SimpleITK  1.3.0.dev466
ImageRegistrationMethodBSpline1/ImageRegistrationMethodBSpline1.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 
27 def command_iteration(method) :
28  print("{0:3} = {1:10.5f}".format(method.GetOptimizerIteration(),
29  method.GetMetricValue()))
30 
31 if len ( sys.argv ) < 4:
32  print( "Usage: {0} <fixedImageFilter> <movingImageFile> <outputTransformFile>".format(sys.argv[0]))
33  sys.exit ( 1 )
34 
35 
36 fixed = sitk.ReadImage(sys.argv[1], sitk.sitkFloat32)
37 
38 moving = sitk.ReadImage(sys.argv[2], sitk.sitkFloat32)
39 
40 transformDomainMeshSize=[8]*moving.GetDimension()
42  transformDomainMeshSize )
43 
44 print("Initial Parameters:");
45 print(tx.GetParameters())
46 
48 R.SetMetricAsCorrelation()
49 
50 R.SetOptimizerAsLBFGSB(gradientConvergenceTolerance=1e-5,
51  numberOfIterations=100,
52  maximumNumberOfCorrections=5,
53  maximumNumberOfFunctionEvaluations=1000,
54  costFunctionConvergenceFactor=1e+7)
55 R.SetInitialTransform(tx, True)
56 R.SetInterpolator(sitk.sitkLinear)
57 
58 R.AddCommand( sitk.sitkIterationEvent, lambda: command_iteration(R) )
59 
60 outTx = R.Execute(fixed, moving)
61 
62 print("-------")
63 print(outTx)
64 print("Optimizer stop condition: {0}".format(R.GetOptimizerStopConditionDescription()))
65 print(" Iteration: {0}".format(R.GetOptimizerIteration()))
66 print(" Metric value: {0}".format(R.GetMetricValue()))
67 
68 sitk.WriteTransform(outTx, sys.argv[3])
69 
70 if ( not "SITK_NOSHOW" in os.environ ):
71 
72  resampler = sitk.ResampleImageFilter()
73  resampler.SetReferenceImage(fixed);
74  resampler.SetInterpolator(sitk.sitkLinear)
75  resampler.SetDefaultPixelValue(100)
76  resampler.SetTransform(outTx)
77 
78  out = resampler.Execute(moving)
79  simg1 = sitk.Cast(sitk.RescaleIntensity(fixed), sitk.sitkUInt8)
80  simg2 = sitk.Cast(sitk.RescaleIntensity(out), sitk.sitkUInt8)
81  cimg = sitk.Compose(simg1, simg2, simg1//2.+simg2//2.)
82  sitk.Show( cimg, "ImageRegistration1 Composition" )