Failure to run PneuNets.pyscn [SoftRobots.inverse]

[GriffTDG]

Hello! I am currently trying to run the simulation PneuNets.pyscn on the most recent binaries version of SOFA. I believe I have properly imported the plugins SoftRobots and SoftRobots.inverse, as I have been able to run some other of the examples included in these plugins, although I have noticed certain ones do not run. When I run the PneuNets.pyscn I get the error this error in the SOFA terminal:

[ERROR]   [SofaPython3::SceneLoader] Unable to completely load the scene from file 'C:\Users\TristanGriffith\SOFA\v22.06.00\plugins\SoftRobots.Inverse\docs\sofapython3\component\constraint\SurfacePressureActuator\PneuNets.pyscn'.
Python exception:
  TypeError: Unknown Attribute(s):
 - "drawAsEdges" with value: "1

I can run the SurfacePressureActuator just fine, but I am having similar issues when I try and run the SurfacePressureActuatorGS.
It seems to me like the scene setup is either outdated or something is going wrong with STLIB.
This is what the rest of the terminal says when running this person:

[WARNING] [ObjectFactory] Default template for class CableConstraint already registered (Vec3d), do not register Vec3d as the default
[WARNING] [ObjectFactory] Class already registered: CableConstraint<Vec2d>
[WARNING] [ObjectFactory] Class already registered: CableConstraint<Vec3d>
[WARNING] [ObjectFactory] Default template for class PartialRigidificationConstraint already registered (Rigid3d), do not register Rigid3d as the default
[WARNING] [ObjectFactory] Class already registered: PartialRigidificationConstraint<Rigid3d>
[WARNING] [ObjectFactory] Default template for class SurfacePressureConstraint already registered (Vec3d), do not register Vec3d as the default
[WARNING] [ObjectFactory] Class already registered: SurfacePressureConstraint<Vec3d>
[WARNING] [ObjectFactory] Default template for class UnilateralPlaneConstraint already registered (Vec3d), do not register Vec3d as the default
[WARNING] [ObjectFactory] Class already registered: UnilateralPlaneConstraint<Vec3d>
[WARNING] [ObjectFactory] Default template for class AnimationEditor already registered (Vec3d), do not register Vec3d as the default
[WARNING] [ObjectFactory] Class already registered: AnimationEditor<Rigid3d>
[WARNING] [ObjectFactory] Class already registered: AnimationEditor<Vec3d>
[WARNING] [ObjectFactory] Default template for class DataVariationLimiter already registered (Vec3d), do not register Vec3d as the default
[WARNING] [ObjectFactory] Class already registered: DataVariationLimiter<Vec1d>
[WARNING] [ObjectFactory] Class already registered: DataVariationLimiter<Vec1i>
[WARNING] [ObjectFactory] Class already registered: DataVariationLimiter<Vec2d>
[WARNING] [ObjectFactory] Class already registered: DataVariationLimiter<Vec2i>
[WARNING] [ObjectFactory] Class already registered: DataVariationLimiter<Vec3d>
[WARNING] [ObjectFactory] Class already registered: DataVariationLimiter<Vec3i>
[WARNING] [ObjectFactory] Class already registered: SerialPortBridgeGeneric
[WARNING] [ObjectFactory] Default template for class CenterOfMass already registered (Vec3d), do not register Vec3d as the default
[WARNING] [ObjectFactory] Class already registered: CenterOfMass<Vec3d>
[WARNING] [ObjectFactory] Default template for class VolumeFromTriangles already registered (Vec3d), do not register Vec3d as the default
[WARNING] [ObjectFactory] Class already registered: VolumeFromTriangles<Vec3d>
[WARNING] [ObjectFactory] Default template for class VolumeFromTetrahedrons already registered (Vec3d), do not register Vec3d as the default
[WARNING] [ObjectFactory] Class already registered: VolumeFromTetrahedrons<Vec3d>
[WARNING] [ObjectFactory] Default template for class PREquivalentStiffnessForceField already registered (Rigid3d), do not register Rigid3d as the default
[WARNING] [ObjectFactory] Class already registered: PREquivalentStiffnessForceField<Rigid3d>
[WARNING] [ObjectFactory] Default template for class PartialRigidificationForceField already registered (Vec3d,Rigid3d), do not register Vec3d,Rigid3d as the default
[WARNING] [ObjectFactory] Class already registered: PartialRigidificationForceField<Vec3d,Rigid3d>
[WARNING] [ObjectFactory] Default template for class PipeForceField already registered (Vec3d), do not register Vec3d as the default
[WARNING] [ObjectFactory] Class already registered: PipeForceField<Vec3d>
[INFO]    [PluginManager] Loaded plugin: C:/Users/TristanGriffith/SOFA/v22.06.00/plugins/SoftRobots/bin/SoftRobots.dll
[INFO]    [SofaPython3] Added 'C:/Users/TristanGriffith/SOFA/v22.06.00/plugins/SoftRobots/lib/python3/site-packages' to sys.path
[INFO]    [PluginManager] 15 plugins have been loaded from C:/Users/TristanGriffith/SOFA/v22.06.00/config/loadedPlugins.ini
[WARNING] [Qt] The constructor with a shareWidget is deprecated, use the regular contructor instead.

