
+

Helper function to be able to index waves stored in wave reference waves in wave assignment statements.

+

The case where wv contains wave references is also covered by the optional parameters. While returned regular waves can be indexed within the assignment as shown in the first example, this does not work for wave reference waves. Thus, the parameters allow to index through the function call.

+

Example for source containing regular waves: 


+
+
+

Make/FREE data1 = p +Make/FREE data2 = p^2 +Make/FREE/WAVE source = {data1, data2}

+

Make/FREE dest +dest[] = WaveRef(source[0])[p] + WaveRef(source[1])[p] // note the direct indexing [p] following WaveRef(…) here

+

+

+

Example for source containing wave ref waves: 


+
+
+

Make/FREE data1 = p +Make/FREE/WAVE interm = {data1, data1} +Make/FREE/WAVE source = {interm, interm}

+

Make/FREE/WAVE/N=2 dest +dest[] = WaveRef(source[p], row = 0) // direct indexing does not work here, so we index through the optional function parameter

+

+

+

row, col, layer, chunk are evaluated in this order until one argument is not given.

+

+UTF_NOINSTRUMENTATION

+
+
Parameters:
+
    +

  • w – input wave ref wave

    • +

  • row – [optional, default = n/a] when param set returns wv[row] typed

    • +

  • col – [optional, default = n/a] when param row and this set returns wv[row][col] typed

    • +

  • layer – [optional, default = n/a] when param row, col and this set returns wv[row][col][layer] typed

    • +

  • chunk – [optional, default = n/a] when param row, col, layer and this set returns wv[row][layer][chunk] typed

    • +
+
+
Returns:
+

untyped waveref of wv or typed wave ref of wv when indexed

+
+
+
+ +
+
+string WaveText(WaveOrNull w, variable row = defaultValue, variable col = defaultValue, variable layer = defaultValue, variable chunk = defaultValue)
+

Compensate IP not having a way to dynamically extract a string from an untyped, i.e. numeric, wave.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+wave SelectWave(variable condition, WaveOrNull waveIfFalse, WaveOrNull waveIfTrue)
+

Helper function for multithread statements where ? : does not work with wave references.

+

The order of arguments is modelled after SelectString/SelectNumber.

+
+ +
+
+wave RemoveUnusedRows(wave wv)
+

Remove unused rows from the passed wave and return a copy of it.

+

If the wave is empty with index being zero, we return a wave with one point so that we:

    +

  • can store something non-empty

    • +

  • preserve the dimension labels (this can get lost for empty waves when duplication/saving)

    • +
+

+

+

See also

+

EnsureLargeEnoughWave()

+
+

+
+ +
+
+wave DuplicateWaveToFree(wave w)
+

Duplicates the input wave to a free wave and returns the free wave reference.

+
+ +
+
+wave ZapNaNs(wave data)
+

Removes all NaNs from the input wave.

+
+ +
+
+variable ChangeFreeWaveName(wave wv, string name)
+

Give the free wave wv the name name

+
+ +
+
+wave ZapNullRefs(WaveRefWave input)
+
+ +
+
+wave SplitWavesToDimension(WaveRefWave input, variable sdim = defaultValue)
+

Split multidimensional waves inside input to the given dimension.

+
+
Parameters:
+
    +

  • input – wave reference wave

    • +

  • sdim – [optional, defaults to 1] dimensionality to split to

    • +
+
+
+
+ +
+
+variable FindFirstNaNIndex(wave wv)
+

Returns the first row index that is NaN from the floating point wave wv, NaN if no index is NaN.

+
+ +
+
+variable SetDimensionLabelsFromWaveContents(wave wv, string prefix = defaultValue, string suffix = defaultValue, variable strict = defaultValue)
+

Sets the DimLabels for elements of a 1d numerical or text wave based on the content of the wave For numerical waves the wave element is treated as integer For textual waves the elements must translate to a valid DimLabel.

+
+
Parameters:
+
    +

  • wv – input wave

    • +

  • prefix – [optional: default “” for numerical waves and NUM_ for textual waves] prefix of the dimlabel For numerical waves it is recommended to provide an own prefix.

    • +

  • suffix – [optional: default “”] suffix of the dimlabel

    • +

  • strict – [optional: default 0] When this flag is set then each constructed DimLabels for text wave elements are checked if it results in a valid DimLabel, it is also checked if duplicate Dimlabels would be created.

    • +
+
+
+
+ +
+
+wave ConvertFreeWaveToPermanent(wave freeWave, dfref dfr, string wName)
+

Converts a free wave to a permanent wave with Overwrite.

+
+
Parameters:
+
    +

  • freeWave – [in] wave that should be converted to a permanent wave

    • +

  • dfr – [in] data folder where permanent wave is stored

    • +

  • wName – [in] name of permanent wave that is created

    • +
+
+
Returns:
+

wave reference to the permanent wave

+
+
+
+ +
+
+wave MoveFreeWaveToPermanent(wave freeWave, dfref dfr, string wvName)
+
+ +
+
+variable DuplicateWaveAndKeepTargetRef(WaveOrNull source, WaveOrNull target)
+

Duplicate a source wave to a target wave and keep the target wave reference intact. Use with free/local waves. For global waves use “Duplicate/O source, target”.

+
+
Parameters:
+
    +

  • source – source wave

    • +

  • target – target wave

    • +
+
+
+
+ +
+
+variable SearchForDuplicates(wave wv)
+

Detects duplicate values in a 1d wave.

+
+
Returns:
+

one if duplicates could be found, zero otherwise

+
+
+
+ +
+
+wave FindNeighbourDuplicates(wave wv)
+

Return the indizes of elements which need to be dropped so that no two neighbouring points are equal/both NaN.

+
+ +
+
+wave MoveWaveWithOverwrite(wave dest, wave src, variable recursive = defaultValue)
+

Move the source wave to the location of the given destination wave. The destination wave must be a permanent wave.

+

Workaround for MoveWave having no /O flag.

+
+
Parameters:
+
    +

  • dest – permanent wave

    • +

  • src – wave (free or permanent)

    • +

  • recursive – [optional, defaults to false] Overwrite referenced waves in dest with the ones from src (wave reference waves only with matching sizes)

    • +
+
+
Returns:
+

new wave reference to dest wave

+
+
+
+ +
+
+variable ZeroWave(wave wv)
+

Zero the wave using differentiation and integration.

+

Overwrites the input wave Preserves the WaveNote and adds the entry NOTE_KEY_ZEROED

+

2D waves are zeroed along each row

+
+
Returns:
+

0 if nothing was done, 1 if zeroed

+
+
+
+ +
+
+variable ZeroWaveImpl(wave wv)
+

Zeroes a wave in place.

+
+ +
+
+variable GetDecimatedWaveSize(variable numRows, variable decimationFactor, variable method)
+

Return the size of the decimated wave.

+

Query that to create the output wave before calling DecimateWithMethod().

+
+
Parameters:
+
    +

  • numRows – number of rows in the input wave

    • +

  • decimationFactor – decimation factor, must be an integer and larger than 1

    • +

  • method – one of DecimationMethods

    • +
+
+
+
+ +
+
+string GetLastNonEmptyEntry(WaveText wv, string colLabel, variable endRow)
+

Searches the column colLabel in wv for an non-empty entry with a row number smaller or equal to endRow.

+

Return an empty string if nothing could be found.

+
+
Parameters:
+
    +

  • wv – text wave to search in

    • +

  • colLabel – column label from wv

    • +

  • endRow – maximum row index to consider

    • +
+
+
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___wave_builder_8ipf.html b/file/_m_i_e_s___wave_builder_8ipf.html new file mode 100644 index 0000000000..e87ee3f0de --- /dev/null +++ b/file/_m_i_e_s___wave_builder_8ipf.html @@ -0,0 +1,1469 @@ + + + + + + + + File MIES_WaveBuilder.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_WaveBuilder.ipf

+

WB Stimulus set creation

+
+

Constants for WB_GetControlWithDeltaIdx

+

The numeric values are row indizes in the waves returned by WB_GetControlWithDeltaWvs().

+
+
+static const double WB_IDX_DURATION = 0
+
+ +
+
+static const double WB_IDX_AMPLITUDE = 2
+
+ +
+
+static const double WB_IDX_OFFSET = 4
+
+ +
+
+static const double WB_IDX_SIN_CHIRP_SAW_FREQUENCY = 6
+
+ +
+
+static const double WB_IDX_TRAIN_PULSE_DURATION = 8
+
+ +
+
+static const double WB_IDX_PSC_EXP_RISE_TIME = 10
+
+ +
+
+static const double WB_IDX_PSC_EXP_DECAY_TIME_1_2 = 12
+
+ +
+
+static const double WB_IDX_PSC_EXP_DECAY_TIME_2_2 = 14
+
+ +
+
+static const double WB_IDX_PSC_RATIO_DECAY_TIMES = 16
+
+ +
+
+static const double WB_IDX_LOW_PASS_FILTER_CUT_OFF = 20
+
+ +
+
+static const double WB_IDX_HIGH_PASS_FILTER_CUT_OFF = 22
+
+ +
+
+static const double WB_IDX_CHIRP_END_FREQUENCY = 24
+
+ +
+
+static const double WB_IDX_NOISE_FILTER_ORDER = 26
+
+ +
+
+static const double WB_IDX_PT_FIRST_MIXED_FREQUENCY = 28
+
+ +
+
+static const double WB_IDX_PT_LAST_MIXED_FREQUENCY = 30
+
+ +
+
+static const double WB_IDX_NUMBER_OF_PULSES = 45
+
+ +
+
+static const double WB_IDX_ITI = 99
+
+ +
+
+

Functions that build wave types

+
+
+static variable WB_SquareSegment(SegmentParameters *pa)
+
+ +
+
+static variable WB_RampSegment(SegmentParameters *pa)
+
+ +
+
+variable WB_IsValidCutoffFrequency(variable freq)
+

Check if the given frequency is a valid setting for the noise epoch.

+
+ +
+
+variable WB_IsValidScaledCutoffFrequency(variable freq)
+

Check if the given frequency is a valid setting for the noise epoch.

+

Requires a scaled frequency as input, see DisplayHelpTopic "FilterIIR"

+
+ +
+
+static variable WB_NoiseSegment(SegmentParameters *pa)
+
+ +
+
+static std::tuple<variable, variable> WB_TrigGetBoundsForInflectionPoints(SegmentParameters *pa, variable offset)
+
+ +
+
+static variable WB_CheckTrigonometricSegmentParameters(SegmentParameters *pa)
+
+ +
+
+static std::tuple<WaveDouble, WaveDouble> WB_TrigCalculateInflectionPoints(SegmentParameters *pa, variable k0, variable k1, variable k2, variable k3)
+

Calculate the x values where the trigonometric epoch has inflection points.

+

For zero offset, the inflection points coincide with the zero crossings/roots. In case nothing can be calculated the inflectionPoints wave has one NaN entry.

+

The formula without chirp can be solved for \(f(x) == 0\) as:

+
+\[\begin{split}f(x) &= a \cdot \sin(k_0 \cdot x) \\ +k_0 \cdot x &= c \cdot \pi \\ +x &= \frac{c \cdot \pi}{k_0}\end{split}\]
+

And for cosine:

+
+\[x = \frac{(c + \frac{1}{2}) \cdot \pi}{k_0}\]
+

With chirp and sine:

+
+\[\begin{split}f(x) &= a \cdot \sin(k_2 \cdot e^{k_1 \cdot x}- k_3) \\ +k_2 \cdot e^{k_1 \cdot x} - k_3 &= c \cdot \pi \\ +e^{k_1 \cdot x} &= \frac{c \cdot \pi + k_3}{k_2} \\ +k_1 \cdot x &= \ln\left(\frac{c \cdot \pi + k_3}{k_2}\right) \\ +x &= \frac{1}{k_1} \cdot \ln\left(\frac{c \cdot \pi + k_3}{k_2}\right)\end{split}\]
+

And analogous for cosine:

+
+\[x = \frac{1}{k_1} \cdot \ln\left(\frac{(c + \frac{1}{2}) \cdot \pi + k_3}{k_2}\right)\]
+

+
+ +
+
+static std::tuple<WaveDouble, WaveDouble> WB_TrigSegment(SegmentParameters *pa)
+
+ +
+
+static variable WB_SawToothSegment(SegmentParameters *pa)
+
+ +
+
+static variable WB_CreatePulse(wave wv, variable pulseType, variable amplitude, variable first, variable last)
+
+ +
+
+string WB_ToEpochTypeString(variable epochType)
+

Convert the numeric epoch type to a stringified version.

+
+ +
+
+variable WB_ToEpochType(string epochTypeStr)
+

Convert the stringified epoch type to a numerical one.

+
+ +
+
+string WB_GetWaveNoteEntry(string text, variable entryType, string key = defaultValue, variable sweep = defaultValue, variable epoch = defaultValue)
+

Query stimset wave note entries.

+

Format of the wave note:

+

The wave note version is tracked through STIMSET_NOTE_VERSION

+

Lines separated by \r (carriage return) in UTF-8 encoding. +The lines hold Igor Pro style key value pairs in the form key = value; +where value can contain any character except ; (semicolon).

+

Four types of entries can be distinguished:

+
    +

  • Version: In the very first line (line 1)

    • +

  • Sweep specific entries have an epoch of nan: (line 2, 7)

    • +

  • Epoch specific: (line 3 - 6)

    • +

  • Stimset specific: (line 12)

    • +
+

Additional infos on selected entries: +- ITI is in seconds +- Flipping is done on a per stimset basis +- Durations are in stimset build ms +- Pulse Train Pulses are absolute pulse starting times in epoch build ms +- Pulse To Pulse Length is in stimset build ms +- Function params (encoded) contains the analysis function parameters. The values have the format described at GetWaveBuilderWaveTextParam(). +- Inflection Points are in epoch build ms. For offset zero these coincide with the roots.

+
+
Added with version 10:
    +

  • start and end indices for pulses in pulse trains (end index is part of the pulse)

    • +

  • length of each segment

    • +

  • inflection point positions (left side index)

    • +
+
+
+

Example:

+
 1Version = 2;
+ 2Sweep = 0;Epoch = nan;ITI = 1;
+ 3Sweep = 0;Epoch = 0;Type = Square pulse;Duration = 500;Amplitude = 0;
+ 4Sweep = 0;Epoch = 1;Type = Ramp;Duration = 150;Amplitude = 1;Offset = 0;
+ 5Sweep = 0;Epoch = 2;Type = Square pulse;Duration = 300;Amplitude = 0;
+ 6Sweep = 0;Epoch = 3;Type = Pulse Train;Duration = 960.005;Amplitude = 1;Offset = 0;Pulse Type = Square;Frequency = 20;Pulse To Pulse Length = 50;Pulse duration = 10;Number of pulses = 20;Mixed frequency = False;First mixed frequency = 0;Last mixed frequency = 0;Poisson distribution = False;Random seed = 0.963638;Pulse Train Pulses = 0,50,100,150,200,250,300,350,400,450,500,550,600,650,700,750,800,850,900,950,;Definition mode = Duration;
+ 7Sweep = 1;Epoch = nan;ITI = 2;
+ 8Sweep = 1;Epoch = 0;Type = Square pulse;Duration = 500;Amplitude = 0;
+ 9Sweep = 1;Epoch = 1;Type = Ramp;Duration = 150;Amplitude = 1;Offset = 0;
+10Sweep = 1;Epoch = 2;Type = Square pulse;Duration = 300;Amplitude = 0;
+11Sweep = 1;Epoch = 3;Type = Pulse Train;Duration = 960.005;Amplitude = 1;Offset = 0;Pulse Type = Square;Frequency = 20;Pulse To Pulse Length = 50;Pulse duration = 10;Number of pulses = 20;Mixed frequency = False;First mixed frequency = 0;Last mixed frequency = 0;Poisson distribution = False;Random seed = 0.963638;Pulse Train Pulses = 0,50,100,150,200,250,300,350,400,450,500,550,600,650,700,750,800,850,900,950,;Definition mode = Duration;
+12Stimset;Sweep Count = 2;Epoch Count = 4;Pre DAQ = ;Mid Sweep = ;Post Sweep = ;Post Set = ;Post DAQ = ;Pre Sweep = ;Generic = PSQ_Ramp;Pre Set = ;Function params (encoded)= NumberOfSpikes:variable=5,Elements:string=%20%3B%2C;Flip = 0;Random Seed = 0.963638;Wavebuilder Error = 0;Checksum = 65446509;
+
+
+

+
+
Parameters:
+
    +

  • text – stimulus set wave note

    • +

  • entryType – one of StimsetWaveNoteEntryTypes

    • +

  • key – [optional] named entry to return, not required for VERSION_ENTRY

    • +

  • sweep – [optional] number of the sweep

    • +

  • epoch – [optional] number of the epoch

    • +
+
+
+
+ +
+
+variable WB_GetWaveNoteEntryAsNumber(string text, variable entryType, string key = defaultValue, variable sweep = defaultValue, variable epoch = defaultValue)
+
+ +
+
+static std::tuple<WaveDouble, WaveDouble, WaveDouble, variable> WB_PulseTrainSegment(SegmentParameters *pa, variable mode)
+
+ +
+
+static variable WB_PSCSegment(SegmentParameters *pa)
+
+ +
+
+static variable WB_CustomWaveSegment(SegmentParameters *pa, wave customWave)
+
+ +
+
+static wave WB_FillWaveFromFormula(string formula, variable channelType, variable sweep)
+

Create a wave segment as combination of existing stim sets.

+
+ +
+
+

Functions

+
+
+wave WB_CreateAndGetStimSet(string setName)
+

Return the stim set wave and create it permanently in the datafolder hierarchy.

+
+
Returns:
+

stimset wave ref or an invalid wave ref

+
+
+
+ +
+
+string WB_GetParameterWaveName(string stimset, variable type, variable nwbFormat = defaultValue)
+

Return the name of one of the three stimset parameter waves.

+
+
Parameters:
+
    +

  • stimset – name of stimset

    • +

  • type – indicate parameter wave (WP, WPT, or SegWvType), see ParameterWaveTypes

    • +

  • nwbFormat – [optional, defaults to false] nwbFormat has type as suffix

    • +
+
+
Returns:
+

name as string

+
+
+
+ +
+
+wave WB_GetWaveParamForSet(string setName)
+

Return the wave WP for a stim set.

+
+
Returns:
+

valid/invalid wave reference

+
+
+
+ +
+
+wave WB_GetWaveTextParamForSet(string setName)
+

Return the wave WPT for a stim set.

+
+
Returns:
+

valid/invalid wave reference

+
+
+
+ +
+
+wave WB_GetSegWvTypeForSet(string setName)
+

Return the wave SegmentWvType for a stim set.

+
+
Returns:
+

valid/invalid wave reference

+
+
+
+ +
+
+static variable WB_StimsetNeedsUpdate(string setName)
+

Check if stimset needs to be created.

+

Stimset is recreated

    +

  • if one of the parameter waves was modified

    • +

  • the custom wave that was used to build the stimset was modified

    • +
+

+
+
Returns:
+

1 if stimset needs to be recreated, 0 otherwise

+
+
+
+ +
+
+static variable WB_StimsetHasLatestNoteVersion(string setName)
+

Check if the stimset wave note has the latest version.

+
+ +
+
+static variable WB_ParameterWvsNewerThanStim(string setName)
+

Check if parameter waves’ are newer than the saved stimset.

+
+
Parameters:
+

setName – string containing name of stimset

+
+
Returns:
+

1 if Parameter waves were modified, 0 otherwise

+
+
+
+ +
+
+variable WB_GetStimsetChecksum(wave stimset, string setName, variable dataAcqOrTP)
+

Return a checksum of the stimsets and its parameter waves.

+

Uses the entry from the stimset wave note if available.

+
+ +
+
+static variable WB_CalculateStimsetChecksum(wave stimset, string setName)
+

Calculcate the checksum of the stimsets and its parameter waves.

+
+ +
+
+variable WB_GetLastModStimSet(string setName)
+

Get modification date of saved stimset wave.

+
+
Parameters:
+

setName – string containing name of stimset

+
+
Returns:
+

date of last modification as double precision Igor date/time value

+
+
+
+ +
+
+wave WB_GetStimSetForWaveBuilder()
+

Return the current stimset wave for the wavebuilder.

+
+ +
+
+static wave WB_GetStimSet(string setName = defaultValue)
+

Return the stim set wave.

+

As opposed to WB_CreateAndGetStimSet this function returns a free wave only

+
+
Parameters:
+

setName – [optional, defaults to WaveBuilderPanel GUI settings] name of the set

+
+
Returns:
+

free wave with the stim set, invalid wave ref if the WP* parameter waves could not be found.

+
+
+
+ +
+
+static wave WB_GetControlWithDeltaIdx()
+

Return a free wave with indizes referencing the values with delta values.

+

Indizes are into WP

and reference the entry with the value itself.

+

Constants are defined at

+ControlDeltaIndizes.
+

See also

+

AddDimLabelsToWP()

+
+

+
+ +
+
+static wave WB_GetControlWithDeltaWvs(wave WP, wave SegWvType)
+

Return a free wave with wave references where the values with delta reside in.

+

+

See also

+

AddDimLabelsToWP()

+
+

+
+ +
+
+variable WB_GetDeltaDimLabel(wave wv, variable index, DeltaControlNames *s)
+

Return the WP/WPT/SegWvType dimension labels for the related delta controls given the index into WP of the value itself.

+
+
Returns:
+

0 on success, 1 otherwise

+
+
+
+ +
+
+static variable WB_AddDelta(string setName, wave WP, wave WPOrig, WaveText WPT, wave SegWvType, wave SegWvTypeOrig, variable sweep, variable numSweeps)
+

Add delta to appropriate parameters.

+

Relies on alternating sequence of parameter and delta’s in parameter waves as documented in WB_MakeWaveBuilderWave().

+
+
Parameters:
+
    +

  • setName – name of the stimset

    • +

  • WP – wavebuilder parameter wave (temporary copy)

    • +

  • WPOrig – wavebuilder parameter wave (original)

    • +

  • WPT – wavebuilder text parameter wave

    • +

  • SegWvType – segment parameter wave (temporary copy)

    • +

  • SegWvTypeOrig – segment parameter wave (original)

    • +

  • sweep – sweep number

    • +

  • numSweeps – total number of sweeps

    • +
+
+
+
+ +
+
+static variable WB_CalculateParameterWithDelta(variable operation, variable *value, variable *delta, variable dme, string ldelta, variable originalValue, variable sweep, variable numSweeps, string setName, string paramName)
+

Calculate the new value of a parameter taking into account the delta operation.

+
+
Parameters:
+
    +

  • operation – [in] delta operation, one of WaveBuilderDeltaOperationModes

    • +

  • value – [inout] parameter value (might be incremented by former delta application calls)

    • +

  • delta – [inout] delta value

    • +

  • dme – [in] delta multiplier or exponent

    • +

  • ldelta – [in] explicit list of delta values

    • +

  • originalValue – [in] unmodified parameter value

    • +

  • sweep – [in] sweep number

    • +

  • numSweeps – [in] number of sweeps

    • +

  • setName – [in] name of the stimulus set (used for error reporting)

    • +

  • paramName – [in] name of the parameter (used for error reporting)

    • +
+
+
+
+ +
+
+static wave WB_MakeWaveBuilderWave(wave WP, WaveText WPT, wave SegWvType, variable stepCount, variable numEpochs, variable channelType, variable updateEpochIDWave, string stimset = defaultValue)
+
+ +
+
+static variable WB_UpdateEpochID(variable epochIndex, variable epochDuration, variable accumulatedDuration)
+

Update the accumulated stimset duration for the mouse selection via GetEpochID()

+
+
Parameters:
+
    +

  • epochIndex – [in] index of the epoch

    • +

  • epochDuration – [in] duration of the current segment

    • +

  • accumulatedDuration – [in] accumulated duration in the stimset for the first step

    • +
+
+
+
+ +
+
+variable WB_GetITI(wave stimset, variable sweep)
+

Query the stimset wave note for the sweep/set specific ITI.

+
+ +
+
+variable WB_UpgradeCustomWaveInWPT(WaveText wv, variable channelType, variable i)
+

Try to recover a custom wave when in the old format (aka with only a wave name and not a full path)

+
+
Parameters:
+
    +

  • wv – WPT wave reference

    • +

  • channelType – AD/DA or TTL channel type

    • +

  • i – index of epoch containing custom wave

    • +
+
+
+
+ +
+
+static variable WB_ApplyOffset(SegmentParameters *pa)
+
+ +
+
+static variable WB_InitializeSeed(wave WP, wave SegWvType, variable epoch, variable type, variable stepCount)
+

Initialize the seed value of the pseudo random number generator.

+
+ +
+
+variable WB_UpdateEpochCombineList(WaveText epochCombineList, variable channelType)
+

Update the shorthand/stimset wave for the epoch type Combine

+

The rows are sorted by creationDate of the WP/stimset wave to try to keep the shorthands constants even when new stimsets are added.

+
+ +
+
+static string WB_GenerateUniqueLabel(variable idx)
+

Generate a unique textual representation of an index.

+

Returns the alphabet for 1-26, and then A1, B1, …, Z1000

+
+ +
+
+variable WB_ParseCombinerFormula(variable channelType, string formula, variable sweep, FormulaProperties *fp)
+

Parse the formula from the epoch type Combine

+
+
Parameters:
+
    +

  • channelType – [in] One of CHANNEL_TYPE_DA or CHANNEL_TYPE_TTL

    • +

  • formula – [in] math formula to execute, all operators which Igor can grok are allowed

    • +

  • sweep – [in] current sweep (aka step)

    • +

  • fp – [out] parsed formula structure, with shorthands replaced by stimsets, empty on parse error, ready to be executed by WB_FillWaveFromFormula()

    • +
+
+
Returns:
+

0 on success, 1 on parse errors (currently not many are found)

+
+
+
+ +
+
+variable WB_FormulaSwitchToStimset(variable channelType, string formula, FormulaProperties *fp)
+

Replace shorthands with the real stimset names suffixed with ?

+
+ +
+
+static variable WB_PrepareFormulaForExecute(FormulaProperties *fp, variable sweep)
+

Add wave ranges to every stimset (location marked by ?) and add a left hand side to the formula.

+
+ +
+
+string WB_FormulaSwitchToShorthand(variable channelType, string formula)
+

Replace all stimsets suffixed with ? by their shorthands.

+
+ +
+
+wave WB_CustomWavesFromStimSet(string stimsetList)
+

Get all custom waves that are used by the supplied stimset.

+

used by WaveBuilder and NeuroDataWithoutBorders

+
+
Returns:
+

a wave of wave references

+
+
+
+ +
+
+wave WB_CustomWavesPathFromStimSet(string stimsetList)
+

Get all custom waves that are used by the supplied stimset.

+
+
Returns:
+

a text wave with paths to custom waves.

+
+
+
+ +
+
+static wave WB_UpgradeCustomWaves(string stimsetList)
+

Try to upgrade all epochs with custom waves from the stimsetlist.

+

you can only use this function if the custom wave is present in the current experiment. do not try to upgrade when loading stimsets. The custom waves have to be loaded first.

+
+
Returns:
+

a text wave with paths to custom waves.

+
+
+
+ +
+
+static string WB_StimsetChildren(string stimset = defaultValue)
+

Search for stimsets in formula epochs.

+

a stimset (parent) can depend on other stimsets (child)

+
+
Returns:
+

non-unique list of all (child) stimsets

+
+
+
+ +
+
+variable WB_StimsetFamilyNames(string *knownNames, string *parent = defaultValue)
+

Get children of current parent stimset.

+
+
Parameters:
+
    +

  • parent – [optional: defaults to current WB panel] specify parent stimset.

    • +

  • knownNames – [out] unique list of stimsets

    • +
+
+
Returns:
+

number of parents stimsets that were moved to child stimsets

+
+
+
+ +
+
+string WB_StimsetRecursion(string parent = defaultValue, string knownStimsets = defaultValue)
+

Recursively descents into parent stimsets.

+

You can not recurse into a stimset that depends on itself.

+
+
Returns:
+

list of stimsets that derive from the input stimset

+
+
+
+ +
+
+string WB_StimsetRecursionForList(string stimsetQueue)
+

Recursively descents into parent stimsets.

+
+
Parameters:
+

stimsetQueue – can be a list of stimsets (separated by ;) or a simple string

+
+
Returns:
+

list of stimsets that derive from the input stimsets

+
+
+
+ +
+
+variable WB_ParameterWavesExist(string stimset)
+

check if parameter waves exist

+
+
Returns:
+

1 if parameter waves exist, 0 otherwise

+
+
+
+ +
+
+variable WB_StimsetExists(string stimset)
+

check if (custom) stimset exists

+
+
Returns:
+

1 if stimset wave was found, 0 otherwise

+
+
+
+ +
+
+variable WB_KillParameterWaves(string stimset)
+

Kill Parameter waves for stimset.

+
+ +
+
+variable WB_KillStimset(string stimset)
+

Kill (custom) stimset.

+
+ +
+
+variable WB_StimsetIsFromThirdParty(string stimset)
+

Determine if the stimset is third party or from MIES.

+

Third party stimsets don’t have all parameter waves

+
+
Returns:
+

true if from third party, false otherwise

+
+
+
+ +
+
+variable WB_AddAnalysisParameterIntoWPT(WaveText WPT, string name, variable var = defaultValue, string str = defaultValue, wave wv = defaultValue)
+

Internal use only.

+
+ +
+
+variable WB_SetAnalysisFunctionGeneric(variable stimulusType, string analysisFunction, WaveText WPT)
+

Internal use only.

+
+ +
+
+static variable WB_SaveStimSetParameterWaves(string setName, wave SegWvType, wave WP, WaveText WPT, variable stimulusType)
+
+ +
+
+string WB_SaveStimSet(string baseName, variable stimulusType, wave SegWvType, wave WP, WaveText WPT, variable setNumber, variable saveAsBuiltin)
+
+ +
+
+wave WB_GetEpochLengths(string setName)
+

Return a wave with the length of all epochs.

+
+
Returns:
+

wave with epoch lengths or an invalid wave reference in case we don’t have any epochs

+
+
+
+ +
+
+static variable WB_CheckStimsetContents(wave stimset)
+
+ +
+
+static variable WB_CheckForEmptyEpochs(string setname)
+
+ +
+
+static string WB_AssembleSetName(string basename, variable stimulusType, variable setNumber, string suffix = defaultValue, variable lengthLimit = defaultValue)
+

Return the name of a stimulus set build up from the passed parts.

+
+
Returns:
+

complete stimulus set name or an empty string in case the basename is too long

+
+
+
+ +
+
+variable WB_SplitStimsetName(string setName, string *setPrefix, variable *stimulusType, variable *setNumber)
+

Split the full setname into its three parts: prefix, stimulusType and set number.

+

Counterpart to WB_AssembleSetName()

+
+ +
+
+variable WB_MakeStimsetThirdParty(string setName)
+

Changes an existing stimset to a third party stimset.

+
+ +
+
+variable WB_UpdateChangedStimsets(string device = defaultValue, variable stimulusType = defaultValue)
+

Propagate added/removed stimsets to DA_Ephys panels and our epoch combine list.

+
+ +
+
+static std::tuple<variable, variable, variable, variable> WB_GetIndicesForSignalDuration(variable startTime, variable duration, variable sampleInterval)
+

Returns the start and end indices for a wave given a FP duration. The length within the wave is calculated in a way, that at least the points to fill duration are included. So the effective duration never gets shortened.

+
+
Parameters:
+
    +

  • startTime – floating point start time of the range

    • +

  • duration – floating point duration time

    • +

  • sampleInterval – floating point sample interval

    • +
+
+
Return values:
+
    +

  • startIndex – index where the range starts

    • +

  • endIndex – index where the range ends, this is inclusive for e.g. data[startIndex, endIndex] = amplitude

    • +

  • startOffset – floating point error of start in wave regarding startTime argument: >= -0.5 * sampleInterval && < 0.5 * sampleInterval

    • +

  • durationError – floating point error of duration in wave regarding duration argument: >= 0 && < sampleInterval

    • +
+
+
+
+ +
+
+variable WB_GetStimSetType(string setName)
+

Return the type, CHANNEL_TYPE_DAC, CHANNEL_TYPE_TTL or CHANNEL_TYPE_UNKNOWN, of the stimset.

+

All callers must ensure that they can handle the unexpected CHANNEL_TYPE_UNKNOWN properly.

+
+ +
+
+string WB_ExtractAnalysisFuncFromStimSet(wave stimSet, variable eventType)
+

Extract the analysis function name from the wave note of the stim set.

+
+
Returns:
+

Analysis function for the given event type, empty string if none is set

+
+
+
+ +
+
+string WB_ExtractAnalysisFunctionParams(wave stimSet)
+

Return the analysis function parameters as comma (,) separated list.

+

+

See also

+

GetWaveBuilderWaveTextParam() for the exact format.

+
+

+
+ +
+
+

Variables

+
+
+static const double PULSE_TRAIN_MODE_DUR = 0x01
+
+ +
+
+static const double PULSE_TRAIN_MODE_PULSE = 0x02
+
+ +
+
+static const double WB_PULSE_TRAIN_TYPE_SQUARE = 0
+
+ +
+
+static const double WB_PULSE_TRAIN_TYPE_TRIANGLE = 1
+
+ +
+
+static const double WB_TRIG_TYPE_SIN = 0
+
+ +
+
+static const double WB_TRIG_TYPE_COS = 1
+
+ +
+
+static const double DELTA_OPERATION_EXPLICIT = 6
+
+ +
+
+
+struct SegmentParameters
+
+

Public Members

+
+
+variable duration
+
+ +
+
+variable deltaDur
+
+ +
+
+variable amplitude
+
+ +
+
+variable deltaAmp
+
+ +
+
+variable offset
+
+ +
+
+variable frequency
+
+ +
+
+variable deltaFreq
+
+ +
+
+variable pulseDuration
+
+ +
+
+variable tauRise
+
+ +
+
+variable tauDecay1
+
+ +
+
+variable tauDecay2
+
+ +
+
+variable tauDecay2Weight
+
+ +
+
+variable lowPassCutOff
+
+ +
+
+variable highPassCutOff
+
+ +
+
+variable filterOrder
+
+ +
+
+variable endFrequency
+
+ +
+
+variable numberOfPulses
+
+ +
+
+variable poisson
+
+ +
+
+variable logChirp
+
+ +
+
+variable randomSeed
+
+ +
+
+variable trigFuncType
+
+ +
+
+variable noiseType
+
+ +
+
+variable noiseGenMode
+
+ +
+
+variable noiseGenModePTMixedFreq
+
+ +
+
+variable buildResolution
+
+ +
+
+variable pulseType
+
+ +
+
+variable mixedFreq
+
+ +
+
+variable mixedFreqShuffle
+
+ +
+
+variable firstFreq
+
+ +
+
+variable lastFreq
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___wave_builder___macro_8ipf.html b/file/_m_i_e_s___wave_builder___macro_8ipf.html new file mode 100644 index 0000000000..9ed7ffb8ba --- /dev/null +++ b/file/_m_i_e_s___wave_builder___macro_8ipf.html @@ -0,0 +1,287 @@ + + + + + + + + File MIES_WaveBuilder_Macro.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_WaveBuilder_Macro.ipf

+

WBPM WaveBuilder panel macro

+
+

Functions

+
+
+void WaveBuilder()
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___wave_builder_panel_8ipf.html b/file/_m_i_e_s___wave_builder_panel_8ipf.html new file mode 100644 index 0000000000..d4951f45b1 --- /dev/null +++ b/file/_m_i_e_s___wave_builder_panel_8ipf.html @@ -0,0 +1,909 @@ + + + + + + + + File MIES_WaveBuilderPanel.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_WaveBuilderPanel.ipf

+

WBP Panel for creating stimulus sets

+
+

Parameters for WBP_TranslateControlContents()

+
+
+static const double FROM_PANEL_TO_WAVE = 0x1
+
+ +
+
+static const double FROM_WAVE_TO_PANEL = 0x2
+
+ +
+
+

Unnamed Group

+
+
+string WBP_GetAnalysisFunctions_V3()
+

Wrapper functions to be used in GUI recreation macros This avoids having to hardcode the parameter values.

+
+ +
+
+

Functions

+
+
+variable WB_OpenStimulusSetInWaveBuilder()
+
+ +
+
+string WBP_CreateWaveBuilderPanel()
+
+ +
+
+variable WBP_StartupSettings()
+
+ +
+
+static variable WBP_AddEpochHLTraces(dfref dfr, variable epochHLType, variable epoch, variable numEpochs)
+

Add epoch highlightning traces Uses fill-to-next on specially created waves added before and after the current trace.

+
+ +
+
+static variable WBP_DisplaySetInPanel()
+
+ +
+
+static variable WBP_UpdateDependentControls(string checkBoxCtrl, variable checked)
+

Reponsible for adjusting controls which depend on other controls.

+

Must be called before the changed settings are written into the parameter waves.

+
+ +
+
+static variable WBP_UpdatePanelIfAllowed()
+
+ +
+
+static variable WBP_ParameterWaveToPanel(variable stimulusType)
+

Passes the data from the WP wave to the panel.

+
+ +
+
+static variable WBP_SetControl(string win, string control, variable value = defaultValue, string str = defaultValue)
+

Generic wrapper for setting a control’s value.

+
+ +
+
+variable WBP_ButtonProc_DeleteSet(WMButtonAction *ba)
+
+ +
+
+variable WBP_CheckProc(WMCheckboxAction *cba)
+
+ +
+
+variable WBP_InitialTabHook(WMTabControlAction *tca)
+

Additional initialhook called in ACL_DisplayTab

+
+ +
+
+variable WBP_FinalTabHook(WMTabControlAction *tca)
+

Additional finalhook called in ACL_DisplayTab

+
+ +
+
+variable WBP_ButtonProc_SaveSet(WMButtonAction *ba)
+
+ +
+
+static variable WBP_GetWaveTypeFromControl(string control)
+
+ +
+
+static variable WBP_ExtractRowNumberFromControl(string control)
+

Returns the row index into the parameter wave of the parameter represented by the named control.

+

+All entries are per epoch type and per epoch number except when the $suffix is ALL which denotes that it is a setting for the full stimset.

+
+
Parameters:
+

control – name of the control, the expected format is $str_$sep$row_$suffix where $str may contain any characters but $suffix is not allowed to include the substring _$sep.

+
+
+
+ +
+
+variable WBP_UpdateControlAndWave(string control, variable var = defaultValue, string str = defaultValue)
+

Update the named control and pass its new value into the parameter wave.

+
+ +
+
+variable WBP_SetVarProc_UpdateParam(WMSetVariableAction *sva)
+
+ +
+
+static variable WBP_LowPassDeltaLimits()
+
+ +
+
+static variable WBP_HighPassDeltaLimits()
+
+ +
+
+static variable WBP_ChangeWaveType()
+
+ +
+
+variable WBP_GetStimulusType()
+
+ +
+
+variable WBP_PopMenuProc_WaveType(WMPopupAction *pa)
+
+ +
+
+string WBP_GetListOfWaves()
+
+ +
+
+variable WBP_SetVarProc_SetSearchString(WMSetVariableAction *sva)
+
+ +
+
+variable WBP_PopMenuProc_WaveToLoad(WMPopupAction *pa)
+
+ +
+
+string WBP_ReturnListSavedSets()
+
+ +
+
+variable WBP_IsBuiltinStimset(string setName)
+

Return true if the given stimset is a builtin, false otherwise.

+
+ +
+
+static variable WBP_LoadSet(string setName)
+
+ +
+
+static variable SetAnalysisFunctionIfFuncExists(string win, string ctrl, string stimset, string funcList, string func)
+
+ +
+
+static variable WBP_UpdateEpochControls()
+
+ +
+
+variable WBP_SetVarProc_EpochToEdit(WMSetVariableAction *sva)
+
+ +
+
+variable WBP_PopupMenu_LoadSet(WMPopupAction *pa)
+
+ +
+
+static variable WBP_CutOffCrossOver()
+
+ +
+
+static variable WBP_ReturnPulseDurationMax()
+

Checks to see if the pulse duration in square pulse stimulus trains is too long.

+
+ +
+
+dfref WBP_GetFolderPath()
+
+ +
+
+string WBP_ReturnFoldersList()
+
+ +
+
+variable WBP_PopMenuProc_FolderSelect(WMPopupAction *pa)
+
+ +
+
+variable WBP_CheckProc_PreventUpdate(WMCheckboxAction *cba)
+
+ +
+
+variable WBP_PopupMenu(WMPopupAction *pa)
+
+ +
+
+static string WBP_ConvertDeltaLblToCtrlNames(string allControls, string dimLabel)
+

Convert from the row index of a delta related control to a list of control names.

+
+ +
+
+static variable WBP_AdjustDeltaControls(string control)
+

Depending on the delta operation the visibility of related controls is adjusted.

+
+
Parameters:
+

control – delta operation control name

+
+
+
+ +
+
+variable WBP_ButtonProc_NewSeed(WMButtonAction *ba)
+
+ +
+
+variable WBP_PopupMenu_AnalysisFunctions(WMPopupAction *pa)
+
+ +
+
+static variable WBP_UpgradePRNG()
+
+ +
+
+static variable WBP_AnaFuncsToWPT()
+
+ +
+
+string WBP_GetAnalysisFunctions(variable versionBitMask)
+

Return a list of analysis functions including NONE, usable for popup menues.

+

+

See also

+

AFM_GetAnalysisFunctions

+
+

+
+ +
+
+string WBP_GetNoiseTypes()
+

Return a list of noise types, usable for popup menues.

+
+ +
+
+string WBP_GetNoiseBuildResolution()
+

Return a list of build resolutions , usable for popup menues.

+
+ +
+
+variable WBP_ButtonProc_OpenAnaFuncs(WMButtonAction *ba)
+
+ +
+
+variable WBP_SetVarCombineEpochFormula(WMSetVariableAction *sva)
+
+ +
+
+static string WBP_TranslateControlContents(string control, variable direction, string data)
+

Convert a control entry for the panel or the wave.

+

Useful if the visualization is different from the stored data.

+
+
Parameters:
+
+
+
+
+ +
+
+static variable WBP_ClearFolders()
+
+ +
+
+variable WBP_MainWindowHook(WMWinHookStruct *s)
+

Wavebuilder panel window hook.

+

The epoch selection is done on the mouseup event if there exists no marquee. This allows to still use the zooming capability.

+
+ +
+
+string WBP_GetFFTSpectrumPanel()
+
+ +
+
+variable WBP_ShowFFTSpectrumIfReq(wave segmentWave, variable sweep)
+
+ +
+
+static std::tuple<RGBColor> WBP_GetSweepColor(variable sweep)
+

Return distinct colors the sweeps of the wavebuilder.

+

These are backwards compared to the trace colors

+
+ +
+
+static variable WBP_DeleteAnalysisParameter(string name)
+

Delete the given analysis parameter.

+
+
Parameters:
+

name – name of the parameter

+
+
+
+ +
+
+string WBP_GetParameterTypes()
+

Return a list of all possible analysis parameter types.

+
+ +
+
+static string WBP_GetAnalysisParameters()
+

Return the analysis parameters.

+
+ +
+
+static string WBP_GetAnalysisGenericFunction()
+
+ +
+
+string WBP_GetAnalysisParameterNames()
+

Return the analysis parameter names for the currently selected stimset.

+
+ +
+
+static variable WBP_UpdateParameterWave()
+

Fill the listwave from the stimset analysis parameters extracted from its WPT.

+
+ +
+
+static variable WBP_ToggleAnalysisParamGUI()
+

Toggle the analysis parameter GUI.

+
+
Returns:
+

one if the panel was killed, zero if it was created

+
+
+
+ +
+
+variable WBP_ButtonProc_DeleteParam(WMButtonAction *ba)
+
+ +
+
+variable WBP_ButtonProc_AddParam(WMButtonAction *ba)
+
+ +
+
+variable WBP_ButtonProc_OpenAnaParamGUI(WMButtonAction *ba)
+
+ +
+
+variable WBP_ListBoxProc_AnalysisParams(WMListboxAction *lba)
+
+ +
+
+variable WBP_ButtonProc_LoadSet(WMButtonAction *ba)
+
+ +
+
+string WBP_RegenerateEpochParameterNamesCode()
+

Function to regenerate code for GetEpochParameterNames()

+
+ +
+
+static wave WBP_ListControlsPerStimulusType(variable epochType)
+

Return a list of all parameter names of the given epochType.

+
+ +
+
+string WBP_GetDeltaModes()
+
+ +
+
+string WBP_GetTriggerTypes()
+
+ +
+
+string WBP_GetPulseTypes()
+
+ +
+
+

Variables

+
+
+static const string panel = "WaveBuilder"
+
+ +
+
+static const string WaveBuilderGraph = "WaveBuilder#WaveBuilderGraph"
+
+ +
+
+static const string AnalysisParamGUI = "WaveBuilder#AnalysisParamGUI"
+
+ +
+
+static const string DEFAULT_SET_PREFIX = "StimulusSetA"
+
+ +
+
+static const string SEGWVTYPE_CONTROL_REGEXP = ".*_S[[:digit:]]+"
+
+ +
+
+static const string WP_CONTROL_REGEXP = ".*_P[[:digit:]]+"
+
+ +
+
+static const string WPT_CONTROL_REGEXP = ".*_T[[:digit:]]+"
+
+ +
+
+static const string SEGWVTYPE_ALL_CONTROL_REGEXP = "^.*_ALL$"
+
+ +
+
+static const double WBP_WAVETYPE_WP = 0x1
+
+ +
+
+static const double WBP_WAVETYPE_WPT = 0x2
+
+ +
+
+static const double WBP_WAVETYPE_SEGWVTYPE = 0x4
+
+ +
+
+static const string HIDDEN_CONTROLS_CUSTOM_COMBINE = "SetVar_WaveBuilder_P0;SetVar_WaveBuilder_P1;SetVar_WaveBuilder_P2;SetVar_WaveBuilder_P3;SetVar_WB_DurDeltaMult_P52;SetVar_WB_AmpDeltaMult_P50;popup_WaveBuilder_op_P70;popup_WaveBuilder_op_P71;popup_WaveBuilder_op_P72;setvar_explDeltaValues_T11;setvar_explDeltaValues_T12_DD02;setvar_explDeltaValues_T13"
+
+ +
+
+static const string HIDDEN_CONTROLS_SQUARE_PULSE = "popup_WaveBuilder_op_P71;setvar_explDeltaValues_T12_DD02"
+
+ +
+
+static const double EPOCH_HL_TYPE_LEFT = 0x01
+
+ +
+
+static const double EPOCH_HL_TYPE_RIGHT = 0x02
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_m_i_e_s___wave_data_folder_getters_8ipf.html b/file/_m_i_e_s___wave_data_folder_getters_8ipf.html new file mode 100644 index 0000000000..1787cd5ca6 --- /dev/null +++ b/file/_m_i_e_s___wave_data_folder_getters_8ipf.html @@ -0,0 +1,4374 @@ + + + + + + + + File MIES_WaveDataFolderGetters.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File MIES_WaveDataFolderGetters.ipf

+

Collection of Wave and Datafolder getter functions.

+

    +

  • All functions with return types DF or Wave return an existing wave or datafolder.

    • +

  • Prefer functions which return a DFREF over functions which return strings. The latter ones are only useful if you need to know if the folder exists.

    • +

  • Modifying wave getter functions might require to introduce wave versioning, see Wave versioning support

    • +
+

+
+

Experiment Documentation

+
+
+static const double LBN_NUMERICAL_DESCRIPTION_VERSION = 2
+
+ +
+
+static const double LBN_TEXTUAL_DESCRIPTION_VERSION = 1
+
+ +
+
+static const double SWEEP_SETTINGS_WAVE_VERSION = 39
+
+ +
+
+dfref GetLabNotebookFolder()
+

Return the datafolder reference to the lab notebook.

+
+ +
+
+string GetLabNotebookFolderAsString()
+

Return the full path to the lab notebook, e.g. root:MIES:LabNoteBook.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetDevSpecLabNBFolder(string device)
+

Return the data folder reference to the device specific lab notebook.

+
+ +
+
+string GetDevSpecLabNBFolderAsString(string device)
+

Return the full path to the device specific lab notebook, e.g. root:MIES:LabNoteBook:ITC18USB:Device0.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+wave DAQ_LBN_GETTER_PROTO(string win)
+
+ +
+
+wave GetLBTextualValues(string device)
+

Returns a wave reference to the text labnotebook.

+

Rows:

    +

  • Filled at runtime

    • +
+

+

Columns:

    +

  • Filled at runtime

    • +
+

+

Layers:

    +

  • 0-7: data for a particular headstage using the layer index

    • +

  • 8: headstage independent data

    • +
+

+
+ +
+
+static variable UpgradeLabNotebook(string device)
+

Handle upgrades of the numerical/textual labnotebooks in one step.

+

This function is idempotent and must stay that way.

+

Supported upgrades:

    +

  • Addition of the third column “TimeStampSinceIgorEpochUTC”

    • +

  • Addition of nineth layer for headstage independent data

    • +

  • Conversion of numeric labnotebook to 64bit floats

    • +

  • Removal of invalid units for “Stim Scale Factor”, “DA Gain” and “AD Gain”

    • +

  • Addition of fourth column “EntrySourceType”

    • +

  • Fix unit and tolerance of “Repeat Sets”

    • +

  • Reapplying the dimension labels as the old ones were cut off after 31 bytes

    • +

  • Making dimension labels valid liberal object names

    • +

  • Extending the row dimension to 6 for the key waves

    • +

  • Fixing empty column dimension labels in key waves

    • +
+

+
+ +
+
+static string FixInvalidLabnotebookKey(string name)
+
+ +
+
+static variable SetLBKeysRowDimensionLabels(wave wv)
+
+ +
+
+wave GetLBTextualKeys(string device)
+

Return a wave reference to the text labnotebook keys.

+

Rows:

    +

  • 0: Parameter Name

    • +

  • 1: Parameter Unit

    • +

  • 2: Parameter Tolerance

    • +
+

+

Columns:

    +

  • 0: Sweep Number

    • +

  • 1: Time Stamp in local time zone

    • +

  • 2: Time Stamp in UTC

    • +

  • 3: Source entry type, one of DataAcqModes

    • +

  • 4: Acquisition state, one of AcquisitionStates

    • +

  • other columns are filled at runtime

    • +
+

+
+ +
+
+wave GetLBNumericalKeys(string device)
+

Return a wave reference to the numeric labnotebook keys.

+

Rows:

    +

  • 0: Name

    • +

  • 1: Units

    • +

  • 2: Tolerance

    • +

  • 3: Description

    • +

  • 4: Headstage Contingency

    • +

  • 5: ClampMode

    • +
+

+

Columns:

    +

  • 0: Sweep Number

    • +

  • 1: Time Stamp in local time zone

    • +

  • 2: Time Stamp in UTC

    • +

  • 3: Source entry type, one of DataAcqModes

    • +

  • 4: Acquisition state, one of AcquisitionStates

    • +

  • other columns are filled at runtime

    • +
+

+
+ +
+
+wave GetLBNumericalDescription(variable forceReload = defaultValue)
+

Return a wave reference to the static and read-only labnotebook descriptions for the numerical entries.

+

Requirements for each entry [

    +

  • 0: Parameter Not empty

    • +

  • 1: Units Something ParseUnit() can grok or degC, bitMask, % or On/Off

    • +

  • 2: Tolerance LABNOTEBOOK_NO_TOLERANCE or a positive number including zero

    • +

  • 3: Description Not empty

    • +

  • 4: Headstage Contingency One of ALL, DEPEND, INDEP

    • +

  • 5: Clamp Mode One of IC, VC, IC;I=0, IC;VC, IC;VC;I=0 or empty

    • +
+
+

See also

+

CheckLBNDescriptions()]:

+
+

+
+ +
+
+wave GetLBTextualDescription(variable forceReload = defaultValue)
+
+ +
+
+static wave GetLBDescription_Impl(string name, variable forceReload)
+
+ +
+
+variable SaveLBNumericalDescription()
+
+ +
+
+variable SaveLBTextualDescription()
+
+ +
+
+static variable SaveLBDescription_Impl(string name, variable version)
+
+ +
+
+static variable UpgradeResultsNotebook()
+

Handle upgrades of the numerical/textual results logbooks in one step.

+

This function is idempotent and must stay that way.

+

Supported upgrades:

    +

  • Fixing empty column dimension labels in key waves

    • +
+

+
+ +
+
+wave GetLBNumericalValues(string device)
+

Return a wave reference to the numeric labnotebook keys.

+

Rows:

    +

  • Filled at runtime

    • +
+

+

Columns:

    +

  • Filled at runtime

    • +
+

+

Layers:

    +

  • 0-7: data for a particular headstage using the layer index

    • +

  • 8: headstage independent data

    • +
+

+
+ +
+
+wave GetNumericalResultsKeys()
+

Return a wave reference to the numerical results keys.

+

Rows:

    +

  • 0: Parameter Name

    • +

  • 1: Parameter Unit

    • +

  • 2: Parameter Tolerance

    • +
+

+

Columns:

    +

  • 0: Sweep Number (always NaN)

    • +

  • 1: Time Stamp in local time zone

    • +

  • 2: Time Stamp in UTC

    • +

  • 3: Source entry type, one of DataAcqModes

    • +

  • 4: Acquisition state, one of AcquisitionStates

    • +

  • other columns are filled at runtime

    • +
+

+
+ +
+
+wave GetNumericalResultsValues()
+

Return a wave reference to the numerical results values.

+

Rows:

    +

  • Filled at runtime

    • +
+

+

Columns:

    +

  • Filled at runtime

    • +
+

+

Layers:

    +

  • 0-7: data for a particular headstage using the layer index

    • +

  • 8: headstage independent data

    • +
+

+
+ +
+
+wave GetTextualResultsKeys()
+

Return a wave reference to the textual results keys.

+

One user of the results wave is Sweep Formula. It stores the code and various meta information in it every time it is executed.

+

Rows:

    +

  • 0: Parameter Name

    • +

  • 1: Parameter Unit

    • +

  • 2: Parameter Tolerance

    • +
+

+

Columns:

    +

  • SweepNum: Sweep number (always NaN)

    • +

  • TimeStamp: Time stamp in local time zone since igor epoch

    • +

  • TimeStampSinceIgorEpochUTC: time stamp in UTC since igor epoch

    • +

  • EntrySourceType: One of DataAcqModes

    • +

  • AcquisitionState: One of AcquisitionStates

    • +

  • Sweep Formula code: Executed code from SweepFormula

    • +

  • Sweep Formula sweeps/channels: Displayed sweeps and channels as 2D array in the form $sweep0;$channelType0;$channelNumber0;,$sweep1;$channelType1;$channelNumber1;,...

    +

    See also

    +

    SFH_NewSelectDataWave

    +
    +

    • +

  • Sweep Formula displayed sweeps: Displayed sweeps (deprecated)

    • +

  • Sweep Formula active channels: Active channels (deprecated)

    • +

  • Sweep Formula experiment: Name of the experiment

    • +

  • Sweep Formula device: Device

    • +

  • Sweep Formula cursor X: Information about each available cursor, see GetCursorInfos() for the exact format.

    • +

  • Sweep Formula store [X]: Stored data from SweepFormula store operation. The X is dynamic and the first argument passed.

    • +

  • Other columns are created and filled at runtime

    • +
+

+
+ +
+
+wave GetTextualResultsValues()
+

Return a wave reference to the numerical results values.

+

Rows:

    +

  • Filled at runtime

    • +
+

+

Columns:

    +

  • Filled at runtime

    • +
+

+

Layers:

    +

  • 0-7: data for a particular headstage using the layer index

    • +

  • 8: headstage independent data

    • +
+

+
+ +
+
+wave GetLBRowCache(wave values)
+

Return the labnotebook cache wave holding the first and last rows into values of each sweep number.

+

Uses the values wave modification count to reset itself upon a change.

+

The stored information is the returned first/last parameter from GetLastSettingNoCache().

+

Rows:

    +

  • Sweep numbers (only existing sweeps)

    • +
+

+

Columns:

    +

  • 0: First row

    • +

  • 1: Last row

    • +
+

+

Layers:

+

+
+ +
+
+wave GetLBIndexCache(wave values)
+

Index wave which serves as a labnotebook cache.

+

Rows:

    +

  • Sweep numbers

    • +
+

+

Columns:

    +

  • One for each LBN key

    • +
+

+

Layers:

+

+

The wave can be indexed with sweepNumber, settings column and entrySourceType to return the row index of the labnotebok wave where the desired value can be found.

+

Contents:

+

+
+ +
+
+wave GetLBNidCache(wave numericalValues)
+

Free wave to cache the sweeps of one RAC/SCI ID.

+

Type of content:

    +

  • valid wave

    • +

  • invalid wave reference (uncached entry)

    • +

  • wave of size zero (non-existant entry)

    • +
+

+

Rows:

    +

  • One for each sweep number

    • +
+

+

Columns:

    +

  • RAC (repeated acquisition cycle IDs) sweeps

    • +

  • SCI (simset cycle IDs) sweeps

    • +
+

+
+ +
+
+static variable SetSweepSettingsDimLabels(wave dest, WaveText sourceKey)
+

Uses the parameter names from the sourceKey columns and write them as dimension into the columns of dest.

+
+ +
+
+wave GetSweepSettingsWave(string device)
+

Returns a wave reference to the sweepSettingsWave.

+

sweepSettingsWave is used to save stimulus settings for each data sweep and create waveNotes for tagging data sweeps

+

Additional columns, necessary for unassociated channels, are created on runtime.

+

Rows:

    +

  • One row

    • +
+

+

Columns:

+

+

Layers:

    +

  • 0-7: data for a particular headstage using the layer index

    • +

  • 8: headstage independent data

    • +
+

+
+ +
+
+wave GetSweepSettingsKeyWave(string device)
+

Returns a wave reference to the sweepSettingsKeyWave.

+

sweepSettingsKeyWave is used to index save stimulus settings for each data sweep and create waveNotes for tagging data sweeps

+

Rows:

    +

  • 0: Parameter

    • +

  • 1: Units

    • +

  • 2: Tolerance Factor

    • +
+

+

Columns:

    +

  • 0: Stim Scale Factor

    • +

  • 1: DAC

    • +

  • 2: ADC

    • +

  • 3: DA Gain

    • +

  • 4: AD Gain

    • +

  • 5: Set sweep count

    • +

  • 6: Insert TP on/off

    • +

  • 7: Inter-trial interval (used after the sweep it is documented for)

    • +

  • 8: TTL rack zero bits (ITC hardware), bit sum in INDEP_HEADSTAGE layer of the active DAEphys TTL channels (called TTLBit)

    • +

  • 9: TTL rack one bits, same for the second rack

    • +

  • 10: TTL rack zero channel (ITC hardware), device type dependent hardware channel used for acquisition in INDEP_HEADSTAGE layer

    • +

  • 11: TTL rack one channel (ITC hardware), same for the second rack

    • +

  • 12: Delay onset user

    • +

  • 13: Delay onset auto

    • +

  • 14: Delay termination

    • +

  • 15: Delay distributed DAQ

    • +

  • 16: Distributed DAQ

    • +

  • 17: Repeat Sets

    • +

  • 18: Scaling zero

    • +

  • 19: Indexing

    • +

  • 20: Locked indexing

    • +

  • 21: Repeated Acquisition

    • +

  • 22: Random Repeated Acquisition

    • +

  • 23: Sampling interval DA

    • +

  • 24: Sampling interval AD

    • +

  • 25: Sampling interval TTL

    • +

  • 26: Sampling interval multiplier

    • +

  • 27: Stim set length

    • +

  • 28: oodDAQ Pre Feature

    • +

  • 29: oodDAQ Post Feature

    • +

  • 30: oodDAQ Resolution

    • +

  • 31: Optimized Overlap dDAQ

    • +

  • 32: Delay onset oodDAQ

    • +

  • 33: Repeated Acquisition Cycle ID

    • +

  • 34: Stim Wave Checksum (can be used to disambiguate cases where two stimsets are named the same but have different contents)

    • +

  • 35: Multi Device mode

    • +

  • 36: Background Testpulse

    • +

  • 37: Background DAQ

    • +

  • 38: Sampling interval multiplier

    • +

  • 39: TP during ITI

    • +

  • 40: Amplifier change via I=0

    • +

  • 41: Skip analysis functions

    • +

  • 42: Repeat sweep on async alarm

    • +

  • 43: Set Cycle Count

    • +

  • 44: Stimset cycle ID

    • +

  • 45: Digitizer Hardware Type, one of HardwareDACTypeConstants

    • +

  • 46: Fixed frequency acquisition

    • +

  • 47: Headstage Active, binary flag that indicates the enabled headstage(s), the index is the headstage number

    • +

  • 48: Clamp Mode

    • +

  • 49: Igor Pro bitness

    • +

  • 50: DA ChannelType, one of DaqChannelTypeConstants

    • +

  • 51: AD ChannelType, one of DaqChannelTypeConstants

    • +

  • 52: oodDAQ member, true if headstage takes part in oodDAQ mode, false otherwise

    • +

  • 53: Autobias % (DAEphys->Settings->Amplifier)

    • +

  • 54: Autobias Interval (DAEphys->Settings->Amplifier)

    • +

  • 55: TP after DAQ

    • +

  • 56: Epochs version

    • +

  • 57: Get/Set Inter-trial interval

    • +

  • 58: Double precision data

    • +

  • 59: Save amplifier settings

    • +

  • 60: Require amplifier

    • +

  • 61: Skip Ahead

    • +
+

+
+ +
+
+wave GetSweepSettingsTextWave(string device)
+

Returns a wave reference to SweepSettingsTxtData.

