Try to get the position, displacement and force from the SOFA #4855

Milagroslikeyoshi · 2024-07-27T05:44:29Z

Milagroslikeyoshi
Jul 27, 2024

Hi,
I am now trying to analysis the displacement of the gripper tip(the pneumatic gripper example in softrobot).
I can run the simulation, but how can I get the data saved in the MechanicalObject? I can see them in the GUI?
What I want to do is to plot the position of the gripper tip. Could you please help me?
I see the writestate function, but I think it export all the points, I just need one of the tip point.
Thanks a lot!

hugtalbot · 2024-07-30T09:58:38Z

hugtalbot
Jul 30, 2024
Maintainer

Hi @Milagroslikeyoshi

For such need, Python is the answer.
Here is an example:

# Required import for python
import Sofa
import SofaRuntime
from scipy import sparse
from scipy import linalg
from matplotlib import pyplot as plt
import numpy as np

timeVector=[]
positionVector=[]

class PlotPositionController(Sofa.Core.Controller):
    def __init__(self, *args, **kwargs):
        Sofa.Core.Controller.__init__(self, *args, **kwargs)
        self.mechanical_object = kwargs.get("mechanical_object")

    def onAnimateEndEvent(self, event):
        time = self.mechanical_object.getContext().time.value
        timeVector.append(time)
        pos = self.mechanical_object.position.value
        positionVector.append(pos[318][2])       ## Replace this index 318 by the index of the tip point

        plt.plot(timeVector,positionVector)
        plt.show(block=False)


# Function called when the scene graph is being created
def createScene(root):

    root.addObject('VisualStyle', displayFlags="showBehaviorModels showForceFields")

    root.addObject("RequiredPlugin", pluginName=['Sofa.Component.Constraint.Projective',
    'Sofa.Component.Engine.Select',
    'Sofa.Component.LinearSolver.Direct',
    'Sofa.Component.Mass',
    'Sofa.Component.ODESolver.Backward',
    'Sofa.Component.SolidMechanics.FEM.Elastic',
    'Sofa.Component.StateContainer',
    'Sofa.Component.Topology.Container.Grid',
    'Sofa.Component.Visual'
    ])

    root.addObject('DefaultAnimationLoop')
    root.addObject('DefaultVisualManagerLoop')

    root.addObject('EulerImplicitSolver', rayleighStiffness="0.1", rayleighMass="0.1")
    root.addObject('SparseLDLSolver', template="CompressedRowSparseMatrixd")

    MO = root.addObject('MechanicalObject', name="DoFs")
    root.addObject('MeshMatrixMass', name="mass", totalMass="320")
    root.addObject('RegularGridTopology', name="grid", nx="4", ny="4", nz="20", xmin="-9", xmax="-6", ymin="0", ymax="3", zmin="0", zmax="19")
    root.addObject('BoxROI', name="box", box="-10 -1 -0.0001  -5 4 0.0001")
    root.addObject('FixedProjectiveConstraint', indices="@box.indices")
    root.addObject('HexahedronFEMForceField', name="FEM", youngModulus="4000", poissonRatio="0.3", method="large")

    root.addObject(PlotPositionController('PlotPositionController', name='plotPosition', mechanical_object=MO))

    return root

0 replies

Milagroslikeyoshi · 2024-07-30T13:32:11Z

Milagroslikeyoshi
Jul 30, 2024
Author

Thank you for your answers! @hugtalbot
But I failed to run the simulation...I can't get the plot from the codes below:
I don't know why I can't get the figure....
I am sorry I am a green hand for sofa and python.

