diff --git a/Modules/Segmentation/Interactions/mitkCloseRegionTool.cpp b/Modules/Segmentation/Interactions/mitkCloseRegionTool.cpp new file mode 100644 index 0000000000..4e5cd15b69 --- /dev/null +++ b/Modules/Segmentation/Interactions/mitkCloseRegionTool.cpp @@ -0,0 +1,120 @@ +/*============================================================================ + +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 "mitkCloseRegionTool.h" + +// us +#include +#include +#include +#include + +#include + +#include +#include + +namespace mitk +{ + MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, CloseRegionTool, "Close tool"); +} + +const char **mitk::CloseRegionTool::GetXPM() const +{ + return nullptr; +} + +us::ModuleResource mitk::CloseRegionTool::GetIconResource() const +{ + us::Module *module = us::GetModuleContext()->GetModule(); + us::ModuleResource resource = module->GetResource("Close_48x48.png"); + return resource; +} + +us::ModuleResource mitk::CloseRegionTool::GetCursorIconResource() const +{ + us::Module *module = us::GetModuleContext()->GetModule(); + us::ModuleResource resource = module->GetResource("Close_Cursor_32x32.png"); + return resource; +} + +const char *mitk::CloseRegionTool::GetName() const +{ + return "Close"; +} + + +template +void DoITKRegionClosing(const itk::Image* oldSegImage, + mitk::Image::Pointer& filledRegionImage, itk::Index seedIndex, mitk::Label::PixelType& seedLabel) +{ + typedef itk::Image InputImageType; + typedef itk::Image OutputImageType; + typedef itk::ConnectedThresholdImageFilter RegionGrowingFilterType; + using FillHoleFilter = itk::BinaryFillholeImageFilter; + + seedLabel = oldSegImage->GetPixel(seedIndex); + + typename OutputImageType::Pointer itkResultImage; + filledRegionImage = nullptr; + + try + { + auto regionGrower = RegionGrowingFilterType::New(); + regionGrower->SetInput(oldSegImage); + regionGrower->SetReplaceValue(1); + regionGrower->AddSeed(seedIndex); + + regionGrower->SetLower(seedLabel); + regionGrower->SetUpper(seedLabel); + + auto filler = FillHoleFilter::New(); + filler->SetInput(regionGrower->GetOutput()); + filler->SetForegroundValue(1); + filler->Update(); + + itkResultImage = filler->GetOutput(); + } + catch (const itk::ExceptionObject&) + { + return; // can't work + } + catch (...) + { + return; + } + mitk::CastToMitkImage(itkResultImage, filledRegionImage); +} + +mitk::Image::Pointer mitk::CloseRegionTool::GenerateFillImage(const Image* workingSlice, Point3D seedPoint, mitk::Label::PixelType& seedLabelValue) const +{ + itk::Index<2> seedIndex; + workingSlice->GetGeometry()->WorldToIndex(seedPoint, seedIndex); + + Image::Pointer fillImage; + + AccessFixedDimensionByItk_n(workingSlice, DoITKRegionClosing, 2, (fillImage, seedIndex, seedLabelValue)); + + auto labelSetImage = dynamic_cast(this->GetWorkingData()); + if (seedLabelValue == labelSetImage->GetExteriorLabel()->GetValue()) + { + return nullptr; + } + + return fillImage; +} + +void mitk::CloseRegionTool::PrepareFilling(const Image* /*workingSlice*/, Point3D /*seedPoint*/) +{ + m_FillLabelValue = m_SeedLabelValue; + m_MergeStyle = MultiLabelSegmentation::MergeStyle::Merge; +}; diff --git a/Modules/Segmentation/Interactions/mitkFillRegionTool.h b/Modules/Segmentation/Interactions/mitkCloseRegionTool.h similarity index 64% copy from Modules/Segmentation/Interactions/mitkFillRegionTool.h copy to Modules/Segmentation/Interactions/mitkCloseRegionTool.h index 3643b13992..1d907a2582 100644 --- a/Modules/Segmentation/Interactions/mitkFillRegionTool.h +++ b/Modules/Segmentation/Interactions/mitkCloseRegionTool.h @@ -1,60 +1,64 @@ /*============================================================================ 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 mitkFillRegionTool_h_Included -#define mitkFillRegionTool_h_Included +#ifndef mitkCloseRegionTool_h_Included +#define mitkCloseRegionTool_h_Included -#include "mitkSetRegionTool.h" +#include "mitkFillRegionBaseTool.h" #include namespace us { class ModuleResource; } namespace mitk { /** - \brief Fill the inside of a contour with the foreground pixel value. + \brief Closes/Fills the inside of a contour with the foreground pixel value. - \sa SetRegionTool + \sa FillRegionBaseTool \ingroup Interactions Finds the outer contour of a shape in 2D (possibly including holes) and sets all the pixels inside to the foreground pixel value (filling holes in a segmentation). If clicked on the background, the outer contour might contain the whole image and thus fill the whole image with the foreground pixel value. \warning Only to be instantiated by mitk::ToolManager. */ - class MITKSEGMENTATION_EXPORT FillRegionTool : public SetRegionTool + class MITKSEGMENTATION_EXPORT CloseRegionTool : public FillRegionBaseTool { public: - mitkClassMacro(FillRegionTool, SetRegionTool); + mitkClassMacro(CloseRegionTool, FillRegionBaseTool); itkFactorylessNewMacro(Self); itkCloneMacro(Self); const char **GetXPM() const override; us::ModuleResource GetCursorIconResource() const override; us::ModuleResource GetIconResource() const override; const char *GetName() const override; protected: - FillRegionTool(); // purposely hidden - ~FillRegionTool() override; + CloseRegionTool() = default; // purposely hidden + ~CloseRegionTool() = default; + + Image::Pointer GenerateFillImage(const Image* workingSlice, Point3D seedPoint, mitk::Label::PixelType& seedLabelValue) const override; + void PrepareFilling(const Image* workingSlice, Point3D seedPoint) override; + }; } // namespace #endif diff --git a/Modules/Segmentation/Interactions/mitkEditableContourTool.cpp b/Modules/Segmentation/Interactions/mitkEditableContourTool.cpp index f25e261373..81db18aa4a 100644 --- a/Modules/Segmentation/Interactions/mitkEditableContourTool.cpp +++ b/Modules/Segmentation/Interactions/mitkEditableContourTool.cpp @@ -1,471 +1,459 @@ /*============================================================================ 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 "mitkEditableContourTool.h" #include mitk::EditableContourTool::EditableContourTool() : FeedbackContourTool("EditableContourTool"), m_AutoConfirm(true), m_AddMode(true) {} mitk::EditableContourTool::~EditableContourTool() { this->ReleaseHelperObjects(); this->ReleaseInteractors(); } void mitk::EditableContourTool::ConnectActionsAndFunctions() { CONNECT_FUNCTION("InitObject", OnInitContour); CONNECT_FUNCTION("AddPoint", OnAddPoint); CONNECT_FUNCTION("CtrlAddPoint", OnAddPoint); CONNECT_FUNCTION("Drawing", OnDrawing); CONNECT_FUNCTION("EndDrawing", OnEndDrawing); CONNECT_FUNCTION("FinishContour", OnFinish); CONNECT_FUNCTION("CtrlMovePoint", OnMouseMoved); } void mitk::EditableContourTool::Activated() { Superclass::Activated(); this->ResetToStartState(); this->EnableContourInteraction(true); } void mitk::EditableContourTool::Deactivated() { this->ClearSegmentation(); Superclass::Deactivated(); } void mitk::EditableContourTool::ConfirmSegmentation(bool resetStatMachine) { auto referenceImage = this->GetReferenceData(); auto workingImage = this->GetWorkingData(); if (nullptr != referenceImage && nullptr != workingImage) { std::vector sliceInfos; const auto currentTimePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint(); TimeStepType workingImageTimeStep = workingImage->GetTimeGeometry()->TimePointToTimeStep(currentTimePoint); auto contour = this->GetContour(); if (nullptr == contour || contour->IsEmpty()) return; auto workingSlice = this->GetAffectedImageSliceAs2DImage(m_PlaneGeometry, workingImage, workingImageTimeStep)->Clone(); sliceInfos.emplace_back(workingSlice, m_PlaneGeometry, workingImageTimeStep); auto projectedContour = ContourModelUtils::ProjectContourTo2DSlice(workingSlice, contour); int activePixelValue = ContourModelUtils::GetActivePixelValue(workingImage); if (!m_AddMode) { activePixelValue = 0; } ContourModelUtils::FillContourInSlice(projectedContour, workingSlice, workingImage, activePixelValue); this->WriteBackSegmentationResults(sliceInfos); } this->ReleaseHelperObjects(); this->ReleaseInteractors(); if (resetStatMachine) this->ResetToStartState(); } void mitk::EditableContourTool::ClearSegmentation() { this->ReleaseHelperObjects(); this->ReleaseInteractors(); this->ResetToStartState(); } bool mitk::EditableContourTool::IsEditingContour() const { return (nullptr != GetContour()) && !this->IsDrawingContour(); }; bool mitk::EditableContourTool::IsDrawingContour() const { return m_PreviewContour.IsNotNull(); }; -bool mitk::EditableContourTool::IsPositionEventInsideImageRegion(mitk::InteractionPositionEvent *positionEvent, - mitk::BaseData *data) -{ - bool isPositionEventInsideImageRegion = - nullptr != data && data->GetGeometry()->IsInside(positionEvent->GetPositionInWorld()); - - if (!isPositionEventInsideImageRegion) - MITK_WARN("EditableContourTool") << "PositionEvent is outside ImageRegion!"; - - return isPositionEventInsideImageRegion; -} - mitk::Point3D mitk::EditableContourTool::PrepareInitContour(const Point3D& clickedPoint) { //default implementation does nothing return clickedPoint; } void mitk::EditableContourTool::OnInitContour(StateMachineAction *, InteractionEvent *interactionEvent) { auto positionEvent = dynamic_cast(interactionEvent); if (nullptr == positionEvent) return; auto workingDataNode = this->GetWorkingDataNode(); if (nullptr != this->GetContour()) { this->ConfirmSegmentation(false); } if (!IsPositionEventInsideImageRegion(positionEvent, workingDataNode->GetData())) { this->ResetToStartState(); return; } m_LastEventSender = positionEvent->GetSender(); m_LastEventSlice = m_LastEventSender->GetSlice(); auto contour = this->CreateNewContour(); m_ContourNode = mitk::DataNode::New(); m_ContourNode->SetData(contour); m_ContourNode->SetName("working contour node"); m_ContourNode->SetProperty("layer", IntProperty::New(100)); m_ContourNode->AddProperty("fixedLayer", BoolProperty::New(true)); m_ContourNode->SetProperty("helper object", mitk::BoolProperty::New(true)); m_ContourNode->AddProperty("contour.color", ColorProperty::New(1.0f, 1.0f, 0.0f), nullptr, true); m_ContourNode->AddProperty("contour.points.color", ColorProperty::New(1.0f, 0.0f, 0.1f), nullptr, true); m_ContourNode->AddProperty("contour.controlpoints.show", BoolProperty::New(true), nullptr, true); m_PreviewContour = this->CreateNewContour(); m_PreviewContourNode = mitk::DataNode::New(); m_PreviewContourNode->SetData(m_PreviewContour); m_PreviewContourNode->SetName("active preview node"); m_PreviewContourNode->SetProperty("layer", IntProperty::New(101)); m_PreviewContourNode->AddProperty("fixedLayer", BoolProperty::New(true)); m_PreviewContourNode->SetProperty("helper object", mitk::BoolProperty::New(true)); m_PreviewContourNode->AddProperty("contour.color", ColorProperty::New(0.1f, 1.0f, 0.1f), nullptr, true); m_PreviewContourNode->AddProperty("contour.width", mitk::FloatProperty::New(4.0f), nullptr, true); m_ClosureContour = this->CreateNewContour(); m_ClosureContourNode = mitk::DataNode::New(); m_ClosureContourNode->SetData(m_ClosureContour); m_ClosureContourNode->SetName("active closure node"); m_ClosureContourNode->SetProperty("layer", IntProperty::New(101)); m_ClosureContourNode->AddProperty("fixedLayer", BoolProperty::New(true)); m_ClosureContourNode->SetProperty("helper object", mitk::BoolProperty::New(true)); m_ClosureContourNode->AddProperty("contour.color", ColorProperty::New(0.0f, 1.0f, 0.1f), nullptr, true); m_ClosureContourNode->AddProperty("contour.width", mitk::FloatProperty::New(2.0f), nullptr, true); m_CurrentRestrictedArea = this->CreateNewContour(); auto dataStorage = this->GetToolManager()->GetDataStorage(); dataStorage->Add(m_ContourNode, workingDataNode); dataStorage->Add(m_PreviewContourNode, workingDataNode); dataStorage->Add(m_ClosureContourNode, workingDataNode); m_ReferenceDataSlice = this->GetAffectedReferenceSlice(positionEvent); auto origin = m_ReferenceDataSlice->GetSlicedGeometry()->GetOrigin(); m_ReferenceDataSlice->GetSlicedGeometry()->WorldToIndex(origin, origin); m_ReferenceDataSlice->GetSlicedGeometry()->IndexToWorld(origin, origin); m_ReferenceDataSlice->GetSlicedGeometry()->SetOrigin(origin); // Remember PlaneGeometry to determine if events were triggered in the same plane m_PlaneGeometry = interactionEvent->GetSender()->GetCurrentWorldPlaneGeometry(); // Map click to pixel coordinates auto click = positionEvent->GetPositionInWorld(); click = this->PrepareInitContour(click); this->InitializePreviewContour(click); // Set initial start point contour->AddVertex(click, true); m_PreviewContour->AddVertex(click, false); m_ClosureContour->AddVertex(click); mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); } void mitk::EditableContourTool::FinalizePreviewContour(const Point3D& /*clickedPoint*/) { // Remove duplicate first vertex, it's already contained in m_ContourNode m_PreviewContour->RemoveVertexAt(0); m_PreviewContour->SetControlVertexAt(m_PreviewContour->GetNumberOfVertices() - 1); } void mitk::EditableContourTool::InitializePreviewContour(const Point3D& clickedPoint) { //default implementation only clears the preview and sets the start point m_PreviewContour = this->CreateNewContour(); m_PreviewContour->AddVertex(clickedPoint); m_PreviewContourNode->SetData(m_PreviewContour); } void mitk::EditableContourTool::UpdatePreviewContour(const Point3D& clickedPoint) { //default implementation draws just a simple line to position if (m_PreviewContour->GetNumberOfVertices() > 2) { auto contour = this->GetContour(); this->InitializePreviewContour(contour->GetVertexAt(contour->GetNumberOfVertices() - 1)->Coordinates); } if (m_PreviewContour->GetNumberOfVertices() == 2) { m_PreviewContour->RemoveVertexAt(m_PreviewContour->GetNumberOfVertices()-1); } m_PreviewContour->AddVertex(clickedPoint); } void mitk::EditableContourTool::OnAddPoint(StateMachineAction*, InteractionEvent* interactionEvent) { auto positionEvent = dynamic_cast(interactionEvent); if (nullptr == positionEvent) return; if (m_PlaneGeometry.IsNotNull()) { // Check if the point is in the correct slice if (m_PlaneGeometry->DistanceFromPlane(positionEvent->GetPositionInWorld()) > mitk::sqrteps) return; } this->FinalizePreviewContour(positionEvent->GetPositionInWorld()); // Merge contours auto contour = this->GetContour(); contour->Concatenate(m_PreviewContour); this->InitializePreviewContour(positionEvent->GetPositionInWorld()); mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); } void mitk::EditableContourTool::OnDrawing(StateMachineAction*, InteractionEvent* interactionEvent) { auto* positionEvent = dynamic_cast(interactionEvent); if (!positionEvent) return; m_PreviewContourNode->SetVisibility(false); auto contour = this->GetContour(); contour->AddVertex(positionEvent->GetPositionInWorld(), false); UpdateClosureContour(positionEvent->GetPositionInWorld()); assert(positionEvent->GetSender()->GetRenderWindow()); mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); } void mitk::EditableContourTool::OnEndDrawing(StateMachineAction*, InteractionEvent* interactionEvent) { auto* positionEvent = dynamic_cast(interactionEvent); if (!positionEvent) return; auto contour = this->GetContour(); auto controlVs = contour->GetControlVertices(0); if (!controlVs.empty()) { //add the last control point (after that the draw part start) m_CurrentRestrictedArea->AddVertex(controlVs.back()->Coordinates); } m_PreviewContourNode->SetVisibility(true); contour->SetControlVertexAt(contour->GetNumberOfVertices() - 1); //add the just created/set last control point (with it the draw part ends) m_CurrentRestrictedArea->AddVertex(contour->GetVertexAt(contour->GetNumberOfVertices() - 1)->Coordinates); this->InitializePreviewContour(positionEvent->GetPositionInWorld()); mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); } void mitk::EditableContourTool::OnMouseMoved(StateMachineAction*, InteractionEvent* interactionEvent) { auto positionEvent = dynamic_cast(interactionEvent); if (nullptr == positionEvent) return; if (m_PlaneGeometry.IsNotNull()) { // Check if the point is in the correct slice if (m_PlaneGeometry->DistanceFromPlane(positionEvent->GetPositionInWorld()) > mitk::sqrteps) return; } this->UpdatePreviewContour(positionEvent->GetPositionInWorld()); this->UpdateClosureContour(positionEvent->GetPositionInWorld()); RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); } void mitk::EditableContourTool::OnFinish(StateMachineAction *, InteractionEvent *interactionEvent) { auto positionEvent = dynamic_cast(interactionEvent); if (nullptr == positionEvent) return; if (m_PlaneGeometry.IsNotNull()) { // Check if the point is in the correct slice if (m_PlaneGeometry->DistanceFromPlane(positionEvent->GetPositionInWorld()) > mitk::sqrteps) return; } this->FinalizePreviewContour(positionEvent->GetPositionInWorld()); this->FinishTool(); // Merge contours auto contour = this->GetContour(); contour->Concatenate(m_PreviewContour); auto numberOfTimesteps = static_cast(contour->GetTimeSteps()); for (int i = 0; i <= numberOfTimesteps; ++i) contour->Close(i); this->ReleaseHelperObjects(false); if (m_AutoConfirm) { this->ConfirmSegmentation(); } } void mitk::EditableContourTool::ReleaseHelperObjects(bool includeWorkingContour) { this->RemoveHelperObjectsFromDataStorage(includeWorkingContour); if (includeWorkingContour) { m_ContourNode = nullptr; m_CurrentRestrictedArea = nullptr; } m_PreviewContourNode = nullptr; m_PreviewContour = nullptr; m_ClosureContourNode = nullptr; m_ClosureContour = nullptr; } void mitk::EditableContourTool::RemoveHelperObjectsFromDataStorage(bool includeWorkingContour) { auto dataStorage = this->GetToolManager()->GetDataStorage(); if (nullptr == dataStorage) return; if (includeWorkingContour) { if (m_ContourNode.IsNotNull()) dataStorage->Remove(m_ContourNode); } if (m_PreviewContourNode.IsNotNull()) dataStorage->Remove(m_PreviewContourNode); if (m_ClosureContourNode.IsNotNull()) dataStorage->Remove(m_ClosureContourNode); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } mitk::ContourModel::Pointer mitk::EditableContourTool::CreateNewContour() const { auto workingData = this->GetWorkingData(); if (nullptr == workingData) { this->InteractiveSegmentationBugMessage( "Cannot create new contour. No valid working data is set. Application is in invalid state."); mitkThrow() << "Cannot create new contour. No valid working data is set. Application is in invalid state."; } auto contour = ContourModel::New(); // generate a time geometry that is always visible as the working contour should always be. auto contourTimeGeometry = ProportionalTimeGeometry::New(); contourTimeGeometry->SetStepDuration(std::numeric_limits::max()); contourTimeGeometry->SetTimeStepGeometry(contour->GetTimeGeometry()->GetGeometryForTimeStep(0)->Clone(), 0); contour->SetTimeGeometry(contourTimeGeometry); return contour; } void mitk::EditableContourTool::UpdateClosureContour(mitk::Point3D endpoint) { if (m_ClosureContour->GetNumberOfVertices() > 2) { m_ClosureContour = this->CreateNewContour(); m_ClosureContourNode->SetData(m_ClosureContour); } if (m_ClosureContour->GetNumberOfVertices() == 0) { auto contour = this->GetContour(); m_ClosureContour->AddVertex(contour->GetVertexAt(0)->Coordinates); m_ClosureContour->Update(); } if (m_ClosureContour->GetNumberOfVertices() == 2) { m_ClosureContour->RemoveVertexAt(0); } m_ClosureContour->AddVertexAtFront(endpoint); } void mitk::EditableContourTool::EnableContourInteraction(bool on) { if (m_ContourInteractor.IsNotNull()) { m_ContourInteractor->EnableInteraction(on); } } void mitk::EditableContourTool::ReleaseInteractors() { this->EnableContourInteraction(false); m_ContourInteractor = nullptr; } mitk::ContourModel* mitk::EditableContourTool::GetContour() { if (this->m_ContourNode.IsNotNull()) { return dynamic_cast(this->m_ContourNode->GetData()); } return nullptr; }; const mitk::ContourModel* mitk::EditableContourTool::GetContour() const { if (this->m_ContourNode.IsNotNull()) { return dynamic_cast(this->m_ContourNode->GetData()); } return nullptr; }; \ No newline at end of file diff --git a/Modules/Segmentation/Interactions/mitkEditableContourTool.h b/Modules/Segmentation/Interactions/mitkEditableContourTool.h index 8be7c24ac9..1189e3b406 100644 --- a/Modules/Segmentation/Interactions/mitkEditableContourTool.h +++ b/Modules/Segmentation/Interactions/mitkEditableContourTool.h @@ -1,127 +1,125 @@ /*============================================================================ 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 mitkEditbaleContourTool_h_Included #define mitkEditbaleContourTool_h_Included #include namespace mitk { /** * Base class for lasso like tools that allow to draw closed contours with multiple ancor points. * The segments between the ancor points may be freehand contour segments or computed segments * (e.g. straight lines or live wire). Derive from the class to implement the computation of the non-freehand * segments. * @sa LassoTool LivewWireTool2D */ class MITKSEGMENTATION_EXPORT EditableContourTool : public FeedbackContourTool { public: mitkClassMacro(EditableContourTool, FeedbackContourTool); /// \brief Convert current contour to binary segmentations. virtual void ConfirmSegmentation(bool resetStatMachine = true); /// \brief Delete all current contours. virtual void ClearSegmentation(); itkBooleanMacro(AutoConfirm); itkSetMacro(AutoConfirm, bool); itkGetMacro(AutoConfirm, bool); itkBooleanMacro(AddMode); itkSetMacro(AddMode, bool); itkGetMacro(AddMode, bool); /* Indicated if a contour is drawn, but not confirmed yet. This the tool is in interactor mode to allow users to edit the contour. This state can be reached if AutoConfirm is false, after the finalizing double click before the contour is confirmed.