void mitk::PaintbrushTool::CheckIfCurrentSliceHasChanged(const InteractionPositionEvent *event)
{
const PlaneGeometry* planeGeometry( dynamic_cast<const PlaneGeometry*> (event->GetSender()->GetCurrentWorldGeometry2D() ) );
DataNode* workingNode( m_ToolManager->GetWorkingData(0) );
if (!workingNode)
return;
Image::Pointer image = dynamic_cast<Image*>(workingNode->GetData());
if ( !image || !planeGeometry )
return;
if(m_CurrentPlane.IsNull() || m_WorkingSlice.IsNull())
{
m_CurrentPlane = const_cast<PlaneGeometry*>(planeGeometry);
m_WorkingSlice = SegTool2D::GetAffectedImageSliceAs2DImage(event, image)->Clone();
m_WorkingNode->ReplaceProperty( "color", workingNode->GetProperty("color") );
m_WorkingNode->SetData(m_WorkingSlice);
}
else
{
bool isSameSlice (false);
isSameSlice = mitk::MatrixEqualElementWise(planeGeometry->GetIndexToWorldTransform()->GetMatrix(),m_CurrentPlane->GetIndexToWorldTransform()->GetMatrix());
isSameSlice = mitk::Equal(planeGeometry->GetIndexToWorldTransform()->GetOffset(),m_CurrentPlane->GetIndexToWorldTransform()->GetOffset());
if (!isSameSlice)
{
m_ToolManager->GetDataStorage()->Remove(m_WorkingNode);
m_CurrentPlane = NULL;
m_WorkingSlice = NULL;
m_WorkingNode = NULL;
m_CurrentPlane = const_cast<PlaneGeometry*>(planeGeometry);
m_WorkingSlice = SegTool2D::GetAffectedImageSliceAs2DImage(event, image)->Clone();
m_WorkingNode = mitk::DataNode::New();
m_WorkingNode->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( mitk::LevelWindow(0, 1) ) );
m_WorkingNode->SetProperty( "binary", mitk::BoolProperty::New(true) );
m_WorkingNode->SetData(m_WorkingSlice);
//So that the paintbrush contour vanished in the previous render window
RenderingManager::GetInstance()->RequestUpdateAll();
}
}
if(!m_ToolManager->GetDataStorage()->Exists(m_WorkingNode))
{
m_WorkingNode->SetProperty( "outline binary", mitk::BoolProperty::New(true) );
m_WorkingNode->SetProperty( "color", workingNode->GetProperty("color") );
m_WorkingNode->SetProperty( "name", mitk::StringProperty::New("Paintbrush_Node") );
m_WorkingNode->SetProperty( "helper object", mitk::BoolProperty::New(true) );
m_WorkingNode->SetProperty( "opacity", mitk::FloatProperty::New(0.8) );
m_WorkingNode->SetProperty( "includeInBoundingBox", mitk::BoolProperty::New(false));
m_WorkingNode->SetVisibility(false, mitk::BaseRenderer::GetInstance( mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget4")));
m_ToolManager->GetDataStorage()->Add(m_WorkingNode);
}
}
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();
}
}
}
bool mitk::ComplexExternalTool::OnMouseReleased(Action* action, const StateEvent* stateEvent)
{
// 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's working image corresponds to that
FeedbackContourTool::SetFeedbackContourVisible(false);
const PositionEvent* positionEvent = dynamic_cast<const PositionEvent*>(stateEvent->GetEvent());
if (!positionEvent) return false;
assert( positionEvent->GetSender()->GetRenderWindow() );
mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() );
if (!FeedbackContourTool::OnMouseReleased( action, stateEvent )) return false;
DataNode* workingNode( m_ToolManager->GetWorkingData(0) );
if (!workingNode) return false;
Image* image = dynamic_cast<Image*>(workingNode->GetData());
const PlaneGeometry* planeGeometry( dynamic_cast<const PlaneGeometry*> (positionEvent->GetSender()->GetCurrentWorldGeometry2D() ) );
if ( !image || !planeGeometry ) return false;
int affectedDimension( -1 );
int affectedSlice( -1 );
if ( FeedbackContourTool::DetermineAffectedImageSlice( image, planeGeometry, affectedDimension, affectedSlice ) )
{
// 2. Slice is known, now we try to get it as a 2D image and project the contour into index coordinates of this slice
mitk::Image::Pointer workingSlice = FeedbackContourTool::GetAffectedImageSliceAs2DImage( positionEvent, image );
if ( workingSlice.IsNull() )
{
std::cerr << "Unable to extract slice." << std::endl;
return false;
}
// etc etc. Example will be extended later. Look at other tools in MITK to see what to do here.
