diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/CMakeLists.txt b/Plugins/org.mitk.gui.qt.semanticrelations/CMakeLists.txt index 2ffd63c2e3..970cb000dd 100644 --- a/Plugins/org.mitk.gui.qt.semanticrelations/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.semanticrelations/CMakeLists.txt @@ -1,7 +1,7 @@ project(org_mitk_gui_qt_semanticrelations) mitk_create_plugin( EXPORT_DIRECTIVE MITK_GUI_SEMANTICRELATIONS_EXPORT EXPORTED_INCLUDE_SUFFIXES src - MODULE_DEPENDS MitkPersistence MitkSemanticRelationsUI MitkRenderWindowManager + MODULE_DEPENDS MitkPersistence MitkSemanticRelationsUI MitkRenderWindowManager MitkMultilabel MitkSegmentationUI ) diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidget.cpp b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidget.cpp index 910b6cefaa..4a6872c152 100644 --- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidget.cpp +++ b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidget.cpp @@ -1,461 +1,496 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // semantic relations plugin #include "QmitkLesionInfoWidget.h" #include "QmitkDataNodeAddToSemanticRelationsAction.h" #include "QmitkFocusOnLesionAction.h" #include "QmitkSemanticRelationsNodeSelectionDialog.h" // semantic relations UI module #include // semantic relations module #include #include #include #include #include -// registration ontology module -//#include +// segmentation +#include +#include // qt #include #include #include #include #include QmitkLesionInfoWidget::QmitkLesionInfoWidget(mitk::DataStorage* dataStorage, berry::IWorkbenchPartSite::Pointer workbenchPartSite, QWidget* parent /*= nullptr*/) : QWidget(parent) , m_DataStorage(dataStorage) , m_WorkbenchPartSite(workbenchPartSite) , m_SemanticRelationsDataStorageAccess(std::make_unique(dataStorage)) , m_SemanticRelationsIntegration(std::make_unique()) { Initialize(); } void QmitkLesionInfoWidget::Initialize() { m_Controls.setupUi(this); m_Controls.lesionTreeView->setAlternatingRowColors(true); m_Controls.lesionTreeView->setSelectionMode(QAbstractItemView::SingleSelection); m_Controls.lesionTreeView->setSelectionBehavior(QAbstractItemView::SelectRows); m_Controls.lesionTreeView->setContextMenuPolicy(Qt::CustomContextMenu); m_StorageModel = new QmitkLesionTreeModel(m_Controls.lesionTreeView); if (m_DataStorage.IsExpired()) { return; } auto dataStorage = m_DataStorage.Lock(); m_StorageModel->SetDataStorage(dataStorage); m_Controls.lesionTreeView->setModel(m_StorageModel); SetUpConnections(); } void QmitkLesionInfoWidget::SetUpConnections() { connect(m_StorageModel, &QmitkLesionTreeModel::ModelUpdated, this, &QmitkLesionInfoWidget::OnModelUpdated); connect(m_Controls.addLesionPushButton, &QPushButton::clicked, this, &QmitkLesionInfoWidget::OnAddLesionButtonClicked); connect(m_Controls.lesionTreeView->selectionModel(), &QItemSelectionModel::currentChanged, this, &QmitkLesionInfoWidget::OnSelectionChanged); connect(m_Controls.lesionTreeView, &QTreeView::customContextMenuRequested, this, &QmitkLesionInfoWidget::OnLesionListContextMenuRequested); } void QmitkLesionInfoWidget::SetCaseID(const mitk::SemanticTypes::CaseID& caseID) { m_CaseID = caseID; m_StorageModel->SetCaseID(caseID); } void QmitkLesionInfoWidget::SetDataNodeSelection(const QList& dataNodeSelection) { m_StorageModel->SetDataNodeSelection(dataNodeSelection); } ////////////////////////////////////////////////////////////////////////// // Implementation of the QT_SLOTS ////////////////////////////////////////////////////////////////////////// void