SofaCarving crash in SofaPython3

[BeforeSilence]

Hi,

I'm trying to convert a scene in ".scn" to “.py”. In this scene, I want to use carving module to remove some elements from tissue(liver). It works in ".scn" file. However, once I change to ".py", the SofaCarving module does not work while collison is ok.

When I load my '.py' file, there will be an "[INFO]No python3 dir found in D:/Set_Apps/v20.12.03/plugins/SofaCarving"
If this mean SofaPython3 does not support SofaCarving?

Looking forward to help.

The following is my code.

import Sofa


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


def main():
    import SofaRuntime
    import Sofa.Gui
    SofaRuntime.importPlugin("SofaOpenglVisual")
    SofaRuntime.importPlugin("SofaImplicitOdeSolver")

    root = Sofa.Core.Node("root")
    createScene(root)
    Sofa.Simulation.init(root)

    if not USE_GUI:
        for iteration in range(10):
            Sofa.Simulation.animate(root, root.dt.value)
    else:
        Sofa.Gui.GUIManager.Init("myscene", "qglviewer")
        Sofa.Gui.GUIManager.createGUI(root, __file__)
        Sofa.Gui.GUIManager.SetDimension(1080, 1080)
        Sofa.Gui.GUIManager.MainLoop(root)
        Sofa.Gui.GUIManager.closeGUI()

def createScene(root):
    
    root.gravity=[0, 0, 0]
    root.dt=0.05
    root.showBoundingTree = 0
    root.addObject('RequiredPlugin', pluginName="SofaOpenglVisual SofaBoundaryCondition SofaGeneralLoader SofaGeneralSimpleFem SofaImplicitOdeSolver SofaLoader SofaMeshCollision SofaRigid SofaMiscCollision SofaTopologyMapping")
    root.addObject('RequiredPlugin',name="Carving",pluginName="SofaCarving")

    root.addObject('VisualStyle',displayFlags="")
    root.addObject('DefaultPipeline',verbose="0")
    root.addObject('BruteForceDetection',name="N2")
    root.addObject('DefaultContactManager',response="default")
  root.addObject('MinProximityIntersection',name="Proximity",alarmDistance="0.08",contactDistance="0.05",useSurfaceNormals="false")
    root.addObject('DefaultCollisionGroupManager')
    root.addObject('CarvingManager',active="true",carvingDistance="-0.01")
  
    TT = root.addChild('TT')
    
    TT.addObject('EulerImplicitSolver',name="cg_odesolver",printLog="false",rayleighStiffness="0.1",rayleighMass="0.1")
    TT.addObject('CGLinearSolver',iterations="25",name="linear solver",tolerance="1.0e-9",threshold="1.0e-9")
    TT.addObject('MeshGmshLoader',filename="mesh/liver.msh",name="loader",scale="1")
    TT.addObject('TetrahedronSetTopologyContainer', name="topo", src="@loader")
   
    TT.addObject('MechanicalObject',template="Vec3d",src="@loader",name="Volume")
    TT.addObject('TetrahedronSetGeometryAlgorithms', template="Vec3d", name="GeomAlgo")
    #TT.addObject('include',href="Objects/TetrahedronSetTopology.xml",src="@loader")
    
    TT.addObject('DiagonalMass',massDensity="0.5")
    TT.addObject('FixedConstraint',indices="1 3 50")
    TT.addObject('TetrahedralCorotationalFEMForceField',name="CFEM",youngModulus="160",poissonRatio="0.3",method="large")
    
    T=TT.addChild('T')
    T.addObject('TetrahedronSetGeometryAlgorithms',name="GeomAlgo",template="Vec3d")
    T.addObject('TriangleSetTopologyContainer', name="Container")
    T.addObject('TriangleSetTopologyModifier', name="Modifier")
    T.addObject('Tetra2TriangleTopologicalMapping', input="@../topo", output="@Container")
    #T.addObject('Tetra2TriangleTopologicalMapping',input="@Container",output="@Container")
    T.addObject('TriangleCollisionModel', tags="CarvingSurface")

    Visu = T.addChild('Visu')
    Visu.addObject('OglModel',name="Visual",material="Default Diffuse 1 0 1 0 1 Ambient 0 1 1 1 1 Specular 1 1 1 0 1 Emissive 0 1 1 0 1 Shininess 1 100")
    Visu.addObject('IdentityMapping',input="@Volume",output="@Visual")

