GDCM  2.2.6
ConvertPIL.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 save a DICOM image with PIL 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 PIL import Image, ImageOps
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  result = numpy.frombuffer(gdcm_array, dtype=dtype)
63  maxV = float(result[result.argmax()])
64  ## linear gamma adjust
65  #result = result + .5*(maxV-result)
66  ## log gamma
67  result = numpy.log(result+50) ## 50 is apprx background level
68  maxV = float(result[result.argmax()])
69  result = result*(2.**8/maxV) ## histogram stretch
70  result.shape = d
71  return result
72 
73 if __name__ == "__main__":
74  import sys
75  r = gdcm.ImageReader()
76  filename = sys.argv[1]
77  r.SetFileName( filename )
78  if not r.Read(): sys.exit(1)
79  numpy_array = gdcm_to_numpy( r.GetImage() )
80  ## L is 8 bit grey
81  ## http://www.pythonware.com/library/pil/handbook/concepts.htm
82  pilImage = Image.frombuffer('L',
83  numpy_array.shape,
84  numpy_array.astype(numpy.uint8),
85  'raw','L',0,1)
86  ## cutoff removes background noise and spikes
87  pilImage = ImageOps.autocontrast(pilImage, cutoff=.1)
88  pilImage.save(sys.argv[1]+'.jpg')

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