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Add MotionCorrection, CorrectedImageStack and DeltaFOverF to ophys tutorial #629

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merged 3 commits into from
Nov 25, 2024

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ehennestad
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@ehennestad ehennestad commented Nov 20, 2024

Motivation

Add NWB types to tutorial to reach 100% tutorial coverage

How to test the behavior?

Run ophys live script

Checklist

  • Have you ensured the PR description clearly describes the problem and solutions?
  • Have you checked to ensure that there aren't other open or previously closed Pull Requests for the same change?
  • If this PR fixes an issue, is the first line of the PR description fix #XX where XX is the issue number?

bendichter
bendichter previously approved these changes Nov 20, 2024
@bendichter bendichter marked this pull request as ready for review November 20, 2024 12:49
@bendichter bendichter marked this pull request as draft November 20, 2024 12:54
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The test fails when trying to read the output nwb with pynwb, with the following error message:

 "Could not construct CorrectedImageStack object due to: CorrectedImageStack.__init__: missing argument 'original'"

The original property of the CorrectedImageStack object is set, and also present when I read the file back with matnwb.

@rly do you know why this might be happening? @ehennestad , could you provide a sample file?

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ehennestad commented Nov 20, 2024

The object in question should be added as a link. Issue #559 already discusses how the matnwb api is not enforcing links for types that should be links

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codecov bot commented Nov 20, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 95.16%. Comparing base (e070e20) to head (60f37a6).

Additional details and impacted files
@@           Coverage Diff           @@
##           master     #629   +/-   ##
=======================================
  Coverage   95.16%   95.16%           
=======================================
  Files         113      113           
  Lines        4734     4734           
=======================================
  Hits         4505     4505           
  Misses        229      229           

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@ehennestad ehennestad marked this pull request as ready for review November 21, 2024 07:40
@ehennestad ehennestad changed the title Add MotionCorrection, CorrectedImageStack and DeltaFOverF to ophys tu… Add MotionCorrection, CorrectedImageStack and DeltaFOverF to ophys tutorial Nov 21, 2024
@bendichter bendichter self-requested a review November 25, 2024 13:25
@bendichter bendichter merged commit d46adae into master Nov 25, 2024
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2 participants