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Update ImagingExtractor #365

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Update ImagingExtractor #365

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@pauladkisson pauladkisson commented Sep 24, 2024 •
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This PR is the first of a series that implement breaking changes to fully standardize the roiextractors api and update/streamline the testing suite. Some of the main goals include

  • removing channels argument to enforce 1 channel/extractor
  • Switching to modularized mixins for testing and supporting pytest fixtures/parameterization
  • Standard input validation, numpy indexing for 'get' methods, etc.

This PR focuses on ImagingExtractor, FrameSliceImagingExtractor, and NumpyImagingExtractor

@pauladkisson
updated imaging extractor to reflect 1-channel imaging extractors
4043df4
@pauladkisson
updated get_dtype to abstract to facilitate more efficient implementa…
b3fc00c 
…tions
@pauladkisson
removed channel from get_frames and get_video
889f721
@pauladkisson
removed write_imaging
ae8f055
@pauladkisson
cleaned up numpyimagingextractor init
76aa346
@pauladkisson
removed channels from numpyimagingextractor
c9c3a54
@pauladkisson
removed get_available_channels from imagingextractor
bd954c4
@pauladkisson
updated testing with no channels
6431da8
@pauladkisson
updated get_frames to allow frame_idxs out of order
358923e
@pauladkisson
moved check_imaging_equal to imagingextractor itself
0dfab19
@pauladkisson
added imagingextractor_mixin
0d45f9f
@pauladkisson
added test_numpy_imaging_extractor with mixin
a4797ee
@pauladkisson
fixed imaging extractor to pass tests
1cd743d
@pauladkisson
switched to fixtures to allow more complex setup
8db166f
@pauladkisson
added from file test
1bdf12e
@pauladkisson
fixed frame_slice so that it passes tests
fc43167
@pauladkisson
moved input handling to frame_slice method instead of init
ca7bcc3
@pauladkisson
updated frame validation
36ed953
@pauladkisson
updated frame validation
2d1f3f2
@pauladkisson
refactored frame slice tests into their own mixin
cd26c34
@pauladkisson
added tests for frame_slice method
211f9c3
@pauladkisson
Merge branch '0.6.0dev' into 0.6.0
7ea7142
@pauladkisson
reorganized tests to pass while PR is in progress
2e8dc4f
@pauladkisson
ignore old_tests
777393e
@pauladkisson
Merge branch '0.6.0dev' into 0.6.0
667ebb8
@pauladkisson
fixed python 3.9 isinstance bug
ae8d6e6
@pauladkisson
refactored input validation for get_video and get_frames into their o…
30279d2 
…wn private methods
@pauladkisson pauladkisson marked this pull request as ready for review September 24, 2024 22:00
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pauladkisson commented Sep 24, 2024 •
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A roadmap for future PRs for this dev effort:

@pauladkisson pauladkisson mentioned this pull request Sep 28, 2024
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Hey, this escaped my radar. Let's have a call once you are back from the retreat to have a brief discussion before I do a full review.

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@h-mayorquin h-mayorquin Awaiting requested review from h-mayorquin

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