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fix (pipeline): catch error when there are no suitable segmentation types in the imgtools csv #13

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Mar 6, 2024
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fix (pipeline): catch error when there are no suitable segmentation types in the imgtools csv #13

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9 changes: 7 additions & 2 deletions src/readii/pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,8 +58,13 @@ def main():
raise FileNotFoundError("Output for med-imagetools not found for this image set. Check the data_directory argument or run med-imagetools.")

print("Getting segmentation type...")
# Get segType from imageFileList to generate the image metadata file and set up feature extraction
segType = getSegmentationType(imageFileListPath)
try:
# Get segType from imageFileList to generate the image metadata file and set up feature extraction
segType = getSegmentationType(imageFileListPath)
except RuntimeError as e:
print(str(e))
print("Feature extraction not complete.")


# Check if image metadata file has already been created
imageMetadataPath = os.path.join(outputDir, "ct_to_seg_match_list_" + datasetName + ".csv")
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