diff --git a/Modules/SegmentationUI/Qmitk/QmitkSlicesInterpolator.cpp b/Modules/SegmentationUI/Qmitk/QmitkSlicesInterpolator.cpp index b33b8093b6..1cdc1b20e8 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkSlicesInterpolator.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkSlicesInterpolator.cpp @@ -1,1984 +1,1991 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkSlicesInterpolator.h" #include "QmitkRenderWindow.h" #include "QmitkRenderWindowWidget.h" #include "mitkApplyDiffImageOperation.h" #include "mitkColorProperty.h" #include "mitkCoreObjectFactory.h" #include "mitkDiffImageApplier.h" #include "mitkInteractionConst.h" #include "mitkLevelWindowProperty.h" #include "mitkOperationEvent.h" #include "mitkProgressBar.h" #include "mitkProperties.h" #include "mitkRenderingManager.h" #include "mitkSegTool2D.h" #include "mitkSliceNavigationController.h" #include "mitkSurfaceToImageFilter.h" #include "mitkToolManager.h" #include "mitkUndoController.h" #include #include #include #include #include #include #include #include #include #include #include #include // Includes for the merge operation #include "mitkImageToContourFilter.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include namespace { template itk::SmartPointer GetData(const mitk::DataNode* dataNode) { return nullptr != dataNode ? dynamic_cast(dataNode->GetData()) : nullptr; } } float SURFACE_COLOR_RGB[3] = {0.49f, 1.0f, 0.16f}; const std::map QmitkSlicesInterpolator::createActionToSlicer(const QList& windows) { std::map actionToSliceDimension; for (auto* window : windows) { std::string windowName; auto renderWindowWidget = dynamic_cast(window->parentWidget()); if (renderWindowWidget) { windowName = renderWindowWidget->GetCornerAnnotationText(); } else { windowName = window->GetRenderer()->GetName(); } auto slicer = window->GetSliceNavigationController(); actionToSliceDimension[new QAction(QString::fromStdString(windowName), nullptr)] = slicer; } return actionToSliceDimension; } // Check whether the given contours are coplanar bool AreContoursCoplanar(mitk::SurfaceInterpolationController::ContourPositionInformation leftHandSide, mitk::SurfaceInterpolationController::ContourPositionInformation rightHandSide) { // Here we check two things: // 1. Whether the normals of both contours are at least parallel // 2. Whether both contours lie in the same plane // Check for coplanarity: // a. Span a vector between two points one from each contour // b. Calculate dot product for the vector and one of the normals // c. If the dot is zero the two vectors are orthogonal and the contours are coplanar double vec[3]; vec[0] = leftHandSide.ContourPoint[0] - rightHandSide.ContourPoint[0]; vec[1] = leftHandSide.ContourPoint[1] - rightHandSide.ContourPoint[1]; vec[2] = leftHandSide.ContourPoint[2] - rightHandSide.ContourPoint[2]; double n[3]; n[0] = rightHandSide.ContourNormal[0]; n[1] = rightHandSide.ContourNormal[1]; n[2] = rightHandSide.ContourNormal[2]; double dot = vtkMath::Dot(n, vec); double n2[3]; n2[0] = leftHandSide.ContourNormal[0]; n2[1] = leftHandSide.ContourNormal[1]; n2[2] = leftHandSide.ContourNormal[2]; // The normals of both contours have to be parallel but not of the same orientation double lengthLHS = leftHandSide.ContourNormal.GetNorm(); double lengthRHS = rightHandSide.ContourNormal.GetNorm(); double dot2 = vtkMath::Dot(n, n2); bool contoursParallel = mitk::Equal(fabs(lengthLHS * lengthRHS), fabs(dot2), 0.001); if (mitk::Equal(dot, 0.0, 0.001) && contoursParallel) return true; else return false; } mitk::Image::Pointer ExtractSliceFromImage(mitk::Image* image, const mitk::PlaneGeometry * contourPlane, unsigned int timeStep) { vtkSmartPointer reslice = vtkSmartPointer::New(); // set to false to extract a slice reslice->SetOverwriteMode(false); reslice->Modified(); mitk::ExtractSliceFilter::Pointer extractor = mitk::ExtractSliceFilter::New(reslice); extractor->SetInput(image); extractor->SetTimeStep(timeStep); extractor->SetWorldGeometry(contourPlane); extractor->SetVtkOutputRequest(false); extractor->SetResliceTransformByGeometry(image->GetTimeGeometry()->GetGeometryForTimeStep(timeStep)); extractor->Update(); mitk::Image::Pointer slice = extractor->GetOutput(); return slice; } template std::vector GetPixelValuesPresentInImage(mitk::LabelSetImage* labelSetImage) { std::vector pixelsPresent; mitk::ImagePixelReadAccessor readAccessor(labelSetImage); std::size_t numberOfPixels = 1; for (size_t dim = 0; dim < VImageDimension; ++dim) numberOfPixels *= static_cast(readAccessor.GetDimension(dim)); auto src = readAccessor.GetData(); for (std::size_t i = 0; i < numberOfPixels; ++i) { mitk::Label::PixelType pixelVal = *(src + i); if ( (std::find(pixelsPresent.begin(), pixelsPresent.end(), pixelVal) == pixelsPresent.end()) && (pixelVal != mitk::LabelSetImage::UnlabeledValue) ) pixelsPresent.push_back(pixelVal); } return pixelsPresent; } template ModifyLabelActionTrigerred ModifyLabelProcessing(mitk::LabelSetImage* labelSetImage, mitk::SurfaceInterpolationController::Pointer surfaceInterpolator, unsigned int timePoint) { auto currentLayerID = labelSetImage->GetActiveLayer(); auto numTimeSteps = labelSetImage->GetTimeSteps(); ModifyLabelActionTrigerred actionTriggered = ModifyLabelActionTrigerred::Null; mitk::SurfaceInterpolationController::ContourPositionInformationList ¤tContourList = surfaceInterpolator->GetContours(timePoint, currentLayerID); mitk::LabelSetImage::Pointer labelSetImage2 = labelSetImage->Clone(); mitk::ImagePixelReadAccessor readAccessor(labelSetImage2.GetPointer()); for (auto& contour : currentContourList) { mitk::Label::PixelType contourPixelValue; itk::Index<3> itkIndex; labelSetImage2->GetGeometry()->WorldToIndex(contour.ContourPoint, itkIndex); if (VImageDimension == 4) { itk::Index time3DIndex; for (size_t i = 0; i < itkIndex.size(); ++i) time3DIndex[i] = itkIndex[i]; time3DIndex[3] = timePoint; contourPixelValue = readAccessor.GetPixelByIndexSafe(time3DIndex); } else if (VImageDimension == 3) { itk::Index geomIndex; for (size_t i = 0; i < itkIndex.size(); ++i) geomIndex[i] = itkIndex[i]; contourPixelValue = readAccessor.GetPixelByIndexSafe(geomIndex); } if (contour.LabelValue != contourPixelValue) { if (contourPixelValue == 0) // Erase label { for (size_t t = 0; t < numTimeSteps; ++t) surfaceInterpolator->RemoveContours(contour.LabelValue, t, currentLayerID); actionTriggered = ModifyLabelActionTrigerred::Erase; } else { contour.LabelValue = contourPixelValue; actionTriggered = ModifyLabelActionTrigerred::Merge; } } } return actionTriggered; } QmitkSlicesInterpolator::QmitkSlicesInterpolator(QWidget *parent, const char * /*name*/) : QWidget(parent), m_Interpolator(mitk::SegmentationInterpolationController::New()), m_SurfaceInterpolator(mitk::SurfaceInterpolationController::GetInstance()), m_ToolManager(nullptr), m_Initialized(false), m_LastSNC(nullptr), m_LastSliceIndex(0), m_2DInterpolationEnabled(false), m_3DInterpolationEnabled(false), m_PreviousActiveLabelValue(0), m_CurrentActiveLabelValue(0), m_PreviousLayerIndex(0), m_CurrentLayerIndex(0), m_FirstRun(true) { m_GroupBoxEnableExclusiveInterpolationMode = new QGroupBox("Interpolation", this); QVBoxLayout *vboxLayout = new QVBoxLayout(m_GroupBoxEnableExclusiveInterpolationMode); m_EdgeDetector = mitk::FeatureBasedEdgeDetectionFilter::New(); m_PointScorer = mitk::PointCloudScoringFilter::New(); m_CmbInterpolation = new QComboBox(m_GroupBoxEnableExclusiveInterpolationMode); m_CmbInterpolation->addItem("Disabled"); m_CmbInterpolation->addItem("2-Dimensional"); m_CmbInterpolation->addItem("3-Dimensional"); vboxLayout->addWidget(m_CmbInterpolation); m_BtnApply2D = new QPushButton("Confirm for single slice", m_GroupBoxEnableExclusiveInterpolationMode); vboxLayout->addWidget(m_BtnApply2D); m_BtnApplyForAllSlices2D = new QPushButton("Confirm for all slices", m_GroupBoxEnableExclusiveInterpolationMode); vboxLayout->addWidget(m_BtnApplyForAllSlices2D); m_BtnApply3D = new QPushButton("Confirm", m_GroupBoxEnableExclusiveInterpolationMode); vboxLayout->addWidget(m_BtnApply3D); // T28261 // m_BtnSuggestPlane = new QPushButton("Suggest a plane", m_GroupBoxEnableExclusiveInterpolationMode); // vboxLayout->addWidget(m_BtnSuggestPlane); m_BtnReinit3DInterpolation = new QPushButton("Reinit Interpolation", m_GroupBoxEnableExclusiveInterpolationMode); vboxLayout->addWidget(m_BtnReinit3DInterpolation); m_ChkShowPositionNodes = new QCheckBox("Show Position Nodes", m_GroupBoxEnableExclusiveInterpolationMode); vboxLayout->addWidget(m_ChkShowPositionNodes); this->HideAllInterpolationControls(); connect(m_CmbInterpolation, SIGNAL(currentIndexChanged(int)), this, SLOT(OnInterpolationMethodChanged(int))); connect(m_BtnApply2D, SIGNAL(clicked()), this, SLOT(OnAcceptInterpolationClicked())); connect(m_BtnApplyForAllSlices2D, SIGNAL(clicked()), this, SLOT(OnAcceptAllInterpolationsClicked())); connect(m_BtnApply3D, SIGNAL(clicked()), this, SLOT(OnAccept3DInterpolationClicked())); connect(m_BtnReinit3DInterpolation, SIGNAL(clicked()), this, SLOT(OnReinit3DInterpolation())); connect(m_ChkShowPositionNodes, SIGNAL(toggled(bool)), this, SLOT(OnShowMarkers(bool))); connect(m_ChkShowPositionNodes, SIGNAL(toggled(bool)), this, SIGNAL(SignalShowMarkerNodes(bool))); QHBoxLayout *layout = new QHBoxLayout(this); layout->addWidget(m_GroupBoxEnableExclusiveInterpolationMode); this->setLayout(layout); itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); command->SetCallbackFunction(this, &QmitkSlicesInterpolator::OnInterpolationInfoChanged); InterpolationInfoChangedObserverTag = m_Interpolator->AddObserver(itk::ModifiedEvent(), command); itk::ReceptorMemberCommand::Pointer command2 = itk::ReceptorMemberCommand::New(); command2->SetCallbackFunction(this, &QmitkSlicesInterpolator::OnSurfaceInterpolationInfoChanged); SurfaceInterpolationInfoChangedObserverTag = m_SurfaceInterpolator->AddObserver(itk::ModifiedEvent(), command2); auto command3 = itk::ReceptorMemberCommand::New(); command3->SetCallbackFunction(this, &QmitkSlicesInterpolator::OnInterpolationAborted); InterpolationAbortedObserverTag = m_Interpolator->AddObserver(itk::AbortEvent(), command3); // feedback node and its visualization properties m_FeedbackNode = mitk::DataNode::New(); mitk::CoreObjectFactory::GetInstance()->SetDefaultProperties(m_FeedbackNode); m_FeedbackNode->SetProperty("binary", mitk::BoolProperty::New(true)); m_FeedbackNode->SetProperty("outline binary", mitk::BoolProperty::New(true)); m_FeedbackNode->SetProperty("color", mitk::ColorProperty::New(255.0, 255.0, 0.0)); m_FeedbackNode->SetProperty("texture interpolation", mitk::BoolProperty::New(false)); m_FeedbackNode->SetProperty("layer", mitk::IntProperty::New(20)); m_FeedbackNode->SetProperty("levelwindow", mitk::LevelWindowProperty::New(mitk::LevelWindow(0, 1))); m_FeedbackNode->SetProperty("name", mitk::StringProperty::New("Interpolation feedback")); m_FeedbackNode->SetProperty("opacity", mitk::FloatProperty::New(0.8)); m_FeedbackNode->SetProperty("helper object", mitk::BoolProperty::New(true)); m_InterpolatedSurfaceNode = mitk::DataNode::New(); m_InterpolatedSurfaceNode->SetProperty("color", mitk::ColorProperty::New(SURFACE_COLOR_RGB)); m_InterpolatedSurfaceNode->SetProperty("name", mitk::StringProperty::New("Surface Interpolation feedback")); m_InterpolatedSurfaceNode->SetProperty("opacity", mitk::FloatProperty::New(0.5)); m_InterpolatedSurfaceNode->SetProperty("line width", mitk::FloatProperty::New(4.0f)); m_InterpolatedSurfaceNode->SetProperty("includeInBoundingBox", mitk::BoolProperty::New(false)); m_InterpolatedSurfaceNode->SetProperty("helper object", mitk::BoolProperty::New(true)); m_InterpolatedSurfaceNode->SetVisibility(false); m_3DContourNode = mitk::DataNode::New(); m_3DContourNode->SetProperty("color", mitk::ColorProperty::New(0.0, 0.0, 0.0)); m_3DContourNode->SetProperty("hidden object", mitk::BoolProperty::New(true)); m_3DContourNode->SetProperty("name", mitk::StringProperty::New("Drawn Contours")); m_3DContourNode->SetProperty("material.representation", mitk::VtkRepresentationProperty::New(VTK_WIREFRAME)); m_3DContourNode->SetProperty("material.wireframeLineWidth", mitk::FloatProperty::New(2.0f)); m_3DContourNode->SetProperty("3DContourContainer", mitk::BoolProperty::New(true)); m_3DContourNode->SetProperty("includeInBoundingBox", mitk::BoolProperty::New(false)); m_3DContourNode->SetVisibility(false); QWidget::setContentsMargins(0, 0, 0, 0); if (QWidget::layout() != nullptr) { QWidget::layout()->setContentsMargins(0, 0, 0, 0); } // For running 3D Interpolation in background // create a QFuture and a QFutureWatcher connect(&m_Watcher, SIGNAL(started()), this, SLOT(StartUpdateInterpolationTimer())); connect(&m_Watcher, SIGNAL(finished()), this, SLOT(OnSurfaceInterpolationFinished())); connect(&m_Watcher, SIGNAL(finished()), this, SLOT(StopUpdateInterpolationTimer())); m_Timer = new QTimer(this); connect(m_Timer, SIGNAL(timeout()), this, SLOT(ChangeSurfaceColor())); } void QmitkSlicesInterpolator::SetDataStorage(mitk::DataStorage::Pointer storage) { if (m_DataStorage == storage) { return; } if (m_DataStorage.IsNotNull()) { m_DataStorage->RemoveNodeEvent.RemoveListener( mitk::MessageDelegate1(this, &QmitkSlicesInterpolator::NodeRemoved) ); } m_DataStorage = storage; m_SurfaceInterpolator->SetDataStorage(storage); if (m_DataStorage.IsNotNull()) { m_DataStorage->RemoveNodeEvent.AddListener( mitk::MessageDelegate1(this, &QmitkSlicesInterpolator::NodeRemoved) ); } } mitk::DataStorage *QmitkSlicesInterpolator::GetDataStorage() { if (m_DataStorage.IsNotNull()) { return m_DataStorage; } else { return nullptr; } } void QmitkSlicesInterpolator::InitializeWindow(QmitkRenderWindow* window) { auto slicer = window->GetSliceNavigationController(); if (slicer == nullptr) { MITK_WARN << "Tried setting up interpolation for a render window that does not have a slice navigation controller set"; return; } // Has to be initialized m_LastSNC = slicer; m_TimePoints.insert(slicer, slicer->GetSelectedTimePoint()); itk::MemberCommand::Pointer deleteCommand = itk::MemberCommand::New(); deleteCommand->SetCallbackFunction(this, &QmitkSlicesInterpolator::OnSliceNavigationControllerDeleted); m_ControllerToDeleteObserverTag[slicer] = slicer->AddObserver(itk::DeleteEvent(), deleteCommand); itk::MemberCommand::Pointer timeChangedCommand = itk::MemberCommand::New(); timeChangedCommand->SetCallbackFunction(this, &QmitkSlicesInterpolator::OnTimeChanged); m_ControllerToTimeObserverTag[slicer] = slicer->AddObserver(mitk::SliceNavigationController::TimeGeometryEvent(nullptr, 0), timeChangedCommand); itk::MemberCommand::Pointer sliceChangedCommand = itk::MemberCommand::New(); sliceChangedCommand->SetCallbackFunction(this, &QmitkSlicesInterpolator::OnSliceChanged); m_ControllerToSliceObserverTag[slicer] = slicer->AddObserver(mitk::SliceNavigationController::GeometrySliceEvent(nullptr, 0), sliceChangedCommand); } void QmitkSlicesInterpolator::Initialize(mitk::ToolManager *toolManager, const QList& windows) { Q_ASSERT(!windows.empty()); if (m_Initialized) { // remove old observers this->Uninitialize(); } m_ToolManager = toolManager; if (m_ToolManager) { // set enabled only if a segmentation is selected mitk::DataNode *node = m_ToolManager->GetWorkingData(0); QWidget::setEnabled(node != nullptr); // react whenever the set of selected segmentation changes m_ToolManager->WorkingDataChanged += mitk::MessageDelegate(this, &QmitkSlicesInterpolator::OnToolManagerWorkingDataModified); m_ToolManager->ReferenceDataChanged += mitk::MessageDelegate( this, &QmitkSlicesInterpolator::OnToolManagerReferenceDataModified); // connect to the slice navigation controller. after each change, call the interpolator for (auto* window : windows) { this->InitializeWindow(window); } m_ActionToSlicer = createActionToSlicer(windows); } m_Initialized = true; } void QmitkSlicesInterpolator::Uninitialize() { if (m_ToolManager.IsNotNull()) { m_ToolManager->WorkingDataChanged -= mitk::MessageDelegate(this, &QmitkSlicesInterpolator::OnToolManagerWorkingDataModified); m_ToolManager->ReferenceDataChanged -= mitk::MessageDelegate( this, &QmitkSlicesInterpolator::OnToolManagerReferenceDataModified); } for (auto* slicer : m_ControllerToTimeObserverTag.keys()) { slicer->RemoveObserver(m_ControllerToDeleteObserverTag.take(slicer)); slicer->RemoveObserver(m_ControllerToTimeObserverTag.take(slicer)); slicer->RemoveObserver(m_ControllerToSliceObserverTag.take(slicer)); } - auto dataIter = m_SegmentationObserverTags.begin(); - while (dataIter != m_SegmentationObserverTags.end()) - { - auto labelSetImage = (*dataIter).first; - labelSetImage->RemoveObserver((*dataIter).second); - for (size_t layerID = 0; layerID < labelSetImage->GetNumberOfLayers(); ++layerID) - { - this->OnRemoveLabelSetConnection(labelSetImage, layerID); - } - ++dataIter; - } - m_SegmentationObserverTags.clear(); + this->ClearSegmentationObservers(); m_ActionToSlicer.clear(); m_ToolManager = nullptr; m_Initialized = false; } QmitkSlicesInterpolator::~QmitkSlicesInterpolator() { if (m_Initialized) { // remove old observers this->Uninitialize(); } WaitForFutures(); if (m_DataStorage.IsNotNull()) { m_DataStorage->RemoveNodeEvent.RemoveListener( mitk::MessageDelegate1(this, &QmitkSlicesInterpolator::NodeRemoved) ); if (m_DataStorage->Exists(m_3DContourNode)) m_DataStorage->Remove(m_3DContourNode); if (m_DataStorage->Exists(m_InterpolatedSurfaceNode)) m_DataStorage->Remove(m_InterpolatedSurfaceNode); } // remove observer m_Interpolator->RemoveObserver(InterpolationAbortedObserverTag); m_Interpolator->RemoveObserver(InterpolationInfoChangedObserverTag); m_SurfaceInterpolator->RemoveObserver(SurfaceInterpolationInfoChangedObserverTag); m_SurfaceInterpolator->UnsetSelectedImage(); delete m_Timer; } /** External enableization... */ void QmitkSlicesInterpolator::setEnabled(bool enable) { QWidget::setEnabled(enable); // Set the gui elements of the different interpolation modi enabled if (enable) { if (m_2DInterpolationEnabled) { this->Show2DInterpolationControls(true); m_Interpolator->Activate2DInterpolation(true); } else if (m_3DInterpolationEnabled) { this->Show3DInterpolationControls(true); this->Show3DInterpolationResult(true); } } // Set all gui elements of the interpolation disabled else { this->HideAllInterpolationControls(); this->Show3DInterpolationResult(false); } } void QmitkSlicesInterpolator::On2DInterpolationEnabled(bool status) { OnInterpolationActivated(status); m_Interpolator->Activate2DInterpolation(status); } void QmitkSlicesInterpolator::On3DInterpolationEnabled(bool status) { On3DInterpolationActivated(status); } void QmitkSlicesInterpolator::OnInterpolationDisabled(bool status) { if (status) { OnInterpolationActivated(!status); On3DInterpolationActivated(!status); this->Show3DInterpolationResult(false); } } void QmitkSlicesInterpolator::HideAllInterpolationControls() { this->Show2DInterpolationControls(false); this->Show3DInterpolationControls(false); } void QmitkSlicesInterpolator::Show2DInterpolationControls(bool show) { m_BtnApply2D->setVisible(show); m_BtnApplyForAllSlices2D->setVisible(show); } void QmitkSlicesInterpolator::Show3DInterpolationControls(bool show) { m_BtnApply3D->setVisible(show); // T28261 // m_BtnSuggestPlane->setVisible(show); m_ChkShowPositionNodes->setVisible(show); m_BtnReinit3DInterpolation->setVisible(show); } void QmitkSlicesInterpolator::OnInterpolationMethodChanged(int index) { switch (index) { case 0: // Disabled m_GroupBoxEnableExclusiveInterpolationMode->setTitle("Interpolation"); this->HideAllInterpolationControls(); this->OnInterpolationActivated(false); this->On3DInterpolationActivated(false); this->Show3DInterpolationResult(false); m_Interpolator->Activate2DInterpolation(false); break; case 1: // 2D m_GroupBoxEnableExclusiveInterpolationMode->setTitle("Interpolation (Enabled)"); this->HideAllInterpolationControls(); this->Show2DInterpolationControls(true); this->OnInterpolationActivated(true); this->On3DInterpolationActivated(false); m_Interpolator->Activate2DInterpolation(true); break; case 2: // 3D m_GroupBoxEnableExclusiveInterpolationMode->setTitle("Interpolation (Enabled)"); this->HideAllInterpolationControls(); this->Show3DInterpolationControls(true); this->OnInterpolationActivated(false); this->On3DInterpolationActivated(true); m_Interpolator->Activate2DInterpolation(false); break; default: MITK_ERROR << "Unknown interpolation method!"; m_CmbInterpolation->setCurrentIndex(0); break; } } void QmitkSlicesInterpolator::OnShowMarkers(bool state) { mitk::DataStorage::SetOfObjects::ConstPointer allContourMarkers = m_DataStorage->GetSubset(mitk::NodePredicateProperty::New("isContourMarker", mitk::BoolProperty::New(true))); for (mitk::DataStorage::SetOfObjects::ConstIterator it = allContourMarkers->Begin(); it != allContourMarkers->End(); ++it) { it->Value()->SetProperty("helper object", mitk::BoolProperty::New(!state)); } } void QmitkSlicesInterpolator::OnToolManagerWorkingDataModified() { + this->ClearSegmentationObservers(); + if (m_ToolManager->GetWorkingData(0) != nullptr) { m_Segmentation = dynamic_cast(m_ToolManager->GetWorkingData(0)->GetData()); auto labelSetImage = dynamic_cast(m_ToolManager->GetWorkingData(0)->GetData()); m_BtnReinit3DInterpolation->setEnabled(true); try { if (m_SegmentationObserverTags.find(labelSetImage) == m_SegmentationObserverTags.end()) { auto command2 = itk::MemberCommand::New(); command2->SetCallbackFunction(this, &QmitkSlicesInterpolator::OnModifyLabelChanged); auto workingImage = dynamic_cast(m_ToolManager->GetWorkingData(0)->GetData()); m_SegmentationObserverTags[workingImage] = workingImage->AddObserver(itk::ModifiedEvent(), command2); } } catch (const std::exception& e) { MITK_ERROR << "Error casting node data to LabelSetImage\n"; } } else { // If no workingdata is set, remove the interpolation feedback this->GetDataStorage()->Remove(m_FeedbackNode); m_FeedbackNode->SetData(nullptr); this->GetDataStorage()->Remove(m_3DContourNode); m_3DContourNode->SetData(nullptr); this->GetDataStorage()->Remove(m_InterpolatedSurfaceNode); m_InterpolatedSurfaceNode->SetData(nullptr); m_BtnReinit3DInterpolation->setEnabled(false); m_CmbInterpolation->setCurrentIndex(0); return; } // Updating the current selected segmentation for the 3D interpolation this->SetCurrentContourListID(); if (m_2DInterpolationEnabled) { OnInterpolationActivated(true); // re-initialize if needed } } void QmitkSlicesInterpolator::OnToolManagerReferenceDataModified() { } void QmitkSlicesInterpolator::OnTimeChanged(itk::Object *sender, const itk::EventObject &e) { // Check if we really have a GeometryTimeEvent if (!dynamic_cast(&e)) return; mitk::SliceNavigationController *slicer = dynamic_cast(sender); Q_ASSERT(slicer); const auto timePoint = slicer->GetSelectedTimePoint(); m_TimePoints[slicer] = timePoint; if (m_Watcher.isRunning()) m_Watcher.waitForFinished(); if (timePoint != m_SurfaceInterpolator->GetCurrentTimePoint()) { m_SurfaceInterpolator->SetCurrentTimePoint(timePoint); if (m_3DInterpolationEnabled) { m_3DContourNode->SetData(nullptr); m_InterpolatedSurfaceNode->SetData(nullptr); } m_SurfaceInterpolator->Modified(); } if (m_LastSNC == slicer) { slicer->SendSlice(); // will trigger a new interpolation } } void QmitkSlicesInterpolator::OnSliceChanged(itk::Object *sender, const itk::EventObject &e) { // Check whether we really have a GeometrySliceEvent if (!dynamic_cast(&e)) return; mitk::SliceNavigationController *slicer = dynamic_cast(sender); if(m_2DInterpolationEnabled) { this->On2DInterpolationEnabled(m_2DInterpolationEnabled); } if (TranslateAndInterpolateChangedSlice(e, slicer)) { slicer->GetRenderer()->RequestUpdate(); } } bool QmitkSlicesInterpolator::TranslateAndInterpolateChangedSlice(const itk::EventObject &e, mitk::SliceNavigationController *slicer) { if (!m_2DInterpolationEnabled) return false; try { const mitk::SliceNavigationController::GeometrySliceEvent &event = dynamic_cast(e); mitk::TimeGeometry *tsg = event.GetTimeGeometry(); if (tsg && m_TimePoints.contains(slicer) && tsg->IsValidTimePoint(m_TimePoints[slicer])) { mitk::SlicedGeometry3D *slicedGeometry = dynamic_cast(tsg->GetGeometryForTimePoint(m_TimePoints[slicer]).GetPointer()); if (slicedGeometry) { m_LastSNC = slicer; mitk::PlaneGeometry *plane = dynamic_cast(slicedGeometry->GetPlaneGeometry(event.GetPos())); if (plane) { Interpolate(plane, m_TimePoints[slicer], slicer); } return true; } } } catch (const std::bad_cast &) { return false; // so what } return false; } void QmitkSlicesInterpolator::OnLayerChanged() { auto* workingNode = m_ToolManager->GetWorkingData(0); if (workingNode != nullptr) { m_3DContourNode->SetData(nullptr); this->Show3DInterpolationResult(false); } if (m_3DInterpolationEnabled) { m_SurfaceInterpolator->Modified(); } if (m_2DInterpolationEnabled) { m_FeedbackNode->SetData(nullptr); this->OnInterpolationActivated(true); m_LastSNC->SendSlice(); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); this->UpdateVisibleSuggestion(); } void QmitkSlicesInterpolator::Interpolate(mitk::PlaneGeometry *plane, mitk::TimePointType timePoint, mitk::SliceNavigationController *slicer) { if (m_ToolManager) { mitk::DataNode *node = m_ToolManager->GetWorkingData(0); if (node) { m_Segmentation = dynamic_cast(node->GetData()); if (m_Segmentation) { if (!m_Segmentation->GetTimeGeometry()->IsValidTimePoint(timePoint)) { MITK_WARN << "Cannot interpolate segmentation. Passed time point is not within the time bounds of WorkingImage. Time point: " << timePoint; return; } const auto timeStep = m_Segmentation->GetTimeGeometry()->TimePointToTimeStep(timePoint); int clickedSliceDimension = -1; int clickedSliceIndex = -1; // calculate real slice position, i.e. slice of the image mitk::SegTool2D::DetermineAffectedImageSlice(m_Segmentation, plane, clickedSliceDimension, clickedSliceIndex); mitk::Image::Pointer interpolation = m_Interpolator->Interpolate(clickedSliceDimension, clickedSliceIndex, plane, timeStep); m_FeedbackNode->SetData(interpolation); // maybe just have a variable that stores the active label color. if (m_ToolManager) { auto* workingNode = m_ToolManager->GetWorkingData(0); if (workingNode != nullptr) { auto* activeLabel = dynamic_cast(workingNode->GetData())->GetActiveLabelSet()->GetActiveLabel(); if (nullptr != activeLabel) { auto activeColor = activeLabel->GetColor(); m_FeedbackNode->SetProperty("color", mitk::ColorProperty::New(activeColor)); } } } m_LastSNC = slicer; m_LastSliceIndex = clickedSliceIndex; } } } } void QmitkSlicesInterpolator::OnSurfaceInterpolationFinished() { mitk::Surface::Pointer interpolatedSurface = m_SurfaceInterpolator->GetInterpolationResult(); mitk::DataNode *workingNode = m_ToolManager->GetWorkingData(0); mitk::PlaneGeometry::Pointer slicingPlane = mitk::PlaneGeometry::New(); mitk::Vector3D slicingPlaneNormalVector; FillVector3D(slicingPlaneNormalVector,0.0,1.0,0.0); mitk::Point3D origin; FillVector3D(origin, 0.0, 0.0, 0.0); slicingPlane->InitializePlane(origin, slicingPlaneNormalVector); if (interpolatedSurface.IsNotNull() && workingNode) { m_BtnApply3D->setEnabled(true); // T28261 // m_BtnSuggestPlane->setEnabled(true); m_InterpolatedSurfaceNode->SetData(interpolatedSurface); m_3DContourNode->SetData(m_SurfaceInterpolator->GetContoursAsSurface()); this->Show3DInterpolationResult(true); if (!m_DataStorage->Exists(m_InterpolatedSurfaceNode)) { m_DataStorage->Add(m_InterpolatedSurfaceNode); } } else if (interpolatedSurface.IsNull()) { m_BtnApply3D->setEnabled(false); // T28261 // m_BtnSuggestPlane->setEnabled(false); if (m_DataStorage->Exists(m_InterpolatedSurfaceNode)) { this->Show3DInterpolationResult(false); } } m_BtnReinit3DInterpolation->setEnabled(true); for (auto* slicer : m_ControllerToTimeObserverTag.keys()) { slicer->GetRenderer()->RequestUpdate(); } m_SurfaceInterpolator->ReinitializeInterpolation(); } void QmitkSlicesInterpolator::OnAcceptInterpolationClicked() { auto* workingNode = m_ToolManager->GetWorkingData(0); auto* planeGeometry = m_LastSNC->GetCurrentPlaneGeometry(); auto* interpolatedPreview = dynamic_cast(m_FeedbackNode->GetData()); if (nullptr == workingNode || nullptr == interpolatedPreview) return; auto* segmentationImage = dynamic_cast(workingNode->GetData()); if (nullptr == segmentationImage) return; const auto timePoint = m_LastSNC->GetSelectedTimePoint(); if (!segmentationImage->GetTimeGeometry()->IsValidTimePoint(timePoint)) { MITK_WARN << "Cannot accept interpolation. Time point selected by SliceNavigationController is not within the time bounds of segmentation. Time point: " << timePoint; return; } const auto timeStep = segmentationImage->GetTimeGeometry()->TimePointToTimeStep(timePoint); auto interpolatedSlice = mitk::SegTool2D::GetAffectedImageSliceAs2DImage(planeGeometry, segmentationImage, timeStep)->Clone(); auto labelSet = segmentationImage->GetActiveLabelSet(); auto activeValue = labelSet->GetActiveLabel()->GetValue(); mitk::TransferLabelContentAtTimeStep( interpolatedPreview, interpolatedSlice, labelSet, timeStep, 0, mitk::LabelSetImage::UnlabeledValue, false, { {0, mitk::LabelSetImage::UnlabeledValue}, {1, activeValue} } ); mitk::SegTool2D::WriteBackSegmentationResult(workingNode, planeGeometry, interpolatedSlice, timeStep); m_FeedbackNode->SetData(nullptr); } void QmitkSlicesInterpolator::AcceptAllInterpolations(mitk::SliceNavigationController *slicer) { /* * What exactly is done here: * 1. We create an empty diff image for the current segmentation * 2. All interpolated slices are written into the diff image * 3. Then the diffimage is applied to the original segmentation */ if (m_Segmentation) { mitk::Image::Pointer segmentation3D = m_Segmentation; unsigned int timeStep = 0; const auto timePoint = slicer->GetSelectedTimePoint(); if (4 == m_Segmentation->GetDimension()) { const auto* geometry = m_Segmentation->GetTimeGeometry(); if (!geometry->IsValidTimePoint(timePoint)) { MITK_WARN << "Cannot accept all interpolations. Time point selected by passed SliceNavigationController is not within the time bounds of segmentation. Time point: " << timePoint; return; } mitk::Image::Pointer activeLabelImage; try { auto labelSetImage = dynamic_cast(m_Segmentation); activeLabelImage = labelSetImage->CreateLabelMask(labelSetImage->GetActiveLabelSet()->GetActiveLabel()->GetValue(), true, 0); } catch (const std::exception& e) { MITK_ERROR << e.what() << " | NO LABELSETIMAGE IN WORKING NODE\n"; } m_Interpolator->SetSegmentationVolume(activeLabelImage); timeStep = geometry->TimePointToTimeStep(timePoint); auto timeSelector = mitk::ImageTimeSelector::New(); timeSelector->SetInput(m_Segmentation); timeSelector->SetTimeNr(timeStep); timeSelector->Update(); segmentation3D = timeSelector->GetOutput(); } // Create an empty diff image for the undo operation auto diffImage = mitk::Image::New(); diffImage->Initialize(segmentation3D); // Create scope for ImageWriteAccessor so that the accessor is destroyed right after use { mitk::ImageWriteAccessor accessor(diffImage); // Set all pixels to zero auto pixelType = mitk::MakeScalarPixelType(); // For legacy purpose support former pixel type of segmentations (before multilabel) if (itk::IOComponentEnum::UCHAR == m_Segmentation->GetImageDescriptor()->GetChannelDescriptor().GetPixelType().GetComponentType()) pixelType = mitk::MakeScalarPixelType(); memset(accessor.GetData(), 0, pixelType.GetSize() * diffImage->GetDimension(0) * diffImage->GetDimension(1) * diffImage->GetDimension(2)); } // Since we need to shift the plane it must be clone so that the original plane isn't altered auto slicedGeometry = m_Segmentation->GetSlicedGeometry(); auto planeGeometry = slicer->GetCurrentPlaneGeometry()->Clone(); int sliceDimension = -1; int sliceIndex = -1; mitk::SegTool2D::DetermineAffectedImageSlice(m_Segmentation, planeGeometry, sliceDimension, sliceIndex); const auto numSlices = m_Segmentation->GetDimension(sliceDimension); mitk::ProgressBar::GetInstance()->AddStepsToDo(numSlices); std::atomic_uint totalChangedSlices; // Reuse interpolation algorithm instance for each slice to cache boundary calculations auto algorithm = mitk::ShapeBasedInterpolationAlgorithm::New(); // Distribute slice interpolations to multiple threads const auto numThreads = std::min(std::thread::hardware_concurrency(), numSlices); // const auto numThreads = 1; std::vector> sliceIndices(numThreads); for (std::remove_const_t sliceIndex = 0; sliceIndex < numSlices; ++sliceIndex) sliceIndices[sliceIndex % numThreads].push_back(sliceIndex); std::vector threads; threads.reserve(numThreads); // This lambda will be executed by the threads auto interpolate = [=, &interpolator = m_Interpolator, &totalChangedSlices](unsigned int threadIndex) { auto clonedPlaneGeometry = planeGeometry->Clone(); auto origin = clonedPlaneGeometry->GetOrigin(); // Go through the sliced indices for (auto sliceIndex : sliceIndices[threadIndex]) { slicedGeometry->WorldToIndex(origin, origin); origin[sliceDimension] = sliceIndex; slicedGeometry->IndexToWorld(origin, origin); clonedPlaneGeometry->SetOrigin(origin); auto interpolation = interpolator->Interpolate(sliceDimension, sliceIndex, clonedPlaneGeometry, timeStep, algorithm); if (interpolation.IsNotNull()) { // Setting up the reslicing pipeline which allows us to write the interpolation results back into the image volume auto reslicer = vtkSmartPointer::New(); // Set overwrite mode to true to write back to the image volume reslicer->SetInputSlice(interpolation->GetSliceData()->GetVtkImageAccessor(interpolation)->GetVtkImageData()); reslicer->SetOverwriteMode(true); reslicer->Modified(); auto diffSliceWriter = mitk::ExtractSliceFilter::New(reslicer); diffSliceWriter->SetInput(diffImage); diffSliceWriter->SetTimeStep(0); diffSliceWriter->SetWorldGeometry(clonedPlaneGeometry); diffSliceWriter->SetVtkOutputRequest(true); diffSliceWriter->SetResliceTransformByGeometry(diffImage->GetTimeGeometry()->GetGeometryForTimeStep(0)); diffSliceWriter->Modified(); diffSliceWriter->Update(); ++totalChangedSlices; } mitk::ProgressBar::GetInstance()->Progress(); } }; m_Interpolator->EnableSliceImageCache(); // Do the interpolation here. for (size_t threadIndex = 0; threadIndex < numThreads; ++threadIndex) { interpolate(threadIndex); } m_Interpolator->DisableSliceImageCache(); const mitk::Label::PixelType newDestinationLabel = dynamic_cast(m_Segmentation)->GetActiveLabelSet()->GetActiveLabel()->GetValue(); // Do and Undo Operations if (totalChangedSlices > 0) { // Create do/undo operations auto* doOp = new mitk::ApplyDiffImageOperation(mitk::OpTEST, m_Segmentation, diffImage, timeStep); auto* undoOp = new mitk::ApplyDiffImageOperation(mitk::OpTEST, m_Segmentation, diffImage, timeStep); undoOp->SetFactor(-1.0); auto comment = "Confirm all interpolations (" + std::to_string(totalChangedSlices) + ")"; auto* undoStackItem = new mitk::OperationEvent(mitk::DiffImageApplier::GetInstanceForUndo(), doOp, undoOp, comment); mitk::OperationEvent::IncCurrGroupEventId(); mitk::OperationEvent::IncCurrObjectEventId(); mitk::UndoController::GetCurrentUndoModel()->SetOperationEvent(undoStackItem); mitk::DiffImageApplier::GetInstanceForUndo()->SetDestinationLabel(newDestinationLabel); // Apply the changes to the original image mitk::DiffImageApplier::GetInstanceForUndo()->ExecuteOperation(doOp); } m_FeedbackNode->SetData(nullptr); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSlicesInterpolator::FinishInterpolation(mitk::SliceNavigationController *slicer) { // this redirect is for calling from outside if (slicer == nullptr) OnAcceptAllInterpolationsClicked(); else AcceptAllInterpolations(slicer); } void QmitkSlicesInterpolator::OnAcceptAllInterpolationsClicked() { QMenu orientationPopup(this); for (auto it = m_ActionToSlicer.begin(); it != m_ActionToSlicer.end(); ++it) orientationPopup.addAction(it->first); connect(&orientationPopup, SIGNAL(triggered(QAction *)), this, SLOT(OnAcceptAllPopupActivated(QAction *))); orientationPopup.exec(QCursor::pos()); } void