/*
 * 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
