ENH: Make Clone action clone a segment when a segment is selected in …

…subject hierarchy

Previously, "Clone" action duplicated the entire segmentation node, even when right-clicked on a segment.
This commit changes the behavior so that if the user right-clicks on a Segment and chooses Clone then only that selected segment will be cloned.

Libs/MRML/Core/vtkMRMLSubjectHierarchyNode.cxx

@@ -120,8 +120,9 @@ class vtkSubjectHierarchyItem : public vtkObject
   /// \param parent Parent item pointer under which this item is inserted
   /// \param name Name of the item
   /// \param level Level string of the item (\sa vtkMRMLSubjectHierarchyConstants). It will be added as a special attribute
+  /// \param positionUnderParent Position of the item under the parent item. If set to -1 then it will be appended after the last item under the parent.
   /// \return ID of the item in the hierarchy that was assigned automatically when adding
-  vtkIdType AddToTree(vtkSubjectHierarchyItem* parent, std::string name, std::string level);
+  vtkIdType AddToTree(vtkSubjectHierarchyItem* parent, std::string name, std::string level, int positionUnderParent = -1);
 
   /// Get name of the item. If has data node associated then return name of data node, \sa Name member otherwise
   std::string GetName();
@@ -317,7 +318,7 @@ vtkIdType vtkSubjectHierarchyItem::AddToTree(vtkSubjectHierarchyItem* parent, vt
 }
 
 //---------------------------------------------------------------------------
-vtkIdType vtkSubjectHierarchyItem::AddToTree(vtkSubjectHierarchyItem* parent, std::string name, std::string level)
+vtkIdType vtkSubjectHierarchyItem::AddToTree(vtkSubjectHierarchyItem* parent, std::string name, std::string level, int positionUnderParent/*=-1*/)
 {
   this->ID = vtkSubjectHierarchyItem::NextSubjectHierarchyItemID;
   vtkSubjectHierarchyItem::NextSubjectHierarchyItemID++;
@@ -338,7 +339,14 @@ vtkIdType vtkSubjectHierarchyItem::AddToTree(vtkSubjectHierarchyItem* parent, st
     {
     // Add under parent
     vtkSmartPointer<vtkSubjectHierarchyItem> childPointer(this);
-    this->Parent->Children.push_back(childPointer);
+    if (positionUnderParent<0 || positionUnderParent >= this->Parent->Children.size())
+      {
+      this->Parent->Children.push_back(childPointer);
+      }
+    else
+      {
+      this->Parent->Children.insert(this->Parent->Children.begin() + positionUnderParent, childPointer);
+      }
 
     // Add to cache (DataNode is nullptr, so no need to add to node cache)
     vtkSubjectHierarchyItem::ItemCache[this->ID] = this;
@@ -2564,7 +2572,7 @@ vtkIdType vtkMRMLSubjectHierarchyNode::CreateItem(vtkIdType parentItemID, vtkMRM
 }
 
 //---------------------------------------------------------------------------
-vtkIdType vtkMRMLSubjectHierarchyNode::CreateHierarchyItem(vtkIdType parentItemID, std::string name, std::string level)
+vtkIdType vtkMRMLSubjectHierarchyNode::CreateHierarchyItem(vtkIdType parentItemID, std::string name, std::string level, int positionUnderParent/*=-1*/)
 {
   vtkSubjectHierarchyItem* parentItem = this->Internal->FindItemByID(parentItemID);
   if (!parentItem)
@@ -2580,7 +2588,7 @@ vtkIdType vtkMRMLSubjectHierarchyNode::CreateHierarchyItem(vtkIdType parentItemI
   this->Internal->AddItemObservers(item);
 
   // Add item to the tree
-  vtkIdType itemID = item->AddToTree(parentItem, name, level);
+  vtkIdType itemID = item->AddToTree(parentItem, name, level, positionUnderParent);
 
   // Request owner plugin search (it may depend on the parent etc.)
   this->RequestOwnerPluginSearch(itemID);