+

SweepSettingsTxtData is passed to ED_AddEntriesToLabnotebook to add entries to the labnotebook.

+

Rows:

    +

  • Only one

    • +
+

+

Columns:

+

+

Layers:

    +

  • 0-7: data for a particular headstage using the layer index

    • +

  • 8: headstage independent data

    • +
+

+
+ +
+
+wave GetSweepSettingsTextKeyWave(string device)
+

Returns a wave reference to the SweepSettingsKeyTxtData.

+

SweepSettingsKeyTxtData is used to index SweepSettingsTxtData.

+

Rows:

    +

  • Only one

    • +
+

+

Columns:

    +

  • 0: Stim set

    • +

  • 1: DA unit

    • +

  • 2: AD unit

    • +

  • 3: TTL rack zero stim sets (ITC hardware), string list in INDEP_HEADSTAGE layer with empty entries indexed by [0, NUM_DA_TTL_CHANNELS[

    • +

  • 4: TTL rack one stim sets (ITC hardware), same for the second rack

    • +

  • 5: Analysis function pre daq

    • +

  • 6: Analysis function mid sweep

    • +

  • 7: Analysis function post sweep

    • +

  • 8: Analysis function post set

    • +

  • 9: Analysis function post daq

    • +

  • 10: Analysis function pre sweep

    • +

  • 11: Analysis function generic

    • +

  • 12: Analysis function pre set

    • +

  • 13: Analysis function parameters

    • +

  • 14: oodDAQ regions list

      +

    • Format: $begin1-$end1;$begin2-$end2;....

      • +

    • Unit: stimset build ms.

      • +
    +

    • +

  • 15: Electrode

    • +

  • 16: High precision sweep start timestamp in ISO8601 format

    • +

  • 17: Stimset wave note

    • +

  • 18: TTL rack zero set sweep counts (ITC hardware)

    • +

  • 19: TTL rack one set sweep counts (ITC hardware)

    • +

  • 20: TTL set sweep counts (NI hardware), string list in INDEP_HEADSTAGE layer with empty entries indexed by [0, NUM_DA_TTL_CHANNELS[

    • +

  • 21: TTL stim sets (NI hardware), string list in INDEP_HEADSTAGE layer with empty entries indexed by [0, NUM_DA_TTL_CHANNELS[

    • +

  • 22: TTL channels (NI hardware), string list in INDEP_HEADSTAGE layer with empty entries indexed by [0, NUM_DA_TTL_CHANNELS[

    • +

  • 23: Follower Device, list of follower devices (not supported anymore and therefore always empty)

    • +

  • 24: MIES version, multi line mies version string

    • +

  • 25: Igor Pro version

    • +

  • 26: Digitizer Hardware Name

    • +

  • 27: Digitizer Serial Numbers

    • +

  • 28: Epochs

    • +

  • 29: JSON config file [path] (| separated list of full file paths)

    • +

  • 30: JSON config file [SHA-256 hash] (| separated list of hashes)

    • +

  • 31: JSON config file [stimset nwb file path]

    • +

  • 32: Igor Pro build

    • +

  • 33: Indexing End Stimset

    • +

  • 34: TTL Indexing End Stimset (hardware agnostic), string list in INDEP_HEADSTAGE layer with empty entries indexed by [0, NUM_DA_TTL_CHANNELS[

    • +

  • 35: TTL Stimset wave note (hardware agnostic), same string list formatting

    • +

  • 36: TTL Stim Wave Checksum (hardware agnostic) URL-encoded payload, see URL-encoding for background information, same string list formatting

    • +

  • 37: TTL Stim set length (hardware agnostic), same string list formatting

    • +

  • 38: TTL rack zero set cycle counts (ITC hardware)

    • +

  • 39: TTL rack one set cycle counts (ITC hardware)

    • +

  • 40: TTL set cycle counts (NI hardware), string list in INDEP_HEADSTAGE layer with empty entries indexed by [0, NUM_DA_TTL_CHANNELS[

    • +

  • 41: Device (aka DAEphys panel name)

    • +
+

+
+ +
+
+

Wavebuilder

+
+
+static const double WP_WAVE_LAYOUT_VERSION = 13
+
+ +
+
+static const double WPT_WAVE_LAYOUT_VERSION = 11
+
+ +
+
+static const double SEGWVTYPE_WAVE_LAYOUT_VERSION = 7
+
+ +
+
+dfref GetWaveBuilderPath()
+

Returns a data folder reference to the base.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetWaveBuilderPathAsString()
+

Returns the full path to the base path, e.g. root:MIES:WaveBuilder.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetWaveBuilderDataPath()
+

Returns a data folder reference to the data.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetWaveBuilderDataPathAsString()
+

Returns the full path to the data folder, e.g root:MIES:WaveBuilder:Data.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetWaveBuilderDataDAPath()
+

Returns a data folder reference to the data.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetWaveBuilderDataDAPathAsString()
+

Returns the full path to the data folder, e.g root:MIES:WaveBuilder:Data:DA.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetWaveBuilderDataTTLPath()
+

Returns a data folder reference to the data.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetWaveBuilderDataTTLPathAsString()
+

Returns the full path to the data folder, e.g root:MIES:WaveBuilder:Data:TTL.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetWBSvdStimSetParamPath()
+

Returns a data folder reference to the stimulus set parameter.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetWBSvdStimSetParamPathAS()
+

Returns the full path to the stimulus set parameter folder, e.g. root:MIES:WaveBuilder:SavedStimulusSetParameters.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetWBSvdStimSetPath()
+

Returns a data folder reference to the stimulus set.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetWBSvdStimSetPathAsString()
+

Returns the full path to the stimulus set, e.g. root:MIES:WaveBuilder:SavedStimulusSets.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetWBSvdStimSetParamDAPath()
+

Returns a data folder reference to the stimulus set parameters of DA type.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetWBSvdStimSetParamDAPathAS()
+

Returns the full path to the stimulus set parameters of DA type, e.g. root:MIES:WaveBuilder:SavedStimulusSetParameters:DA.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetWBSvdStimSetParamTTLPath()
+

Returns a data folder reference to the stimulus set parameters of TTL type.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetWBSvdStimSetParamTTLAsString()
+

Returns the full path to the stimulus set parameters of TTL type, e.g. root:MIES:WaveBuilder:SavedStimulusSetParameters:TTL.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetWBSvdStimSetDAPath()
+

Returns a data folder reference to the stimulus set of DA type.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetWBSvdStimSetDAPathAsString()
+

Returns the full path to the stimulus set of DA type, e.g. root:MIES:WaveBuilder:SavedStimulusSet:DA.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetWBSvdStimSetTTLPath()
+

Returns a data folder reference to the stimulus set of TTL type.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetWBSvdStimSetTTLPathAsString()
+

Returns the full path to the stimulus set of TTL type, e.g. root:MIES:WaveBuilder:SavedStimulusSet:TTL.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+wave GetTestPulse()
+

Return the testpulse wave.

+

This wave will be written in TP_CreateTestPulseWave() and will use the real sampling interval.

+
+ +
+
+wave GetTestPulseAsFree()
+
+ +
+
+static variable GetWPVersion()
+

Automated testing helper.

+
+ +
+
+variable UpgradeWaveParam(wave wv)
+

Upgrade the wave layout of WP to the most recent one as defined in WP_WAVE_LAYOUT_VERSION

+
+ +
+
+static variable AddDimLabelsToWP(wave wv)
+
+ +
+
+wave GetWaveBuilderWaveParam()
+

Return the parameter wave for the wave builder panel.

+

Rows:

    +

  • Variables synced to GUI controls, see e.g. WB_MakeWaveBuilderWave in MIES_WaveBuilder for an up to date list

    • +
+

+

Columns:

    +

  • Segment/Epoch

    • +
+

+

Layers hold different stimulus wave form types:

    +

  • Square pulse

    • +

  • Ramp

    • +

  • Noise

    • +

  • Sin

    • +

  • Saw tooth

    • +

  • Pulse train

    • +

  • PSC

    • +

  • Load custom wave

    • +

  • Combine

    • +
+

+
+ +
+
+wave GetWaveBuilderWaveParamAsFree()
+

Return a free wave version of GetWaveBuilderWaveParam()

+

+

See also

+

GetWaveBuilderWaveParam()

+
+

+
+ +
+
+static variable GetWPTVersion()
+

Automated testing helper.

+
+ +
+
+variable UpgradeWaveTextParam(WaveText wv)
+

Upgrade the wave layout of WPT to the most recent one as defined in WPT_WAVE_LAYOUT_VERSION

+
+ +
+
+static variable AddDimLabelsToWPT(wave wv)
+

Add dimension labels to the WaveBuilder WPT wave.

+
+ +
+
+wave GetWaveBuilderWaveTextParam()
+

Return the parameter text wave for the wave builder panel.

+

Rows:

    +

  • 0: Name of the custom wave for EPOCH_TYPE_CUSTOM (legacy format: wave name only, current format: absolute path including the wave name)

    • +

  • 1: Analysis function, pre daq (deprecated)

    • +

  • 2: Analysis function, mid sweep (deprecated)

    • +

  • 3: Analysis function, post sweep (deprecated)

    • +

  • 4: Analysis function, post set (deprecated)

    • +

  • 5: Analysis function, post daq (deprecated)

    • +

  • 6: Formula

    • +

  • 7: Formula version: “[[:digit:]]+”

    • +

  • 8: Analysis function, pre sweep (deprecated)

    • +

  • 9: Analysis function, generic

    • +

  • 10: Unused

    • +

  • 11-26: Explicit delta values. ; separated list as long as the number of sweeps.

    • +

  • 27: Analysis function, pre set (deprecated)

    • +

  • 28: Explicit delta value for “Inter trial interval”

    • +

  • 29: Analysis function parameters. See below for a detailed explanation.

    • +

  • 30-50: unused

    • +
+

+

Formula and Formula Version are in the EPOCH_TYPE_COMBINE layer, the custom wave name is in the EPOCH_TYPE_CUSTOM layer. 11 to 26 are for all epoch types. The rest is layer independent (aka a setting for the full set) in INDEP_EPOCH_TYPE.

+

Columns:

    +

  • Segment/Epoch, the very last index is reserved for textual settings for the complete set

    • +
+

+

Layers hold different stimulus wave form types:

    +

  • Square pulse/Set specific settings

    • +

  • Ramp

    • +

  • Noise

    • +

  • Sin

    • +

  • Saw tooth

    • +

  • Pulse train

    • +

  • PSC

    • +

  • Load custom wave

    • +

  • Combine

    • +
+

+

Analysis function parameters

+

Format of a single parameter:

    +

  • name:(variable|string|wave|textwave)=value

    • +
+

+

For these building blocks the following restrictions hold

+

+

Multiple entries are separated by comma (,).

+
+ +
+
+wave GetWaveBuilderWaveTextParamAsFree()
+

Return a free wave version of GetWaveBuilderWaveTextParam()

+

+

See also

+

GetWaveBuilderWaveTextParam()

+
+

+
+ +
+
+static variable GetSegWvTypeVersion()
+

Automated testing helper.

+
+ +
+
+variable UpgradeSegWvType(wave wv)
+

Upgrade the wave layout of SegWvType to the most recent one as defined in SEGWVTYPE_WAVE_LAYOUT_VERSION

+
+ +
+
+static variable AddDimLabelsToSegWvType(wave wv)
+

Add dimension labels to the WaveBuilder SegWvType wave.

+
+ +
+
+wave GetSegmentTypeWave()
+

Returns the segment type wave used by the wave builder panel Remember to change WB_TOTAL_NUMBER_OF_EPOCHS if changing the wave layout.

+

Rows:

    +

  • 0 - 93: epoch types using one of WaveBuilderEpochTypes

    • +

  • 94: Inter trial interval delta operation, one of WaveBuilderDeltaOperationModes

    • +

  • 95: Inter trial interval delta multiplier/exponent [a. u.]

    • +

  • 96: Inter trial interval delta [s]

    • +

  • 97: Stimset global RNG seed

    • +

  • 98: Data flipping (1 or 0)

    • +

  • 99: Inter trial interval [s]

    • +

  • 100: total number of segments/epochs

    • +

  • 101: total number of steps

    • +
+

+
+ +
+
+wave GetSegmentTypeWaveAsFree()
+

Return a free wave version of GetSegmentTypeWave()

+

+

See also

+

GetSegmentTypeWave()

+
+

+
+ +
+
+wave GetEpochID()
+

Return the wave identifiying the begin and end times of the current epoch.

+
+ +
+
+wave GetWaveBuilderDispWave()
+

Return the wave for visualization of the stim set in the wavebuilder panel.

+
+ +
+
+wave GetWBEpochCombineList(variable channelType)
+
+ +
+
+wave GetSegmentWave(variable duration = defaultValue)
+

Returns the segment wave which stores the stimulus set of one segment/epoch.

+
+
Parameters:
+

duration – time of the stimulus in ms

+
+
+
+ +
+
+wave GetEpochParameterNames()
+
+ +
+
+

SweepFormula PSX

+
+
+static const double PSX_WAVE_VERSION = 2
+
+ +
+
+static const double PSX_EVENT_WAVE_COLUMNS = 14
+
+ +
+
+variable UpgradePSXEventWave(wave psxEvent)
+
+ +
+
+wave GetPSXEventWaveAsFree()
+

Return a 2D events wave as free wave.

+

Rows:

    +

  • count

    • +
+

+

Cols:

    +

  • 0/index: Event index

    • +

  • 1/peak_t: Event time [ms]

    • +

  • 2/peak: Event amplitude in deconvoluted data [y unit of data]

    • +

  • 3/post_min: Minimum of filtered and offsetted data in the range [time, time + 2ms]

    • +

  • 4/post_min_t: X location of [2]

    • +

  • 5/pre_max: Maximum of filtered and offsetted data in the range [time - 2ms, time], averaged over +/- 0.1 ms

    • +

  • 6/pre_max_t: X location of [5]

    • +

  • 7/rel_peak: Relative amplitude: [2] - [4]

    • +

  • 8/isi: Time difference to previous event [ms]

    • +

  • 9/tau: Decay constant tau of exponential fit

    • +

  • 10/Fit manual QC call: One of PSXStates

    • +

  • 11/Fit result: 1 for success, everything smaller than 0 is failure:

    +

    • +

  • 12/Event manual QC call: One of PSXStates

    • +

  • 13/Rise Time: rise time as calculated by PSX_CalculateRiseTime()

    • +
+

+
+ +
+
+variable SetPSXEventDimensionLabels(wave wv)
+
+ +
+
+wave GetPSXSingleEventFitWaveFromDFR(dfref dfr)
+
+ +
+
+wave GetPSXEventFitWaveAsFree()
+
+ +
+
+wave GetPSXEventColorsWaveAsFree(variable numEvents)
+
+ +
+
+wave GetPSXEventMarkerWaveAsFree(variable numEvents)
+
+ +
+
+static wave GetWaveFromFolder(dfref dfr, string name)
+
+ +
+
+wave GetPSXEventWaveFromDFR(dfref dfr)
+
+ +
+
+wave GetPSXPeakXWaveFromDFR(dfref dfr)
+
+ +
+
+wave GetPSXPeakYWaveFromDFR(dfref dfr)
+
+ +
+
+wave GetPSXPeakYAtFiltWaveFromDFR(dfref dfr)
+
+ +
+
+wave GetPSXEventColorsWaveFromDFR(dfref dfr)
+
+ +
+
+wave GetPSXEventMarkerWaveFromDFR(dfref dfr)
+
+ +
+
+wave GetPSXEventFitWaveFromDFR(dfref dfr)
+
+ +
+
+wave GetPSXSweepDataWaveFromDFR(dfref dfr)
+
+ +
+
+wave GetPSXSweepDataFiltOffWaveFromDFR(dfref dfr)
+
+ +
+
+wave GetPSXSweepDataFiltOffDeconvWaveFromDFR(dfref dfr)
+
+ +
+
+wave GetPSXEventLocationLabels(dfref dfr)
+
+ +
+
+wave GetPSXEventLocationTicks(dfref dfr)
+
+ +
+
+string GetPSXFolderForComboAsString(dfref dfr, variable index)
+
+ +
+
+dfref GetPSXFolderForCombo(dfref dfr, variable index)
+
+ +
+
+wave GetPSXComboListBox(dfref dfr)
+
+ +
+
+string GetPSXSingleEventFolderAsString(dfref comboDFR)
+
+ +
+
+dfref GetPSXSingleEventFolder(dfref comboDFR)
+
+ +
+
+wave GetPSXAverageWave(dfref dfr, variable state)
+

Return the average wave of the given state for the PSX event plot.

+

dfr can be either singleEventDFR for the per-combo averages or workDFR for the average over all events disregarding the combo.

+
+ +
+
+wave GetPSXAcceptedAverageFitWaveFromDFR(dfref dfr)
+
+ +
+
+

Test Pulse

+
+
+wave GetTPStorage(string device)
+

Return a wave reference for TPStorage.

+

Stores properties of the testpulse during TP

+

ROWS:

    +

  • One entry per step

    • +
+

+

COLS:

    +

  • NUM_HEADSTAGES

    • +
+

+

LAYERS:

    +

  • 0: Amplifier holding command (Voltage Clamp)

    • +

  • 1: Amplifier bias current (Current Clamp)

    • +

  • 2: (Peak/Instantaneous) Resistance

    • +

  • 3: (Steady State) Resistance

    • +

  • 4: Time in s (arbitrary zero)

    • +

  • 5: Delta time in s relative to the entry in the first row of layer 3

    • +

  • 6: (Steady State) Resistance slope

    • +

  • 7: Pressure in psi

    • +

  • 8: Timestamp since igor epoch (with timezone offsets)

    • +

  • 9: Timestamp in UTC since igor epoch

    • +

  • 10: Pressure changed

    • +

  • 11: Holding current (pA, Voltage Clamp)

    • +

  • 12: Vrest (mV, Current Clamp)

    • +

  • 13: AD channel

    • +

  • 14: DA channel

    • +

  • 15: Headstage

    • +

  • 16: ClampMode

    • +

  • 17: UserPressure

    • +

  • 18: PressureMethod (see PressureModeConstants)

    • +

  • 19: ValidState (true if the entry is considered valid, false otherwise)

    • +

  • 20: UserPressureType (see PressureTypeConstants)

    • +

  • 21: UserPressureTimeStampUTC timestamp since Igor Pro epoch in UTC where the user pressure was acquired

    • +

  • 22: TPMarker unique number identifying this set of TPs

    • +

  • 23: Cell state: Pressure control values defining the cell state, one of CellStateValues

    • +

  • 24: Testpulse Cycle Id (changes whenever TP is started, allows to group TPs together)

    • +

  • 25: Auto TP Amplitude: success/fail state

    • +

  • 26: Auto TP Baseline: success/fail state

    • +

  • 27: Auto TP Baseline Range Exceeded: True/False

    • +

  • 28: Auto TP Cycle ID: Unique number which is constant until the “Auto TP” state is switched (aka on->off or off->on)

    • +

  • 29: Auto TP Baseline Fit result: One of TPBaselineFitResults

    • +

  • 30: Auto TP Delta V [mV]

    • +
+

+
+ +
+
+wave GetAcqTPStorage()
+

Return a free wave reference for AcqTPStorage wave for passing to ACQ4.

+

The wave stores PeakResistance, SteadyStateResistance, and TimeStamp in rows and headstages in cols

+
+ +
+
+dfref GetDeviceTestPulse(string device)
+

Return a datafolder reference to the test pulse folder.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetDeviceTestPulseAsString(string device)
+

Return the path to the test pulse folder, e.g. root:mies:HardwareDevices:ITC1600:Device0:TestPulse.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+wave GetScaledDataWave(string device)
+

Return a wave which holds undecimated and scaled data.

+

ScaledDataWave is initialized in

+

For ITC on initialization the channels are filled with NaN and the headstages data unit is set. In

+ +Unversioned Wave:
+

See also

+

DC_InitScaledDataWave Each channel contains scaled data that takes the gain from the headstage into account. In the channel wave the voltage output to the DAC and read from the ADC is translated back to the headstages input/output signal (e.g. mV / pA). The x-time interval is milliseconds.

+
+
+

See also

+

SCOPE_ITC_UpdateOscilloscope all channels are copied from the DAQDataWave to the scaledDataWave and properly scaled. For NI on initialization the non-ADC channels are copied from the DAQDataWave to the scaledDataWave and properly scaled. The ADC channels are scaled by a gain factor that is applied in hardware (or the device XOP). Thus, in

+
+
+

See also

+

SCOPE_NI_UpdateOscilloscope and

+
+
+

See also

+

SCOPE_SU_UpdateOscilloscope the ADC channel data is simply copied from the DAQDataWave to the scaledDataWave.

+
+

+

Rows:

    +

  • StopCollectionPoint

    • +
+

+

Columns:

    +

  • Number of active channels

    • +
+

+

Type:

+

+

Version 1: WAVEREF wave, initially with size 0 sized in

+

See also

+

DC_MakeHelperWaves to number of hardware channels as in config wave

+
+

+
+ +
+
+wave GetOscilloscopeWave(string device)
+

Return a wave for displaying scaled data in the oscilloscope window.

+

Contents can be decimated for faster display.

+
+ +
+
+wave GetScaledTPTempWave(string device)
+

Return a wave for temporary storing scaled data for PowerSpectrum input.

+
+ +
+
+wave GetTPOscilloscopeWave(string device)
+

Return a wave for displaying scaled TP data in the oscilloscope window for the “TP during DAQ” channels or for TP power spectrum during Test Pulse.

+

Rows:

    +

  • Holds exactly one TP

    • +
+

+

Columns:

+

+
+ +
+
+wave GetStoredTestPulseWave(string device)
+

Return a wave reference wave for storing the full test pulses.

+
+ +
+
+wave GetTPResults(string device)
+

Return the testpulse results wave.

+

Rows:

    +

  • 0: Resistance Instantaneous: [MΩ]

    • +

  • 1: Baseline Steady State: [mV] for IC, [pA] for VC

    • +

  • 2: Resistance Steady State: [MΩ]

    • +

  • 3: Elevated Steady State: [mV] for IC, [pA] for VC

    • +

  • 4: Elevated Instantaneous: [mV] for IC, [pA] for VC

    • +

  • 5: Auto TP Amplitude: Pass/Fail

    • +

  • 6: Auto TP Baseline: Pass/Fail

    • +

  • 7: Auto TP Baseline range exceeded: True/False

    • +

  • 8: Auto TP Baseline fit result: One of TPBaselineFitResults

    • +

  • 9: Auto TP Delta V: [mV]

    • +
+

+

Columns:

    +

  • NUM_HEADSTAGES

    • +
+

+
+ +
+
+wave GetTPResultsBuffer(string device)
+

Return the testpulse results buffer wave.

+

Same layout as GetTPResults() but as many layers as the buffer size.

+
+ +
+
+

Amplifier

+
+
+dfref GetAmplifierFolder()
+

Return the datafolder reference to the amplifier.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetAmplifierFolderAsString()
+

Return the path to the amplifierm e.g. root:mies:Amplifiers”.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+wave GetAmplifierParamStorageWave(string device)
+

Return a wave reference to the amplifier parameter storage wave.

+

Rows:

    +

  • 0-31: Amplifier settings identified by dimension labels

    • +
+

+

Columns:

    +

  • Only one

    • +
+

+

Layers:

    +

  • 0-7: Headstage identifier

    • +
+

+

Contents:

    +

  • numerical amplifier settings

    • +
+

+
+ +
+
+wave GetAmplifierSettingsWave()
+

Return a free wave reference for the amplifier settings, data wave.

+

Rows:

    +

  • Only one

    • +
+

+

Columns:

    +

  • Amplifier parameters as described in the amplifier settings key wave

    • +
+

+

Layers:

    +

  • 0-7: data for a particular headstage using the layer index

    • +

  • 8: headstage independent data

    • +
+

+
+ +
+
+wave GetAmplifierSettingsKeyWave()
+

Return a free wave reference for the amplifier settings, key wave.

+

Rows:

    +

  • 0: Parameter

    • +

  • 1: Units

    • +

  • 2: Tolerance factor

    • +
+

+

Columns:

    +

  • Various settings

    • +
+

+
+ +
+
+wave GetAmplifierSettingsTextWave()
+

Return a free wave for the amplifier text settings, data wave.

+

Rows:

    +

  • Only one

    • +
+

+

Columns:

    +

  • Amplifier parameters as described in the amplifier settings text key wave

    • +
+

+

Layers:

    +

  • 0-7: data for a particular headstage using the layer index

    • +

  • 8: headstage independent data

    • +
+

+
+ +
+
+wave GetAmplifierSettingsTextKeyWave()
+

Return a free wave for the amplifier text settings, key wave.

+

Rows:

    +

  • 0: Parameter

    • +

  • 1: Units

    • +

  • 2: Tolerance factor

    • +
+

+

Columns:

    +

  • Various settings

    • +
+

+
+ +
+
+wave GetAmplifierTelegraphServers()
+

Return wave reference to the W_TelegraphServers wave.

+

Call AI_FindConnectedAmps() to create that wave, otherwise an empty wave is returned.

+
+ +
+
+wave GetAmplifierMultiClamps()
+

Return wave reference to the W_MultiClamps wave.

+

Call AI_FindConnectedAmps() to create that wave, if that was not done an empty wave is returned.

+
+ +
+
+

Asynchronous Measurements

+
+
+wave GetAsyncSettingsWave()
+

Return a free wave for the asyncSettingsWave, data wave.

+

asyncSettingsWave is used to save async settings for each data sweep and create waveNotes for tagging data sweeps

+

Rows:

    +

  • One row

    • +
+

+

Columns:

    +

  • Same as GetAsyncSettingsKeyWave

    • +
+

+

Layers:

+

+
+ +
+
+wave GetAsyncSettingsKeyWave(wave settingsWave, variable channel, string title, string unit)
+

Return a free wave for the asyncSettingsKeyWave.

+

asyncSettingsKeyWave is used to index async settings for each data sweep and create waveNotes for tagging data sweeps

+

Rows:

    +

  • 0: Parameter

    • +

  • 1: Units

    • +

  • 2: Tolerance Factor

    • +
+

+

Columns:

    +

  • 0: Async AD $Channel OnOff

    • +

  • 1: Async AD $Channel Gain

    • +

  • 2: Async Alarm $Channel OnOff

    • +

  • 3: Async Alarm $Channel Min

    • +

  • 4: Async Alarm $Channel Max

    • +

  • 5: Async AD $Channel [$Title]

    • +
+

+
+ +
+
+wave GetAsyncSettingsTextWave()
+

Return a free wave for the AsyncSettingsTxtWave.

+

AsyncSettingsTxtData is used to store the async text settings used on a particular headstage and then create waveNotes for the sweep data

+

Rows:

    +

  • Only one

    • +
+

+

Columns:

    +

  • Same as GetAsyncSettingsTextKeyWave

    • +
+

+

Layers:

+

+
+ +
+
+wave GetAsyncSettingsTextKeyWave(WaveText settingsWave, variable channel)
+

Return a free wave for the AsyncSettingsKeyTxtData.

+

AsyncSettingsKeyTxtData is used to index Txt Key Wave

+

Rows:

    +

  • Just one

    • +
+

+

Columns:

    +

  • 0: Async $Channel Title

    • +

  • 1: Async $Channel Unit

    • +
+

+
+ +
+
+

Pressure Control

+
+
+string P_GetDevicePressureFolderAS(string device)
+

Returns device specific pressure folder as string.

+
+ +
+
+dfref P_DeviceSpecificPressureDFRef(string device)
+

Creates device specific pressure folder - used to store data for pressure regulators.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string P_GetPressureFolderAS(string device)
+

Returns pressure folder as string.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref P_PressureFolderReference(string device)
+

Returns the data folder reference for the main pressure folder “root:MIES:Pressure”.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+wave P_GetITCData(string device)
+

Returns a wave reference to the DAQ data wave used for pressure pulses.

+

Rows:

+

+

Columns:

    +

  • 0: DA data

    • +

  • 1: AD data

    • +

  • 2: TTL data rack 0

    • +

  • 3: TTL data rack 1 (available if supported by the device)

    • +
+

+
+ +
+
+wave P_GetITCChanConfig(string device)
+

Returns a wave reference to the DAQ config wave used for pressure pulses.

+

Rows:

    +

  • 0: DA channel specifications

    • +

  • 1: AD channel specifications

    • +

  • 2: TTL rack 0 specifications

    • +

  • 3: TTL rack 1 specifications (available if supported by the device)

    • +
+

+

Columns:

    +

  • 0: Channel Type

    • +

  • 1: Channel number

    • +

  • 2: Sampling interval

    • +

  • 3: Decimation

    • +
+

+
+ +
+
+static variable SetPressureWaveDimLabels(wave wv)
+

Set the dimension labels for the numeric pressure wave.

+
+ +
+
+wave P_GetPressureDataWaveRef(string device)
+

Returns wave reference of wave used to store data used in functions that run pressure regulators creates the wave if it does not exist.

+

Rows:

    +

  • 0 - 7: Headstage 0 through 7

    • +
+

+

Columns:

    +

  • 0: Pressure method. -1 = none, 0 = Approach, 1 = Seal, 2 = Break In, 3 = Clear

    • +

  • 1: List position of DAC (used for presssure control) selected for headstage

    • +

  • 2: Type of DAC, index into HARDWARE_DAC_TYPES

    • +

  • 3: Device ID used by Instrutech DACs or index into HW_NI_ListDevices depending on column 2

    • +

  • 4: DA channel used for pressure regulation.

    • +

  • 5: Gain of DA channel used for presssure regulation.

    • +

  • 6: AD channel used for pressure regulation.

    • +

  • 7: Gain of AD channel used for pressure regulation.

    • +

  • 8: TTL channel A used for pressure regulation.

    • +

  • 9: Pipette pressure setting while pipette is positioned in air/outside of bath.

    • +

  • 10: Pipette pressure setting for pipette positioned in the bath.

    • +

  • 11: Pipette pressure setting for pipette positioned in the slice.

    • +

  • 12: Pipette pressure setting for pipette positioned near the target cell.

    • +

  • 13: Pipette pressure setting for pipette at the initialization of seal formation.

    • +

  • 14: Maximum Pipette pressure setting for seal formation.

    • +

  • 15: Distance between the bottom of the recording chamber to the surface of the bath solution.

    • +

  • 16: Distance between the bottom of the recording chamber and the top of the tissue slice.

    • +

  • 17: Distance between the bottom of the recording chamber and the soma of the target cell.

    • +

  • 18: X position (in the stage frame) of the soma of the target cell.

    • +

  • 19: Y position (in the stage frame) of the soma of the target cell.

    • +

  • 20: Place holder for future data.

    • +

  • 21: Realtime pressure

    • +

  • 22: Last steady state resistance value.

    • +

  • 23: Slope of the peak TP resistance over the last 5 seconds.

    • +

  • 24: State of the TP (0 = OFF, 1 = ON).

    • +

  • 25: Slope threshold. Used to determine if pressure should be incremented during sealing.

    • +

  • 26: Time of last slope check

    • +

  • 27: Last pressure command.

    • +

  • 28: State of pressure pulse (0 = OFF, 1 = ON).

    • +

  • 29: Last amplifier voltage command.

    • +

  • 30: Manual pressure command amplitude in psi.

    • +

  • 31: Manual pressure pulse command amplitude in psi.

    • +

  • 32: Manual pressure pulse duation in ms.

    • +

  • 33: Peak resistance on previous method cycle.

    • +

  • 34: Peak resistance on active method cycle.

    • +

  • 35: Time of last peak resistance check.

    • +

  • 36: Calibration constant for positive pulse.

    • +

  • 37: Calibration constant for negative pulse.

    • +

  • 38: Checkbox state of “Approach Near”.

    • +

  • 39: Checkbox state of “Seal Atmosphere”.

    • +

  • 40: Selected headstage by the slider.

    • +

  • 41: User pressure offset in psi.

    • +

  • 42: Total sum of user pressure offsets in psi.

    • +

  • 43: Total sum of user pressure offsets since last pulse in psi.

    • +

  • 44: TTL channel B used for pressure regulation.

    • +

  • 45: User pressure deviceID

    • +

  • 46: User pressure device hardware type

    • +

  • 47: User pressure ADC

    • +
+

+
+ +
+
+wave P_PressureDataTxtWaveRef(string device)
+

Returns wave reference for wave used to store text used in pressure control.

+

Rows:

    +

  • 0 - 7: Headstage 0 through 7

    • +
+

+

Columns:

    +

  • 0: Digitial to analog converter device type string.

    • +

  • 1: DA unit.

    • +

  • 2: AD unit.

    • +
+

+
+ +
+
+

Analysis Browser

+
+
+dfref GetAnalysisFolder()
+

Return the datafolder reference to the root folder for the analysis browser.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetAnalysisFolderAS()
+

Return the full path to the root analysis folder, e.g. root:MIES:analysis.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetAnalysisExpFolder(string expFolder)
+

Return the datafolder reference to the per experiment folder.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetAnalysisExpFolderAS(string expFolder)
+

Return the full path to the per experiment folder, e.g. root:MIES:Analysis:my_experiment.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetAnalysisDeviceFolder(string expFolder, string device)
+

Return the datafolder reference to the per device folder of an experiment.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetAnalysisDeviceFolderAS(string expFolder, string device)
+

Return the full path to the per device folder of an experiment, e.g. root:MIES:Analysis:my_experiment:ITC18USB_Dev_0.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetAnalysisDevChannelFolder(string expFolder, string device)
+

Return the datafolder reference to the sweep to channel relation of a device and experiment pair.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetAnalysisDevChannelFolderAS(string expFolder, string device)
+

Return the full path to the sweep to channel relation folder of a device and experiment pair, e.g. root:MIES:Analysis:my_experiment:ITC18USB_Dev_0:channel.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetAnalysisDeviceConfigFolder(string expFolder, string device)
+

Return the datafolder reference to the sweep config folder of a device and experiment pair.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetAnalysisDeviceConfigFolderAS(string expFolder, string device)
+

Return the full path to the sweep config folder of a device and experiment pair, e.g. root:MIES:Analysis:my_experiment:ITC18USB_Dev_0:config.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetAnalysisDeviceTestpulse(string expFolder, string device)
+

Return the datafolder reference to the testpulse folder of a device and experiment pair.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetAnalysisDeviceTestpulseAS(string expFolder, string device)
+

Return the full path to the testpulse folder of a device and experiment pair, e.g. root:MIES:Analysis:my_experiment:ITC18USB_Dev_0:testpulse.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetAnalysisLabNBFolder(string expFolder, string device)
+

Return the datafolder reference to the labnotebook folder of a device and experiment pair.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetAnalysisLabNBFolderAS(string expFolder, string device)
+

Return the full path to the labnotebook folder of a device and experiment pair, e.g. root:MIES:Analysis:my_experiment:ITC18USB_Dev_0:labnotebook.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetAnalysisSweepPath(string expFolder, string device)
+

Return the datafolder reference to the sweep folder of a device and experiment pair.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetAnalysisSweepPathAsString(string expFolder, string device)
+

Return the full path to the sweep folder of a device and experiment pair, e.g. root:MIES:Analysis:my_experiment:ITC18USB_Dev_0:sweep.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetAnalysisSweepDataPath(string expFolder, string device, variable sweep)
+

Return the datafolder reference to the per sweep folder.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetAnalysisSweepDataPathAS(string expFolder, string device, variable sweep)
+

Return the full path to the the per sweep folder, e.g. root:MIES:Analysis:my_experiment:ITC18USB_Dev_0:sweep:X_$sweep.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetAnalysisStimSetPath(string expFolder, string device)
+

Return the datafolder reference to the stim set folder.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetAnalysisStimSetPathAS(string expFolder, string device)
+

Return the full path to the stim set folder, e.g. root:MIES:Analysis:my_experiment::stimset.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetAnalysisResultsFolder(string expFolder)
+

Return the datafolder reference to results folder of an experiment.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetAnalysisResultsFolderAsString(string expFolder)
+

Return the datafolder reference to results folder of an experiment, e.g. root:MIES:Analysis:my_experiment:results.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+wave GetAnalysisResultsWave(string expFolder, variable type)
+

Return one of the four results waves.

+
+
Parameters:
+
+
+
+
+ +
+
+wave GetAnalysisChannelStorage(string dataFolder, string device)
+

wave is used to relate it’s index to sweepWave and deviceWave.

+
+ +
+
+wave GetAnalysisChannelStimWave(string dataFolder, string device)
+

Return a wave containing all stimulus channels in the NWB file as a “;”-separated List wave is used to relate it’s index to sweepWave and deviceWave.

+
+ +
+
+wave GetAnalysisChannelAcqWave(string dataFolder, string device)
+

Return a wave containing all acquisition channels in the NWB file as a “;”-separated List wave is used to relate it’s index to sweepWave and deviceWave.

+
+ +
+
+wave GetAnalysisChannelSweepWave(string dataFolder, string device)
+

Return a wave containing all sweeps in a unique fashion. wave is used to relate it’s index to channelWave and deviceWave.

+
+ +
+
+wave GetAnalysisDeviceWave(string dataFolder)
+

Return a wave containing all devices wave is used to relate it’s index to sweepWave and channelWave.

+
+ +
+
+wave GetAnalysisStoredTestPulses(string dataFolder, string device)
+

Return wave with all stored test pulses.

+
+ +
+
+wave GetAnalysisBrowserMap()
+

Return AnalysisBrowser indexing storage wave.

+

Rows:

    +

  • Experiments found in current Directory

    • +
+

+

Columns:

    +

  • 0: DiscLocation: Path to Experiment on Disc

    • +

  • 1: FileName: Name of File in experiment column in ExperimentBrowser

    • +

  • 2: DataFolder Data folder inside current Igor experiment

    • +

  • 3: FileType File Type identifier for routing to loader functions, one of AnalysisBrowserFileTypes

    • +
+

+
+ +
+
+wave GetAnalysisBrowserGUIFolderList()
+

Return the text wave used in the folder listbox of the analysis browser.

+
+ +
+
+wave GetAnalysisBrowserGUIFolderSelection()
+

Return the selection wave used in the folder listbox of the analysis browser.

+
+ +
+
+wave GetAnalysisBrowserGUIFolderColors()
+

Return the color wave used in the folder listbox of the analysis browser.

+
+ +
+
+wave GetExperimentBrowserGUIList()
+

Return the text wave used in the listbox of the experiment browser.

+

The “experiment” column in the second layer maps to the corresponding row in the experimentMap.

+
+ +
+
+wave GetExperimentBrowserGUISel()
+

Return the selection wave used in the listbox of the experiment browser.

+
+ +
+
+wave GetAnalysisConfigWave(string dataFolder, string device, variable sweep)
+

Return the configSweep wave of a given sweep from the analysis subfolder.

+
+ +
+
+wave ANALYSIS_LBN_GETTER_PROTO(string expFolder, string device)
+

UTF_NOINSTRUMENTATION.

+
+ +
+
+wave GetAnalysLBNumericalValues(string expFolder, string device)
+

Return the numerical labnotebook values in the analysis browser of a device and experiment pair.

+
+ +
+
+wave GetAnalysLBTextualValues(string expFolder, string device)
+

Return the textual labnotebook keys in the analysis browser of a device and experiment pair.

+
+ +
+
+wave GetAnalysLBNumericalKeys(string expFolder, string device)
+

Return the numerical labnotebook keys in the analysis browser of a device and experiment pair.

+
+ +
+
+wave GetAnalysLBTextualKeys(string expFolder, string device)
+

Return the textual labnotebook keys in the analysis browser of a device and experiment pair.

+
+ +
+
+

Getters relating to caching

+

Return the datafolder reference to the wave cache UTF_NOINSTRUMENTATION

+
+
+dfref GetCacheFolder()
+
+ +
+
+string GetCacheFolderAS()
+

Return the full path to the wave cache datafolder, e.g. root:MIES:Cache UTF_NOINSTRUMENTATION.

+
+ +
+
+wave GetCacheValueWave()
+

Return the wave reference wave holding the cached data.

+

Dimension sizes and NOTE_INDEX value must coincide with other two cache waves. UTF_NOINSTRUMENTATION

+
+ +
+
+wave GetCacheKeyWave()
+

Return the wave reference wave holding the cache keys.

+

Dimension sizes and NOTE_INDEX value must coincide with other two cache waves. UTF_NOINSTRUMENTATION

+
+ +
+
+wave GetCacheStatsWave()
+

Return the wave reference wave holding the cache stats.

+

Rows:

    +

  • One for each cache entry

    • +
+

+

Columns:

    +

  • 0: Number of cache hits (Incremented for every read)

    • +

  • 1: Number of cache misses (Increment for every failed lookup)

    • +

  • 2: Modification timestamp (Updated on write)

    • +

  • 3: Size in bytes (Updated on write)

    • +
+

+

Dimension sizes and NOTE_INDEX value must coincide with other two cache waves. UTF_NOINSTRUMENTATION

+
+ +
+
+ +

Return the datafolder reference to the debug folder

+

UTF_NOINSTRUMENTATION

+
+
+dfref GetDebugPanelFolder()
+
+ +
+
+string GetDebugPanelFolderAS()
+

Return the full path to the debug datafolder, e.g. root:MIES:Debug.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+wave GetDebugPanelListWave()
+

Return the list wave for the debug panel.

+
+ +
+
+wave GetDebugPanelListSelWave()
+

Return the list selection wave for the debugging panel.

+
+ +
+
+

AnalysisFunctionGetters Getters used by analysis functions

+
+
+wave GetAnalysisFuncIndexingHelper(string device)
+

Return a wave reference which holds an headstage-dependent index.

+

Can be used by analysis function to count the number of invocations.

+
+ +
+
+wave GetAnalysisFuncDAScaleDeltaV(string device)
+

Return a wave reference which holds the “Delta V” values of all sweeps from one repeated acquisition cycle.

+

Used by PSQ_AdjustDAScale().

+

Rows:

    +

  • Sweeps

    • +
+

+

Columns:

    +

  • Headstages

    • +
+

+
+ +
+
+wave GetAnalysisFuncDAScaleDeltaI(string device)
+

Return a wave reference which holds the “Delta I” values of all sweeps from one repeated acquisition cycle.

+

Used by PSQ_AdjustDAScale().

+

Rows:

    +

  • Sweeps

    • +
+

+

Columns:

    +

  • Headstages

    • +
+

+
+ +
+
+wave GetAnalysisFuncDAScaleRes(string device)
+

Return a wave reference to the fitted resistance values and its error.

+

Used by PSQ_AdjustDAScale().

+

Rows:

    +

  • Headstages

    • +
+

+

Columns:

    +

  • Value

    • +

  • Error (standard deviation)

    • +
+

+
+ +
+
+wave GetAnalysisFuncDAScaleResFit(string device, variable headstage)
+

Return a wave reference to the fitted resistance wave created by CurveFit

+

Used by PSQ_AdjustDAScale().

+
+ +
+
+wave GetAnalysisFuncDAScaleSpikeFreq(string device, variable headstage)
+

Return a wave reference to the spikes frequency wave.

+

Used by PSQ_AdjustDAScale().

+
+ +
+
+wave GetAnalysisFuncDAScaleFreqFit(string device, variable headstage)
+

Return a wave reference to the spikes frequency wave.

+

Used by PSQ_AdjustDAScale().

+
+ +
+
+wave GetAnalysisFuncDAScales(string device, variable headstage)
+

Return a wave reference to the DAScale wave.

+

Used by PSQ_AdjustDAScale().

+
+ +
+
+

Async Framework

+
+
+wave GetDFREFbuffer(dfref dfr)
+

Return wave reference to wave with data folder reference buffer for delayed readouts 1d wave for data folder references, starts with size 0 when jobs should be read out in order, the waiting data folders are buffered in this wave e.g. if the next read out would be job 2, but a data folder from job 3 is returned the data folder is buffered until the one from job 2 appears from the output queue.

+
+ +
+
+wave GetWorkloadTracking(dfref dfr)
+

Returns wave ref for workload tracking 2d wave row stores work load classes named through dimension label column 0 stores how many work loads were pushed to Async column 1 stores how many work loads were read out from Async.

+
+ +
+
+wave GetSerialExecutionBuffer(dfref dfr)
+

Returns wave ref for buffering results when THREADING_DISABLED is defined 1D wave using NOTE_INDEX logic.

+
+ +
+
+string GetAsyncHomeStr()
+

Returns string path to async framework home data folder.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetAsyncHomeDF()
+

Returns reference to async framework home data folder.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+

Functions

+
+
+wave GetLogbookValuesFromKeys(wave keyWave)
+

Return a wave reference to the corresponding Logbook keys wave from an values wave input.

+
+ +
+
+wave GetLogbookKeysFromValues(wave valuesWave)
+

Return a wave reference to the corresponding Logbook values wave from an keys wave input.

+
+ +
+
+wave GetChanAmpAssign(string device)
+

Return a wave reference to the channel <-> amplifier relation wave (numeric part)

+

Rows:

    +

  • 0-3: V-Clamp: DA channel, DA gain, AD channel, AD gain

    • +

  • 4-7: I-Clamp: DA channel, DA gain, AD channel, AD gain

    • +

  • 8: Amplifier Serial number as returned by AxonTelegraphFindServers. This differs compared to the ones returned by MCC_FindServers, as the latter are strings with leading zeros. E.g.: “00000123” vs 123 E.g.: “Demo” vs 0

    • +

  • 9: Amplifier Channel ID

    • +
+

+

Columns:

    +

  • Head stage number

    • +
+

+
+ +
+
+wave GetChanAmpAssignUnit(string device)
+

Return a wave reference to the channel <-> amplifier relation wave (textual part)

+

Rows:

    +

  • 0: DA unit (V-Clamp mode)

    • +

  • 1: AD unit (V-Clamp mode)

    • +

  • 2: DA unit (I-Clamp mode)

    • +

  • 3: AD unit (I-Clamp mode)

    • +
+

+

Columns:

    +

  • Head stage number

    • +
+

+
+ +
+
+static variable ExistsWithCorrectLayoutVersion(WaveOrNull wv, variable versionOfNewWave)
+

Check if wv exists and has the correct version UTF_NOINSTRUMENTATION.

+
+ +
+
+static variable WaveVersionIsAtLeast(WaveOrNull wv, variable existingVersion)
+

Check if the given wave’s version is equal or larger than the given version, if version is not set false is returned.

+
+ +
+
+static variable IsWaveVersioned(wave wv)
+

Returns 1 if the wave has a valid version information attached, 0 otherwise.

+
+ +
+
+static variable WaveVersionIsSmaller(WaveOrNull wv, variable existingVersion)
+

Check if the given wave’s version is smaller than the given version, if version is not set true is returned.

+
+ +
+
+variable GetWaveVersion(WaveOrNull wv)
+

return the Version of the Wave, returns NaN if no version was set UTF_NOINSTRUMENTATION

+
+ +
+
+static variable SetWaveVersion(wave wv, variable val)
+

Set the wave layout version of wave.

+
+ +
+
+static variable IsValidWaveVersion(variable value)
+

A valid wave version is a positive non-zero integer.

+
+ +
+
+variable ClearWaveNoteExceptWaveVersion(wave wv)
+

Clear the wave note but keep any valid wave version.

+
+ +
+
+dfref UpgradeDataFolderLocation(string oldFolder, string newFolder)
+

Move/Rename a datafolder across different locations.

+

Both parameters must be absolute datafolder locations. Cases where both exist are also handled gracefully.

+

Function/DF GetMyFolder()
+    return UpgradeDataFolderLocation("root:old", "root:new")
+End
+
+
+

+
+
Returns:
+

DFREF to the newFolder with the contents of oldFolder

+
+
+
+ +
+
+wave UpgradeWaveLocationAndGetIt(WaveLocationMod *p)
+

Rename/Move a wave to a new location.

+

Valid transformations (and all combinations of them):

    +

  • Moving into a new datafolder

    • +

  • Renaming to a new name

    • +

  • Nothing

    • +
+

+

The function is idempotent (i.e. it can be called also on already relocated waves). Cases where new == old are also handled gracefully.

+

Function/WAVE GetMyWave(device)
+    string device
+
+    variable versionOfNewWave = 1
+    string newName = "newAndNiceName"
+    DFREF newDFR = GetNewAndFancyFolder(device)
+
+    STRUCT WaveLocationMod p
+    p.dfr     = $(GetSomeFolder(device) + ":oldSubFolder")
+    p.newDFR  = newDFR
+    p.name    = "oldAndUglyName"
+    p.newName = newName
+
+    WAVE/Z wv = UpgradeWaveLocationAndGetIt(p)
+
+    if(ExistsWithCorrectLayoutVersion(wv, versionOfNewWave))
+        return wv
+    elseif(WaveExists(wv))
+        // handle upgrade
+    else
+        Make/R/N=(10, 2) newDFR:newName/Wave=wv
+    end
+
+    SetWaveVersion(wv, versionOfNewWave)
+
+    return wv
+End
+
+
+

+
+
Returns:
+

wave reference to the wave in the new location, an invalid one if the wave does not exist at the specified former location

+
+
+
+ +
+
+wave GetTPResultAsyncBuffer(string device)
+

Return a wave reference to the tp result async buffer wave.

+

Rows:

    +

  • buffered partial result entries

    • +
+

+

Column 0 (ASYNCDATA):

    +

  • Layers:

      +

    • 0: marker

      • +

    • 1: received channels

      • +

    • 2: now Column 1: baseline level Column 2: steady state res Column 3: instantaneous res Column 4: baseline position Column 5: steady state res position Column 6: instantaneous res position Column 7: average elevated level (steady state) Column 8: average elevated level (instantaneous)

      • +
    +

    • +
+

+

Layers:

    +

  • NUM_HEADSTAGES positions with value entries at hsIndex

    • +
+

+
+ +
+
+wave GetChannelClampMode(string device)
+

Return a wave reference to the channel clamp mode wave.

+

Only specialized code which does not have a headstage, or needs to know the clamp mode for unassociated channels, should use this function.

+

Rows:

    +

  • Channel numbers

    • +
+

+

Columns:

    +

  • 0: DAC

    • +

  • 1: ADC

    • +
+

+

Layers:

    +

  • 0: Clamp Mode

    • +

  • 1: Headstage

    • +
+

+
+ +
+
+wave GetHSProperties(string device)
+

Return properties for the headstages during TP/DAQ.

+

+

See also

+

DC_UpdateHSProperties()

+
+

+
+ +
+
+dfref GetDAQDevicesFolder()
+

Return the DAQ devices folder “root:mies:HardwareDevices”.

+
+ +
+
+string GetDAQDevicesFolderAsString()
+

Return a data folder reference to the DAQ devices folder.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetActiveDAQDevicesTimerFolder()
+

Return the active DAQ devices timer folder “root:mies:HardwareDevices:ActiveDAQDevices:Timer”.

+
+ +
+
+string GetActiveDAQDevicesTimerAS()
+

Return a data folder reference to the active DAQ devices timer folder.

+
+ +
+
+dfref GetActiveDAQDevicesFolder()
+

Return the active DAQ devices folder “root:mies:HardwareDevices:ActiveDAQDevices”.

+
+ +
+
+string GetActiveDAQDevicesFolderAS()
+

Return a data folder reference to the active DAQ devices folder.

+
+ +
+
+dfref GetDeviceTypePath(string deviceType)
+

Return a datafolder reference to the device type folder.

+
+ +
+
+string GetDeviceTypePathAsString(string deviceType)
+

Return the path to the device type folder, e.g. root:mies:HardwareDevices:ITC1600.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetDevicePath(string device)
+

Return a datafolder reference to the device folder.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetDeviceInfoPathAsString()
+

Return the path to the device info folder, e.g. root:mies:HardwareDevices:DeviceInfo.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetDeviceInfoPath()
+

Return a datafolder reference to the device info folder.

+
+ +
+
+string GetDevicePathAsString(string device)
+

Return the path to the device folder, e.g. root:mies:HardwareDevices:ITC1600:Device0.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetDeviceDataPath(string device)
+

Return a datafolder reference to the device data folder.

+
+ +
+
+string GetDeviceDataPathAsString(string device)
+

Return the path to the device folder, e.g. root:mies:HardwareDevices:ITC1600:Device0:Data.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetMiesPath()
+

Returns a data folder reference to the mies base folder.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetMiesPathAsString()
+

Returns the base folder for all MIES functionality, e.g. root:MIES UTF_NOINSTRUMENTATION.

+
+ +
+
+dfref GetSweepFormulaPath()
+

Returns a data folder reference to the sweep formula folder.

+
+ +
+
+string GetSweepFormulaPathAsString()
+

Returns the temporary folder for Sweep formula, e.g. root:MIES:SweepFormula.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetCalledOncePath()
+

Returns a data folder reference to the call once folder.

+
+ +
+
+string GetCalledOncePathAsString()
+

Returns a name of the data folder for the call once folder, e.g. root:MIES:CalledOnce.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetSingleSweepFolder(dfref dfr, variable sweepNo)
+

Return a datafolder reference to a subfolder below dfr for splitted sweep specific data, e.g. dfr:X_5.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetSingleSweepFolderAsString(dfref dfr, variable sweepNo)
+

Return the path to a subfolder below dfr for splitted sweep specific data.

+
+ +
+
+wave GetDAQDataWave(string device, variable mode)
+

Return the DAQ data wave.

+

ITC hardware:

    +

  • 2D signed 16bit integer wave, the colums are for the channel

    • +
+

+

NI/SU hardware:

    +

  • Wave reference wave, one referencing each channel

    • +
+

+

Rows:

    +

  • data

    • +
+

+

Columns:

    +

  • one for each active DA, AD, TTL channel (in that order)

    • +
+

+

For scaling and gain information see SWS_GetChannelGains().

+

Note: TP_PROPERTIES_HASH: Unique hash for a combination of all properties which influence the test pulse.

+
+
Parameters:
+
+
+
+
+ +
+
+wave GetSUCompositeTTLWave(string device)
+
+ +
+
+wave GetNIDAQChannelWave(string device, variable channel, variable mode)
+

Get the single NI/Sutter channel waves.

+

Special use function, normal callers should use GetDAQDataWave() instead.

+
+ +
+
+wave GetSutterSingleSampleDACOutputWave(string device)
+

Get a single point output wave for Sutter device.

+
+ +
+
+wave GetSutterSingleSampleADCInputWave(string device)
+

Get a single point input wave for Sutter device.

+
+ +
+
+wave GetEpochsWave(string device)
+

Return the epochs text wave.

+

Rows:

    +

  • epochs

    • +
+

+

Column numbers must use global column number constants

+

Columns:

+
    +

  • 0: Start time in sec

    • +

  • 1: End time in sec

    • +

  • 2: Tags

    • +

  • 3: Tree Level

    • +
+
+

See also

+

epochColumnNumber.

+
+

+

Layers: index the GUI channel numbers

    +

  • NUM_DA_TTL_CHANNELS

    • +
+

+

Chunks: index the XOP channel types

    +

  • XOP_CHANNEL_TYPE_COUNT

    • +
+

+

Version History

+

Wave

+

    +

  • 1: Initial version

    • +

  • 2: Renamed column Name to Tags

    • +

  • 3: Added chunks dimension indexing over channel types

    • +
+

+

Tags format

+

Initial version in a2172f03 (Added generations of epoch information wave, 2019-05-22), parsed in PA plot since 4e534e29 (Pulse Averaging: Pulse starting times are now read from the lab notebook, 2020-10-07).

+

In d150d896 (DC_AddEpochsFromStimSetNote: Add sub sub epoch information, 2021-02-02) tree level 3 info for pulse train pulses was added, which is read out since ba209bbd (PA plot: Gather more pulse infos, 2021-02-02).

+

And in 2371cfb0 (Epochs: Revise naming, 2021-09-22) we changed the naming of the tags and also adapted PA_RetrievePulseStartTimesFromEpochs.

+

For these three formats we have tests in RPI_WorksWithOldData(). When changing the tags format this test needs to be updated.

+
+ +
+
+wave GetEpochsWaveAsFree()
+
+ +
+
+static variable SetEpochsDimensionLabelAndVersion(wave wv)
+
+ +
+
+variable SetEpochsDimensionLabelsSingleChannel(wave wv)
+
+ +
+
+dfref GetEpochsVisualizationFolder(dfref dfr)
+

Return the folder for the epoch visualization waves below the sweepfolder/databrowser specific folder.

+
+ +
+
+wave GetDAQConfigWave(string device)
+

Return the DAQ config wave.

+

Rows:

    +

  • One for each channel, the order is DA, AD, TTL (same as in the DAQDataWave)

    • +
+

+

Columns:

    +

  • channel type, one of XopChannelConstants

    • +

  • channel number (0-based)

    • +

  • sampling interval in microseconds (1e-6)

    • +

  • decimation mode (always zero)

    • +

  • data offset

    • +

  • headstage number

    • +

  • clamp mode

    • +
+

+

The wave note holds a list of channel units. The order is the same as the rows. TTL channels don’t have units. Querying the channel unit should always be done via AFH_GetChannelUnit() or AFH_GetChannelUnits().

+

This wave is also used for NI devices as configuration template. There is one difference though: While for ITC devices there is one TTL row for each rack, for NI devices there is one TTL row for each channel (up to 8 currently) The channel number column holds the hardware channel number for the NI device

+

ITC hardware: The number of TTL bits which are stored in each TTL channel is hardware dependent and can be queried with HW_ITC_GetRackRange().

+

Version 1 changes:

    +

  • Columns now have dimension labels

    • +

  • One more column with the channel data offset

    • +

  • Due to the wave versioning the channel unit is now stored with the CHANNEL_UNIT_KEY as key and it is now separated not with semicolon anymore but a comma.

    • +
+

+

Version 2 changes:

    +

  • DAQChannelType column added

    • +
+

+

Version 3 changes:

    +

  • Change wave to double precision

    • +

  • Headstage column added

    • +

  • ClampMode column added

    • +
+

+
+ +
+
+wave GetDQMActiveDeviceList()
+

Returns a reference to the wave of active devices for data acquisition in multi device mode.

+

The wave is used in data acquisition in multiple device mode to keep track of active devices.

+

Columns:

    +

  • DeviceID id of an active device

    • +

  • ADChannelToMonitor index of first active AD channel in DAQDataWave

    • +

  • HardwareType type of hardware of the device

    • +

  • ActiveChunk if a channel of the device is used for TP while DAQ this column saves the number of the last evaluated test pulse

    • +
+

+

Version changes:

    +

  • 1: Added column activeChunk

    • +

  • 2: Changed precision to double

    • +

  • 3: Removed column 2 with StopCollectionPoint as it is no longer used

    • +
+

+
+ +
+
+wave GetTTLWave(string device)
+

Return the intermediate storage wave for the TTL data.

+
+ +
+
+wave GetStimsetAcqIDHelperWave(string device)
+

Return the stimset acquistion cycle ID helper wave.

+

Only valid during DAQ.

+

Rows:

    +

  • NUM_DA_TTL_CHANNELS

    • +
+

+

Columns:

    +

  • 0: Stimset fingerprint of the previous sweep

    • +

  • 1: Current stimset acquisition cycle ID

    • +
+

+
+ +
+
+dfref GetDevSpecLabNBTempFolder(string device)
+

Return the data folder reference to the device specific lab notebook folder for temporary waves.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetDevSpecLabNBTempFolderAS(string device)
+

Return the full path to the device specific lab notebook temp folder, e.g. root:MIES:LabNoteBook:ITC18USB:Device0:Temp.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetResultsFolderAsString()
+

Return the full path to the results folder, e.g. root:MIES:Results.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetResultsFolder()
+

Return the data folder reference to the results folder.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+wave GetIndexingStorageWave(string device)
+

Return the indexing storage wave.

+

Rows:

+

+

Columns:

    +

  • 0: Popup menu index of Wave (stimset)

    • +

  • 1: Popup menu index of Indexing end wave (stimset)

    • +
+

+

All zero-based as returned by GetPopupMenuIndex().

+

Layers:

    +

  • Channels

    • +
+

+
+ +
+
+dfref GetTempPath()
+

Return the temporary folder below the MIES hierarchy, e.g. root:mies:trash.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetUniqueTempPath()
+

Return a unique temporary folder below the MIES hierarchy, e.g. root:mies:trash$digit.

+

As soon as you discard the latest reference to the folder it will be slated for removal at some point in the future.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetStaticDataFolder()
+

Return the datafolder reference to the static data location, e.g. root:mies:StaticData:

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetStaticDataFolderAS()
+

Return the full path to the static data location.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetActDAQDevicesTestPulseFolder()
+

Return the datafolder reference to the active DAQ devices folder, e.g. root:MIES:HardwareDevices:ActiveDAQDevices:TestPulse.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetActiveDAQDevicesTestPulseFolderAsString()
+

Return the full path to the active DAQ devices location for the test pulse.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+wave GetActiveDevicesTPMD()
+

Return the active devices wave for TP MD.

+

Rows:

    +

  • Devices taking part in TP MD Columns:

    • +

  • 0: DeviceID

    • +

  • 1: ActiveChunk

    • +
+

+

The $NOTE_INDEX wave note entry holds the number of active devices. In addition it is also the next free row index.