/*
// 5. Write the modified 2D working data slice back into the image
OverwriteSliceImageFilter::Pointer slicewriter = OverwriteSliceImageFilter::New();
slicewriter->SetInput( image );
slicewriter->SetCreateUndoInformation( true );
slicewriter->SetSliceImage( temporarySlice );
slicewriter->SetSliceDimension( affectedDimension );
slicewriter->SetSliceIndex( affectedSlice );
slicewriter->SetTimeStep( positionEvent->GetSender()->GetTimeStep( image ) );
slicewriter->Update();
*/
// 6. Make sure the result is drawn again --> is visible then.
assert( positionEvent->GetSender()->GetRenderWindow() );
mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() );
}
else
{
InteractiveSegmentationBugMessage( "FeedbackContourTool could not determine which slice of the image you are drawing on." );
}
return true;
}
mitk::Image::Pointer mitk::SegTool2D::GetAffectedWorkingSlice(const InteractionPositionEvent* positionEvent)
{
DataNode* workingNode( m_ToolManager->GetWorkingData(0) );
if ( !workingNode ) return NULL;
Image* workingImage = dynamic_cast<Image*>(workingNode->GetData());
if ( !workingImage ) return NULL;
return GetAffectedImageSliceAs2DImage( positionEvent, workingImage );
}
void mitk::SegTool2D::WriteBackSegmentationResult (const PlaneGeometry* planeGeometry, Image* slice, unsigned int timeStep)
{
if(!planeGeometry || !slice) return;
DataNode* workingNode( m_ToolManager->GetWorkingData(0) );
Image* image = dynamic_cast<Image*>(workingNode->GetData());
//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->GetGeometry( 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 ========================*/
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void mitk::LiveWireTool2D::ConfirmSegmentation()
{
DataNode *workingNode(m_ToolManager->GetWorkingData(0));
if (!workingNode)
return;
Image *workingImage = dynamic_cast<Image *>(workingNode->GetData());
if (!workingImage)
return;
// for all contours in list (currently created by tool)
std::vector<std::pair<mitk::DataNode::Pointer, mitk::PlaneGeometry::Pointer>>::iterator itWorkingContours =
this->m_WorkingContours.begin();
std::vector<SliceInformation> sliceList;
sliceList.reserve(m_WorkingContours.size());
while (itWorkingContours != this->m_WorkingContours.end())
{
// if node contains data
if (itWorkingContours->first->GetData())
{
// if this is a contourModel
mitk::ContourModel *contourModel = dynamic_cast<mitk::ContourModel *>(itWorkingContours->first->GetData());
if (contourModel)
{
// for each timestep of this contourModel
for (TimeStepType currentTimestep = 0; currentTimestep < contourModel->GetTimeGeometry()->CountTimeSteps();
++currentTimestep)
{
// get the segmentation image slice at current timestep
mitk::Image::Pointer workingSlice =
this->GetAffectedImageSliceAs2DImage(itWorkingContours->second, workingImage, currentTimestep);
mitk::ContourModel::Pointer projectedContour =
mitk::ContourModelUtils::ProjectContourTo2DSlice(workingSlice, contourModel, true, false);
mitk::ContourModelUtils::FillContourInSlice(projectedContour, workingSlice, workingImage, 1.0);
// write back to image volume
SliceInformation sliceInfo(workingSlice, itWorkingContours->second, currentTimestep);
sliceList.push_back(sliceInfo);
this->WriteSliceToVolume(sliceInfo);
}
}
}
++itWorkingContours;
}
this->WriteBackSegmentationResult(sliceList, false);
this->ClearSegmentation();
}
void mitk::SegTool2D::WriteSliceToVolume(mitk::SegTool2D::SliceInformation sliceInfo)
{
DataNode* workingNode( m_ToolManager->GetWorkingData(0) );
Image* image = dynamic_cast<Image*>(workingNode->GetData());
/*============= BEGIN undo/redo feature block ========================*/
// Create undo operation by caching the not yet modified slices
mitk::Image::Pointer originalSlice = GetAffectedImageSliceAs2DImage(sliceInfo.plane, image, sliceInfo.timestep);
