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

  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 <climits>
#include "itkImage.h"
#include "itkImageFileWriter.h"
#include "itkImageFileReader.h"
#include "itkCastImageFilter.h"
#include "itkRescaleIntensityImageFilter.h"

namespace ants
{
template <unsigned int ImageDimension, typename TPIXELTYPE>
int
ConvertType(int argc, char * argv[], double MINVAL, double MAXVAL)
{
  using outPixelType = TPIXELTYPE;
  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());
  const double desiredMinimum = MINVAL;
  double       desiredMaximum = MAXVAL;
  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
ConvertImagePixelType(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(), "ConvertImagePixelType");
  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 out.ext TYPE-OPTION " << std::endl;
    std::cout << " ext is the extension you want, e.g. tif.  " << std::endl;
    std::cout << " TYPE-OPTION  :  TYPE " << std::endl;
    std::cout << "  0  :  char   " << std::endl;
    std::cout << "  1  :  unsigned char   " << std::endl;
    std::cout << "  2  :  short   " << std::endl;
    std::cout << "  3  :  unsigned short   " << std::endl;
    std::cout << "  4  :  int   " << std::endl;
    std::cout << "  5  :  unsigned int   " << std::endl;
    std::cout
      << " Note that some pixel types are not supported by some image formats. e.g.  int is not supported by jpg. "
      << std::endl;
    std::cout << " You can easily extend this for other pixel types with a few lines of code and adding usage info. "
              << std::endl;
    std::cout << " The image intensity will be scaled to the dynamic range of the pixel type.  E.g. uchar => 0  (min), "
                 "255 (max). "
              << 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;
  }
  unsigned int typeoption = 0;
  if (argc > 3)
  {
    typeoption = std::stoi(argv[3]);
  }
  // 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();

  if (typeoption == 0)
  {
    switch (imageIO->GetNumberOfDimensions())
    {
      case 2:
      {
        ConvertType<2, char>(argc, argv, SCHAR_MIN, SCHAR_MAX);
      }
      break;
      case 3:
      {
        ConvertType<3, char>(argc, argv, SCHAR_MIN, SCHAR_MAX);
      }
      break;
      default:
        std::cout << "Unsupported dimension" << std::endl;
        return EXIT_FAILURE;
    }
  }
  else if (typeoption == 1)
  {
    switch (imageIO->GetNumberOfDimensions())
    {
      case 2:
      {
        ConvertType<2, unsigned char>(argc, argv, 0, UCHAR_MAX);
      }
      break;
      case 3:
      {
        ConvertType<3, unsigned char>(argc, argv, 0, UCHAR_MAX);
      }
      break;
      default:
        std::cout << "Unsupported dimension" << std::endl;
        return EXIT_FAILURE;
    }
  }
  else if (typeoption == 2)
  {
    switch (imageIO->GetNumberOfDimensions())
    {
      case 2:
      {
        ConvertType<2, short>(argc, argv, SHRT_MIN, SHRT_MAX);
      }
      break;
      case 3:
      {
        ConvertType<3, short>(argc, argv, SHRT_MIN, SHRT_MAX);
      }
      break;
      default:
        std::cout << "Unsupported dimension" << std::endl;
        return EXIT_FAILURE;
    }
  }
  else if (typeoption == 3)
  {
    switch (imageIO->GetNumberOfDimensions())
    {
      case 2:
      {
        ConvertType<2, unsigned short>(argc, argv, 0, USHRT_MAX);
      }
      break;
      case 3:
      {
        ConvertType<3, unsigned short>(argc, argv, 0, USHRT_MAX);
      }
      break;
      default:
        std::cout << "Unsupported dimension" << std::endl;
        return EXIT_FAILURE;
    }
  }
  else if (typeoption == 4)
  {
    switch (imageIO->GetNumberOfDimensions())
    {
      case 2:
      {
        ConvertType<2, int>(argc, argv, INT_MIN, INT_MAX);
      }
      break;
      case 3:
      {
        ConvertType<3, int>(argc, argv, INT_MIN, INT_MAX);
      }
      break;
      default:
        std::cout << "Unsupported dimension" << std::endl;
        return EXIT_FAILURE;
    }
  }
  else if (typeoption == 5)
  {
    switch (imageIO->GetNumberOfDimensions())
    {
      case 2:
      {
        ConvertType<2, unsigned int>(argc, argv, 0, UINT_MAX);
      }
      break;
      case 3:
      {
        ConvertType<3, unsigned int>(argc, argv, 0, UINT_MAX);
      }
      break;
      default:
        std::cout << "Unsupported dimension" << std::endl;
        return EXIT_FAILURE;
    }
  }
  return EXIT_SUCCESS;
}
} // namespace ants