+
+ +
+
+wave GetDA_EphysGuiStateNum(string device)
+

Returns wave (DA_EphysGuiState) that stores the DA_Ephys GUI state DA_EphysGuiState is stored in the device specific folder e.g. root:MIES:HardwareDevices:ITC18USB:Device0.

+

Rows:

    +

  • Column specific GUI control settings usually associated with control name number

    • +
+

+

Columns:

    +

  • 0: State of control Check_DataAcqHS_RowNum. 0 = UnChecked, 1 = Checked

    • +

  • 1: Clamp mode of HS number that matches Row number. 0 = VC, 1 = IC, 2 = NC.

    • +

  • 2: State of control Check_DA_RowNum. 0 = UnChecked, 1 = Checked

    • +

  • 3: Internal number stored in control Gain_DA_RowNum. Gain is user/hardware defined.

    • +

  • 4: Internal number stored in setvar:Scale_DA_RowNum. Scalar is user defined.

    • +

  • 5: PopupMenu Index of popupMenu:Wave_DA_RowNum. Stores index of active DA stimulus set during data acquisition. Stores index of next DA stimulus set when data acquistion is not active.

    • +

  • 6: PopupMenu Index of popupMenu:IndexEnd_DA_RowNum. Stores the index of the last DA stimulus set used in indexed aquisition mode.

    • +

  • 7: State of checkbox control Check_AD_RowNum. 0 = UnChecked, 1 = Checked

    • +

  • 8: Internal number stored in Gain_AD_RowNum. Gain is user/hardware defined.

    • +

  • 9: State of checkbox control Check_TTL_RowNum. 0 = UnChecked, 1 = Checked

    • +

  • 10: PopupMenu Index of popupMenu:Wave_TTL_RowNum. Stores index of active TTL stimulus set during data acquisition. Stores index of next TTL stimulus set when data acquistion is not active.

    • +

  • 11: PopupMenu Index of popupMenu:IndexEnd_TTL_RowNum. Stores the index of the last TTL stimulus set used in indexed aquisition mode.

    • +

  • 12: State of control Check_AsyncAD_RowNum. 0 = UnChecked, 1 = Checked

    • +

  • 13: Internal number stored in control SetVar_AsyncAD_Gain_RowNum. Gain is user/hardware defined.

    • +

  • 14: State of control check_AsyncAlarm_RowNum. 0 = UnChecked, 1 = Checked

    • +

  • 15: Internal number stored in control min_AsyncAD__RowNum. The minium value alarm trigger.

    • +

  • 16: Internal number stored in control max_AsyncAD_RowNum. The max value alarm trigger.

    • +

  • 17+: Unique controls

    • +
+

+

UTF_NOINSTRUMENTATION

+
+ +
+
+wave GetDA_EphysGuiStateTxT(string device)
+

Return a wave reference to the textual GUI state wave.

+

Rows:

    +

  • Column specific GUI control settings usually associated with control name number

    • +
+

+

Columns:

    +

  • 0: (DA) First stimset name

    • +

  • 1: (DA) Last stimset name

    • +

  • 2: (DA) Unit

    • +

  • 3: (DA) Search string

    • +

  • 4: (AD) Unit

    • +

  • 5: (TTL) First stimset name

    • +

  • 6: (TTL) Last stimset name

    • +

  • 7: (TTL) Search string

    • +

  • 8: (Async) Title

    • +

  • 9: (Async) Unit

    • +

  • 10+: Unique controls (SetVariable and PopupMenu only)

    • +
+

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetNWBFolder()
+

Return the datafolder reference to the NeuroDataWithoutBorders folder, e.g. root:MIES:NWB.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetNWBFolderAS()
+

Return the full path to the NeuroDataWithoutBorders folder.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+wave GetDeviceMapping()
+

Return a wave mapping the deviceIDs (numeric) to the device name(NI HW only) and user visible device name.

+

Rows:

    +

  • DeviceIDs, supports 32 as the ITC XOP does

    • +
+

+

COLS:

    +

  • One column for each supported HW type

    • +
+

+

LAYERS:

    +

  • 0: Main device (aka device of a DA_Ephys panel), used for deriving datafolders for storage

    • +

  • 1: Name of the device used for pressure control (maybe empty)

    • +
+

+
+ +
+
+wave GetCellElectrodeNames(string device)
+

Returns the names of the electrodes.

+

The electrodes represents the physically connected part to the cell whereas the headstage refers to the logical entity inside MIES.

+

Will be written into the labnotebook and used for the NWB export.

+
+ +
+
+wave GetPressureTypeWv(string device)
+

Returns a 1D wave with the same number of rows as headstages used to store the pressure type.

+

Available pressure types are one of PressureTypeConstants

+

ROWS:

    +

  • One row for each headstage

    • +
+

+

+

See also

+

P_UpdatePressureType

+
+

+
+ +
+
+dfref GetDevicePulseAverageFolder(dfref dfr)
+

Return the pulse averaging folder.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetDevicePulseAverageFolderAS(dfref dfr)
+

Return the full path to the pulse averaging folder, e.g. dfr:PulseAveraging.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetDevicePulseAverageHelperFolder(dfref dfr)
+

Return the pulse averaging helper folder.

+

This holds various helper waves for the graph generation.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+string GetDevicePulseAverageHelperFolderAS(dfref dfr)
+

Return the full path to the pulse averaging helper folder, e.g. dfr:Helper.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+wave GetPulseAverageWave(dfref dfr, variable length, variable channelType, variable channelNumber, variable region, variable pulseIndex)
+

Return a wave reference to the single pulse defined by the given parameters.

+
+
Parameters:
+
    +

  • dfr – datafolder reference where to create the empty wave if it does not exist

    • +

  • length – Length in points of the new wave

    • +

  • channelType – channel type, one of XopChannelConstants

    • +

  • channelNumber – channel number

    • +

  • region – region index (a region is the range with data in a dDAQ/oodDAQ measurement)

    • +

  • pulseIndex – pulse number, 0-based

    • +
+
+
+
+ +
+
+wave GetPulseAverageWaveNoteWave(dfref dfr, variable length, variable channelType, variable channelNumber, variable region, variable pulseIndex)
+

Return a wave reference to the single pulse defined by the given parameters.

+
+
Parameters:
+
    +

  • dfr – datafolder reference where to create the empty wave if it does not exist

    • +

  • length – Length in points of the new wave

    • +

  • channelType – channel type, one of XopChannelConstants

    • +

  • channelNumber – channel number

    • +

  • region – region index (a region is the range with data in a dDAQ/oodDAQ measurement)

    • +

  • pulseIndex – pulse number, 0-based

    • +
+
+
+
+ +
+
+wave GetPulseAverageSetIndizes(dfref dfr, variable channelNumber, variable region)
+

Returns the pulse average set properties wave.

+

These are row indizes into GetPulseAverageProperties()/GetPulseAveragePropertiesWaves() for the pulses which belong to the given set.

+
+ +
+
+wave GetPulseAverageSetImageWave(dfref dfr, variable channelNumber, variable region)
+

Returns the pulse average image wave.

+

This is used for the image display mode.

+

NOTE_INDEX is used for marking the length of the used columns as there is one pulse per column.

+
+ +
+
+wave GetPulseAverageProperties(dfref dfr)
+

Return the pulse average properties wave.

+

It is filled by PA_GenerateAllPulseWaves() and consumed by others.

+
+ +
+
+wave GetPulseAveragePropertiesWaves(dfref dfr)
+

Return the pulse average properties wave with wave references.

+

Belongs to GetPulseAverageProperties() and also has the same NOTE_INDEX count stored there.

+
+ +
+
+wave GetPulseAverageDisplayMapping(dfref dfr)
+

Return the mapping wave for pulse averaging between region/channel to activeRegion/activeChannel.

+

Belongs to GetPulseAverageProperties() and also has the same NOTE_INDEX count stored there.

+
+ +
+
+wave GetArtefactRemovalListWave(dfref dfr)
+

Return the artefact removal listbox wave for the databrowser or the sweepbrowser.

+
+ +
+
+wave GetArtefactRemovalDataWave(dfref dfr)
+

Return the artefact removal wave databrowser or the sweepbrowser.

+
+ +
+
+wave GetOverlaySweepsListWave(dfref dfr)
+

Return the overlay sweeps listbox wave for the databrowser or the sweepbrowser.

+
+ +
+
+wave GetOverlaySweepsListSelWave(dfref dfr)
+

Return the overlay sweeps listbox selection wave for the databrowser or the sweepbrowser.

+
+ +
+
+wave GetOverlaySweepHeadstageRemoval(dfref dfr)
+

Return the overlay sweeps wave with the parsed headstage removal info.

+

Rows:

+

+

Columns:

+

+
+ +
+
+wave GetOverlaySweepSelectionChoices(string win, dfref dfr, variable skipUpdate = defaultValue)
+

Return the overlay sweeps wave with all sweep selection choices for the databrowser or the sweepbrowser.

+
+ +
+
+wave GetChannelSelectionWave(dfref dfr)
+

Return the channel selection wave for the databrowser or sweep browser.

+
+ +
+
+wave GetAxisLabelCacheWave()
+

Return a free wave used for the axis label cache.

+
+ +
+
+wave GetSweepBrowserMap(dfref dfr)
+

Return the sweepBrowser map wave from the given DFR.

+
+ +
+
+wave GetAnalysisFunctionStorage(string device)
+

Return the storage wave for the analysis functions.

+

Only contains valid functions. An analysis function is valid if it has a compatible signature and can be found within the locations searched by AFH_GetAnalysisFunctions().

+

Rows:

    +

  • Head stage number

    • +
+

+

Columns:

+

+
+ +
+
+wave GetSetEventFlag(string device)
+

Used for storing a true/false state that the pre and/or post set event should be fired after the sweep which is currently prepared in DC_PlaceDataInDAQDataWave().

+

Rows:

    +

  • NUM_DA_TTL_CHANNELS

    • +
+

+

Columns:

    +

  • PRE_SET_EVENT

    • +

  • POST_SET_EVENT

    • +
+

+
+ +
+
+wave GetRAPerfWave(string device)
+

Return the wave for storing timestamps for perf testing repeated acquisition.

+
+ +
+
+wave WBP_GetAnalysisParamGUIListWave()
+

Return the list wave for the analysis parameter GUI.

+
+ +
+
+wave WBP_GetAnalysisParamGUISelWave()
+

Return the selection wave for the analysis parameter GUI.

+
+ +
+
+wave WBP_GetAnalysisParamGUIHelpWave()
+

Return the help wave for the analysis parameter GUI.

+
+ +
+
+wave GetAnaFuncDashboardListWave(dfref dfr)
+

Return the analysis function dashboard listbox wave for the databrowser or the sweepbrowser.

+
+ +
+
+wave GetAnaFuncDashboardInfoWave(dfref dfr)
+

Return the analysis function dashboard info wave for the databrowser or the sweepbrowser.

+
+ +
+
+wave GetAnaFuncDashboardSelWave(dfref dfr)
+

Return the analysis function dashboard listbox selection wave for the databrowser or the sweepbrowser.

+
+ +
+
+wave GetAnaFuncDashboardColorWave(dfref dfr)
+

Return the analysis function dashboard listbox color wave for the databrowser or the sweepbrowser.

+
+ +
+
+wave GetAnaFuncDashboardHelpWave(dfref dfr)
+

Return the analysis function dashboard help wave for the databrowser or the sweepbrowser.

+
+ +
+
+wave GetDeviceInfoWave(string device)
+

Return a wave with device information.

+

   Entries:
+
+
+ AD: - For devices that have mixed channels for HS, Unassoc AD the number of the channels combined
    +

  • For devices that have separate channels for HS and Unassoc AD the number of the headstages DA: - For devices that have mixed channels for HS, Unassoc DA the number of the channels combined

    • +

  • For devices that have separate channels for HS and Unassoc DA the number of the headstages TTL: - Number of TTL channels Rack: - Number of Racks for ITC, NaN for other HW HardwareType: - One of

    +

    See also

    +

    HardwareDACTypeConstants like HARDWARE_SUTTER_DAC AuxAD: - For devices with HS independent AD channels the number of the separate AD channels, NaN for devices with mixed channels AuxDA: - For devices with HS independent DA channels the number of the separate DA channels, NaN for devices with mixed channels

    +
    +

    • +
+

+
+ +
+
+wave GetElapsedTimeWave()
+

Return a wave suitable for storing elapsed time.

+

Helper function for DEBUGPRINT_ELAPSED_WAVE() and StoreElapsedTime().

+
+ +
+
+wave GetSweepFormulaX(dfref dfr, variable graphNr)
+

Return the X wave for the sweep formula.

+
+ +
+
+wave GetSweepFormulaY(dfref dfr, variable graphNr)
+

Return the Y wave for the sweep formula.

+
+ +
+
+wave GetPopupExtMenuWave()
+

Return the global temporary wave for extended popup menu.

+
+ +
+
+string GetGraphUserDataFolderAsString()
+

Return the reference to the graph user data datafolder as string.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+dfref GetGraphUserDataFolderDFR()
+

Return the reference to the graph user data datafolder.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+static string BuildGraphName(string graph)
+

UTF_NOINSTRUMENTATION.

+
+ +
+
+string GetGraphUserDataAsString(string graph)
+

Return the path to the text wave for the graph user data as string.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+wave GetGraphUserData(string graph)
+

Return the text wave for the graph user data.

+
+
Parameters:
+

graph – existing graph

+
+
+
+ +
+
+wave GetPAGraphData()
+

Return the wave for trace counts per graph for pulse averaging plot rows one per graph, dimlabel is graph name.

+

Columns:

    +

  • 0: trace names of all average traces

    • +

  • 1: trace names of all deconvolution traces

    • +

  • 2: list of used image names

    • +
+

+
+ +
+
+std::tuple<WAVE, string> GetPAPermanentAverageWave(dfref dfr, variable channel, variable region)
+

Return permanent average wave for PA plot for a given channel/region as well as its base name Returns a null wave if the permanent wave does not exist.

+
+ +
+
+wave GetPulseInfoWave()
+

Return a free wave for storing timing information of single pulses.

+

Rows:

    +

  • Pulses

    • +
+

+

Columns:

    +

  • Length [ms]: Total length including baseline

    • +

  • PulseStart [ms]: Start of the pulse (aka begin of active)

    • +

  • PulseEnd [ms]: End of the pulse (aka end of active)

    • +
+

+
+ +
+
+wave GetOverrideResults()
+

Return the wave used for storing mock data for tests.

+

This wave is created by MSQ_CreateOverrideResults(), PSQ_CreateOverrideResults() or TP_CreateOverrideResults() and does also not follow our usual rules so it might not exist.

+
+ +
+
+wave GetAcqStateTracking()
+

Return the wave used for storing acquisition state transitions during testing.

+
+ +
+
+wave GetValidAcqStateTransitions()
+

Return a wave with all valid acquisition state transitions.

+

It is AS_NUM_STATES x AS_NUM_STATES matrix were the old states are in the rows and the new states in the columns. Every valid transition has a 1 in it.

+
+ +
+
+string GetDANDIFolderAsString()
+

UTF_NOINSTRUMENTATION.

+
+ +
+
+dfref GetDANDIFolder()
+

Return the data folder reference to the DANDI folder.

+

UTF_NOINSTRUMENTATION

+
+ +
+
+wave GetDandiSetProperties()
+

Return a free wave with the DANDI set properties.

+

Rows:

    +

  • one row for each asset

    • +
+

+

Columns:

    +

  • ID

    • +

  • created timestamp (ISO8601)

    • +

  • modified timestamp (ISO8601)

    • +

  • file path of the asset inside the DANDI set

    • +
+

+
+ +
+
+wave GetDandiDialogWave(wave props)
+
+ +
+
+wave GetDACAmplitudes(variable numDACEntries)
+

Return a free wave with the DAC amplitudes.

+

Rows:

    +

  • One for each active DAC

    • +
+

+

Columns:

    +

  • DASCALE: DA Scale from the DAEphys GUI

    • +

  • TPAMP: Testpulse amplitude (clamp mode dependent)

    • +
+

+
+ +
+
+wave GetYvsXFormulas()
+

Return a free text wave to store single y vs x formula combinations from sweepformula code.

+

Rows:

    +

  • One for each y vs x formula combination

    • +
+

+
+ +
+
+wave GetYandXFormulas()
+

Return a free text wave to store y and x formula combinations from sweepformula code.

+

Rows:

    +

  • One for each formula Columns:

    • +

  • FORMULA_X: formula for x wave

    • +

  • FORMULA_Y: formula for y wave

    • +
+

+
+ +
+
+wave GetTPSettingsFree()
+

Free wave version of GetTPSettingsFree()

+
+ +
+
+wave GetTPSettings(string device)
+

Return the testpulse GUI settings.

+

Rows:

    +

  • Buffer size: Number of elements to average

    • +

  • Resistance tolerance: Tolerance for labnotebook change reporting of resistance values, see GetTPResults()

    • +

  • Baseline percentage: Fraction which the baseline occupies relative to the total testpulse length, before and after the pulse itself.

    • +

  • Pulse duration [ms]

    • +

  • Amplitude VC

    • +

  • Amplitude IC

    • +

  • Auto TP: On/Off (Requires to also call TP_AutoTPGenerateNewCycleID() when writing)

    • +

  • Auto TP: Maximum current [pA]

    • +

  • Auto TP: Voltage [mV]

    • +

  • Auto TP: +/- Voltage [mV]

    • +

  • Auto TP: Percentage [%]

    • +

  • Auto TP: Interval [s]

    • +

  • Auto TP: Cycle ID

    • +
+

+

Columns:

    +

  • LABNOTEBOOK_LAYER_COUNT

    • +
+

+
+ +
+
+wave GetTPSettingsCalculated(string device)
+

Return the calculated/derived TP settings.

+

The entries in this wave are only valid during DAQ/TP and are updated via DC_UpdateGlobals().

+
+ +
+
+wave GetTPSettingsCalculatedAsFree()
+
+ +
+
+static variable SetTPSettingsCalculatedProperties(wave wv)
+
+ +
+
+wave GetTPSettingsLabnotebookKeyWave(string device)
+

Returns a wave reference to the TP settings key wave.

+

Rows:

    +

  • 0: Parameter

    • +

  • 1: Units

    • +

  • 2: Tolerance Factor

    • +
+

+

Columns (all entries headstage dependent except otherwise noted):

    +

  • 0: TP Baseline Fraction (INDEP_HEADSTAGE)

    • +

  • 1: TP Amplitude VC

    • +

  • 2: TP Amplitude IC

    • +

  • 3: TP Pulse Duration (INDEP_HEADSTAGE)

    • +

  • 4: TP Auto On/Off

    • +

  • 5: TP Auto max current

    • +

  • 6: TP Auto voltage

    • +

  • 7: TP Auto voltage range

    • +

  • 8: TP buffer size (INDEP_HEADSTAGE)

    • +

  • 9: Minimum TP resistance for tolerance (INDEP_HEADSTAGE)

    • +

  • 10: Send TP settings to all headstages (INDEP_HEADSTAGE)

    • +

  • 11: TP Auto percentage (INDEP_HEADSTAGE)

    • +

  • 12: TP Auto interval (INDEP_HEADSTAGE)

    • +

  • 13: TP Auto QC

    • +

  • 14: TP Cycle ID

    • +
+

+
+ +
+
+wave GetTPSettingsLabnotebook(string device)
+

Get TP settings wave for the labnotebook.

+

See GetTPSettingsLabnotebookKeyWave() for the dimension label description.

+
+ +
+
+wave GetFormulaGatherWave()
+

Returns a free wave for gathering formula results.

+

The wave stores the wave reference waves returned from SF_ExecuteFormula for the X and Y formulas. In SF_GatherFormulaResults() all formula pairs for on graph subwindow are gathered.

+
+ +
+
+wave GetSFVarStorage(string graph)
+

Returns variable storage of data browser referenced by dfr.

+
+ +
+
+wave GetSFVarAssignments()
+

Returns a wave where variable assignments are collected into.

+
+ +
+
+wave GetActiveChannelMapTTLGUIToHW()
+

Returns a wave where GetActiveChannels fills in the mapping between GUI and hardware TTL channels The wave is initialized here with no active channels.

+
+ +
+
+wave GetActiveChannelMapTTLHWToGUI()
+

Returns a wave where GetActiveChannels fills in the mapping between hardware and GUI TTL channels The wave is initialized here with no active channels.

+
+ +
+
+wave GetLogFileNames()
+

Returns a wave with the names of all log files.

+
+ +
+
+wave GetNewSamplingIntervalsAsFree()
+

Used as temporary wave to store various sampling intervals in ms.

+
+ +
+
+wave GetSUDeviceInfo()
+

Return wave with Sutter device info.

+

ROWS:

    +

  • NUMBEROFDACS: number of IPA devices

    • +

  • MASTERDEVICE: Serial of master device

    • +

  • LISTOFDEVICES: Serials of SubDevices

    • +

  • LISTOFHEADSTAGES: Number of Headstages per Device

    • +

  • SUMHEADSTAGES: Sum of Headstages

    • +

  • AI: Number of analog ins

    • +

  • AO: Number of analog outs

    • +

  • DIOPortWidth: Number of digital outs

    • +
+

+
+ +
+
+wave GetSUDeviceInput(string device)
+

Return wave with Sutter input list wave.

+

ROWS:

    +

  • entries

    • +
+

+

COLS:

    +

  • INPUTWAVE: full path to input wave

    • +

  • CHANNEL: sutter hardware channel number

    • +

  • ENCODEINFO: additional information for multi-device configuration

    • +
+

+
+ +
+
+wave GetSUDeviceOutput(string device)
+

Return wave with Sutter output list wave.

+

ROWS:

    +

  • entries

    • +
+

+

COLS:

    +

  • OUTPUTWAVE: full path to output wave

    • +

  • CHANNEL: sutter hardware channel number

    • +

  • ENCODEINFO: additional information for multi-device configuration

    • +
+

+
+ +
+
+wave GetSUDeviceInputGains(string device)
+

Return wave with Sutter gains for input.

+

ROWS:

    +

  • entries

    • +
+

+

COLS:

    +

  • GAINFACTOR: gain factor

    • +

  • OFFSET: offset

    • +
+

+
+ +
+
+wave GetSutterDACTTLSampleInterval()
+

Returns valid TTL channel sample intervals of sutter IPA hardware in microseconds.

+
+ +
+
+wave GetSutterADCSampleInterval()
+

Returns valid ADC channel sample intervals of sutter IPA hardware in microseconds.

+
+ +
+
+std::tuple<WaveText, WaveDouble> GetLogbookSortedKeys(wave values)
+

Gets from a Logbook values wave the wave with sortedKeys and associated indices in a separate wave.

+
+ +
+
+dfref GetSetFolder(variable channelType)
+

Return the stimset folder from the numeric channelType, CHANNEL_TYPE_DAC or CHANNEL_TYPE_TTL.

+
+
Returns:
+

Data Folder reference to Stimset dataFolder

+
+
+
+ +
+
+string GetSetFolderAsString(variable channelType)
+

Return the stimset folder from the numeric channelType, CHANNEL_TYPE_DAC or CHANNEL_TYPE_TTL.

+
+
Returns:
+

String with full path to Stimset dataFolder

+
+
+
+ +
+
+dfref GetSetParamFolder(variable channelType)
+

Get the stimset parameter folder.

+
+
Parameters:
+

channelType – CHANNEL_TYPE_DAC or CHANNEL_TYPE_TTL

+
+
Returns:
+

dataFolder as DFREF

+
+
+
+ +
+
+string GetSetParamFolderAsString(variable channelType)
+

Get the stimset parameter folder.

+
+
Parameters:
+

channelType – CHANNEL_TYPE_DAC or CHANNEL_TYPE_TTL

+
+
Returns:
+

dataFolder as String

+
+
+
+ +
+
+

Variables

+
+
+static const double ANALYSIS_BROWSER_LISTBOX_WAVE_VERSION = 1
+
+ +
+
+static const double ANALYSIS_BROWSER_FOLDER_LISTBOX_WAVE_VERSION = 1
+
+ +
+
+static const double ANALYSIS_BROWSER_FOLDERCOL_LISTBOX_WAVE_VERSION = 1
+
+ +
+
+static const double ANALYSIS_BROWSER_FOLDERSEL_LISTBOX_WAVE_VERSION = 1
+
+ +
+
+static const double NUM_COLUMNS_LIST_WAVE = 12
+
+ +
+
+static const string WAVE_NOTE_LAYOUT_KEY = "WAVE_LAYOUT_VERSION"
+
+ +
+
+static const double WAVE_TYPE_NUMERICAL = 0x1
+
+ +
+
+static const double WAVE_TYPE_TEXTUAL = 0x2
+
+ +
+
+static const double PULSE_WAVE_VERSION = 4
+
+ +
+
+static const string TP_SETTINGS_LABELS = "bufferSize;resistanceTol;sendToAllHS;baselinePerc;durationMS;amplitudeVC;amplitudeIC;autoTPEnable;autoAmpMaxCurrent;autoAmpVoltage;autoAmpVoltageRange;autoTPPercentage;autoTPInterval;autoTPCycleID"
+
+ +
+
+static const string LOGBOOK_SUFFIX_SORTEDKEYS = "_sorted"
+
+ +
+
+static const string LOGBOOK_SUFFIX_SORTEDKEYSINDICES = "_indices"
+
+ +
+
+static const double EPOCHS_WAVE_VERSION = 3
+
+ +
+
+static const double DQM_ACTIVE_DEV_WAVE_VERSION = 3
+
+ +
+
+static const double TP_SETTINGSCALCULATED_WAVE_VERSION = 3
+
+ +
+
+static const double TP_SETTINGS_WAVE_VERSION = 2
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/file/_zero_m_q___interop_8ipf.html b/file/_zero_m_q___interop_8ipf.html new file mode 100644 index 0000000000..78647e6cef --- /dev/null +++ b/file/_zero_m_q___interop_8ipf.html @@ -0,0 +1,524 @@ + + + + + + + + File ZeroMQ_Interop.ipf — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File ZeroMQ_Interop.ipf

+
+

Flags for zeromq_set()

+

Sets the default flags (no debug, no ipv6, busy wait on receive)

+
+
+const double ZeroMQ_SET_FLAGS_DEFAULT = 0x1
+
+ +
+
+const double ZeroMQ_SET_FLAGS_DEBUG = 0x2
+

Enable debug output.

+
+ +
+
+const double ZeroMQ_SET_FLAGS_IPV6 = 0x4
+

Enable ipv6 support.

+
+ +
+
+const double ZeroMQ_SET_FLAGS_NOBUSYWAITRECV = 0x8
+

Don’t do busy waiting on zeromq_server_recv() and zeromq_client_recv() instead immediately return if no messages are available.

+
+ +
+
+const double ZeroMQ_SET_FLAGS_LOGGING = 0x10
+

Log incoming and outgoing messages.

+
+ +
+
+

Error codes

+

+
+
+const double ZeroMQ_UNKNOWN_SET_FLAG = 10003
+
+ +
+
+const double ZeroMQ_INTERNAL_ERROR = 10004
+
+ +
+
+const double ZeroMQ_INVALID_ARG = 10005
+
+ +
+
+const double ZeroMQ_HANDLER_ALREADY_RUNNING = 10006
+
+ +
+
+const double ZeroMQ_HANDLER_NO_CONNECTION = 10007
+
+ +
+
+const double ZeroMQ_MISSING_PROCEDURE_FILES = 10008
+
+ +
+
+const double ZeroMQ_INVALID_MESSAGE_FORMAT = 10009
+
+ +
+
+const double ZeroMQ_INVALID_LOGGING_TEMPLATE = 10010
+
+ +
+
+const double ZeroMQ_MESSAGE_FILTER_DUPLICATED = 10011
+
+ +
+
+const double ZeroMQ_MESSAGE_FILTER_MISSING = 10012
+
+ +
+
+

Functions which might be useful for outside callers

+

+
+
+variable ZeroMQ_WaveExists(string pathToWave)
+
+ +
+
+wave ZeroMQ_GetWave(string pathToWave)
+
+ +
+
+variable ZeroMQ_DataFolderExists(string pathToDataFolder)
+
+ +
+
+string ZeroMQ_FunctionList(string matchStr)
+
+ +
+
+string ZeroMQ_FunctionInfo(string functionNameStr)
+
+ +
+
+variable ZeroMQ_ShowHelp(string topic)
+
+ +
+
+

Variables

+
+
+const string ZeroMQ_HEARTBEAT = "heartbeat"
+
+ +
+
+const double REQ_SUCCESS = 0
+
+ +
+
+const double REQ_UNKNOWN_ERROR = 1
+
+ +
+
+const double REQ_INVALID_JSON_OBJECT = 3
+
+ +
+
+const double REQ_INVALID_VERSION = 4
+
+ +
+
+const double REQ_INVALID_OPERATION = 5
+
+ +
+
+const double REQ_INVALID_OPERATION_FORMAT = 6
+
+ +
+
+const double REQ_INVALID_MESSAGEID = 7
+
+ +
+
+const double REQ_OUT_OF_MEMORY = 8
+
+ +
+
+const double REQ_PROC_NOT_COMPILED = 100
+
+ +
+
+const double REQ_NON_EXISTING_FUNCTION = 101
+
+ +
+
+const double REQ_TOO_FEW_FUNCTION_PARAMS = 102
+
+ +
+
+const double REQ_TOO_MANY_FUNCTION_PARAMS = 103
+
+ +
+
+const double REQ_UNSUPPORTED_FUNC_SIG = 104
+
+ +
+
+const double REQ_UNSUPPORTED_FUNC_RET = 105
+
+ +
+
+const double REQ_INVALID_PARAM_FORMAT = 106
+
+ +
+
+const double REQ_FUNCTION_ABORTED = 107
+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/filelist.html b/filelist.html new file mode 100644 index 0000000000..547171b9e7 --- /dev/null +++ b/filelist.html @@ -0,0 +1,7364 @@ + + + + + + + + File list — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

File list

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/genindex.html b/genindex.html new file mode 100644 index 0000000000..cf17a7b9a6 --- /dev/null +++ b/genindex.html @@ -0,0 +1,13353 @@ + + + + + + + Index — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + +
+
+
+
+ + +

Index

+ +
+ A + | B + | C + | D + | E + | F + | G + | H + | I + | J + | K + | L + | M + | N + | O + | P + | Q + | R + | S + | T + | U + | V + | W + | X + | Y + | Z + +
+

A

+ + + +
+ +

B

+ + + +
+ +

C

+ + + +
+ +

D

+ + + +
+ +

E

+ + + +
+ +

F

+ + + +
+ +

G

+ + + +
+ +

H

+ + + +
+ +

I

+ + + +
+ +

J

+ + + +
+ +

K

+ + + +
+ +

L

+ + + +
+ +

M

+ + + +
+ +

N

+ + + +
+ +

O

+ + + +
+ +

P

+ + + +
+ +

Q

+ + + +
+ +

R

+ + + +
+ +

S

+ + + +
+ +

T

+ + + +
+ +

U

+ + + +
+ +

V

+ + + +
+ +

W

+ + + +
+ +

X

+ + + +
+ +

Y

+ + + +
+ +

Z

+ + + +
+ + + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/group/group___analysis_function_parameter_helpers.html b/group/group___analysis_function_parameter_helpers.html new file mode 100644 index 0000000000..8c1552e486 --- /dev/null +++ b/group/group___analysis_function_parameter_helpers.html @@ -0,0 +1,318 @@ + + + + + + + + Group AnalysisFunctionParameterHelpers — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Group AnalysisFunctionParameterHelpers

+
+
+group AnalysisFunctionParameterHelpers
+
+

Functions

+
+
+string AFH_GetListOfAnalysisParamNames(string params)
+

Return a semicolon separated list of user parameters.

+
+
Parameters:
+

params – serialized parameters, usually just AnalysisFunction_V3.params

+
+
+
+ +
+
+variable AFH_IsParameterPresent(string name, string params)
+

Check if the given analysis parameter is present.

+
+
Parameters:
+
+
+
Returns:
+

one if present, zero otherwise

+
+
+
+ +
+
+string AFH_GetAnalysisParamType(string name, string params, variable typeCheck = defaultValue, string expectedType = defaultValue)
+

Return the type of the user parameter.

+
+
Parameters:
+
+
+
Returns:
+

one of AnalysisFunctionParameterTypes or an empty string

+
+
+
+ +
+
+variable AFH_GetAnalysisParamNumerical(string name, string params, variable defValue = defaultValue)
+

Return a numerical user parameter.

+
+
Parameters:
+
    +

  • name – parameter name

    • +

  • params – serialized parameters, usually just AnalysisFunction_V3.params

    • +

  • defValue – [optional, defaults to NaN] return this value if the parameter could not be found

    • +
+
+
+
+ +
+
+string AFH_GetAnalysisParamTextual(string name, string params, string defValue = defaultValue, variable percentDecoded = defaultValue)
+

Return a textual user parameter.

+
+
Parameters:
+
    +

  • name – parameter name

    • +

  • params – serialized parameters, usually just AnalysisFunction_V3.params

    • +

  • defValue – [optional, defaults to an empty string] return this value if the parameter could not be found

    • +

  • percentDecoded – [optional, defaults to true] if the return value should be percent decoded or not.

    • +
+
+
+
+ +
+
+wave AFH_GetAnalysisParamWave(string name, string params, wave defValue = defaultValue)
+

Return a numerical wave user parameter.

+
+
Parameters:
+
    +

  • name – parameter name

    • +

  • params – serialized parameters, usually just AnalysisFunction_V3.params

    • +

  • defValue – [optional, defaults to an invalid wave ref] return this value if the parameter could not be found

    • +
+
+
Returns:
+

wave reference to free numeric wave, or invalid wave ref in case the parameter could not be found.

+
+
+
+ +
+
+wave AFH_GetAnalysisParamTextWave(string name, string params, WaveText defValue = defaultValue, variable percentDecoded = defaultValue)
+

Return a textual wave user parameter.

+
+
Parameters:
+
    +

  • name – parameter name

    • +

  • params – serialized parameters, usually just AnalysisFunction_V3.params

    • +

  • defValue – [optional, defaults to an invalid wave ref] return this value if the parameter could not be found

    • +

  • percentDecoded – [optional, defaults to true] if the return value should be percent decoded or not.

    • +
+
+
Returns:
+

wave reference to free text wave, or invalid wave ref in case the parameter could not be found.

+
+
+
+ +
+
+variable AFH_IsValidAnalysisParameter(string name)
+

Check if the given name is a valid user parameter name.

+
+ +
+
+variable AFH_IsValidAnalysisParamType(string type)
+

Check if the given type is a valid user parameter type.

+
+ +
+
+string AFH_GetAnalysisParameter(string name, string params, string expectedType = defaultValue)
+

Return an user parameter’s value as string.

+
+
Parameters:
+
+
+
+
+ +
+
+string AFH_RemoveAnalysisParameter(string name, string params)
+

Delete the given user parameter name.

+
+
Parameters:
+
+
+
Returns:
+

serialized parameters with name removed

+
+
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/group/group___background_functions.html b/group/group___background_functions.html new file mode 100644 index 0000000000..74abf54796 --- /dev/null +++ b/group/group___background_functions.html @@ -0,0 +1,211 @@ + + + + + + + + Group BackgroundFunctions — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Group BackgroundFunctions

+
+
+group BackgroundFunctions
+
+

Functions

+
+
+variable BW_BackgroundWatchdog(WMBackgroundStruct *s)
+

Helper background task for debugging.

+
+ +
+
+variable DQM_FIFOMonitor(BackgroundStruct *s)
+

Fifo monitor for DAQ Multi Device.

+
+ +
+
+variable DQM_Timer(WMBackgroundStruct *s)
+

Background function for tracking ITI.

+
+ +
+
+variable DQS_BkrdDataAcq(string device)
+

Fifo monitor for DAQ Single Device.

+
+ +
+
+variable DQS_FIFOMonitor(WMBackgroundStruct *s)
+

Fifo monitor for DAQ Single Device.

+
+ +
+
+variable DQS_Timer(WMBackgroundStruct *s)
+

Keep track of time during ITI.

+
+ +
+
+variable P_ITC_FIFOMonitorProc(WMBackgroundStruct *s)
+

Monitor the device FIFO and terminates acquisition when sufficient data has been collected.

+
+ +
+
+variable TPM_BkrdTPFuncMD(BackgroundStruct *s)
+

Background TP Multi Device.

+
+ +
+
+variable TPS_TestPulseFunc(BackgroundStruct *s)
+

Background TP Single Device.

+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/group/group___labnotebook_query_functions.html b/group/group___labnotebook_query_functions.html new file mode 100644 index 0000000000..ac5b5e28be --- /dev/null +++ b/group/group___labnotebook_query_functions.html @@ -0,0 +1,585 @@ + + + + + + + + Group LabnotebookQueryFunctions — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Group LabnotebookQueryFunctions

+
+
+group LabnotebookQueryFunctions
+

The labnotebook querying functions can be categorized into the following categories:

+

Return the stored settings of a single sweep. The functions return a wave with LABNOTEBOOK_LAYER_COUNT rows, where the first NUM_HEADSTAGES hold headstage dependent data and the row returned by GetIndexForHeadstageIndepData() the headstage independent data.

+

+

Return the headstage independent data of a single sweep. Trimmed down a special default value in case the setting could not be found.

+

+

If you want to query the information on a per-channel basis the following functions are helpful. They also take care of unassociated channels automatically.

+

+

Return the data of one of the sweeps of a repeated acquistion cycle (RAC). The functions return only the first valid setting searching the sweeps from the end to the begin of the RAC.

+

+

Return the data of all sweeps of a repeated acquistion cycle (RAC) with the following functions:

+

+

All the above functions are concerned with querying data from the labnotebook where the sweep number is known. In case you are looking for data from an arbitrary sweep use one of the following functions:

+

+
+

Functions

+
+
+variable GetLastSettingIndep(wave numericalValues, variable sweepNo, string setting, variable entrySourceType, variable defValue = defaultValue)
+

Return a headstage independent setting from the numerical labnotebook.

+

+

See also

+

GetLastSetting()

+
+

+
+
Returns:
+

the headstage independent setting or defValue

+
+
+
+ +
+
+string GetLastSettingTextIndep(WaveText textualValues, variable sweepNo, string setting, variable entrySourceType, string defValue = defaultValue)
+

Return a headstage independent setting from the textual labnotebook.

+

+

See also

+

GetLastSetting()

+
+

+
+
Returns:
+

the headstage independent setting or defValue

+
+
+
+ +
+
+variable GetLastSettingIndepRAC(wave numericalValues, variable sweepNo, string setting, variable entrySourceType, variable defValue = defaultValue)
+

Return a headstage independent setting from the numerical labnotebook of the sweeps in the same RA cycle.

+

+

See also

+

GetLastSetting()

+
+

+
+
Returns:
+

the headstage independent setting or defValue

+
+
+
+ +
+
+variable GetLastSettingIndepSCI(wave numericalValues, variable sweepNo, string setting, variable headstage, variable entrySourceType, variable defValue = defaultValue)
+

Return a headstage independent setting from the numerical labnotebook of the sweeps in the same SCI cycle.

+

+

See also

+

GetLastSetting()

+
+

+
+
Returns:
+

the headstage independent setting or defValue

+
+
+
+ +
+
+string GetLastSettingTextIndepSCI(wave numericalValues, WaveText textualValues, variable sweepNo, string setting, variable headstage, variable entrySourceType, string defValue = defaultValue)
+

Return a headstage independent setting from the textual labnotebook of the sweeps in the same SCI cycle.

+

+

See also

+

GetLastSetting()

+
+

+
+
Returns:
+

the headstage independent setting or defValue

+
+
+
+ +
+
+string GetLastSettingTextIndepRAC(wave numericalValues, WaveText textualValues, variable sweepNo, string setting, variable entrySourceType, string defValue = defaultValue)
+

Return a headstage independent setting from the numerical labnotebook of the sweeps in the same RA cycle.

+
+
Returns:
+

the headstage independent setting or defValue

+
+
+
+ +
+
+std::tuple<WaveOrNull, variable> GetLastSettingChannel(wave numericalValues, WaveTextOrNull textualValues, variable sweepNo, string setting, variable channelNumber, variable channelType, variable entrySourceType)
+

Return a numerical or text setting for the given channel.

+

It also returns headstage independent entries when the given channel refers to an active channel.

+

+

See also

+

GetLastSettingChannelInternal()

+
+

+
+
Returns:
+

the wave containing the setting and the index into it.

+
+
+
+ +
+
+wave GetLastSetting(wave values, variable sweepNo, string setting, variable entrySourceType)
+

Return a numeric/textual wave with the latest value of a setting from the numerical/labnotebook labnotebook for the given sweep number.

+
+
Parameters:
+
    +

  • values – numerical/textual labnotebook

    • +

  • sweepNo – sweep number

    • +

  • setting – name of the setting to query

    • +

  • entrySourceType – type of the labnotebook entry, one of DataAcqModes. If you don’t care about the entry source type pass UNKNOWN_MODE.

    • +
+
+
Returns:
+

a free wave with LABNOTEBOOK_LAYER_COUNT rows. In case the setting could not be found an invalid wave reference is returned.

+
+
+
+ +
+
+wave GetLastSettingNoCache(wave values, variable sweepNo, string setting, variable entrySourceType, variable *first = defaultValue, variable *last = defaultValue, variable *rowIndex = defaultValue, variable settingCol = defaultValue)
+

Return a wave with the latest value of a setting from the numerical/textual labnotebook for the given sweep number. Uncached version, general users should prefer GetLastSetting().

+
+
Parameters:
+
    +

  • values – numerical/textual labnotebook

    • +

  • sweepNo – sweep number

    • +

  • setting – name of the setting to query

    • +

  • entrySourceType – type of the labnotebook entry, one of DataAcqModes

    • +

  • first – [inout] [optional] Can be used to query and return the labnotebook row range. Useful for routines which must make a lot of queries to the same sweep and want to avoid the overhead of calculating first and last. Passing LABNOTEBOOK_GET_RANGE will set the calculated values of first and last after the function returns. Passing a value greater or equal zero will use these values instead.

    • +

  • last – [inout] [optional] see first

    • +

  • rowIndex – [out] [optional] return the row where the setting could be found, otherwise it is set to LABNOTEBOOK_MISSING_VALUE

    • +

  • settingCol – [optional, default: determined by function] if the caller has already determined the setting column, it can set this argument then GetLastSettingNoCache saves the find

    • +
+
+
Returns:
+

a free wave with LABNOTEBOOK_LAYER_COUNT rows. In case the setting could not be found an invalid wave reference is returned.

+
+
+
+ +
+
+wave GetLastSettingTextRAC(wave numericalValues, WaveText textualValues, variable sweepNo, string setting, variable entrySourceType)
+

Return the last textual value of the sweeps in the same RA cycle.

+

+

See also

+

GetLastSetting()

+
+

+
+ +
+
+wave GetLastSettingRAC(wave numericalValues, variable sweepNo, string setting, variable entrySourceType)
+

Return the last numerical value of the sweeps in the same RA cycle.

+

+

See also

+

GetLastSetting()

+
+

+
+ +
+
+wave GetLastSettingIndepEachRAC(wave numericalValues, variable sweepNo, string setting, variable entrySourceType, variable defValue = defaultValue)
+

Return the last numerical value for the given setting of each sweep in the same RA cycle.

+

The returned wave will have NaN for sweeps which do not have that entry. This is done in order to keep the indizes intact.

+

+

See also

+

GetLastSetting()

+
+

+
+ +
+
+wave GetLastSettingTextIndepEachRAC(wave numericalValues, WaveText textualValues, variable sweepNo, string setting, variable entrySourceType, string defValue = defaultValue)
+

Return the last textual value for the given setting of each sweep in the same RA cycle.

+

The returned wave will have NaN for sweeps which do not have that entry. This is done in order to keep the indizes intact.

+

+

See also

+

GetLastSetting()

+
+

+
+ +
+
+wave GetLastSettingEachRAC(wave numericalValues, variable sweepNo, string setting, variable headstage, variable entrySourceType)
+

Return the last numerical value for the given setting of each sweep for a given headstage in the same RA cycle.

+

The returned wave will have NaN for sweeps which do not have that entry. This is done in order to keep the indizes intact.

+

+

See also

+

GetLastSetting

+
+

+
+ +
+
+wave GetLastSettingTextEachRAC(wave numericalValues, WaveText textualValues, variable sweepNo, string setting, variable headstage, variable entrySourceType)
+

Return the last textual value for the given setting of each sweep for a given headstage in the same RA cycle.

+

The returned wave will have NaN for sweeps which do not have that entry. This is done in order to keep the indizes intact.

+

+

See also

+

GetLastSetting()

+
+

+
+ +
+
+wave GetLastSettingTextSCI(wave numericalValues, WaveText textualValues, variable sweepNo, string setting, variable headstage, variable entrySourceType)
+

Return the last textual value of the sweeps in the same stimset cycle.

+

+

See also

+

GetLastSetting()

+
+

+
+ +
+
+wave GetLastSettingSCI(wave numericalValues, variable sweepNo, string setting, variable headstage, variable entrySourceType)
+

Return the last numerical value of the sweeps in the same stimset cycle.

+

+

See also

+

GetLastSetting()

+
+

+
+ +
+
+wave GetLastSettingIndepEachSCI(wave numericalValues, variable sweepNo, string setting, variable headstage, variable entrySourceType, variable defValue = defaultValue)
+

Return the last numerical value for the given setting of each sweep in the same stimset cycle.

+

The returned wave will have NaN for sweeps which do not have that entry. This is done in order to keep the indizes intact.

+

+

See also

+

GetLastSetting()

+
+

+
+ +
+
+wave GetLastSettingTextIndepEachSCI(wave numericalValues, WaveText textualValues, variable sweepNo, variable headstage, string setting, variable entrySourceType, string defValue = defaultValue)
+

Return the last textual value for the given setting of each sweep in the same stimset cycle.

+

The returned wave will have NaN for sweeps which do not have that entry. This is done in order to keep the indizes intact.

+

+

See also

+

GetLastSetting()

+
+

+
+ +
+
+wave GetLastSettingEachSCI(wave numericalValues, variable sweepNo, string setting, variable headstage, variable entrySourceType)
+

Return the last numerical value for the given setting of each sweep for a given headstage in the same stimset cycle.

+

The returned wave will have NaN for sweeps which do not have that entry. This is done in order to keep the indizes intact.

+

+

See also

+

GetLastSetting

+
+

+
+ +
+
+wave GetLastSettingTextEachSCI(wave numericalValues, WaveText textualValues, variable sweepNo, string setting, variable headstage, variable entrySourceType)
+

Return the last textual value for the given setting of each sweep for a given headstage in the same stimset cycle.

+

The returned wave will have NaN for sweeps which do not have that entry. This is done in order to keep the indizes intact.

+

+

See also

+

GetLastSetting()

+
+

+
+ +
+
+wave GetSweepsWithSetting(wave labnotebookValues, string setting)
+

Return a wave with all sweep numbers which have a non-empty entry for setting.

+
+
Parameters:
+
    +

  • labnotebookValues – numerical/textual labnotebook

    • +

  • setting – name of the value to search

    • +
+
+
Returns:
+

a 1D free wave with the matching sweep numbers. In case the setting could not be found an invalid wave reference is returned.

+
+
+
+ +
+
+wave GetLastSweepWithSetting(wave numericalValues, string setting, variable *sweepNo)
+

Return the last numerical value of a setting from the labnotebook and the sweep it was set.

+
+
Parameters:
+
    +

  • numericalValues – [in] numerical labnotebook

    • +

  • setting – [in] name of the value to search

    • +

  • sweepNo – [out] sweep number the value was last set

    • +
+
+
Returns:
+

a free wave with LABNOTEBOOK_LAYER_COUNT rows. In case the setting could not be found an invalid wave reference is returned.

+
+
+
+ +
+
+variable GetLastSweepWithSettingIndep(wave numericalValues, string setting, variable *sweepNo, variable defValue = defaultValue)
+

Return the last numerical value of a headstage independent setting from the labnotebook and the sweep it was set.

+
+
Parameters:
+
    +

  • numericalValues – [in] numerical labnotebook

    • +

  • setting – [in] name of the value to search

    • +

  • sweepNo – [out] sweep number the value was last set

    • +

  • defValue – [in] [optional, defaults to NaN] value to return in case nothing could be found

    • +
+
+
+
+ +
+
+wave GetLastSweepWithSettingText(WaveText textualValues, string setting, variable *sweepNo)
+

Return the last textual value of a setting from the labnotebook and the sweep it was set.

+
+
Parameters:
+
    +

  • textualValues – [in] textual labnotebook

    • +

  • setting – [in] name of the value to search

    • +

  • sweepNo – [out] sweep number the value was last set

    • +
+
+
Returns:
+

a free wave with LABNOTEBOOK_LAYER_COUNT rows. In case the setting could not be found an invalid wave reference is returned.

+
+
+
+ +
+
+string GetLastSweepWithSettingTextI(wave numericalValues, string setting, variable *sweepNo, string defValue = defaultValue)
+

Return the last textual value of a headstage independent setting from the labnotebook and the sweep it was set.

+
+
Parameters:
+
    +

  • numericalValues – [in] numerical labnotebook

    • +

  • setting – [in] name of the value to search

    • +

  • sweepNo – [out] sweep number the value was last set

    • +

  • defValue – [in] [optional, defaults to an empty string] value to return in case nothing could be found

    • +
+
+
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/group/group___stimset_a_p_i_functions.html b/group/group___stimset_a_p_i_functions.html new file mode 100644 index 0000000000..081047ff5f --- /dev/null +++ b/group/group___stimset_a_p_i_functions.html @@ -0,0 +1,311 @@ + + + + + + + + Group StimsetAPIFunctions — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Group StimsetAPIFunctions

+
+
+group StimsetAPIFunctions
+

Code example: 

Function StimsetAPIExample()
+    string setName, stimsets
+    variable numEpochs
+
+    // create new stimulus set
+    setName = ST_CreateStimSet("myset", CHANNEL_TYPE_DAC)
+
+    // check that it is there
+    stimsets = ST_GetStimsetList(channelType = CHANNEL_TYPE_DAC, searchString = "my*")
+    printf "Stimsets %s\r", stimsets
+
+    // inspect global stimulus parameters
+    WAVE globalParams = ST_GetStimsetParameters(setName)
+    print globalParams
+
+    // use two epochs
+    ST_SetStimsetParameter(setName, "Total number of epochs", var = 2)
+
+    // and three steps/sweeps
+    ST_SetStimsetParameter(setName, "Total number of steps", var = 3)
+
+    // inspect the just set entry
+    numEpochs = ST_GetStimSetParameterAsVariable(setName, "Total number of epochs")
+    printf "Number of epochs: %d\r", numEpochs
+
+    ST_SetStimsetParameter(setName, "Type of Epoch 0", var = EPOCH_TYPE_SQUARE_PULSE)
+    ST_SetStimsetParameter(setName, "Type of Epoch 1", var = EPOCH_TYPE_PULSE_TRAIN)
+
+    // get the list of possible parameters for the square pulse
+    WAVE epochParams = ST_GetStimsetParameters(setName, epochType = EPOCH_TYPE_SQUARE_PULSE)
+    print epochParams
+
+    // and pulse train
+    WAVE epochParams = ST_GetStimsetParameters(setName, epochType = EPOCH_TYPE_PULSE_TRAIN)
+    print epochParams
+
+    // configure square pulse
+    ST_SetStimsetParameter(setName, "Duration", epochIndex = 0, var = 500)
+    ST_SetStimsetParameter(setName, "Amplitude", epochIndex = 0, var = 0)
+
+    // configure pulse train
+    ST_SetStimsetParameter(setName, "Duration", epochIndex = 1, var = 1500)
+    ST_SetStimsetParameter(setName, "Amplitude", epochIndex = 1, var = 1)
+    ST_SetStimsetParameter(setName, "Sin/chirp/saw frequency", epochIndex = 1, var = 10)
+    ST_SetStimsetParameter(setName, "Train pulse duration", epochIndex = 1, var = 20)
+
+    // set an analysis function
+    ST_SetStimsetParameter(setName, "Analysis function (generic)", str = "TestAnalysisFunction_V3")
+
+    // add analysis parameter
+    AFH_AddAnalysisParameter(setName, "myVarParam", var = 1.23456)
+
+    // use an explicit delta list for the ITI
+    ST_SetStimsetParameter(setName, "Inter trial interval op", str = "Explicit")
+    ST_SetStimsetParameter(setName, "Inter trial interval ldel", str = "5;7")
+End
+
+
+

+

+
+

Functions for manipulating stimulus sets

+
+
+string ST_GetStimsetList(variable channelType = defaultValue, string searchString = defaultValue, string *WBstimSetList = defaultValue, string *thirdPartyStimSetList = defaultValue)
+

Return a sorted list of all DA/TTL stim set waves.

+
+
Parameters:
+
    +

  • channelType – [in] [optional, defaults to all] CHANNEL_TYPE_DAC or CHANNEL_TYPE_TTL

    • +

  • searchString – [in] [optional, defaults to “*”] search string in wildcard syntax

    • +

  • WBstimSetList – [out] [optional] returns the list of stim sets built with the wavebuilder

    • +

  • thirdPartyStimSetList – [out] [optional] returns the list of third party stim sets not built with the wavebuilder

    • +
+
+
+
+ +
+
+string ST_CreateStimSet(string baseName, variable stimulusType, variable setNumber = defaultValue, variable saveAsBuiltin = defaultValue)
+

Create a new stimset with one square pulse epoch with 1ms duration.

+
+
Parameters:
+
    +

  • baseName – user choosable part of the stimset name

    • +

  • stimulusType – one of CHANNEL_TYPE_DAC or CHANNEL_TYPE_TTL

    • +

  • setNumber – [optional, defaults to 0] stimset number, allows for convenient alphabetic increasing names used in indexing

    • +

  • saveAsBuiltin – [optional, defaults to false] allows to create builtin stimsets when enabled

    • +
+
+
+
+ +
+
+variable ST_RemoveStimSet(string setName)
+

Remove the given stimulus set and update all relevant GUIs.

+
+ +
+
+wave ST_GetStimsetParameters(string setName, variable epochType = defaultValue)
+

Returns the available stimsets parameters.

+

Return the epoch-independent parameters when epochType is not present.

+
+ +
+
+variable ST_GetStimsetParameterAsVariable(string setName, string entry, variable epochIndex = defaultValue)
+

Return the given stimset numeric parameter.

+
+
Parameters:
+
    +

  • setName – name of the stimset

    • +

  • entry – name of the parameter, can be global or epoch

    • +

  • epochIndex – [optional, when not given this sets global parameters] epoch index (0-based)

    • +
+
+
+
+ +
+
+string ST_GetStimsetParameterAsString(string setName, string entry, variable epochIndex = defaultValue)
+

Return the given stimset string parameter.

+
+
Parameters:
+
    +

  • setName – name of the stimset

    • +

  • entry – name of the parameter, can be global or epoch

    • +

  • epochIndex – [optional, when not given this sets global parameters] epoch index (0-based)

    • +
+
+
+
+ +
+
+variable ST_SetStimsetParameter(string setName, string entry, variable epochIndex = defaultValue, variable var = defaultValue, string str = defaultValue)
+

Set the given stimset parameter.

+

If you use this function in analysis functions be sure to use an event which happens before the stimset is read, for example PRE_DAQ_EVENT, PRE_SET_EVENT or PRE_SWEEP_CONFIG_EVENT. The last one is always called for each sweep before it is configured.

+
+
Parameters:
+
    +

  • setName – name of the stimset

    • +

  • entry – name of the parameter, can be global or epoch

    • +

  • epochIndex – [optional, when not given this sets global parameters] epoch index (0-based)

    • +

  • var – [optional, one of var/str must be present] numeric parameter to set

    • +

  • str – [optional, one of var/str must be present] string parameter to set

    • +
+
+
Returns:
+

0 on success, 1 on error

+
+
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/group/group___wave_versioning_support.html b/group/group___wave_versioning_support.html new file mode 100644 index 0000000000..9a506c3b77 --- /dev/null +++ b/group/group___wave_versioning_support.html @@ -0,0 +1,319 @@ + + + + + + + + Group WaveVersioningSupport — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Group WaveVersioningSupport

+
+
+group WaveVersioningSupport
+

The wave getter functions always return an existing wave. This can result in problems if the layout of the wave changes.

+

Layout in this context means:

    +

  • Sizes of all dimensions

    • +

  • Labels of all dimensions

    • +

  • Wave data type

    • +

  • Prefilled wave content or wave note

    • +
+

+

This also means that the name and location of the wave does not influence the wave version. Use UpgradeWaveLocationAndGetIt() if you need to move the wave. The main reason is that for being able to query the wave version you already need to know where it is.

+

In order to enable smooth upgrades between old and new wave layouts the following code pattern can be used: 

Function/Wave GetMyWave(device)
+    string device
+
+    DFREF dfr = GetMyPath(device)
+    variable versionOfNewWave = 2
+
+    Wave/Z/SDFR=dfr wv = myWave
+
+    if(ExistsWithCorrectLayoutVersion(wv, versionOfNewWave))
+        return wv
+    elseif(WaveExists(wv)) // handle upgrade
+        if(WaveVersionIsAtLeast(wv, 1)) // 1->2
+            Redimension/D wv
+        else // no-version->2
+            // change the required dimensions and leave all others untouched with -1
+            // the extended dimensions are initialized with zero
+            Redimension/D/N=(10, -1, -1, -1) wv
+        endif
+    else
+        Make/R/N=(10, 2) dfr:myWave/Wave=wv
+    endif
+
+    SetWaveVersion(wv, versionOfNewWave)
+
+    return wv
+End
+
+
+

+

+

Now everytime the layout of myWave changes, raise versionOfNewWave by 1 and add a new WaveVersionIsAtLeast branch. When GetMyWave is called the first time, the wave is redimensioned or rebuilt as double wave depending on the current version, and on successive calls the wave is returned as is.

+

Hints:

    +

  • Wave layout versioning is mandatory if you change the layout of the wave

    • +

  • Wave layout versions start with 1 and are integers

    • +

  • Rule of thumb: Raise the version if you change anything in or below the Make line

    • +

  • Wave versioning needs a special wave note style, see GetNumberFromWaveNote

    • +
+

+
+

Functions

+
+
+static variable ExistsWithCorrectLayoutVersion(WaveOrNull wv, variable versionOfNewWave)
+

Check if wv exists and has the correct version UTF_NOINSTRUMENTATION.

+
+ +
+
+static variable WaveVersionIsAtLeast(WaveOrNull wv, variable existingVersion)
+

Check if the given wave’s version is equal or larger than the given version, if version is not set false is returned.

+
+ +
+
+static variable IsWaveVersioned(wave wv)
+

Returns 1 if the wave has a valid version information attached, 0 otherwise.

+
+ +
+
+static variable WaveVersionIsSmaller(WaveOrNull wv, variable existingVersion)
+

Check if the given wave’s version is smaller than the given version, if version is not set true is returned.

+
+ +
+
+variable GetWaveVersion(WaveOrNull wv)
+

return the Version of the Wave, returns NaN if no version was set UTF_NOINSTRUMENTATION

+
+ +
+
+static variable SetWaveVersion(wave wv, variable val)
+

Set the wave layout version of wave.

+
+ +
+
+static variable IsValidWaveVersion(variable value)
+

A valid wave version is a positive non-zero integer.

+
+ +
+
+variable ClearWaveNoteExceptWaveVersion(wave wv)
+

Clear the wave note but keep any valid wave version.

+
+ +
+
+dfref UpgradeDataFolderLocation(string oldFolder, string newFolder)
+

Move/Rename a datafolder across different locations.

+

Both parameters must be absolute datafolder locations. Cases where both exist are also handled gracefully.

+

Function/DF GetMyFolder()
+    return UpgradeDataFolderLocation("root:old", "root:new")
+End
+
+
+

+
+
Returns:
+

DFREF to the newFolder with the contents of oldFolder

+
+
+
+ +
+
+wave UpgradeWaveLocationAndGetIt(WaveLocationMod *p)
+

Rename/Move a wave to a new location.

+

Valid transformations (and all combinations of them):

    +

  • Moving into a new datafolder

    • +

  • Renaming to a new name

    • +

  • Nothing

    • +
+

+

The function is idempotent (i.e. it can be called also on already relocated waves). Cases where new == old are also handled gracefully.

+

Function/WAVE GetMyWave(device)
+    string device
+
+    variable versionOfNewWave = 1
+    string newName = "newAndNiceName"
+    DFREF newDFR = GetNewAndFancyFolder(device)
+
+    STRUCT WaveLocationMod p
+    p.dfr     = $(GetSomeFolder(device) + ":oldSubFolder")
+    p.newDFR  = newDFR
+    p.name    = "oldAndUglyName"
+    p.newName = newName
+
+    WAVE/Z wv = UpgradeWaveLocationAndGetIt(p)
+
+    if(ExistsWithCorrectLayoutVersion(wv, versionOfNewWave))
+        return wv
+    elseif(WaveExists(wv))
+        // handle upgrade
+    else
+        Make/R/N=(10, 2) newDFR:newName/Wave=wv
+    end
+
+    SetWaveVersion(wv, versionOfNewWave)
+
+    return wv
+End
+
+
+

+
+
Returns:
+

wave reference to the wave in the new location, an invalid one if the wave does not exist at the specified former location

+
+
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/grouplist.html b/grouplist.html new file mode 100644 index 0000000000..02a8bfa1e2 --- /dev/null +++ b/grouplist.html @@ -0,0 +1,218 @@ + + + + + + + + Group list — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Group list

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/index.html b/index.html new file mode 100644 index 0000000000..d465cd0bac --- /dev/null +++ b/index.html @@ -0,0 +1,144 @@ + + + + + + + + Table of Contents — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Table of Contents

+
+ +
+

The user documentation can be reached at User documentation, developer documentation is everything else. +The documentation for the ZeroMQ-XOP is located here.

