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[scene] A scene with haptics and insertion in a liver represented by a .msh tetrahedral mesh (#42)
* [scene] Created a starting point for a scene with haptics WIP Friction is deactivated - needle gets stuck during retreat
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‎scenes/InsertionGeomagic.py‎

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import Sofa
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g_needleLength=0.100 #(m)
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g_needleNumberOfElems=20 #(# of edges)
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g_needleBaseOffset=[0.15,0.04,0.04]
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g_needleRadius = 0.001 #(m)
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g_needleMechanicalParameters = {
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"radius":g_needleRadius,
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"youngModulus":1e11,
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"poissonRatio":0.3
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}
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g_needleTotalMass=0.01
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g_gelRegularGridParameters = {
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"n":[8, 8, 8],
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"min":[-0.125, -0.125, -0.350],
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"max":[0.125, 0.125, -0.100]
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} #Again all in mm
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g_gelMechanicalParameters = {
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"youngModulus":9e4,
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"poissonRatio":0.45,
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"method":"large"
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}
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g_gelTotalMass = 1
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g_cubeColor=[0.8, 0.34, 0.34, 0.3]
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g_gelFixedBoxROI=[-0.350, -0.280, -0.360, 0.130, 0.130, -0.200 ]
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# Function called when the scene graph is being created
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def createScene(root):
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root.gravity=[0,0,0]
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root.dt = 0.01
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root.addObject("RequiredPlugin",pluginName=['Sofa.Component.AnimationLoop',
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'Sofa.Component.Constraint.Lagrangian.Solver',
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'Sofa.Component.ODESolver.Backward',
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'Sofa.Component.Visual',
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'Sofa.Component.Constraint.Lagrangian.Correction',
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'Sofa.Component.Constraint.Lagrangian.Model',
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'Sofa.Component.LinearSolver.Direct',
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'Sofa.Component.Mapping.Linear',
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'Sofa.Component.Mass',
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'Sofa.Component.SolidMechanics.FEM.Elastic',
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'Sofa.Component.StateContainer',
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'Sofa.Component.Topology.Container.Dynamic',
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'Sofa.Component.Topology.Mapping',
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'Sofa.Component.Mapping.NonLinear',
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'Sofa.Component.Topology.Container.Grid',
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'Sofa.Component.Constraint.Projective',
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'Sofa.Component.SolidMechanics.Spring',
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'Sofa.GL.Component.Rendering3D',
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'Sofa.GUI.Component',
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'Sofa.Component.Engine.Select',
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'MultiThreading',
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'CollisionAlgorithm',
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'ConstraintGeometry',
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'Geomagic',
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'Sofa.Component.Haptics',
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'Sofa.Component.IO.Mesh'
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])
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root.addObject("ConstraintAttachButtonSetting")
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root.addObject("VisualStyle", displayFlags="showVisualModels hideBehaviorModels showCollisionModels hideMappings hideForceFields showWireframe showInteractionForceFields" )
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root.addObject("FreeMotionAnimationLoop")
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root.addObject("GenericConstraintSolver", tolerance=0.00001, maxIt=5000, printLog=False, computeConstraintForces=True)
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root.addObject("CollisionLoop")
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root.addObject("GeomagicDriver"
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, name='GeomagicDevice'
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, deviceName='Default Device'
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, scale='0.02'
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, drawDeviceFrame='false'
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, drawDevice='false'
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, manualStart='0'
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, positionBase='0.12 0 0'
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, orientationBase='0 0.174 0 -0.985'
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)
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toolController = root.addChild("ToolController")
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toolController.addObject("MechanicalObject", name="mstate_baseMaster", position="@GeomagicDevice.positionDevice", template="Rigid3d", showObjectScale=0.01, showObject="false", drawMode=1)