QmitkLesionInfoWidget::OnModelUpdated() { m_Controls.lesionTreeView->expandAll(); int columns = m_Controls.lesionTreeView->model()->columnCount(); for (int i = 0; i < columns; ++i) { m_Controls.lesionTreeView->resizeColumnToContents(i); } } void QmitkLesionInfoWidget::OnAddLesionButtonClicked() { if (m_CaseID.empty()) { QMessageBox msgBox(QMessageBox::Warning, "No case ID set.", "In order to add a lesion, please specify the current case / patient."); msgBox.exec(); return; } mitk::SemanticTypes::Lesion newLesion = mitk::GenerateNewLesion(); try { m_SemanticRelationsIntegration->AddLesion(m_CaseID, newLesion); } catch (mitk::SemanticRelationException& e) { MITK_INFO << "Could not add a new lesion. " << e; } } void QmitkLesionInfoWidget::OnSelectionChanged(const QModelIndex& current, const QModelIndex& /*previous*/) { // only the UID is needed to identify a representing lesion QVariant data = m_StorageModel->data(current, Qt::UserRole); if (!data.canConvert()) { return; } auto lesion = data.value()->GetData().GetLesion(); if (false == mitk::SemanticRelationsInference::InstanceExists(m_CaseID, lesion)) { // no UID of a existing lesion found; cannot create a lesion return; } // if selected data nodes are set, reset to empty list to // hide "selected data nodes presence background highlighting" in the model if (!m_StorageModel->GetSelectedDataNodes().isEmpty()) { m_StorageModel->SetDataNodeSelection(QList()); } emit LesionSelectionChanged(lesion); } void QmitkLesionInfoWidget::OnLesionListContextMenuRequested(const QPoint& pos) { if (nullptr == m_SemanticRelationsIntegration) { return; } if (m_CaseID.empty()) { QMessageBox msgBox(QMessageBox::Warning, "No case ID set.", "In order to access the context menu entries a case ID has to be set."); msgBox.exec(); return; } QModelIndex index = m_Controls.lesionTreeView->indexAt(pos); if (!index.isValid()) { // no item clicked; cannot retrieve the current lesion return; } QVariant data = m_StorageModel->data(index, Qt::UserRole); mitk::SemanticTypes::Lesion selectedLesion; if (data.canConvert()) { selectedLesion = data.value()->GetData().GetLesion(); } else { return; } QMenu* menu = new QMenu(m_Controls.lesionTreeView); QAction* linkToSegmentation = new QAction("Link to segmentation", this); linkToSegmentation->setEnabled(true); connect(linkToSegmentation, &QAction::triggered, [this, selectedLesion] { OnLinkToSegmentation(selectedLesion); }); menu->addAction(linkToSegmentation); QAction* setLesionName = new QAction("Set lesion name", this); setLesionName->setEnabled(true); connect(setLesionName, &QAction::triggered, [this, selectedLesion] { OnSetLesionName(selectedLesion); }); menu->addAction(setLesionName); QAction* setLesionClass = new QAction("Set lesion class", this); setLesionClass->setEnabled(true); connect(setLesionClass, &QAction::triggered, [this, selectedLesion] { OnSetLesionClass(selectedLesion); }); menu->addAction(setLesionClass); - QAction* propageLesionToImage = new QAction("Propagate lesion to image", this); - propageLesionToImage->setEnabled(true); - connect(propageLesionToImage, &QAction::triggered, [this, selectedLesion] { OnPropagateLesion(selectedLesion); }); - menu->addAction(propageLesionToImage); + QAction* createNewSegmentation = new QAction("Create new lesion", this); + createNewSegmentation->setEnabled(true); + connect(createNewSegmentation, &QAction::triggered, [this, selectedLesion] { OnCreateNewSegmentation(selectedLesion); }); + menu->addAction(createNewSegmentation); QAction* removeLesion = new QAction("Remove