#Grabthe cube
import Sofa
import math
import SofaRuntime
from scipy import sparse
from scipy import linalg
from matplotlib import pyplot as plt
import numpy as np

from wholeGripperController import WholeGripperController

timeVector=[]
positionVector=[]

youngModulusFingers = 500
youngModulusStiffLayerFingers = 1500

radius = 70
angle1 = 120 * math.pi / 180  # Angle between 1st and 2nd finger in radian
angle2 = 240 * math.pi / 180  # Angle between 1st and 3rd finger in radian
translateFinger1 = [0, 0, 0]
translateFinger2 = [0, radius + radius * math.sin(angle1 - math.pi / 2), radius * math.cos(angle1 - math.pi / 2)]
translateFinger3 = [0, radius + radius * math.sin(angle2 - math.pi / 2), radius * math.cos(angle2 - math.pi / 2)]
translations = [translateFinger1, translateFinger2, translateFinger3]
angles = [0, angle1, angle2]

class PlotPositionController(Sofa.Core.Controller):
    def __init__(self, *args, **kwargs):
        Sofa.Core.Controller.__init__(self, *args, **kwargs)
        self.mechanical_object = kwargs.get("mechanical_object")

    def onAnimateEndEvent(self, event):
        time = self.mechanical_object.getContext().time.value
        timeVector.append(time)
        pos = self.mechanical_object.position.value
        positionVector.append(pos[318][2])

        plt.plot(timeVector,positionVector)
        plt.show(block=False)


def createScene(rootNode):
    rootNode.addObject('RequiredPlugin',
                       pluginName='SoftRobots SofaPython3')

    rootNode.addObject('VisualStyle',
                       displayFlags='showVisualModels hideBehaviorModels hideCollisionModels hideBoundingCollisionModels hideForceFields showInteractionForceFields hideWireframe')
    rootNode.gravity.value = [-9810, 0, 0]
    rootNode.addObject('FreeMotionAnimationLoop')
    rootNode.addObject('GenericConstraintSolver', tolerance=1e-12, maxIterations=10000)
    rootNode.addObject('DefaultPipeline')
    rootNode.addObject('BruteForceBroadPhase')
    rootNode.addObject('BVHNarrowPhase')
    rootNode.addObject('DefaultContactManager', response='FrictionContactConstraint', responseParams='mu=0.6')
    rootNode.addObject('LocalMinDistance', name='Proximity', alarmDistance=5, contactDistance=1, angleCone=0.0)

    rootNode.addObject('BackgroundSetting', color=[0, 0.168627, 0.211765, 1.])
    rootNode.addObject('OglSceneFrame', style='Arrows', alignment='TopRight')
   
    planeNode = rootNode.addChild('Plane')
    planeNode.addObject('MeshOBJLoader', name='loader', filename='data/mesh/floorFlat.obj', triangulate=True,
                        rotation=[0, 0, 270], scale=10, translation=[-122, 0, 0])
    planeNode.addObject('MeshTopology', src='@loader')
    planeNode.addObject('MechanicalObject', src='@loader')
    planeNode.addObject('TriangleCollisionModel', simulated=False, moving=False)
    planeNode.addObject('LineCollisionModel', simulated=False, moving=False)
    planeNode.addObject('PointCollisionModel', simulated=False, moving=False)
    planeNode.addObject('OglModel', name='Visual', src='@loader', color=[1, 0, 0, 1])

    cube = rootNode.addChild('cube')
    cube.addObject('EulerImplicitSolver', name='odesolver')
    cube.addObject('SparseLDLSolver', name='linearSolver')
    cube.addObject('MechanicalObject', template='Rigid3', position=[-100, 70, 0, 0, 0, 0, 1])
    cube.addObject('UniformMass', totalMass=0.001)
    cube.addObject('UncoupledConstraintCorrection')

    # collision
    cubeCollis = cube.addChild('cubeCollis')
    cubeCollis.addObject('MeshOBJLoader', name='loader', filename='data/mesh/smCube27.obj', triangulate=True,
                         scale=6)
    cubeCollis.addObject('MeshTopology', src='@loader')
    cubeCollis.addObject('MechanicalObject')
    cubeCollis.addObject('TriangleCollisionModel')
    cubeCollis.addObject('LineCollisionModel')
    cubeCollis.addObject('PointCollisionModel')
    cubeCollis.addObject('RigidMapping')

