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Add parameters to mean adaptive thresh #937

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merged 49 commits into from
Oct 14, 2022

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JorgeGtz
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@JorgeGtz JorgeGtz commented Aug 23, 2022

Describe your changes
Adding parameters of block size and offset to both, mean and Gaussian adaptive threshold functions.

This will add flexibility to tune the behavior of the adaptive threshold depending on the image (resolution, size of the objects, and degree of change in brightness).

We have been using these functions as automatic methods, with block size and offset fixed, but that is not an optimal usage of the adaptive thresholds. The important characteristic of these adaptive methods is that they use a different threshold value for each pixel, depending on the value of the pixels in a surrounding block.

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  • New feature or feature enhancement

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  • PR functionality reviewed in a Jupyter Notebook
  • All tests pass
  • Test coverage remains 100%
  • Documentation tested
  • New documentation pages added to plantcv/mkdocs.yml
  • Changes to function input/output signatures added to updating.md
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@JorgeGtz JorgeGtz added the work in progress Mark work in progress label Aug 23, 2022
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codecov bot commented Aug 24, 2022

Codecov Report

Merging #937 (8ce5f85) into release-4.0 (4390066) will not change coverage.
The diff coverage is 100.00%.

❗ Current head 8ce5f85 differs from pull request most recent head 00c5d74. Consider uploading reports for the commit 00c5d74 to get more accurate results

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@@              Coverage Diff               @@
##           release-4.0      #937    +/-   ##
==============================================
  Coverage       100.00%   100.00%            
==============================================
  Files              161       147    -14     
  Lines             6840      6640   -200     
==============================================
- Hits              6840      6640   -200     
Flag Coverage Δ
unittests 100.00% <100.00%> (ø)

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

Impacted Files Coverage Δ
plantcv/parallel/multiprocess.py 100.00% <100.00%> (ø)
plantcv/plantcv/find_objects.py 100.00% <100.00%> (ø)
plantcv/plantcv/hyperspectral/analyze_spectral.py 100.00% <100.00%> (ø)
plantcv/plantcv/roi/roi2mask.py 100.00% <100.00%> (ø)
plantcv/plantcv/roi/roi_methods.py 100.00% <100.00%> (ø)
plantcv/plantcv/threshold/threshold_methods.py 100.00% <100.00%> (ø)
plantcv/plantcv/transform/color_correction.py 100.00% <100.00%> (ø)
...lantcv/plantcv/visualize/auto_threshold_methods.py 100.00% <100.00%> (ø)
plantcv/plantcv/transform/__init__.py
plantcv/learn/__init__.py
... and 12 more

@JorgeGtz JorgeGtz added enhancement Enhancements to existing features ready to review and removed work in progress Mark work in progress labels Aug 29, 2022
@nfahlgren nfahlgren added this to the PlantCV v4.0 milestone Sep 4, 2022
nfahlgren and others added 23 commits October 14, 2022 15:32
@nfahlgren nfahlgren changed the base branch from 4.x to release-4.0 October 14, 2022 20:54
@nfahlgren nfahlgren merged commit 04d8ae5 into release-4.0 Oct 14, 2022
@nfahlgren nfahlgren deleted the add-parameters-to-mean-adaptive-thresh branch October 14, 2022 21:11
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