diff --git a/Modules/Multilabel/mitkLabelSetImage.cpp b/Modules/Multilabel/mitkLabelSetImage.cpp index ba98605702..e65768edba 100644 --- a/Modules/Multilabel/mitkLabelSetImage.cpp +++ b/Modules/Multilabel/mitkLabelSetImage.cpp @@ -1,1740 +1,1743 @@ /*============================================================================ 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 "mitkLabelSetImage.h" #include #include #include #include #include #include #include #include #include #include namespace mitk { template void ClearBufferProcessing(ImageType* itkImage) { itkImage->FillBuffer(0); } void ClearImageBuffer(mitk::Image* image) { if (image->GetDimension() == 4) { //remark: this extra branch was added, because LabelSetImage instances can be //dynamic (4D), but AccessByItk by support only supports 2D and 3D. //The option to change the CMake default dimensions for AccessByItk was //dropped (for details see discussion in T28756) AccessFixedDimensionByItk(image, ClearBufferProcessing, 4); } else { AccessByItk(image, ClearBufferProcessing); } } } const mitk::LabelSetImage::LabelValueType mitk::LabelSetImage::UNLABELED_VALUE = 0; mitk::LabelSetImage::LabelSetImage() : mitk::Image(), m_ActiveLabelValue(0), m_UnlabeledLabelLock(false), m_ActiveLayer(0), m_activeLayerInvalid(false) { m_LookupTable = mitk::LookupTable::New(); m_LookupTable->SetType(mitk::LookupTable::MULTILABEL); // Add some DICOM Tags as properties to segmentation image DICOMSegmentationPropertyHelper::DeriveDICOMSegmentationProperties(this); } mitk::LabelSetImage::LabelSetImage(const mitk::LabelSetImage &other) : Image(other), m_ActiveLabelValue(other.m_ActiveLabelValue), m_LookupTable(other.m_LookupTable->Clone()), m_UnlabeledLabelLock(other.m_UnlabeledLabelLock), m_ActiveLayer(other.GetActiveLayer()), m_activeLayerInvalid(false) { GroupIndexType i = 0; for (auto groupImage : other.m_LayerContainer) { this->AddLayer(groupImage->Clone(), other.GetConstLabelsByValue(other.GetLabelValuesByGroup(i))); i++; } m_Groups = other.m_Groups; // Add some DICOM Tags as properties to segmentation image DICOMSegmentationPropertyHelper::DeriveDICOMSegmentationProperties(this); } void mitk::LabelSetImage::Initialize(const mitk::Image *other) { mitk::PixelType pixelType(mitk::MakeScalarPixelType()); if (other->GetDimension() == 2) { const unsigned int dimensions[] = {other->GetDimension(0), other->GetDimension(1), 1}; Superclass::Initialize(pixelType, 3, dimensions); } else { Superclass::Initialize(pixelType, other->GetDimension(), other->GetDimensions()); } auto originalGeometry = other->GetTimeGeometry()->Clone(); this->SetTimeGeometry(originalGeometry); // initialize image memory to zero ClearImageBuffer(this); // Transfer some general DICOM properties from the source image to derived image (e.g. Patient information,...) DICOMQIPropertyHelper::DeriveDICOMSourceProperties(other, this); // Add a inital LabelSet ans corresponding image data to the stack if (this->GetNumberOfLayers() == 0) { AddLayer(); } } mitk::LabelSetImage::~LabelSetImage() { for (auto [value, label] : m_LabelMap) { this->ReleaseLabel(label); } m_LabelMap.clear(); } unsigned int mitk::LabelSetImage::GetActiveLayer() const { if (m_LayerContainer.size() == 0) mitkThrow() << "Cannot return active layer index. No layer is available."; return m_ActiveLayer; } unsigned int mitk::LabelSetImage::GetNumberOfLayers() const { return m_LayerContainer.size(); } void mitk::LabelSetImage::RemoveGroup(GroupIndexType indexToDelete) { if (!this->ExistGroup(indexToDelete)) mitkThrow() << "Cannot remove group. Group does not exist. Invalid group index: "<GetNumberOfLayers() == 1) { //last layer is about to be deleted newActiveIndex = 0; } else { //we have to add/subtract one more because we have not removed the layer yet, thus the group count is to 1 high. newActiveIndex = indexToDelete+1 < GetNumberOfLayers() ? indexToDelete : GetNumberOfLayers() - 2; newActiveIndexBeforeDeletion = indexToDelete + 1 < GetNumberOfLayers() ? indexToDelete+1 : indexToDelete -1; } } if (activeIndex == indexToDelete) { // we are deleting the active layer, it should not be copied back into the vector m_activeLayerInvalid = true; //copy the image content of the upcoming new active layer; SetActiveLayer(newActiveIndexBeforeDeletion); } auto relevantLabels = m_GroupToLabelMap[indexToDelete]; { std::lock_guard guard(m_LabelNGroupMapsMutex); // remove labels of group for (auto labelValue : relevantLabels) { auto label = m_LabelMap[labelValue]; this->ReleaseLabel(label); m_LabelToGroupMap.erase(labelValue); m_LabelMap.erase(labelValue); this->InvokeEvent(LabelRemovedEvent(labelValue)); } // remove the group entries in the maps and the image. m_Groups.erase(m_Groups.begin() + indexToDelete); m_GroupToLabelMap.erase(m_GroupToLabelMap.begin() + indexToDelete); m_LayerContainer.erase(m_LayerContainer.begin() + indexToDelete); } //update old indexes in m_GroupToLabelMap to new layer indexes for (auto& element : m_LabelToGroupMap) { if (element.second > indexToDelete) element.second = element.second -1; } //correct active layer index m_ActiveLayer = newActiveIndex; this->InvokeEvent(LabelsChangedEvent(relevantLabels)); this->InvokeEvent(GroupRemovedEvent(indexToDelete)); this->Modified(); } mitk::LabelSetImage::LabelValueVectorType mitk::LabelSetImage::ExtractLabelValuesFromLabelVector(const LabelVectorType& labels) { LabelValueVectorType result; for (auto label : labels) { result.emplace_back(label->GetValue()); } return result; } mitk::LabelSetImage::LabelValueVectorType mitk::LabelSetImage::ExtractLabelValuesFromLabelVector(const ConstLabelVectorType& labels) { LabelValueVectorType result; for (auto label : labels) { result.emplace_back(label->GetValue()); } return result; } mitk::LabelSetImage::ConstLabelVectorType mitk::LabelSetImage::ConvertLabelVectorConst(const LabelVectorType& labels) { ConstLabelVectorType result(labels.begin(), labels.end()); return result; }; const mitk::LabelSetImage::LabelValueVectorType mitk::LabelSetImage::GetAllLabelValues() const { LabelValueVectorType result; for (auto [value, label] : m_LabelMap) { result.emplace_back(value); } return result; } mitk::LabelSetImage::LabelValueVectorType mitk::LabelSetImage::GetUsedLabelValues() const { LabelValueVectorType result = { UNLABELED_VALUE }; for (auto [value, label] : m_LabelMap) { result.emplace_back(value); } return result; } mitk::LabelSetImage::GroupIndexType mitk::LabelSetImage::AddLayer(ConstLabelVector labels) { mitk::Image::Pointer newImage = mitk::Image::New(); newImage->Initialize(this->GetPixelType(), this->GetDimension(), this->GetDimensions(), this->GetImageDescriptor()->GetNumberOfChannels()); newImage->SetTimeGeometry(this->GetTimeGeometry()->Clone()); ClearImageBuffer(newImage); return this->AddLayer(newImage, labels); } mitk::LabelSetImage::GroupIndexType mitk::LabelSetImage::AddLayer(mitk::Image* layerImage, ConstLabelVector labels) { GroupIndexType newGroupID = m_Groups.size(); if (nullptr == layerImage) mitkThrow() << "Cannot add group. Passed group image is nullptr."; bool equalGeometries = Equal( *(this->GetTimeGeometry()), *(layerImage->GetTimeGeometry()), NODE_PREDICATE_GEOMETRY_DEFAULT_CHECK_COORDINATE_PRECISION, NODE_PREDICATE_GEOMETRY_DEFAULT_CHECK_DIRECTION_PRECISION, false); if (!equalGeometries) mitkThrow() << "Cannot add group. Passed group image has not the same geometry like segmentation."; if (layerImage->GetPixelType() != MakePixelType()) mitkThrow() << "Cannot add group. Passed group image has incorrect pixel type. Only LabelValueType is supported. Invalid pixel type: "<< layerImage->GetPixelType().GetTypeAsString(); // push a new working image for the new layer m_LayerContainer.push_back(layerImage); m_Groups.push_back(""); m_GroupToLabelMap.push_back({}); for (auto label : labels) { if (m_LabelMap.end() != m_LabelMap.find(label->GetValue())) { mitkThrow() << "Cannot add layer. Labels that should be added with layer use at least one label value that is already in use. Conflicted label value: " << label->GetValue(); } auto labelClone = label->Clone(); DICOMSegmentationPropertyHelper::SetDICOMSegmentProperties(labelClone); this->AddLabelToMap(labelClone->GetValue(), labelClone, newGroupID); this->RegisterLabel(labelClone); } this->Modified(); this->InvokeEvent(GroupAddedEvent(newGroupID)); return newGroupID; } void mitk::LabelSetImage::ReplaceGroupLabels(const GroupIndexType groupID, const ConstLabelVectorType& labelSet) { if (m_LayerContainer.size() <= groupID) { mitkThrow() << "Trying to replace labels of non-existing group. Invalid group id: "< guard(m_LabelNGroupMapsMutex); oldLabels = this->m_GroupToLabelMap[groupID]; for (auto labelID : oldLabels) { this->RemoveLabelFromMap(labelID); this->InvokeEvent(LabelRemovedEvent(labelID)); } } this->InvokeEvent(LabelsChangedEvent(oldLabels)); this->InvokeEvent(GroupModifiedEvent(groupID)); //add new labels to group for (auto label : labelSet) { this->AddLabel(label->Clone(), groupID, true, false); } } void mitk::LabelSetImage::ReplaceGroupLabels(const GroupIndexType groupID, const LabelVectorType& labelSet) { return ReplaceGroupLabels(groupID, ConvertLabelVectorConst(labelSet)); } mitk::Image* mitk::LabelSetImage::GetGroupImage(GroupIndexType groupID) { if (!this->ExistGroup(groupID)) mitkThrow() << "Error, cannot return group image. Group ID is invalid. Invalid ID: " << groupID; return groupID == this->GetActiveLayer() ? this : m_LayerContainer[groupID]; } const mitk::Image* mitk::LabelSetImage::GetGroupImage(GroupIndexType groupID) const { if (!this->ExistGroup(groupID)) mitkThrow() << "Error, cannot return group image. Group ID is invalid. Invalid ID: " << groupID; return groupID == this->GetActiveLayer() ? this : m_LayerContainer.at(groupID).GetPointer(); } const mitk::Image* mitk::LabelSetImage::GetGroupImageWorkaround(GroupIndexType groupID) const { if (!this->ExistGroup(groupID)) mitkThrow() << "Error, cannot return group image. Group ID is invalid. Invalid ID: " << groupID; if (groupID == this->GetActiveLayer() && this->GetMTime()> m_LayerContainer[groupID]->GetMTime()) { //we have to transfer the content first into the group image if (4 == this->GetDimension()) { AccessFixedDimensionByItk_n(this, ImageToLayerContainerProcessing, 4, (groupID)); } else { AccessByItk_1(this, ImageToLayerContainerProcessing, groupID); } } return m_LayerContainer[groupID].GetPointer(); } const std::string& mitk::LabelSetImage::GetGroupName(GroupIndexType groupID) const { if (!this->ExistGroup(groupID)) mitkThrow() << "Error, cannot return group name. Group ID is invalid. Invalid ID: " << groupID; return m_Groups[groupID]; } void mitk::LabelSetImage::SetGroupName(GroupIndexType groupID, const std::string& name) { if (!this->ExistGroup(groupID)) mitkThrow() << "Error, cannot set group name. Group ID is invalid. Invalid ID: " << groupID; m_Groups[groupID] = name; this->InvokeEvent(GroupModifiedEvent(groupID)); } void mitk::LabelSetImage::SetActiveLayer(unsigned int layer) { try { if (4 == this->GetDimension()) { if ((layer != GetActiveLayer() || m_activeLayerInvalid) && (layer < this->GetNumberOfLayers())) { BeforeChangeLayerEvent.Send(); if (m_activeLayerInvalid) { // We should not write the invalid layer back to the vector m_activeLayerInvalid = false; } else { AccessFixedDimensionByItk_n(this, ImageToLayerContainerProcessing, 4, (GetActiveLayer())); } m_ActiveLayer = layer; AccessFixedDimensionByItk_n(this, LayerContainerToImageProcessing, 4, (GetActiveLayer())); AfterChangeLayerEvent.Send(); } } else { if ((layer != GetActiveLayer() || m_activeLayerInvalid) && (layer < this->GetNumberOfLayers())) { BeforeChangeLayerEvent.Send(); if (m_activeLayerInvalid) { // We should not write the invalid layer back to the vector m_activeLayerInvalid = false; } else { AccessByItk_1(this, ImageToLayerContainerProcessing, GetActiveLayer()); } m_ActiveLayer = layer; AccessByItk_1(this, LayerContainerToImageProcessing, GetActiveLayer()); AfterChangeLayerEvent.Send(); } } } catch (itk::ExceptionObject &e) { mitkThrow() << e.GetDescription(); } this->Modified(); } void mitk::LabelSetImage::SetActiveLabel(LabelValueType label) { m_ActiveLabelValue = label; if (label != UNLABELED_VALUE) { auto groupID = this->GetGroupIndexOfLabel(label); if (groupID!