ConfidenceConnected3D.cxx

/*=========================================================================

  Program:   Insight Segmentation & Registration Toolkit
  Module:    ConfidenceConnected3D.cxx
  Language:  C++
  Date:      $Date$
  Version:   $Revision$

  Copyright (c) Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.

     This software is distributed WITHOUT ANY WARRANTY; without even 
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
     PURPOSE.  See the above copyright notices for more information.

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

#ifdef __BORLANDC__
#define ITK_LEAN_AND_MEAN
#endif

//  Software Guide : BeginCommandLineArgs
//  INPUTS: {brainweb165a10f17.mha}
//  OUTPUTS: {WhiteMatterSegmentation.mhd}
//  Software Guide : EndCommandLineArgs


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

// Software Guide : BeginLatex
//
// This example is a 3D version of the previous ConfidenceConnected example.
// In this particular case, we are extracting the white matter from an input
// Brain MRI dataset.
//
// Software Guide : EndLatex 


int main( int argc, char *argv[] )
{
  if( argc < 3 )
    {
    std::cerr << "Missing Parameters " << std::endl;
    std::cerr << "Usage: " << argv[0];
    std::cerr << " inputImage  outputImage " << std::endl;
    return 1;
    }


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

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

  smoothing->SetInput( reader->GetOutput() );
  confidenceConnected->SetInput( smoothing->GetOutput() );
  caster->SetInput( confidenceConnected->GetOutput() );
  writer->SetInput( caster->GetOutput() );

  smoothing->SetNumberOfIterations( 2 );
  smoothing->SetTimeStep( 0.05 );

  confidenceConnected->SetMultiplier( 2.5 );
  confidenceConnected->SetNumberOfIterations( 5 );
  confidenceConnected->SetInitialNeighborhoodRadius( 2 );
  confidenceConnected->SetReplaceValue( 255 );
  
  InternalImageType::IndexType index1;
  index1[0] = 118; 
  index1[1] = 133;
  index1[2] = 92;
  confidenceConnected->AddSeed( index1 );

  InternalImageType::IndexType index2;
  index2[0] = 63;
  index2[1] = 135;
  index2[2] = 94;
  confidenceConnected->AddSeed( index2 );
 
  InternalImageType::IndexType index3;
  index3[0] = 63;
  index3[1] = 157;
  index3[2] = 90;
  confidenceConnected->AddSeed( index3 );
 
  InternalImageType::IndexType index4;
  index4[0] = 111;
  index4[1] = 150;
  index4[2] = 90;
  confidenceConnected->AddSeed( index4 );
 
  InternalImageType::IndexType index5;
  index5[0] = 111;
  index5[1] = 50;
  index5[2] = 88;
  confidenceConnected->AddSeed( index5 );

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


  return EXIT_SUCCESS;
}