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

#include <sstream>
#include <string>
#include <tclap/CmdLine.h>
#include <itkImage.h>
#include <fpa/Filters/Image/Mori.h>
#include "Functions.h"

// -------------------------------------------------------------------------
const unsigned int Dim = 3;
typedef short                     TPixel;
typedef unsigned char             TLabel;
typedef itk::Image< TPixel, Dim > TImage;
typedef itk::Image< TLabel, Dim > TLabels;

// -------------------------------------------------------------------------
int main( int argc, char* argv[] )
{
  typedef TCLAP::ValueArg< std::string >   _TStringArg;
  typedef TCLAP::ValueArg< double >        _TRealArg;
  typedef TCLAP::ValueArg< unsigned long > _TUIntArg;
  typedef TCLAP::ValueArg< TPixel >        _TPixelArg;

  // Parse input line
  _TStringArg in( "i", "input", "Input image", true, "", "file" );
  _TStringArg out( "o", "output", "Output image", true, "", "file" );
  _TStringArg signal( "s", "signal", "Output signal", false, "", "file" );
  _TStringArg aSeed( "p", "seed", "Input seed", true, "", "\"x y z\"" );
  _TPixelArg mThr( "t", "min_thr", "Minimum threshold", false, -850, "value (-850)" );
  _TUIntArg sKernel( "k", "kernel", "Kernel size", false, 20, "value (20)" );
  _TRealArg sThr( "r", "signal_thr", "Signal threshold", false, 100, "value (100)" );
  _TRealArg sInfluence( "f", "signal_influence", "Signal influence", false, 0.5, "value (0.5)" );
  _TPixelArg lower( "l", "lower", "Lower threshold", false, -1024, "value (-1024)" );
  _TPixelArg upper( "u", "upper", "Upper threshold", false, 0, "value (0)" );
  _TPixelArg delta( "d", "delta", "Delta threshold", false, 1, "value (1)" );
  try
  {
    TCLAP::CmdLine cmd( "Mori segmentation", ' ', "1.0.0" );
    cmd.add( delta );
    cmd.add( upper );
    cmd.add( lower );
    cmd.add( sInfluence );
    cmd.add( sThr );
    cmd.add( sKernel );
    cmd.add( mThr );
    cmd.add( aSeed );
    cmd.add( signal );
    cmd.add( out );
    cmd.add( in );
    cmd.parse( argc, argv );
  }
  catch( TCLAP::ArgException& err )
  {
    std::cerr
      << "===============================" << std::endl
      << "Error caught: " << std::endl
      << err.error( ) << " " << err.argId( )
      << "===============================" << std::endl
      << std::endl;
    return( 1 );

  } // yrt

  // Get seed
  std::istringstream sSeed( aSeed.getValue( ) );
  TImage::PointType seed;
  sSeed >> seed[ 0 ] >> seed[ 1 ] >> seed[ 2 ];

  try
  {
    // Read image
    TImage::Pointer input_image;
    CTBronchi::ReadImage( input_image, in.getValue( ) );

    // Mori segmentation
    typedef fpa::Filters::Image::Mori< TImage, TLabels > _TMori;
    _TMori::Pointer mori = _TMori::New( );
    mori->SetInput( input_image );
    mori->SetSeed( seed );
    mori->SetInsideValue( 1 );
    mori->SetOutsideValue( 0 );
    mori->SetMinimumThreshold( mThr.getValue( ) );
    mori->SetSignalKernelSize( sKernel.getValue( ) );
    mori->SetSignalThreshold( sThr.getValue( ) );
    mori->SetSignalInfluence( sInfluence.getValue( ) );
    mori->SetThresholds(
      lower.getValue( ), upper.getValue( ), delta.getValue( )
      );
    double t = CTBronchi::MeasureTime( mori );
    std::cout << "Mori executed in " << t << " s" << std::endl;

    // Write result
    CTBronchi::WriteImage( mori->GetOutput( ), out.getValue( ) );

    // Write signal
    if( signal.getValue( ) != "" )
    {
      std::stringstream signalStr;
      unsigned long nthr = mori->GetNumberOfEvaluatedThresholds( );
      signalStr << "# nThr = " << nthr << std::endl;
      signalStr << "# Opt  = " << mori->GetOptimumThreshold( ) << std::endl;
      for( unsigned long j = 0; j < nthr; ++j )
      {
        typename _TMori::TPeak p;
        double x, y;
        mori->GetSignalValues( j, x, y, p );
        signalStr << x << " " << y << std::endl;

      } // rof
      std::ofstream oStrSignals( signal.getValue( ).c_str( ) );
      oStrSignals << signalStr.str( );
      oStrSignals.close( );

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

  } // yrt
  return( 0 );
}

// eof - $RCSfile$