//connected threshold
#if defined(_MSC_VER)
#pragma warning ( disable : 4786 )
#endif

#ifdef __BORLANDC__
#define ITK_LEAN_AND_MEAN
#endif


#include "itkConnectedThresholdImageFilter.h"
#include "itkImage.h"
#include "itkCastImageFilter.h"
#include "itkCurvatureFlowImageFilter.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"


int main( int argc, char *argv[])
{
  if( argc < 7 )
    {
    std::cerr << "Missing Parameters " << std::endl;
    std::cerr << "Usage: " << argv[0];
    std::cerr << " inputImage  outputImage seed1X seed2Y seed3Z seed2X seed2Y seed3Z lowerThreshold upperThreshold" << std::endl;
    return 1;
    }


  typedef   float           InternalPixelType;
  const     unsigned int    Dimension = 3;
  typedef itk::Image< InternalPixelType, Dimension >  InternalImageType;


  typedef short OutputPixelType;
  typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
  typedef itk::CastImageFilter< InternalImageType, OutputImageType >
    CastingFilterType;
  CastingFilterType::Pointer caster = CastingFilterType::New();
                        

  typedef  itk::ImageFileReader< InternalImageType > ReaderType;
  typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;

  ReaderType::Pointer reader = ReaderType::New();
  WriterType::Pointer writer = WriterType::New();

  reader->SetFileName( argv[1] );
  writer->SetFileName( argv[2] );


  typedef itk::CurvatureFlowImageFilter< InternalImageType, InternalImageType >
    CurvatureFlowImageFilterType;

  CurvatureFlowImageFilterType::Pointer smoothing = 
                         CurvatureFlowImageFilterType::New();

  typedef itk::ConnectedThresholdImageFilter< InternalImageType, 
                                    InternalImageType > ConnectedFilterType;

  ConnectedFilterType::Pointer connectedThreshold = ConnectedFilterType::New();
  //  if(atoi(argv[8]) > 1)
  //{
   smoothing->SetNumberOfIterations( 2 );
   smoothing->SetTimeStep(0.125 );
   smoothing->SetInput( reader->GetOutput() );
   connectedThreshold->SetInput( smoothing->GetOutput() );
  //} else {

  //  connectedThreshold->SetInput(reader->GetOutput() );
    //}
   caster->SetInput( connectedThreshold->GetOutput() );
   writer->SetInput( caster->GetOutput() );
 
 

  const InternalPixelType lowerThreshold = atof( argv[9] );
  const InternalPixelType upperThreshold = atof( argv[10] );


  connectedThreshold->SetLower(  lowerThreshold  );
  connectedThreshold->SetUpper(  upperThreshold  );

  connectedThreshold->SetReplaceValue( 255 );


  InternalImageType::IndexType  index;
  
  index[0] = atoi( argv[3] );
  index[1] = atoi( argv[4] );
  index[2] = atoi( argv[5] );

  InternalImageType::IndexType  index2;
  
  index2[0] = atoi( argv[6] );
  index2[1] = atoi( argv[7] );
  index2[2] = atoi( argv[8] );

  connectedThreshold->AddSeed( index );
  connectedThreshold->AddSeed( index2 );

  try
    {
    writer->Update();
    }
  catch( itk::ExceptionObject & excep )
    {
    std::cerr << "Exception caught !" << std::endl;
    std::cerr << excep << std::endl;
    }

  return 0;
}