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();
}
}
}
}
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);
}
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();
}
void mitk::OtsuTool3D::ConfirmSegmentation()
{
GetTargetSegmentationNode()->SetData(dynamic_cast<mitk::Image*>(m_BinaryPreviewNode->GetData()));
m_ToolManager->ActivateTool(-1);
}