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DeformableRegistration1.cxx
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DeformableRegistration1.cxx
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/*=========================================================================
*
* 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.
*
*=========================================================================*/
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkHistogramMatchingImageFilter.h"
// Software Guide : BeginLatex
//
// The finite element (FEM) library within the Insight Toolkit can be
// used to solve deformable image registration problems. The first step in
// implementing a FEM-based registration is to include the appropriate
// header files.
//
// \index{Registration!Finite Element-Based}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
#include "itkFEMRegistrationFilter.h"
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Next, we use \code{typedef}s to instantiate all necessary classes. We
// define the image and element types we plan to use to solve a
// two-dimensional registration problem. We define multiple element
// types so that they can be used without recompiling the code.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
typedef itk::Image<unsigned char, 2> DiskImageType;
typedef itk::Image<float, 2> ImageType;
typedef itk::fem::Element2DC0LinearQuadrilateralMembrane ElementType;
typedef itk::fem::Element2DC0LinearTriangularMembrane ElementType2;
typedef itk::fem::FEMObject<2> FEMObjectType;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Note that in order to solve a three-dimensional registration
// problem, we would simply define 3D image and element types in lieu
// of those above. The following declarations could be used for a 3D
// problem:
//
// SoftwareGuide : EndLatex
// SoftwareGuide : BeginCodeSnippet
typedef itk::Image<unsigned char, 3> FileImage3DType;
typedef itk::Image<float, 3> Image3DType;
typedef itk::fem::Element3DC0LinearHexahedronMembrane Element3DType;
typedef itk::fem::Element3DC0LinearTetrahedronMembrane Element3DType2;
typedef itk::fem::FEMObject<3> FEMObject3DType;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Once all the necessary components have been instantiated, we can
// instantiate the \doxygen{FEMRegistrationFilter}, which depends on the
// image input and output types.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
typedef itk::fem::FEMRegistrationFilter<ImageType,ImageType,FEMObjectType>
RegistrationType;
// Software Guide : EndCodeSnippet
int main(int argc, char *argv[])
{
const char *fixedImageName, *movingImageName;
if ( argc < 2 )
{
std::cout << "Image file names missing" << std::endl;
std::cout << "Usage: " << argv[0] << " fixedImageFile movingImageFile"
<< std::endl;
return EXIT_FAILURE;
}
else
{
fixedImageName = argv[1];
movingImageName = argv[2];
}
// Software Guide : BeginLatex
//
// In order to begin the registration, we declare an instance of the
// \code{FEMRegistrationFilter} and set its parameters. For simplicity, we will call
// it \code{registrationFilter}.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
RegistrationType::Pointer registrationFilter = RegistrationType::New();
registrationFilter->SetMaxLevel(1);
registrationFilter->SetUseNormalizedGradient( true );
registrationFilter->ChooseMetric( 0 );
unsigned int maxiters = 20;
float E = 100;
float p = 1;
registrationFilter->SetElasticity(E, 0);
registrationFilter->SetRho(p, 0);
registrationFilter->SetGamma(1., 0);
registrationFilter->SetAlpha(1.);
registrationFilter->SetMaximumIterations( maxiters, 0 );
registrationFilter->SetMeshPixelsPerElementAtEachResolution(4, 0);
registrationFilter->SetWidthOfMetricRegion(1, 0);
registrationFilter->SetNumberOfIntegrationPoints(2, 0);
registrationFilter->SetDoLineSearchOnImageEnergy( 0 );
registrationFilter->SetTimeStep(1.);
registrationFilter->SetEmployRegridding(false);
registrationFilter->SetUseLandmarks(false);
// Software Guide : EndCodeSnippet
// Read the image files
typedef itk::ImageFileReader< DiskImageType > FileSourceType;
FileSourceType::Pointer movingfilter = FileSourceType::New();
movingfilter->SetFileName( movingImageName );
FileSourceType::Pointer fixedfilter = FileSourceType::New();
fixedfilter->SetFileName( fixedImageName );
std::cout << " reading moving " << movingImageName << std::endl;
std::cout << " reading fixed " << fixedImageName << std::endl;
try
{
movingfilter->Update();
}
catch( itk::ExceptionObject & e )
{
std::cerr << "Exception caught during reference file reading " << std::endl;
std::cerr << e << std::endl;
return EXIT_FAILURE;
}
try
{
fixedfilter->Update();
}
catch( itk::ExceptionObject & e )
{
std::cerr << "Exception caught during target file reading " << std::endl;
