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#include "antsUtilities.h"
#include <algorithm>
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkMatrixOffsetTransformBase.h"
#include "itkWarpImageMultiTransformFilter.h"
#include "itkGridImageSource.h"
namespace ants
{
template <unsigned int ImageDimension>
int
CreateWarpedGridImage(int argc, char * argv[])
{
using RealType = float;
using RealImageType = 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();
using GridSourceType = itk::GridImageSource<RealImageType>;
typename GridSourceType::Pointer gridder = GridSourceType::New();
gridder->SetSpacing(reader->GetOutput()->GetSpacing());
gridder->SetOrigin(reader->GetOutput()->GetOrigin());
gridder->SetSize(reader->GetOutput()->GetLargestPossibleRegion().GetSize());
using ArrayType = typename GridSourceType::ArrayType;
using BoolArrayType = typename GridSourceType::BoolArrayType;
ArrayType gridSpacing;
ArrayType gridSigma;
BoolArrayType which;
which.Fill(false);
for (itk::SizeValueType i = 0; i < 2; i++)
{
which[i] = true;
}
if (argc > 4)
{
std::vector<unsigned int> directions = ConvertVector<unsigned int>(std::string(argv[4]));
if (directions.size() != ImageDimension)
{
std::cout << "Incorrect direction size." << std::endl;
return EXIT_FAILURE;
}
else
{
for (itk::SizeValueType i = 0; i < ImageDimension; i++)
{
which[i] = static_cast<bool>(directions[i]);
}
}
}
for (itk::SizeValueType i = 0; i < ImageDimension; i++)
{
gridSpacing[i] =
static_cast<typename ArrayType::ValueType>(reader->GetOutput()->GetLargestPossibleRegion().GetSize()[i]) *
static_cast<typename ArrayType::ValueType>(reader->GetOutput()->GetSpacing()[i]) /
static_cast<typename ArrayType::ValueType>(25.0);
gridSigma[i] = gridSpacing[i] / static_cast<typename ArrayType::ValueType>(10.0);
}
if (argc > 5)
{
std::vector<RealType> spacing = ConvertVector<RealType>(std::string(argv[5]));
if (spacing.size() != ImageDimension)
{
std::cout << "Incorrect spacing size." << std::endl;
return EXIT_FAILURE;
}
else
{
for (itk::SizeValueType i = 0; i < ImageDimension; i++)
{
gridSpacing[i] = spacing[i];
gridSigma[i] = gridSpacing[i] / 10.0;
}
}
}
if (argc > 6)
{
std::vector<typename ArrayType::ValueType> sigma =
ConvertVector<typename ArrayType::ValueType>(std::string(argv[6]));
if (sigma.size() != ImageDimension)
{
std::cout << "Incorrect sigma size." << std::endl;
return EXIT_FAILURE;
}
else
{
for (itk::SizeValueType i = 0; i < ImageDimension; i++)
{
gridSigma[i] = sigma[i] / static_cast<typename ArrayType::ValueType>(10.0);
}
}
}
gridder->SetGridSpacing(gridSpacing);
gridder->SetSigma(gridSigma);
gridder->SetWhichDimensions(which);
gridder->Update();
typename RealImageType::Pointer grid = gridder->GetOutput();
grid->SetDirection(reader->GetOutput()->GetDirection());
grid->SetOrigin(reader->GetOutput()->GetOrigin());
grid->SetSpacing(reader->GetOutput()->GetSpacing());
using TransformType = itk::MatrixOffsetTransformBase<double, ImageDimension, ImageDimension>;
using WarperType = itk::WarpImageMultiTransformFilter<RealImageType, RealImageType, VectorImageType, TransformType>;
typename WarperType::Pointer warper = WarperType::New();
warper->SetInput(grid);
warper->SetEdgePaddingValue(0);
warper->SetSmoothScale(1);
warper->PushBackDisplacementFieldTransform(reader->GetOutput());
warper->SetOutputParametersFromImage(reader->GetOutput());
warper->Update();
std::string file = std::string(argv[3]);
using ImageWriterType = itk::ImageFileWriter<RealImageType>;
typename ImageWriterType::Pointer gridWriter = ImageWriterType::New();
gridWriter->SetFileName(file.c_str());
gridWriter->SetInput(warper->GetOutput());
gridWriter->Update();
return EXIT_SUCCESS;
}
// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int
CreateWarpedGridImage(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(), "CreateWarpedGridImage");
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::cout << "Usage: " << argv[0] << " ImageDimension deformationField "
<< "outputImage [directions, e.g. 1x0x0] [gridSpacing, e.g. 10x10x10] [gridSigma, e.g. 1x1x1]"
<< 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;
}
switch (std::stoi(argv[1]))
{
case 2:
{
return CreateWarpedGridImage<2>(argc, argv);
}
break;
case 3:
{
return CreateWarpedGridImage<3>(argc, argv);
}
break;
default:
std::cout << "Unsupported dimension" << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
} // namespace ants
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