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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"
#include "itkFEMRegistrationFilter.h"
/* Example of FEM-base deformable registration in 3D */
const unsigned int Dimension = 3;
typedef itk::Image<unsigned char, Dimension> FileImageType;
typedef itk::Image<float, Dimension> ImageType;
typedef itk::fem::Element3DC0LinearHexahedronMembrane ElementType;
typedef itk::fem::Element3DC0LinearTetrahedronMembrane ElementType2;
typedef itk::fem::FEMObject<Dimension> FEMObjectType;
typedef itk::fem::FEMRegistrationFilter<ImageType,ImageType,FEMObjectType> RegistrationType;
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];
}
// Setup registration parameters
RegistrationType::Pointer registrationFilter = RegistrationType::New();
registrationFilter->SetMaxLevel(1);
registrationFilter->SetUseNormalizedGradient( true );
registrationFilter->ChooseMetric( 0 );
unsigned int maxiters = 20;
float E = 10;
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->SetDescentDirectionMinimize();
registrationFilter->SetDoLineSearchOnImageEnergy( 0 );
registrationFilter->SetTimeStep(1.);
registrationFilter->SetEmployRegridding(false);
registrationFilter->SetUseLandmarks(false);
// Read the image files
typedef itk::ImageFileReader< FileImageType > FileSourceType;
FileSourceType::Pointer movingfilter = FileSourceType::New();
movingfilter->SetFileName( movingImageName );
FileSourceType::Pointer fixedfilter = FileSourceType::New();
fixedfilter->SetFileName( fixedImageName );
std::cout << " reading moving ";
std::cout << movingImageName << std::endl;
std::cout << " reading fixed ";
std::cout << fixedImageName << std::endl;
try
{
movingfilter->Update();
}
catch( itk::ExceptionObject & e )
{
std::cerr << "Exception caught during reference file reading ";
std::cerr << std::endl << e << std::endl;
return EXIT_FAILURE;
}
try
{
fixedfilter->Update();
}
catch( itk::ExceptionObject & e )
{
std::cerr << "Exception caught during target file reading ";
std::cerr << std::endl << e << std::endl;
return EXIT_FAILURE;
}
// Rescale the image intensities so that they fall between 0 and 255
typedef itk::RescaleIntensityImageFilter<
FileImageType, 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();
registrationFilter->SetFixedImage(fixedrescalefilter->GetOutput());
registrationFilter->SetMovingImage(IntensityEqualizeFilter->GetOutput());
itk::ImageFileWriter<ImageType>::Pointer writer;
writer = itk::ImageFileWriter<ImageType>::New();
writer->SetFileName("fixed.mhd");
writer->SetInput(registrationFilter->GetFixedImage() );
writer->Write();
itk::ImageFileWriter<ImageType>::Pointer writer2;
writer2 = itk::ImageFileWriter<ImageType>::New();
writer2->SetFileName("moving.mhd");
writer2->SetInput(registrationFilter->GetMovingImage() );
writer2->Write();
// Create the material properties
itk::fem::MaterialLinearElasticity::Pointer m;
m = itk::fem::MaterialLinearElasticity::New();
m->SetGlobalNumber(0);
m->SetYoungsModulus(registrationFilter->GetElasticity()); // Young's modulus used in the membrane
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);
// Run registration
registrationFilter->RunRegistration();
// Warp the moving image and write it to a file.
writer->SetFileName("warpedMovingImage.mhd");
writer->SetInput( registrationFilter->GetWarpedImage() );
try
{
writer->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
// output the displacement field
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;
}
return EXIT_SUCCESS;
}
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