Slicer crashes when setting master Sequence Node to SequenceBrowserNode

Development
1

Operating system: Ubuntu Debian 18.04 (KDE neon 5.19)
Slicer version: 4.11.0-2020-06-05
Expected behavior:
Actual behavior:

Hi everyone,

I’m having some troubles managing sequences (create them and remove them completely) from python scripts for background nodes (ie ScalarVolumeNodes) and label nodes (ie LabelMapVolumeNodes). My problem is that I can create and delete everything once (sequence node for both background and label, sequence browser node, and both proxys). Buth when I attempt to create a sequence again after its removal, slicer crashes in this line:

SeqBrowNode.SetAndObserveMasterSequenceNodeID(SeqNode.GetID())

The way I manage a sequence creation is like this:

SeqBrowN = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLSequenceBrowserNode')
SeqBrowN.SetName('SOME_SEQBROWN_NAME')

SeqN = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLSequenceNode')
SeqN.SetName('SOME_SEQN_NAME')

for frame_i in range(frames):
      NodeForSequence = slicer.mrmlScene.GetNodeByID('SOME_PREFIX' + str(frame_i))
      SeqN.SetDataNodeAtValue(NodeForSequence,str(frame_i))

SeqBrowN.SetAndObserveMasterSequenceNodeID(SeqN.GetID()) # Here I get the crash
sequencesModule.widgetRepresentation().setActiveBrowserNode(SeqBrowN)

The way I manage removal:

for seq_i in range(self.getNumberOfMySequences()):

    # Build background name
    name_i = str(seq_i + 1) + self.getBackgName()

    # Custom background SequenceNodes
    backgSeqNode = slicer.mrmlScene.GetNodesByClassByName('vtkMRMLSequenceNode',name_i).GetItemAsObject(0)
    while ( backgSeqNode != None ):
      backgSeqNode.RemoveAllObservers()
      slicer.mrmlScene.RemoveNode(backgSeqNode)
      backgSeqNode = slicer.mrmlScene.GetNodesByClassByName('vtkMRMLSequenceNode',name_i).GetItemAsObject(0)
    
    # Custom background ScalarVolumeNodes (proxys)
    backgProxyNode = slicer.mrmlScene.GetNodesByClassByName('vtkMRMLScalarVolumeNode',name_i).GetItemAsObject(0) 
    while ( backgProxyNode != None ):
      slicer.mrmlScene.RemoveNode(backgProxyNode)
      backgProxyNode = slicer.mrmlScene.GetNodesByClassByName('vtkMRMLScalarVolumeNode',name_i).GetItemAsObject(0)
    
  # Custom background SeqBrowNode
  name_SeqBrow = self.getBackgName()
  backgSeqBrowNode = slicer.mrmlScene.GetNodesByClassByName('vtkMRMLSequenceBrowserNode',name_SeqBrow).GetItemAsObject(0)
  while ( backgSeqBrowNode != None ):
    backgSeqBrowNode.RemoveAllObservers()  
    slicer.mrmlScene.RemoveNode(backgSeqBrowNode)
    backgSeqBrowNode = slicer.mrmlScene.GetNodesByClassByName('vtkMRMLSequenceBrowserNode',name_SeqBrow).GetItemAsObject(0)

I think I’m not removing correctly or maybe the synchronization is the problem. Any suggestion or similar code to look for and learn?

Thanks!!
Lucca

2

In the first example there does not seem to be anything wrong, so the issue is most likely the content of NodeForSequence. Can you send a code snippet that I can use as is to reproduce the crash? Or at least a link to your source code repository so that I can see the full context of the code.

To delete nodes, just call slicer.mrmlScene.RemoveNode(). No need for removing observers manually. Remove browser node first, then proxy nodes and sequence nodes.

3

Hi Andras,

First, thank you very much for your reply. I checked the NodeForSequence and they were correct (ScalarVolumeNodes). I could solved this by setting a ‘NodeAboutToBeRemoved’ callback on sequenceNodes and using RemoveSynchronizedSequenceNode’ s method of sequenceBrowserNode with its master SequenceNode that was about to be deleted. This stops slicer’s crashes and doesn’t give warnings. However, I don’t understand why it works.

I’m not sure how to encapsulate a snippet of code to reproduce as is, but I can try to make a reduced version. Meanwhile, here is the full code. Is relatively large, but functions mentioned are:

  • def createCardIAcSequence(self): (line 1466)
  • def deleteCardIAcSeqNodes(self,delete_only_shortSeq = False): (line 1549)

Thanks again