*/ bool IsEditingContour() const; /* Indicate if a contour is currently drawn by the user (state between the initializing double click and the finalizing double click).*/ bool IsDrawingContour() const; protected: EditableContourTool(); ~EditableContourTool() override; void ConnectActionsAndFunctions() override; void Activated() override; void Deactivated() override; virtual Point3D PrepareInitContour(const Point3D& clickedPoint); virtual void FinalizePreviewContour(const Point3D& clickedPoint); virtual void InitializePreviewContour(const Point3D& clickedPoint); virtual void UpdatePreviewContour(const Point3D& clickedPoint); /// \brief Initialize tool. virtual void OnInitContour(StateMachineAction *, InteractionEvent *interactionEvent); /// \brief Add a control point and finish current segment. virtual void OnAddPoint(StateMachineAction *, InteractionEvent *interactionEvent); /// \brief Draw a contour according to the mouse movement when mouse button is pressed and mouse is moved. virtual void OnDrawing(StateMachineAction *, InteractionEvent *interactionEvent); virtual void OnEndDrawing(StateMachineAction *, InteractionEvent *interactionEvent); /// \brief Computation of the preview contour. virtual void OnMouseMoved(StateMachineAction *, InteractionEvent *interactionEvent); /// \brief Finish EditableContour tool. virtual void OnFinish(StateMachineAction *, InteractionEvent *interactionEvent); /// \brief Finish contour interaction. virtual void FinishTool() = 0; void EnableContourInteraction(bool on); void ReleaseInteractors(); virtual void ReleaseHelperObjects(bool includeWorkingContour = true); virtual void RemoveHelperObjectsFromDataStorage(bool includeWorkingContour = true); ContourModel::Pointer CreateNewContour() const; virtual void UpdateClosureContour(mitk::Point3D endpoint); - bool IsPositionEventInsideImageRegion(InteractionPositionEvent *positionEvent, BaseData *data); - mitk::ContourModel* GetContour(); const mitk::ContourModel* GetContour() const; mitk::DataNode::Pointer m_ContourNode; mitk::ContourModel::Pointer m_PreviewContour; mitk::DataNode::Pointer m_PreviewContourNode; mitk::ContourModel::Pointer m_ClosureContour; mitk::DataNode::Pointer m_ClosureContourNode; mitk::ContourModel::Pointer m_CurrentRestrictedArea; /** Slice of the reference data the tool is currently actively working on to define contours.*/ mitk::Image::Pointer m_ReferenceDataSlice; PlaneGeometry::ConstPointer m_PlaneGeometry; mitk::DataInteractor::Pointer m_ContourInteractor; bool m_AutoConfirm; bool m_AddMode; }; } #endif diff --git a/Modules/Segmentation/Interactions/mitkEraseRegionTool.cpp b/Modules/Segmentation/Interactions/mitkEraseRegionTool.cpp index e1d480645d..928c0507f4 100644 --- a/Modules/Segmentation/Interactions/mitkEraseRegionTool.cpp +++ b/Modules/Segmentation/Interactions/mitkEraseRegionTool.cpp @@ -1,59 +1,93 @@ /*============================================================================ 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 "mitkEraseRegionTool.h" #include "mitkEraseRegionTool.xpm" +#include +#include +#include // us #include #include #include #include namespace mitk { MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, EraseRegionTool, "Erase tool"); } -mitk::EraseRegionTool::EraseRegionTool() : SetRegionTool(0) -{ - FeedbackContourTool::SetFeedbackContourColor(1.0, 1.0, 0.0); -} - -mitk::EraseRegionTool::~EraseRegionTool() -{ -} - const char **mitk::EraseRegionTool::GetXPM() const { return mitkEraseRegionTool_xpm; } us::ModuleResource mitk::EraseRegionTool::GetIconResource() const { us::Module *module = us::GetModuleContext()->GetModule(); us::ModuleResource resource = module->GetResource("Erase_48x48.png"); return resource; } us::ModuleResource mitk::EraseRegionTool::GetCursorIconResource() const { us::Module *module = us::GetModuleContext()->GetModule(); us::ModuleResource resource = module->GetResource("Erase_Cursor_32x32.png"); return resource; } const char *mitk::EraseRegionTool::GetName() const { return "Erase"; } + +template +void DoFillImage(itk::Image* image) +{ + image->FillBuffer(1); +}; + +mitk::Image::Pointer mitk::EraseRegionTool::GenerateFillImage(const Image* workingSlice, Point3D seedPoint, mitk::Label::PixelType& seedLabelValue) const +{ + auto labelSetImage = dynamic_cast(this->GetWorkingData()); + + itk::Index<2> seedIndex; + workingSlice->GetGeometry()->WorldToIndex(seedPoint, seedIndex); + + using AccessorType = ImagePixelReadAccessor; + AccessorType accessor(workingSlice); + seedLabelValue = accessor.GetPixelByIndex(seedIndex); + Image::Pointer fillImage; + + if ( seedLabelValue == labelSetImage->GetExteriorLabel()->GetValue()) + { //clicked on background remove everything which is not locked. + fillImage = workingSlice->Clone(); + AccessByItk(fillImage, DoFillImage); + } + else + { + fillImage = Superclass::GenerateFillImage(workingSlice, seedPoint, seedLabelValue); + } + + return fillImage; +} + +void mitk::EraseRegionTool::PrepareFilling(const Image* /*workingSlice*/, Point3D /*seedPoint*/) +{ + auto labelSetImage = dynamic_cast(this->GetWorkingData()); + if (nullptr != labelSetImage) + { + m_FillLabelValue = labelSetImage->GetExteriorLabel()->GetValue(); + } +}; diff --git a/Modules/Segmentation/Interactions/mitkEraseRegionTool.h b/Modules/Segmentation/Interactions/mitkEraseRegionTool.h index 5316ce5dc1..abeeeb476b 100644 --- a/Modules/Segmentation/Interactions/mitkEraseRegionTool.h +++ b/Modules/Segmentation/Interactions/mitkEraseRegionTool.h @@ -1,61 +1,64 @@ /*============================================================================ 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 mitkEraseRegionTool_h_Included #define mitkEraseRegionTool_h_Included -#include "mitkSetRegionTool.h" +#include "mitkFillRegionBaseTool.h" #include namespace us { class ModuleResource; } namespace mitk { /** \brief Erase the inside of a contour by filling the inside of a contour with the background pixel value. \sa SetRegionTool \ingroup Interactions Finds the outer contour of a shape in 2D (possibly including single patches) and sets all the pixels inside to the background pixel value (erasing a segmentation). If clicked on the background, the outer contour might contain the whole image and thus fill the whole image with the background pixel value. \warning Only to be instantiated by mitk::ToolManager. */ - class MITKSEGMENTATION_EXPORT EraseRegionTool : public SetRegionTool + class MITKSEGMENTATION_EXPORT EraseRegionTool : public FillRegionBaseTool { public: - mitkClassMacro(EraseRegionTool, SetRegionTool); + mitkClassMacro(EraseRegionTool, FillRegionBaseTool); itkFactorylessNewMacro(Self); itkCloneMacro(Self); - const char **GetXPM() const override; + const char **GetXPM() const override; us::ModuleResource GetCursorIconResource() const override; us::ModuleResource GetIconResource() const override; const char *GetName() const override; protected: - EraseRegionTool(); // purposely hidden - ~EraseRegionTool() override; + EraseRegionTool() = default; // purposely hidden + ~EraseRegionTool() = default; + + Image::Pointer GenerateFillImage(const Image* workingSlice, Point3D seedPoint, mitk::Label::PixelType& seedLabelValue) const override; + void PrepareFilling(const Image* workingSlice, Point3D seedPoint) override; }; } // namespace #endif diff --git a/Modules/Segmentation/Interactions/mitkFillRegionBaseTool.cpp b/Modules/Segmentation/Interactions/mitkFillRegionBaseTool.cpp new file mode 100644 index 0000000000..403b705cd7 --- /dev/null +++ b/Modules/Segmentation/Interactions/mitkFillRegionBaseTool.cpp @@ -0,0 +1,149 @@ +/*============================================================================ + +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 "mitkFillRegionBaseTool.h" +#include "mitkToolManager.h" + +#include "mitkBaseRenderer.h" +#include "mitkDataStorage.h" + +#include "mitkITKImageImport.h" +#include "mitkImageAccessByItk.h" + +#include "mitkRenderingManager.h" + +#include + +mitk::FillRegionBaseTool::FillRegionBaseTool() : SegTool2D("MouseReleaseOnly") +{ +} + +mitk::FillRegionBaseTool::~FillRegionBaseTool() +{ +} + +void mitk::FillRegionBaseTool::ConnectActionsAndFunctions() +{ + CONNECT_FUNCTION("Release", OnClick); +} + + +template +void DoITKRegionGrowing(const itk::Image* oldSegImage, + mitk::Image::Pointer& filledRegionImage, itk::Index seedIndex, mitk::Label::PixelType& seedLabel ) +{ + typedef itk::Image InputImageType; + typedef itk::Image OutputImageType; + typedef itk::ConnectedThresholdImageFilter RegionGrowingFilterType; + + seedLabel = oldSegImage->GetPixel(seedIndex); + + typename OutputImageType::Pointer itkResultImage; + filledRegionImage = nullptr; + + try + { + typename RegionGrowingFilterType::Pointer regionGrower = RegionGrowingFilterType::New(); + regionGrower->SetInput(oldSegImage); + regionGrower->SetReplaceValue(1); + regionGrower->AddSeed(seedIndex); + + regionGrower->SetLower(seedLabel); + regionGrower->SetUpper(seedLabel); + + regionGrower->Update(); + + itkResultImage = regionGrower->GetOutput(); + } + catch (const itk::ExceptionObject&) + { + return; // can't work + } + catch (...) + { + return; + } + mitk::CastToMitkImage(itkResultImage, filledRegionImage); +} + +void mitk::FillRegionBaseTool::OnClick(StateMachineAction*, InteractionEvent* interactionEvent) +{ + auto positionEvent = dynamic_cast(interactionEvent); + if (nullptr == positionEvent) + return; + + auto labelSetImage = dynamic_cast(this->GetWorkingData()); + if (nullptr == labelSetImage) + { + return; + } + + if (!IsPositionEventInsideImageRegion(positionEvent, labelSetImage)) + { + return; + } + + m_LastEventSender = positionEvent->GetSender(); + m_LastEventSlice = m_LastEventSender->GetSlice(); + + auto workingSlice = this->GetAffectedWorkingSlice(positionEvent); + + auto click = positionEvent->GetPositionInWorld(); + + m_SeedLabelValue = 0; + auto fillImage = this->GenerateFillImage(workingSlice, click, m_SeedLabelValue); + + if (fillImage.IsNull()) + { + return; //nothing to fill; + } + + auto label = labelSetImage->GetLabel(m_SeedLabelValue, labelSetImage->GetActiveLayer()); + + if (label->GetLocked() && label->GetValue()!=labelSetImage->GetActiveLabel()->GetValue()) + { + ErrorMessage.Send("Label of selected region is locked. Tool operation has no effect."); + return; + } + + this->PrepareFilling(workingSlice, click); + + //as fill region tools should always allow to manipulate active label + //(that is what the user expects/knows when using tools so far: + //the active label can always be changed even if locked) + //we realize that by cloning the relevant label set and changing the lock state + //this fillLabelSet is used for the transfer. + auto fillLabelSet = labelSetImage->GetActiveLabelSet()->Clone(); + auto activeLabelClone = fillLabelSet->GetLabel(labelSetImage->GetActiveLabel()->GetValue()); + if (nullptr != activeLabelClone) + { + activeLabelClone->SetLocked(false); + } + + TransferLabelContent(fillImage, workingSlice, fillLabelSet, 0, labelSetImage->GetExteriorLabel()->GetValue(), false, { {1, m_FillLabelValue} }, m_MergeStyle); + + this->WriteBackSegmentationResult(positionEvent, workingSlice); + + mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); +} + +mitk::Image::Pointer mitk::FillRegionBaseTool::GenerateFillImage(const Image* workingSlice, Point3D seedPoint, mitk::Label::PixelType& seedLabelValue) const +{ + itk::Index<2> seedIndex; + workingSlice->GetGeometry()->WorldToIndex(seedPoint, seedIndex); + + Image::Pointer fillImage; + + AccessFixedDimensionByItk_n(workingSlice, DoITKRegionGrowing, 2, (fillImage, seedIndex, seedLabelValue)); + + return fillImage; +} diff --git a/Modules/Segmentation/Interactions/mitkFillRegionBaseTool.h b/Modules/Segmentation/Interactions/mitkFillRegionBaseTool.h new file mode 100644 index 0000000000..8235310900 --- /dev/null +++ b/Modules/Segmentation/Interactions/mitkFillRegionBaseTool.h @@ -0,0 +1,83 @@ +/*============================================================================ + +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 mitkFillRegionBaseTool_h_Included +#define mitkFillRegionBaseTool_h_Included + +#include "mitkCommon.h" +#include "mitkContourModelUtils.h" +#include "mitkContourUtils.h" //TODO remove legacy support +#include "mitkImage.h" +#include "mitkSegTool2D.h" +#include + +#include "mitkDataNode.h" + +#include "mitkImageCast.h" + +namespace mitk +{ + /** + \brief Base class for tools that fill a connected region of a 2D slice + + \sa Tool + + \ingroup Interaction + \ingroup ToolManagerEtAl + + \warning Only to be instantiated by mitk::ToolManager. + + $Author: nolden $ + */ + class MITKSEGMENTATION_EXPORT FillRegionBaseTool : public SegTool2D + { + public: + mitkClassMacro(FillRegionBaseTool, SegTool2D); + + protected: + FillRegionBaseTool(); // purposely hidden + ~FillRegionBaseTool() override; + + void ConnectActionsAndFunctions() override; + + /// \brief Add a control point and finish current segment. + virtual void OnClick(StateMachineAction*, InteractionEvent* interactionEvent); + + /** Function that generates the mask image that indicates which pixels should be filled. + * Caller of this function assumes that all pixels that should be filled have the value 1. + * Pixels that should stay untouched should have the value 0. + * The default implementation marks the connected reagion around seedPoint, that has + * the same pixel value/label like the seedPoint. + * You may reimplement this function to change the strategy to determin the fill region. + * @param workingSlice part of the segmentation image that should be used to determin the fill image. + * @param seedPoint The world coordinate position where the user has cliced. + * @param [out] seedLabelValue The function should return the label value that should be assumed + * as clicked on, given the seedPoint. + * @return Return the image maske that indicates which pixels should be filled. Returning + * a null pointer indicates that there is nothing to fill. + */ + virtual Image::Pointer GenerateFillImage(const Image* workingSlice, Point3D seedPoint, mitk::Label::PixelType& seedLabelValue) const; + + /** Function that is called by OnClick before the filling is executed. If you want to do special + * preperation (e.g. change m_FillLabelValue, you can overwrite this function. */ + virtual void PrepareFilling(const Image* workingSlice, Point3D seedPoint) = 0; + + Label::PixelType m_FillLabelValue = 0; + Label::PixelType m_SeedLabelValue = 0; + + MultiLabelSegmentation::MergeStyle m_MergeStyle = MultiLabelSegmentation::MergeStyle::Replace; + private: + }; + +} // namespace + +#endif diff --git a/Modules/Segmentation/Interactions/mitkFillRegionTool.cpp b/Modules/Segmentation/Interactions/mitkFillRegionTool.cpp index 1ef851a209..cdde1d0b95 100644 --- a/Modules/Segmentation/Interactions/mitkFillRegionTool.cpp +++ b/Modules/Segmentation/Interactions/mitkFillRegionTool.cpp @@ -1,58 +1,59 @@ /*============================================================================ 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 "mitkFillRegionTool.h" -#include "mitkFillRegionTool.xpm" - // us #include #include #include #include namespace mitk { MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, FillRegionTool, "Fill tool"); } -mitk::FillRegionTool::FillRegionTool() : SetRegionTool(1) -{ -} - -mitk::FillRegionTool::~FillRegionTool() -{ -} - const char **mitk::FillRegionTool::GetXPM() const { - return mitkFillRegionTool_xpm; + return nullptr; } us::ModuleResource mitk::FillRegionTool::GetIconResource() const { us::Module *module = us::GetModuleContext()->GetModule(); us::ModuleResource resource = module->GetResource("Fill_48x48.png"); return resource; } us::ModuleResource mitk::FillRegionTool::GetCursorIconResource() const { us::Module *module = us::GetModuleContext()->GetModule(); us::ModuleResource resource = module->GetResource("Fill_Cursor_32x32.png"); return resource; } const char *mitk::FillRegionTool::GetName() const { return "Fill"; } + +void mitk::FillRegionTool::PrepareFilling(const Image* /*workingSlice*/, Point3D /*seedPoint*/) +{ + auto labelSetImage = dynamic_cast(this->GetWorkingData()); + + if (nullptr == labelSetImage) mitkThrow() << "Invalid state of FillRegionTool. Working image is not of correct type."; + + m_FillLabelValue = labelSetImage->GetActiveLabel()->GetValue(); + m_MergeStyle = MultiLabelSegmentation::MergeStyle::Merge; +}; + diff --git a/Modules/Segmentation/Interactions/mitkFillRegionTool.h b/Modules/Segmentation/Interactions/mitkFillRegionTool.h index 3643b13992..e7a1247858 100644 --- a/Modules/Segmentation/Interactions/mitkFillRegionTool.h +++ b/Modules/Segmentation/Interactions/mitkFillRegionTool.h @@ -1,60 +1,62 @@ /*============================================================================ 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 mitkFillRegionTool_h_Included #define mitkFillRegionTool_h_Included -#include "mitkSetRegionTool.h" +#include "mitkFillRegionBaseTool.h" #include namespace us { class ModuleResource; } namespace mitk { /** \brief Fill the inside of a contour with the foreground pixel value. \sa SetRegionTool \ingroup Interactions Finds the outer contour of a shape in 2D (possibly including holes) and sets all the pixels inside to the foreground pixel value (filling holes in a segmentation). If clicked on the background, the outer contour might contain the whole image and thus fill the whole image with the foreground pixel value. \warning Only to be instantiated by mitk::ToolManager. */ - class MITKSEGMENTATION_EXPORT FillRegionTool : public SetRegionTool + class MITKSEGMENTATION_EXPORT FillRegionTool : public FillRegionBaseTool { public: - mitkClassMacro(FillRegionTool, SetRegionTool); + mitkClassMacro(FillRegionTool, FillRegionBaseTool); itkFactorylessNewMacro(Self); itkCloneMacro(Self); - const char **GetXPM() const override; + const char **GetXPM() const override; us::ModuleResource GetCursorIconResource() const override; us::ModuleResource GetIconResource() const