/*  
	Philip Radin
	Open Source Practice
	10/17/2007
*/

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

#ifdef __BORLANDC__
#define ITK_LEAN_AND_MEAN
#endif
#include "itkConfidenceConnectedImageFilter.h"
#include "itkImage.h"

#include "itkExtractImageFilter.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"


int main( int argc, char *argv[] )
{
  if( argc < 5 )
    {
    std::cerr << "Missing Parameters " << std::endl;
    std::cerr << "Usage: " << argv[0];
    std::cerr << " inputImage  outputImage seedX seedY seedZ" << std::endl;
    return 1;
    }

  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;

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

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

  typedef itk::ConfidenceConnectedImageFilter<InternalImageType, InternalImageType> 
    ConnectedFilterType;
  ConnectedFilterType::Pointer confidenceConnected = ConnectedFilterType::New();

  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[4] );
  index[1] = atoi( argv[5] );
  index[2] = atoi( argv[6] );

  confidenceConnected->SetSeed( index );
  confidenceConnected->SetInitialNeighborhoodRadius( 2 );

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

// Extract a Z slice and save it as PNG.

typedef unsigned short Input2DPixelType;
typedef unsigned char Output2DPixelType;

typedef itk::Image< Input2DPixelType, 3 > Input2DImageType;
typedef itk::Image< Output2DPixelType, 2 > Output2DImageType;
typedef itk::ImageFileWriter< Output2DImageType > Writer2DType;

Writer2DType::Pointer writer2D = Writer2DType::New();

typedef itk::ExtractImageFilter< Input2DImageType, Output2DImageType > Filter2DType;
Filter2DType::Pointer filter2D = Filter2DType::New();

confidenceConnected->Update();
Input2DImageType::RegionType inputRegion = confidenceConnected->GetOutput()->GetLargestPossibleRegion();

Input2DImageType::SizeType size = inputRegion.GetSize();
size[2] = 0;

Input2DImageType::IndexType start = inputRegion.GetIndex();
const unsigned int sliceNumber = atoi( argv[6] );
start[0] = 0;
start[1] = 0;
start[2] = sliceNumber;

Input2DImageType::RegionType desiredRegion;
desiredRegion.SetSize( size );
desiredRegion.SetIndex( start );

filter2D->SetInput( confidenceConnected->GetOutput());
filter2D->SetExtractionRegion( desiredRegion );

writer2D->SetInput( filter2D->GetOutput() );
writer2D->SetFileName( argv[3] );

try
{
	writer2D->Update();
}
catch( itk::ExceptionObject & err )
{
	std::cerr << "ExceptionObject caught !" << std::endl;
	std::cerr << err << std::endl;
	return EXIT_FAILURE;
}

  return 0;
}