Libs/MRML/Core/vtkMRMLSubjectHierarchyNode.h

@@ -206,8 +206,10 @@ class VTK_MRML_EXPORT vtkMRMLSubjectHierarchyNode : public vtkMRMLNode
   /// \param parentItemID Parent item under which the created item is inserted. If top-level then use \sa GetSceneItemID
   /// \param name Name of the item. Only used if there is no data node associated
   /// \param level Level of the hierarchy item. It will be stored as attribute (\sa vtkMRMLSubjectHierarchyConstants)
+  /// \param positionUnderParent Position of the item under the parent item. If set to -1 then it will be appended
+  ///   after the last item under the parent.
   /// \return ID of the item in the hierarchy that was assigned automatically when adding
-  vtkIdType CreateHierarchyItem(vtkIdType parentItemID, std::string name, std::string level);
+  vtkIdType CreateHierarchyItem(vtkIdType parentItemID, std::string name, std::string level, int positionUnderParent = -1);
   /// Convenience function to create subject item in the hierarchy under a specified parent.
   /// \param parentItemID Parent item under which the created item is inserted. If top-level then use \sa GetSceneItemID
   /// \param name Name of the item. Only used if there is no data node associated

Modules/Loadable/Segmentations/SubjectHierarchyPlugins/qSlicerSubjectHierarchySegmentationsPlugin.cxx

@@ -712,10 +712,19 @@ void qSlicerSubjectHierarchySegmentationsPlugin::onSegmentAdded(vtkObject* calle
 
   if (segmentShItemID == vtkMRMLSubjectHierarchyNode::INVALID_ITEM_ID)
     {
+    // Get position of segment under parent
+    int positionUnderParent = -1;
+    vtkSegmentation* segmentation = segmentationNode->GetSegmentation();
+    if (segmentation)
+      {
+      positionUnderParent = segmentation->GetSegmentIndex(segmentId);
+      }
+
     // Add the segment in subject hierarchy to allow individual handling (e.g. visibility)
     vtkIdType segmentShItemID = shNode->CreateHierarchyItem(
       segmentationShItemID, (segment->GetName() ? segment->GetName() : ""),
-      vtkMRMLSubjectHierarchyConstants::GetSubjectHierarchyVirtualBranchAttributeName());
+      vtkMRMLSubjectHierarchyConstants::GetSubjectHierarchyVirtualBranchAttributeName(),
+      segmentation->GetSegmentIndex(segmentId));
     shNode->SetItemAttribute(segmentShItemID, vtkMRMLSegmentationNode::GetSegmentIDAttributeName(), segmentId);
     // Set plugin for the new item (automatically selects the segment plugin based on confidence values)
     qSlicerSubjectHierarchyPluginHandler::instance()->findAndSetOwnerPluginForSubjectHierarchyItem(segmentShItemID);

Modules/Loadable/Segmentations/SubjectHierarchyPlugins/qSlicerSubjectHierarchySegmentsPlugin.cxx

@@ -67,9 +67,10 @@ class qSlicerSubjectHierarchySegmentsPluginPrivate: public QObject
 public:
   QIcon SegmentIcon;
 
-  QAction* ShowOnlyCurrentSegmentAction;
-  QAction* ShowAllSegmentsAction;
-  QAction* JumpSlicesAction;
+  QAction* ShowOnlyCurrentSegmentAction{nullptr};
+  QAction* ShowAllSegmentsAction{nullptr};
+  QAction* JumpSlicesAction{nullptr};
+  QAction* CloneSegmentAction{nullptr};
 };
 
 //-----------------------------------------------------------------------------
@@ -80,9 +81,6 @@ qSlicerSubjectHierarchySegmentsPluginPrivate::qSlicerSubjectHierarchySegmentsPlu
 : q_ptr(&object)
 , SegmentIcon(QIcon(":Icons/Segment.png"))
 {
-  this->ShowOnlyCurrentSegmentAction = nullptr;
-  this->ShowAllSegmentsAction = nullptr;
-  this->JumpSlicesAction = nullptr;
 }
 
