# ConvertPIL.py

    ############################################################################
    #
    #  Program: GDCM (Grassroots DICOM). A DICOM library
    #  Module:  $URL$
    #
    #  Copyright (c) 2006-2010 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.
    #
    ############################################################################

    """
    save a DICOM image with PIL via numpy

    Caveats:
    - Does not support UINT12/INT12

    Usage:

     python ConvertNumpy.py "IM000000"

    Thanks:
      plotting example - Ray Schumacher 2009
    """

    import gdcm
    import numpy
    from PIL import Image, ImageOps

    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.UINT16 :numpy.uint16,
                    gdcm.PixelFormat.INT16  :numpy.int16,
                    gdcm.PixelFormat.UINT32 :numpy.uint32,
                    gdcm.PixelFormat.INT32  :numpy.int32,
                    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().GetScalarType()
        print 'pf', pf
        print image.GetPixelFormat().GetScalarTypeAsString()
        assert pf in get_gdcm_to_numpy_typemap().keys(), \
               "Unsupported array type %s"%pf
        d = image.GetDimension(0), image.GetDimension(1)
        print 'Image Size: %d x %d' % (d[0], d[1])
        dtype = get_numpy_array_type(pf)
        gdcm_array = image.GetBuffer()
        result = numpy.frombuffer(gdcm_array, dtype=dtype)
        maxV = float(result[result.argmax()])
        ## linear gamma adjust
        #result = result + .5*(maxV-result)
        ## log gamma
        result = numpy.log(result+50) ## 50 is apprx background level
        maxV = float(result[result.argmax()])
        result = result*(2.**8/maxV) ## histogram stretch
        result.shape = d
        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() )
      ## L is 8 bit grey
      ## http://www.pythonware.com/library/pil/handbook/concepts.htm
      pilImage = Image.frombuffer('L',
                               numpy_array.shape,
                               numpy_array.astype(numpy.uint8),
                               'raw','L',0,1)
      ## cutoff removes background noise and spikes
      pilImage = ImageOps.autocontrast(pilImage, cutoff=.1)
      pilImage.save(sys.argv[1]+'.jpg')