GDCM 2.2.0

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ConvertNumpy.py

    ############################################################################
    #
    #  Program: GDCM (Grassroots DICOM). A DICOM library
    #
    #  Copyright (c) 2006-2011 Mathieu Malaterre
    #  All rights reserved.
    #  See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
    #
    #     This software is distributed WITHOUT ANY WARRANTY; without even
    #     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
    #     PURPOSE.  See the above copyright notice for more information.
    #
    ############################################################################

    """
    This module add support for converting a gdcm.Image to a numpy array.

    Caveats:
    - Does not support UINT12/INT12

    Removed:
    - float16 is defined in GDCM API but no implementation exist for it ...
    """

    import gdcm
    import numpy

    def get_gdcm_to_numpy_typemap():
        """Returns the GDCM Pixel Format to numpy array type mapping."""
        _gdcm_np = {gdcm.PixelFormat.UINT8  :numpy.int8,
                    gdcm.PixelFormat.INT8   :numpy.uint8,
                    #gdcm.PixelFormat.UINT12 :numpy.uint12,
                    #gdcm.PixelFormat.INT12  :numpy.int12,
                    gdcm.PixelFormat.UINT16 :numpy.uint16,
                    gdcm.PixelFormat.INT16  :numpy.int16,
                    gdcm.PixelFormat.UINT32 :numpy.uint32,
                    gdcm.PixelFormat.INT32  :numpy.int32,
                    #gdcm.PixelFormat.FLOAT16:numpy.float16,
                    gdcm.PixelFormat.FLOAT32:numpy.float32,
                    gdcm.PixelFormat.FLOAT64:numpy.float64 }
        return _gdcm_np

    def get_numpy_array_type(gdcm_pixel_format):
        """Returns a numpy array typecode given a GDCM Pixel Format."""
        return get_gdcm_to_numpy_typemap()[gdcm_pixel_format]

    def gdcm_to_numpy(image):
        """Converts a GDCM image to a numpy array.
        """
        pf = image.GetPixelFormat()

        assert pf.GetScalarType() in get_gdcm_to_numpy_typemap().keys(), \
               "Unsupported array type %s"%pf

        shape = image.GetDimension(0) * image.GetDimension(1), pf.GetSamplesPerPixel()
        if image.GetNumberOfDimensions() == 3:
          shape = shape[0] * image.GetDimension(2), shape[1]

        dtype = get_numpy_array_type(pf.GetScalarType())
        gdcm_array = image.GetBuffer()
        result = numpy.frombuffer(gdcm_array, dtype=dtype)
        result.shape = shape
        return result

    if __name__ == "__main__":
      import sys
      r = gdcm.ImageReader()
      filename = sys.argv[1]
      r.SetFileName( filename )
      if not r.Read():
        sys.exit(1)

      numpy_array = gdcm_to_numpy( r.GetImage() )
      print numpy_array