Collision not work through python

[MikeP]

I am using Sofa and Sofapython3 v20.12. I recently watched the SOFA Training Session 2020 which was extremely helpful. I tried to replicate the example that Hugo does during the session in python. I successfully managed to replicate everything he did using SofaPython3 and everything has worked except the last part, which includes a rigid object colliding with a deformable liver object. The code I used is:

import sys, os

sys.path.append(os.path.abspath("./bindings/Sofa/package"))
sys.path.append(os.path.abspath("./bindings/SofaRuntime/package"))
sys.path.append(os.path.abspath("./bindings/SofaTypes/package"))

import Sofa
# Choose in your script to activate or not the GUI
USE_GUI = True

# Function called when the scene graph is being created
def createScene(root):
    # Set time step and gravity of the Scene
    root.gravity=[0, 0, 0]
    root.dt=0.01
    # Scene must now include a VisualLoop
    root.addObject('DefaultVisualManagerLoop')
    # Scene must now include a AnimationLoop
    root.addObject('DefaultAnimationLoop')

    # In order to simulate collision, a collision pipeline needs to be created
    root.addObject('CollisionPipeline', verbose=0, draw=0)
    root.addObject('BruteForceDetection', name="N2")
    root.addObject('NewProximityIntersection', name="Proximity", alarmDistance=0.5, contactDistance=0.25)
    root.addObject('CollisionResponse', name="Response", response="default")

    # Load mesh file to accessed by other objects in child nodes
    root.addObject('MeshGmshLoader', name="meshLoaderCoarse", filename="mesh/liver.msh")
    # Load finer mesh for visual model.
    root.addObject('MeshObjLoader', name="meshLoaderFine", filename="mesh/liver-smooth.obj")

    # Add child node
    liver = root.addChild('Liver')
    # Add physics solver to determine effect of forces on the object
    liver.addObject('EulerImplicitSolver')
    liver.addObject('CGLinearSolver', iterations=200, tolerance=1e-09, threshold=1e-09)
    # Load tetrhedron mesh from loaded mesh and storing it in a container
    liver.addObject('TetrahedronSetTopologyContainer', name="topo", src="@../meshLoaderCoarse")
    liver.addObject('TetrahedronSetGeometryAlgorithms', name="GeomAlgo", template="Vec3d")
    # Add rigid body with its degrees of freedom and initial position
    liver.addObject('MechanicalObject', name="MechanicalModel", template="Vec3d", showObject=1)
    # Add a mechaincal model for example Elasticity
    liver.addObject('TetrahedronFEMForceField', name="FEM", youngModulus=600, poissonRatio=0.4, method="large")
    liver.addObject('MeshMatrixMass', massDensity=1)
    liver.addObject('ConstantForceField', totalForce=[100,0,0])
    # Add constraint to the model at the following points
    liver.addObject('FixedConstraint', indices=[1,3,50])

    # Only a surface mesh is required for a visual model, which can be extracted from the TetrahedronSetTopologyContainer using the below child node.
    surfaceMesh = liver.addChild('ExtractSurface')
    surfaceMesh.addObject('TriangleSetTopologyContainer', name="Container")
    surfaceMesh.addObject('TriangleSetTopologyModifier', name="Modifier")
    surfaceMesh.addObject('Tetra2TriangleTopologicalMapping', input="@../topo", output="@Container")

    # In order to create a visual model which moves with the physics model,the visual mesh must be mapped to the physics mesh
    # This is done by creating a child node of the particle for the visual model
    visual = surfaceMesh.addChild('Visual')
    # Add a visual model using the same mesh that was loaded
    visual.addObject('OglModel', name="VisualModel", color="red")
    # Add mapping of the visual model to the 'Liver' physics model.
    visual.addObject('IdentityMapping', name="VMapping", input="@../../MechanicalModel", output="@VisualModel")

