// @author T. Piekos
// Confidence Connected Segmentation w/ITK
// 10.18.2007

// code derived from sample code provided

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImage.h"
#include "itkConfidenceConnectedImageFilter.h"
#include "itkCastImageFilter.h"

using namespace std;
using namespace itk;

int main(int argc, char *argv[])
{
	if (argc < 6)
	{
		cerr << "Missing Parameters: [input file] [output file] [xseed] [yseed] [zseed]" << endl;
		return -1;
	}

	// define the image type
	typedef	unsigned short			InternalPixelType;
	const	unsigned int	Dimension = 3;
	typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
	typedef unsigned short OutputPixelType;
	typedef itk::Image< OutputPixelType, Dimension > OutputImageType;

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

	// set up the reader
	ReaderType::Pointer reader = ReaderType::New();
	reader->SetFileName(argv[1]);
	
	// set up the writer
	WriterType::Pointer writer = WriterType::New();
	writer->SetFileName(argv[2]);

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

	ConnectedFilterType::Pointer confidenceConnected = ConnectedFilterType::New();
	
	// there was something with smoothing in the sample code,
	// removed
	
	confidenceConnected->SetInput( reader->GetOutput() );
	writer->SetInput( confidenceConnected->GetOutput() );

	confidenceConnected->SetMultiplier( 2.5 );
	confidenceConnected->SetNumberOfIterations( 5 );
	confidenceConnected->SetReplaceValue( 255 );

  	InternalImageType::IndexType  index;

  	index[0] = atoi( argv[3] );
  	index[1] = atoi( argv[4] );

	// add a third dimension not in the sample code
	index[2] = atoi( argv[5] );
	
	confidenceConnected->SetSeed( index );
	
	confidenceConnected->SetInitialNeighborhoodRadius( 2 );
	
	try
    {
    	writer->Update();
    }
  	catch( itk::ExceptionObject & excep )
    {
    	cerr << "Exception caught !" << endl;
    	cerr << excep << endl;
    }

	return 0;

}