    # visualization
    cubeVisu = cube.addChild('cubeVisu')
    cubeVisu.addObject('MeshOBJLoader', name='loader', filename='data/mesh/smCube27.obj')
    cubeVisu.addObject('OglModel', name='Visual', src='@loader', color=[0.0, 0.1, 0.5], scale=6.2)
    cubeVisu.addObject('RigidMapping')

    for i in range(3):
        ##########################################
        # Finger Model	 						 #
        ##########################################
        finger = rootNode.addChild('finger' + str(i + 1))
        finger.addObject('EulerImplicitSolver', name='odesolver', rayleighStiffness=0.1, rayleighMass=0.1)
        finger.addObject('SparseLDLSolver', name='preconditioner')

        finger.addObject('MeshVTKLoader', name='loader', filename='data/mesh/pneunetCutCoarse.vtk',
                         rotation=[360 - angles[i] * 180 / math.pi, 0, 0], translation=translations[i])
        finger.addObject('MeshTopology', src='@loader', name='container')

        MO=finger.addObject('MechanicalObject', name='tetras', template='Vec3', showIndices=False, showIndicesScale=4e-5)
        finger.addObject('UniformMass', totalMass=0.04)
        finger.addObject('TetrahedronFEMForceField', template='Vec3', name='FEM', method='large', poissonRatio=0.3,
                         youngModulus=youngModulusFingers)

        finger.addObject('BoxROI', name='boxROI', box=[-10, 0, -20, 0, 30, 20], doUpdate=False)
        finger.addObject('BoxROI', name='boxROISubTopo', box=[-100, 22.5, -8, -19, 28, 8], strict=False)
        if i == 0:
            finger.addObject('RestShapeSpringsForceField', points='@boxROI.indices', stiffness=1e12,
                             angularStiffness=1e12)
        else:
            finger.addObject('RestShapeSpringsForceField', points='@../finger1/boxROI.indices', stiffness=1e12,
                             angularStiffness=1e12)

        finger.addObject('LinearSolverConstraintCorrection')

        ##########################################
        # Sub topology						   #
        ##########################################
        modelSubTopo = finger.addChild('modelSubTopo')
        if i == 0:
            modelSubTopo.addObject('TetrahedronSetTopologyContainer', position='@loader.position',
                                   tetrahedra='@boxROISubTopo.tetrahedraInROI', name='container')
        else:
            modelSubTopo.addObject('TetrahedronSetTopologyContainer', position='@loader.position',
                                   tetrahedra='@../../finger1/boxROISubTopo.tetrahedraInROI', name='container')
        modelSubTopo.addObject('TetrahedronFEMForceField', template='Vec3', name='FEM', method='large',
                               poissonRatio=0.3, youngModulus=youngModulusStiffLayerFingers - youngModulusFingers)

        ##########################################
        # Constraint							 #
        ##########################################
        cavity = finger.addChild('cavity')
        cavity.addObject('MeshSTLLoader', name='loader', filename='data/mesh/pneunetCavityCut.stl',
                         translation=translations[i], rotation=[360 - angles[i] * 180 / math.pi, 0, 0])
        cavity.addObject('MeshTopology', src='@loader', name='topo')
        cavity.addObject('MechanicalObject', name='cavity')
        cavity.addObject('SurfacePressureConstraint', name='SurfacePressureConstraint', template='Vec3', value=0.0001,
                         triangles='@topo.triangles', valueType='pressure')
        cavity.addObject('BarycentricMapping', name='mapping', mapForces=False, mapMasses=False)

        ##########################################
        # Collision							  #
        ##########################################

        collisionFinger = finger.addChild('collisionFinger')
        collisionFinger.addObject('MeshSTLLoader', name='loader', filename='data/mesh/pneunetCut.stl',
                                  translation=translations[i], rotation=[360 - angles[i] * 180 / math.pi, 0, 0])
        collisionFinger.addObject('MeshTopology', src='@loader', name='topo')
        collisionFinger.addObject('MechanicalObject', name='collisMech')
        collisionFinger.addObject('TriangleCollisionModel', selfCollision=False)
        collisionFinger.addObject('LineCollisionModel', selfCollision=False)
        collisionFinger.addObject('PointCollisionModel', selfCollision=False)
        collisionFinger.addObject('BarycentricMapping')

