Пример #1
0
void mitk::BinaryThresholdULTool::CreateNewSegmentationFromThreshold(DataNode* node)
{
  if (node)
  {
    Image::Pointer feedBackImage = dynamic_cast<Image*>( m_ThresholdFeedbackNode->GetData() );
    if (feedBackImage.IsNotNull())
    {
      // create a new image of the same dimensions and smallest possible pixel type
      DataNode::Pointer emptySegmentation = GetTargetSegmentationNode();

      if (emptySegmentation)
      {
        // actually perform a thresholding and ask for an organ type
        for (unsigned int timeStep = 0; timeStep < feedBackImage->GetTimeSteps(); ++timeStep)
        {
          try
          {
            ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New();
            timeSelector->SetInput( feedBackImage );
            timeSelector->SetTimeNr( timeStep );
            timeSelector->UpdateLargestPossibleRegion();
            Image::Pointer feedBackImage3D = timeSelector->GetOutput();

            if (feedBackImage3D->GetDimension() == 2)
            {
              AccessFixedDimensionByItk_2( feedBackImage3D, ITKSetVolume, 2, dynamic_cast<Image*>(emptySegmentation->GetData()), timeStep );
            }
            else
            {
              AccessFixedDimensionByItk_2( feedBackImage3D, ITKSetVolume, 3, dynamic_cast<Image*>(emptySegmentation->GetData()), timeStep );
            }

          }
          catch(...)
          {
            Tool::ErrorMessage("Error accessing single time steps of the original image. Cannot create segmentation.");
          }
        }

        //since we are maybe working on a smaller image, pad it to the size of the original image
        if (m_OriginalImageNode.GetPointer() != m_NodeForThresholding.GetPointer())
        {
          mitk::PadImageFilter::Pointer padFilter = mitk::PadImageFilter::New();

          padFilter->SetInput(0, dynamic_cast<mitk::Image*> (emptySegmentation->GetData()));
          padFilter->SetInput(1, dynamic_cast<mitk::Image*> (m_OriginalImageNode->GetData()));
          padFilter->SetBinaryFilter(true);
          padFilter->SetUpperThreshold(1);
          padFilter->SetLowerThreshold(1);
          padFilter->Update();

          emptySegmentation->SetData(padFilter->GetOutput());
        }

        m_ToolManager->SetWorkingData( emptySegmentation );
        m_ToolManager->GetWorkingData(0)->Modified();
      }
    }
  }
}
Пример #2
0
void mitk::OtsuTool3D::ConfirmSegmentation()
{
  mitk::LabelSetImage::Pointer resultImage = mitk::LabelSetImage::New();
  resultImage->InitializeByLabeledImage(dynamic_cast<mitk::Image *>(m_BinaryPreviewNode->GetData()));
  GetTargetSegmentationNode()->SetData(resultImage);

  m_ToolManager->ActivateTool(-1);
}
Пример #3
0
void mitk::FastMarchingTool3D::ConfirmSegmentation()
{
  // combine preview image with current working segmentation
  if (dynamic_cast<mitk::Image*>(m_ResultImageNode->GetData()))
  {
    //logical or combination of preview and segmentation slice
    OutputImageType::Pointer segmentationImageInITK = OutputImageType::New();

    mitk::Image::Pointer workingImage = dynamic_cast<mitk::Image*>(GetTargetSegmentationNode()->GetData());
    if(workingImage->GetTimeSlicedGeometry()->GetTimeSteps() > 1)
    {
      mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
      timeSelector->SetInput( workingImage );
      timeSelector->SetTimeNr( m_CurrentTimeStep );
      timeSelector->UpdateLargestPossibleRegion();
      CastToItkImage( timeSelector->GetOutput(), segmentationImageInITK );
    }
    else
    {
      CastToItkImage( workingImage, segmentationImageInITK );
    }

    typedef itk::OrImageFilter<OutputImageType, OutputImageType> OrImageFilterType;
    OrImageFilterType::Pointer orFilter = OrImageFilterType::New();

    orFilter->SetInput(0, m_ThresholdFilter->GetOutput());
    orFilter->SetInput(1, segmentationImageInITK);
    orFilter->Update();

    //set image volume in current time step from itk image
    workingImage->SetVolume( (void*)(m_ThresholdFilter->GetOutput()->GetPixelContainer()->GetBufferPointer()), m_CurrentTimeStep);
    this->m_ResultImageNode->SetVisibility(false);
    this->ClearSeeds();
    workingImage->Modified();
  }

  mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
Пример #4
0
void mitk::OtsuTool3D::ConfirmSegmentation()
{
  GetTargetSegmentationNode()->SetData(dynamic_cast<mitk::Image*>(m_BinaryPreviewNode->GetData()));
  m_ToolManager->ActivateTool(-1);
}