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yoninachmany/README.md

Last active July 11, 2019 10:04
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README.md

If models not already downloaded in /home/ubuntu/models/ (need 8.6 G)

  1. Make models directory: sudo mkdir /home/ubuntu/models
  2. For view classification model: in models directory, download clf_urls.txt and run wget -i clf_urls.txt
  3. For image segmentation models: in models directory, download seg_urls.txt and run wget -i seg_urls.txt

Before running

  1. Replace ./models/ with /home/ubuntu/models/ in Python files

To run on your own study 0. If data comes from AWS, configure credentials: aws configure

  1. Replace "Image" with "a" in predict_viewclass_v2.py
  2. Make data directory: mkdir /home/ubuntu/data
  3. Comment out dicomdir = "dicomsample"
  4. For segment_a4c_a2c_a3c_plax_psax.py, copy OptionParser import and code from predict_viewclass_v2.py
  5. Run Python file with -d <study_dir> option

To run on your own studies

  1. Run Python file with -d <study_dir> option
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