diff --git a/Modules/Segmentation/Interactions/mitkAutoSegmentationWithPreviewTool.cpp b/Modules/Segmentation/Interactions/mitkAutoSegmentationWithPreviewTool.cpp index c38e65a00c..be1696c826 100644 --- a/Modules/Segmentation/Interactions/mitkAutoSegmentationWithPreviewTool.cpp +++ b/Modules/Segmentation/Interactions/mitkAutoSegmentationWithPreviewTool.cpp @@ -1,584 +1,595 @@ /*============================================================================ 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 "mitkAutoSegmentationWithPreviewTool.h" #include "mitkToolManager.h" #include "mitkColorProperty.h" #include "mitkProperties.h" #include "mitkDataStorage.h" #include "mitkRenderingManager.h" #include "mitkImageAccessByItk.h" #include "mitkImageCast.h" #include "mitkLabelSetImage.h" #include "mitkMaskAndCutRoiImageFilter.h" #include "mitkPadImageFilter.h" #include "mitkNodePredicateGeometry.h" #include "mitkSegTool2D.h" mitk::AutoSegmentationWithPreviewTool::AutoSegmentationWithPreviewTool(bool lazyDynamicPreviews): m_LazyDynamicPreviews(lazyDynamicPreviews) { m_ProgressCommand = ToolCommand::New(); } mitk::AutoSegmentationWithPreviewTool::AutoSegmentationWithPreviewTool(bool lazyDynamicPreviews, const char* interactorType, const us::Module* interactorModule) : AutoSegmentationTool(interactorType, interactorModule), m_LazyDynamicPreviews(lazyDynamicPreviews) { m_ProgressCommand = ToolCommand::New(); } mitk::AutoSegmentationWithPreviewTool::~AutoSegmentationWithPreviewTool() { } +void mitk::AutoSegmentationWithPreviewTool::SetMergeStyle(MultiLabelSegmentation::MergeStyle mergeStyle) +{ + m_MergeStyle = mergeStyle; +} + +void mitk::AutoSegmentationWithPreviewTool::SetOverwriteStyle(MultiLabelSegmentation::OverwriteStyle overwriteStyle) +{ + m_OverwriteStyle = overwriteStyle; +} + + bool mitk::AutoSegmentationWithPreviewTool::CanHandle(const BaseData* referenceData, const BaseData* workingData) const { if (!Superclass::CanHandle(referenceData, workingData)) return false; if (workingData == nullptr) return true; auto* labelSet = dynamic_cast(workingData); if (labelSet != nullptr) return true; auto* image = dynamic_cast(workingData); if (image == nullptr) return false; //if it is a normal image and not a label set image is used as working data //it must have the same pixel type as a label set. return MakeScalarPixelType< DefaultSegmentationDataType >() == image->GetPixelType(); } void mitk::AutoSegmentationWithPreviewTool::Activated() { Superclass::Activated(); this->GetToolManager()->RoiDataChanged += MessageDelegate(this, &AutoSegmentationWithPreviewTool::OnRoiDataChanged); this->GetToolManager()->SelectedTimePointChanged += MessageDelegate(this, &AutoSegmentationWithPreviewTool::OnTimePointChanged); m_ReferenceDataNode = this->GetToolManager()->GetReferenceData(0); m_SegmentationInputNode = m_ReferenceDataNode; m_LastTimePointOfUpdate = RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint(); if (m_PreviewSegmentationNode.IsNull()) { m_PreviewSegmentationNode = DataNode::New(); m_PreviewSegmentationNode->SetProperty("color", ColorProperty::New(0.0, 1.0, 0.0)); m_PreviewSegmentationNode->SetProperty("name", StringProperty::New(std::string(this->GetName())+" preview")); m_PreviewSegmentationNode->SetProperty("opacity", FloatProperty::New(0.3)); m_PreviewSegmentationNode->SetProperty("binary", BoolProperty::New(true)); m_PreviewSegmentationNode->SetProperty("helper object", BoolProperty::New(true)); } if (m_SegmentationInputNode.IsNotNull()) { this->ResetPreviewNode(); this->InitiateToolByInput(); } else { this->GetToolManager()->ActivateTool(-1); } } void mitk::AutoSegmentationWithPreviewTool::Deactivated() { this->GetToolManager()->RoiDataChanged -= MessageDelegate(this, &AutoSegmentationWithPreviewTool::OnRoiDataChanged); this->GetToolManager()->SelectedTimePointChanged -= MessageDelegate(this, &AutoSegmentationWithPreviewTool::OnTimePointChanged); m_SegmentationInputNode = nullptr; m_ReferenceDataNode = nullptr; m_WorkingPlaneGeometry = nullptr; try { if (DataStorage *storage = this->GetToolManager()->GetDataStorage()) { storage->Remove(m_PreviewSegmentationNode); RenderingManager::GetInstance()->RequestUpdateAll(); } } catch (...) { // don't care } if (m_PreviewSegmentationNode.IsNotNull()) { m_PreviewSegmentationNode->SetData(nullptr); } Superclass::Deactivated(); } void mitk::AutoSegmentationWithPreviewTool::ConfirmSegmentation() { bool labelChanged = this->EnsureUpToDateUserDefinedActiveLabel(); if ((m_LazyDynamicPreviews && m_CreateAllTimeSteps) || labelChanged) { // The tool should create all time steps but is currently in lazy mode, // thus ensure that a preview for all time steps is