SOFA brain simulation error with Barycentric Mapping (Rigid3d, Vec3d)

[cdelor02]

Hello all. I am working on a modified version of the liver.py example contained in the SofaPython3 plugin examples. I am trying to make and visualize a brain. The overall goal is to then add a robot model into this scene to poke and prod against the brain, and acquire (force) data from the brain surface. I can get the brain model to appear in SOFA, however I am met with this error:

[WARNING] [DefaultContactManager] Option "default" for data "response" has been renamed since v21.12 (PR#2522). You have until v22.06 to fix your scene. Use "PenalityContactForceField" instead.
[WARNING] [TetrahedronSetGeometryAlgorithms(GeomAlgo)] Requested template 'Rigid3d' cannot be found in the list of available templates [Vec2d, Vec3d]. Falling back to default template: 'Vec3d'.
[WARNING] [TetrahedralCorotationalFEMForceField(FEM)] Requested template 'Rigid3d' cannot be found in the list of available templates [Vec3d]. Falling back to default template: 'Vec3d'.
[ERROR]   [SofaPython3::SceneLoader] Unable to completely load the scene from file 'mybrain.py3scn'.
Python exception:
  ValueError: Object type BarycentricMapping<Vec3d,Vec3d> was not created
The object is in the factory but cannot be created.
Requested template : None
Used template      : Vec3d,Vec3d (default)
Reason(s)          : Data attribute 'input' does not point to a mechanical state of data type 'Vec3d' and none can be found in the parent node context.
Also tried to create the object with the template 'Vec3d,Rigid3d' but failed for the following reason(s):
    1. Data attribute 'input' does not point to a mechanical state of data type 'Vec3d' and none can be found in the parent node context.

I am not sure why my changing of which mesh I use from the liver example should result in such an error. A GitHub issue from 2019 discussed this same issue, their solution being to change the scaling of their object however either I am not doing it correctly/it is not the source of my issue. I have attached a screenshot of my terminal errors as well as a .zip file of my relevant files, in the correct directory arrangement that they are in my own directory. Thank you.

Details: SOFA v21.12, Windows 10, Python3.7

brainsim.zip

[hugtalbot]

Hey @cdelor02

It seems you did not only change the mesh. You might have change the template of the liver from template="Vec3d" to template="Rigid3d"right ? I guess you do want your brain to be soft/deformable, if so you should keep the template="Vec3d".

Could you share your scene?

In addition, the two first warnings you get are pretty clear:

• TetrahedronSetGeometryAlgorithms / TetrahedralCorotationalFEMForceField can not be instantiated for rigid objects (template="Rigid3d") since they are made to compute deformation on soft objects.
• the possible options for the data field response in the DefaultContactManager changed in v21.12. As explained in the warning : "default" has been replaced by "PenalityContactForceField"

[cdelor02]

I would like to have the brain be deformable so I can use my robot to press against it, so I have kept the use of Vec3d as opposed to using Rigid3d in my script, mybrain.py3scn. I am using Vec3d however the Python exception is saying there is an error with the BarycentricMapping<Vec3d,Vec3d>, even though I am using Vec3d? By scene do you mean a .scn file? I am only using a .py3scn script at the moment, which is in the zipped file in sofapython3/mybrain.py3scn.

For the first warning I get, I am not using Rigid3d templates so I do not know why the TetrahedralCorotationalFEMForceField would try to instantiate for them?
For the second, I should go into the DefaultContactManager and change where it mentions "default" to instead be "PenalityContactForceField" ?
EDIT: I found where I need to change "default" to "PenalityContactForceField", however my other questions still stand.

[hugtalbot]

@cdelor02 could you please share the scene/mesh is possible ? it would ease the testing/support

[cdelor02]

I have pasted my script below. Apologies if this just escalates the problem, I have combined my two objects (fingerlike robot and brain model) into one script, however it seems to introduce more issues. I am not able to have the brain exhibit physical properties and be able to be touched and prodded by the robot.

from stlib3.physics.deformable import ElasticMaterialObject
from stlib3.physics.collision import CollisionMesh
from stlib3.scene import MainHeader, ContactHeader
from splib3.loaders import loadPointListFromFile
from stlib3.physics.constraints import FixedBox
from softrobots.actuators import PullingCable
import Sofa.constants.Key as Key
import SofaRuntime
import Sofa.Core
import Sofa


scripts_dir = "C:\\Users\\Charlie\\Documents\\pcle_davinci_soft_actuator_experiment\\soft_robot_scripts"

class FingerController(Sofa.Core.Controller):
    def __init__(self, *args, **kwargs):
        Sofa.Core.Controller.__init__(self,args,kwargs)
        self.cable = args[0]
        self.name = "FingerController"

    def onKeypressedEvent(self, e):
        displacement = self.cable.CableConstraint.value[0]
        if e["key"] == Key.uparrow: #plus:
            displacement += 1.