DiffSliceOperation* undoOperation = new DiffSliceOperation(const_cast<mitk::Image*>(image), originalSlice, dynamic_cast<SlicedGeometry3D*>(originalSlice->GetGeometry()), sliceInfo.timestep, sliceInfo.plane);
/*============= END undo/redo feature block ========================*/
//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(sliceInfo.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( sliceInfo.timestep );
extractor->SetWorldGeometry( sliceInfo.plane );
extractor->SetVtkOutputRequest(false);
extractor->SetResliceTransformByGeometry( image->GetGeometry( sliceInfo.timestep ) );
extractor->Modified();
extractor->Update();
//the image was modified within the pipeline, but not marked so
image->Modified();
image->GetVtkImageData()->Modified();
/*============= BEGIN undo/redo feature block ========================*/
//specify the undo operation with the edited slice
DiffSliceOperation* doOperation = new DiffSliceOperation(image, extractor->GetOutput(),dynamic_cast<SlicedGeometry3D*>(sliceInfo.slice->GetGeometry()), sliceInfo.timestep, sliceInfo.plane);
//create an operation event for the undo stack
OperationEvent* undoStackItem = new OperationEvent( DiffSliceOperationApplier::GetInstance(), doOperation, 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
undoOperation = NULL;
doOperation = NULL;
/*============= END undo/redo feature block ========================*/
}
void mitk::SetRegionTool::OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
assert(positionEvent->GetSender()->GetRenderWindow());
// 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's
// working image corresponds to that
FeedbackContourTool::SetFeedbackContourVisible(false);
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
int timeStep = positionEvent->GetSender()->GetTimeStep();
DataNode *workingNode(m_ToolManager->GetWorkingData(0));
if (!workingNode)
return;
auto *image = dynamic_cast<Image *>(workingNode->GetData());
const PlaneGeometry *planeGeometry((positionEvent->GetSender()->GetCurrentWorldPlaneGeometry()));
if (!image || !planeGeometry)
return;
Image::Pointer slice = FeedbackContourTool::GetAffectedImageSliceAs2DImage(positionEvent, image);
if (slice.IsNull())
{
MITK_ERROR << "Unable to extract slice." << std::endl;
return;
}
ContourModel *feedbackContour(FeedbackContourTool::GetFeedbackContour());
ContourModel::Pointer projectedContour = FeedbackContourTool::ProjectContourTo2DSlice(
slice, feedbackContour, false, false); // false: don't add 0.5 (done by FillContourInSlice)
// false: don't constrain the contour to the image's inside
if (projectedContour.IsNull())
return;
auto *labelImage = dynamic_cast<LabelSetImage *>(image);
int activeColor = 1;
if (labelImage != nullptr)
{
activeColor = labelImage->GetActiveLabel()->GetValue();
}
mitk::ContourModelUtils::FillContourInSlice(
projectedContour, timeStep, slice, image, m_PaintingPixelValue * activeColor);
this->WriteBackSegmentationResult(positionEvent, slice);
}
bool mitk::CorrectorTool2D::OnMouseReleased(Action* action, const StateEvent* stateEvent)
{
// 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's working image corresponds to that
FeedbackContourTool::SetFeedbackContourVisible(false);
const PositionEvent* positionEvent = dynamic_cast<const PositionEvent*>(stateEvent->GetEvent());
if (!positionEvent) return false;
assert( positionEvent->GetSender()->GetRenderWindow() );
mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() );
if ( FeedbackContourTool::CanHandleEvent(stateEvent) < 1.0 ) return false;
DataNode* workingNode( m_ToolManager->GetWorkingData(0) );
if (!workingNode) return false;
Image* image = dynamic_cast<Image*>(workingNode->GetData());
const PlaneGeometry* planeGeometry( dynamic_cast<const PlaneGeometry*> (positionEvent->GetSender()->GetCurrentWorldGeometry2D() ) );
if ( !image || !planeGeometry ) return false;
// 2. Slice is known, now we try to get it as a 2D image and project the contour into index coordinates of this slice
