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

  Program:   Advanced Normalization Tools
  Module:    $RCSfile: ResampleImageBySpacing.cxx,v $
  Language:  C++
  Date:      $Date: 2009/03/31 21:22:00 $
  Version:   $Revision: 1.17 $

  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 "ReadWriteData.h"
#include "itkResampleImageFilter.h"
#include "itkIdentityTransform.h"
#include "itkLinearInterpolateImageFunction.h"
#include "itkNearestNeighborInterpolateImageFunction.h"
#include "itkRecursiveGaussianImageFilter.h"
#include "itkIntensityWindowingImageFilter.h"
#include "itkDiscreteGaussianImageFilter.h"

namespace ants
{
// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int ResampleImageBySpacing( std::vector<std::string> args, std::ostream* /*out_stream = NULL */ )
{
  args.insert( args.begin(), "ResampleImageBySpacing" );
  int     argc = args.size();
  char* * argv = new char *[args.size() + 1];
  for( unsigned int i = 0; i < args.size(); ++i )
    {
    argv[i] = new char[args[i].length() + 1];
    std::strncpy( argv[i], args[i].c_str(), args[i].length() );
    argv[i][args[i].length()] = '\0';
    }
  argv[argc] = ITK_NULLPTR;
  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 )
    {
    std::cout << "Usage: " << std::endl;
    std::cout << argv[0]
             <<
      "  ImageDimension inputImageFile  outputImageFile outxspc outyspc {outzspacing}  {dosmooth?}  {addvox} {nn-interp?}"
             << std::endl;
    std::cout << " addvox pads each dimension by addvox " << std::endl;
    std::cout << "  " << std::endl;
//    std::cout << " interp 0 = linear, 1 = nn " << 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 Dimension = atoi(argv[1]);

  if( Dimension == 2 )
    {
    typedef   float InputPixelType;
    typedef   float InternalPixelType;
    typedef   float OutputPixelType;

    typedef itk::Image<InputPixelType,    2> InputImageType;
    typedef itk::Image<InternalPixelType, 2> InternalImageType;
    typedef itk::Image<OutputPixelType,   2> OutputImageType;

    InputImageType::Pointer inputImage;
    ReadImage<InputImageType>( inputImage, argv[2] );

    const InputImageType::SpacingType& inputSpacing = inputImage->GetSpacing();

    OutputImageType::SpacingType spacing;
    for( int i = 0; i < 2; i++ )
      {
      spacing[i] = inputSpacing[i];
      }

    std::cout <<  " spacing " << spacing << " dim " << 2 << std::endl;

    bool dosmooth = 1;
    if( argc > 4 )
      {
      spacing[0] = atof(argv[4]);
      }
    if( argc > 5 )
      {
      spacing[1] = atof(argv[5]);
      }
    if( argc > 6 )
      {
      dosmooth = atoi(argv[6]);
      }
    int addvox = 0;
    if( argc > 7 )
      {
      addvox = atoi(argv[7]);
      }
    bool nn = false;
    if( argc > 8 )
      {
      nn = atoi(argv[7]);
      }

    std::cout <<  " spacing2 " << spacing << std::endl;

    InternalImageType::Pointer smoothedImage = inputImage;
    if( dosmooth )
      {
      for( int sm = 0; sm < 2; sm++ )
        {
        typedef itk::RecursiveGaussianImageFilter<
            OutputImageType,
            OutputImageType> GaussianFilterType;

        GaussianFilterType::Pointer smootherX = GaussianFilterType::New();
        smootherX->SetInput( smoothedImage );
        const float sig = atof(argv[4 + sm]) / inputSpacing[sm] - 1.0;
        std::cout << " smoothing by : " << sig << " dir " << sm << std::endl;
        smootherX->SetSigma( sig );
        smootherX->SetDirection( sm );
        smootherX->SetNormalizeAcrossScale( false );
        if( sig > 0 && dosmooth )
          {
          try
            {
            smootherX->Update();
            }
          catch( itk::ExceptionObject & excep )
            {
            std::cout << "Exception catched !" << std::endl;
            std::cout << excep << std::endl;
            }
          smoothedImage = smootherX->GetOutput();
          }
        }
      }

    // InternalImageType::ConstPointer smoothedImage = smootherY->GetOutput();

    // InternalImageType::ConstPointer smoothedImage = reader->GetOutput();
    // smoothedImage =SmoothImage<ImageType>(reader->GetOutput() , );

    typedef itk::ResampleImageFilter<
        InternalImageType, OutputImageType>  ResampleFilterType;

    ResampleFilterType::Pointer resampler = ResampleFilterType::New();

    typedef itk::IdentityTransform<double, 2> TransformType;

    typedef itk::LinearInterpolateImageFunction<
        InternalImageType, double>  InterpolatorType;
    typedef itk::NearestNeighborInterpolateImageFunction<
        InternalImageType, double>  InterpolatorType2;

    InterpolatorType::Pointer  interpolator = InterpolatorType::New();
    InterpolatorType2::Pointer interpolator2 = InterpolatorType2::New();

    resampler->SetInterpolator( interpolator );
    if( nn == 1 )
      {
      resampler->SetInterpolator( interpolator2 );
      }

    InternalImageType::IndexType ind;
    ind.Fill(1);
    resampler->SetDefaultPixelValue( inputImage->GetPixel(ind) ); // zero regions without source

    // Use the inputImage as initial template
    resampler->SetOutputParametersFromImage( inputImage );
    // Reset spacing by explicit specification
    std::cout << " out space " << spacing << std::endl;
    resampler->SetOutputSpacing( spacing );