override; const char *GetName() const override; protected: - FillRegionTool(); // purposely hidden - ~FillRegionTool() override; + void PrepareFilling(const Image* workingSlice, Point3D seedPoint) override; + + FillRegionTool() = default; // purposely hidden + ~FillRegionTool() = default; }; } // namespace #endif diff --git a/Modules/Segmentation/Interactions/mitkPickingTool.cpp b/Modules/Segmentation/Interactions/mitkPickingTool.cpp index 6f94213db6..d757a07db4 100644 --- a/Modules/Segmentation/Interactions/mitkPickingTool.cpp +++ b/Modules/Segmentation/Interactions/mitkPickingTool.cpp @@ -1,276 +1,275 @@ /*============================================================================ 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 "mitkPickingTool.h" #include "mitkProperties.h" #include "mitkToolManager.h" #include "mitkInteractionPositionEvent.h" // us #include #include #include #include #include "mitkITKImageImport.h" #include "mitkImageAccessByItk.h" #include "mitkImageCast.h" #include "mitkImageTimeSelector.h" -#include "mitkImageTimeSelector.h" #include #include #include #include namespace mitk { MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, PickingTool, "PickingTool"); } mitk::PickingTool::PickingTool() : SegWithPreviewTool(false, "PressMoveReleaseAndPointSetting") { this->ResetsToEmptyPreviewOn(); } mitk::PickingTool::~PickingTool() { } bool mitk::PickingTool::CanHandle(const BaseData* referenceData, const BaseData* workingData) const { if (!Superclass::CanHandle(referenceData,workingData)) return false; auto* image = dynamic_cast(referenceData); if (image == nullptr) return false; return true; } const char **mitk::PickingTool::GetXPM() const { return nullptr; } const char *mitk::PickingTool::GetName() const { return "Picking"; } us::ModuleResource mitk::PickingTool::GetIconResource() const { us::Module *module = us::GetModuleContext()->GetModule(); us::ModuleResource resource = module->GetResource("Pick_48x48.png"); return resource; } void mitk::PickingTool::Activated() { Superclass::Activated(); m_PointSet = mitk::PointSet::New(); //ensure that the seed points are visible for all timepoints. dynamic_cast(m_PointSet->GetTimeGeometry())->SetStepDuration(std::numeric_limits::max()); m_PointSetNode = mitk::DataNode::New(); m_PointSetNode->SetData(m_PointSet); m_PointSetNode->SetName(std::string(this->GetName()) + "_PointSet"); m_PointSetNode->SetBoolProperty("helper object", true); m_PointSetNode->SetColor(0.0, 1.0, 0.0); m_PointSetNode->SetVisibility(true); this->GetDataStorage()->Add(m_PointSetNode, this->GetToolManager()->GetWorkingData(0)); } void mitk::PickingTool::Deactivated() { this->ClearSeeds(); // remove from data storage and disable interaction GetDataStorage()->Remove(m_PointSetNode); m_PointSetNode = nullptr; m_PointSet = nullptr; Superclass::Deactivated(); } void mitk::PickingTool::ConnectActionsAndFunctions() { CONNECT_FUNCTION("ShiftSecondaryButtonPressed", OnAddPoint); CONNECT_FUNCTION("ShiftPrimaryButtonPressed", OnAddPoint); CONNECT_FUNCTION("DeletePoint", OnDelete); } void mitk::PickingTool::OnAddPoint(StateMachineAction*, InteractionEvent* interactionEvent) { if (!this->IsUpdating() && m_PointSet.IsNotNull()) { const auto positionEvent = dynamic_cast(interactionEvent); if (positionEvent != nullptr) { m_PointSet->InsertPoint(m_PointSet->GetSize(), positionEvent->GetPositionInWorld()); this->UpdatePreview(); } } } void mitk::PickingTool::OnDelete(StateMachineAction*, InteractionEvent* /*interactionEvent*/) { if (!this->IsUpdating() && m_PointSet.IsNotNull()) { // delete last seed point if (this->m_PointSet->GetSize() > 0) { m_PointSet->RemovePointAtEnd(0); this->UpdatePreview(); } } } void mitk::PickingTool::ClearPicks() { this->ClearSeeds(); this->UpdatePreview(); } bool mitk::PickingTool::HasPicks() const { return this->m_PointSet.IsNotNull() && this->m_PointSet->GetSize()>0; } void mitk::PickingTool::ClearSeeds() { if (this->m_PointSet.IsNotNull()) { // renew pointset this->m_PointSet = mitk::PointSet::New(); //ensure that the seed points are visible for all timepoints. dynamic_cast(m_PointSet->GetTimeGeometry())->SetStepDuration(std::numeric_limits::max()); this->m_PointSetNode->SetData(this->m_PointSet); } } template void DoITKRegionGrowing(const itk::Image* oldSegImage, mitk::Image* segmentation, const mitk::PointSet* seedPoints, unsigned int timeStep, const mitk::BaseGeometry* inputGeometry, const mitk::Label::PixelType outputValue, const mitk::Label::PixelType backgroundValue, bool& emptyTimeStep) { typedef itk::Image InputImageType; typedef itk::Image OutputImageType; typedef typename InputImageType::IndexType IndexType; typedef itk::ConnectedThresholdImageFilter RegionGrowingFilterType; using IndexMapType = std::map < mitk::Label::PixelType, std::vector >; IndexMapType indexMap; // convert world coordinates to image indices for (auto pos = seedPoints->Begin(); pos != seedPoints->End(); ++pos) { IndexType seedIndex; inputGeometry->WorldToIndex(pos->Value(), seedIndex); const auto selectedLabel = oldSegImage->GetPixel(seedIndex); if (selectedLabel != backgroundValue) { indexMap[selectedLabel].push_back(seedIndex); } } typename OutputImageType::Pointer itkResultImage; try { bool first = true; typename RegionGrowingFilterType::Pointer regionGrower = RegionGrowingFilterType::New(); regionGrower->SetInput(oldSegImage); regionGrower->SetReplaceValue(outputValue); for (const auto& [label, indeces] : indexMap) { // perform region growing in desired segmented region regionGrower->ClearSeeds(); for (const auto& index : indeces) { regionGrower->AddSeed(index); } regionGrower->SetLower(label); regionGrower->SetUpper(label); regionGrower->Update(); if (first) { itkResultImage = regionGrower->GetOutput(); } else { typename itk::OrImageFilter::Pointer orFilter = itk::OrImageFilter::New(); orFilter->SetInput1(regionGrower->GetOutput()); orFilter->SetInput2(itkResultImage); orFilter->Update(); itkResultImage = orFilter->GetOutput(); } first = false; itkResultImage->DisconnectPipeline(); } } catch (const itk::ExceptionObject&) { return; // can't work } catch (...) { return; } if (itkResultImage.IsNotNull()) { segmentation->SetVolume((void*)(itkResultImage->GetPixelContainer()->GetBufferPointer()),timeStep); } emptyTimeStep = itkResultImage.IsNull(); } void mitk::PickingTool::DoUpdatePreview(const Image* /*inputAtTimeStep*/, const Image* oldSegAtTimeStep, LabelSetImage* previewImage, TimeStepType timeStep) { if (nullptr != oldSegAtTimeStep && nullptr != previewImage && m_PointSet.IsNotNull()) { bool emptyTimeStep = true; if (this->HasPicks()) { Label::PixelType backgroundValue = 0; auto labelSetImage = dynamic_cast(oldSegAtTimeStep); if (nullptr != labelSetImage) { backgroundValue = labelSetImage->GetExteriorLabel()->GetValue(); } AccessFixedDimensionByItk_n(oldSegAtTimeStep, DoITKRegionGrowing, 3, (previewImage, this->m_PointSet, timeStep, oldSegAtTimeStep->GetGeometry(), this->GetUserDefinedActiveLabel(), backgroundValue, emptyTimeStep)); } if (emptyTimeStep) { this->ResetPreviewContentAtTimeStep(timeStep); } } } diff --git a/Modules/Segmentation/Interactions/mitkSegTool2D.cpp b/Modules/Segmentation/Interactions/mitkSegTool2D.cpp index ca9a769dfd..80f4bcba3a 100644 --- a/Modules/Segmentation/Interactions/mitkSegTool2D.cpp +++ b/Modules/Segmentation/Interactions/mitkSegTool2D.cpp @@ -1,757 +1,769 @@ /*============================================================================ 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 "mitkSegTool2D.h" #include "mitkToolManager.h" #include "mitkBaseRenderer.h" #include "mitkDataStorage.h" #include "mitkPlaneGeometry.h" // Include of the new ImageExtractor #include "mitkMorphologicalOperations.h" #include "mitkPlanarCircle.h" #include "usGetModuleContext.h" // Includes for 3DSurfaceInterpolation #include "mitkImageTimeSelector.h" #include "mitkImageToContourFilter.h" #include "mitkSurfaceInterpolationController.h" // includes for resling and overwriting #include #include #include #include #include "mitkOperationEvent.h" #include "mitkUndoController.h" #include #include "mitkAbstractTransformGeometry.h" #include "mitkLabelSetImage.h" #include "mitkContourModelUtils.h" #include "itkImageRegionIterator.h" #define ROUND(a) ((a) > 0 ? (int)((a) + 0.5) : -(int)(0.5 - (a))) bool mitk::SegTool2D::m_SurfaceInterpolationEnabled = true; mitk::SegTool2D::SliceInformation::SliceInformation(const mitk::Image* aSlice, const mitk::PlaneGeometry* aPlane, mitk::TimeStepType aTimestep) : slice(aSlice), plane(aPlane), timestep(aTimestep) { } mitk::SegTool2D::SegTool2D(const char *type, const us::Module *interactorModule) : Tool(type, interactorModule), m_Contourmarkername("Position") { Tool::m_EventConfig = "DisplayConfigBlockLMB.xml"; } mitk::SegTool2D::~SegTool2D() { } bool mitk::SegTool2D::FilterEvents(InteractionEvent *interactionEvent, DataNode *) { const auto *positionEvent = dynamic_cast(interactionEvent); bool isValidEvent = (positionEvent && // Only events of type mitk::InteractionPositionEvent interactionEvent->GetSender()->GetMapperID() == BaseRenderer::Standard2D // Only events from the 2D renderwindows ); return isValidEvent; } 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; } // coronal else if (imageNormal0.GetNorm() <= eps) { affectedDimension = 0; } else { affectedDimension = -1; // no idea return false; } // determine slice number in image BaseGeometry *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) { std::vector slices = { SliceInformation(slice, plane, 0)}; Self::UpdateSurfaceInterpolation(slices, workingImage, detectIntersection); } void mitk::SegTool2D::RemoveContourFromInterpolator(const SliceInformation& sliceInfo) { mitk::SurfaceInterpolationController::ContourPositionInformation contourInfo; contourInfo.contourNormal = sliceInfo.plane->GetNormal(); contourInfo.contourPoint = sliceInfo.plane->GetOrigin(); mitk::SurfaceInterpolationController::GetInstance()->RemoveContour(contourInfo); } void mitk::SegTool2D::UpdateSurfaceInterpolation(const std::vector& sliceInfos, const Image* workingImage, bool detectIntersection) { if (!m_SurfaceInterpolationEnabled) return; //Remark: the ImageTimeSelector is just needed to extract a timestep/channel of //the image in order to get the image dimension (time dimension and channel dimension //stripped away). Therfore it is OK to always use time step 0 and channel 0 mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); timeSelector->SetInput(workingImage); timeSelector->SetTimeNr(0); timeSelector->SetChannelNr(0); timeSelector->Update(); const auto dimRefImg = timeSelector->GetOutput()->GetDimension(); if (dimRefImg != 3) return; std::vector contourList; contourList.reserve(sliceInfos.size()); ImageToContourFilter::Pointer contourExtractor = ImageToContourFilter::New(); std::vector relevantSlices = sliceInfos; if (detectIntersection) { relevantSlices.clear(); for (const auto& sliceInfo : sliceInfos) { // Test whether there is something to extract or whether the slice just contains intersections of others mitk::Image::Pointer slice2 = sliceInfo.slice->Clone(); mitk::MorphologicalOperations::Erode(slice2, 2, mitk::MorphologicalOperations::Ball); contourExtractor->SetInput(slice2); contourExtractor->Update(); mitk::Surface::Pointer contour = contourExtractor->GetOutput(); if (contour->GetVtkPolyData()->GetNumberOfPoints() == 0) { Self::RemoveContourFromInterpolator(sliceInfo); } else { relevantSlices.push_back(sliceInfo); } } } if (relevantSlices.empty()) return; for (const auto& sliceInfo : relevantSlices) { contourExtractor->SetInput(sliceInfo.slice); contourExtractor->Update(); mitk::Surface::Pointer contour = contourExtractor->GetOutput(); if (contour->GetVtkPolyData()->GetNumberOfPoints() == 0) { Self::RemoveContourFromInterpolator(sliceInfo); } else { contour->DisconnectPipeline(); contourList.push_back(contour); } } mitk::SurfaceInterpolationController::GetInstance()->AddNewContours(contourList); } mitk::Image::Pointer mitk::SegTool2D::GetAffectedImageSliceAs2DImage(const InteractionPositionEvent *positionEvent, const Image *image, unsigned int component /*= 0*/) { if (!positionEvent) { return nullptr; } assert(positionEvent->GetSender()); // sure, right? const auto timeStep = positionEvent->GetSender()->GetTimeStep(image); // get the timestep of the visible part (time-wise) of the image return GetAffectedImageSliceAs2DImage(positionEvent->GetSender()->GetCurrentWorldPlaneGeometry(), image, timeStep, component); } mitk::Image::Pointer mitk::SegTool2D::GetAffectedImageSliceAs2DImageByTimePoint(const PlaneGeometry* planeGeometry, const Image* image, TimePointType timePoint, unsigned int component /*= 0*/) { if (!image || !planeGeometry) { return nullptr; } if (!image->GetTimeGeometry()->IsValidTimePoint(timePoint)) return nullptr; return SegTool2D::GetAffectedImageSliceAs2DImage(planeGeometry, image, image->GetTimeGeometry()->TimePointToTimeStep(timePoint), component); } mitk::Image::Pointer mitk::SegTool2D::GetAffectedImageSliceAs2DImage(const PlaneGeometry *planeGeometry, const Image *image, TimeStepType timeStep, unsigned int component /*= 0*/) { if (!image || !planeGeometry) { return nullptr; } // 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)); // additionally extract the given component // default is 0; the extractor checks for multi-component images extractor->SetComponent(component); extractor->Modified(); extractor->Update(); Image::Pointer slice = extractor->GetOutput(); return slice; } mitk::Image::Pointer mitk::SegTool2D::GetAffectedWorkingSlice(const InteractionPositionEvent *positionEvent) const { const auto workingNode = this->GetWorkingDataNode(); if (!workingNode) { return nullptr; } const auto *workingImage = dynamic_cast(workingNode->GetData()); if (!workingImage) { return nullptr; } return GetAffectedImageSliceAs2DImage(positionEvent, workingImage); } mitk::Image::Pointer mitk::SegTool2D::GetAffectedReferenceSlice(const InteractionPositionEvent *positionEvent) const { DataNode* referenceNode = this->GetReferenceDataNode(); if (!referenceNode) { return nullptr; } auto *referenceImage = dynamic_cast(referenceNode->GetData()); if (!referenceImage) { return nullptr; } int displayedComponent = 0; if (referenceNode->GetIntProperty("Image.Displayed Component", displayedComponent)) { // found the displayed component return GetAffectedImageSliceAs2DImage(positionEvent, referenceImage, displayedComponent); } else { return GetAffectedImageSliceAs2DImage(positionEvent, referenceImage); } } mitk::Image::Pointer mitk::SegTool2D::GetAffectedReferenceSlice(const PlaneGeometry* planeGeometry, TimeStepType timeStep) const { DataNode* referenceNode = this->GetReferenceDataNode(); if (!referenceNode) { return nullptr; } auto* referenceImage = dynamic_cast(referenceNode->GetData()); if (!referenceImage) { return nullptr; } int displayedComponent = 0; if (referenceNode->GetIntProperty("Image.Displayed Component", displayedComponent)) { // found the displayed component return GetAffectedImageSliceAs2DImage(planeGeometry, referenceImage, timeStep, displayedComponent); } else { return GetAffectedImageSliceAs2DImage(planeGeometry, referenceImage, timeStep); } } void mitk::SegTool2D::Activated() { Superclass::Activated(); this->GetToolManager()->SelectedTimePointChanged += mitk::MessageDelegate(this, &mitk::SegTool2D::OnTimePointChangedInternal); m_LastTimePointTriggered = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint(); } void mitk::SegTool2D::Deactivated() { this->GetToolManager()->SelectedTimePointChanged -= mitk::MessageDelegate(this, &mitk::SegTool2D::OnTimePointChangedInternal); Superclass::Deactivated(); } void mitk::SegTool2D::OnTimePointChangedInternal() { if (m_IsTimePointChangeAware && nullptr != this->GetWorkingDataNode()) { const auto timePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint(); if (timePoint != m_LastTimePointTriggered) { m_LastTimePointTriggered = timePoint; this->OnTimePointChanged(); } } } void mitk::SegTool2D::OnTimePointChanged() { //default implementation does nothing } mitk::DataNode* mitk::SegTool2D::GetWorkingDataNode() const { if (nullptr != this->GetToolManager()) { return this->GetToolManager()->GetWorkingData(0); } return nullptr; } mitk::Image* mitk::SegTool2D::GetWorkingData() const { auto node = this->GetWorkingDataNode(); if (nullptr != node) { return dynamic_cast(node->GetData()); } return nullptr; } mitk::DataNode* mitk::SegTool2D::GetReferenceDataNode() const { if (nullptr != this->GetToolManager()) { return this->GetToolManager()->GetReferenceData(0); } return nullptr; } mitk::Image* mitk::SegTool2D::GetReferenceData() const { auto node = this->GetReferenceDataNode(); if (nullptr != node) { return dynamic_cast(node->GetData()); } return nullptr; } void mitk::SegTool2D::WriteBackSegmentationResult(const InteractionPositionEvent *positionEvent, const Image * segmentationResult) { if (!positionEvent) return; const PlaneGeometry *planeGeometry((positionEvent->GetSender()->GetCurrentWorldPlaneGeometry())); const auto *abstractTransformGeometry( dynamic_cast(positionEvent->GetSender()->GetCurrentWorldPlaneGeometry())); if (planeGeometry && segmentationResult && !abstractTransformGeometry) { const auto workingNode = this->GetWorkingDataNode(); auto *image = dynamic_cast(workingNode->GetData()); const auto timeStep = positionEvent->GetSender()->GetTimeStep(image); this->WriteBackSegmentationResult(planeGeometry, segmentationResult, timeStep); } } void mitk::SegTool2D::WriteBackSegmentationResult(const DataNode* workingNode, const PlaneGeometry* planeGeometry, const Image* segmentationResult, TimeStepType timeStep) { if (!planeGeometry || !segmentationResult) return; SliceInformation sliceInfo(segmentationResult, const_cast(planeGeometry), timeStep); Self::WriteBackSegmentationResults(workingNode, { sliceInfo }, true); } void mitk::SegTool2D::WriteBackSegmentationResult(const PlaneGeometry *planeGeometry, const Image * segmentationResult, TimeStepType timeStep) { if (!planeGeometry || !segmentationResult) return; SliceInformation sliceInfo(segmentationResult, const_cast(planeGeometry), timeStep); WriteBackSegmentationResults({ sliceInfo }, true); } void mitk::SegTool2D::WriteBackSegmentationResults(const std::vector &sliceList, bool writeSliceToVolume) { if (sliceList.empty()) { return; } if (nullptr == m_LastEventSender) { MITK_WARN << "Cannot write tool results. Tool seems to be in an invalid state, as no interaction event was recieved but is expected."; return; } const auto workingNode = this->GetWorkingDataNode(); mitk::SegTool2D::WriteBackSegmentationResults(workingNode, sliceList, writeSliceToVolume); // the first geometry is needed otherwise restoring the position is not working const auto* plane3 = dynamic_cast(dynamic_cast( m_LastEventSender->GetSliceNavigationController()->GetCurrentGeometry3D()) ->GetPlaneGeometry(0)); unsigned int slicePosition = m_LastEventSender->GetSliceNavigationController()->GetSlice()->GetPos(); /* A cleaner solution would be to add a contour marker for each slice info. It currently does not work as the contour markers expect that the plane is always the plane of slice 0. Had not the time to do it properly no. Should be solved by T28146*/ this->AddContourmarker(plane3, slicePosition); } void mitk::SegTool2D::WriteBackSegmentationResults(const DataNode* workingNode, const std::vector& sliceList, bool writeSliceToVolume) { if (sliceList.empty()) { return; } if (nullptr == workingNode) { mitkThrow() << "Cannot write slice to working node. Working node is invalid."; } auto* image = dynamic_cast(workingNode->GetData()); if (nullptr == image) { mitkThrow() << "Cannot write slice to working node. Working node does not contain an image."; } for (const auto& sliceInfo : sliceList) { if (writeSliceToVolume && nullptr != sliceInfo.plane && sliceInfo.slice.IsNotNull()) { mitk::SegTool2D::WriteSliceToVolume(image, sliceInfo, true); } } mitk::SegTool2D::UpdateSurfaceInterpolation(sliceList, image, false); // also mark its node as modified (T27308). Can be removed if T27307 // is properly solved if (workingNode != nullptr) workingNode->Modified(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void mitk::SegTool2D::WriteSliceToVolume(Image* workingImage, const PlaneGeometry* planeGeometry, const Image* slice, TimeStepType timeStep, bool allowUndo) { SliceInformation sliceInfo(slice, planeGeometry, timeStep); WriteSliceToVolume(workingImage, sliceInfo , allowUndo); } void mitk::SegTool2D::WriteSliceToVolume(Image* workingImage, const SliceInformation &sliceInfo, bool allowUndo) { if (nullptr == workingImage) { mitkThrow() << "Cannot write slice to working node. Working node does not contain an image."; } DiffSliceOperation* undoOperation = nullptr; if (allowUndo) { /*============= BEGIN undo/redo feature block ========================*/ // Create undo operation by caching the not yet modified slices mitk::Image::Pointer originalSlice = GetAffectedImageSliceAs2DImage(sliceInfo.plane, workingImage, sliceInfo.timestep); undoOperation = new DiffSliceOperation(workingImage, originalSlice, dynamic_cast(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 reslice = vtkSmartPointer::New(); // Set the slice as 'input' // casting const away is needed and OK as long the OverwriteMode of // mitkVTKImageOverwrite is true. // Reason: because then the input slice is not touched but // used to overwrite the input of the ExtractSliceFilter. auto noneConstSlice = const_cast(sliceInfo.slice.GetPointer()); reslice->SetInputSlice(noneConstSlice->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(workingImage); extractor->SetTimeStep(sliceInfo.timestep); extractor->SetWorldGeometry(sliceInfo.plane); extractor->SetVtkOutputRequest(false); extractor->SetResliceTransformByGeometry(workingImage->GetGeometry(sliceInfo.timestep)); extractor->Modified(); extractor->Update(); // the image was modified within the pipeline, but not marked so workingImage->Modified(); workingImage->GetVtkImageData()->Modified(); if (allowUndo) { /*============= BEGIN undo/redo feature block ========================*/ // specify the redo operation with the edited slice auto* doOperation = new DiffSliceOperation(workingImage, extractor->GetOutput(), dynamic_cast(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 UndoStackItem::IncCurrObjectEventId(); UndoStackItem::IncCurrGroupEventId(); UndoController::GetCurrentUndoModel()->SetOperationEvent(undoStackItem); /*============= END undo/redo feature block ========================*/ } } void mitk::SegTool2D::SetShowMarkerNodes(bool status) { m_ShowMarkerNodes = status; } void mitk::SegTool2D::SetEnable3DInterpolation(bool enabled) { m_SurfaceInterpolationEnabled = enabled; } int mitk::SegTool2D::AddContourmarker(const PlaneGeometry* planeGeometry, unsigned int sliceIndex) { if (planeGeometry == nullptr) return -1; us::ServiceReference serviceRef = us::GetModuleContext()->GetServiceReference(); PlanePositionManagerService *service = us::GetModuleContext()->GetService(serviceRef); unsigned int size = service->GetNumberOfPlanePositions(); unsigned int id = service->AddNewPlanePosition(planeGeometry, sliceIndex); mitk::PlanarCircle::Pointer contourMarker = mitk::PlanarCircle::New(); mitk::Point2D p1; planeGeometry->Map(planeGeometry->GetCenter(), p1); mitk::Point2D p2 = p1; p2[0] -= planeGeometry->GetSpacing()[0]; p2[1] -= planeGeometry->GetSpacing()[1]; contourMarker->PlaceFigure(p1); contourMarker->SetCurrentControlPoint(p1); contourMarker->SetPlaneGeometry(planeGeometry->Clone()); std::stringstream markerStream; auto workingNode = this->GetWorkingDataNode(); 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 (planeGeometry) { if (id == size) { this->GetToolManager()->GetDataStorage()->Add(rotatedContourNode, workingNode); } else { mitk::NodePredicateProperty::Pointer isMarker = mitk::NodePredicateProperty::New("isContourMarker", mitk::BoolProperty::New(true)); mitk::DataStorage::SetOfObjects::ConstPointer markers = this->GetToolManager()->GetDataStorage()->GetDerivations(workingNode, isMarker); for (auto 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; } } this->GetToolManager()->GetDataStorage()->Add(rotatedContourNode, workingNode); } } return id; } void mitk::SegTool2D::InteractiveSegmentationBugMessage(const std::string &message) const { 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 << " https://phabricator.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; } void mitk::SegTool2D::WritePreviewOnWorkingImage( Image *targetSlice, const Image *sourceSlice, const Image *workingImage, int paintingPixelValue) { if (nullptr == targetSlice) { mitkThrow() << "Cannot write preview on working image. Target slice does not point to a valid instance."; } if (nullptr == sourceSlice) { mitkThrow() << "Cannot write preview on working image. Source slice does not point to a valid instance."; } if (nullptr == workingImage) { mitkThrow() << "Cannot write preview on working image. Working image does not point to a valid instance."; } auto constVtkSource = sourceSlice->GetVtkImageData(); /*Need to const cast because Vtk interface does not support const correctly. (or I am not experienced enough to use it correctly)*/ auto nonConstVtkSource = const_cast(constVtkSource); ContourModelUtils::FillSliceInSlice(nonConstVtkSource, targetSlice->GetVtkImageData(), workingImage, paintingPixelValue, 1.0); } + +bool mitk::SegTool2D::IsPositionEventInsideImageRegion(mitk::InteractionPositionEvent* positionEvent, + const mitk::BaseData* data) +{ + bool isPositionEventInsideImageRegion = + nullptr != data && data->GetGeometry()->IsInside(positionEvent->GetPositionInWorld()); + + if (!isPositionEventInsideImageRegion) + MITK_WARN("EditableContourTool") << "PositionEvent is outside ImageRegion!"; + + return isPositionEventInsideImageRegion; +} diff --git a/Modules/Segmentation/Interactions/mitkSegTool2D.h b/Modules/Segmentation/Interactions/mitkSegTool2D.h index 1c58bbf035..ed13ab6d29 100644 --- a/Modules/Segmentation/Interactions/mitkSegTool2D.h +++ b/Modules/Segmentation/Interactions/mitkSegTool2D.h @@ -1,294 +1,298 @@ /*============================================================================ 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 mitkSegTool2D_h_Included #define mitkSegTool2D_h_Included #include "mitkCommon.h" #include "mitkImage.h" #include "mitkTool.h" #include #include "mitkInteractionPositionEvent.h" #include "mitkInteractionConst.h" #include "mitkPlanePositionManager.h" #include "mitkRestorePlanePositionOperation.h" #include namespace mitk { class BaseRenderer; /** \brief Abstract base class for segmentation tools. \sa Tool \ingroup Interaction \ingroup ToolManagerEtAl Implements 2D segmentation specific helper methods, that might be of use to all kind of 2D segmentation tools. At the moment these are: - Determination of the slice where the user paints upon (DetermineAffectedImageSlice) - Projection of a 3D contour onto a 2D plane/slice SegTool2D tries to structure the interaction a bit. If you pass "PressMoveRelease" as the interaction type of your derived tool, you might implement the methods OnMousePressed, OnMouseMoved, and OnMouseReleased. Yes, your guess about when they are called is correct. \warning Only to be instantiated by mitk::ToolManager. $Author$ */ class MITKSEGMENTATION_EXPORT SegTool2D : public Tool { public: mitkClassMacro(SegTool2D, Tool); /** \brief Calculates for a given Image and PlaneGeometry, which slice of the image (in index corrdinates) is meant by the plane. \return false, if no slice direction seems right (e.g. rotated planes) \param image \param plane \param affectedDimension The image dimension, which is constant for all points in the plane, e.g. Axial --> 2 \param affectedSlice The index of the image slice */ static bool DetermineAffectedImageSlice(const Image *image, const PlaneGeometry *plane, int &affectedDimension, int &affectedSlice); /** * @brief Updates the surface interpolation by extracting the contour form the given slice. * @param slice the slice from which the contour should be extracted * @param workingImage the segmentation image * @param plane the plane in which the slice lies * @param detectIntersection if true the slice is eroded before contour extraction. If the slice is empty after the * erosion it is most * likely an intersecting contour an will not be added to the SurfaceInterpolationController */ static void UpdateSurfaceInterpolation(const Image *slice, const Image *workingImage, const PlaneGeometry *plane, bool detectIntersection); /** * \brief Extract the slice of an image that the user just scribbles on. The given component denotes the vector component of an vector image. * * \param positionEvent Event that specifies the plane that should be used to slice * \param image Image that should be sliced * \param component The component to be extracted of a given multi-component image. -1 is the default parameter to denote an invalid component. * * \return 'nullptr' if SegTool2D is either unable to determine which slice was affected, or if there was some problem * getting the image data at that position. */ static Image::Pointer GetAffectedImageSliceAs2DImage(const InteractionPositionEvent* positionEvent, const Image* image, unsigned int component = 0); /** * \brief Extract the slice of an image cut by given plane. The given component denotes the vector component of a vector image. * * \param planeGeometry Geometry defining the slice that should be cut out. * \param image Image that should be sliced * \param timeStep TimeStep of the image that shold be sliced * \param component The component to be extracted of a given multi-component image. -1 is the default parameter to denote an invalid component. * * \return 'nullptr' if SegTool2D is either unable to determine which slice was affected, or if there was some problem * getting the image data at that position. */ static Image::Pointer GetAffectedImageSliceAs2DImage(const PlaneGeometry* planeGeometry, const Image* image, TimeStepType timeStep, unsigned int component = 0); static Image::Pointer GetAffectedImageSliceAs2DImageByTimePoint(const PlaneGeometry* planeGeometry, const Image* image, TimePointType timePoint, unsigned int component = 0); /** Convenience overloaded version that can be called for a given planeGeometry, slice image and time step. * Calls static WriteBackSegmentationResults*/ static void WriteBackSegmentationResult(const DataNode* workingNode, const PlaneGeometry* planeGeometry, const Image* segmentationResult, TimeStepType timeStep); /** Convenience overloaded version that can be called for a given planeGeometry, slice image and time step. * For more details see protected WriteSliceToVolume version.*/ static void WriteSliceToVolume(Image* workingImage, const PlaneGeometry* planeGeometry, const Image* slice, TimeStepType timeStep, bool allowUndo); void SetShowMarkerNodes(bool); /** * \brief Enables or disables the 3D interpolation after writing back the 2D segmentation result, and defaults to * true. */ void SetEnable3DInterpolation(bool); void Activated() override; void Deactivated() override; itkSetMacro(IsTimePointChangeAware, bool); itkGetMacro(IsTimePointChangeAware, bool); itkBooleanMacro(IsTimePointChangeAware); protected: SegTool2D(); // purposely hidden SegTool2D(const char *, const us::Module *interactorModule = nullptr); // purposely hidden ~SegTool2D() override; /** * @brief returns the segmentation node that should be modified by the tool. */ DataNode* GetWorkingDataNode() const; Image* GetWorkingData() const; DataNode* GetReferenceDataNode() const; Image* GetReferenceData() const; /** * This function can be reimplemented by derived classes to react on changes of the current * time point. Default implementation does nothing.*/ virtual void OnTimePointChanged(); struct SliceInformation { mitk::Image::ConstPointer slice; const mitk::PlaneGeometry *plane = nullptr; mitk::TimeStepType timestep = 0; SliceInformation() = default; SliceInformation(const mitk::Image* aSlice, const mitk::PlaneGeometry* aPlane, mitk::TimeStepType aTimestep); }; /** * @brief Updates the surface interpolation by extracting the contour form the given slice. * @param sliceInfos vector of slice information instances from which the contours should be extracted * @param workingImage the segmentation image * @param detectIntersection if true the slice is eroded before contour extraction. If the slice is empty after the * erosion it is most * likely an intersecting contour an will not be added to the SurfaceInterpolationController */ static void UpdateSurfaceInterpolation(const std::vector& sliceInfos, const Image* workingImage, bool detectIntersection); /** * \brief Filters events that cannot be handled by 2D segmentation tools * * Currently an event is discarded if it was not sent by a 2D renderwindow and if it is * not of type InteractionPositionEvent */ bool FilterEvents(InteractionEvent *interactionEvent, DataNode *dataNode) override; /** \brief Extract the slice of the currently selected working image that the user just scribbles on. \return nullptr if SegTool2D is either unable to determine which slice was affected, or if there was some problem getting the image data at that position, or just no working image is selected. */ Image::Pointer GetAffectedWorkingSlice(const InteractionPositionEvent *) const; /** \brief Extract the slice of the currently selected reference image that the user just scribbles on. \return nullptr if SegTool2D is either unable to determine which slice was affected, or if there was some problem getting the image data at that position, or just no reference image is selected. */ Image::Pointer GetAffectedReferenceSlice(const InteractionPositionEvent *) const; /** Overload version that gets the reference slice passed on the passed plane geometry and timestep.*/ Image::Pointer GetAffectedReferenceSlice(const PlaneGeometry* planeGeometry, TimeStepType timeStep) const; /** Convenience version that can be called for a given event (which is used to deduce timepoint and plane) and a slice image. * Calls non static WriteBackSegmentationResults*/ void WriteBackSegmentationResult(const InteractionPositionEvent *, const Image* segmentationResult); /** Convenience version that can be called for a given planeGeometry, slice image and time step. * Calls non static WriteBackSegmentationResults*/ void WriteBackSegmentationResult(const PlaneGeometry *planeGeometry, const Image* segmentationResult, TimeStepType timeStep); /** Overloaded version that calls the static version and also adds the contour markers. * @remark If the sliceList is empty, this function does nothing.*/ void WriteBackSegmentationResults(const std::vector &sliceList, bool writeSliceToVolume = true); /** \brief Writes all provided source slices into the data of the passed workingNode. * The function does the following: 1) for every passed slice write it to workingNode (and generate and undo/redo step); * 2) update the surface interpolation and 3) marke the node as modified. * @param workingNode Pointer to the node that contains the working image. * @param sliceList Vector of all slices that should be written into the workingNode. If the list is * empty, the function call does nothing. * @param writeSliceToVolume If set to false the write operation (WriteSliceToVolume will be skipped) * and only the surface interpolation will be updated. * @pre workingNode must point to a valid instance and contain an image instance as data.*/ static void WriteBackSegmentationResults(const DataNode* workingNode, const std::vector& sliceList, bool writeSliceToVolume = true); /** Writes the provided source slice into the target slice with the given pixel value. * If passed workingImage is a LabelSetImage the label set rules will be applied when * writing all non zero source pixels into the target slice (e.g. locked lables will not be touched) * with the given paintingPixelValue. * @param targetSlice Pointer to the slice that should be filled with the content of the sourceSlice. * @param sourceSlice Pointer to the slice that is the source/preview every pixel will be (tried to be) transfered . * @param workingImage Will be used to check if LabeSetImageRules have to be applied and the label set state. * @param paintingPixelValue Value that will be used to paint onto target slice. * @pre targetSlice must point to a valid instance. * @pre sourceSlice must point to a valid instance. * @pre workingImage must point to a valid instance.*/ static void WritePreviewOnWorkingImage( Image *targetSlice, const Image *sourceSlice, const Image *workingImage, int paintingPixelValue); /** Writes a provided slice into the passed working image. The content of working image that is covered * by the slice will be completly overwritten. If asked for it also generates the needed * undo/redo steps. * @param workingImage Pointer to the image that is the target of the write operation. * @param sliceInfo SliceInfo instance that containes the slice image, the defining plane geometry and time step. * @param allowUndo Indicates if undo/redo operations should be registered for the write operation * performed by this call. true: undo/redo will be generated; false: no undo/redo will be generated, so * this operation cannot be revoked by the user. * @pre workingImage must point to a valid instance.*/ static void WriteSliceToVolume(Image* workingImage, const SliceInformation &sliceInfo, bool allowUndo); /** \brief Adds a new node called Contourmarker to the datastorage which holds a mitk::PlanarFigure. By selecting this node the slicestack will be reoriented according to the passed PlanarFigure's Geometry */ int AddContourmarker(const PlaneGeometry* planeGeometry, unsigned int sliceIndex); void InteractiveSegmentationBugMessage(const std::string &message) const; + /** Helper function to check if a position events points to a point inside the boundingbox of a passed + data instance.*/ + static bool IsPositionEventInsideImageRegion(InteractionPositionEvent* positionEvent, const BaseData* data); + BaseRenderer *m_LastEventSender = nullptr; unsigned int m_LastEventSlice = 0; itkGetMacro(LastTimePointTriggered, TimePointType); private: /** Internal method that gets triggered as soon as the tool manager indicates a * time point change. If the time point has changed since last time and tool * is set to be time point change aware, OnTimePointChanged() will be called.