ITK  5.2.0
Insight Toolkit
Examples/RegistrationITKv4/LandmarkWarping2.cxx
/*=========================================================================
*
* Copyright NumFOCUS
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
// Software Guide : BeginLatex
//
// This example illustrates how to deform an image using a KernelBase spline
// and two sets of landmarks.
//
// \index{WarpImageFilter}
// \index{LandmarkDisplacementFieldSource}
//
// In addition to standard headers included in previous examples, this
// example requires the following includes:
//
// Software Guide : EndLatex
#include "itkImage.h"
// Software Guide : BeginCodeSnippet
#include "itkVector.h"
#include <fstream>
// Software Guide : EndCodeSnippet
int
main(int argc, char * argv[])
{
if (argc < 3)
{
std::cerr << "Missing Parameters " << std::endl;
std::cerr << "Usage: " << argv[0];
std::cerr << " landmarksFile fixedImage ";
std::cerr << "movingImage deformedMovingImage" << std::endl;
return EXIT_FAILURE;
}
constexpr unsigned int Dimension = 2;
using VectorComponentType = float;
using DisplacementFieldType = itk::Image<VectorType, Dimension>;
using PixelType = unsigned char;
using FixedImageType = itk::Image<PixelType, Dimension>;
using MovingImageType = itk::Image<PixelType, Dimension>;
using FixedReaderType = itk::ImageFileReader<FixedImageType>;
using MovingReaderType = itk::ImageFileReader<MovingImageType>;
using MovingWriterType = itk::ImageFileWriter<MovingImageType>;
FixedReaderType::Pointer fixedReader = FixedReaderType::New();
fixedReader->SetFileName(argv[2]);
try
{
fixedReader->Update();
}
catch (const itk::ExceptionObject & excp)
{
std::cerr << "Exception thrown " << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
MovingReaderType::Pointer movingReader = MovingReaderType::New();
MovingWriterType::Pointer movingWriter = MovingWriterType::New();
movingReader->SetFileName(argv[3]);
movingWriter->SetFileName(argv[4]);
FixedImageType::ConstPointer fixedImage = fixedReader->GetOutput();
// Software Guide : BeginLatex
//
// After reading in the fixed and moving images, the \code{deformer} object
// is instantiated from the \code{itk::LandmarkDisplacementFieldSource}
// class, and parameters of the image space and orientation are set.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using DisplacementSourceType =
DisplacementSourceType::Pointer deformer = DisplacementSourceType::New();
deformer->SetOutputSpacing(fixedImage->GetSpacing());
deformer->SetOutputOrigin(fixedImage->GetOrigin());
deformer->SetOutputRegion(fixedImage->GetLargestPossibleRegion());
deformer->SetOutputDirection(fixedImage->GetDirection());
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Source and target landmarks are then created, and the points themselves
// are read in from a file stream.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using LandmarkContainerType = DisplacementSourceType::LandmarkContainer;
using LandmarkPointType = DisplacementSourceType::LandmarkPointType;
LandmarkContainerType::Pointer sourceLandmarks =
LandmarkContainerType::New();
LandmarkContainerType::Pointer targetLandmarks =
LandmarkContainerType::New();
LandmarkPointType sourcePoint;
LandmarkPointType targetPoint;
std::ifstream pointsFile;
pointsFile.open(argv[1]);
unsigned int pointId = 0;
pointsFile >> sourcePoint;
pointsFile >> targetPoint;
while (!pointsFile.fail())
{
sourceLandmarks->InsertElement(pointId, sourcePoint);
targetLandmarks->InsertElement(pointId, targetPoint);
++pointId;
pointsFile >> sourcePoint;
pointsFile >> targetPoint;
}
pointsFile.close();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The source and target landmark objects are then assigned to
// \code{deformer}.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
deformer->SetSourceLandmarks(sourceLandmarks);
deformer->SetTargetLandmarks(targetLandmarks);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// After calling \code{UpdateLargestPossibleRegion()} on the
// \code{deformer}, the displacement field may be obtained via the
// \code{GetOutput()} method.
//
// Software Guide : EndLatex
try
{
deformer->UpdateLargestPossibleRegion();
}
catch (const itk::ExceptionObject & excp)
{
std::cerr << "Exception thrown " << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
DisplacementFieldType::Pointer displacementField = deformer->GetOutput();
using InterpolatorPrecisionType = double;
using TransformPrecisionType = float;
using FilterType = itk::ResampleImageFilter<MovingImageType,
MovingImageType,
InterpolatorPrecisionType,
TransformPrecisionType>;
FilterType::Pointer warper = FilterType::New();
using InterpolatorType =
InterpolatorPrecisionType>;
InterpolatorType::Pointer interpolator = InterpolatorType::New();
warper->SetInterpolator(interpolator);
using DisplacementFieldTransformType =
auto displacementTransform = DisplacementFieldTransformType::New();
displacementTransform->SetDisplacementField(displacementField);
warper->SetTransform(displacementTransform);
warper->SetOutputSpacing(displacementField->GetSpacing());
warper->SetOutputOrigin(displacementField->GetOrigin());
warper->SetOutputDirection(displacementField->GetDirection());
warper->SetSize(displacementField->GetLargestPossibleRegion().GetSize());
warper->SetInput(movingReader->GetOutput());
movingWriter->SetInput(warper->GetOutput());
try
{
movingWriter->Update();
}
catch (const itk::ExceptionObject & excp)
{
std::cerr << "Exception thrown " << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
itkDisplacementFieldTransform.h
itk::GTest::TypedefsAndConstructors::Dimension2::VectorType
ImageBaseType::SpacingType VectorType
Definition: itkGTestTypedefsAndConstructors.h:53
itk::Vector
A templated class holding a n-Dimensional vector.
Definition: itkVector.h:62
itkImageFileReader.h
itkImage.h
itk::DisplacementFieldTransform
Provides local/dense/high-dimensionality transformation via a a displacement field.
Definition: itkDisplacementFieldTransform.h:86
itk::ImageFileReader
Data source that reads image data from a single file.
Definition: itkImageFileReader.h:75
itk::LinearInterpolateImageFunction
Linearly interpolate an image at specified positions.
Definition: itkLinearInterpolateImageFunction.h:50
itk::ImageFileWriter
Writes image data to a single file.
Definition: itkImageFileWriter.h:87
itkImageFileWriter.h
itkVector.h
itk::ResampleImageFilter
Resample an image via a coordinate transform.
Definition: itkResampleImageFilter.h:90
itk::Image
Templated n-dimensional image class.
Definition: itkImage.h:86
itkResampleImageFilter.h
itkLandmarkDisplacementFieldSource.h
itk::GTest::TypedefsAndConstructors::Dimension2::Dimension
constexpr unsigned int Dimension
Definition: itkGTestTypedefsAndConstructors.h:44
itk::LandmarkDisplacementFieldSource
Computes a displacement field from two sets of landmarks.
Definition: itkLandmarkDisplacementFieldSource.h:49