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

  Program:   Advanced Normalization Tools
  Module:    $RCSfile: PermuteFlipImageOrientationAxes.cxx,v $
  Language:  C++
  Date:      $Date: 2009/01/30 16:40:33 $
  Version:   $Revision: 1.19 $

  Copyright (c) ConsortiumOfANTS. All rights reserved.
  See accompanying COPYING.txt or
 http://sourceforge.net/projects/advants/files/ANTS/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 "itkImage.h"
#include "itkConstantPadImageFilter.h"
#include "itkIdentityTransform.h"
#include "itkLinearInterpolateImageFunction.h"
#include "itkRecursiveGaussianImageFilter.h"
#include "itkPermuteAxesImageFilter.h"
#include "itkFlipImageFilter.h"

#include "ReadWriteData.h"

namespace ants
{
template <unsigned int Dimension>
int PermuteFlipImageOrientationAxes( int argc, char * argv[] )
{
  typedef   float InputPixelType;
  typedef   float OutputPixelType;

  typedef itk::Image<InputPixelType,    Dimension> InputImageType;
  typedef itk::Image<OutputPixelType,   Dimension> OutputImageType;

  typename InputImageType::Pointer inputImage = ITK_NULLPTR;
  ReadImage<InputImageType>(inputImage, argv[1]);

  // Create a filter
  typedef OutputImageType ShortImage;
  typename itk::PermuteAxesImageFilter<ShortImage>::Pointer permute;
  permute = itk::PermuteAxesImageFilter<ShortImage>::New();
  permute->SetInput( inputImage );

  unsigned int upperFactors[Dimension];
  unsigned int lowerFactors[Dimension];
  for( unsigned int q = 0; q < Dimension; ++q )
    {
    upperFactors[q] = 0;
    lowerFactors[q] = 0;
    }

  bool flipaboutorigin = false;
  if( Dimension == 2 )
    {
    if( argc > 3 )
      {
      upperFactors[0] = atoi(argv[3]);
      }
    if( argc > 4 )
      {
      upperFactors[1] = atoi(argv[4]);
      }
    if( argc > 5 )
      {
      lowerFactors[0] = atoi(argv[5]);
      }
    if( argc > 6 )
      {
      lowerFactors[1] = atoi(argv[6]);
      }
    if( argc > 7 )
      {
      flipaboutorigin = atoi(argv[7]);
      }
    }
  else if( Dimension == 3 )
    {
    if( argc > 3 )
      {
      upperFactors[0] = atoi(argv[3]);
      }
    if( argc >  4 )
      {
      upperFactors[1] = atoi(argv[4]);
      }
    if( argc > 5 )
      {
      upperFactors[2] = atoi(argv[5]);
      }
    if( argc > 6 )
      {
      lowerFactors[0] = atoi(argv[6]);
      }
    if( argc > 7 )
      {
      lowerFactors[1] = atoi(argv[7]);
      }
    if( argc > 8  )
      {
      lowerFactors[2] = atoi(argv[8]);
      }
    if( argc > 9 )
      {
      flipaboutorigin = atoi(argv[9]);
      }
    }

  permute->SetOrder( upperFactors );
  permute->Update();

  typedef itk::FlipImageFilter<ShortImage> FlipType;
  typename FlipType::FlipAxesArrayType flip;
  for( unsigned int i = 0; i < Dimension; i++ )
    {
    flip[i] = lowerFactors[i];
    }
  typename FlipType::Pointer flipper = FlipType::New();
  flipper->SetFlipAboutOrigin(flipaboutorigin);
  flipper->SetFlipAxes(flip);
  flipper->SetInput( permute->GetOutput() );
  flipper->Update();

  typename InputImageType::Pointer image = flipper->GetOutput();
  WriteImage<OutputImageType>(image, argv[2]);

  return EXIT_SUCCESS;
}

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

  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 < 3 )
    {
    std::cout << "Usage: " << std::endl;
    std::cout << argv[0]
             <<
      " ImageDimension  inputImageFile  outputImageFile xperm yperm {zperm}  xflip yflip {zflip}  {FlipAboutOrigin}"
             << std::endl;
    std::cout << " for 3D:  " << argv[0]
             << " 3  in.nii out.nii   2 0 1  1 1 1  \n would map z=>x, x=>y, y=>z and flip each " << std::endl;
    std::cout << " for 2D:  " << argv[0] << " 2  in.nii out.nii   1 0  1 0  \n would map x=>y, y=>x and flip x  "
             << std::endl;
    std::cout << std::endl;
    std::cout << " 0 1 2 for permute factors gives no axis permutation " << std::endl;
    std::cout << " 1 2 0 maps y to x,  z to y and x to z " << std::endl;
    std::cout << " the flip values are boolean -  0 1 0 would flip the y-axis only " << std::endl;
    std::cout <<  std::endl << " The FlipAboutOrigin boolean lets you flip about the coordinate set in the origin "
             << 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
  switch( atoi(argv[1]) )
    {
    case 2:
      {
      PermuteFlipImageOrientationAxes<2>(argc - 1, argv + 1);
      }
      break;
    case 3:
      {
      PermuteFlipImageOrientationAxes<3>(argc - 1, argv + 1);
      }
      break;
    default:
      std::cout << "Unsupported dimension" << std::endl;
      return EXIT_FAILURE;
    }
  return EXIT_SUCCESS;
}
} // namespace ants
