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#include "antsUtilities.h"
#include "ReadWriteData.h"
#include "itkExtractImageFilter.h"
#include "itkPasteImageFilter.h"
namespace ants
{
template <unsigned int ImageDimension>
int
ExtractSliceFromImage(int argc, char * argv[])
{
using PixelType = float;
using ImageType = itk::Image<PixelType, ImageDimension>;
using SliceType = itk::Image<PixelType, ImageDimension - 1>;
typename ImageType::Pointer inputImage;
ReadImage<ImageType>(inputImage, argv[2]);
bool keepInputDim = false;
if (argc == 7)
{
std::istringstream(argv[6]) >> keepInputDim;
}
if (!keepInputDim)
{
typename ImageType::RegionType region;
typename ImageType::RegionType::SizeType size = inputImage->GetLargestPossibleRegion().GetSize();
size[atoi(argv[4])] = 0;
typename ImageType::IndexType index;
index.Fill(0);
index[atoi(argv[4])] = std::stoi(argv[5]);
region.SetIndex(index);
region.SetSize(size);
using ExtracterType = itk::ExtractImageFilter<ImageType, SliceType>;
typename ExtracterType::Pointer extracter = ExtracterType::New();
extracter->SetInput(inputImage);
extracter->SetExtractionRegion(region);
if (ImageDimension < 4)
{
extracter->SetDirectionCollapseToIdentity();
}
else
{
extracter->SetDirectionCollapseToSubmatrix();
}
extracter->Update();
ANTs::WriteImage<SliceType>(extracter->GetOutput(), argv[3]);
}
else
{
// extract the slice by setting the selected dimension to 1.
typename ImageType::RegionType region;
typename ImageType::RegionType::SizeType size = inputImage->GetLargestPossibleRegion().GetSize();
size[atoi(argv[4])] = 1; // set size to 1 in selected direction
typename ImageType::IndexType index;
index.Fill(0);
index[atoi(argv[4])] = std::stoi(argv[5]);
region.SetIndex(index);
region.SetSize(size);
using ExtracterType = itk::ExtractImageFilter<ImageType, ImageType>;
typename ExtracterType::Pointer extracter = ExtracterType::New();
extracter->SetInput(inputImage);
extracter->SetExtractionRegion(region);
if (ImageDimension < 4)
{
extracter->SetDirectionCollapseToIdentity();
}
else
{
extracter->SetDirectionCollapseToSubmatrix();
}
extracter->Update();
// Create a blank image from the input image
typename ImageType::Pointer outImage = ImageType::New();
outImage->CopyInformation(inputImage);
outImage->SetRegions(inputImage->GetLargestPossibleRegion());
outImage->AllocateInitialized();
// paste image slice to higher dimensionl image
using PasteFilterType = itk::PasteImageFilter<ImageType>;
typename PasteFilterType::Pointer pasteFilter = PasteFilterType::New();
pasteFilter->SetSourceImage(extracter->GetOutput());
pasteFilter->SetDestinationImage(outImage);
pasteFilter->SetDestinationIndex(index);
pasteFilter->SetSourceRegion(extracter->GetOutput()->GetBufferedRegion());
pasteFilter->Update();
ANTs::WriteImage<ImageType>(pasteFilter->GetOutput(), 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
ExtractSliceFromImage(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(), "ExtractSliceFromImage");
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 < 6)
{
std::cout << "Usage: " << argv[0]
<< " imageDimension inputImage outputSlice direction(e.g. 0, 1, 2) slice_number "
"[KeepSliceInOriginalSpace (0 or 1)]"
<< 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 ExtractSliceFromImage<2>(argc, argv);
}
break;
case 3:
{
return ExtractSliceFromImage<3>(argc, argv);
}
break;
case 4:
{
return ExtractSliceFromImage<4>(argc, argv);
}
break;
default:
std::cout << "Unsupported dimension" << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
} // namespace ants
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