lesion", this); removeLesion->setEnabled(true); connect(removeLesion, &QAction::triggered, [this, selectedLesion] { OnRemoveLesion(selectedLesion); }); menu->addAction(removeLesion); if (!m_WorkbenchPartSite.Expired()) { QmitkFocusOnLesionAction* focusOnLesion = new QmitkFocusOnLesionAction(this, m_WorkbenchPartSite.Lock()); focusOnLesion->SetDataStorage(m_DataStorage.Lock()); focusOnLesion->SetSelectedLesion(selectedLesion); menu->addAction(focusOnLesion); } menu->popup(QCursor::pos()); } void QmitkLesionInfoWidget::OnLinkToSegmentation(mitk::SemanticTypes::Lesion selectedLesion) { if (m_DataStorage.IsExpired()) { return; } auto dataStorage = m_DataStorage.Lock(); QmitkSemanticRelationsNodeSelectionDialog* dialog = new QmitkSemanticRelationsNodeSelectionDialog(this, "Select segmentation to link to the selected lesion.", ""); dialog->setWindowTitle("Select segmentation node"); dialog->SetDataStorage(dataStorage); dialog->SetNodePredicate(mitk::NodePredicates::GetSegmentationPredicate()); dialog->SetSelectOnlyVisibleNodes(true); dialog->SetCaseID(m_CaseID); // set the last added segmentation node as pre-selected data node const mitk::DataNode* lastSegmentation = m_StorageModel->GetLastSegmentation(); QList selectedDataNodes; if (nullptr != lastSegmentation) { selectedDataNodes.push_back(const_cast(lastSegmentation)); dialog->SetCurrentSelection(selectedDataNodes); } int dialogReturnValue = dialog->exec(); if (QDialog::Rejected == dialogReturnValue) { return; } mitk::DataNode::Pointer selectedDataNode = nullptr; selectedDataNodes = dialog->GetSelectedNodes(); if (!selectedDataNodes.isEmpty()) { // only single selection allowed selectedDataNode = selectedDataNodes.front(); } if (nullptr == selectedDataNode || false == mitk::NodePredicates::GetSegmentationPredicate()->CheckNode(selectedDataNode)) { QMessageBox msgBox(QMessageBox::Warning, "No valid segmentation node selected.", "In order to link the selected lesion to a segmentation, please specify a valid segmentation node."); msgBox.exec(); return; } mitk::BaseData* baseData = selectedDataNode->GetData(); if (nullptr == baseData) { QMessageBox msgBox(QMessageBox::Warning, "No valid base data.", "In order to link the selected lesion to a segmentation, please specify a valid segmentation node."); msgBox.exec(); return; } - // if the segmentation is not contained in the semantic relations, add it - if (!mitk::SemanticRelationsInference::InstanceExists(selectedDataNode)) - { - try - { - AddToSemanticRelationsAction::Run(dataStorage, selectedDataNode); - } - catch (const mitk::SemanticRelationException& e) - { - std::stringstream exceptionMessage; exceptionMessage << e; - QMessageBox msgBox(QMessageBox::Warning, - "Could not link the selected lesion.", - "The program wasn't able to correctly link the selected lesion with the selected segmentation.\n" - "Reason:\n" + QString::fromStdString(exceptionMessage.str() + "\n")); - msgBox.exec(); - } - } - - // link the segmentation - try - { - m_SemanticRelationsIntegration->LinkSegmentationToLesion(selectedDataNode, selectedLesion); - } - catch (const mitk::SemanticRelationException& e) - { - std::stringstream exceptionMessage; exceptionMessage << e; - QMessageBox msgBox(QMessageBox::Warning, - "Could not link the selected lesion.", - "The program wasn't able to correctly link the selected lesion with the selected segmentation.