The described behavior seems reasonable to me, you need to update references when you add/change nodes in the scene but not when you copy existing state into a SceneView node.

What's it the real problem here?

There is inconsistency between:
a) a vtkMRMLSceneViewNode created from Slicer session
b) and a vtkMRMLSceneViewNode loaded from MRML scene file.

In a) vtkMRMLSceneViewNode::Nodes scene doesn't have references
In b) vtkMRMLSceneViewNode::Nodes scene has references (because vtkMRMLSceneViewNode::UpdateScene() is called.

In case of b), there is a problem because:
1) vtkMRMLSceneViewNode::Nodes scene contains references to the main scene nodes.
2) at destruction time, the main scene is deleted, deleting all nodes (2a) and vtkMRMLSceneViewNodes (2b). vtkMRMLSceneViewNode::Nodes scene deletes mrml nodes that can attempt to remove reference from scene. It browses through the reference list which contains pointers on MRML nodes of the main scene, but these pointers have already been deleted in 2a which result in crash.

These errors are shown in py_LoadAnnotationRulerScene and vtkMRMLSceneViewNodeStoreSceneTest::references().

I suggest:

• call UpdateScene after "StoreScene"
• vtkMRMLSceneViewNode::UpdateScene(mainScene) should not copy main scene reference nodes (vtkMRMLScene::ReferenceNodes) into the scene view node scene reference nodes (vtkMRMLSceneViewNode::Nodes::ReferenceNodes), but copy only the main scene node IDs (vtkMRMLScene::ReferenceNodeIDs). The scene view node scene reference nodes (vtkMRMLSceneViewNode::Nodes::ReferenceNodes) must be computed from the nodes in its internal scene (vtkMRMLSceneViewNode::Nodes) whose IDs match the ones of the main scene reference nodes (vtkMRMLScene::ReferenceNodes).

ViewNode builds it's own ReferencingNodes vector rather than copying one from the scene. Also cleans references when reusing ViewNode.

http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=20067

Dear issue reporter,

Good news :) Slicer developers SOLVED the problem you reported - YOU now need to VERIFY and CLOSE this issue.