m_WorkingSlice = FeedbackContourTool::GetAffectedImageSliceAs2DImage( positionEvent, image );
if ( m_WorkingSlice.IsNull() )
{
MITK_ERROR << "Unable to extract slice." << std::endl;
return false;
}
CorrectorAlgorithm::Pointer algorithm = CorrectorAlgorithm::New();
algorithm->SetInput( m_WorkingSlice );
algorithm->SetContour( FeedbackContourTool::GetFeedbackContour() );
try
{
algorithm->UpdateLargestPossibleRegion();
}
catch ( std::exception& e )
{
MITK_ERROR << "Caught exception '" << e.what() << "'" << std::endl;
}
mitk::Image::Pointer resultSlice = mitk::Image::New();
resultSlice->Initialize(algorithm->GetOutput());
resultSlice->SetVolume(algorithm->GetOutput()->GetData());
this->WriteBackSegmentationResult(positionEvent, resultSlice);
return true;
}
void mitk::SegTool2D::WriteBackSegmentationResult (const PlaneGeometry* planeGeometry, Image* slice, unsigned int timeStep)
{
if(!planeGeometry || !slice) return;
SliceInformation sliceInfo (slice, const_cast<mitk::PlaneGeometry*>(planeGeometry), timeStep);
this->WriteSliceToVolume(sliceInfo);
DataNode* workingNode( m_ToolManager->GetWorkingData(0) );
Image* image = dynamic_cast<Image*>(workingNode->GetData());
this->UpdateSurfaceInterpolation(slice, image, planeGeometry, false);
if (m_SurfaceInterpolationEnabled)
this->AddContourmarker();
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()->GetCurrentWorldPlaneGeometry() ) );
const AbstractTransformGeometry* abstractTransformGeometry( dynamic_cast<const AbstractTransformGeometry*> (positionEvent->GetSender()->GetCurrentWorldPlaneGeometry() ) );
if( planeGeometry && slice && !abstractTransformGeometry)
{
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);
}
}
/**
Close the contour, project it to the image slice and fill it in 2D.
*/
bool mitk::ContourTool::OnMouseReleased( StateMachineAction*, InteractionEvent* interactionEvent )
{
// 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's working image corresponds to that
FeedbackContourTool::SetFeedbackContourVisible(false);
mitk::InteractionPositionEvent* positionEvent = dynamic_cast<mitk::InteractionPositionEvent*>( interactionEvent );
//const PositionEvent* positionEvent = dynamic_cast<const PositionEvent*>(stateEvent->GetEvent());
if (!positionEvent) return false;
assert( positionEvent->GetSender()->GetRenderWindow() );
mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() );
DataNode* workingNode( m_ToolManager->GetWorkingData(0) );
if (!workingNode) return false;
Image* image = dynamic_cast<Image*>(workingNode->GetData());
const PlaneGeometry* planeGeometry( dynamic_cast<const PlaneGeometry*> (positionEvent->GetSender()->GetCurrentWorldPlaneGeometry() ) );
if ( !image || !planeGeometry ) return false;
const AbstractTransformGeometry* abstractTransformGeometry( dynamic_cast<const AbstractTransformGeometry*> (positionEvent->GetSender()->GetCurrentWorldPlaneGeometry() ) );
if ( !image || abstractTransformGeometry ) return false;
// 2. Slice is known, now we try to get it as a 2D image and project the contour into index coordinates of this slice
Image::Pointer slice = SegTool2D::GetAffectedImageSliceAs2DImage( positionEvent, image );
if ( slice.IsNull() )
{
MITK_ERROR << "Unable to extract slice." << std::endl;
return false;
}
ContourModel* feedbackContour = FeedbackContourTool::GetFeedbackContour();
ContourModel::Pointer projectedContour = FeedbackContourTool::ProjectContourTo2DSlice( slice, feedbackContour, true, false ); // true: actually no idea why this is neccessary, but it works :-(
if (projectedContour.IsNull()) return false;
int timestep = positionEvent->GetSender()->GetTimeStep();
FeedbackContourTool::FillContourInSlice( projectedContour, timestep, slice, m_PaintingPixelValue );
this->WriteBackSegmentationResult(positionEvent, slice);
// 4. Make sure the result is drawn again --> is visible then.