        elif e["key"] == Key.downarrow: #minus:
            displacement -= 1.
            if displacement < 0:
                displacement = 0
        self.cable.CableConstraint.value = [displacement]



def main():
    import SofaRuntime
    import Sofa.Gui
    SofaRuntime.importPlugin("SofaOpenglVisual")
    SofaRuntime.importPlugin("SofaImplicitOdeSolver")
    root = Sofa.Core.Node("root")
    createScene(root)



def createScene(root):
    root.gravity = [0, -9.81, 0]
    root.dt      = 0.02
    root.addObject('DefaultVisualManagerLoop')
    root.addObject('DefaultAnimationLoop')

    root.addObject('VisualStyle', displayFlags="showCollisionModels")
    root.addObject('RequiredPlugin', pluginName="SofaImplicitOdeSolver SofaLoader SofaOpenglVisual SofaBoundaryCondition SofaGeneralLoader SofaGeneralSimpleFem SofaDeformable SofaEngine SoftRobots")
    root.addObject('DefaultPipeline', name="CollisionPipeline")
    root.addObject('BruteForceBroadPhase', name="BroadPhase")
    root.addObject('BVHNarrowPhase', name="NarrowPhase")
    root.addObject('DefaultContactManager', name="CollisionResponse", response="PenalityContactForceField")
    root.addObject('DiscreteIntersection')


    # add brain to scene
    brain  = root.addChild("Brain")
    ebrain = ElasticMaterialObject(brain,
                                   volumeMeshFileName="../brain/source/brain.vtk", 
                                   surfaceMeshFileName="../brain/source/brain.stl",
                                   surfaceColor=[0.9,0.6,0.6])

    FixedBox(ebrain, doVisualization=False)

    root.addObject('MeshObjLoader', name="BrainSurface", filename=scripts_dir + "\\cablegripper_modified_example\\brain\\source\\test.obj")
    brain.addObject('MeshGmshLoader', name="meshLoader", scale=0.1, filename=scripts_dir + "\\cablegripper_modified_example\\brain\\source\\brainmsh.msh")
    brain.addObject('TetrahedronSetTopologyContainer', name="topo", src="@meshLoader")
    brain.addObject('MechanicalObject', name="dofs", src="@meshLoader")

    brain.addObject('TetrahedronSetGeometryAlgorithms', template="Vec3d", name="GeomAlgo")
    brain.addObject('DiagonalMass', name="Mass", massDensity="1.0")
    brain.addObject('TetrahedralCorotationalFEMForceField', template="Vec3d", 
                    name="FEM", method="large", poissonRatio="0.3", 
                    youngModulus="3000", computeGlobalMatrix="0")
    brain.addObject('FixedConstraint', name="FixedConstraint", indices="3 39 64")
    
    visu = brain.addChild("Visu")
    visu.addObject("OglModel", name="VisualModel", src="@../../BrainSurface", 
                   color=[0.9, 0.6, 0.6], translation=[-100.0, 80.0, 0.0], 
                   rotation=[180.0, 0.0, 0.0])


    # add finger to scene
    finger = root.addChild("Finger")
    eobject = ElasticMaterialObject(finger,
                                    volumeMeshFileName="../data/mesh/finger.vtk",
                                    surfaceMeshFileName="../data/mesh/finger.stl",
                                    surfaceColor=[0.0,0.7,0.8])
    finger.addChild(eobject)
    FixedBox(eobject, doVisualization=True, atPositions=[-10, -10, -10, 10, 10, 10])
    cable = PullingCable(eobject, cableGeometry=loadPointListFromFile("../data/mesh/cable.json"))

    finger.addObject(FingerController(cable))

    CollisionMesh(eobject, surfaceMeshFileName="../data/mesh/finger.stl", name="part0", collisionGroup=[1,2])

    CollisionMesh(eobject,
                  surfaceMeshFileName="../data/mesh/fingerCollision_part1.stl",
                  name="CollisionMeshAuto1", collisionGroup=[1])

    CollisionMesh(eobject,
                  surfaceMeshFileName="../data/mesh/fingerCollision_part2.stl",
                  name="CollisionMeshAuto2", collisionGroup=[2])

    MainHeader(root, plugins=["SoftRobots"])
    root.VisualStyle.displayFlags = "showBehavior showCollisionModels"
    ContactHeader(root, alarmDistance=4, contactDistance=3, frictionCoef=0.08)

    return root


if __name__ == '__main__':
    main()

And the new errors from the script are below. The distinct errors are at the bottom, talking about errors in TetrahedronSetTopologyContainer(container), which I saw a pull request about however I wasn't able to go from there to a solution to my particular error.