 //------------------------------------------------------------------------------
@@ -101,6 +99,12 @@ void qSlicerSubjectHierarchySegmentsPluginPrivate::init()
   // Jump slices action
   this->JumpSlicesAction = new QAction("Jump slices",q);
   QObject::connect(this->JumpSlicesAction, SIGNAL(triggered()), q, SLOT(jumpSlices()));
+
+  // Clone segment action
+  this->CloneSegmentAction = new QAction("Clone", q);
+  qSlicerSubjectHierarchyAbstractPlugin::setActionPosition(this->CloneSegmentAction,
+    qSlicerSubjectHierarchyAbstractPlugin::SectionNode, 0.5); // put it right after "Rename" action
+  QObject::connect(this->CloneSegmentAction, SIGNAL(triggered()), q, SLOT(cloneSegment()));
 }
 
 //-----------------------------------------------------------------------------
@@ -606,6 +610,33 @@ QColor qSlicerSubjectHierarchySegmentsPlugin::getDisplayColor(vtkIdType itemID,
   return QColor::fromRgbF(colorArray[0], colorArray[1], colorArray[2]);
 }
 
+//---------------------------------------------------------------------------
+QList<QAction*> qSlicerSubjectHierarchySegmentsPlugin::itemContextMenuActions()const
+{
+  Q_D(const qSlicerSubjectHierarchySegmentsPlugin);
+  QList<QAction*> actions;
+  actions << d->CloneSegmentAction;
+  return actions;
+}
+
+//---------------------------------------------------------------------------
+void qSlicerSubjectHierarchySegmentsPlugin::showContextMenuActionsForItem(vtkIdType itemID)
+{
+  Q_D(const qSlicerSubjectHierarchySegmentsPlugin);
+
+  qSlicerSubjectHierarchySegmentationsPlugin* segmentationsPlugin = qobject_cast<qSlicerSubjectHierarchySegmentationsPlugin*>(
+    qSlicerSubjectHierarchyPluginHandler::instance()->pluginByName("Segmentations"));
+
+  // Segments plugin shows all segmentations plugin functions in segment context menu
+  segmentationsPlugin->showContextMenuActionsForItem(itemID);
+
+  // Owned Segment
+  if (this->canOwnSubjectHierarchyItem(itemID) && this->isThisPluginOwnerOfItem(itemID))
+    {
+    d->CloneSegmentAction->setVisible(true);
+    }
+}
+
 //---------------------------------------------------------------------------
 QList<QAction*> qSlicerSubjectHierarchySegmentsPlugin::visibilityContextMenuActions()const
 {
@@ -844,6 +875,67 @@ void qSlicerSubjectHierarchySegmentsPlugin::jumpSlices()
     }
 }
 
