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#include "antsUtilities.h"
#include <algorithm>
#include "ReadWriteData.h"
#include "itkDeformationFieldGradientTensorImageFilter.h"
#include "itkDeterminantTensorImageFilter.h"
#include "itkGeometricJacobianDeterminantImageFilter.h"
#include "itkLogImageFilter.h"
#include "itkMaximumImageFilter.h"
namespace ants
{
template <unsigned int ImageDimension>
int
CreateJacobianDeterminantImage(int argc, char * argv[])
{
using RealType = double;
using ImageType = itk::Image<RealType, ImageDimension>;
using VectorType = itk::Vector<RealType, ImageDimension>;
using VectorImageType = itk::Image<VectorType, ImageDimension>;
/**
* Read in vector field
*/
using ReaderType = itk::ImageFileReader<VectorImageType>;
typename ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(argv[2]);
reader->Update();
typename ImageType::Pointer jacobian = nullptr;
typename ImageType::Pointer minimumConstantImage = ImageType::New();
minimumConstantImage->CopyInformation(reader->GetOutput());
minimumConstantImage->SetRegions(reader->GetOutput()->GetRequestedRegion());
minimumConstantImage->Allocate();
minimumConstantImage->FillBuffer(0.001);
bool calculateLogJacobian = false;
if (argc > 4)
{
calculateLogJacobian = static_cast<bool>(std::stoi(argv[4]));
}
bool calculateGeometricJacobian = false;
if (argc > 5)
{
calculateGeometricJacobian = static_cast<bool>(std::stoi(argv[5]));
}
bool returnDeformationGradient = false;
if (argc > 6)
{
returnDeformationGradient = static_cast<bool>(std::stoi(argv[6]));
}
if (calculateGeometricJacobian)
{
using JacobianFilterType = itk::GeometricJacobianDeterminantImageFilter<VectorImageType, RealType, ImageType>;
typename JacobianFilterType::Pointer jacobianFilter = JacobianFilterType::New();
jacobianFilter->SetInput(reader->GetOutput());
jacobian = jacobianFilter->GetOutput();
jacobian->Update();
jacobian->DisconnectPipeline();
}
else
{
using JacobianFilterType = itk::DeformationFieldGradientTensorImageFilter<VectorImageType, RealType>;
typename JacobianFilterType::Pointer jacobianFilter = JacobianFilterType::New();
jacobianFilter->SetInput(reader->GetOutput());
jacobianFilter->SetCalculateJacobian(true);
jacobianFilter->SetUseImageSpacing(true);
jacobianFilter->SetOrder(2);
jacobianFilter->SetUseCenteredDifference(true);
if ( returnDeformationGradient ) {
jacobianFilter->Update();
ANTs::WriteImage<typename JacobianFilterType::OutputImageType>(jacobianFilter->GetOutput(), argv[3]);
return EXIT_SUCCESS;
}
using DeterminantFilterType =
itk::DeterminantTensorImageFilter<typename JacobianFilterType::OutputImageType, RealType>;
typename DeterminantFilterType::Pointer determinantFilter = DeterminantFilterType::New();
determinantFilter->SetInput(jacobianFilter->GetOutput());
determinantFilter->Update();
minimumConstantImage->FillBuffer(0.0);
using MaxFilterType = itk::MaximumImageFilter<ImageType, ImageType, ImageType>;
typename MaxFilterType::Pointer maxFilter = MaxFilterType::New();
maxFilter->SetInput1(determinantFilter->GetOutput());
maxFilter->SetInput2(minimumConstantImage);
jacobian = maxFilter->GetOutput();
jacobian->Update();
jacobian->DisconnectPipeline();
}
if (calculateLogJacobian)
{
minimumConstantImage->FillBuffer(0.001);
using MaxFilterType = itk::MaximumImageFilter<ImageType, ImageType, ImageType>;
typename MaxFilterType::Pointer maxFilter = MaxFilterType::New();
maxFilter->SetInput1(jacobian);
maxFilter->SetInput2(minimumConstantImage);
using LogFilterType = itk::LogImageFilter<ImageType, ImageType>;
typename LogFilterType::Pointer logFilter = LogFilterType::New();
logFilter->SetInput(maxFilter->GetOutput());
logFilter->Update();
ANTs::WriteImage<ImageType>(logFilter->GetOutput(), argv[3]);
}
else
{
ANTs::WriteImage<ImageType>(jacobian, argv[3]);
}
return EXIT_SUCCESS;
}
// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int
CreateJacobianDeterminantImage(std::vector<std::string> args, std::ostream * itkNotUsed(out_stream))
{
// put the arguments coming in as 'args' into standard (argc,argv) format;
// 'args' doesn't have the command name as first, argument, so add it manually;
// 'args' may have adjacent arguments concatenated into one argument,
// which the parser should handle
args.insert(args.begin(), "CreateJacobianDeterminantImage");
int argc = args.size();
char ** argv = new char *[args.size() + 1];
for (unsigned int i = 0; i < args.size(); ++i)
{
// allocate space for the string plus a null character
argv[i] = new char[args[i].length() + 1];
std::strncpy(argv[i], args[i].c_str(), args[i].length());
// place the null character in the end
argv[i][args[i].length()] = '\0';
}
argv[argc] = nullptr;
// class to automatically cleanup argv upon destruction
class Cleanup_argv
{
public:
Cleanup_argv(char ** argv_, int argc_plus_one_)
: argv(argv_)
, argc_plus_one(argc_plus_one_)
{}
~Cleanup_argv()
{
for (unsigned int i = 0; i < argc_plus_one; ++i)
{
delete[] argv[i];
}
delete[] argv;
}
private:
char ** argv;
unsigned int argc_plus_one;
};
Cleanup_argv cleanup_argv(argv, argc + 1);
// antscout->set_stream( out_stream );
if (argc < 3)
{
std::cout << "Usage: " << argv[0]
<< " imageDimension deformationField outputImage [doLogJacobian=0] [useGeometric=0] [deformationGradient=0]" << std::endl;
std::cout << "deformationGradient cannot be written to nifti: try mhd or nrrd." << std::endl;
return EXIT_FAILURE;
}
switch (std::stoi(argv[1]))
{
case 2:
{
return CreateJacobianDeterminantImage<2>(argc, argv);
}
break;
case 3:
{
return CreateJacobianDeterminantImage<3>(argc, argv);
}
break;
default:
std::cout << "Unsupported dimension" << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
} // namespace ants
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