    Instrument = root.addChild('Instrument')
    Instrument.addObject('EulerImplicitSolver',name="cg_odesolver",printLog="false")
    Instrument.addObject('CGLinearSolver',iterations="25",name="linear solver",tolerance="1.0e-9",threshold="1.0e-9")
    Instrument.addObject('MechanicalObject',template="Rigid3d",name="instrumentState",tags="Omni",rotation="90 45 0",translation="0 0 1")
    Instrument.addObject('UniformMass',template="Rigid3d",name="mass",totalMass="5")
    visuIns = Instrument.addChild('visuIns')
    visuIns.addObject('MeshObjLoader',name="meshLoader_0",filename="mesh/dental_instrument_light.obj",scale3d="1 1 1",translation="-0.412256 -0.067639 3.35",rotation="180 0 150",handleSeams="1")
    visuIns.addObject('OglModel',template="ExtVec3f",name="InstrumentVisualModel",src="@meshLoader_0",material="Default Diffuse 1 1 0.2 0.2 1 Ambient 1 0.2 0.04 0.04 1 Specular 0 1 0.2 0.2 1 Emissive 0 1 0.2 0.2 1 Shininess 0 45")
    visuIns.addObject('RigidMapping',template="Rigid,ExtVec3f",name="MM->VM mapping",input="@instrumentState",output="@InstrumentVisualModel")

    colIns = Instrument.addChild('colIns')
    colIns.addObject('MechanicalObject',template="Vec3d",name="Particle",position="-0.2 -0.2 -0.2")
    colIns.addObject('SphereCollisionModel',name="ParticleModel",radius="0.2",tags="CarvingTool")
    #colIns.addObject('SphereCollisionModel',name="ParticleModel",radius="0.2")
    colIns.addObject('RigidMapping',template="Rigid,Vec3d",name="MM->CM mapping",input="@instrumentState",output="@Particle")

    return root


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

[epernod]

No the warning just say there is no specific python folder/script for SofaCarving. But you should be able to use it inside your python scene like in .scn
could you put the full log when you launch the python scene.
Thx.

[BeforeSilence]

Thanks and sorry for my late reply.

Here is my log.

[INFO]    [SceneCheckerVisitor] Validating node "root" with checks: [SceneCheckDuplicatedName, SceneCheckMissingRequiredPlugin, SceneCheckUsingAlias]
[INFO]    [SceneCheckerVisitor] Finished validating node "root".
[INFO]    [PluginManager] Loaded plugin: D:/Set_Apps/v20.12.03/bin/SofaCarving.dll
[INFO]    [SofaPython3] No python3 dir found in D:/Set_Apps/v20.12.03/plugins/SofaCarving
[WARNING] [UniformMass(mass)] Template Rigid3d incorrect, used Rigid3d,RigidMass<3,double>
[WARNING] [OglModel(InstrumentVisualModel)] Template ExtVec3f incorrect, used Vec3d
[WARNING] [RigidMapping(MM->VM mapping)] Template Rigid,ExtVec3f incorrect, used Rigid3d,Vec3d
[DEPRECATED] [RigidMapping(MM->VM mapping)] The deprecated template 'Rigid' has been replaced by Rigid3d. As they have different precisions this may result in undefined behavior. To remove this message, please update your scene to use the generic 'Vec3' templates or one of 'Vec3f/Vec3d' that match your the precision of your Sofa binary.
[DEPRECATED] [RigidMapping(MM->CM mapping)] The deprecated template 'Rigid' has been replaced by Rigid3d. As they have different precisions this may result in undefined behavior. To remove this message, please update your scene to use the generic 'Vec3' templates or one of 'Vec3f/Vec3d' that match your the precision of your Sofa binary.
[INFO]    [SceneCheckerVisitor] Validating node "root" with checks: [SceneCheckDuplicatedName, SceneCheckMissingRequiredPlugin, SceneCheckUsingAlias]
[INFO]    [SceneCheckerVisitor] Finished validating node "root".

