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add tutorial reproducing new icephys tables
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| session_start_time = datetime(2018, 3, 1, 12, 0, 0, 'TimeZone', 'local'); | ||
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| nwbfile = NwbFile( ... | ||
| 'session_description', 'my first synthetic recording', ... | ||
| 'identifier', 'EXAMPLE_ID', ... | ||
| 'session_start_time', session_start_time, ... | ||
| 'general_experimenter', 'Dr. Bilbo Baggins', ... | ||
| 'general_lab', 'Bag End Laboratory', ... | ||
| 'general_institution', 'University of Middle Earth at the Shire', ... | ||
| 'general_experiment_description', 'I went on an adventure with thirteen dwarves to reclaim vast treasures.', ... | ||
| 'general_session_id', 'LONELYMTN' ... | ||
| ); | ||
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| device_name = 'Heka ITC-1600'; | ||
| device_link = types.untyped.SoftLink(['/general/devices/' device_name]); | ||
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| nwbfile.general_devices.set(device_name, types.core.Device()); | ||
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| electrode_name = 'ele0'; | ||
| electrode_link = types.untyped.SoftLink( ... | ||
| ['/general/intracellular_ephys/' electrode_name] ... | ||
| ); | ||
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| electrode_object_view = types.untyped.ObjectView( .... | ||
| ['/general/intracellular_ephys/' electrode_name] ... | ||
| ); | ||
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| nwbfile.general_intracellular_ephys.set( .... | ||
| electrode_name, types.core.IntracellularElectrode( ... | ||
| 'description', 'a mock intracellular electrode', ... | ||
| 'device', device_link) ... | ||
| ); | ||
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| nwbfile.stimulus_presentation.set( ... | ||
| 'ccss', types.core.VoltageClampStimulusSeries( ... | ||
| 'data', [1, 2, 3, 4, 5], ... | ||
| 'starting_time', 123.6, ... | ||
| 'starting_time_rate', 10e3, ... | ||
| 'electrode', electrode_link, ... | ||
| 'gain', 0.02, ... | ||
| 'sweep_number', uint64(15), ... | ||
| 'stimulus_description', 'N/A' ... | ||
| ) ... | ||
| ); | ||
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| nwbfile.acquisition.set( ... | ||
| 'vcs', types.core.VoltageClampSeries( ... | ||
| 'data', [0.1, 0.2, 0.3, 0.4, 0.5], ... | ||
| 'data_conversion', 1e-12, ... | ||
| 'data_resolution', NaN, ... | ||
| 'starting_time', 123.6, ... | ||
| 'starting_time_rate', 20e3, ... | ||
| 'electrode', electrode_link, ... | ||
| 'gain', 0.02, ... | ||
| 'capacitance_slow', 100e-12, ... | ||
| 'resistance_comp_correction', 70.0, ... | ||
| 'stimulus_description', 'N/A', ... | ||
| 'sweep_number', uint64(15) ... | ||
| ) ... | ||
| ); | ||
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| %% | ||
| ic_rec_table = types.core.IntracellularRecordingsTable( ... | ||
| 'categories', {'electrodes', 'stimiuli', 'responses'}, ... | ||
| 'colnames', {'recordings_tag'}, ... | ||
| 'description', [ ... | ||
| 'A table to group together a stimulus and response from a single ', ... | ||
| 'electrode and a single simultaneous recording and for storing ', ... | ||
| 'metadata about the intracellular recording.'], ... | ||
| 'id', types.hdmf_common.ElementIdentifiers( ... | ||
| 'data', int64([10, 11, 12]) ... | ||
| ) ... | ||
| ); | ||
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| ic_rec_table.electrodes = types.core.IntracellularElectrodesTable( ... | ||
| 'description', 'Table for storing intracellular electrode related metadata.', ... | ||
| 'colnames', {'electrode'}, ... | ||
| 'id', types.hdmf_common.ElementIdentifiers( ... | ||
| 'data', int64([0, 1, 2]) ... | ||
| ), ... | ||
| 'electrode', types.hdmf_common.VectorData( ... | ||
| 'data', repmat(electrode_object_view, 3, 1), ... | ||
| 'description', 'Column for storing the reference to the intracellular electrode' ... | ||
| ) ... | ||
| ); | ||
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| ic_rec_table.responses = types.core.IntracellularResponsesTable( ... | ||
| 'description', 'Table for storing intracellular response related metadata.', ... | ||
| 'colnames', {'response'}, ... | ||
| 'id', types.hdmf_common.ElementIdentifiers( ... | ||
| 'data', int64([0, 1, 2]) ... | ||
| ), ... | ||
| 'response', types.core.TimeSeriesReferenceVectorData( ... | ||
| 'description', 'Column storing the reference to the recorded response for the recording (rows)', ... | ||
| 'data', struct( ... | ||
| 'idx_start', [0, 2, 0], ... | ||
| 'count', [5, 3, 5], ... | ||
