GMSH Loader in Sofa v23.12.00 on Windows #4727

oystebje · 2024-05-07T14:41:55Z

oystebje
May 7, 2024

Hello,

My colleague is trying to run my SOFA scene on her laptop, but she is not able to load the gmsh (.msh) file in SofaPython3. We have tried opening the "liver.msh" file from the example "examples/Demos/liver.scn". This works well when opening the XML-scene, but not when opening it from our python scene.

Here is the error message:

I'm still using SOFA v22.06.00, while she is on SOFA v23.12.00. Everything works well on my laptop. Have there been any updates to the MeshGmshLoader in v23 that could cause this issue?

Here is the scene we have tried:

import Sofa


def createScene(rootNode):
     
    rootNode.dt=0.01
    rootNode.gravity=[0, -9.81e3, 0] 

    confignode = rootNode.addChild("Config")
    confignode.addObject('RequiredPlugin', name="Sofa.Component.Collision.Geometry")
    confignode.addObject('RequiredPlugin', name="SofaPython3", printLog=False)
    confignode.addObject('OglSceneFrame', style="Arrows", alignment="TopRight")
    
    rootNode.addObject('DefaultVisualManagerLoop')
    rootNode.addObject('DefaultPipeline', name="pipeline", depth="6", verbose="0")
    rootNode.addObject('BruteForceBroadPhase')
    rootNode.addObject('BVHNarrowPhase')
    rootNode.addObject('DefaultContactManager', name="response", response="FrictionContactConstraint") 
    rootNode.addObject('LocalMinDistance', alarmDistance="3.408", contactDistance="1.136", angleCone="0.0")
    rootNode.addObject('FreeMotionAnimationLoop')
    #rootNode.addObject('LCPConstraintSolver', tolerance="0.001", maxIt="1000", computeConstraintForces="True", mu="0.000001")

    #rootNode.addObject('RequiredPlugin', name='Geomagic')
    #driver = rootNode.addObject('GeomagicDriver', name='GeomagicDevice', deviceName="Default Device", scale="30", drawDeviceFrame="1", positionBase="0 0 0", drawDevice="0", orientationBase="0 0.707 0 -0.707")  #scale attribute only affects position
    
    #LIVER NODE BEGIN*************************************************************************************************************************************************************************
    liver = rootNode.addChild('liver')
    liver.gravity = [0, -9.81e3, 0]
    liver.addObject('EulerImplicitSolver', name="cg_odesolver")
    liver.addObject('CGLinearSolver', name="linear solver", iterations="25", tolerance="1e-09", threshold="1e-09")

    liver.addObject('MeshGmshLoader', name="meshLoader", filename="mesh/liver.msh", rotation="90 270 -182", translation="0 -31.5 -26", scale3d="26 26 26")
    liver.addObject('TetrahedronSetTopologyContainer', name="topo",  src="@meshLoader")
   
    liver.addObject('MechanicalObject', name="liverDofs", src="@meshLoader")
    liver.addObject('TetrahedronSetGeometryAlgorithms', template="Vec3d", name="GeomAlgo")
    liver.addObject('DiagonalMass', name="mass", massDensity="1.09e-9", topology="@topo", geometryState="@liverDofs") 
    liver.addObject('TetrahedralCorotationalFEMForceField', template="Vec3d", name="FEM", poissonRatio="0.29", youngModulus="5.05") 
    liver.addObject('PrecomputedConstraintCorrection', recompute="true")
    liver.addObject('FixedConstraint', name="FixedConstraint", indices="1 2 5 6 7 11 12 13 14 15 16 17 18 19 20 21 22 23 24")
    #LIVER NODE END***************************************************************************************************************************************************************************
    
    return rootNode

    

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

Answered by epernod

May 15, 2024

Hi @oystebje

I tested your scene and except some warnings due to aliases or required plugin missing, it works fine on my side. But I'm on master, not 23.12.

To investigate:

Could you try to open this example: https://github.com/sofa-framework/SofaPython3/blob/master/examples/liver.py
It is the same the "examples/Demos/liver.scn" but in python.
Could you update your scene line 33 to change the TopologyContainer with this: liver.addObject('TetrahedronSetTopologyContainer', name="topo", position="@meshLoader.position", tetrahedra="@meshLoader.tetrahedra")
passing only the points and tetrahedra, it will force the component to recompute the list of triangles and edges with the correct struct…

View full answer

adrianbacallado · 2024-05-07T15:14:55Z

adrianbacallado
May 7, 2024

Hello!

Maybe the version of SOFA could be the problem, but before that I think you may need to import the IO plugin, as:
confignode.addObject('RequiredPlugin', name="Sofa.Component.IO.Mesh")

I hope this helps!

