SpikeInterface / SpikeInterface/spikeinterface
Probe appears to be missing when interpolating 'bad channels' in recording
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Description
Hi,
I am trying to identify and interpolate 'bad' channels in my recording. Whenever I try to save the newly obtained preprocessed interpolated recording, I get the following warning:
"UserWarning: There is no Probe attached to this recording. Creating a dummy one with contact positions
warn("There is no Probe attached to this recording. Creating a dummy one with contact positions")"
There seems to be a probe attached to the recording (The statement recording.has_probe() returns "True"). Whenever I try to save the recording without this interpolation step, I don't get this warning.
Roughly the steps I take:
recording = se.read_openephys(self.oe_path)
recording = recording.set_probe(probe, in_place=False)
bad_channel_ids, channel_labels = spre.detect_bad_channels(recording=recording, method='coherence+psd')
recording = spre.interpolate_bad_channels(recording=recording, bad_channel_ids=bad_channel_ids)
recording.has_probe()
recording_saved = recording.save(folder=session.preprocessed_folder, format='binary')
In a similar issue I read that it is potentially not a problem, since the relevant information (channels locations, groups) are still passed (https://github.com/SpikeInterface/spikeinterface/issues/2895).
Possibly someone knows why I get this specific warning in this case (and whether it is a problem at all).
Much appreciated,
Sietse
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Research direction
Start by reproducing the warning with read_openephys, set_probe, detect_bad_channels, interpolate_bad_channels, and save as shown. Trace how interpolation and binary saving handle probe metadata; done means determining whether the probe is lost or replaced with a dummy and documenting or correcting the behavior.
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Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100