    InputImageType::SizeType inputSize = inputImage->GetLargestPossibleRegion().GetSize();
    typedef InputImageType::SizeType::SizeValueType SizeValueType;
    InputImageType::SizeType size;
    for( int i = 0; i < 2; i++ )
      {
      size[i] = static_cast<SizeValueType>(inputSize[i] * inputSpacing[i] / spacing[i] + addvox);
      }

    std::cout << " output size " << size << " spc " << spacing << std::endl;
    resampler->SetSize( size );
    resampler->SetInput( smoothedImage );
    TransformType::Pointer transform = TransformType::New();
    transform->SetIdentity();
    resampler->SetTransform( transform );
    resampler->Update();
    WriteImage<OutputImageType>( resampler->GetOutput(), argv[3] );
    }

  if( Dimension == 3 )
    {
    typedef   float InputPixelType;
    typedef   float InternalPixelType;
    typedef   float OutputPixelType;

    typedef itk::Image<InputPixelType,    3> InputImageType;
    typedef itk::Image<InternalPixelType, 3> InternalImageType;
    typedef itk::Image<OutputPixelType,   3> OutputImageType;
    InputImageType::Pointer inputImage;
    ReadImage<InputImageType>( inputImage, argv[2] );

    const InputImageType::SpacingType& inputSpacing = inputImage->GetSpacing();

    OutputImageType::SpacingType spacing;
    for( int i = 0; i < 3; i++ )
      {
      spacing[i] = inputSpacing[i];
      }

    std::cout <<  " spacing " << spacing << " dim " << 3 << std::endl;

    bool dosmooth = 1;
    if( argc > 4 )
      {
      spacing[0] = atof(argv[4]);
      }
    if( argc > 5 )
      {
      spacing[1] = atof(argv[5]);
      }
    if( argc > 6 )
      {
      spacing[2] = atof(argv[6]);
      }
    if( argc > 7 )
      {
      dosmooth = atoi(argv[7]);
      }
    int addvox = 0;
    if( argc > 8 )
      {
      addvox = atoi(argv[8]);
      }
    bool nn = false;
    if( argc > 9 )
      {
      nn = atoi(argv[9]);
      }

    std::cout <<  " spacing2 " << spacing << std::endl;

    InternalImageType::Pointer smoothedImage = inputImage;
    if( dosmooth )
      {
      for( int sm = 0; sm < 3; sm++ )
        {
        typedef itk::RecursiveGaussianImageFilter<
            OutputImageType,
            OutputImageType> GaussianFilterType;

        GaussianFilterType::Pointer smootherX = GaussianFilterType::New();
        smootherX->SetInput( smoothedImage );
        const float sig = atof(argv[4 + sm]) / inputSpacing[sm] - 1.0;
        std::cout << " smoothing by : " << sig << " dir " << sm << std::endl;
        smootherX->SetSigma( sig );
        smootherX->SetDirection( sm );
        smootherX->SetNormalizeAcrossScale( false );
        if( sig > 0 && dosmooth )
          {
          try
            {
            smootherX->Update();
            }
          catch( itk::ExceptionObject & excep )
            {
            std::cout << "Exception catched !" << std::endl;
            std::cout << excep << std::endl;
            }
          smoothedImage = smootherX->GetOutput();
          }
        }
      }

    // InternalImageType::ConstPointer smoothedImage = smootherY->GetOutput();

    // InternalImageType::ConstPointer smoothedImage = reader->GetOutput();
    // smoothedImage =SmoothImage<ImageType>(reader->GetOutput() , );

    typedef itk::ResampleImageFilter<
        InternalImageType, OutputImageType>  ResampleFilterType;

    ResampleFilterType::Pointer resampler = ResampleFilterType::New();

    typedef itk::IdentityTransform<double, 3> TransformType;

    typedef itk::LinearInterpolateImageFunction<
        InternalImageType, double>  InterpolatorType;
    typedef itk::NearestNeighborInterpolateImageFunction<
        InternalImageType, double>  InterpolatorType2;

    InterpolatorType::Pointer  interpolator = InterpolatorType::New();
    InterpolatorType2::Pointer interpolator2 = InterpolatorType2::New();

    resampler->SetInterpolator( interpolator );
    if( nn == 1 )
      {
      resampler->SetInterpolator( interpolator2 );
      }

    InternalImageType::IndexType ind;
    ind.Fill(1);
    resampler->SetDefaultPixelValue( inputImage->GetPixel(ind) ); // zero regions without source

    // Use the inputImage as initial template
    resampler->SetOutputParametersFromImage( inputImage );
    // Reset spacing by explicit specification
    std::cout << " out space " << spacing << std::endl;
    resampler->SetOutputSpacing( spacing );

    InputImageType::SizeType inputSize = inputImage->GetLargestPossibleRegion().GetSize();
    typedef InputImageType::SizeType::SizeValueType SizeValueType;
    InputImageType::SizeType size;
    for( int i = 0; i < 3; i++ )
      {
      size[i] = static_cast<SizeValueType>(inputSize[i] * inputSpacing[i] / spacing[i] + addvox);
      }

    std::cout << " output size " << size << " spc " << spacing << std::endl;
    resampler->SetSize( size );
    resampler->SetInput( smoothedImage );
    TransformType::Pointer transform = TransformType::New();
    transform->SetIdentity();
    resampler->SetTransform( transform );
    resampler->Update();
    WriteImage<OutputImageType>( resampler->GetOutput(), argv[3] );
    }
  return EXIT_SUCCESS;
}
} // namespace ants