SimpleITK  
ImageRegistrationMethod4/ImageRegistrationMethod4.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""" A SimpleITK example demonstrating image registration using Mattes mutual
21 information as the metric. """
22
23import sys
24import os
25import SimpleITK as sitk
26
27
28def command_iteration(method):
29 """ Callback invoked when the optimization has an iteration. """
30 print(
31 f"{method.GetOptimizerIteration():3} "
32 + f"= {method.GetMetricValue():10.5f} "
33 + f": {method.GetOptimizerPosition()}"
34 )
35
36
37def main(args):
38 """ A SimpleITK example demonstrating image registration using Mattes mutual
39 information as the metric. """
40
41 if len(args) < 3:
42 print(
43 "Usage:",
44 "ImageRegistrationMethod4",
45 "<fixedImageFilter> <movingImageFile>",
46 "<outputTransformFile> <numberOfBins> <samplingPercentage>",
47 )
48 sys.exit(1)
49
50 fixed = sitk.ReadImage(args[1], sitk.sitkFloat32)
51 moving = sitk.ReadImage(args[2], sitk.sitkFloat32)
52
53 numberOfBins = 24
54 samplingPercentage = 0.10
55
56 if len(args) > 4:
57 numberOfBins = int(args[4])
58 if len(args) > 5:
59 samplingPercentage = float(args[5])
60
62 R.SetMetricAsMattesMutualInformation(numberOfBins)
63 R.SetMetricSamplingPercentage(samplingPercentage, sitk.sitkWallClock)
64 R.SetMetricSamplingStrategy(R.RANDOM)
65 R.SetOptimizerAsRegularStepGradientDescent(1.0, 0.001, 200)
66 R.SetInitialTransform(sitk.TranslationTransform(fixed.GetDimension()))
67 R.SetInterpolator(sitk.sitkLinear)
68
69 R.AddCommand(sitk.sitkIterationEvent, lambda: command_iteration(R))
70
71 outTx = R.Execute(fixed, moving)
72
73 print("-------")
74 print(outTx)
75 print(f"Optimizer stop condition: {R.GetOptimizerStopConditionDescription()}")
76 print(f" Iteration: {R.GetOptimizerIteration()}")
77 print(f" Metric value: {R.GetMetricValue()}")
78
79 sitk.WriteTransform(outTx, args[3])
80
81 resampler = sitk.ResampleImageFilter()
82 resampler.SetReferenceImage(fixed)
83 resampler.SetInterpolator(sitk.sitkLinear)
84 resampler.SetDefaultPixelValue(100)
85 resampler.SetTransform(outTx)
86
87 out = resampler.Execute(moving)
88 simg1 = sitk.Cast(sitk.RescaleIntensity(fixed), sitk.sitkUInt8)
89 simg2 = sitk.Cast(sitk.RescaleIntensity(out), sitk.sitkUInt8)
90 cimg = sitk.Compose(simg1, simg2, simg1 // 2.0 + simg2 // 2.0)
91
92 return {"fixed": fixed, "moving": moving, "composition": cimg}
93
94
95if __name__ == "__main__":
96 return_dict = main(sys.argv)
97 if "SITK_NOSHOW" not in os.environ:
98 sitk.Show(return_dict["composition"], "ImageRegistration4 Composition")
An interface method to the modular ITKv4 registration framework.
Resample an image via a coordinate transform.
Translation of a 2D or 3D coordinate space.
SITKIO_EXPORT Image ReadImage(const PathType &filename, PixelIDValueEnum outputPixelType=sitkUnknown, const std::string &imageIO="")
ReadImage is a procedural interface to the ImageFileReader class which is convenient for most image r...
Image Compose(const std::vector< Image > &images)
ComposeImageFilter combine several scalar images into a multicomponent image.
void SITKIO_EXPORT Show(const Image &image, const std::string &title="", const bool debugOn=ProcessObject::GetGlobalDefaultDebug())
SITKCommon_EXPORT void WriteTransform(const Transform &transform, const PathType &filename)
Image RescaleIntensity(Image &&image1, double outputMinimum=0, double outputMaximum=255)
Applies a linear transformation to the intensity levels of the input Image .
Image Cast(const Image &image, PixelIDValueEnum pixelID)