[INFO]    [SceneCheckerVisitor] Validating node "root" with checks: [SceneCheckDuplicatedName, SceneCheckMissingRequiredPlugin, SceneCheckUsingAlias, SceneCheckDeprecatedComponents, SceneCheckCollisionResponse]
[INFO]    [SceneCheckerVisitor] Finished validating node "root".
[SUGGESTION] [SparseLDLSolver(preconditioner)] Template is empty
By default SparseLDLSolver uses blocks with a single scalar (to handle all cases of simulations).
If you are using only 3D DOFs, you may consider using blocks of Matrix3 to speedup the calculations.
If it is the case, add template="CompressedRowSparseMatrixMat3x3d" to this object in your scene
Otherwise, if you want to disable this message, add template="CompressedRowSparseMatrixd" .
[ERROR]   [SofaPython3::SceneLoader] Unable to completely load the scene from file 'C:\Users\TristanGriffith\SOFA\v22.06.00\plugins\SoftRobots.Inverse\docs\sofapython3\component\constraint\SurfacePressureActuator\PneuNets.pyscn'.
Python exception:
  TypeError: Unknown Attribute(s):
 - "drawAsEdges" with value: "1

  C:\Users\TristanGriffith\SOFA\v22.06.00\plugins\SoftRobots.Inverse\docs\sofapython3\component\constraint\SurfacePressureActuator\PneuNets.pyscn(41): createScene

[INFO]    [SceneCheckerVisitor] Validating node "root" with checks: [SceneCheckDuplicatedName, SceneCheckMissingRequiredPlugin, SceneCheckUsingAlias, SceneCheckDeprecatedComponents, SceneCheckCollisionResponse]
[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 beginning of your scene (if it is a .scn):
  <RequiredPlugin name="Sofa.Component.AnimationLoop"/> <!-- Needed to use components [FreeMotionAnimationLoop] -->
  <RequiredPlugin name="Sofa.Component.Collision.Geometry"/> <!-- Needed to use components [SphereCollisionModel] -->
  <RequiredPlugin name="Sofa.Component.Constraint.Lagrangian.Correction"/> <!-- Needed to use components [UncoupledConstraintCorrection] -->
  <RequiredPlugin name="Sofa.Component.IO.Mesh"/> <!-- Needed to use components [MeshVTKLoader] -->
  <RequiredPlugin name="Sofa.Component.LinearSolver.Direct"/> <!-- Needed to use components [SparseLDLSolver] -->
  <RequiredPlugin name="Sofa.Component.LinearSolver.Iterative"/> <!-- Needed to use components [CGLinearSolver] -->
  <RequiredPlugin name="Sofa.Component.Mass"/> <!-- Needed to use components [UniformMass] -->
  <RequiredPlugin name="Sofa.Component.ODESolver.Backward"/> <!-- Needed to use components [EulerImplicitSolver] -->
  <RequiredPlugin name="Sofa.Component.Setting"/> <!-- Needed to use components [BackgroundSetting] -->
  <RequiredPlugin name="Sofa.Component.SolidMechanics.FEM.Elastic"/> <!-- Needed to use components [TetrahedronFEMForceField] -->
  <RequiredPlugin name="Sofa.Component.StateContainer"/> <!-- Needed to use components [MechanicalObject] -->
  <RequiredPlugin name="Sofa.Component.Topology.Container.Dynamic"/> <!-- Needed to use components [TetrahedronSetTopologyContainer, TetrahedronSetTopologyModifier] -->
  <RequiredPlugin name="Sofa.Component.Visual"/> <!-- Needed to use components [VisualStyle] -->
  <RequiredPlugin name="Sofa.GL.Component.Rendering3D"/> <!-- Needed to use components [OglSceneFrame] -->