1 reply

oystebje May 14, 2024
Author

Hi @adrianbacallado

Thanks for the reply! We have tried this but unfortunately no luck. Still the same error.

hugtalbot · 2024-05-15T04:57:44Z

hugtalbot
May 15, 2024
Maintainer

Hi @oystebje

Thanks for noticing this. The topology components are getting stricter regarding the input info/mesh.
I will take a look at it and keep you posted.

0 replies

epernod · 2024-05-15T08:42:28Z

epernod
May 15, 2024
Maintainer

Hi @oystebje

I tested your scene and except some warnings due to aliases or required plugin missing, it works fine on my side. But I'm on master, not 23.12.

To investigate:

Could you try to open this example: https://github.com/sofa-framework/SofaPython3/blob/master/examples/liver.py
It is the same the "examples/Demos/liver.scn" but in python.
Could you update your scene line 33 to change the TopologyContainer with this: liver.addObject('TetrahedronSetTopologyContainer', name="topo", position="@meshLoader.position", tetrahedra="@meshLoader.tetrahedra")
passing only the points and tetrahedra, it will force the component to recompute the list of triangles and edges with the correct structure.

Hope it helps.

1 reply

oystebje May 15, 2024
Author

@hugtalbot @epernod thanks alot! Replacing line 33 worked well, so that solved the problem for us.

For completeness, here is the code that worked:

import Sofa

def createScene(rootNode):
     
    rootNode.dt=0.01
    rootNode.gravity=[0, -9.81e3, 0] 

    confignode = rootNode.addChild("Config")
    confignode.addObject('RequiredPlugin', name="Sofa.Component.Collision.Geometry")
    confignode.addObject('RequiredPlugin', name="SofaPython3", printLog=False)
    confignode.addObject('OglSceneFrame', style="Arrows", alignment="TopRight")
    
    rootNode.addObject('DefaultVisualManagerLoop')
    rootNode.addObject('DefaultPipeline', name="pipeline", depth="6", verbose="0")
    rootNode.addObject('BruteForceBroadPhase')
    rootNode.addObject('BVHNarrowPhase')
    rootNode.addObject('DefaultContactManager', name="response", response="FrictionContactConstraint") 
    rootNode.addObject('LocalMinDistance', alarmDistance="3.408", contactDistance="1.136", angleCone="0.0")
    rootNode.addObject('FreeMotionAnimationLoop')
    #rootNode.addObject('LCPConstraintSolver', tolerance="0.001", maxIt="1000", computeConstraintForces="True", mu="0.000001")

    #rootNode.addObject('RequiredPlugin', name='Geomagic')
    #driver = rootNode.addObject('GeomagicDriver', name='GeomagicDevice', deviceName="Default Device", scale="30", drawDeviceFrame="1", positionBase="0 0 0", drawDevice="0", orientationBase="0 0.707 0 -0.707")  #scale attribute only affects position
    
    #LIVER NODE BEGIN*************************************************************************************************************************************************************************
    liver = rootNode.addChild('liver')
    liver.gravity = [0, -9.81e3, 0]
    liver.addObject('EulerImplicitSolver', name="cg_odesolver")
    liver.addObject('CGLinearSolver', name="linear solver", iterations="25", tolerance="1e-09", threshold="1e-09")

    liver.addObject('MeshGmshLoader', name="meshLoader", filename="mesh/liver.msh", rotation="90 270 -182", translation="0 -31.5 -26", scale3d="26 26 26")
    liver.addObject('TetrahedronSetTopologyContainer', name="topo", position="@meshLoader.position", tetrahedra="@meshLoader.tetrahedra")
    liver.addObject('MechanicalObject', name="liverDofs", src="@meshLoader")
    liver.addObject('TetrahedronSetGeometryAlgorithms', template="Vec3d", name="GeomAlgo")
    liver.addObject('DiagonalMass', name="mass", massDensity="1.09e-9", topology="@topo", geometryState="@liverDofs") 
    liver.addObject('TetrahedralCorotationalFEMForceField', template="Vec3d", name="FEM", poissonRatio="0.29", youngModulus="5.05") 
    liver.addObject('PrecomputedConstraintCorrection', recompute="true")
    liver.addObject('FixedConstraint', name="FixedConstraint", indices="1 2 5 6 7 11 12 13 14 15 16 17 18 19 20 21 22 23 24")
    #LIVER NODE END***************************************************************************************************************************************************************************
    
    return rootNode

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

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GMSH Loader in Sofa v23.12.00 on Windows #4727

oystebje May 7, 2024

Replies: 3 comments · 2 replies

adrianbacallado May 7, 2024

oystebje May 14, 2024 Author

hugtalbot May 15, 2024 Maintainer

epernod May 15, 2024 Maintainer

oystebje May 15, 2024 Author

oystebje
May 7, 2024

Replies: 3 comments 2 replies

adrianbacallado
May 7, 2024

oystebje May 14, 2024
Author

hugtalbot
May 15, 2024
Maintainer

epernod
May 15, 2024
Maintainer

oystebje May 15, 2024
Author