Alternative for TetrahedronSetTopologyAlgorithms?

[Mathieu]

Hello,

I am quite new to SOFA and wanted to have a closer look at some examples of this github repository: https://github.com/StanfordASL/soft-robot-control

I followed all the instructions and SOFA is running correctly, but they used an object called TetrahedronSetTopologyAlgorithms that has been removed since SOFA v20.12 (I use this version from the master branch, together with SofaPython3). Is there an alternative to this object working with v20.12?

The full terminal message is the following:

(sofa) srl@srl-20:~$ $SOFA_BLD/master/bin/runSofa -l $SP3_BLD/lib/libSofaPython3.so /home/srl/sofa-plugins/soft-robot-control/launch_sofa.py
[INFO]    [runSofa] PluginRepository paths = /home/srl/sofa/build/master/plugins:/home/srl/sofa/build/master/lib
[INFO]    [runSofa] DataRepository paths = /home/srl/sofa/src/share:/home/srl/sofa/src/examples:/home/srl/sofa/build/master:/home/srl/sofa/build/master
[INFO]    [runSofa] GuiDataRepository paths = /home/srl/sofa/src/applications/projects/runSofa/resources:/home/srl/sofa/src/modules/SofaGuiQt/src/sofa/gui/qt/resources
[INFO]    [SofaPython3]  Initializing with python version 3.8.8 (default, Feb 24 2021, 21:48:08) 
[GCC 7.3.0]
[INFO]    [SofaPython3] Registering a scene loader for [.py, .py3, .pyscn, .py3scn] files.
[INFO]    [SofaPython3] Shared library name is 'libpython3.8m.so'
[INFO]    [SofaPython3] Intializing python
[INFO]    [SofaPython3] Added '/home/srl/sofa-plugins/SofaPython3/build/site-packages' to sys.path
[INFO]    [SofaPython3] Added '/home/srl/sofa-plugins/SofaPython3/build/site-packages/python3/site-packages' to sys.path
[INFO]    [SofaPython3] Added '/home/srl/sofa-plugins/SofaPython3/build/lib/python3/site-packages' to sys.path
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa-plugins/SofaPython3/build/lib/libSofaPython3.so
[INFO]    [runSofa] Loading automatically plugin list in /home/srl/sofa/build/master/lib/plugin_list.conf.default
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaSimpleFem.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaRigid.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaDeformable.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaObjectInteraction.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaMeshCollision.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaEngine.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaExplicitOdeSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaImplicitOdeSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaLoader.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaGeneralVisual.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaGraphComponent.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaGeneralMeshCollision.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaBoundaryCondition.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaGeneralAnimationLoop.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaGeneralDeformable.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaGeneralEngine.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaGeneralExplicitOdeSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaGeneralImplicitOdeSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaGeneralLinearSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaGeneralRigid.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaGeneralObjectInteraction.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaGeneralSimpleFem.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaGeneralTopology.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaTopologyMapping.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaUserInteraction.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaConstraint.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaGeneralLoader.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaExporter.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaSparseSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaPreconditioner.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaHaptics.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaValidation.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaDenseSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaNonUniformFem.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaOpenglVisual.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaMiscTopology.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaMiscExtra.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaMiscForceField.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaMiscEngine.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaMiscSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaMiscFem.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaMiscMapping.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libCImgPlugin.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSofaMiscCollision.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libLMConstraint.so
[INFO]    [PluginManager] Loaded plugin: /home/srl/sofa/build/master/lib/libSoftRobots.so
Warning: Setting a new default format with a different version or profile after the global shared context is created may cause issues with context sharing.
The constructor with a QGLFormat is deprecated, use the regular contructor instead.

[ERROR]   [SofaPython3::SceneLoader] ValueError: Object type TetrahedronSetTopologyAlgorithms<> was not created  
The object is not in the factory.  
This component has been REMOVED since SOFA v20.12 (deprecated since v20.12). Please consider updating your scene. If this component is crucial to you please report that to sofa-dev@ so that we can reconsider this component for future re-integration.  

At:
  /home/srl/sofa-plugins/soft-robot-control/robots/environments.py(253): __init__
  /home/srl/sofa-plugins/soft-robot-control/examples/diamond/diamond.py(155): run_scp
  launch_sofa.py(30): createScene

[INFO]    [SceneCheckerVisitor] Validating node "root" with checks: [SceneCheckDuplicatedName, SceneCheckMissingRequiredPlugin, SceneCheckUsingAlias]
[WARNING] [SceneCheckMissingRequiredPlugin] This scene is using component defined in plugins but is not importing the required plugins.  
  Your scene may not work on a sofa environment with different pre-loaded plugins.  
  To fix your scene and remove this warning you just need to cut & paste the following lines at the begining of your scene (if it is a .scn):   
  <RequiredPlugin pluginName='SofaConstraint'/> <!-- Needed to use components [FreeMotionAnimationLoop, GenericConstraintSolver, ]-->  

[INFO]    [SceneCheckerVisitor] Finished validating node "root".
[WARNING] [RealGUI] Global Bounding Box seems very small; Your viewer settings (based on the bbox) are likely invalid, switching to default value of [-1,-1,-1,1,1,1].This is caused by using component which does not implement properly the updateBBox function.You can remove this warning by manually forcing a value in the parameter bbox="minX minY minZ maxX maxY maxZ" in your root node 

The two files in which the error comes from, namely

/home/srl/sofa-plugins/soft-robot-control/robots/environments.py(253): __init__
  /home/srl/sofa-plugins/soft-robot-control/examples/diamond/diamond.py(155): run_scp
  launch_sofa.py(30): createScene

can be found respectively here: https://github.com/StanfordASL/soft-robot-control/blob/main/robots/environments.py and here: https://github.com/StanfordASL/soft-robot-control/blob/main/examples/diamond/diamond.py

Thank you a lot for your help,

Best,
Mathieu

[Hugo]

Dear @dubied

Thanks for your message and sorry for our latency.
All components *SetTopologyAlgorithms have indeed been removed, or it should be rather said that they are no longer needed in the scene graph.

You can just remove them, the scene behavior won’t be affected.
Best wishes,

Hugo

[Hugo]

Sorry wrong nickname, @mdubied

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