assert( positionEvent->GetSender()->GetRenderWindow() );
return true;
}
bool mitk::SetRegionTool::OnMouseReleased( StateMachineAction*, InteractionEvent* interactionEvent )
{
// 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's working image corresponds to that
FeedbackContourTool::SetFeedbackContourVisible(false);
mitk::InteractionPositionEvent* positionEvent = dynamic_cast<mitk::InteractionPositionEvent*>( interactionEvent );
if (!positionEvent) return false;
assert( positionEvent->GetSender()->GetRenderWindow() );
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
int timeStep = positionEvent->GetSender()->GetTimeStep();
if (!m_FillContour && !m_StatusFillWholeSlice) return true;
DataNode* workingNode( m_ToolManager->GetWorkingData(0) );
if (!workingNode) return false;
Image* image = dynamic_cast<Image*>(workingNode->GetData());
const AbstractTransformGeometry* abstractTransformGeometry( dynamic_cast<const AbstractTransformGeometry*> (positionEvent->GetSender()->GetCurrentWorldPlaneGeometry() ) );
const PlaneGeometry* planeGeometry( dynamic_cast<const PlaneGeometry*> (positionEvent->GetSender()->GetCurrentWorldPlaneGeometry() ) );
if ( !image || !planeGeometry || abstractTransformGeometry ) return false;
Image::Pointer slice = FeedbackContourTool::GetAffectedImageSliceAs2DImage( positionEvent, image );
if ( slice.IsNull() )
{
MITK_ERROR << "Unable to extract slice." << std::endl;
return false;
}
ContourModel* feedbackContour( FeedbackContourTool::GetFeedbackContour() );
ContourModel::Pointer projectedContour = FeedbackContourTool::ProjectContourTo2DSlice( slice, feedbackContour, false, false ); // false: don't add 0.5 (done by FillContourInSlice)
// false: don't constrain the contour to the image's inside
if (projectedContour.IsNull()) return false;
FeedbackContourTool::FillContourInSlice( projectedContour, timeStep, slice, m_PaintingPixelValue );
this->WriteBackSegmentationResult(positionEvent, slice);
m_WholeImageContourInWorldCoordinates = NULL;
m_SegmentationContourInWorldCoordinates = NULL;
return true;
}
void mitk::SetRegionTool::OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
m_LastEventSender = positionEvent->GetSender();
m_LastEventSlice = m_LastEventSender->GetSlice();
// 1. Get the working image
Image::Pointer workingSlice = FeedbackContourTool::GetAffectedWorkingSlice(positionEvent);
if (workingSlice.IsNull())
return; // can't do anything without the segmentation
// if click was outside the image, don't continue
const BaseGeometry *sliceGeometry = workingSlice->GetGeometry();
itk::Index<3> projectedPointIn2D;
sliceGeometry->WorldToIndex(positionEvent->GetPositionInWorld(), projectedPointIn2D);
if (!sliceGeometry->IsIndexInside(projectedPointIn2D))
{
MITK_ERROR << "point apparently not inside segmentation slice" << std::endl;
return; // can't use that as a seed point
}
typedef itk::Image<DefaultSegmentationDataType, 2> InputImageType;
typedef InputImageType::IndexType IndexType;
typedef itk::ConnectedThresholdImageFilter<InputImageType, InputImageType> RegionGrowingFilterType;
RegionGrowingFilterType::Pointer regionGrower = RegionGrowingFilterType::New();
// convert world coordinates to image indices
IndexType seedIndex;
sliceGeometry->WorldToIndex(positionEvent->GetPositionInWorld(), seedIndex);
// perform region growing in desired segmented region
InputImageType::Pointer itkImage = InputImageType::New();
CastToItkImage(workingSlice, itkImage);
regionGrower->SetInput(itkImage);
regionGrower->AddSeed(seedIndex);
InputImageType::PixelType bound = itkImage->GetPixel(seedIndex);
regionGrower->SetLower(bound);