| 'timeseries', [ ... | ||
| types.untyped.ObjectView('/acquisition/vcs'), ... | ||
| types.untyped.ObjectView('/acquisition/vcs'), ... | ||
| types.untyped.ObjectView('/acquisition/vcs') ... | ||
| ] ... | ||
| )... | ||
| )... | ||
| ); | ||
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| ic_rec_table.stimuli = types.core.IntracellularStimuliTable( ... | ||
| 'description', 'Table for storing intracellular stimulus related metadata.', ... | ||
| 'colnames', {'stimulus'}, ... | ||
| 'id', types.hdmf_common.ElementIdentifiers( ... | ||
| 'data', int64([0, 1, 2]) ... | ||
| ), ... | ||
| 'stimulus', types.core.TimeSeriesReferenceVectorData( ... | ||
| 'description', 'Column storing the reference to the recorded stimulus for the recording (rows)', ... | ||
| 'data', struct( ... | ||
| 'idx_start', [0, 1, -1], ... | ||
| 'count', [5, 3, -1], ... | ||
| 'timeseries', [ ... | ||
| types.untyped.ObjectView('/stimulus/presentation/ccss'), ... | ||
| types.untyped.ObjectView('/stimulus/presentation/ccss'), ... | ||
| types.untyped.ObjectView('/acquisition/vcs') ... | ||
| ] ... | ||
| )... | ||
| )... | ||
| ); | ||
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| % add category | ||
| ic_rec_table.categories = [ic_rec_table.categories, {'recording_lab_data'}]; | ||
| ic_rec_table.dynamictable.set( ... | ||
| 'recording_lab_data', types.hdmf_common.DynamicTable( ... | ||
| 'description', 'category table for lab-specific recording metadata', ... | ||
| 'colnames', {'location'}, ... | ||
| 'id', types.hdmf_common.ElementIdentifiers( ... | ||
| 'data', int64([0, 1, 2]) ... | ||
| ), ... | ||
| 'location', types.hdmf_common.VectorData( ... | ||
| 'data', {'Mordor', 'Gondor', 'Rohan'}, ... | ||
| 'description', 'Recording location in Middle Earth' ... | ||
| ) ... | ||
| ) ... | ||
| ); | ||
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| % Add voltage threshold as column of electrodes table | ||
| ic_rec_table.electrodes.colnames = [ic_rec_table.electrodes.colnames {'voltage_threshold'}]; | ||
| ic_rec_table.electrodes.vectordata.set('voltage_threshold', types.hdmf_common.VectorData( ... | ||
| 'data', [0.1, 0.12, 0.13], ... | ||
| 'description', 'Just an example column on the electrodes category table' ... | ||
| ) ... | ||
| ); | ||
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| nwbfile.general_intracellular_ephys_intracellular_recordings = ic_rec_table; | ||
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| %% Add a simultaneous recording | ||
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| % create simultaneous recordings table with custom column | ||
| % 'simultaneous_recording_tag' | ||
| ic_sim_recs_table = types.core.SimultaneousRecordingsTable( ... | ||
| 'description', [ ... | ||
| 'A table for grouping different intracellular ', ... | ||
| 'recordings from theIntracellularRecordingsTable table together ', ... | ||
| 'that were recorded simultaneously from different electrodes.'... | ||
| ], ... | ||
| 'colnames', {'recordings', 'simultaneous_recording_tag'}, ... | ||
| 'id', types.hdmf_common.ElementIdentifiers( ... | ||
| 'data', int64(12) ... | ||
| ), ... | ||
| 'recordings', types.hdmf_common.DynamicTableRegion( ... | ||
| 'table', types.untyped.ObjectView( ... | ||
| '/general/intracellular_ephys/intracellular_recordings' ... | ||
| ), ... | ||
| 'data', [0, 1, 2], ... | ||
| 'description', [ | ||
| 'Column with references to one or more rows in ', ... | ||
| 'the IntracellularRecordingsTable table' | ||
| ] ... | ||
| ), ... | ||
| 'recordings_index', types.hdmf_common.VectorIndex( ... | ||
| 'description', 'Index for VectorData "recordings"', ... | ||
| 'target', types.untyped.ObjectView( ... | ||
| '/general/intracellular_ephys/simultaneous_recordings/recordings' ... | ||
| ), ... | ||
| 'data', 3 ... | ||
| ), ... | ||
| 'simultaneous_recording_tag', types.hdmf_common.VectorData( ... | ||
| 'description', 'A custom tag for simultaneous_recordings', ... | ||
| 'data', {'LabTag1'} ... | ||
| ) ... | ||
| ); | ||
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| % add a column | ||
| ic_sim_recs_table.colnames = [ic_sim_recs_table.colnames, {'simultaneous_recording_type'}]; | ||
| ic_sim_recs_table.vectordata.set( ... | ||
| 'simultaneous_recording_type', types.hdmf_common.VectorData(... | ||
| 'description', 'Description of the type of simultaneous_recording', ... | ||
| 'data', {'SimultaneousRecordingType1'} ... | ||
| ) ... | ||
| ); | ||
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| nwbfile.general_intracellular_ephys_simultaneous_recordings = ic_sim_recs_table; | ||