+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/installation.html b/installation.html new file mode 100644 index 0000000000..01d3ba4c62 --- /dev/null +++ b/installation.html @@ -0,0 +1,363 @@ + + + + + + + + Installation instructions — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Installation instructions

+
+

Installing Igor Pro

+

Requirements: Windows 10 64bit or MaxOSX 64bit (analysis only)

+ +
+
+

Igor Pro Update Nightly

+

We rely on a fixed intermediate Igor Pro version. This is not available as +installer package but only as zip file.

+
+

Update steps

+
    +

  • When you open a new MIES version you might get the following message in the history:

    +
    +
    Your Igor Pro version is too old to be usable for MIES.
+
    +
    +
    +
    • +
+

and a dialog appears with a button which opens this documentation.

+

In that case please perform the following steps:

+
    +

  • Download the package for Igor Pro 9 (Windows) or Igor Pro 9 (MacOSX). +Either from within Igor Pro or from a web browser.

    • +

  • Close Igor Pro

    • +
  • +
    Windows: Replace the folders IgorBinaries_x64 and IgorBinaries_Win32

    in C:\Program Files\WaveMetrics\Igor Pro 9 with the ones from the +downloaded zip package. This requires admin access.

    +
    +
    +
    • +

  • MacOSX: Install from image as usual

    • +

  • Restart Igor Pro

    • +
+
+
+
+

Installation using the installer (preferred)

+

Select the installer for the latest release from here.

+

Pressure control may be implemented with ITC and/or NIDAQ hardware. For +NIDAQ hardware, install the NIDAQ Tool +MX +package from Wavemetrics.

+

Install version 2.2.2 of the Multiclamp Commander (64bit) from here.

+
+

Signed installer

+

Starting with release 2.3 the installer executable is signed with an Extended +Validation (EV) Code Signing certificate. See Wikipedia +for more information. Signing the installer should avoid most issues with +antivirus software treating the MIES installer as potentially malicious. The +public key of the certificate can be downloaded from here.

+
+
+

Silent installation

+

The installer is developed using NSIS which also +supports silent installation. The installer requires admin privileges also with +silent installation.

+

To perform a silent installation pass the /S command line option which will +install with the following settings:

+
    +

  • Install for Igor Pro 9 64bit

    • +

  • Admin installation into %PROGRAMFILES%MIES for the current user, pass /ALLUSER to install for all users

    • +

  • Install all Hardware XOPs

    • +
+

Previously existing MIES installations of the admin will be silently uninstalled.

+
+
+

Installer details and limitations

+

The installer uses the Nullsoft Installer System NSIS. +NSIS allows to create installers that require admin privileges and installers that +run with user privileges only. By default an installer requiring admin privileges +is created by executing tools/create-installer.sh from a MingW64 bash. +With tools/create-installer.sh 1 a user mode installer can be created.

+

The installer tries to detect if and where the required Igor Pro versions are is installed. +It defaults then to the 64-bit version if the found Igor Pro(s) which is reflected +in the default selection of the corresponding installer dialog. In silent mode the +found defaults are automatically used. If in silent mode no Igor Pro installations are +detected then only the main MIES files get installed.

+
+

Installer with admin privileges

+

When run as user the installer asks for privilege elevation.

+

Installs by default to the user folder e.g. \Users\Admin\Documents\MIES folder. +Igor Pro integration through shortcuts is put to the user Igor Pro procedures/extension folders in +\Users\Admin\Documents\WaveMetrics\Igor Pro X Folder.

+

Installs with /ALLUSER or corresponding dialog selection to the \Program Files\MIES folder. +Igor Pro integration through shortcuts is put to the global Igor Pro procedures/extension folders in +\Program Files\Wavemetrics\Igor Pro X Folder.

+

Prior installation it is detected by checking the installed programs list of windows (Apps & Features) +if MIES is already installed. If it is installed then the uninstaller is called first. +If the installation was run silent then the uninstaller is also called silent.

+

A limitation is that the installer can not detect if another user has a user installation of MIES. +Thus such installation will remain in parallel and result in a double installation for that user (global and local). +The local installation of this user has to be uninstalled. This can be done when the user is logged in through +windows Apps & Features.

+
+
+

Installer with user privileges

+

Installs by default to the user folder e.g. \Users\User\Documents\MIES folder. +Igor Pro integration through shortcuts is put to the user Igor Pro procedures/extension folders in +\Users\User\Documents\WaveMetrics\Igor Pro X Folder.

+

Installation for all users is not supported as it would require administrative privileges. +Thus the dialog option is greyed out. When /ALLUSER is specified an error message is shown. +If /ALLUSER and /S for silent installation is specified the installer silently quits.

+

Prior installation it is detected by checking the installed programs list of windows (Apps & Features) +if MIES is already installed. If it is installed then the uninstaller is called first. +If the installation was run silent then the uninstaller is also called silent. +The user can only uninstall previous installations from himself. If the previous installation +was done by an admin the uninstaller will ask for privilege elevation.

+
+
+

Corrupted installations

+

After the installer has called a potential uninstaller it checks if the target Igor Pro procedures folder +for the MIES integration has no shortcut to MIES. If there still exists a shortcut to MIES then further installation +is aborted. The graphical installer gives a message box requesting a manual cleanup. +Such case typically happens if shortcuts in the Igor Pro folders for integrating MIES were created manually. +Then the shortcuts have to be removed manually first before a MIES installation is run.

+
+
+
+
+

Manual Installation

+

The manual installation instructions are here for historical/compatibility +reasons or in case you are on MacOSX. Windows users should always prefer to +install via the Installer package.

+
+

Windows (with hardware support)

+

Install the Visual C++ Redistributable package <https://github.com/AllenInstitute/MIES/blob/main/tools/installer/vc_redist.x64.exe>`__.

+
    +

  • Quit Igor Pro

    • +

  • Create the following shortcuts in C:\Users\$username\Documents\WaveMetrics\Igor Pro 9 User Files

    +
      +

    • In User Procedures a shortcut pointing to

      +
        +

      • Packages\IPNWB

        • +

      • Packages\MIES

        • +
      +
      • +

    • In Igor Procedures a shortcut pointing to Packages\MIES_Include.ipf

      • +

    • In Igor Extensions (64-bit) a shortcut pointing to XOPs-IP9-64bit

      • +

    • In Igor Help Files a shortcut pointing to HelpFiles-IP9

      • +
    +
    • +

  • Start Igor Pro

    • +
+
+
+

Windows (without hardware)

+

In case you don’t have the hardware connected/available which some XOPs +require, you can also install MIES without any hardware related XOPs present.

+

Install the Visual C++ Redistributable package <https://github.com/AllenInstitute/MIES/blob/main/tools/installer/vc_redist.x64.exe>`__.

+
    +

  • Quit Igor Pro

    • +

  • Create the following shortcuts in +C:\Users\$username\Documents\WaveMetrics\Igor Pro 9 User Files

    +
      +

    • In User Procedures a shortcut pointing to

      +
        +

      • Packages\IPNWB

        • +

      • Packages\MIES

        • +
      +
      • +

    • In Igor Procedures a shortcut pointing to Packages\MIES_Include.ipf

      • +

    • In Igor Extensions (64-bit) a shortcut pointing to

      +
        +

      • XOPs-IP9-64bit\JSON-64.xop

        • +

      • XOPs-IP9-64bit\MIESUtils-64.xop

        • +

      • XOPs-IP9-64bit\ZeroMQ-64.xop

        • +

      • XOPs-IP9-64bit\TUFXOP-64.xop

        • +

      • XOPs-IP9-64bit\mies-nwb2-compound-XOP-64.xop

        • +
      +
      • +

    • In Igor Help Files a shortcut pointing to HelpFiles-IP9

      • +
    +
    • +

  • Start Igor Pro

    • +
+
+
+

MacOSX (without hardware)

+

Analysis support only. Data acquisition and NWBv2 export are not supported on MacOSx.

+
    +

  • Quit Igor Pro

    • +

  • Get the MIES source code, see +here +for instructions.

    • +

  • Create the following symlinks in +/Users/$username/Documents/WaveMetrics/Igor Pro 9 User Files

    +
      +

    • In User Procedures a symlink pointing to

      +
        +

      • Packages/IPNWB

        • +

      • Packages/MIES

        • +
      +
      • +

    • In Igor Procedures a symlink pointing to Packages\MIES_Include.ipf

      • +

    • In Igor Extensions (64-bit) a symlink pointing to

      +
        +

      • XOPs-MacOSX-IP9-64bit

        • +
      +
      • +

    • In Igor Help Files a shortcut pointing to HelpFiles-IP9

      • +
    +
    • +

  • Start Igor Pro

    • +
+
+
+
+ + +
+
+
+
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Labnotebook descriptions

+ + ++++++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Numerical entries

Name

Unit

Tolerance

Description

Headstage Contingency

ClampMode

SweepNum

    +
  • +
+

Sweep number: Non-repeating non-negative numeric identifier for sweep time series. Increments in the order of acquisition. Starts at zero.

ALL

TimeStamp

s

    +
  • +
+

Time Stamp: Seconds since Igor epoch (1/1/1904) in local time zone with millisecond precision. Written at time of labnotebook entry.

ALL

TimeStampSinceIgorEpochUTC

s

    +
  • +
+

Time Stamp: Seconds since Igor epoch (1/1/1904) in coordinated universal time zone (UTC) with millisecond precision. Written at time of labnotebook entry.

ALL

EntrySourceType

    +
  • +
+

Entry source type: type of the labnotebook entry, 0 for data acquisition, 1 for test pulse, NaN for all other types including user entries.

ALL

AcquisitionState

    +
  • +
+

Stores the current numbered state of data acquistion.

ALL

TP Baseline Vm

mV

1

Testpulse Baseline: Average membrane potential, see https://alleninstitute.github.io/MIES/CalculateTPLikePropsFromSweep.html

DEPEND

IC;I=0

TP Baseline pA

pA

50

Testpulse Baseline: Average holding current, see https://alleninstitute.github.io/MIES/CalculateTPLikePropsFromSweep.html

DEPEND

VC

TP Peak Resistance

MΩ

runtime

Testpulse Peak Resistance: Instantaneous resistance measurement calculated from testpulse profil, https://alleninstitute.github.io/MIES/CalculateTPLikePropsFromSweep.html

DEPEND

TP Steady State Resistance

MΩ

runtime

Testpulse Steady State Resistance: Resistance measurement obtained from the end of the applied testpulse profile, see https://alleninstitute.github.io/MIES/CalculateTPLikePropsFromSweep.html

DEPEND

Fast compensation capacitance

F

1e-12

Fast capacitance compensation: Cp Fast sets the parameters of current injected into the headstage atvoltage steps to charge (and discharge) the fast component of electrodecapacitance. The adjustable fields display estimates of the magnitudeand time constant for this capacitance.

+

For theoretical details see the MultiClamp700B Manual.

+

DEPEND

Slow compensation capacitance

F

1e-12

Slow capacitance compensation: Settings for Cp Slow determine the parameters of current injected intothe headstage at voltage steps to charge and discharge the slow componentof electrode capacitance. The adjustable fields display estimates of themagnitude and time constant for this capacitance.

+

For theoretical details see the MultiClamp700B Manual.

+

DEPEND

Fast compensation time

s

1e-6

Fast compensation time: Time constant for Fast compensation

+

For theoretical details see the MultiClamp700B Manual.

+

DEPEND

Slow compensation time

s

1e-6

Slow compensation time: Time constant for slow compensation

+

For theoretical details see the MultiClamp700B Manual.

+

DEPEND

Headstage Active

On/Off

    +
  • +
+

Headtage Active State: Specifies if the hardware associated with the headstage is in use.

DEPEND

DAC

0.1

Digital Analog Channel used for testpulse or data acquisition

ALL

ADC

0.1

Analog digital channel used for testpulse or data acquisition

ALL

Clamp Mode

    +
  • +
+

Amplifier clamp state: One of 0 (VC aka Voltage Clamp), 1 (IC aka Current Clamp), 2 (I=0 aka I Equal Zero)

ALL

TP Baseline Fraction

0.01

Testpulse baseline fraction: Fraction of the full test pulse length used for baseline. Proportional to test pulse repeat frequency f = ???.

+

See also https://alleninstitute.github.io/MIES/CalculateTPLikePropsFromSweep.html

+

INDEP

TP Amplitude VC

pA

    +
  • +
+

Testpulse Amplitude: Current injected during testpulse

DEPEND

VC

TP Amplitude IC

mV

    +
  • +
+

Testpulse Amplitude: Applied potential relative to the holding potential of the amplifier.

+

See also https://alleninstitute.github.io/MIES/CalculateTPLikePropsFromSweep.html.

+

DEPEND

IC;I=0

TP Pulse Duration

ms

    +
  • +
+

Duration of the applied testpulse without baseline.

+

See also https://alleninstitute.github.io/MIES/CalculateTPLikePropsFromSweep.html.

+

INDEP

Stim Scale Factor

.0001

Scalar applied to the stimulus set at acquisition time.

ALL

DA Gain

.000001

Digital Analog amplifier gain: Termed external command sensitivity in the Multiclamp Commander.

+

For theoretical details see the MultiClamp700B Manual.

+

ALL

AD Gain

.000001

Analog digital amplifier gain for current and voltag clamp.

+

For theoretical details see the MultiClamp700B Manual.

+

ALL

Set Sweep Count

0.1

Non-negative sweep (timeseries) index for the stimulus set.

ALL

TP Insert Checkbox

On/Off

    +
  • +
+

Inserted Testpulse:

INDEP

Inter-trial interval

s

0.01

Target interval for consecutive sweeps, start to start, in seconds

INDEP

Inter-trial interval (effective)

s

    +
  • +
+

Realised interval for consecutive sweeps, start to start, in seconds including repurposed time

INDEP

TTL rack zero bits

bit mask

    +
  • +
+

ITC hardware specific: Bit mask for active DAEphys TTL channels of rack zero.

+

See also https://alleninstitute.github.io/MIES/file/_m_i_e_s___mies_utilities_8ipf.html?highlight=getttlbits#_CPPv310GetTTLBits4wave8variable8variable and https://alleninstitute.github.io/MIES/file/_m_i_e_s___mies_utilities_8ipf.html?highlight=getttlstimsets#_CPPv314GetTTLStimSets4wave4wave8variable.

+

INDEP

TTL rack one bits

bit mask

    +
  • +
+

ITC hardware specific: Bit mask for active DAEphys TTL channels of rack one.

+

See also https://alleninstitute.github.io/MIES/file/_m_i_e_s___mies_utilities_8ipf.html?highlight=getttlbits#_CPPv310GetTTLBits4wave8variable8variable and https://alleninstitute.github.io/MIES/file/_m_i_e_s___mies_utilities_8ipf.html?highlight=getttlstimsets#_CPPv314GetTTLStimSets4wave4wave8variable.

+

INDEP

TTL rack zero channel

    +
  • +
+

ITC hardware specific: ITC XOP TTL hardware channel for rack zero, e.g., ITC 1600 = 0, ITC 18USB = 1

INDEP

TTL rack one channel

    +
  • +
+

ITC hardware specific: ITC XOP TTL hardware channel for rack one, e.g., ITC 1600 = 3. Of the ITC devices, only the ITC1600 can have up to two racks.

INDEP

Delay onset user

ms

1

User defined delay of stimset onset in milliseconds across all active channels. Occurs immediately after an optionally inserted Testpulse. Output is constant zero during the delay.

+

See https://alleninstitute.github.io/MIES/#id2 for a visualization of the sweep delays during data acquisition.

+

INDEP

Delay onset auto

ms

1

Automatically defined delay in milliseconds due to the Testpulse (optionally) inserted at sweep onset.

+

See https://alleninstitute.github.io/MIES/#id2 for a visualization of the sweep delays during data acquisition.

+

INDEP

Delay termination

ms

1

User defined delay of sweep termination in milliseconds across all active channels. Occurs immediately after stimulus set termination. Output is constant zero during the delay.

+

See https://alleninstitute.github.io/MIES/#id2 for a visualization of the sweep delays during data acquisition.

+

INDEP

Delay distributed DAQ

ms

1

Distributed data acquisition distributes in time the selected stimsets across all active channels in a single sweep. The delay is the time in milliseconds between stimsets on each active channel.

+

See https://alleninstitute.github.io/MIES/index.html#id3 for visualization of the delay.

+

INDEP

Distributed DAQ

On/Off

    +
  • +
+

Distributed data acquisition distributes in time the selected stimsets across all active channels in a single sweep.

+

See https://alleninstitute.github.io/MIES/index.html#id3 for visualization of the delay.

+

INDEP

Repeat Sets

1

User defined value that sets the minimum number of times a stimulus set is acquired within a repeated acquisition cycle.

+

See https://alleninstitute.github.io/MIES/index.html#id1 for a visualisation of set repetition and indexing.

+

INDEP

Scaling zero

On/Off

    +
  • +
+

The DA scaling for active channels is set to zero after the stimulus set has cycled once. Only applies with locked indexing.

+

See https://alleninstitute.github.io/MIES/index.html#id1 for a visualisation of scaling to zero.

+

INDEP

Indexing

On/Off

    +
  • +
+

Enables the acquistion of multiple stimulus sets, for an active channel, on a single repeated acquisition cycle.

+

See https://alleninstitute.github.io/MIES/index.html#id1 for a visualisation of indexing.

+

INDEP

Locked indexing

On/Off

    +
  • +
+

Enables the acquistion of multiple stimulus sets, for an active channel, on a single repeated acquisition cycle. +A special form of indexing where the transition to the next stimulus set happens on the same sweep for all active channels.

+

See https://alleninstitute.github.io/MIES/index.html#id1 for a visualisation of indexing.

+

INDEP

Repeated Acquisition

On/Off

    +
  • +
+

Automated acquisition of more than one sweep.

+

See https://alleninstitute.github.io/MIES/index.html#id1 for a visualisation of repeated acquisition.

+

INDEP

Random Repeated Acquisition

On/Off

    +
  • +
+

Randomizes the sweep acquisition order within a stimulus set.

+

See https://alleninstitute.github.io/MIES/index.html#id1 for a visualisation of indexing.

+

INDEP

Sampling interval DA

ms

1

Time interval between consecutive DA data points.

INDEP

Sampling interval AD

ms

1

Time interval between consecutive AD data points.

INDEP

Sampling interval TTL

ms

1

Time interval between consecutive TTL data points.

INDEP

Sampling interval multiplier

0.1

The hardware limited minimum interval between consecutive data points is called the minimum sampling interval. +This interval can be prolonged by the user configured sampling interval multiplier.

INDEP

Stim set length

0.1

Number of points in each sweep of the stimulus set. This is determined by the acquisition sampling interval.

ALL

oodDAQ Pre Feature

ms

1

oodDAQ pre delay is the leading time envelope for non-zero parts of the stimulus set sweeps.

+

See https://alleninstitute.github.io/MIES/#id4 for a visualisation of oodDAQ.

+

INDEP

oodDAQ Post Feature

ms

1

oodDAQ post delay is the trailing time envelope for non-zero parts of the stimulus set sweeps.

+

See https://alleninstitute.github.io/MIES/#id4 for a visualisation of oodDAQ.

+

INDEP

oodDAQ Resolution

ms

1

The minimum search step for the oodDAQ time offset calculation.

+

See https://alleninstitute.github.io/MIES/#id4 for a visualisation of oodDAQ.

+

INDEP

Optimized Overlap dDAQ

On/Off

    +
  • +
+

Optimized overlap distributed data acquisition (oodDAQ) offsets in time stimulus set sweeps across headstages. The offset is determined such that the non-zero parts, plus user defined envelope (pre and post delay), of the stimset sweeps don’t overlap on different headstages.

+

See https://alleninstitute.github.io/MIES/#id4 for a visualisation of oodDAQ.

+

INDEP

Delay onset oodDAQ

ms

1

Calculated total oodDAQ offset used for acquisition.

+

See https://alleninstitute.github.io/MIES/#id4 for a visualisation of oodDAQ.

+

DEPEND

Pulse To Pulse Length

ms

1

Not used in newer MIES versions.

ALL

Repeated Acq Cycle ID

1

The “Repeated Acq Cycle ID” labels each repeated acquisition with a unique integer number. +Sweeps belonging to the same repeated acquisition cycle have the same ID. +For yoked devices the follower and lead devices will have the same ID, +which also helps in that case to group sweeps together.

INDEP

Stim Wave Checksum

1

The “Stim Wave Checksum” is a unique identifier for the stimulus set contents.

+

Changes in this ID catches cases where the stimset has the same name but different contents.

+

DEPEND

Multi Device mode

On/Off

    +
  • +
+

Support for multiple DAQ devices acquiring data simultaneously. When turned off, legacy single device mode is used.

INDEP

Background Testpulse

On/Off

    +
  • +
+

When enabled, a running testpulse does not block the Igor Pro user interface.

INDEP

Background DAQ

On/Off

    +
  • +
+

When enabled, data acquisition does not block the Igor Pro user interface.

INDEP

TP buffer size

0.1

Size of the running average window for the testpulse results.

INDEP

TP during ITI

On/Off

    +
  • +
+

When checked the testpulse runs during the inter-trial-interval.

INDEP

Amplifier change via I=0

On/Off

    +
  • +
+

Switching between voltage and current clamp passes through I=0 mode if enabled.

+

For theoretical details see the MultiClamp700B Manual.

+

INDEP

Skip analysis functions

On/Off

    +
  • +
+

Analysis functions attached to simulus sets are not called when enabled.

INDEP

Repeat sweep on async alarm

On/Off

    +
  • +
+

When an asynchronous’ channel alarm is triggered (user configurable) the last sweep is continously reacquired until the alarm state is cleared.

INDEP

TP after DAQ

On/Off

    +
  • +
+

Run the testpulse immediately after data acquisition finished or was stopped prematurely.

INDEP

Set Cycle Count

1

The number of stimulus set repetitions in one repeated acquisition cycle.

DEPEND

Stimset Acq Cycle ID

1

+
+
This identifier changes if one of the folllowing properties change:
    +

  • Repeated acquisition cycle ID

    • +

  • Stimulus set

    • +

  • Stimulus set checksum

    • +

  • Stimulus set cycle count

    • +
+
+
+
+

The primary use case is for querying all labnotebook entries of all sweeps from the current set. +In analysis function terms all sweeps which are acquired between pre set event and post set event, see +also https://alleninstitute.github.io/MIES/file/_m_i_e_s___analysis_functions_8ipf.html.

+

A visualisation is available at https://alleninstitute.github.io/MIES/#id1.

+

DEPEND

DAQ stop reason

    +
  • +
+

Documents why data acquisition was stopped.

INDEP

Digitizer Hardware Type

1

Hardware type (integer) of the DAEphys panel digitizer.

INDEP

Fixed frequency acquisition

kHz

1

The sampling frequency of the digitizer in kHz when fixed frequency acquisition is enabled.

INDEP

Igor Pro bitness

    +
  • +
+

Architecture bitness (32 or 64) of Igor Pro.

INDEP

DA ChannelType

1

Acquisition mode of the given DA channel. Can be one of Testpulse (2), data acquisition (1) or unknown (-1).

DEPEND

AD ChannelType

1

Acquisition mode of the given AD channel. Can be one of Testpulse (2), data acquisition (1) or unknown (-1).

DEPEND

oodDAQ member

On/Off

    +
  • +
+

Set to one for headstages taking part in oodDAQ, set to zero for TP during DAQ headstages.

DEPEND

V-Clamp Holding Enable

On/Off

    +
  • +
+

Enables the holding potential in Voltage Clamp.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

VC

V-Clamp Holding Level

mV

0.9

Holding potential in Voltage Clamp.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

VC

Osc Killer Enable

On/Off

    +
  • +
+

Disables or reduces capacitance neutralization (Current Clamp) or RS compensation (Voltage Clamp) when oscillations are detected.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC;VC

RsComp Bandwidth

Hz

0.9

The lowpass filter cutoff frequency of the series compensation signal.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

VC

RsComp Correction

%

0.9

Percentage of active series resistance compensation applied.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

VC

RsComp Enable

On/Off

    +
  • +
+

Compensates the series resistance in voltage clamp.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

VC

RsComp Prediction

%

0.9

Open loop amplification of output current transient.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

VC

Whole Cell Comp Enable

On/Off

    +
  • +
+

Voltage clamp whole cell capacitance and resistance compensation.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

VC

Whole Cell Comp Cap

pF

0.9

Voltage clamp capacitance for whole cell compensation.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

VC

Whole Cell Comp Resist

MΩ

0.9

Voltage clamp resistance for whole cell compensation.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

VC

I-Clamp Holding Enable

On/Off

    +
  • +
+

Bias current in current clamp.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC

I-Clamp Holding Level

pA

0.9

Bias current level in current clamp.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC

Neut Cap Enabled

On/Off

    +
  • +
+

Pipette Capacitance Neutralization.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC

Neut Cap Value

pF

0.9

User defined pipette capacitance.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC

Bridge Bal Enable

On/Off

    +
  • +
+

Pipette series resistance bridge balance.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC

Bridge Bal Value

MΩ

0.9

User defined pipette series resistance.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC

Serial Number

    +
  • +
+

Vendor defined amplifier serial number. More than one headstage can share one amplifier.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC;VC;I=0

Channel ID

    +
  • +
+

Amplifier headstage channel. Unique for each headstage of a given amplifier.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC;VC;I=0

ComPort ID

    +
  • +
+

Always -1 for 700B amplifiers.

DEPEND

IC;VC;I=0

AxoBus ID

    +
  • +
+

Always -1 for 700B amplifiers.

DEPEND

IC;VC;I=0

Operating Mode

    +
  • +
+

Clamp mode of the headstage.

DEPEND

IC;VC;I=0

Scaled Out Signal

    +
  • +
+

Type of output signal:

+
    +

  • Membrane Current

    • +

  • Membrane Potential

    • +

  • Pipette Potential

    • +

  • 100x AC Membrane Potential

    • +

  • External Command Potential

    • +

  • Auxiliary 1 Potential

    • +

  • Auxiliary 2 Current

    • +
+

DEPEND

IC;VC;I=0

Alpha

    +
  • +
+

Output gain for primary output signal.

DEPEND

IC;VC;I=0

Scale Factor

    +
  • +
+

Gain scale factor (for Alpha == 1) of primary output signal

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC;VC;I=0

Scale Factor Units

    +
  • +
+

Units of the scaled output signal

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC;VC;I=0

LPF Cutoff

    +
  • +
+

Primary output low pass filter cut off value (Bessel)

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC;VC;I=0

Membrane Cap

pF

0.9

User configured whole cell membrane capacitance.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

VC

Ext Cmd Sens

    +
  • +
+

Scaling between the external command voltage sent to the COMMAND input BNCs on the amplifier front panel, and voltage or current steps delivered to the cell.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC;VC

Raw Out Signal

    +
  • +
+

User configured signal type of secondary output

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC;VC;I=0

Raw Scale Factor

    +
  • +
+

Gain scale factor (for Alpha == 1) of secondary output signal.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC;VC;I=0

Raw Scale Factor Units

    +
  • +
+

Number denoting the unit of the Raw Scale Factor.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC;VC;I=0

Hardware Type

    +
  • +
+

Identifier of the amplifier hardware, will be 1 for the 700B. A string version is available in the textual labnotebook as “HardwareTypeString”.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC;VC;I=0

Secondary Alpha

    +
  • +
+

Output gain for secondary output

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC;VC;I=0

Secondary LPF Cutoff

    +
  • +
+

Secondary output lowpass filter cutoff frequency, in Hz.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC;VC;I=0

Series Resistance

MΩ

    +
  • +
+

Measured series resistance

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC;VC;I=0

Pipette Offset

mV

0.1

Removes the differential voltage between the ground and the pipette.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC;VC;I=0

Slow current injection

On/Off

    +
  • +
+

Varies holding level to hit a certain voltage.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC

Slow current injection level

V

0.1

Holding level for “Slow current injection”.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC

Slow current injection settling time

s

    +
  • +
+

Time constant for “Slow current injection”.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

IC

Autobias Vcom

mV

0.1

During the inter trial interval (“ITI”) autobias adjusts the holding current to maintain the user defined “Autobias Vcom” within “Autobias Vcom variance”. The autobias evaluates a user defined part (“Autobias (%)”) of the Testpulse baseline at the “Autobias Interval” (DaEphys->Settings->Amplifier).

DEPEND

IC

Autobias Vcom variance

mV

0.1

During the inter trial interval (“ITI”) autobias adjusts the holding current to maintain the user defined “Autobias Vcom” within “Autobias Vcom variance”. The autobias evaluates a user defined part (“Autobias (%)”) of the Testpulse baseline at the “Autobias Interval” (DaEphys->Settings->Amplifier).

DEPEND

IC

Autobias Ibias max

pA

0.1

During the inter trial interval (“ITI”) autobias adjusts the holding current to maintain the user defined “Autobias Vcom” within “Autobias Vcom variance”. The autobias evaluates a user defined part (“Autobias (%)”) of the Testpulse baseline at the “Autobias Interval” (DaEphys->Settings->Amplifier).

DEPEND

IC

Autobias Interval

s

0.1

During the inter trial interval (“ITI”) autobias adjusts the holding current to maintain the user defined “Autobias Vcom” within “Autobias Vcom variance”. The autobias evaluates a user defined part (“Autobias (%)”) of the Testpulse baseline at the “Autobias Interval” (DaEphys->Settings->Amplifier).

INDEP

IC

Autobias %

0.1

During the inter trial interval (“ITI”) autobias adjusts the holding current to maintain the user defined “Autobias Vcom” within “Autobias Vcom variance”. The autobias evaluates a user defined part (“Autobias (%)”) of the Testpulse baseline at the “Autobias Interval” (DaEphys->Settings->Amplifier).

INDEP

IC

Autobias

On/Off

    +
  • +
+

During the inter trial interval (“ITI”) autobias adjusts the holding current to maintain the user defined “Autobias Vcom” within “Autobias Vcom variance”. The autobias evaluates a user defined part (“Autobias (%)”) of the Testpulse baseline at the “Autobias Interval” (DaEphys->Settings->Amplifier).

DEPEND

IC

Sweep Rollback

0.1

Sweep rollback allows to remove existing sweeps by decreasing the device sweep counter. This entry documents that sweep rollback has happened and the new target sweep number. (removed)

INDEP

Skip Sweeps

0.1

Whenever the user issues a “Skip Sweeps” command this entry documents the new and to be jumped to sweep number.

INDEP

Async 0 On/Off

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async 1 On/Off

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async 2 On/Off

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async 3 On/Off

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async 4 On/Off

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async 5 On/Off

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async 6 On/Off

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async 7 On/Off

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async 0 Gain

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async 1 Gain

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async 2 Gain

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async 3 Gain

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async 4 Gain

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async 5 Gain

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async 6 Gain

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async 7 Gain

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 0 On/Off

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 1 On/Off

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 2 On/Off

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 3 On/Off

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 4 On/Off

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 5 On/Off

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 6 On/Off

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 7 On/Off

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 0 Min

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 1 Min

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 2 Min

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 3 Min

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 4 Min

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 5 Min

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 6 Min

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 7 Min

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 0 Max

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 1 Max

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 2 Max

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 3 Max

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 4 Max

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 5 Max

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 6 Max

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 7 Max

.001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 0 State

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 1 State

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 2 State

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 3 State

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 4 State

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 5 State

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 6 State

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async Alarm 7 State

On/Off

    +
  • +
+

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async AD 0 [Set Temperature]

degC

0

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async AD 1 [Bath Temperature]

degC

17.5

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async AD 2

.0001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async AD 3

.0001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async AD 4

.0001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async AD 5

.0001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async AD 6

.0001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

Async AD 7

.0001

Single AD channel read at the end of the sweep. Commonly used for reading experimental hardware states. From temperature controllers, for example.

+

Alarm is triggered when enabled and minimum or maximum is exceeded.

+

The value is stored in a new labnotebook column called “Async AD$X: $Name” where X is the asynchronous channel and $Name the title of the entry.

+

INDEP

IC;VC;I=0

TP Auto

On/Off

    +
  • +
+

Automatic adjustment of testpulse baeline fraction and IC amplitude

DEPEND

IC

TP Auto max current

pA

0.1

Maximum allowed current for automatic testpulse

DEPEND

IC

TP Auto voltage

mV

0.1

Target voltage of the pulse

DEPEND

IC

TP Auto voltage range

mV

0.1

Acceptable deviation from the set voltage to the measured voltage

DEPEND

IC

TP Auto percentage

%

1

Scaling factor for the amplitude adjustment

INDEP

IC

TP Auto interval

s

0.1

Interval how often to try tuning the Auto testpulse parameters

INDEP

IC

TP Auto QC

On/Off

    +
  • +
+

Determines if the desired auto testpulse propertes were reached or not.

DEPEND

IC

TP Cycle ID

1

An arbitrary but unique number where all testpulse from the same run have the same ID. “Fast” testpulse restarting is considered to be the same run.

INDEP

IC;VC;I=0

Minimum TP resistance for tolerance

MΩ

1

Testpulse resistance values which differ more than this value from their value on the last TP run are documented in the sweep wave note.

INDEP

IC;VC;I=0

Send TP settings to all headstages

On/Off

    +
  • +
+

GUI control for headstage dependent testpulse settings.

INDEP

IC;VC;I=0

Epochs version

1

Version number of the stored epoch information.

INDEP

IC;VC;I=0

Get/Set Inter-trial interval

On/Off

    +
  • +
+

Determines if the ITI is readout from the stimset in each sweep or the ITI from GUI control is used.

INDEP

IC;VC;I=0

Double precision data

On/Off

    +
  • +
+

Stored data is stored with double (ON) or single precision (OFF).

INDEP

IC;VC;I=0

Save amplifier settings

On/Off

    +
  • +
+

ON if amplifier settings should be stored, OFF if not.

INDEP

IC;VC;I=0

Require amplifier

On/Off

    +
  • +
+

ON if data acquisition was done with an amplifier, OFF if not.

INDEP

IC;VC;I=0

Skip Ahead

1

Determines how many sweeps are skipped from the stimset whan starting data acquisition.

INDEP

IC;VC;I=0

Skip Sweeps source

0.1

Stores who is responsible for sweep skipping. Current values are 0x1 for the user and 0x2 for automatic/internal reasons.

INDEP

IC;VC;I=0

+ + ++++++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Textual entries

Name

Unit

Tolerance

Description

Headstage Contingency

ClampMode

TimeStamp

s

    +
  • +
+

Time Stamp: Seconds since Igor epoch (1/1/1904) in local time zone with millisecond precision. Written at time of labnotebook entry.

ALL

TimeStampSinceIgorEpochUTC

s

    +
  • +
+

Time Stamp: Seconds since Igor epoch (1/1/1904) in coordinated universal time zone (UTC) with millisecond precision. Written at time of labnotebook entry.

ALL

EntrySourceType

    +
  • +
+

Entry source type: type of the labnotebook entry, 0 for data acquisition, 1 for test pulse, NaN for all other types including user entries.

ALL

AcquisitionState

    +
  • +
+

Stores the current numbered state of data acquistion.

ALL

Stim Wave Name

    +
  • +
+

Stimulus set name

DEPEND

DA unit

    +
  • +
+

User-defined analog output unit. Depends on the clamp mode. Typically pA or mV.

DEPEND

AD unit

    +
  • +
+

User-defined analog input unit. Depends on the clamp mode. Typically pA or mV.

DEPEND

TTL rack zero stim sets

    +
  • +
+

Names of the TTL stimulus sets for each channel of rack zero. Semi-colon separated string list. Up to 4 entries. Empty entries for inactive TTL channels. ITC hardware only.

INDEP

TTL rack one stim sets

    +
  • +
+

Names of the TTL stimulus sets for each channel of rack one. Semi-colon separated string list .Up to 4 entries. Empty entries for inactive TTL channels. ITC hardware only.

INDEP

Pre DAQ function

    +
  • +
+

Name of analysis function used for Pre DAQ event. Used for Version 1 and 2 analysis functions. Deprecated. See also: https://alleninstitute.github.io/MIES/file/_m_i_e_s___analysis_functions_8ipf.html

DEPEND

Mid Sweep function

    +
  • +
+

Name of analysis function used for Mid Sweep event. Used for Version 1 and 2 analysis functions. Deprecated. See also: https://alleninstitute.github.io/MIES/file/_m_i_e_s___analysis_functions_8ipf.html

DEPEND

Post Sweep function

    +
  • +
+

Name of analysis function used for Post Sweep event. Used for Version 1 and 2 analysis functions. Deprecated. See also: https://alleninstitute.github.io/MIES/file/_m_i_e_s___analysis_functions_8ipf.html

DEPEND

Post Set function

    +
  • +
+

Name of analysis function used for Post Set event. Used for Version 1 and 2 analysis functions. Deprecated. See also: https://alleninstitute.github.io/MIES/file/_m_i_e_s___analysis_functions_8ipf.html

DEPEND

Post DAQ function

    +
  • +
+

Name of analysis function used for Post DAQ event. Used for Version 1 and 2 analysis functions. Deprecated. See also: https://alleninstitute.github.io/MIES/file/_m_i_e_s___analysis_functions_8ipf.html

DEPEND

Pre Sweep Config function

    +
  • +
+

Name of analysis function used for Pre Sweep Config event (event occurs before config). Used for Version 1 and 2 analysis functions. Deprecated. See also: https://alleninstitute.github.io/MIES/file/_m_i_e_s___analysis_functions_8ipf.html

DEPEND

Generic function

    +
  • +
+

Stores the name of the analysis function run on each headstage. Version 3 of analysis functions only. See also: https://alleninstitute.github.io/MIES/file/_m_i_e_s___analysis_functions_8ipf.html

DEPEND

Pre Set function

    +
  • +
+

Name of analysis function used for Pre Sweep event. Used for Version 1 and 2 analysis functions. Deprecated. See also: https://alleninstitute.github.io/MIES/file/_m_i_e_s___analysis_functions_8ipf.html

DEPEND

Function params (encoded)

    +
  • +
+

A comma-separated list of analysis parameter names, types, and values. For formatting, see documentation: +https://alleninstitute.github.io/MIES/file/_m_i_e_s___wave_data_folder_getters_8ipf.html#_CPPv427GetWaveBuilderWaveTextParamv

DEPEND

oodDAQ regions

    +
  • +
+

Semi-colon separated list of optimized overlap distributed data acquisition (oodDAQ) regions (parts of the stimulus with a non-zero signal plus the oodDAQ pre and post-delay). Unit: stimset build ms (does not include user or auto onset delays).

DEPEND

Electrode

    +
  • +
+

User-defined names of headstages. Names are stored in the cellElectrodeNames wave. Names are also stored in the MIES NWBV2 file. Electrode names in cellElectrodeNames are meant to be manually updated each time the user changes pipettes. The default names are the MIES headstage number. See documentation: https://alleninstitute.github.io/MIES/file/_m_i_e_s___wave_data_folder_getters_8ipf.html#_CPPv421GetCellElectrodeNames6string and https://pynwb.readthedocs.io/en/stable/pynwb.icephys.html#pynwb.icephys.IntracellularElectrode

DEPEND

High precision sweep start

    +
  • +
+

High precision sweep start timestamp in ISO8601 format. See documentation: https://alleninstitute.github.io/MIES/file/_m_i_e_s___wave_data_folder_getters_8ipf.html?highlight=high%20precision%20sweep%20start#_CPPv427GetSweepSettingsTextKeyWave6string

INDEP

Stim Wave Note

    +
  • +
+

Wave note of the DA stimulus set. Textual description of the stimulus set. See documentation: https://alleninstitute.github.io/MIES/file/_m_i_e_s___wave_builder_8ipf.html#_CPPv419WB_GetWaveNoteEntry6string8variable6string8variable8variable

DEPEND

TTL rack zero set sweep counts

    +
  • +
+

Non-negative sweep (timeseries) index for the TTL stimulus set of rack zero. Semi-colon separated string list. Up to 4 entries. Empty entries for inactive TTL channels. ITC hardware only.

INDEP

TTL rack one set sweep counts

    +
  • +
+

Non-negative sweep (timeseries) index for the TTL stimulus set of rack one. Semi-colon separated string list. Up to 4 entries. Empty entries for inactive TTL channels. ITC hardware only.

INDEP

TTL set sweep counts

    +
  • +
+

Non-negative sweep (timeseries) index for the TTL stimulus set. Semi-colon separated string list. Up to 8 entries. Empty entries for inactive TTL channels. Non-ITC hardware only.

INDEP

TTL stim sets

    +
  • +
+

Names of the TTL stimulus sets for each TTL channel. Semi-colon separated string list. Up to 8 entries. Empty entries for inactive TTL channels. Non-ITC hardware only.

INDEP

TTL channels

    +
  • +
+

List of active TTL channels. Semi-colon separated string list. Up to 8 entries. Both the entry and the list position encode the channel number. Empty entries for inactive TTL channels. Non-ITC hardware only.

INDEP

Follower Device

    +
  • +
+

Semi-colon separated list of follower (time locked) devices. ITC hardware only.

INDEP

Device

    +
  • +
+

Name of the DAEphys panel used for acquiring the sweep.

INDEP

MIES version

    +
  • +
+

MIES version.e.g., Release_1.4_20170929-16-g497e7aa8 +Extended version includes the date and time of last commit e.g., 2018-05-08T14:42:50+02:00 and the submodule status, e.g., +160000 6c47163858d99986b27c70f6226e8fca894ed5f7 0tPackages/IPNWB +160000 ed7e824a6e065e383ae31bb304383e13d7c7ccb5 0tPackages/ITCXOP2 +160000 2bd259940cb332339ed3c82b74632f06c9b68a15 0tPackages/ZeroMQ +160000 657e9e8abdc92aa299301796d710a0a717da4ef8 0tPackages/unit-testing

INDEP

Igor Pro version

    +
  • +
+

Igor Pro version number. e.g., 9.0.1.2

INDEP

Digitizer Hardware Name

    +
  • +
+

Device hardware name. +ITC device names: https://alleninstitute.github.io/MIES/file/_m_i_e_s___constants_8ipf.html?highlight=device_types_itc#_CPPv416DEVICE_TYPES_ITC +NI device names: given name (not model)

INDEP

Digitizer Serial Numbers

    +
  • +
+

Hardware serial number is unique for each device. Formatting varies across hardware types.

INDEP

Epochs

    +
  • +
+

Epoch information of the sweep of the DA channel per headstage. It contains start, end times, treelevel and tag information. The tag information is a list of key-value pairs, all possible tags are described in https://alleninstitute.github.io/MIES/epoch_information.html#naming. The epoch information is a serialized wave, documented at https://alleninstitute.github.io/MIES/file/_m_i_e_s___wave_data_folder_getters_8ipf.html?highlight=getepochswave#_CPPv413GetEpochsWave6string, using : as row separator and , as column separator.

DEPEND

JSON config file [path]

    +
  • +
+

Absolute file path (Igor style / HFS) to the experiment configuration file for the DA_ephys panel.

INDEP

JSON config file [SHA-256 hash]

    +
  • +
+

Hash (an identifier that uniquely defines the contents of the file) of the absolute file path (Igor style / HFS) to the experiment configuration file for the DA_ephys panel. If the Hash changes, it indicates the file contents have been altered.

INDEP

JSON config file [stimset nwb file path]

    +
  • +
+

Absolute path to the stimsets loaded with experiment configuration. Formatting matches the Stim set file name user entry in the config file.

INDEP

Igor Pro build

    +
  • +
+

Igor pro build version (the build count). Used to identify nightly builds.

INDEP

Indexing End Stimset

    +
  • +
+

The last DA stimulus set in the indexing list.

DEPEND

TTL Indexing End Stimset

    +
  • +
+

The last TTL stimulus set in the indexing list.

INDEP

TTL Stimset wave note

    +
  • +
+

Wave note of the TTL stimulus set. Textual description of the stimulus set. See documentation: https://alleninstitute.github.io/MIES/file/_m_i_e_s___wave_builder_8ipf.html#_CPPv419WB_GetWaveNoteEntry6string8variable6string8variable8variable

INDEP

TTL Stim Wave Checksum

    +
  • +
+

List of TTL stimset checksums. URL-encoded semi-colon separated string list, see https://en.wikipedia.org/wiki/Percent-encoding. Up to 8 entries. Empty entries for inactive TTL channels. For all hardware types.

INDEP

TTL Stim set length

    +
  • +
+

List of TTL stimset lengths in points. Semi-colon separated string list. Up to 8 entries. Empty entries for inactive TTL channels. For all hardware types.

INDEP

TTL rack zero set cycle counts

    +
  • +
+

The number of TTL stimulus set repetitions in one repeated acquisition cycle of rack zero. Semi-colon separated string list. Up to 4 entries. Empty entries for inactive TTL channels. ITC hardware only.

INDEP

TTL rack one set cycle counts

    +
  • +
+

The number of TTL stimulus set repetitions in one repeated acquisition cycle of rack one. Semi-colon separated string list. Up to 4 entries. Empty entries for inactive TTL channels. ITC hardware only.

INDEP

TTL set cycle counts

    +
  • +
+

The number of TTL stimulus set repetitions in one repeated acquisition cycle. Semi-colon separated string list. Up to 8 entries. Empty entries for inactive TTL channels. ITC hardware only.

INDEP

OperatingModeString

    +
  • +
+

Amplifier clamp mode as a text string. i.e., v-clamp, i-clamp, I = 0

DEPEND

ScaledOutSignalString

    +
  • +
+

Amplifier output signal type encoded as string. +One of:

+
    +

  • Membrane Current

    • +

  • Membrane Potential

    • +

  • Pipette Potential

    • +

  • 100x AC Membrane Potential

    • +

  • External Command Potential

    • +

  • Auxiliary 1 Potential

    • +

  • Auxiliary 2 Current

    • +
+

DEPEND

ScaleFactorUnitsString

    +
  • +
+

Units of the scaled output signal encoded as a string.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

RawOutSignalString

    +
  • +
+

User-configured signal type of secondary output encoded as a string.

+

For more details, see the MultiClamp700B Manual.

+

DEPEND

RawScaleFactorUnitsString

    +
  • +
+

String denoting the unit of the Raw Scale Factor.

+

For more details see the MultiClamp700B Manual.

+

DEPEND

User comment

    +
  • +
+

Free-form user comment without a timestamp. Duplicate of entries in the user-comment notebook.

INDEP

HardwareTypeString

    +
  • +
+

Amplifer hardware type string. e.g., MultiClamp 700B

DEPEND

Async AD0 Title

    +
  • +
+

User name of indicated asynchronous channel.

INDEP

Async AD1 Title

    +
  • +
+

User name of indicated asynchronous channel.

INDEP

Async AD2 Title

    +
  • +
+

User name of indicated asynchronous channel.

INDEP

Async AD3 Title

    +
  • +
+

User name of indicated asynchronous channel.

INDEP

Async AD4 Title

    +
  • +
+

User name of indicated asynchronous channel.

INDEP

Async AD5 Title

    +
  • +
+

User name of indicated asynchronous channel.

INDEP

Async AD6 Title

    +
  • +
+

User name of indicated asynchronous channel.

INDEP

Async AD7 Title

    +
  • +
+

User name of indicated asynchronous channel.

INDEP

Async AD0 Unit

    +
  • +
+

User-defined unit of indicated asynchronous channel.

INDEP

Async AD1 Unit

    +
  • +
+

User-defined unit of indicated asynchronous channel.

INDEP

Async AD2 Unit

    +
  • +
+

User-defined unit of indicated asynchronous channel.

INDEP

Async AD3 Unit

    +
  • +
+

User-defined unit of indicated asynchronous channel.

INDEP

Async AD4 Unit

    +
  • +
+

User-defined unit of indicated asynchronous channel.

INDEP

Async AD5 Unit

    +
  • +
+

User-defined unit of indicated asynchronous channel.

INDEP

Async AD6 Unit

    +
  • +
+

User-defined unit of indicated asynchronous channel.

INDEP

Async AD7 Unit

    +
  • +
+

User-defined unit of indicated asynchronous channel.

INDEP

TTL Epochs Channel 0

    +
  • +
+

Epochs of TTL Channel 0

INDEP

TTL Epochs Channel 1

    +
  • +
+

Epochs of TTL Channel 1

INDEP

TTL Epochs Channel 2

    +
  • +
+

Epochs of TTL Channel 2

INDEP

TTL Epochs Channel 3

    +
  • +
+

Epochs of TTL Channel 3

INDEP

TTL Epochs Channel 4

    +
  • +
+

Epochs of TTL Channel 4

INDEP

TTL Epochs Channel 5

    +
  • +
+

Epochs of TTL Channel 5

INDEP

TTL Epochs Channel 6

    +
  • +
+

Epochs of TTL Channel 6

INDEP

TTL Epochs Channel 7

    +
  • +
+

Epochs of TTL Channel 7

INDEP

+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/labnotebook-docs.html b/labnotebook-docs.html new file mode 100644 index 0000000000..cdb4231846 --- /dev/null +++ b/labnotebook-docs.html @@ -0,0 +1,375 @@ + + + + + + + + Labnotebook documentation for developers — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Labnotebook documentation for developers

+
+

Overview

+

In MIES, metadata of sweeps and test pulses get stored in a data structure +called a labnotebook. The general structure is like a paper-based lab journal +with columnar data entry storage. Each measurement has an associated date and +time of the data acquisition and nothing is ever erased. After data +acquisition, setup specific settings, and other metadata are written to the +labnotebook.

+

Our digital version consists of an array of (key,`value`) pairs. Each +(key,`value`) pair is used to describe one metadata entry of a sweep. The +data values get separated by their type into numerical and textual data storage +containers. Each storage container consists of a *Keys and a corresponding +*Values dataset. While *Keys contains textual, unique references to the +data entities, *Values contains numeric or text values to the corresponding +key. Such separation means that four multidimensional data waves contain the +data for this digital labnotebook. The available data storage containers, +therefore, are numericalKeys, numericalValues, textualKeys, and +textualValues.

+

In PXP files, the analysis browser stores labnotebooks in +root:MIES:Analysis:$fileName:$device:labnotebook: whereas the data browser +stores files in root:MIES:LabNoteBook:$hardware:$device:. In NWB files, the +labnotebook arrays reside in /general/labnotebook/$device.

+

The results waves with analysis results have the same layout as the +labnotebook waves. They are stored for PXP files in root:MIES:Results and +for NWBv2 files in /general/results.

+
+
+

Layout

+

The key array is two dimensional and has 3 rows

+
    +

  • 0: Parameter Name

    • +

  • 1: Parameter Unit

    • +

  • 2: Parameter Tolerance

    • +
+

and an arbitrary number of columns. Each column in the key array describes +one metadata entry in each column of the value array. The value array is +three dimensional and has an arbitrary number of rows (one row for each added +labnotebook entry) an arbitrary number of columns (one for each metadata entry) +and nine layers (the first eight hold headstage dependent data, the nineth +headstage independent data).

+
+
+

Encoding

+

The numerical arrays are IEEE-754 64bit floating point values, the textual +arrays are UTF-8 encoded.

+
+

Example key array

+

Rows are vertical, columns are horizontal.

+ + + + + + + + + + + + + + + + + + + + + +

SweepNum

TimeStampSinceIgorEpochUTC

EntrySourceType

V-Clamp Holding Level

…

mV

…

0.9

…

+
+
+

Specification of the entries

+
    +

  • Parameter Name: Non-empty string

    • +

  • Parameter Unit: SI/imperial unit with prefix or % or On/Off or empty

    • +

  • Parameter Tolerance: Smallest meaningful difference or empty/- if it does not apply.

    • +
+
+
+

Example value array

+

Rows are vertical, columns are horizontal and only showing the first layer.

+ + + + + + + + + + + + + + + +

0

3548850546.923

0

0.0004854951403103769

…

0

3548850566.0

1

NaN

…

+
+
+

Addition of new entries

+

When writing a new value into the labnotebook a new row is appended/filled in +the value array. This means we never overwrite old entries. Due to sweep +rollback (aka deleting existing sweeps and acquiring new sweeps) it can happen +that duplicated sweep numbers are present in the labnotebook. Each row holds +the entry source type, which tells you about the subsystem the entry originated +from, the possible values are

+
    +

  • 0: data acquisition

    • +

  • 1: test pulse

    • +

  • NaN: all other subsystems including user entries.

    • +
+
+
+
+

Caveats

+
    +

  • Due to the design of the labnotebook you can never rely on the exact column +number of an entry being constant or meaningful. Just because it is in the +current version in row 5 does not mean it will be in the same row in the +next version or in the next dataset.

    • +

  • The dimensions of the arrays given above are minimum dimensions, they can +anytime increase but will never decrease.

    • +

  • Although we strive to not remove entries from the labnotebook, you should +handle non-existing values gracefully or abort.

    • +

  • Entries which are not present are either NaN or an empty string.

    • +

  • Some entries are, for historical reasons, present in both the first layer and +the headstage independent layer (nineth layer). New code should query the data +from the headstage independent layer only.

    • +

  • In case unassociated DA/AD channels were used (these are channels which are +not connected to a headstage) during acquisition there are additional entries +present which are formatted like $entry UNASSOC_$channelNumber (old style) +or $entry u_(AD|DA)$channelNumber (new style) and only have entries in the +ninth layer (as it is by definition headstage independent data).

    • +

  • One important concept is valid entries vs placeholder entries. All non-NaN +or non-empty string entries are valid entries. Therefore only valid entries +override other placeholder entries. But placeholder entries never override +valid entries.

    • +

  • This document describes the latest version of the labnotebook only. Some +things will be different for older versions. In case you need to read these +and got into trouble please contact MIES@alleninstitute.org for +assistance.

    • +

  • For internal technical reasons the value arrays will have some empty rows at the +end.

    • +
+
+
+

Common Tasks

+
+

Getting a list of all available labnotebook entries

+

Iterate over the columns of each key array and extract the name from the +first row.

+
+
+

Searching a labnotebook entry for a given sweep number

+
    +

  • Search the first row of the key arrays for the desired entry, remember the column +index and which array holds the entry. Abort if it could not be found.

    • +

  • Search the first row of the key array for the SweepNum entry and remember +the column index. Abort if it could not be found.

    • +

  • Search in the column of the sweep number in the corresponding value array +from back to front for the desired sweep number. The result of that search is a +consecutive range of rows.

    • +

  • (Optional) Extract from the row range the entries with the desired entry +source type.

    • +

  • Search in the row range and the entry’s column from back to front for the latest +value of the desired entry. If the entry is present in the nineth layer the +setting is headstage independent, otherwise the layer index with a +non-empty/NaN entry denotes the headstage.

    • +

  • Get the unit of the entry from the key arrays third row.

    • +
+
+
+

Searching the last sweep which has a given labnotebook entry

+
    +

  • Search the first row of the key arrays for the desired entry, remember the column +index and which array holds the entry. Abort if it could not be found.

    • +

  • Search the first row of the key array for the SweepNum entry and remember +the column index. Abort if it could not be found.

    • +

  • Search the corresponding value array from back to front for a +non-empty/NaN entry in the given column. If the entry is present in the +nineth layer the setting is headstage independent, otherwise the layer index +with a non-empty/NaN entry denotes the headstage. Depending on your needs +you might want to filter depending on entry source type as well.

    • +

  • Read out the sweep number for the match from the sweep number column.

    • +
+
+
+

Getting all sweeps of a repeated acquisition cycle RAC

+
    +

  • The entry named Repeated Acq Cycle ID is the same for sweeps which stem +from the same repeated acquisition cycle.

    • +

  • Search the first row of the key arrays for the Repeated Acq Cycle ID +entry, remember the column index and which array holds the entry. Abort if it +could not be found.

    • +

  • Search the first row of the key array for the SweepNum entry and remember +the column index. Abort if it could not be found.

    • +

  • Search the corresponding value array from back to front for a +non-empty/NaN entry in the given sweep number column. The result of that +search is a consecutive range of rows.

    • +

  • Search in this row range and the RAC column from back to front for a +non-empty entry.

    • +

  • Now collect all sweep numbers which have that RAC value

    • +
+

The related entry Stimset Acq Cycle ID (SCI) is an identifier which is +constant for a given headstage if the data stems from the same stimset, the +same RAC and had the same stimset cycle count.

+
+
+
+

Existing code

+
+

Igor Pro

+

See Group LabnotebookQueryFunctions for a list of all functions for querying the labnotebook.

+
+
+

Python

+

An example on how to query the labnotebook can be found +here +in the method MiesNwb.notebook.

+
+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/mies-concepts.html b/mies-concepts.html new file mode 100644 index 0000000000..5ae68c9f0f --- /dev/null +++ b/mies-concepts.html @@ -0,0 +1,279 @@ + + + + + + + + Important MIES concepts for developers — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Important MIES concepts for developers

+

This document should help new developers understand some of the guiding +principles behind MIES.

+
+

Coding Guidelines

+

Can be found here.

+
+
+

Documentation

+

Our documentation toolchain consists of doxygen/breathe/sphinx. All +documentation for the code should be in procedure files. All public accessible +functions should have a documentation block, for complex interfaces the use of +@param is recommended. See AFH_ExtractOneDimDataFromSweep() for an +example.

+

Caller/Callee graphs can be created by executing doxygen in Packages/doc +and can be browsed at Packages/doc/html/index.html.

+

The full documentation can be generated with tools/build-documentation.sh.

+
+
+

Global objects

+

Global objects like variables, strings, waves and datafolders should only be +used if necessary. Local variables, strings, free waves and free datafolders +should therefore be preferred if possible.

+

Reasons to use global objects:

+
    +

  • Persistent storage

    • +

  • Performance reasons

    • +
+

All access to global objects must be handled via getter functions in +File MIES_WaveDataFolderGetters.ipf or File MIES_GlobalStringAndVariableAccess.ipf. +The documentation for these getter functions must include the wave layout, and +purpose of the object. This documentation should be the primary, and only, +source for finding out what the object holds. Using a single access point for +global objects allows to quickly find all users of that object.

+

For waves we use wave versioning, see Group WaveVersioningSupport. This is +done in order to enable a smooth upgrade when the wave layout changes and old +experiments are loaded with the old wave layout.

+

The use of dimension labels in waves for better readability is recommended.

+

User data on GUI objects or traces should only be used sparingly.

+
+
+

Convenience Wrapper

+

Some Igor Pro functionality is wrapped in separate functions for better +readability and error checking. These include interacting with GUI controls, +see File MIES_GuiUtilities.ipf, checking strings IsEmpty() or numbers +IsFinite().

+

Setting GUI values programmatically must always be done via +PGC_SetAndActivateControl() as that calls the GUI procedure as well.

+
+
+

Assertions

+

We employ assertions to check function invariants . The relevant +functions are ASSERT() and ASSERT_TS(). Adding assertions +to the code greatly improves the error reporting capabilities of MIES and +should be used where appropriate.

+
+
+

Debug output

+

MIES uses the DEBUGGING_ENABLED symbol for toggling compilation with and +without debug output. The relevant functions are DEBUGPRINT(), +DEBUGPRINT_TS(), DEBUGPRINTv(), +DEBUGPRINTs() and DEBUGPRINTSTACKINFO(). The debug mode +can be toggled on a per-file basis from MIES Panels->Advanced->Open debug +panel or globally via EnableDebugMode()/DisableDebugMode().

+
+
+

Dynamically growing waves

+

Often one is adding entries to a wave one at a time. In order to minimize the +performance cost one can employ a technique where the actual size of the wave +and the used size differ in order to minimize the number of resize operations. +The relevant functions are EnsureLargeEnoughWave() (with example +code), SetNumberInWaveNote(), GetNumberFromWaveNote() and +RemoveUnusedRows().

+
+
+

Datafolders

+

The current data folder (cdf) should never be set or expected to be something +fixed. For dealing with that environment the following functions have been +created: UniqueWaveName(), UniqueDataFolder(), +createDFWithAllParents() and GetListOfObjects().

+
+
+

Deleting waves and datafolders

+

Due to the way Igor Pro works deleting a datafolder/wave may not succeed as the +object is currently in use. Use KillOrMoveToTrash() to work around +that issue.

+
+
+

Wave cache

+

In order to avoid having to do the same lengthy calculation over and over again +MIES has a wave cache. To use that cache you have to implement a function +which derives a key from all the input parameters and is unique for the +combination of parameters and different for all other combinations. This key is +then used to store and retrieve the wave from the cache. See File MIES_Cache.ipf for further examples.

+
+
+

Background functions

+

For DAQ we use a variety of background functions, all are listed at Group BackgroundFunctions. For debugging purposes the background watchdog panel +from MIES Panels->Advanced->Start Background … allows to view the state of +the background functions during execution.

+
+
+

Structured wave metadata

+

Structured metadata can be stored and retrieved into/from the wave note using +GetNumberFromWaveNote()/SetNumberInWaveNote(), +GetStringFromWaveNote()/SetStringInWaveNote() and +AddEntryIntoWaveNoteAsList()/HasEntryInWaveNoteList().