    # In order to simulate collisions, a collision model and mesh must be added and mapped to the physics model
    collision = liver.addChild('Collision')
    collision.addObject('MeshTopology', src="@../../meshLoaderFine")
    collision.addObject('MechanicalObject', name="CollisionMO", scale=1.0)
    collision.addObject('TriangleCollisionModel', name="CollisionModel", contactStiffness=3)
    collision.addObject('BarycentricMapping', name="CollisionMapping", input="@../MechanicalModel", output="@CollisionMO")

    # Create a new child node of root to create a new object in the Simulation
    sphere = root.addChild('Sphere')
    sphere.addObject('EulerImplicitSolver', rayleighStiffness=0)
    sphere.addObject('CGLinearSolver', iterations=200, tolerance=1e-06, threshold=1e-06)
    sphere.addObject('MechanicalObject', name="mySphere", template="Rigid3d", position=[-2,10,0,0,0,0,1], showObject=1, showObjectScale=0.5)
    sphere.addObject('UniformMass', totalMass=1)
    sphere.addObject('ConstantForceField', force=[0,-1,0,0,0,0])
    sphere.addObject('SphereCollisionModel', name="SphereCollision", listRadius=1, simulated=1, moving=1, contactStiffness=100)

    return root

def main():
    import SofaRuntime
    import Sofa.Gui
    # Make sure to load all SOFA libraries
    SofaRuntime.importPlugin("SofaComponentAll")
    #Create the root node
    root = Sofa.Core.Node("root")
    # Call the below 'createScene' function to create the scene graph
    createScene(root)
    Sofa.Simulation.init(root)

    if not USE_GUI:
        for iteration in range(10):
            Sofa.Simulation.animate(root, root.dt.value)
    else:
        # Find out the supported GUIs
        print ("Supported GUIs are: " + Sofa.Gui.GUIManager.ListSupportedGUI(","))
        # Launch the GUI (qt or qglviewer)
        Sofa.Gui.GUIManager.Init("myscene", "qglviewer")
        Sofa.Gui.GUIManager.createGUI(root, __file__)
        Sofa.Gui.GUIManager.SetDimension(1080, 1080)
        # Initialization of the scene will be done here
        Sofa.Gui.GUIManager.MainLoop(root)
        Sofa.Gui.GUIManager.closeGUI()
        print("GUI was closed")

    print("Simulation is done.")

# Function used only if this script is called from a python environment
if __name__ == '__main__':
    main()

When I used runSofa the animation works perfectly, however when I used python3 the rigid sphere passes through the liver and no interactions are shown. Additionally, in the terminal the following warning is displayed:

[WARNING] [IntersectorMap] Element Intersector SphereCollisionModel<StdRigidTypes<3u, double> >-TriangleCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> > NOT FOUND within :  OBBCollisionModel<StdRigidTypes<3u, double> >-OBBCollisionModel<StdRigidTypes<3u, double> >  TOBB<StdRigidTypes<3u, double> >-TOBB<StdRigidTypes<3u, double> >  
  CubeCollisionModel-CubeCollisionModel  Cube-Cube  
  SphereCollisionModel<StdRigidTypes<3u, double> >-OBBCollisionModel<StdRigidTypes<3u, double> >  TSphere<StdRigidTypes<3u, double> >-TOBB<StdRigidTypes<3u, double> >  
  SphereCollisionModel<StdRigidTypes<3u, double> >-SphereCollisionModel<StdRigidTypes<3u, double> >  TSphere<StdRigidTypes<3u, double> >-TSphere<StdRigidTypes<3u, double> >  
  SphereCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-OBBCollisionModel<StdRigidTypes<3u, double> >  TSphere<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TOBB<StdRigidTypes<3u, double> >  
  SphereCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-SphereCollisionModel<StdRigidTypes<3u, double> >  TSphere<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TSphere<StdRigidTypes<3u, double> >  
  SphereCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-SphereCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  TSphere<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TSphere<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  
  CapsuleCollisionModel<StdRigidTypes<3u, double> >-OBBCollisionModel<StdRigidTypes<3u, double> >  TCapsule<StdRigidTypes<3u, double> >-TOBB<StdRigidTypes<3u, double> >  
  CapsuleCollisionModel<StdRigidTypes<3u, double> >-SphereCollisionModel<StdRigidTypes<3u, double> >  TCapsule<StdRigidTypes<3u, double> >-TSphere<StdRigidTypes<3u, double> >  
  CapsuleCollisionModel<StdRigidTypes<3u, double> >-SphereCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  TCapsule<StdRigidTypes<3u, double> >-TSphere<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  
  CapsuleCollisionModel<StdRigidTypes<3u, double> >-CapsuleCollisionModel<StdRigidTypes<3u, double> >  TCapsule<StdRigidTypes<3u, double> >-TCapsule<StdRigidTypes<3u, double> >  
  CapsuleCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-OBBCollisionModel<StdRigidTypes<3u, double> >  TCapsule<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TOBB<StdRigidTypes<3u, double> >  
  CapsuleCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-SphereCollisionModel<StdRigidTypes<3u, double> >  TCapsule<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TSphere<StdRigidTypes<3u, double> >  
  CapsuleCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-SphereCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  TCapsule<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TSphere<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  
  CapsuleCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-CapsuleCollisionModel<StdRigidTypes<3u, double> >  TCapsule<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TCapsule<StdRigidTypes<3u, double> >  
  CapsuleCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-CapsuleCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  TCapsule<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TCapsule<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> > 

