[Insight-users] problem using itkGeodesicActiveContourLevelSetImageFilter

[john smith]

Hello,

I am reading a 3D volume, rescale it to [0,255], extract a 3D region from
this volume, use the itkGeodesicActiveContourLevelSetImageFilter over the
extracted region and finally get a slice from the output of the GAC filter.
Well I have wrote some code, which doesn't give any debug errors. I have
loaded a small extracted region (5x5x5) as input for the
itkGeodesicActiveContourLevelSetImageFilte.After finishing the debug of the
code, the compiler seems to still runing, for 3 hours so far. I cannot
understand the reason why debuger is still runing and I didn't get any
result, while I do not get any debug error when using breakpoints. Here is
my code. I hope someone could help me.

Thanks


    ///////////filter rescale
       FilterType_rescale::Pointer filter_rescale =
FilterType_rescale::New();
       filter_rescale->SetOutputMinimum(   0 );
       filter_rescale->SetOutputMaximum( value_norm );

//////extract region filter
       FilterType_region::Pointer filter_region = FilterType_region::New();
        OutputImageType::IndexType start_region;
        start_region[0] = ui->doubleSpinBox_start_x->value();
        start_region[1] = ui->doubleSpinBox_start_y->value();
        start_region[2] = ui->doubleSpinBox_start_z->value();

        OutputImageType::SizeType size_region;
        size_region[0] = ui->doubleSpinBox_size_x->value();
        size_region[1] = ui->doubleSpinBox_size_y->value();
        size_region[2] = ui->doubleSpinBox_size_z->value();

        OutputImageType::RegionType desiredRegion_region;
        desiredRegion_region.SetSize(  size_region  );
        desiredRegion_region.SetIndex( start_region );

        filter_region->SetRegionOfInterest( desiredRegion_region );

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


        reader->SetFileName( fileName.toStdString()  );


        filter_rescale->SetInput( reader->GetOutput() );
        filter_region->SetInput( filter_rescale->GetOutput() );
        ////////////////////////////////////////////////////////////
        /////////////////////GAC algorithm in extracted region
         ThresholdingFilterType::Pointer thresholder =
ThresholdingFilterType::New();

  thresholder->SetLowerThreshold( -1000.0 );
  thresholder->SetUpperThreshold(     0.0 );

  thresholder->SetOutsideValue(  0  );
  thresholder->SetInsideValue(  255 );


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

  GradientFilterType::Pointer  gradientMagnitude =
GradientFilterType::New();

  SigmoidFilterType::Pointer sigmoid = SigmoidFilterType::New();

  sigmoid->SetOutputMinimum(  0.0  );
  sigmoid->SetOutputMaximum(  1.0  );


   FastMarchingFilterType::Pointer  fastMarching =
FastMarchingFilterType::New();

   GeodesicActiveContourFilterType::Pointer geodesicActiveContour =
                                     GeodesicActiveContourFilterType::New();



  const double propagationScaling =
ui->doubleSpinBox_propagationScaling->value();
  geodesicActiveContour->SetPropagationScaling( propagationScaling );
  geodesicActiveContour->SetCurvatureScaling( 1.0 );
  geodesicActiveContour->SetAdvectionScaling( 1.0 );


  geodesicActiveContour->SetMaximumRMSError( 0.02 );
  geodesicActiveContour->SetNumberOfIterations( 800 );


  smoothing->SetInput( filter_region->GetOutput() );
  gradientMagnitude->SetInput( smoothing->GetOutput() );
  sigmoid->SetInput( gradientMagnitude->GetOutput() );

  geodesicActiveContour->SetInput(  fastMarching->GetOutput() );
  geodesicActiveContour->SetFeatureImage( sigmoid->GetOutput() );

  thresholder->SetInput( geodesicActiveContour->GetOutput() );

  //////////////////////////

    FilterType_extract_GAC::Pointer filter_extract_z =
FilterType_extract_GAC::New();

    WriterType::Pointer writer_z = WriterType::New();
    writer_z->SetFileName( "result_z.png" );

  filter_region->Update();
  InputImageType::RegionType inputRegion =
           filter_region->GetOutput()->GetLargestPossibleRegion();

  InputImageType::SizeType size = inputRegion.GetSize();

  // get the size of the hole 3D image
  size_x = size[0];
  size_y = size[1];
  size_z = size[2];

  // get slices of z coordinate
  size[2] = 0;

   InputImageType::IndexType start = inputRegion.GetIndex();
 // const unsigned int sliceNumber = 90;
  ui->verticalScrollBar_z->setRange(0,size_z-1);
  unsigned int sliceNumber = ui->verticalScrollBar_z->value();
  start[2] = sliceNumber;
 // ui->verticalScrollBar_z->setValue(sliceNumber);


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

  filter_extract_z->SetExtractionRegion( desiredRegion );

  ////////////////////////////

  filter_extract_z->SetInput( thresholder->GetOutput() );
  writer_z->SetInput( filter_extract_z->GetOutput() );


  smoothing->SetTimeStep( 0.0625 );
  smoothing->SetNumberOfIterations(  5 );
  smoothing->SetConductanceParameter( 9.0 );

  const double sigma = ui->doubleSpinBox_sigma->value();
  gradientMagnitude->SetSigma(  sigma  );

  const double alpha =  ui->doubleSpinBox_alpha->value();
  const double beta  =  ui->doubleSpinBox_beta->value();
  sigmoid->SetAlpha( alpha );
  sigmoid->SetBeta(  beta  );


  NodeContainer::Pointer seeds = NodeContainer::New();

  InputImageType::IndexType  seedPosition;

  seedPosition[0] = ui->doubleSpinBox_seed_x->value();
  seedPosition[1] = ui->doubleSpinBox_seed_y->value();
  seedPosition[2] = ui->doubleSpinBox_seed_z->value();

  const double initialDistance =
ui->doubleSpinBox_initial_distance->value();

  NodeType node;

  const double seedValue = - initialDistance;

  node.SetValue( seedValue );
  node.SetIndex( seedPosition );


  seeds->Initialize();
  seeds->InsertElement( 0, node );

   fastMarching->SetTrialPoints(  seeds  );

   fastMarching->SetSpeedConstant( 1.0 );




  fastMarching->SetOutputSize(
           reader->GetOutput()->GetBufferedRegion().GetSize() );

    try
    {
        writer_z->Update();

    }
  catch( itk::ExceptionObject & excep )
    {
    std::cerr << "Exception caught !" << std::endl;
    std::cerr << excep << std::endl;
    }
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