SpikeInterface / SpikeInterface/spikeinterface
`read_kilosort_as_analyzer` : read original `spike_templates.npy` instead of `spike_clusters.npy` from kilosort output
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Description
We should read the spike_templates.npy file in read_phy
Alternatively I propose to allow an argument to BasePhyKilosortSortingExtractor init that tells whether to try to use spike_clusters.npy if found or not and add an argument which was used.
The terminology should not be misleading because kilosort output can be manually refined by phy
https://github.com/SpikeInterface/spikeinterface/issues/4366#issuecomment-3854954921
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First steps
- Read the whole issue, then the project's contributing guide.
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- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start in src/spikeinterface/extractors/phykilosortextractors.py around line 341 and review the linked discussion in issue #4366. Determine whether the reader should use spike_templates.npy by default or expose an option for spike_clusters.npy, and clarify the terminology for manually refined Phy output. Done means the selected behavior and argument are consistently represented in the reader.
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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
- 45/100