JVM crashes after modifying the graph in TrackScheme.

[tinevez]

It can happen that the Mastodon crashes when modifying the graph several times via its highlight or focus.

The diagnosis is as follow (based on the unify-views branch):

A graphChanged event ends up in calling the paint() method of the TrackSchemePanel.

The paint() method does mainly two things, in the following order:

• It recompute the graph layout: All TrackScheme vertices get a new value for X. This calls the layout() method of the LineageTreeLayout class.

• It regenerates the ScreenEntities for the new layout. This involves creating new ScreenVertexes and ScreenEdges properly linked to the TrackScheme items currently displayed. This calls the cropAndScale() method of the LineageTreeLayout class.

  Between the call of layout() and cropAndScale(), the ScreenEntities are invalid. They may correspond to TrackScheme items that moved or disappeared because of the graph change event.

This issue is caused by the fact that several classes are notified when the layout() method is finished, and interrogate the ScreenEntities. For instance for this bug:

1. A graphChanged event ends up in calling the paint() method of the TrackSchemePanel.

2. The paint() method calls the layout() method of the LineageTreeLayout class.

3. When the layout is done, The LayoutListener of the class are notified (via `layoutChanged()).

4. One of these listener is the InertialScreenTransformListener. It notifies its TransformListener (via transformChanged()).

5. This transform listener is theInteractiveDisplayCanvasComponent`. It has several listeners it forward this event to.

6. One of them is the MouseHighlightHandler. Calling its transformChanged() method causes it to try an grab the currently highlighted edge or vertex.

7. To do so, it calls the getEdgeAt() or getVertexAt() method of the AbstractTrackSchemeOverlay class.

8. These two methods rely on ScreenEntities to retrieve the desired TrackScheme item, but at this time, they are not valid. They link to TrackScheme items that may have been deleted or moved. Calling a second graph modification event with these items is what causes the crash.

[tpietzsch]

@tinevez thanks for finding this out!

[tpietzsch]

@tinevez I have a tentative fix for this. It requires addition of a RefPool.getIfExists() method, so it touches all mastodon projects:

https://github.com/bigdataviewer/mastodon-collection/tree/safe-get-object https://github.com/bigdataviewer/mastodon-graph/tree/safe-get-object https://github.com/fiji/TrackMate3/tree/safe-get-object

Can you have a look? If everything is ok, I'll merge and release...

[tinevez]

Sorry for delayed response.

Yes it works! The crash is gone!