=this->GetActiveLayer()) this->SetActiveLayer(groupID); } Modified(); } void mitk::LabelSetImage::ClearBuffer() { try { ClearImageBuffer(this); this->Modified(); } catch (itk::ExceptionObject &e) { mitkThrow() << e.GetDescription(); } } void mitk::LabelSetImage::MergeLabel(PixelType pixelValue, PixelType sourcePixelValue) { try { AccessByItk_2(this, MergeLabelProcessing, pixelValue, sourcePixelValue); } catch (itk::ExceptionObject &e) { mitkThrow() << e.GetDescription(); } this->SetActiveLabel(pixelValue); this->InvokeEvent(LabelModifiedEvent(sourcePixelValue)); this->InvokeEvent(LabelModifiedEvent(pixelValue)); this->InvokeEvent(LabelsChangedEvent({ sourcePixelValue, pixelValue })); Modified(); } void mitk::LabelSetImage::MergeLabels(PixelType pixelValue, const std::vector& vectorOfSourcePixelValues) { try { for (unsigned int idx = 0; idx < vectorOfSourcePixelValues.size(); idx++) { AccessByItk_2(this, MergeLabelProcessing, pixelValue, vectorOfSourcePixelValues[idx]); this->InvokeEvent(LabelModifiedEvent(vectorOfSourcePixelValues[idx])); } } catch (itk::ExceptionObject &e) { mitkThrow() << e.GetDescription(); } this->SetActiveLabel(pixelValue); this->InvokeEvent(LabelModifiedEvent(pixelValue)); auto modifiedValues = vectorOfSourcePixelValues; modifiedValues.push_back(pixelValue); this->InvokeEvent(LabelsChangedEvent(modifiedValues)); Modified(); } void mitk::LabelSetImage::RemoveLabel(LabelValueType pixelValue) { GroupIndexType groupID = 0; { std::lock_guard guard(m_LabelNGroupMapsMutex); if (m_LabelMap.find(pixelValue) == m_LabelMap.end()) return; groupID = this->GetGroupIndexOfLabel(pixelValue); //first erase the pixel content (also triggers a LabelModified event) this->EraseLabel(pixelValue); this->RemoveLabelFromMap(pixelValue); if (m_ActiveLabelValue == pixelValue) { this->SetActiveLabel(0); } } this->InvokeEvent(LabelRemovedEvent(pixelValue)); this->InvokeEvent(LabelsChangedEvent({ pixelValue })); this->InvokeEvent(GroupModifiedEvent(groupID)); } void mitk::LabelSetImage::RemoveLabelFromMap(LabelValueType pixelValue) { if (m_LabelMap.find(pixelValue) == m_LabelMap.end()) mitkThrow()<<"Invalid state of instance. RemoveLabelFromMap was called for unknown label id. invalid label id: "<GetGroupIndexOfLabel(pixelValue); this->ReleaseLabel(m_LabelMap[pixelValue]); //now remove the label entry itself m_LabelMap.erase(pixelValue); m_LabelToGroupMap.erase(pixelValue); auto labelsInGroup = m_GroupToLabelMap[groupID]; labelsInGroup.erase(std::remove(labelsInGroup.begin(), labelsInGroup.end(), pixelValue), labelsInGroup.end()); m_GroupToLabelMap[groupID] = labelsInGroup; } void mitk::LabelSetImage::RemoveLabels(const LabelValueVectorType& vectorOfLabelPixelValues) { for (const auto labelValue : vectorOfLabelPixelValues) { this->RemoveLabel(labelValue); } this->InvokeEvent(LabelsChangedEvent(vectorOfLabelPixelValues)); } void mitk::LabelSetImage::EraseLabel(LabelValueType pixelValue) { try { auto groupID = this->GetGroupIndexOfLabel(pixelValue); mitk::Image* groupImage = this->GetGroupImage(groupID); if (4 == this->GetDimension()) { AccessFixedDimensionByItk_1(groupImage, EraseLabelProcessing, 4, pixelValue); } else { AccessByItk_1(groupImage, EraseLabelProcessing, pixelValue); } groupImage->Modified(); } catch (const itk::ExceptionObject& e) { mitkThrow() << e.GetDescription(); } this->InvokeEvent(LabelModifiedEvent(pixelValue)); this->InvokeEvent(LabelsChangedEvent({ pixelValue })); Modified(); } void mitk::LabelSetImage::EraseLabels(const LabelValueVectorType& labelValues) { for (auto labelValue : labelValues) { this->EraseLabel(labelValue); } } mitk::LabelSetImage::LabelValueType mitk::LabelSetImage::GetUnusedLabelValue() const { auto usedValues = this->GetUsedLabelValues(); return usedValues.back() + 1; } mitk::Label* mitk::LabelSetImage::AddLabel(mitk::Label* label, GroupIndexType groupID, bool addAsClone, bool correctLabelValue) { if (nullptr == label) mitkThrow() << "Invalid use of AddLabel. label is not valid."; mitk::Label::Pointer newLabel = label; { std::lock_guard guard(m_LabelNGroupMapsMutex); unsigned int max_size = mitk::Label::MAX_LABEL_VALUE + 1; if (m_LayerContainer.size() >= max_size) return nullptr; if (addAsClone) newLabel = label->Clone(); auto pixelValue = newLabel->GetValue(); auto usedValues = this->GetUsedLabelValues(); auto finding = std::find(usedValues.begin(), usedValues.end(), pixelValue); if (!usedValues.empty() && usedValues.end() != finding) { if (correctLabelValue) { pixelValue = this->GetUnusedLabelValue(); newLabel->SetValue(pixelValue); } else { mitkThrow() << "Cannot add label due to conflicting label value that already exists in the MultiLabelSegmentation. Conflicting label value: " << pixelValue; } } // add DICOM information of the label DICOMSegmentationPropertyHelper::SetDICOMSegmentProperties(newLabel); this->AddLabelToMap(pixelValue, newLabel, groupID); this->RegisterLabel(newLabel); } this->InvokeEvent(LabelAddedEvent(newLabel->GetValue())); m_ActiveLabelValue = newLabel->GetValue(); this->Modified(); return newLabel; } mitk::Label* mitk::LabelSetImage::AddLabelWithContent(Label* label, const Image* labelContent, GroupIndexType groupID, LabelValueType contentLabelValue, bool addAsClone, bool correctLabelValue) { if (nullptr == labelContent) mitkThrow() << "Invalid use of AddLabel. labelContent is not valid."; if (!Equal(*(this->GetTimeGeometry()), *(labelContent->GetTimeGeometry()), mitk::NODE_PREDICATE_GEOMETRY_DEFAULT_CHECK_COORDINATE_PRECISION, mitk::NODE_PREDICATE_GEOMETRY_DEFAULT_CHECK_DIRECTION_PRECISION)) mitkThrow() << "Invalid use of AddLabel. labelContent has not the same geometry like the segmentation."; auto newLabel = this->AddLabel(label, groupID, addAsClone, correctLabelValue); mitk::TransferLabelContent(labelContent, this->GetGroupImage(groupID), this->GetConstLabelsByValue(this->GetLabelValuesByGroup(groupID)), mitk::LabelSetImage::UNLABELED_VALUE, mitk::LabelSetImage::UNLABELED_VALUE, false, { {contentLabelValue, newLabel->GetValue()}}, mitk::MultiLabelSegmentation::MergeStyle::Replace, mitk::MultiLabelSegmentation::OverwriteStyle::RegardLocks); this->Modified(); return newLabel; } mitk::Label* mitk::LabelSetImage::AddLabel(const std::string& name, const mitk::Color& color, GroupIndexType groupID) { mitk::Label::Pointer newLabel = mitk::Label::New(); newLabel->SetName(name); newLabel->SetColor(color); return AddLabel(newLabel,groupID,false); } void mitk::LabelSetImage::RenameLabel(LabelValueType pixelValue, const std::string& name, const mitk::Color& color) { std::shared_lock guard(m_LabelNGroupMapsMutex); mitk::Label* label = GetLabel(pixelValue); if (nullptr == label) mitkThrow() << "Cannot rename label.Unknown label value provided. Unknown label value:" << pixelValue; label->SetName(name); label->SetColor(color); this->UpdateLookupTable(pixelValue); + m_LookupTable->Modified(); + // change DICOM information of the label DICOMSegmentationPropertyHelper::SetDICOMSegmentProperties(label); } mitk::Label *mitk::LabelSetImage::GetActiveLabel() { if (m_ActiveLabelValue == UNLABELED_VALUE) return nullptr; auto finding = m_LabelMap.find(m_ActiveLabelValue); return finding == m_LabelMap.end() ? nullptr : finding->second; } const mitk::Label* mitk::LabelSetImage::GetActiveLabel() const { if (m_ActiveLabelValue == UNLABELED_VALUE) return nullptr; auto finding = m_LabelMap.find(m_ActiveLabelValue); return finding == m_LabelMap.end() ? nullptr : finding->second; } void mitk::LabelSetImage::UpdateCenterOfMass(PixelType pixelValue) { if (4 == this->GetDimension()) { AccessFixedDimensionByItk_1(this->GetGroupImage(this->GetGroupIndexOfLabel(pixelValue)), CalculateCenterOfMassProcessing, 4, pixelValue); } else { AccessByItk_1(this->GetGroupImage(this->GetGroupIndexOfLabel(pixelValue)), CalculateCenterOfMassProcessing, pixelValue); } } void mitk::LabelSetImage::SetLookupTable(mitk::LookupTable* lut) { m_LookupTable = lut; this->Modified(); } void mitk::LabelSetImage::UpdateLookupTable(PixelType pixelValue) { const mitk::Color& color = this->GetLabel(pixelValue)->GetColor(); double rgba[4]; m_LookupTable->GetTableValue(static_cast(pixelValue), rgba); rgba[0] = color.GetRed(); rgba[1] = color.GetGreen(); rgba[2] = color.GetBlue(); if (GetLabel(pixelValue)->GetVisible()) rgba[3] = GetLabel(pixelValue)->GetOpacity(); else rgba[3] = 0.0; m_LookupTable->SetTableValue(static_cast(pixelValue), rgba); } unsigned int mitk::LabelSetImage::GetNumberOfLabels(unsigned int layer) const { if (layer >= m_Groups.size()) mitkThrow() << "Cannot get number of labels in group. Group is unknown. Invalid index:" << layer; return m_GroupToLabelMap[layer].size(); } unsigned int mitk::LabelSetImage::GetTotalNumberOfLabels() const { return m_LabelMap.size(); } void mitk::LabelSetImage::MaskStamp(mitk::Image *mask, bool forceOverwrite) { try { mitk::PadImageFilter::Pointer padImageFilter = mitk::PadImageFilter::New(); padImageFilter->SetInput(0, mask); padImageFilter->SetInput(1, this); padImageFilter->SetPadConstant(0); padImageFilter->SetBinaryFilter(false); padImageFilter->SetLowerThreshold(0); padImageFilter->SetUpperThreshold(1); padImageFilter->Update(); mitk::Image::Pointer paddedMask = padImageFilter->GetOutput(); if (paddedMask.IsNull()) return; AccessByItk_2(this, MaskStampProcessing, paddedMask, forceOverwrite); } catch (...) { mitkThrow() << "Could not stamp the provided mask on the selected label."; } } void mitk::LabelSetImage::InitializeByLabeledImage(mitk::Image::Pointer image) { if (image.IsNull() || image->IsEmpty() || !image->IsInitialized()) mitkThrow() << "Invalid labeled image."; try { this->Initialize(image); unsigned int byteSize = sizeof(LabelSetImage::PixelType); for (unsigned int dim = 0; dim < image->GetDimension(); ++dim) { byteSize *= image->GetDimension(dim); } mitk::ImageWriteAccessor *accessor = new mitk::ImageWriteAccessor(static_cast(this)); memset(accessor->GetData(), 0, byteSize); delete accessor; auto geometry = image->GetTimeGeometry()->Clone(); this->SetTimeGeometry(geometry); if (image->GetDimension() == 3) { AccessTwoImagesFixedDimensionByItk(this, image, InitializeByLabeledImageProcessing, 3); } else if (image->GetDimension() == 4) { AccessTwoImagesFixedDimensionByItk(this, image, InitializeByLabeledImageProcessing, 4); } else { mitkThrow() << image->GetDimension() << "-dimensional label set images not yet supported"; } } catch (Exception& e) { mitkReThrow(e) << "Could not initialize by provided labeled image."; } catch (...) { mitkThrow() << "Could not initialize by provided labeled image due to unknown error."; } this->Modified(); } template void mitk::LabelSetImage::InitializeByLabeledImageProcessing(LabelSetImageType *labelSetImage, ImageType *image) { typedef itk::ImageRegionConstIteratorWithIndex SourceIteratorType; typedef itk::ImageRegionIterator TargetIteratorType; TargetIteratorType targetIter(labelSetImage, labelSetImage->GetRequestedRegion()); targetIter.GoToBegin(); SourceIteratorType sourceIter(image, image->GetRequestedRegion()); sourceIter.GoToBegin(); while (!sourceIter.IsAtEnd()) { const auto originalSourceValue = sourceIter.Get(); const auto sourceValue = static_cast(originalSourceValue); if (originalSourceValue > mitk::Label::MAX_LABEL_VALUE) { mitkThrow() << "Cannot initialize MultiLabelSegmentation by image. Image contains a pixel value that exceeds the label value range. Invalid pixel value:" << originalSourceValue; } targetIter.Set(sourceValue); if (LabelSetImage::UNLABELED_VALUE!=sourceValue && !this->ExistLabel(sourceValue)) { if (this->GetTotalNumberOfLabels() >= mitk::Label::MAX_LABEL_VALUE) { mitkThrow() << "Cannot initialize MultiLabelSegmentation by image. Image contains to many labels."; } std::stringstream name; name << "object-" << sourceValue; double rgba[4]; this->GetLookupTable()->GetTableValue(sourceValue, rgba); mitk::Color color; color.SetRed(rgba[0]); color.SetGreen(rgba[1]); color.SetBlue(rgba[2]); auto label = mitk::Label::New(); label->SetName(name.str().c_str()); label->SetColor(color); label->SetOpacity(rgba[3]); label->SetValue(sourceValue); this->AddLabel(label,0,false); } ++sourceIter; ++targetIter; } } template void mitk::LabelSetImage::MaskStampProcessing(ImageType *itkImage, mitk::Image *mask, bool forceOverwrite) { typename ImageType::Pointer itkMask; mitk::CastToItkImage(mask, itkMask); typedef itk::ImageRegionConstIterator SourceIteratorType; typedef itk::ImageRegionIterator TargetIteratorType; SourceIteratorType sourceIter(itkMask, itkMask->GetLargestPossibleRegion()); sourceIter.GoToBegin(); TargetIteratorType targetIter(itkImage, itkImage->GetLargestPossibleRegion()); targetIter.GoToBegin(); const auto activeLabel = this->GetActiveLabel()->GetValue(); while (!sourceIter.IsAtEnd()) { PixelType sourceValue = sourceIter.Get(); PixelType targetValue = targetIter.Get(); if ((sourceValue != UNLABELED_VALUE) && (forceOverwrite || !this->IsLabelLocked(targetValue))) // skip unlabeled pixels and locked labels { targetIter.Set(activeLabel); } ++sourceIter; ++targetIter; } this->Modified(); } template void mitk::LabelSetImage::CalculateCenterOfMassProcessing(ImageType *itkImage, LabelValueType pixelValue) { if (ImageType::GetImageDimension() != 3) { return; } auto labelGeometryFilter = itk::LabelGeometryImageFilter::New(); labelGeometryFilter->SetInput(itkImage); labelGeometryFilter->Update(); auto centroid = labelGeometryFilter->GetCentroid(pixelValue); mitk::Point3D pos; pos[0] = centroid[0]; pos[1] = centroid[1]; pos[2] = centroid[2]; this->GetLabel(pixelValue)->SetCenterOfMassIndex(pos); this->GetSlicedGeometry()->IndexToWorld(pos, pos); this->GetLabel(pixelValue)->SetCenterOfMassCoordinates(pos); } template void mitk::LabelSetImage::LayerContainerToImageProcessing(itk::Image *target, unsigned int layer) { typedef itk::Image ImageType; typename ImageType::Pointer itkSource; // mitk::CastToItkImage(m_LayerContainer[layer], itkSource); itkSource = ImageToItkImage(m_LayerContainer[layer]); typedef itk::ImageRegionConstIterator SourceIteratorType; typedef itk::ImageRegionIterator TargetIteratorType; SourceIteratorType sourceIter(itkSource, itkSource->GetLargestPossibleRegion()); sourceIter.GoToBegin(); TargetIteratorType targetIter(target, target->GetLargestPossibleRegion()); targetIter.GoToBegin(); while (!sourceIter.IsAtEnd()) { targetIter.Set(sourceIter.Get()); ++sourceIter; ++targetIter; } } template void mitk::LabelSetImage::ImageToLayerContainerProcessing(const itk::Image *source, unsigned int layer) const { typedef itk::Image ImageType; typename ImageType::Pointer itkTarget; // mitk::CastToItkImage(m_LayerContainer[layer], itkTarget); itkTarget = ImageToItkImage(m_LayerContainer[layer]); typedef itk::ImageRegionConstIterator SourceIteratorType; typedef itk::ImageRegionIterator TargetIteratorType; SourceIteratorType sourceIter(source, source->GetLargestPossibleRegion()); sourceIter.GoToBegin(); TargetIteratorType targetIter(itkTarget, itkTarget->GetLargestPossibleRegion()); targetIter.GoToBegin(); while (!sourceIter.IsAtEnd()) { targetIter.Set(sourceIter.Get()); ++sourceIter; ++targetIter; } m_LayerContainer[layer]->Modified(); } template void mitk::LabelSetImage::EraseLabelProcessing(ImageType *itkImage, PixelType pixelValue) { typedef itk::ImageRegionIterator IteratorType; IteratorType iter(itkImage, itkImage->GetLargestPossibleRegion()); iter.GoToBegin(); while (!iter.IsAtEnd()) { PixelType value = iter.Get(); if (value == pixelValue) { iter.Set(0); } ++iter; } } template void mitk::LabelSetImage::MergeLabelProcessing(ImageType *itkImage, PixelType pixelValue, PixelType index) { typedef itk::ImageRegionIterator IteratorType; IteratorType iter(itkImage, itkImage->GetLargestPossibleRegion()); iter.GoToBegin(); while (!iter.IsAtEnd()) { if (iter.Get() == index) { iter.Set(pixelValue); } ++iter; } } void mitk::LabelSetImage::AddLabelToMap(LabelValueType labelValue, mitk::Label* label, GroupIndexType groupID) { if (m_LabelMap.find(labelValue)!=m_LabelMap.end()) mitkThrow() << "Segmentation is in an invalid state: Label value collision. A label was added with a LabelValue already in use. LabelValue: " << labelValue; if (!this->ExistGroup(groupID)) mitkThrow() << "Cannot add label. Defined group is unknown. Invalid group index: " << groupID; m_LabelMap[labelValue] = label; m_LabelToGroupMap[labelValue] = groupID; auto groupFinding = std::find(m_GroupToLabelMap[groupID].begin(), m_GroupToLabelMap[groupID].end(), labelValue); if (groupFinding == m_GroupToLabelMap[groupID].end()) { m_GroupToLabelMap[groupID].push_back(labelValue); } } void mitk::LabelSetImage::RegisterLabel(mitk::Label* label) { if (nullptr == label) mitkThrow() << "Invalid call of RegisterLabel with a nullptr."; UpdateLookupTable(label->GetValue()); + m_LookupTable->Modified(); auto command = itk::MemberCommand::New(); command->SetCallbackFunction(this, &LabelSetImage::OnLabelModified); m_LabelModEventGuardMap.emplace(label->GetValue(), ITKEventObserverGuard(label, itk::ModifiedEvent(), command)); } void mitk::LabelSetImage::ReleaseLabel(Label* label) { if (nullptr == label) mitkThrow() << "Invalid call of ReleaseLabel with a nullptr."; m_LabelModEventGuardMap.erase(label->GetValue()); } void mitk::LabelSetImage::ApplyToLabels(const LabelValueVectorType& values, std::function&& lambda) { auto labels = this->GetLabelsByValue(values); std::for_each(labels.begin(), labels.end(), lambda); this->InvokeEvent(LabelsChangedEvent(values)); } void mitk::LabelSetImage::VisitLabels(const LabelValueVectorType& values, std::function&& lambda) const { auto labels = this->GetConstLabelsByValue(values); std::for_each(labels.begin(), labels.end(), lambda); } void mitk::LabelSetImage::OnLabelModified(const Object* sender, const itk::EventObject&) { auto label = dynamic_cast(sender); if (nullptr == label) mitkThrow() << "LabelSet is in wrong state. LabelModified event is not send by a label instance."; Superclass::Modified(); this->InvokeEvent(LabelModifiedEvent(label->GetValue())); } bool mitk::LabelSetImage::ExistLabel(LabelValueType value) const { auto finding = m_LabelMap.find(value); return m_LabelMap.end() != finding; } bool mitk::LabelSetImage::ExistLabel(LabelValueType value, GroupIndexType groupIndex) const { auto finding = m_LabelToGroupMap.find(value); if (m_LabelToGroupMap.end() != finding) { return finding->second == groupIndex; } return false; } bool mitk::LabelSetImage::ExistGroup(GroupIndexType index) const { return index < m_LayerContainer.size(); } mitk::LabelSetImage::GroupIndexType mitk::LabelSetImage::GetGroupIndexOfLabel(LabelValueType value) const { auto finding = m_LabelToGroupMap.find(value); if (m_LabelToGroupMap.end() == finding) { mitkThrow()<< "Cannot deduce group index. Passed label value does not exist. Value: "<< value; } return finding->second; } const mitk::Label* mitk::LabelSetImage::GetLabel(LabelValueType value) const { auto finding = m_LabelMap.find(value); if (m_LabelMap.end() != finding) { return finding->second; } return nullptr; }; mitk::Label* mitk::LabelSetImage::GetLabel(LabelValueType value) { auto finding = m_LabelMap.find(value); if (m_LabelMap.end() != finding) { return finding->second; } return nullptr; }; bool mitk::LabelSetImage::IsLabelLocked(LabelValueType value) const { if (value == UNLABELED_VALUE) { return m_UnlabeledLabelLock; } const auto label = this->GetLabel(value); return label->GetLocked(); } const mitk::LabelSetImage::ConstLabelVectorType mitk::LabelSetImage::GetLabels() const { ConstLabelVectorType result; for (auto [value, label] : m_LabelMap) { result.emplace_back(label); } return result; } const mitk::LabelSetImage::LabelVectorType mitk::LabelSetImage::GetLabels() { LabelVectorType result; for (auto [value, label] : m_LabelMap) { result.emplace_back(label); } return result; } const mitk::LabelSetImage::LabelVectorType mitk::LabelSetImage::GetLabelsByValue(const LabelValueVectorType& labelValues, bool ignoreMissing) { LabelVectorType result; for (const auto& labelValue : labelValues) { auto* label = this->GetLabel(labelValue); if (label != nullptr) { result.emplace_back(label); } else if (!ignoreMissing) mitkThrow() << "Error cannot get labels by Value. At least one passed value is unknown. Unknown value: " << labelValue; } return result; } const mitk::LabelSetImage::ConstLabelVectorType mitk::LabelSetImage::GetConstLabelsByValue(const LabelValueVectorType& labelValues, bool ignoreMissing) const { ConstLabelVectorType result; for (const auto& labelValue : labelValues) { const auto* label = this->GetLabel(labelValue); if (label != nullptr) { result.emplace_back(label); } else if (!ignoreMissing) mitkThrow() << "Error cannot get labels by Value. At least one passed value is unknown. Unknown value: " << labelValue; } return result; } const mitk::LabelSetImage::LabelValueVectorType mitk::LabelSetImage::GetLabelValuesByGroup(GroupIndexType index) const { if (!this->ExistGroup(index)) mitkThrow() << "Cannot get labels of an invalid group. Invalid group index: " << index; return m_GroupToLabelMap[index]; } const mitk::LabelSetImage::LabelValueVectorType mitk::LabelSetImage::GetLabelValuesByName(GroupIndexType index, const std::string_view name) const { LabelValueVectorType result; auto searchName = [&result, name](const Label* l) { if(l->GetName() == name) result.push_back(l->GetValue()); }; this->VisitLabels(this->GetLabelValuesByGroup(index), searchName); return result; } std::vector mitk::LabelSetImage::GetLabelClassNames() const { std::set names; auto searchName = [&names](const Label* l) { names.emplace(l->GetName()); }; this->VisitLabels(this->GetAllLabelValues(), searchName); return std::vector(names.begin(), names.end()); } std::vector mitk::LabelSetImage::GetLabelClassNamesByGroup(GroupIndexType index) const { std::set names; auto searchName = [&names](const Label* l) { names.emplace(l->GetName()); }; this->VisitLabels(this->GetLabelValuesByGroup(index), searchName); return std::vector(names.begin(), names.end()); } void mitk::LabelSetImage::SetAllLabelsVisible(bool visible) { auto setVisibility = [visible,this](Label* l) { l->SetVisible(visible); this->UpdateLookupTable(l->GetValue()); }; this->ApplyToLabels(this->GetAllLabelValues(), setVisibility); this->m_LookupTable->Modified(); } void mitk::LabelSetImage::SetAllLabelsVisibleByGroup(GroupIndexType group, bool visible) { auto setVisibility = [visible, this](Label* l) { l->SetVisible(visible); this->UpdateLookupTable(l->GetValue()); }; this->ApplyToLabels(this->GetLabelValuesByGroup(group), setVisibility); this->m_LookupTable->Modified(); } void mitk::LabelSetImage::SetAllLabelsVisibleByName(GroupIndexType group, const std::string_view name, bool visible) { auto setVisibility = [visible, this](Label* l) { l->SetVisible(visible); this->UpdateLookupTable(l->GetValue()); }; this->ApplyToLabels(this->GetLabelValuesByName(group, name), setVisibility); this->m_LookupTable->Modified(); } void mitk::LabelSetImage::SetAllLabelsLocked(bool locked) { auto setLock = [locked](Label* l) { l->SetLocked(locked); }; this->ApplyToLabels(this->GetAllLabelValues(), setLock); } void mitk::LabelSetImage::SetAllLabelsLockedByGroup(GroupIndexType group, bool locked) { auto setLock = [locked](Label* l) { l->SetLocked(locked); }; this->ApplyToLabels(this->GetLabelValuesByGroup(group), setLock); } void mitk::LabelSetImage::SetAllLabelsLockedByName(GroupIndexType group, const std::string_view name, bool locked) { auto setLock = [locked](Label* l) { l->SetLocked(locked); }; this->ApplyToLabels(this->GetLabelValuesByName(group, name), setLock); } bool mitk::Equal(const mitk::LabelSetImage &leftHandSide, const mitk::LabelSetImage &rightHandSide, ScalarType eps, bool verbose) { bool returnValue = true; /* LabelSetImage members */ MITK_INFO(verbose) << "--- LabelSetImage Equal ---"; // m_LookupTable; const mitk::LookupTable* lhsLUT = leftHandSide.GetLookupTable(); const mitk::LookupTable* rhsLUT = rightHandSide.GetLookupTable(); returnValue = *lhsLUT == *rhsLUT; if (!returnValue) { MITK_INFO(verbose) << "Lookup tables not equal."; return returnValue; ; } // number layers returnValue = leftHandSide.GetNumberOfLayers() == rightHandSide.GetNumberOfLayers(); if (!returnValue) { MITK_INFO(verbose) << "Number of layers not equal."; return false; } // total number labels returnValue = leftHandSide.GetTotalNumberOfLabels() == rightHandSide.GetTotalNumberOfLabels(); if (!returnValue) { MITK_INFO(verbose) << "Total number of labels not equal."; return false; } // active layer returnValue = leftHandSide.GetActiveLayer() == rightHandSide.GetActiveLayer(); if (!returnValue) { MITK_INFO(verbose) << "Active layer not equal."; return false; } if (4 == leftHandSide.GetDimension()) { MITK_INFO(verbose) << "Can not compare image data for 4D images - skipping check."; } else { // working image data returnValue = mitk::Equal((const mitk::Image &)leftHandSide, (const mitk::Image &)rightHandSide, eps, verbose); if (!returnValue) { MITK_INFO(verbose) << "Working image data not equal."; return false; } } if (leftHandSide.GetTotalNumberOfLabels() != rightHandSide.GetTotalNumberOfLabels()) { MITK_INFO(verbose) << "Number of labels are not equal."; return false; } for (unsigned int layerIndex = 0; layerIndex < leftHandSide.GetNumberOfLayers(); layerIndex++) { if (4 == leftHandSide.GetDimension()) { MITK_INFO(verbose) << "Can not compare image data for 4D images - skipping check."; } else { // layer image data returnValue = mitk::Equal(*leftHandSide.GetGroupImage(layerIndex), *rightHandSide.GetGroupImage(layerIndex), eps, verbose); if (!returnValue) { MITK_INFO(verbose) << "Layer image data not equal."; return false; } } // label data auto leftLabelsInGroup = leftHandSide.GetLabelValuesByGroup(layerIndex); auto rightLabelsInGroup = rightHandSide.GetLabelValuesByGroup(layerIndex); if (leftLabelsInGroup.size()!=rightLabelsInGroup.size()) { MITK_INFO(verbose) << "Number of layer labels is not equal. Invalid layer:" <; ConstLabelMapType ConvertLabelVectorToMap(const mitk::ConstLabelVector& labelV) { ConstLabelMapType result; for (auto label : labelV) { const auto value = label->GetValue(); auto finding = result.find(value); if (finding != result.end()) mitkThrow() << "Operation failed. Cannot convert label vector into label map, because at least one label value is not unique. Violating label value: " << value; result.insert(std::make_pair(value, label)); } return result; } /** Functor class that implements the label transfer and is used in conjunction with the itk::BinaryFunctorImageFilter. * For details regarding the usage of the filter and the functor patterns, please see info of itk::BinaryFunctorImageFilter. */ template class LabelTransferFunctor { public: LabelTransferFunctor() {}; LabelTransferFunctor(const ConstLabelMapType& destinationLabels, mitk::Label::PixelType sourceBackground, mitk::Label::PixelType destinationBackground, bool destinationBackgroundLocked, mitk::Label::PixelType sourceLabel, mitk::Label::PixelType newDestinationLabel, mitk::MultiLabelSegmentation::MergeStyle mergeStyle, mitk::MultiLabelSegmentation::OverwriteStyle overwriteStyle) : m_DestinationLabels(destinationLabels), m_SourceBackground(sourceBackground), m_DestinationBackground(destinationBackground), m_DestinationBackgroundLocked(destinationBackgroundLocked), m_SourceLabel(sourceLabel), m_NewDestinationLabel(newDestinationLabel), m_MergeStyle(mergeStyle), m_OverwriteStyle(overwriteStyle) { }; ~LabelTransferFunctor() {}; bool operator!