*/ void OnTimePointChangedInternal(); static void RemoveContourFromInterpolator(const SliceInformation& sliceInfo); // The prefix of the contourmarkername. Suffix is a consecutive number const std::string m_Contourmarkername; bool m_ShowMarkerNodes = false; static bool m_SurfaceInterpolationEnabled; bool m_IsTimePointChangeAware = true; TimePointType m_LastTimePointTriggered = 0.; }; } // namespace #endif diff --git a/Modules/Segmentation/Interactions/mitkSetRegionTool.cpp b/Modules/Segmentation/Interactions/mitkSetRegionTool.cpp deleted file mode 100644 index 486679ddaf..0000000000 --- a/Modules/Segmentation/Interactions/mitkSetRegionTool.cpp +++ /dev/null @@ -1,138 +0,0 @@ -/*============================================================================ - -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 "mitkSetRegionTool.h" - -#include "mitkToolManager.h" - -#include "mitkBaseRenderer.h" - -#include -#include - -#include -#include - -mitk::SetRegionTool::SetRegionTool(int paintingPixelValue) - : FeedbackContourTool("PressMoveRelease"), m_PaintingPixelValue(paintingPixelValue) -{ -} - -mitk::SetRegionTool::~SetRegionTool() -{ -} - -void mitk::SetRegionTool::ConnectActionsAndFunctions() -{ - CONNECT_FUNCTION("PrimaryButtonPressed", OnMousePressed); - CONNECT_FUNCTION("Release", OnMouseReleased); - CONNECT_FUNCTION("Move", OnMouseMoved); -} - -void mitk::SetRegionTool::Activated() -{ - Superclass::Activated(); -} - -void mitk::SetRegionTool::Deactivated() -{ - Superclass::Deactivated(); -} - -void mitk::SetRegionTool::OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent) -{ - auto *positionEvent = dynamic_cast(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_WARN << "Point outside of segmentation slice." << std::endl; - return; // can't use that as a seed point - } - - typedef itk::Image InputImageType; - typedef InputImageType::IndexType IndexType; - typedef itk::ConnectedThresholdImageFilter 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::Pointer fillHolesFilter = - itk::BinaryFillholeImageFilter::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(this->GetToolManager()->GetWorkingData(0)); - if (!workingNode) - return; - - mitk::ImageToContourModelFilter::Pointer contourextractor = mitk::ImageToContourModelFilter::New(); - contourextractor->SetInput(resultImage); - contourextractor->Update(); - - mitk::ContourModel::Pointer awesomeContour = contourextractor->GetOutput(); - - this->UpdateCurrentFeedbackContour(awesomeContour); - - FeedbackContourTool::SetFeedbackContourVisible(true); - mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); -} - -void mitk::SetRegionTool::OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent) -{ - auto *positionEvent = dynamic_cast(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 - mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); - - this->WriteBackFeedbackContourAsSegmentationResult(positionEvent, m_PaintingPixelValue); -} - -void mitk::SetRegionTool::OnMouseMoved(mitk::StateMachineAction *, mitk::InteractionEvent *) -{ -} diff --git a/Modules/Segmentation/Interactions/mitkSetRegionTool.h b/Modules/Segmentation/Interactions/mitkSetRegionTool.h deleted file mode 100644 index 9fab9b8030..0000000000 --- a/Modules/Segmentation/Interactions/mitkSetRegionTool.h +++ /dev/null @@ -1,60 +0,0 @@ -/*============================================================================ - -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 mitkSetRegionTool_h_Included -#define mitkSetRegionTool_h_Included - -#include "mitkCommon.h" -#include "mitkFeedbackContourTool.h" -#include - -namespace mitk -{ - class Image; - class StateMachineAction; - class InteractionEvent; - /** - \brief Fills or erases a 2D region - - \sa FeedbackContourTool - \sa ExtractImageFilter - - \ingroup Interactions - - Finds the outer contour of a shape in 2D (possibly including holes or single patches) and sets all - the inside pixels to a specified value. This might fill holes or erase segmentations. - - \warning Only to be instantiated by mitk::ToolManager. - */ - class MITKSEGMENTATION_EXPORT SetRegionTool : public FeedbackContourTool - { - public: - mitkClassMacro(SetRegionTool, FeedbackContourTool); - - protected: - SetRegionTool(int paintingPixelValue = 1); // purposely hidden - ~SetRegionTool() override; - - void ConnectActionsAndFunctions() override; - - void Activated() override; - void Deactivated() override; - - virtual void OnMousePressed(StateMachineAction *, InteractionEvent *); - virtual void OnMouseReleased(StateMachineAction *, InteractionEvent *); - virtual void OnMouseMoved(StateMachineAction *, InteractionEvent *); - int m_PaintingPixelValue; - }; - -} // namespace - -#endif diff --git a/Modules/Segmentation/Interactions/mitkTool.h b/Modules/Segmentation/Interactions/mitkTool.h index af0224ea3c..2eec4b6f7b 100644 --- a/Modules/Segmentation/Interactions/mitkTool.h +++ b/Modules/Segmentation/Interactions/mitkTool.h @@ -1,272 +1,273 @@ /*============================================================================ 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 mitkTool_h_Included #define mitkTool_h_Included #include "itkObjectFactoryBase.h" #include "itkVersion.h" #include "mitkCommon.h" #include "mitkDataNode.h" #include "mitkEventStateMachine.h" #include "mitkInteractionEventObserver.h" #include "mitkLabelSetImage.h" #include "mitkMessage.h" #include "mitkNodePredicateAnd.h" #include "mitkNodePredicateDataType.h" #include "mitkNodePredicateDimension.h" #include "mitkNodePredicateNot.h" #include "mitkNodePredicateOr.h" #include "mitkNodePredicateProperty.h" #include "mitkToolEvents.h" #include "mitkToolFactoryMacro.h" #include #include #include #include #include #include #include "usServiceRegistration.h" namespace us { class ModuleResource; } namespace mitk { class ToolManager; /** \brief Base class of all tools used by mitk::ToolManager. \sa ToolManager \sa SegTool2D \ingroup Interaction \ingroup ToolManagerEtAl Every tool is a mitk::EventStateMachine, which can follow any transition pattern that it likes. Every derived tool should always call SuperClass::Deactivated() at the end of its own implementation of Deactivated, because mitk::Tool resets the interaction configuration in this method. Only if you are very sure that you covered all possible things that might happen to your own tool, you should consider not to reset the configuration. To learn about the MITK implementation of state machines in general, have a look at \ref InteractionPage. To derive a non-abstract tool, you inherit from mitk::Tool (or some other base class further down the inheritance tree), and in your own parameterless constructor (that is called from the itkFactorylessNewMacro that you use) you pass a state machine name (interactor type). Names and .xml-files for valid state machines can be found in different "Interaction" directories (which might be enhanced by you). You have to implement at least GetXPM() and GetName() to provide some identification. Each Tool knows its ToolManager, which can provide the data that the tool should work on. \warning Only to be instantiated by mitk::ToolManager (because SetToolManager has to be called). All other uses are unsupported. $Author$ */ class MITKSEGMENTATION_EXPORT Tool : public EventStateMachine, public InteractionEventObserver { public: typedef mitk::Label::PixelType DefaultSegmentationDataType; /** * \brief To let GUI process new events (e.g. qApp->processEvents() ) */ Message<> GUIProcessEventsMessage; /** * \brief To send error messages (to be shown by some GUI) */ Message1 ErrorMessage; /** * \brief To send whether the tool is busy (to be shown by some GUI) */ Message1 CurrentlyBusy; /** * \brief To send general messages (to be shown by some GUI) */ Message1 GeneralMessage; mitkClassMacro(Tool, EventStateMachine); // no New(), there should only be subclasses /** \brief Returns an icon in the XPM format. This icon has to fit into some kind of button in most applications, so make it smaller than 25x25 pixels. XPM is e.g. supported by The Gimp. But if you open any XPM file in your text editor, you will see that you could also "draw" it with an editor. */ + [[deprecated]] virtual const char **GetXPM() const = 0; /** * \brief Returns the path of an icon. * * This icon is preferred to the XPM icon. */ virtual std::string GetIconPath() const { return ""; } /** * \brief Returns the path of a cursor icon. * */ virtual us::ModuleResource GetCursorIconResource() const; /** * @brief Returns the tool button icon of the tool wrapped by a usModuleResource * @return a valid ModuleResource or an invalid if this function * is not reimplemented */ virtual us::ModuleResource GetIconResource() const; /** \brief Returns the name of this tool. Make it short! This name has to fit into some kind of button in most applications, so take some time to think of a good name! */ virtual const char *GetName() const = 0; /** \brief Name of a group. You can group several tools by assigning a group name. Graphical tool selectors might use this information to group tools. (What other reason could there be?) */ virtual const char *GetGroup() const; virtual void InitializeStateMachine(); /** * \brief Interface for GUI creation. * * This is the basic interface for creation of a GUI object belonging to one tool. * * Tools that support a GUI (e.g. for display/editing of parameters) should follow some rules: * * - A Tool and its GUI are two separate classes * - There may be several instances of a GUI at the same time. * - mitk::Tool is toolkit (Qt, wxWidgets, etc.) independent, the GUI part is of course dependent * - The GUI part inherits both from itk::Object and some GUI toolkit class * - The GUI class name HAS to be constructed like "toolkitPrefix" tool->GetClassName() + "toolkitPostfix", e.g. * MyTool -> wxMyToolGUI * - For each supported toolkit there is a base class for tool GUIs, which contains some convenience methods * - Tools notify the GUI about changes using ITK events. The GUI must observe interesting events. * - The GUI base class may convert all ITK events to the GUI toolkit's favoured messaging system (Qt -> signals) * - Calling methods of a tool by its GUI is done directly. * In some cases GUIs don't want to be notified by the tool when they cause a change in a tool. * There is a macro CALL_WITHOUT_NOTICE(method()), which will temporarily disable all notifications during a * method call. */ virtual itk::Object::Pointer GetGUI(const std::string &toolkitPrefix, const std::string &toolkitPostfix); virtual NodePredicateBase::ConstPointer GetReferenceDataPreference() const; virtual NodePredicateBase::ConstPointer GetWorkingDataPreference() const; DataNode::Pointer CreateEmptySegmentationNode(const Image *original, const std::string &organName, const mitk::Color &color) const; DataNode::Pointer CreateSegmentationNode(Image *image, const std::string &organName, const mitk::Color &color) const; /** Function used to check if a tool can handle the referenceData and (if specified) the working data. @pre referenceData must be a valid pointer @param referenceData Pointer to the data that should be checked as valid reference for the tool. @param workingData Pointer to the data that should be checked as valid working data for this tool. This parameter can be null if no working data is specified so far.*/ virtual bool CanHandle(const BaseData *referenceData, const BaseData *workingData) const; protected: friend class ToolManager; virtual void SetToolManager(ToolManager *); /** Returns the pointer to the tool manager of the tool. May be null.*/ ToolManager* GetToolManager() const; /** Returns the data storage provided by the toolmanager. May be null (e.g. if ToolManager is not set).*/ mitk::DataStorage* GetDataStorage() const; void ConnectActionsAndFunctions() override; /** \brief Called when the tool gets activated. Derived tools should call their parents implementation at the beginning of the overriding function. */ virtual void Activated(); /** \brief Called when the tool gets deactivated. Derived tools should call their parents implementation at the end of the overriding function. */ virtual void Deactivated(); /** \brief Let subclasses change their event configuration. */ std::string m_EventConfig; Tool(const char *, const us::Module *interactorModule = nullptr); // purposely hidden ~Tool() override; void Notify(InteractionEvent *interactionEvent, bool isHandled) override; bool FilterEvents(InteractionEvent *, DataNode *) override; private: ToolManager* m_ToolManager; // for reference data NodePredicateDataType::Pointer m_PredicateImages; NodePredicateDimension::Pointer m_PredicateDim3; NodePredicateDimension::Pointer m_PredicateDim4; NodePredicateOr::Pointer m_PredicateDimension; NodePredicateAnd::Pointer m_PredicateImage3D; NodePredicateProperty::Pointer m_PredicateBinary; NodePredicateNot::Pointer m_PredicateNotBinary; NodePredicateProperty::Pointer m_PredicateSegmentation; NodePredicateNot::Pointer m_PredicateNotSegmentation; NodePredicateProperty::Pointer m_PredicateHelper; NodePredicateNot::Pointer m_PredicateNotHelper; NodePredicateAnd::Pointer m_PredicateImageColorful; NodePredicateAnd::Pointer m_PredicateImageColorfulNotHelper; NodePredicateAnd::Pointer m_PredicateReference; // for working data NodePredicateAnd::Pointer m_IsSegmentationPredicate; std::string m_InteractorType; std::map m_DisplayInteractionConfigs; const us::Module *m_InteractorModule; }; } // namespace #endif diff --git a/Modules/Segmentation/Resources/Close_48x48.png b/Modules/Segmentation/Resources/Close_48x48.png new file mode 100644 index 0000000000..9f1da9fd4e Binary files /dev/null and b/Modules/Segmentation/Resources/Close_48x48.png differ diff --git a/Modules/Segmentation/Resources/Close_Cursor_32x32.png b/Modules/Segmentation/Resources/Close_Cursor_32x32.png new file mode 100644 index 0000000000..9953754248 Binary files /dev/null and b/Modules/Segmentation/Resources/Close_Cursor_32x32.png differ diff --git a/Modules/Segmentation/Resources/Interactions/MouseReleaseOnly.xml b/Modules/Segmentation/Resources/Interactions/MouseReleaseOnly.xml new file mode 100644 index 0000000000..98f74e2964 --- /dev/null +++ b/Modules/Segmentation/Resources/Interactions/MouseReleaseOnly.xml @@ -0,0 +1,10 @@ + + + + + + + + + + \ No newline at end of file diff --git a/Modules/Segmentation/files.cmake b/Modules/Segmentation/files.cmake index 93b40ede21..6253ea9559 100644 --- a/Modules/Segmentation/files.cmake +++ b/Modules/Segmentation/files.cmake @@ -1,108 +1,112 @@ set(CPP_FILES Algorithms/mitkCalculateSegmentationVolume.cpp Algorithms/mitkContourModelSetToImageFilter.cpp Algorithms/mitkContourSetToPointSetFilter.cpp Algorithms/mitkContourUtils.cpp Algorithms/mitkCorrectorAlgorithm.cpp Algorithms/mitkDiffImageApplier.cpp Algorithms/mitkDiffSliceOperation.cpp Algorithms/mitkDiffSliceOperationApplier.cpp Algorithms/mitkFeatureBasedEdgeDetectionFilter.cpp Algorithms/mitkImageLiveWireContourModelFilter.cpp Algorithms/mitkImageToContourFilter.cpp #Algorithms/mitkImageToContourModelFilter.cpp Algorithms/mitkImageToLiveWireContourFilter.cpp Algorithms/mitkManualSegmentationToSurfaceFilter.cpp Algorithms/mitkOtsuSegmentationFilter.cpp Algorithms/mitkSegmentationHelper.cpp Algorithms/mitkSegmentationObjectFactory.cpp Algorithms/mitkShapeBasedInterpolationAlgorithm.cpp Algorithms/mitkShowSegmentationAsSmoothedSurface.cpp Algorithms/mitkShowSegmentationAsSurface.cpp Algorithms/mitkVtkImageOverwrite.cpp Controllers/mitkSegmentationInterpolationController.cpp Controllers/mitkToolManager.cpp Controllers/mitkSegmentationModuleActivator.cpp Controllers/mitkToolManagerProvider.cpp DataManagement/mitkContour.cpp DataManagement/mitkContourSet.cpp DataManagement/mitkExtrudedContour.cpp Interactions/mitkAddContourTool.cpp Interactions/mitkAutoCropTool.cpp Interactions/mitkSegWithPreviewTool.cpp Interactions/mitkBinaryThresholdBaseTool.cpp Interactions/mitkBinaryThresholdTool.cpp Interactions/mitkBinaryThresholdULTool.cpp + Interactions/mitkCloseRegionTool.cpp Interactions/mitkContourModelInteractor.cpp Interactions/mitkContourModelLiveWireInteractor.cpp Interactions/mitkEditableContourTool.cpp Interactions/mitkLiveWireTool2D.cpp Interactions/mitkLassoTool.cpp Interactions/mitkContourTool.cpp Interactions/mitkDrawPaintbrushTool.cpp Interactions/mitkErasePaintbrushTool.cpp Interactions/mitkEraseRegionTool.cpp Interactions/mitkFeedbackContourTool.cpp + Interactions/mitkFillRegionBaseTool.cpp Interactions/mitkFillRegionTool.cpp Interactions/mitkOtsuTool3D.cpp Interactions/mitkPaintbrushTool.cpp Interactions/mitkRegionGrowingTool.cpp Interactions/mitkSegmentationsProcessingTool.cpp - Interactions/mitkSetRegionTool.cpp Interactions/mitkSegTool2D.cpp Interactions/mitkSubtractContourTool.cpp Interactions/mitkTool.cpp Interactions/mitkToolCommand.cpp Interactions/mitkPickingTool.cpp Interactions/mitknnUnetTool.cpp Interactions/mitkSegmentationInteractor.cpp #SO Interactions/mitkProcessExecutor.cpp Rendering/mitkContourMapper2D.cpp Rendering/mitkContourSetMapper2D.cpp Rendering/mitkContourSetVtkMapper3D.cpp Rendering/mitkContourVtkMapper3D.cpp SegmentationUtilities/BooleanOperations/mitkBooleanOperation.cpp SegmentationUtilities/MorphologicalOperations/mitkMorphologicalOperations.cpp #Added from ML Controllers/mitkSliceBasedInterpolationController.cpp Algorithms/mitkSurfaceStampImageFilter.cpp ) set(RESOURCE_FILES Add_48x48.png Add_Cursor_32x32.png AI_48x48.png AI_Cursor_32x32.png + Close_48x48.png + Close_Cursor_32x32.png Erase_48x48.png Erase_Cursor_32x32.png Fill_48x48.png Fill_Cursor_32x32.png LiveWire_48x48.png LiveWire_Cursor_32x32.png NewAdd_48x48.png NewAdd_Cursor_32x32.png Otsu_48x48.png Paint_48x48.png Paint_Cursor_32x32.png Pick_48x48.png RegionGrowing_48x48.png RegionGrowing_Cursor_32x32.png Subtract_48x48.png Subtract_Cursor_32x32.png Threshold_48x48.png TwoThresholds_48x48.png Wipe_48x48.png Wipe_Cursor_32x32.png Interactions/dummy.xml Interactions/EditableContourTool.xml Interactions/PickingTool.xml + Interactions/MouseReleaseOnly.xml Interactions/PressMoveRelease.xml Interactions/PressMoveReleaseAndPointSetting.xml Interactions/PressMoveReleaseWithCTRLInversion.xml Interactions/PressMoveReleaseWithCTRLInversionAllMouseMoves.xml Interactions/SegmentationToolsConfig.xml Interactions/ContourModelModificationConfig.xml Interactions/ContourModelModificationInteractor.xml ) diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox index 8fff9e1c8c..5098e80b45 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox +++ b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox @@ -1,415 +1,422 @@ /** \page org_mitk_views_segmentation The Segmentation View \imageMacro{segmentation-dox.svg,"Icon of the segmentation view",2.00} Some of the features described below are closed source additions to the open source toolkit MITK and are not available in every application. \tableofcontents \section org_mitk_views_segmentationoverview Overview Segmentation is the act of partitioning an image into subsets by either manual or automated delineation to create i.e. a distinction between foreground and background. A multilabel segmentation can contain more than one label and more than one layer. This allows you to create different labels for different regions of interest encapsulated in one single image. The difference between labels and layers is that labels on one layer cannot overlap but labels on different layers can. The MITK segmentation plugin allows you to create multilabel segmentations of anatomical and pathological structures in medical images. The plugin consists of two views:
  • Segmentation View: Manual and (semi-)automatic segmentation
  • \subpage org_mitk_views_segmentationutilities : Segmentation post-processing
In this documentation, the features and usage of the segmentation view will be described. For an introduction to the segmentation utilities please be referred to the respective documentation pages. \imageMacro{QmitkSegmentationPlugin_Overview.png,"Segmentation plugin overview", 16.00} \section org_mitk_views_segmentationpreferences Preferences The segmentation plugin offers a number of preferences which can be set via the MITK Workbench application preferences: \imageMacro{QmitkSegmentationPreferences.png,"Segmentation preferences", 10.00}
  • Slim view: Allows to show or hide the tool button description of the segmentation view
  • 2D display: Specify whether the segmentation is drawn as outline or as a transparent overlay
  • Show only selected nodes: Enable if only the selected segmentation and the reference image should be visible
  • Smoothed surface creation: Set certain smoothing parameters for surface creation
  • Default label set preset: Start a new segmentation with this preset instead of a default label
  • Label creation: Assign default names and colors to new labels or ask users for them
  • Label suggestions: Specify custom suggestions for label names and colors
\section org_mitk_views_segmentationtechnicalissues Technical issues The segmentation plugin makes a number of assumptions:
  • Images must be 2D, 3D, or 3D+t.