        ##########################################
        # Visualization						  #
        ##########################################
        modelVisu = finger.addChild('visu')
        modelVisu.addObject('MeshSTLLoader', name='loader', filename='data/mesh/pneunetCut.stl')
        modelVisu.addObject('OglModel', src='@loader', color=[0.7, 0.7, 0.7, 0.6], translation=translations[i],
                            rotation=[360 - angles[i] * 180 / math.pi, 0, 0])
        modelVisu.addObject('BarycentricMapping')
        
    rootNode.addObject(PlotPositionController('PlotPositionController', name='plotPosition', mechanical_object=MO))
    rootNode.addObject(WholeGripperController(node=rootNode))

    return rootNode

Controller:

import Sofa.Core
from Sofa.constants import *
import math


def moveRestPos(rest_pos, dx, dy, dz):
    out = []
    for i in range(0,len(rest_pos)) :
        out += [[rest_pos[i][0]+dx, rest_pos[i][1]+dy, rest_pos[i][2]+dz]]
    return out


def rotateRestPos(rest_pos,rx,centerPosY,centerPosZ):
    out = []
    for i in range(0,len(rest_pos)) :
        newRestPosY = (rest_pos[i][1] - centerPosY)*math.cos(rx) - (rest_pos[i][2] - centerPosZ)*math.sin(rx) +  centerPosY
        newRestPosZ = (rest_pos[i][1] - centerPosY)*math.sin(rx) + (rest_pos[i][2] - centerPosZ)*math.cos(rx) +  centerPosZ
        out += [[rest_pos[i][0], newRestPosY, newRestPosZ]]
    return out


class WholeGripperController(Sofa.Core.Controller):

    def __init__(self, *a, **kw):

        Sofa.Core.Controller.__init__(self, *a, **kw)
        self.node = kw["node"]
        self.constraints = []
        self.dofs = []
        for i in range(1,4):
            self.dofs.append(self.node.getChild('finger' + str(i)).tetras)
            self.constraints.append(self.node.getChild('finger'+str(i)).cavity.SurfacePressureConstraint)

        self.centerPosY = 70
        self.centerPosZ = 0
        self.rotAngle = 0

        return

    def onKeypressedEvent(self,e):

        increment = 0.01

        if e["key"] == Sofa.constants.Key.plus:
            for i in range(3):
                pressureValue = self.constraints[i].value.value[0] + increment
                if pressureValue > 1.5:
                    pressureValue = 1.5
                self.constraints[i].value = [pressureValue]

        if e["key"] == Sofa.constants.Key.minus:
            for i in range(3):
                pressureValue = self.constraints[i].value.value[0] - increment
                if pressureValue < 0:
                    pressureValue = 0
                self.constraints[i].value = [pressureValue]

        elif e["key"] == Sofa.constants.Key.uparrow:
            for i in range(3):
                results = moveRestPos(self.dofs[i].rest_position.value, 3.0, 0.0, 0.0)
                self.dofs[i].rest_position.value = results

        elif e["key"] == Sofa.constants.Key.downarrow:
            for i in range(3):
                results = moveRestPos(self.dofs[i].rest_position.value, -3.0, 0.0, 0.0)
                self.dofs[i].rest_position.value = results

        elif e["key"] == Sofa.constants.Key.leftarrow:
            dy = 3.0*math.cos(self.rotAngle)
            dz = 3.0*math.sin(self.rotAngle)
            for i in range(3):
                results = moveRestPos(self.dofs[i].rest_position.value, 0.0, dy, dz)
                self.dofs[i].rest_position.value = results
            self.centerPosY = self.centerPosY + dy
            self.centerPosZ = self.centerPosZ + dz

        elif e["key"] == Sofa.constants.Key.rightarrow:
            dy = -3.0*math.cos(self.rotAngle)
            dz = -3.0*math.sin(self.rotAngle)
            for i in range(3):
                results = moveRestPos(self.dofs[i].rest_position.value, 0.0, dy, dz)
                self.dofs[i].rest_position.value = results
            self.centerPosY = self.centerPosY + dy
            self.centerPosZ = self.centerPosZ + dz

        # Direct rotation
        elif e["key"] == "A":
            for i in range(3):
                results = rotateRestPos(self.dofs[i].rest_position.value, math.pi / 16, self.centerPosY, self.centerPosZ)
                self.dofs[i].rest_position.value = results
            self.rotAngle = self.rotAngle + math.pi/16