########## SIG 11 - SIGSEGV: segfault ##########
45: sofa::helper::BackTrace::dump - 0x7ffab3f56f1044: sofa::helper::BackTrace::sig - 0x7ffab3f5705c43: seh_filter_exe - 0x7ffb60730cc042: seh_filter_exe - 0x7ffb60730cc041: _C_specific_handler - 0x7ffb2e14b85040: _chkstk - 0x7ffb62e9230039: RtlRaiseException - 0x7ffb62e4107038: KiUserExceptionDispatcher - 0x7ffb62e90f2037: sofa::component::collision::TopologicalChangeManager::removeItemsFromTriangleModel - 0x7ffa9f8e9fb436: sofa::component::collision::TopologicalChangeManager::removeItemsFromCollisionModel - 0x7ffa9f8e8fec35: sofa::component::collision::CarvingManager::doCarve - 0x7ffa99e44bd434: sofa::component::collision::CarvingManager::handleEvent - 0x7ffa99e45b8433: sofa::simulation::PropagateEventVisitor::processObject - 0x7ffabb0e363032: sofa::simulation::DefaultAnimationLoop::step - 0x7ffabb0b976031: sofa::simulation::PropagateEventVisitor::processNodeTopDown - 0x7ffabb0e35f030: sofa::simulation::graph::DAGNode::executeVisitorTopDown - 0x7ffb23b69ed029: sofa::simulation::graph::DAGNode::doExecuteVisitor - 0x7ffb23b692b828: sofa::simulation::Node::executeVisitor - 0x7ffabb0d58b027: sofa::simulation::DefaultAnimationLoop::step - 0x7ffabb0b976026: sofa::simulation::Simulation::animate - 0x7ffabb0e562825: sofa::gui::qt::RealGUI::step - 0x7ffa98a5735024: QMetaObject::activate - 0x7ffa8db5b31023: QTimer::timerEvent - 0x7ffa8db6864022: QObject::event - 0x7ffa8db6138021: QApplicationPrivate::notify_helper - 0x7ffa9835832020: QApplication::notify - 0x7ffa9835593019: QCoreApplication::notifyInternal2 - 0x7ffa8db3a8d018: QEventDispatcherWin32::event - 0x7ffa8db841b017: QApplicationPrivate::notify_helper - 0x7ffa9835832016: QApplication::notify - 0x7ffa9835593015: QCoreApplication::notifyInternal2 - 0x7ffa8db3a8d014: QCoreApplicationPrivate::sendPostedEvents - 0x7ffa8db3c6d013: qt_plugin_query_metadata - 0x7ffa87bc16e012: QEventDispatcherWin32::processEvents - 0x7ffa8db845e011: CallWindowProcW - 0x7ffb620be46010: DispatchMessageW - 0x7ffb620be0409: QEventDispatcherWin32::processEvents - 0x7ffa8db845e08: qt_plugin_query_metadata - 0x7ffa87bc16e07: QEventLoop::exec - 0x7ffa8db365706: QCoreApplication::exec - 0x7ffa8db397305: sofa::gui::qt::RealGUI::mainLoop - 0x7ffa98a5490c4: sofa::gui::GUIManager::MainLoop - 0x7ffaf04a184c3: sofa::gui::GUIManager::MainLoop - 0x7ffaf04a184c2: sofa::gui::GUIManager::MainLoop - 0x7ffaf04a184c1: BaseThreadInitThunk - 0x7ffb62c770200: RtlUserThreadStart - 0x7ffb62e42680[WARNING] [SofaSimulationTree] the library has not been cleaned up (sofa::simulation::tree::cleanup() has never been called, see sofa/helper/init.h)

[epernod]

Hi,

• ok from what I see in your log, you have several problem of templates:

[WARNING] [UniformMass(mass)] Template Rigid3d incorrect, used Rigid3d,RigidMass<3,double>
[WARNING] [OglModel(InstrumentVisualModel)] Template ExtVec3f incorrect, used Vec3d
[WARNING] [RigidMapping(MM->VM mapping)] Template Rigid,ExtVec3f incorrect, used Rigid3d,Vec3d

I'm not sure if it is the cause the of the crash but I suggest to solve them first.

• Then in a more general way, I see you are using: v20.12.03, this release is 2 years old, I would highly recommend to use our latest release v22.06.00
• Finally looking at your scene, there is an error in the topology components. You should have:

TT.addObject('TetrahedronSetTopologyContainer', name="topo", src="@loader")
TT.addObject('TetrahedronSetTopologyModifier', name="topoMod")
TT.addObject('TetrahedronSetGeometryAlgorithms', template="Vec3d", name="GeomAlgo")

and

T.addObject('TriangleSetTopologyContainer', name="Container")
T.addObject('TriangleSetTopologyModifier', name="Modifier")
T.addObject('TriangleSetGeometryAlgorithms',name="GeomAlgo",template="Vec3d")
T.addObject('Tetra2TriangleTopologicalMapping', input="@../topo", output="@Container")

I will push this python scene inside the plugin examples.

[epernod]

Here it is: #3457