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/*
* ResetDirection2.cxx
*
* Created on: Nov 14, 2008
* 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 <algorithm>
#include <iostream>
#include <fstream>
#include <cstdio>
#include "antsAllocImage.h"
#include "itkImage.h"
#include "itkImageFileWriter.h"
#include "itkImageFileReader.h"
#include "itkCastImageFilter.h"
#include "itkRescaleIntensityImageFilter.h"
namespace ants
{
template <unsigned int ImageDimension>
int
ResetDirection(int argc, char * argv[])
{
if (argc < 3)
{
std::cout << "Usage: " << argv[0] << " infile.nii outfile.nii direction matrix in a row " << 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;
}
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::DirectionType direction = outim->GetDirection();
// direction->SetIdentity();
// direction.Fill(0);
// for (unsigned int i=0;i<ImageDimension;i++) direction[i][i]=1;
char ** dtext = argv + 3;
for (unsigned int i = 0; i < ImageDimension; i++)
{
for (unsigned int j = 0; j < ImageDimension; j++)
{
direction[i][j] = atof(dtext[i * ImageDimension + j]);
std::cout << "direction[" << i << "][" << j << "]=" << direction[i][j] << std::endl;
}
}
using Iterator = itk::ImageRegionIteratorWithIndex<ImageType>;
typename ImageType::Pointer varimage = AllocImage<ImageType>(outim);
varimage->SetDirection(direction);
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
SetDirectionByMatrix(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(), "SetDirectionByMatrix");
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] << " infile.nii outfile.nii d01 d02 d03 d10 .... " << 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:
{
return ResetDirection<2>(argc, argv);
}
break;
case 3:
{
return ResetDirection<3>(argc, argv);
}
break;
case 4:
{
return ResetDirection<4>(argc, argv);
}
break;
default:
std::cout << "Unsupported dimension " << imageIO->GetNumberOfDimensions() << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
} // namespace ants
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