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HED augmentations for digital pathology image #649

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merged 57 commits into from
Jul 21, 2023

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Geeks-Sid
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Added H&E based augmentations for Histopathology images (can be used for other RGB images)
Solves #510

Proposed Changes

  • Added a hed transform that will allow to make precise changes to digital pathology images, particularly H&E images.

Checklist

  • I have read the CONTRIBUTING guide.
  • My PR is based from the current GaNDLF master .
  • Non-breaking change (does not break existing functionality): provide as many details as possible for any breaking change.
  • Function/class source code documentation added/updated.
  • Code has been blacked for style consistency.
  • If applicable, version information has been updated in GANDLF/version.py.
  • If adding a git submodule, add to list of exceptions for black styling in pyproject.toml file.
  • Usage documentation has been updated, if appropriate.
  • History has been updated, if appropriate.
  • Tests added or modified to cover the changes; if coverage is reduced, please give explanation.
  • If customized dependency installation is required (i.e., a separate pip install step is needed for PR to be functional), please ensure it is reflected in all the files that control the CI, namely: python-test.yml, and all docker files [1,2,3].

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github-actions bot commented May 16, 2023

MLCommons CLA bot All contributors have signed the MLCommons CLA ✍️ ✅

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codecov bot commented May 22, 2023

Codecov Report

Merging #649 (7fe43db) into master (bca8bbd) will increase coverage by 0.04%.
The diff coverage is 97.05%.

❗ Current head 7fe43db differs from pull request most recent head 1cc449a. Consider uploading reports for the commit 1cc449a to get more accurate results

@@            Coverage Diff             @@
##           master     #649      +/-   ##
==========================================
+ Coverage   94.62%   94.67%   +0.04%     
==========================================
  Files         116      117       +1     
  Lines        8062     8162     +100     
==========================================
+ Hits         7629     7727      +98     
- Misses        433      435       +2     
Flag Coverage Δ
unittests 94.67% <97.05%> (+0.04%) ⬆️

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

Impacted Files Coverage Δ
GANDLF/data/augmentation/rgb_augs.py 100.00% <ø> (ø)
GANDLF/data/augmentation/hed_augs.py 96.15% <96.15%> (ø)
GANDLF/data/augmentation/__init__.py 100.00% <100.00%> (ø)
GANDLF/parseConfig.py 84.53% <100.00%> (+0.75%) ⬆️
testing/test_full.py 99.16% <100.00%> (+<0.01%) ⬆️

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@Geeks-Sid
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@sarthakpati I am not able to hit the transform function, can you assist me with the code coverage.

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@sarthakpati sarthakpati marked this pull request as draft July 18, 2023 13:38
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@sarthakpati sarthakpati marked this pull request as ready for review July 21, 2023 12:53
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LGTM pending tests

@sarthakpati sarthakpati merged commit da3bfa4 into mlcommons:master Jul 21, 2023
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@github-actions github-actions bot locked and limited conversation to collaborators Jul 21, 2023
@Geeks-Sid Geeks-Sid deleted the hed_adv branch July 21, 2023 14:01
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2 participants