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Set sparse=False during waveform extraction #1039

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merged 43 commits into from
Aug 5, 2024

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@khl02007 khl02007 commented Jul 19, 2024

Description

Waveforms are extracted with spikeinterface.extract_waveforms, which accepts an argument that extracts only the waveforms from electrodes with significant signal (i.e. if sparse=True). This introduces some issues when saving the results to NWB file as this causes the number of electrodes with signal to be different across units. It used to be that sparse=False by default but that has changed in a recent version of spikeinterface. This change forces sparse to be False if not specified in WaveformParameters.

Checklist:

  • This PR should be accompanied by a release: (yes/no/unsure)
  • If release, I have updated the CITATION.cff
  • This PR makes edits to table definitions: (yes/no)
  • If table edits, I have included an alter snippet for release notes.
  • If this PR makes changes to position, I ran the relevant tests locally.
  • I have updated the CHANGELOG.md with PR number and description.
  • I have added/edited docs/notebooks to reflect the changes

khl02007 and others added 30 commits May 9, 2023 23:56
@edeno edeno linked an issue Jul 19, 2024 that may be closed by this pull request
@edeno edeno merged commit 907098a into LorenFrankLab:master Aug 5, 2024
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MetricCuration populate problem
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