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Improve NWB support

Open kir0ul opened this issue 3 years ago • 4 comments
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This PR does the following:

  • Save F_chan2 and Fneu_chan2 to 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):

image image

kir0ul avatar Jun 11 '22 04:06 kir0ul

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

kir0ul avatar Jun 13 '22 15:06 kir0ul

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

kir0ul avatar Jun 29 '22 03:06 kir0ul

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!

chriski777 avatar Aug 08 '22 21:08 chriski777

Codecov Report

Merging #840 (7668607) into main (34b1bfd) will increase coverage by 0.82%. The diff coverage is 73.48%.

@@            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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codecov-commenter avatar Aug 11 '22 13:08 codecov-commenter

@chriski777 @rly Tests are ok now :heavy_check_mark: so I think this is finally ready for review! :slightly_smiling_face:

kir0ul avatar Aug 22 '22 15:08 kir0ul

@kir0ul, sorry for the late reply! Looks great to me so I'll merge it! Thanks!!!

chriski777 avatar Aug 28 '22 20:08 chriski777