regionGrower->SetUpper(bound);
regionGrower->SetReplaceValue(1);
itk::BinaryFillholeImageFilter<InputImageType>::Pointer fillHolesFilter =
itk::BinaryFillholeImageFilter<InputImageType>::New();
fillHolesFilter->SetInput(regionGrower->GetOutput());
fillHolesFilter->SetForegroundValue(1);
// Store result and preview
mitk::Image::Pointer resultImage = mitk::GrabItkImageMemory(fillHolesFilter->GetOutput());
resultImage->SetGeometry(workingSlice->GetGeometry());
// Get the current working color
DataNode *workingNode(m_ToolManager->GetWorkingData(0));
if (!workingNode)
return;
mitk::ImageToContourModelFilter::Pointer contourextractor = mitk::ImageToContourModelFilter::New();
contourextractor->SetInput(resultImage);
contourextractor->Update();
mitk::ContourModel::Pointer awesomeContour = contourextractor->GetOutput();
FeedbackContourTool::SetFeedbackContour(awesomeContour);
FeedbackContourTool::SetFeedbackContourVisible(true);
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
}
int mitk::SegTool2D::AddContourmarker()
{
if (m_LastEventSender == NULL)
return -1;
us::ServiceReference<PlanePositionManagerService> serviceRef =
us::GetModuleContext()->GetServiceReference<PlanePositionManagerService>();
PlanePositionManagerService* service = us::GetModuleContext()->GetService(serviceRef);
unsigned int slicePosition = m_LastEventSender->GetSliceNavigationController()->GetSlice()->GetPos();
// the first geometry is needed otherwise restoring the position is not working
const mitk::PlaneGeometry* plane = dynamic_cast<const PlaneGeometry*> (dynamic_cast< const mitk::SlicedGeometry3D*>(
m_LastEventSender->GetSliceNavigationController()->GetCurrentGeometry3D())->GetPlaneGeometry(0));
unsigned int size = service->GetNumberOfPlanePositions();
unsigned int id = service->AddNewPlanePosition(plane, slicePosition);
mitk::PlanarCircle::Pointer contourMarker = mitk::PlanarCircle::New();
mitk::Point2D p1;
plane->Map(plane->GetCenter(), p1);
mitk::Point2D p2 = p1;
p2[0] -= plane->GetSpacing()[0];
p2[1] -= plane->GetSpacing()[1];
contourMarker->PlaceFigure( p1 );
contourMarker->SetCurrentControlPoint( p1 );
contourMarker->SetPlaneGeometry( const_cast<PlaneGeometry*>(plane));
std::stringstream markerStream;
mitk::DataNode* workingNode (m_ToolManager->GetWorkingData(0));
markerStream << m_Contourmarkername ;
markerStream << " ";
markerStream << id+1;
DataNode::Pointer rotatedContourNode = DataNode::New();
rotatedContourNode->SetData(contourMarker);
rotatedContourNode->SetProperty( "name", StringProperty::New(markerStream.str()) );
rotatedContourNode->SetProperty( "isContourMarker", BoolProperty::New(true));
rotatedContourNode->SetBoolProperty( "PlanarFigureInitializedWindow", true, m_LastEventSender );
rotatedContourNode->SetProperty( "includeInBoundingBox", BoolProperty::New(false));
rotatedContourNode->SetProperty( "helper object", mitk::BoolProperty::New(!m_ShowMarkerNodes));
rotatedContourNode->SetProperty( "planarfigure.drawcontrolpoints", BoolProperty::New(false));
rotatedContourNode->SetProperty( "planarfigure.drawname", BoolProperty::New(false));
rotatedContourNode->SetProperty( "planarfigure.drawoutline", BoolProperty::New(false));
rotatedContourNode->SetProperty( "planarfigure.drawshadow", BoolProperty::New(false));
if (plane)
{
if ( id == size )
{
m_ToolManager->GetDataStorage()->Add(rotatedContourNode, workingNode);
}
else
{
mitk::NodePredicateProperty::Pointer isMarker = mitk::NodePredicateProperty::New("isContourMarker", mitk::BoolProperty::New(true));
mitk::DataStorage::SetOfObjects::ConstPointer markers = m_ToolManager->GetDataStorage()->GetDerivations(workingNode,isMarker);