available. this->UpdatePreview(true); } CreateResultSegmentationFromPreview(); RenderingManager::GetInstance()->RequestUpdateAll(); if (!m_KeepActiveAfterAccept) { this->GetToolManager()->ActivateTool(-1); } } void mitk::AutoSegmentationWithPreviewTool::InitiateToolByInput() { //default implementation does nothing. //implement in derived classes to change behavior } mitk::Image* mitk::AutoSegmentationWithPreviewTool::GetPreviewSegmentation() { if (m_PreviewSegmentationNode.IsNull()) { return nullptr; } return dynamic_cast(m_PreviewSegmentationNode->GetData()); } mitk::DataNode* mitk::AutoSegmentationWithPreviewTool::GetPreviewSegmentationNode() { return m_PreviewSegmentationNode; } const mitk::Image* mitk::AutoSegmentationWithPreviewTool::GetSegmentationInput() const { if (m_SegmentationInputNode.IsNull()) { return nullptr; } return dynamic_cast(m_SegmentationInputNode->GetData()); } const mitk::Image* mitk::AutoSegmentationWithPreviewTool::GetReferenceData() const { if (m_ReferenceDataNode.IsNull()) { return nullptr; } return dynamic_cast(m_ReferenceDataNode->GetData()); } template void ClearBufferProcessing(ImageType* itkImage) { itkImage->FillBuffer(0); } void mitk::AutoSegmentationWithPreviewTool::ResetPreviewContentAtTimeStep(unsigned int timeStep) { auto previewImage = GetImageByTimeStep(this->GetPreviewSegmentation(), timeStep); if (nullptr != previewImage) { AccessByItk(previewImage, ClearBufferProcessing); } } void mitk::AutoSegmentationWithPreviewTool::ResetPreviewContent() { auto previewImage = this->GetPreviewSegmentation(); if (nullptr != previewImage) { auto castedPreviewImage = dynamic_cast(previewImage); if (nullptr == castedPreviewImage) mitkThrow() << "Application is on wrong state / invalid tool implementation. Preview image should always be of type LabelSetImage now."; castedPreviewImage->ClearBuffer(); } } void mitk::AutoSegmentationWithPreviewTool::ResetPreviewNode() { if (m_IsUpdating) { mitkThrow() << "Used tool is implemented incorrectly. ResetPreviewNode is called while preview update is ongoing. Check implementation!"; } itk::RGBPixel previewColor; previewColor[0] = 0.0f; previewColor[1] = 1.0f; previewColor[2] = 0.0f; const auto image = this->GetSegmentationInput(); if (nullptr != image) { LabelSetImage::ConstPointer workingImage = dynamic_cast(this->GetToolManager()->GetWorkingData(0)->GetData()); if (workingImage.IsNotNull()) { auto newPreviewImage = workingImage->Clone(); if (this->GetResetsToEmptyPreview()) { newPreviewImage->ClearBuffer(); } if (newPreviewImage.IsNull()) { MITK_ERROR << "Cannot create preview helper objects. Unable to clone working image"; return; } m_PreviewSegmentationNode->SetData(newPreviewImage); // Let's paint the feedback node green... auto* activeLayer = newPreviewImage->GetActiveLabelSet(); auto* activeLabel = activeLayer->GetActiveLabel(); activeLabel->SetColor(previewColor); activeLayer->UpdateLookupTable(activeLabel->GetValue()); } else { Image::ConstPointer workingImageBin = dynamic_cast(this->GetToolManager()->GetWorkingData(0)->GetData()); if (workingImageBin.IsNotNull()) { Image::Pointer newPreviewImage; if (this->GetResetsToEmptyPreview()) { newPreviewImage = Image::New(); newPreviewImage->Initialize(workingImageBin); } else { auto newPreviewImage = workingImageBin->Clone(); } if (newPreviewImage.IsNull()) { MITK_ERROR << "Cannot create preview helper objects. Unable to clone working image"; return; } m_PreviewSegmentationNode->SetData(newPreviewImage); } else { mitkThrow() << "Tool is an invalid state. Cannot setup preview node. Working data is an unsupported class and should have not been accepted by CanHandle()."; } } m_PreviewSegmentationNode->SetColor(previewColor); m_PreviewSegmentationNode->SetOpacity(0.5); int layer(50); m_ReferenceDataNode->GetIntProperty("layer", layer); m_PreviewSegmentationNode->SetIntProperty("layer", layer + 1); if (DataStorage *ds = this->GetToolManager()->GetDataStorage()) { if (!ds->Exists(m_PreviewSegmentationNode)) ds->Add(m_PreviewSegmentationNode, m_ReferenceDataNode); } } } void mitk::AutoSegmentationWithPreviewTool::TransferImageAtTimeStep(const Image* sourceImage, Image* destinationImage, const TimeStepType timeStep) { try { Image::ConstPointer sourceImageAtTimeStep = this->GetImageByTimeStep(sourceImage, timeStep); if (sourceImageAtTimeStep->GetPixelType() != destinationImage->GetPixelType()) { mitkThrow() << "Cannot transfer images. Tool is in an invalid state, source image and destination image do not have the same pixel type. " << "Source pixel type: " << sourceImage->GetPixelType().GetTypeAsString() << "; destination pixel type: " << destinationImage->GetPixelType().GetTypeAsString(); } if (!Equal(*(sourceImage->GetGeometry(timeStep)), *(destinationImage->GetGeometry(timeStep)), NODE_PREDICATE_GEOMETRY_DEFAULT_CHECK_COORDINATE_PRECISION, NODE_PREDICATE_GEOMETRY_DEFAULT_CHECK_DIRECTION_PRECISION, false)) { mitkThrow() << "Cannot transfer images. Tool is in an invalid state, source image and destination image do not have the same geometry."; } if (nullptr != this->GetWorkingPlaneGeometry()) { auto sourceSlice = SegTool2D::GetAffectedImageSliceAs2DImage(this->GetWorkingPlaneGeometry(), sourceImage, timeStep); SegTool2D::WriteBackSegmentationResult(this->GetTargetSegmentationNode(), m_WorkingPlaneGeometry, sourceSlice, timeStep); } else { //take care of the full segmentation volume auto sourceLSImage = dynamic_cast(sourceImage); auto destLSImage = dynamic_cast(destinationImage); - TransferLabelContent(sourceLSImage, destLSImage, { {this->GetUserDefinedActiveLabel(),this->GetUserDefinedActiveLabel()} }, MultiLabelSegmentation::MergeStyle::Replace, - MultiLabelSegmentation::OverwriteStyle::RegardLocks, timeStep); + TransferLabelContent(sourceLSImage, destLSImage, { {this->GetUserDefinedActiveLabel(),this->GetUserDefinedActiveLabel()} }, m_MergeStyle, + m_OverwriteStyle, timeStep); } } catch (...) { Tool::ErrorMessage("Error accessing single time steps of the original image. Cannot create segmentation."); throw; } } void mitk::AutoSegmentationWithPreviewTool::CreateResultSegmentationFromPreview() { const auto segInput = this->GetSegmentationInput(); auto previewImage = this->GetPreviewSegmentation(); if (nullptr != segInput && nullptr != previewImage) { DataNode::Pointer resultSegmentationNode = GetTargetSegmentationNode(); if (resultSegmentationNode.IsNotNull()) { const auto timePoint = RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint(); auto resultSegmentation = dynamic_cast(resultSegmentationNode->GetData()); // REMARK: the following code in this scope assumes that previewImage and resultSegmentation // are clones of the working image (segmentation provided to the tool). Therefore they have // the same time geometry. if (previewImage->GetTimeSteps() != resultSegmentation->GetTimeSteps()) { mitkThrow() << "Cannot perform threshold. Internal tool state is invalid." << " Preview segmentation and segmentation result image have different time geometries."; } if (m_CreateAllTimeSteps) { for (unsigned int timeStep = 0; timeStep < previewImage->GetTimeSteps(); ++timeStep) { this->TransferImageAtTimeStep(previewImage, resultSegmentation, timeStep); } } else { const auto timeStep = resultSegmentation->GetTimeGeometry()->TimePointToTimeStep(timePoint); this->TransferImageAtTimeStep(previewImage, resultSegmentation, timeStep); } // since we are maybe working on a smaller image, pad it to the size of the original image if (m_ReferenceDataNode.GetPointer() != m_SegmentationInputNode.GetPointer()) { PadImageFilter::Pointer padFilter = PadImageFilter::New(); padFilter->SetInput(0, resultSegmentation); padFilter->SetInput(1, dynamic_cast(m_ReferenceDataNode->GetData())); padFilter->SetBinaryFilter(true); padFilter->SetUpperThreshold(1); padFilter->SetLowerThreshold(1); padFilter->Update(); resultSegmentationNode->SetData(padFilter->GetOutput()); } if (m_OverwriteExistingSegmentation) { //if we overwrite the segmentation (and not just store it as a new result //in the data storage) we update also the tool manager state. this->GetToolManager()->SetWorkingData(resultSegmentationNode); this->GetToolManager()->GetWorkingData(0)->Modified(); } this->EnsureTargetSegmentationNodeInDataStorage(); } } } void mitk::AutoSegmentationWithPreviewTool::OnRoiDataChanged() { DataNode::ConstPointer node = this->GetToolManager()->GetRoiData(0); if (node.IsNotNull()) { MaskAndCutRoiImageFilter::Pointer roiFilter = MaskAndCutRoiImageFilter::New(); Image::Pointer image = dynamic_cast(m_SegmentationInputNode->GetData()); if (image.IsNull()) return; roiFilter->SetInput(image); roiFilter->SetRegionOfInterest(node->GetData()); roiFilter->Update(); DataNode::Pointer tmpNode = DataNode::New(); tmpNode->SetData(roiFilter->GetOutput()); m_SegmentationInputNode = tmpNode; } else m_SegmentationInputNode = m_ReferenceDataNode; this->ResetPreviewNode(); this->InitiateToolByInput(); this->UpdatePreview(); } void mitk::AutoSegmentationWithPreviewTool::OnTimePointChanged() { if (m_IsTimePointChangeAware && m_PreviewSegmentationNode.IsNotNull() && m_SegmentationInputNode.IsNotNull()) { const auto timePoint = RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint(); const bool isStaticSegOnDynamicImage = m_PreviewSegmentationNode->GetData()->GetTimeSteps() == 1 && m_SegmentationInputNode->GetData()->GetTimeSteps() > 1; if (timePoint!