=(const LabelTransferFunctor& other)const { return !(*this == other); } bool operator==(const LabelTransferFunctor& other) const { return this->m_SourceBackground == other.m_SourceBackground && this->m_DestinationBackground == other.m_DestinationBackground && this->m_DestinationBackgroundLocked == other.m_DestinationBackgroundLocked && this->m_SourceLabel == other.m_SourceLabel && this->m_NewDestinationLabel == other.m_NewDestinationLabel && this->m_MergeStyle == other.m_MergeStyle && this->m_OverwriteStyle == other.m_OverwriteStyle && this->m_DestinationLabels == other.m_DestinationLabels; } LabelTransferFunctor& operator=(const LabelTransferFunctor& other) { this->m_DestinationLabels = other.m_DestinationLabels; this->m_SourceBackground = other.m_SourceBackground; this->m_DestinationBackground = other.m_DestinationBackground; this->m_DestinationBackgroundLocked = other.m_DestinationBackgroundLocked; this->m_SourceLabel = other.m_SourceLabel; this->m_NewDestinationLabel = other.m_NewDestinationLabel; this->m_MergeStyle = other.m_MergeStyle; this->m_OverwriteStyle = other.m_OverwriteStyle; return *this; } inline TOutputpixel operator()(const TDestinationPixel& existingDestinationValue, const TSourcePixel& existingSourceValue) { if (existingSourceValue == this->m_SourceLabel) { if (mitk::MultiLabelSegmentation::OverwriteStyle::IgnoreLocks == this->m_OverwriteStyle) { return this->m_NewDestinationLabel; } else { if (existingDestinationValue == m_DestinationBackground) { if (!m_DestinationBackgroundLocked) { return this->m_NewDestinationLabel; } } else { auto labelFinding = this->m_DestinationLabels.find(existingDestinationValue); if (labelFinding==this->m_DestinationLabels.end() || !labelFinding->second->GetLocked()) { return this->m_NewDestinationLabel; } } } } else if (mitk::MultiLabelSegmentation::MergeStyle::Replace == this->m_MergeStyle && existingSourceValue == this->m_SourceBackground && existingDestinationValue == this->m_NewDestinationLabel && (mitk::MultiLabelSegmentation::OverwriteStyle::IgnoreLocks == this->m_OverwriteStyle || !this->m_DestinationBackgroundLocked)) { return this->m_DestinationBackground; } return existingDestinationValue; } private: ConstLabelMapType m_DestinationLabels; mitk::Label::PixelType m_SourceBackground = 0; mitk::Label::PixelType m_DestinationBackground = 0; bool m_DestinationBackgroundLocked = false; mitk::Label::PixelType m_SourceLabel = 1; mitk::Label::PixelType m_NewDestinationLabel = 1; mitk::MultiLabelSegmentation::MergeStyle m_MergeStyle = mitk::MultiLabelSegmentation::MergeStyle::Replace; mitk::MultiLabelSegmentation::OverwriteStyle m_OverwriteStyle = mitk::MultiLabelSegmentation::OverwriteStyle::RegardLocks; }; /**Helper function used by TransferLabelContentAtTimeStep to allow the templating over different image dimensions in conjunction of AccessFixedPixelTypeByItk_n.*/ template void TransferLabelContentAtTimeStepHelper(const itk::Image* itkSourceImage, mitk::Image* destinationImage, const mitk::ConstLabelVector& destinationLabels, mitk::Label::PixelType sourceBackground, mitk::Label::PixelType destinationBackground, bool destinationBackgroundLocked, mitk::Label::PixelType sourceLabel, mitk::Label::PixelType newDestinationLabel, mitk::MultiLabelSegmentation::MergeStyle mergeStyle, mitk::MultiLabelSegmentation::OverwriteStyle overwriteStyle) { typedef itk::Image ContentImageType; typename ContentImageType::Pointer itkDestinationImage; mitk::CastToItkImage(destinationImage, itkDestinationImage); auto sourceRegion = itkSourceImage->GetLargestPossibleRegion(); auto relevantRegion = itkDestinationImage->GetLargestPossibleRegion(); bool overlapping = relevantRegion.Crop(sourceRegion); if (!overlapping) { mitkThrow() << "Invalid call of TransferLabelContentAtTimeStep; sourceImage and destinationImage seem to have no overlapping image region."; } typedef LabelTransferFunctor LabelTransferFunctorType; typedef itk::BinaryFunctorImageFilter FilterType; LabelTransferFunctorType transferFunctor(ConvertLabelVectorToMap(destinationLabels), sourceBackground, destinationBackground, destinationBackgroundLocked, sourceLabel, newDestinationLabel, mergeStyle, overwriteStyle); auto transferFilter = FilterType::New(); transferFilter->SetFunctor(transferFunctor); transferFilter->InPlaceOn(); transferFilter->SetInput1(itkDestinationImage); transferFilter->SetInput2(itkSourceImage); transferFilter->GetOutput()->SetRequestedRegion(relevantRegion); transferFilter->Update(); } void mitk::TransferLabelContentAtTimeStep( const Image* sourceImage, Image* destinationImage, const mitk::ConstLabelVector& destinationLabels, const TimeStepType timeStep, mitk::Label::PixelType sourceBackground, mitk::Label::PixelType destinationBackground, bool destinationBackgroundLocked, LabelValueMappingVector labelMapping, MultiLabelSegmentation::MergeStyle mergeStyle, MultiLabelSegmentation::OverwriteStyle overwriteStlye) { if (nullptr == sourceImage) { mitkThrow() << "Invalid call of TransferLabelContentAtTimeStep; sourceImage must not be null."; } if (nullptr == destinationImage) { mitkThrow() << "Invalid call of TransferLabelContentAtTimeStep; destinationImage must not be null."; } if (sourceImage == destinationImage && labelMapping.size() > 1) { MITK_DEBUG << "Warning. Using TransferLabelContentAtTimeStep or TransferLabelContent with equal source and destination and more then on label to transfer, can lead to wrong results. Please see documentation and verify that the usage is OK."; } Image::ConstPointer sourceImageAtTimeStep = SelectImageByTimeStep(sourceImage, timeStep); Image::Pointer destinationImageAtTimeStep = SelectImageByTimeStep(destinationImage, timeStep); if (nullptr == sourceImageAtTimeStep) { mitkThrow() << "Invalid call of TransferLabelContentAtTimeStep; sourceImage does not have the requested time step: " << timeStep; } if (nullptr == destinationImageAtTimeStep) { mitkThrow() << "Invalid call of TransferLabelContentAtTimeStep; destinationImage does not have the requested time step: " << timeStep; } if (!Equal(*(sourceImageAtTimeStep->GetGeometry()), *(destinationImageAtTimeStep->GetGeometry()), mitk::NODE_PREDICATE_GEOMETRY_DEFAULT_CHECK_COORDINATE_PRECISION, mitk::NODE_PREDICATE_GEOMETRY_DEFAULT_CHECK_DIRECTION_PRECISION)) { if (IsSubGeometry(*(sourceImageAtTimeStep->GetGeometry()), *(destinationImageAtTimeStep->GetGeometry()), mitk::NODE_PREDICATE_GEOMETRY_DEFAULT_CHECK_COORDINATE_PRECISION, mitk::NODE_PREDICATE_GEOMETRY_DEFAULT_CHECK_DIRECTION_PRECISION)) { //we have to pad the source image //because ImageToImageFilters always check for origin matching even if //the requested output region is fitting :( auto padFilter = mitk::PadImageFilter::New(); padFilter->SetInput(0, sourceImageAtTimeStep); padFilter->SetInput(1, destinationImageAtTimeStep); padFilter->SetPadConstant(Label::UNLABELED_VALUE); padFilter->SetBinaryFilter(false); padFilter->Update(); sourceImageAtTimeStep = padFilter->GetOutput(); } else { mitkThrow() << "Invalid call of TransferLabelContentAtTimeStep; source image has neither the same geometry than destination image nor has the source image a sub geometry."; } } auto destLabelMap = ConvertLabelVectorToMap(destinationLabels); for (const auto& [sourceLabel, newDestinationLabel] : labelMapping) { if (LabelSetImage::UNLABELED_VALUE!=newDestinationLabel && destLabelMap.end() == destLabelMap.find(newDestinationLabel)) { mitkThrow() << "Invalid call of TransferLabelContentAtTimeStep. Defined destination label does not exist in destinationImage. newDestinationLabel: " << newDestinationLabel; } AccessFixedPixelTypeByItk_n(sourceImageAtTimeStep, TransferLabelContentAtTimeStepHelper, (Label::PixelType), (destinationImageAtTimeStep, destinationLabels, sourceBackground, destinationBackground, destinationBackgroundLocked, sourceLabel, newDestinationLabel, mergeStyle, overwriteStlye)); } destinationImage->Modified(); } void mitk::TransferLabelContent( const Image* sourceImage, Image* destinationImage, const mitk::ConstLabelVector& destinationLabels, mitk::Label::PixelType sourceBackground, mitk::Label::PixelType destinationBackground, bool destinationBackgroundLocked, LabelValueMappingVector labelMapping, MultiLabelSegmentation::MergeStyle mergeStyle, MultiLabelSegmentation::OverwriteStyle overwriteStlye) { if (nullptr == sourceImage) { mitkThrow() << "Invalid call of TransferLabelContent; sourceImage must not be null."; } if (nullptr == destinationImage) { mitkThrow() << "Invalid call of TransferLabelContent; destinationImage must not be null."; } const auto sourceTimeStepCount = sourceImage->GetTimeGeometry()->CountTimeSteps(); if (sourceTimeStepCount != destinationImage->GetTimeGeometry()->CountTimeSteps()) { mitkThrow() << "Invalid call of TransferLabelContent; mismatch between images in number of time steps."; } for (mitk::TimeStepType i = 0; i < sourceTimeStepCount; ++i) { TransferLabelContentAtTimeStep(sourceImage, destinationImage, destinationLabels, i, sourceBackground, destinationBackground, destinationBackgroundLocked, labelMapping, mergeStyle, overwriteStlye); } } void mitk::TransferLabelContentAtTimeStep( const LabelSetImage* sourceImage, LabelSetImage* destinationImage, const TimeStepType timeStep, LabelValueMappingVector labelMapping, MultiLabelSegmentation::MergeStyle mergeStyle, MultiLabelSegmentation::OverwriteStyle overwriteStlye) { if (nullptr == sourceImage) { mitkThrow() << "Invalid call of TransferLabelContentAtTimeStep; sourceImage must not be null."; } auto destinationLabels = destinationImage->GetConstLabelsByValue(destinationImage->GetLabelValuesByGroup(destinationImage->GetActiveLayer())); for (const auto& mappingElement : labelMapping) { if (LabelSetImage::UNLABELED_VALUE != mappingElement.first && !sourceImage->ExistLabel(mappingElement.first, sourceImage->GetActiveLayer())) { mitkThrow() << "Invalid call of TransferLabelContentAtTimeStep. Defined source label does not exist in sourceImage. SourceLabel: " << mappingElement.first; } } TransferLabelContentAtTimeStep(sourceImage, destinationImage, destinationLabels, timeStep, LabelSetImage::UNLABELED_VALUE, LabelSetImage::UNLABELED_VALUE, destinationImage->GetUnlabeledLabelLock(), labelMapping, mergeStyle, overwriteStlye); } void mitk::TransferLabelContent( const LabelSetImage* sourceImage, LabelSetImage* destinationImage, LabelValueMappingVector labelMapping, MultiLabelSegmentation::MergeStyle mergeStyle, MultiLabelSegmentation::OverwriteStyle overwriteStlye) { if (nullptr == sourceImage) { mitkThrow() << "Invalid call of TransferLabelContent; sourceImage must not be null."; } if (nullptr == destinationImage) { mitkThrow() << "Invalid call of TransferLabelContent; destinationImage must not be null."; } const auto sourceTimeStepCount = sourceImage->GetTimeGeometry()->CountTimeSteps(); if (sourceTimeStepCount != destinationImage->GetTimeGeometry()->CountTimeSteps()) { mitkThrow() << "Invalid call of TransferLabelContent; images have no equal number of time steps."; } for (mitk::TimeStepType i = 0; i < sourceTimeStepCount; ++i) { TransferLabelContentAtTimeStep(sourceImage, destinationImage, i, labelMapping, mergeStyle, overwriteStlye); } } diff --git a/Modules/Segmentation/Interactions/mitkSegWithPreviewTool.cpp b/Modules/Segmentation/Interactions/mitkSegWithPreviewTool.cpp index 314b7b9fee..6070914a34 100644 --- a/Modules/Segmentation/Interactions/mitkSegWithPreviewTool.cpp +++ b/Modules/Segmentation/Interactions/mitkSegWithPreviewTool.cpp @@ -1,851 +1,852 @@ /*============================================================================ 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); previewImage->Modified(); } } 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()); } + newPreviewImage->GetLookupTable()->Modified(); 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; } diff --git a/Modules/SegmentationUI/Qmitk/QmitkMultiLabelInspector.cpp b/Modules/SegmentationUI/Qmitk/QmitkMultiLabelInspector.cpp index e302703f9d..bfa89b7021 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkMultiLabelInspector.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkMultiLabelInspector.cpp @@ -1,1424 +1,1426 @@ /*============================================================================ 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 // mitk #include #include #include #include // Qmitk #include #include #include #include // Qt #include #include #include #include #include namespace { void ActivateLabelHighlights(mitk::DataNode* node, const mitk::LabelSetImage::LabelValueVectorType highlightedValues) { const std::string propertyName = "org.mitk.multilabel.labels.highlighted"; mitk::IntVectorProperty::Pointer prop = dynamic_cast(node->GetNonConstProperty(propertyName)); if (nullptr == prop) { prop = mitk::IntVectorProperty::New(); node->SetProperty(propertyName, prop); } mitk::IntVectorProperty::VectorType intValues(highlightedValues.begin(), highlightedValues.end()); prop->SetValue(intValues); prop->Modified(); //see T30386; needed because VectorProperty::SetValue does currently trigger no modified mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void DeactivateLabelHighlights(mitk::DataNode* node) { std::string propertyName = "org.mitk.multilabel.labels.highlighted"; mitk::IntVectorProperty::Pointer prop = dynamic_cast(node->GetNonConstProperty(propertyName)); if (nullptr != prop) { prop->SetValue({}); prop->Modified(); //see T30386; needed because VectorProperty::SetValue does currently trigger no modified mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } } QmitkMultiLabelInspector::QmitkMultiLabelInspector(QWidget* parent/* = nullptr*/) : QWidget(parent), m_Controls(new Ui::QmitkMultiLabelInspector), m_SegmentationNodeDataMTime(0) { m_Controls->setupUi(this); m_Model = new QmitkMultiLabelTreeModel(this); m_Controls->view->setModel(m_Model); m_ColorItemDelegate = new QmitkLabelColorItemDelegate(this); auto visibleIcon = QmitkStyleManager::ThemeIcon(QLatin1String(":/Qmitk/visible.svg")); auto invisibleIcon = QmitkStyleManager::ThemeIcon(QLatin1String(":/Qmitk/invisible.svg")); m_VisibilityItemDelegate = new QmitkLabelToggleItemDelegate(visibleIcon, invisibleIcon, this); auto lockIcon = QmitkStyleManager::ThemeIcon(QLatin1String(":/Qmitk/lock.svg")); auto unlockIcon = QmitkStyleManager::ThemeIcon(QLatin1String(":/Qmitk/unlock.svg")); m_LockItemDelegate = new QmitkLabelToggleItemDelegate(lockIcon, unlockIcon, this); auto* view = this->m_Controls->view; view->setItemDelegateForColumn(1, m_LockItemDelegate); view->setItemDelegateForColumn(2, m_ColorItemDelegate); view->setItemDelegateForColumn(3, m_VisibilityItemDelegate); auto* header = view->header(); header->setSectionResizeMode(0,QHeaderView::Stretch); header->setSectionResizeMode(1, QHeaderView::ResizeToContents); header->setSectionResizeMode(2, QHeaderView::ResizeToContents); header->setSectionResizeMode(3, QHeaderView::ResizeToContents); view->setContextMenuPolicy(Qt::CustomContextMenu); connect(m_Model, &QAbstractItemModel::modelReset, this, &QmitkMultiLabelInspector::OnModelReset); connect(m_Model, &QAbstractItemModel::dataChanged, this, &QmitkMultiLabelInspector::OnDataChanged); connect(view->selectionModel(), SIGNAL(selectionChanged(const QItemSelection&, const QItemSelection&)), SLOT(OnChangeModelSelection(const QItemSelection&, const QItemSelection&))); connect(view, &QAbstractItemView::customContextMenuRequested, this, &QmitkMultiLabelInspector::OnContextMenuRequested); connect(view, &QAbstractItemView::doubleClicked, this, &QmitkMultiLabelInspector::OnItemDoubleClicked); connect(view, &QAbstractItemView::entered, this, &QmitkMultiLabelInspector::OnEntered); connect(view, &QmitkMultiLabelTreeView::MouseLeave, this, &QmitkMultiLabelInspector::OnMouseLeave); } QmitkMultiLabelInspector::~QmitkMultiLabelInspector() { delete m_Controls; } void QmitkMultiLabelInspector::Initialize() { m_LastValidSelectedLabels = {}; m_ModelManipulationOngoing = false; m_Model->SetSegmentation(m_Segmentation); m_Controls->view->expandAll(); m_LastValidSelectedLabels = {}; //in singel selection mode, if at least one label exist select the first label of the mode. if (m_Segmentation.IsNotNull() && !this->GetMultiSelectionMode() && m_Segmentation->GetTotalNumberOfLabels() > 0) { auto firstIndex = m_Model->FirstLabelInstanceIndex(QModelIndex()); auto labelVariant = firstIndex.data(QmitkMultiLabelTreeModel::ItemModelRole::LabelInstanceValueRole); if (labelVariant.isValid()) { this->SetSelectedLabel(labelVariant.value()); m_Controls->view->selectionModel()->setCurrentIndex(firstIndex, QItemSelectionModel::NoUpdate); } } } void QmitkMultiLabelInspector::SetMultiSelectionMode(bool multiMode) { m_Controls->view->setSelectionMode(multiMode ? QAbstractItemView::SelectionMode::MultiSelection : QAbstractItemView::SelectionMode::SingleSelection); } bool QmitkMultiLabelInspector::GetMultiSelectionMode() const { return QAbstractItemView::SelectionMode::MultiSelection == m_Controls->view->selectionMode(); } void QmitkMultiLabelInspector::SetAllowVisibilityModification(bool visibilityMod) { m_AllowVisibilityModification = visibilityMod; this->m_Model->SetAllowVisibilityModification(visibilityMod); } void QmitkMultiLabelInspector::SetAllowLabelModification(bool labelMod) { m_AllowLabelModification = labelMod; } bool QmitkMultiLabelInspector::GetAllowVisibilityModification() const { return m_AllowVisibilityModification; } void QmitkMultiLabelInspector::SetAllowLockModification(bool lockMod) { m_AllowLockModification = lockMod; this->m_Model->SetAllowLockModification(lockMod); } bool QmitkMultiLabelInspector::GetAllowLockModification() const { return m_AllowLockModification; } bool QmitkMultiLabelInspector::GetAllowLabelModification() const { return m_AllowLabelModification; } void QmitkMultiLabelInspector::SetDefaultLabelNaming(bool defaultLabelNaming) { m_DefaultLabelNaming = defaultLabelNaming; } void QmitkMultiLabelInspector::SetMultiLabelSegmentation(mitk::LabelSetImage* segmentation) { if (segmentation != m_Segmentation) { m_Segmentation = segmentation; this->Initialize(); emit SegmentationChanged(); } } mitk::LabelSetImage* QmitkMultiLabelInspector::GetMultiLabelSegmentation() const { return m_Segmentation; } void QmitkMultiLabelInspector::SetMultiLabelNode(mitk::DataNode* node) { if (node != this->m_SegmentationNode.GetPointer()) { m_SegmentationObserver.Reset(); m_SegmentationNode = node; m_SegmentationNodeDataMTime = 0; if (m_SegmentationNode.IsNotNull()) { auto& widget = *this; auto checkAndSetSeg = [&widget, node](const itk::EventObject&) { if (widget.m_SegmentationNodeDataMTime < node->GetDataReferenceChangedTime()) { auto newSeg = dynamic_cast(node->GetData()); if (nullptr == newSeg) mitkThrow() << "Invalid usage. Node set does not contain a segmentation."; widget.m_SegmentationNodeDataMTime = node->GetDataReferenceChangedTime(); widget.SetMultiLabelSegmentation(newSeg); } }; m_SegmentationObserver.Reset(node, itk::ModifiedEvent(), checkAndSetSeg); checkAndSetSeg(itk::ModifiedEvent()); } else { this->SetMultiLabelSegmentation(nullptr); } } } mitk::DataNode* QmitkMultiLabelInspector::GetMultiLabelNode() const { return m_SegmentationNode; } bool QmitkMultiLabelInspector::GetModelManipulationOngoing() const { return m_ModelManipulationOngoing; } void QmitkMultiLabelInspector::OnModelReset() { m_LastValidSelectedLabels = {}; m_ModelManipulationOngoing = false; } void QmitkMultiLabelInspector::OnDataChanged(const QModelIndex& topLeft, const QModelIndex& /*bottomRight*/, const QList& /*roles*/) { if (!m_ModelManipulationOngoing && topLeft.isValid()) m_Controls->view->expand(topLeft); } bool EqualLabelSelections(const QmitkMultiLabelInspector::LabelValueVectorType& selection1, const QmitkMultiLabelInspector::LabelValueVectorType& selection2) { if (selection1.size() == selection2.size()) { // lambda to compare node pointer inside both lists return std::is_permutation(selection1.begin(), selection1.end(), selection2.begin()); } return false; } void QmitkMultiLabelInspector::SetSelectedLabels(const LabelValueVectorType& selectedLabels) { if (EqualLabelSelections(this->GetSelectedLabels(), selectedLabels)) { return; } this->UpdateSelectionModel(selectedLabels); m_LastValidSelectedLabels = selectedLabels; } void QmitkMultiLabelInspector::UpdateSelectionModel(const LabelValueVectorType& selectedLabels) { // create new selection by retrieving the corresponding indexes of the labels QItemSelection newCurrentSelection; for (const auto& labelID : selectedLabels) { QModelIndexList matched = m_Model->match(m_Model->index(0, 0), QmitkMultiLabelTreeModel::ItemModelRole::LabelInstanceValueRole, QVariant(labelID), 1, Qt::MatchRecursive); if (!matched.empty()) { newCurrentSelection.select(matched.front(), matched.front()); } } m_Controls->view->selectionModel()->select(newCurrentSelection, QItemSelectionModel::ClearAndSelect|QItemSelectionModel::Current); } void QmitkMultiLabelInspector::SetSelectedLabel(mitk::LabelSetImage::LabelValueType selectedLabel) { this->SetSelectedLabels({ selectedLabel }); } QmitkMultiLabelInspector::LabelValueVectorType QmitkMultiLabelInspector::GetSelectedLabelsFromSelectionModel() const { LabelValueVectorType result; QModelIndexList selectedIndexes = m_Controls->view->selectionModel()->selectedIndexes(); for (const auto& index : std::as_const(selectedIndexes)) { QVariant qvariantDataNode = m_Model->data(index, QmitkMultiLabelTreeModel::ItemModelRole::LabelInstanceValueRole); if (qvariantDataNode.canConvert()) { result.push_back(qvariantDataNode.value()); } } return result; } QmitkMultiLabelInspector::LabelValueVectorType QmitkMultiLabelInspector::GetSelectedLabels() const { return m_LastValidSelectedLabels; } mitk::Label* QmitkMultiLabelInspector::GetFirstSelectedLabelObject() const { if (m_LastValidSelectedLabels.empty() || m_Segmentation.IsNull()) return nullptr; return m_Segmentation->GetLabel(m_LastValidSelectedLabels.front()); } void QmitkMultiLabelInspector::OnChangeModelSelection(const QItemSelection& /*selected*/, const QItemSelection& /*deselected*/) { if (!m_ModelManipulationOngoing) { auto internalSelection = GetSelectedLabelsFromSelectionModel(); if (internalSelection.empty()) { //empty selections are not allowed by UI interactions, there should always be at least on label selected. //but selections are e.g. also cleared if the model is updated (e.g. due to addition of labels) UpdateSelectionModel(m_LastValidSelectedLabels); } else { m_LastValidSelectedLabels = internalSelection; emit CurrentSelectionChanged(GetSelectedLabels()); } } } void QmitkMultiLabelInspector::WaitCursorOn() const { QApplication::setOverrideCursor(QCursor(Qt::WaitCursor)); } void QmitkMultiLabelInspector::WaitCursorOff() const { this->RestoreOverrideCursor(); } void QmitkMultiLabelInspector::RestoreOverrideCursor() const { QApplication::restoreOverrideCursor(); } mitk::Label* QmitkMultiLabelInspector::GetCurrentLabel() const { auto currentIndex = this->m_Controls->view->currentIndex(); auto labelVariant = currentIndex.data(QmitkMultiLabelTreeModel::ItemModelRole::LabelDataRole); mitk::Label::Pointer currentIndexLabel = nullptr; if (labelVariant.isValid()) { auto uncastedLabel = labelVariant.value(); currentIndexLabel = static_cast(uncastedLabel); } return currentIndexLabel; } QmitkMultiLabelInspector::IndexLevelType QmitkMultiLabelInspector::GetCurrentLevelType() const { auto currentIndex = this->m_Controls->view->currentIndex(); auto labelInstanceVariant = currentIndex.data(QmitkMultiLabelTreeModel::ItemModelRole::LabelInstanceDataRole); auto labelVariant = currentIndex.data(QmitkMultiLabelTreeModel::ItemModelRole::LabelDataRole); if (labelInstanceVariant.isValid() ) { return IndexLevelType::LabelInstance; } else if (labelVariant.isValid()) { return IndexLevelType::LabelClass; } return IndexLevelType::Group; } QmitkMultiLabelInspector::LabelValueVectorType QmitkMultiLabelInspector::GetCurrentlyAffactedLabelInstances() const { auto currentIndex = m_Controls->view->currentIndex(); return m_Model->GetLabelsInSubTree(currentIndex); } QmitkMultiLabelInspector::LabelValueVectorType QmitkMultiLabelInspector::GetLabelInstancesOfSelectedFirstLabel() const { if (m_Segmentation.IsNull()) return {}; if (this->GetSelectedLabels().empty()) return {}; const auto index = m_Model->indexOfLabel(this->GetSelectedLabels().front()); return m_Model->GetLabelInstancesOfSameLabelClass(index); } mitk::Label* QmitkMultiLabelInspector::AddNewLabelInstanceInternal(mitk::Label* templateLabel) { if (!m_AllowLabelModification) mitkThrow() << "QmitkMultiLabelInspector is configured incorrectly. Set AllowLabelModification to true to allow the usage of AddNewLabelInstance."; if (nullptr == templateLabel) mitkThrow() << "QmitkMultiLabelInspector is in an invalid state. AddNewLabelInstanceInternal was called with a non existing label as template"; auto groupID = m_Segmentation->GetGroupIndexOfLabel(templateLabel->GetValue()); m_ModelManipulationOngoing = true; auto newLabel = m_Segmentation->AddLabel(templateLabel, groupID, true); m_ModelManipulationOngoing = false; this->SetSelectedLabel(newLabel->GetValue()); auto index = m_Model->indexOfLabel(newLabel->GetValue()); if (index.isValid()) { m_Controls->view->expand(index.parent()); } else { mitkThrow() << "Segmentation or