diff --git a/Modules/Segmentation/Interactions/mitkSegWithPreviewTool.cpp b/Modules/Segmentation/Interactions/mitkSegWithPreviewTool.cpp index 38991559a2..e20ac8569b 100644 --- a/Modules/Segmentation/Interactions/mitkSegWithPreviewTool.cpp +++ b/Modules/Segmentation/Interactions/mitkSegWithPreviewTool.cpp @@ -1,849 +1,850 @@ /*============================================================================ 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 "mitkSegWithPreviewTool.h" #include "mitkToolManager.h" #include "mitkColorProperty.h" #include "mitkProperties.h" #include "mitkDataStorage.h" #include "mitkRenderingManager.h" #include #include "mitkImageAccessByItk.h" #include "mitkImageCast.h" #include "mitkLabelSetImage.h" #include "mitkMaskAndCutRoiImageFilter.h" #include "mitkPadImageFilter.h" #include "mitkNodePredicateGeometry.h" #include "mitkSegTool2D.h" mitk::SegWithPreviewTool::SegWithPreviewTool(bool lazyDynamicPreviews): Tool("dummy"), m_LazyDynamicPreviews(lazyDynamicPreviews) { m_ProgressCommand = ToolCommand::New(); } mitk::SegWithPreviewTool::SegWithPreviewTool(bool lazyDynamicPreviews, const char* interactorType, const us::Module* interactorModule) : Tool(interactorType, interactorModule), m_LazyDynamicPreviews(lazyDynamicPreviews) { m_ProgressCommand = ToolCommand::New(); } mitk::SegWithPreviewTool::~SegWithPreviewTool() { } void mitk::SegWithPreviewTool::SetMergeStyle(MultiLabelSegmentation::MergeStyle mergeStyle) { m_MergeStyle = mergeStyle; this->Modified(); } void mitk::SegWithPreviewTool::SetOverwriteStyle(MultiLabelSegmentation::OverwriteStyle overwriteStyle) { m_OverwriteStyle = overwriteStyle; this->Modified(); } void mitk::SegWithPreviewTool::SetLabelTransferScope(LabelTransferScope labelTransferScope) { m_LabelTransferScope = labelTransferScope; this->Modified(); } void mitk::SegWithPreviewTool::SetLabelTransferMode(LabelTransferMode labelTransferMode) { m_LabelTransferMode = labelTransferMode; this->Modified(); } void mitk::SegWithPreviewTool::SetSelectedLabels(const SelectedLabelVectorType& labelsToTransfer) { m_SelectedLabels = labelsToTransfer; this->Modified(); } bool mitk::SegWithPreviewTool::CanHandle(const BaseData* referenceData, const BaseData* workingData) const { if (!Superclass::CanHandle(referenceData, workingData)) return false; if (workingData == nullptr) return false; auto* referenceImage = dynamic_cast(referenceData); if (referenceImage == nullptr) return false; auto* labelSet = dynamic_cast(workingData); if (labelSet != nullptr) return true; auto* workingImage = dynamic_cast(workingData); if (workingImage == nullptr) return false; // If the working image is a normal image and not a label set image // it must have the same pixel type as a label set. return MakeScalarPixelType< DefaultSegmentationDataType >() == workingImage->GetPixelType(); } void mitk::SegWithPreviewTool::Activated() { Superclass::Activated(); this->GetToolManager()->RoiDataChanged += MessageDelegate(this, &SegWithPreviewTool::OnRoiDataChanged); this->GetToolManager()->SelectedTimePointChanged += MessageDelegate(this, &SegWithPreviewTool::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); } + m_IsPreviewGenerated = false; } void mitk::SegWithPreviewTool::Deactivated() { this->GetToolManager()->RoiDataChanged -= MessageDelegate(this, &SegWithPreviewTool::OnRoiDataChanged); this->GetToolManager()->SelectedTimePointChanged -= MessageDelegate(this, &SegWithPreviewTool::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::SegWithPreviewTool::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); } this->ConfirmCleanUp(); } void mitk::SegWithPreviewTool::InitiateToolByInput() { //default implementation does nothing. //implement in derived classes to change behavior } mitk::LabelSetImage* mitk::SegWithPreviewTool::GetPreviewSegmentation() { if (m_PreviewSegmentationNode.IsNull()) { return nullptr; } return dynamic_cast(m_PreviewSegmentationNode->GetData()); } const mitk::LabelSetImage* mitk::SegWithPreviewTool::GetPreviewSegmentation() const { if (m_PreviewSegmentationNode.IsNull()) { return nullptr; } return dynamic_cast(m_PreviewSegmentationNode->GetData()); } mitk::DataNode* mitk::SegWithPreviewTool::GetPreviewSegmentationNode() { return