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#include "itkConstNeighborhoodIterator.h"
#include "itkDecomposeTensorFunction.h"
#include "itkImageRegionIteratorWithIndex.h"
//#include "itkVectorFieldGradientImageFunction.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkNeighborhoodAlgorithm.h"
#include "itkTimeProbe.h"
#include "itkVariableSizeMatrix.h"
#include "itkVectorImageFileReader.h"
#include "itkVector.h"
#include "itkZeroFluxNeumannBoundaryCondition.h"
#include "itkANTSImageRegistrationOptimizer.h"
template <class TImage, class TDeformationField>
typename TDeformationField::PixelType
TransformVector(TDeformationField* field, typename TImage::IndexType index )
{
enum { ImageDimension = TImage::ImageDimension };
typename TDeformationField::PixelType vec=field->GetPixel(index);
typename TDeformationField::PixelType newvec;
newvec.Fill(0);
for (unsigned int row=0; row<ImageDimension; row++)
for (unsigned int col=0; col<ImageDimension; col++)
newvec[row]+=vec[col]*field->GetDirection()[row][col];
return newvec;
}
template <unsigned int ImageDimension>
int CreateJacobianDeterminantImage( int argc, char *argv[] )
{
typedef float RealType;
typedef itk::Image<RealType, ImageDimension> ImageType;
typedef itk::Vector<RealType, ImageDimension> VectorType;
typedef itk::Image<VectorType, ImageDimension> VectorImageType;
/**
* Read in vector field
*/
typedef itk::VectorImageFileReader<ImageType, VectorImageType> ReaderType;
typename ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName( argv[2] );
reader->SetUseAvantsNamingConvention( true );
reader->Update();
typename VectorImageType::Pointer vecimg=reader->GetOutput();
/** smooth before finite differencing */
typedef itk::ANTSImageRegistrationOptimizer<ImageDimension, float> RegistrationOptimizerType;
typedef typename RegistrationOptimizerType::Pointer RegistrationOptimizerPointer;
RegistrationOptimizerPointer reg=RegistrationOptimizerType::New();
reg->SmoothDeformationFieldGauss(vecimg,3);
typename VectorImageType::SpacingType spacing
= vecimg->GetSpacing();
typename ImageType::Pointer jacobian = ImageType::New();
jacobian->SetOrigin( vecimg->GetOrigin() );
jacobian->SetSpacing( vecimg->GetSpacing() );
jacobian->SetRegions( vecimg->GetLargestPossibleRegion() );
jacobian->SetDirection( vecimg->GetDirection());
jacobian->Allocate();
itk::TimeProbe timer;
timer.Start();
bool calculateLogJacobian = false;
if ( argc > 4 )
{
calculateLogJacobian = static_cast<bool>( atoi( argv[4] ) );
}
typedef itk::ConstNeighborhoodIterator<VectorImageType>
ConstNeighborhoodIteratorType;
typename ConstNeighborhoodIteratorType::RadiusType radius;
radius.Fill( 2 );
itk::ZeroFluxNeumannBoundaryCondition<VectorImageType> nbc;
ConstNeighborhoodIteratorType bit;
itk::ImageRegionIterator<ImageType> It;
// Find the data-set boundary "faces"
typename itk::NeighborhoodAlgorithm
::ImageBoundaryFacesCalculator<VectorImageType>::FaceListType faceList;
typename itk::NeighborhoodAlgorithm
::ImageBoundaryFacesCalculator<VectorImageType> bC;
faceList = bC( vecimg,
vecimg->GetLargestPossibleRegion(), radius );
typedef itk::VariableSizeMatrix<RealType> MatrixType;
typedef itk::DecomposeTensorFunction<MatrixType, RealType> DecomposerType;
typename DecomposerType::Pointer decomposer = DecomposerType::New();
typename itk::NeighborhoodAlgorithm::ImageBoundaryFacesCalculator
<VectorImageType>::FaceListType::iterator fit;
for ( fit = faceList.begin(); fit != faceList.end(); ++fit )
{
bit = ConstNeighborhoodIteratorType( radius, vecimg, *fit );
bit.OverrideBoundaryCondition( &nbc );
bit.GoToBegin();
It = itk::ImageRegionIterator<ImageType>( jacobian, *fit );
It.GoToBegin();
while ( !bit.IsAtEnd() )
{
MatrixType J;
J.SetSize( ImageDimension, ImageDimension );
for( unsigned int i = 0; i < ImageDimension; i++ )
{
for( unsigned int j = 0; j < ImageDimension; j++ )
{
RealType x = bit.GetCenterPixel()[j];
RealType xp1 = bit.GetNext( i )[j];
RealType xp2 = bit.GetNext( i, 2 )[j];
RealType xm1 = bit.GetPrevious( i )[j];
RealType xm2 = bit.GetPrevious( i, 2 )[j];
RealType h = 0.5;
xp1 = xp1*h + x*(1.0-h);
xm1 = xm1*h + x*(1.0-h);
xp2 = xp2*h + xp1*(1.0-h);
xp2 = xm2*h + xm1*(1.0-h);
J[i][j] = ( -xp2 + 8.0*xp1 - 8.0*xm1 + xm2 ) / ( 12.0*spacing[i] );
}
J[i][i] += 1.0;
}
try
{
RealType jacDet = decomposer->EvaluateDeterminant( J );
if (jacDet < 1.e-4 && calculateLogJacobian ) jacDet=1.e-4;
if (vnl_math_isnan(jacDet)) jacDet=1;
It.Set( ( calculateLogJacobian ? vcl_log( jacDet ) : jacDet ) );
}
catch(...)
{
It.Set( itk::NumericTraits<RealType>::max() );
}
++bit;
++It;
}
}
timer.Stop();
// std::cout << "Elapsed time: " << timer.GetMeanTime() << std::endl;
typedef itk::ImageFileWriter<ImageType> RealImageWriterType;
typename RealImageWriterType::Pointer realwriter = RealImageWriterType::New();
realwriter->SetFileName( argv[3] );
realwriter->SetInput( jacobian );
realwriter->Update();
return 0;
}
int main( int argc, char *argv[] )
{
if ( argc < 3 )
{
std::cout << "Usage: " << argv[0] << " ImageDimension deformationField outputImage log-jac?(default-false)" << std::endl;
exit( 1 );
}
switch( atoi( argv[1] ) )
{
case 2:
CreateJacobianDeterminantImage<2>( argc, argv );
break;
case 3:
CreateJacobianDeterminantImage<3>( argc, argv );
break;
default:
std::cerr << "Unsupported dimension" << std::endl;
exit( EXIT_FAILURE );
}
}
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