\n" - "Reason:\n" + QString::fromStdString(exceptionMessage.str())); - msgBox.exec(); - } + LinkSegmentationToLesion(selectedDataNode, selectedLesion); } void QmitkLesionInfoWidget::OnSetLesionName(mitk::SemanticTypes::Lesion selectedLesion) { // use the lesion information to set the input text for the dialog QmitkLesionTextDialog* inputDialog = new QmitkLesionTextDialog(this); inputDialog->setWindowTitle("Set lesion name"); inputDialog->SetLineEditText(selectedLesion.name); int dialogReturnValue = inputDialog->exec(); if (QDialog::Rejected == dialogReturnValue) { return; } selectedLesion.name = inputDialog->GetLineEditText().toStdString(); m_SemanticRelationsIntegration->OverwriteLesion(m_CaseID, selectedLesion); } void QmitkLesionInfoWidget::OnSetLesionClass(mitk::SemanticTypes::Lesion selectedLesion) { // use the lesion information to set the input text for the dialog QmitkLesionTextDialog* inputDialog = new QmitkLesionTextDialog(this); inputDialog->setWindowTitle("Set lesion class"); inputDialog->SetLineEditText(selectedLesion.lesionClass.classType); // prepare the completer for the dialogs input text field mitk::LesionClassVector allLesionClasses = mitk::SemanticRelationsInference::GetAllLesionClassesOfCase(m_CaseID); QStringList wordList; for (const auto& lesionClass : allLesionClasses) { wordList << QString::fromStdString(lesionClass.classType); } QCompleter* completer = new QCompleter(wordList, this); completer->setCaseSensitivity(Qt::CaseInsensitive); inputDialog->GetLineEdit()->setCompleter(completer); int dialogReturnValue = inputDialog->exec(); if (QDialog::Rejected == dialogReturnValue) { return; } // retrieve the new input lesion class type and check for an already existing lesion class types std::string newLesionClassType = inputDialog->GetLineEditText().toStdString(); mitk::SemanticTypes::LesionClass existingLesionClass = mitk::FindExistingLesionClass(newLesionClassType, allLesionClasses); if (existingLesionClass.UID.empty()) { // could not find lesion class information for the new lesion class type // create a new lesion class for the selected lesion existingLesionClass = mitk::GenerateNewLesionClass(newLesionClassType); } selectedLesion.lesionClass = existingLesionClass; m_SemanticRelationsIntegration->OverwriteLesion(m_CaseID, selectedLesion); } -void QmitkLesionInfoWidget::OnPropagateLesion(mitk::SemanticTypes::Lesion selectedLesion) +void QmitkLesionInfoWidget::OnCreateNewSegmentation(mitk::SemanticTypes::Lesion selectedLesion) { if (m_DataStorage.IsExpired()) { return; } auto dataStorage = m_DataStorage.Lock(); - QmitkSemanticRelationsNodeSelectionDialog* dialog = new QmitkSemanticRelationsNodeSelectionDialog(this, "Select data node to propagate the selected lesion.", ""); + QmitkSemanticRelationsNodeSelectionDialog* dialog = new QmitkSemanticRelationsNodeSelectionDialog(this, "Select image to segment lesion on.", ""); dialog->setWindowTitle("Select image node"); dialog->SetDataStorage(dataStorage); dialog->SetNodePredicate(mitk::NodePredicates::GetImagePredicate()); dialog->SetSelectOnlyVisibleNodes(true); dialog->SetCaseID(m_CaseID); dialog->SetLesion(selectedLesion); int dialogReturnValue = dialog->exec(); if (QDialog::Rejected == dialogReturnValue) { return; } auto nodes = dialog->GetSelectedNodes(); mitk::DataNode::Pointer selectedDataNode = nullptr; if (!nodes.isEmpty()) { // only single selection allowed selectedDataNode = nodes.front(); } if (nullptr == selectedDataNode || false == mitk::NodePredicates::GetImagePredicate()->CheckNode(selectedDataNode)) { QMessageBox msgBox(QMessageBox::Warning, "No valid image node selected.", - "In order to propagate the selected lesion to an image, please specify a valid image node."); + "In order to create a new