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Update spike sorting V1 code and notebook to run sorters other than mountainsort4
#844
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pull to sync; to make a forked repo
Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
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Thanks for your contributions @donghoon-shin !
I have a couple code comments on black
, pop
, and sorter name validation. Having the py-script of the notebook (see how here) would make it easier to give comments on those changes. In particular, it looks like you left some things commented out, which might make it hard to run outside the lab's DB. I think I would put these in if
clauses to avoid w/e error you intend to avoid by commenting out
chris's suggestion Co-authored-by: Chris Brozdowski <[email protected]>
chris's suggestion Co-authored-by: Chris Brozdowski <[email protected]>
…y tested ironclust
@CBroz1 I fixed as your comments except for the ones that I commented. Please let me know! |
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Thanks for converting the notebook @donghoon-shin !
I had some comments about comments there, and then extracting common kwargs outside of the if/then
.
It took me a sec to find your comment. I'm in the habit of leaving items unresolved until both author and reviewer are on the same page
Thanks again for the contribution!
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sgc.LabMember.insert_from_nwbfile(nwb_file_name) | ||
# + | ||
# sgc.LabMember.insert_from_nwbfile(nwb_file_name) |
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Please uncomment and put in some form of conditional like
# sgc.LabMember.insert_from_nwbfile(nwb_file_name) | |
if not (sgc.LabMember & 'lab_member_name = "Firstname Lastname"'): | |
sgc.LabMember.insert_from_nwbfile(nwb_file_name) |
Jupytext makes it easier to comment on specific lines, but it can be inconsistent in the py
-> ipynb
direction, so I unfortunately generally apply comments by hand in the notebook.
@@ -52,33 +54,54 @@ | |||
# insert SortGroup | |||
# | |||
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sgs.SortGroup.set_group_by_shank(nwb_file_name=nwb_file_name2) | |||
# + | |||
# sgs.SortGroup.set_group_by_shank(nwb_file_name=nwb_file_name2) |
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Please either set this in a conditional or provide some context about why this is commented out. e.g., a markdown cell saying "If you haven't already done X, please uncomment the line below"
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@donghoon-shin can you make the changes to the notebook and verify that everything runs? |
Co-authored-by: Chris Brozdowski <[email protected]>
The notebook needs to be cleaned up more. I have started adding some more documentation to make it more thorough. |
mountainsort4
mountainsort4
mountainsort4
In conversation with @khl02007 , this is good to go. There will be a followup PR that will do some notebook cleanup. |
Description
src/spyglass/spikesorting/v1/sorting.py
: modifyingsorter_params
dictionary ; spikeinterface.run_sorter parameters based on spikesorting algorithms.notebooks/10_Spike_SortingV1.ipynb
: Change a few notebook cells so that it can run without error until spike sorting. Also added more instructions on running other spikesorting algorithms such as kilosort2.5, kilosort3, and mountainsort5.Checklist:
CITATION.cff
CHANGELOG.md