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/*=========================================================================1
Program: Advanced Normalization Tools
Copyright (c) ConsortiumOfANTS. All rights reserved.
See accompanying COPYING.txt or
https://github.com/stnava/ANTs/blob/master/ANTSCopyright.txt 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 "antsUtilities.h"
#include "antsUtilities.h"
#include "ReadWriteData.h"
#include "itkantsReadWriteTransform.h"
#include "itkPreservationOfPrincipalDirectionTensorReorientationImageFilter.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkWarpTensorImageMultiTransformFilter.h"
#include "itkTransformFileReader.h"
#include "itkTransformFactory.h"
namespace ants
{
template <int ImageDimension>
void
ReorientTensorImage(char * moving_image_filename, char * output_image_filename, char * transform_filename)
{
if (ImageDimension != 3)
{
std::cout << "ReorientTensorImage only supports 3D image volumes" << std::endl;
return;
}
using RealType = double;
using TensorPixelType = itk::DiffusionTensor3D<RealType>;
using TensorImageType = itk::Image<TensorPixelType, ImageDimension>;
using ImageType = itk::Image<float, ImageDimension>;
using AffineTransformType = itk::MatrixOffsetTransformBase<double, ImageDimension, ImageDimension>;
itk::TransformFactory<AffineTransformType>::RegisterTransform();
using ImageFileReaderType = itk::ImageFileReader<ImageType>;
typename TensorImageType::Pointer img_mov;
// No reason to use log-euclidean space
ReadTensorImage<TensorImageType>(img_mov, moving_image_filename, false);
typename ImageType::Pointer img_ref = nullptr;
typename ImageFileReaderType::Pointer reader_img_ref = ImageFileReaderType::New();
using PPDReorientType =
itk::PreservationOfPrincipalDirectionTensorReorientationImageFilter<TensorImageType>;
typename PPDReorientType::Pointer reo = PPDReorientType::New();
reo->SetInput(img_mov);
using TransformType = itk::Transform<RealType, ImageDimension, ImageDimension>;
using CompositeTransformType = itk::CompositeTransform<RealType, ImageDimension>;
// Read the transform from the file
typename TransformType::Pointer transform = itk::ants::ReadTransform<RealType, ImageDimension>(transform_filename, false);
// Check if the transform is a composite transform
if (transform->GetNameOfClass() == "CompositeTransform")
{
typename CompositeTransformType::Pointer composite_transform =
dynamic_cast<CompositeTransformType *>(transform.GetPointer());
if (composite_transform)
{
reo->SetCompositeTransform(composite_transform);
}
else
{
std::cerr << "Error: Failed to cast to CompositeTransformType." << std::endl;
return;
}
}
else
{
// Create a new composite transform and add the individual transform we just read
typename CompositeTransformType::Pointer composite_transform = CompositeTransformType::New();
composite_transform->AddTransform(transform);
reo->SetCompositeTransform(composite_transform);
}
reo->Update();
typename TensorImageType::Pointer img_output = reo->GetOutput();
// No reason to use log-euclidean space here
WriteTensorImage<TensorImageType>(img_output, output_image_filename, false);
}
// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int
ReorientTensorImage(std::vector<std::string> args, std::ostream * /*out_stream = nullptr */)
{
// 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(), "ReorientTensorImage");
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 != 5)
{
std::cout << "Usage: " << argv[0] << " Dimension infile.nii outfile.nii <composite.h5/warp.nii.gz/affine.mat/affine.txt> "
<< std::endl
<< "antsApplyTransforms now applies reorientation automatically. If resampled your tensors into fixed space "
<< "with antsApplyTransforms -e 2, the reorientation is already done."
<< std::endl;
if (argc >= 2 && (std::string(argv[1]) == std::string("--help") || std::string(argv[1]) == std::string("-h")))
{
return EXIT_SUCCESS;
}
return EXIT_FAILURE;
}
char * moving_image_filename = nullptr;
char * output_image_filename = nullptr;
char * transform_filename = nullptr;
int dim = std::stoi(argv[1]);
moving_image_filename = argv[2];
output_image_filename = argv[3];
transform_filename = argv[4];
if (dim != 3)
{
std::cout << "ReorientTensorImage only supports 3D image volumes" << std::endl;
return EXIT_FAILURE;
}
ReorientTensorImage<3>(moving_image_filename, output_image_filename, transform_filename);
return EXIT_SUCCESS;
}
} // namespace ants
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