QmitkMultiLabelTreeModel is in an invalid state. Label is not present in the model after adding it to the segmentation. Label value: " << newLabel->GetValue(); } emit ModelUpdated(); return newLabel; } mitk::Label* QmitkMultiLabelInspector::AddNewLabelInstance() { auto currentLabel = this->GetFirstSelectedLabelObject(); if (nullptr == currentLabel) return nullptr; auto result = this->AddNewLabelInstanceInternal(currentLabel); // this is needed as workaround for (T27307). It circumvents the fact that modifications // of data (here the segmentation) does not directly trigger the modification of the // owning node (see T27307). Therefore other code (like renderers or model views) that e.g. // listens to the datastorage for modification would not get notified. if (m_SegmentationNode.IsNotNull()) { m_SegmentationNode->Modified(); } return result; } mitk::Label* QmitkMultiLabelInspector::AddNewLabelInternal(const mitk::LabelSetImage::GroupIndexType& containingGroup) { auto newLabel = mitk::LabelSetImageHelper::CreateNewLabel(m_Segmentation); bool canceled = false; if (!m_DefaultLabelNaming) emit LabelRenameRequested(newLabel, false, canceled); if (canceled) return nullptr; m_ModelManipulationOngoing = true; m_Segmentation->AddLabel(newLabel, containingGroup, false); m_ModelManipulationOngoing = false; this->SetSelectedLabel(newLabel->GetValue()); auto index = m_Model->indexOfLabel(newLabel->GetValue()); if (!index.isValid()) mitkThrow() << "Segmentation or QmitkMultiLabelTreeModel is in an invalid state. Label is not present in the " "model after adding it to the segmentation. Label value: " << newLabel->GetValue(); m_Controls->view->expand(index.parent()); emit ModelUpdated(); return newLabel; } mitk::Label* QmitkMultiLabelInspector::AddNewLabel() { if (!m_AllowLabelModification) mitkThrow() << "QmitkMultiLabelInspector is configured incorrectly. Set AllowLabelModification to true to allow the usage of AddNewLabel."; if (m_Segmentation.IsNull()) { return nullptr; } auto currentLabel = this->GetFirstSelectedLabelObject(); mitk::LabelSetImage::GroupIndexType groupID = nullptr != currentLabel ? m_Segmentation->GetGroupIndexOfLabel(currentLabel->GetValue()) : 0; auto result = AddNewLabelInternal(groupID); // this is needed as workaround for (T27307). It circumvents the fact that modifications // of data (here the segmentation) does not directly trigger the modification of the // owning node (see T27307). Therefore other code (like renderers or model views) that e.g. // listens to the datastorage for modification would not get notified. if (m_SegmentationNode.IsNotNull()) { m_SegmentationNode->Modified(); } return result; } void QmitkMultiLabelInspector::DeleteLabelInstance() { if (!m_AllowLabelModification) mitkThrow() << "QmitkMultiLabelInspector is configured incorrectly. Set AllowLabelModification to true to allow the usage of DeleteLabelInstance."; if (m_Segmentation.IsNull()) return; auto label = this->GetFirstSelectedLabelObject(); if (nullptr == label) return; auto index = m_Model->indexOfLabel(label->GetValue()); auto instanceName = index.data(Qt::DisplayRole); auto question = "Do you really want to delete label instance \"" + instanceName.toString() + "\"?"; auto answer = QMessageBox::question(this, QString("Delete label instances"), question, QMessageBox::Yes | QMessageBox::Cancel, QMessageBox::Yes); if (answer == QMessageBox::Yes) { this->DeleteLabelInternal({ label->GetValue() }); // this is needed as workaround for (T27307). It circumvents the fact that modifications // of data (here the segmentation) does not directly trigger the modification of the // owning node (see T27307). Therefore other code (like renderers or model views) that e.g. // listens to the datastorage for modification would not get notified. if (m_SegmentationNode.IsNotNull()) { m_SegmentationNode->Modified(); } } } void QmitkMultiLabelInspector::DeleteLabel() { if (!m_AllowLabelModification) mitkThrow() << "QmitkMultiLabelInspector is configured incorrectly. Set AllowLabelModification to true to allow the usage of DeleteLabel."; if (m_Segmentation.IsNull()) return; const auto label = this->GetFirstSelectedLabelObject(); if (nullptr == label) return; const auto relevantLabels = this->GetLabelInstancesOfSelectedFirstLabel(); if (relevantLabels.empty()) return; auto question = "Do you really want to delete label \"" + QString::fromStdString(label->GetName()); question = relevantLabels.size()==1 ? question + "\"?" : question + "\" with all "+QString::number(relevantLabels.size()) +" instances?"; auto answer = QMessageBox::question(this, QString("Delete label"), question, QMessageBox::Yes | QMessageBox::Cancel, QMessageBox::Yes); if (answer == QMessageBox::Yes) { this->DeleteLabelInternal(relevantLabels); // this is needed as workaround for (T27307). It circumvents the fact that modifications // of data (here the segmentation) does not directly trigger the modification of the // owning node (see T27307). Therefore other code (like renderers or model views) that e.g. // listens to the datastorage for modification would not get notified. if (m_SegmentationNode.IsNotNull()) { m_SegmentationNode->Modified(); } } } void QmitkMultiLabelInspector::DeleteLabelInternal(const LabelValueVectorType& labelValues) { if (!m_AllowLabelModification) mitkThrow() << "QmitkMultiLabelInspector is configured incorrectly. Set AllowLabelModification to true to allow the usage of DeleteLabelInternal."; if (m_Segmentation.IsNull()) { return; } QVariant nextLabelVariant; this->WaitCursorOn(); m_ModelManipulationOngoing = true; for (auto labelValue : labelValues) { if (labelValue == labelValues.back()) { auto currentIndex = m_Model->indexOfLabel(labelValue); auto nextIndex = m_Model->ClosestLabelInstanceIndex(currentIndex); nextLabelVariant = nextIndex.data(QmitkMultiLabelTreeModel::ItemModelRole::LabelInstanceValueRole); } m_Segmentation->RemoveLabel(labelValue); } m_ModelManipulationOngoing = false; this->WaitCursorOff(); if (nextLabelVariant.isValid()) { auto newLabelValue = nextLabelVariant.value(); this->SetSelectedLabel(newLabelValue); auto index = m_Model->indexOfLabel(newLabelValue); //we have to get index again, because it could have changed due to remove operation. if (index.isValid()) { m_Controls->view->expand(index.parent()); } else { mitkThrow() << "Segmentation or QmitkMultiLabelTreeModel is in an invalid state. Label is not present in the model after adding it to the segmentation. Label value: " << newLabelValue; } } else { this->SetSelectedLabels({}); } emit ModelUpdated(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } mitk::Label* QmitkMultiLabelInspector::AddNewGroup() { if (!m_AllowLabelModification) mitkThrow() << "QmitkMultiLabelInspector is configured incorrectly. Set AllowLabelModification to true to allow the usage of AddNewLabel."; if (m_Segmentation.IsNull()) { return nullptr; } mitk::LabelSetImage::GroupIndexType groupID = 0; mitk::Label* newLabel = nullptr; m_ModelManipulationOngoing = true; try { this->WaitCursorOn(); groupID = m_Segmentation->AddLayer(); m_Segmentation->SetActiveLayer(groupID); this->WaitCursorOff(); newLabel = this->AddNewLabelInternal(groupID); } catch (mitk::Exception& e) { this->WaitCursorOff(); m_ModelManipulationOngoing = false; MITK_ERROR << "Exception caught: " << e.GetDescription(); QMessageBox::information(this, "Add group", "Could not add a new group. See error log for details."); } m_ModelManipulationOngoing = false; emit ModelUpdated(); // this is needed as workaround for (T27307). It circumvents the fact that modifications // of data (here the segmentation) does not directly trigger the modification of the // owning node (see T27307). Therefore other code (like renderers or model views) that e.g. // listens to the datastorage for modification would not get notified. if (m_SegmentationNode.IsNotNull()) { m_SegmentationNode->Modified(); } return newLabel; } void QmitkMultiLabelInspector::RemoveGroupInternal(const mitk::LabelSetImage::GroupIndexType& groupID) { if (!m_AllowLabelModification) mitkThrow() << "QmitkMultiLabelInspector is configured incorrectly. Set AllowLabelModification to true to allow the usage of RemoveLabel."; if (m_Segmentation.IsNull()) return; if (m_Segmentation->GetNumberOfLayers() < 2) return; auto currentIndex = m_Model->indexOfGroup(groupID); auto nextIndex = m_Model->ClosestLabelInstanceIndex(currentIndex); auto labelVariant = nextIndex.data(QmitkMultiLabelTreeModel::ItemModelRole::LabelInstanceValueRole); try { this->WaitCursorOn(); m_ModelManipulationOngoing = true; m_Segmentation->RemoveGroup(groupID); m_ModelManipulationOngoing = false; this->WaitCursorOff(); } catch (mitk::Exception& e) { m_ModelManipulationOngoing = false; this->WaitCursorOff(); MITK_ERROR << "Exception caught: " << e.GetDescription(); QMessageBox::information(this, "Delete group", "Could not delete the currently active group. See error log for details."); return; } if (labelVariant.isValid()) { auto newLabelValue = labelVariant.value(); this->SetSelectedLabel(newLabelValue); auto index = m_Model->indexOfLabel(newLabelValue); //we have to get index again, because it could have changed due to remove operation. if (index.isValid()) { m_Controls->view->expand(index.parent()); } else { mitkThrow() << "Segmentation or QmitkMultiLabelTreeModel is in an invalid state. Label is not present in the model after adding it to the segmentation. Label value: " << newLabelValue; } } else { this->SetSelectedLabels({}); } emit ModelUpdated(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkMultiLabelInspector::RemoveGroup() { if (!m_AllowLabelModification) mitkThrow() << "QmitkMultiLabelInspector is configured incorrectly. Set AllowLabelModification to true to allow the usage of RemoveLabel."; if (m_Segmentation.IsNull()) return; if (m_Segmentation->GetNumberOfLayers() < 2) { QMessageBox::information(this, "Delete group", "Cannot delete last remaining group. A segmentation must contain at least a single group."); return; } const auto* selectedLabel = this->GetFirstSelectedLabelObject(); if (selectedLabel == nullptr) return; const auto groupID = m_Segmentation->GetGroupIndexOfLabel(selectedLabel->GetValue()); auto groupName = QString::fromStdString(mitk::LabelSetImageHelper::CreateDisplayGroupName(m_Segmentation, groupID)); auto question = QStringLiteral("Do you really want to delete group \"%1\" including all of its labels?").arg(groupName); auto answer = QMessageBox::question(this, QString("Delete group \"%1\"").arg(groupName), question, QMessageBox::Yes | QMessageBox::No, QMessageBox::Yes); if (answer != QMessageBox::Yes) return; this->RemoveGroupInternal(groupID); } void QmitkMultiLabelInspector::OnDeleteGroup() { if (!m_AllowLabelModification) mitkThrow() << "QmitkMultiLabelInspector is configured incorrectly. Set AllowLabelModification to true to allow the usage of RemoveLabel."; if (m_Segmentation.IsNull()) return; auto currentIndex = this->m_Controls->view->currentIndex(); auto groupIDVariant = currentIndex.data(QmitkMultiLabelTreeModel::ItemModelRole::GroupIDRole); if (groupIDVariant.isValid()) { auto groupID = groupIDVariant.value(); auto groupName = QString::fromStdString(mitk::LabelSetImageHelper::CreateDisplayGroupName(m_Segmentation, groupID)); auto question = QStringLiteral("Do you really want to delete group \"%1\" including all of its labels?").arg(groupName); auto answer = QMessageBox::question(this, QString("Delete group \"%1\"").arg(groupName), question, QMessageBox::Yes | QMessageBox::No, QMessageBox::Yes); if (answer != QMessageBox::Yes) return; this->RemoveGroupInternal(groupID); // this is needed as workaround for (T27307). It circumvents the fact that modifications // of data (here the segmentation) does not directly trigger the modification of the // owning node (see T27307). Therefore other code (like renderers or model views) that e.g. // listens to the datastorage for modification would not get notified. if (m_SegmentationNode.IsNotNull()) { m_SegmentationNode->Modified(); } } }; void QmitkMultiLabelInspector::OnContextMenuRequested(const QPoint& /*pos*/) { if (m_Segmentation.IsNull() || !this->isEnabled()) return; const auto indexLevel = this->GetCurrentLevelType(); auto currentIndex = this->m_Controls->view->currentIndex(); //this ensures correct highlighting is the context menu is triggered while //another context menu is already open. if (currentIndex.isValid() && this->m_AboutToShowContextMenu) this->OnEntered(this->m_Controls->view->currentIndex()); QMenu* menu = new QMenu(this); if (IndexLevelType::Group == indexLevel) { if (m_AllowLabelModification) { QAction* addInstanceAction = new QAction(QmitkStyleManager::ThemeIcon(QStringLiteral(":/Qmitk/icon_label_add.svg")), "&Add label", this); QObject::connect(addInstanceAction, &QAction::triggered, this, &QmitkMultiLabelInspector::OnAddLabel); menu->addAction(addInstanceAction); if (m_Segmentation->GetNumberOfLayers() > 1) { QAction* removeAction = new