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| %% add sequential recording | ||
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| nwbfile.general_intracellular_ephys_sequential_recordings = types.core.SequentialRecordingsTable( ... | ||
| 'description', [ ... | ||
| 'A table for grouping different intracellular recording ', ... | ||
| 'simultaneous_recordings from the SimultaneousRecordingsTable ', ... | ||
| 'table together. This is typically used to group together ', ... | ||
| 'simultaneous_recordings where the a sequence of stimuli of ', ... | ||
| 'the same type with varying parameters have been presented in ', ... | ||
| 'a sequence.' ... | ||
| ], ... | ||
| 'colnames', {'simultaneous_recordings', 'stimulus_type'}, ... | ||
| 'id', types.hdmf_common.ElementIdentifiers( ... | ||
| 'data', int64(15) ... | ||
| ), ... | ||
| 'simultaneous_recordings', types.hdmf_common.DynamicTableRegion( ... | ||
| 'table', types.untyped.ObjectView('/general/intracellular_ephys/simultaneous_recordings'), ... | ||
| 'description', [ ... | ||
| 'Column with references to one or more rows in the ', ... | ||
| 'SimultaneousRecordingsTable table', ... | ||
| ], ... | ||
| 'data', 0 ... | ||
| ), ... | ||
| 'simultaneous_recordings_index', types.hdmf_common.VectorIndex( ... | ||
| 'target', types.untyped.ObjectView( ... | ||
| '/general/intracellular_ephys/sequential_recordings/simultaneous_recordings' ... | ||
| ), ... | ||
| 'description', 'Index for VectorData "simultaneous_recordings"', ... | ||
| 'data', 1 ... | ||
| ), ... | ||
| 'stimulus_type', types.hdmf_common.VectorData( ... | ||
| 'description', 'Column storing the type of stimulus used for the sequential recording', ... | ||
| 'data', {'square'} ... | ||
| ) ... | ||
| ); | ||
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| %% add repetition | ||
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| nwbfile.general_intracellular_ephys_repetitions = types.core.RepetitionsTable( ... | ||
| 'description', [ ... | ||
| 'A table for grouping different intracellular recording sequential ', ... | ||
| 'recordings together. With each SimultaneousRecording typically ', ... | ||
| 'representing a particular type of stimulus, the RepetitionsTable ', ... | ||
| 'table is typically used to group sets of stimuli applied in sequence.' ... | ||
| ], ... | ||
| 'colnames', {'sequential_recordings'}, ... | ||
| 'id', types.hdmf_common.ElementIdentifiers( ... | ||
| 'data', int64(17) ... | ||
| ), ... | ||
| 'sequential_recordings', types.hdmf_common.DynamicTableRegion( ... | ||
| 'table', types.untyped.ObjectView('/general/intracellular_ephys/sequential_recordings'), ... | ||
| 'description', 'Column with references to one or more rows in the SequentialRecordingsTable table', ... | ||
| 'data', 0 ... | ||
| ), ... | ||
| 'sequential_recordings_index', types.hdmf_common.VectorIndex( ... | ||
| 'target', types.untyped.ObjectView('/general/intracellular_ephys/repetitions/sequential_recordings'), ... | ||
| 'description', 'Index for VectorData "sequential_recordings"', ... | ||
| 'data', 1 ... | ||
| ) ... | ||
| ); | ||
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| %% add experimental condition | ||
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| nwbfile.general_intracellular_ephys_experimental_conditions = types.core.ExperimentalConditionsTable( ... | ||
| 'description', [ ... | ||
| 'A table for grouping different intracellular recording ', ... | ||
| 'repetitions together that belong to the same experimental ', ... | ||
| 'conditions.' ... | ||
| ], ... | ||
| 'colnames', {'repetitions', 'tag'}, ... | ||
| 'id', types.hdmf_common.ElementIdentifiers( ... | ||
| 'data', int64([19, 21]) ... | ||
| ), ... | ||
| 'repetitions', types.hdmf_common.DynamicTableRegion( ... | ||
| 'table', types.untyped.ObjectView('/general/intracellular_ephys/repetitions'), ... | ||
| 'description', 'Column with references to one or more rows in the RepetitionsTable table', ... | ||
| 'data', [0, 0] ... | ||
| ), ... | ||
| 'repetitions_index', types.hdmf_common.VectorIndex( ... | ||
| 'target', types.untyped.ObjectView('/general/intracellular_ephys/experimental_conditions/repetitions'), ... | ||
| 'description', 'Index for VectorData "repetitions"', ... | ||
| 'data', [1, 2] ... | ||
| ), ... | ||
| 'tag', types.hdmf_common.VectorData( ... | ||
| 'description', 'integer tag for a experimental condition', ... | ||
| 'data', [1,3] ... | ||
| ) ... | ||
| ); | ||
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| %% write | ||
| nwbExport(nwbfile, 'test_new_icephys.nwb'); | ||
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