[Insight-users] RGB Fuzzy Connectedness

[Juan Paredes]

Hi ITK users,

I'm attempting to run fuzzy connectedness segmentation on a RGB image. Based on ITK documentation examples, I have  compiled  the code  and build the executable but when I run it the program aborts and the following error message it is displayed:

.../vnl_matrix.txx :  1184: matrix has non-finite elements

Any suggestion to fix the problem?.

Here, it is the code:



#include "itkVectorConfidenceConnectedImageFilter.h"
#include "itkSimpleFuzzyConnectednessRGBImageFilter.h"


#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkVector.h"
#include "itkArray2D.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 outputmap seedX seedY multiplier " << std::endl;
    return 1;
    }

  typedef   unsigned char                         PixelComponentType;
  const   unsigned char        VDim = 3;
  typedef   itk::Vector< PixelComponentType, VDim >   InputPixelType;
  const     unsigned int    Dimension = 2;
  typedef itk::Image< InputPixelType, Dimension >  InputImageType;

  typedef unsigned char OutputPixelType;
  typedef itk::Image< OutputPixelType, Dimension > OutputImageType;

                
  typedef  itk::VectorConfidenceConnectedImageFilter< InputImageType, 
                                    OutputImageType > ConnectedFilterType;
  

  ConnectedFilterType::Pointer confidenceConnected = ConnectedFilterType::New();

  typedef itk::SimpleFuzzyConnectednessRGBImageFilter< InputImageType, OutputImageType >  FuzzySegmentationFilterType;
  
  FuzzySegmentationFilterType::Pointer fuzzysegmenter = FuzzySegmentationFilterType::New();

  typedef FuzzySegmentationFilterType::FuzzySceneType  FuzzySceneType; 

  typedef  itk::ImageFileReader<  InputImageType   > ReaderType;
  typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;
  typedef  itk::ImageFileWriter< FuzzySceneType  >    FuzzyWriterType;


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

  FuzzyWriterType::Pointer fwriter = FuzzyWriterType::New();

  reader->SetFileName( argv[1] );
  writer->SetFileName( argv[2] ); 
  fwriter->SetFileName( argv[3] );

  InputImageType::IndexType index;

  index[0] = atoi(argv[4]);
  index[1] = atoi(argv[5]);


  confidenceConnected->SetInput( reader->GetOutput() );

  WriterType::Pointer confidenceWriter = WriterType::New();
  confidenceWriter->SetInput( confidenceConnected->GetOutput() );
  confidenceWriter->SetFileName("confConPre.png");
  confidenceWriter->Update();

    
  fuzzysegmenter->SetInput( reader->GetOutput() );
   
  const double multiplier = atof( argv[6] );

  confidenceConnected->SetMultiplier( multiplier );

  const unsigned int iterations = 2;
    
  confidenceConnected->SetNumberOfIterations( iterations );

  confidenceConnected->SetReplaceValue( 255 );

  confidenceConnected->SetSeed( index );
   
  //confidenceConnected->AddSeed( index );

  confidenceConnected->SetInitialNeighborhoodRadius( 3 );

  typedef ConnectedFilterType::MeanVectorType   MeanVectorType; 
    
  const MeanVectorType & mean = confidenceConnected->GetMean();

  typedef ConnectedFilterType::CovarianceMatrixType   CovarianceMatrixType; 
    
  const CovarianceMatrixType & covariance = confidenceConnected->GetCovariance();
  
  std::cout << "Covariance matrix = " << std::endl;
  std::cout << covariance << std::endl;
    
  fuzzysegmenter->SetObjectSeed( index );
  
  const double * mean1 = mean.data_block();

  const double * cov1 = covariance.data_block();

  double ccov[3][3]; 
  
  double mmean[3];
  
  int z=0;
  for (int x=0; x<3; ++x)
  for (int y=0; y<3; ++y)
  {
      ccov[x][y]= cov1[z];
      ++z;
  }

 
  for (int i=0; i<3; ++i)
  mmean[i]= mean1[i];

  fuzzysegmenter->SetMean(  mmean );  
  fuzzysegmenter->SetVariance( ccov );
  fuzzysegmenter->SetThreshold( 0.5 );
  
  writer->SetInput( fuzzysegmenter->GetOutput() );
  
  fwriter->SetInput( fuzzysegmenter->GetFuzzyScene() );
  

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


  return 0;
}


 
---------------------------------
No need to miss a message. Get email on-the-go 
with Yahoo! Mail for Mobile. Get started.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://public.kitware.com/pipermail/insight-users/attachments/20070220/fd9f50fb/attachment.html