/*=========================================================================1

  Program:   Advanced Normalization Tools
  Module:    $RCSfile: DeNrrd.cxx,v $
  Language:  C++
  Date:      $Date: 2009/03/17 18:55:26 $
  Version:   $Revision: 1.2 $

  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 <itkImageSeriesReader.h>
#include <itkGDCMImageIO.h>
#include <itkGDCMSeriesFileNames.h>
#include <itkExceptionObject.h>
#include <itkImageRegionIteratorWithIndex.h>
#include <itkImageFileWriter.h>
#include <itkImageFileReader.h>
#include <itkMetaDataObject.h>
#include <itkNrrdImageIO.h>
#include <itkVectorImage.h>
#include <itkVariableLengthVector.h>

#include <itkMetaDataDictionary.h>

#include <iostream>
#include <sys/stat.h>

#include <fstream>
#include <stdio.h>

#include <cstring>
#include <sstream>


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

  const 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 < 4 )
    {
    std::cerr << "Usage: " << argv[0] << " inImage.nrrd outImage.nii gradients.txt"
             << 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;
    }

  const char * const input_image_filename = argv[1];
  const char * const output_image_filename = argv[2];
  const char * const output_gradients_filename = argv[3];

  typedef float                             PixelType;
  typedef itk::VectorImage<PixelType,3>	    DiffusionImageType;

  typedef itk::ImageFileReader<DiffusionImageType,
  itk::DefaultConvertPixelTraits< PixelType > > FileReaderType;
  FileReaderType::Pointer reader = FileReaderType::New();
  reader->SetFileName(input_image_filename);
  reader->Update();

  itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
  //io->SetNrrdVectorType( nrrdKindList );
  io->SetFileType( itk::ImageIOBase::ASCII );

  //std::cout  << "Number of dwi values " << reader->GetOutput()->GetNumberOfComponentsPerPixel() << std::endl;

  std::string v_string;
  std::string b_string;

  itk::MetaDataDictionary & mdd = reader->GetOutput()->GetMetaDataDictionary();

  if ( mdd.HasKey("modality") )
    {
    std::string modality;
    itk::ExposeMetaData<std::string>(mdd, "modality", modality);
    if ( modality.compare("DWMRI") != 0 )
      {
      std::cerr << "Data in not DWMRI" << std::endl;
      return EXIT_FAILURE;
      }
    }
  else
    {
    std::cerr << "Error: No b-value found" << std::endl;
    return EXIT_FAILURE;
    }


  if ( mdd.HasKey( "DWMRI_b-value" ) )
    {
    itk::ExposeMetaData<std::string>(mdd, "DWMRI_b-value", b_string);
    //std::cout << "BValue = " << b_string << std::endl;
    }
  else
    {
    std::cerr << "Error: No b-value found" << std::endl;
    return EXIT_FAILURE;
    }

  std::ofstream gradientfile;
  gradientfile.open(output_gradients_filename);
  gradientfile << "VERSION: 2" << std::endl;

  for ( unsigned int i=0; i<reader->GetOutput()->GetNumberOfComponentsPerPixel(); i++ )
    {
    char gradKey[20];
    sprintf( gradKey, "DWMRI_gradient_%04d", i );
    itk::ExposeMetaData<std::string>(mdd, gradKey, v_string);
    //std::cout << "Gradient = " << v_string << std::endl;

    std::istringstream iss(v_string);
    double x, y, z;
    iss >> x >> y >> z;

    if ( (x*x + y*y + z*z ) == 0 )
      {
      gradientfile << v_string << " 0" << std::endl;
      }
    else
      {
      gradientfile << v_string << " " << b_string << std::endl;
      }
    }

  gradientfile.close();

  /*
  OutputImageType::Pointer outImage = OutputImageType::New();
  OutputImageType::SizeType outSize;
  outSize[0] = reader->GetOutput()->GetLargestPossibleRegion().GetSize()[0];
  outSize[1] = reader->GetOutput()->GetLargestPossibleRegion().GetSize()[1];
  outSize[2] = reader->GetOutput()->GetLargestPossibleRegion().GetSize()[2];
  outSize[3] = reader->GetOutput()->GetNumberOfComponentsPerPixel();
  OutputImageType::RegionType outRegion;
  outRegion.SetSize( outSize );
  outImage->SetRegions( outRegion );
  outImage->Allocate();

  OutputImageType::SpacingType spacing;
  spacing[0] = reader->GetOutput()->GetSpacing()[0];
  spacing[1] = reader->GetOutput()->GetSpacing()[1];
  spacing[2] = reader->GetOutput()->GetSpacing()[2];
  spacing[3] = 1.0;
  outImage->SetSpacing(spacing);

  OutputImageType::PointType origin;
  origin[0] = reader->GetOutput()->GetOrigin()[0];
  origin[1] = reader->GetOutput()->GetOrigin()[1];
  origin[2] = reader->GetOutput()->GetOrigin()[2];
  outImage->SetOrigin(origin);

  OutputImageType::DirectionType dirMat;
  for ( unsigned int i=0; i<3; i++ )
    for ( unsigned int j=0; j<3; j++)
      dirMat(i,j) = reader->GetOutput()->GetDirection()(i,j);
  dirMat(3,3) = 1.0;
  outImage->SetDirection(dirMat);

  for ( unsigned int x=0; x<outSize[0]; x++ )
    for ( unsigned int y=0; y<outSize[1]; y++ )
      for ( unsigned int z=0; z<outSize[2]; z++ )
        for ( unsigned int t=0; t<outSize[3]; t++ )
          {
          OutputImageType::IndexType oIdx;
          oIdx[0] = x;
          oIdx[1] = y;
          oIdx[2] = z;
          oIdx[3] = t;

          DiffusionImageType::IndexType dIdx;
          dIdx[0] = x;
          dIdx[1] = y;
          dIdx[2] = z;

          outImage->SetPixel(oIdx,reader->GetOutput()->GetPixel(dIdx)[t]);

          }
*/


  typedef itk::ImageFileWriter<DiffusionImageType> FileWriterType;
  FileWriterType::Pointer writer = FileWriterType::New();
  writer->SetFileName(output_image_filename);
  writer->SetInput( reader->GetOutput() );
  writer->Update();

  return EXIT_SUCCESS;
}
} // namespace ants
