search

CINPLA / expipe-plugin-cinpla

Plugins for expipe command line interface
http://expipe-plugin-cinpla.readthedocs.io/en/latest/
GNU General Public License v3.0
1 stars 3 forks source link

removing excess spikes #85

Closed mariapfj closed 1 week ago

mariapfj commented 1 week ago

Getting an error message when spikesorting projects\ec109\maria\mec-social-nwb\actions\137-310121-7 and projects\ec109\maria\novel-env-nwb\145-211021-1

ValueError: The sorting object has spikes exceeding the recording duration. You have to remove those spikes with the spikeinterface.curation.remove_excess_spikes() function

There already seems to be a function for removing excess spikes in src/expipe_plugin_cinpla/scripts/curation.py (I'm assuming this is the one referred to in the error message), any idea why this issue occurs for these specific recordings? Do I need to run the function in question manually? (if yes feel free to mention specifically which variables it requires) :)

alejoe91 commented 1 week ago

Hi @mariapfj Is that the full error? I'll take a look

mariapfj commented 1 week ago

Postprocessing Extracting waveforms ERROR: unable to process 137-310121-7 Traceback (most recent call last): File "/fp/projects01/ec109/software/expipe-plugin-cinpla/src/expipe_plugin_cinpla/widgets/process.py", line 300, in on_run process.process_ecephys( File "/fp/projects01/ec109/software/expipe-plugin-cinpla/src/expipe_plugin_cinpla/scripts/process.py", line 245, in process_ecephys compute_and_set_unit_groups(sorting, recording_cmr) File "/fp/projects01/ec109/software/expipe-plugin-cinpla/src/expipe_plugin_cinpla/scripts/utils.py", line 295, in compute_and_set_unit_groups we_mem = si.extract_waveforms(recording, sorting, folder=None, mode="memory", sparse=False) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/fp/homes01/u01/ec-mariapfj/.local/lib/python3.11/site-packages/spikeinterface/core/waveform_extractor.py", line 1670, in extract_waveforms we = WaveformExtractor.create( ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/fp/homes01/u01/ec-mariapfj/.local/lib/python3.11/site-packages/spikeinterface/core/waveform_extractor.py", line 271, in create raise ValueError( ValueError: The sorting object has spikes exceeding the recording duration. You have to remove those spikes with the spikeinterface.curation.remove_excess_spikes() function