raylim commited on
Commit
0d1b788
·
unverified ·
1 Parent(s): ddfa8f1

Update AEON inference to require sex parameter

Browse files

- Remove 'Unknown' from sex choices in CLI arguments
- Update docstrings to indicate sex is required
- Clarify that sex must be 'Male' or 'Female' for inference

src/mosaic/analysis.py CHANGED
@@ -673,7 +673,7 @@ def analyze_slide(
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  slide_path: Path to the whole slide image file
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  seg_config: Segmentation configuration, one of "Biopsy", "Resection", or "TCGA"
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  site_type: Site type, either "Primary" or "Metastatic"
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- sex: Patient sex ("Unknown", "Male", "Female")
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  tissue_site: Tissue site name
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  cancer_subtype: Cancer subtype (OncoTree code or "Unknown" for inference)
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  cancer_subtype_name_map: Dictionary mapping cancer subtype names to codes
 
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  slide_path: Path to the whole slide image file
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  seg_config: Segmentation configuration, one of "Biopsy", "Resection", or "TCGA"
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  site_type: Site type, either "Primary" or "Metastatic"
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+ sex: Patient sex ("Male" or "Female") - required
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  tissue_site: Tissue site name
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  cancer_subtype: Cancer subtype (OncoTree code or "Unknown" for inference)
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  cancer_subtype_name_map: Dictionary mapping cancer subtype names to codes
src/mosaic/inference/aeon.py CHANGED
@@ -224,9 +224,9 @@ def parse_args():
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  parser.add_argument(
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  "--sex",
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  type=str,
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- choices=["Male", "Female", "Unknown"],
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  default=None,
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- help="Patient sex (Male or Female)",
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  )
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  parser.add_argument(
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  "--tissue-site",
 
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  parser.add_argument(
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  "--sex",
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  type=str,
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+ choices=["Male", "Female"],
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  default=None,
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+ help="Patient sex (Male or Female, required for inference)",
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  )
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  parser.add_argument(
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  "--tissue-site",