=m_LastTimePointOfUpdate && (isStaticSegOnDynamicImage || m_LazyDynamicPreviews)) { //we only need to update either because we are lazzy //or because we have a static segmentation with a dynamic image this->UpdatePreview(); } } } bool mitk::AutoSegmentationWithPreviewTool::EnsureUpToDateUserDefinedActiveLabel() { bool labelChanged = true; const auto workingImage = dynamic_cast(this->GetToolManager()->GetWorkingData(0)->GetData()); if (const auto& labelSetImage = dynamic_cast(workingImage)) { // this is a fix for T28131 / T28986, which should be refactored if T28524 is being worked on auto newLabel = labelSetImage->GetActiveLabel(labelSetImage->GetActiveLayer())->GetValue(); labelChanged = newLabel != m_UserDefinedActiveLabel; m_UserDefinedActiveLabel = newLabel; } else { m_UserDefinedActiveLabel = 1; labelChanged = false; } return labelChanged; } void mitk::AutoSegmentationWithPreviewTool::UpdatePreview(bool ignoreLazyPreviewSetting) { const auto inputImage = this->GetSegmentationInput(); auto previewImage = this->GetPreviewSegmentation(); int progress_steps = 200; const auto workingImage = dynamic_cast(this->GetToolManager()->GetWorkingData(0)->GetData()); this->EnsureUpToDateUserDefinedActiveLabel(); this->CurrentlyBusy.Send(true); m_IsUpdating = true; this->UpdatePrepare(); const auto timePoint = RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint(); try { if (nullptr != inputImage && nullptr != previewImage) { m_ProgressCommand->AddStepsToDo(progress_steps); if (previewImage->GetTimeSteps() > 1 && (ignoreLazyPreviewSetting || !m_LazyDynamicPreviews)) { for (unsigned int timeStep = 0; timeStep < previewImage->GetTimeSteps(); ++timeStep) { Image::ConstPointer feedBackImage; Image::ConstPointer currentSegImage; auto previewTimePoint = previewImage->GetTimeGeometry()->TimeStepToTimePoint(timeStep); auto inputTimeStep = inputImage->GetTimeGeometry()->TimePointToTimeStep(previewTimePoint); if (nullptr != this->GetWorkingPlaneGeometry()) { //only extract a specific slice defined by the working plane as feedback image. feedBackImage = SegTool2D::GetAffectedImageSliceAs2DImage(this->GetWorkingPlaneGeometry(), inputImage, inputTimeStep); currentSegImage = SegTool2D::GetAffectedImageSliceAs2DImageByTimePoint(this->GetWorkingPlaneGeometry(), workingImage, previewTimePoint); } else { //work on the whole feedback image feedBackImage = this->GetImageByTimeStep(inputImage, inputTimeStep); currentSegImage = this->GetImageByTimePoint(workingImage, previewTimePoint); } this->DoUpdatePreview(feedBackImage, currentSegImage, previewImage, timeStep); } } else { Image::ConstPointer feedBackImage; Image::ConstPointer currentSegImage; if (nullptr != this->GetWorkingPlaneGeometry()) { feedBackImage = SegTool2D::GetAffectedImageSliceAs2DImageByTimePoint(this->GetWorkingPlaneGeometry(), inputImage, timePoint); currentSegImage = SegTool2D::GetAffectedImageSliceAs2DImageByTimePoint(this->GetWorkingPlaneGeometry(), workingImage, timePoint); } else { feedBackImage = this->GetImageByTimePoint(inputImage, timePoint); currentSegImage = this->GetImageByTimePoint(workingImage, timePoint); } auto timeStep = previewImage->GetTimeGeometry()->TimePointToTimeStep(timePoint); this->DoUpdatePreview(feedBackImage, currentSegImage, previewImage, timeStep); } RenderingManager::GetInstance()->RequestUpdateAll(); } } catch (itk::ExceptionObject & excep) { MITK_ERROR << "Exception caught: " << excep.GetDescription(); m_ProgressCommand->SetProgress(progress_steps); std::string msg = excep.GetDescription(); ErrorMessage.Send(msg); } catch (...) { m_ProgressCommand->SetProgress(progress_steps); m_IsUpdating = false; CurrentlyBusy.Send(false); throw; } this->UpdateCleanUp(); m_LastTimePointOfUpdate = timePoint; m_ProgressCommand->SetProgress(progress_steps); m_IsUpdating = false; CurrentlyBusy.Send(false); } bool mitk::AutoSegmentationWithPreviewTool::IsUpdating() const { return m_IsUpdating; } void mitk::AutoSegmentationWithPreviewTool::UpdatePrepare() { // default implementation does nothing //reimplement in derived classes for special behavior } void mitk::AutoSegmentationWithPreviewTool::UpdateCleanUp() { // default implementation does nothing //reimplement in derived classes for special behavior } mitk::TimePointType mitk::AutoSegmentationWithPreviewTool::GetLastTimePointOfUpdate() const { return m_LastTimePointOfUpdate; } diff --git a/Modules/Segmentation/Interactions/mitkAutoSegmentationWithPreviewTool.h b/Modules/Segmentation/Interactions/mitkAutoSegmentationWithPreviewTool.h index 26db3a4def..09ec1d6634 100644 --- a/Modules/Segmentation/Interactions/mitkAutoSegmentationWithPreviewTool.h +++ b/Modules/Segmentation/Interactions/mitkAutoSegmentationWithPreviewTool.h @@ -1,210 +1,225 @@ /*============================================================================ 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 