SimpleITK  1.3.0.dev466
N4BiasFieldCorrection/N4BiasFieldCorrection.py
1 #!/usr/bin/env python
2 #=========================================================================
3 #
4 # Copyright Insight Software Consortium
5 #
6 # Licensed under the Apache License, Version 2.0 (the "License");
7 # you may not use this file except in compliance with the License.
8 # You may obtain a copy of the License at
9 #
10 # http://www.apache.org/licenses/LICENSE-2.0.txt
11 #
12 # Unless required by applicable law or agreed to in writing, software
13 # distributed under the License is distributed on an "AS IS" BASIS,
14 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15 # See the License for the specific language governing permissions and
16 # limitations under the License.
17 #
18 #=========================================================================
19 
20 from __future__ import print_function
21 
22 import SimpleITK as sitk
23 import sys
24 import os
25 
26 if len ( sys.argv ) < 2:
27  print( "Usage: N4BiasFieldCorrection inputImage " + \
28  "outputImage [shrinkFactor] [maskImage] [numberOfIterations] " +\
29  "[numberOfFittingLevels]" )
30  sys.exit ( 1 )
31 
32 
33 inputImage = sitk.ReadImage( sys.argv[1] )
34 
35 if len ( sys.argv ) > 4:
36  maskImage = sitk.ReadImage( sys.argv[4], sitk.sitkUint8 )
37 else:
38  maskImage = sitk.OtsuThreshold( inputImage, 0, 1, 200 )
39 
40 if len ( sys.argv ) > 3:
41  inputImage = sitk.Shrink( inputImage, [ int(sys.argv[3]) ] * inputImage.GetDimension() )
42  maskImage = sitk.Shrink( maskImage, [ int(sys.argv[3]) ] * inputImage.GetDimension() )
43 
44 inputImage = sitk.Cast( inputImage, sitk.sitkFloat32 )
45 
47 
48 numberFittingLevels = 4
49 
50 if len ( sys.argv ) > 6:
51  numberFittingLevels = int( sys.argv[6] )
52 
53 if len ( sys.argv ) > 5:
54  corrector.SetMaximumNumberOfIterations( [ int( sys.argv[5] ) ] *numberFittingLevels )
55 
56 
57 output = corrector.Execute( inputImage, maskImage )
58 
59 sitk.WriteImage( output, sys.argv[2] )
60 
61 
62 if ( not "SITK_NOSHOW" in os.environ ):
63  sitk.Show( output, "N4 Corrected" )