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Fix scalefactors error visium hd 3.x #343

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merged 1 commit into from
Nov 8, 2025
Merged

Fix scalefactors error visium hd 3.x #343

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8 changes: 8 additions & 0 deletions src/spatialdata_io/readers/visium_hd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -133,6 +133,14 @@ def visium_hd(
CELL_GEOJSON_PATH = SEGMENTED_OUTPUTS_PATH / VisiumHDKeys.CELL_SEGMENTATION_GEOJSON_PATH
NUCLEUS_GEOJSON_PATH = SEGMENTED_OUTPUTS_PATH / VisiumHDKeys.NUCLEUS_SEGMENTATION_GEOJSON_PATH
SCALE_FACTORS_PATH = SEGMENTED_OUTPUTS_PATH / VisiumHDKeys.SPATIAL / VisiumHDKeys.SCALEFACTORS_FILE
if not SCALE_FACTORS_PATH.exists():
# Visium HD 3.0.0 does not have the SEGMENTATION_OUTPUTS folder
scale_factors_file = next(
(file for file in path.rglob("*") if file.name.endswith(VisiumHDKeys.SCALEFACTORS_FILE)),
None,
)
assert scale_factors_file is not None, "Scale factors file not found in any of the subdirectories."
SCALE_FACTORS_PATH = scale_factors_file
BARCODE_MAPPINGS_PATH = next(
(file for file in path.rglob("*") if file.name.endswith(VisiumHDKeys.BARCODE_MAPPINGS_FILE)),
None,
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