QmitkSlicesInterpolator::OnAccept3DInterpolationClicked() { auto referenceImage = GetData(m_ToolManager->GetReferenceData(0)); auto* segmentationDataNode = m_ToolManager->GetWorkingData(0); auto labelSetImage = dynamic_cast(segmentationDataNode->GetData()); auto activeLabelColor = labelSetImage->GetActiveLabelSet()->GetActiveLabel()->GetColor(); std::string activeLabelName = labelSetImage->GetActiveLabelSet()->GetActiveLabel()->GetName(); auto segmentation = GetData(segmentationDataNode); if (referenceImage.IsNull() || segmentation.IsNull()) return; const auto* segmentationGeometry = segmentation->GetTimeGeometry(); const auto timePoint = m_LastSNC->GetSelectedTimePoint(); if (!referenceImage->GetTimeGeometry()->IsValidTimePoint(timePoint) || !segmentationGeometry->IsValidTimePoint(timePoint)) { MITK_WARN << "Cannot accept interpolation. Current time point is not within the time bounds of the patient image and segmentation."; return; } auto interpolatedSurface = GetData(m_InterpolatedSurfaceNode); if (interpolatedSurface.IsNull()) return; auto surfaceToImageFilter = mitk::SurfaceToImageFilter::New(); surfaceToImageFilter->SetImage(referenceImage); surfaceToImageFilter->SetMakeOutputBinary(true); surfaceToImageFilter->SetUShortBinaryPixelType(itk::IOComponentEnum::USHORT == segmentation->GetPixelType().GetComponentType()); surfaceToImageFilter->SetInput(interpolatedSurface); surfaceToImageFilter->Update(); mitk::Image::Pointer interpolatedSegmentation = surfaceToImageFilter->GetOutput(); auto timeStep = segmentationGeometry->TimePointToTimeStep(timePoint); const mitk::Label::PixelType newDestinationLabel = labelSetImage->GetActiveLabelSet()->GetActiveLabel()->GetValue(); TransferLabelContentAtTimeStep( interpolatedSegmentation, labelSetImage, labelSetImage->GetActiveLabelSet(), timeStep, 0, 0, false, {{1, newDestinationLabel}}, mitk::MultiLabelSegmentation::MergeStyle::Merge, mitk::MultiLabelSegmentation::OverwriteStyle::RegardLocks); // m_CmbInterpolation->setCurrentIndex(0); this->Show3DInterpolationResult(false); std::string name = segmentationDataNode->GetName() + " 3D-interpolation - " + activeLabelName; mitk::TimeBounds timeBounds; if (1 < interpolatedSurface->GetTimeSteps()) { name += "_t" + std::to_string(timeStep); auto* polyData = vtkPolyData::New(); polyData->DeepCopy(interpolatedSurface->GetVtkPolyData(timeStep)); auto surface = mitk::Surface::New(); surface->SetVtkPolyData(polyData); interpolatedSurface = surface; timeBounds = segmentationGeometry->GetTimeBounds(timeStep); } else { timeBounds = segmentationGeometry->GetTimeBounds(0); } auto* surfaceGeometry = static_cast(interpolatedSurface->GetTimeGeometry()); surfaceGeometry->SetFirstTimePoint(timeBounds[0]); surfaceGeometry->SetStepDuration(timeBounds[1] - timeBounds[0]); // Typical file formats for surfaces do not save any time-related information. As a workaround at least for MITK scene files, we have the // possibility to seralize this information as properties. interpolatedSurface->SetProperty("ProportionalTimeGeometry.FirstTimePoint", mitk::FloatProperty::New(surfaceGeometry->GetFirstTimePoint())); interpolatedSurface->SetProperty("ProportionalTimeGeometry.StepDuration", mitk::FloatProperty::New(surfaceGeometry->GetStepDuration())); auto interpolatedSurfaceDataNode = mitk::DataNode::New(); interpolatedSurfaceDataNode->SetData(interpolatedSurface); interpolatedSurfaceDataNode->SetName(name); interpolatedSurfaceDataNode->SetOpacity(0.7f); interpolatedSurfaceDataNode->SetColor(activeLabelColor); m_DataStorage->Add(interpolatedSurfaceDataNode, segmentationDataNode); } void QmitkSlicesInterpolator::OnReinit3DInterpolation() { // Step 1. Load from the isContourPlaneGeometry nodes the contourNodes. mitk::NodePredicateProperty::Pointer pred = mitk::NodePredicateProperty::New("isContourPlaneGeometry", mitk::BoolProperty::New(true)); mitk::DataStorage::SetOfObjects::ConstPointer contourNodes = m_DataStorage->GetDerivations(m_ToolManager->GetWorkingData(0), pred); if (contourNodes->Size() != 0) { std::vector contourPlanes; std::vector contourList; if (m_ToolManager->GetWorkingData(0) != nullptr) { try { auto labelSetImage = dynamic_cast(m_ToolManager->GetWorkingData(0)->GetData()); auto activeLayerID = labelSetImage->GetActiveLayer(); const auto timePoint = m_LastSNC->GetSelectedTimePoint(); if (!labelSetImage->GetTimeGeometry()->IsValidTimePoint(timePoint)) { MITK_ERROR << "Invalid time point requested for interpolation pipeline."; return; } // Adding layer, label and timeStep information for the contourNodes. for (auto it = contourNodes->Begin(); it != contourNodes->End(); ++it) { auto contourNode = it->Value(); auto layerID = dynamic_cast(contourNode->GetProperty("layerID"))->GetValue(); auto labelID = dynamic_cast(contourNode->GetProperty("labelID"))->GetValue(); auto timeStep = dynamic_cast(contourNode->GetProperty("timeStep"))->GetValue(); auto px = dynamic_cast(contourNode->GetProperty("px"))->GetValue(); auto py = dynamic_cast(contourNode->GetProperty("py"))->GetValue(); auto pz = dynamic_cast(contourNode->GetProperty("pz"))->GetValue(); // auto layerImage = labelSetImage->GetLayerImage(layerID); auto planeGeometry = dynamic_cast(contourNode->GetData())->GetPlaneGeometry(); labelSetImage->SetActiveLayer(layerID); auto sliceImage = ExtractSliceFromImage(labelSetImage, planeGeometry, timeStep); labelSetImage->SetActiveLayer(activeLayerID); mitk::ImageToContourFilter::Pointer contourExtractor = mitk::ImageToContourFilter::New(); contourExtractor->SetInput(sliceImage); contourExtractor->SetContourValue(labelID); contourExtractor->Update(); mitk::Surface::Pointer contour = contourExtractor->GetOutput(); if (contour->GetVtkPolyData()->GetNumberOfPoints() == 0) continue; vtkSmartPointer intArray = vtkSmartPointer::New(); intArray->InsertNextValue(labelID); intArray->InsertNextValue(layerID); intArray->InsertNextValue(timeStep); contour->GetVtkPolyData()->GetFieldData()->AddArray(intArray); vtkSmartPointer doubleArray = vtkSmartPointer::New(); doubleArray->InsertNextValue(px); doubleArray->InsertNextValue(py); doubleArray->InsertNextValue(pz); contour->GetVtkPolyData()->GetFieldData()->AddArray(doubleArray); contour->DisconnectPipeline(); contourList.push_back(contour); contourPlanes.push_back(planeGeometry); } labelSetImage->SetActiveLayer(activeLayerID); // size_t activeLayer = labelSetImage->GetActiveLayer(); for (size_t l = 0; l < labelSetImage->GetNumberOfLayers(); ++l) { this->OnAddLabelSetConnection(l); } // labelSetImage->SetActiveLayer(activeLayer); m_SurfaceInterpolator->CompleteReinitialization(contourList, contourPlanes); } catch(const std::exception& e) { MITK_ERROR << "Exception thrown casting toolmanager working data to labelsetImage"; } } } else { m_BtnApply3D->setEnabled(false); QMessageBox errorInfo; errorInfo.setWindowTitle("Reinitialize surface interpolation"); errorInfo.setIcon(QMessageBox::Information); errorInfo.setText("No contours available for the selected segmentation!"); errorInfo.exec(); } } void QmitkSlicesInterpolator::OnAcceptAllPopupActivated(QAction *action) { try { auto iter = m_ActionToSlicer.find(action); if (iter != m_ActionToSlicer.end()) { mitk::SliceNavigationController *slicer = iter->second; AcceptAllInterpolations(slicer); } } catch (...) { /* Showing message box with possible memory error */ QMessageBox errorInfo; errorInfo.setWindowTitle("Interpolation Process"); errorInfo.setIcon(QMessageBox::Critical); errorInfo.setText("An error occurred during interpolation. Possible cause: Not enough memory!"); errorInfo.exec(); // additional error message on std::cerr std::cerr << "Ill construction in " __FILE__ " l. " << __LINE__ << std::endl; } } void QmitkSlicesInterpolator::OnInterpolationActivated(bool on) { m_2DInterpolationEnabled = on; try { if (m_DataStorage.IsNotNull()) { if (on && !m_DataStorage->Exists(m_FeedbackNode)) { m_DataStorage->Add(m_FeedbackNode); } } } catch (...) { // don't care (double add/remove) } if (m_ToolManager) { mitk::DataNode *workingNode = m_ToolManager->GetWorkingData(0); mitk::DataNode *referenceNode = m_ToolManager->GetReferenceData(0); QWidget::setEnabled(workingNode != nullptr); m_BtnApply2D->setEnabled(on); m_FeedbackNode->SetVisibility(on); if (!on) { mitk::RenderingManager::GetInstance()->RequestUpdateAll(); return; } if (workingNode) { auto labelSetImage = dynamic_cast(workingNode->GetData()); if (nullptr == labelSetImage) { MITK_ERROR << "NO LABELSETIMAGE IN WORKING NODE\n"; mitk::RenderingManager::GetInstance()->RequestUpdateAll(); return; } auto* activeLabel = labelSetImage->GetActiveLabelSet()->GetActiveLabel(); auto* segmentation = dynamic_cast(workingNode->GetData()); if (nullptr != activeLabel && nullptr != segmentation) { auto activeLabelImage = labelSetImage->CreateLabelMask(activeLabel->GetValue(), true, 0); m_Interpolator->SetSegmentationVolume(activeLabelImage); if (referenceNode) { mitk::Image *referenceImage = dynamic_cast(referenceNode->GetData()); m_Interpolator->SetReferenceVolume(referenceImage); // may