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Read gain scaling from .rec header. #1448

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merged 3 commits into from
Apr 9, 2024
Merged

Read gain scaling from .rec header. #1448

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7d0e575
Fix issue #1441: Read gain scaling from .rec header.
gkBCCN Mar 28, 2024
035b1aa
Make the note more explicit about what is hardcoded.
zm711 Mar 29, 2024
83a84b2
ADD: scaling attribute and warning if not scaleable...
gkBCCN Apr 9, 2024
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19 changes: 12 additions & 7 deletions neo/rawio/spikegadgetsrawio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,10 +55,10 @@ def __init__(self, filename="", selected_streams=None):

Notes
-----
This file format has multiple version. New versions include the gain for scaling.
The current implementation does not contain this feature because we don't have
files to test this. So now the gain is "hardcoded" to 1, and so units are
not handled correctly.
This file format has multiple versions:
- Newer versions include the gain for scaling to microvolts [uV].
- If the scaling is not found in the header, it will be "hardcoded" to 1,
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in which case the units are not handled correctly.
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Examples
--------
Expand Down Expand Up @@ -173,12 +173,17 @@ def _parse_header(self):

chan_ind = 0
for trode in sconf:
if "spikeScalingToUv" in trode.attrib:
gain = float(trode.attrib["spikeScalingToUv"])
units = "uV"
else:
gain = 1 # revert to hardcoded gain
units = ""

for schan in trode:
name = "trode" + trode.attrib["id"] + "chan" + schan.attrib["hwChan"]
chan_id = schan.attrib["hwChan"]
# TODO LATER : handle gain correctly according the file version
units = ""
gain = 1.0

offset = 0.0
signal_channels.append(
(name, chan_id, self._sampling_rate, "int16", units, gain, offset, stream_id)
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