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ENH: Add DeformAVolumeWithAThinPlateSpline
Adapted from: https://itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ThinPlateSplineWarp_8cxx-example.html However, we use itk mesh IO to read the point sets, and use the reference image interface to ResampleImageFilter. Both were added since that example was created.
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‎ITKRepositoryImport.todo

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* ../ITK/Examples/Registration/DeformationFieldJacobian.cxx
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* ../ITK/Examples/Registration/ImageRegistration5.tcl
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* ../ITK/Examples/Registration/ImageRegistration5.py
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* ../ITK/Examples/Registration/ThinPlateSplineWarp.cxx
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* ../ITK/Examples/Registration/ImageRegistration4.tcl
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* ../ITK/Examples/Registration/ImageRegistration16.cxx
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* ../ITK/Examples/Registration/ImageRegistration4.py

‎src/Core/Transform/CMakeLists.txt

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compare_to_baseline(EXAMPLE_NAME GlobalRegistrationTwoImagesBSpline
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BASELINE_PREFIX GlobalRegistrationTwoImagesBSpline
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)
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add_example(DeformAVolumeWithAThinPlateSpline)
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compare_to_baseline(EXAMPLE_NAME DeformAVolumeWithAThinPlateSpline
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BASELINE_PREFIX DeformedImageBaseline
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)

‎src/Core/Transform/DeformAVolumeWithAThinPlateSpline/CMakeLists.txt

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cmake_minimum_required(VERSION 3.16.3)
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project(DeformAVolumeWithAThinPlateSpline)
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find_package(ITK REQUIRED)
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include(${ITK_USE_FILE})
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add_executable(DeformAVolumeWithAThinPlateSpline Code.cxx)
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target_link_libraries(DeformAVolumeWithAThinPlateSpline ${ITK_LIBRARIES})
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install(TARGETS DeformAVolumeWithAThinPlateSpline
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DESTINATION bin/ITKSphinxExamples/Core/Transform
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COMPONENT Runtime
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)
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install(FILES Code.cxx CMakeLists.txt Code.py
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DESTINATION share/ITKSphinxExamples/Code/Core/Transform/DeformAVolumeWithAThinPlateSpline
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COMPONENT Code
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)
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enable_testing()
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set(source_landmarks ${CMAKE_CURRENT_BINARY_DIR}/SourceLandmarks.vtk)
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set(target_landmarks ${CMAKE_CURRENT_BINARY_DIR}/TargetLandmarks.vtk)
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set(input_image ${CMAKE_CURRENT_BINARY_DIR}/brainweb165a10f17.mha)
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set(deformed_image DeformedImage.mha)
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set(checkerboard_image CheckerBoardImage.mha)
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add_test(NAME DeformAVolumeWithAThinPlateSplineTest
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COMMAND ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/DeformAVolumeWithAThinPlateSpline
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${source_landmarks}
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${target_landmarks}
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${input_image}
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${deformed_image}
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${checkerboard_image}
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)
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if(ITK_WRAP_PYTHON)
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find_package(PythonInterp REQUIRED)
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string(REPLACE . "Python." deformed_image "${deformed_image}")
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add_test(NAME DeformAVolumeWithAThinPlateSplineTestPython
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COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/Code.py
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${source_landmarks}
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${target_landmarks}
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${input_image}
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${deformed_image}
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${checkerboard_image}
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)
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endif()

‎src/Core/Transform/DeformAVolumeWithAThinPlateSpline/CheckerBoard.png.cid

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‎src/Core/Transform/DeformAVolumeWithAThinPlateSpline/Code.cxx