be nullptr } } } } this->UpdateVisibleSuggestion(); } void QmitkSlicesInterpolator::Run3DInterpolation() { m_SurfaceInterpolator->Interpolate(); } void QmitkSlicesInterpolator::StartUpdateInterpolationTimer() { m_Timer->start(500); } void QmitkSlicesInterpolator::StopUpdateInterpolationTimer() { if(m_ToolManager) { auto* workingNode = m_ToolManager->GetWorkingData(0); auto activeColor = dynamic_cast(workingNode->GetData())->GetActiveLabelSet()->GetActiveLabel()->GetColor(); m_InterpolatedSurfaceNode->SetProperty("color", mitk::ColorProperty::New(activeColor)); m_3DContourNode->SetProperty("color", mitk::ColorProperty::New(activeColor)); } m_Timer->stop(); } void QmitkSlicesInterpolator::ChangeSurfaceColor() { float currentColor[3]; m_InterpolatedSurfaceNode->GetColor(currentColor); m_InterpolatedSurfaceNode->SetProperty("color", mitk::ColorProperty::New(SURFACE_COLOR_RGB)); m_InterpolatedSurfaceNode->Update(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(mitk::RenderingManager::REQUEST_UPDATE_3DWINDOWS); } void QmitkSlicesInterpolator::PrepareInputsFor3DInterpolation() { if (m_DataStorage.IsNotNull() && m_ToolManager && m_3DInterpolationEnabled) { auto *workingNode = m_ToolManager->GetWorkingData(0); if (workingNode != nullptr) { int ret = QMessageBox::Yes; if (m_SurfaceInterpolator->EstimatePortionOfNeededMemory() > 0.5) { QMessageBox msgBox; msgBox.setText("Due to short handed system memory the 3D interpolation may be very slow!"); msgBox.setInformativeText("Are you sure you want to activate the 3D interpolation?"); msgBox.setStandardButtons(QMessageBox::No | QMessageBox::Yes); ret = msgBox.exec(); } auto labelSetImage = dynamic_cast(workingNode->GetData()); auto activeLabel = labelSetImage->GetActiveLabelSet()->GetActiveLabel()->GetValue(); m_SurfaceInterpolator->AddActiveLabelContoursForInterpolation(activeLabel); if (m_Watcher.isRunning()) m_Watcher.waitForFinished(); if (ret == QMessageBox::Yes) { // Maybe set the segmentation node here m_Future = QtConcurrent::run(this, &QmitkSlicesInterpolator::Run3DInterpolation); m_Watcher.setFuture(m_Future); } else { m_CmbInterpolation->setCurrentIndex(0); } } else { QWidget::setEnabled(false); m_ChkShowPositionNodes->setEnabled(m_3DInterpolationEnabled); } } if (!m_3DInterpolationEnabled) { this->Show3DInterpolationResult(false); m_BtnApply3D->setEnabled(m_3DInterpolationEnabled); // T28261 // m_BtnSuggestPlane->setEnabled(m_3DInterpolationEnabled); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSlicesInterpolator::On3DInterpolationActivated(bool on) { m_3DInterpolationEnabled = on; try { // this->PrepareInputsFor3DInterpolation(); m_SurfaceInterpolator->Modified(); } catch (...) { MITK_ERROR << "Error with 3D surface interpolation!"; } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSlicesInterpolator::EnableInterpolation(bool on) { // only to be called from the outside world // just a redirection to OnInterpolationActivated OnInterpolationActivated(on); } void QmitkSlicesInterpolator::Enable3DInterpolation(bool on) { // only to be called from the outside world // just a redirection to OnInterpolationActivated this->On3DInterpolationActivated(on); } void QmitkSlicesInterpolator::UpdateVisibleSuggestion() { mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSlicesInterpolator::OnInterpolationInfoChanged(const itk::EventObject & /*e*/) { // something (e.g. undo) changed the interpolation info, we should refresh our display this->UpdateVisibleSuggestion(); } void QmitkSlicesInterpolator::OnInterpolationAborted(const itk::EventObject& /*e*/) { m_CmbInterpolation->setCurrentIndex(0); m_FeedbackNode->SetData(nullptr); } void QmitkSlicesInterpolator::OnSurfaceInterpolationInfoChanged(const itk::EventObject & /*e*/) { if (m_Watcher.isRunning()) m_Watcher.waitForFinished(); if (m_3DInterpolationEnabled) { m_3DContourNode->SetData(nullptr); m_InterpolatedSurfaceNode->SetData(nullptr); auto *workingNode = m_ToolManager->GetWorkingData(0); auto labelSetImage = dynamic_cast(workingNode->GetData()); auto activeLabel = labelSetImage->GetActiveLabelSet()->GetActiveLabel()->GetValue(); m_SurfaceInterpolator->AddActiveLabelContoursForInterpolation(activeLabel); m_Future = QtConcurrent::run(this, &QmitkSlicesInterpolator::Run3DInterpolation); m_Watcher.setFuture(m_Future); } } void QmitkSlicesInterpolator::SetCurrentContourListID() { // New ContourList = hide current interpolation Show3DInterpolationResult(false); if (m_DataStorage.IsNotNull() && m_ToolManager && m_LastSNC) { mitk::DataNode *workingNode = m_ToolManager->GetWorkingData(0); try{ auto labelSetImage = dynamic_cast(workingNode->GetData()); for (size_t layerID = 0; layerID < labelSetImage->GetNumberOfLayers(); ++layerID) { this->OnAddLabelSetConnection(layerID); } } catch (std::exception &e) { MITK_ERROR << e.what() << "\n"; } if (workingNode) { QWidget::setEnabled(true); const auto timePoint = m_LastSNC->GetSelectedTimePoint(); // In case the time is not valid use 0 to access the time geometry of the working node unsigned int time_position = 0; if (!workingNode->GetData()->GetTimeGeometry()->IsValidTimePoint(timePoint)) { MITK_WARN << "Cannot accept interpolation. Time point selected by SliceNavigationController is not within the time bounds of WorkingImage. Time point: " << timePoint; return; } // Sets up the surface interpolator to accept time_position = workingNode->GetData()->GetTimeGeometry()->TimePointToTimeStep(timePoint); mitk::Vector3D spacing = workingNode->GetData()->GetGeometry(time_position)->GetSpacing(); double minSpacing = 100; double maxSpacing = 0; for (int i = 0; i < 3; i++) { if (spacing[i] < minSpacing) { minSpacing = spacing[i]; } if (spacing[i] > maxSpacing) { maxSpacing = spacing[i]; } } m_SurfaceInterpolator->SetMaxSpacing(maxSpacing); m_SurfaceInterpolator->SetMinSpacing(minSpacing); m_SurfaceInterpolator->SetDistanceImageVolume(50000); mitk::Image::Pointer segmentationImage; segmentationImage = dynamic_cast(workingNode->GetData()); m_SurfaceInterpolator->SetCurrentInterpolationSession(segmentationImage); m_SurfaceInterpolator->SetCurrentTimePoint(timePoint); } else { QWidget::setEnabled(false); } } } void QmitkSlicesInterpolator::Show3DInterpolationResult(bool status) { if (m_InterpolatedSurfaceNode.IsNotNull()) m_InterpolatedSurfaceNode->SetVisibility(status); if (m_3DContourNode.IsNotNull()) { auto allRenderWindows = mitk::BaseRenderer::GetAll3DRenderWindows(); for (auto mapit = allRenderWindows.begin(); mapit != allRenderWindows.end(); ++mapit) { m_3DContourNode->SetVisibility(status, mapit->second); } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSlicesInterpolator::OnActiveLabelChanged(mitk::Label::PixelType) { m_3DContourNode->SetData(nullptr); m_FeedbackNode->SetData(nullptr); m_InterpolatedSurfaceNode->SetData(nullptr); if (m_Watcher.isRunning()) m_Watcher.waitForFinished(); if (m_3DInterpolationEnabled) { m_SurfaceInterpolator->Modified(); } if (m_2DInterpolationEnabled) { m_FeedbackNode->SetData(nullptr); this->OnInterpolationActivated(true); m_LastSNC->SendSlice(); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); this->UpdateVisibleSuggestion(); } void QmitkSlicesInterpolator::CheckSupportedImageDimension() { if (m_ToolManager->GetWorkingData(0)) { m_Segmentation = dynamic_cast(m_ToolManager->GetWorkingData(0)->GetData()); if (m_3DInterpolationEnabled && m_Segmentation && ((m_Segmentation->GetDimension() != 3) || (m_Segmentation->GetDimension() != 4)) ) { QMessageBox info; info.setWindowTitle("3D Interpolation Process"); info.setIcon(QMessageBox::Information); info.setText("3D Interpolation is only supported for 3D/4D images at the moment!"); info.exec(); m_CmbInterpolation->setCurrentIndex(0); } } } void QmitkSlicesInterpolator::OnSliceNavigationControllerDeleted(const itk::Object *sender, const itk::EventObject & /*e*/) { // Don't know how to avoid const_cast here?! mitk::SliceNavigationController *slicer = dynamic_cast(const_cast(sender)); if (slicer) { m_ControllerToTimeObserverTag.remove(slicer); m_ControllerToSliceObserverTag.remove(slicer); m_ControllerToDeleteObserverTag.remove(slicer); } } void QmitkSlicesInterpolator::WaitForFutures() { if (m_Watcher.isRunning()) { m_Watcher.waitForFinished(); } if (m_PlaneWatcher.isRunning()) { m_PlaneWatcher.waitForFinished(); } } void QmitkSlicesInterpolator::NodeRemoved(const mitk::DataNode* node) { if ((m_ToolManager && m_ToolManager->GetWorkingData(0) == node) || node == m_3DContourNode || node == m_FeedbackNode || node == m_InterpolatedSurfaceNode) { WaitForFutures(); } } void QmitkSlicesInterpolator::OnAddLabelSetConnection(unsigned int layerID) { if (m_ToolManager->GetWorkingData(0) != nullptr) { try { auto workingImage = dynamic_cast(m_ToolManager->GetWorkingData(0)->GetData()); auto labelSet = workingImage->GetLabelSet(layerID); labelSet->RemoveLabelEvent += mitk::MessageDelegate1( this, &QmitkSlicesInterpolator::OnRemoveLabel); labelSet->ActiveLabelEvent += mitk::MessageDelegate1( this, &QmitkSlicesInterpolator::OnActiveLabelChanged); workingImage->AfterChangeLayerEvent += mitk::MessageDelegate( this, &QmitkSlicesInterpolator::OnLayerChanged); m_SurfaceInterpolator->AddLabelSetConnection(layerID); } catch(const std::exception& e) { MITK_ERROR << e.what() << '\n'; } } } void QmitkSlicesInterpolator::OnAddLabelSetConnection() { if (m_ToolManager->GetWorkingData(0) != nullptr) { try { auto workingImage = dynamic_cast(m_ToolManager->GetWorkingData(0)->GetData()); workingImage->GetActiveLabelSet()->RemoveLabelEvent += mitk::MessageDelegate1( this, &QmitkSlicesInterpolator::OnRemoveLabel); workingImage->GetActiveLabelSet()->ActiveLabelEvent += mitk::MessageDelegate1( this, &QmitkSlicesInterpolator::OnActiveLabelChanged); workingImage->AfterChangeLayerEvent += mitk::MessageDelegate( this, &QmitkSlicesInterpolator::OnLayerChanged); m_SurfaceInterpolator->AddLabelSetConnection(); } catch(const std::exception& e) { MITK_ERROR << e.what() << '\n'; } } } void QmitkSlicesInterpolator::OnRemoveLabelSetConnection(mitk::LabelSetImage* labelSetImage, unsigned int layerID) { size_t previousLayerID = labelSetImage->GetActiveLayer(); labelSetImage->SetActiveLayer(layerID); labelSetImage->GetActiveLabelSet()->RemoveLabelEvent -= mitk::MessageDelegate1( this, &QmitkSlicesInterpolator::OnRemoveLabel); labelSetImage->GetActiveLabelSet()->ActiveLabelEvent -= mitk::MessageDelegate1( this, &QmitkSlicesInterpolator::OnActiveLabelChanged); labelSetImage->AfterChangeLayerEvent -= mitk::MessageDelegate( this, &QmitkSlicesInterpolator::OnLayerChanged); m_SurfaceInterpolator->RemoveLabelSetConnection(labelSetImage, layerID); labelSetImage->SetActiveLayer(previousLayerID); } void QmitkSlicesInterpolator::OnRemoveLabelSetConnection() { if (m_ToolManager->GetWorkingData(0) != nullptr) { try { auto workingImage = dynamic_cast(m_ToolManager->GetWorkingData(0)->GetData()); workingImage->GetActiveLabelSet()->RemoveLabelEvent -= mitk::MessageDelegate1( this, &QmitkSlicesInterpolator::OnRemoveLabel); workingImage->GetActiveLabelSet()->ActiveLabelEvent -= mitk::MessageDelegate1( this, &QmitkSlicesInterpolator::OnActiveLabelChanged); workingImage->AfterChangeLayerEvent -= mitk::MessageDelegate( this, &QmitkSlicesInterpolator::OnLayerChanged); } catch(const std::exception& e) { MITK_ERROR << e.what() << '\n'; } } } void QmitkSlicesInterpolator::OnRemoveLabel(mitk::Label::PixelType /*removedLabelValue*/) { if (m_ToolManager->GetWorkingData(0) != nullptr) { try { auto labelSetImage = dynamic_cast(m_ToolManager->GetWorkingData(0)->GetData()); auto currentLayerID = labelSetImage->GetActiveLayer(); auto numTimeSteps = labelSetImage->GetTimeGeometry()->CountTimeSteps(); for (size_t t = 0; t < numTimeSteps; ++t) { m_SurfaceInterpolator->RemoveContours(m_PreviousActiveLabelValue,t,currentLayerID); } } catch(const std::exception& e) { MITK_ERROR << "Bad cast error for labelSetImage"; } } } void QmitkSlicesInterpolator::OnModifyLabelChanged(const itk::Object *caller, const itk::EventObject & /*event*/) { auto *tempImage = dynamic_cast(const_cast(caller) ) ; if( tempImage == nullptr) { MITK_ERROR << "Unable to cast caller to LabelSetImage."; return; } ModifyLabelActionTrigerred actionTriggered = ModifyLabelActionTrigerred::Null; if(m_ToolManager->GetWorkingData(0) != nullptr) { auto labelSetImage = dynamic_cast(m_ToolManager->GetWorkingData(0)->GetData()); if (labelSetImage == tempImage) { const auto timePoint = m_LastSNC->GetSelectedTimePoint(); if (!labelSetImage->GetTimeGeometry()->IsValidTimePoint(timePoint)) { MITK_ERROR << "Invalid time point requested for interpolation pipeline."; return; } auto timeStep = labelSetImage->GetTimeGeometry()->TimePointToTimeStep(timePoint); auto numLayersInCurrentSegmentation = m_SurfaceInterpolator->GetNumberOfLayersInCurrentSegmentation(); // This handles the add layer or remove layer operation. if (labelSetImage->GetNumberOfLayers() != numLayersInCurrentSegmentation) { bool addLayer = (labelSetImage->GetNumberOfLayers() == (numLayersInCurrentSegmentation +1) ); bool removeLayer = (labelSetImage->GetNumberOfLayers() == (numLayersInCurrentSegmentation - 1) ); m_SurfaceInterpolator->SetNumberOfLayersInCurrentSegmentation(labelSetImage->GetNumberOfLayers()); if (addLayer) { m_SurfaceInterpolator->OnAddLayer(); this->OnAddLabelSetConnection(); } if (removeLayer) { m_SurfaceInterpolator->OnRemoveLayer(); } return; } // Get the pixels present in the image. // This portion of the code deals with the merge and erase labels operations. auto imageDimension = labelSetImage->GetDimension(); if (imageDimension == 4) { actionTriggered = ModifyLabelProcessing<4>(labelSetImage, m_SurfaceInterpolator, timeStep); } else { actionTriggered = ModifyLabelProcessing<3>(labelSetImage, m_SurfaceInterpolator, timeStep); } if (actionTriggered == ModifyLabelActionTrigerred::Erase) { m_InterpolatedSurfaceNode->SetData(nullptr); } auto currentLayerID = labelSetImage->GetActiveLayer(); if (actionTriggered == ModifyLabelActionTrigerred::Merge) { this->MergeContours(timeStep, currentLayerID); m_SurfaceInterpolator->Modified(); } } } } void QmitkSlicesInterpolator::MergeContours(unsigned int timeStep, unsigned int layerID) { std::vector& contours = m_SurfaceInterpolator->GetContours(timeStep,layerID); std::this_thread::sleep_for(std::chrono::milliseconds(1000)); for (size_t i = 0; i < contours.size(); ++i) { for (size_t j = i+1; j < contours.size(); ++j) { // And Labels are the same and Layers are the same. bool areContoursCoplanar = AreContoursCoplanar(contours[i],contours[j]); if ( areContoursCoplanar && (contours[i].LabelValue == contours[j].LabelValue) ) { // Update the contour by re-extracting the slice from the corresponding plane. mitk::Image::Pointer slice = ExtractSliceFromImage(m_Segmentation, contours[i].Plane, timeStep); mitk::ImageToContourFilter::Pointer contourExtractor = mitk::ImageToContourFilter::New(); contourExtractor->SetInput(slice); contourExtractor->SetContourValue(contours[i].LabelValue); contourExtractor->Update(); mitk::Surface::Pointer contour = contourExtractor->GetOutput(); contours[i].Contour = contour; // Update the interior point of the contour contours[i].ContourPoint = m_SurfaceInterpolator->ComputeInteriorPointOfContour(contours[i],dynamic_cast(m_Segmentation)); // Setting the contour polygon data to an empty vtkPolyData, // as source label is empty after merge operation. contours[j].Contour->SetVtkPolyData(vtkSmartPointer::New()); } } } auto segmentationNode = m_SurfaceInterpolator->GetSegmentationImageNode(); if (segmentationNode == nullptr) { MITK_ERROR << "segmentation Image Node not found\n"; } auto isContourPlaneGeometry = mitk::NodePredicateProperty::New("isContourPlaneGeometry", mitk::BoolProperty::New(true)); mitk::DataStorage::SetOfObjects::ConstPointer contourNodes = m_DataStorage->GetDerivations(segmentationNode, isContourPlaneGeometry); // Remove empty contour nodes. auto isContourEmpty = [] (const mitk::SurfaceInterpolationController::ContourPositionInformation& contour) { return (contour.Contour->GetVtkPolyData()->GetNumberOfPoints() == 0); }; auto it = std::remove_if(contours.begin(), contours.end(), isContourEmpty); contours.erase(it, contours.end()); } + +void QmitkSlicesInterpolator::ClearSegmentationObservers() +{ + auto dataIter = m_SegmentationObserverTags.begin(); + while (dataIter != m_SegmentationObserverTags.end()) + { + auto labelSetImage = (*dataIter).first; + labelSetImage->RemoveObserver((*dataIter).second); + for (size_t layerID = 0; layerID < labelSetImage->GetNumberOfLayers(); ++layerID) + { + this->OnRemoveLabelSetConnection(labelSetImage, layerID); + } + ++dataIter; + } + m_SegmentationObserverTags.clear(); +} diff --git a/Modules/SegmentationUI/Qmitk/QmitkSlicesInterpolator.h b/Modules/SegmentationUI/Qmitk/QmitkSlicesInterpolator.h index fddec42bf3..9ab6eec6d3 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkSlicesInterpolator.h +++ b/Modules/SegmentationUI/Qmitk/QmitkSlicesInterpolator.h @@ -1,425 +1,426 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkSlicesInterpolator_h #define QmitkSlicesInterpolator_h #include "mitkDataNode.h" #include "mitkDataStorage.h" #include "mitkSegmentationInterpolationController.h" #include "mitkSliceNavigationController.h" #include "mitkSurfaceInterpolationController.h" #include "mitkToolManager.h" #include #include "mitkFeatureBasedEdgeDetectionFilter.h" #include "mitkPointCloudScoringFilter.h" #include #include #include #include #include #include #include #include "mitkVtkRepresentationProperty.h" #include "vtkProperty.h" // For running 3D interpolation in background #include #include #include #include namespace mitk { class PlaneGeometry; class SliceNavigationController; } class QPushButton; class QmitkRenderWindow; enum ModifyLabelActionTrigerred { Null, Erase, Merge }; /** \brief GUI for slices interpolation. \ingroup ToolManagerEtAl \ingroup Widgets \sa QmitkInteractiveSegmentation \sa mitk::SegmentationInterpolation