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Ensure synthesis metrics have an option to take voided image #981

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merged 24 commits into from
Dec 20, 2024

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sarthakpati
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@sarthakpati sarthakpati commented Dec 19, 2024

Fixes #957

Proposed Changes

  • the synthesis metrics for BraTS rely on something called a "void image", which was not accounted for before.
  • it is now possible to either use a mask or a "void image" for normalization (sarthakpati@1c4afd7)
  • updated ncc metrics to get results from a masked region
  • updated spellings and typos

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.

@sarthakpati sarthakpati requested a review from a team as a code owner December 19, 2024 16:03
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github-actions bot commented Dec 19, 2024

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

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Just one comment about possibly separating functions.

@sarthakpati sarthakpati merged commit f9aabec into mlcommons:master Dec 20, 2024
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@github-actions github-actions bot locked and limited conversation to collaborators Dec 20, 2024
@sarthakpati sarthakpati deleted the synthesis_metrics_debug branch December 20, 2024 15:30
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[BUG] inpainting metrics are not computed correctly
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