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#include "antsUtilities.h"
#include "antsAllocImage.h"
#include <algorithm>
#include "itkVectorIndexSelectionCastImageFilter.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "vnl/algo/vnl_determinant.h"
#include "itkANTSImageRegistrationOptimizer.h"
#include "itkTimeVaryingVelocityFieldIntegrationImageFilter.h"
#include "itkWarpImageFilter.h"
#include "itkTimeVaryingVelocityFieldTransform.h"
#include "itkImageFileWriter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "vnl/algo/vnl_determinant.h"
#include "itkDiscreteGaussianImageFilter.h"
#include "itkVectorLinearInterpolateImageFunction.h"
#include "itkGradientRecursiveGaussianImageFilter.h"
#include "itkVectorCurvatureAnisotropicDiffusionImageFilter.h"
#include "itkLaplacianRecursiveGaussianImageFilter.h"
#include "itkGradientRecursiveGaussianImageFilter.h"
#include "ReadWriteData.h"
namespace ants
{
template <unsigned int ImageDimension>
int
IntegrateVelocityField(int argc, char * argv[])
{
int argct = 1;
std::string imgfn = std::string(argv[argct]);
argct++;
std::string vectorfn = std::string(argv[argct]);
argct++;
std::string outname = std::string(argv[argct]);
argct++;
using PixelType = float;
PixelType timezero = 0;
PixelType timeone = 1;
PixelType dT = 0.01;
if (argc > argct)
{
timezero = atof(argv[argct]);
}
argct++;
if (argc > argct)
{
timeone = atof(argv[argct]);
}
argct++;
if (argc > argct)
{
dT = atof(argv[argct]);
}
argct++;
std::cout << " time-0 " << timezero << " dt " << dT << " time-1 " << timeone << std::endl;
PixelType starttime = timezero;
PixelType finishtime = timeone;
using PixelType = float;
using VectorType = itk::Vector<PixelType, ImageDimension>;
using DisplacementFieldType = itk::Image<VectorType, ImageDimension>;
using TimeVaryingVelocityFieldType = itk::Image<VectorType, ImageDimension + 1>;
using ImageType = itk::Image<PixelType, ImageDimension>;
typename ImageType::Pointer image;
ReadImage<ImageType>(image, imgfn.c_str());
using tvt = TimeVaryingVelocityFieldType;
typename tvt::Pointer timeVaryingVelocity;
ReadImage<tvt>(timeVaryingVelocity, vectorfn.c_str());
VectorType zero;
zero.Fill(0);
typename DisplacementFieldType::Pointer deformation = AllocImage<DisplacementFieldType>(image, zero);
if (!timeVaryingVelocity)
{
std::cerr << " No TV Field " << std::endl;
return EXIT_FAILURE;
}
if (starttime < 0)
{
starttime = 0;
}
if (starttime > 1)
{
starttime = 1;
}
if (finishtime < 0)
{
finishtime = 0;
}
if (finishtime > 1)
{
finishtime = 1;
}
using IntegratorType =
itk::TimeVaryingVelocityFieldIntegrationImageFilter<TimeVaryingVelocityFieldType, DisplacementFieldType>;
typename IntegratorType::Pointer integrator = IntegratorType::New();
integrator->SetInput(timeVaryingVelocity);
integrator->SetLowerTimeBound(starttime);
integrator->SetUpperTimeBound(finishtime);
integrator->SetNumberOfIntegrationSteps((unsigned int)1 / dT);
integrator->Update();
ANTs::WriteImage<DisplacementFieldType>(integrator->GetOutput(), outname.c_str());
return 0;
}
// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int
ANTSIntegrateVelocityField(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(), "ANTSIntegrateVelocityField");
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 < 4)
{
std::cerr << "Usage: " << argv[0] << " reference_image VelocityIn.mhd DeformationOut.nii.gz time0 time1 dT "
<< 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;
}
std::cout << " start " << std::endl;
std::string ifn = std::string(argv[1]);
itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(ifn.c_str(), itk::IOFileModeEnum::ReadMode);
imageIO->SetFileName(ifn.c_str());
imageIO->ReadImageInformation();
unsigned int dim = imageIO->GetNumberOfDimensions();
std::cout << " dim " << dim << std::endl;
switch (dim)
{
case 2:
{
IntegrateVelocityField<2>(argc, argv);
}
break;
case 3:
{
IntegrateVelocityField<3>(argc, argv);
}
break;
case 4:
{
IntegrateVelocityField<4>(argc, argv);
}
break;
default:
std::cerr << "Unsupported dimension" << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
} // namespace ants
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