[vtkusers] Error message about vtk

Wed Nov 3 09:10:25 EDT 2010

The problem is this: when I run the program, till the diffusion filtering process, it works well. However, after that, once I click the fast marching button, the crash occurred. 

If I skip the diffusion filtering process and run the fast marching function directly, then it works well.

I am really confused. Do you know why? I appreciated your help so far very much!

Thanks a lot,

Xiaopeng

发件人: Jothy [mailto:jothybasu at gmail.com] 
发送时间: 2010년 11월 3일 수요일 오후 9:55
收件人: Xiaopeng Yang
抄送: vtk
主题: Re: [vtkusers] Error message about vtk

Are you setting importer->SetImportVoidPointer(data);

"data" is the output from itk.

I hope you had a look at http://vtk.org/gitweb?p=VTK.git;a=blob;f=Imaging/Testing/Cxx/ImportExport.cxx

Jothy

On Wed, Nov 3, 2010 at 12:40 PM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Thank you so much for your warmhearted help! My code is kind of huge. Let me explain briefly: the program is coded for segmentation using ITK, visualization by VTK, and interface by QT. It consists of image loading, diffusion filtering, then fast marching segmentation using diffusion filtering output as input. I attach the code here and hope you guys can help me to find inappropriate part. Thank you very much in advance!

//connect vtk to itk

template <typename ITK_Exporter, typename VTK_Importer>

void ConnectPipelines(ITK_Exporter exporter, VTK_Importer* importer)

{

  importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback());

  importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback());

  importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());

  importer->SetSpacingCallback(exporter->GetSpacingCallback());

  importer->SetOriginCallback(exporter->GetOriginCallback());

  importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());

  importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback());

  importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback());

  importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());

  importer->SetDataExtentCallback(exporter->GetDataExtentCallback());

  importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback());

  importer->SetCallbackUserData(exporter->GetCallbackUserData());

}

//Paramter definiation

#define N_SEEDS 11

typedef    float    InputPixelType;

typedef    float    OutputPixelType;

typedef itk::Image< InputPixelType,  3 >   InputImageType;

typedef itk::Image< OutputPixelType, 3 >   OutputImageType;

typedef itk::ImageSeriesReader< InputImageType >     ReaderType;

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

typedef itk::GDCMImageIO                        ImageIOType;

typedef itk::GDCMSeriesFileNames                NamesGeneratorType;

ImageIOType::Pointer gdcmIO = ImageIOType::New();

NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();

typedef itk::VTKImageExport< OutputImageType > ExportFilterType;

typedef itk::RescaleIntensityImageFilter< 

             OutputImageType, InputImageType > RescaleFilterType;

RescaleFilterType::Pointer rescaler = RescaleFilterType::New();

typedef itk::BinaryThresholdImageFilter< InputImageType, 

                    OutputImageType    >    ThresholdingFilterType;

SimpleView::SimpleView() 

{

  this->ui = new Ui_SimpleView;

this->ui->setupUi(this);

  // Set up action signals and slots

connect(this->ui->actionOpen, SIGNAL(triggered()), this, SLOT(slotOpen())); 

connect(this->ui->pushButton_14, SIGNAL(clicked()), this, SLOT(slotContour()));

};

void SimpleView::slotOpen()

{

  QString directory = QFileDialog::getExistingDirectory(this,

                                    tr("Choose a directory"), QDir::currentPath());

  namesGenerator->SetInputDirectory(directory); 

  const ReaderType::FileNamesContainer & filenames = 

                            namesGenerator->GetInputFileNames();

  unsigned int numberOfFilenames =  filenames.size();

  std::cout << numberOfFilenames << " images loaded" << std::endl; 

  for(unsigned int fni = 0; fni<numberOfFilenames; fni++)

    {

    std::cout << "filename # " << fni << " = ";

    std::cout << filenames[fni] << std::endl;

    }

  reader->SetImageIO( gdcmIO );

  reader->SetFileNames( filenames );

  //reader->Update();

  //Diffusion filter

  typedef itk::GradientAnisotropicDiffusionImageFilter<

               InputImageType, OutputImageType >  FilterType;

  FilterType::Pointer filter = FilterType::New();

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

  // Set parameters for diffusion filter

  const unsigned int numberOfIterations = 5;

  const double       timeStep = 0.0625;

  const double       conductance = 3;

  filter->SetNumberOfIterations( numberOfIterations );

  filter->SetTimeStep( timeStep );

  filter->SetConductanceParameter( conductance );

  filter->Update();

  RescaleFilterType::Pointer rescaler = RescaleFilterType::New();

  rescaler->SetOutputMinimum(   0 );

  rescaler->SetOutputMaximum( 255 );

rescaler->SetInput( filter->GetOutput() );

}

void SimpleView::slotContour() {

  long int seed_points[N_SEEDS][3] = {

                                                            {     186,  206, 138    },

                                                            {     138,  218, 124    },

                                                            {     226,  201, 124    },

                                                            {     309,  220, 124    },

                                                            {     147,  305, 83     },

                                                            {     111,  228, 83     },

                                                            {     171,  176, 83     },

                                                            {     245,  178, 83     },

                                                            {     202,  243, 83     },

                                                            {     112,  242, 45     },

                                                            {     98,  253, 7 }                                         

                                                        };

  const InputPixelType  timeThreshold = 85;

  ThresholdingFilterType::Pointer thresholder1 = ThresholdingFilterType::New();

  thresholder1->SetLowerThreshold(           0.0  );

  thresholder1->SetUpperThreshold( timeThreshold  );

  thresholder1->SetOutsideValue(  0  );

  thresholder1->SetInsideValue(  255 );

  typedef   itk::GradientMagnitudeRecursiveGaussianImageFilter< 

                               InputImageType, 

                               InputImageType >  GradientFilterType;

  typedef   itk::SigmoidImageFilter<

                               InputImageType, 

                               InputImageType >  SigmoidFilterType;

