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/*
* SetSpacing.cxx
*
* Created on: Mar 5, 2009
* Author: songgang
*/
/*=========================================================================
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 "antsAllocImage.h"
#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
SetSpacing(int itkNotUsed(argc), char * argv[])
{
using outPixelType = float;
using inPixelType = float;
using ImageType = itk::Image<inPixelType, ImageDimension>;
using OutImageType = itk::Image<outPixelType, ImageDimension>;
using readertype = itk::ImageFileReader<ImageType>;
using writertype = itk::ImageFileWriter<OutImageType>;
typename readertype::Pointer reader = readertype::New();
reader->SetFileName(argv[1]);
reader->Update();
typename OutImageType::Pointer outim = reader->GetOutput();
typename OutImageType::SpacingType spacing = outim->GetSpacing();
std::cout << " Old Spacing " << outim->GetSpacing();
for (unsigned int d = 0; d < ImageDimension; d++)
{
spacing[d] = atof(argv[d+3]);
}
std::cout << " New Spacing " << spacing << std::endl;
using Iterator = itk::ImageRegionIteratorWithIndex<ImageType>;
typename ImageType::Pointer varimage = AllocImage<ImageType>(outim);
varimage->SetSpacing(spacing);
Iterator vfIter2(varimage, varimage->GetLargestPossibleRegion());
for (vfIter2.GoToBegin(); !vfIter2.IsAtEnd(); ++vfIter2)
{
vfIter2.Set(outim->GetPixel(vfIter2.GetIndex()));
}
typename writertype::Pointer writer = writertype::New();
writer->SetFileName(argv[2]);
writer->SetInput(varimage);
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
SetSpacing(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(), "SetSpacing");
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: " << argv[0] << " Dimension infile.hdr outfile.nii SpacingX SpacingY {SpacingZ} "
<< 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
switch (std::stoi(argv[1]))
{
case 2:
{
return SetSpacing<2>(argc - 1, argv + 1);
}
break;
case 3:
{
return SetSpacing<3>(argc - 1, argv + 1);
}
break;
default:
std::cout << "Unsupported dimension" << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
} // namespace ants
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