segmentation, please specify a valid image node."); msgBox.exec(); return; } - mitk::BaseData* baseData = selectedDataNode->GetData(); - if (nullptr == baseData) + mitk::Image* selectedImage = dynamic_cast(selectedDataNode->GetData()); + if (nullptr == selectedImage) { QMessageBox msgBox(QMessageBox::Warning, - "No valid base data.", - "In order to propagate the selected lesion to an image, please specify a valid image node."); + "No valid image.", + "In order to create a new segmentation, please specify a valid image node."); msgBox.exec(); return; } + mitk::LabelSetImage::Pointer segmentation = mitk::LabelSetImage::New(); try { - /* - auto allSegmentationsOfLesion = m_SemanticRelationsDataStorageAccess->GetAllSegmentationsOfLesion(m_CaseID, selectedLesion); - mitk::FindClosestSegmentationMask(); - */ + segmentation->Initialize(selectedImage); } - catch (const mitk::SemanticRelationException& e) + catch (mitk::Exception& e) { std::stringstream exceptionMessage; exceptionMessage << e; QMessageBox msgBox(QMessageBox::Warning, - "Could not propagate the selected lesion.", - "The program wasn't able to correctly propagate the selected lesion to the selected image.\n" + "Could not initialize segmentation.", + "The segmentation could not be correctly initialized with the selected image geometry.\n" "Reason:\n" + QString::fromStdString(exceptionMessage.str())); msgBox.exec(); + return; + } + + auto segmentationDialog = new QmitkNewSegmentationDialog(this); + segmentationDialog->setWindowTitle("New lesion segmentation"); + + dialogReturnValue = segmentationDialog->exec(); + if (dialogReturnValue == QDialog::Rejected) + { + return; + } + + QString segmentatioName = segmentationDialog->GetSegmentationName(); + if (segmentatioName.isEmpty()) + { + segmentatioName = "Unnamed"; } + segmentation->GetActiveLabelSet()->AddLabel(segmentatioName.toStdString(), segmentationDialog->GetColor()); + + mitk::DataNode::Pointer segmentationNode = mitk::DataNode::New(); + segmentationNode->SetData(segmentation); + segmentationNode->SetName(segmentatioName.toStdString()); + dataStorage->Add(segmentationNode, selectedDataNode); + + LinkSegmentationToLesion(segmentationNode, selectedLesion); } void QmitkLesionInfoWidget::OnRemoveLesion(mitk::SemanticTypes::Lesion selectedLesion) { try { m_SemanticRelationsIntegration->RemoveLesion(m_CaseID, selectedLesion); } catch (const mitk::SemanticRelationException& e) { std::stringstream exceptionMessage; exceptionMessage << e; QMessageBox msgBox(QMessageBox::Warning, "Could not remove the selected lesion.", "The program wasn't able to correctly remove the selected lesion from the semantic relations model.\n" "Reason:\n" + QString::fromStdString(exceptionMessage.str())); msgBox.exec(); } } + +void QmitkLesionInfoWidget::LinkSegmentationToLesion(const mitk::DataNode* selectedDataNode, mitk::SemanticTypes::Lesion selectedLesion) +{ + if (m_DataStorage.IsExpired()) + { + return; + } + + auto dataStorage = m_DataStorage.Lock(); + + // if the segmentation is not contained in the semantic relations, add it + if (!mitk::SemanticRelationsInference::InstanceExists(selectedDataNode)) + { + try + { + AddToSemanticRelationsAction::Run(dataStorage, selectedDataNode); + } + catch (const mitk::SemanticRelationException& e) + { + std::stringstream exceptionMessage; exceptionMessage << e; + QMessageBox msgBox(QMessageBox::Warning, + "Could not link the selected lesion.", + "The program wasn't able to correctly link the selected lesion with the selected segmentation.