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

#include <string>
#include <tclap/CmdLine.h>
#include <itkImage.h>
#include "MoriLabelling.h"
#include "Functions.h"

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

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

  // Parse input line
  _TStringArg in( "i", "input", "Input image", true, "", "file" );
  _TStringArg labels( "l", "labels", "Input labels", true, "", "file" );
  _TStringArg vesselness( "v", "vesselness", "Input vesselness", true, "", "file" );
  _TStringArg out( "o", "output", "Output image", true, "", "file" );
  _TRealArg vThr( "a", "vesselness_thr", "Vesselness threshold (%)", false, 5, "value (5)" );
  _TPixelArg uThr( "u", "upper_thr", "Upper threshold", false, -400, "value (-400)" );
  try
  {
    TCLAP::CmdLine cmd( "Labelling", ' ', "1.0.0" );
    cmd.add( uThr );
    cmd.add( vThr );
    cmd.add( out );
    cmd.add( vesselness );
    cmd.add( labels );
    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
      << std::endl;
    return( 1 );

  } // yrt

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

    // Read input labels
    TLabels::Pointer input_labels;
    CTBronchi::ReadImage( input_labels, labels.getValue( ) );

    // Read input vesselness
    TScalarImage::Pointer input_vesselness;
    CTBronchi::ReadImage( input_vesselness, vesselness.getValue( ) );

    // Create labels
    typedef CTBronchi::MoriLabelling< TImage, TLabels, TScalarImage > _TLabelling;
    _TLabelling::Pointer labelling = _TLabelling::New( );
    labelling->SetInput( input_image );
    labelling->SetInputLabels( input_labels );
    labelling->SetInputVesselness( input_vesselness );
    labelling->SetVesselnessThreshold( vThr.getValue( ) );
    labelling->SetUpperThreshold( uThr.getValue( ) );
    labelling->SetInsideValue( 1 );
    labelling->SetOutsideValue( 2 );
    labelling->SetFillValue( 2 );
    double t = CTBronchi::MeasureTime( labelling );
    std::cout << "Labelling executed in " << t << " s" << std::endl;

    // Write result
    CTBronchi::WriteImage( labelling->GetOutput( ), out.getValue( ) );
  }
  catch( std::exception& err )
  {
    std::cerr
      << "===============================" << std::endl
      << "Error caught: " << std::endl
      << err.what( ) << std::endl
      << "===============================" << std::endl
      << std::endl;
    return( 1 );

  } // yrt
  return( 0 );
}

// eof - $RCSfile$