# ConvertMPL.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.
    #
    ############################################################################

    """
    display a DICOM image with matPlotLib via numpy

    Caveats:
    - Does not support UINT12/INT12

    Usage:

     python ConvertNumpy.py "IM000000"

    Thanks:
      plotting example - Ray Schumacher 2009
    """

    import gdcm
    import numpy
    from pylab import *

    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()
        ## use float for accurate scaling
        result = numpy.frombuffer(gdcm_array, dtype=dtype).astype(float)
        ## optional gamma scaling
        #maxV = float(result[result.argmax()])
        #result = result + .5*(maxV-result)
        #result = numpy.log(result+50) ## apprx background level
        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() )

      subplot(111)# one plot, on left
      title(filename)
      ## many colormaps are available
      imshow(numpy_array, interpolation='bilinear', cmap=cm.jet)
      ## set the plot sizes and placement
      subplots_adjust(bottom=0.1, right=0.8, top=0.9)
      cax = axes([0.85, 0.1, 0.075, 0.8])
      colorbar(cax=cax)
      title('values')
      get_current_fig_manager().window.title('plot')
      show()