While mitk::SegmentationInterpolation does the bookkeeping of interpolation (keeping track of which slices contain how much segmentation) and the algorithmic work, QmitkSlicesInterpolator is responsible to watch the GUI, to notice, which slice is currently visible. It triggers generation of interpolation suggestions and also triggers acception of suggestions. \todo show/hide feedback on demand Last contributor: $Author: maleike $ */ class MITKSEGMENTATIONUI_EXPORT QmitkSlicesInterpolator : public QWidget { Q_OBJECT public: QmitkSlicesInterpolator(QWidget *parent = nullptr, const char *name = nullptr); /** To be called once before real use. */ void Initialize(mitk::ToolManager *toolManager, const QList& windows); /** * @brief * */ void Uninitialize(); ~QmitkSlicesInterpolator() override; /** * @brief Set the Data Storage object * * @param storage */ void SetDataStorage(mitk::DataStorage::Pointer storage); /** * @brief Get the Data Storage object * * @return mitk::DataStorage* */ mitk::DataStorage *GetDataStorage(); /** Just public because it is called by itk::Commands. You should not need to call this. */ void OnToolManagerWorkingDataModified(); /** Just public because it is called by itk::Commands. You should not need to call this. */ void OnToolManagerReferenceDataModified(); /** * @brief Reacts to the time changed event. * * @param sender */ void OnTimeChanged(itk::Object *sender, const itk::EventObject &); /** * @brief Reacts to the slice changed event * * @param sender */ void OnSliceChanged(itk::Object *sender, const itk::EventObject &); void OnSliceNavigationControllerDeleted(const itk::Object *sender, const itk::EventObject &); /** Just public because it is called by itk::Commands. You should not need to call this. */ void OnInterpolationInfoChanged(const itk::EventObject &); /** Just public because it is called by itk::Commands. You should not need to call this. */ void OnInterpolationAborted(const itk::EventObject &); /** Just public because it is called by itk::Commands. You should not need to call this. */ void OnSurfaceInterpolationInfoChanged(const itk::EventObject &); private: /** * @brief Set the visibility of the 3d interpolation */ void Show3DInterpolationResult(bool); /** * @brief Function that reacts to a change in the activeLabel of the working segmentation image. * */ void OnActiveLabelChanged(mitk::Label::PixelType); /** * @brief Function that reacts to a change in the layer. * */ void OnLayerChanged(); /** * @brief Function that handles label removal from the segmentation image. * */ void OnRemoveLabel(mitk::Label::PixelType removedLabelValue); /** * @brief Function that to changes in the segmentation image. It handles the layer removal, addition, label erasure, * */ void OnModifyLabelChanged(const itk::Object *caller, const itk::EventObject & /*event*/); /** * @brief Add the necessary subscribers to the label set image, for UI responsiveness. * It deals with remove label, change active label, layer changes and change in the label. * */ void OnAddLabelSetConnection(); /** * @brief Add the necessary subscribers to the current LabelSetImage at the layer input, for UI responsiveness. * It deals with remove label, change active label, layer changes and change in the label. * * @param layerID */ void OnAddLabelSetConnection(unsigned int layerID); /** * @brief Remove the subscribers for the different events to the segmentation image. * */ void OnRemoveLabelSetConnection(); /** * @brief Merge contours for the current layerID and current timeStep. * * @param timeStep * @param layerID */ void MergeContours(unsigned int timeStep, unsigned int layerID); /** * @brief Prepare Inputs for 3D Interpolation. * */ void PrepareInputsFor3DInterpolation(); signals: void SignalRememberContourPositions(bool); void SignalShowMarkerNodes(bool); public slots: virtual void setEnabled(bool); /** Call this from the outside to enable/disable interpolation */ void EnableInterpolation(bool); void Enable3DInterpolation(bool); /** Call this from the outside to accept all interpolations */ void FinishInterpolation(mitk::SliceNavigationController *slicer = nullptr); protected slots: /** Reaction to button clicks. */ void OnAcceptInterpolationClicked(); /* Opens popup to ask about which orientation should be interpolated */ void OnAcceptAllInterpolationsClicked(); /* Reaction to button clicks */ void OnAccept3DInterpolationClicked(); /** * @brief Reaction to reinit 3D Interpolation. Re-reads the plane geometries of the image * that should have generated the * */ void OnReinit3DInterpolation(); /* * Will trigger interpolation for all slices in given orientation (called from popup menu of * OnAcceptAllInterpolationsClicked) */ void OnAcceptAllPopupActivated(QAction *action); /** Called on activation/deactivation */ void OnInterpolationActivated(bool); void On3DInterpolationActivated(bool); void OnInterpolationMethodChanged(int index); // Enhancement for 3D interpolation void On2DInterpolationEnabled(bool); void On3DInterpolationEnabled(bool); void OnInterpolationDisabled(bool); void OnShowMarkers(bool); void Run3DInterpolation(); /** * @brief Function triggers when the surface interpolation thread completes running. * It is responsible for retrieving the data, rendering it in the active color label, * storing the surface information in the feedback node. * */ void OnSurfaceInterpolationFinished(); void StartUpdateInterpolationTimer(); void StopUpdateInterpolationTimer(); void ChangeSurfaceColor(); /** * @brief Removes all observers to the labelSetImage at the layerID specified. * Is used when changing the segmentation image. * * @param labelSetImage * @param layerID */ void OnRemoveLabelSetConnection(mitk::LabelSetImage* labelSetImage, unsigned int layerID); protected: const std::map createActionToSlicer(const QList& windows); std::map m_ActionToSlicer; void AcceptAllInterpolations(mitk::SliceNavigationController *slicer); /** Retrieves the currently selected PlaneGeometry from a SlicedGeometry3D that is generated by a SliceNavigationController and calls Interpolate to further process this PlaneGeometry into an interpolation. \param e is a actually a mitk::SliceNavigationController::GeometrySliceEvent, sent by a SliceNavigationController \param slicer the SliceNavigationController */ bool TranslateAndInterpolateChangedSlice(const itk::EventObject &e, mitk::SliceNavigationController *slicer); /** Given a PlaneGeometry, this method figures out which slice of the first working image (of the associated ToolManager) should be interpolated. The actual work is then done by our SegmentationInterpolation object. */ void Interpolate(mitk::PlaneGeometry *plane, mitk::TimePointType timePoint, mitk::SliceNavigationController *slicer); // void InterpolateSurface(); /** Called internally to update the interpolation suggestion. Finds out about the focused render window and requests an interpolation. */ void UpdateVisibleSuggestion(); void SetCurrentContourListID(); private: void InitializeWindow(QmitkRenderWindow* window); void HideAllInterpolationControls(); void Show2DInterpolationControls(bool show); void Show3DInterpolationControls(bool show); void CheckSupportedImageDimension(); void WaitForFutures(); void NodeRemoved(const mitk::DataNode* node); + void ClearSegmentationObservers(); mitk::SegmentationInterpolationController::Pointer m_Interpolator; mitk::SurfaceInterpolationController::Pointer m_SurfaceInterpolator; mitk::FeatureBasedEdgeDetectionFilter::Pointer m_EdgeDetector; mitk::PointCloudScoringFilter::Pointer m_PointScorer; mitk::ToolManager::Pointer m_ToolManager; bool m_Initialized; QHash m_ControllerToTimeObserverTag; QHash m_ControllerToSliceObserverTag; QHash m_ControllerToDeleteObserverTag; std::map m_SegmentationObserverTags; unsigned int InterpolationInfoChangedObserverTag; unsigned int SurfaceInterpolationInfoChangedObserverTag; unsigned int InterpolationAbortedObserverTag; QGroupBox *m_GroupBoxEnableExclusiveInterpolationMode; QComboBox *m_CmbInterpolation; QPushButton *m_BtnApply2D; QPushButton *m_BtnApplyForAllSlices2D; QPushButton *m_BtnApply3D; // T28261 // QPushButton *m_BtnSuggestPlane; QCheckBox *m_ChkShowPositionNodes; QPushButton *m_BtnReinit3DInterpolation; mitk::DataNode::Pointer m_FeedbackNode; mitk::DataNode::Pointer m_InterpolatedSurfaceNode; mitk::DataNode::Pointer m_3DContourNode; mitk::Image *m_Segmentation; mitk::SliceNavigationController *m_LastSNC; unsigned int m_LastSliceIndex; QHash m_TimePoints; bool m_2DInterpolationEnabled; bool m_3DInterpolationEnabled; unsigned int m_numTimesLabelSetConnectionAdded; mitk::DataStorage::Pointer m_DataStorage; QFuture m_Future; QFutureWatcher m_Watcher; QFuture m_ModifyFuture; QFutureWatcher m_ModifyWatcher; QTimer *m_Timer; QFuture m_PlaneFuture; QFutureWatcher m_PlaneWatcher; mitk::Label::PixelType m_PreviousActiveLabelValue; mitk::Label::PixelType m_CurrentActiveLabelValue; unsigned int m_PreviousLayerIndex; unsigned int m_CurrentLayerIndex; bool m_FirstRun; }; #endif