Fix radiomics pipeline: swapped arguments and path type error#556
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wasserth merged 1 commit intowasserth:masterfrom Mar 30, 2026
Merged
Fix radiomics pipeline: swapped arguments and path type error#556wasserth merged 1 commit intowasserth:masterfrom
wasserth merged 1 commit intowasserth:masterfrom
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Fix two bugs in the radiomics feature extraction pipeline: 1. get_radiomics_features_for_entire_dir() passed ct_file as the first argument to get_radiomics_features(), but the function signature expects (seg_file, img_file). This reversed the CT and mask roles, causing incorrect feature extraction and keying all results under the CT filename instead of individual mask names. 2. In python_api.py, the TemporaryDirectory context manager returns a string, but the code used the / operator on it (tmp_folder / "ct.nii.gz"), which raises TypeError. Wrap with Path() to fix. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Summary
get_radiomics_features_for_entire_dir()instatistics.pypassedct_fileas the first argument toget_radiomics_features(), but the function signature is(seg_file, img_file). This reversed the CT and mask roles, producing incorrect radiomics features and keying all results under the CT filename instead of individual mask names.python_api.py,tempfile.TemporaryDirectory()returns astr, but the code used the/operator on it (tmp_folder / "ct.nii.gz"), which raisesTypeErrorwhen radiomics is called on aNifti1Imageinput. Wrapped withPath()to fix.Both bugs make the radiomics pipeline (
--radiomicsflag) non-functional.Test plan
totalsegmentatorwith--radiomicsflag on a nifti input and verify features are computed per-maskNifti1Imageobject via the Python API withradiomics=Trueand verify noTypeErrorstatistics_radiomics.jsonkeys are mask names (e.g.,liver,spleen) not the CT filename