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Add support for DICOM WSI by using OpenSlide #959

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Merged
sarthakpati merged 9 commits into from
Oct 31, 2024
Merged

Add support for DICOM WSI by using OpenSlide #959

sarthakpati merged 9 commits into from
Oct 31, 2024

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@benmalef
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@benmalef benmalef commented Oct 30, 2024 •
edited by sarthakpati
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Fixes #ISSUE_NUMBER

Proposed Changes

Checklist

  • CONTRIBUTING guide has been followed.
  • PR is based on 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 (ensure typing is used to provide type hints, including and not limited to using Optional if a variable has a pre-defined value).
  • Code has been blacked for style consistency and linting.
  • 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.
  • 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].
  • The logging library is being used and no print statements are left.

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github-actions bot commented Oct 30, 2024 •
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MLCommons CLA bot All contributors have signed the MLCommons CLA ✍️ ✅

@sarthakpati sarthakpati changed the title Change the tiffslide to openslide. Change the tiffslide to openslide Oct 31, 2024
sarthakpati
sarthakpati requested changes Oct 31, 2024
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Great work! Minor comments to address.

benmalef and others added 8 commits October 31, 2024 18:46
@benmalef @sarthakpati
Update Dockerfile-CPU
8be7537 
Co-authored-by: Sarthak Pati <patis@iu.edu>
@benmalef @sarthakpati
Update Dockerfile-ROCm
bf7abfc 
Co-authored-by: Sarthak Pati <patis@iu.edu>
@benmalef @sarthakpati
Update GANDLF/compute/inference_loop.py
adcd561 
Co-authored-by: Sarthak Pati <patis@iu.edu>
@benmalef @sarthakpati
Update GANDLF/data/inference_dataloader_histopath.py
9185b70 
Co-authored-by: Sarthak Pati <patis@iu.edu>
@benmalef @sarthakpati
Update GANDLF/data/inference_dataloader_histopath.py
20cf01b 
Co-authored-by: Sarthak Pati <patis@iu.edu>
@benmalef @sarthakpati
Update GANDLF/data/patch_miner/opm/patch.py
cfd0a7a 
Co-authored-by: Sarthak Pati <patis@iu.edu>
@benmalef @sarthakpati
Update setup.py
7b118cc 
Co-authored-by: Sarthak Pati <patis@iu.edu>
@benmalef
blacked .
94feb7f
@sarthakpati sarthakpati marked this pull request as ready for review October 31, 2024 18:19
@sarthakpati sarthakpati requested a review from a team as a code owner October 31, 2024 18:19
@sarthakpati sarthakpati changed the title Change the tiffslide to openslide Add support for DICOM WSI by using OpenSlide Oct 31, 2024
@sarthakpati sarthakpati merged commit e69e4d5 into mlcommons:master Oct 31, 2024
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@github-actions github-actions bot locked and limited conversation to collaborators Oct 31, 2024
@benmalef benmalef deleted the change_lib_from_tiffslide_to_openslide branch April 10, 2025 16:11
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@benmalef @sarthakpati