diff --git a/Modules/Segmentation/Interactions/mitkSegTool2D.cpp b/Modules/Segmentation/Interactions/mitkSegTool2D.cpp index a718ed6449..712d33244f 100644 --- a/Modules/Segmentation/Interactions/mitkSegTool2D.cpp +++ b/Modules/Segmentation/Interactions/mitkSegTool2D.cpp @@ -1,468 +1,470 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkSegTool2D.h" #include "mitkToolManager.h" #include "mitkDataStorage.h" #include "mitkBaseRenderer.h" #include "mitkPlaneGeometry.h" #include "mitkExtractImageFilter.h" #include "mitkExtractDirectedPlaneImageFilter.h" //Include of the new ImageExtractor #include "mitkExtractDirectedPlaneImageFilterNew.h" #include "mitkPlanarCircle.h" #include "mitkOverwriteSliceImageFilter.h" #include "mitkOverwriteDirectedPlaneImageFilter.h" #include "mitkMorphologicalOperations.h" #include "usGetModuleContext.h" //Includes for 3DSurfaceInterpolation #include "mitkImageToContourFilter.h" #include "mitkSurfaceInterpolationController.h" //includes for resling and overwriting #include #include #include #include #include #include "mitkOperationEvent.h" #include "mitkUndoController.h" #define ROUND(a) ((a)>0 ? (int)((a)+0.5) : -(int)(0.5-(a))) bool mitk::SegTool2D::m_SurfaceInterpolationEnabled = true; mitk::SegTool2D::SegTool2D(const char* type) :Tool(type), m_LastEventSender(NULL), m_LastEventSlice(0), m_Contourmarkername ("Position"), m_ShowMarkerNodes (false) { } mitk::SegTool2D::~SegTool2D() { } float mitk::SegTool2D::CanHandleEvent( InteractionEvent const *stateEvent) const { const InteractionPositionEvent* positionEvent = dynamic_cast( stateEvent ); if (!positionEvent) return 0.0; if ( positionEvent->GetSender()->GetMapperID() != BaseRenderer::Standard2D ) return 0.0; // we don't want anything but 2D return 1.0; } bool mitk::SegTool2D::DetermineAffectedImageSlice( const Image* image, const PlaneGeometry* plane, int& affectedDimension, int& affectedSlice ) { assert(image); assert(plane); // compare normal of plane to the three axis vectors of the image Vector3D normal = plane->GetNormal(); Vector3D imageNormal0 = image->GetSlicedGeometry()->GetAxisVector(0); Vector3D imageNormal1 = image->GetSlicedGeometry()->GetAxisVector(1); Vector3D imageNormal2 = image->GetSlicedGeometry()->GetAxisVector(2); normal.Normalize(); imageNormal0.Normalize(); imageNormal1.Normalize(); imageNormal2.Normalize(); imageNormal0.SetVnlVector( vnl_cross_3d(normal.GetVnlVector(),imageNormal0.GetVnlVector()) ); imageNormal1.SetVnlVector( vnl_cross_3d(normal.GetVnlVector(),imageNormal1.GetVnlVector()) ); imageNormal2.SetVnlVector( vnl_cross_3d(normal.GetVnlVector(),imageNormal2.GetVnlVector()) ); double eps( 0.00001 ); // axial if ( imageNormal2.GetNorm() <= eps ) { affectedDimension = 2; } // sagittal else if ( imageNormal1.GetNorm() <= eps ) { affectedDimension = 1; } // frontal else if ( imageNormal0.GetNorm() <= eps ) { affectedDimension = 0; } else { affectedDimension = -1; // no idea return false; } // determine slice number in image Geometry3D* imageGeometry = image->GetGeometry(0); Point3D testPoint = imageGeometry->GetCenter(); Point3D projectedPoint; plane->Project( testPoint, projectedPoint ); Point3D indexPoint; imageGeometry->WorldToIndex( projectedPoint, indexPoint ); affectedSlice = ROUND( indexPoint[affectedDimension] ); MITK_DEBUG << "indexPoint " << indexPoint << " affectedDimension " << affectedDimension << " affectedSlice " << affectedSlice; // check if this index is still within the image if ( affectedSlice < 0 || affectedSlice >= static_cast(image->GetDimension(affectedDimension)) ) return false; return true; } 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(); if (contour->GetVtkPolyData()->GetNumberOfPoints() != 0 && workingImage->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); } } mitk::Image::Pointer mitk::SegTool2D::GetAffectedImageSliceAs2DImage(const InteractionPositionEvent* positionEvent, const Image* image) { if (!positionEvent) return NULL; assert( positionEvent->GetSender() ); // sure, right? unsigned int timeStep = positionEvent->GetSender()->GetTimeStep( image ); // get the timestep of the visible part (time-wise) of the image // first, we determine, which slice is affected const PlaneGeometry* planeGeometry( dynamic_cast (positionEvent->GetSender()->GetCurrentWorldGeometry2D() ) ); return this->GetAffectedImageSliceAs2DImage(planeGeometry, image, timeStep); } mitk::Image::Pointer mitk::SegTool2D::GetAffectedImageSliceAs2DImage(const PlaneGeometry* planeGeometry, const Image* image, unsigned int timeStep) { if ( !image || !planeGeometry ) return NULL; //Make sure that for reslicing and overwriting the same alogrithm is used. We can specify the mode of the vtk reslicer vtkSmartPointer reslice = vtkSmartPointer::New(); //set to false to extract a slice reslice->SetOverwriteMode(false); reslice->Modified(); //use ExtractSliceFilter with our specific vtkImageReslice for overwriting and extracting mitk::ExtractSliceFilter::Pointer extractor = mitk::ExtractSliceFilter::New(reslice); extractor->SetInput( image ); extractor->SetTimeStep( timeStep ); extractor->SetWorldGeometry( planeGeometry ); extractor->SetVtkOutputRequest(false); extractor->SetResliceTransformByGeometry( image->GetTimeGeometry()->GetGeometryForTimeStep( timeStep ) ); extractor->Modified(); extractor->Update(); Image::Pointer slice = extractor->GetOutput(); /*============= BEGIN undo feature block ========================*/ //specify the undo operation with the non edited slice m_undoOperation = new DiffSliceOperation(const_cast(image), extractor->GetVtkOutput(), slice->GetGeometry(), timeStep, const_cast(planeGeometry)); /*============= END undo feature block ========================*/ return slice; } mitk::Image::Pointer mitk::SegTool2D::GetAffectedWorkingSlice(const InteractionPositionEvent* positionEvent) { DataNode* workingNode( m_ToolManager->GetWorkingData(0) ); if ( !workingNode ) return NULL; Image* workingImage = dynamic_cast(workingNode->GetData()); if ( !workingImage ) return NULL; return GetAffectedImageSliceAs2DImage( positionEvent, workingImage ); } mitk::Image::Pointer mitk::SegTool2D::GetAffectedReferenceSlice(const InteractionPositionEvent* positionEvent) { DataNode* referenceNode( m_ToolManager->GetReferenceData(0) ); if ( !referenceNode ) return NULL; Image* referenceImage = dynamic_cast(referenceNode->GetData()); if ( !referenceImage ) return NULL; return GetAffectedImageSliceAs2DImage( positionEvent, referenceImage ); } void mitk::SegTool2D::WriteBackSegmentationResult (const InteractionPositionEvent* positionEvent, Image* slice) { if(!positionEvent) return; const PlaneGeometry* planeGeometry( dynamic_cast (positionEvent->GetSender()->GetCurrentWorldGeometry2D() ) ); if( planeGeometry && slice) { DataNode* workingNode( m_ToolManager->GetWorkingData(0) ); Image* image = dynamic_cast(workingNode->GetData()); unsigned int timeStep = positionEvent->GetSender()->GetTimeStep( image ); this->WriteBackSegmentationResult(planeGeometry, slice, timeStep); } } void mitk::SegTool2D::WriteBackSegmentationResult (const PlaneGeometry* planeGeometry, Image* slice, unsigned int timeStep) { if(!planeGeometry || !slice) return; SliceInformation sliceInfo (slice, const_cast(planeGeometry), timeStep); this->WriteSliceToVolume(sliceInfo); DataNode* workingNode( m_ToolManager->GetWorkingData(0) ); Image* image = dynamic_cast(workingNode->GetData()); this->UpdateSurfaceInterpolation(slice, image, planeGeometry, false); + if (m_SurfaceInterpolationEnabled) + this->AddContourmarker(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void mitk::SegTool2D::WriteBackSegmentationResult(std::vector sliceList) { std::vector contourList; contourList.reserve(sliceList.size()); ImageToContourFilter::Pointer contourExtractor = ImageToContourFilter::New(); DataNode* workingNode( m_ToolManager->GetWorkingData(0) ); Image* image = dynamic_cast(workingNode->GetData()); for (unsigned int i = 0; i < sliceList.size(); ++i) { SliceInformation currentSliceInfo = sliceList.at(i); this->WriteSliceToVolume(currentSliceInfo); if (m_SurfaceInterpolationEnabled && image->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); } void mitk::SegTool2D::WriteSliceToVolume(mitk::SegTool2D::SliceInformation sliceInfo) { DataNode* workingNode( m_ToolManager->GetWorkingData(0) ); Image* image = dynamic_cast(workingNode->GetData()); //Make sure that for reslicing and overwriting the same alogrithm is used. We can specify the mode of the vtk reslicer vtkSmartPointer reslice = vtkSmartPointer::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(true); 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 feature block ========================*/ //specify the undo operation with the edited slice m_doOperation = new DiffSliceOperation(image, extractor->GetVtkOutput(),sliceInfo.slice->GetGeometry(), sliceInfo.timestep, sliceInfo.plane ); //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::SegTool2D::SetShowMarkerNodes(bool status) { m_ShowMarkerNodes = status; } void mitk::SegTool2D::SetEnable3DInterpolation(bool enabled) { m_SurfaceInterpolationEnabled = enabled; } unsigned int mitk::SegTool2D::AddContourmarker() { us::ServiceReference serviceRef = us::GetModuleContext()->GetServiceReference(); 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 (dynamic_cast< const mitk::SlicedGeometry3D*>( m_LastEventSender->GetSliceNavigationController()->GetCurrentGeometry3D())->GetGeometry2D(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->SetGeometry2D( const_cast(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; } void mitk::SegTool2D::InteractiveSegmentationBugMessage( const std::string& message ) { MITK_ERROR << "********************************************************************************" << std::endl << " " << message << std::endl << "********************************************************************************" << std::endl << " " << std::endl << " If your image is rotated or the 2D views don't really contain the patient image, try to press the button next to the image selection. " << std::endl << " " << std::endl << " Please file a BUG REPORT: " << std::endl << " http://bugs.mitk.org" << std::endl << " Contain the following information:" << std::endl << " - What image were you working on?" << std::endl << " - Which region of the image?" << std::endl << " - Which tool did you use?" << std::endl << " - What did you do?" << std::endl << " - What happened (not)? What did you expect?" << std::endl; }