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

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

  sigmoid->SetOutputMinimum(  0.0  );        

  sigmoid->SetOutputMaximum(  1.0  );        

  typedef  itk::FastMarchingImageFilter< InputImageType, 

                              InputImageType >    FastMarchingFilterType;

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

  gradientMagnitude->SetInput( rescaler->GetOutput() ); // using rescaler from diffusion filter as input 

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

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

  thresholder1->SetInput( fastMarching->GetOutput() );

  //thresholder1->Update();

  const double sigma = 1.3;                 

  gradientMagnitude->SetSigma(  sigma  );

  const double alpha =  -0.05;                 

  const double beta =  0.3;              

  sigmoid->SetAlpha( alpha );

  sigmoid->SetBeta(  beta  );

  typedef FastMarchingFilterType::NodeContainer           NodeContainer;

  typedef FastMarchingFilterType::NodeType                NodeType;

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

  InputImageType::IndexType  seedPosition, seedPosition2;   

  const double initialDistance = 2.0;

  NodeType node, node1, node2;

  const double seedValue = -1*initialDistance;

  for (int i = 0; i<N_SEEDS; i++)   {

      seedPosition[0] = seed_points[i][0];

      seedPosition[1] = seed_points[i][1];

      seedPosition[2] = seed_points[i][2];

      node.SetValue( seedValue );

      node.SetIndex( seedPosition );

      seeds->InsertElement( i, node );

      std::cout << "Seed Position " << seedPosition << std::endl;

  }

  fastMarching->SetTrialPoints(  seeds  );

  fastMarching->SetOutputSize( 

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

  const double stoppingTime = 100;

  fastMarching->SetStoppingValue(  stoppingTime  );

  ExportFilterType::Pointer itkExporter2 = ExportFilterType::New();

  itkExporter2->SetInput( thresholder1->GetOutput() );

  vtkImageImport* vtkImporter2 = vtkImageImport::New();  

  ConnectPipelines(itkExporter2, vtkImporter2);

  vtkImageViewer2 *imageViewer = vtkImageViewer2::New();

  this->ui->qvtkWidget->SetRenderWindow(imageViewer->GetRenderWindow());

  vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();

  imageViewer->SetupInteractor(iren);

  imageViewer->SetInput(vtkImporter2->GetOutput());

  imageViewer->SetColorLevel(127);

  imageViewer->SetColorWindow(255);

  imageViewer->Render();

  imageViewer->GetRenderer()->ResetCamera();

  vtkSliderRepresentation2D *SliderRepres = vtkSliderRepresentation2D::New();

  int min = imageViewer->GetSliceMin();

  int max = imageViewer->GetSliceMax();

  SliderRepres->SetMinimumValue(min);

  SliderRepres->SetMaximumValue(max);

  SliderRepres->SetValue(static_cast<int>((min + max) / 2));

  SliderRepres->GetPoint1Coordinate()->SetCoordinateSystemToNormalizedDisplay();

  SliderRepres->GetPoint1Coordinate()->SetValue(0.92, 0.9);

  SliderRepres->GetPoint2Coordinate()->SetCoordinateSystemToNormalizedDisplay();

  SliderRepres->GetPoint2Coordinate()->SetValue(0.92, 0.1);

  SliderRepres->SetSliderLength(0.03);

  SliderRepres->SetSliderWidth(0.03);

  SliderRepres->SetEndCapLength(0.03);

  SliderRepres->SetEndCapWidth(0.05);

  SliderRepres->SetTubeWidth(0.005);

  SliderRepres->SetLabelFormat("%3.0lf");

  SliderRepres->SetTitleHeight(0.05);

  SliderRepres->SetLabelHeight(0.05);

  vtkSliderWidget *SliderWidget = vtkSliderWidget::New();

  SliderWidget->SetInteractor(iren);

  SliderWidget->SetRepresentation(SliderRepres);

  SliderWidget->KeyPressActivationOff();

  SliderWidget->SetAnimationModeToAnimate();

  SliderWidget->SetEnabled(true);

  vtkSliderCallback2 *SliderCb = vtkSliderCallback2::New();

  SliderCb->SetImageViewer(imageViewer);

  SliderWidget->AddObserver(vtkCommand::InteractionEvent, SliderCb);  

  imageViewer->SetSlice(static_cast<int>(SliderRepres->GetValue()));

imageViewer->SetSliceOrientationToXY();

SliderRepres->Delete();

SliderCb->Delete();

iren->Start();

iren->Delete();

}

发件人: Jothy [mailto:jothybasu at gmail.com] 
发送时间: 2010년 11월 3일 수요일 오후 9:15
收件人: Xiaopeng Yang
抄送: vtk
主题: Re: [vtkusers] Error message about vtk

You could post the code snippet, so that ppl can look into it to help you better!

Jothy

On Wed, Nov 3, 2010 at 11:54 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Dear All,

About the error message I mentioned in the last email. Did anybody know what causes the probem?

Best regards,

Yang

发件人: vtkusers-bounces at vtk.org [mailto:vtkusers-bounces at vtk.org] 代表 Xiaopeng Yang
发送时间: 2010년 11월 3일 수요일 오전 10:22
收件人: 'vtk'
主题: [vtkusers] Error message about vtk

Hi 

I got the following error when I run a segmentation algorithm. Could anyone explain the cause of this error?

Thanks,

Xiaopeng

Untitled.png

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