ITK  5.0.0
Insight Segmentation and Registration Toolkit
Examples/RegistrationITKv4/LandmarkWarping2.cxx
/*=========================================================================
*
* Copyright Insight Software Consortium
*
* 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( 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( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown " << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
DisplacementFieldType::ConstPointer displacementField = deformer->GetOutput();
using FilterType = itk::WarpImageFilter< MovingImageType,
MovingImageType,
DisplacementFieldType >;
FilterType::Pointer warper = FilterType::New();
using InterpolatorType = itk::LinearInterpolateImageFunction<
MovingImageType, double >;
InterpolatorType::Pointer interpolator = InterpolatorType::New();
warper->SetInterpolator( interpolator );
warper->SetOutputSpacing( displacementField->GetSpacing() );
warper->SetOutputOrigin( displacementField->GetOrigin() );
warper->SetDisplacementField( displacementField );
warper->SetInput( movingReader->GetOutput() );
movingWriter->SetInput( warper->GetOutput() );
try
{
movingWriter->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown " << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}