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knossos-project / knossos_utils

Python library for interacting with KNOSSOS data sets and annotation files
GNU General Public License v2.0
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Parsing of edges between different things is not yet supported #34

Closed hash-ir closed 8 months ago

hash-ir commented 11 months ago

Hi,

I get a warning when I load an annotated skeleton using knossos-utils. Warning: Parsing of edges between different things is not yet supported, skipping edge: 56451 -> 18342 and this warning is presented for many edges. This comes from here.

I don't quite understand what this would mean. I use the annotated skeleton to assign labels to the vertices of the mesh (using a kd-tree search). Is it safe to ignore this warning? I use knossos-utils==0.1

Optiligence commented 11 months ago

If you have nodes in several trees in KNOSSOS and nodes from different trees are connected, knossos_utils doesn’t seem to be able to properly work with those edges.

hash-ir commented 11 months ago

That explains it, thank you. Is there also a way in Knossos to combine those trees?

Optiligence commented 11 months ago

You can merge trees via the context menu on trees in the skeleton table with the tracing advanced mode active.