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Update Suite2pSegmentationExtractor to support multi channel and multi plane outputs #242

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merged 31 commits into from
Nov 6, 2023

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weiglszonja
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@weiglszonja weiglszonja commented Sep 14, 2023

Related issue: #234
Also in catalystneuro/pinto-lab-to-nwb#9

The interface PR: catalystneuro/neuroconv#601

@weiglszonja weiglszonja marked this pull request as draft September 14, 2023 14:54
weiglszonja and others added 3 commits September 14, 2023 17:05
# Conflicts:
#	src/roiextractors/extractors/suite2p/suite2psegmentationextractor.py
@weiglszonja weiglszonja self-assigned this Sep 14, 2023
@weiglszonja weiglszonja linked an issue Sep 14, 2023 that may be closed by this pull request
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@CodyCBakerPhD
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@weiglszonja Can you also include some of the fixes/improvements from https://github.com/catalystneuro/roiextractors/pull/227/files while working on this? Such as safe loading (based on file existence) for each of the response series types

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codecov bot commented Oct 31, 2023

Codecov Report

Merging #242 (c26c4ca) into main (80ecc1f) will increase coverage by 0.04%.
The diff coverage is 93.75%.

Impacted file tree graph

@@            Coverage Diff             @@
##             main     #242      +/-   ##
==========================================
+ Coverage   78.96%   79.00%   +0.04%     
==========================================
  Files          39       39              
  Lines        2985     3029      +44     
==========================================
+ Hits         2357     2393      +36     
- Misses        628      636       +8     
Flag Coverage Δ
unittests 79.00% <93.75%> (+0.04%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files Coverage Δ
...extractors/suite2p/suite2psegmentationextractor.py 89.61% <93.75%> (-3.12%) ⬇️

@weiglszonja weiglszonja marked this pull request as ready for review November 3, 2023 15:27
@CodyCBakerPhD CodyCBakerPhD self-requested a review November 3, 2023 15:27
@weiglszonja weiglszonja requested review from alessandratrapani and removed request for CodyCBakerPhD November 3, 2023 15:27
@CodyCBakerPhD CodyCBakerPhD self-requested a review November 3, 2023 15:27
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CodyCBakerPhD commented Nov 3, 2023

@pauladkisson @alessandratrapani Can I get your help reviewing this PR? Thanks in advance

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Looks good to me! :)
I just added two minor comments on the test functions for channel names. Probably I am wrong, but I wanted to be sure.

@CodyCBakerPhD CodyCBakerPhD merged commit 8041fb0 into main Nov 6, 2023
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@CodyCBakerPhD CodyCBakerPhD deleted the update_suite2psegmentationextractor branch November 6, 2023 15:42
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[Feature]: Suite2p multiple optical channels
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