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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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* https://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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#include "itkImageFileReader.h"
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#include "itkImageFileWriter.h"
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#include "itkImage.h"
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#include "itkResampleImageFilter.h"
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#include "itkThinPlateSplineKernelTransform.h"
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#include "itkPointSet.h"
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#include "itkMesh.h"
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#include "itkMeshFileReader.h"
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#include "itkCheckerBoardImageFilter.h"
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int
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main(int argc, char * argv[])
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{
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if (argc != 6)
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{
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std::cerr << "Usage: " << argv[0];
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std::cerr << " <SourceLandmarks>";
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std::cerr << " <TargetLandmarks>";
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std::cerr << " <InputImage>";
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std::cerr << " <DeformedImage>";
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std::cerr << " <CheckerBoardImage>";
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std::cerr << std::endl;
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return EXIT_FAILURE;
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}
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const char * sourceLandmarksFile = argv[1];
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const char * targetLandmarksFile = argv[2];
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const char * inputImageFile = argv[3];
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const char * deformedImageFile = argv[4];
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const char * checkerboardImageFile = argv[5];
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constexpr unsigned int Dimension = 3;
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using CoordinateRepType = double;
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using TransformType = itk::ThinPlateSplineKernelTransform<CoordinateRepType, Dimension>;
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using PointSetType = TransformType::PointSetType;
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using PixelType = unsigned char;
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using MeshType = itk::Mesh<PointSetType::PixelType, Dimension, PointSetType::MeshTraits>;
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using ImageType = itk::Image<PixelType, Dimension>;
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auto sourceLandmarks = PointSetType::New();
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auto targetLandmarks = PointSetType::New();
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ImageType::Pointer inputImage;
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try
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{
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auto sourceLandmarksMesh = itk::ReadMesh<MeshType>(sourceLandmarksFile);
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sourceLandmarks->SetPoints(sourceLandmarksMesh->GetPoints());
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auto targetLandmarksMesh = itk::ReadMesh<MeshType>(targetLandmarksFile);
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targetLandmarks->SetPoints(targetLandmarksMesh->GetPoints());
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inputImage = itk::ReadImage<ImageType>(inputImageFile);
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}
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catch (itk::ExceptionObject & error)
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{
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std::cerr << "Error: " << error << std::endl;
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return EXIT_FAILURE;
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}
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using TransformType = itk::ThinPlateSplineKernelTransform<CoordinateRepType, Dimension>;
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auto thinPlateSpline = TransformType::New();
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thinPlateSpline->SetSourceLandmarks(sourceLandmarks);
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thinPlateSpline->SetTargetLandmarks(targetLandmarks);
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thinPlateSpline->ComputeWMatrix();
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using ResamplerType = itk::ResampleImageFilter<ImageType, ImageType>;
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auto resampler = ResamplerType::New();
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resampler->SetInput(inputImage);
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using InterpolatorType = itk::LinearInterpolateImageFunction<ImageType, CoordinateRepType>;
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auto interpolator = InterpolatorType::New();
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resampler->SetInterpolator(interpolator);
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resampler->SetUseReferenceImage(true);
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resampler->SetReferenceImage(inputImage);
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resampler->SetTransform(thinPlateSpline);
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using CheckerBoardFilterType = itk::CheckerBoardImageFilter<ImageType>;
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auto checkerboardFilter = CheckerBoardFilterType::New();
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checkerboardFilter->SetInput1(inputImage);
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checkerboardFilter->SetInput2(resampler->GetOutput());
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try
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{
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resampler->Update();
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checkerboardFilter->Update();
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itk::WriteImage(resampler->GetOutput(), deformedImageFile);
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itk::WriteImage(checkerboardFilter->GetOutput(), checkerboardImageFile);
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}
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catch (itk::ExceptionObject & error)
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{
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std::cerr << "Error: " << error << std::endl;
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return EXIT_FAILURE;
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}
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return EXIT_SUCCESS;
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}

‎src/Core/Transform/DeformAVolumeWithAThinPlateSpline/Code.py

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#!/usr/bin/env python
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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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# https://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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import argparse
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import itk
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import numpy as np
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parser = argparse.ArgumentParser(
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description="Deform a Volume With a Thin Plate Spline."
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)
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parser.add_argument("source_landmarks")
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parser.add_argument("target_landmarks")
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parser.add_argument("input_image")
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parser.add_argument("deformed_image")
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parser.add_argument("checker_board_image")
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args = parser.parse_args()
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Dimension = 3
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thin_plate_spline = itk.ThinPlateSplineKernelTransform[itk.D, Dimension].New()
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source_landmarks_mesh = itk.meshread(args.source_landmarks)
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# Cast points from float32 to float64
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points = itk.array_from_vector_container(source_landmarks_mesh.GetPoints())
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points = points.astype(np.float64)
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source_landmarks = thin_plate_spline.GetSourceLandmarks()
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source_landmarks.SetPoints(itk.vector_container_from_array(points.flatten()))
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target_landmarks_mesh = itk.meshread(args.target_landmarks)
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# Cast points from float32 to float64
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points = itk.array_from_vector_container(target_landmarks_mesh.GetPoints())
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points = points.astype(np.float64)
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target_landmarks = thin_plate_spline.GetTargetLandmarks()
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target_landmarks.SetPoints(itk.vector_container_from_array(points.flatten()))
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thin_plate_spline.ComputeWMatrix()
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input_image = itk.imread(args.input_image)
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deformed_image = itk.resample_image_filter(
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input_image,
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use_reference_image=True,
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reference_image=input_image,
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transform=thin_plate_spline,
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)
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itk.imwrite(deformed_image, args.deformed_image)
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checker_board = itk.checker_board_image_filter(input_image, deformed_image)
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itk.imwrite(checker_board, args.checker_board_image)

‎src/Core/Transform/DeformAVolumeWithAThinPlateSpline/DeformedImage.png.cid

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‎src/Core/Transform/DeformAVolumeWithAThinPlateSpline/DeformedImageBaseline.mha.cid

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‎src/Core/Transform/DeformAVolumeWithAThinPlateSpline/Documentation.rst

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:name: DeformAVolumeWithAThinPlateSpline
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Deform a Volume With a Thin Plate Spline
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========================================
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.. index::
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single: ThinPlateSplineKernelTransform
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Synopsis
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--------
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This example deforms a 3D volume with the thin plate spline.
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Results
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-------
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.. figure:: InputImage.png
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:width: 640px
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:alt: Input image
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Input image
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.. figure:: DeformedImage.png
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:width: 640px
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:alt: Deformed image
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Deformed image
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.. figure:: CheckerBoard.png
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:width: 640px
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:alt: CheckerBoard image
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CheckerBoard image
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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: 1,16-
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C++
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...
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.. literalinclude:: Code.cxx
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:language: c++
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:lines: 18-
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Classes demonstrated
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--------------------
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.. breathelink:: itk::ThinPlateSplineKernelTransform

‎src/Core/Transform/DeformAVolumeWithAThinPlateSpline/InputImage.png.cid

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