/*=========================================================================

  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 "itkImage.h"
#include "itkImageFileWriter.h"
#include "itkImageFileReader.h"
#include "itkCastImageFilter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "ReadWriteData.h"
#include "TensorFunctions.h"

namespace ants
{
template <unsigned int ImageDimension>
int
CopyImageHeaderInformation(int argc, char * argv[])
{
  using inPixelType = float;
  using ImageType = itk::Image<inPixelType, ImageDimension>;
  using readertype = itk::ImageFileReader<ImageType>;

  typename readertype::Pointer reader = readertype::New();
  reader->SetFileName(argv[1]);
  reader->Update();
  //  std::cout << " Spacing " << reader->GetOutput()->GetSpacing() << std::endl;
  // std::cout << " Origin " << reader->GetOutput()->GetOrigin() << std::endl;
  // std::cout << " Direction " << std::endl << reader->GetOutput()->GetDirection() << std::endl;
  // std::cout << " Size " << std::endl << reader->GetOutput()->GetLargestPossibleRegion().GetSize() << std::endl;

  bool istensor = false;
  if (argc > 7)
  {
    if (std::stoi(argv[7]))
    {
      istensor = true;
    }
  }
  if (istensor)
  {
    using TensorType = itk::Vector<float, 6>;
    using TensorFieldType = itk::Image<TensorType, ImageDimension>;
    typename TensorFieldType::Pointer timage;
    ReadTensorImage<TensorFieldType>(timage, argv[2], false);
    //      std::cout<< " tim dir " << timage->GetDirection() << std::endl;
    if (argc > 6)
    {
      if (std::stoi(argv[6]))
      {
        timage->SetSpacing(reader->GetOutput()->GetSpacing());
      }
    }
    if (argc > 5)
    {
      if (std::stoi(argv[5]))
      {
        timage->SetOrigin(reader->GetOutput()->GetOrigin());
      }
    }
    if (argc > 4)
    {
      if (std::stoi(argv[4]))
      {
        timage->SetDirection(reader->GetOutput()->GetDirection());
      }
    }

    //      std::cout<< " tim dir " << timage->GetDirection() << std::endl;
    WriteTensorImage<TensorFieldType>(timage, argv[3], false);

    return EXIT_SUCCESS;
  }

  typename readertype::Pointer reader2 = readertype::New();
  reader2->SetFileName(argv[2]);
  reader2->Update();

  // MakeNewImage(typename TImage::Pointer image1, typename TImage::PixelType initval)
  typename ImageType::Pointer newimage = MakeNewImage<ImageType>(reader2->GetOutput(), -1);

  if (argc > 6)
  {
    if (std::stoi(argv[6]))
    {
      newimage->SetSpacing(reader->GetOutput()->GetSpacing());
    }
  }
  if (argc > 5)
  {
    if (std::stoi(argv[5]))
    {
      newimage->SetOrigin(reader->GetOutput()->GetOrigin());
    }
  }
  if (argc > 4)
  {
    if (std::stoi(argv[4]))
    {
      newimage->SetDirection(reader->GetOutput()->GetDirection());
    }
  }

  ANTs::WriteImage<ImageType>(newimage, argv[3]);

  return EXIT_FAILURE;
}

// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int
CopyImageHeaderInformation(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(), "CopyImageHeaderInformation");

  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 < 4)
  {
    std::cout << "Usage:  " << argv[0]
              << " refimage.ext imagetocopyrefimageinfoto.ext imageout.ext   boolcopydirection  boolcopyorigin "
                 "boolcopyspacing  {bool-Image2-IsTensor}"
              << 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();
  unsigned int dim = imageIO->GetNumberOfDimensions();

  switch (dim)
  {
    case 2:
    {
      CopyImageHeaderInformation<2>(argc, argv);
    }
    break;
    case 3:
    {
      CopyImageHeaderInformation<3>(argc, argv);
    }
    break;
    case 4:
    {
      CopyImageHeaderInformation<4>(argc, argv);
    }
    break;
    default:
      std::cout << "Unsupported dimension : " << dim << std::endl;
      return EXIT_FAILURE;
  }
  return EXIT_SUCCESS;
}
} // namespace ants
