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[BUG] Parallel batch processing example: label information from CSV #757

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ysuter opened this issue Mar 29, 2022 · 1 comment
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[BUG] Parallel batch processing example: label information from CSV #757

ysuter opened this issue Mar 29, 2022 · 1 comment
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@ysuter
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ysuter commented Mar 29, 2022

Description
When using the example parallel batch processing (examples)/batchprocessing_parallel.py), the label information fetched from the input CSV file does not get passed to the feature extractor. This leads to a feature extraction not considering the provided label information.
This is correctly done in the non-parallel versions. The example works fine if the label is provided in the setting file.

To Reproduce
Use the example setting with batch_processing_parallel.py together with an input CSV file to extract features based on a multi-label segmentation. The CVS-file contains the same image/mask pair on multiple lines, with the only difference being the label column with different values. With the current batch_processing_parallel.py, the label information from the CSV file is not considered by the feature extraction (extracted on the same label). In this case, the label information is provided in the CSV, not the settings file.

Expected behavior
Feature extraction on the multi-label image based on the label information provided in the input CSV file.

Version:

  • OS: Ubuntu 20.04.3
  • Python version: 3.7.7
  • PyRadiomics version 3.0.1

Related PR: #756
If the feature vector should also contain the label information, adding the label to both the feature extractor and the updated feature vector would be an alternative.

@ysuter ysuter added the bug label Mar 29, 2022
@ysuter ysuter changed the title [BUG] [BUG] Parallel batch processing example: label information from CSV Mar 29, 2022
@JoostJM
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JoostJM commented Apr 3, 2022

Thanks for the fix! The PR is merged.

@JoostJM JoostJM closed this as completed Apr 3, 2022
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