BlueBrain / BlueBrain/VessMorphoVis
CLI Bugs
- Dominant language
- Python
- Stars
- 50
- Forks
- 6
- PR merge metrics
- No merged PRs in 30d
Description
Hey,
first of all thanks for this great library, it's a big help.
I wanted to report some bugs I encountered when using the CLI to reconstruct a mesh.
- The _tessellation-level_ option is called _tessellation-ratio_ in the code. This fails when _arguments.tessellation_ratio_ is called
https://github.com/BlueBrain/VessMorphoVis/blob/90446383cef5caa4f9a8d8613a4a9a04c293fdf6/vmv/options/vessmorphovis_options.py#L171
Quickfixing this by changing the line to _arguments.tessellation_level_ allows the program to continue, but setting the tessellation to another value than 1.0 will cause a _TypeError: Converting py args to operator properties: : keyword "apply_as" unrecognized_ in the mesh builder.
- vmv.file does not have a function _read_morphology_from_file_
https://github.com/BlueBrain/VessMorphoVis/blob/90446383cef5caa4f9a8d8613a4a9a04c293fdf6/vmv/interface/cli/mesh_reconstruction.py#L298
- _only cli_options.mesh.export_obj_ is used to determine if _vmv.file.export_mesh_object_ should be called, this ignores for example export-vascular-mesh-stl
https://github.com/BlueBrain/VessMorphoVis/blob/90446383cef5caa4f9a8d8613a4a9a04c293fdf6/vmv/interface/cli/mesh_reconstruction.py#L112
- _vmv.file.export_mesh_object_ gets wrong arguments
https://github.com/BlueBrain/VessMorphoVis/blob/90446383cef5caa4f9a8d8613a4a9a04c293fdf6/vmv/interface/cli/mesh_reconstruction.py#L113-L116
- Even when _mesh_objects_ from _vmv.scene.get_list_of_meshes_in_scene()_ is just one mesh, it's still a list object
https://github.com/BlueBrain/VessMorphoVis/blob/90446383cef5caa4f9a8d8613a4a9a04c293fdf6/vmv/interface/cli/mesh_reconstruction.py#L100-L109
I just fixed it by setting mesh_object = mesh_objects[0] when len(mesh_objects) == 1
When these points were fixed, everything worked as expected.
If you have any questions I can provide more accurate descriptions.
Contributor guide
Research direction
Start in vmv/interface/cli/mesh_reconstruction.py at the referenced lines, then inspect vmv/options/vessmorphovis_options.py and the vmv.file functions involved in mesh loading and export. Reproduce CLI mesh reconstruction and trace each reported argument, export-condition, missing-function, and mesh-list failure. Done means all listed CLI paths complete successfully with the requested tessellation and export options.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100