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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 +1 -1
- src/mosaic/inference/aeon.py +2 -2
src/mosaic/analysis.py
CHANGED
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@@ -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 ("
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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
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src/mosaic/inference/aeon.py
CHANGED
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@@ -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"
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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",
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