suite2p
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Improve NWB support
This PR does the following:
- Save
F_chan2andFneu_chan2to NWB (fixes https://github.com/MouseLand/suite2p/issues/817), - Add planes fluorescence containers to NWB,
- Separate ROIs for each plane in NWB,
- Test round trip writing + reading NWB file.
Here are below some screenshots that show the structure differences of the resulting NWB file (left: before this PR, right: after this PR):

Apparently something happened on the GH side, could someone restart the CI?
fatal: unable to connect to github.com:
github.com[0: 192.30.255.113]: errno=Unknown error
Fixed the merge conflicts, but not sure why there's a segmentation fault on MacOS as tests run fine on my Linux machine.
cc @rly
Hey @kir0ul, thanks for this PR. Ah, yep the segmentation fault error on the Mac happens for some reason with the latest version of PyTorch. I'll take a look at this PR and try to merge it soon!
Codecov Report
Merging #840 (7668607) into main (34b1bfd) will increase coverage by
0.82%. The diff coverage is73.48%.
@@ Coverage Diff @@
## main #840 +/- ##
==========================================
+ Coverage 26.93% 27.76% +0.82%
==========================================
Files 55 55
Lines 9819 9866 +47
==========================================
+ Hits 2645 2739 +94
+ Misses 7174 7127 -47
| Impacted Files | Coverage Δ | |
|---|---|---|
| suite2p/run_s2p.py | 81.36% <ø> (+0.25%) |
:arrow_up: |
| suite2p/io/nwb.py | 75.00% <73.48%> (+24.18%) |
:arrow_up: |
| suite2p/gui/rungui.py | 0.00% <0.00%> (ø) |
|
| suite2p/detection/detect.py | 78.63% <0.00%> (ø) |
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@chriski777 @rly Tests are ok now :heavy_check_mark: so I think this is finally ready for review! :slightly_smiling_face:
@kir0ul, sorry for the late reply! Looks great to me so I'll merge it! Thanks!!!