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/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: $RCSfile: DeformableRegistration10.cxx,v $
Language: C++
Date: $Date: 2009-11-21 21:23:25 $
Version: $Revision: 1.7 $
Copyright (c) Insight Software Consortium. All rights reserved.
See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
#include "itkConfigure.h"
#ifndef USE_FFTWD
#error "This program needs FFTWD to work."
#endif
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkCurvatureRegistrationFilter.h"
#include "itkFastSymmetricForcesDemonsRegistrationFunction.h"
#include "itkMultiResolutionPDEDeformableRegistration.h"
#include "itkHistogramMatchingImageFilter.h"
#include "itkCastImageFilter.h"
#include "itkWarpImageFilter.h"
#include "itkLinearInterpolateImageFunction.h"
#include "itkExceptionObject.h"
const unsigned int Dimension = 3;
// The following section of code implements a Command observer
// that will monitor the evolution of the registration process.
//
class CommandIterationUpdate : public itk::Command
{
public:
typedef CommandIterationUpdate Self;
typedef itk::Command Superclass;
typedef itk::SmartPointer<CommandIterationUpdate> Pointer;
itkNewMacro( CommandIterationUpdate );
protected:
CommandIterationUpdate() {};
typedef itk::Image< float, Dimension > InternalImageType;
typedef itk::Vector< float, Dimension > VectorPixelType;
typedef itk::Image< VectorPixelType, Dimension > DeformationFieldType;
typedef itk::CurvatureRegistrationFilter<
InternalImageType,
InternalImageType,
DeformationFieldType,
itk::FastSymmetricForcesDemonsRegistrationFunction<InternalImageType,InternalImageType,DeformationFieldType> > RegistrationFilterType;
public:
void Execute(itk::Object *caller, const itk::EventObject & event)
{
Execute( (const itk::Object *)caller, event);
}
void Execute(const itk::Object * object, const itk::EventObject & event)
{
const RegistrationFilterType * filter =
dynamic_cast< const RegistrationFilterType * >( object );
if( !(itk::IterationEvent().CheckEvent( &event )) )
{
return;
}
std::cout << filter->GetMetric() << std::endl;
}
};
int main( int argc, char *argv[] )
{
if( argc < 4 )
{
std::cerr << "Missing Parameters " << std::endl;
std::cerr << "Usage: " << argv[0];
std::cerr << " fixedImageFile movingImageFile ";
std::cerr << " outputImageFile " << std::endl;
return EXIT_FAILURE;
}
typedef short PixelType;
typedef itk::Image< PixelType, Dimension > FixedImageType;
typedef itk::Image< PixelType, Dimension > MovingImageType;
typedef itk::Image< float, Dimension > JacobianImageType;
typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType;
typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType;
FixedImageReaderType::Pointer fixedImageReader =
FixedImageReaderType::New();
MovingImageReaderType::Pointer movingImageReader =
MovingImageReaderType::New();
fixedImageReader->SetFileName( argv[1] );
movingImageReader->SetFileName( argv[2] );
typedef float InternalPixelType;
typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
typedef itk::CastImageFilter< FixedImageType,
InternalImageType > FixedImageCasterType;
typedef itk::CastImageFilter< MovingImageType,
InternalImageType > MovingImageCasterType;
FixedImageCasterType::Pointer fixedImageCaster =
FixedImageCasterType::New();
MovingImageCasterType::Pointer movingImageCaster =
MovingImageCasterType::New();
fixedImageCaster->SetInput( fixedImageReader->GetOutput() );
movingImageCaster->SetInput( movingImageReader->GetOutput() );
typedef itk::HistogramMatchingImageFilter<
InternalImageType,
InternalImageType > MatchingFilterType;
MatchingFilterType::Pointer matcher = MatchingFilterType::New();
matcher->SetInput( movingImageCaster->GetOutput() );
matcher->SetReferenceImage( fixedImageCaster->GetOutput() );
matcher->SetNumberOfHistogramLevels( 1024 );
matcher->SetNumberOfMatchPoints( 7 );
matcher->ThresholdAtMeanIntensityOn();
typedef itk::Vector< float, Dimension > VectorPixelType;
typedef itk::Image< VectorPixelType, Dimension > DeformationFieldType;
typedef itk::CurvatureRegistrationFilter<
InternalImageType,
InternalImageType,
DeformationFieldType,
itk::FastSymmetricForcesDemonsRegistrationFunction<InternalImageType,InternalImageType,DeformationFieldType> > RegistrationFilterType;
RegistrationFilterType::Pointer filter = RegistrationFilterType::New();
filter->SetTimeStep( 1 );
filter->SetConstraintWeight( 0.1 );
CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
filter->AddObserver( itk::IterationEvent(), observer );
typedef itk::MultiResolutionPDEDeformableRegistration<
InternalImageType,
InternalImageType,
DeformationFieldType > MultiResRegistrationFilterType;
MultiResRegistrationFilterType::Pointer multires = MultiResRegistrationFilterType::New();
multires->SetRegistrationFilter( filter );
multires->SetNumberOfLevels( 3 );
multires->SetFixedImage( fixedImageCaster->GetOutput() );
multires->SetMovingImage( matcher->GetOutput() );
unsigned int nIterations[4] = { 10, 20, 50, 50 };
multires->SetNumberOfIterations( nIterations );
multires->Update();
typedef itk::WarpImageFilter<
MovingImageType,
MovingImageType,
DeformationFieldType > WarperType;
typedef itk::LinearInterpolateImageFunction<
MovingImageType,
double > InterpolatorType;
WarperType::Pointer warper = WarperType::New();
InterpolatorType::Pointer interpolator = InterpolatorType::New();
FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();
warper->SetInput( movingImageReader->GetOutput() );
warper->SetInterpolator( interpolator );
warper->SetOutputSpacing( fixedImage->GetSpacing() );
warper->SetOutputOrigin( fixedImage->GetOrigin() );
warper->SetOutputDirection( fixedImage->GetDirection() );
warper->SetDeformationField( multires->GetOutput() );
// Write warped image out to file
typedef unsigned short OutputPixelType;
typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
typedef itk::CastImageFilter<
MovingImageType,
OutputImageType > CastFilterType;
typedef itk::ImageFileWriter< OutputImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
CastFilterType::Pointer caster = CastFilterType::New();
writer->SetFileName( argv[3] );
caster->SetInput( warper->GetOutput() );
writer->SetInput( caster->GetOutput() );
writer->Update();
if( argc > 4 ) // if a fourth line argument has been provided...
{
typedef itk::ImageFileWriter< DeformationFieldType > FieldWriterType;
FieldWriterType::Pointer fieldWriter = FieldWriterType::New();
fieldWriter->SetFileName( argv[4] );
fieldWriter->SetInput( multires->GetOutput() );
try
{
fieldWriter->Update();
}
catch ( itk::ExceptionObject e )
{
e.Print( std::cerr );
}
}
return EXIT_SUCCESS;
}
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