Adding mechanism to curate each extracted patch

[shubhaminnani]

Added to code to curate the patches, discard the patches if tissue in patch is less than 30%, and if there is any other artifact as glass reflection, pen markings.

Fixes #652

Proposed Changes

• added the code to curate the tiles after patching

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].

[github-actions]

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

[sarthakpati]

Thanks for your contribution!

Minor syntactic changes requested.

[sarthakpati]

MLCommons CLA bot: Thank you very much for your submission, we really appreciate it. Before we can accept your contribution, we ask that you sign the MLCommons CLA (Apache 2). Please use this [Google form] (https://forms.gle/Ew1KkBVpyeJDuRw67) to initiate authorization. If you are from an MLCommons member organization, we will request that you be added to the CLA. If you are not from a member organization, we will email you a CLA to sign. For any questions, please contact support@mlcommons.org.0 out of 1 committers have signed the MLCommons CLA.❌ @shubhaminnaniYou can retrigger this bot by commenting recheck in this Pull Request

Thanks for the contribution, @shubhaminnani! Let me know once you have signed and submitted the CLA, and I can re-check this.

[codecov]

Codecov Report

Merging #653 (dad52e2) into master (e6cec23) will increase coverage by 0.02%.
The diff coverage is 90.90%.

❗ Current head dad52e2 differs from pull request most recent head 68e00a3. Consider uploading reports for the commit 68e00a3 to get more accurate results

@@            Coverage Diff             @@
##           master     #653      +/-   ##
==========================================
+ Coverage   94.60%   94.62%   +0.02%     
==========================================
  Files         116      116              
  Lines        8038     8056      +18     
==========================================
+ Hits         7604     7623      +19     
+ Misses        434      433       -1     

Flag	Coverage Δ
unittests	94.62% <90.90%> (+0.02%)	⬆️

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

Impacted Files	Coverage Δ
GANDLF/data/patch_miner/opm/patch_manager.py	91.19% <ø> (ø)
GANDLF/data/patch_miner/opm/utils.py	94.53% <88.88%> (-0.62%)	⬇️
GANDLF/cli/patch_extraction.py	95.65% <100.00%> (+6.52%)	⬆️

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[sarthakpati]

This will be a major round of changes that stems from the fact that there is no unit test coverage for this code addition. Going back from there, I am seeing a bunch of places where the code is brittle and can cause breaks/crashes.

[sarthakpati]

Hey @shubhaminnani, I have converted this PR to draft until it is ready for review once again (at least once the tests are all passing). All the best! 👍🏽

[sarthakpati]

Minor changes requested.

[sarthakpati]

LGTM pending tests.

[sarthakpati]

LGTM