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MaxwellIO: Fix issue due to disparity between routed and mapped channels #1703

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MaxwellIO: Fix issue due to disparity between routed and mapped channels #1703

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6e02e3c
Fix issue due to disparity between routed and mapped channels
May 9, 2025
4cb378b
Update maxwellrawio.py
LeMuellerGuy May 9, 2025
17ade48
Update maxwellrawio.py
LeMuellerGuy May 11, 2025
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20 changes: 15 additions & 5 deletions neo/rawio/maxwellrawio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,20 @@ def __init__(self, filename="", rec_name=None):

def _source_name(self):
return self.filename

def _get_ids_and_electrodes(self, version, stream_id, h5file, mapping):
if int(version) == 20160704:
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Could you document where this version number comes from in a comment? Was this dev docs etc. I think knowing magic numbers at all times.

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I took the version number from the existing code. My best guess is that it is actually the release date of the first file version, where the structure was a little different. Our lab works with the MaxTwo device which was released later on so I assume that it never used this version because it needs additional fields to correctly represent the multiple wells of the MaxTwo device. There is also an option for legacy data formats in the software supplied by maxwell, so I assume it must be that.

channel_ids = np.array(mapping["channel"])
electrode_ids = np.array(mapping["electrode"])
else:
channel_ids = np.array(h5file["wells"][stream_id][self.rec_name]["groups"]["routed"]["channels"])
electrode_ids = np.array(mapping["electrode"])
channel_ids = channel_ids[channel_ids >= 0]
routed_channel_ids_mask = np.isin(np.array(mapping["channel"]), channel_ids)
unique_channel_ids_mask = np.unique(mapping["channel"][routed_channel_ids_mask],
return_index=True)[1]
return channel_ids, electrode_ids[unique_channel_ids_mask]


def _parse_header(self):
import h5py
Expand Down Expand Up @@ -175,11 +189,7 @@ def _parse_header(self):
}
self._stream_buffer_slice[stream_id] = slice(None)

channel_ids = np.array(mapping["channel"])
electrode_ids = np.array(mapping["electrode"])
mask = channel_ids >= 0
channel_ids = channel_ids[mask]
electrode_ids = electrode_ids[mask]
channel_ids, electrode_ids = self._get_ids_and_electrodes(version, stream_id, h5file, mapping)

for i, chan_id in enumerate(channel_ids):
elec_id = electrode_ids[i]
Expand Down