I probably won’t need this, but I would appreciate insight into the problem and its cause to help my understanding and ability to figure it out in the future.

Thanks,
Michael Pienaar

[Hugo]

Hey @quantanovo

Thank you very much for your interest in SOFA, for your feedback regarding the YouTube tutorial videos and SofaPython3.
The problem you point out is strange indeed. @jnbrunet could this be due to a missing binding for OBBs?
In the meantime @quantanovo could you try replacing the NewProximityIntersection by LocalMinDistance instead? Let us know if it helps.

Best wishes,

Hugo

[MikeP]

Hi @Hugo

Thank you so much for the response as well as the providing the training session as it has been extremely helpful!
Unfortunately, LocalMinDistance does not work either and provides a similar warning:

[WARNING] [IntersectorMap] Element Intersector SphereCollisionModel<StdRigidTypes<3u, double> >-TriangleCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> > NOT FOUND within :  OBBCollisionModel<StdRigidTypes<3u, double> >-OBBCollisionModel<StdRigidTypes<3u, double> >  TOBB<StdRigidTypes<3u, double> >-TOBB<StdRigidTypes<3u, double> >  
  RayCollisionModel-LineCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  nullptr  
  RayCollisionModel-PointCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  nullptr  
  RayCollisionModel-SphereCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  Ray-TSphere<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  
  RayCollisionModel-TriangleCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  Ray-TTriangle<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  
  CubeCollisionModel-CubeCollisionModel  Cube-Cube  
  LineCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-LineCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  TLine<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TLine<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  
  LineCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-PointCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  TLine<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TPoint<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  
  LineCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-SphereCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  TLine<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TSphere<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  
  PointCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-PointCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  TPoint<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TPoint<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  
  SphereCollisionModel<StdRigidTypes<3u, double> >-OBBCollisionModel<StdRigidTypes<3u, double> >  TSphere<StdRigidTypes<3u, double> >-TOBB<StdRigidTypes<3u, double> >  
  SphereCollisionModel<StdRigidTypes<3u, double> >-SphereCollisionModel<StdRigidTypes<3u, double> >  TSphere<StdRigidTypes<3u, double> >-TSphere<StdRigidTypes<3u, double> >  
  SphereCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-OBBCollisionModel<StdRigidTypes<3u, double> >  TSphere<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TOBB<StdRigidTypes<3u, double> >  
  SphereCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-PointCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  TSphere<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TPoint<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  
  SphereCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-SphereCollisionModel<StdRigidTypes<3u, double> >  TSphere<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TSphere<StdRigidTypes<3u, double> >  
  SphereCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-SphereCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  TSphere<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TSphere<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  
  CapsuleCollisionModel<StdRigidTypes<3u, double> >-OBBCollisionModel<StdRigidTypes<3u, double> >  TCapsule<StdRigidTypes<3u, double> >-TOBB<StdRigidTypes<3u, double> >  
  CapsuleCollisionModel<StdRigidTypes<3u, double> >-SphereCollisionModel<StdRigidTypes<3u, double> >  TCapsule<StdRigidTypes<3u, double> >-TSphere<StdRigidTypes<3u, double> >  