        # Indirect rotation
        elif e["key"] == "Q":
            for i in range(3):
                results = rotateRestPos(self.dofs[i].rest_position.value, -math.pi / 16, self.centerPosY, self.centerPosZ)
                self.dofs[i].rest_position.value = results
            self.rotAngle = self.rotAngle - math.pi/16

5 replies

hugtalbot Jul 30, 2024
Maintainer

You need to pause the animation to see the plot (clicking again on Animate)

Milagroslikeyoshi Jul 30, 2024
Author

Actually, nothing happened on the matplotlib even if I paused the animation.
To be honest, I confused of the relationship of "class PlotPositionController(Sofa.Core.Controller)" and the "class WholeGripperController(Sofa.Core.Controller)". If I want to get the real-time plot of the position of the tip point, how should I set the structure of this two class? what's more, I set MO=finger.addObject('MechanicalObject', name='tetras', template='Vec3', showIndices=False, showIndicesScale=4e-5) in the circle "for i in range(3):", I don't know whether it is ok? Thank you again...

hugtalbot Jul 30, 2024
Maintainer

Actually, nothing happened on the matplotlib even if I paused the animation.

You might have an error showing up in the command window, don't you?

Milagroslikeyoshi Jul 30, 2024
Author

Here's the info:

[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:
root.addObject('RequiredPlugin', name='Sofa.Component.AnimationLoop') # Needed to use components [FreeMotionAnimationLoop]
root.addObject('RequiredPlugin', name='Sofa.Component.Collision.Detection.Algorithm') # Needed to use components [BVHNarrowPhase,BruteForceBroadPhase,CollisionPipeline]
root.addObject('RequiredPlugin', name='Sofa.Component.Collision.Detection.Intersection') # Needed to use components [LocalMinDistance]
root.addObject('RequiredPlugin', name='Sofa.Component.Collision.Geometry') # Needed to use components [LineCollisionModel,PointCollisionModel,TriangleCollisionModel]
root.addObject('RequiredPlugin', name='Sofa.Component.Collision.Response.Contact') # Needed to use components [DefaultContactManager]
root.addObject('RequiredPlugin', name='Sofa.Component.Constraint.Lagrangian.Correction') # Needed to use components [LinearSolverConstraintCorrection,UncoupledConstraintCorrection]
root.addObject('RequiredPlugin', name='Sofa.Component.Constraint.Lagrangian.Solver') # Needed to use components [GenericConstraintSolver]
root.addObject('RequiredPlugin', name='Sofa.Component.Engine.Select') # Needed to use components [BoxROI]
root.addObject('RequiredPlugin', name='Sofa.Component.IO.Mesh') # Needed to use components [MeshOBJLoader,MeshSTLLoader,MeshVTKLoader]
root.addObject('RequiredPlugin', name='Sofa.Component.LinearSolver.Direct') # Needed to use components [SparseLDLSolver]
root.addObject('RequiredPlugin', name='Sofa.Component.Mapping.Linear') # Needed to use components [BarycentricMapping]
root.addObject('RequiredPlugin', name='Sofa.Component.Mapping.NonLinear') # Needed to use components [RigidMapping]
root.addObject('RequiredPlugin', name='Sofa.Component.Mass') # Needed to use components [UniformMass]
root.addObject('RequiredPlugin', name='Sofa.Component.ODESolver.Backward') # Needed to use components [EulerImplicitSolver]
root.addObject('RequiredPlugin', name='Sofa.Component.Setting') # Needed to use components [BackgroundSetting]
root.addObject('RequiredPlugin', name='Sofa.Component.SolidMechanics.FEM.Elastic') # Needed to use components [TetrahedronFEMForceField]
root.addObject('RequiredPlugin', name='Sofa.Component.SolidMechanics.Spring') # Needed to use components [RestShapeSpringsForceField]
root.addObject('RequiredPlugin', name='Sofa.Component.StateContainer') # Needed to use components [MechanicalObject]
root.addObject('RequiredPlugin', name='Sofa.Component.Topology.Container.Constant') # Needed to use components [MeshTopology]
root.addObject('RequiredPlugin', name='Sofa.Component.Topology.Container.Dynamic') # Needed to use components [TetrahedronSetTopologyContainer]
root.addObject('RequiredPlugin', name='Sofa.Component.Visual') # Needed to use components [VisualStyle]
root.addObject('RequiredPlugin', name='Sofa.GL.Component.Rendering3D') # Needed to use components [OglModel,OglSceneFrame]

[WARNING] [SceneCheckUsingAlias] This scene is using hard coded aliases. Aliases can be very confusing, use with caution.