+
+
+

DA_Ephys panel

+

The main data acquisition panel is created via the window macro +DA_Ephys(). After changing it, be sure to call MIES +Panels->Advanced->Reset And Store … for setting the default values and +recreating the window macro.

+

Access to the GUI control settings is done via the GUI state wave which caches +the settings for performance reasons. The functions +DAG_GetNumericalValue() and DAG_GetTextualValue() can be used to +query the values of (nearly) all GUI controls.

+

The names of GUI controls which come in groups, like headstages, DA/AD/TTL +channels must be derived by calling GetPanelControl(). Their state can be +queried with DAG_GetChannelState().

+
+
+

Versioned panels

+

All panels are versioned. The version number must be increased if a stored +panel in an old experiment would misbehave with new code. The relevant +constants are DA_EPHYS_PANEL_VERSION, DATABROWSER_PANEL_VERSION, +SWEEPBROWSER_PANEL_VERSION and WAVEBUILDER_PANEL_VERSION.

+
+
+

Tabbed panels

+

For TabControl GUI elements we use routines from ACL_TabUtilities.ipf and +ACL_UserdataEditor.ipf for convenient programming.

+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/namespace/namespace_bkg_watcher.html b/namespace/namespace_bkg_watcher.html new file mode 100644 index 0000000000..72908c2a8e --- /dev/null +++ b/namespace/namespace_bkg_watcher.html @@ -0,0 +1,289 @@ + + + + + + + + Namespace BkgWatcher — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Namespace BkgWatcher

+
+
+namespace BkgWatcher
+
+

Functions

+
+
+static variable ASSERT(variable var, string errorMsg)
+
+ +
+
+static variable SetValDisplay(string win, string control, variable var = defaultValue, string str = defaultValue, string format = defaultValue)
+
+ +
+
+static string GetValDisplayAsString(string win, string control)
+
+ +
+
+static variable IsBackgroundTaskRunning(string task)
+
+ +
+
+variable BW_StartPanel()
+
+ +
+
+variable BW_CreatePanel()
+
+ +
+
+variable BW_StartTask()
+
+ +
+
+variable BW_StopTask()
+
+ +
+
+variable BW_PanelUpdate()
+
+ +
+
+variable BW_BackgroundWatchdog(WMBackgroundStruct *s)
+

Helper background task for debugging.

+
+ +
+
+variable BW_ButtonProc_ShowTask(WMButtonAction *ba)
+
+ +
+
+variable BW_ButtonProc_QuitTask(WMButtonAction *ba)
+
+ +
+
+variable BW_WindowHook(WMWinHookStruct *s)
+
+ +
+
+variable BW_ButtonProc_StartTask(WMButtonAction *ba)
+
+ +
+
+variable BW_ButtonProc_StopTask(WMButtonAction *ba)
+
+ +
+
+

Variables

+
+
+static const string PANEL = "BW_MiesBackgroundWatchPanel"
+
+ +
+
+static const string TASK = "BW_BackgroundWatchdog"
+
+ +
+
+static const string CONTROL_PREFIX = "bckrdw"
+
+ +
+
+static const double INVALIDATE_STATE = -1
+
+ +
+
+static const double XGRID = 20
+
+ +
+
+static const double XOFFS = 240
+
+ +
+
+static const double YGRID = 20
+
+ +
+
+static const double CONTROL_TYPE_VALDISPLAY = 4
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/namespacelist.html b/namespacelist.html new file mode 100644 index 0000000000..e4fe409330 --- /dev/null +++ b/namespacelist.html @@ -0,0 +1,165 @@ + + + + + + + + Namespace list — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Namespace list

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/objects.inv b/objects.inv new file mode 100644 index 0000000000..befb4ff679 Binary files /dev/null and b/objects.inv differ diff --git a/releasenotes.html b/releasenotes.html new file mode 100644 index 0000000000..49272fe601 --- /dev/null +++ b/releasenotes.html @@ -0,0 +1,5692 @@ + + + + + + + + Release notes — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Release notes

+
+
+
+

Release 2.8

+
+

Controls

+

All added, removed or renamed controls of the main GUIs are listed. These lists are intended to help upgrading the JSON +configuration files. Controls, like GroupBox’es, which can not be read/written with the configuration code are not included.

+
+

AnalysisBrowser

+
+
Added
+

None

+
+
+
Removed
+

None

+
+
+
Renamed
+

None

+
+
+
+

DA_Ephys

+
+
Added
+

None

+
+
+
Removed
+

None

+
+
+
Renamed
+

None

+
+
+
+

Databrowser

+
+
Added
+

None

+
+
+
Removed
+

None

+
+
+
Renamed
+

None

+
+
+
+

Wavebuilder

+
+
Added
+

None

+
+
+
Removed
+

None

+
+
+
Renamed
+

None

+
+
+
+
+

Sweep Formula

+
    +

  • Breaking change: vs is now per formula allowing different x-formulas for +different y-formulas in the same graph

    • +

  • Add merge, fit, fitline and dataset

    • +

  • Add support for tweaking epoch ranges via epochs(ST) + [1, -2]

    • +

  • Use datasets in output of epochs

    • +

  • Ensure that all internal numeric waves are double precision

    • +

  • Keep sweep number information in derived data via operation stack

    • +

  • Use headstage trace colors for labnotebook

    • +

  • psx:

    +
      +

    • Use the opposite sign of kernelAmp for the rise time

      • +

    • Handle edge cases better

      • +

    • Add psxDeconvFilter as helper operation

      • +

    • Add support for multiple ranges

      • +

    • Make deconvoluation more robust

      • +
    +
    • +

  • psxStats: Abort on intersecting ranges

    • +

  • Make trace colors work with swapped axis

    • +

  • Fix parser errors on valid constructs

    • +

  • Add data type forwarding for primitive operations like +, -, *, /

    • +

  • Allow plotting of multi-datasets stored as array elements

    • +

  • More flexible handling of legend shrinking

    • +

  • Don’t kill and recreate the main panel. This also implies that the plot +window is not brought to the front anymore on update.

    • +
+
+
+

AnalysisBrowser

+
    +

  • Add on-the-fly upgrade to new sweep wave format

    • +

  • Fix file management when removing and restoring files in edge case

    • +
+
+
+

DataBrowser

+

None

+
+
+

DataBrowser/SweepBrowser

+
    +

  • Make the panel naming more consistent

    • +

  • Fix sorting of sweeps in overlay sweeps in edge case

    • +

  • Enhance accuracy of epoch info in display

    • +

  • Fix labnotebook/results name gathering speed for popup menu

    • +
+
+

Dashboard

+
    +

  • Fix calculation of failed sweeps for Rheobase

    • +

  • Allow to select multiple individual rows

    • +

  • Decorate the analysis function name with the operation mode (PSQ_DASCale only)

    • +
+
+
+
+

DA_Ephys

+
    +

  • Add experimental support for Sutter hardware (amplifier support is pending)

    • +

  • The data format of the sweep waves has changed

    • +

  • Skip updating the DA/TTL data for oscilloscope display

    • +

  • Do not add epoch information to the sweep wave note

    • +

  • Fix edge-cases for TP property calculation

    • +

  • Check gain, scale and unit of unassociated DA/AD channels

    • +

  • Zero the DAC after running the testpulse for single device mode (already done for multi device)

    • +

  • Streamline analysis parameter checking and also check all present analysis +parameters

    • +

  • Forbid analysis parameters which are neither required nor optional. +The check is only done if we have required/optional parameters at all.

    • +

  • Fix out-of-bounds checking for NI hardware, we previously only looked at the first DA channel

    • +
+
+
+

JSON Configuration

+

None

+
+
+

Downsample

+

None

+
+
+

Analysis Functions

+
    +

  • Add “Adaptive Suprathreshold” operation mode for PSQ_DASCale()

    • +

  • Adapt AnalysisFunction_V3 for Sutter hardware support

    • +

  • Avoid calling analysis functions mid sweep when the acquisition has not yet +started (aka fifo position is zero)

    • +

  • Make casing of user epoch DA Suppression don’t depend on the hardware type for PSQ_Ramp

    • +
+
+
+

Foreign Function interface

+ +
+
+

Pulse Average Plot

+

None

+
+
+

Publisher

+

None

+
+
+

General

+
    +

  • Add headstage and clampmode information in DAQ config wave

    • +

  • CheckInstallation: Check that all non-hardware XOPs are present

    • +

  • Add experimental support for MacOSX (data analysis only), needs a manual installation

    • +

  • Fix GetLastSettingTextIndepSCI

    • +

  • Fix ST_GetStimsetList incorrectly matching against saved stimsets

    • +

  • Avoid creating global objects in the current datafolder

    • +

  • Nicify documentation layout

    • +

  • Ignore case when querying analysis parameters in AFH_GetAnalysisXXX` functions

    • +

  • Fix minor issues with Windows 11

    • +

  • Update EV certificate for window installer signing

    • +
+
+
+

TUF XOP

+

None

+
+
+

ITC XOP 2

+
    +

  • Avoid creating V_ITCError/V_ITCXOPError as global variables for ITCSetGlobals2

    • +
+
+
+

ZeroMQ XOP

+

None

+
+
+

MCC XOP

+

None

+
+
+

MIESUtils XOP

+

None

+
+
+

JSON XOP

+
    +

  • Update to version-892-g9251933

    • +
+
+
+

Labnotebook

+
    +

  • Fix labnotebook querying of settings from aborted sweeps which were written +by analysis functions in their PRE_DAQ_EVENT

    • +

  • Speedup labnotebook querying by using a sorted key wave as lookup help

    • +
+
+

New numerical keys

+

The following new labnotebook keys denote the per channel type sampling +intervals, the old key Sampling Interval is gone. For ITC and NI hardware +the numerical values of all three labnotebook entries will always be the same.

+
    +

  • Sampling interval DA

    • +

  • Sampling interval AD

    • +

  • Sampling interval TTL

    • +
+
+
+

New textual keys

+
    +

  • PSQ_FMT_LBN_DA_AT_FI_OFFSET

    • +

  • PSQ_FMT_LBN_DA_AT_FREQ

    • +

  • PSQ_FMT_LBN_DA_AT_FREQ_SUPRA

    • +

  • PSQ_FMT_LBN_DA_AT_DASCALE_SUPRA

    • +

  • PSQ_FMT_LBN_DA_AT_FI_SLOPES

    • +

  • PSQ_FMT_LBN_DA_AT_FI_OFFSETS

    • +

  • PSQ_FMT_LBN_DA_AT_MAX_SLOPE

    • +

  • PSQ_FMT_LBN_DA_AT_VALID_SLOPE_PASS

    • +

  • PSQ_FMT_LBN_DA_AT_INIT_VALID_SLOPE_PASS

    • +

  • PSQ_FMT_LBN_DA_AT_ENOUGH_FI_POINTS_PASS

    • +

  • PSQ_FMT_LBN_DA_AT_FUTURE_DASCALES

    • +

  • PSQ_FMT_LBN_DA_AT_FUTURE_DASCALES_PASS

    • +
+
+
+

Changed numerical entries

+

None

+
+
+

Changed textual entries

+

None

+
+
+

Renamed numerical entries

+

None

+
+
+

Renamed textual entries

+

None

+
+
+

Removed numerical entries

+
    +

  • Sampling interval

    • +
+
+
+

Removed textual entries

+

None

+
+
+
+

Epoch information

+
    +

  • Fix sorting to be numerically correct

    • +

  • Avoid deleting the last epoch in edge case

    • +

  • Make epoch information sample point exact (except ooDAQ regions), see here

    • +

  • Allow to recreate epoch information from the labnotebook including user +epochs from the analysis functions (DA only). These are now automatically +recreated for Databrowser/Sweepbrowser display and Sweep Formula.

    • +

  • Make start/end times and inflection points for pulse train epochs sample exact

    • +
+
+
+

NWB/IPNWB

+
    +

  • Update list of available stimsets after loading stimsets from NWB

    • +

  • Fix epoch info export for TTL channels with ITC1600

    • +

  • Fix string type of nwb_version in NWB file to ease DANDI handling

    • +

  • Increase precision of SamplingRate in source attribute

    • +

  • Fix forgotten stimsets when storing TTL data with ITC1600 hardware from rack one

    • +

  • Fix export of custom waves referenced from stimsets we are depending on only

    • +

  • Add epoch size in points to wave note

    • +

  • Create separate NWB files for each device

    • +

  • Use chunked compression for stimsets when saving

    • +
+
+

File format

+
    +

  • The sweep waves are now completely hardware independent. They consist of 1D +text waves referencing the individual channel waves, see GetSweepWave().

    • +
+
+
+
+

Pressure Control

+

None

+
+
+

WaveBuilder

+
    +

  • Fix combine stimsets referencing multiple stimsets where one stimset name is +a substring of another stimset name

    • +

  • Sort the analysis parameter entries in the panel

    • +

  • Ignore case when splitting stimset names into parts

    • +

  • Fix multi-level recursive combine stimsets

    • +

  • Fix creation order when a combine stimset references a non-existing stimset

    • +

  • Enhance error reporting on failure to create stimset

    • +

  • Don’t allow stimsets to have non-finite entries

    • +
+
+
+

Work Sequencing Engine

+

None

+
+
+

Internal

+
    +

  • Adapt FindIndizes with new property PROP_NOT to negate the matching logic

    • +

  • Add EnableWaveCache()/DisableWaveCache()

    • +

  • check-code.sh:

    +
      +

    • Add check to ensure that all macros are in their own files

      • +

    • Don’t allow semicolons at end of line

      • +

    • Check correct casing of doxygen commands

      • +

    • Tighten function-call-in-for-loop check

      • +

    • Bail out if we find ResizeControlsHook

      • +
    +
    • +

  • Factor out macros into their own files

    • +

  • Add read/write support for wave reference waves in JSON waves notes

    • +

  • Change FindIndizes to return double precision waves

    • +

  • Split large utility ipf files into smaller files

    • +
+
+
+

CI

+
    +

  • Disable report generation for release branches

    • +

  • Use code formatting with ipt

    • +

  • Add job to compile test each commit

    • +

  • Upgrade documentation toolchain

    • +

  • Enable wave leak detection

    • +

  • Upgrade all container images to latest debian stable (bookworm)

    • +

  • Verify NWB files with DANDI (ignoring some warnings though)

    • +
+
+
+

Tests

+
    +

  • Add testing with ITC1600 and fix the tests

    • +

  • Introduce TestBeginCommon/TestEndCommon/TestCaseBeginCommon/TestCaseEndCommon

    • +

  • Update to newer github action versions to avoid nodejs deprecation warning

    • +

  • Update pynwb for read tests

    • +
+
+
+

Async Framework

+

Nonet

+
+
+

Logging

+
    +

  • Archive logfiles on Igor Pro shutdown

    • +

  • Readd timestamps to the JSON newline entries

    • +
+
+
+

Installer

+
    +

  • Add NWBv2 compound XOP for installations without hardware XOPs

    • +
+
+
+
+

Release 2.7

+
+

Controls

+

All added, removed or renamed controls of the main GUIs are listed. These lists are intended to help upgrading the JSON +configuration files. Controls, like GroupBox’es, which can not be read/written with the configuration code are not included.

+
+

AnalysisBrowser

+
+
Added
+
    +

  • listbox_AB_Folders

    • +

  • button_AB_AddFiles

    • +

  • button_AB_Remove

    • +

  • button_AB_Open

    • +
+
+
+
Removed
+
    +

  • setvar_baseFolder

    • +
+
+
+
Renamed
+
    +

  • button_base_folder_scan -> button_AB_refresh

    • +

  • button_select_directory -> button_AB_AddFolder

    • +
+
+
+
+

DA_Ephys

+
+
Added
+

None

+
+
+
Removed
+
    +

  • button_Hardware_AddFollower

    • +

  • button_Hardware_Independent

    • +

  • button_Hardware_Lead1600

    • +

  • button_Hardware_RemoveYoke

    • +

  • group_Hardware_Yoke

    • +

  • group_Hardware_YokeInner

    • +

  • popup_Hardware_AvailITC1600s

    • +

  • popup_Hardware_YokedDACs

    • +

  • setvar_Hardware_Status

    • +

  • setvar_Hardware_YokeList

    • +

  • title_hardware_1600inst

    • +
+
+
+
Renamed
+

None

+
+
+
+

Databrowser

+
+
Added
+

None

+
+
+
Removed
+

None

+
+
+
Renamed
+

None

+
+
+
+

Wavebuilder

+
+
Added
+

None

+
+
+
Removed
+

None

+
+
+
Renamed
+

None

+
+
+
+
+

Sweep Formula

+
    +

  • Completely rework the internals to handle multiple datasets with different +sampling intervals in all cases. This change should not affect user code.

    • +

  • merge: Remove it as it is not needed anymore

    • +

  • store:

    +
      +

    • Make stored sweeps and channel unambiguous in the results wave, we now store the full 2D wave

      • +

    • Change serialization format to use JSON wave serialization. +This allows to store multiple waves with all metadata.

      • +
    +
    • +

  • select:

    +
      +

    • Fix data gathering for cases where we did not yet have splitted sweep data

      • +

    • Add support for TTL channels and unassociated channels

      • +

    • Add an optional fourth argument that allows to query sweeps with a specific clamp mode

      • +
    +
    • +

  • data:

    +
      +

    • Silently ignore non-existing epochs when requesting data from multiple sweeps

      • +

    • Clip too large epoch ranges for old data instead of asserting out

      • +
    +
    • +

  • powerspectrum: Add it

    • +

  • Fix parser issues with signed numbers/arrays

    • +

  • Fix buggy computation for formulas like (1)/(1)/(1)/(1)

    • +

  • Make the sweep brower retrievable from the plot via the context menu

    • +

  • Add with keyword to plot multiple y formulas against the same x formula/axis

    • +

  • epochs: Only return the full tag if no shortname is present

    • +

  • epochs/data: Add support for multiple epochs in wildcard syntax, e.g. ["TP_*", "E1*"]

    • +

  • apfrequency: Add more modes for normalization

    • +

  • Add variable support for faster and shorter formulas

    • +

  • avg: Add support for two different averaging modes

    • +

  • tp:

    +
      +

    • Fix property calculation

      • +

    • Add tpss, tpinst, tpbase, tpfit modes

      • +
    +
    • +

  • //+/-/*: Add support for working with multiple datasets

    • +

  • Add operations psx/psxprep/psxstats/psxkernel/psxrisetime for miniature analysis. The below instructional video should help you get started. There is also extensive documentation for the operations and the gui available.

    • +
+
+
    +

  • Plotter:

    +
      +

    • Add more support for customization by operations: SF_META_XAXISLABEL/SF_META_XVALUES/SF_META_MOD_MARKER/SF_META_SHOW_LEGEND/SF_META_XTICKLABELS/SF_META_XTICKPOSITIONS/SF_META_TRACE_MODE/SF_META_CUSTOM_LEGEND

      • +

    • Remove partially broken support for plotting multidimensional text waves

      • +

    • Enhance legend by adding more information on the applied operations, but also compress the text output

      • +

    • Adapt logic how x-waves are mapped to y-waves

      • +

    • Warn by more than 1000 traces and forbid more than 10000 traces. Please file an issue if that breaks your code.

      • +

    • Use our standard trace coloring for averaged sweeps

      • +

    • Restore axes ranges, cursors and annotations positions afte replotting the same SF code

      • +

    • Automatically use different markers or line styles if formulas are different in the same plot

      • +
    +
    • +
+
+
+

AnalysisBrowser

+
    +

  • Allow to load all Stimsets from files containing only stimsets

    • +

  • Revise GUI to allow loading single files and open multiple folders

    • +

  • Handle loading NWBv1 with duplicated sweeps better

    • +
+
+
+

DataBrowser

+

None

+
+
+

DataBrowser/SweepBrowser

+
    +

  • LogbookViewer: Update plot for textual entries in case the labnotebook got resized

    • +

  • LogbookViewer: Avoid plotting the same entry again within a sweep

    • +

  • Always enable tooltips for epoch visualization

    • +

  • Add support for creating a browser in automation mode without additional external subwindows

    • +

  • Improve hiding/showing of the subwindows

    • +

  • Show epoch information also for unassociated DA and TTL channels

    • +

  • Use the GUI channel numbers for TTL data plots in the axis labels

    • +

  • Use the correct colors for TTL channels

    • +

  • Output correct headstage when viewing textual labnotebook entries

    • +
+
+

Dashboard

+
    +

  • Fix rare case of not updating the display due to incorrect cache key deriviation

    • +

  • Handle sweeps without analysis functions better

    • +

  • Accept broken sweeps from PSQ_SquarePulse without PRE_SET_EVENT labnotebook entries

    • +

  • Handle data from previous PSQ analysis function versions better

    • +
+
+
+
+

DA_Ephys

+
    +

  • Be less chatty when no amplifier is connected to a headstage

    • +

  • Support NI hardware USB-6346

    • +

  • Output a help message in case no hardware was found when scanning

    • +

  • Support acquisition without amplifier better

    • +

  • Improve the version check for old NIDAQmx XOPs to not result in an compilation error

    • +

  • Don’t bug out when having oodDAQ enabled and only “TP during DAQ” channels present

    • +

  • Retry amplifier calls on error automatically after waiting 100ms

    • +

  • Make data acquisition more robust in edge cases with ITC hardware

    • +

  • Unify “Delay onset auto” calcuation to avoid epoch gaps at treelevel 0

    • +

  • Fix the search fields for DA/TTL stimsets

    • +

  • Warn about too short stimset epochs before DAQ/TP

    • +

  • Check also unassociated DA channels before DAQ/TP

    • +

  • Fix acquisition with random option

    • +

  • Disallow “TP during DAQ” on unassociated channels

    • +

  • Fix adding empty TTL related labnotebook entries without active TTL channels

    • +

  • Add none entries for the DA/AD channel selection on the hardware tab instead of using an invalid index

    • +
+
+
+

JSON Configuration

+
    +

  • Support saving and restore of plaintext notebook windows

    • +

  • Support saving and restore of MCC gain values

    • +

  • Support upgrading old configuration files. Just load an old configuration +file and save it under a new name. All settings from the old files are taken +over. Rig files are also supported.

    • +

  • Allow saving and restoring of all major MIES GUIs

    • +

  • Support saving and restoring DA_Ephys panels with headstages without associated amplifier

    • +
+
+
+

Downsample

+

None

+
+
+

Analysis Functions

+
    +

  • PSQ_Chirp:

    +
      +

    • Rework chirp cycle code completely as the old heuristic did fail in various occasions

      • +

    • Fix spike detection and add Chirp Spike Evaluation user epoch for visual inspection

      • +

    • Add analysis function parameter BaselineTargetVThreshold

      • +
    +
    • +

  • PSQ_DAScale:

    +
      +

    • Add analysis function parameter BaselineTargetVThreshold

      • +
    +
    • +

  • PSQ_Ramp:

    +
      +

    • Add analysis function parameter BaselineTargetVThreshold

      • +
    +
    • +

  • PSQ_Rheobase:

    +
      +

    • Add analysis function parameter BaselineTargetVThreshold

      • +
    +
    • +

  • SetControlInEvent:

    +
      +

    • Support setting notebooks in general and not only for special cases

      • +

    • Add XXX_CheckParam function to catch errors earlier

      • +
    +
    • +

  • Create the databrowser in automation mode for SweepFormula execution to not +interfere with other open databrowsers for the following analysis functions:

    +
      +

    • PSQ_PipetteInBath

      • +

    • PSQ_SealEvaluation

      • +

    • PSQ_TrueRestingMembranePotential

      • +

    • PSQ_AccessResistanceSmoke

      • +
    +
    • +
+
+
+

Foreign Function interface

+

None

+
+
+

Pulse Average Plot

+

None

+
+
+

Publisher

+

None

+
+
+

General

+
    +

  • Add version checking for ITCXOP2

    • +

  • Add generic functions for dealing with JSON formatted wave notes, see MIES_JSONWaveNotes.ipf

    • +

  • EP_GetEpochs: Add support for old epoch tag formats

    • +

  • Better handle cases in IgorBeforeQuitHook/IgorBeforeNewHook where an +experiment was opened from a read-only location

    • +

  • Add table with all analysis parameters

    • +

  • Allow multithreading also in preemptive threads

    • +

  • Upload the ITCXOP2 logfile as well when uploading logfiles

    • +

  • Add documentation for dDAQ and oodDAQ

    • +

  • Fix wave leaks found with latest IP9 and igortest’s new wave leak detection support

    • +

  • Add support for wildcard matching in FindIndizes

    • +

  • Make graph menu option HorizExpandWithVisX more reliable

    • +

  • Remove support for yoking with ITC hardware

    • +

  • Require a newer IP9 build, r39935, to avoid a bogus save dialog on creating a +new experiment

    • +

  • Remove workarounds for fixed IP9 bugs

    • +

  • Revise JSON layout for MIES log files

    • +

  • Teach GetActiveChannels to return the GUI/HW channel mapping for TTL channels for all hardware types

    • +

  • Add routines JSONToWave and WaveToJSON for igor wave serialization to JSON and back

    • +

  • The complete Sweep Rollback feature was removed as maintaining it and keeping it working 100% reliable was too difficult

    • +

  • Add user ping support (enabled by default), can be disabled via config file or menu option permanently

    • +

  • Don’t deploy the release packages anymore. All users should by now either use the installer or do an installation from git

    • +
+
+
+

TUF XOP

+ +
+
+

ITC XOP 2

+
    +

  • Error out when free waves can not be used in certain cases

    • +

  • Rewrite ITCCloseAll2 to be more robust

    • +

  • Add support for JSON newlines formatted logfiles

    • +

  • Make debugging flag global instead of local to the thread

    • +
+
+
+

ZeroMQ XOP

+
    +

  • Enhance wave serialization examples in Readme.md

    • +

  • Add timesteamp in XOP when creating a logfile entry

    • +

  • Fix dimension label serialization with empty entries in between

    • +
+
+
+

MCC XOP

+

None

+
+
+

MIESUtils XOP

+

None

+
+
+

JSON XOP

+ +
+
+

Labnotebook

+
    +

  • Improve labnotebook key upgrade for IP9 compatibility with existing data

    • +

  • Add descriptions for the textual labnotebook entries

    • +
+
+

New numerical keys

+
    +

  • PSQ_FMT_LBN_TARGETV_THRESHOLD

    • +

  • PSQ_FMT_LBN_CR_STIMSET_QC

    • +

  • Skip Sweeps source: Reason for the sweep skipping

    • +

  • Skip Ahead: Number of ahead skipped sweeps

    • +

  • Double precision data

    • +

  • Save amplifier settings

    • +

  • Require amplifier

    • +
+
+
+

New textual keys

+
    +

  • Device: DAEphys device used for acquisition

    • +

  • TTL Epochs Channel 0-7: TTL epoch information

    • +
+
+
+

Changed numerical entries

+

None

+
+
+

Changed textual entries

+
    +

  • TTL Stim set length: Holds now the decimanted length instead of the undecimated

    • +
+
+
+

Renamed numerical entries

+

None

+
+
+

Renamed textual entries

+

None

+
+
+

Removed numerical entries

+
    +

  • Sweep Rollback: The complete Sweep Rollback feature was removed as maintaining it was too difficult

    • +

  • PSQ_FMT_LBN_CR_CYCLES: Replaced with user epoch Chirp Cycle Evaluation/U_CR_CE

    • +
+
+
+

Removed textual entries

+
    +

  • PSQ_FMT_LBN_CR_STIMSET_QC

    • +
+
+
+
+

Epoch information

+
    +

  • Add Chirp Cycle Evaluation/U_CR_CE for PSQ_Chirp

    • +

  • Add epoch information for new trigonometric epoch types: Ex_TG_Cx, Ex_TG_Cx_Hx, Ex_TG_Ix

    • +

  • Add epoch information for TTL channels

    • +
+
+
+

NWB/IPNWB

+
    +

  • Raise pynwb version used for read test CI to 2.4.0

    • +

  • IPNWB: Minor API fixes

    • +

  • IPNWB: Fix reading very old data (pre NWBv1.0.5)

    • +

  • Avoid bogus warning about third-part stimsets when custom waves are present in the DA/TTL stimset folder

    • +
+
+

File format

+

None

+
+
+
+

Pressure Control

+

None

+
+
+

WaveBuilder

+
    +

  • Improve calculation of the inflection points for trigonometric stimsets

    • +

  • Allow longer stimulus set names, the new maximum is 31 characters

    • +

  • Don’t allow to save empty stimsets or stimsets with empty epochs

    • +
+
+
+

Work Sequencing Engine

+

None

+
+
+

Internal

+
    +

  • Add support for the ListBox GUI type to PGC_SetAndActivateControl

    • +

  • Make MIES version gathering for git checkouts compatible with git 2.38 and higher

    • +

  • Add AccelerateHideTracesPerTrace/AccelerateHideTracesAndColor together with IP code generating this code

    • +

  • check-code.sh: Warn about function statements in for loops and fix most of those cases

    • +

  • Rename confusing minimumSize argument of EnsureLargeEnoughWave

    • +

  • Use DC_DocumentChannelProperty now also exclusively for TTL labnotebook entries

    • +

  • Start using pip package hashes for the documentation packages to enforce +better software supply chain security

    • +
+
+
+

Tests

+
    +

  • Add CheckThatZeroMQMessagingWorks to abort early on ZMQ transport problems

    • +

  • PGC_SetAndActivateControl: Enhance test coverage

    • +

  • Tests: Add ScaleZeroWithCycling

    • +

  • Tests: Add single/multi device tests with RA and a single sweep

    • +

  • Add SWEEPFORMULA_DEBUG define to check_mies_compilation.sh

    • +

  • Check in all experiments for bug messages

    • +

  • Reorganize test folders

    • +

  • Add improved AcquireData_NG to make hardware test parmeterization easier and shorter, also with documentation

    • +

  • Allow tweaking test execution more fine-grained

    • +

  • Make tests work with ITC1600 again

    • +

  • Fix adapting the number of usable async channels to the data acquisition hardware

    • +

  • Adopt latest version of igortest and remove workarounds for fixed bugs

    • +

  • Add some for the AnalysisBrowser

    • +

  • Add tests for checking various acquisition delays

    • +

  • Drop confusing tests which used override functions

    • +

  • Enhance the hardware tests exceution speed a bit by caching the list of available hardware devices

    • +

  • Prefer igortest compilation test support instead of our own hack

    • +

  • Switch to cobertura as output format for coverage information, see also the coverage history

    • +

  • Gather logfiles and the IP diagnostics folder after each CI run with Igor Pro

    • +

  • Make ITC testing more robust and avoid often occurring crashes

    • +

  • Move to github actions for CI and say good-bye to our old on-premise bamboo instance

    • +

  • Add tests with historic MIES data

    • +

  • Add pre-commit config and CI

    • +
+
+
+

Async Framework

+

None

+
+
+

Logging

+
    +

  • Handle logfiles larger than 2GB better when uploading them. Also split them for faster access above a certain threshold.

    • +
+
+
+

Installer

+
    +

  • Remove old MIES installations with developer (/CIS) installer

    • +
+
+
+
+

Release 2.6

+
+

Controls

+

All added, removed or renamed controls of the main GUIs are listed. These lists are intended to help upgrading the JSON +configuration files. Controls, like GroupBox’es, which can not be read/written with the configuration code are not included.

+
+

DA_Ephys

+
+
Added
+

None

+
+
+
Removed
+

None

+
+
+
Renamed
+

None

+
+
+
+

Databrowser

+
+
Added
+

None

+
+
+
Removed
+

None

+
+
+
Renamed
+

None

+
+
+
+

Wavebuilder

+
+
Added
+

None

+
+
+
Removed
+

None

+
+
+
Renamed
+

None

+
+
+
+
+

Sweep Formula

+
    +

  • Rework builtin help +- Index with links at the bottom, with back buttons +- In-Editor help via tooltip +- Enhance it in various places

    • +

  • Add basic syntax coloring to Editor

    • +

  • Enhance test coverag

    • +
+
+
+

AnalysisBrowser

+

None

+
+
+

DataBrowser

+

None

+
+
+

DataBrowser/SweepBrowser

+
    +

  • Fix Selected checkbox in Logbook panel

    • +
+
+

Dashboard

+
    +

  • Handle manually stopped sweeps better

    • +
+
+
+
+

DA_Ephys

+

None

+
+
+

JSON Configuration

+
    +

  • Add LPF primary output

    • +
+
+
+

Downsample

+

None

+
+
+

Analysis Functions

+
    +

  • PSQ_Chirp:

    +
      +

    • Add UserOnsetDelay/UseTrueRestingMembranePotentialVoltage/AsyncQCChannels analysis parameter

      • +

    • Make SamplingMultiplier/NumberOfFailedSweeps an required analysis parameter

      • +
    +
    • +

  • PSQ_SealEvaluation:

    +
      +

    • Make BaselineChunkLength a lower limit for WaveBuilder epoch length +instead of an exact match. This allows to have longer epochs that what is +used for baseline evaluation.

      • +

    • Made SweepFormula execution more robust

      • +

    • Make it work with other DACs than zero

      • +

    • Make SamplingMultiplier/BaselineRMSShortThreshold/BaselineRMSLongThreshold +required analysis parameters

      • +

    • Add NextIndexingEndStimSetName/AsyncQCChannels analysis parameter

      • +
    +
    • +

  • Add PSQ_AccessResistanceSmoke

    • +

  • Add PSQ_TrueRestingMembranePotential

    • +

  • PSQ_PipetteInBath:

    +
      +

    • Made SweepFormula execution more robust

      • +

    • Make SamplingMultiplier/BaselineRMSShortThreshold/BaselineRMSLongThreshold +required analysis parameters

      • +

    • Add NextIndexingEndStimSetName/AsyncQCChannels analysis parameter

      • +
    +
    • +

  • Allow to change the indexing state in POST_DAQ_EVENT

    • +

  • PSQ_SquarePulse:

    +
      +

    • Use the correct labnotebook prefix again and not the one for +PSQ_SealEvaluation. Broken since 1a64ca17 (PSQ_SealEvaluation: Add it, +2022-02-22).

      • +

    • Add AsyncQCChannels analysis parameter

      • +
    +
    • +

  • PSQ_DAScale:

    +
      +

    • Avoid warning from FitResistance about missing labnotebook keys if the sweep did not pass.

      • +

    • Add AsyncQCChannels analysis parameter

      • +
    +
    • +

  • PSQ_Rheobase:

    +
      +

    • Add AsyncQCChannels analysis parameter

      • +
    +
    • +

  • PSQ_Ramp:

    +
      +

    • Add AsyncQCChannels analysis parameter

      • +
    +
    • +
+
+
+

Foreign Function interface

+

None

+
+
+

Publisher

+
    +

  • Reorganize ZeroMQ publishing functions and move all of them into File MIES_Publish.ipf

    • +

  • Add example output for each message

    • +

  • Publish DAQ/TP start and stop, see also PUB_DAQStateChange(). There is no message sent for TP during ITI.

    • +
+
+
+

Pulse Average Plot

+

None

+
+
+

General

+
    +

  • Fix invalid backup path syntax which newer IP9 versions don’t accept

    • +

  • Remove support for Igor Pro 8

    • +

  • Use Xoshiro++256 as default pseudo random number generator

    • +

  • Asynchronous channels: Make them work with NI hardware

    • +

  • Output special error message on MCC bug where the DA gain is always zero

    • +
+
+
+

TUF XOP

+

None

+
+
+

ITC XOP 2

+

None

+
+
+

ZeroMQ XOP

+

None

+
+
+

MCC XOP

+

None

+
+
+

MIESUtils XOP

+

None

+
+
+

Labnotebook

+ +
+

New numerical keys

+
    +

  • Get/Set Inter-trial interval

    • +

  • PSQ_FMT_LBN_AR_ACCESS_RESISTANCE

    • +

  • PSQ_FMT_LBN_AR_ACCESS_RESISTANCE_PASS

    • +

  • PSQ_FMT_LBN_AR_STEADY_STATE_RESISTANCE

    • +

  • PSQ_FMT_LBN_AR_RESISTANCE_RATIO

    • +

  • PSQ_FMT_LBN_AR_RESISTANCE_RATIO_PASS

    • +

  • PSQ_FMT_LBN_VM_FULL_AVG

    • +

  • PSQ_FMT_LBN_VM_FULL_AVG_ADIFF

    • +

  • PSQ_FMT_LBN_VM_FULL_AVG_ADIFF_PASS

    • +

  • PSQ_FMT_LBN_VM_FULL_AVG_RDIFF

    • +

  • PSQ_FMT_LBN_VM_FULL_AVG_RDIFF_PASS

    • +

  • PSQ_FMT_LBN_VM_FULL_AVG_PASS

    • +

  • PSQ_FMT_LBN_ASYNC_PASS

    • +

  • Async Alarm XX State

    • +
+
+
+

New textual keys

+

None

+
+
+

Changed numerical entries

+

None

+
+
+

Changed textual entries

+

None

+
+
+

Renamed numerical entries

+

None

+
+
+

Renamed textual entries

+

None

+
+
+
+

Epoch information

+
    +

  • EP_GetEpochs: Allow to query epoch information during MID_SWEEP_EVENT

    • +
+
+
+

NWB/IPNWB

+

None

+
+

File format

+

None

+
+
+
+

Pressure Control

+

None

+
+
+

WaveBuilder

+
    +

  • Use Xoshiro++266 as pseudo random number generator (PRNG) for new stimsets. +For compatibility reasons the existing PRNGs are kept for existing stimsets.

    • +
+
+
+

Work Sequencing Engine

+

None

+
+
+

Internal

+
    +

  • Add new option PROP_GREP to FindIndizes()

    • +

  • Update documentation toolchain

    • +
+
+
+

Tests

+

None

+
+
+

Async Framework

+

None

+
+
+

Logging

+

None

+
+
+

Installer

+
    +

  • Remove support for IP8 and add support for IP10 (not yet available though at the time of writing)

    • +
+
+
+
+

Release 2.5

+
+

Controls

+

All added, removed or renamed controls of the main GUIs are listed. These lists are intended to help upgrading the JSON +configuration files. Controls, like GroupBox’es, which can not be read/written with the configuration code are not included.

+
+

DA_Ephys

+
+
Added
+

None

+
+
+
Removed
+

None

+
+
+
Renamed
+

None

+
+
+
+

Databrowser

+
+
Added
+
    +

  • button_sweepformula_all_code

    • +

  • check_limit_x_selected_sweeps

    • +

  • popupext_resultsKeys

    • +
+
+
+
Removed
+
    +

  • button_DataBrowser_setaxis

    • +
+
+
+
Renamed
+

None

+
+
+
+

Wavebuilder

+
+
Added
+

None

+
+
+
Removed
+
    +

  • button_WaveBuilder_setaxisA

    • +
+
+
+
Renamed
+

None

+
+
+
+
+

Sweep Formula

+
    +

  • Make tp more robust

    • +

  • Add store operation, see here

    • +

  • We now store all executed code in the results waves with metadata and allow browsing old code again

    • +

  • Change argument order in epochs operation to match the order of the data operation

    • +

  • Add select operation as replacement for passing channels and sweeps to various operations. +This now also adds full support for accessing non-displayed sweeps.

    • +

  • The operations data, epochs, tp and labnotebook now accept selections via select. +For convenience this parameter is optional, this means data([100-200]) now +returns all displayed data in the range from 100ms to 200ms.

    • +
+
+
+

AnalysisBrowser

+

None

+
+
+

DataBrowser

+

None

+
+
+

DataBrowser/SweepBrowser

+
    +

  • Fix placement of textual entries in the logbook graph

    • +

  • Add option to show only displayed sweeps in logbook graph

    • +

  • Fix updating textual entries after each new sweep

    • +

  • Use graph font size of 10 for logbook graph by default

    • +

  • Always re-execute the sweep formula code when the current selection changes

    • +

  • Show description of numerical labnotebook entries when hovering over the y-axis label

    • +

  • Allow resetting the axis scaling via the wellknown Ctrl+A shortcut in all circumstances with subwindows. +This makes the reset scaling button superfluous.

    • +
+
+

Dashboard

+
    +

  • PSQ_Chirp: Handle missing spike pass wave gracefully

    • +

  • Convert baseline voltage correctly in debug plotting routine for chirp bounds

    • +

  • Output more detailed error message on baseline QC failures

    • +

  • Handle aborted data acquisition better

    • +

  • Ignore set but disabled analysis functions

    • +
+
+
+
+

DA_Ephys

+
    +

  • Check free memory when storing every TP

    • +

  • Fix testpulse caching with NI hardware

    • +

  • Handle corrupt package settings files and create a default one in this case

    • +

  • Add optional daily logfile upload (defaults to off)

    • +

  • Prevent saving incompatible sweep and config wave combinations gracefully

    • +

  • Fix indexing error when restarting data acquisition during PSQ_Ramp execution

    • +

  • Make restarting data acquisition more robust in case it asserts out due to +lingering runtime errors

    • +

  • Don’t enable “Sweep rollback” on unlocking

    • +

  • Make the TP power spectrum work again with odd number of rows in the DAQDataWave

    • +

  • Add a new type of logbook: The results waves, textual and numerical, +hold analysis results from Sweep Formula. Their layout is the same as for the +standard labnotebooks.

    • +
+
+
+

JSON Configuration

+

None

+
+
+

Downsample

+

None

+
+
+

Analysis Functions

+
    +

  • PSQ_DAScale/PSQ_Rheobase/PSQ_Ramp/PSQ_Chirp:

    +
      +

    • Store the PSQ_FMT_LBN_TARGETV value with the correct amplitude. Broken since +0a86df51 (PSQ Analysis functions: Store the baseline voltage when +evaluated, 2021-01-15).

      • +
    +
    • +

  • PSQ_Chirp:

    +
      +

    • Handle scalingFactor of zero gracefully

      • +

    • Bugfix: Use correct conversion from V to mV in production code

      • +

    • Add support for setting autobias target voltage

      • +
    +
    • +

  • PSQ_PipetteInBath:

    +
      +

    • Handle turned on overlay sweeps correctly

      • +

    • Use correct conversion value for storing PSQ_FMT_LBN_PB_RESISTANCE. +Broken since 6e32699f (PSQ_PipetteInBath: Add it, 2021-12-08).

      • +
    +
    • +

  • Add PSQ_SealEvaluation

    • +

  • Analysis functions can now read and write epoch information also during the post sweep and set event, see +see here.

    • +

  • Add PSQ_PipetteInBath

    • +
+
+
+

Foreign Function interface

+

None

+
+
+

Pulse Average Plot

+

None

+
+
+

General

+
    +

  • Require newer IP9 versions to fix some stability issues

    • +
+
+
+

TUF XOP

+
    +

  • Add XOP

    • +
+
+
+

ITC XOP 2

+
    +

  • Automatically retry opening devices with ITC1600 hardware in known error +situations, see also here.

    • +
+
+
+

ZeroMQ XOP

+

None

+
+
+

MCC XOP

+

None

+
+
+

MIESUtils XOP

+

None

+
+
+

Labnotebook

+
    +

  • The units of all user entries written in the analysis functions are now +documented here and +here

    • +

  • We now store additional values for each numerical labnotebook entry: +- Description +- Headstage contingency +- Applicable clamp modes

    +

    See here for the generated table with all stock numerical entries

    +
    • +
+
+

New numerical keys

+
    +

  • PSQ_FMT_LBN_LEAKCUR_PASS

    • +

  • PSQ_FMT_LBN_LEAKCUR

    • +

  • PSQ_FMT_LBN_PB_RESISTANCE_PASS

    • +

  • PSQ_FMT_LBN_PB_RESISTANCE

    • +

  • PSQ_FMT_LBN_SE_RESISTANCE_A

    • +

  • PSQ_FMT_LBN_SE_RESISTANCE_B

    • +

  • PSQ_FMT_LBN_SE_RESISTANCE_MAX

    • +

  • PSQ_FMT_LBN_SE_RESISTANCE_PASS

    • +

  • PSQ_FMT_LBN_SE_TESTPULSE_GROUP

    • +
+
+
+

New textual keys

+
    +

  • Follower Device: Always add it, even if empty

    • +
+
+
+

Changed numerical entries

+
    +

  • PSQ_FMT_LBN_INITIAL_SCALE: Remove unit

    • +

  • MSQ_FMT_LBN_SPIKE_COUNTS: Remove unit

    • +

  • MSQ_FMT_LBN_ACTIVE_HS: Add LABNOTEBOOK_BINARY_UNIT as unit

    • +
+

The following entries now have a correct - (LABNOTEBOOK_NO_TOLERANCE) as tolerance:

+
+
    +

  • Serial Number

    • +

  • Channel ID

    • +

  • ComPort ID

    • +

  • AxoBus ID

    • +

  • Operating Mode

    • +

  • Scaled Out Signal

    • +

  • Alpha

    • +

  • Scale Factor

    • +

  • Scale Factor Units

    • +

  • LPF Cutoff

    • +

  • Membrane Cap

    • +

  • Ext Cmd Sens

    • +

  • Raw Out Signal

    • +

  • Raw Scale Factor

    • +

  • Raw Scale Factor Units

    • +

  • Hardware Type

    • +

  • Secondary Alpha

    • +

  • Secondary LPF Cutoff

    • +

  • Slow current injection settling time

    • +

  • TP Amplitude VC

    • +

  • TP Amplitude IC

    • +

  • TP Pulse Duration

    • +
+
+

Changed unit to MΩ from MOhm for the following entries:

+
+
    +

  • TP Peak Resistance

    • +

  • TP Steady State Resistance

    • +

  • Whole Cell Comp Resist

    • +

  • Bridge Bal Value

    • +

  • Series Resistance

    • +

  • Minimum TP resistance for tolerance

    • +
+
+

Remove a. u. units for the following entries:

+
+
    +

  • Sweep Rollback

    • +

  • Skip Sweeps

    • +

  • DAC

    • +

  • ADC

    • +

  • Set Sweep Count

    • +

  • TTL rack zero channel

    • +

  • TTL rack one channel

    • +

  • Repeat Sets

    • +

  • Sampling interval multiplier

    • +

  • Stim set length

    • +

  • Repeated Acq Cycle ID

    • +

  • Stim Wave Checksum

    • +

  • Sampling interval multiplier

    • +

  • Set Cycle Count

    • +

  • Stimset Acq Cycle ID

    • +

  • Digitizer Hardware Type

    • +

  • Clamp Mode

    • +

  • Igor Pro bitness

    • +

  • DA ChannelType

    • +

  • AD ChannelType

    • +

  • Autobias %

    • +

  • Epochs version

    • +
+
+
+
+

Changed textual entries

+

None

+
+
+

Renamed numerical entries

+

None

+
+
+

Renamed textual entries

+

None

+
+
+
+

Epoch information

+
    +

  • Always shorten too long user epoch entries, even if acquisition finished as planned

    • +

  • Clip oodDAQ region epochs to the available stimset length

    • +

  • Fix the unacquired epoch length when too long user epochs are present

    • +
+
+
+

NWB/IPNWB

+
    +

  • Export results waves into NWBv2

    • +
+
+

File format

+

None

+
+
+
+

Pressure Control

+

None

+
+
+

WaveBuilder

+
    +

  • Make saving stimsets faster by avoiding duplicated update calls

    • +

  • Avoid deleting existing stimsets on save errors due to analysis function parameter checks

    • +

  • Keep selected x-axis range on display update

    • +

  • Allow resetting the axis scaling via the wellknown Ctrl+A shortcut in all circumstances with subwindows. +This makes the reset scaling button superfluous.

    • +
+
+
+

Work Sequencing Engine

+
    +

  • Add wrappers for toggling Store every testpulse

    • +

  • IVS_RunGigOhmSealQC now runs the PSQ_SealEvaluation analysis function

    • +

  • IVS_runBaselineCheckQC now runs the PSQ_PipetteInBath analysis function

    • +

  • Fix returned sweep number in published zeromq messages

    • +
+
+
+

Internal

+
    +

  • Upgrade IUTF to a version which also support code coverage for macros

    • +

  • Add development hints for writing analysis functions, see here

    • +

  • Add linting tool in tools/check-code.sh to avoid common issues

    • +

  • Add the full stacktrace to the log entries for BUG and BUG_TS

    • +

  • Add threadsafe variant BUG_TS

    • +

  • Make the extended GUI popup menu names work also with non-liberal input names

    • +

  • Add constants XXX_TO_YYY for converting between different decimal +multipliers for values with units here. +Using that is also enforced with additional checks in tools/check-code.sh.

    • +
+
+
+

Tests

+
    +

  • Add tests for TPStorage wave

    • +

  • Add generic range checks for USER labnotebook entries in the PSQ analysis functions

    • +

  • Skip outdated deployment on main branch

    • +

  • Make the tests work with a real amplifier and model cell

    • +

  • Check amplifier presence before locking

    • +

  • Only perform expensive checks in CI

    • +

  • Create code coverage reports from tests on the main branch

    • +
+
+
+

Async Framework

+

None

+
+
+

Logging

+

None

+
+
+

Installer

+
    +

  • Install TUF XOP without hardware XOPs

    • +
+
+
+
+

Release 2.4

+
+

Controls

+

All added, removed or renamed controls of the main GUIs are listed. These lists are intended to help upgrading the JSON +configuration files. Controls, like GroupBox’es, which can not be read/written with the configuration code are not included.

+
+

DA_Ephys

+
+
Added
+
    +

  • check_TP_SendToAllHS

    • +

  • check_DataAcq_AutoTP

    • +

  • setvar_DataAcq_IinjMax

    • +

  • setvar_DataAcq_targetVoltage

    • +

  • setvar_DataAcq_targetVoltageRange

    • +

  • setvar_Settings_autoTP_int

    • +

  • setvar_Settings_autoTP_perc

    • +
+
+
+
Removed
+

None

+
+
+
Renamed
+

None

+
+
+
+

Databrowser

+
+
Added
+
    +

  • button_sweepFormula_tofront

    • +
+
+
+
Removed
+

None

+
+
+
Renamed
+

None

+
+
+
+

Wavebuilder

+
+
Added
+

None

+
+
+
Removed
+

None

+
+
+
Renamed
+

None

+
+
+
+
+

Sweep Formula

+
    +

  • Allow = in strings

    • +

  • Add epoch command to extract epoch information, see the documentation

    • +

  • Fix bugs in comment character (#) handling

    • +

  • Add and keyword to create multiple graphs from one session, see the +documentation

    • +

  • Improved error handling and made parsing more robust

    • +

  • Fixed handling of , and use a more consistent parsing strategy

    • +

  • Fix plotting of 2D vs 0D data

    • +

  • Heavily revised the documentation

    • +

  • data now accepts an epoch short name as range

    • +
+
+
+

AnalysisBrowser

+

None

+
+
+

DataBrowser

+

None

+
+
+

DataBrowser/SweepBrowser

+
    +

  • Make browsing old labnotebooks prior to 5c9a5e4c (Add “Acquisition State” as +default labnotebook entry, 2020-11-27) work again

    • +

  • Show the tree level in epoch visualization tooltips as well

    • +

  • Require the modifier key ALT for changing sweeps with the mouse wheel

    • +

  • Use a separate axis for displaying epoch information and don’t require DA data to be shown anymore

    • +

  • Make overlay sweeps selections faster

    • +

  • Allow selecting sweeps and set sweep/cycle counts

    • +

  • Select a better default x axis when displaying TPStorage data without any acquired sweeps

    • +

  • Preselect device and experiment in the SweepBrowser for enhanced usability

    • +
+
+

Dashboard

+
    +

  • Support sampling frequency QC failure

    • +
+
+
+
+

DA_Ephys

+
    +

  • Fix updating indexing metadata on changing stimsets in the DA tab with the ALL popup menues

    • +

  • Handle adding new stimsets when the DA/TTL tabs already had some selected better

    • +

  • Use the correct GUI procedure for Popup_Settings_DecMethod

    • +

  • Fix some edge cases where pending comments in the SetVariable or the comment +notebook were not handled correctly. The fallout was that these comments were +not saved to NWB.

    • +

  • Use 35% as default baseline for the Testpulse

    • +

  • Added Auto testpulse adaptation, see the documentation. This +also added the following new entries to TPStorage: TPCycleID, +AutoTPAmplitude, AutoTPBaseline, AutoTPBaselineRangeExceeded, +AutoTPCycleID, AutoTPBaselineFitResult, AutoTPDeltaV

    • +

  • Avoid creating the ITC1600 Device 0 path for yoking if not needed

    • +
+
+
+

JSON Configuration

+
    +

  • Switch back to Headstage 0 after configuration

    • +

  • Assert out on missing or invalid stimulus set file

    • +
+
+
+

Downsample

+

None

+
+
+

Analysis Functions

+
    +

  • PSQ_DAScale/PSQ_SquarePulse/PSQ_Rheobase/PSQ_Ramp/PSQ_Chirp:

    +
      +

    • Enforce that we have the expected sampling frequency of 50kHz. See the +analysis function parameters SamplingMultiplier and +SamplingFrequency to accomodate other hardware than ITC.

      • +

    • Make setting the SamplingMultiplier more robust. Previously it was not +always set due to a combination of three unrelated bugs.

      • +

    • Make the baseline QC RMS long/short thresholds configurable via the +analysis parameters BaselineRMSShortThreshold and BaselineRMSLongThreshold. +The used values are written into the labnotebook as well.

      • +

    • The time slices used for baseline QC (called chunks in MIES) are now stored +as user epochs with the tag Name=Baseline Chunk;Index=<X>;ShortName=U_BLC<X>.

      • +
    +
    • +

  • It is now possible to add user epochs in the PRE_SWEEP_CONFIG_EVENT and +the PRE_SET_EVENT events in addition to the MID_SWEEP_EVENT.

    • +

  • PSQ_Ramp: Add user epochs for the unacquired data region due to the restart during DAQ

    • +

  • PSQ_Chirp:

    +
      +

    • Fix pulse retrieval for certain edge cases of epoch information

      • +

    • Baseline QC is now always done, even if the spike check fails

      • +

    • Complain if NumberOfFailedSweeps is larger than the number of sweeps in the stimset

      • +

    • Add BoundsEvaluationMode to selectively evaluate only lower or upper parts of the chirp

      • +

    • Rename LowerRelativeBound/UpperRelativeBound to InnerRelativeBound/OuterRelativeBound

      • +
    +
    • +

  • SC_SpikeControl: Enhance reaction to too-many failed spikes and add +the new DaScaleTooManySpikesOperator and DaScaleTooManySpikesModifier +analysis parameters.

    • +

  • Introduce a new signature for XXX_CheckParam functions. The old signature +is still supported, see also here.

    • +
+
+
+

Foreign Function interface

+
    +

  • New ZeroMQ messages on clamp mode switch, auto TP success/fail, pressure breakin, amplifier auto bridge balance

    • +
+
+
+

Pulse Average Plot

+

None

+
+
+

General

+
    +

  • Remove support for 32bit Igor Pro versions

    • +

  • Better inform users about the next steps when trying to turn of ASLR for ITC hardware

    • +

  • PGC_SetAndActivateControl: Require valid values for popup menus and sliders

    • +

  • PGC_SetAndActivateControl: Make setting a disabled control an error by default

    • +

  • Nicified the HTML documentation a bit

    • +
+
+
+

ITC XOP 2

+

None

+
+
+

ZeroMQ XOP

+

None

+
+
+

MCC XOP

+

None

+
+
+

MIESUtils XOP

+

None

+
+
+

Labnotebook

+
+

New numerical keys

+
    +

  • PSQ_FMT_LBN_SAMPLING_PASS: Pass/Fail state of the sampling interval check

    • +

  • PSQ_FMT_LBN_RMS_SHORT_PASS: Short RMS baseline threshold [V]

    • +

  • PSQ_FMT_LBN_RMS_LONG_PASS: Long RMS baseline threshold [V]

    • +

  • TP Auto On/Off

    • +

  • TP Auto max current

    • +

  • TP Auto voltage

    • +

  • TP Auto voltage range

    • +

  • TP buffer size (INDEP_HEADSTAGE)

    • +

  • Minimum TP resistance for tolerance (INDEP_HEADSTAGE)

    • +

  • Send TP settings to all headstages (INDEP_HEADSTAGE)

    • +

  • TP Auto percentage (INDEP_HEADSTAGE)

    • +

  • TP Auto interval (INDEP_HEADSTAGE)

    • +

  • TP Auto QC

    • +

  • TP Cycle ID

    • +
+
+
+

New textual keys

+

None

+
+
+

Changed numerical entries

+
    +

  • Set Cycle Count: This was previously erroneously set to 0 for TP +channels, it is now always NaN in this case.

    • +

  • TP buffer size: Is now only present when the TP ran and therefore uses +TEST_PULSE_MODE as entrySourceType

    • +

  • TP Amplitude IC: New unit mV

    • +

  • TP Amplitude VC: New unit pA

    • +
+
+
+

Changed textual entries

+

None

+
+
+

Renamed numerical entries

+

None

+
+
+

Renamed textual entries

+

None

+
+
+
+

Epoch information

+
    +

  • Add short names for all stock epochs in the format ShortName=XX. This allows to use names like TP in +the sweepformula epochs command instead of the complete tag. See here for the detailed documentation.

    • +

  • Don’t add epoch information for third-party stimsets or for TP during DAQ simsets

    • +

  • Handle prematurely stopped sweeps better. The epochs are now shortend to only +cover really acquired data. Epochs which are completely outside the acquired +data are dropped. Unacquired data is now also properly tagged with the +special epoch Unacquired data.

    • +

  • Disallow some characters in epoch tags

    • +

  • Add support for user epochs via EP_AddUserEpoch, see the documentation.

    • +

  • Revise naming so that we now have always key value pairs like A=B and also a more uniform naming.

    • +
+
+
+

NWB/IPNWB

+
    +

  • Export MIES epoch information into NWBv2 files. The epoch information is +stored in /intervals/epochs. See Epoch Information for the +epoch documentation and code examples how to read it.

    • +

  • Store the Zero MQ XOP logfile as well if present

    • +

  • Only store logfile entries from the same day and not the whole files

    • +
+
+

File format

+

None

+
+
+
+

Pressure Control

+

None

+
+
+

WaveBuilder

+
    +

  • Fixed recreation of third party stimsets

    • +
+
+
+

Work Sequencing Engine

+
    +

  • Return success/fail state from IVS_ExportAllData

    • +
+
+
+

Internal

+
    +

  • Added mies-nwb2-compound XOP for writting epoch information into NWBv2 files

    • +

  • Fixed and documented the best approach for try/catch situations

    • +

  • GetLastSettingChannel: Make returning INDEP_HEADSTAGE entries work again

    • +

  • GetSweepsWithSetting: Don’t return invalid sweep numbers

    • +

  • Updated JSON XOP

    • +

  • Rewrote much of the testpulse settings code during testpulse runs for auto testpulse

    • +

  • Upgraded documentation toolchain

    • +

  • Use a proper name for the DAQ device in the code instead of panelTitle

    • +
+
+
+

Tests

+
    +

  • Add epoch consistency checks to all tests with hardware

    • +

  • Use the best test assertion for each case and avoid constructs like CHECK(1 == i)

    • +

  • Some test cases were failing with ITC1600 hardware

    • +
+
+
+

Async Framework

+

None

+
+
+

Logging

+

None

+
+
+

Installer

+
    +

  • Sign the installer with an EV code signing certificate. This should avoid +most problems with antivirus and security software. See here +for details.

    • +

  • Always install the ZeroMQ XOP

    • +
+
+
+
+

Release 2.3

+
+

Controls

+

All added, removed or renamed controls of the main GUIs are listed. These lists are intended to help upgrading the JSON +configuration files. Controls, like GroupBox’es, which can not be read/written with the configuration code are not included.

+
+

DA_Ephys

+

None

+
+
+

Databrowser/Sweepbrowser

+
+
Added
+
    +

  • check_BrowserSettings_VisEpochs

    • +

  • popup_Device

    • +

  • popup_experiment

    • +

  • popupext_TPStorageKeys

    • +
+
+
+
Removed
+

None

+
+
+
Renamed
+

None

+
+
+
+

Wavebuilder

+
+
Added
+

None

+
+
+
Removed
+
    +

  • setvar_explDeltaValues_T12

    • +
+
+
+
Renamed
+

None

+
+
+
+
+

Sweep Formula

+

None

+
+
+

AnalysisBrowser

+
    +

  • Display the exact file type in the listbox

    • +

  • Allow resaving an NWBv1 file as NWBv2

    • +
+
+
+

DataBrowser

+
    +

  • Make selecting the first existing sweep on locking more robust

    • +
+
+
+

DataBrowser/SweepBrowser

+
    +

  • Make deleting the datafolder on panel close more reliable

    • +

  • Allow browsing TPStorage/Labnotebook waves. This also makes the dedicated +panels for the sweepbrowser unnecessary and these have been removed.