QAction(QmitkStyleManager::ThemeIcon(QStringLiteral(":/Qmitk/icon_group_delete.svg")), "Delete group", this); QObject::connect(removeAction, &QAction::triggered, this, &QmitkMultiLabelInspector::OnDeleteGroup); menu->addAction(removeAction); } } if (m_AllowLockModification) { menu->addSeparator(); QAction* lockAllAction = new QAction(QmitkStyleManager::ThemeIcon(QLatin1String(":/Qmitk/lock.svg")), "Lock group", this); QObject::connect(lockAllAction, &QAction::triggered, this, &QmitkMultiLabelInspector::OnLockAffectedLabels); menu->addAction(lockAllAction); QAction* unlockAllAction = new QAction(QmitkStyleManager::ThemeIcon(QLatin1String(":/Qmitk/unlock.svg")), "Unlock group", this); QObject::connect(unlockAllAction, &QAction::triggered, this, &QmitkMultiLabelInspector::OnUnlockAffectedLabels); menu->addAction(unlockAllAction); } if (m_AllowVisibilityModification) { menu->addSeparator(); QAction* viewAllAction = new QAction(QmitkStyleManager::ThemeIcon(QLatin1String(":/Qmitk/visible.svg")), "Show group", this); QObject::connect(viewAllAction, &QAction::triggered, this, &QmitkMultiLabelInspector::OnSetAffectedLabelsVisible); menu->addAction(viewAllAction); QAction* hideAllAction = new QAction(QmitkStyleManager::ThemeIcon(QLatin1String(":/Qmitk/invisible.svg")), "Hide group", this); QObject::connect(hideAllAction, &QAction::triggered, this, &QmitkMultiLabelInspector::OnSetAffectedLabelsInvisible); menu->addAction(hideAllAction); menu->addSeparator(); auto opacityAction = this->CreateOpacityAction(); if (nullptr != opacityAction) menu->addAction(opacityAction); } } else if (IndexLevelType::LabelClass == indexLevel) { if (m_AllowLabelModification) { QAction* addInstanceAction = new QAction(QmitkStyleManager::ThemeIcon(QStringLiteral(":/Qmitk/icon_label_add_instance.svg")), "Add label instance", this); QObject::connect(addInstanceAction, &QAction::triggered, this, &QmitkMultiLabelInspector::OnAddLabelInstance); menu->addAction(addInstanceAction); QAction* renameAction = new QAction(QIcon(":/Qmitk/RenameLabel.png"), "&Rename label", this); QObject::connect(renameAction, SIGNAL(triggered(bool)), this, SLOT(OnRenameLabel(bool))); menu->addAction(renameAction); QAction* removeAction = new QAction(QmitkStyleManager::ThemeIcon(QStringLiteral(":/Qmitk/icon_label_delete.svg")), "&Delete label", this); QObject::connect(removeAction, &QAction::triggered, this, &QmitkMultiLabelInspector::OnDeleteAffectedLabel); menu->addAction(removeAction); } if (m_AllowLockModification) { menu->addSeparator(); QAction* lockAllAction = new QAction(QmitkStyleManager::ThemeIcon(QLatin1String(":/Qmitk/lock.svg")), "Lock label instances", this); QObject::connect(lockAllAction, &QAction::triggered, this, &QmitkMultiLabelInspector::OnLockAffectedLabels); menu->addAction(lockAllAction); QAction* unlockAllAction = new QAction(QmitkStyleManager::ThemeIcon(QLatin1String(":/Qmitk/unlock.svg")), "Unlock label instances", this); QObject::connect(unlockAllAction, &QAction::triggered, this, &QmitkMultiLabelInspector::OnUnlockAffectedLabels); menu->addAction(unlockAllAction); } if (m_AllowVisibilityModification) { menu->addSeparator(); QAction* viewAllAction = new QAction(QmitkStyleManager::ThemeIcon(QLatin1String(":/Qmitk/visible.svg")), "Show label instances", this); QObject::connect(viewAllAction, &QAction::triggered, this, &QmitkMultiLabelInspector::OnSetAffectedLabelsVisible); menu->addAction(viewAllAction); QAction* hideAllAction = new QAction(QmitkStyleManager::ThemeIcon(QLatin1String(":/Qmitk/invisible.svg")), "Hide label instances", this); QObject::connect(hideAllAction, &QAction::triggered, this, &QmitkMultiLabelInspector::OnSetAffectedLabelsInvisible); menu->addAction(hideAllAction); menu->addSeparator(); auto opacityAction = this->CreateOpacityAction(); if (nullptr!=opacityAction) menu->addAction(opacityAction); } } else { auto selectedLabelValues = this->GetSelectedLabels(); if (selectedLabelValues.empty()) return; if (this->GetMultiSelectionMode() && selectedLabelValues.size() > 1) { if (m_AllowLabelModification) { QAction* mergeAction = new QAction(QIcon(":/Qmitk/MergeLabels.png"), "Merge selection on current label", this); QObject::connect(mergeAction, SIGNAL(triggered(bool)), this, SLOT(OnMergeLabels(bool))); menu->addAction(mergeAction); QAction* removeLabelsAction = new QAction(QmitkStyleManager::ThemeIcon(QStringLiteral(":/Qmitk/icon_label_delete_instance.svg")), "&Delete selected labels", this); QObject::connect(removeLabelsAction, SIGNAL(triggered(bool)), this, SLOT(OnDeleteLabels(bool))); menu->addAction(removeLabelsAction); QAction* clearLabelsAction = new QAction(QIcon(":/Qmitk/EraseLabel.png"), "&Clear selected labels", this); QObject::connect(clearLabelsAction, SIGNAL(triggered(bool)), this, SLOT(OnClearLabels(bool))); menu->addAction(clearLabelsAction); } if (m_AllowVisibilityModification) { if (m_AllowLabelModification) menu->addSeparator(); QAction* viewOnlyAction = new QAction(QmitkStyleManager::ThemeIcon(QLatin1String(":/Qmitk/visible.svg")), "Hide everything but this", this); QObject::connect(viewOnlyAction, SIGNAL(triggered(bool)), this, SLOT(OnSetOnlyActiveLabelVisible(bool))); menu->addAction(viewOnlyAction); menu->addSeparator(); auto opacityAction = this->CreateOpacityAction(); if (nullptr != opacityAction) menu->addAction(opacityAction); } } else { if (m_AllowLabelModification) { QAction* addInstanceAction = new QAction(QmitkStyleManager::ThemeIcon(QStringLiteral(":/Qmitk/icon_label_add_instance.svg")), "&Add label instance", this); QObject::connect(addInstanceAction, &QAction::triggered, this, &QmitkMultiLabelInspector::OnAddLabelInstance); menu->addAction(addInstanceAction); const auto selectedLabelIndex = m_Model->indexOfLabel(selectedLabelValues.front()); if (m_Model->GetLabelInstancesOfSameLabelClass(selectedLabelIndex).size() > 1) // Only labels that actually appear as instance (having additional instances) { QAction* renameAction = new QAction(QIcon(":/Qmitk/RenameLabel.png"), "&Rename label instance", this); QObject::connect(renameAction, SIGNAL(triggered(bool)), this, SLOT(OnRenameLabel(bool))); menu->addAction(renameAction); QAction* removeInstanceAction = new QAction(QmitkStyleManager::ThemeIcon(QStringLiteral(":/Qmitk/icon_label_delete_instance.svg")), "&Delete label instance", this); QObject::connect(removeInstanceAction, &QAction::triggered, this, &QmitkMultiLabelInspector::DeleteLabelInstance); menu->addAction(removeInstanceAction); } else { QAction* renameAction = new QAction(QIcon(":/Qmitk/RenameLabel.png"), "&Rename label", this); QObject::connect(renameAction, SIGNAL(triggered(bool)), this, SLOT(OnRenameLabel(bool))); menu->addAction(renameAction); } QAction* removeLabelAction = new QAction(QmitkStyleManager::ThemeIcon(QStringLiteral(":/Qmitk/icon_label_delete.svg")), "Delete &label", this); QObject::connect(removeLabelAction, &QAction::triggered, this, &QmitkMultiLabelInspector::DeleteLabel); menu->addAction(removeLabelAction); QAction* clearAction = new QAction(QIcon(":/Qmitk/EraseLabel.png"), "&Clear content", this); QObject::connect(clearAction, SIGNAL(triggered(bool)), this, SLOT(OnClearLabel(bool))); menu->addAction(clearAction); } if (m_AllowVisibilityModification) { if (m_AllowLabelModification) menu->addSeparator(); QAction* viewOnlyAction = new QAction(QmitkStyleManager::ThemeIcon(QLatin1String(":/Qmitk/visible.svg")), "Hide everything but this", this); QObject::connect(viewOnlyAction, SIGNAL(triggered(bool)), this, SLOT(OnSetOnlyActiveLabelVisible(bool))); menu->addAction(viewOnlyAction); menu->addSeparator(); auto opacityAction = this->CreateOpacityAction(); if (nullptr != opacityAction) menu->addAction(opacityAction); } } } QObject::connect(menu, &QMenu::aboutToHide, this, &QmitkMultiLabelInspector::OnMouseLeave); m_AboutToShowContextMenu = true; menu->popup(QCursor::pos()); } QWidgetAction* QmitkMultiLabelInspector::CreateOpacityAction() { auto selectedLabelValues = this->GetSelectedLabels(); auto relevantLabelValues = !this->GetMultiSelectionMode() || selectedLabelValues.size() <= 1 ? this->GetCurrentlyAffactedLabelInstances() : selectedLabelValues; std::vector relevantLabels; if (!relevantLabelValues.empty()) { for (auto value : relevantLabelValues) { auto label = this->m_Segmentation->GetLabel(value); if (nullptr == label) mitkThrow() << "Invalid state. Internal model returned a label value that does not exist in segmentation. Invalid value:" << value; relevantLabels.emplace_back(label); } auto* opacitySlider = new QSlider; opacitySlider->setMinimum(0); opacitySlider->setMaximum(100); opacitySlider->setOrientation(Qt::Horizontal); auto opacity = relevantLabels.front()->GetOpacity(); opacitySlider->setValue(static_cast(opacity * 100)); auto segmentation = m_Segmentation; auto node = m_SegmentationNode; auto onChangeLambda = [segmentation, relevantLabels](const int value) { auto opacity = static_cast(value) / 100.0f; for (auto label : relevantLabels) { label->SetOpacity(opacity); segmentation->UpdateLookupTable(label->GetValue()); } segmentation->GetLookupTable()->Modified(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); }; QObject::connect(opacitySlider, &QSlider::valueChanged, this, onChangeLambda); auto onPressedLambda = [node]() { DeactivateLabelHighlights(node); }; QObject::connect(opacitySlider, &QSlider::sliderPressed, this, onPressedLambda); auto onReleasedLambda = [node, relevantLabelValues]() { ActivateLabelHighlights(node, relevantLabelValues); }; QObject::connect(opacitySlider, &QSlider::sliderReleased, this, onReleasedLambda); QLabel* opacityLabel = new QLabel("Opacity: "); QVBoxLayout* opacityWidgetLayout = new QVBoxLayout; opacityWidgetLayout->setContentsMargins(4, 4, 4, 4); opacityWidgetLayout->addWidget(opacityLabel); opacityWidgetLayout->addWidget(opacitySlider); QWidget* opacityWidget = new QWidget; opacityWidget->setLayout(opacityWidgetLayout); QWidgetAction* opacityAction = new QWidgetAction(this); opacityAction->setDefaultWidget(opacityWidget); return opacityAction; } return nullptr; } void QmitkMultiLabelInspector::OnClearLabels(bool /*value*/) { QString question = "Do you really want to clear the selected labels?"; QMessageBox::StandardButton answerButton = QMessageBox::question( this, "Clear selected labels", question, QMessageBox::Yes | QMessageBox::Cancel, QMessageBox::Yes); if (answerButton == QMessageBox::Yes) { this->WaitCursorOn(); m_Segmentation->EraseLabels(this->GetSelectedLabels()); this->WaitCursorOff(); // this is needed as workaround for (T27307). It circumvents the fact that modifications // of data (here the segmentation) does not directly trigger the modification of the // owning node (see T27307). Therefore other code (like renderers or model views) that e.g. // listens to the datastorage for modification would not get notified. if (m_SegmentationNode.IsNotNull()) { m_SegmentationNode->Modified(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } } void QmitkMultiLabelInspector::OnDeleteAffectedLabel() { if (!m_AllowLabelModification) mitkThrow() << "QmitkMultiLabelInspector is configured incorrectly. Set AllowLabelModification to true to allow the usage of RemoveLabel."; if (m_Segmentation.IsNull()) { return; } auto affectedLabels = GetCurrentlyAffactedLabelInstances(); auto currentLabel = m_Segmentation->GetLabel(affectedLabels.front()); QString question = "Do you really want to delete all instances of label \"" + QString::fromStdString(currentLabel->GetName()) + "\"?"; QMessageBox::StandardButton answerButton = QMessageBox::question(this, "Delete label", question, QMessageBox::Yes | QMessageBox::Cancel, QMessageBox::Yes); if (answerButton == QMessageBox::Yes) { this->DeleteLabelInternal(affectedLabels); // this is needed as workaround for (T27307). It circumvents the fact that modifications // of data (here the segmentation) does not directly trigger the modification of the // owning node (see T27307). Therefore other code (like renderers or model views) that e.g. // listens to the datastorage for modification would not get notified. if (m_SegmentationNode.IsNotNull()) { m_SegmentationNode->Modified(); } } } void QmitkMultiLabelInspector::OnDeleteLabels(bool /*value*/) { QString question = "Do you really want to remove the selected labels?"; QMessageBox::StandardButton answerButton = QMessageBox::question( this, "Remove selected labels", question, QMessageBox::Yes | QMessageBox::Cancel, QMessageBox::Yes); if (answerButton == QMessageBox::Yes) { this->WaitCursorOn(); m_Segmentation->RemoveLabels(this->GetSelectedLabels()); this->WaitCursorOff(); // this is needed as workaround for (T27307). It circumvents the fact that modifications // of data (here the segmentation) does not directly trigger the modification of the // owning node (see T27307). Therefore other code (like renderers or model views) that e.g. // listens to the datastorage for modification would not get notified. if (m_SegmentationNode.IsNotNull()) { m_SegmentationNode->Modified(); } } } void QmitkMultiLabelInspector::OnMergeLabels(bool /*value*/) { auto currentLabel = GetCurrentLabel(); QString question = "Do you really want to merge selected labels into \"" + QString::fromStdString(currentLabel->GetName())+"\"?"; QMessageBox::StandardButton answerButton = QMessageBox::question( this, "Merge selected label", question, QMessageBox::Yes | QMessageBox::Cancel, QMessageBox::Yes); if (answerButton == QMessageBox::Yes) { this->WaitCursorOn(); m_Segmentation->MergeLabels(currentLabel->GetValue(), this->GetSelectedLabels()); this->WaitCursorOff(); // this is needed as workaround for (T27307). It circumvents the fact that modifications // of data (here the segmentation) does not directly trigger the modification of the // owning node (see T27307). Therefore other code (like renderers or model views) that e.g. // listens to the datastorage for modification would not get notified. if (m_SegmentationNode.IsNotNull()) { m_SegmentationNode->Modified(); } } } void QmitkMultiLabelInspector::OnAddLabel() { auto currentIndex = this->m_Controls->view->currentIndex(); auto groupIDVariant = currentIndex.data(QmitkMultiLabelTreeModel::ItemModelRole::GroupIDRole); if (groupIDVariant.isValid()) { auto groupID = groupIDVariant.value(); this->AddNewLabelInternal(groupID); // this is needed as workaround for (T27307). It circumvents the fact that modifications // of data (here the segmentation) does not directly trigger the modification of the // owning node (see T27307). Therefore other code (like renderers or model views) that e.g. // listens to the datastorage for modification would not get notified. if (m_SegmentationNode.IsNotNull()) { m_SegmentationNode->Modified(); } } } void QmitkMultiLabelInspector::OnAddLabelInstance() { auto currentLabel = this->GetCurrentLabel(); if (nullptr == currentLabel) return; this->AddNewLabelInstanceInternal(currentLabel); // this is needed as workaround for (T27307). It circumvents the fact that modifications // of data (here the segmentation) does not directly trigger the modification of the // owning node (see T27307). Therefore other code (like renderers or model views) that e.g. // listens to the datastorage for modification would not get notified. if (m_SegmentationNode.IsNotNull()) { m_SegmentationNode->Modified(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkMultiLabelInspector::OnClearLabel(bool /*value*/) { auto currentLabel = GetFirstSelectedLabelObject(); QString question = "Do you really want to clear the contents of label \"" + QString::fromStdString(currentLabel->GetName())+"\"?"; QMessageBox::StandardButton answerButton = QMessageBox::question(this, "Clear label", question, QMessageBox::Yes | QMessageBox::Cancel, QMessageBox::Yes); if (answerButton == QMessageBox::Yes) { this->WaitCursorOn(); m_Segmentation->EraseLabel(currentLabel->GetValue()); this->WaitCursorOff(); // this is needed as workaround for (T27307). It circumvents the fact that modifications // of data (here the segmentation) does not directly trigger the modification of the // owning node (see T27307). Therefore other code (like renderers or model views) that e.g. // listens to the datastorage for modification would not get notified. if (m_SegmentationNode.IsNotNull()) { m_SegmentationNode->Modified(); } } } void QmitkMultiLabelInspector::OnRenameLabel(bool /*value*/) { auto relevantLabelValues = this->GetCurrentlyAffactedLabelInstances(); auto currentLabel = this->GetCurrentLabel(); bool canceled = false; emit LabelRenameRequested(currentLabel, true, canceled); if (canceled) return; for (auto value : relevantLabelValues) { if (value != currentLabel->GetValue()) { auto label = this->m_Segmentation->GetLabel(value); if (nullptr == label) mitkThrow() << "Invalid state. Internal model returned a label value that does not exist in segmentation. Invalid value:" << value; label->SetName(currentLabel->GetName()); label->SetColor(currentLabel->GetColor()); m_Segmentation->UpdateLookupTable(label->GetValue()); + m_Segmentation->GetLookupTable()->Modified(); mitk::DICOMSegmentationPropertyHelper::SetDICOMSegmentProperties(label); // this is needed as workaround for (T27307). It circumvents the fact that modifications // of data (here the segmentation) does not directly trigger the modification of the // owning node (see T27307). Therefore other code (like renderers or model views) that e.g. // listens to the datastorage for modification would not get notified. if (m_SegmentationNode.IsNotNull()) { m_SegmentationNode->Modified(); } } } emit ModelUpdated(); } void QmitkMultiLabelInspector::SetLockOfAffectedLabels(bool locked) const { auto relevantLabelValues = this->GetCurrentlyAffactedLabelInstances(); if (!relevantLabelValues.empty()) { for (auto value : relevantLabelValues) { auto label = this->m_Segmentation->GetLabel(value); if (nullptr == label) mitkThrow() << "Invalid state. Internal model returned a label value that does not exist in segmentation. Invalid value:" << value; label->SetLocked(locked); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkMultiLabelInspector::OnUnlockAffectedLabels() { this->SetLockOfAffectedLabels(false); } void QmitkMultiLabelInspector::OnLockAffectedLabels() { this->SetLockOfAffectedLabels(true); } void QmitkMultiLabelInspector::SetVisibilityOfAffectedLabels(bool visible) const { auto relevantLabelValues = this->GetCurrentlyAffactedLabelInstances(); if (!relevantLabelValues.empty()) { for (auto value : relevantLabelValues) { auto label = this->m_Segmentation->GetLabel(value); if (nullptr == label) mitkThrow() << "Invalid state. Internal model returned a label value that does not exist in segmentation. Invalid value:" << value; label->SetVisible(visible); m_Segmentation->UpdateLookupTable(label->GetValue()); } m_Segmentation->GetLookupTable()->Modified(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkMultiLabelInspector::OnSetAffectedLabelsVisible() { this->SetVisibilityOfAffectedLabels(true); } void QmitkMultiLabelInspector::OnSetAffectedLabelsInvisible() { this->SetVisibilityOfAffectedLabels(false); } void QmitkMultiLabelInspector::OnSetOnlyActiveLabelVisible(bool /*value*/) { auto selectedLabelValues = this->GetSelectedLabels(); if (selectedLabelValues.empty()) return; m_Segmentation->SetAllLabelsVisible(false); for (auto selectedValue : selectedLabelValues) { auto currentLabel = m_Segmentation->GetLabel(selectedValue); currentLabel->SetVisible(true); m_Segmentation->UpdateLookupTable(selectedValue); } + m_Segmentation->GetLookupTable()->Modified(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); this->PrepareGoToLabel(selectedLabelValues.front()); } void QmitkMultiLabelInspector::OnItemDoubleClicked(const QModelIndex& index) { if (!index.isValid()) return; if (index.column() > 0) return; auto labelVariant = index.data(QmitkMultiLabelTreeModel::ItemModelRole::LabelInstanceValueRole); if (!labelVariant.isValid()) return; const auto labelID = labelVariant.value(); if (QApplication::queryKeyboardModifiers().testFlag(Qt::AltModifier)) { this->OnRenameLabel(false); return; } this->PrepareGoToLabel(labelID); } void QmitkMultiLabelInspector::PrepareGoToLabel(mitk::Label::PixelType labelID) const { this->WaitCursorOn(); m_Segmentation->UpdateCenterOfMass(labelID); const auto currentLabel = m_Segmentation->GetLabel(labelID); const mitk::Point3D& pos = currentLabel->GetCenterOfMassCoordinates(); this->WaitCursorOff(); if (pos.GetVnlVector().max_value() > 0.0) { emit GoToLabel(currentLabel->GetValue(), pos); } } void QmitkMultiLabelInspector::OnEntered(const QModelIndex& index) { if (m_SegmentationNode.IsNotNull()) { auto labelVariant = index.data(QmitkMultiLabelTreeModel::ItemModelRole::LabelInstanceValueRole); auto highlightedValues = m_Model->GetLabelsInSubTree(index); ActivateLabelHighlights(m_SegmentationNode, highlightedValues); } m_AboutToShowContextMenu = false; } void QmitkMultiLabelInspector::OnMouseLeave() { if (m_SegmentationNode.IsNotNull() && !m_AboutToShowContextMenu) { DeactivateLabelHighlights(m_SegmentationNode); } else { m_AboutToShowContextMenu = false; } } diff --git a/Modules/SegmentationUI/Qmitk/QmitkMultiLabelSegWithPreviewToolGUIBase.cpp b/Modules/SegmentationUI/Qmitk/QmitkMultiLabelSegWithPreviewToolGUIBase.cpp index 004cd80513..5d8ef26003 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkMultiLabelSegWithPreviewToolGUIBase.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkMultiLabelSegWithPreviewToolGUIBase.cpp @@ -1,149 +1,150 @@ /*============================================================================ 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 "QmitkMultiLabelSegWithPreviewToolGUIBase.h" #include "mitkSegWithPreviewTool.h" #include #include QmitkMultiLabelSegWithPreviewToolGUIBase::QmitkMultiLabelSegWithPreviewToolGUIBase() : QmitkSegWithPreviewToolGUIBase(false) { auto enableMLSelectedDelegate = [this](bool enabled) { auto tool = this->GetConnectedToolAs(); return nullptr != tool ? (tool->GetLabelTransferScope() == mitk::SegWithPreviewTool::LabelTransferScope::AllLabels || !tool->GetSelectedLabels().empty()) && enabled : false; }; m_EnableConfirmSegBtnFnc = enableMLSelectedDelegate; } void QmitkMultiLabelSegWithPreviewToolGUIBase::InitializeUI(QBoxLayout* mainLayout) { auto radioTransferAll = new QRadioButton("Transfer all labels", this); radioTransferAll->setToolTip("Transfer all preview labels when confirmed."); radioTransferAll->setChecked(true); connect(radioTransferAll, &QAbstractButton::toggled, this, &QmitkMultiLabelSegWithPreviewToolGUIBase::OnRadioTransferAllClicked); mainLayout->addWidget(radioTransferAll); m_RadioTransferAll = radioTransferAll; auto radioTransferSelected = new QRadioButton("Transfer selected labels", this); radioTransferSelected->setToolTip("Transfer the selected preview labels when confirmed."); radioTransferSelected->setChecked(false); mainLayout->addWidget(radioTransferSelected); m_RadioTransferSelected = radioTransferSelected; m_LabelSelectionList = new QmitkSimpleLabelSetListWidget(this); m_LabelSelectionList->setObjectName(QString::fromUtf8("m_LabelSelectionList")); QSizePolicy sizePolicy2(QSizePolicy::Minimum, QSizePolicy::MinimumExpanding); sizePolicy2.setHorizontalStretch(0); sizePolicy2.setVerticalStretch(0); sizePolicy2.setHeightForWidth(m_LabelSelectionList->sizePolicy().hasHeightForWidth()); m_LabelSelectionList->setSizePolicy(sizePolicy2); m_LabelSelectionList->setMaximumSize(QSize(10000000, 10000000)); m_LabelSelectionList->setVisible(false); mainLayout->addWidget(m_LabelSelectionList); connect(m_LabelSelectionList, &QmitkSimpleLabelSetListWidget::SelectedLabelsChanged, this, &QmitkMultiLabelSegWithPreviewToolGUIBase::OnLabelSelectionChanged); this->OnRadioTransferAllClicked(true); Superclass::InitializeUI(mainLayout); } void QmitkMultiLabelSegWithPreviewToolGUIBase::OnLabelSelectionChanged(const QmitkSimpleLabelSetListWidget::LabelVectorType& selectedLabels) { auto tool = this->GetConnectedToolAs(); if (nullptr != tool) { mitk::SegWithPreviewTool::SelectedLabelVectorType labelIDs; for (const auto& label : selectedLabels) { labelIDs.push_back(label->GetValue()); } tool->SetSelectedLabels(labelIDs); this->ActualizePreviewLabelVisibility(); this->EnableWidgets(true); //used to actualize the ConfirmSeg btn via the delegate; } } void QmitkMultiLabelSegWithPreviewToolGUIBase::ActualizePreviewLabelVisibility() { auto tool = this->GetConnectedToolAs(); if (nullptr != tool) { auto preview = tool->GetPreviewSegmentation(); if (nullptr != preview) { auto labels = preview->GetLabelsByValue(preview->GetLabelValuesByGroup(preview->GetActiveLayer())); auto selectedLabels = tool->GetSelectedLabels(); for (auto label : labels) { bool isVisible = tool->GetLabelTransferScope() == mitk::SegWithPreviewTool::LabelTransferScope::AllLabels || (std::find(selectedLabels.begin(), selectedLabels.end(), label->GetValue()) != selectedLabels.end()); label->SetVisible(isVisible); preview->UpdateLookupTable(label->GetValue()); } + preview->GetLookupTable()->Modified(); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkMultiLabelSegWithPreviewToolGUIBase::OnRadioTransferAllClicked(bool checked) { m_LabelSelectionList->setVisible(!checked); auto tool = this->GetConnectedToolAs(); if (nullptr != tool) { if (checked) { tool->SetLabelTransferScope(mitk::SegWithPreviewTool::LabelTransferScope::AllLabels); } else { tool->SetLabelTransferScope(mitk::SegWithPreviewTool::LabelTransferScope::SelectedLabels); } } this->ActualizePreviewLabelVisibility(); } void QmitkMultiLabelSegWithPreviewToolGUIBase::EnableWidgets(bool enabled) { Superclass::EnableWidgets(enabled); if (nullptr != m_LabelSelectionList) { m_LabelSelectionList->setEnabled(enabled); } if (nullptr != m_RadioTransferAll) { m_RadioTransferAll->setEnabled(enabled); } if (nullptr != m_RadioTransferSelected) { m_RadioTransferSelected->setEnabled(enabled); } } void QmitkMultiLabelSegWithPreviewToolGUIBase::SetLabelSetPreview(const mitk::LabelSetImage* preview) { if (nullptr != m_LabelSelectionList) { m_LabelSelectionList->SetLabelSetImage(preview); } }