CollisionPipeline: 1 created with alias "DefaultPipeline" This alias will be REMOVED at the SOFA release v22.06, please update your scenes.
[INFO] [SceneCheckerVisitor] Finished validating node "root".
[WARNING] [TetrahedronFEMForceField(FEM)] buildDampingMatrix not implemented: for compatibility reason, the deprecated API (addBToMatrix) will be used. This compatibility will disapear in the future, and will cause issues in simulations. Please update the code of TetrahedronFEMForceField to ensure right behavior: the function addBToMatrix has been replaced by buildDampingMatrix
[WARNING] [TetrahedronFEMForceField(FEM)] buildDampingMatrix not implemented: for compatibility reason, the deprecated API (addBToMatrix) will be used. This compatibility will disapear in the future, and will cause issues in simulations. Please update the code of TetrahedronFEMForceField to ensure right behavior: the function addBToMatrix has been replaced by buildDampingMatrix
[WARNING] [TetrahedronFEMForceField(FEM)] buildDampingMatrix not implemented: for compatibility reason, the deprecated API (addBToMatrix) will be used. This compatibility will disapear in the future, and will cause issues in simulations. Please update the code of TetrahedronFEMForceField to ensure right behavior: the function addBToMatrix has been replaced by buildDampingMatrix
[WARNING] [TetrahedronFEMForceField(FEM)] buildDampingMatrix not implemented: for compatibility reason, the deprecated API (addBToMatrix) will be used. This compatibility will disapear in the future, and will cause issues in simulations. Please update the code of TetrahedronFEMForceField to ensure right behavior: the function addBToMatrix has been replaced by buildDampingMatrix
[WARNING] [TetrahedronFEMForceField(FEM)] buildDampingMatrix not implemented: for compatibility reason, the deprecated API (addBToMatrix) will be used. This compatibility will disapear in the future, and will cause issues in simulations. Please update the code of TetrahedronFEMForceField to ensure right behavior: the function addBToMatrix has been replaced by buildDampingMatrix
[WARNING] [TetrahedronFEMForceField(FEM)] buildDampingMatrix not implemented: for compatibility reason, the deprecated API (addBToMatrix) will be used. This compatibility will disapear in the future, and will cause issues in simulations. Please update the code of TetrahedronFEMForceField to ensure right behavior: the function addBToMatrix has been replaced by buildDampingMatrix
[INFO] [SofaViewer] QtViewer::keyPressEvent, CONTROL pressed
[INFO] [SofaViewer] QtViewer::keyPressEvent, CONTROL pressed
[INFO] [SofaViewer] QtViewer::keyPressEvent, CONTROL pressed
[INFO] [SofaViewer] QtViewer::keyPressEvent, CONTROL pressed

hugtalbot Jul 31, 2024
Maintainer

In your Python class PlotPositionController, could you add in the onAnimateEndEvent function a print(self.mechanical_object.name.value) please ? or just a print(self.mechanical_object) ?

@Milagroslikeyoshi · 2024-10-07T06:15:35Z

github-actions[bot]
bot Oct 7, 2024

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@Milagroslikeyoshi
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.

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Try to get the position, displacement and force from the SOFA #4855

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Try to get the position, displacement and force from the SOFA #4855

Milagroslikeyoshi Jul 27, 2024

Replies: 3 comments · 5 replies

hugtalbot Jul 30, 2024 Maintainer

Milagroslikeyoshi Jul 30, 2024 Author

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hugtalbot Jul 30, 2024
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Milagroslikeyoshi Jul 30, 2024
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hugtalbot Jul 31, 2024
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