mitkAutoSegmentationWithPreviewTool_h_Included #define mitkAutoSegmentationWithPreviewTool_h_Included #include "mitkAutoSegmentationTool.h" #include "mitkCommon.h" #include "mitkDataNode.h" #include "mitkToolCommand.h" #include namespace mitk { /** \brief Base class for any auto segmentation tool that provides a preview of the new segmentation. This tool class implements a lot basic logic to handle auto segmentation tools with preview, Time point and ROI support. Derived classes will ask to update the segmentation preview if needed (e.g. because the ROI or the current time point has changed) or because derived tools indicated the need to update themselves. This class also takes care to properly transfer a confirmed preview into the segementation result. \ingroup ToolManagerEtAl \sa mitk::Tool \sa QmitkInteractiveSegmentation */ class MITKSEGMENTATION_EXPORT AutoSegmentationWithPreviewTool : public AutoSegmentationTool { public: mitkClassMacro(AutoSegmentationWithPreviewTool, AutoSegmentationTool); void Activated() override; void Deactivated() override; void ConfirmSegmentation(); itkSetMacro(CreateAllTimeSteps, bool); itkGetMacro(CreateAllTimeSteps, bool); itkBooleanMacro(CreateAllTimeSteps); itkSetMacro(KeepActiveAfterAccept, bool); itkGetMacro(KeepActiveAfterAccept, bool); itkBooleanMacro(KeepActiveAfterAccept); itkSetMacro(IsTimePointChangeAware, bool); itkGetMacro(IsTimePointChangeAware, bool); itkBooleanMacro(IsTimePointChangeAware); itkSetMacro(ResetsToEmptyPreview, bool); itkGetMacro(ResetsToEmptyPreview, bool); itkBooleanMacro(ResetsToEmptyPreview); + /*itk macro was not used on purpose, to aviod the change of mtime.*/ + void SetMergeStyle(MultiLabelSegmentation::MergeStyle mergeStyle); + itkGetMacro(MergeStyle, MultiLabelSegmentation::MergeStyle); + + /*itk macro was not used on purpose, to aviod the change of mtime.*/ + void SetOverwriteStyle(MultiLabelSegmentation::OverwriteStyle overwriteStyle); + itkGetMacro(OverwriteStyle, MultiLabelSegmentation::OverwriteStyle); + bool CanHandle(const BaseData* referenceData, const BaseData* workingData) const override; /** Triggers the actualization of the preview * @param ignoreLazyPreviewSetting If set true UpdatePreview will always * generate the preview for all time steps. If set to false, UpdatePreview * will regard the setting specified by the constructor. * To define the update generation for time steps implement DoUpdatePreview. * To alter what should be done directly before or after the update of the preview, * reimplement UpdatePrepare() or UpdateCleanUp().*/ void UpdatePreview(bool ignoreLazyPreviewSetting = false); /** Indicate if currently UpdatePreview is triggered (true) or not (false).*/ bool IsUpdating() const; protected: ToolCommand::Pointer m_ProgressCommand; /** Member is always called if GetSegmentationInput() has changed * (e.g. because a new ROI was defined, or on activation) to give derived * classes the posibility to initiate their state accordingly. * Reimplement this function to implement special behavior. */ virtual void InitiateToolByInput(); /** This member function offers derived classes the possibility to alter what should happen directly before the update of the preview is performed. It is called by UpdatePreview. Default implementation does nothing.*/ virtual void UpdatePrepare(); /** This member function offers derived classes the possibility to alter what should happen directly after the update of the preview is performed. It is called by UpdatePreview. Default implementation does nothing.*/ virtual void UpdateCleanUp(); /** This function does the real work. Here the preview for a given * input image should be computed and stored in the also passed * preview image at the passed time step. * It also provides the current/old segmentation at the time point, * which can be used, if the preview depends on the the segmenation so far. */ virtual void DoUpdatePreview(const Image* inputAtTimeStep, const Image* oldSegAtTimeStep, Image* previewImage, TimeStepType timeStep) = 0; AutoSegmentationWithPreviewTool(bool lazyDynamicPreviews = false); // purposely hidden AutoSegmentationWithPreviewTool(bool lazyDynamicPreviews, const char* interactorType, const us::Module* interactorModule = nullptr); // purposely hidden ~AutoSegmentationWithPreviewTool() override; /** Returns the image that contains the preview of the current segmentation. * Returns null if the node is not set or does not contain an image.*/ Image* GetPreviewSegmentation(); DataNode* GetPreviewSegmentationNode(); /** Returns the input that should be used for any segmentation/preview or tool update. * It is either the data of ReferenceDataNode itself or a part of it defined by a ROI mask * provided by the tool manager. Derived classes should regard this as the relevant * input data for any processing. * Returns null if the node is not set or does not contain an image.