    • +

  • Make the labnotebook key menues better viewable with a lot (> 400) of entries

    • +

  • Make epoch viewing generally available for users (IP9 only)

    • +

  • Revamp settings tab

    • +
+
+

Dashboard

+
    +

  • Make the failure messages for PSQ analysis functions more robust and include per sweep information

    • +

  • Disable/Enable the Passed Sweeps/Failed Sweeps checkboxes with the Dashboard Enable checkbox

    • +

  • Handle bogus sweep data without “Baseline QC” entry better

    • +

  • Show result message for prematurely stopped sweeps

    • +
+
+
+
+

DA_Ephys

+
    +

  • Allow PCIe-6341 as new NI device for data acquisition

    • +

  • Read NWB version correctly for per-sweep NWB export

    • +

  • Try restarting DAQ/TP automatically on mismatched MCC gains instead of telling the user to do it

    • +
+
+
+

JSON Configuration

+

None

+
+
+

Downsample

+

None

+
+
+

Analysis Functions

+
    +

  • Fix PSQ_DAScale/PSQ_Chirp failing to work with headstage numbers different than zero

    • +

  • Remove PRE_SWEEP_EVENT and repurpose it as PRE_SWEEP_CONFIG_EVENT. Users +had difficulties using PRE_SWEEP_EVENT as that happened after configuring +the sweep and thus did not allow tweaking settings for the current sweep +anymore. We therefore decided to remove that event and repurpose it as +PRE_SWEEP_CONFIG_EVENT which is now issued before the sweep is configured. +See the analysis function +documentation.

    • +

  • Teach ``SetControlInEvent`` to accept ``Pre Sweep`` entries as ``Pre Sweep Config`` entries but warn users

    • +

  • ``PSQ_DAScale``: Find the correct last passing rheobase sweep

    • +

  • Add ``AFH_GetHeadstageFromActiveADC``

    • +

  • Rework decision logic for post pulse baseline chunks. These could have been erroneously failed in edge cases.

    • +

  • ``PSQ_Chirp``: Use the fitted resistance instead of the resistance at a single point

    • +
+
+
+

Foreign Function interface

+

None

+
+
+

Pulse Average Plot

+
    +

  • Make updating the scale bars more robust

    • +
+
+
+

General

+
    +

  • Update manual installation instructions

    • +

  • Add a pull request template for github

    • +

  • Check also some common debug defines in the installation check

    • +

  • Allow downloading stimsets from DANDI

    • +

  • Add new acquisition state AS_PRE_SWEEP_CONFIG

    • +

  • MIES now requires the released version of Igor Pro 9, instead of supporting +an intermediate beta version. Igor Pro 8 is still supported but +support for it will be removed in one of the next releases.

    • +

  • Add cell state as new entry into TPStorage

    • +
+
+
+

ITC XOP 2

+

None

+
+
+

ZeroMQ XOP

+

None

+
+
+

MCC XOP

+

None

+
+
+

MIESUtils XOP

+

None

+
+
+

Labnotebook

+
    +

  • The labnotebook waves are upgraded so that all keys are valid liberal object names (required by Igor Pro 9). This +required invalid keys to be renamed. See below for a list of renamed stock entries. +Also user entries are renamed as well.

    • +

  • Error out when trying to add labnotebook entries with invalid keys

    • +
+
+

New numerical keys

+
    +

  • TP after DAQ: If the testpulse is run after data acquisition or not

    • +

  • DAQ stop reason: Enumeration value explaining why data acquisition was stopped, see DQ_STOP_REASON for +all possible values.

    • +

  • Epochs Version: Version of the epoch information

    • +

  • Add the version of the major builtin analysis functions to the labnotebook:

    +
      +

    • USER_Chirp version

      • +

    • USER_DA Scale version

      • +

    • USER_F Rheo E version

      • +

    • USER_Ramp version

      • +

    • USER_Rheobase version

      • +

    • USER_Spike Control version

      • +

    • USER_Squ. Pul. version

      • +
    +
    • +
+
+
+

New textual keys

+
    +

  • Indexing End Stimset: The ending stimset for locked/unlocked indexing of DA channels

    • +

  • The following entries are now also available for TTL channels. These are +stored hardware agnostic with NUM_DA_TTL_CHANNELS entries in the +INDEP_HEADSTAGE layer:

    +
      +

    • TTL Indexing End Stimset

      • +

    • TTL Stimset length

      • +

    • TTL Stimset checksum

      • +

    • TTL Stimset wave note (URL encoded)

      • +
    +
    • +

  • Set cycle counts for TTL channels:

    +
      +

    • TTL rack zero set cycle counts (ITC hardware)

      • +

    • TTL rack one set cycle counts (ITC hardware)

      • +

    • TTL set cycle counts (NI hardware)

      • +
    +
    • +
+
+
+

Changed numerical entries

+
    +

  • Delta I: Use the correct unit A (amperes)

    • +
+
+
+

Renamed numerical entries

+
    +

  • Async AD $Channel: $Title -> Async AD $Channel [$Title]

    • +
+
+
+

Changed textual entries

+

None

+
+
+

Renamed textual entries

+
    +

  • JSON config file: path -> JSON config file [path]

    • +

  • JSON config file: stimset nwb file path -> JSON config file [stimset nwb file path]

    • +

  • JSON config file: SHA-256 hash -> JSON config file [SHA-256 hash]

    • +
+
+
+
+

Epoch information

+
    +

  • Add missing trailing baseline for:

    +
    +
      +

    • Stimsets when acquiring on multiple headstages with different length stimsets

      • +

    • Pulse train epochs in edge cases

      • +
    +
    +
    • +
+
+
+

NWB/IPNWB

+
    +

  • Make per-sweep NWB export faster by pushing it into the ASYNC framework. This +makes the overhead smaller than 20ms on recent PCs. Please note that the +stimsets are not written anymore to the NWB in this mode.

    • +

  • We now save again always all four labnotebook waves in NWB. The previous +optimization which skipped empty ones turned out to be harmful +to downstream users which were not prepared for this.

    • +

  • /general/generated_by: Store the HDF5 library version and sweep epoch version

    • +

  • Store the correct device name for NI devices

    • +
+
+

File format

+

None

+
+
+
+

Pressure Control

+
    +

  • Fix gathering pressure changes in TPStorage

    • +

  • Publish pressure method changes and sealed state via ZeroMQ. See +FFI_GetAvailableMessageFilters +for all available message filters

    • +
+
+
+

WaveBuilder

+
    +

  • Rename function for adding analysis parameters programmatically: WBP_AddAnalysisParameter -> AFH_AddAnalysisParameter

    • +

  • Create an API for creating, modifying and deleting stimsets programmatically. +See Simset API +for examples and documentation.

    • +

  • Make all parameter waves have valid liberal object names as dimension labels (required for Igor Pro 9)

    • +
+
+
+

Work Sequencing Engine

+

None

+
+
+

Internal

+
    +

  • Many more functions are now marked as threadsafe. In addition the labnotebook +getters now also work in preemptive threads.

    • +

  • Add a convenient way to debug threadsafe functions. See Debugging threadsafe functions +for instructions. This introduced the THREADING_DISABLED define which allows code to handle this case gracefully.

    • +

  • Fix compile errors with Igor Pro 9 due to duplicated case labels

    • +

  • Make dimension labels valid liberal names (required for Igor Pro 9)

    • +

  • Rework LBN getters for the databrowser/sweepbrowser completely

    • +

  • Add menu entry for resetting the analysis browser

    • +

  • Make the release package work as installation source again

    • +

  • DC_PlaceDataInDAQDataWave was refactored to be readable and maintainable again

    • +

  • Postpone writing the epoch information into the sweep settings wave to after finishing the sweeps

    • +
+
+
+

Tests

+
    +

  • Add tests to execute all window macros

    • +

  • Add tests to check that all GUIs don’t have invalid control procedures

    • +

  • Other fixes and additions all over the place

    • +
+
+
+

Async Framework

+
    +

  • Enhance ASYN_AddParam to allow for user defined parameter names and add +ASYNC_FetchWave/ASYNC_FetchVariable/ASYNC_FetchString for convenient +readout.

    • +
+
+
+

Logging

+
    +

  • Add log entries in failures cases of DAQ stop reason

    • +
+
+
+

Installer

+

None

+
+
+
+

Release 2.2

+

This version is the first version of MIES with support for upcoming Igor Pro 9. And it will also be the last with +support for Igor Pro 8.

+
+

Controls

+

All added, removed or renamed controls of the main GUIs are listed here. These lists are intended to help upgrading the JSON +configuration files manually. Controls which can not be read/written with the configuration code, like GroupBox’es, are not included.

+
+

DA_Ephys

+
+
Added
+

None

+
+
+
Removed
+
    +

  • Check_Settings_Append

    • +

  • setvar_Settings_DecMethodFac

    • +

  • title_hardware_Follow

    • +

  • title_hardware_Release

    • +
+
+
+
Renamed
+

None

+
+
+
+

Databrowser

+
+
Added
+
    +

  • check_BrowserSettings_DS

    • +

  • check_pulseAver_ShowImage

    • +

  • check_pulseAver_drawXZeroLine

    • +

  • check_pulseAver_fixedPulseLength

    • +

  • check_pulseAver_hideFailedPulses

    • +

  • check_pulseAver_searchFailedPulses

    • +

  • check_pulseAver_showTraces

    • +

  • popup_pulseAver_colorscales

    • +

  • popup_pulseAver_pulseSortOrder

    • +

  • setvar_pulseAver_failedPulses_level

    • +

  • setvar_pulseAver_numberOfSpikes

    • +

  • setvar_pulseAver_vert_scale_bar

    • +
+
+
+
Removed
+

None

+
+
+
Renamed
+
    +

  • check_pulseAver_indTraces → check_pulseAver_indPulses

    • +

  • check_pulseAver_zeroTrac → check_pulseAver_zero

    • +

  • setvar_pulseAver_fallbackLength → setvar_pulseAver_overridePulseLength

    • +
+
+
+
+

Wavebuilder

+
+
Added
+

None

+
+
+
Removed
+

None

+
+
+
Renamed
+

None

+
+
+
+
+

Sweep Formula

+
    +

  • Add area operation

    • +

  • Fix most cases of ignored minus signs in formulas

    • +

  • Make it more user friendly on errors by not just asserting out

    • +
+
+
+

AnalysisBrowser

+

None

+
+
+

DataBrowser

+
+

Dashboard

+
    +

  • Display the headstages for each sweep

    • +

  • Add support for multipatch seq analysis functions

    • +

  • Add “enable checkbox” for the dashboard

    • +

  • Show the dashboard result message as tooltip

    • +

  • Add support for all sweeps even without having an analysis function attached to the stimulus set

    • +
+
+
+
+

DataBrowser/SweepBrowser

+
    +

  • Fix restoring from backup so that it works again and also restore all sweeps and not only the displayed ones

    • +

  • The axes’ locations are now more predictable for zooming in/out via mouse wheel

    • +

  • Don’t display data from TP during DAQ channels

    • +

  • Always create backup waves when splitting the sweep

    • +

  • Speedup plotting of many traces by grouping AppendToGraph calls. This is mostly noticable in Igor Pro 8, less in +Igor Pro 9.

    • +

  • Make overlay sweeps with headstage removal faster

    • +

  • Select the current sweep when enabling overlay sweeps

    • +

  • Add new trace popup for convenient stimulus set opening in the wavebuilder

    • +

  • Fix displaying TTL data with only “TP during DAQ” data

    • +

  • Use a different marker for the first headstage. + can be easily hidden by axis ticks, but # not

    • +
+
+
+

SweepBrowser

+
    +

  • Add dashboard support

    • +

  • Show the sweep number in the sweep control and not the index into the list of sweeps

    • +
+
+
+

DA_Ephys

+
    +

  • Closing the DAEphys panel that is running TP now waits for the TP analysis to finish before closing

    • +

  • Ignore TP during DAQ channels for locked indexing

    • +

  • Prevent sweep skipping from crossing stimulus set borders

    • +

  • Handle relocking a device with data better. We now don’t start at sweep zero but at the next sweep after the last acquired

    • +

  • Remove decimation factor control

    • +

  • Make rerunning the TP with the same settings faster

    • +

  • Don’t disable dDAQ and oodDAQ checkboxes during data aquisition anymore

    • +

  • Don’t allow dialogs during background function execution, this should prevent Igor Pro crashes

    • +

  • Add new trace popup for convenient stimulus set opening

    • +

  • Warn users about permanent data loss when using sweep rollback

    • +

  • Fix TP during DAQ channels with TTL channels

    • +

  • Fix auto pipette offset taking “Apply on mode switch” into account

    • +

  • Remove the “Enable async acquisition” checkbox from the settings panel. Enable async from the async tab of the DA_Ephys panel.

    • +

  • Change sweep rollback to move the data to an archive folder instead of deleting it

    • +
+
+
+

JSON Configuration

+
    +

  • Remove the old experiment configuration. The new JSON based configuration now completely replaces it.

    • +

  • Add menu option to open all JSON configuration files in a notebook

    • +

  • Add entry “Sweep Rollback allowed” defaulting to false. This means users who are configuring MIES must explicitly +allow sweep rollback. This was done to make the chance of misuse smaller

    • +
+
+
+

Downsample

+

None

+
+
+

Analysis Functions

+
    +

  • SetControlInEvent: Warn when trying to set a control which can not be set

    • +

  • Add SC_SpikeControl

    • +

  • Convert ReachTargetVoltage to V3 format

    • +

  • Use correct labnotebook prefix for headstage active entry in MSQ_DAScale

    • +

  • Make MSQ_FastRheoEst/MSQ_DAScale/MSQ_SpikeControl/ReachTargetVoltage compatible with locked indexing

    • +

  • Add option to query the autobias target voltage from the user in ReachTargetVoltage

    • +

  • Make execution faster by not trying to redo baseline QC when it was already done

    • +
+
+
+

Pulse Average Plot

+
    +

  • Completely rework it for better performance

    • +

  • Add documentation for time align code

    • +

  • Add support for failed spike detection. Failed spikes can be highlighted or hidden in the PA plot.

    • +

  • Allow one PA plot per browser window

    • +

  • Add X/Y scale bars with zoom support

    • +

  • Make averaging faster by adding support for incremental updates and parallelizing the calculations

    • +

  • Make adding new sweeps during data acquisition much faster

    • +

  • Nicify GUI controls and add more help entries

    • +

  • Rework the time alignment code for faster execution

    • +

  • Allow displaying deconvoluted pulses without visualized average wave

    • +

  • Add image plot mode with external subwindows for the color scales and the option to +choose the pulse sorting order

    • +

  • Add option Draw X zero line to draw a line crossing the plots at x == 0

    • +

  • Add option to always use a fixed pulse length

    • +

  • Read pulse starting times from the labnotebook if present and only fallback to calculating them

    • +

  • Add Tests

    • +

  • Ignore spikes which are narrower than 0.2 ms

    • +
+
+
+

Foreign Function interface

+
    +

  • Add FFI_GetAvailableMessageFilters to query all available subscriber message filters

    • +
+
+
+

General

+
    +

  • Add a menu option for resetting the package settings to their default

    • +

  • Adapt Check Installation for Igor Pro 9

    • +

  • Make querying the labnotebok faster by adding support for incremental updates for the cache waves

    • +

  • An early version of MIES user documentation

    • +

  • Make the Igor Pro version check much more user friendly to use. We now don’t bug out on old Igor Pro +versions anymore but display a dialog and allow direct download of the new version. +This also includes up-to-date links in the documentation.

    • +

  • Sweep Rollback: Fix and avoid deleting the wrong sweeps. In some cases deleted sweeps can be reconstructed via +RecreateSweepWaveFromBackupAndLBN. Please create an issue if you need help with that.

    • +

  • Enhance the user experience when old NIDAQ-mx XOP versions are used with MIES

    • +

  • Make unlocked indexing work with TP during DAQ

    • +

  • Add menu option for opening the package settings in a notebook

    • +

  • Add sub sub epoch information for pulse train pulses

    • +

  • Fix POST_SET_EVENT/PRE_SET_EVENT determination in DC_PlaceDataInDAQDataWave for headstages in special cases.

    • +

  • Add option to upload the MIES and ZeroMQ log files

    • +
+
+
+

ITC XOP 2

+

None

+
+
+

ZeroMQ XOP

+
    +

  • Add support for logging in JSONL-format on disk. This is used for debugging and performance gathering. Enabled by default.

    • +

  • Add support for publisher/subscriber sockets

    • +
+
+
+

MCC XOP

+

None

+
+
+

MIESUtils XOP

+

None

+
+
+

Labnotebook

+
    +

  • Set the exact same timestamps for all entries added with one call. Previously these could differ in the +sub-millisecond range.

    • +

  • Store timestamps with enough resolution in textual labnotebook, so instead of 3.6968e+09 we now store 3696770484.463

    • +

  • Fix storing the wrong value for the alarm checkbox for the asynchronous tab

    • +

  • With asynchronous acquisition unused channels don’t result in empty labnotebook entries anymore

    • +
+
+

New numerical keys

+ +
+
+

New textual keys

+ +
+
+

Changed numerical entries

+

None

+
+
+

Changed textual entries

+

None

+
+
+
+

NWB/IPNWB

+
    +

  • Add the Igor Pro build version to the generated_by dataset from ndx-MIES

    • +

  • Make it faster by only saving the filled rows for the labnotebook and TP storage waves

    • +

  • Skip sweeps on export which don’t have a config wave

    • +

  • Store the MIES log file in the same place as the Igor Pro history

    • +
+
+

File format

+

None

+
+
+
+

Pressure Control

+
    +

  • We now enforce that NI hardware uses differential setup for the AI channels

    • +
+
+
+

WaveBuilder

+
    +

  • Use WP and SegWvType with double precision for new waves. We keep the existing single precision waves +as we want to generate the exact stimulus sets again.

    • +

  • Jump to the selected analysis function if possible when “Open” is pressed

    • +

  • Make selecting epochs with the mouse work with flipping enabled

    • +

  • Add help entry for delta modes

    • +

  • Warn on too long explicit delta value list

    • +
+
+
+

Work Sequencing Engine

+
    +

  • Remove existing file first when exporting into NWB

    • +

  • Publish QC results from background functions via ZeroMQ publisher socket

    • +
+
+
+

Internal

+
    +

  • Enhance error reporting in ASSERT_TS with outputting the stacktrace in IP9

    • +

  • Make NumericWaveToList faster by using wfprintf

    • +

  • Make GetAllDevices faster

    • +

  • Fix various corner cases in RA_SkipSweeps

    • +

  • Unify naming for HardwareDataWave/ITCDataWave to DAQDataWave

    • +

  • Minor fixes for Igor Pro 9

    • +

  • Make compiling slightly faster by not compiling the background watchter panel by default

    • +

  • Add debug visualization for epochs in the Databrowser/Sweepbrowser

    • +

  • Fix GetSweepSettings for the textual labnotebook

    • +

  • Add GetActiveChannels which allow to determine which channels were active for a given sweep

    • +
+
+
+

Tests

+
    +

  • Cleanup initialization code and add RunWithOpts

    • +

  • Add basic dashboard testing

    • +
+
+
+

Async Framework

+
    +

  • Add tracking jobs by workload parameters. This allows to check if all jobs of a given workload are finished.

    • +
+
+
+

Logging

+
    +

  • Add support for logging in JSONL-format on disk. This is used for debugging and performance gathering.

    • +

  • Store assertions, Igor starting/stopping/quitting/compiling, NWB export and device/pressure locking

    • +
+
+
+

Installer

+
    +

  • Skip vc_redist installation as non-admin

    • +

  • Use latest 2019 vc_redist package

    • +
+
+
+
+

Release 2.1

+
+

Sweep Formula

+
    +

  • Add an easy to use scripting language to evaluate acquired data termed Sweep Formula

    • +
+
+
+

AnalysisBrowser

+
    +

  • Load user comments from NWB files

    • +

  • Store the starting directory in the package settings

    • +
+
+
+

DataBrowser

+
    +

  • Use a per-instance folder. Now users can have multiple databrowsers open with +different settings as each databrowser graph has its own folder.

    • +

  • Enable resizing for BrowserHistorySettings Panel

    • +

  • Properly select NONE with multiple devices with data

    • +

  • Make all axes scaling options available from SweepBrowser

    • +
+
+
+

DataBrowser/SweepBrowser

+
    +

  • Fix loading and displaying of old experiments

    • +

  • Make it much faster by custom trace user data handling, incremental sweep +updates and avoiding full updates when they are not necessary.

    • +

  • The graph is now always plotted correctly even when using overlay sweeps with +headstage removal and special sweeps.

    • +

  • Make the highlightning for overlay sweeps much more responsive.

    • +

  • Allow to only overlay the sweeps from the current RAC/SCI

    • +

  • Adapt tick labels for splitted TTL axis

    • +

  • Pulse Average:

    +
    +
      +

    • Fetch the pulse times for each sweep

      • +

    • Make it much faster

      • +

    • Never grey out controls, this allows tweaking the settings while it is disabled

      • +
    +
    +
    • +

  • Restore always all cursors

    • +

  • Show the headstage number in the graph as well

    • +

  • Replace Labnotebook popup menus with our own cascaded solution which avoids +long menues.

    • +

  • Add all channel checkboxes

    • +

  • Default “Display last sweep acquired” to ON

    • +

  • Ignore invalid headstages in removal list of overlay sweeps

    • +
+
+
+

DA_Ephys

+
    +

  • Fix oodDAQ offset bug introduced in 88323d8d (Replacement of oodDAQ offset +calculation routines, 2019-06-13) with more than two stimsets.

    • +

  • Cache the HardwareDataWave for the Testpulse

    • +

  • Initialize all channel data to NaN

    • +

  • Fix AD unit querying bug for ADs above 8

    • +

  • Allow TP during DAQ for Indexing

    • +

  • Fix an off-by-one error for the fifo position

    • +

  • Rework device selection logic: This is now more intuitive.

    • +

  • Add a button for rescanning the list of changed hardware devices. This is +required as that list is now cached.

    • +

  • Add support for decimated oscilloscope wave which greatly speeds up the display

    • +

  • Handle stopped DAQ properly and avoid “Uninitialized raCycleID detected” assertions

    • +

  • Fix that with TP during DAQ all test pulse channels are stored

    • +

  • Apply search string for all controls as well

    • +

  • Rework oodDAQ algorithm: The new algorithm is much faster and does not require a resolution parameter anymore

    • +

  • Make I=0 clamp mode work again

    • +

  • Reset the session start time on “Save and Clear Experiment”

    • +

  • Perform analysis parameter checks very early (even before “PRE DAQ” event)

    • +

  • Add increment selection to “DA Scale” and manual pressure set variables via context menu

    • +

  • Avoid using async channels for DAQ as well

    • +

  • Make it usable with lots of sweeps much better

    • +

  • Handle changing power spectrum checkbox during TP

    • +

  • Parallelize curve fits on TPStorage data

    • +
+
+
+

ExperimentConfig

+
    +

  • Introduce new configuration management:

    +
      +

    • Support all panels and controls

      • +

    • Support setting all amplifier entries per headstage

      • +

    • Configuration files are in standard JSON format

      • +

    • Support for global and rig specific config files which complement each other

      • +
    +
    • +

  • Fix MCC opening bug in demo mode

    • +

  • Add configuration field Amplifier Channel to specify channel explicitly

    • +

  • Support multiple locations for the json settings files

    • +
+
+
+

Downsample

+

None

+
+
+

Analysis Functions

+
    +

  • Parameters now have no restrictions anymore on the type of content. +Previously some characters were not allowed.

    • +

  • Explicitly ignore TP during DAQ channels

    • +

  • Fix an off-by-one issue as we use the lastKnownRowIndex/lastValidRowIndex as +zero-based indizes and not as length. We now also pass these values as NaN +if they do not make sense for the current event.

    • +

  • AnalysisFunction_V3: Introduce scaledDataWave member

    • +

  • Add an analysis function for measuring the mid sweep event timings

    • +

  • Fix level calculation for NI hardware in PSQ_Ramp

    • +
  • +
    Adapt Supra mode for PSQ_DAScale:
      +

    • Plot the spike frequency vs DAScale

      • +

    • Add new LBN entry of the slope of that plot

      • +

    • Support new FinalSlopePercent parameter as additional set passing +criteria

      • +

    • Add new LBN entry which denotes if the FinalSlopePercent was reached +or not

      • +

    • Store pulse duration in LBN

      • +
    +
    +
    +
    • +

  • SetControlInEvent: Add support setting notebook contents

    • +

  • Add support for check and help functions. Port the existing analysis +functions to use that new feature.

    • +

  • Fixed the analysis function parameter check routine

    • +
+
+
+

Foreign Function interface

+

None

+
+
+

General

+
    +

  • Drop support for Igor Pro 7

    • +

  • Enhance the first time usage ITC error message

    • +

  • Added MIES_MassExperimentProcessing.ipf for batch converting Igor experiment files to NWBv2.

    • +

  • Upload Igor Pro crash dumps every day

    • +

  • Nicify About MIES dialog

    • +

  • Add MIES settings which are persistent across restarts

    • +

  • Add menu option to open the diagnostics directory

    • +

  • Switch the default branch to main from master to foster inclusive +terminology. For existing clones execute git remote set-head origin main +to switch the remote HEAD to main as well.

    • +
+
+
+

ITC XOP 2

+
    +

  • Remove unnecessary ITCMM DLLs

    • +

  • Add powershell scripts for disabling ASLR

    • +
+
+
+

ZeroMQ XOP

+
    +

  • Don’t restart the message handler if not required. This makes it possible to +create a new experiment via ZeroMQ.

    • +
+
+
+

MCC XOP

+

None

+
+
+

MIESUtils XOP

+

None

+
+
+

Labnotebook

+
    +

  • Add functions for querying labnotebook data via channel number and type

    • +

  • Change naming scheme of unassociated channels:

    +
    +

    We support two types of unassociated keys. Old style, prior to 403c8ec2 +(Merge pull request #370 from AllenInstitute/feature/sweepformula_enable, +2019-11-13) but after its introduction in ad8dc8ec (Allow AD/DA channels +not associated with a headstage again, 2015-10-22) are written as $Name UNASSOC_$ChannelNumber. +New style has the format $Name u_(AD|DA)$ChannelNumber, this includes +the channel type to make them more self explaining.

    +
    +
    • +

  • Remove “Pulse Train Pulses” and “Pulse to Pulse Length” labnotebook entries due severe bugs in the calculation

    • +

  • Fix too short dimension labels

    • +

  • Some units and tolerances were fixed for the numerical labnotebook

    • +
+
+

New numerical keys

+
    +

  • PSQ_FMT_LBN_DA_fI_SLOPE for fitted slope in the f-I plot for PSQ_DAScale

    • +

  • PSQ_FMT_LBN_DA_fI_SLOPE_REACHED for fitted slope in the f-I plot exceeds target value for PSQ_DAScale

    • +

  • PSQ_FMT_LBN_PULSE_DUR for PSQ_DAScale

    • +

  • PSQ_FMT_LBN_SPIKE_DETECT for PSQ_DAScale

    • +
+
+
+

New textual keys

+ +
+
+

Changed numerical entries

+
    +

  • oodDAQ regions: Now uses floating point numbers instead of intergers

    • +
+
+
+

Changed textual entries

+
    +

  • Function params -> Function params (encoded): This entry now holds the serialized analysis function +parameter strings where the values are percent encoded.

    • +
+
+
+
+

NWB/IPNWB

+
    +

  • Write the Igor Pro history by default

    • +

  • Add support for exporting into NWBv2 (2.2.4 to be exact). Additional MIES +data and metadata is tagged using ndx-MIES. +Export support into NWBv1 is unchanged.

    • +

  • Various bugfixes for exporting really old or buggy MIES data into NWB.

    • +

  • Support export of I=0 data better

    • +

  • Don’t delete third party stimsets after exporting into NWB.

    • +

  • Mark /general/stimsets as custom for NWBv1

    • +
+
+

File format

+

None

+
+
+
+

Pressure Control

+
    +

  • Allow adjusting the pressure with the mouse wheel

    • +
+
+
+

WaveBuilder

+
    +

  • Raise the stimset wave note version

    • +

  • Make the analysis function paramter panel nicer and resizable

    • +

  • Changed encoding of the analysis function parameters to use percent-encoding

    • +

  • Add duration entry for combined stimset

    • +

  • Add a search string for the wavebuilder stimsets for loading

    • +

  • Add wave note entry for mixed frequency shuffle

    • +

  • Force stimset rebuilding on too old wave note version

    • +

  • Fix forgotten delta mode for pulse duration for pulse train pulse

    • +
+
+
+

Work Sequencing Engine

+
    +

  • Remove AnalyaisMaster panel and HDF5 operations

    • +
+
+
+

Internal

+
    +

  • Packages/doc/developers.rst: Update CI section

    • +

  • Add JSON-XOP

    • +

  • Add preliminary support for Igor Pro 9

    • +

  • Use mathjax instead of images for the documentation

    • +

  • Fix version generation with latest tag

    • +

  • CreateMiesVersion: Support more git install locations

    • +

  • Started cleanup of DC_PlaceDataInHardwareDataWave

    • +

  • Check that ASLR is turned off on Windows 10 64-bit. This is required for ITC hardware to work, see https://github.com/AllenInstitute/ITCXOP2/#windows-10.

    • +

  • Add generic wave cache accessor CA_TemporaryWaveKey for using the returned wave in multihread statements as target junk wave

    • +

  • Add ROVar/ROStr for mapping global variables and strings to a read-only version

    • +

  • Update our documentation toolchain to sphinx 3

    • +

  • Remove Tango procedure files

    • +

  • Fixed some minor memory leaks

    • +
+
+
+

Tango

+
    +

  • Remove it completely

    • +

  • Add empty MIES_TangoInteract.ipf to avoid compile errors on old experiments

    • +
+
+
+

Tests

+
    +

  • Lots of additions and fixes

    • +

  • TTL channels are now much more checked on ITC1600

    • +

  • Switch to Windows 10 on CI server and greatly cleanup the test scripts

    • +

  • Perform compile testing on 32bit and 64bit Igor Pro

    • +

  • Added test and pynwb validation tests for NWBV2

    • +

  • Port tests to use rtFunctionErrors=1

    • +
+
+
+

Async Framework

+
    +

  • Make ASYNC_Start and ASYNC_Stop idempotent

    • +

  • Start and Stop of ASYNC framework is now globally done by CompileHooks

    • +
+
+
+

Installer

+
    +

  • Add more documentation for admins how it works

    • +

  • Added support for /ALLUSER parameter to installer

    • +

  • Switch installer to support Igor Pro 8 and 9

    • +

  • Add special installation mode for CI server via /CIS and /SKIPHWXOP flags

    • +

  • Fix edge case of user vs admin installations due to NSIS ShellLink plugin

    • +

  • Enhance deinstallation logic to catch more edge cases

    • +

  • Make ITC hardware work out of the box on new Windowses. Requires that +unsigned powershell scripts can be executed.

    • +
+
+
+
+

Release 2.0

+
+

AnalysisBrowser

+
    +

  • Labnotebook browser: Fixes for new TPStorage wave layout

    • +

  • Add support for loading TPStorage waves from NWB

    • +

  • Make it possible to load version 2 PXP files, i.e. PXP files with NI hardware +acquired data can now be loaded

    • +

  • Allow loading TTL channel data from NI hardware

    • +
+
+
+

DataBrowser

+
+
+

DataBrowser/SweepBrowser

+
    +

  • Pulse Average:

    +
      +

    • Use inf as default range for the PA deconvolution

      • +

    • Use full resolution for diagonal traces only, show the other traces with +reduced resolution for speedup reasons

      • +

    • Don’t change the x axis range for deconvolution

      • +

    • Automatic Time Alignment for Pulse Averaging

      • +

    • Adapt individual traces’ opacity and line size

      • +

    • Speedup plot creation and resize behaviour

      • +

    • Allow zeroing individual traces

      • +

    • Add deconvolution support

      • +
    +
    • +

  • Move TTL channel display to the bottom

    • +
+
+
+

DA_Ephys

+
    +

  • Allow TP stopping/restarting to be much faster for special cases

    • +

  • Make “Pipette Offset” faster, especially for a large number of active headstages

    • +

  • Add “TP during DAQ” feature which allows to have a testpulse on some +headstages and DAQ on other headstages

    • +

  • TestPulseMarker is now saved in TPStorage as well as in the stored TPWaves

    • +

  • TestPulse: Implemented handling of Oscilloscope scaling depending of GUI setting

    • +

  • Minimize the number of amplifier select calls

    • +

  • Allow but delay clamp mode changes during DAQ

    • +

  • Add entries to DA_Ephys to record User Pressure during TP

    • +

  • GetTPStorage: Raise version to hold user pressure value and type as well

    • +

  • Use the correct order for testpulse stopping and calling DAP_CheckSettings +which fires the PRE_DAQ analysis event

    • +

  • SCOPE_CreateGraph replaced Tag approach for TP Resistance values

    • +

  • Testpulse analysis is now done in a separate thread

    • +

  • Add possibility to acquire data with fixed frequency

    • +

  • Fix inserted TP length with active TTL channels

    • +

  • When synchronizing MIES to the MCC we now ignore sendToAll state

    • +

  • Use one GUI control procedure for TP and DAQ

    • +

  • SWS_SweepSaving: Call SCOPE_UpdateOscilloscopeData with correct fifo position

    • +

  • Optimization: PowerSpectrum uses fast line draw on Igor Pro 8

    • +

  • oodDAQ: Make the optimizing code faster and cache everything possible and +nicify interface for callers

    • +

  • Enabled live view for peak+steadystate resistance graph in IP8

    • +

  • Ensure that the ITI is always reached for manual sweep starts as well

    • +
+
+
+

ExperimentConfig

+
    +

  • Add user pressure settings

    • +

  • Add “Respect ITI for manual initialization”

    • +
+
+
+

Downsample

+
    +

  • Nothing

    • +
+
+
+

Analysis Functions

+
    +

  • PSQ_Ramp: Added support for NI hardware

    • +

  • PSQ_Rheobase:

    +
      +

    • Handle DaScale of zero better

      • +

    • Search again with small DAScale values

      • +
    +
    • +

  • PSQ_DAScale:

    +
      +

    • Add optional analysis parameter to choose operator for Supra

      • +

    • Fix average calculation for NI hardware

      • +

    • Enable “TP inserting”

      • +

    • Add optional support adjusting DAScale when out of band

      • +
    +
    • +

  • PSQ_SquarePulse:

    +
      +

    • Catch spiking with DAScale of zero

      • +

    • Handle known case better in Dashboard

      • +
    +
    • +

  • Add support for optional parameters in _GetParams

    • +

  • Add MSQ_DA_SCALE analysis function

    • +

  • Add SetControlInEvent analysis function

    • +

  • Add PSQ_FastRheoEstimate

    • +

  • Better checks for analysis parameters before DAQ

    • +

  • PSQ_EvaluateBaselineProperties: Fix incorrect fifo time usage

    • +

  • Dashboard: Fix querying the scale exceeded value for Rheobase

    • +
+
+
+

Foreign Function interface

+
    +

  • Nothing

    • +
+
+
+

General

+
    +

  • Make the repository publically +available. Due to restrictions on github’s side we have compressed the NWB +and PXP files. See the README.md for instructions when checking out the +repository.

    • +

  • Making stopping the async framework more robust

    • +

  • ExtractOneDimDataFromSweep:

    +
      +

    • Create a copy for NI hardware as well

      • +

    • Make it compatible with mid-sweep NI layout

      • +
    +
    • +

  • AFH_GetAnalysisParam*: Tighten logic and add tests

    • +

  • AFH_GetAnalysisParamType: Add support for requesting a specific type

    • +

  • GetListOfObjects: Return never empty list elements

    • +

  • Add support for NI PXI-6259 devices

    • +

  • Restore IP7 style responsive behaviour in IP8

    • +

  • ASSERT: Enhance diagnostic output

    • +

  • Use zero as TP amplitude for unassociated DACs

    • +

  • GetChannelClampMode: Extend to also hold headstage information

    • +

  • DAP_CheckHeadStage: Check AD/DA headstages more thorough

    • +

  • DQ_ApplyAutoBias: Modernize code

    • +

  • Query the values for the labnotebook earlier before starting the sweep

    • +

  • ToggleCheckBoxes/EqualizeCheckBoxes: Update GUI state wave as well

    • +

  • Documentation: Make all graphs zoomable

    • +

  • Change of InstResistance, SSResistance, BaseLineAverage to be double precision

    • +

  • Fixed a bug which resulted in a RTE for long stimsets with NI hardware

    • +

  • Enhance fWaveAveraging with MatrixOP

    • +

  • SCOPE_UpdateGraph: Use more accurate relative time axis update

    • +

  • Bugfix: Sweep SkipAhead resets to -1 in GUI on DAQ, following DAQ fails

    • +

  • DAP_CheckStimset: Check all reachable stimsets

    • +

  • Only stop the TP if we can start DAQ

    • +

  • DAP_CheckHeadStage: Check for empty waves in analysis parameters as well

    • +

  • Device Map: Drop internal device name

    • +

  • TP_RecordTP: Avoid erroring out on low memory condition

    • +

  • EnsureLargeEnoughWave: Add support for checking free memory before increasing the size of the wave

    • +

  • Rework TPStorage completly: Holds now NUM_HEADSTAGES columns and also holds +every Testpulse result. We now also always append to the current TPStorage +wave so there is only one now.

    • +

  • Acquisition support for NI DAC devices in multi device mode

    • +

  • DC_PlaceDataInITCDataWave: Don’t use interpolation for gathering data from TTL stimsets

    • +

  • CheckInstallation: More thorough checks for NIDAQ XOP version

    • +

  • SI_CalculateMinSampInterval: Fix minimum sampling interval for ITC hardware with PCI cards

    • +

  • HW_ITC_MoreData/HW_ITC_MoreData_TS: Fix return value for offset usage

    • +

  • CalculateTPLikePropsFromSweep: Fix some edge cases found during evaluation

    • +

  • Add documentation for how the testpulse properties are calculated

    • +

  • Fix RTE at end of blowout protocol

    • +
+
+
+

ITC XOP 2

+
    +

  • Update help file

    • +
+
+
+

ZeroMQ XOP

+
    +

  • Nothing

    • +
+
+
+

MCC XOP

+
    +

  • Nothing

    • +
+
+
+

MIESUtils XOP

+
    +

  • Update help file

    • +
+
+
+

Labnotebook

+
+

New numerical keys

+
    +

  • “oodDAQ member”: This entry is a true/false entry denoting if a +headstage takes part in oodDAQ or not.

    • +

  • “DA ChannelType” and “AD ChannelType”: Denotes if the channel was used +for TP or DAQ.

    • +

  • “Fixed Frequency acquisition”

    • +

  • “Igor Pro bitness”

    • +
+
+
+

New textual keys

+
    +

  • “TTL rack zero set sweep counts”

    • +

  • “TTL rack one set sweep counts”

    • +

  • “TTL set sweep counts (NI hardware)”

    • +

  • “TTL stim sets (NI hardware)”

    • +

  • “TTL channels (NI hardware)”

    • +

  • “Digitizer Hardware Name”

    • +

  • “Digitizer Serial Numbers”

    • +
+
+
+

Changed numerical entries

+
    +

  • Change “Minimum Sampling Interval” to “Sampling Interval”

    • +

  • Document the correct TTL bits for RACK_ONE

    • +
+
+
+

Changed textual entries

+
    +

  • Nothing

    • +
+
+
+
+

NWB/IPNWB

+
    +

  • Write the correct stimulus set for TTL channels for ITC hardware

    • +

  • Add more functions for reading NWB file information

    • +

  • Rename chunkedLayout parameter and add single chunk compression option

    • +

  • Clarify group naming in Readme.rst

    • +

  • Add an error message when loading NWB v2 files

    • +

  • NWB_ExportAllData: Make compression mode configurable

    • +

  • Set correct electrode number for associated DA/AD: +Bug introduced in 7c37bf08 (NWB: Use Labnotebook property electrodeName +if available, 2016-08-06).

    +

    With default electrode names, which are just strings with the electrode +numbers, the buggy source attributes are

    +

    ITC1600_Dev_0;Sweep=0;AD=10;ElectrodeNumber=0;ElectrodeName=6

    +

    (note the difference between the ElectrodeName and the ElectrodeNumber)

    +

    where as it should be

    +

    ITC1600_Dev_0;Sweep=0;AD=10;ElectrodeNumber=6;ElectrodeName=6

    +

    One side effect of that bug is also that all TimeSeries attributes +written by NWB_GetTimeSeriesProperties are fetched for the first +headstage and not for the correct ones.

    +
    • +

  • Handle deleted stimsets gracefully when exporting the experiment

    • +

  • Flush file after every sweep in a separate thread

    • +

  • Compress stored testpulses using “single chunk compression” to make the NWB +files smaller

    • +
+
+

File format

+
    +

  • Fix NWB group for unassociated DA channels. We need to store them +in /stimulus/presentation and not in /acquisition/timeseries as ADC data.

    • +
+
+
+
+

Pressure Control

+
    +

  • Make manual mode respect user access (during TP)

    • +

  • P_UpdateSSRSlopeAndSSR: Extract correct layer from TPStorage

    • +

  • Only call P_PressureControl every 90ms during TP

    • +
+
+
+

WaveBuilder

+
    +

  • Add required column to the analysis parameter panel

    • +

  • Add the required setting for all analysis parameters and don’t loose it on +user changes.

    • +

  • Add wave note entry for empty epoch as well

    • +

  • Fix wave recreation logic for multiple modifications done in under a second

    • +

  • Invert log chirp setting written to wave note

    • +

  • Call WBP_UpdateITCPanelPopUps from all stimset loading functions

    • +

  • Update DAQ GUI controls on sampling interval change

    • +
+
+
+

Work Sequencing Engine

+
    +

  • Nothing

    • +
+
+
+

Internal

+
    +

  • Allow using NI USB 6001 devices in evil mode

    • +

  • Documentation: Make sphinx build pass without unexpected errors

    • +
+
+
+

Tests

+
    +

  • Hardware Tests:

    +
      +

    • Make the test suite pass with NI hardware and ITC-1600

      • +

    • Use multi data test case feature to run the tests for each device +see also here

      • +

    • Check the created NWB file thoroughly

      • +

    • Use the new UTF reentry functionality, thus making the tests much easier +to understand, adapt and run for debugging.

      • +

    • Add a test to ensure that TP is stopped before PRE_DAQ_EVENT

      • +

    • Check that the sweep numbers are ascending in TEST_CASE_END_OVERRIDE

      • +

    • Perform common checks after every test case

      • +

    • Add tests which check the sampling interval for various combinations

      • +
    +
    • +

  • Compilation Testing: Test evil mode as well

    • +

  • AI_QueryGainsFromMCC: Override safety check for holding potential during automated testing

    • +

  • BUG: Assert out during automated testing

    • +
+
+
+

Async Framework

+
    +

  • Added a generic framework for executing code in a separate thread

    • +
+
+
+

Installer

+
    +

  • vc_redist package was not installed by the installer

    • +
+
+
+

Tango

+
    +

  • Nothing

    • +
+
+
+
+

Release 1.7

+
+

DA_Ephys

+
    +

  • Support stimsets with per-sweep ITI. This also changes how the ITI is +calculated for a set of sweeps, as now only the active sets are taken into +account and not all sets in range anymore.

    • +

  • Complain if the calculated number of sweeps in the set is zero

    • +

  • Check free disc space before acquisition

    • +

  • Add minimum sampling interval table for ITC16/ITC16USB

    • +

  • Complain better on known ITC issues for first time users

    • +

  • Fix acquisition order when changing tabs during DAQ with indexing turned on

    • +

  • Avoid indexing errors when changing Repeat Sets/Lists during DAQ

    • +

  • Apply on mode switch: Fix cases where the headstage and the DA/AD +numerical values don’t match

    • +

  • Apply on mode switch: Fix some edge cases with indexing

    • +

  • Make TPStorage resizing faster

    • +

  • Testpulse Multi Device: Try selecting the device first +This handles some edge case experiments better which have the TP stored as +running and are then reopened.

    • +
+
+
+

ExperimentConfig

+
    +

  • Changed I-Clamp primary gain to 5 from 1

    • +

  • Recursively create the folders to save the experiment

    • +
+
+
+

General

+
    +

  • Support stopping Igor Pro via Quit/N while the testpulse is running. We +now don’t crash anymore.

    • +

  • Save and clear: Delete Databrowser, Cache and reset history capturing

    • +
+
+
+

ITC XOP 2

+
    +

  • Use current version of ITCXOP2 for IP8 as well

    • +
+
+
+

MCC XOP

+
    +

  • The XOP now works on a real 32bit Windows

    • +
+
+
+

MIESUtils XOP

+
    +

  • New function MU_GetFreeDiskSpace

    • +
+
+
+

Labnotebook

+
+

New numerical keys

+
    +

  • Digitizer Hardware Type

    • +
+
+
+
+

Pressure Control

+
    +

  • Make breakin work again with NI hardware

    • +

  • P_SetAndGetPressure now returns the real psi and not the calibrated one

    • +
+
+
+

WaveBuilder

+
    +

  • Reorganize controls and add per sweep ITI controls

    • +

  • Due to the new per-sweep ITI the version of the stimset wave note has changed as well

    • +

  • Create a newly saved stimset in the stimset folder so that it can be used +immediately without the need to recreate it.

    • +

  • Speedup delta calculation

    • +
+
+
+

Internal

+
    +

  • Fix the bitrotted sampling interval calculation code

    • +

  • Documentation: Don’t syntax highlight verbatim blocks

    • +

  • Enhance the debug panel

    • +

  • DEBUGPRINT/DEBUGPRINTw: Add support for outputting waves

    • +

  • Updated BackgroundWatchdog: New Panel Design, works with any background task +shows up to 15 tasks

    • +
+
+
+

Tango

+
    +

  • Changed the delimiter character from ; to | for the cmdID passing

    • +
+
+
+
+

Release 1.6

+
+

AnalysisBrowser

+
    +

  • Use try/catch for opening the HDF5 file. This allows us to continue on +corrupt HDF5 files.

    • +

  • Properly update all sweep controls on sweep loading

    • +
+
+
+

DataBrowser

+
    +

  • Auto assign locked devices as well on panel creation

    • +

  • Add dashboard for inspecting analysis function results

    • +
+
+
+

DataBrowser/SweepBrowser

+
    +

  • Enhance vertical axis ticks for on/off entries

    • +

  • Don’t plot anything if no sweeps are selected with OVS

    • +

  • Nicify visualization of textual entries

    • +
+
+
+

DA_Ephys

+
    +

  • Update the calculated onset delay during DAQ

    • +

  • Allow only one of dDAQ/oodDAQ being checked at a time

    • +

  • Fix the stimset search controls for single channel controls

    • +

  • Load builtin stimsets on first device locking

    • +

  • Implement “Repeat sweep on async alarm” checkbox

    • +

  • Allow stopping DAQ with ESC

    • +

  • Allow stopping the testpulse always with ESC

    • +

  • Fix DAQ restart logic when changing the stimset and TP after DAQ is enabled

    • +

  • Fix forgotten update of stimsets in GUI with unlocked indexing

    • +

  • Fix indexing with reversed stimset order

    • +

  • Fix locked indexing bug. When the first stimset is not the one with the most +sweeps we fail to produce the correct acquisition order.

    • +

  • Document the really used ITI when it is changed mid sweep

    • +

  • Fix TP settings change if TP is running, no more bugging out

    • +
+
+
+

ExperimentConfig

+
    +

  • Add Testpulse amplitude in current clamp (IC) to configuration

    • +

  • Close the user config notebook immediately if it is not used anymore

    • +
+
+
+

Downsample

+

None

+
+
+

Analysis Functions

+
    +

  • Patch Seq:

    +
      +

    • Skip only to the end of the currently active set

      • +

    • PSQ_Rheobase: Add labnotebook entry if the DAScale range was exceeded

      • +

    • Make the sampling multiplier a required analysis parameter

      • +

    • PSQ_SquarePulse: Add sweep/set pass/fail entries

      • +

    • Shorten overlong keys

      • +

    • PSQ_SPIKE_LEVEL: Change to 0.01mV

      • +

    • PSQ_DeterminePulseDuration: Handle pulses with negative amplitude properly

      • +

    • Disallow TTL channels

      • +

    • Force RA to true

      • +

    • PSQ_DAScale: Only calculate/store/display resistance in sub threshold mode

      • +

    • PSQ_DAScale: Enforce I-Clamp mode

      • +

    • PSQ_DAScale: Add test for supra mode

      • +

    • PSQ_DAScale: Check also the DAScale values

      • +

    • PSQ_DaScale: Add new operation mode

      • +

    • Force dDAQ/oodDAQ to off

      • +

    • Force settings instead of complaining if possible

      • +

    • Rename SubThreshold to DAScale

      • +

    • Enfore minimum stimset length in PRE_DAQ_EVENT

      • +

    • PSQ_Rheobase: Stop the sweep early if baseline QC passed

      • +

    • PSQ_Rheobase: Handle failing baseline QC properly

      • +

    • Add PSQ_Ramp with tests, documentation and flow chart

      • +

    • Port to V3 API

      • +

    • Fix spike detection logic

      • +

    • Support indexing

      • +

    • PSQ_SearchForSpikes: Fix searching for multiple spikes and finding none

      • +

    • Patch Seq Rheobase: Increase post pulse baseline chunk size to 500ms

      • +

    • PSQ_Rheobase: Fix stimset length check

      • +
    +
    • +

  • Introduce Analysis functions V3. All new analysis functions should use this format.

    • +

  • Add support for analysis parameters which can be attached to stimsets and are passed into the analysis function.

    • +

  • Set realDataLength to NaN for PRE_DAQ_EVENT

    • +

  • Explain behaviour on early aborting

    • +

  • Allow switching multi device/single device in PRE_DAQ_EVENT

    • +

  • Don’t start DAQ if Abort happened during PRE_DAQ_EVENT

    • +

  • Ensure that MID_SWEEP_EVENT is always reached

    • +

  • Analysis parameters: Add method to request the types as well +A breaking change is that the names now must be separated with commas +(,) as that is more in line how we store the entries in the stimset.

    • +

  • Add PRE_SET_EVENT and fix POST_SET_EVENT for indexing

    • +
+
+
+

Foreign Function interface

+

None

+
+
+

General

+
    +

  • Readd 32-bit support. Users should always prefer 64-bit as we will phase out 32-bit support.

    • +

  • Add support for Igor Pro 8

    • +

  • PGC_SetAndActivateControl: Do nothing if the checkbox is already in the desired state

    • +

  • Stimset wave note: Store sweep and epoch count as well

    • +

  • Add document explaining some MIES coding concepts for new developers

    • +

  • IgorBeforeNewHook: Save experiment after cleaning up

    • +

  • AFH_ExtractOneDimDataFromSweep: More documentation and add support for TTL channels

    • +

  • All hardware dependent XOPs are now not a compilation requirement anymore

    • +

  • Reorganize menu

    • +

  • Add a cache for the labnotebook queries, this speeds up reading out the +labnotebook by around two orders of magnitude

    • +

  • Add shortcuts to most common MIES panels

    • +

  • Use fast line drawing for oscilloscope traces (Igor Pro 8 only)

    • +

  • Make Multi Device DAQ the default

    • +

  • Let NWB_ExportAllData use the given NWB via overrideFilePath and not use the +standard NWB file derived from the experiment name

    • +
+
+
+

Installer

+
    +

  • Add 32bit support, auto uninstall, add support for installing without hardware XOPs instead of modules

    • +

  • Remove module support

    • +
+
+
+

ITC XOP 2

+
    +

  • Modularize the repository and use submodules

    • +

  • ITCConfigAllChannels2/ITCConfigChannel2: Add possibility to offset into data +wave. This changes the ITCChanConfigWave format.

    • +

  • Add matching PDBs

    • +
+
+
+

ZeroMQ XOP

+
    +

  • Modularize the repository and use submodules

    • +

  • Fix a crash with long function names from Igor Pro 8 (XOP is still compiled +without long name support)

    • +
+
+
+

MCC XOP

+
    +

  • The XOP now searches the AxMultiClampMsg.dll in the default installation +folder. So we don’t need to ship it.

    • +
+
+
+

Labnotebook

+
    +

  • GetLastSetting*: Return an invalid wave reference if nothing could be found

    • +

  • Fix labnotebook getter for text entries using RAC logic

    • +

  • Enhance documentation of the labnotebook querying functions

    • +

  • Add documentation for developers on how to use the labnotebook

    • +

  • DC_DocumentChannelProperty: Initialize sweep settings wave properly for +unassociated channels The labnotebook entries for in these cases does not +follow our standard scheme as zeros where used as placeholders instead of +NaNs.

    +

    Detecting invalid data entries:

    +
      +

    • Only labnotebook entries with UNASSOC in the name are concerned.

      • +

    • These labnotebook entries never have entries in the headstage +dependent layers so these layers can alywas be ignored.

      • +

    • The only valid entry is in the INDEP_HEADSTAGE (9th) layer.

      • +

    • Write only valid analysis functions into the labnotebook

      • +
    +
    • +
+
+

New numerical keys

+
    +

  • “Sweep Rollback”: Documents the sweep where the user used sweep rollback

    • +

  • “Multi Device mode”: On/Off

    • +

  • “Background Testpulse”: On/Off

    • +

  • “Background DAQ”: On/Off

    • +

  • “Sampling interval multiplier”: (Integer value) Factor used for reducing the sampling rate

    • +

  • “TP buffer size”: (Integer value) Size of the TP buffer used for averaging

    • +

  • “TP during ITI”: On/Off

    • +

  • “Amplifier change via I=0”: On/Off

    • +

  • “Skip analysis functions”: On/Off

    • +

  • “Repeat sweep on async alarm”: On/Off

    • +

  • “Autobias Vcom”: Voltage [mV]

    • +

  • “Autobias Vcom variance”: Voltage variance [mV]

    • +

  • “Autobias Ibias max”: Maximum current [pA]

    • +

  • “Autobias”: On/Off

    • +

  • “Set Cycle count”: Number of times a stimset was completely acquired in a row

    • +

  • “Stimset acquisition cycle ID”: Unique identifier which is constant for all +sweeps of an RAC with the same stimset and set cycle count.

    • +
+
+
+

New textual keys

+
    +

  • “Stim Wave Note”: The stimset wave note, useful for querying epoch specific settings

    • +
+
+
+

Changed numerical entries

+
    +

  • Fix casing of “Stim Wave Checksum”

    • +

  • Nearly all patch seq entries were fine tuned.

    • +
+
+
+

Changed textual entries

+
    +

  • Nearly all patch seq entries were fine tuned.

    • +

  • The analysis function entries now have consistent casing:

    +
      +

    • “Pre DAQ function”

      • +

    • “Mid Sweep function”

      • +

    • “Post Sweep function”

      • +

    • “Post Set function”

      • +

    • “Post DAQ function”

      • +
    +
    • +
+
+
+
+

NWB/IPNWB

+
    +

  • Store the Igor Pro history in NWB on interactive export

    • +
+
+

File format

+

None

+
+
+
+

Pressure Control

+
    +

  • MAX/MIN_REGULATOR_PRESSURE: Unify constants

    • +
+
+
+

WaveBuilder

+
    +

  • Remove deprecated analysis functions if possible on stimset saving

    • +

  • Delete intermediate waves on panel close

    • +

  • Support stimsets with more than 20 sweeps

    • +

  • Add GUI for handling analysis parameters

    • +

  • Sort the list of shown stimsets across channel types

    • +

  • Add stimset checksum to the stimset wavenote

    • +

  • Fail with a good error message on unknown delta modes on stimset creation

    • +

  • Upgrade WP/WPT waves to hold per entry delta operations and multipliers

    • +

  • WPT now gained layers for epoch type specific data

    • +

  • Add a new delta operation named “Explicit delta values” which allows to set +the delta value for each sweep

    • +

  • Don’t error out on the combine epoch tab with no stimsets available

    • +
+
+
+

Work Sequencing Engine

+
    +

  • Added support for WSE to interact with patchSeq Wave Set

    • +
+
+
+

Internal

+
    +

  • Add cache statistics

    • +

  • FindIndizes: Support input waves with layers

    • +

  • AFH_GetChannelUnit/AFH_GetChannelUnits: Add functions for querying the channel units from the ITCChanConfigWave

    • +

  • DAP_CheckSettings: Add checks for asynchronous acquisition

    • +

  • Mies Version: Add date and time of last commit

    • +

  • Remove stale wrapper functions

    • +

  • Removed stock XOPs/Procedures/HelpFiles with shortcuts to their original location

    • +

  • Add MIESUtils XOP with MU_WaveModCount, WaveModCount is available in IP8

    • +

  • Unify GetLastSetting and GetLastSettingText

    • +

  • Wave cache: Allow to operate on a non-duplicated wave

    • +

  • Enhance indexing documentation, add a human readable description how indexing should work

    • +
+
+
+

Tango

+
    +

  • Add upstream license file

    • +
+
+
+
+

Release 1.5

+
+

AnalysisBrowser

+
    +

  • Accept dropped NWB files

    • +

  • Make initial scanning of NWB files much faster

    • +
+
+
+

DataBrowser

+
    +

  • Default to sweeps axis type for labnotebook browsing

    • +

  • Make “Export Traces” work

    • +
+
+
+

DataBrowser/SweepBrowser

+
    +

  • Artefact removal: Handle no AD channels in graph gracefully

    • +

  • Rework and unify UI

    • +

  • Use correct trace color for unassociated channels

    • +
+
+
+

DA_Ephys

+
    +

  • Don’t stop and restart TP if DAQ is ongoing

    • +

  • Oscilloscope resistance values: Use sub MOhm for < 10MOhm

    • +

  • Fix error on stopping single device DAQ during repeated acquisition

    • +

  • Stop single device DAQ properly if aborted during ITI

    • +

  • Zero ITC channels if DAQ is stopped during ITI

    • +

  • Enable analysis functions by default

    • +

  • Properly support “TP after DAQ” when aborting currently running DAQ

    • +

  • Unify stopping for single/multi device

    • +

  • Make DAQ faster for short stimsets (100ms) with less overhead

    • +

  • Store only the AD data when storing the full testpulses

    • +

  • Store nearly all GUI controls value in a numerical/textual GUI state +immediately on change. This allows much faster querying and makes RA faster by around 100ms.

    • +

  • Fix skipping sweeps when called during ITI

    • +

  • Implement foreground single device RA. This gives a more accurate ITI for short (< 100ms) stimsets.

    • +

  • Add automated blowout feature

    • +

  • Amplifier: Set stored clamp mode instead of complaining only if the stored and the one active in the MCC panel differ

    • +

  • Avoid endless loop in case the monitoring thread dies for multi device testpulse

    • +

  • Cache used waves for multi device test pulse

    • +

  • Open Arduino panel and initialize it for yoked DAQ automatically

    • +
+
+
+

ExperimentConfig

+

None

+
+
+

Downsample

+

None

+
+
+

Analysis Functions

+
    +

  • Add central storage wave to make calling them faster

    • +

  • Add PSQ_Rheobase with tests, documentation and flow chart

    • +

  • Add PSQ_SquarePulse with tests, documentation and flow chart

    • +
+
+
+

Foreign Function interface

+

None

+
+
+

General

+
    +

  • Reorganize the MIES menu entries

    • +

  • Enhance the mies version information to include submodule information as well

    • +

  • Add many more labnotebook querying functions which respects RA cycle ID

    • +

  • PGC_SetAndActivateControl: Send the limited val for SetVariable controls

    • +

  • TPStorageWave: Store the validity of the entries

    • +

  • Add windows installer based on NSIS

    • +

  • Adapt sweep wave note layout

    • +

  • Add manual tests for yoked DAQ

    • +

  • Disable Indexing and “TP after DAQ” for yoked DAQ as it is currently broken

    • +
+
+
+

ITC XOP 2

+

None

+
+
+

ZeroMQ XOP

+

None

+
+
+

Labnotebook

+
    +

  • Textual Labnotebook: Normalize EOLs in entries to n

    • +

  • The new analysis functions write some labnotebook entries. See their documentation for details.

    • +
+
+

New numerical keys

+

None

+
+
+

New textual keys

+
    +

  • “Igor Pro version”: Igor Pro version

    • +

  • “High precision sweep start”: ISO8601 timestamp of the sweep start with sub-second precision

    • +
+
+
+

Changed numerical entries

+

None

+
+
+

Changed textual entries

+
    +

  • “Async Unit”: The textual entry for the “Async Unit” should be the plain unit +instead of “Async AD *: *”. Same for the unit of the async entry itself.

    • +

  • “Timestamp”: Store sub-second precision in Timestamp columns

    • +
+
+
+
+

NWB/IPNWB

+
    +

  • Add option to export all stimsets into NWB on interactive export

    • +

  • Use labnotebook high precision timestamp for starting_time calculation

    • +

  • Fix NWB export naming and metadata for unassociated channels and TTL channels

    • +

  • Export full testpulses into NWB on interactive export

    • +
+
+

File format

+
    +

  • Unassociatetd channels now neither have a channel suffix (_$num) for the +group name if TTL channels are present.

    • +
+
+
+
+

Pressure Control

+

None

+
+
+

WaveBuilder

+
    +

  • Introduce builtin stimset concepts: All stimsets starting with MIES_ are +considered to be builtin and should not be created by users.

    • +

  • Fix epoch selection by mouse for really short epochs

    • +
+
+
+

Work Sequencing Engine

+

More general check for test pulse running in QC functions

+
+
+

Internal

+
    +

  • Reorganize repository: Move all separate projects into their own repository +and include them via git submodules.

    • +

  • Add automated testing with hardware on windows

    • +

  • Enhance wording of failed assertions. It now also includes a backtrace and the MIES version.

