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thewtexthewtex
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Merge pull request #304 from thewtex/landmark-python
2 parents 9ab3696 + 5f34106 commit 035c21f

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4 files changed

+146
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‎src/Registration/Common/RegisterImageToAnotherUsingLandmarks/CMakeLists.txt

Lines changed: 7 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -14,11 +14,17 @@ install(TARGETS RegisterImageToAnotherUsingLandmarks
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COMPONENT Runtime
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)
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install(FILES Code.cxx CMakeLists.txt
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install(FILES Code.cxx CMakeLists.txt Code.py
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DESTINATION share/ITKSphinxExamples/Code/Registration/Common/RegisterImageToAnotherUsingLandmarks/
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COMPONENT Code
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)
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enable_testing()
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add_test(NAME RegisterImageToAnotherUsingLandmarksTest
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COMMAND ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/RegisterImageToAnotherUsingLandmarks)
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if(ITK_WRAP_PYTHON)
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add_test(NAME RegisterImageToAnotherUsingLandmarksTestPython
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COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/Code.py
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)
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endif()

‎src/Registration/Common/RegisterImageToAnotherUsingLandmarks/Code.cxx

Lines changed: 5 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -40,9 +40,9 @@ main(int itkNotUsed(argc), char * itkNotUsed(argv)[])
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ImageType::Pointer movingImage = ImageType::New();
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CreateMovingImage(movingImage);
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using Rigid2DTransformType = itk::Rigid2DTransform<double>;
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using TransformType = itk::Rigid2DTransform<double>;
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using LandmarkBasedTransformInitializerType =
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itk::LandmarkBasedTransformInitializer<Rigid2DTransformType, ImageType, ImageType>;
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itk::LandmarkBasedTransformInitializer<TransformType, ImageType, ImageType>;
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LandmarkBasedTransformInitializerType::Pointer landmarkBasedTransformInitializer =
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LandmarkBasedTransformInitializerType::New();
@@ -87,7 +87,7 @@ main(int itkNotUsed(argc), char * itkNotUsed(argv)[])
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landmarkBasedTransformInitializer->SetFixedLandmarks(fixedLandmarks);
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landmarkBasedTransformInitializer->SetMovingLandmarks(movingLandmarks);
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Rigid2DTransformType::Pointer transform = Rigid2DTransformType::New();
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TransformType::Pointer transform = TransformType::New();
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transform->SetIdentity();
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landmarkBasedTransformInitializer->SetTransform(transform);
@@ -97,12 +97,9 @@ main(int itkNotUsed(argc), char * itkNotUsed(argv)[])
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ResampleFilterType::Pointer resampleFilter = ResampleFilterType::New();
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resampleFilter->SetInput(movingImage);
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resampleFilter->SetTransform(transform);
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resampleFilter->SetSize(fixedImage->GetLargestPossibleRegion().GetSize());
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resampleFilter->SetOutputOrigin(fixedImage->GetOrigin());
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resampleFilter->SetOutputSpacing(fixedImage->GetSpacing());
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resampleFilter->SetOutputDirection(fixedImage->GetDirection());
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resampleFilter->SetUseReferenceImage(true);
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resampleFilter->SetReferenceImage(fixedImage);
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resampleFilter->SetDefaultPixelValue(200);
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resampleFilter->GetOutput();
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// Write the output
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using WriterType = itk::ImageFileWriter<ImageType>;

‎src/Registration/Common/RegisterImageToAnotherUsingLandmarks/Code.py

Lines changed: 127 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,127 @@
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#!/usr/bin/env python3
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# =========================================================================
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#
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# Copyright NumFOCUS
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0.txt
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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#
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# =========================================================================*/
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import itk
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Dimension = 2
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PixelType = itk.ctype("unsigned char")
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ImageType = itk.Image[PixelType, Dimension]
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def create_fixed_image():
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start = [
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0,
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] * Dimension
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size = [
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100,
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] * Dimension
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region = itk.ImageRegion[Dimension](start, size)
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ImageType = itk.Image[PixelType, Dimension]
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image = ImageType.New()
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image.SetRegions(region)
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image.Allocate()
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image.FillBuffer(0)
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image[11:20, 11:20] = 255
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itk.imwrite(image, "fixedPython.png")
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return image
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def create_moving_image():
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start = [
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0,
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] * Dimension
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size = [
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100,
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] * Dimension
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region = itk.ImageRegion[Dimension](start, size)
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ImageType = itk.Image[PixelType, Dimension]
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image = ImageType.New()
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image.SetRegions(region)
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image.Allocate()
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image.FillBuffer(0)
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image[51:60, 51:60] = 100
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itk.imwrite(image, "movingPython.png")
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return image
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fixed_image = create_fixed_image()
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moving_image = create_moving_image()
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77+
LandmarkPointType = itk.Point[itk.D, Dimension]
78+
LandmarkContainerType = itk.vector[LandmarkPointType]
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80+
fixed_landmarks = LandmarkContainerType()
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moving_landmarks = LandmarkContainerType()
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fixed_point = LandmarkPointType()
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moving_point = LandmarkPointType()
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86+
fixed_point[0] = 10
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fixed_point[1] = 10
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moving_point[0] = 50
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moving_point[1] = 50
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fixed_landmarks.push_back(fixed_point)
91+
moving_landmarks.push_back(moving_point)
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93+
fixed_point[0] = 20
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fixed_point[1] = 10
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moving_point[0] = 60
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moving_point[1] = 50
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fixed_landmarks.push_back(fixed_point)
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moving_landmarks.push_back(moving_point)
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100+
fixed_point[0] = 20
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fixed_point[1] = 20
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moving_point[0] = 60
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moving_point[1] = 60
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fixed_landmarks.push_back(fixed_point)
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moving_landmarks.push_back(moving_point)
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107+
TransformInitializerType = itk.LandmarkBasedTransformInitializer[
108+
itk.Transform[itk.D, Dimension, Dimension]
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]
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transform_initializer = TransformInitializerType.New()
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transform_initializer.SetFixedLandmarks(fixed_landmarks)
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transform_initializer.SetMovingLandmarks(moving_landmarks)
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transform = itk.Rigid2DTransform[itk.D].New()
116+
transform_initializer.SetTransform(transform)
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transform_initializer.InitializeTransform()
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119+
output = itk.resample_image_filter(
120+
moving_image,
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transform=transform,
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use_reference_image=True,
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reference_image=fixed_image,
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default_pixel_value=200,
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)
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itk.imwrite(output, "outputPython.png")

‎src/Registration/Common/RegisterImageToAnotherUsingLandmarks/Documentation.rst

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@@ -36,6 +36,13 @@ Results
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Code
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----
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Python
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......
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.. literalinclude:: Code.py
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:language: python
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:lines: 1, 20-
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C++
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...
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