
#include "antsUtilities.h"
#include <algorithm>

#include <stdio.h>

#include "itkCastImageFilter.h"
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkExtractImageFilter.h"
#include "itkLabelStatisticsImageFilter.h"

#include <string>
#include <vector>

namespace ants
{

template <unsigned int ImageDimension>
int ExtractRegionFromImage( int argc, char *argv[] )
{
  typedef float PixelType;

  typedef itk::Image<PixelType, ImageDimension> ImageType;
  typedef itk::ImageFileReader<ImageType>       ReaderType;
  typename ReaderType::Pointer reader = ReaderType::New();
  reader->SetFileName( argv[2] );
  reader->Update();

  typename ImageType::RegionType region;
  typename ImageType::RegionType::SizeType size;
  typename ImageType::RegionType::IndexType index;

  if( argc == 6 )
    {
    std::vector<int> minIndex;
    std::vector<int> maxIndex;
    minIndex = ConvertVector<int>( std::string( argv[4] ) );
    maxIndex = ConvertVector<int>( std::string( argv[5] ) );
    for( unsigned int i = 0; i < ImageDimension; i++ )
      {
      index[i] = minIndex[i];
      size[i] = maxIndex[i] - minIndex[i] + 1;
      }
    region.SetSize( size );
    region.SetIndex( index );
    }
  else
    {
    typedef itk::Image<unsigned short, ImageDimension>      ShortImageType;
    typedef itk::CastImageFilter<ImageType, ShortImageType> CasterType;
    typename CasterType::Pointer caster = CasterType::New();
    caster->SetInput( reader->GetOutput() );
    caster->Update();

    typedef itk::LabelStatisticsImageFilter<ShortImageType, ShortImageType>
      StatsFilterType;
    typename StatsFilterType::Pointer stats = StatsFilterType::New();
    stats->SetLabelInput( caster->GetOutput() );
    stats->SetInput( caster->GetOutput() );
    stats->Update();

    region = stats->GetRegion( atoi( argv[4] ) );
    }

  std::cout << region << std::endl;

  typedef itk::ExtractImageFilter<ImageType, ImageType> CropperType;
  typename CropperType::Pointer cropper = CropperType::New();
  cropper->SetInput( reader->GetOutput() );
  cropper->SetExtractionRegion( region );
  cropper->SetDirectionCollapseToSubmatrix();
  cropper->Update();

  typedef itk::ImageFileWriter<ImageType> WriterType;
  typename WriterType::Pointer writer = WriterType::New();
  writer->SetInput( cropper->GetOutput() );
  writer->SetFileName( argv[3] );
  writer->Update();

  return EXIT_SUCCESS;
}

// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int ExtractRegionFromImage( std::vector<std::string> args, std::ostream* /*out_stream = NULL */ )
{
  // 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(), "ExtractRegionFromImage" );

  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] = ITK_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 < 5 || argc > 6 )
    {
    std::cout << "Usage 1: " << argv[0] << " ImageDimension "
             << "inputImage outputImage minIndex maxIndex " << std::endl;
    std::cout << "Usage 2: " << argv[0] << " ImageDimension "
             << "inputImage outputImage label " << 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;
    }

  switch( atoi( argv[1] ) )
    {
    case 2:
      {
      ExtractRegionFromImage<2>( argc, argv );
      }
      break;
    case 3:
      {
      ExtractRegionFromImage<3>( argc, argv );
      }
      break;
    default:
      std::cout << "Unsupported dimension" << std::endl;
      return EXIT_FAILURE;
    }
  return EXIT_SUCCESS;
}
} // namespace ants
