SpikeInterface / SpikeInterface/spikeinterface
spykingcircus2 Insufficient system resources exist to complete the requested service
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- Dominant language
- Python
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Description
Dear Spikeinterface community,
I am using spykingcircus2 to do spike-sorting. After applying bandpass filter, motion correction, whitening to the raw data on spikeinterface, I checked the result on phy and felt that the default settings in spykingcircus2 seemed to work well with a single-shank (64 channels). However, when I switched to multple shank (96 channels) recording, I bumped into this error
OSError: [WinError 1450] Insufficient system resources exist to complete the requested service
It looks like the issue is with the computer. However, I can apply kilosort4 to this dataset on Spikeinterface without any problem. Does anyone know what issue I might have with spykingcircus2?
Below is my code and the log.json
rec_of_interest=get_preprocessed_recording(oe_folder,analysis_methods)
recording_saved=spre.astype(recording_saved,np.float32)
recording_corrected_dict=motion_correction_shankbyshank(recording_saved,oe_folder,analysis_methods)
if len(recording_corrected_dict)>1:
recording_corrected=recording_corrected_dict
else:
recording_corrected=recording_corrected_dict[0]
rec_for_sorting = spre.whiten(
recording=recording_corrected,
mode="local",
radius_um=150,
#int_scale=200,#this can be added to replicate kilosort behaviour
)
print(f"run spike sorting with {this_sorter}")
sorter_params = ss.get_default_sorter_params(this_sorter)
sorter_params.update({"apply_motion_correction": False,"apply_preprocessing": False})
sorter_params['general'].update({"radius_um":150})
if len(recording_corrected_dict)>1:
rec_for_sorting=si.aggregate_channels(rec_for_sorting)
sorting_spikes = ss.run_sorter_by_property(
sorter_name=this_sorter,
recording=rec_for_sorting,
remove_existing_folder=True,
grouping_property='group',
folder=oe_folder / result_folder_name,
verbose=True,
**sorter_params
)
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- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the supplied code around ss.run_sorter_by_property and the attached spikeinterface_log.json, reproducing the spykingcircus2 run with the single-shank and multishank recordings. Compare the sorter configuration and resource use at the failure point; done means identifying the cause of WinError 1450 and documenting a confirmed fix or limitation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100