  CapsuleCollisionModel<StdRigidTypes<3u, double> >-SphereCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  TCapsule<StdRigidTypes<3u, double> >-TSphere<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  
  CapsuleCollisionModel<StdRigidTypes<3u, double> >-CapsuleCollisionModel<StdRigidTypes<3u, double> >  TCapsule<StdRigidTypes<3u, double> >-TCapsule<StdRigidTypes<3u, double> >  
  CapsuleCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-OBBCollisionModel<StdRigidTypes<3u, double> >  TCapsule<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TOBB<StdRigidTypes<3u, double> >  
  CapsuleCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-SphereCollisionModel<StdRigidTypes<3u, double> >  TCapsule<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TSphere<StdRigidTypes<3u, double> >  
  CapsuleCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-SphereCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  TCapsule<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TSphere<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  
  CapsuleCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-CapsuleCollisionModel<StdRigidTypes<3u, double> >  TCapsule<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TCapsule<StdRigidTypes<3u, double> >  
  CapsuleCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-CapsuleCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  TCapsule<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TCapsule<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  
  TriangleCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-LineCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  nullptr  
  TriangleCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-PointCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  TTriangle<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TPoint<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  
  TriangleCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-SphereCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  TTriangle<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TSphere<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  
  TriangleCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >-TriangleCollisionModel<StdVectorTypes<Vec<3u, double>, Vec<3u, double>, double> >  nullptr  

Kind regards,
Mike

[Hugo]

Hey @quantanovo

I tested it with the recent v20.12.01 release of SOFA it seems to work well.
Could you try it as well?

Only a set of RequiredPlugin was missing:

    root.addObject('RequiredPlugin', pluginName="SofaGeneralLoader")
    root.addObject('RequiredPlugin', pluginName="SofaLoader")
    root.addObject('RequiredPlugin', pluginName="SofaImplicitOdeSolver")
    root.addObject('RequiredPlugin', pluginName="SofaSimpleFem")
    root.addObject('RequiredPlugin', pluginName="SofaOpenglVisual")

Hope this helps.
Best

Hugo

[MikeP]

Hi @Hugo

Apologies for the late reply.

I have rebuilt SOFA with the latest release and unfortunately it still does not work. I have converted a few collision examples into python scripts such as SphereModel.scn and TriangleModel.scn and they both give a similar warning as above. That being said, the SphereModel example still works, but the TriangleModel example does not.

Considering, that you have tested it on your side and it works, then it must be something wrong on my side. I’m clueless what it could be especially since I did rebuild it from sources again.

Regards,
Mike

[Hugo]

Hi @quantanovo

I understand that you have updated your SOFA (and SofaPython3) sources and compiled again. Despite this it does not work properly. Is this correct?

Could you tell me what a “git log” command gives you from the SOFA sources?
Are you fetching SofaPython3 when configuring the project in the CMake phase ?

Best,

Hugo

[MikeP]

Hi @Hugo

I apologize for the late reply. I decided to reinstall sofa v20.12.01 from the binaries. And this solved my issue.

Kind regards,
Michael

[Hugo]

Great to hear, thanks @quantanovo for letting us know and closing the topic!
Looking forward to seeing your simulation achievements!

Hugo

[chiarasapo]

I have the exact same problem, should I go back to the previous version too? Or do you think that there is another solution? Thanks in advance!

[Author]

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