Error during Inference. ValueError: Found Multiple nodes named (name). #1918
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Hi @hemanyaradadia, We have run into this before, and the issue seems to stem from the "py/state": {"name": "nose", "weight": 1.0}when it should contain "py/state": {"py/tuple": ["nose", 1.0]}. While I can (and will shortly) write a file converter to reformat the file into the expected format, this still does not explain the root cause of the behavior. We use the
I am testing this on my computer as well and will report back, but would you be able to share the environment information for the Windows computer that does not have this Thanks, Related |
TLDRThe change in Action Plan (developer)The underlying theme in these discussions is that "pickling across versions" is an "antipattern" and we should perhaps find a different way to serialize our Action Plan (user)Report to us that you are having this problem (including your environment info if possible), until a new release is published, use this script to convert incompatible skeleton.json files (that use a dictionary for the Journaling the possibility that something might be happening inside
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Hi @roomrys, Thanks for the reply. The skeleton file I am using was created on the mentioned Windows 10 computer. I had installed SLEAP using conda from the package. conda env info for the windows computerInterestingly, this environment has the same version of |
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Hi @hemanyaradadia, This is a file format compatibility issue that will be officially addressed in our future release (by constraining the version of A (temporary) peace offeringApologies you have run into this, but thank you for reporting! Until this issue is officially addressed in a release, you can run this script to convert the incompatible skeleton.json that uses a To run the script:
Results: Converting your skeletonI set your current skeleton.json as the {"directed": true, "graph": {"name": "Skeleton-3", "num_edges_inserted": 5}, "links": [{"edge_insert_idx": 0, "key": 0, "source": {"py/object": "sleap.skeleton.Node", "py/state": {"name": "nose", "weight": 1.0}}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"name": "right-ear", "weight": 1.0}}, "type": {"py/reduce": [{"py/type": "sleap.skeleton.EdgeType"}, {"py/tuple": [1]}]}}, {"edge_insert_idx": 1, "key": 0, "source": {"py/id": 1}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"name": "left-ear", "weight": 1.0}}, "type": {"py/id": 3}}, {"edge_insert_idx": 2, "key": 0, "source": {"py/id": 2}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"name": "thorax", "weight": 1.0}}, "type": {"py/id": 3}}, {"edge_insert_idx": 3, "key": 0, "source": {"py/id": 4}, "target": {"py/id": 5}, "type": {"py/id": 3}}, {"edge_insert_idx": 4, "key": 0, "source": {"py/id": 5}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"name": "tail-base", "weight": 1.0}}, "type": {"py/id": 3}}], "multigraph": true, "nodes": [{"id": {"py/id": 1}}, {"id": {"py/id": 2}}, {"id": {"py/id": 4}}, {"id": {"py/id": 5}}, {"id": {"py/id": 6}}]}and this is the output skeleton.json that was saved as {"directed": true, "graph": {"name": "Skeleton-3", "num_edges_inserted": 5}, "links": [{"edge_insert_idx": 0, "key": 0, "source": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["nose", 1.0]}}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["right-ear", 1.0]}}, "type": {"py/reduce": [{"py/type": "sleap.skeleton.EdgeType"}, {"py/tuple": [1]}]}}, {"edge_insert_idx": 1, "key": 0, "source": {"py/id": 1}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["left-ear", 1.0]}}, "type": {"py/id": 3}}, {"edge_insert_idx": 2, "key": 0, "source": {"py/id": 2}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["thorax", 1.0]}}, "type": {"py/id": 3}}, {"edge_insert_idx": 3, "key": 0, "source": {"py/id": 4}, "target": {"py/id": 5}, "type": {"py/id": 3}}, {"edge_insert_idx": 4, "key": 0, "source": {"py/id": 5}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["tail-base", 1.0]}}, "type": {"py/id": 3}}], "multigraph": true, "nodes": [{"id": {"py/id": 1}}, {"id": {"py/id": 2}}, {"id": {"py/id": 4}}, {"id": {"py/id": 5}}, {"id": {"py/id": 6}}]}(notice the differences in the Then when loading each skeleton.json as a In [1]: from sleap import Skeleton
In [2]: input_json = "dict_state.json"
In [3]: output_json = "tuple_state.json"
In [4]: skeleton_input = Skeleton.load_json(input_json)
In [5]: skeleton_input
Out[5]: Skeleton(name='Skeleton-3', description='None', nodes=['name', 'name', 'name', 'name', 'name'], edges=[('name', 'name'), ('name', 'name'), ('name', 'name'), ('name', 'name'), ('name', 'name')],
symmetries=[])
In [6]: skeleton_output = Skeleton.load_json(output_json)
In [7]: skeleton_output
Out[7]: Skeleton(name='Skeleton-3', description='None', nodes=['nose', 'right-ear', 'left-ear', 'thorax', 'tail-base'], edges=[('nose', 'right-ear'), ('nose', 'left-ear'), ('right-ear', 'thorax'), ('left-ear', 'thorax'), ('thorax', 'tail-base')], symmetries=[])Let us know if you run into further trouble. Thanks, |
Yes, I also originally thought it might be a I see that your Although, this is still strange because, while we do not have a pin on the Line 58 in 864c994 I am wondering if perhaps the Windows computer might have a "conda from source" installation which uses the development branch in which Again, this is our fault as we list dependency constraints, I am working on building a 1.3.4 mac conda packages as those have no upper bound on the Thanks, |
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Hi @roomrys, Thanks for the script to convert the skeleton |
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We have released SLEAP 1.3.4 (off #1927) which adds additional dependency constraints to prevent this from happening, but we are also switching to manually handling the I will leave this issue open until our next release (where we include a conversion script as well). |
roomrys
added
the
fixed in future release
and others
Bug description
Running Inference and Tracking throws up 'ValueError: Found multiple nodes named (name).' on a Linux system. While running the same command on a Windows 10 system, it works without any error.
Expected behaviour
A .slp output file with predictions/track in each frame.
Actual behaviour
The error shows up in the terminal. While .slp file is generated but without any predictions or frames. Essentially an empty .slp project file.
Your personal set up
Environment packages
Logs
CLI command and resulting outputSkeleton .json file used
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