\n" + "Reason:\n" + QString::fromStdString(exceptionMessage.str() + "\n")); + msgBox.exec(); + } + } + + // link the segmentation + try + { + m_SemanticRelationsIntegration->LinkSegmentationToLesion(selectedDataNode, selectedLesion); + } + catch (const mitk::SemanticRelationException& e) + { + std::stringstream exceptionMessage; exceptionMessage << e; + QMessageBox msgBox(QMessageBox::Warning, + "Could not link the selected lesion.", + "The program wasn't able to correctly link the selected lesion with the selected segmentation.\n" + "Reason:\n" + QString::fromStdString(exceptionMessage.str())); + msgBox.exec(); + } +} diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidget.h b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidget.h index 6864f1ca0f..f675f664fa 100644 --- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidget.h +++ b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidget.h @@ -1,105 +1,107 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef QMITKLESIONINFOWIDGET_H #define QMITKLESIONINFOWIDGET_H // semantic relations plugin #include // semantic relations UI module #include // semantic relations module #include #include // mitk #include // berry #include // qt #include /* * @brief The QmitkLesionInfoWidget is a widget that shows and modifies the currently available lesion data of the semantic relations model. * * The widget provides a dialogs to add nodes from the data storage to the semantic relations model. * It provides functionality to create new lesions and link them with segmentation nodes. * * The QmitkLesionInfoWidget provides three QListWidgets, that show the lesion data and the referenced segmentation data, as * well as the connected image data, depending on the selected lesion. */ class QmitkLesionInfoWidget : public QWidget { Q_OBJECT public: static const QBrush DEFAULT_BACKGROUND_COLOR; static const QBrush SELECTED_BACKGROUND_COLOR; static const QBrush CONNECTED_BACKGROUND_COLOR; QmitkLesionInfoWidget(mitk::DataStorage* dataStorage, berry::IWorkbenchPartSite::Pointer workbenchPartSite, QWidget* parent = nullptr); void SetCaseID(const mitk::SemanticTypes::CaseID& caseID); void SetDataNodeSelection(const QList& dataNodeSelection); Q_SIGNALS: void LesionSelectionChanged(const mitk::SemanticTypes::Lesion&); private Q_SLOTS: void OnModelUpdated(); /* * @brief Generates a new, empty lesion to add to the semantic relations model for the current case ID. */ void OnAddLesionButtonClicked(); // slots for the mouse click events of tree view's selection model void OnSelectionChanged(const QModelIndex& current, const QModelIndex& previous); void OnLesionListContextMenuRequested(const QPoint&); // slots for the context menu actions of the lesion list widget void OnLinkToSegmentation(mitk::SemanticTypes::Lesion); void OnSetLesionName(mitk::SemanticTypes::Lesion); void OnSetLesionClass(mitk::SemanticTypes::Lesion); - void OnPropagateLesion(mitk::SemanticTypes::Lesion); + void OnCreateNewSegmentation(mitk::SemanticTypes::Lesion); void OnRemoveLesion(mitk::SemanticTypes::Lesion); private: void Initialize(); void SetUpConnections(); + void LinkSegmentationToLesion(const mitk::DataNode* selectedDataNode, mitk::SemanticTypes::Lesion selectedLesion); + Ui::QmitkLesionInfoWidgetControls m_Controls; QmitkLesionTreeModel* m_StorageModel; mitk::SemanticTypes::CaseID m_CaseID; mitk::WeakPointer m_DataStorage; berry::IWorkbenchPartSite::WeakPtr m_WorkbenchPartSite; std::unique_ptr m_SemanticRelationsDataStorageAccess; std::unique_ptr m_SemanticRelationsIntegration; }; #endif // QMITKLESIONINFOWIDGET_H