std::cerr << e << std::endl;
return EXIT_FAILURE;
}
// Rescale the image intensities so that they fall between 0 and 255
typedef itk::RescaleIntensityImageFilter<DiskImageType,ImageType> FilterType;
FilterType::Pointer movingrescalefilter = FilterType::New();
FilterType::Pointer fixedrescalefilter = FilterType::New();
movingrescalefilter->SetInput(movingfilter->GetOutput());
fixedrescalefilter->SetInput(fixedfilter->GetOutput());
const double desiredMinimum = 0.0;
const double desiredMaximum = 255.0;
movingrescalefilter->SetOutputMinimum( desiredMinimum );
movingrescalefilter->SetOutputMaximum( desiredMaximum );
movingrescalefilter->UpdateLargestPossibleRegion();
fixedrescalefilter->SetOutputMinimum( desiredMinimum );
fixedrescalefilter->SetOutputMaximum( desiredMaximum );
fixedrescalefilter->UpdateLargestPossibleRegion();
// Histogram match the images
typedef itk::HistogramMatchingImageFilter<ImageType,ImageType> HEFilterType;
HEFilterType::Pointer IntensityEqualizeFilter = HEFilterType::New();
IntensityEqualizeFilter->SetReferenceImage( fixedrescalefilter->GetOutput() );
IntensityEqualizeFilter->SetInput( movingrescalefilter->GetOutput() );
IntensityEqualizeFilter->SetNumberOfHistogramLevels( 100);
IntensityEqualizeFilter->SetNumberOfMatchPoints( 15);
IntensityEqualizeFilter->ThresholdAtMeanIntensityOn();
IntensityEqualizeFilter->Update();
// Set the images for registration filter
registrationFilter->SetFixedImage(fixedrescalefilter->GetOutput());
registrationFilter->SetMovingImage(IntensityEqualizeFilter->GetOutput());
itk::ImageFileWriter<ImageType>::Pointer writer;
writer = itk::ImageFileWriter<ImageType>::New();
std::string ofn="fixed.mha";
writer->SetFileName(ofn.c_str());
writer->SetInput(registrationFilter->GetFixedImage() );
try
{
writer->Write();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
ofn="moving.mha";
itk::ImageFileWriter<ImageType>::Pointer writer2;
writer2 = itk::ImageFileWriter<ImageType>::New();
writer2->SetFileName(ofn.c_str());
writer2->SetInput(registrationFilter->GetMovingImage() );
try
{
writer2->Write();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// In order to initialize the mesh of elements, we must first create
// ``dummy'' material and element objects and assign them to the
// registration filter. These objects are subsequently used to
// either read a predefined mesh from a file or generate a mesh using
// the software. The values assigned to the fields within the
// material object are arbitrary since they will be replaced with
// those specified earlier. Similarly, the element
// object will be replaced with those from the desired mesh.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Create the material properties
itk::fem::MaterialLinearElasticity::Pointer m;
m = itk::fem::MaterialLinearElasticity::New();
m->SetGlobalNumber(0);
// Young's modulus of the membrane
m->SetYoungsModulus(registrationFilter->GetElasticity());
m->SetCrossSectionalArea(1.0); // Cross-sectional area
m->SetThickness(1.0); // Thickness
m->SetMomentOfInertia(1.0); // Moment of inertia
m->SetPoissonsRatio(0.); // Poisson's ratio -- DONT CHOOSE 1.0!!
m->SetDensityHeatProduct(1.0); // Density-Heat capacity product
// Create the element type
ElementType::Pointer e1=ElementType::New();
e1->SetMaterial(m.GetPointer());
registrationFilter->SetElement(e1.GetPointer());
registrationFilter->SetMaterial(m);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Now we are ready to run the registration:
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
registrationFilter->RunRegistration();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// To output the image resulting from the registration, we can call
// \code{GetWarpedImage()}. The image is written in floating point
// format.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
itk::ImageFileWriter<ImageType>::Pointer warpedImageWriter;
warpedImageWriter = itk::ImageFileWriter<ImageType>::New();
warpedImageWriter->SetInput( registrationFilter->GetWarpedImage() );
warpedImageWriter->SetFileName("warpedMovingImage.mha");
try
{
warpedImageWriter->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We can also output the displacement field resulting from the
// registration; we can call \code{GetDisplacementField()} to get the
// multi-component image.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
typedef itk::ImageFileWriter<RegistrationType::FieldType> DispWriterType;
DispWriterType::Pointer dispWriter = DispWriterType::New();
dispWriter->SetInput( registrationFilter->GetDisplacementField() );
dispWriter->SetFileName("displacement.mha");
try
{
dispWriter->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
// Software Guide : EndCodeSnippet
return EXIT_SUCCESS;
}