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19import itk
20from sys import argv
21
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27
28if len(argv) < 4:
29 print("Missing Parameters")
30 print(
31 "Usage: ImageRegistration5.py fixedImageFile movingImageFile outputImagefile"
32 )
33 exit()
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53
54fixedImageReader.SetFileName(argv[1])
55movingImageReader.SetFileName(argv[2])
56
57fixedImageReader.Update()
58movingImageReader.Update()
59
60fixedImage = fixedImageReader.GetOutput()
61movingImage = movingImageReader.GetOutput()
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65
66
67registration = RegistrationType.New()
68imageMetric = MetricType.New()
69transform = TransformType.New()
70optimizer = OptimizerType.New()
71
72registration.SetOptimizer(optimizer)
73registration.SetMetric(imageMetric)
74
75registration.SetFixedImage(fixedImage)
76registration.SetMovingImage(movingImage)
77
78
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80
81
82transform.SetAngle(0.0)
83
84
85fixedSpacing = fixedImage.GetSpacing()
86fixedOrigin = fixedImage.GetOrigin()
87fixedSize = fixedImage.GetLargestPossibleRegion().GetSize()
88
89centerFixed = (
90 fixedOrigin.GetElement(0)
91 + fixedSpacing.GetElement(0) * fixedSize.GetElement(0) / 2.0,
92 fixedOrigin.GetElement(1)
93 + fixedSpacing.GetElement(1) * fixedSize.GetElement(1) / 2.0,
94)
95
96
97movingSpacing = movingImage.GetSpacing()
98movingOrigin = movingImage.GetOrigin()
99movingSize = movingImage.GetLargestPossibleRegion().GetSize()
100
101centerMoving = (
102 movingOrigin.GetElement(0)
103 + movingSpacing.GetElement(0) * movingSize.GetElement(0) / 2.0,
104 movingOrigin.GetElement(1)
105 + movingSpacing.GetElement(1) * movingSize.GetElement(1) / 2.0,
106)
107
108
109center = transform.GetCenter()
110center.SetElement(0, centerFixed[0])
111center.SetElement(1, centerFixed[1])
112
113
114translation = transform.GetTranslation()
115translation.SetElement(0, centerMoving[0] - centerFixed[0])
116translation.SetElement(1, centerMoving[1] - centerFixed[1])
117
118registration.SetInitialTransform(transform)
119
120initialParameters = transform.GetParameters()
121
122print("Initial Parameters: ")
123print(f"Angle: {initialParameters.GetElement(0):f}")
124print(
125 f"Center: {initialParameters.GetElement(1):f}, {initialParameters.GetElement(2):f}"
126)
127print(
128 "Translation: %f, %f"
129 % (initialParameters.GetElement(3), initialParameters.GetElement(4))
130)
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138translationScale = 1.0 / 1000.0
139
141optimizerScales.SetElement(0, 1.0)
142optimizerScales.SetElement(1, translationScale)
143optimizerScales.SetElement(2, translationScale)
144optimizerScales.SetElement(3, translationScale)
145optimizerScales.SetElement(4, translationScale)
146
147optimizer.SetScales(optimizerScales)
148
149optimizer.SetRelaxationFactor(0.6)
150optimizer.SetLearningRate(0.1)
151optimizer.SetMinimumStepLength(0.001)
152optimizer.SetNumberOfIterations(200)
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157
158registration.SetNumberOfLevels(1)
159registration.SetSmoothingSigmasPerLevel([0])
160registration.SetShrinkFactorsPerLevel([1])
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164
165
166def iterationUpdate():
167 currentParameter = transform.GetParameters()
168 print(
169 "M: %f P: %f %f %f %f %f "
170 % (
171 optimizer.GetValue(),
172 currentParameter.GetElement(0),
173 currentParameter.GetElement(1),
174 currentParameter.GetElement(2),
175 currentParameter.GetElement(3),
176 currentParameter.GetElement(4),
177 )
178 )
179
180
181iterationCommand = itk.PyCommand.New()
182iterationCommand.SetCommandCallable(iterationUpdate)
183optimizer.AddObserver(itk.IterationEvent(), iterationCommand)
184
185print("Starting registration")
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191registration.Update()
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197finalParameters = registration.GetOutput().Get().GetParameters()
198
199print("Final Registration Parameters ")
200print(f"Angle in radians = {finalParameters.GetElement(0):f}")
201print(f"Rotation Center X = {finalParameters.GetElement(1):f}")
202print(f"Rotation Center Y = {finalParameters.GetElement(2):f}")
203print(f"Translation in X = {finalParameters.GetElement(3):f}")
204print(f"Translation in Y = {finalParameters.GetElement(4):f}")
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210
212resampler.SetTransform(registration.GetTransform())
213resampler.SetInput(movingImageReader.GetOutput())
214
215region = fixedImage.GetLargestPossibleRegion()
216
217resampler.SetSize(region.GetSize())
218resampler.SetOutputOrigin(fixedImage.GetOrigin())
219resampler.SetOutputSpacing(fixedImage.GetSpacing())
220resampler.SetOutputDirection(fixedImage.GetDirection())
221resampler.SetDefaultPixelValue(100)
222
225outputCast.SetInput(resampler.GetOutput())
226
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229
230
232writer.SetFileName(argv[3])
233writer.SetInput(outputCast.GetOutput())
234writer.Update()
Casts input pixels to output pixel type.
Data source that reads image data from a single file.
Writes image data to a single file.
Interface method for the current registration framework.
Templated n-dimensional image class.
Class implementing a mean squares metric.
Class to hold and manage different parameter types used during optimization.
Regular Step Gradient descent optimizer.
Resample an image via a coordinate transform.