GDCM  2.4.5
ConvertMPL.py
1 ############################################################################
2 #
3 # Program: GDCM (Grassroots DICOM). A DICOM library
4 #
5 # Copyright (c) 2006-2011 Mathieu Malaterre
6 # All rights reserved.
7 # See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
8 #
9 # This software is distributed WITHOUT ANY WARRANTY; without even
10 # the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
11 # PURPOSE. See the above copyright notice for more information.
12 #
13 ############################################################################
14 
15 """
16 display a DICOM image with matPlotLib via numpy
17 
18 Caveats:
19 - Does not support UINT12/INT12
20 
21 Usage:
22 
23  python ConvertNumpy.py "IM000000"
24 
25 Thanks:
26  plotting example - Ray Schumacher 2009
27 """
28 
29 import gdcm
30 import numpy
31 from pylab import *
32 
33 
34 def get_gdcm_to_numpy_typemap():
35  """Returns the GDCM Pixel Format to numpy array type mapping."""
36  _gdcm_np = {gdcm.PixelFormat.UINT8 :numpy.int8,
37  gdcm.PixelFormat.INT8 :numpy.uint8,
38  gdcm.PixelFormat.UINT16 :numpy.uint16,
39  gdcm.PixelFormat.INT16 :numpy.int16,
40  gdcm.PixelFormat.UINT32 :numpy.uint32,
41  gdcm.PixelFormat.INT32 :numpy.int32,
42  gdcm.PixelFormat.FLOAT32:numpy.float32,
43  gdcm.PixelFormat.FLOAT64:numpy.float64 }
44  return _gdcm_np
45 
46 def get_numpy_array_type(gdcm_pixel_format):
47  """Returns a numpy array typecode given a GDCM Pixel Format."""
48  return get_gdcm_to_numpy_typemap()[gdcm_pixel_format]
49 
50 def gdcm_to_numpy(image):
51  """Converts a GDCM image to a numpy array.
52  """
53  pf = image.GetPixelFormat().GetScalarType()
54  print 'pf', pf
55  print image.GetPixelFormat().GetScalarTypeAsString()
56  assert pf in get_gdcm_to_numpy_typemap().keys(), \
57  "Unsupported array type %s"%pf
58  d = image.GetDimension(0), image.GetDimension(1)
59  print 'Image Size: %d x %d' % (d[0], d[1])
60  dtype = get_numpy_array_type(pf)
61  gdcm_array = image.GetBuffer()
62  ## use float for accurate scaling
63  result = numpy.frombuffer(gdcm_array, dtype=dtype).astype(float)
64  ## optional gamma scaling
65  #maxV = float(result[result.argmax()])
66  #result = result + .5*(maxV-result)
67  #result = numpy.log(result+50) ## apprx background level
68  result.shape = d
69  return result
70 
71 if __name__ == "__main__":
72  import sys
73  r = gdcm.ImageReader()
74  filename = sys.argv[1]
75  r.SetFileName( filename )
76  if not r.Read(): sys.exit(1)
77  numpy_array = gdcm_to_numpy( r.GetImage() )
78 
79  subplot(111)# one plot, on left
80  title(filename)
81  ## many colormaps are available
82  imshow(numpy_array, interpolation='bilinear', cmap=cm.jet)
83  ## set the plot sizes and placement
84  subplots_adjust(bottom=0.1, right=0.8, top=0.9)
85  cax = axes([0.85, 0.1, 0.075, 0.8])
86  colorbar(cax=cax)
87  title('values')
88  get_current_fig_manager().window.title('plot')
89  show()

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