[INFO]    [SceneCheckerVisitor] Finished validating node "root".
[ERROR]   [TetrahedronSetTopologyContainer(container)] Cannot find edge 0 [493, 451] in triangle 0 [13 493 451] in the provided edge list (@/model/container.edges). It shows an inconsistency between the edge list (@/model/container.edges) and the triangle list (@/model/container.triangles). Either fix the topology (probably in a mesh file), or provide only the triangle list to '/model/container' and not the edges. In the latter case, the edge list will be computed from triangles.
[ERROR]   [TetrahedronSetTopologyContainer(container)] Cannot find edge 0 [493, 451] in triangle 0 [13 493 451] in the provided edge list (@/model/container.edges). It shows an inconsistency between the edge list (@/model/container.edges) and the triangle list (@/model/container.triangles). Either fix the topology (probably in a mesh file), or provide only the triangle list to '/model/container' and not the edges. In the latter case, the edge list will be computed from triangles.
[WARNING] [TetrahedronSetTopologyContainer(container)] TrianglesAroundEdge buffer can't be created as EdgesInTriangle buffer creation failed.
[ERROR]   [TetrahedronSetTopologyContainer(container)] Cannot find triangle 0 [176, 436, 599] in tetrahedron 0
[WARNING] [TetrahedronSetTopologyContainer(container)]  In getTetrahedronArray, cannot find edge for tetrahedron 0and edge 0
[ERROR]   [TetrahedronSetTopologyContainer(container)] Cannot find triangle 0 [176, 436, 599] in tetrahedron 0
[WARNING] [TetrahedronSetTopologyContainer(container)] TetrahedraAroundTriangle buffer can't be created as trianglesInTetrahedron buffer creation failed.

[hugtalbot]

Hi @GriffTDG

Thank you for your interest in SOFA and SoftRobots.Inverse.
However, so far the SoftRobots.Inverse plugin is a private plugin, I can not significantly help myself usually.

But here it seems that a component had a Data (option) named "drawAsEdges" which is not existing anymore. Could you try to edit the scene file and remove the Data drawAsEdges="1" ?

Maybe @EulalieCoevoet can give us some insight.

Best wishes.

[EulalieCoevoet]

Hi @GriffTDG,

Thanks for reporting this, there are indeed a lot of outdated examples. We'll do our best to update them all for the next release (v23.06).

Meanwhile here's a working scene:

import os

path = os.path.dirname(os.path.abspath(__file__)) + '/mesh/'


def createScene(rootNode):
    rootNode.addObject('RequiredPlugin', pluginName=['SoftRobots', 'SoftRobots.Inverse'])
    rootNode.addObject('VisualStyle',
                       displayFlags='showVisualModels showBehaviorModels showCollisionModels '
                                    'hideBoundingCollisionModels hideForceFields '
                                    'showInteractionForceFields hideWireframe')

    rootNode.addObject('FreeMotionAnimationLoop')
    rootNode.addObject('QPInverseProblemSolver')

    ##########################################
    # Goal                                   #
    ##########################################
    goal = rootNode.addChild('goal')
    goal.addObject('EulerImplicitSolver', firstOrder=True)
    goal.addObject('CGLinearSolver', iterations=100, tolerance=1e-5, threshold=1e-5)
    goal.addObject('MechanicalObject', name='goalMO', position=[[-230, 15, 0]])
    goal.addObject('SphereCollisionModel', radius=5, group=3)
    goal.addObject('UncoupledConstraintCorrection')

    ##########################################
    # FEM Model                              #
    ##########################################
    model = rootNode.addChild('model')
    model.addObject('EulerImplicitSolver', rayleighStiffness=0.2, rayleighMass=0.2)
    model.addObject('SparseLDLSolver')

    model.addObject('MeshVTKLoader', name='loader', filename=path + 'PneuNets.vtk')
    model.addObject('MeshTopology', src='@loader', name='container')

    model.addObject('MechanicalObject')
    model.addObject('UniformMass', totalMass=0.5)
    model.addObject('TetrahedronFEMForceField', template='Vec3', poissonRatio=0.3,
                    youngModulus=100)

    model.addObject('BoxROI', name='boxROI', box=[-10, 0, -20, 0, 30, 20], drawBoxes=True,
                    position=model.MechanicalObject.position.linkpath,
                    tetrahedra=model.container.tetrahedra.linkpath)
    model.addObject('BoxROI', name='boxROISubTopo', box=[-175, 22.5, -8, -19, 28, 8], drawBoxes=False,
                    position="@tetras.rest_position", tetrahedra=model.container.tetrahedra.linkpath)
    model.addObject('RestShapeSpringsForceField', points=model.boxROI.indices.linkpath, stiffness=1e12)
    model.addObject('LinearSolverConstraintCorrection')