  • Images must be single-values, i.e. CT, MRI or "normal" ultrasound. Images from color doppler or photographic (RGB) images are only partially supported (please be aware that some tools might not be compatible with this image type).
  • Segmentations are handled as multilabel images of the same extent as the original image.
\section org_mitk_views_segmentationdataselection Data selection & creating new segmentations To select a reference image for the segmentation, click on the Selected image selection widget and choose a suitable image from the selection available in the data manager. Once an image is selected, a new segmentation can be created on this reference image by clicking the button to the right of the Selected segmentation selection widget. A new multilabel segmentation with an initial label is automatically generated. The new segmentation will be added to the data manager as sub-node of the reference image. This item is then automatically selected in the data selection, which allows to start editing the new segmentation right away. \imageMacro{"QmitkSegmentation_DataSelection.png","Data selection",12} Alternatively to creating a new segmentation, an existing one can be edited as well. If a reference image is selected for which a segmentation already exists in the data manager, the auto selection mode will automatically select a fitting segmentation. Clicking on the segmentation selection widget a drop down list will open, containing all suitable segmentations for the selected reference dataset available in the data manager. \section org_mitk_views_segmentationlayers Segmentation layers For each multilabel segmentation different layers can be added or deleted. The layers can be used independently and layers can be switched using the left and right arrows. A layer is a set of labels that occupy a non-overlapping anatomical space. The best way to describe them is by a real use case: Imagine you are working on a radiotherapy planning application. In the first layer of your segmentation session, you would like to trace the contours of the liver and neighboring organs. You can accommodate all these segmentations in separate labels because they all occupy different anatomical regions and do not overlap. Now say you would like to segment the arteries and veins inside the liver. If you don't trace them in a different layer, you will overwrite the previous ones. You may also need a third layer for segmenting the different irrigation territories in the liver and a fourth layer to contain the lesion you would like to treat. \imageMacro{"QmitkSegmentation_LayerSelection.png","Layer selection",12} \section org_mitk_views_segmentationlabels Segmentation labels For each layer, one or more labels can be added. Pressing the double arrow on the right, all created labels are shown in the 'Label Table'. The following label properties are available:
  • Name:
    • the name of the label. Can be a predefined one or any other.
  • Locked:
    • whether the label is locked or editable. A locked label cannot be overwritten by another.
  • Color:
    • the color of the label.
  • Visible:
    • whether the label is currently visible or hidden.
\imageMacro{"QmitkSegmentation_LabelTable.png","The 'Label Table' shows all labels in the current segmentation session",12} The 'New Label' button can be used to add a new label. This will automatically add a new label with a distinct name and color to the list of available labels.\n In the current implementation of the plugin, the maximum number of labels is restricted to 255. If you need more, you will have to create a new segmentation session. \subsection org_mitk_views_segmentationlabelsuggestions Label name and color suggestions When renaming labels or creating new labels with enforced manual naming in the Segmentation preferences, entering names is supported by auto-completion for common label names. The list of predefined label names and colors for the auto-completion feature can be either extented or replaced by a custom list of label name and color suggestions. This custom list must be specified as a JSON file, just containing an array of objects, each with a mandatory "name" string and an optional "color" string. The JSON file can be set in the Segmentation preferences as well as a few options on how to apply these suggestions. \subsection org_mitk_views_segmentationlabelpresets Saving and loading label set presets Label set presets are useful to share a certain style or scheme between different segmentation sessions or to provide templates for new segmentation sessions. The properties of all labels in all layers like their names, colors, and visibilities are saved as a label set preset by clicking on the 'Save label set preset' button. Label set presets are applied to any segmentation session by clicking on the 'Load label set preset' button. If a label for a certain value already exists, its properties are overridden by the preset. If a label for a certain value does not yet exist, an empty label with the label properties of the preset is created. The actual segmentations of labels are unaffected as label set presets only store label properties. \subsubsection org_mitk_views_segmentationdefaultlabelpresets Applying label set presets by default If you work on a repetetive segmentation task, manually loading the same label set preset for each and every new segmentation can be tedious. To streamline your workflow, you can set a default label set preset in the Segmentation preferences (Ctrl+P). When set, this label set preset will be applied to all new segmentations instead of creating the default red "New label 1" label. \subsection org_mitk_views_segmentationlabelsearch Searching for a label It may happen that many labels (e.g. > 200) are present in a segmentation session and therefore manual searching can be time-consuming. The 'Label Search' edit box allows for quickly finding a label by providing assistance for label name completion. If the label is found, it will become the active one after pressing 'enter'. To start editing a label needs to be activated by clicking on the corresponding row in the 'Label Table'. Only one label can be active at the time. Then the segmentation tools in the toolbox can be used for mask generation. \subsection org_mitk_views_multilabelsegmentationoperationsonlabels Operations on labels Depending on the selection in the 'Label Table', several actions are offered: \subsubsection org_mitk_views_segmentationoperationssingleselection Operations with single label selection Right-clicking on any label opens a pop-up menu that offers the following actions to be performed on the selected label:
  • Rename...
    • : change the name and / or color of the selected label.
  • Remove...
    • : delete the selected label.
  • Erase...
    • : only clear the contents of the selected label.
  • Merge...
    • : merge two labels by selecting a second label.
  • Random color
    • : assign a random color to the label.
  • View only
    • : make all labels except the current selected label invisible.
  • View/Hide all
    • : make all labels visible / invisible
  • Lock/Unlock all
    • : lock or unlock all labels.
  • Create surface
    • : generate a surface out of the selected label.
  • Create mask
    • : generate a mask out of the selected label. A mask is a binary image with "1" inside and "0" outside.
  • Create cropped mask
    • : generate a binary mask out of the selected label. Crop changes the extent of the resulting image to the extent of the label.
\imageMacro{"QmitkSegmentation_OperationsSingleSelection.png","Context menu for single label selection",12} \subsubsection org_mitk_views_segmentationoperationsmultiselection Operations with multiple label selection Shift-clickink on multiple labels allows to select more than one label. If more than one label is selected, different options will appear in the menu:
  • Merge selection on current label
    • : transfer the contents of the selected labels in the 'Label Table' into the current one.
  • Remove selected labels
    • : delete the selected labels.
  • Erase selected labels
    • : only clear the contents of the selected labels.
\imageMacro{"QmitkSegmentation_OperationsMultiSelection.png","Context menu for multiple label selection",12} \section org_mitk_views_segmentationtooloverview Segmentation tool overview MITK offers a comprehensive set of slice-based 2D and (semi-)automated 3D segmentation tools. The manual 2D tools require some user interaction and can only be applied to a single image slice whereas the 3D tools operate on the whole image. The 3D tools usually only require a small amount of user interaction, i.e. placing seed points or setting / adjusting parameters. You can switch between the different toolsets by selecting the 2D or 3D tab in the segmentation view. \imageMacro{QmitkSegmentation_ToolOverview.png,"An overview of the existing 2D and 3D tools in MITK.",5.50} \section org_mitk_views_segmentation2dsegmentation 2D segmentation tools With 2D manual contouring you define which voxels are part of the segmentation and which are not. This allows you to create segmentations of any structures of interest in an image. You can also use manual contouring to correct segmentations that result from sub-optimal automatic methods. The drawback of manual contouring is that you might need to define contours on many 2D slices. However, this is mitigated by the interpolation feature, which will make suggestions for a segmentation. To start using one of the editing tools, click its button from the displayed toolbox. The selected editing tool will be active and its corresponding button will stay pressed until you click the button again. Selecting a different tool also deactivates the previous one.\n If you have to delineate a lot of images, shortcuts to switch between tools becomes convenient. For that, just hit the first letter of each tool to activate it (A for Add, S for Subtract, etc.). All of the editing tools work by the same principle: using the mouse (left button) to click anywhere in a 2D window (any of the orientations axial, sagittal, or coronal), moving the mouse while holding the mouse button and releasing the button to finish the editing action. Multi-step undo and redo is fully supported by all editing tools by using the application-wide undo / redo buttons in the toolbar. Remark: Clicking and moving the mouse in any of the 2D render windows will move the crosshair that defines what part of the image is displayed. This behavior is disabled as long as any of the manual segmentation tools are active - otherwise you might have a hard time concentrating on the contour you are drawing. \subsection org_mitk_views_segmentationaddsubtracttools Add and subtract tools \imageMacro{QmitkSegmentation_IMGIconAddSubtract.png,"Add and subtract tools",7.70} Use the left mouse button to draw a closed contour. When releasing the mouse button, the contour will be added (Add tool) to or removed (Subtract tool) from the current segmentation. Adding and subtracting voxels can be iteratively repeated for the same segmentation. Holding CTRL / CMD while drawing will invert the current tool's behavior (i.e. instead of adding voxels, they will be subtracted). \subsection org_mitk_views_segmentationlassotool Lasso tool \imageMacro{QmitkSegmentation_Lasso.png,"Lasso tool",7.70} The tool is a more advanced version of the add/substract tool. It offers you the following features:
  1. Generating a polygon segmentation (click left mouse button to set ancor point)
  2. Freehand contouring (like the add tool; press left mouse button while moving the mouse)
  3. Move ancor points (select an ancor point, press left mouse button while moving the mouse)
  4. Add new ancor points (press CTRL while click left mouse to add an ancor to the contour)
  5. Delete an ancor point (press Del while ancor point is selected)
  6. Segmentation can be added to the label (Add mode) or substracted (Substract mode)
To start a segmentation double left click where the first ancor point should be. To end the segmentation double left click where the last ancor point should be. Please note that:
  • feature 3-6 are only available, if auto confirm is *not* activated
  • feature 3-5 is not available for freehand contour segments
\subsection org_mitk_views_segmentationpaintwipetools Paint and wipe tools \imageMacro{QmitkSegmentation_IMGIconPaintWipe.png,"Paint and wipe tools",7.68} Use the Size slider to change the radius of the round paintbrush tool. Move the mouse in any 2D window and press the left button to draw or erase pixels. Holding CTRL / CMD while drawing will invert the current tool's behavior (i.e. instead of painting voxels, they will be wiped). \subsection org_mitk_views_segmentationregiongrowingtool Region growing tool \imageMacro{QmitkSegmentation_IMGIconRegionGrowing.png,"Region growing tool",3.81} Click at one point in a 2D slice widget to add an image region to the segmentation with the region growing tool. Region Growing selects all pixels around the mouse cursor that have a similar gray value as the pixel below the mouse cursor. This allows to quickly create segmentations of structures that have a good contrast to surrounding tissue. The tool operates based on the current level window, so changing the level window to optimize the contrast for the ROI is encouraged. Moving the mouse up / down is different from left / right: Moving up the cursor while holding the left mouse button widens the range for the included grey values; moving it down narrows it. Moving the mouse left and right will shift the range. The tool will select more or less pixels, corresponding to the changing gray value range. \if THISISNOTIMPLEMENTEDATTHEMOMENT A common issue with region growing is the so called "leakage" which happens when the structure of interest is connected to other pixels, of similar gray values, through a narrow "bridge" at the border of the structure. The Region Growing tool comes with a "leakage detection/removal" feature. If leakage happens, you can left-click into the leakage region and the tool will try to automatically remove this region (see illustration below). \imageMacro{QmitkSegmentation_Leakage.png,"Leakage correction feature of the region growing tool",11.28} \endif \subsection org_mitk_views_segmentationfilltool Fill tool \imageMacro{QmitkSegmentation_IMGIconFill.png,"Fill tool",3.81} -Left-click inside a segmentation with holes to completely fill all holes. Left-click inside a hole to fill only this specific hole. +Left-click inside a region/segmentation to flood fill all connected pixels that have the same label with the active label. This tool will only work on regions of unlocked labels or on regions that are not labeled at all. \subsection org_mitk_views_segmentationerasetool Erase tool - \imageMacro{QmitkSegmentation_IMGIconErase.png,"Erase tool",3.79} This tool removes a connected part of pixels that form a segmentation. -You may use it to remove single segmentations (left-click on specific segmentation) or to clear a whole slice at once (left-click outside a segmentation). +You may use it to remove single segmented regions (left-click on specific segmentation) or to clear a whole slice at once (left-click at the non-labeled background). +This tool will only work and regions of unlocked labels or on regions of the active label. + +\subsection org_mitk_views_segmentationclosetool Close tool +\imageMacro{QmitkSegmentation_IMGIconClose.png,"Close tool",3.79} + +Left-click inside the region/segmentation to fill all "holes" (pixels labelled with another label or no label) inside the region. +Therefore this tool behaves like a local closing operation. This tool will not work, when a non-labeled region is selected and holes of locked labels will not be filled. +\remark This tool always uses the label of the selected region (even if this label is not the active label). Therefore you can use this tool on regions of the active label and of none locked labels (without the need to change the active label). \subsection org_mitk_views_segmentationlivewiretool Live wire tool \imageMacro{QmitkSegmentation_IMGIconLiveWire.png,"Live wire tool",3.01} The Live Wire Tool acts as a magnetic lasso with a contour snapping to edges of objects. \imageMacro{QmitkSegmentation_IMGLiveWireUsage.PNG,"Steps for using the Live Wire Tool",16.00} The tool handling is the same like the Lasso tool (see for more info), except it generates live wire contours instead of straight lines. \subsection org_mitk_views_segmentationinterpolation 2D and 3D Interpolation Creating segmentations using 2D manual contouring for large image volumes may be very time-consuming, because structures of interest may cover a large range of slices. Note: Interpolation is currently disabled for segmentations containing more than one label. The segmentation view offers two helpful features to mitigate this drawback:
  • 2D Interpolation
  • 3D Interpolation
The 2D Interpolation creates suggestions for a segmentation whenever you have a slice that
  • has got neighboring slices with segmentations (these do not need to be direct neighbors but could also be a couple of slices away) AND
  • is completely clear of a manual segmentation, i.e. there will be no suggestion if there is even only a single pixel of segmentation in the current slice.
\imageMacro{QmitkSegmentation_2DInterpolation.png,"2D interpolation usage",3.01} Interpolated suggestions are displayed as outlines, until you confirm them as part of the segmentation. To confirm single slices, click the Confirm for single slice button below the toolbox. You may also review the interpolations visually and then accept all of them at once by selecting Confirm for all slices. The 3D interpolation creates suggestions for 3D segmentations. That means if you start contouring, from the second contour onwards, the surface of the segmented area will be interpolated based on the given contour information. The interpolation works with all available manual tools. Please note that this is currently a pure mathematical interpolation, i.e. image intensity information is not taken into account. With each further contour the interpolation result will be improved, but the more contours you provide the longer the recalculation will take. To achieve an optimal interpolation result and in this way a most accurate segmentation you should try to describe the surface with sparse contours by segmenting in arbitrary oriented planes. The 3D interpolation is not meant to be used for parallel slice-wise segmentation, but rather segmentations in i.e. the axial, coronal and sagittal plane. \imageMacro{QmitkSegmentation_3DInterpolationWrongRight.png,"3D interpolation usage",16.00} You can accept the interpolation result by clicking the Confirm-button below the tool buttons. In this case the 3D interpolation will be deactivated automatically so that the result can be post-processed without any interpolation running in the background. Additional to the surface, black contours are shown in the 3D render window, which mark all the drawn contours used for the interpolation. You can navigate between the drawn contours by clicking on the corresponding position nodes in the data manager which are stored as sub-nodes of the selected segmentation. If you do not want to see these nodes just uncheck the Show Position Nodes checkbox and these nodes will be hidden. If you want to delete a drawn contour we recommend to use the Erase-Tool since undo / redo is not yet working for 3D interpolation. The current state of the 3D interpolation can be saved across application restart. For that, just click on save project during the interpolation is active. After restarting the application and load your project you can click on "Reinit Interpolation" within the 3D interpolation GUI area. \section org_mitk_views_segmentation3dsegmentation 3D segmentation tools The 3D tools operate on the whole image and require usually a small amount of interaction like placing seed-points or specifying certain parameters. All 3D tools provide an immediate segmentation feedback, which is displayed as a transparent green overlay. For accepting a preview you have to press the Confirm button of the selected tool. The following 3D tools are available: \subsection org_mitk_views_segmentation3dthresholdtool 3D Threshold tool The thresholding tool simply applies a 3D threshold to the patient image. All pixels with values equal or above the selected threshold are labeled as part of the segmentation. You can change the threshold by either moving the slider of setting a certain value in the spinbox. \imageMacro{QmitkSegmentation_3DThresholdTool.png,"3D Threshold tool",10.00} \subsection org_mitk_views_segmentation3dulthresholdTool 3D upper / lower threshold tool The Upper/Lower Thresholding tool works similar to the simple 3D threshold tool but allows you to define an upper and lower threshold. All pixels with values within this threshold interval will be labeled as part of the segmentation. \imageMacro{QmitkSegmentation_3DULThresholdTool.png,"3D upper / lower threshold tool",10.00} \subsection org_mitk_views_segmentation3dotsutool 3D Otsu tool The 3D Otsu tool provides a more sophisticated thresholding algorithm. It allows you to define a number of regions. Based on the image histogram the pixels will then be divided into different regions. The more regions you define the longer the calculation will take. You can select afterwards which of these regions you want to confirm as segmentation. \imageMacro{QmitkSegmentation_3DOtsuTool.png,"3D Otsu tool",10.00} \subsection org_mitk_views_segmentation3drgtool 3D Region growing tool The 3D Region Growing tool works similar to the 2D pendant. At the beginning you have to place a seedpoint and define a threshold interval. If you press Run Segmentation a preview is calculated. By moving the Adapt region growing slider you can interactively adapt the segmentation result. \imageMacro{QmitkSegmentation_3DRGTool.png,"3D Region growing tool",10.00} \subsection org_mitk_views_segmentationpickingtool Picking Tool The Picking tool offers two modes that allow you to manipulate "islands" within your segmentation. This is especially useful if e.g. a thresholding provided you with several areas within your image but you are just interested in one special region. - Picking mode: Allows you to select certain "islands". When the pick is confirmed, the complete content of the active label will be removed except the pick. This mode is beneficial if you have a lot segmentation noise and want to pick the relevant parts and dismiss the rest. Hint: You can also pick from other labels, but this will only work if these labels are unlocked. - Relabel mode: Allows you to select certain "islands". When the pick is confirmed, it will be relabeled and added to the active label content. Hint: This mode ignores the locks of other labels, hence you do not need to unlock them explicitly. \imageMacro{QmitkSegmentation_PickingTool.png,"Picking tool",10.00} \subsection org_mitk_views_segmentationnnUNetTool nnU-Net Tool (Ubuntu only) \imageMacro{QmitkSegmentation_nnUnetTool.png,"nnUNet tool",10.00} This tool provides a GUI to the deep learning-based segmentation algorithm called the nnUNet. With this tool, you can get a segmentation mask predicted for the loaded image in MITK. Be ready with the pre-trained weights (a.k.a RESULTS_FOLDER) for your organ or task concerned, before using the tool. For a detailed explanation of the parameters and pre-trained weights folder structure etc., please refer to https://github.com/MIC-DKFZ/nnUNet.
