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Mcsh5 offsets and proper scaling in uV for return_scaled #2988

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merged 9 commits into from
Jul 5, 2024
Merged

Mcsh5 offsets and proper scaling in uV for return_scaled #2988

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45deefa
Adding offsets to allow return_scaled
yger Jun 6, 2024
432890e
Scaling of offset/gain in uV
yger Jun 6, 2024
4228deb
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 6, 2024
e729585
Docs and negative sign
yger Jun 6, 2024
bda5ff4
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 6, 2024
78d9c78
Merge branch 'main' into mcsh5_offsets
yger Jun 10, 2024
ec951f8
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 10, 2024
6391d43
Update src/spikeinterface/extractors/mcsh5extractors.py
yger Jul 3, 2024
2407d2f
Update src/spikeinterface/extractors/mcsh5extractors.py
samuelgarcia Jul 5, 2024
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15 changes: 12 additions & 3 deletions src/spikeinterface/extractors/mcsh5extractors.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,9 @@ def __init__(self, file_path, stream_id=0):
# set gain
self.set_channel_gains(mcs_info["gain"])

# set offsets
self.set_channel_offsets(mcs_info["offset"])

# set other properties
self.set_property("electrode_labels", mcs_info["electrode_labels"])

Expand Down Expand Up @@ -101,7 +104,11 @@ def get_traces(self, start_frame=None, end_frame=None, channel_indices=None):


def openMCSH5File(filename, stream_id):
"""Open an MCS hdf5 file, read and return the recording info."""
"""Open an MCS hdf5 file, read and return the recording info.
Specs can be found online
https://www.multichannelsystems.com/downloads/documentation?page=3
"""

import h5py

rf = h5py.File(filename, "r")
Expand All @@ -122,7 +129,8 @@ def openMCSH5File(filename, stream_id):
Tick = info["Tick"][0] / 1e6
exponent = info["Exponent"][0]
convFact = info["ConversionFactor"][0]
gain = convFact.astype(float) * (10.0**exponent)
gain_uV = 1e6 * (convFact.astype(float) * (10.0**exponent))
offset_uV = -1e6 * (info["ADZero"].astype(float) * (10.0**exponent)) * gain_uV

nRecCh, nFrames = data.shape
channel_ids = [f"Ch{ch}" for ch in info["ChannelID"]]
Expand Down Expand Up @@ -150,8 +158,9 @@ def openMCSH5File(filename, stream_id):
"num_channels": nRecCh,
"channel_ids": channel_ids,
"electrode_labels": electrodeLabels,
"gain": gain,
"gain": gain_uV,
"dtype": dtype,
"offset": offset_uV,
}

return mcs_info
Expand Down