    ##########################################
    # Sub topology                           #
    ##########################################
    modelSubTopo = model.addChild('modelSubTopo')
    modelSubTopo.addObject('TetrahedronSetTopologyContainer', position='@loader.position',
                           tetrahedra=model.boxROISubTopo.tetrahedraInROI.linkpath, name='container')
    modelSubTopo.addObject('TetrahedronFEMForceField', template='Vec3', poissonRatio=0.3,
                           youngModulus=200)

    ##########################################
    # Effector                               #
    ##########################################
    effector = model.addChild('effector')
    effector.addObject('MechanicalObject', position=[-195, 15, 0])
    effector.addObject('PositionEffector', template='Vec3', indices=[0], effectorGoal=goal.goalMO.position.linkpath,
                       useDirections=[1, 1, 0])
    effector.addObject('BarycentricMapping')

    ##########################################
    # Actuator                               #
    ##########################################
    cavity = model.addChild('cavity')
    cavity.addObject('MeshSTLLoader', name='loader', filename=path + 'PneuNets_Cavity.stl')
    cavity.addObject('MeshTopology', src=cavity.loader.linkpath, name='topo')
    cavity.addObject('MechanicalObject', name='cavity')
    cavity.addObject('SurfacePressureActuator', template='Vec3', triangles=cavity.topo.triangles.linkpath,
                     maxVolumeGrowthVariation=500, minPressure=0)
    cavity.addObject('BarycentricMapping')

    ##########################################
    # Visualization                          #
    ##########################################
    modelVisu = model.addChild('visu')
    modelVisu.addObject('MeshSTLLoader', filename=path + "PneuNets.stl", name="loader")
    modelVisu.addObject('OglModel', src=modelVisu.loader.linkpath, color=[0.7, 0.7, 0.7, 0.6])
    modelVisu.addObject('BarycentricMapping')

    return rootNode

[GriffTDG]

Thank you both for the replies, sorry about the delay in my response. I tried running the above scene but was met with this

[ERROR] [SofaPython3::SceneLoader] Unable to completely load the scene from file 'C:\Users\TristanGriffith\SOFA\v22.06.00\plugins\SoftRobots.Inverse\docs\sofapython3\component\constraint\SurfacePressureActuator\PneuNets2.pyscn'.
Python exception:
KeyError: 'linkpath'

At:
C:\Users\TristanGriffith\SOFA\v22.06.00\plugins\SoftRobots.Inverse\docs\sofapython3\component\constraint\SurfacePressureActuator\PneuNets2.pyscn(72): createScene

I quickly looked at some other working examples for comparison and changed the line 72 that said:
cavity.addObject('MeshTopology', src=cavity.loader.linkpath, name='topo')
to:
cavity.addObject('MeshTopology', src='@loader', name='topo')
which was able to run further but gave me a similar error on line 83.

Other examples didn't have the src= part for the OglModel, so I cut it out and was able to get the simulation to work with the code below:

import os

path = os.path.dirname(os.path.abspath(file)) + '/mesh/'

def createScene(rootNode):
rootNode.addObject('RequiredPlugin', pluginName=['SoftRobots', 'SoftRobots.Inverse'])
rootNode.addObject('VisualStyle',
displayFlags='showVisualModels showBehaviorModels showCollisionModels '
'hideBoundingCollisionModels hideForceFields '
'showInteractionForceFields hideWireframe')

rootNode.addObject('FreeMotionAnimationLoop')
rootNode.addObject('QPInverseProblemSolver')

##########################################
# Goal                                   #
##########################################
goal = rootNode.addChild('goal')
goal.addObject('EulerImplicitSolver', firstOrder=True)
goal.addObject('CGLinearSolver', iterations=100, tolerance=1e-5, threshold=1e-5)
goal.addObject('MechanicalObject', name='goalMO', position=[[-230, 15, 0]])
goal.addObject('SphereCollisionModel', radius=5, group=3)
goal.addObject('UncoupledConstraintCorrection')

