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Add GDCM dependency to Dockerfile

Open danielsnider opened this issue 5 years ago • 16 comments

My DICOM images seem to be compressed and ask for GDCM. It would be great to add GDCM to the ocr Dockerfile :-).

This is what I see:

root@38a72d18ad9b:/code# ./entrypoint.sh --input /data
DEBUG Found 1 contender files in data
DEBUG Checking 1 dicom files for validation.
Found 1 valid dicom files
Traceback (most recent call last):
  File "/code/main.py", line 172, in <module>
    main()
  File "/code/main.py", line 108, in main
    verbose=args.verbose)
  File "/code/user/__init__.py", line 31, in __init__
    self.image = dicom._get_pixel_array()
  File "/opt/anaconda2/lib/python2.7/site-packages/pydicom-1.0.0a1-py2.7.egg/pydicom/dataset.py", line 1053, in _get_pixel_array
    self._pixel_array = self._pixel_data_numpy()
  File "/opt/anaconda2/lib/python2.7/site-packages/pydicom-1.0.0a1-py2.7.egg/pydicom/dataset.py", line 690, in _pixel_data_numpy
    raise NotImplementedError("Pixel Data is compressed in a "
NotImplementedError: Pixel Data is compressed in a format pydicom does not yet handle. Cannot return array. Pydicom might be able to convert the pixel data using GDCM if it is installed.

Sidenote: Commenting on line main.py#L157... if you catch all exceptions it would be great to at minimum print the exception instead of hiding it. Not seeing the error is the worst kind of error.

danielsnider avatar Jan 02 '19 22:01 danielsnider