void mitk::SegTool2D::WriteBackSegmentationResult(std::vector<mitk::SegTool2D::SliceInformation> sliceList, bool writeSliceToVolume)
{
std::vector<mitk::Surface::Pointer> contourList;
contourList.reserve(sliceList.size());
ImageToContourFilter::Pointer contourExtractor = ImageToContourFilter::New();
DataNode* workingNode( m_ToolManager->GetWorkingData(0) );
Image* image = dynamic_cast<Image*>(workingNode->GetData());
mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
timeSelector->SetInput( image );
timeSelector->SetTimeNr( 0 );
timeSelector->SetChannelNr( 0 );
timeSelector->Update();
Image::Pointer dimRefImg = timeSelector->GetOutput();
for (unsigned int i = 0; i < sliceList.size(); ++i)
{
SliceInformation currentSliceInfo = sliceList.at(i);
if(writeSliceToVolume)
this->WriteSliceToVolume(currentSliceInfo);
if (m_SurfaceInterpolationEnabled && dimRefImg->GetDimension() == 3)
{
currentSliceInfo.slice->DisconnectPipeline();
contourExtractor->SetInput(currentSliceInfo.slice);
contourExtractor->Update();
mitk::Surface::Pointer contour = contourExtractor->GetOutput();
contour->DisconnectPipeline();
contourList.push_back(contour);
}
}
mitk::SurfaceInterpolationController::GetInstance()->AddNewContours(contourList);
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void mitk::SegTool2D::WriteBackSegmentationResult (const InteractionPositionEvent* positionEvent, Image* slice)
{
if(!positionEvent) return;
const PlaneGeometry* planeGeometry( dynamic_cast<const PlaneGeometry*> (positionEvent->GetSender()->GetCurrentWorldGeometry2D() ) );
if( planeGeometry && slice)
{
DataNode* workingNode( m_ToolManager->GetWorkingData(0) );
Image* image = dynamic_cast<Image*>(workingNode->GetData());
unsigned int timeStep = positionEvent->GetSender()->GetTimeStep( image );
this->WriteBackSegmentationResult(planeGeometry, slice, timeStep);
slice->DisconnectPipeline();
ImageToContourFilter::Pointer contourExtractor = ImageToContourFilter::New();
contourExtractor->SetInput(slice);
contourExtractor->Update();
mitk::Surface::Pointer contour = contourExtractor->GetOutput();
if (m_3DInterpolationEnabled && contour->GetVtkPolyData()->GetNumberOfPoints() > 0 && image->GetDimension() == 3)
{
unsigned int pos = this->AddContourmarker(positionEvent);
us::ServiceReference<PlanePositionManagerService> serviceRef =
us::GetModuleContext()->GetServiceReference<PlanePositionManagerService>();
PlanePositionManagerService* service = us::GetModuleContext()->GetService(serviceRef);
mitk::SurfaceInterpolationController::GetInstance()->AddNewContour( contour, service->GetPlanePosition(pos));
contour->DisconnectPipeline();
}
}
}
void mitk::SegTool2D::UpdateSurfaceInterpolation(const Image *slice,
const Image *workingImage,
const PlaneGeometry *plane,
bool detectIntersection)
{
if (!m_SurfaceInterpolationEnabled)
return;
ImageToContourFilter::Pointer contourExtractor = ImageToContourFilter::New();
mitk::Surface::Pointer contour;
if (detectIntersection)
{
// Test whether there is something to extract or whether the slice just contains intersections of others
mitk::Image::Pointer slice2 = slice->Clone();
mitk::MorphologicalOperations::Erode(slice2, 2, mitk::MorphologicalOperations::Ball);
contourExtractor->SetInput(slice2);
contourExtractor->Update();
contour = contourExtractor->GetOutput();
if (contour->GetVtkPolyData()->GetNumberOfPoints() == 0)
{
// Remove contour!