##########################################
# FEM Model                              #
##########################################
model = rootNode.addChild('model')
model.addObject('EulerImplicitSolver', rayleighStiffness=0.2, rayleighMass=0.2)
model.addObject('SparseLDLSolver')

model.addObject('MeshVTKLoader', name='loader', filename=path + 'PneuNets.vtk')
model.addObject('MeshTopology', src='@loader', name='container')

model.addObject('MechanicalObject')
model.addObject('UniformMass', totalMass=0.5)
model.addObject('TetrahedronFEMForceField', template='Vec3', poissonRatio=0.3,
                youngModulus=100)

model.addObject('BoxROI', name='boxROI', box=[-10, 0, -20, 0, 30, 20], drawBoxes=True,
                position=model.MechanicalObject.position.linkpath,
                tetrahedra=model.container.tetrahedra.linkpath)
model.addObject('BoxROI', name='boxROISubTopo', box=[-175, 22.5, -8, -19, 28, 8], drawBoxes=False,
                position="@tetras.rest_position", tetrahedra=model.container.tetrahedra.linkpath)
model.addObject('RestShapeSpringsForceField', points=model.boxROI.indices.linkpath, stiffness=1e12)
model.addObject('LinearSolverConstraintCorrection')

##########################################
# Sub topology                           #
##########################################
modelSubTopo = model.addChild('modelSubTopo')
modelSubTopo.addObject('TetrahedronSetTopologyContainer', position='@loader.position',
                       tetrahedra=model.boxROISubTopo.tetrahedraInROI.linkpath, name='container')
modelSubTopo.addObject('TetrahedronFEMForceField', template='Vec3', poissonRatio=0.3,
                       youngModulus=200)

##########################################
# Effector                               #
##########################################
effector = model.addChild('effector')
effector.addObject('MechanicalObject', position=[-195, 15, 0])
effector.addObject('PositionEffector', template='Vec3', indices=[0], effectorGoal=goal.goalMO.position.linkpath,
                   useDirections=[1, 1, 0])
effector.addObject('BarycentricMapping')

##########################################
# Actuator                               #
##########################################
cavity = model.addChild('cavity')
cavity.addObject('MeshSTLLoader', name='loader', filename=path + 'PneuNets_Cavity.stl')
cavity.addObject('MeshTopology', src='@loader', name='topo')
cavity.addObject('MechanicalObject', name='cavity')
cavity.addObject('SurfacePressureActuator', template='Vec3', triangles=cavity.topo.triangles.linkpath,
                 maxVolumeGrowthVariation=500, minPressure=0)
cavity.addObject('BarycentricMapping')

##########################################
# Visualization                          #
##########################################
modelVisu = model.addChild('visu')
modelVisu.addObject('MeshSTLLoader', filename=path + "PneuNets.stl", name="loader")
modelVisu.addObject('OglModel', color=[0.7, 0.7, 0.7, 0.6])
modelVisu.addObject('BarycentricMapping')

return rootNode

Thanks again for the help. I was wondering if there were any sorts of guides out there for setting up new simulations in comparison to the older examples. Or maybe more accurately how the old models should be updated/converted? I am part of a research project that is trying to use a lot of the principles shown in the SoftRobots and SoftRobots.Inverse, and it would be nice to know which key things should be done differently when making new simulations based on those shown in the examples.

The main thing for the project is the use of the surface pressure constraint/actuator along a thin hollow tube.

[GriffTDG]

Sorry, one more addition! In this new PneuNets code is the SurfacePressureActuator driven by volume or pressure? Since we are trying to drive it through the use of pressure how would you change this to pressure if it was on volume?

[EulalieCoevoet]

Hi,

linkpath is a new feature of SofaPython3, it should be in the last release of SOFA (v22.12), right @hugtalbot ?

The component SurfacePressureActuator outputs both pressure and volume growth. In runSofa GUI, you can double click on the component and see all the inputs and outputs.

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In accordance with our forum management policy, the last reply is more than 4 months old and is therefore closed. Our objective is to keep the forum up to date and offer the best support experience.

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⚠️ ⚠️ ⚠️
@GriffTDG
In accordance with our forum management policy, the last reply is more than 4 months old and is therefore closed. Our objective is to keep the forum up to date and offer the best support experience.

Please feel free to reopen it if the topic is still active by providing us with an update. Please feel free to open a new thread at any time - we'll be happy to help where and when we can.