+//------------------------------------------------------------------------------
+void qSlicerSubjectHierarchySegmentsPlugin::cloneSegment()
+{
+  vtkMRMLSubjectHierarchyNode* shNode = qSlicerSubjectHierarchyPluginHandler::instance()->subjectHierarchyNode();
+  if (!shNode)
+    {
+    qCritical() << Q_FUNC_INFO << ": Failed to access subject hierarchy node";
+    return;
+    }
+  vtkIdType currentItemID = qSlicerSubjectHierarchyPluginHandler::instance()->currentItem();
+  if (currentItemID == vtkMRMLSubjectHierarchyNode::INVALID_ITEM_ID)
+    {
+    qCritical() << Q_FUNC_INFO << ": Invalid current item";
+    return;
+    }
+
+  // Get segmentation node
+  vtkIdType segmentationShItemID = shNode->GetItemParent(currentItemID);
+  if (segmentationShItemID == vtkMRMLSubjectHierarchyNode::INVALID_ITEM_ID)
+    {
+    qCritical() << Q_FUNC_INFO << ": Failed to find segmentation subject hierarchy item for segment item " << shNode->GetItemName(currentItemID).c_str();
+    return;
+    }
+  vtkMRMLSegmentationNode* segmentationNode = vtkMRMLSegmentationNode::SafeDownCast(shNode->GetItemDataNode(segmentationShItemID));
+  if (!segmentationNode || !segmentationNode->GetSegmentation())
+    {
+    qCritical() << Q_FUNC_INFO << ": Unable to find segmentation node for segment subject hierarchy item " << shNode->GetItemName(currentItemID).c_str();
+    return;
+    }
+
+  // Get segment ID
+  std::string segmentId = shNode->GetItemAttribute(currentItemID, vtkMRMLSegmentationNode::GetSegmentIDAttributeName());
+
+  // Get segment and segmentation object
+  vtkSegmentation* segmentation = segmentationNode->GetSegmentation();
+  vtkSegment* segment = segmentation->GetSegment(segmentId);
+  if (!segment)
+    {
+    qCritical() << Q_FUNC_INFO << " failed: error getting the segment object";
+    return;
+    }
+
+  // Copy
+  vtkNew<vtkSegment> segmentCopy;
+  segmentCopy->DeepCopy(segment);
+
+  // Find the next segment's ID, because we want to insert the copied segment right below the current segment
+  int segmentIndex = segmentation->GetSegmentIndex(segmentId);
+  std::string insertBeforeSegmentId;
+  if (segmentIndex + 1 < segmentation->GetNumberOfSegments())
+    {
+    insertBeforeSegmentId = segmentation->GetNthSegmentID(segmentIndex + 1);
+    }
+
+  std::string targetSegmentId = segmentation->GenerateUniqueSegmentID(segmentId);
+  if (!segmentation->AddSegment(segmentCopy, targetSegmentId, insertBeforeSegmentId))
+    {
+    qCritical() << Q_FUNC_INFO << " failed: error adding cloned segment '" << segmentId.c_str() << "' to segmentation";
+    return;
+    }
+}
 //---------------------------------------------------------------------------
 bool qSlicerSubjectHierarchySegmentsPlugin::showItemInView(
   vtkIdType itemID, vtkMRMLAbstractViewNode* viewNode, vtkIdList* allItemsToShow)

Modules/Loadable/Segmentations/SubjectHierarchyPlugins/qSlicerSubjectHierarchySegmentsPlugin.h

@@ -108,6 +108,13 @@ class Q_SLICER_SEGMENTATIONS_PLUGINS_EXPORT qSlicerSubjectHierarchySegmentsPlugi
   ///   qSlicerTerminologyItemDelegate::ColorAutoGeneratedRole : bool
   QColor getDisplayColor(vtkIdType itemID, QMap<int, QVariant> &terminologyMetaData)const override;
 
+  /// Get item context menu item actions to add to tree view
+  QList<QAction*> itemContextMenuActions()const override;
+
+  /// Show context menu actions valid for a given subject hierarchy item.
+  /// \param itemID Subject Hierarchy item to show the context menu items for
+  void showContextMenuActionsForItem(vtkIdType itemID) override;
+
   /// Get visibility context menu item actions to add to tree view.
   /// These item visibility context menu actions can be shown in the implementations of \sa showVisibilityContextMenuActionsForItem
   QList<QAction*> visibilityContextMenuActions()const override;
@@ -132,6 +139,9 @@ protected slots:
   /// Jump to slices in slice views to show current segment
   void jumpSlices();
 
+  /// Clone the selected segment
+  void cloneSegment();
+
 protected:
   QScopedPointer<qSlicerSubjectHierarchySegmentsPluginPrivate> d_ptr;
 

Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyCloneNodePlugin.cxx

@@ -124,6 +124,13 @@ void qSlicerSubjectHierarchyCloneNodePlugin::showContextMenuActionsForItem(vtkId
     return;
     }
 
+  vtkIdType parentItemID = shNode->GetItemParent(itemID);
+  if (parentItemID && shNode->IsItemVirtualBranchParent(parentItemID))
+    {
+    // This generic plugin does not know how to clone virtual branch items
+    return;
+    }
+
   // Show clone node for every non-scene items
   d->CloneItemAction->setVisible(true);
 }