Out of bounds error during mesh creation

[tischi]

@constantinpape

There are several segments that cause an error when the current code is trying to create a mesh.
I suspect that those segments that are cut off by the image boundary.

An example is: label 89 at time point 1

If you have any ideas, let me know.

Anyway I will work on this more at some point (embl-cba/imagej-utils#44)

[constantinpape]

Ok, I don't want to pull master in mobie-viewer right now because I have some experimental changes for reading private buckets, but I can check it out some time next week.
In the meantime, can you maybe post the error's trace back?

[tischi]

I was more thinking about whether you can see anything "funny" in the input data. The java error is pretty deep in the code and (for my taste) complicated imglib2 stuff, I don't think I would like to bother you with that ;-)

[constantinpape]

I was more thinking about whether you can see anything "funny" in the input data.

Ok, I will check it out once I update master.

The java error is pretty deep in the code and (for my taste) complicated imglib2 stuff, I don't think I would like to bother you with that ;-)

I became pretty good at reading obscure java tracebacks recently ;).

[constantinpape]

I tried running it with the current master, but ran into this issue: mobie/mobie-viewer-fiji#216

[constantinpape]

Cannot check this due to mobie/mobie-viewer-fiji#501.

[constantinpape]

Can confirm that the error still exists:

java.lang.ArrayIndexOutOfBoundsException: 262144
	at net.imglib2.img.basictypeaccess.array.AbstractIntArray.getValue(AbstractIntArray.java:61)
	at net.imglib2.type.numeric.integer.GenericIntType.getInt(GenericIntType.java:137)
	at net.imglib2.type.numeric.integer.UnsignedIntType.get(UnsignedIntType.java:180)
	at net.imglib2.type.numeric.integer.UnsignedIntType.getIntegerLong(UnsignedIntType.java:197)
	at net.imglib2.type.numeric.integer.AbstractIntegerType.getRealDouble(AbstractIntegerType.java:62)
	at de.embl.cba.tables.mesh.MeshExtractor.generateMesh(MeshExtractor.java:597)
	at org.embl.mobie.viewer.mesh.MeshCreator.createMesh(MeshCreator.java:74)
	at org.embl.mobie.viewer.mesh.MeshCreator.createCustomTriangleMesh(MeshCreator.java:106)
	at org.embl.mobie.viewer.mesh.MeshCreator.createSmoothCustomTriangleMesh(MeshCreator.java:95)
	at org.embl.mobie.viewer.volume.SegmentsVolumeViewer.updateSelectedSegments(SegmentsVolumeViewer.java:204)
	at org.embl.mobie.viewer.volume.SegmentsVolumeViewer.lambda$updateView$0(SegmentsVolumeViewer.java:172)
	at java.lang.Thread.run(Thread.java:748)
Exception in thread "Thread-91" java.lang.RuntimeException: Could not create mesh for segment 89.0 at time point 1
	at org.embl.mobie.viewer.mesh.MeshCreator.createCustomTriangleMesh(MeshCreator.java:116)
	at org.embl.mobie.viewer.mesh.MeshCreator.createSmoothCustomTriangleMesh(MeshCreator.java:95)
	at org.embl.mobie.viewer.volume.SegmentsVolumeViewer.updateSelectedSegments(SegmentsVolumeViewer.java:204)
	at org.embl.mobie.viewer.volume.SegmentsVolumeViewer.lambda$updateView$0(SegmentsVolumeViewer.java:172)
	at java.lang.Thread.run(Thread.java:748)