for ( mitk::DataStorage::SetOfObjects::const_iterator iter = markers->begin();
iter != markers->end();
++iter)
{
std::string nodeName = (*iter)->GetName();
unsigned int t = nodeName.find_last_of(" ");
unsigned int markerId = atof(nodeName.substr(t+1).c_str())-1;
if(id == markerId)
{
return id;
}
}
m_ToolManager->GetDataStorage()->Add(rotatedContourNode, workingNode);
}
}
return id;
}
bool mitk::CorrectorTool2D::OnMouseReleased(Action* action, const StateEvent* stateEvent)
{
// 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's working image corresponds to that
FeedbackContourTool::SetFeedbackContourVisible(false);
const PositionEvent* positionEvent = dynamic_cast<const PositionEvent*>(stateEvent->GetEvent());
if (!positionEvent) return false;
assert( positionEvent->GetSender()->GetRenderWindow() );
mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() );
if (!FeedbackContourTool::OnMouseReleased( action, stateEvent )) return false;
DataNode* workingNode( m_ToolManager->GetWorkingData(0) );
if (!workingNode) return false;
Image* image = dynamic_cast<Image*>(workingNode->GetData());
const PlaneGeometry* planeGeometry( dynamic_cast<const PlaneGeometry*> (positionEvent->GetSender()->GetCurrentWorldGeometry2D() ) );
if ( !image || !planeGeometry ) return false;
int affectedDimension( -1 );
int affectedSlice( -1 );
FeedbackContourTool::DetermineAffectedImageSlice( image, planeGeometry, affectedDimension, affectedSlice );
// 2. Slice is known, now we try to get it as a 2D image and project the contour into index coordinates of this slice
m_WorkingSlice = FeedbackContourTool::GetAffectedImageSliceAs2DImage( positionEvent, image );
if ( m_WorkingSlice.IsNull() )
{
MITK_ERROR << "Unable to extract slice." << std::endl;
return false;
}
CorrectorAlgorithm::Pointer algorithm = CorrectorAlgorithm::New();
algorithm->SetInput( m_WorkingSlice );
algorithm->SetContour( FeedbackContourTool::GetFeedbackContour() );
try
{
algorithm->UpdateLargestPossibleRegion();
}
catch ( std::exception& e )
{
MITK_ERROR << "Caught exception '" << e.what() << "'" << std::endl;
}
if ( affectedDimension != -1 )
{
// 5. Write the modified 2D working data slice back into the image
OverwriteSliceImageFilter::Pointer slicewriter = OverwriteSliceImageFilter::New();
slicewriter->SetInput( image );
slicewriter->SetCreateUndoInformation( true );
slicewriter->SetSliceImage( algorithm->GetOutput() );
slicewriter->SetSliceDimension( affectedDimension );
slicewriter->SetSliceIndex( affectedSlice );
slicewriter->SetTimeStep( positionEvent->GetSender()->GetTimeStep( image ) );
slicewriter->Update();
if( m_RememberContourPositions )
{
this->AddContourmarker( positionEvent );
}
}
else if ( affectedDimension == -1 )
{
OverwriteDirectedPlaneImageFilter::Pointer slicewriter = OverwriteDirectedPlaneImageFilter::New();
slicewriter->SetInput( image );
slicewriter->SetCreateUndoInformation( false );
slicewriter->SetSliceImage( m_WorkingSlice );
slicewriter->SetPlaneGeometry3D( m_WorkingSlice->GetGeometry() );
slicewriter->SetTimeStep( positionEvent->GetSender()->GetTimeStep( image ) );
slicewriter->Update();
if( m_RememberContourPositions )
{
this->AddContourmarker( positionEvent );
}
}
else
{
InteractiveSegmentationBugMessage( "FeedbackContourTool could not determine which slice of the image you are drawing on." );
}
// 6. Make sure the result is drawn again --> is visible then.
assert( positionEvent->GetSender()->GetRenderWindow() );
mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() );
return true;
}
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();
}
