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

[Author]

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