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@drgmo drgmo commented Jan 18, 2026

--fix:
try-except-block prevents prevent the process from crashing when feature files listed in the slide table are missing or inaccessible.

--background:

encode_slides_: Iterates over os.listdir(feat_dir). This naturally filters out missing files because it only attempts to process files that the OS reports as present.
encode_patients_: Iterates over a pandas DataFrame (patient_groups). If the csv contains a reference to a slide filename that does not exist on disk, the direct file access causes a FileNotFoundError or OSError, crashing the entire pipeline

@mducducd mducducd self-requested a review January 19, 2026 10:22
)
continue

# feats, agg_feats = self._validate_and_read_features_with_agg(
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I think we can remove this

@mducducd mducducd merged commit 32e78f4 into KatherLab:main Jan 23, 2026
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2 participants