SimpleITK  
ImageRegistrationMethod1/ImageRegistrationMethod1.py
1 #!/usr/bin/env python
2 # =========================================================================
3 #
4 # Copyright NumFOCUS
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 import SimpleITK as sitk
21 import sys
22 import os
23 
24 
25 def command_iteration(method):
26  print(
27  f"{method.GetOptimizerIteration():3} "
28  + f"= {method.GetMetricValue():10.5f} "
29  + f": {method.GetOptimizerPosition()}"
30  )
31 
32 
33 def main(args):
34  if len(args) < 3:
35  print(
36  "Usage:",
37  "ImageRegistrationMethod1",
38  "<fixedImageFilter> <movingImageFile>",
39  "<outputTransformFile>",
40  )
41  sys.exit(1)
42 
43  fixed = sitk.ReadImage(args[1], sitk.sitkFloat32)
44 
45  moving = sitk.ReadImage(args[2], sitk.sitkFloat32)
46 
48  R.SetMetricAsMeanSquares()
49  R.SetOptimizerAsRegularStepGradientDescent(4.0, 0.01, 200)
50  R.SetInitialTransform(sitk.TranslationTransform(fixed.GetDimension()))
51  R.SetInterpolator(sitk.sitkLinear)
52 
53  R.AddCommand(sitk.sitkIterationEvent, lambda: command_iteration(R))
54 
55  outTx = R.Execute(fixed, moving)
56 
57  print("-------")
58  print(outTx)
59  print(f"Optimizer stop condition: {R.GetOptimizerStopConditionDescription()}")
60  print(f" Iteration: {R.GetOptimizerIteration()}")
61  print(f" Metric value: {R.GetMetricValue()}")
62 
63  sitk.WriteTransform(outTx, args[3])
64 
65  resampler = sitk.ResampleImageFilter()
66  resampler.SetReferenceImage(fixed)
67  resampler.SetInterpolator(sitk.sitkLinear)
68  resampler.SetDefaultPixelValue(100)
69  resampler.SetTransform(outTx)
70 
71  out = resampler.Execute(moving)
72  simg1 = sitk.Cast(sitk.RescaleIntensity(fixed), sitk.sitkUInt8)
73  simg2 = sitk.Cast(sitk.RescaleIntensity(out), sitk.sitkUInt8)
74  cimg = sitk.Compose(simg1, simg2, simg1 // 2.0 + simg2 // 2.0)
75 
76  return_images = {"fixed": fixed,
77  "moving": moving,
78  "composition": cimg}
79  return return_images
80 
81 
82 if __name__ == "__main__":
83  return_dict = main(sys.argv)
84  if "SITK_NOSHOW" not in os.environ:
85  sitk.Show(return_dict["composition"], "ImageRegistration1 Composition")
itk::simple::WriteTransform
SITKCommon_EXPORT void WriteTransform(const Transform &transform, const std::string &filename)
itk::simple::RescaleIntensity
Image RescaleIntensity(const Image &image1, double outputMinimum=0, double outputMaximum=255)
Applies a linear transformation to the intensity levels of the input Image .
itk::simple::Show
void SITKIO_EXPORT Show(const Image &image, const std::string &title="", const bool debugOn=ProcessObject::GetGlobalDefaultDebug())
itk::simple::ReadImage
SITKIO_EXPORT Image ReadImage(const std::vector< std::string > &fileNames, PixelIDValueEnum outputPixelType=sitkUnknown, const std::string &imageIO="")
ReadImage is a procedural interface to the ImageSeriesReader class which is convenient for most image...
itk::simple::TranslationTransform
Translation of a 2D or 3D coordinate space.
Definition: sitkTranslationTransform.h:33
itk::simple::Cast
Image Cast(const Image &image, PixelIDValueEnum pixelID)
itk::simple::ResampleImageFilter
Resample an image via a coordinate transform.
Definition: sitkResampleImageFilter.h:52
itk::simple::Compose
Image Compose(const Image &image1, const Image &image2, const Image &image3, const Image &image4, const Image &image5)
ComposeImageFilter combine several scalar images into a multicomponent image.
itk::simple::ImageRegistrationMethod
An interface method to the modular ITKv4 registration framework.
Definition: sitkImageRegistrationMethod.h:89