m_PreviewSegmentationNode; } const mitk::Image* mitk::SegWithPreviewTool::GetSegmentationInput() const { if (m_SegmentationInputNode.IsNull()) { return nullptr; } return dynamic_cast(m_SegmentationInputNode->GetData()); } const mitk::Image* mitk::SegWithPreviewTool::GetReferenceData() const { if (m_ReferenceDataNode.IsNull()) { return nullptr; } return dynamic_cast(m_ReferenceDataNode->GetData()); } template void ClearBufferProcessing(ImageType* itkImage) { itkImage->FillBuffer(0); } void mitk::SegWithPreviewTool::ResetPreviewContentAtTimeStep(unsigned int timeStep) { auto previewImage = GetImageByTimeStep(this->GetPreviewSegmentation(), timeStep); if (nullptr != previewImage) { AccessByItk(previewImage, ClearBufferProcessing); } } void mitk::SegWithPreviewTool::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::SegWithPreviewTool::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); if (newPreviewImage->GetNumberOfLayers() == 0) { newPreviewImage->AddLayer(); newPreviewImage->SetActiveLayer(0); } auto* activeLabel = newPreviewImage->GetActiveLabel(); if (nullptr == activeLabel) { activeLabel = newPreviewImage->AddLabel("toolresult", previewColor, newPreviewImage->GetActiveLayer()); newPreviewImage->UpdateLookupTable(activeLabel->GetValue()); } else if (m_UseSpecialPreviewColor) { // Let's paint the feedback node green... activeLabel->SetColor(previewColor); newPreviewImage->UpdateLookupTable(activeLabel->GetValue()); } activeLabel->SetVisible(true); } 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); } } } mitk::SegWithPreviewTool::LabelMappingType mitk::SegWithPreviewTool::GetLabelMapping() const { LabelSetImage::LabelValueType offset = 0; if (LabelTransferMode::AddLabel == m_LabelTransferMode && LabelTransferScope::ActiveLabel!=m_LabelTransferScope) { //If we are not just working on active label and transfer mode is add, we need to compute an offset for adding the //preview labels instat of just mapping them to existing segmentation labels. const auto segmentation = this->GetTargetSegmentation(); if (nullptr == segmentation) mitkThrow() << "Invalid state of SegWithPreviewTool. Cannot GetLabelMapping if no target segmentation is set."; auto labels = segmentation->GetLabels(); auto maxLabelIter = std::max_element(std::begin(labels), std::end(labels), [](const Label::Pointer& a, const Label::Pointer& b) { return a->GetValue() < b->GetValue(); }); if (maxLabelIter != labels.end()) { offset = maxLabelIter->GetPointer()->GetValue(); } } LabelMappingType labelMapping = {}; switch (this->m_LabelTransferScope) { case LabelTransferScope::SelectedLabels: { for (auto label : this->m_SelectedLabels) { labelMapping.push_back({label, label + offset}); } } break; case LabelTransferScope::AllLabels: { const auto labelValues = this->GetPreviewSegmentation()->GetLabelValuesByGroup(this->GetPreviewSegmentation()->GetActiveLayer()); for (auto labelValue : labelValues) { labelMapping.push_back({ labelValue, labelValue + offset}); } } break; default: { if (m_SelectedLabels.empty()) mitkThrow() << "Failed to generate label transfer mapping. Tool is in an invalid state, as " "LabelTransferScope==ActiveLabel but no label is indicated as selected label. Check " "implementation of derived tool class."; if (m_SelectedLabels.size() > 1) mitkThrow() << "Failed to generate label transfer mapping. Tool is in an invalid state, as " "LabelTransferScope==ActiveLabel but more then one selected label is indicated." "Should be only one. Check implementation of derived tool class."; labelMapping.push_back({m_SelectedLabels.front(), this->GetUserDefinedActiveLabel()}); } break; } return labelMapping; } void mitk::SegWithPreviewTool::TransferImageAtTimeStep(const Image* sourceImage, Image* destinationImage, const TimeStepType timeStep, const LabelMappingType& labelMapping) { 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); auto resultSlice = SegTool2D::GetAffectedImageSliceAs2DImage(this->GetWorkingPlaneGeometry(), destinationImage, timeStep)->Clone(); auto destLSImage = dynamic_cast(destinationImage); //We need to transfer explictly to a copy of the current