    • +

  • Reorganized procedure files to enhance function grouping and naming

    • +

  • Make PGC_SetAndActivateControl faster

    • +

  • PGC_SetAndActivateControl: Allow to switch tabs

    • +

  • PGC_SetAndActivateControl: Allow setting popup menues by string

    • +

  • HW ITC: Support interactive mode

    • +

  • Upgrade documentation generation toolchain to latest versions

    • +
+
+
+

Tango

+

None

+
+
+
+

Release 1.4

+
+

AnalysisBrowser

+
    +
  • +
    SweepBrowser Export:
      +

    • Fix x range determination by number of pulses

      • +

    • Use correct region for pulse range calculation

      • +

    • Fix operation on zoomed in graphs

      • +
    +
    +
    +
    • +

  • SweepBrowser: Remove both unused sub panels on the right

    • +
+
+
+

DataBrowser

+
    +

  • Rework UI to use much less horizontal space and make it more compact

    • +

  • Fix overlay sweeps for experiments with non-standard sweep ordering

    • +
+
+
+

DataBrowser/SweepBrowser

+
    +
  • +
    Pulse Average:
      +

    • Make individual traces more transparent

      • +

    • Enhance display of poisson distributed pulses

      • +
    +
    +
    +
    • +

  • Overlay Sweeps: Add mode for overlaying sweeps in a non-commulative way

    • +
+
+
+

DA_Ephys

+
    +

  • Avoid complaining into the history if the ITI is too short

    • +

  • Speedup repeated acqusition in case no ITI is left for the background function

    • +

  • Testpulse Multidevice: Extract the first chunk only after it is finished

    • +

  • Disable more GUI controls during DAQ

    • +

  • Set DA channels to zero on normal stop as well (required if analysis function aborts early)

    • +
  • +
    TP_Delta:
      +

    • Prefer a fixed time period for the instantaneous calculation

      • +

    • Fix Steady state resistance calculation for non-default baselines

      • +
    +
    +
    +
    • +

  • Avoid inifite loop in DAQ Multidevice (hard to trigger though)

    • +

  • New User settings for All V-clamp or I-clamp settings

    • +

  • Add jump ahead feature which allows the user to skip future sweeps

    • +

  • Make the autobias percentage and the interval configurable

    • +
+
+
+

Analysis Functions

+ +
+
+

ExperimentConfig

+
    +

  • Added some more config fields

    • +
+
+
+

Downsample

+

None

+
+
+

Foreign Function interface

+

None

+
+
+

General

+
    +

  • Avoid calling analysis functions twice on mid sweep event

    • +

  • Allow skipping the last sweep with repeated acquisition on

    • +
+
+
+

ITC XOP 2

+

None

+
+
+

ZeroMQ XOP

+

None

+
+
+

Labnotebook

+

None. The new analysis functions write some labnotebook entries. See their +documentation for details.

+
+

New numerical keys

+

None

+
+
+

New textual keys

+

None

+
+
+

Changed numerical entries

+

None

+
+
+

Changed textual entries

+

None

+
+
+
+

NWB/IPNWB

+

None

+
+

File format

+

None

+
+
+
+

Pressure Control

+

None

+
+
+

WaveBuilder

+
    +

  • Fix combine stimset creation without Wavebuilder panel open

    • +
  • +
    Pulse Train epoch:
      +

    • Adjust pulse positions relative to the begin of the stimset

      • +

    • Fix number of pulses control updating with multiple pulse train epochs in one stimset

      • +

    • Add mixed frequency mode

      • +
    +
    +
    +
    • +
  • +
    Noise epoch:
      +

    • Fix high/low filter values and document them properly

      • +

    • Add the possibility to create multiple epochs using the exact same RNG seed

      • +
    +
    +
    +
    • +

  • Avoid runtime error on custom wave epoch on empty folder selection

    • +

  • Add automated regression tests

    • +
+
+
+

Work Sequencing Engine

+

None

+
+
+

Internal

+
    +

  • Convert Abort with message to DoAbortNow to facilitate automated testing with hardware in future versions.

    • +

  • Fix skipped documentation for DAP_EphysPanelStartUpSettings() due to buggy code conversion script.

    • +

  • ED_AddEntryToLabnotebook: Add optional overrideSweepNo parameter

    • +

  • Get rid of some ITC hardware related waves

    • +
+
+
+

Tango

+

None

+
+
+
+

Release 1.3

+
+

AnalysisBrowser

+
    +

  • Make the NWB menu entries available when only this module is loaded

    • +
+
+
+

DataBrowser

+
    +

  • Reset overlay sweep folder on device locking

    • +

  • Labnotebook entry graph: Make the vertical axis scale to the visible data by default

    • +
+
+
+

DataBrowser/SweepBrowser

+
    +

  • Pulse averaging: Fix work preventing logic again

    • +

  • PulseAveraging: Handle invalid pulse coordinates more gracefully

    • +

  • Fix Display of TTL waves

    • +
+
+
+

DA_Ephys

+
    +

  • Testpulse Multidevice: +- Use the correct testpulse length for the cutoff at the end (minor) +- Fix invalid extracted chunks for special baseline values +- Push stopCollection point further to the end +- Rewrite fifo handling logic to always extract the last chunk +- Remove device restarting logic

    • +

  • Fix the total number of sweeps calculation for locked indexing. Broken since 0.9.

    • +

  • Prevent locking a ITC device which is not present

    • +

  • Repeated Acquisition: Don’t try starting TP during ITI if there is no time left

    • +

  • Oscilloscope: Prevent sub MOhm values for Rss and Rpeak

    • +

  • Oscilloscope: Don’t use autoscaling in DAQ mode.

    • +

  • Background functions: Unify DAQ/TP bkg functions period to 5 ticks (12/60s = 83ms)

    • +

  • Speedup DAQ via optimizing the way we write into the oscilloscope wave

    • +

  • Experiment Documentation: Rework and speedup the sweep wave note creation with changed entries

    • +

  • Turn off analysis functions by default

    • +

  • Analysis Functions: Implement support for new mid sweep return type

    • +

  • Add support for skipping forward and back some sweeps during data acquisition

    • +

  • Repeated Acquisition: Immediately finish if we have only one trial

    • +

  • Analysis Functions: Prevent Post Sweep/Set/DAQ event execution on forced DAQ stopping

    • +

  • Experiment Documentation: Avoid bugging out on very long text entries

    • +

  • Pulse averaging: Fix fallback logic for non existing pulse lengths

    • +

  • Correct the default channels and other settings for device 1 to 9 of the type ITC1600

    • +

  • Handle non-active headstage gracefully if the user presses Approach (pressure mode)

    • +

  • Try out all possible MultiClampCommander paths

    • +

  • Add possibility to store each testpulse

    • +
+
+
+

ExperimentConfig

+
    +

  • Remove workaround for buggy MultiClampCommander 64-bit App (Requires latest beta version of MCC App)

    • +

  • Fixed incorrect GetPanelControl constants to set the Min/Max Temp alarm. Fixed now

    • +

  • Add User Config field to save each TP sweep

    • +

  • Added new fields to User Configuration: +- Enable/Disable Autobias current +- Enable/Disable Cap Neutralization +- Set User onset and termination delay +- Select initial stim set and amplitude to begin data acquisition

    • +
+
+
+

Downsample

+
    +

  • Avoid erroring out on invalid target rate

    • +
+
+
+

Foreign Function interface

+

None

+
+
+

General

+
    +

  • Remove 32bit, Manipulator and RemoteControl support

    • +

  • Avoid gossiping (aka printing messages) too much during operation instead use ControlWindowToFront when it is really important

    • +

  • Prevent erroneous save dialog when quitting MIES when nothing has changed

    • +

  • Readme.md: Unify full installation instructions for 32/64 bit

    • +

  • Readme.md: Enhance installation instructions without hardware

    • +

  • Raise required Igor Pro version to 7.04

    • +
+
+
+

Labnotebook

+
    +

  • Fix adding the basic entries to all layers. Broken since the switch to Igor Pro 7.

    • +
+
+
+

ITC XOP 2

+
    +

  • Fix some erroneous tests

    • +

  • Add BSD-3-Clause License

    • +
+
+
+

ZeroMQ XOP

+
    +

  • Add help file in Igor Pro Help format

    • +

  • Nicify documentation and enhance compilation instructions

    • +

  • Add example C++ client

    • +

  • Add MacOSX XOPs

    • +

  • Upgrade to new XOPSupport 7.01

    • +

  • Recompile XOP support libraries with runtime DLL setting

    • +

  • Fix some compilation warnings found by clang on MacOSX

    • +

  • Remove dependency of the tests on MIES

    • +

  • Add BSD-3-Clause License

    • +
+
+

New numerical keys

+
    +

  • “Stim Wave Checksum”, 32bit CRC of the stimset and its parameter waves (if present)

    • +

  • “Repeated Acq Cycle ID” holds an integer value which is unique for every +repeated acquisition cycle. This allows to determine if two sweeps belong to +the same repeaqted acquisition. Before this was only possible via an +heuristic which could not be correct all the time.

    • +
+
+
+

New textual keys

+

None

+
+
+

Changed numerical entries

+
    +

  • Write “TTL rack zero/one channel” only in the headstage independent layer

    • +

  • Write asyn entries also in the headstage independent layer (For backwards compatibility we keep it in the zeroth layer)

    • +
+
+
+

Changed textual entries

+
    +

  • Write asyn entries also in the headstage independent layer (For backwards compatibility we keep it in the zeroth layer)

    • +
+
+
+
+

NWB/IPNWB

+
    +

  • Link to the specification we implement

    • +

  • Nicify documentation

    • +

  • Add BSD-3-Clause License

    • +

  • Add example code for reading as well

    • +

  • H5_LoadDataset: Use HDF5 Error and dump routine in case of error

    • +

  • CreateCommonGroups: Write required datasets always

    • +

  • GeneralInfo: Include all other root folder elements as well

    • +
+
+
+

Pressure Control

+

None

+
+
+

WaveBuilder

+
    +

  • Fix loading default stimset values for DA type

    • +

  • Fix loading of TTL stimsets

    • +

  • Update the stimset related DA_EPHYS panel controls if only the number of sweeps of stimset changed

    • +

  • Prevent keeping non-existing analysis functions attached to a stimset during load and save cycle

    • +

  • Warn the user if the stimset references a non existing analysis function on loading

    • +
+
+
+

Work Sequencing Engine

+

None

+
+

File format

+

None

+
+
+
+

Internal

+
    +

  • Switch continuous integration server to use Igor Pro 64-bit for unit and compilation testing

    • +

  • GetLastSetting: Return a double precision wave

    • +

  • EnsureLargeEnoughWave: Avoid enlarging minimum sized waves immediately

    • +

  • DA_EPHYS: Introduce a RNG seed value for each locked device

    • +

  • ExtractOneDimDataFromSweep: Add assertion for catching sweep <-> config mixups

    • +

  • ED_AddEntriesToLabnotebook: Add convenience function for easy addition of user labnotebook entries

    • +

  • FindIndizes: Simplify interface

    • +

  • Count global initializes at zero instead of NaN

    • +

  • FindRange: Make it possible to search for NaNs

    • +

  • DeepCopyWaveRefWave: Avoid claiming to support multi dimensional src waves

    • +

  • ParseISO8601TimeStamp: Accept more format variations written by the api-python code

    • +
+
+
+

Tango

+

None. But be aware that now the 64-bit version of the Tango XOP always is used.

+
+
+
+

Release 1.2

+
+

General

+
    +

  • Add menu entry for loading stimsets from an NWB file

    • +

  • Entry type heuristic: Handle old labnotebooks without entry source type and no TP data properly

    • +

  • Rework TPStorage contents

    • +

  • Don’t allow aborting SaveExperimentWrapper in SAVE_AND_SPLIT mode

    • +

  • Keep the NWB file open on SAVE_AND_SPLIT

    • +

  • Averaging: Fix rounding error due to single precision intermediate wave

    • +

  • Upgrade to NIDAQ XOPs version 1.10 final

    • +
+
+
+

DA_Ephys

+
    +

  • oodDAQ:

    +
      +

    • Fix some edge cases (works around a FindLevel limitation in older Igor 7 versions)

      • +

    • Allow to use analysis functions in this mode as well

      • +

    • Inform the user if the pre/post oodDAQ delays are out of range

      • +
    +
    • +

  • Make clamp mode changing faster and add controls for changing the clamp mode once for all active headstages

    • +

  • Change inital onset user delay to 0ms

    • +

  • Added checkbox control to de/activate all headstages simultaneously

    • +

  • Complain and abort DAQ/TP if the requested settings would exceed the signed 16bit range of the ITCDataWave

    • +

  • Remove backup waves as well on sweep rollback

    • +

  • Move the free memory check into DC_ConfigureDataForITC and make it +non-skippable. This should make it less likely that Igor crashes due to out +of memory during DAQ.

    • +

  • Move the FIFO checking to a separate thread for DAQ MD in order to prevent a +crash on heavy load on the Igor main thread

    • +

  • Disable active headstage checkboxes during DAQ

    • +

  • Disable background/multi device checkboxes during DAQ/TP

    • +

  • Add support for stopping and restarting DAQ on stimset change

    • +

  • Prevent foreground DAQ with RA

    • +

  • Stop DAQ/TP before unlocking the device

    • +
+
+
+

AnalysisBrowser

+
    +

  • Better code for deriving the initial filesystem folder

    • +

  • Allow loading stimsets, including dependent stimsets and custom waves, from NWB/PXP

    • +
+
+
+

DataBrowser/SweepBrowser

+
    +

  • Fix oodDAQ display with only TTL data shown

    • +

  • Unify oodDAQ and dDAQ display. The region slider can now be used to select +oodDAQ regions or dDAQ headstage regions.

    • +

  • Add new overlay sweeps functionality with the following features:

    +
      +

    • Select sweeps by popup menu (stimset and stimset plus clamp mode), checkbox +clicking or “prev”/”next” buttons

      • +

    • The user can choose the offset and the stepping for all popupmenu +selections except “none”.

      • +

    • Allow to ignore headstages per sweep by context menu selection or +listbox entries

      • +

    • Regenerate the graph of overlayed sweeps on every change, this also +makes it possible to allow all other settings to be available while +overlay sweeps is active

      • +
    +
    • +

  • Make averaging work in dDAQ mode

    • +

  • Speedup displaying lots of sweeps a lot (by more than one magnitude for averaging turned on)

    • +

  • ArtefactRemoval: +- Make range highlightning optional +- Speed it up and fix some edge cases +- Replace range with first value instead of NaN

    • +

  • Zero traces: Skip superfluous invocations

    • +

  • Add pulse averaging

    +
      +

    • Allow the user to average pulses from a pulse train stimset.

      • +

    • New graphs are created for each region and active channel to the right +hand side of the databrowser/sweep browser.

      • +
    +
    • +

  • Adjust waves for onset delay for oodDAQ view

    • +

  • Enhance axis positioning in dDAQ mode

    • +

  • Time alignment: Make it usable again

    • +

  • Add checkbox for hiding normal sweeps:

    +
      +

    • Use our headstage colors if normal sweeps are hidden

      • +
    +
    • +
+
+
+

SweepBrowser

+
    +

  • SweepBrowser: Enhance export functionality

    +
      +

    • Use a real panel for querying user input instead of DoPrompt

      • +

    • Add new options:

      +
        +

      • Source graph

        • +

      • Target graph

        • +

      • Target left/bottom axis

        • +

      • Target left/bottom axis name

        • +
      +
      • +
    +
    • +
+
+
+

DataBrowser

+
    +

  • Add panel versioning

    • +

  • Lock to device on panel opening if we only have data from one.

    • +

  • Unify all settings to use checkboxes

    • +
+
+
+

Labnotebook

+
    +

  • Document the train pulse starting times and pulse lengths

    • +

  • GetLastSetting/GetLastSettingText/… learned to treat edge cases including +DAQ/TP and sweep number rollback properly. This is a change in the +labnotebook reading routines only.

    • +
+
+

New numerical keys

+
    +

  • Pulse To Pulse Length: Distance in ms of two pulses in pulse train stimsets

    • +
+
+
+

New textual keys

+
    +

  • Pulse Train Pulses: List of pulse train starting times in ms (relative to the stimset start)

    • +
+
+
+
+

NWB/IPNWB

+
    +

  • Raise version to 0.16

    • +

  • Truncate the written wave notes to avoid triggering the “64k” limit on attribute sizes.

    • +

  • Add rtFunctionErrors pragma

    • +

  • ReadLabNoteBooks: Don’t assert out if we could not find the labnotebook

    • +

  • Require Igor Pro 7

    • +

  • Allow exporting unassociated channel data of all channel types

    • +

  • Add generic routines for loading datasets into free waves

    • +

  • Flush the NWB file to disc on Igor experiment save

    • +
+
+

File format

+
    +

  • Allow creating NWB files with only TPStorage waves or stimsets

    • +

  • Store dependent stimsets, due to formula epochs, and referenced custom waves +in NWB as well when storing the stimset of a sweep.

    • +
+
+
+
+

Pressure Control

+
    +

  • Fix NI device resetting code on device close

    • +
+
+
+

User Config

+
    +

  • Add a config file and code to allow setting the required MIES settings in an +automated way.

    • +
+
+
+

WaveBuilder

+
    +

  • Square Pulse Train:

    +
      +

    • Rename Square Pulse Train to Pulse Train

      • +

    • The pulse type can now be either square (as before) or triangle.

      • +

    • Add amplitude related entries to wave note

      • +

    • Make poisson distributed pulses reproducible. This also adds “New Seed” and +a “Seed / Sweep” controls.

      • +

    • Add the pulse starting times to the stimset wave notes

      • +
    +
    • +

  • Fix flipping with multi sweep stimsets

    • +

  • Speedup sawtooth on Igor Pro 7.02 and later

    • +

  • CustomWave: Use the same offset than all other epoch types. This also fixes +the problem that the wrong “offset”/”delta offset” was added to the +segment wave note.

    • +

  • More use of the magical speedup keywords

    • +

  • Use differnt colors for sweeps in the wavebuilder

    • +

  • Show the delta mode also for the custom wave

    • +

  • Show user analysis functions from UserAnalysisFunctions.ipf as well in the popup menues

    • +

  • Prevent RTE due to non existing bottom axis on empty graph

    • +

  • Improved detection of the need to regenerate the stimset from the parameter +waves. Recreate the stimsets if one of the following elements changed:

    +
      +

    • any custom wave has changed

      • +

    • any stimsets within a formula have changed

      • +
    +
    • +

  • Rework stimset wave note generation: +We now document the settings of each sweep (aka step) and not only of the first +including delta. This also changes the format of the sweep wave note.

    +

    Example of the new stimset wave note format:

    +
    Sweep = 0;Epoch = 0;Type = Square pulse;Duration = 1000;Amplitude = 0;
+Sweep = 0;Epoch = 1;Type = Pulse Train;Duration = 1840.01;Amplitude = 1;Offset = 0;Pulse Type = Square;Frequency = 5;Pulse duration = 40;Number of pulses = 10;Poisson distribution = False;Random seed = 0.943029;Definition mode = Duration;
+Stimset;ITI = 0;Pre DAQ = ;Mid Sweep = ;Post Sweep = ;Post Set = ;Post DAQ = ;Flip = 0;
+
    +
    +
    • +
+
+
+

Work Sequencing Engine

+

None

+
+
+

Downsample

+

None

+
+
+

Foreign Function interface

+
    +

  • FFI_ReturnTPValues: Return a null wave if the testpulse has not yet been running

    • +
+
+
+

ITC XOP 2

+
    +

  • Change /V flag handling of ITCSetDAC2 to match the documentation

    • +

  • Fix a potential crash in ITCInitialize2/U (we don’t use this flag)

    • +

  • Add PDB files

    • +
+
+
+

ZeroMQ XOP

+
    +

  • Return a newly added and more specific error message on catching std::bad_alloc exceptions.

    • +

  • Try handling out of memory cases more gracefully, in some cases caller are even responed to with a specific error message.

    • +

  • Update to latest libzmq version (84d94b4f)

    • +

  • Add PDB files

    • +
+
+
+

Internal

+
    +

  • GetTPStorage: Fix wave note formatting on upgrade

    • +

  • Replace GetClampModeString by a more versatile solution, namely the GetActiveHSProperties wave

    • +

  • Fix sweep splitting for changed sweep waves

    • +

  • PGC_SetAndActivateControl: Set popStr for PopupMenues if not supplied

    • +

  • Prevent storing sweep data with differing channel number in config and sweep

    • +

  • PGC_SetAndActivateControl: Respect the valid data range for SetVariable controls

    • +

  • Add rtFunctionErrors pragma which should catch more programming errors

    • +

  • Finalize transition to always existing count variable

    • +

  • Add infrastructure and bamboo jobs for automated unit testing

    • +

  • Update to latest version of the igor unit testing framework and enable JUNIT output for the tests

    • +

  • Use the parent experiment name for deriving the NWB filename. The result is +that sibling experiments now use the same NWB file as the parent +experiment.

    • +
+
+
+

Tango

+
    +

  • TI_ConfigureMCCforIVSCC: Use correct clamp mode

    • +

  • TI_saveNWBFile: Take the full path

    • +
+
+
+
+

Release 1.1

+
+

General

+
    +

  • Add more user analysis functions

    • +
+
+
+

DA_Ephys

+
    +

  • DA Tab: Add controls for changing all channels in a given clamp mode

    • +

  • Bugfix: Use existing GUI procedures for DA1-7 search controls

    • +
+
+
+

WaveBuilder

+
    +

  • Add panel versioning

    • +

  • WP/WPT waves received a wave version upgrade and changed dimensions labels

    • +

  • Custom epoch: Enhance GUI usability for wave selection

    • +

  • Bugfix: Use existing GUI procedure for delta type controls

    • +

  • Avoid useless stimset recreation on epoch selection by mouse

    • +

  • Fix minor GUI layout issues

    • +

  • GPB-Noise: Complete rewrite epoch generation +The old approach had the user-visible drawback that it was very very slow +for durations larger than 1000ms.

    +

    The new approach has the following properties:

    +
      +

    • Fast creation, at least a magnitude faster, by using IFFT and FilterIIR

      • +

    • Unified approach for white, pink and brown noise

      • +

    • Fix interchanged definitions for pink and brown noise

      • +

    • Only one filter coefficient, ranging from 1 to 100, with delta remains

      • +

    • 1/f increment was replaced by the experimental build resolution option

      • +

    • The amplitude is now peak-to-peak and not standard deviation

      • +

    • The phase is now uniform distributed between [-pi, pi) using the +Mersenne-Twister as pseudo random number generator

      • +

    • epoch noise tab cleanup

      • +

    • FFT phase and spectrum is displayed for each sweep

      • +
    +

    Keeping the old method for compatibility with existing parameter stimset waves was deemed +not worth the effort.

    +
    • +
+
+
+

DataBrowser

+
    +

  • Bugfix: Use correct location for channel selection wave

    • +
+
+
+

DataBrowser/SweepBrowser

+
    +

  • Add Artefact removal panel

    • +
+
+
+

Pressure Control

+
    +

  • Set pressure to atmosphere on disabling the headstage

    • +

  • Bugfix: Avoid spurious control on unrelated windows

    • +
+
+
+

Labnotebook

+
    +

  • Enhance EntrySourceType heuristics for very old labnotebooks

    • +
+
+

New numerical keys

+

None

+
+
+

New textual keys

+

None

+
+
+
+

NWB/IPNWB

+

None

+
+

File format

+

None

+
+
+
+

Internal

+
    +

  • Add script to build documentation on Linux using docker

    • +

  • Bugfix: Add missing files to the release package

    • +

  • Add panel for tuning debug mode on a per-file level

    • +
+
+
+
+

Release 1.0

+
+

General

+
    +

  • Require Igor Pro 7.01

    • +

  • Switch to completely rewritten ITC XOP

    • +

  • Ignore errors on closing the experiment

    • +

  • Status message displays saved file name after saving config

    • +

  • Avoid runtime error after DAQ in edge cases

    • +

  • Avoid RTE on DAQ with RA

    • +

  • Fix indexing with stimsets with multiple steps

    • +

  • Yoking: Sync dDAQ settings properly

    • +

  • Make TP MD testpulse creation faster

    • +

  • Enhance data saving speed

    • +

  • Add new data acquisition mode: Optimized overlap distributed +acquisition

    • +

  • CheckInstallation: Look for a valid MIES version too

    • +

  • Testpulse MD: Streamline ITC XOP calling sequence

    • +

  • Stop device before closing

    • +

  • TP MD: Rework and fix crashes with 64bit XOP

    • +
+
+
+

DA_Ephys

+
    +

  • Generalize controls for setting multiple channel values

    • +

  • Propagate amplifier settings before DAQ/TP

    • +

  • Add checks for DA/AD gain and unit in pre DAQ/TP checks

    • +

  • Read the pressure settings from the waves on device locking

    • +

  • Prevent impossible clamp mode switch

    • +

  • Fixes bug where positive going fast capacitative artifact could lead +to incorrect peak R calculation

    • +

  • Increase performance on oscilloscope update

    • +

  • Fix MIES auto pipette offset for overload edge case

    • +

  • Delete data waves before TP if requested

    • +

  • Allow to increase the sweep counter again on rollback

    • +

  • Remove the “Overwrite data waves” checkbox

    • +

  • Fix graph updating logic in corner case for TP MD

    • +

  • Fix restarting the test pulse for multiple headstage on settings +change

    • +

  • Allow to display the power spectrum of the TP as an option

    • +

  • Fail locking on device open error

    • +

  • Fix auto pipette offset buttons for unsychronized clamp mode

    • +

  • Try to regenerate root:mies:version more eagerly

    • +

  • Autobias: Initialize actualCurrent properly

    • +

  • Autobias: Correct indexing of TP result waves

    • +

  • Fix Autopipette offset with MIES->MCC syncing

    • +

  • Use double precision for TPStorage

    • +

  • Create the Acqusition TPSTorage wave with double precision as well

    • +

  • Check for mismatched clamp mode early enough that we can complain +properly to the user

    • +

  • Prevent Random Acq together with Indexing

    • +

  • Increased MINIMUM_ITCDATAWAVE_EXPONENT from 17 to 20. This means +the acquired data will now always be at least 2^20 points long

    • +

  • Bring command window to front on most common setup verification +errors

    • +
+
+
+

NWB/IPNWB

+
    +

  • Honour overrideFilePath for export in all cases

    • +

  • Prevent duplicated datasets on export

    • +

  • Allow to export older experiments

    • +

  • Raise IPNWB version to 0.15

    • +

  • Support writing unassociated AD channels

    • +

  • Add support for reading NWB files we created ourselves

    • +
+
+

File format

+
    +

  • Raise version to 1.0.5

    • +

  • Add /general/generated_by

    • +

  • Add mandatory tags attribute to /epochs

    • +

  • Change source attributes from TimeSeries

    • +

  • Document the channel suffix as TTLBit using source attribute

    • +

  • Skip writing /general/version

    • +

  • Add device to /general/intracellular_ephys/electrode_X

    • +

  • Fix type of /general/intracellular_ephys/electrode_x

    • +

  • Use Labnotebook property electrodeName if available for the +electrode_name

    • +

  • Change stimset writing logic (skips writing the raw stimset waves for +most cases)

    • +

  • Use plain TimeSeries for unknown clamp modes

    • +
+
+
+
+

Wavebuilder

+
    +

  • Combined epoch: Fix accessing third party stim sets

    • +

  • Combined epoch: Fix wrong formula generation in edge case

    • +

  • Custom epoch: Update epoch controls

    • +

  • Custom epoch: Enhance upgrade path

    • +

  • Custom epoch: Highlight them in the preview

    • +

  • Fix window hook for epoch selection

    • +

  • Make stimset handling logic more robust

    • +
+
+
+

AnalysisBrowser

+
    +

  • Fix reading experiments without “Set Sweep Count” entries

    • +

  • Ignore LoadData errors

    • +

  • Handle experiments with no data gracefully

    • +

  • Don’t add duplicated experiment names

    • +

  • Handle multiple experiments with the same name properly

    • +

  • Don’t error out on non-existing datafolders

    • +

  • Fix “Scan folder” cleanup logic

    • +
+
+
+

Databrowser/Sweepbrowser

+
    +

  • Add dedicated support for viewing dDAQ/oodDAQ data

    • +

  • Speedup wave averaging a bit

    • +

  • Add support displaying textual labnotebook data

    • +
+
+
+

Databrowser

+
    +

  • Remove the lock button

    • +

  • Add channel/headstage selection dialog

    • +
+
+
+

SweepBrowser

+
    +

  • Add headstage controls in selection dialog

    • +
+
+
+

Work Sequencing Engine

+
    +

  • Various fixes

    • +

  • Support pulling of TP values out of the TP storage wave

    • +
+
+
+

Downsample

+
    +

  • Fix not finding any device data

    • +
+
+
+

Labnotebook

+
    +

  • Raise version to 6

    • +

  • Write forgotten async text settings to the labnotebook

    • +

  • Streamline labnotebook naming with the new names being:

    +
      +

    • numericalValues

      • +

    • numericalKeys

      • +

    • textualValues

      • +

    • textualKeys

      • +
    +
    • +

  • Avoid wasted memory in textual labnotebook

    • +

  • Fix units and tolerance of “Repeat Sets” for new entries

    • +

  • Upgrade labnotebook to correct “Repeat Sets” units and tolerance

    • +

  • Upgrade labnotebook to hold a “EntrySourceType” column

    • +
+
+

New numerical keys

+
    +

  • “Sampling interval multiplier”

    • +

  • “Minimum sampling interval”

    • +

  • “Stim set length”

    • +

  • “oodDAQ Pre Feature”

    • +

  • “oodDAQ Post Feature”

    • +

  • “oodDAQ Resolution”

    • +

  • “Optimized Overlap dDAQ”

    • +

  • “Delay onset oodDAQ”

    • +

  • “EntrySourceType”

    • +
+
+
+

New textual keys

+
    +

  • “Electrode” (defaults to headstage number)

    • +

  • “oodDAQ regions”

    • +
+
+
+
+

Pressure control

+
    +

  • Set the initial seal pressure to -0.2

    • +

  • P_LoadPressureButtonState: Use headstage value from wave instead of +GUI query

    • +

  • Allow the user to offset the applied pressure

    • +

  • Update to seal and break method

    • +

  • Fix “all” usage for Manual pressure

    • +

  • Initialize pressure waves with correct defaults

    • +

  • Don’t overwrite pressure wave data on upgrade

    • +

  • Create P_SetPressureMode to allow external processes to use pressure +controls in MIES/Igor.

    • +

  • Set pressure to 0 psi at disable

    • +

  • Add user pressure

    • +

  • Use DAP_AbortIfUnlocked for pressure related controls

    • +

  • Fixed bug where displayed pressure included the calibration constant

    • +
+
+
+

Internal

+
    +

  • Upgrade HDF5 XOP to a version which allows to force the dimension +space to SIMPLE for attributes

    • +

  • Remove unnecessary files from Release package

    • +

  • DAP_EphysPanelStartUpSettings: Make it more usable

    • +

  • Update Packages/unit-testing to 26f3f77f9

    • +

  • AI_SendToAmp: Add option for setting/getting values in MIES units

    • +

  • Rework follower/leader check functions

    • +

  • Remove doNotCreateSVAR hack for ListOfFollowerITC1600s

    • +

  • Add HDF5 Browser ipf from IP7

    • +

  • Update Helpfiles from IP7 final

    • +

  • Add EVILKITTENEATING_MODE for turning off all safety checks

    • +

  • Add script for generating a changelog (which the author of these lines +forgot about)

    • +

  • Add wave caching framework

    • +

  • doxygen-filter-ipf: Make output sphinx compatible

    • +

  • Switch to doxygen/breathe/sphinx for developer documentation

    • +

  • ED_createTextNotes: Accept incoming waves with only one layer

    • +

  • Disambiguate labnotebook entry search for TP/DAQ keys

    • +

  • Add ZeroMQ.XOP

    • +

  • Autostart ZeroMQ Message Handler on Igor Start

    • +

  • Foreground DAQ/TP: Do Idle Processing in loop

    • +

  • Convert procedures to UTF8-encoding

    • +
+
+
+

Tango

+
    +

  • Avoid using “MS Shell Dlg” font

    • +
+

For older releases use git log!

+
+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/reportingbugs.html b/reportingbugs.html new file mode 100644 index 0000000000..4a33bc9927 --- /dev/null +++ b/reportingbugs.html @@ -0,0 +1,145 @@ + + + + + + + + Bug reporting — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Bug reporting

+

In case you find an issue/bug/problem in MIES please create an +issue here.

+

We need the following information to be able to help you:

+
    +

  • Output of MIES Panels->Advanced->Check installation

    • +

  • Screenshots of error dialogs or similiar

    • +

  • Steps to reproduce

    • +
+

The following things are, depending on the type of issue, also required:

+
    +

  • Acquired data as packed experiment (pxp)

    • +

  • In case the generated NWB file is concerned, please include that as +well

    • +

  • In case the issue concerns the ZeroMQ XOP, the messages in textform +will tremendeously help

    • +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/search.html b/search.html new file mode 100644 index 0000000000..38dd33e6da --- /dev/null +++ b/search.html @@ -0,0 +1,124 @@ + + + + + + + Search — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + + + + + + +
+
+
+
+ +

Search

+ + + + +

+ Searching for multiple words only shows matches that contain + all words. +

+ + +
+ + + +
+ + +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/searchindex.js b/searchindex.js new file mode 100644 index 0000000000..aba77255de --- /dev/null +++ b/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"alltitles": {"Abbreviation legend": [[7, "id2"]], "Added": [[184, "added"], [184, "id1"], [184, "id4"], [184, "id7"], [184, "id16"], [184, "id20"], [184, "id24"], [184, "id28"], [184, "id72"], [184, "id76"], [184, "id80"], [184, "id121"], [184, "id125"], [184, "id129"], [184, "id169"], [184, "id173"], [184, "id177"], [184, "id217"], [184, "id221"], [184, "id260"], [184, "id264"], [184, "id268"]], "Adding support for new NI hardware": [[26, "adding-support-for-new-ni-hardware"]], "Addition of new entries": [[180, "addition-of-new-entries"]], "All event graph": [[5, "all-event-graph"]], "All parameters of the stock analysis functions": [[7, "id1"]], "Analysis Functions": [[184, "analysis-functions"], [184, "id39"], [184, "id91"], [184, "id140"], [184, "id188"], [184, "id232"], [184, "id279"], [184, "id309"], [184, "id336"], [184, "id376"], [184, "id401"], [184, "id422"]], "Analysis function parameters": [[7, "analysis-function-parameters"]], "AnalysisBrowser": [[9, "analysisbrowser"], [184, "analysisbrowser"], [184, "id10"], [184, "id15"], [184, "id32"], [184, "id84"], [184, "id133"], [184, "id181"], [184, "id225"], [184, "id272"], [184, "id304"], [184, "id330"], [184, "id370"], [184, "id395"], [184, "id418"], [184, "id441"], [184, "id465"], [184, "id500"]], "Argument Setup Stack": [[4, "argument-setup-stack"]], "Array Evaluation": [[4, "array-evaluation"]], "Artefact Removal": [[15, "artefact-removal"]], "Assertions": [[181, "assertions"]], "Async Framework": [[10, "async-framework"], [184, "async-framework"], [184, "id67"], [184, "id116"], [184, "id164"], [184, "id211"], [184, "id255"], [184, "id299"], [184, "id328"], [184, "id355"]], "Automatic test pulse tuning": [[11, "automatic-test-pulse-tuning"]], "Available CI servers": [[26, "available-ci-servers"]], "Background functions": [[181, "background-functions"]], "Branch naming scheme": [[26, "branch-naming-scheme"]], "Bug reporting": [[185, "bug-reporting"]], "Building the documentation": [[26, "building-the-documentation"]], "CI": [[184, "ci"]], "CalculateTPLikePropsFromSweep Algorithm": [[0, "calculatetplikepropsfromsweep-algorithm"]], "Calculation": [[0, "calculation"], [6, "calculation"]], "Caveats": [[180, "caveats"]], "Changed numerical entries": [[184, "changed-numerical-entries"], [184, "id53"], [184, "id104"], [184, "id152"], [184, "id199"], [184, "id243"], [184, "id290"], [184, "id319"], [184, "id346"], [184, "id386"], [184, "id409"], [184, "id432"], [184, "id454"]], "Changed textual entries": [[184, "changed-textual-entries"], [184, "id54"], [184, "id105"], [184, "id153"], [184, "id200"], [184, "id245"], [184, "id291"], [184, "id320"], [184, "id347"], [184, "id387"], [184, "id410"], [184, "id433"], [184, "id455"]], "Changing execution order of a work load class": [[10, 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121, 123, 134, 150, 164, 168, 170, 184, 211], "chunked_compress": [29, 170], "chunkedlayout": [3, 184], "chunklength": 53, "chunklengthtim": 53, "chunkpass": 53, "chunksep": 150, "chunkstarttimemax": 53, "chusep": 150, "ci": [53, 93, 108, 113, 159], "ci_expensive_check": 26, "ci_igor_revis": 93, "ci_instrument_test": 26, "circl": [4, 5], "circular": 121, "circumst": [9, 26, 184], "claim": 184, "clamp": [0, 1, 2, 3, 4, 6, 11, 19, 33, 35, 40, 49, 58, 64, 67, 68, 77, 103, 108, 111, 127, 129, 130, 135, 168, 179, 180, 184, 230], "clampamp": [134, 170, 222, 231], "clampmod": [3, 4, 6, 33, 35, 40, 51, 64, 67, 68, 115, 130, 134, 135, 168, 170, 179, 184, 222, 224, 230, 231], "clampmode_entry_kei": [64, 170], "clampmodechangeopt": 67, "clang": 184, "clarif": [36, 158], "clarifi": 184, "class": [1, 2, 29, 35, 55, 64, 137, 168, 224], "classic": [36, 161], "classif": [4, 137, 234], "classifi": 4, "claus": 184, "clean": [26, 41, 67, 147, 184], "cleanup": [8, 38, 55, 92, 147, 153, 178, 184], 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141, 148, 150, 164, 168, 173, 179, 180, 184, 207], "columnar": 180, "columnsinwav": 6, "com": [1, 26, 34, 36, 52, 64, 88, 134, 148, 162, 164, 178, 184, 195, 233], "comapt": 107, "combin": [4, 5, 7, 9, 13, 27, 29, 41, 43, 46, 53, 55, 60, 61, 64, 66, 77, 88, 99, 105, 130, 132, 134, 136, 137, 139, 165, 168, 175, 181, 184, 195, 200, 235], "combo": [5, 137, 168], "combodfr": [137, 168], "combofold": 137, "comboindex": [137, 233], "comboindizesfromtrac": 137, "combokei": [61, 64, 137], "come": [26, 181], "comma": [34, 49, 51, 130, 165, 168, 179, 184], "command": [3, 4, 26, 40, 80, 121, 127, 141, 162, 168, 178, 179, 184], "comment": [1, 2, 4, 8, 26, 41, 67, 84, 86, 131, 135, 141, 179, 184], "comment_panel": [67, 170], "comment_panel_notebook": [67, 170], "commit": [8, 26, 86, 113, 179, 184], "common": [2, 4, 8, 26, 29, 33, 34, 36, 37, 51, 53, 59, 63, 64, 126, 141, 148, 151, 157, 158, 161, 184], "common_control_group_count_num": [64, 170], "common_control_group_count_txt": [64, 170], 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"conf_getstringfromsavedcontrol": [63, 170], "conf_getstringfromset": [63, 170], "conf_getuserpressur": [63, 170], "conf_getvariablefromsavedcontrol": [63, 170], "conf_getvariablefromset": [63, 170], "conf_getwavefromsavedcontrolarrai": [63, 170], "conf_getwindownam": [63, 170], "conf_joinrigfil": [63, 170], "conf_jsontowindow": [63, 170], "conf_loadconfigusedfordaephyspanel": [63, 170], "conf_mcc_midexp": [63, 170], "conf_notebooktojson": [63, 170], "conf_onexistsetandactivatecontrolstr": [63, 170], "conf_onexistsetandactivatecontrolvar": [63, 170], "conf_openconfiginnotebook": [63, 170], "conf_parsejson": [63, 170], "conf_position_mcc_win": [63, 170], "conf_primedevicelist": [63, 170], "conf_removerigelementsfromdaephysjson": [63, 170], "conf_requireconfigblockexist": [63, 170], "conf_restoreamplifierset": [63, 170], "conf_restorecontrol": [63, 170], "conf_restoredaephi": [63, 170], "conf_restoreheadstageassoci": [63, 170], "conf_restorenotebookwindow": [63, 170], "conf_restoreuserpressur": [63, 170], "conf_restorewindow": [63, 170], "conf_savedaephi": [63, 170], "conf_savewindow": [63, 170], "conf_setdaephyschannelpopup": [63, 170], "conf_transferpreviousdaephysjson": [63, 170], "conf_traversalfind": [63, 170], "conf_updatepackagesettingsfromconfigfil": [63, 170], "conf_windowtojson": [63, 170], "confid": 7, "config": [0, 26, 41, 46, 49, 59, 63, 64, 66, 77, 83, 105, 106, 107, 112, 115, 117, 134, 139, 144, 168, 179, 188, 233], "config_dontrestor": [63, 64], "config_dontsav": [63, 64], "config_filehash": 64, "config_filenam": 64, "config_grouppath": 63, "config_nicenam": 63, "config_paneltyp": 64, "config_pushbuttononrestor": 63, "config_radiocouplingfunc": 63, "config_restoreprior": 63, "config_stimsetnwbpath": 64, "config_sweep_": [41, 64], "config_t": 66, "config_windowhandl": 63, "configfunc": 66, "configsweep": [41, 168], "configur": [0, 11, 20, 27, 46, 49, 58, 63, 64, 66, 72, 77, 107, 133, 134, 168, 174, 179, 195], "configvers": 106, "configwav": [83, 115, 117], "confus": [65, 184], "congratul": 8, "conjunct": 152, "connect": [20, 26, 39, 52, 63, 92, 120, 168, 178, 180, 184], "consecut": [6, 7, 27, 53, 88, 113, 132, 141, 147, 148, 179, 180], "consid": [3, 10, 20, 26, 36, 52, 63, 112, 121, 124, 130, 135, 148, 164, 168, 179, 184], "consist": [0, 2, 4, 6, 26, 27, 130, 159, 180, 181, 184], "const": [0, 6, 29, 30, 31, 33, 38, 40, 41, 44, 49, 51, 52, 53, 54, 55, 57, 58, 59, 60, 62, 63, 64, 65, 66, 67, 78, 80, 81, 83, 87, 88, 90, 97, 99, 101, 113, 114, 119, 121, 122, 123, 124, 125, 127, 130, 132, 135, 136, 137, 141, 142, 144, 146, 152, 165, 167, 168, 169, 182], "constan": 64, "constant": [4, 6, 7, 10, 11, 20, 29, 33, 35, 46, 48, 51, 53, 59, 60, 61, 63, 64, 65, 68, 77, 83, 87, 88, 94, 103, 105, 108, 111, 127, 130, 137, 141, 144, 149, 150, 152, 159, 162, 165, 168, 179, 180, 181, 184, 209, 216, 230, 233], "constantr": 81, "constantwidth": 137, "constrain": [4, 88], "constraint": [4, 27, 135], "construct": [26, 112, 117, 164, 184], "consum": [64, 168], "consumpt": [98, 130], "contact": 180, "contain": [0, 2, 4, 6, 9, 10, 12, 20, 26, 27, 31, 34, 40, 41, 43, 63, 77, 82, 83, 86, 87, 88, 97, 103, 105, 112, 113, 114, 117, 121, 122, 125, 127, 130, 135, 136, 137, 148, 150, 153, 161, 164, 165, 167, 168, 173, 179, 180, 184, 235], "content": [3, 4, 26, 31, 33, 34, 37, 60, 63, 67, 68, 80, 88, 110, 121, 124, 137, 148, 150, 153, 154, 156, 164, 168, 175, 179, 184], "content_typ": 110, "content_type_al": [64, 170], "content_type_com": [64, 170], "content_type_sweep": [64, 110, 170], "content_type_tpstorag": [64, 170], "contenttyp": 110, "context": [4, 19, 41, 87, 175, 184], "contextu": 88, "contig": 84, "contigu": 27, "contin": 179, "conting": [64, 168, 179, 184], "continu": [0, 53, 131, 184], "contorl": 88, "contrari": [36, 158], "contrast": [26, 83, 88], "contribut": 26, "control": [11, 12, 14, 19, 40, 49, 52, 53, 57, 58, 60, 63, 64, 66, 67, 68, 74, 81, 87, 88, 94, 111, 113, 127, 128, 130, 131, 159, 162, 165, 167, 168, 178, 179, 181, 182, 233, 234], "control_panel_typ": [64, 170], "control_prefix": [57, 170, 182, 183], "control_type_button": [64, 170], "control_type_chart": [64, 170], "control_type_checkbox": [64, 170], "control_type_customcontrol": [64, 170], "control_type_groupbox": [64, 170], "control_type_listbox": [64, 170], "control_type_popupmenu": [64, 170], "control_type_setvari": [64, 170], "control_type_slid": [64, 170], "control_type_tab": [64, 170], "control_type_titlebox": [64, 170], "control_type_valdisplai": [57, 64, 170, 182, 183], "controlarrai": 63, "controlarrayindex": 63, "controlarraynam": 63, "controlchannelindex": 67, "controldeltaind": 165, "controlexist": [88, 170], "controlgroup": 63, "controlinfo": [64, 88, 159], "controllist": [60, 88], "controlnam": [68, 88, 233], "controls_disable_during_daq": [64, 170], "controls_disable_during_daq_tp": [64, 170], "controls_disable_during_idx": [64, 170], "controlst": 88, "controltitlelist": 88, "controltyp": [67, 68, 111], "controltypetonam": [88, 170], "controlwindowtofront": [162, 170, 184], "conveni": [3, 29, 31, 33, 36, 40, 46, 51, 53, 64, 109, 133, 136, 148, 174, 184], "convent": [4, 29, 74, 124, 151, 157], "convers": [1, 2, 36, 64, 65, 88, 101, 103, 108, 135, 150, 164, 168, 184], "convert": [0, 4, 6, 25, 33, 36, 40, 52, 59, 63, 64, 67, 77, 83, 88, 101, 108, 112, 117, 119, 121, 128, 135, 141, 148, 150, 153, 158, 164, 165, 167, 168, 184, 233], "convertamplifiermodeshortstr": [108, 170], "convertamplifiermodetostr": [108, 170], "convertfreewavetoperman": [164, 170], "convertfrombytestomib": [150, 170], "convertlisttoregexpwithaltern": [150, 170], "convertlisttotextwav": 150, "convertratetosamplinginterv": [150, 170], "convertsamplingintervaltor": [150, 170], "converttouniquenumb": [150, 170], "convertxoperrorcod": [162, 170], "convieni": 68, "convolut": 61, "coordin": [0, 2, 7, 20, 37, 51, 52, 88, 103, 111, 116, 125, 130, 134, 137, 179, 184, 207], "copi": [5, 8, 60, 61, 63, 67, 77, 80, 117, 123, 130, 148, 154, 162, 164, 165, 168, 184], "copyright": 82, "copyscal": 4, "copysweeptowref": [117, 170], "core": [2, 4, 29, 33, 37], "corner": [88, 184], "correct": [2, 4, 26, 40, 41, 46, 53, 63, 66, 71, 83, 115, 121, 125, 127, 168, 175, 179, 184, 233], "correctli": [26, 58, 127, 130, 184], "correl": 64, "correspond": [2, 4, 10, 14, 20, 27, 41, 54, 63, 64, 66, 87, 126, 130, 168, 178, 180], "corrupt": 184, "cos1": 64, "cos2": 64, "cos3": 64, "cos4": 64, "cosin": 165, "cost": 181, "could": [0, 1, 4, 26, 27, 36, 41, 46, 50, 51, 53, 61, 63, 64, 67, 85, 88, 97, 103, 113, 117, 121, 124, 130, 132, 136, 148, 153, 158, 164, 165, 168, 171, 173, 180, 184], "couldnt_find_empty_slot": [66, 170], "count": [4, 6, 20, 46, 51, 52, 53, 59, 61, 64, 77, 82, 86, 87, 94, 99, 105, 108, 127, 130, 131, 134, 135, 136, 151, 158, 164, 165, 168, 170, 179, 180, 184, 190, 231], "countbird": 136, "counter": [4, 10, 62, 67, 86, 179, 184, 192], "counterpart": [67, 88, 124, 150, 164, 165], "countobject": 64, 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"expconfig_json_amp_autobias_i_bias_max": [63, 170], "expconfig_json_amp_autobias_v": [63, 170], "expconfig_json_amp_autobias_v_rang": [63, 170], "expconfig_json_amp_bridge_bal": [63, 170], "expconfig_json_amp_bridge_balance_en": [63, 170], "expconfig_json_amp_cap_neutr": [63, 170], "expconfig_json_amp_cap_neutralization_en": [63, 170], "expconfig_json_amp_comp_chain": [63, 170], "expconfig_json_amp_gain": [63, 170], "expconfig_json_amp_hold_": [63, 170], "expconfig_json_amp_hold_enable_": [63, 170], "expconfig_json_amp_hold_enable_vc": [63, 170], "expconfig_json_amp_hold_vc": [63, 170], "expconfig_json_amp_lpf": [63, 170], "expconfig_json_amp_pipette_offset_": [63, 170], "expconfig_json_amp_pipette_offset_vc": [63, 170], "expconfig_json_amp_rs_comp_correct": [63, 170], "expconfig_json_amp_rs_comp_en": [63, 170], "expconfig_json_amp_rs_comp_predict": [63, 170], "expconfig_json_amp_whole_cell_capacit": [63, 170], "expconfig_json_amp_whole_cell_en": [63, 170], "expconfig_json_amp_whole_cell_resist": [63, 170], "expconfig_json_ampblock": [63, 170], "expconfig_json_ampchannel": [63, 170], "expconfig_json_ampicad": [63, 170], "expconfig_json_ampicadgain": [63, 170], "expconfig_json_ampicadunit": [63, 170], "expconfig_json_ampicda": [63, 170], "expconfig_json_ampicdagain": [63, 170], "expconfig_json_ampicdaunit": [63, 170], "expconfig_json_ampseri": [63, 170], "expconfig_json_amptitl": [63, 170], "expconfig_json_ampvcad": [63, 170], "expconfig_json_ampvcadgain": [63, 170], "expconfig_json_ampvcadunit": [63, 170], "expconfig_json_ampvcda": [63, 170], "expconfig_json_ampvcdagain": [63, 170], "expconfig_json_ampvcdaunit": [63, 170], "expconfig_json_globalpackagesettingblock": [63, 170], "expconfig_json_hsassocblock": [63, 170], "expconfig_json_hwdevblock": [119, 170], "expconfig_json_icblock": [63, 170], "expconfig_json_ind": [63, 170], "expconfig_json_logfile_upload": [63, 170], "expconfig_json_logfile_upload_default": [63, 170], "expconfig_json_position_mcc": [63, 170], "expconfig_json_pressad": [63, 170], "expconfig_json_pressadgain": [63, 170], "expconfig_json_pressadunit": [63, 170], "expconfig_json_pressconstneg": [63, 170], "expconfig_json_pressconstpo": [63, 170], "expconfig_json_pressda": [63, 170], "expconfig_json_pressdagain": [63, 170], "expconfig_json_pressdaunit": [63, 170], "expconfig_json_pressdev": [63, 170], "expconfig_json_pressttla": [63, 170], "expconfig_json_pressttlb": [63, 170], "expconfig_json_pressureblock": [63, 170], "expconfig_json_save_path": [63, 170], "expconfig_json_stimset_nam": [63, 170], "expconfig_json_userpressblock": [63, 170], "expconfig_json_userpressda": [63, 170], "expconfig_json_userpressdev": [63, 170], "expconfig_json_vcblock": [63, 170], "expconfig_middleexp_off": [63, 170], "expconfig_middleexp_on": [63, 170], "expconfig_minimize_on_restor": [63, 64, 170], "expconfig_reserved_datablock": [63, 170], "expconfig_reserved_tagentri": [63, 170], "expconfig_rigfilesuffix": [63, 170], "expconfig_save_buttons_only_press": [63, 64, 170], "expconfig_save_ctrltyp": [64, 170], "expconfig_save_dis": [64, 170], "expconfig_save_only_relev": [63, 64, 170], "expconfig_save_popupmenu_as_index_onli": [63, 64, 170], "expconfig_save_popupmenu_as_string_onli": [63, 64, 170], "expconfig_save_posit": [64, 170], "expconfig_save_userdata": [64, 170], "expconfig_save_valu": [64, 170], "expconfig_settings_amptitl": [63, 170], "expconfig_settings_fold": [63, 170], "expconfig_udata_buttonpress": [63, 170], "expconfig_udata_ctrlarrai": [63, 170], "expconfig_udata_ctrlarrayindex": [63, 170], "expconfig_udata_exclude_restor": [63, 64, 170], "expconfig_udata_exclude_sav": [64, 170], "expconfig_udata_jsonpath": [63, 170], "expconfig_udata_maxctrlarrayindex": [63, 170], "expconfig_udata_nicenam": [63, 170], "expconfig_udata_paneltyp": [64, 170], "expconfig_udata_radiocoupl": [63, 170], "expconfig_udata_restore_prior": [63, 170], "expconfig_udata_sourcefile_hash": [64, 170], "expconfig_udata_sourcefile_path": [64, 170], "expconfig_udata_stimset_nwb_path": [64, 170], "expconfig_udata_winhandl": [63, 170], "expect": [4, 7, 26, 27, 36, 46, 52, 53, 59, 62, 63, 67, 88, 113, 124, 136, 137, 164, 167, 171, 181, 184], "expectedhash": 62, "expectedtyp": [46, 171], "expectedvers": [62, 154], "expectedwavetyp": 136, "expens": [26, 124, 184], "experi": [1, 3, 9, 11, 12, 14, 26, 36, 41, 43, 59, 60, 61, 63, 64, 67, 74, 80, 86, 92, 100, 118, 121, 124, 153, 161, 162, 165, 168, 179, 181, 184, 185, 233], "experiment": [1, 35, 37, 49, 53, 162, 170, 179, 184, 201, 231], "experiment_descript": [1, 35, 170, 201, 231], "experiment_treeview_column": [41, 170], "experiment_vers": [64, 170], "experimentbrows": [41, 168], "experimentmap": 168, "expfilepath": [41, 233], "expfold": [41, 168], "expir": 26, "explain": [113, 184], "explan": [4, 20, 116, 130, 168], "explicit": [4, 36, 64, 158, 165, 168, 174, 184], "explicitlbl": 135, "explicitli": [1, 4, 14, 61, 184], "exploit": 162, "expnam": 153, "expon": [165, 168], "exponenti": [4, 137, 168], "expontenti": 141, "export": [26, 27, 37, 41, 44, 64, 86, 121, 168, 178, 184], "exportsettingspanel": [44, 45, 170], "exporttyp": 121, "express": [4, 29, 52, 64, 83, 88, 93, 128, 135, 136, 148, 149, 150, 151, 154, 157, 161], "exprtyp": [151, 157], "ext": [179, 184], "ext_panel_settingshistori": [64, 170], "ext_panel_sf_formula": [60, 170], "ext_panel_sf_help": [60, 170], "ext_panel_sf_json": [60, 170], "ext_panel_subwindow": [60, 170], "ext_panel_sweepcontrol": [60, 170], "extallgraph": 137, "extcmdsen": [40, 170, 189, 231], "extend": [12, 26, 27, 41, 64, 83, 103, 121, 135, 168, 175, 178, 179, 184], "extendedoutput": 159, "extens": [2, 3, 26, 29, 36, 37, 64, 83, 87, 130, 150, 153, 178, 184, 198], "extern": [43, 44, 54, 60, 64, 73, 74, 124, 179, 184], "extra": 20, "extract": [4, 20, 34, 46, 67, 88, 94, 113, 117, 123, 130, 134, 135, 136, 137, 148, 154, 164, 165, 167, 180, 184, 215], "extractfromsubrang": [148, 170], "extractlimit": [88, 170], "extractlimitsfromrecmacro": [88, 170], "extractlogbookslic": [113, 170], "extractlogbookslicedeltatim": [113, 170], "extractlogbooksliceempti": [113, 170], "extractlogbookslicesweep": [113, 170], "extractlogbookslicetimestamp": [113, 170], "extractonedimdatafromsweep": [0, 117, 170, 184], "extractstringfrompair": [161, 170], "extractsweepnumb": [0, 117, 170], "extrapol": 53, "f": [5, 7, 20, 27, 36, 53, 64, 113, 148, 157, 161, 165, 179, 184, 233], "f_": 4, "f_flag_req_itc18_18usb_1600": [66, 170], "f_kei": [64, 170], "facil": 74, "facilit": [14, 20, 67, 184], "fact": [4, 46], "factor": [1, 4, 7, 53, 61, 64, 77, 83, 90, 103, 121, 139, 164, 168, 179, 184, 198], "fail": [3, 4, 7, 8, 11, 25, 50, 51, 52, 53, 63, 64, 90, 101, 115, 130, 135, 164, 168, 184], "failedlevel": 7, "failednumberofspik": [134, 170, 215, 231], "failedpuls": [130, 170, 209, 231], "failedpulselevel": [7, 64], "failedpulseslevel": [130, 134, 170, 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"fifomonitormd": 64, "fifopo": [66, 117, 123, 144], "fifteen_second": [58, 170], "fifth": 64, "figur": [14, 20], "file": [1, 2, 9, 14, 27, 177, 178, 179, 180, 181, 185, 201, 221, 225, 233], "file_create_d": [1, 3, 35, 170, 225, 231], "file_list_sep": [64, 153, 170], "file_organ": 1, "fileexist": [36, 153, 170], "filefilt": 153, "fileid": [3, 31, 33, 34, 121], "filenam": [36, 41, 43, 90, 92, 118, 121, 153, 168, 180, 184], "filepath": [36, 90, 153], "filepathwithsuffix": [36, 153], "files": 3, "filesystem": 184, "filetyp": [41, 168], "fill": [3, 4, 8, 15, 17, 18, 20, 21, 22, 23, 24, 26, 34, 35, 37, 44, 51, 53, 60, 61, 66, 70, 77, 83, 87, 95, 115, 127, 130, 132, 134, 137, 141, 156, 164, 165, 167, 168, 180, 184, 188, 204, 208, 211, 230, 232, 235], "filter": [2, 4, 5, 7, 20, 37, 53, 64, 77, 83, 85, 88, 90, 111, 114, 119, 129, 136, 137, 150, 153, 168, 179, 180, 184], "filterbyd": [114, 170], "filteredskipahead": 67, "filterfir": 4, "filterhigh": 4, "filteriir": [4, 165, 184], "filterlow": 4, "filterord": [165, 170, 220, 231], "filterpass": 53, "final": [3, 4, 51, 53, 64, 117, 184], "finalhook": 167, "finalslopeperc": [7, 184], "find": [2, 4, 26, 49, 51, 53, 63, 64, 74, 85, 111, 113, 114, 115, 137, 148, 154, 158, 173, 181, 184, 185], "findcontrol": [88, 170], "findcursoringraph": [154, 170], "finddupl": [36, 148], "findfirstlogentryelementbyd": [114, 170], "findfirstnanindex": [164, 170], "findfirstoutsidecal": [80, 170], "findind": [64, 103, 170, 184], "findindizesprop": 103, "findlastlogentryelementbyd": [114, 170], "findlevel": [0, 61, 64, 111, 130, 135, 148, 184], "findlevel_edge_both": [4, 64, 170], "findlevel_edge_decreas": [64, 170], "findlevel_edge_increas": [64, 170], "findlevel_mode_multi": [64, 148, 170], "findlevel_mode_singl": [64, 148, 170], "findleveledgetyp": 148, "findlevelmod": 148, "findlevelsingl": [148, 170], "findlevelsmult": [148, 170], "findlevelwrapp": [148, 170], "findneighbourdupl": [164, 170], "findnextexperi": [101, 170], "findnextpow": [158, 170], "findnotebook": [88, 170], "findpeak": 137, "findpreviouspow": [158, 170], "findrang": [113, 170, 184], "findrightmosthighbit": [158, 170], "findvalu": [103, 164], "fine": [8, 14, 77, 88, 128, 184], "fingerprint": [77, 168], "finish": [26, 46, 49, 53, 55, 83, 121, 134, 146, 179, 184, 188], "finit": [4, 36, 53, 55, 149, 164, 184], "fire": [168, 184], "firkin": 4, "first": [0, 1, 2, 3, 4, 6, 7, 8, 19, 20, 26, 27, 33, 35, 36, 41, 49, 51, 53, 55, 59, 60, 61, 63, 64, 66, 74, 77, 80, 81, 82, 84, 86, 87, 88, 92, 98, 99, 103, 105, 111, 113, 114, 122, 124, 127, 130, 131, 132, 135, 136, 137, 139, 141, 148, 149, 150, 151, 152, 154, 157, 158, 161, 164, 165, 168, 170, 173, 175, 178, 180, 184, 208, 230, 231], "first_xop_error": [64, 170], "firstcolinp": 103, "firstcolout": 103, "firstdat": 119, "firstedg": 0, "firstfreq": [165, 170, 220, 231], "firstparts": 148, "firstrowinp": 103, "firstsweep": 99, "firstsweeporindex": 60, "fit": [5, 7, 26, 53, 64, 83, 137, 141, 168, 184], "fitcoeffici": 64, "fitdata": 135, "fiteventdecaycustomerror": 168, "fitfunc": [4, 135], "fitlin": [64, 184], "fitoffset": 53, "fitop": 4, "fitparamet": 64, "fitq": [4, 135], "fitresist": [49, 170, 184], "fitresult": [4, 137], "fitsigma": 64, "fitslop": 53, "five": 4, "fix": [2, 4, 6, 8, 10, 11, 14, 20, 26, 27, 67, 83, 84, 88, 105, 125, 134, 137, 148, 168, 178, 179, 181, 184, 195, 233], "fixedpulselength": [130, 134, 170, 215, 231], "fixinvalidlabnotebookkei": [168, 170], "fixup": [49, 125], "flag": [10, 31, 41, 55, 63, 64, 66, 86, 88, 111, 117, 121, 130, 145, 148, 150, 153, 164, 168, 169, 184], "flesh": 8, "flexibl": 184, "flip": [27, 83, 165, 168, 170, 184, 198, 231], "float": [49, 84, 139, 149, 150, 164, 165, 168, 180, 184], "float32": 2, "floatwithminsigdigit": [123, 150, 170], "floor": [10, 49], "flooranddelta": [158, 170], "flow": [159, 184], "flowchart": [8, 51, 52, 53, 141], "flush": [31, 121, 184], "fly": 184, "fmt_lbn_ana_func_vers": [51, 53, 64, 170], "fname": 63, "folder": [4, 6, 10, 26, 33, 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"mies_miesutilities_sweep": 117, "mies_miesutilities_system": 118, "mies_miesutilities_upload": 119, "mies_miesutilities_zeromq": 120, "mies_neurodatawithoutbord": 121, "mies_optimzedoverlapdistributedacquisit": 122, "mies_oscilloscop": 123, "mies_overlaysweep": 124, "mies_packageset": 125, "mies_pictur": 126, "mies_pressurecontrol": 127, "mies_programmaticguicontrol": 128, "mies_publish": 129, "mies_pulseaverag": 130, "mies_repeatedacquisit": 131, "mies_samplinginterv": 132, "mies_stimsetapi": 133, "mies_structur": 134, "mies_sweepformula": 135, "mies_sweepformula_help": 136, "mies_sweepformula_psx": 137, "mies_sweepformula_psx_macro": 138, "mies_sweepsav": 139, "mies_tangointeract": 140, "mies_testpuls": 141, "mies_testpulse_multi": 142, "mies_testpulse_singl": 143, "mies_threadedfifohandl": 144, "mies_threadsafedatashar": 145, "mies_threadsafeutil": 146, "mies_traceuserdata": 147, "mies_utilities_algorithm": 148, "mies_utilities_check": 149, "mies_utilities_convers": 150, "mies_utilities_datafold": 151, "mies_utilities_debugg": 152, "mies_utilities_fil": 153, "mies_utilities_gener": 155, "mies_utilities_gui": 154, "mies_utilities_json": 156, "mies_utilities_list": 157, "mies_utilities_numer": 158, "mies_utilities_programflow": 159, "mies_utilities_sfhcheck": 160, "mies_utilities_str": 161, "mies_utilities_system": 162, "mies_utilities_tim": 163, "mies_utilities_wavehandl": 164, "mies_wavebuild": 165, "mies_wavebuilder_macro": 166, "mies_wavebuilderpanel": 167, "mies_wavedatafoldergett": 168, "miesutil": 184, "min": 4, "miscellan": 6, "modul": [3, 4], "mous": 5, "msq_pulseset": 204, "multiexperimentprocesspref": 205, "multipl": 4, "name": [26, 27], "namespac": [182, 183], "neurodatawithoutbord": 3, "new": [26, 180, 184], "ni": 26, "nightli": 178, "note": [18, 184], "number": 180, "numer": [179, 184], "nwb": [1, 2, 3, 184], "nwbasyncparamet": 206, "nwbv2": 27, "object": 181, "onlin": 3, "ooddaq": [12, 27], "ooddaqparam": 207, "oper": [4, 20], "optim": [12, 27], "order": [10, 20], "organ": 3, "output": 181, "overlai": 19, "overlap": [12, 27], "overview": 180, "p_pressureda": 208, "pa": 20, "pa_constantset": 209, "panel": [5, 181], "paramet": 7, "parser": 4, "plot": [4, 20, 184], "popup": 26, "postplotset": 212, "powerspectrum": 4, "prefer": 178, "prepar": 10, "preprocess": 4, "pressur": 184, "prevent": 26, "principl": [0, 6], "privileg": 178, "pro": [3, 4, 178, 180], "process": 26, "psc": 5, "psp": 5, "psq_ds_dascaleparam": 210, "psq_pulseset": 211, "psx": [4, 5], "psxdeconvfilt": 4, "psxkernel": 4, "psxprep": 4, "psxrisetim": 4, "psxstat": [4, 5], "publish": 184, "puls": [0, 11, 20, 27, 184, 235], "pulseaveragedeconvset": 213, "pulseaverageset": 215, "pulseaveragesetindic": 214, "python": 180, "quick": [4, 10], "rac": 180, "rang": [4, 6], "read": 3, "readchannelparam": 216, "rectd": 217, "region": 27, "releas": [26, 184], "relev": 14, "remov": [15, 184], "renam": 184, "renew": 26, "repeat": 180, "report": 185, "requir": 26, "resourc": 3, "result": 6, "retriev": [0, 6, 26, 27], "root": 4, "run": 6, "runner": 26, "runtim": 26, "sbe_exportset": 218, "scheme": 26, "search": 180, "segmentparamet": 220, "select": [4, 16], "separ": 4, "sequenc": 184, "server": 26, "set": [0, 20, 21, 22, 26], "setscal": 4, "setup": [4, 26], "sf_plotmetadata": 219, "short": 27, "sign": 178, "silent": 178, "singl": 5, "six": 8, "softwar": 26, "sort": 20, "special": 27, "specif": 180, "squar": [0, 4], "stack": 4, "start": 10, "startup": 6, "statist": 4, "stdev": 4, "step": 178, "stimsetapifunct": 174, "stock": 7, "stop": 10, "store": 4, "struct": [186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231], "structur": 181, "subjectinfo": 221, "support": [26, 178], "sweep": [4, 19, 23, 180, 184], "sweepbrows": [14, 184], "sweepformula": [5, 24], "tab": 181, "tabl": 177, "tango": 184, "task": 180, "test": [11, 26, 184], "testpuls": 6, "text": 4, "textual": [179, 184], "thirti": 8, "thread": 10, "threadsaf": 26, "tiledgraphset": 223, "time": [4, 20, 27], "timeseriesproperti": 224, "todo": 233, "top": 5, "toplevelinfo": 225, "tp": 4, "tpanalysisinput": 222, "tpbase": 4, "tpfit": 4, "tpinst": 4, "tpss": 4, "tpstorag": 232, "trace": 20, "train": [27, 235], "tuf": 184, "tune": 11, "type": [10, 235], "ui": 5, "unit": 26, "up": 26, "updat": [26, 178], "us": 178, "user": [27, 178, 184, 234], "util": 4, "uuid": 226, "v": 14, "valu": [4, 180], "variabl": 4, "varianc": 4, "vectordata": 227, "vectorindex": 228, "version": [1, 2, 26, 181], "wave": [4, 181], "wavebuild": [184, 235], "wavelocationmod": 229, "waveversioningsupport": 175, "which": 180, "window": [26, 178], "without": 178, "work": [10, 184], "wrapper": [4, 181], "write": [3, 4, 8], "writechannelparam": 230, "x": 4, "xop": 184, "xvalu": 4, "y": 4, "zeromq": 184, "zeromq_interop": 169}}) \ No newline at end of file diff --git a/struct/struct_a_s_y_n_c___read_out_struct.html b/struct/struct_a_s_y_n_c___read_out_struct.html new file mode 100644 index 0000000000..95a3e8ef45 --- /dev/null +++ b/struct/struct_a_s_y_n_c___read_out_struct.html @@ -0,0 +1,216 @@ + + + + + + + + Struct ASYNC_ReadOutStruct — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct ASYNC_ReadOutStruct

+
+
+struct ASYNC_ReadOutStruct
+

ReadOut Structure for ASYNC.

