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#include "antsUtilities.h"
#include <algorithm>
#include <cstdio>
#include "itkCastImageFilter.h"
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkExtractImageFilter.h"
#include "itkLabelStatisticsImageFilter.h"
#include <string>
#include <vector>
namespace ants
{
template <unsigned int ImageDimension>
int
ExtractRegionFromImageByMask(int argc, char * argv[])
{
using PixelType = float;
using ImageType = itk::Image<PixelType, ImageDimension>;
using ReaderType = itk::ImageFileReader<ImageType>;
typename ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(argv[2]);
reader->Update();
typename ImageType::RegionType region;
typename ImageType::RegionType::SizeType size;
typename ImageType::RegionType::IndexType index;
if (false)
{
std::vector<int> minIndex;
std::vector<int> maxIndex;
minIndex = ConvertVector<int>(std::string(argv[4]));
maxIndex = ConvertVector<int>(std::string(argv[5]));
for (unsigned int i = 0; i < ImageDimension; i++)
{
index[i] = minIndex[i];
size[i] = maxIndex[i] - minIndex[i] + 1;
}
region.SetSize(size);
region.SetIndex(index);
}
else
{
using ShortImageType = itk::Image<unsigned short, ImageDimension>;
// typedef itk::CastImageFilter<ImageType, ShortImageType> CasterType;
// typename CasterType::Pointer caster = CasterType::New();
// caster->SetInput(reader->GetOutput());
// caster->Update();
using ShortImageReaderType = itk::ImageFileReader<ShortImageType>;
typename ShortImageReaderType::Pointer shortReader = ShortImageReaderType::New();
shortReader->SetFileName(argv[4]);
shortReader->Update();
// typedef itk::LabelStatisticsImageFilter<ShortImageType, ShortImageType>
using StatsFilterType = itk::LabelStatisticsImageFilter<ImageType, ShortImageType>;
typename StatsFilterType::Pointer stats = StatsFilterType::New();
// stats->SetLabelInput(caster->GetOutput());
stats->SetLabelInput(shortReader->GetOutput());
// stats->SetInput(caster->GetOutput());
stats->SetInput(reader->GetOutput());
stats->Update();
const unsigned int label = (argc >= 6) ? std::stoi(argv[5]) : 1;
region = stats->GetRegion(label);
std::cout << "bounding box of label=" << label << " : " << region << std::endl;
const unsigned int padWidth = (argc >= 7) ? std::stoi(argv[6]) : 0;
region.PadByRadius(padWidth);
std::cout << "padding radius = " << padWidth << " : " << region << std::endl;
region.Crop(reader->GetOutput()->GetBufferedRegion());
std::cout << "crop with original image region " << reader->GetOutput()->GetBufferedRegion() << " : " << region
<< std::endl;
}
std::cout << "final cropped region: " << region << std::endl;
using CropperType = itk::ExtractImageFilter<ImageType, ImageType>;
typename CropperType::Pointer cropper = CropperType::New();
cropper->SetInput(reader->GetOutput());
cropper->SetExtractionRegion(region);
cropper->SetDirectionCollapseToSubmatrix();
cropper->Update();
using WriterType = itk::ImageFileWriter<ImageType>;
typename WriterType::Pointer writer = WriterType::New();
writer->SetInput(cropper->GetOutput());
writer->SetFileName(argv[3]);
writer->Update();
return EXIT_SUCCESS;
}
// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int
ExtractRegionFromImageByMask(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(), "ExtractRegionFromImageByMask");
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 || argc > 7)
{
std::cout << "Extract a sub-region from image using the bounding"
" box from a label image, with optional padding radius."
<< std::endl
<< "Usage : " << argv[0] << " ImageDimension "
<< "inputImage outputImage labelMaskImage [label=1] [padRadius=0]" << 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 ExtractRegionFromImageByMask<2>(argc, argv);
}
break;
case 3:
{
return ExtractRegionFromImageByMask<3>(argc, argv);
}
break;
default:
std::cout << "Unsupported dimension" << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
} // namespace ants
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