working image to ensure that labelMapping is done and things //like merge style, overwrite style and locks are regarded. TransferLabelContentAtTimeStep(sourceSlice, resultSlice, destLSImage->GetConstLabelsByValue(destLSImage->GetLabelValuesByGroup(destLSImage->GetActiveLayer())), timeStep, 0, 0, destLSImage->GetUnlabeledLabelLock(), labelMapping, m_MergeStyle, m_OverwriteStyle); //We use WriteBackSegmentationResult to ensure undo/redo is supported also by derived tools of this class. SegTool2D::WriteBackSegmentationResult(this->GetTargetSegmentationNode(), m_WorkingPlaneGeometry, resultSlice, timeStep); } else { //take care of the full segmentation volume auto sourceLSImage = dynamic_cast(sourceImage); auto destLSImage = dynamic_cast(destinationImage); TransferLabelContentAtTimeStep(sourceLSImage, destLSImage, timeStep, labelMapping, m_MergeStyle, m_OverwriteStyle); } } catch (mitk::Exception& e) { Tool::ErrorMessage(e.GetDescription()); mitkReThrow(e); } } void mitk::SegWithPreviewTool::CreateResultSegmentationFromPreview() { const auto segInput = this->GetSegmentationInput(); auto previewImage = this->GetPreviewSegmentation(); if (nullptr != segInput && nullptr != previewImage) { DataNode::Pointer resultSegmentationNode = GetTargetSegmentationNode(); if (resultSegmentationNode.IsNotNull()) { const TimePointType 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 referenceImage (segmentation provided to the tool). Therefore they have // the same time geometry. if (previewImage->GetTimeSteps() != resultSegmentation->GetTimeSteps()) { mitkThrow() << "Cannot confirm/transfer segmentation. Internal tool state is invalid." << " Preview segmentation and segmentation result image have different time geometries."; } auto labelMapping = this->GetLabelMapping(); this->PreparePreviewToResultTransfer(labelMapping); if (m_CreateAllTimeSteps) { for (unsigned int timeStep = 0; timeStep < previewImage->GetTimeSteps(); ++timeStep) { this->TransferImageAtTimeStep(previewImage, resultSegmentation, timeStep, labelMapping); } } else { const auto timeStep = resultSegmentation->GetTimeGeometry()->TimePointToTimeStep(timePoint); this->TransferImageAtTimeStep(previewImage, resultSegmentation, timeStep, labelMapping); } // since we are maybe working on a smaller referenceImage, pad it to the size of the original referenceImage 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()); } this->EnsureTargetSegmentationNodeInDataStorage(); } } } void mitk::SegWithPreviewTool::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::SegWithPreviewTool::OnTimePointChanged() { if (m_IsTimePointChangeAware && m_PreviewSegmentationNode.IsNotNull() && m_SegmentationInputNode.IsNotNull()) { const TimePointType 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 referenceImage this->UpdatePreview(); } } } bool mitk::SegWithPreviewTool::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()->GetValue(); labelChanged = newLabel != m_UserDefinedActiveLabel; m_UserDefinedActiveLabel = newLabel; } else { m_UserDefinedActiveLabel = 1; labelChanged = false; } return labelChanged; } void mitk::SegWithPreviewTool::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; m_IsPreviewGenerated = false; this->UpdatePrepare(); const TimePointType 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 referenceImage. feedBackImage = SegTool2D::GetAffectedImageSliceAs2DImage(this->GetWorkingPlaneGeometry(), inputImage, inputTimeStep); currentSegImage = SegTool2D::GetAffectedImageSliceAs2DImageByTimePoint(this->GetWorkingPlaneGeometry(), workingImage, previewTimePoint); } else { //work on the whole feedback referenceImage 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(); if (!previewImage->GetAllLabelValues().empty()) { // check if labels exits for the preview m_IsPreviewGenerated = true; } } } 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::SegWithPreviewTool::IsUpdating() const { return m_IsUpdating; } void mitk::SegWithPreviewTool::UpdatePrepare() { // default implementation does nothing //reimplement in derived classes for special behavior } void mitk::SegWithPreviewTool::UpdateCleanUp() { // default implementation does nothing //reimplement in derived classes for special behavior } void mitk::SegWithPreviewTool::ConfirmCleanUp() { // default implementation does nothing // reimplement in derived classes for special behavior } void mitk::SegWithPreviewTool::TransferLabelInformation(const LabelMappingType& labelMapping, const mitk::LabelSetImage* source, mitk::LabelSetImage* target) { for (const auto& [sourceLabel, targetLabel] : labelMapping) { if (LabelSetImage::UNLABELED_VALUE != sourceLabel && LabelSetImage::UNLABELED_VALUE != targetLabel && !target->ExistLabel(targetLabel, target->GetActiveLayer())) { if (!source->ExistLabel(sourceLabel, source->GetActiveLayer())) { mitkThrow() << "Cannot prepare segmentation for preview transfer. Preview seems invalid as label is missing. Missing label: " << sourceLabel; } auto clonedLabel = source->GetLabel(sourceLabel)->Clone(); clonedLabel->SetValue(targetLabel); target->AddLabel(clonedLabel,target->GetActiveLayer(), false, false); } } } void mitk::SegWithPreviewTool::PreparePreviewToResultTransfer(const LabelMappingType& labelMapping) { DataNode::Pointer resultSegmentationNode = GetTargetSegmentationNode(); if (resultSegmentationNode.IsNotNull()) { auto resultSegmentation = dynamic_cast(resultSegmentationNode->GetData()); if (nullptr == resultSegmentation) { mitkThrow() << "Cannot prepare segmentation for preview transfer. Tool is in invalid state as segmentation is not existing or of right type"; } auto preview = this->GetPreviewSegmentation(); TransferLabelInformation(labelMapping, preview, resultSegmentation); } } mitk::TimePointType mitk::SegWithPreviewTool::GetLastTimePointOfUpdate() const { return m_LastTimePointOfUpdate; } mitk::LabelSetImage::LabelValueType mitk::SegWithPreviewTool::GetActiveLabelValueOfPreview() const { const auto previewImage = this->GetPreviewSegmentation(); const auto activeLabel = previewImage->GetActiveLabel(); if (nullptr == activeLabel) mitkThrow() << this->GetNameOfClass() <<" is in an invalid state, as " "preview has no active label indicated. Check " "implementation of the class."; return activeLabel->GetValue(); } const char* mitk::SegWithPreviewTool::GetGroup() const { return "autoSegmentation"; } mitk::Image::ConstPointer mitk::SegWithPreviewTool::GetImageByTimeStep(const mitk::Image* image, TimeStepType timestep) { return SelectImageByTimeStep(image, timestep); } mitk::Image::Pointer mitk::SegWithPreviewTool::GetImageByTimeStep(mitk::Image* image, TimeStepType timestep) { return SelectImageByTimeStep(image, timestep); } mitk::Image::ConstPointer mitk::SegWithPreviewTool::GetImageByTimePoint(const mitk::Image* image, TimePointType timePoint) { return SelectImageByTimePoint(image, timePoint); } void mitk::SegWithPreviewTool::EnsureTargetSegmentationNodeInDataStorage() const { auto targetNode = this->GetTargetSegmentationNode(); auto dataStorage = this->GetToolManager()->GetDataStorage(); if (!dataStorage->Exists(targetNode)) { dataStorage->Add(targetNode, this->GetToolManager()->GetReferenceData(0)); } } std::string mitk::SegWithPreviewTool::GetCurrentSegmentationName() { auto workingData = this->GetToolManager()->GetWorkingData(0); return nullptr != workingData ? workingData->GetName() : ""; } mitk::DataNode* mitk::SegWithPreviewTool::GetTargetSegmentationNode() const { return this->GetToolManager()->GetWorkingData(0); } mitk::LabelSetImage* mitk::SegWithPreviewTool::GetTargetSegmentation() const { auto node = this->GetTargetSegmentationNode(); if (nullptr == node) return nullptr; return dynamic_cast(node->GetData()); } void mitk::SegWithPreviewTool::TransferLabelSetImageContent(const LabelSetImage* source, LabelSetImage* target, TimeStepType timeStep) { mitk::ImageReadAccessor newMitkImgAcc(source); LabelMappingType labelMapping; const auto labelValues = source->GetLabelValuesByGroup(source->GetActiveLayer()); for (const auto& labelValue : labelValues) { labelMapping.push_back({ labelValue,labelValue }); } TransferLabelInformation(labelMapping, source, target); target->SetVolume(newMitkImgAcc.GetData(), timeStep); } bool mitk::SegWithPreviewTool::ConfirmBeforeDeactivation() { return m_IsPreviewGenerated && m_RequestDeactivationConfirmation; }