+
+

Public Members

+
+
+DFREF dfr
+
+ +
+
+variable rtErr
+
+ +
+
+string rtErrMsg
+
+ +
+
+variable abortCode
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_active_channels.html b/struct/struct_active_channels.html new file mode 100644 index 0000000000..92fc33adf5 --- /dev/null +++ b/struct/struct_active_channels.html @@ -0,0 +1,228 @@ + + + + + + + + Struct ActiveChannels — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct ActiveChannels

+
+
+struct ActiveChannels
+

Helper struct for storing the number of active channels per rack.

+
+

Public Members

+
+
+int32 numDARack1
+
+ +
+
+int32 numADRack1
+
+ +
+
+int32 numTTLRack1
+
+ +
+
+int32 numDARack2
+
+ +
+
+int32 numADRack2
+
+ +
+
+int32 numTTLRack2
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_analysis_function___v3.html b/struct/struct_analysis_function___v3.html new file mode 100644 index 0000000000..e64ba79cd5 --- /dev/null +++ b/struct/struct_analysis_function___v3.html @@ -0,0 +1,280 @@ + + + + + + + + Struct AnalysisFunction_V3 — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct AnalysisFunction_V3

+
+
+struct AnalysisFunction_V3
+

The structure passed into V3 and later analysis functions.

+
+

Public Members

+
+
+variable eventType
+

one of EVENT_TYPE_ANALYSIS_FUNCTIONS

+
+ +
+
+WaveRefWave scaledDACWave
+

scaled and undecimated data from the DAC hardware, wave ref wave where each element is a channel wave. Channels are in the same order as the config wave rows.

+
+ +
+
+variable headStage
+

active headstage index, [0, NUM_HEADSTAGES[

+
+ +
+
+variable sweepNo
+

Potential future number of the sweep. Once the sweep is finished it will be saved with this number. Use GetSweepWave() to query the sweep itself.

+
+ +
+
+variable sweepsInSet
+

Number of sweeps in the currently acquired stimset of the passed headstage.

+
+ +
+
+string params
+

Analysis function parameters set in the stimset’s textual parameter wave. Settable via AFH_AddAnalysisParameter().

+
+ +
+
+variable lastValidRowIndexDA
+

last valid row index for DA channels in rawDAQWave which will be filled with data at the end of DAQ. If the acquisition was aborted, the remaining samples beyond lastValidRowIndexDA are NaN. The total number of rows in rawDAQWave might be higher due to alignment requirements of the data acquisition hardware (e.g. ITC).

+

Always NaN for PRE_DAQ_EVENT/PRE_SET_EVENT events.

+
+ +
+
+variable lastValidRowIndexAD
+

last valid row index for AD/TTL channels in rawDAQWave which will be filled with data at the end of DAQ. The total number of rows in rawDAQWave might be higher due to alignment requirements of the data acquisition hardware (e.g. ITC).

+

Always NaN for PRE_DAQ_EVENT/PRE_SET_EVENT events.

+
+ +
+
+variable lastKnownRowIndexDA
+

last written row index in rawDAQWave/scaledDACWaves DA channel(s) with already acquired data

+

Always NaN for PRE_DAQ_EVENT/PRE_SET_EVENT/PRE_SWEEP_CONFIG_EVENT.

+
+ +
+
+variable lastKnownRowIndexAD
+

last written row index in rawDAQWave/scaledDACWaves AD/TTL channel(s) with already acquired data

+

Always NaN for PRE_DAQ_EVENT/PRE_SET_EVENT/PRE_SWEEP_CONFIG_EVENT.

+
+ +
+
+variable sampleIntervalDA
+

sample interval of DA channel(s) in ms

+
+ +
+
+variable sampleIntervalAD
+

sample interval of AD channel(s) in ms

+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_axon_telegraph___data_struct.html b/struct/struct_axon_telegraph___data_struct.html new file mode 100644 index 0000000000..6fb99b4adc --- /dev/null +++ b/struct/struct_axon_telegraph___data_struct.html @@ -0,0 +1,348 @@ + + + + + + + + Struct AxonTelegraph_DataStruct — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct AxonTelegraph_DataStruct

+
+
+struct AxonTelegraph_DataStruct
+
+

Public Members

+
+
+uint32 Version
+

Structure version. Value should always be 13.

+
+ +
+
+uint32 SerialNum
+
+ +
+
+uint32 ChannelID
+
+ +
+
+uint32 ComPortID
+
+ +
+
+uint32 AxoBusID
+
+ +
+
+uint32 OperatingMode
+
+ +
+
+string OperatingModeString
+
+ +
+
+uint32 ScaledOutSignal
+
+ +
+
+string ScaledOutSignalString
+
+ +
+
+double Alpha
+
+ +
+
+double ScaleFactor
+
+ +
+
+uint32 ScaleFactorUnits
+
+ +
+
+string ScaleFactorUnitsString
+
+ +
+
+double LPFCutoff
+
+ +
+
+double MembraneCap
+
+ +
+
+double ExtCmdSens
+
+ +
+
+uint32 RawOutSignal
+
+ +
+
+string RawOutSignalString
+
+ +
+
+double RawScaleFactor
+
+ +
+
+uint32 RawScaleFactorUnits
+
+ +
+
+string RawScaleFactorUnitsString
+
+ +
+
+uint32 HardwareType
+
+ +
+
+string HardwareTypeString
+
+ +
+
+double SecondaryAlpha
+
+ +
+
+double SecondaryLPFCutoff
+
+ +
+
+double SeriesResistance
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_background_struct.html b/struct/struct_background_struct.html new file mode 100644 index 0000000000..33e72c34e6 --- /dev/null +++ b/struct/struct_background_struct.html @@ -0,0 +1,225 @@ + + + + + + + + Struct BackgroundStruct — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct BackgroundStruct

+
+
+struct BackgroundStruct
+
+

Public Members

+
+
+WMBackgroundStruct wmbs
+
+ +
+
+int32 count
+

Number of invocations of background function.

+
+ +
+
+int32 threadDeadCount
+

DAQ/TP-MD with ITC hardware only: Number of successive tries to get data from the thread.

+
+ +
+
+variable tickslastReceivedFifoPos
+

DAQ-MD with ITC hardware only: ticks count when the fifo position was last updated.

+
+ +
+
+variable lastReceivedFifoPos
+

DAQ-MD with ITC hardware only: last received fifo position.

+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_buffered_draw_info.html b/struct/struct_buffered_draw_info.html new file mode 100644 index 0000000000..b199757c16 --- /dev/null +++ b/struct/struct_buffered_draw_info.html @@ -0,0 +1,204 @@ + + + + + + + + Struct BufferedDrawInfo — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct BufferedDrawInfo

+
+
+struct BufferedDrawInfo
+

Stores information for buffered draw jsonID - stores information about traces and labels to draw/setup traceWaves - wave ref wave with references to the trace waves (which are always non-free)

+
+

Public Members

+
+
+variable jsonID
+
+ +
+
+WaveRefWave traceWaves
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_c_h_i___installation_state.html b/struct/struct_c_h_i___installation_state.html new file mode 100644 index 0000000000..62444527ed --- /dev/null +++ b/struct/struct_c_h_i___installation_state.html @@ -0,0 +1,204 @@ + + + + + + + + Struct CHI_InstallationState — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct CHI_InstallationState

+
+
+struct CHI_InstallationState
+

Collection of counters used for installation checking.

+
+

Public Members

+
+
+variable numErrors
+
+ +
+
+variable numTries
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_check_parameters_struct.html b/struct/struct_check_parameters_struct.html new file mode 100644 index 0000000000..f3cebf530a --- /dev/null +++ b/struct/struct_check_parameters_struct.html @@ -0,0 +1,203 @@ + + + + + + + + Struct CheckParametersStruct — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct CheckParametersStruct

+
+
+struct CheckParametersStruct
+
+

Public Members

+
+
+string params
+
+ +
+
+string setName
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_chirp_bounds_info.html b/struct/struct_chirp_bounds_info.html new file mode 100644 index 0000000000..7390b64abf --- /dev/null +++ b/struct/struct_chirp_bounds_info.html @@ -0,0 +1,216 @@ + + + + + + + + Struct ChirpBoundsInfo — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct ChirpBoundsInfo

+
+
+struct ChirpBoundsInfo
+

Helper strucuture for PSQ_CR_DetermineBoundsState()

+
+

Public Members

+
+
+variable minimumFac
+
+ +
+
+variable centerFac
+
+ +
+
+variable maximumFac
+
+ +
+
+string state
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_data_configuration_result.html b/struct/struct_data_configuration_result.html new file mode 100644 index 0000000000..510a13d2e0 --- /dev/null +++ b/struct/struct_data_configuration_result.html @@ -0,0 +1,612 @@ + + + + + + + + Struct DataConfigurationResult — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct DataConfigurationResult

+
+
+struct DataConfigurationResult
+

Structure to hold the result of data configuration from DC_GetConfiguration()

+
+

Unnamed Group

+
+
+variable globalTPInsert
+

Various GUI settings

+
+ +
+
+variable scalingZero
+
+ +
+
+variable indexingLocked
+
+ +
+
+variable indexing
+
+ +
+
+variable distributedDAQ
+
+ +
+
+variable distributedDAQOptOv
+
+ +
+
+variable distributedDAQOptPre
+
+ +
+
+variable distributedDAQOptPost
+
+ +
+
+variable multiDevice
+
+ +
+
+variable powerSpectrum
+
+ +
+
+WAVE statusHS
+
+ +
+
+

Various delays in points of the DA data wave

+
+
+variable onsetDelayUser
+
+ +
+
+variable onsetDelayAuto
+
+ +
+
+variable onsetDelay
+

Sum of onsetDelayUser and onsetDelayAuto.

+
+ +
+
+variable distributedDAQDelay
+
+ +
+
+variable terminationDelay
+
+ +
+
+

Unnamed Group

+
+
+WAVE offsets
+

[ms]

+

oodDAQ optimization results, see OOdDAQParams_Output

+
+ +
+
+WaveText regions
+
+ +
+
+

Unnamed Group

+
+
+WAVE DACList
+

List of active channels per type

+
+ +
+
+WAVE ADCList
+
+ +
+
+WAVE TTLList
+
+ +
+
+

Unnamed Group

+
+
+WaveDouble DACAmp
+

All waves here use active channel indexing like DataConfigurationResult::DACList and can thus be all indexed together.

+

+

See also

+

GetDACAmplitudes()

+
+

+
+ +
+
+WaveText setName
+

Stimulus set name.

+
+ +
+
+WaveText TTLsetName
+
+ +
+
+WaveRefWave stimSet
+

Stimulus set wave (2D)

+
+ +
+
+WaveRefWave TTLstimSet
+
+ +
+
+WaveDouble setLength
+

+

See also

+

DC_CalculateStimsetLength()

+
+

+
+ +
+
+WaveDouble TTLsetLength
+
+ +
+
+WaveDouble headstageDAC
+

Headstage of DAC if associated, NaN iff unassociated.

+
+ +
+
+WaveDouble setColumn
+

+

See also

+

DC_CalculateChannelColumnNo()

+
+

+
+ +
+
+WaveDouble TTLsetColumn
+
+ +
+
+WaveDouble setCycleCount
+
+ +
+
+WaveDouble TTLcycleCount
+
+ +
+
+

Public Members

+
+
+variable dataAcqOrTP
+

What type of operation is done. Either DAQ(DATA_ACQUISITION_MODE) or TP(TEST_PULSE_MODE)

+
+ +
+
+variable baselineFrac
+

+

See also

+

GetTestpulseBaselineFraction()

+
+

+
+ +
+
+variable decimationFactor
+

+

See also

+

DC_GetDecimationFactor()

+
+

+
+ +
+
+variable numDACEntries
+

Number of DAC’s, always larger than 0.

+
+ +
+
+variable numADCEntries
+

Number of ADC’s, always larger than 0.

+
+ +
+
+variable numTTLEntries
+

Number of TTLs, can be zero.

+
+ +
+
+variable numActiveChannels
+

Sum of numDACEntries/numADCEntries/numTTLEntries.

+
+ +
+
+variable hardwareType
+

One of HardwareDACTypeConstants.

+
+ +
+
+variable samplingIntervalDA
+

Sampling interval for DA channels in μs,.

+

+

See also

+

DAP_GetSampInt()

+
+

+
+ +
+
+variable samplingIntervalAD
+

Sampling interval for AD channels in μs,.

+

+

See also

+

DAP_GetSampInt()

+
+

+
+ +
+
+variable samplingIntervalTTL
+

Sampling interval for TTL channels in μs,.

+

+

See also

+

DAP_GetSampInt()

+
+

+
+ +
+
+WAVE testPulse
+

+

See also

+

GetTestPulse()

+
+

+
+ +
+
+variable testPulseLength
+

Length of the DataConfigurationResult::testPulse wave in points test pulse properties from TP_GetCreationPropertiesInPoints

+
+ +
+
+variable tpPulseStartPoint
+
+ +
+
+variable tpPulseLengthPoints
+
+ +
+
+WAVE gains
+

+

See also

+

SWS_GetChannelGains() with GAIN_BEFORE_DAQ

+
+

+
+ +
+
+WaveDouble insertStart
+

Offset in points where the stimulus set starts in the DAQ data wave.

+
+ +
+
+WaveDouble headstageADC
+

Headstage of ADC if associated, NaN iff unassociated Uses active channel indexing like DataConfigurationResult::ADCList

+
+ +
+
+variable skipAhead
+

Number of sweeps to skip over on start of data acquisition.

+
+ +
+
+variable stopCollectionPoint
+

Maximum number of samples that can be acquired to the data wave For ITC can be higher that planned samples to be acquired (no automatic stop, only programmatic)

+
+ +
+
+variable joinedTTLStimsetSize
+

for ITC, TTL stimset size in DC after TTL stimsets were bit-combined to a joined wave fixing https://github.com/AllenInstitute/MIES/issues/2007 should remove the need for this

+
+ +
+
+WAVE statusTTLFiltered
+

wave indexing GUI TTL channels, 1 - activated, 0 deactivated

+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_delta_control_names.html b/struct/struct_delta_control_names.html new file mode 100644 index 0000000000..3e26feaea1 --- /dev/null +++ b/struct/struct_delta_control_names.html @@ -0,0 +1,222 @@ + + + + + + + + Struct DeltaControlNames — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct DeltaControlNames

+
+
+struct DeltaControlNames
+

Helper structure for WB_GetDeltaDimLabel()

+
+

Public Members

+
+
+string main
+
+ +
+
+string delta
+
+ +
+
+string dme
+
+ +
+
+string op
+
+ +
+
+string ldelta
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_dynamic_table.html b/struct/struct_dynamic_table.html new file mode 100644 index 0000000000..9d4d464d3b --- /dev/null +++ b/struct/struct_dynamic_table.html @@ -0,0 +1,209 @@ + + + + + + + + Struct DynamicTable — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct DynamicTable

+
+
+struct DynamicTable
+
+

Public Members

+
+
+string colnames
+
+ +
+
+string description
+
+ +
+
+string data_type
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_e_p___epoch_creation_data.html b/struct/struct_e_p___epoch_creation_data.html new file mode 100644 index 0000000000..f24b3c6f08 --- /dev/null +++ b/struct/struct_e_p___epoch_creation_data.html @@ -0,0 +1,324 @@ + + + + + + + + Struct EP_EpochCreationData — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct EP_EpochCreationData

+
+
+struct EP_EpochCreationData
+

Helper structure for data used in epoch creation.

+

structure variables for index based positions are prefixed: dw* - index in the data wave (e.g. DAChannel) wb* - index in the stimset wave from the wave builder

+
+

Public Members

+
+
+WaveText epochWave
+

Epochs wave.

+
+ +
+
+variable channel
+

GUI channel number.

+
+ +
+
+variable channelType
+

channel type as of XopChannelConstants

+
+ +
+
+variable sweep
+

sweep of stimset

+
+ +
+
+variable decimationFactor
+

decimation factor from stimset to data wave

+
+ +
+
+variable samplingInterval
+

sampling interval of data wave

+
+ +
+
+variable scale
+

DAScale of channel.

+
+ +
+
+string stimNote
+

stimset wave note

+
+ +
+
+variable dwStimsetSize
+

stimset size in data wave

+
+ +
+
+variable reducedStimsetSize
+

For DA: size of stimset wave that was decimated to the data wave the duration of that stimset can be reduced compared to the duration of the original wavebuilder stimset due to oodDAQ end cutoff, typically DimSize of the stimset in DC For TTL: same as dwStimsetSize note: While for DA the stimset size in DC can only be reduced for TTL channels it can be increased, see structure element dwJoinedTTLStimsetSize

+
+ +
+
+variable dwStimsetBegin
+

begin of stimset in indicces of the data wave

+
+ +
+
+variable wbOodDAQOffset
+

offset from oodDAQ shift in wavebuilder stimset wave indices

+
+ +
+
+variable wbStimsetSize
+

size of the original wavebuilder stimset, used as reference point for flipping calculation

+
+ +
+
+variable wbEffectiveStimsetSize
+

sum of all stimset epochs without extension from delta mechanism (multi sweep, different size)

+
+ +
+
+variable dwJoinedTTLStimsetSize
+

for ITC TTL stimsets are joined in DC to a single 2D wave that ROWS size equals the largest single stimset. This value is the data wave length that is used to decimate the from DC modified stimset into the data wave. The stimset is decimated to the data wave until dwJoinedTTLStimsetSize - 1. The related value for DA channels is s.setLength. For DA channels: NaN

+
+ +
+
+variable flipping
+

set to one if the stimset is flipped, zero otherwise

+
+ +
+
+variable tpTotalLengthPoints
+

test pulse properties transferred from DataConfigurationResult structure, originally calculated by TP_GetCreationPropertiesInPoints

+
+ +
+
+variable tpPulseStartPoint
+
+ +
+
+variable tpPulseLengthPoints
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_element_identifiers.html b/struct/struct_element_identifiers.html new file mode 100644 index 0000000000..d7fcf97b1e --- /dev/null +++ b/struct/struct_element_identifiers.html @@ -0,0 +1,197 @@ + + + + + + + + Struct ElementIdentifiers — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct ElementIdentifiers

+
+
+struct ElementIdentifiers
+
+

Public Members

+
+
+string data_type
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_formula_properties.html b/struct/struct_formula_properties.html new file mode 100644 index 0000000000..9eca45bbf3 --- /dev/null +++ b/struct/struct_formula_properties.html @@ -0,0 +1,216 @@ + + + + + + + + Struct FormulaProperties — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct FormulaProperties

+
+
+struct FormulaProperties
+

Helper structure for formula parsing of the Wavebuilder combine epoch.

+
+

Public Members

+
+
+string formula
+
+ +
+
+string stimsetList
+
+ +
+
+variable numRows
+
+ +
+
+variable numCols
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_general_info.html b/struct/struct_general_info.html new file mode 100644 index 0000000000..593ece6620 --- /dev/null +++ b/struct/struct_general_info.html @@ -0,0 +1,276 @@ + + + + + + + + Struct GeneralInfo — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct GeneralInfo

+
+
+struct GeneralInfo
+

Structure to hold all properties of the NWB file directly below /general

+
+

Public Members

+
+
+string session_id
+
+ +
+
+string experimenter
+
+ +
+
+string institution
+
+ +
+
+string lab
+
+ +
+
+string related_publications
+
+ +
+
+string notes
+
+ +
+
+string experiment_description
+
+ +
+
+string data_collection
+
+ +
+
+string stimulus
+
+ +
+
+string pharmacology
+
+ +
+
+string surgery
+
+ +
+
+string protocol
+
+ +
+
+string virus
+
+ +
+
+string slices
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_h_d_f5_data_info.html b/struct/struct_h_d_f5_data_info.html new file mode 100644 index 0000000000..84c04df223 --- /dev/null +++ b/struct/struct_h_d_f5_data_info.html @@ -0,0 +1,263 @@ + + + + + + + + Struct HDF5DataInfo — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct HDF5DataInfo

+
+
+struct HDF5DataInfo
+
+

Public Members

+
+
+uint32 version
+
+ +
+
+char structName[16]
+
+ +
+
+double datatype_class
+
+ +
+
+char datatype_class_str[32]
+
+ +
+
+double datatype_size
+
+ +
+
+double datatype_sign
+
+ +
+
+double datatype_order
+
+ +
+
+char datatype_str[64]
+
+ +
+
+double dataspace_type
+
+ +
+
+double ndims
+
+ +
+
+double dims[H5S_MAX_RANK]
+
+ +
+
+double maxdims[H5S_MAX_RANK]
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_hardware_data_t_p_input.html b/struct/struct_hardware_data_t_p_input.html new file mode 100644 index 0000000000..e5aced6507 --- /dev/null +++ b/struct/struct_hardware_data_t_p_input.html @@ -0,0 +1,246 @@ + + + + + + + + Struct HardwareDataTPInput — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct HardwareDataTPInput

+
+
+struct HardwareDataTPInput
+

Helper structure for CA_HardwareDataTPKey()

+
+

Public Members

+
+
+variable hardwareType
+
+ +
+
+variable numDACs
+
+ +
+
+variable numActiveChannels
+
+ +
+
+variable numberOfRows
+
+ +
+
+variable samplingInterval
+
+ +
+
+WAVE gains
+
+ +
+
+WAVE DACAmpTP
+
+ +
+
+variable testPulseLength
+
+ +
+
+variable baselineFrac
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_m_s_q___pulse_settings.html b/struct/struct_m_s_q___pulse_settings.html new file mode 100644 index 0000000000..818ee5a8de --- /dev/null +++ b/struct/struct_m_s_q___pulse_settings.html @@ -0,0 +1,210 @@ + + + + + + + + Struct MSQ_PulseSettings — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct MSQ_PulseSettings

+
+
+struct MSQ_PulseSettings
+

Settings structure filled by MSQ_GetPulseSettingsForType()

+
+

Public Members

+
+
+variable prePulseChunkLength
+
+ +
+
+variable pulseDuration
+
+ +
+
+variable postPulseChunkLength
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_multi_experiment_process_prefs.html b/struct/struct_multi_experiment_process_prefs.html new file mode 100644 index 0000000000..ef88a3f25a --- /dev/null +++ b/struct/struct_multi_experiment_process_prefs.html @@ -0,0 +1,209 @@ + + + + + + + + Struct MultiExperimentProcessPrefs — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct MultiExperimentProcessPrefs

+
+
+struct MultiExperimentProcessPrefs
+
+

Public Members

+
+
+uint32 version
+
+ +
+
+uint32 processRunning
+
+ +
+
+char settingsFile[256]
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_n_w_b_async_parameters.html b/struct/struct_n_w_b_async_parameters.html new file mode 100644 index 0000000000..c4212ef58c --- /dev/null +++ b/struct/struct_n_w_b_async_parameters.html @@ -0,0 +1,305 @@ + + + + + + + + Struct NWBAsyncParameters — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct NWBAsyncParameters

+
+
+struct NWBAsyncParameters
+

Helper structure for the ASYNC NWB writing during DAQ.

+

+

See also

+

NWB_ASYNC_SerializeStruct() and NWB_ASYNC_DeserializeStruct()

+
+

+
+

Public Members

+
+
+string device
+
+ +
+
+string userComment
+
+ +
+
+string nwbFilePath
+
+ +
+
+variable sweep
+
+ +
+
+variable compressionMode
+
+ +
+
+variable session_start_time
+
+ +
+
+variable locationID
+
+ +
+
+variable nwbVersion
+
+ +
+
+WAVE DAQDataWave
+
+ +
+
+WAVE DAQConfigWave
+
+ +
+
+WAVE numericalValues
+
+ +
+
+WaveText numericalKeys
+
+ +
+
+WaveText textualValues
+
+ +
+
+WaveText textualKeys
+
+ +
+
+WAVE numericalResultsValues
+
+ +
+
+WaveText numericalResultsKeys
+
+ +
+
+WaveText textualResultsValues
+
+ +
+
+WaveText textualResultsKeys
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_o_od_d_a_q_params.html b/struct/struct_o_od_d_a_q_params.html new file mode 100644 index 0000000000..4f1093b495 --- /dev/null +++ b/struct/struct_o_od_d_a_q_params.html @@ -0,0 +1,243 @@ + + + + + + + + Struct OOdDAQParams — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct OOdDAQParams

+
+
+struct OOdDAQParams
+

Helper structure for Optimized overlap distributed acquisition (oodDAQ) functions.

+
+

Input

+
+
+WaveRefWave stimSets
+

Wave ref wave with different stimsets.

+
+ +
+
+WAVE setColumns
+

Set (aka column) to use for each stimset.

+
+ +
+
+variable preFeaturePoints
+

Time in points which should be kept signal-free before features.

+
+ +
+
+variable postFeaturePoints
+

Time in points which should be kept signal-free after features.

+
+ +
+
+

Output

+

+
+
+WAVE offsets
+

Result of the optimization in points.

+
+ +
+
+WaveText regions
+

the smeared regions in units of time of the DAQDataWave.

+

List of the form begin-end;... which denotes the x-coordinates of

+

See also

+

OOD_GetFeatureRegions()

+
+

+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_p___pressure_d_a.html b/struct/struct_p___pressure_d_a.html new file mode 100644 index 0000000000..37ba27bf89 --- /dev/null +++ b/struct/struct_p___pressure_d_a.html @@ -0,0 +1,224 @@ + + + + + + + + Struct P_PressureDA — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct P_PressureDA

+
+
+struct P_PressureDA
+

Filled by P_GetPressureForDA()

+
+

Public Members

+
+
+variable calPressure
+
+ +
+
+variable calPressureOffset
+

preconditioned for the DAC hardware

+
+ +
+
+variable pressure
+

[psi]

+
+ +
+
+variable first
+
+ +
+
+variable last
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_p_a___constant_settings.html b/struct/struct_p_a___constant_settings.html new file mode 100644 index 0000000000..170d181c43 --- /dev/null +++ b/struct/struct_p_a___constant_settings.html @@ -0,0 +1,258 @@ + + + + + + + + Struct PA_ConstantSettings — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct PA_ConstantSettings

+
+
+struct PA_ConstantSettings
+

Helper structure to store the constantness of various categories of settings.

+
+

Public Members

+
+
+variable singlePulse
+
+ +
+
+variable traces
+
+ +
+
+variable images
+
+ +
+
+variable failedPulses
+
+ +
+
+variable dontResetWaves
+
+ +
+
+variable multipleGraphs
+
+ +
+
+variable showAverage
+
+ +
+
+variable deconvolution
+
+ +
+
+variable hideFailedPulses
+
+ +
+
+variable showIndividualPulses
+
+ +
+
+variable showTraces
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_p_s_q___d_s___d_a_scale_params.html b/struct/struct_p_s_q___d_s___d_a_scale_params.html new file mode 100644 index 0000000000..23e11f6c09 --- /dev/null +++ b/struct/struct_p_s_q___d_s___d_a_scale_params.html @@ -0,0 +1,221 @@ + + + + + + + + Struct PSQ_DS_DAScaleParams — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct PSQ_DS_DAScaleParams

+
+
+struct PSQ_DS_DAScaleParams
+
+

Public Members

+
+
+variable absFrequencyMinDistance
+
+ +
+
+variable maxFrequencyChangePercent
+
+ +
+
+variable daScaleStepMinNorm
+
+ +
+
+variable daScaleStepMaxNorm
+
+ +
+
+variable slopePercentage
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_p_s_q___pulse_settings.html b/struct/struct_p_s_q___pulse_settings.html new file mode 100644 index 0000000000..d152d2ce79 --- /dev/null +++ b/struct/struct_p_s_q___pulse_settings.html @@ -0,0 +1,217 @@ + + + + + + + + Struct PSQ_PulseSettings — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct PSQ_PulseSettings

+
+
+struct PSQ_PulseSettings
+

Settings structure filled by PSQ_GetPulseSettingsForType()

+
+

Public Members

+
+
+variable prePulseChunkLength
+
+ +
+
+variable pulseDuration
+
+ +
+
+variable postPulseChunkLength
+
+ +
+
+variable usesBaselineChunkEpochs
+

Allows to define the baseline chunks by user epochs with shortname U_BLSd other members are ignored with this option. The baseline chunks should be added in PRE_SWEEP_CONFIG_EVENT.

+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_post_plot_settings.html b/struct/struct_post_plot_settings.html new file mode 100644 index 0000000000..e5c6ea0453 --- /dev/null +++ b/struct/struct_post_plot_settings.html @@ -0,0 +1,258 @@ + + + + + + + + Struct PostPlotSettings — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct PostPlotSettings

+
+
+struct PostPlotSettings
+
+

Trace averaging settings

+
+
+variable averageTraces
+
+ +
+
+DFREF averageDataFolder
+
+ +
+
+

Time alignment settings

+
+
+variable timeAlignment
+
+ +
+
+variable timeAlignMode
+
+ +
+
+string timeAlignRefTrace
+
+ +
+
+variable timeAlignLevel
+
+ +
+
+

Public Members

+
+
+variable hideSweep
+
+ +
+
+variable zeroTraces
+

Zero traces settings.

+
+ +
+
+variable visualizeEpochs
+
+ +
+
+PulseAverageSettings pulseAverSett
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_pulse_average_deconv_settings.html b/struct/struct_pulse_average_deconv_settings.html new file mode 100644 index 0000000000..06ed276532 --- /dev/null +++ b/struct/struct_pulse_average_deconv_settings.html @@ -0,0 +1,215 @@ + + + + + + + + Struct PulseAverageDeconvSettings — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct PulseAverageDeconvSettings

+
+
+struct PulseAverageDeconvSettings
+
+

Public Members

+
+
+variable enable
+
+ +
+
+variable smth
+
+ +
+
+variable tau
+
+ +
+
+variable range
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_pulse_average_set_indices.html b/struct/struct_pulse_average_set_indices.html new file mode 100644 index 0000000000..18154714ce --- /dev/null +++ b/struct/struct_pulse_average_set_indices.html @@ -0,0 +1,293 @@ + + + + + + + + Struct PulseAverageSetIndices — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct PulseAverageSetIndices

+
+
+struct PulseAverageSetIndices
+
+

Public Members

+
+
+WaveRefWave setIndices
+
+ +
+
+WaveRefWave setIndicesUnsorted
+
+ +
+
+WaveRefWave setWaves2Unsorted
+
+ +
+
+WAVE properties
+
+ +
+
+WaveRefWave propertiesWaves
+
+ +
+
+WaveRefWave axesNames
+
+ +
+
+WAVE ovlTracesAvg
+
+ +
+
+WAVE ovlTracesDeconv
+
+ +
+
+WAVE imageAvgDataPresent
+
+ +
+
+WAVE imageDeconvDataPresent
+
+ +
+
+DFREF pulseAverageHelperDFR
+
+ +
+
+DFREF pulseAverageDFR
+
+ +
+
+WAVE channels
+
+ +
+
+WAVE regions
+
+ +
+
+WAVE numEntries
+
+ +
+
+WAVE startEntry
+
+ +
+
+WAVE indexHelper
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_pulse_average_settings.html b/struct/struct_pulse_average_settings.html new file mode 100644 index 0000000000..b2a4f318cc --- /dev/null +++ b/struct/struct_pulse_average_settings.html @@ -0,0 +1,333 @@ + + + + + + + + Struct PulseAverageSettings — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct PulseAverageSettings

+
+
+struct PulseAverageSettings
+
+

Time alignment settings

+
+
+variable startingPulse
+

These settings influence the extracted single pulse waves, see also PA_GenerateAllPulseWaves().

+
+ +
+
+variable endingPulse
+
+ +
+
+variable overridePulseLength
+
+ +
+
+variable fixedPulseLength
+
+ +
+
+

Public Members

+
+
+variable showIndividualPulses
+
+ +
+
+variable showAverage
+
+ +
+
+variable regionSlider
+
+ +
+
+variable multipleGraphs
+
+ +
+
+variable zeroPulses
+
+ +
+
+variable autoTimeAlignment
+
+ +
+
+variable enabled
+
+ +
+
+variable hideFailedPulses
+
+ +
+
+variable searchFailedPulses
+
+ +
+
+variable failedPulsesLevel
+
+ +
+
+variable failedNumberOfSpikes
+
+ +
+
+variable yScaleBarLength
+
+ +
+
+variable showImages
+
+ +
+
+variable showTraces
+
+ +
+
+variable drawXZeroLine
+
+ +
+
+variable pulseSortOrder
+
+ +
+
+string imageColorScale
+
+ +
+
+DFREF dfr
+
+ +
+
+PulseAverageDeconvSettings deconvolution
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_read_channel_params.html b/struct/struct_read_channel_params.html new file mode 100644 index 0000000000..4816df1c68 --- /dev/null +++ b/struct/struct_read_channel_params.html @@ -0,0 +1,255 @@ + + + + + + + + Struct ReadChannelParams — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct ReadChannelParams

+
+
+struct ReadChannelParams
+

Loader structure analog to WriteChannelParams.

+
+

Public Members

+
+
+string device
+

name of the measure device, e.g. “ITC18USB_Dev_0”

+
+ +
+
+string channelSuffix
+

custom channel suffix, in case the channel number is ambiguous

+
+ +
+
+variable sweep
+

running number for each measurement

+
+ +
+
+variable channelType
+

channel type, one of IPNWBChannelTypes

+
+ +
+
+variable channelNumber
+

running number of the hardware channel

+
+ +
+
+variable electrodeNumber
+

electrode identifier the channel was acquired with

+
+ +
+
+variable groupIndex
+

constant for all channels in this measurement.

+
+ +
+
+variable ttlBit
+

additional information to make the channel number unambigous, in the range 2^0, …, 2^3

+
+ +
+
+variable samplingRate
+

sampling rate in Hz

+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_rect_d.html b/struct/struct_rect_d.html new file mode 100644 index 0000000000..dabb8d5e63 --- /dev/null +++ b/struct/struct_rect_d.html @@ -0,0 +1,216 @@ + + + + + + + + Struct RectD — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct RectD

+
+
+struct RectD
+

Helper structure for GetPlotArea()

+
+

Public Members

+
+
+double top
+
+ +
+
+double left
+
+ +
+
+double bottom
+
+ +
+
+double right
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_s_b_e___export_settings.html b/struct/struct_s_b_e___export_settings.html new file mode 100644 index 0000000000..06b6323106 --- /dev/null +++ b/struct/struct_s_b_e___export_settings.html @@ -0,0 +1,287 @@ + + + + + + + + Struct SBE_ExportSettings — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct SBE_ExportSettings

+
+
+struct SBE_ExportSettings
+
+

Public Members

+
+
+string dataFolder
+
+ +
+
+variable useCursorRange
+
+ +
+
+variable resetWaveZero
+
+ +
+
+variable manualRangeBegin
+
+ +
+
+variable manualRangeEnd
+
+ +
+
+string leftAxis
+
+ +
+
+string bottomAxis
+
+ +
+
+string targetGraph
+
+ +
+
+string sourceGraph
+
+ +
+
+variable axisEqualizing
+
+ +
+
+variable equalYRange
+
+ +
+
+variable usePulses
+
+ +
+
+variable numPulses
+
+ +
+
+variable preFirstPulse
+
+ +
+
+variable postLastPulse
+
+ +
+
+variable ADC
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_s_f___plot_meta_data.html b/struct/struct_s_f___plot_meta_data.html new file mode 100644 index 0000000000..e204b3f44d --- /dev/null +++ b/struct/struct_s_f___plot_meta_data.html @@ -0,0 +1,222 @@ + + + + + + + + Struct SF_PlotMetaData — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct SF_PlotMetaData

+
+
+struct SF_PlotMetaData
+

Helper struct for data gathered by SF formula plotter in SF_GatherFormulaResults.

+
+

Public Members

+
+
+string dataType
+
+ +
+
+string opStack
+
+ +
+
+string argSetupStack
+
+ +
+
+string xAxisLabel
+
+ +
+
+string yAxisLabel
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_segment_parameters.html b/struct/struct_segment_parameters.html new file mode 100644 index 0000000000..f2adffb822 --- /dev/null +++ b/struct/struct_segment_parameters.html @@ -0,0 +1,371 @@ + + + + + + + + Struct SegmentParameters — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct SegmentParameters

+
+
+struct SegmentParameters
+
+

Public Members

+
+
+variable duration
+
+ +
+
+variable deltaDur
+
+ +
+
+variable amplitude
+
+ +
+
+variable deltaAmp
+
+ +
+
+variable offset
+
+ +
+
+variable frequency
+
+ +
+
+variable deltaFreq
+
+ +
+
+variable pulseDuration
+
+ +
+
+variable tauRise
+
+ +
+
+variable tauDecay1
+
+ +
+
+variable tauDecay2
+
+ +
+
+variable tauDecay2Weight
+
+ +
+
+variable lowPassCutOff
+
+ +
+
+variable highPassCutOff
+
+ +
+
+variable filterOrder
+
+ +
+
+variable endFrequency
+
+ +
+
+variable numberOfPulses
+
+ +
+
+variable poisson
+
+ +
+
+variable logChirp
+
+ +
+
+variable randomSeed
+
+ +
+
+variable trigFuncType
+
+ +
+
+variable noiseType
+
+ +
+
+variable noiseGenMode
+
+ +
+
+variable noiseGenModePTMixedFreq
+
+ +
+
+variable buildResolution
+
+ +
+
+variable pulseType
+
+ +
+
+variable mixedFreq
+
+ +
+
+variable mixedFreqShuffle
+
+ +
+
+variable firstFreq
+
+ +
+
+variable lastFreq
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_subject_info.html b/struct/struct_subject_info.html new file mode 100644 index 0000000000..d0764583b0 --- /dev/null +++ b/struct/struct_subject_info.html @@ -0,0 +1,240 @@ + + + + + + + + Struct SubjectInfo — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct SubjectInfo

+
+
+struct SubjectInfo
+

Structure to hold all properties of the NWB file directly below /general/subject

+
+

Public Members

+
+
+string age
+
+ +
+
+string date_of_birth
+
+ +
+
+string description
+
+ +
+
+string genotype
+
+ +
+
+string sex
+
+ +
+
+string species
+
+ +
+
+string subject_id
+
+ +
+
+string weight
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_t_p_analysis_input.html b/struct/struct_t_p_analysis_input.html new file mode 100644 index 0000000000..275594605c --- /dev/null +++ b/struct/struct_t_p_analysis_input.html @@ -0,0 +1,258 @@ + + + + + + + + Struct TPAnalysisInput — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct TPAnalysisInput

+
+
+struct TPAnalysisInput
+

Helper structure for TP data transfer to analysis.

+
+

Public Members

+
+
+WAVE data
+
+ +
+
+variable clampAmp
+
+ +
+
+variable clampMode
+
+ +
+
+variable duration
+
+ +
+
+variable baselineFrac
+
+ +
+
+variable tpLengthPoints
+
+ +
+
+variable readTimeStamp
+
+ +
+
+variable hsIndex
+
+ +
+
+string device
+
+ +
+
+variable measurementMarker
+
+ +
+
+variable activeADCs
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_tiled_graph_settings.html b/struct/struct_tiled_graph_settings.html new file mode 100644 index 0000000000..8cef2ee8c6 --- /dev/null +++ b/struct/struct_tiled_graph_settings.html @@ -0,0 +1,252 @@ + + + + + + + + Struct TiledGraphSettings — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct TiledGraphSettings

+
+
+struct TiledGraphSettings
+

Parameter to CreateTiledChannelGraph.

+
+

Public Members

+
+
+int16 displayDAC
+
+ +
+
+int16 displayADC
+
+ +
+
+int16 displayTTL
+
+ +
+
+int16 splitTTLBits
+
+ +
+
+int16 overlaySweep
+
+ +
+
+int16 overlayChannels
+
+ +
+
+int16 dDAQDisplayMode
+
+ +
+
+int16 dDAQHeadstageRegions
+
+ +
+
+int16 hideSweep
+
+ +
+
+int16 visualizeEpochs
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_time_series_properties.html b/struct/struct_time_series_properties.html new file mode 100644 index 0000000000..0a931ac843 --- /dev/null +++ b/struct/struct_time_series_properties.html @@ -0,0 +1,244 @@ + + + + + + + + Struct TimeSeriesProperties — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct TimeSeriesProperties

+
+
+struct TimeSeriesProperties
+

Holds class specific entries for TimeSeries objects.

+

Usage for writers 

STRUCT TimeSeriesProperties tsp
+InitTimeSeriesProperties(tsp, channelType, clampMode)
+AddProperty(tsp, "gain", 1.23456)
+// more calls tp AddProperty()
+WriteSingleChannel(locationID, path, p, tsp)
+
+
+

+

and for readers 

STRUCT TimeSeriesProperties tsp
+InitTimeSeriesProperties(tsp, channelType, clampMode)
+ReadTimeSeriesProperties(groupID, channel, tsp)
+
+
+

+
+

Public Members

+
+
+WaveText names
+
+ +
+
+WAVE data
+
+ +
+
+WaveText unit
+
+ +
+
+WAVE isCustom
+

NWBv1: 1 if the entry should be marked as NWB custom.

+
+ +
+
+string missing_fields
+

keep track of missing fields while reading

+
+ +
+
+string neurodata_type
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_toplevel_info.html b/struct/struct_toplevel_info.html new file mode 100644 index 0000000000..8942c3d8ca --- /dev/null +++ b/struct/struct_toplevel_info.html @@ -0,0 +1,224 @@ + + + + + + + + Struct ToplevelInfo — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct ToplevelInfo

+
+
+struct ToplevelInfo
+

Structure to hold all properties of the NWB file directly below /

+
+

Public Members

+
+
+string session_description
+
+ +
+
+variable session_start_time
+

timestamp in seconds since Igor Pro epoch, UTC timezone

+
+ +
+
+string nwb_version
+

NWB specification version.

+
+ +
+
+string identifier
+
+ +
+
+WaveText file_create_date
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_uuid.html b/struct/struct_uuid.html new file mode 100644 index 0000000000..c7b538f548 --- /dev/null +++ b/struct/struct_uuid.html @@ -0,0 +1,234 @@ + + + + + + + + Struct Uuid — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct Uuid

+
+
+struct Uuid
+

Helper structure for GenerateRFC4122UUID()

+
+

Public Members

+
+
+uint32 time_low
+
+ +
+
+uint16 time_mid
+
+ +
+
+uint16 time_hi_and_version
+
+ +
+
+uint16 clock_seq
+
+ +
+
+uint16 node0
+
+ +
+
+uint16 node1
+
+ +
+
+uint16 node2
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_vector_data.html b/struct/struct_vector_data.html new file mode 100644 index 0000000000..76bbe763ab --- /dev/null +++ b/struct/struct_vector_data.html @@ -0,0 +1,209 @@ + + + + + + + + Struct VectorData — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct VectorData

+
+
+struct VectorData
+
+

Public Members

+
+
+string description
+
+ +
+
+string data_type
+
+ +
+
+string path
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_vector_index.html b/struct/struct_vector_index.html new file mode 100644 index 0000000000..a6753db2b2 --- /dev/null +++ b/struct/struct_vector_index.html @@ -0,0 +1,203 @@ + + + + + + + + Struct VectorIndex — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct VectorIndex

+
+
+struct VectorIndex
+
+

Public Members

+
+
+string data_type
+
+ +
+
+VectorData target
+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_wave_location_mod.html b/struct/struct_wave_location_mod.html new file mode 100644 index 0000000000..9c764b6fe1 --- /dev/null +++ b/struct/struct_wave_location_mod.html @@ -0,0 +1,220 @@ + + + + + + + + Struct WaveLocationMod — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct WaveLocationMod

+
+
+struct WaveLocationMod
+

Helper structure for UpgradeWaveLocationAndGetIt()

+
+

Public Members

+
+
+DFREF dfr
+

former location of the wave

+
+ +
+
+DFREF newDFR
+

new location of the wave (can be invalid)

+
+ +
+
+string name
+

former name of the wave

+
+ +
+
+string newName
+

new name of the wave (can be null/empty)

+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/struct/struct_write_channel_params.html b/struct/struct_write_channel_params.html new file mode 100644 index 0000000000..b2492d7aff --- /dev/null +++ b/struct/struct_write_channel_params.html @@ -0,0 +1,298 @@ + + + + + + + + Struct WriteChannelParams — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct WriteChannelParams

+
+
+struct WriteChannelParams
+

Helper structure for WriteSingleChannel()

+
+

Public Members

+
+
+string device
+

name of the measure device, e.g. “ITC18USB_Dev_0”

+
+ +
+
+string stimSet
+

name of the template simulus set

+
+ +
+
+string channelSuffix
+

custom channel suffix, in case the channel number is ambiguous

+
+ +
+
+string channelSuffixDesc
+

description of the channel suffix, will be added to the source attribute

+
+ +
+
+variable samplingRate
+

sampling rate in Hz

+
+ +
+
+variable startingTime
+

timestamp since Igor Pro epoch in UTC of the start of this measurement

+
+ +
+
+variable sweep
+

running number for each measurement

+
+ +
+
+variable channelType
+

channel type, one of IPNWBChannelTypes

+
+ +
+
+variable channelNumber
+

running number of the channel

+
+ +
+
+variable electrodeNumber
+

electrode identifier the channel was acquired with

+
+ +
+
+string electrodeName
+

electrode identifier the channel was acquired with (string version)

+
+ +
+
+variable clampMode
+

clamp mode, one of IPNWB_ClampModes

+
+ +
+
+variable groupIndex
+

Should be filled with the result of GetNextFreeGroupIndex(locationID, path) before

+
+ +
+
+WAVE data
+

channel data

+

the first call and must stay constant for all channels for this measurement. If NaN an automatic solution is provided.

+
+ +
+
+WaveText epochs
+

epoch information (optional)

+
+ +
+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/structlist.html b/structlist.html new file mode 100644 index 0000000000..7bf0bfdd7a --- /dev/null +++ b/structlist.html @@ -0,0 +1,879 @@ + + + + + + + + Struct list — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Struct list

+
+ +
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/testpulse.html b/testpulse.html new file mode 100644 index 0000000000..da50720286 --- /dev/null +++ b/testpulse.html @@ -0,0 +1,144 @@ + + + + + + + + TPStorage — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

TPStorage

+

TODO fill me

+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/todo.html b/todo.html new file mode 100644 index 0000000000..162231f279 --- /dev/null +++ b/todo.html @@ -0,0 +1,309 @@ + + + + + + + + Todos — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

Todos

+
+
+page todo
+

+
+Member AB_LoadDataWrapper  (dfref tmpDFR, string expFilePath, string datafolderPath, string listOfNames, variable typeFlags=defaultValue, variable recursive=defaultValue)
+

this is not 100% correct as users might choose a different name for the unpacked experiment folder

+
+ +
+
+Member AB_LoadSweepsFromNWB  (string discLocation, string dataFolder, string device)
+

: Update this function for the use with SweepTable

+
+ +
+
+Member AB_StoreChannelsBySweep  (variable groupID, variable nwbVersion, string channelList, WaveInteger sweeps, WaveText storage)
+

Update this function for the use with SweepTable

+
+ +
+
+Member CalculateTPLikePropsFromSweep  (wave numericalValues, wave textualValues, wave sweep, wave deltaI, wave deltaV, wave resistance)
+

unify with TP_Delta code

+

+

add support for evaluating “inserted TP” only

+
+ +
+
+Member DAP_FormatStimSetPopupValue  (variable channelType, string searchString=defaultValue)
+

rework the code to have a fixed popValue

+
+ +
+
+Member DC_CalculateChannelColumnNo  (string device, string setName, variable channelNo, variable channelType)
+

this code here is different compared to what RA_BckgTPwithCallToRACounterMD and RA_CounterMD do

+
+ +
+
+Member GetChanneListFromDAQConfigWave  (wave config, variable channelType)
+

change to return a 0/1 wave with constant size a la DAG_GetChannelState

+
+ +
+
+Member GetCursorXPositionAB  (string graph, variable *csrAx, variable *csrBx)
+

make this a generic cursor getter function and merge with cursors() in

+
+ +
+
+Member GetLBNumericalKeys  (string device)
+

move the renaming stuff into one function for all four labnotebook waves

+
+ +
+
+Member GetRunningSingleDevice  ()
+

remove and use background struct members for the deviceID and GetDeviceMapping instead

+
+ +
+
+Member GetTypeListFromITCConfig  (wave config, variable channelType)
+

change to return a 0/1 wave with constant size a la DAG_GetChannelState

+
+ +
+
+Member GetUniqueEntries  (wave wv, variable caseSensitive=defaultValue)
+

this should be removed as it does not belong into this function

+
+ +
+
+Member H5_GetLinkTarget  (string discLocation, string path)
+

Needs HDF5 XOP support for reading link targets use HDF5LinkInfo

+
+ +
+
+Member LoadSweepTable  (variable locationID, variable version)
+

Allow Executions for files with missing SweepTable entry using LoadSweepNumber

+
+ +
+
+File MIES_PressureControl.ipf
+

TPbackground can crash while operating pressure regulators if called in the middle of a TP. Need to call P_Pressure control from TP functions that occur between TPs to prevent this from happening

+
+ +
+
+Member MSQ_ForceSetEvent  (string device, variable headstage)
+

this hack must go away.

+
+ +
+
+Member MSQ_GetLBNEntryForHeadstageSCI  (wave numericalValues, variable sweepNo, variable type, string str, variable headstage)
+

merge with LBN functions once these are reworked.

+
+ +
+
+Member MSQ_GetLBNEntryForHSSCIBool  (wave numericalValues, variable sweepNo, variable type, string str, variable headstage)
+

merge with LBN functions once these are reworked.

+
+ +
+
+Member NUM_ENTRIES_FOR_MULTITHREAD
+

: IP8 convert all call sites to use MultiThread/T=

+
+ +
+
+Member P_UpdatePressureDataStorageWv  (string device)
+

Needs to be reworked for specific controls and allow the value to be directly passed in with an optional parameter

+
+ +
+
+Member PSQ_DS_FitFrequencyCurrentData  (string device, variable sweepNo, WaveOrNull apfreq, WaveOrNull DAScales, variable singleFit=defaultValue)
+

prefer f over g due to https://github.com/AllenInstitute/MIES/issues/1863

+
+ +
+
+Member PSQ_ForceSetEvent  (string device, variable headstage)
+

this hack must go away.

+
+ +
+
+Member PSX_OperationPrep  (variable jsonId, string jsonPath, string graph)
+

: Don’t hardcode trace names

+
+ +
+
+Member PSX_UpdateEventWaves  (string win, variable val=defaultValue, variable index=defaultValue, variable toggle=defaultValue, WaveOrNull indizes=defaultValue, variable writeState=defaultValue, variable stateType=defaultValue, variable comboIndex=defaultValue)
+

Multithread does not work with index waves

+
+ +
+
+Member ResizeControlsSafe  (WMWinHookStruct *s)
+

reported as #5100 to WM

+
+ +
+
+Member SetControlTitleColor  (string win, string controlName, variable R, variable G, variable B)
+

store color in control user data, check for color change before applying change

+
+ +
+
+Member SetPressureWaveDimLabels  (wave wv)
+

If user switched headStage mode while pressure regulation is ongoing, pressure reg either needs to be turned off, or steady state slope values need to be used

+

+

Enable mode switching with TP running (auto stop TP, switch mode, auto startTP)

+

+

Enable headstate switching with TP running (auto stop TP, change headStage state, auto start TP)

+
+ +
+
+Member SplitWavesToDimension  (WaveRefWave input, variable sdim=defaultValue)
+

workaround IP issue 4979 (singleWaves is not a free wave)

+
+ +

+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/user.html b/user.html new file mode 100644 index 0000000000..9e4744b817 --- /dev/null +++ b/user.html @@ -0,0 +1,210 @@ + + + + + + + + User documentation — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

User documentation

+
+ +
+

MIES is a sweep based data acquisition tool written in Igor Pro.

+

MIES has three primary user interfaces: The WaveBuilder, Da_Ephys, and +DataBrowser. The WaveBuilder is used to generate stimulus sets. The DA_Ephys +GUI is used to control and observe data acquisition in real time. The +DataBrowser is used to browse acquired data. All three interfaces are intended +to be operated in parallel.

+

The following recorded presentation from the NWB hackathon 2020 +gives a overview of the possibilities of MIES.

+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/wavebuilder.html b/wavebuilder.html new file mode 100644 index 0000000000..3b02d3423b --- /dev/null +++ b/wavebuilder.html @@ -0,0 +1,163 @@ + + + + + + + + WaveBuilder — MIES Igor (main) Release_2.8_20240925-4-g349947f6c documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

WaveBuilder

+

The WaveBuilder is used to create a series of related sweeps called a stimulus +set. A sweep is composed of up to 99 epochs. Each epoch can contain one of +seven different waveform types, arbitrary combinations of waveform types, or a +custom waveform. A custom waveform can be a sweep from a different stimulus +set, or a waveform generated by the user using other tools. Custom code to +automate analysis or data acquisition may be linked with a stimulus set using +the WaveBuilder.

+

TODO fill me

+
+

Epoch Types

+

TODO fill me

+
+
+

Pulse Train

+

TODO fill me

+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file