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/*=========================================================================
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 <algorithm>
#include <algorithm>
#include <iostream>
#include <fstream>
#include <cstdio>
#include "itkImage.h"
#include "itkImageFileWriter.h"
#include "itkImageFileReader.h"
#include "itkCastImageFilter.h"
#include "itkRescaleIntensityImageFilter.h"
namespace ants
{
template <unsigned int ImageDimension>
int
ConvertType(int argc, char * argv[])
{
using outPixelType = unsigned char;
using floatPixelType = float;
using inPixelType = float;
using ImageType = itk::Image<inPixelType, ImageDimension>;
using IntermediateType = itk::Image<floatPixelType, ImageDimension>;
using OutImageType = itk::Image<outPixelType, ImageDimension>;
using readertype = itk::ImageFileReader<ImageType>;
using writertype = itk::ImageFileWriter<OutImageType>;
typename readertype::Pointer reader = readertype::New();
if (argc < 2)
{
std::cout << "Missing input filename" << std::endl;
throw;
}
reader->SetFileName(argv[1]);
reader->Update();
std::cout << " Updated reader " << std::endl;
using castertype = itk::CastImageFilter<ImageType, IntermediateType>;
typename castertype::Pointer caster = castertype::New();
caster->SetInput(reader->GetOutput());
caster->Update();
// Rescale the image intensities so that they fall between 0 and 255
using FilterType = itk::RescaleIntensityImageFilter<IntermediateType, IntermediateType>;
typename FilterType::Pointer fixedrescalefilter = FilterType::New();
fixedrescalefilter->SetInput(caster->GetOutput());
constexpr double desiredMinimum = 0.0;
constexpr double desiredMaximum = 255.0;
fixedrescalefilter->SetOutputMinimum(desiredMinimum);
fixedrescalefilter->SetOutputMaximum(desiredMaximum);
fixedrescalefilter->UpdateLargestPossibleRegion();
using castertype2 = itk::CastImageFilter<IntermediateType, OutImageType>;
typename castertype2::Pointer caster2 = castertype2::New();
caster2->SetInput(fixedrescalefilter->GetOutput());
caster2->Update();
typename OutImageType::Pointer outim = caster2->GetOutput();
typename OutImageType::SpacingType spc = outim->GetSpacing();
outim->SetSpacing(spc);
std::cout << " Dire in " << reader->GetOutput()->GetDirection() << std::endl;
std::cout << " Dire out " << outim->GetDirection() << std::endl;
typename writertype::Pointer writer = writertype::New();
if (argc < 3)
{
std::cout << "Missing output filename" << std::endl;
throw;
}
writer->SetFileName(argv[2]);
writer->SetInput(outim);
writer->Update();
writer->Write();
return EXIT_SUCCESS;
}
// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int
ConvertToJpg(std::vector<std::string> args, std::ostream * /*out_stream = nullptr */)
{
try
{
// 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(), "ConvertToJpg");
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 < 3)
{
std::cout << "Usage: ConvertToJpg infile.nii out.jpg " << 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;
}
// Get the image dimension
std::string fn = std::string(argv[1]);
itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::IOFileModeEnum::ReadMode);
imageIO->SetFileName(fn.c_str());
imageIO->ReadImageInformation();
switch (imageIO->GetNumberOfDimensions())
{
case 2:
{
ConvertType<2>(argc, argv);
}
break;
case 3:
{
ConvertType<3>(argc, argv);
}
break;
default:
std::cout << "Unsupported dimension" << std::endl;
return EXIT_FAILURE;
}
}
catch (const itk::ExceptionObject & e)
{
e.Print(std::cerr);
return EXIT_FAILURE;
}
catch (const std::exception & e)
{
std::cerr << e.what() << std::endl;
return EXIT_FAILURE;
}
catch (...)
{
std::cerr << "Unknown exception caught" << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
} // namespace ants
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