[WARNING] [SparseLDLSolver(solver)] Template is empty
By default SparseLDLSolver uses blocks with a single double (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" .
[WARNING] [SparseLDLSolver(solver)] Template is empty
By default SparseLDLSolver uses blocks with a single double (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" .
[DEPRECATED] [Node(root)] Calling the method getObject() with extra arguments is not supported anymore.To remove this message please refer to the documentation of the getObject method
At:
  C:\Users\Charlie\Documents\build\lib\python3\site-packages\stlib3\scene\contactheader.py(28): ContactHeader

[WARNING] [DefaultContactManager] Option "FrictionContact" for data "response" has been renamed since v21.12 (PR#2522). You have until v22.06 to fix your scene. Use "FrictionContactConstraint" instead.
[DEPRECATED] [Node(root)] Calling the method getObject() with extra arguments is not supported anymore.To remove this message please refer to the documentation of the getObject method
At:
  C:\Users\Charlie\Documents\build\lib\python3\site-packages\stlib3\scene\contactheader.py(39): ContactHeader

[DEPRECATED] [Node(root)] Calling the method getObject() with extra arguments is not supported anymore.To remove this message please refer to the documentation of the getObject method
At:
  C:\Users\Charlie\Documents\build\lib\python3\site-packages\stlib3\scene\contactheader.py(42): ContactHeader

[INFO]    [SceneCheckerVisitor] Validating node "root" with checks: [SceneCheckDuplicatedName, SceneCheckMissingRequiredPlugin, SceneCheckUsingAlias, SceneCheckDeprecatedComponents, SceneCheckCollisionResponse]
[DEPRECATED] [BruteForceDetection(BruteForceDetection)] SceneCheckDeprecatedComponents: This component has been DEPRECATED since SOFA v21.06 and will be removed in SOFA v21.12. Please consider updating your scene as using deprecated component may result in poor performance and undefined behavior. If this component is crucial to you please report that to sofa-dev@ so we can reconsider this component for future re-integration.
[WARNING] [SceneCheckDuplicatedName]
- Found duplicated names ['VisualStyle', ] in node '/'
Nodes with similar names at the same level in your scene can crash certain operations, please rename them
[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="SofaMeshCollision"/> <!-- Needed to use components [LineCollisionModel, PointCollisionModel, TriangleCollisionModel] -->

[WARNING] [SceneCheckUsingAlias] This scene is using hard coded aliases. Aliases can be very confusing, use with caution.
  - MeshOBJLoader: 1 created with alias "MeshObjLoader"
[WARNING] [SceneCheckCollisionResponse] Only one DefaultContactManager is needed.

[INFO]    [SceneCheckerVisitor] Finished validating node "root".
[DEPRECATED] [BruteForceDetection(BruteForceDetection)] As a replacement, use a BroadPhase component, such as [BruteForceBroadPhase, IncrSAP],
  AND a NarrowPhase component, such as [BVHNarrowPhase, DirectSAPNarrowPhase, IncrSAP, RayTraceNarrowPhase].
  BruteForceBroadPhase and BVHNarrowPhase have been automatically added to your scene for backward compatibility.
[ERROR]   [TetrahedronSetTopologyContainer(container)] Cannot find edge 0 [28, 77] in triangle 0
[ERROR]   [TetrahedronSetTopologyContainer(container)] Cannot find edge 0 [28, 77] in triangle 0
[WARNING] [TetrahedronSetTopologyContainer(container)] TrianglesAroundEdge buffer can't be created as EdgesInTriangle buffer creation failed.
[ERROR]   [TetrahedronSetTopologyContainer(container)] Cannot find triangle 0 [140, 113, 125] in tetrahedron 0
[WARNING] [TetrahedronSetTopologyContainer(container)]  In getTetrahedronArray, cannot find edge for tetrahedron 0and edge 0
[ERROR]   [TetrahedronSetTopologyContainer(container)] Cannot find triangle 0 [140, 113, 125] in tetrahedron 0
[WARNING] [TetrahedronSetTopologyContainer(container)] TetrahedraAroundTriangle buffer can't be created as trianglesInTetrahedron buffer creation failed.

[hugtalbot]

there is definitely a mesh issue from the lines:

[ERROR]   [TetrahedronSetTopologyContainer(container)] Cannot find edge 0 [28, 77] in triangle 0
[ERROR]   [TetrahedronSetTopologyContainer(container)] Cannot find edge 0 [28, 77] in triangle 0

However I am no STLIB expert and I do not know what is under the ElasticMaterialObject but I would also need to take a look at your two meshes. Could you share them @cdelor02 ?

[cdelor02]

I have attached the object, stl, mesh (vtk) files that I am using in my code below. There are files for a brain (test.obj is a brain), and files for a finger. This finger is taken from the SoftRobots CableGripper example, I am simultaneously trying to get my own version of a similar cable-driven finger to work however I am not having success either.

sim_files.zip

[hugtalbot]

Your VTK mesh is only the surface of the brain. It contains only triangles. As explained in earlier comments, you need to have a vtk mesh using volumetric elements (linear tetra or linear hexa) for your brain.

Moreover, you need to make sure they have the same scale (which is not the case here)

[cdelor02]

I see. Is it possible to produce such a volumetric .vtk file in GMSH? I have a .obj and a .stl file, and I have found some mention of being able to do this with .stl files but I tried generating a new .vtk in GMSH but had no luck.

And what are the things that need to have the same scale? The various files of the brain? I assume if I scale one down (which I do need to do, the brain is much larger than I need) I will use the same scaling factor for all of them.

[hugtalbot]

Yes you can. You can take a look at this project : https://github.com/sescaida/gmsh-sofa_tutorial