// =========================================================================
// @author Leonardo Florez Valencia
// @email florez-l@javeriana.edu.co
// =========================================================================

#include <itkImage.h>
#include <itkAbsoluteValueDifferenceImageFilter.h>
#include <itkBinaryThresholdImageFilter.h>
#include <CTBronchi/Functions.h>
#include <CTBronchi/Mori.h>
#include <CTBronchi/MoriLabelling.h>
#include <CTBronchi/RandomWalker.h>

// -------------------------------------------------------------------------
const unsigned int Dim = 3;
typedef short         TInputPixel;
typedef unsigned char TLabelPixel;
typedef itk::Image< TInputPixel, Dim > TImage;
typedef itk::Image< TLabelPixel, Dim > TLabelImage;

// -------------------------------------------------------------------------
int main( int argc, char* argv[] )
{
  std::map< std::string, std::string > args;
  try
  {
    if( CTBronchi::ParseArgs( args, argc, argv ) )
    {
      // Parse seed
      TImage::PointType seed;
      char* str = new char[ args[ "seed" ].size( ) + 1 ];
      strcpy( str, args[ "seed" ].c_str( ) );
      seed[ 0 ] = std::atof( strtok( str, ";" ) );
      seed[ 1 ] = std::atof( strtok( NULL, ";" ) );
      seed[ 2 ] = std::atof( strtok( NULL, ";" ) );

      // Read input image
      TImage::Pointer input_image;
      CTBronchi::ReadImage( input_image, args[ "in" ] );

      // Mori segmentation
      TLabelImage::Pointer mori;
      TInputPixel opt_thr = CTBronchi::Mori( mori, input_image, seed, args );

      // Label image
      TLabelImage::Pointer labels;
      CTBronchi::Label( labels, input_image, mori, opt_thr, args );

      // Final labels
      TLabelImage::Pointer final_labels;
      CTBronchi::RandomWalker( final_labels, input_image, labels, args );

      // Extract label 1
      typedef itk::BinaryThresholdImageFilter< TLabelImage, TLabelImage > TBinThr;
      TBinThr::Pointer bin_thr = TBinThr::New( );
      bin_thr->SetInput( final_labels );
      bin_thr->SetLowerThreshold( 1 );
      bin_thr->SetUpperThreshold( 1 );
      bin_thr->SetInsideValue( 1 );
      bin_thr->SetOutsideValue( 0 );
      double t = CTBronchi::MeasureTime( bin_thr );
      std::cout << "Label extracted in " << t << " s" << std::endl;
      TLabelImage::Pointer segmentation = bin_thr->GetOutput( );

      // Save
      CTBronchi::WriteImage( segmentation, args[ "out" ] );

      // Save difference
      std::map< std::string, std::string >::const_iterator i =
        args.find( "out_diff" );
      if( i != args.end( ) )
      {
        typedef itk::AbsoluteValueDifferenceImageFilter< TLabelImage, TLabelImage, TLabelImage > TDiff;
        TDiff::Pointer diff = TDiff::New( );
        diff->SetInput1( mori );
        diff->SetInput2( segmentation );
        t = CTBronchi::MeasureTime( diff );
        std::cout << "Difference computed in " << t << " s" << std::endl;
        TLabelImage::Pointer difference = diff->GetOutput( );
        CTBronchi::WriteImage( difference, i->second );

      } // fi
    }
    else
      return( 1 );
  }
  catch( std::exception& err )
  {
    std::cerr
      << "===============================" << std::endl
      << "Error caught: " << std::endl
      << err.what( )
      << "===============================" << std::endl
      << std::endl;
    return( 1 );

  } // yrt
  return( 0 );
}

// eof - $RCSfile$