Remark: The tool assumes that you have a Python3 environment with nnUNet (pip) installed. Your machine should be also equipped with a CUDA enabled GPU. \subsubsection org_mitk_views_segmentationnnUNetToolWorkflow Workflow: -# Select the "Python Path" drop-down to see if MITK has automatically detected other Python environments. Click on a fitting environment for the nnUNet inference or click "Select" in the dropdown to choose an unlisted python environment. Note that, while selecting an arbitrary environment folder, only select the base folder, e.g. "myenv". No need to select all the way until "../myenv/bin/python", for example. -# Click on the "nnUNet Results Folder" directory icon to navigate to the results folder on your hard disk. This is equivalent to setting the RESULTS_FOLDER environment variable. If your results folder is as per the nnUNet required folder structure, the configuration, trainers, tasks and folds are automatically parsed and correspondingly loaded in the drop-down boxes as shown below. Note that MITK automatically checks for the RESULTS_FOLDER environment variable value and, if found, auto parses that directory when the tool is started. \imageMacro{QmitkSegmentation_nnUNet_Settings.png,"nnUNet Segmentation Settings",10} -# Choose your required Task-Configuration-Trainer-Planner-Fold parameters, sequentially. By default, all entries are selected inside the "Fold" dropdown (shown: "All"). Note that, even if you uncheck all entries from the "Fold" dropdown (shown: "None"), then too, all folds would be considered for inferencing. -# For ensemble predictions, you will get the option to select parameters irrespective on postprocessing files available in the ensembles folder of RESULTS_FOLDER. Note that, if a postprocessing json file exists for the selected combination then it will used for ensembling, by default. To choose not to, uncheck the "Use PostProcessing JSON" in the "Advanced" section. \imageMacro{QmitkSegmentation_nnUNet_ensemble.png,"nnUNet Segmentation Settings",10} -# If your task is trained with multi-modal inputs, then "Multi-Modal" checkbox is checked and the no.of modalities are preloaded and shown next to "Required Modalities". Instantly, as much node selectors with corresponding modality names should appear below to select the Data Manager along including a selector with preselected with the reference node. Now, select the image nodes in the node selectors accordingly for accurate inferencing. \imageMacro{QmitkSegmentation_nnUNet_multimodal.png,"nnUNet Multi Modal Settings",10.00} -# Click on "Preview". -# In the "Advanced" section, you can also activate other options like "Mixed Precision" and "Enable Mirroring" (for test time data augmentation) pertaining to nnUNet. \imageMacro{QmitkSegmentation_nnUNet_Advanced.png,"nnUNet Advanced Settings",10.00} -# Use "Advanced" > "GPU Id" combobox to change the preferred GPU for inferencing. This is internally equivalent to setting the CUDA_VISIBLE_DEVICES environment variable. -# Every inferred segmentation is cached to prevent a redundant computation. In case, a user doesn't wish to cache a Preview, uncheck the "Enable Caching" in the "Advanced" section. This will ensure that the current parameters will neither be checked against the existing cache nor a segmentation be loaded from it when Preview is clicked. -# You may always clear all the cached segmentations by clicking "Clear Cache" button. \subsubsection org_mitk_views_segmentationnnUNetToolMisc Miscellaneous: -# In case you want to reload/reparse the folders in the "nnUNet Results Folder", eg. after adding new tasks into it, you may do so without reselecting the folder again by clicking the "Refresh Results Folder" button. -# The "Advanced" > "GPU Id" combobox lists the Nvidia GPUs available by parsing the nvidia-smi utility output. In case your machine has Nvidia CUDA enabled GPUs but the nvidia-smi fails for some reason, the "GPU Id" combobox will show no entries. In such a situation, it's still possible to execute inferencing by manually entering the preferred GPU Id, eg. 0 in the combobox. -# The "Advanced" > "Available Models" lists the available pre-trained tasks for download. Make sure you have internet connection. Then, choose a Task from the dropdown and click the Download button. The pre-trained models for the selected Task will be downloaded and placed to the RESULTS_FOLDER directory automatically. -# In the RESULTS_FOLDER directory, inside the trainer-planner folder of every task, MITK keeps a "mitk_export.json" file for fast loading for multi-modal information. It is recommended not to delete this file(s) for a fast responsive UI. Tip: If multi-modal information shown on MITK is not correct for a given task, you may modify this JSON file and try again. \section org_mitk_views_segmentationpostprocessing Additional things you can do with segmentations Segmentations are never an end in themselves. Consequently, the segmentation view adds a couple of "post-processing" actions, accessible through the context-menu of the data manager. \imageMacro{QmitkSegmentation_IMGDataManagerContextMenu.png,"Context menu items for segmentations",10.58}
  • Create polygon %model applies the marching cubes algorithm to the segmentation. This polygon %model can be used for visualization in 3D or other applications such as stereolithography (3D printing).
  • Create smoothed polygon %model uses smoothing in addition to the marching cubes algorithm, which creates models that do not follow the exact outlines of the segmentation, but look smoother.
  • Autocrop can save memory. Manual segmentations have the same extent as the patient image, even if the segmentation comprises only a small sub-volume. This invisible and meaningless margin is removed by autocropping.
\section org_mitk_views_segmentationof3dtimages Segmentation of 3D+t images For segmentation of 3D+t images, some tools give you the option to choose between creating dynamic and static masks.
  • Dynamic masks can be created on each time frame individually.
  • Static masks will be defined on one time frame and will be the same for all other time frames.
In general, segmentation is applied on the time frame that is selected when execution is performed. If you alter the time frame, the segmentation preview is adapted. \section org_mitk_views_segmentationtechnicaldetail Technical information for developers For technical specifications see \subpage QmitkSegmentationTechnicalPage and for information on the extensions of the tools system \subpage toolextensions. */ diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGIconClose.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGIconClose.png new file mode 100644 index 0000000000..c674c53dea Binary files /dev/null and b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGIconClose.png differ diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp index 62f06eb5e3..7d55bfbbf2 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp @@ -1,1009 +1,1009 @@ /*============================================================================ 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 "QmitkSegmentationView.h" #include "mitkPluginActivator.h" // blueberry #include // mitk #include #include #include #include #include #include #include #include #include #include #include #include #include // Qmitk #include #include #include // us #include #include // Qt #include #include #include #include const std::string QmitkSegmentationView::VIEW_ID = "org.mitk.views.segmentation"; QmitkSegmentationView::QmitkSegmentationView() : m_Parent(nullptr) , m_Controls(nullptr) , m_RenderWindowPart(nullptr) , m_ToolManager(nullptr) , m_ReferenceNode(nullptr) , m_WorkingNode(nullptr) , m_DrawOutline(true) , m_SelectionMode(false) , m_MouseCursorSet(false) , m_DefaultLabelNaming(true) { auto isImage = mitk::TNodePredicateDataType::New(); auto isDwi = mitk::NodePredicateDataType::New("DiffusionImage"); auto isDti = mitk::NodePredicateDataType::New("TensorImage"); auto isOdf = mitk::NodePredicateDataType::New("OdfImage"); auto isSegment = mitk::NodePredicateDataType::New("Segment"); auto validImages = mitk::NodePredicateOr::New(); validImages->AddPredicate(mitk::NodePredicateAnd::New(isImage, mitk::NodePredicateNot::New(isSegment))); validImages->AddPredicate(isDwi); validImages->AddPredicate(isDti); validImages->AddPredicate(isOdf); auto isBinary = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); auto isMask = mitk::NodePredicateAnd::New(isBinary, isImage); auto validSegmentations = mitk::NodePredicateOr::New(); validSegmentations->AddPredicate(mitk::TNodePredicateDataType::New()); validSegmentations->AddPredicate(isMask); m_SegmentationPredicate = mitk::NodePredicateAnd::New(); m_SegmentationPredicate->AddPredicate(validSegmentations); m_SegmentationPredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))); m_SegmentationPredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("hidden object"))); m_ReferencePredicate = mitk::NodePredicateAnd::New(); m_ReferencePredicate->AddPredicate(validImages); m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(m_SegmentationPredicate)); m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))); m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("hidden object"))); } QmitkSegmentationView::~QmitkSegmentationView() { if (nullptr != m_Controls) { OnLooseLabelSetConnection(); // deactivate all tools m_ToolManager->ActivateTool(-1); // removing all observers from working data for (NodeTagMapType::iterator dataIter = m_WorkingDataObserverTags.begin(); dataIter != m_WorkingDataObserverTags.end(); ++dataIter) { (*dataIter).first->GetProperty("visible")->RemoveObserver((*dataIter).second); } m_WorkingDataObserverTags.clear(); // removing all observers from reference data for (NodeTagMapType::iterator dataIter = m_ReferenceDataObserverTags.begin(); dataIter != m_ReferenceDataObserverTags.end(); ++dataIter) { (*dataIter).first->GetProperty("visible")->RemoveObserver((*dataIter).second); } m_ReferenceDataObserverTags.clear(); mitk::RenderingManager::GetInstance()->RemoveObserver(m_RenderingManagerObserverTag); ctkPluginContext* context = mitk::PluginActivator::getContext(); ctkServiceReference ppmRef = context->getServiceReference(); mitk::PlanePositionManagerService* service = context->getService(ppmRef); service->RemoveAllPlanePositions(); context->ungetService(ppmRef); m_ToolManager->SetReferenceData(nullptr); m_ToolManager->SetWorkingData(nullptr); } delete m_Controls; } /**********************************************************************/ /* private Q_SLOTS */ /**********************************************************************/ void QmitkSegmentationView::OnReferenceSelectionChanged(QList nodes) { m_ToolManager->ActivateTool(-1); // Remove observer if one was registered to the reference node auto finding = m_ReferenceDataObserverTags.find(m_ReferenceNode); if (finding != m_ReferenceDataObserverTags.end()) { m_ReferenceNode->GetProperty("visible")->RemoveObserver(m_ReferenceDataObserverTags[m_ReferenceNode]); m_ReferenceDataObserverTags.erase(m_ReferenceNode); } if (nodes.empty()) { m_Controls->workingNodeSelector->SetNodePredicate(m_SegmentationPredicate); m_ReferenceNode = nullptr; m_ToolManager->SetReferenceData(m_ReferenceNode); this->UpdateGUI(); return; } m_ReferenceNode = nodes.first(); m_ToolManager->SetReferenceData(m_ReferenceNode); if (m_ReferenceNode.IsNotNull()) { // set a predicate such that a segmentation fits the selected reference image geometry auto segPredicate = mitk::NodePredicateAnd::New(m_SegmentationPredicate.GetPointer(), mitk::NodePredicateSubGeometry::New(m_ReferenceNode->GetData()->GetGeometry())); m_Controls->workingNodeSelector->SetNodePredicate(segPredicate); if (m_SelectionMode) { // hide all image nodes to later show only the automatically selected ones mitk::DataStorage::SetOfObjects::ConstPointer imageNodes = this->GetDataStorage()->GetSubset(m_ReferencePredicate); for (mitk::DataStorage::SetOfObjects::const_iterator iter = imageNodes->begin(); iter != imageNodes->end(); ++iter) { (*iter)->SetVisibility(false); } } m_ReferenceNode->SetVisibility(true); auto command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(this, &QmitkSegmentationView::ValidateSelectionInput); m_ReferenceDataObserverTags[m_ReferenceNode] = m_ReferenceNode->GetProperty("visible")->AddObserver(itk::ModifiedEvent(), command); } this->UpdateGUI(); } void QmitkSegmentationView::OnSegmentationSelectionChanged(QList nodes) { m_ToolManager->ActivateTool(-1); // Remove observer if one was registered auto finding = m_WorkingDataObserverTags.find(m_WorkingNode); if (finding != m_WorkingDataObserverTags.end()) { m_WorkingNode->GetProperty("visible")->RemoveObserver(m_WorkingDataObserverTags[m_WorkingNode]); m_WorkingDataObserverTags.erase(m_WorkingNode); } if (nodes.empty()) { m_WorkingNode = nullptr; m_ToolManager->SetWorkingData(m_WorkingNode); this->UpdateGUI(); return; } if (m_ReferenceNode.IsNull()) { this->UpdateGUI(); return; } mitk::Image::ConstPointer referenceImage = dynamic_cast(m_ReferenceNode->GetData()); if (referenceImage.IsNull()) { this->UpdateGUI(); return; } m_WorkingNode = nodes.first(); m_ToolManager->SetWorkingData(m_WorkingNode); if (m_WorkingNode.IsNotNull()) { if (m_SelectionMode) { // hide all segmentation nodes to later show only the selected ones mitk::DataStorage::SetOfObjects::ConstPointer segmentationNodes = this->GetDataStorage()->GetSubset(m_SegmentationPredicate); for (mitk::DataStorage::SetOfObjects::const_iterator iter = segmentationNodes->begin(); iter != segmentationNodes->end(); ++iter) { (*iter)->SetVisibility(false); } } m_WorkingNode->SetVisibility(true); this->OnEstablishLabelSetConnection(); m_Controls->labelSetWidget->ResetAllTableWidgetItems(); auto command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(this, &QmitkSegmentationView::ValidateSelectionInput); m_WorkingDataObserverTags[m_WorkingNode] = m_WorkingNode->GetProperty("visible")->AddObserver(itk::ModifiedEvent(), command); this->InitializeRenderWindows(referenceImage->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, false); } this->UpdateGUI(); } void QmitkSegmentationView::OnVisibilityShortcutActivated() { if (m_WorkingNode.IsNull()) { return; } bool isVisible = false; m_WorkingNode->GetBoolProperty("visible", isVisible); m_WorkingNode->SetVisibility(!isVisible); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSegmentationView::OnLabelToggleShortcutActivated() { if (m_WorkingNode.IsNull()) { return; } auto workingImage = dynamic_cast(m_WorkingNode->GetData()); if (nullptr == workingImage) { return; } this->WaitCursorOn(); workingImage->GetActiveLabelSet()->SetNextActiveLabel(); workingImage->Modified(); this->WaitCursorOff(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSegmentationView::OnNewSegmentation() { m_ToolManager->ActivateTool(-1); if (m_ReferenceNode.IsNull()) { MITK_ERROR << "'Create new segmentation' button should never be clickable unless a reference image is selected."; return; } mitk::Image::ConstPointer referenceImage = dynamic_cast(m_ReferenceNode->GetData()); if (referenceImage.IsNull()) { QMessageBox::information( m_Parent, "New segmentation", "Please load and select an image before starting some action."); return; } if (referenceImage->GetDimension() <= 1) { QMessageBox::information( m_Parent, "New segmentation", "Segmentation is currently not supported for 2D images"); return; } auto segTemplateImage = referenceImage; if (referenceImage->GetDimension() > 3) { QmitkStaticDynamicSegmentationDialog dialog(m_Parent); dialog.SetReferenceImage(referenceImage.GetPointer()); dialog.exec(); segTemplateImage = dialog.GetSegmentationTemplate(); } mitk::DataNode::Pointer newSegmentationNode; try { this->WaitCursorOn(); newSegmentationNode = mitk::LabelSetImageHelper::CreateNewSegmentationNode(m_ReferenceNode, segTemplateImage); this->WaitCursorOff(); } catch (mitk::Exception& e) { this->WaitCursorOff(); MITK_ERROR << "Exception caught: " << e.GetDescription(); QMessageBox::warning(m_Parent, "New segmentation", "Could not create a new segmentation."); return; } auto newLabelSetImage = dynamic_cast(newSegmentationNode->GetData()); if (nullptr == newLabelSetImage) { // something went wrong return; } const auto labelSetPreset = this->GetDefaultLabelSetPreset(); if (labelSetPreset.empty() || !mitk::LabelSetIOHelper::LoadLabelSetImagePreset(labelSetPreset, newLabelSetImage)) { auto newLabel = mitk::LabelSetImageHelper::CreateNewLabel(newLabelSetImage); if (!m_DefaultLabelNaming) { QmitkNewSegmentationDialog dialog(m_Parent); dialog.SetName(QString::fromStdString(newLabel->GetName())); dialog.SetColor(newLabel->GetColor()); if (QDialog::Rejected == dialog.exec()) return; auto name = dialog.GetName(); if (!name.isEmpty()) newLabel->SetName(name.toStdString()); newLabel->SetColor(dialog.GetColor()); } newLabelSetImage->GetActiveLabelSet()->AddLabel(newLabel); } if (!this->GetDataStorage()->Exists(newSegmentationNode)) { this->GetDataStorage()->Add(newSegmentationNode, m_ReferenceNode); } if (m_ToolManager->GetWorkingData(0)) { m_ToolManager->GetWorkingData(0)->SetSelected(false); } newSegmentationNode->SetSelected(true); m_Controls->workingNodeSelector->SetCurrentSelectedNode(newSegmentationNode); } std::string QmitkSegmentationView::GetDefaultLabelSetPreset() const { auto labelSetPreset = mitk::BaseApplication::instance().config().getString(mitk::BaseApplication::ARG_SEGMENTATION_LABELSET_PRESET.toStdString(), ""); if (labelSetPreset.empty()) labelSetPreset = m_LabelSetPresetPreference.toStdString(); return labelSetPreset; } void QmitkSegmentationView::OnManualTool2DSelected(int id) { this->ResetMouseCursor(); mitk::StatusBar::GetInstance()->DisplayText(""); if (id >= 0) { std::string text = "Active Tool: \""; text += m_ToolManager->GetToolById(id)->GetName(); text += "\""; mitk::StatusBar::GetInstance()->DisplayText(text.c_str()); us::ModuleResource resource = m_ToolManager->GetToolById(id)->GetCursorIconResource(); this->SetMouseCursor(resource, 0, 0); } } void QmitkSegmentationView::OnShowMarkerNodes(bool state) { mitk::SegTool2D::Pointer manualSegmentationTool; unsigned int numberOfExistingTools = m_ToolManager->GetTools().size(); for (unsigned int i = 0; i < numberOfExistingTools; i++) { manualSegmentationTool = dynamic_cast(m_ToolManager->GetToolById(i)); if (nullptr == manualSegmentationTool) { continue; } manualSegmentationTool->SetShowMarkerNodes(state); } } void QmitkSegmentationView::OnLayersChanged() { this->OnEstablishLabelSetConnection(); m_Controls->labelSetWidget->ResetAllTableWidgetItems(); } void QmitkSegmentationView::OnShowLabelTable(bool value) { m_Controls->labelSetWidget->setVisible(value); } void QmitkSegmentationView::OnGoToLabel(const mitk::Point3D& pos) { if (m_RenderWindowPart) { m_RenderWindowPart->SetSelectedPosition(pos); } } void QmitkSegmentationView::OnLabelSetWidgetReset() { this->ValidateSelectionInput(); } /**********************************************************************/ /* private */ /**********************************************************************/ void QmitkSegmentationView::CreateQtPartControl(QWidget* parent) { m_Parent = parent; m_Controls = new Ui::QmitkSegmentationViewControls; m_Controls->setupUi(parent); // *------------------------ // * SHORTCUTS // *------------------------ QShortcut* visibilityShortcut = new QShortcut(QKeySequence(Qt::CTRL | Qt::Key::Key_H), parent); connect(visibilityShortcut, &QShortcut::activated, this, &QmitkSegmentationView::OnVisibilityShortcutActivated); QShortcut* labelToggleShortcut = new QShortcut(QKeySequence(Qt::CTRL | Qt::Key::Key_L, Qt::CTRL | Qt::Key::Key_I), parent); connect(labelToggleShortcut, &QShortcut::activated, this, &QmitkSegmentationView::OnLabelToggleShortcutActivated); // *------------------------ // * DATA SELECTION WIDGETS // *------------------------ m_Controls->referenceNodeSelector->SetDataStorage(GetDataStorage()); m_Controls->referenceNodeSelector->SetNodePredicate(m_ReferencePredicate); m_Controls->referenceNodeSelector->SetInvalidInfo("Select an image"); m_Controls->referenceNodeSelector->SetPopUpTitel("Select an image"); m_Controls->referenceNodeSelector->SetPopUpHint("Select an image that should be used to define the geometry and bounds of the segmentation."); m_Controls->workingNodeSelector->SetDataStorage(GetDataStorage()); m_Controls->workingNodeSelector->SetNodePredicate(m_SegmentationPredicate); m_Controls->workingNodeSelector->SetInvalidInfo("Select a segmentation"); m_Controls->workingNodeSelector->SetPopUpTitel("Select a segmentation"); m_Controls->workingNodeSelector->SetPopUpHint("Select a segmentation that should be modified. Only segmentation with the same geometry and within the bounds of the reference image are selected."); connect(m_Controls->referenceNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkSegmentationView::OnReferenceSelectionChanged); connect(m_Controls->workingNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkSegmentationView::OnSegmentationSelectionChanged); // *------------------------ // * TOOLMANAGER // *------------------------ m_ToolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); m_ToolManager->SetDataStorage(*(this->GetDataStorage())); m_ToolManager->InitializeTools(); - QString segTools2D = tr("Add Subtract Lasso Fill Erase Paint Wipe 'Region Growing' 'Live Wire'"); + QString segTools2D = tr("Add Subtract Lasso Fill Erase Close Paint Wipe 'Region Growing' 'Live Wire'"); QString segTools3D = tr("Threshold 'UL Threshold' Otsu 'Region Growing 3D' Picking"); #ifdef __linux__ segTools3D.append(" nnUNet"); // plugin not enabled for MacOS / Windows #endif std::regex extSegTool2DRegEx("SegTool2D$"); std::regex extSegTool3DRegEx("SegTool3D$"); auto tools = m_ToolManager->GetTools(); for (const auto &tool : tools) { if (std::regex_search(tool->GetNameOfClass(), extSegTool2DRegEx)) { segTools2D.append(QString(" '%1'").arg(tool->GetName())); } else if (std::regex_search(tool->GetNameOfClass(), extSegTool3DRegEx)) { segTools3D.append(QString(" '%1'").arg(tool->GetName())); } } // setup 2D tools m_Controls->toolSelectionBox2D->SetToolManager(*m_ToolManager); m_Controls->toolSelectionBox2D->SetGenerateAccelerators(true); m_Controls->toolSelectionBox2D->SetToolGUIArea(m_Controls->toolGUIArea2D); m_Controls->toolSelectionBox2D->SetDisplayedToolGroups(segTools2D.toStdString()); m_Controls->toolSelectionBox2D->SetLayoutColumns(3); m_Controls->toolSelectionBox2D->SetEnabledMode( QmitkToolSelectionBox::EnabledWithReferenceAndWorkingDataVisible); connect(m_Controls->toolSelectionBox2D, &QmitkToolSelectionBox::ToolSelected, this, &QmitkSegmentationView::OnManualTool2DSelected); // setup 3D Tools m_Controls->toolSelectionBox3D->SetToolManager(*m_ToolManager); m_Controls->toolSelectionBox3D->SetGenerateAccelerators(true); m_Controls->toolSelectionBox3D->SetToolGUIArea(m_Controls->toolGUIArea3D); m_Controls->toolSelectionBox3D->SetDisplayedToolGroups(segTools3D.toStdString()); m_Controls->toolSelectionBox3D->SetLayoutColumns(3); m_Controls->toolSelectionBox3D->SetEnabledMode( QmitkToolSelectionBox::EnabledWithReferenceAndWorkingDataVisible); m_Controls->slicesInterpolator->SetDataStorage(this->GetDataStorage()); // create general signal / slot connections connect(m_Controls->newSegmentationButton, &QToolButton::clicked, this, &QmitkSegmentationView::OnNewSegmentation); connect(m_Controls->slicesInterpolator, &QmitkSlicesInterpolator::SignalShowMarkerNodes, this, &QmitkSegmentationView::OnShowMarkerNodes); connect(m_Controls->layersWidget, &QmitkLayersWidget::LayersChanged, this, &QmitkSegmentationView::OnLayersChanged); connect(m_Controls->labelsWidget, &QmitkLabelsWidget::ShowLabelTable, this, &QmitkSegmentationView::OnShowLabelTable); // *------------------------ // * LABELSETWIDGET // *------------------------ connect(m_Controls->labelSetWidget, &QmitkLabelSetWidget::goToLabel, this, &QmitkSegmentationView::OnGoToLabel); connect(m_Controls->labelSetWidget, &QmitkLabelSetWidget::LabelSetWidgetReset, this, &QmitkSegmentationView::OnLabelSetWidgetReset); m_Controls->labelSetWidget->SetDataStorage(this->GetDataStorage()); m_Controls->labelSetWidget->hide(); auto command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(this, &QmitkSegmentationView::ValidateSelectionInput); m_RenderingManagerObserverTag = mitk::RenderingManager::GetInstance()->AddObserver(mitk::RenderingManagerViewsInitializedEvent(), command); m_RenderWindowPart = this->GetRenderWindowPart(); if (nullptr != m_RenderWindowPart) { this->RenderWindowPartActivated(m_RenderWindowPart); } // Make sure the GUI notices if appropriate data is already present on creation. // Should be done last, if everything else is configured because it triggers the autoselection of data. m_Controls->referenceNodeSelector->SetAutoSelectNewNodes(true); m_Controls->workingNodeSelector->SetAutoSelectNewNodes(true); this->UpdateGUI(); } void QmitkSegmentationView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) { if (m_RenderWindowPart != renderWindowPart) { m_RenderWindowPart = renderWindowPart; } if (nullptr != m_Parent) { m_Parent->setEnabled(true); } if (nullptr == m_Controls) { return; } // tell the interpolation about tool manager, data storage and render window part if (nullptr != m_RenderWindowPart) { QList controllers; controllers.push_back(m_RenderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController()); controllers.push_back(m_RenderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()); controllers.push_back(m_RenderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()); m_Controls->slicesInterpolator->Initialize(m_ToolManager, controllers); } } void QmitkSegmentationView::RenderWindowPartDeactivated(mitk::IRenderWindowPart* /*renderWindowPart*/) { m_RenderWindowPart = nullptr; if (nullptr != m_Parent) { m_Parent->setEnabled(false); } } void QmitkSegmentationView::OnPreferencesChanged(const berry::IBerryPreferences* prefs) { auto labelSuggestions = mitk::BaseApplication::instance().config().getString(mitk::BaseApplication::ARG_SEGMENTATION_LABEL_SUGGESTIONS.toStdString(), ""); m_DefaultLabelNaming = labelSuggestions.empty() ? prefs->GetBool("default label naming", true) : false; // No default label naming when label suggestions are enforced via command-line argument if (nullptr != m_Controls) { m_Controls->labelsWidget->SetDefaultLabelNaming(m_DefaultLabelNaming); bool slimView = prefs->GetBool("slim view", false); m_Controls->toolSelectionBox2D->SetShowNames(!slimView); m_Controls->toolSelectionBox3D->SetShowNames(!slimView); } m_DrawOutline = prefs->GetBool("draw outline", true); m_SelectionMode = prefs->GetBool("selection mode", false); m_LabelSetPresetPreference = prefs->Get("label set preset", ""); this->ApplyDisplayOptions(); } void QmitkSegmentationView::NodeAdded(const mitk::DataNode* node) { if (m_SegmentationPredicate->CheckNode(node)) { this->ApplyDisplayOptions(const_cast(node)); } } void QmitkSegmentationView::NodeRemoved(const mitk::DataNode* node) { if (!m_SegmentationPredicate->CheckNode(node)) { return; } // remove all possible contour markers of the segmentation mitk::DataStorage::SetOfObjects::ConstPointer allContourMarkers = this->GetDataStorage()->GetDerivations( node, mitk::NodePredicateProperty::New("isContourMarker", mitk::BoolProperty::New(true))); ctkPluginContext* context = mitk::PluginActivator::getContext(); ctkServiceReference ppmRef = context->getServiceReference(); mitk::PlanePositionManagerService* service = context->getService(ppmRef); for (mitk::DataStorage::SetOfObjects::ConstIterator it = allContourMarkers->Begin(); it != allContourMarkers->End(); ++it) { std::string nodeName = node->GetName(); unsigned int t = nodeName.find_last_of(" "); unsigned int id = atof(nodeName.substr(t + 1).c_str()) - 1; service->RemovePlanePosition(id); this->GetDataStorage()->Remove(it->Value()); } context->ungetService(ppmRef); service = nullptr; mitk::Image* image = dynamic_cast(node->GetData()); mitk::SurfaceInterpolationController::GetInstance()->RemoveInterpolationSession(image); } void QmitkSegmentationView::OnEstablishLabelSetConnection() { if (m_WorkingNode.IsNull()) { return; } auto workingImage = dynamic_cast(m_WorkingNode->GetData()); if (nullptr == workingImage) { return; } workingImage->GetActiveLabelSet()->AddLabelEvent += mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems); workingImage->GetActiveLabelSet()->RemoveLabelEvent += mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems); workingImage->GetActiveLabelSet()->ModifyLabelEvent += mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems); workingImage->GetActiveLabelSet()->AllLabelsModifiedEvent += mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems); workingImage->GetActiveLabelSet()->ActiveLabelEvent += mitk::MessageDelegate1(m_Controls->labelSetWidget, &QmitkLabelSetWidget::SelectLabelByPixelValue); // Removed in T27851 to have a chance to react to AfterChangeLayerEvent. Did it brake something? // workingImage->BeforeChangeLayerEvent += mitk::MessageDelegate( // this, &QmitkMultiLabelSegmentationView::OnLooseLabelSetConnection); workingImage->AfterChangeLayerEvent += mitk::MessageDelegate( this, &QmitkSegmentationView::UpdateGUI); } void QmitkSegmentationView::OnLooseLabelSetConnection() { if (m_WorkingNode.IsNull()) { return; } auto workingImage = dynamic_cast(m_WorkingNode->GetData()); if (nullptr == workingImage) { return; } // Reset LabelSetWidget Events workingImage->GetActiveLabelSet()->AddLabelEvent -= mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems); workingImage->GetActiveLabelSet()->RemoveLabelEvent -= mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems); workingImage->GetActiveLabelSet()->ModifyLabelEvent -= mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems); workingImage->GetActiveLabelSet()->AllLabelsModifiedEvent -= mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems); workingImage->GetActiveLabelSet()->ActiveLabelEvent -= mitk::MessageDelegate1(m_Controls->labelSetWidget, &QmitkLabelSetWidget::SelectLabelByPixelValue); // Removed in T27851 to have a chance to react to AfterChangeLayerEvent. Did it brake something? // workingImage->BeforeChangeLayerEvent -= mitk::MessageDelegate( // this, &QmitkMultiLabelSegmentationView::OnLooseLabelSetConnection); workingImage->AfterChangeLayerEvent -= mitk::MessageDelegate( this, &QmitkSegmentationView::UpdateGUI); } void QmitkSegmentationView::ApplyDisplayOptions() { if (nullptr == m_Parent) { return; } if (nullptr == m_Controls) { return; // might happen on initialization (preferences loaded) } mitk::DataStorage::SetOfObjects::ConstPointer allImages = this->GetDataStorage()->GetSubset(m_SegmentationPredicate); for (mitk::DataStorage::SetOfObjects::const_iterator iter = allImages->begin(); iter != allImages->end(); ++iter) { this->ApplyDisplayOptions(*iter); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSegmentationView::ApplyDisplayOptions(mitk::DataNode* node) { if (nullptr == node) { return; } auto labelSetImage = dynamic_cast(node->GetData()); if (nullptr != labelSetImage) { // node is a multi label segmentation // its outline property can be set in the segmentation preference page node->SetProperty("labelset.contour.active", mitk::BoolProperty::New(m_DrawOutline)); // force render window update to show outline node->GetData()->Modified(); } else if (nullptr != node->GetData()) { // node is a legacy binary segmentation bool isBinary = false; node->GetBoolProperty("binary", isBinary); if (isBinary) { node->SetProperty("outline binary", mitk::BoolProperty::New(m_DrawOutline)); node->SetProperty("outline width", mitk::FloatProperty::New(2.0)); // force render window update to show outline node->GetData()->Modified(); } } } void QmitkSegmentationView::OnContourMarkerSelected(const mitk::DataNode* node) { QmitkRenderWindow* selectedRenderWindow = nullptr; auto* renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::OPEN); auto* axialRenderWindow = renderWindowPart->GetQmitkRenderWindow("axial"); auto* sagittalRenderWindow = renderWindowPart->GetQmitkRenderWindow("sagittal"); auto* coronalRenderWindow = renderWindowPart->GetQmitkRenderWindow("coronal"); auto* threeDRenderWindow = renderWindowPart->GetQmitkRenderWindow("3d"); bool PlanarFigureInitializedWindow = false; // find initialized renderwindow if (node->GetBoolProperty("PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, axialRenderWindow->GetRenderer())) { selectedRenderWindow = axialRenderWindow; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, sagittalRenderWindow->GetRenderer())) { selectedRenderWindow = sagittalRenderWindow; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, coronalRenderWindow->GetRenderer())) { selectedRenderWindow = coronalRenderWindow; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, threeDRenderWindow->GetRenderer())) { selectedRenderWindow = threeDRenderWindow; } // make node visible if (nullptr != selectedRenderWindow) { std::string nodeName = node->GetName(); unsigned int t = nodeName.find_last_of(" "); unsigned int id = atof(nodeName.substr(t + 1).c_str()) - 1; ctkPluginContext* context = mitk::PluginActivator::getContext(); ctkServiceReference ppmRef = context->getServiceReference(); mitk::PlanePositionManagerService* service = context->getService(ppmRef); selectedRenderWindow->GetSliceNavigationController()->ExecuteOperation(service->GetPlanePosition(id)); context->ungetService(ppmRef); selectedRenderWindow->GetRenderer()->GetCameraController()->Fit(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkSegmentationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList& nodes) { if (0 == nodes.size()) { return; } std::string markerName = "Position"; unsigned int numberOfNodes = nodes.size(); std::string nodeName = nodes.at(0)->GetName(); if ((numberOfNodes == 1) && (nodeName.find(markerName) == 0)) { this->OnContourMarkerSelected(nodes.at(0)); return; } } void QmitkSegmentationView::ResetMouseCursor() { if (m_MouseCursorSet) { mitk::ApplicationCursor::GetInstance()->PopCursor(); m_MouseCursorSet = false; } } void QmitkSegmentationView::SetMouseCursor(const us::ModuleResource& resource, int hotspotX, int hotspotY) { // Remove previously set mouse cursor if (m_MouseCursorSet) { this->ResetMouseCursor(); } if (resource) { us::ModuleResourceStream cursor(resource, std::ios::binary); mitk::ApplicationCursor::GetInstance()->PushCursor(cursor, hotspotX, hotspotY); m_MouseCursorSet = true; } } void QmitkSegmentationView::UpdateGUI() { mitk::DataNode* referenceNode = m_ToolManager->GetReferenceData(0); bool hasReferenceNode = referenceNode != nullptr; mitk::DataNode* workingNode = m_ToolManager->GetWorkingData(0); bool hasWorkingNode = workingNode != nullptr; m_Controls->newSegmentationButton->setEnabled(false); if (hasReferenceNode) { m_Controls->newSegmentationButton->setEnabled(true); } if (hasWorkingNode && hasReferenceNode) { int layer = -1; referenceNode->GetIntProperty("layer", layer); workingNode->SetIntProperty("layer", layer + 1); } m_Controls->layersWidget->UpdateGUI(); m_Controls->labelsWidget->UpdateGUI(); this->ValidateSelectionInput(); } void QmitkSegmentationView::ValidateSelectionInput() { this->UpdateWarningLabel(""); m_Controls->layersWidget->setEnabled(false); m_Controls->labelsWidget->setEnabled(false); m_Controls->labelSetWidget->setEnabled(false); // the argument is actually not used // enable status depends on the tool manager selection m_Controls->toolSelectionBox2D->setEnabled(false); m_Controls->toolSelectionBox3D->setEnabled(false); m_Controls->slicesInterpolator->setEnabled(false); m_Controls->interpolatorWarningLabel->hide(); mitk::DataNode* referenceNode = m_Controls->referenceNodeSelector->GetSelectedNode(); mitk::DataNode* workingNode = m_Controls->workingNodeSelector->GetSelectedNode(); if (nullptr == referenceNode) { return; } if (nullptr == workingNode) { return; } mitk::IRenderWindowPart* renderWindowPart = this->GetRenderWindowPart(); auto workingNodeIsVisible = renderWindowPart && workingNode->IsVisible(renderWindowPart->GetQmitkRenderWindow("axial")->GetRenderer()); if (!workingNodeIsVisible) { this->UpdateWarningLabel(tr("The selected segmentation is currently not visible!")); return; } /* * Here we check whether the geometry of the selected segmentation image is aligned with the worldgeometry. * At the moment it is not supported to use a geometry different from the selected image for reslicing. * For further information see Bug 16063 */ const mitk::BaseGeometry* workingNodeGeo = workingNode->GetData()->GetGeometry(); const mitk::BaseGeometry* worldGeo = renderWindowPart->GetQmitkRenderWindow("3d")->GetSliceNavigationController()->GetCurrentGeometry3D(); if (nullptr != workingNodeGeo && nullptr != worldGeo) { if (mitk::Equal(*workingNodeGeo->GetBoundingBox(), *worldGeo->GetBoundingBox(), mitk::eps, true)) { m_ToolManager->SetReferenceData(referenceNode); m_ToolManager->SetWorkingData(workingNode); m_Controls->layersWidget->setEnabled(true); m_Controls->labelsWidget->setEnabled(true); m_Controls->labelSetWidget->setEnabled(true); m_Controls->toolSelectionBox2D->setEnabled(true); m_Controls->toolSelectionBox3D->setEnabled(true); auto labelSetImage = dynamic_cast(workingNode->GetData()); if (nullptr != labelSetImage) { int numberOfLabels = labelSetImage->GetNumberOfLabels(labelSetImage->GetActiveLayer()); if (2 == numberOfLabels) // fix for T27319: exterior is label 0, first label is label 1 { m_Controls->slicesInterpolator->setEnabled(true); } else { m_Controls->interpolatorWarningLabel->show(); m_Controls->interpolatorWarningLabel->setText("Interpolation only works for single label segmentations."); } } return; } } m_ToolManager->SetReferenceData(referenceNode); m_ToolManager->SetWorkingData(nullptr); this->UpdateWarningLabel(tr("Please perform a reinit on the segmentation image!")); } void QmitkSegmentationView::UpdateWarningLabel(QString text) { if (text.size() == 0) { m_Controls->selectionWarningLabel->hide(); } else { m_Controls->selectionWarningLabel->show(); m_Controls->selectionWarningLabel->setText("" + text + ""); } }