*/ const Image* GetSegmentationInput() const; /** Returns the image that is provided by the ReferenceDataNode. * Returns null if the node is not set or does not contain an image.*/ const Image* GetReferenceData() const; /** Resets the preview node so it is empty and ready to be filled by the tool @remark Calling this function will generate a new preview image, and the old might be invalidated. Therefore this function should not be used within the scope of UpdatePreview (m_IsUpdating == true).*/ void ResetPreviewNode(); /** Resets the complete content of the preview image. The instance of the preview image and its settings * stay the same.*/ void ResetPreviewContent(); /** Resets only the image content of the specified timeStep of the preview image. If the preview image or the specified time step does not exist, nothing happens.*/ void ResetPreviewContentAtTimeStep(unsigned int timeStep); TimePointType GetLastTimePointOfUpdate() const; itkGetConstMacro(UserDefinedActiveLabel, Label::PixelType); itkSetObjectMacro(WorkingPlaneGeometry, PlaneGeometry); itkGetConstObjectMacro(WorkingPlaneGeometry, PlaneGeometry); private: void TransferImageAtTimeStep(const Image* sourceImage, Image* destinationImage, const TimeStepType timeStep); void CreateResultSegmentationFromPreview(); void OnRoiDataChanged(); void OnTimePointChanged(); /**Internal helper that ensures that the stored active label is up to date. This is a fix for T28131 / T28986. It should be refactored if T28524 is being worked on. On the long run, the active label will be communicated/set by the user/toolmanager as a state of the tool and the tool should react accordingly (like it does for other external state changes). @return indicates if the label has changed (true) or not. */ bool EnsureUpToDateUserDefinedActiveLabel(); /** Node that containes the preview data generated and managed by this class or derived ones.*/ DataNode::Pointer m_PreviewSegmentationNode; /** The reference data recieved from ToolManager::GetReferenceData when tool was activated.*/ DataNode::Pointer m_ReferenceDataNode; /** Node that containes the data that should be used as input for any auto segmentation. It might * be the same like m_ReferenceDataNode (if no ROI is set) or a sub region (if ROI is set).*/ DataNode::Pointer m_SegmentationInputNode; /** Indicates if Accepting the threshold should transfer/create the segmentations of all time steps (true) or only of the currently selected timepoint (false).*/ bool m_CreateAllTimeSteps = false; /** Indicates if the tool should kept active after accepting the segmentation or not.*/ bool m_KeepActiveAfterAccept = false; /** Relevant if the working data / preview image has multiple time steps (dynamic segmentations). * This flag has to be set by derived classes accordingly to there way to generate dynamic previews. * If LazyDynamicPreview is true, the tool generates only the preview for the current time step. * Therefore it always has to update the preview if current time point has changed and it has to (re)compute * all timeframes if ConfirmSegmentation() is called.*/ bool m_LazyDynamicPreviews = false; bool m_IsTimePointChangeAware = true; /** Controls if ResetPreviewNode generates an empty content (true) or clones the current segmentation (false).*/ bool m_ResetsToEmptyPreview = false; TimePointType m_LastTimePointOfUpdate = 0.; bool m_IsUpdating = false; Label::PixelType m_UserDefinedActiveLabel = 1; /** This variable indicates if for the tool a working plane geometry is defined. * If a working plane is defined the tool will only work an the slice of the input * and the segmentation. Thus only the relevant input slice will be passed to * DoUpdatePreview(...) and only the relevant slice of the preview will be transfered when * ConfirmSegmentation() is called.*/ PlaneGeometry::Pointer m_WorkingPlaneGeometry; + + /** This variable controles how the label pixel content of the preview should be transfered into the + segmentation- For more details of the behavior see documentation of MultiLabelSegmentation::MergeStyle. */ + MultiLabelSegmentation::MergeStyle m_MergeStyle = MultiLabelSegmentation::MergeStyle::Replace; + /** This variable controles how the label pixel content of the preview should be transfered into the + segmentation- For more details of the behavior see documentation of MultiLabelSegmentation::OverwriteStyle. */ + MultiLabelSegmentation::OverwriteStyle m_OverwriteStyle = MultiLabelSegmentation::OverwriteStyle::RegardLocks; }; } // namespace #endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkAutoSegmentationToolGUIBase.cpp b/Modules/SegmentationUI/Qmitk/QmitkAutoSegmentationToolGUIBase.cpp index 5ca33cd4e2..f4a276d6ff 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkAutoSegmentationToolGUIBase.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkAutoSegmentationToolGUIBase.cpp @@ -1,157 +1,210 @@ /*============================================================================ 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 "QmitkAutoSegmentationToolGUIBase.h" #include #include #include #include #include bool DefaultEnableConfirmSegBtnFunction(bool enabled) { return enabled; } QmitkAutoSegmentationToolGUIBase::QmitkAutoSegmentationToolGUIBase(bool mode2D) : QmitkToolGUI(), m_EnableConfirmSegBtnFnc(DefaultEnableConfirmSegBtnFunction), m_Mode2D(mode2D) { connect(this, SIGNAL(NewToolAssociated(mitk::Tool *)), this, SLOT(OnNewToolAssociated(mitk::Tool *))); } QmitkAutoSegmentationToolGUIBase::~QmitkAutoSegmentationToolGUIBase() { if (m_Tool.IsNotNull()) { m_Tool->CurrentlyBusy -= mitk::MessageDelegate1(this, &QmitkAutoSegmentationToolGUIBase::BusyStateChanged); } } void QmitkAutoSegmentationToolGUIBase::OnNewToolAssociated(mitk::Tool *tool) { if (m_Tool.IsNotNull()) { this->DisconnectOldTool(m_Tool); } m_Tool = dynamic_cast(tool); if (nullptr == m_MainLayout) { // create the visible widgets m_MainLayout = new QVBoxLayout(this); m_ConfirmSegBtn = new QPushButton("Confirm Segmentation", this); connect(m_ConfirmSegBtn, SIGNAL(clicked()), this, SLOT(OnAcceptPreview())); + m_CheckIgnoreLocks = new QCheckBox("Ignore label locks", this); + m_CheckIgnoreLocks->setChecked(m_Tool->GetOverwriteStyle() == mitk::MultiLabelSegmentation::OverwriteStyle::IgnoreLocks); + m_CheckIgnoreLocks->setToolTip("If checked, the lock state of labels will be ignored when the preview segmentation is confermed. Thus also locked label pixels can be changed by the operation."); + + m_CheckMerge = new QCheckBox("Merge with existing content", this); + m_CheckMerge->setChecked(m_Tool->GetMergeStyle()==mitk::MultiLabelSegmentation::MergeStyle::Merge); + m_CheckMerge->setToolTip("If checked, the preview segmantation will be merged with the existing segmantation into a union. If unchecked, the preview content will replace the old segmantation"); + m_CheckProcessAll = new QCheckBox("Process all time steps", this); m_CheckProcessAll->setChecked(false); m_CheckProcessAll->setToolTip("Process all time steps of the dynamic segmentation and not just the currently visible time step."); m_CheckProcessAll->setVisible(!m_Mode2D); //remark: keept m_CheckProcessAll deactivated in 2D because in this refactoring //it should be kept to the status quo and it was not clear how interpolation //would behave. As soon as it is sorted out we can remove that "feature switch" //or the comment. m_CheckCreateNew = new QCheckBox("Create as new segmentation", this); m_CheckCreateNew->setChecked(false); m_CheckCreateNew->setToolTip("Add the confirmed segmentation as a new segmentation instead of overwriting the currently selected."); m_CheckCreateNew->setVisible(!m_Mode2D); //remark: keept m_CheckCreateNew deactivated in 2D because in this refactoring //it should be kept to the status quo and it was not clear how interpolation //would behave. As soon as it is sorted out we can remove that "feature switch" //or the comment. this->InitializeUI(m_MainLayout); m_MainLayout->addWidget(m_ConfirmSegBtn); + m_MainLayout->addWidget(m_CheckIgnoreLocks); + m_MainLayout->addWidget(m_CheckMerge); m_MainLayout->addWidget(m_CheckProcessAll); m_MainLayout->addWidget(m_CheckCreateNew); } if (m_Tool.IsNotNull()) { this->ConnectNewTool(m_Tool); } } void QmitkAutoSegmentationToolGUIBase::OnAcceptPreview() { if (m_Tool.IsNotNull()) { + if (m_CheckIgnoreLocks->isChecked()) + { + m_Tool->SetOverwriteStyle(mitk::MultiLabelSegmentation::OverwriteStyle::IgnoreLocks); + } + else + { + m_Tool->SetOverwriteStyle(mitk::MultiLabelSegmentation::OverwriteStyle::RegardLocks); + } + + if (m_CheckMerge->isChecked()) + { + m_Tool->SetMergeStyle(mitk::MultiLabelSegmentation::MergeStyle::Merge); + } + else + { + m_Tool->SetMergeStyle(mitk::MultiLabelSegmentation::MergeStyle::Replace); + } + if (m_CheckCreateNew->isChecked()) { m_Tool->SetOverwriteExistingSegmentation(false); } else { m_Tool->SetOverwriteExistingSegmentation(true); } m_Tool->SetCreateAllTimeSteps(m_CheckProcessAll->isChecked()); m_ConfirmSegBtn->setEnabled(false); m_Tool->ConfirmSegmentation(); } } void QmitkAutoSegmentationToolGUIBase::DisconnectOldTool(mitk::AutoSegmentationWithPreviewTool* oldTool) { oldTool->CurrentlyBusy -= mitk::MessageDelegate1(this, &QmitkAutoSegmentationToolGUIBase::BusyStateChanged); } void QmitkAutoSegmentationToolGUIBase::ConnectNewTool(mitk::AutoSegmentationWithPreviewTool* newTool) { newTool->CurrentlyBusy += mitk::MessageDelegate1(this, &QmitkAutoSegmentationToolGUIBase::BusyStateChanged); newTool->SetOverwriteExistingSegmentation(true); m_CheckProcessAll->setVisible(newTool->GetTargetSegmentationNode()->GetData()->GetTimeSteps() > 1); this->EnableWidgets(true); } void QmitkAutoSegmentationToolGUIBase::InitializeUI(QBoxLayout* /*mainLayout*/) { //default implementation does nothing } void QmitkAutoSegmentationToolGUIBase::BusyStateChanged(bool isBusy) { if (isBusy) { QApplication::setOverrideCursor(QCursor(Qt::BusyCursor)); } else { QApplication::restoreOverrideCursor(); } this->EnableWidgets(!isBusy); } void QmitkAutoSegmentationToolGUIBase::EnableWidgets(bool enabled) { if (nullptr != m_MainLayout) { if (nullptr != m_ConfirmSegBtn) { m_ConfirmSegBtn->setEnabled(m_EnableConfirmSegBtnFnc(enabled)); } + if (nullptr != m_CheckIgnoreLocks) + { + m_CheckIgnoreLocks->setEnabled(enabled); + } + if (nullptr != m_CheckMerge) + { + m_CheckMerge->setEnabled(enabled); + } if (nullptr != m_CheckProcessAll) { m_CheckProcessAll->setEnabled(enabled); } if (nullptr != m_CheckCreateNew) { m_CheckCreateNew->setEnabled(enabled); } } } + +void QmitkAutoSegmentationToolGUIBase::SetMergeStyle(mitk::MultiLabelSegmentation::MergeStyle mergeStyle) +{ + if (nullptr != m_CheckMerge) + { + m_CheckMerge->setChecked(mergeStyle == mitk::MultiLabelSegmentation::MergeStyle::Merge); + } +}; + +void QmitkAutoSegmentationToolGUIBase::SetOverwriteStyle(mitk::MultiLabelSegmentation::OverwriteStyle overwriteStyle) +{ + if (nullptr != m_CheckIgnoreLocks) + { + m_CheckIgnoreLocks->setChecked(overwriteStyle == mitk::MultiLabelSegmentation::OverwriteStyle::IgnoreLocks); + } +}; + diff --git a/Modules/SegmentationUI/Qmitk/QmitkAutoSegmentationToolGUIBase.h b/Modules/SegmentationUI/Qmitk/QmitkAutoSegmentationToolGUIBase.h index 2c6eddf881..54701e27ca 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkAutoSegmentationToolGUIBase.h +++ b/Modules/SegmentationUI/Qmitk/QmitkAutoSegmentationToolGUIBase.h @@ -1,93 +1,96 @@ /*============================================================================ 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 QmitkAutoSegmentationToolGUIBase_h_Included #define QmitkAutoSegmentationToolGUIBase_h_Included #include "QmitkToolGUI.h" #include "mitkAutoSegmentationWithPreviewTool.h" #include class QCheckBox; class QPushButton; class QBoxLayout; /** \ingroup org_mitk_gui_qt_interactivesegmentation_internal \brief GUI base clase for tools derived from mitk::AutoSegmentationTool. */ class MITKSEGMENTATIONUI_EXPORT QmitkAutoSegmentationToolGUIBase : public QmitkToolGUI { Q_OBJECT public: mitkClassMacro(QmitkAutoSegmentationToolGUIBase, QmitkToolGUI); itkCloneMacro(Self); itkGetConstMacro(Mode2D, bool); protected slots: void OnNewToolAssociated(mitk::Tool *); void OnAcceptPreview(); protected: QmitkAutoSegmentationToolGUIBase(bool mode2D); ~QmitkAutoSegmentationToolGUIBase() override; virtual void DisconnectOldTool(mitk::AutoSegmentationWithPreviewTool* oldTool); virtual void ConnectNewTool(mitk::AutoSegmentationWithPreviewTool* newTool); /**This method is called by OnNewToolAssociated if the UI is initialized the first time to allow derived classes to introduce own UI code. Overwrite to change. The implementation should ensure that alle widgets needed for the tool UI are properly allocated. If one needs to eecute time (e.g. to connect events between the tool and the UI) each time the tool changes, override the functions ConnectNewTool() and DisconnectOldTool().*/ virtual void InitializeUI(QBoxLayout* mainLayout); void BusyStateChanged(bool isBusy) override; using EnableConfirmSegBtnFunctionType = std::function; EnableConfirmSegBtnFunctionType m_EnableConfirmSegBtnFnc; /**This method is used to control/set the enabled state of the tool UI widgets. It is e.g. used if the busy state is changed (see BusyStateChanged). Override the default implmentation, e.g. if a tool adds his own UI elements (normally by overriding InitializeUI()) and wants to control how the widgets are enabled/disabled.*/ virtual void EnableWidgets(bool enabled); template TTool* GetConnectedToolAs() { return dynamic_cast(m_Tool.GetPointer()); }; - + void SetMergeStyle(mitk::MultiLabelSegmentation::MergeStyle mergeStyle); + void SetOverwriteStyle(mitk::MultiLabelSegmentation::OverwriteStyle overwriteStyle); private: + QCheckBox* m_CheckIgnoreLocks = nullptr; + QCheckBox* m_CheckMerge = nullptr; QCheckBox* m_CheckProcessAll = nullptr; QCheckBox* m_CheckCreateNew = nullptr; QPushButton* m_ConfirmSegBtn = nullptr; QBoxLayout* m_MainLayout = nullptr; /**Indicates if the tool is in 2D or 3D mode.*/ bool m_Mode2D; mitk::AutoSegmentationWithPreviewTool::Pointer m_Tool; }; #endif