mitk::SurfaceInterpolationController::ContourPositionInformation contourInfo;
contourInfo.contourNormal = plane->GetNormal();
contourInfo.contourPoint = plane->GetOrigin();
mitk::SurfaceInterpolationController::GetInstance()->RemoveContour(contourInfo);
return;
}
}
contourExtractor->SetInput(slice);
contourExtractor->Update();
contour = contourExtractor->GetOutput();
mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
timeSelector->SetInput(workingImage);
timeSelector->SetTimeNr(0);
timeSelector->SetChannelNr(0);
timeSelector->Update();
Image::Pointer dimRefImg = timeSelector->GetOutput();
if (contour->GetVtkPolyData()->GetNumberOfPoints() != 0 && dimRefImg->GetDimension() == 3)
{
mitk::SurfaceInterpolationController::GetInstance()->AddNewContour(contour);
contour->DisconnectPipeline();
}
else
{
// Remove contour!
mitk::SurfaceInterpolationController::ContourPositionInformation contourInfo;
contourInfo.contourNormal = plane->GetNormal();
contourInfo.contourPoint = plane->GetOrigin();
mitk::SurfaceInterpolationController::GetInstance()->RemoveContour(contourInfo);
}
}
void mitk::SegTool2D::WriteBackSegmentationResult (const PositionEvent* positionEvent, Image* slice)
{
const PlaneGeometry* planeGeometry( dynamic_cast<const PlaneGeometry*> (positionEvent->GetSender()->GetCurrentWorldGeometry2D() ) );
DataNode* workingNode( m_ToolManager->GetWorkingData(0) );
Image* image = dynamic_cast<Image*>(workingNode->GetData());
unsigned int timeStep = positionEvent->GetSender()->GetTimeStep( image );
//Make sure that for reslicing and overwriting the same alogrithm is used. We can specify the mode of the vtk reslicer
vtkSmartPointer<mitkVtkImageOverwrite> reslice = vtkSmartPointer<mitkVtkImageOverwrite>::New();
//Set the slice as 'input'
reslice->SetInputSlice(slice->GetVtkImageData());
//set overwrite mode to true to write back to the image volume
reslice->SetOverwriteMode(true);
reslice->Modified();
mitk::ExtractSliceFilter::Pointer extractor = mitk::ExtractSliceFilter::New(reslice);
extractor->SetInput( image );
extractor->SetTimeStep( timeStep );
extractor->SetWorldGeometry( planeGeometry );
extractor->SetVtkOutputRequest(true);
extractor->SetResliceTransformByGeometry( image->GetTimeSlicedGeometry()->GetGeometry3D( timeStep ) );
extractor->Modified();
extractor->Update();
//the image was modified within the pipeline, but not marked so
image->Modified();
image->GetVtkImageData()->Modified();
/*============= BEGIN undo feature block ========================*/
//specify the undo operation with the edited slice
m_doOperation = new DiffSliceOperation(image, extractor->GetVtkOutput(),slice->GetGeometry(), timeStep, const_cast<mitk::PlaneGeometry*>(planeGeometry));
//create an operation event for the undo stack
OperationEvent* undoStackItem = new OperationEvent( DiffSliceOperationApplier::GetInstance(), m_doOperation, m_undoOperation, "Segmentation" );
//add it to the undo controller
UndoController::GetCurrentUndoModel()->SetOperationEvent( undoStackItem );
//clear the pointers as the operation are stored in the undocontroller and also deleted from there
m_undoOperation = NULL;
m_doOperation = NULL;
/*============= END undo feature block ========================*/
slice->DisconnectPipeline();
ImageToContourFilter::Pointer contourExtractor = ImageToContourFilter::New();
contourExtractor->SetInput(slice);
contourExtractor->Update();
mitk::Surface::Pointer contour = contourExtractor->GetOutput();
if (m_3DInterpolationEnabled && contour->GetVtkPolyData()->GetNumberOfPoints() > 0 )
{
unsigned int pos = this->AddContourmarker(positionEvent);
mitk::ServiceReference serviceRef = mitk::GetModuleContext()->GetServiceReference<PlanePositionManagerService>();
PlanePositionManagerService* service = dynamic_cast<PlanePositionManagerService*>(mitk::GetModuleContext()->GetService(serviceRef));
mitk::SurfaceInterpolationController::GetInstance()->AddNewContour( contour, service->GetPlanePosition(pos));
contour->DisconnectPipeline();
}
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