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needle = root.addChild("Needle")
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needle.addObject("EulerImplicitSolver", firstOrder=True)
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needle.addObject("EigenSparseLU", name="LinearSolver", template="CompressedRowSparseMatrixd")
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needle.addObject("EdgeSetTopologyContainer", name="Container", position=[[g_needleBaseOffset[0], g_needleBaseOffset[1], -(i * g_needleLength/(g_needleNumberOfElems) + g_needleBaseOffset[2])] for i in range(g_needleNumberOfElems + 1)]
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, edges=[[i, i+1] for i in range(g_needleNumberOfElems)])
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needle.addObject("EdgeSetTopologyModifier", name="modifier")
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needle.addObject("PointSetTopologyModifier", name="modifier2")
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needle.addObject("MechanicalObject", name="mstate", template="Rigid3d", showObjectScale=0.002, showObject="false", drawMode=1)
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needle.addObject("UniformMass", totalMass=g_needleTotalMass)
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needle.addObject("BeamFEMForceField", name="FEM", **g_needleMechanicalParameters)
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# needle.addObject("FixedLagrangianConstraint", indices="0" )
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needle.addObject("LinearSolverConstraintCorrection", printLog="false", linearSolver="@LinearSolver")
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needle.addObject("LCPForceFeedback", activate='1', forceCoef='0.01')
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needleBase = needle.addChild("needleBase")
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needleBase.addObject("PointSetTopologyContainer", name="Container_base", position="@../mstate.position")#"@../../GeomagicDevice.positionBase")
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needleBase.addObject("MechanicalObject",name="mstate_base", template="Rigid3d")
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needleBase.addObject("RestShapeSpringsForceField",points=[0],stiffness=1e9, angularStiffness=1e9,external_points=[0],external_rest_shape="@/ToolController/mstate_baseMaster")
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needleBase.addObject("SubsetMapping", indices="0")
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needleBodyCollision = needle.addChild("bodyCollision")
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needleBodyCollision.addObject("EdgeSetTopologyContainer", name="Container_body", src="@../Container")
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needleBodyCollision.addObject("MechanicalObject",name="mstate_body", template="Vec3d", drawMode=0, showObject="false", showObjectScale="10")
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needleBodyCollision.addObject("EdgeGeometry",name="geom_body",mstate="@mstate_body", topology="@Container_body")
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needleBodyCollision.addObject("EdgeNormalHandler", name="NeedleBeams", geometry="@geom_body")
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needleBodyCollision.addObject("IdentityMapping")
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needleTipCollision = needle.addChild("tipCollision")
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needleTipCollision.addObject("MechanicalObject",name="mstate_tip",position=[g_needleBaseOffset[0], g_needleBaseOffset[1], -(g_needleLength+g_needleBaseOffset[2])],template="Vec3d", showObject="false", showObjectScale=20)
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needleTipCollision.addObject("PointGeometry",name="geom_tip",mstate="@mstate_tip")
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needleTipCollision.addObject("RigidMapping",globalToLocalCoords=True,index=g_needleNumberOfElems)
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needleVisual = needle.addChild("visual")
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needleVisual.addObject("QuadSetTopologyContainer", name="Container_visu")
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needleVisual.addObject("QuadSetTopologyModifier", name="Modifier")
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needleVisual.addObject("Edge2QuadTopologicalMapping", nbPointsOnEachCircle=8, radius=g_needleRadius, input="@../Container", output="@Container_visu")
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needleVisual.addObject("MechanicalObject", name="mstate_visu", showObjectScale="0.0002", showObject="false", drawMode="1")
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needleVisual.addObject("TubularMapping", nbPointsOnEachCircle=8, radius=g_needleRadius, input="@../mstate", output="@mstate_visu")
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needleOGL = needleVisual.addChild("OGL")
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needleOGL.addObject("OglModel", position="@../Container_visu.position",
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vertices="@../Container_visu.position",
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quads="@../Container_visu.quads",
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color="0.4 0.34 0.34",
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material="texture Ambient 1 0.4 0.34 0.34 1.0 Diffuse 0 0.4 0.34 0.34 1.0 Specular 1 0.4 0.34 0.34 0.1 Emissive 1 0.5 0.54 0.54 .01 Shininess 1 20",
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name="visualOgl")
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needleOGL.addObject("IdentityMapping")
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#gelTopo = root.addChild("GelGridTopo")
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#gelTopo.addObject("RegularGridTopology", name="HexaTop", **g_gelRegularGridParameters)
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volume = root.addChild("Volume")
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volume.addObject("EulerImplicitSolver")
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volume.addObject("EigenSimplicialLDLT", name="LinearSolver", template='CompressedRowSparseMatrixMat3x3d')
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#volume.addObject("TetrahedronSetTopologyContainer", name="TetraContainer", position="@../GelGridTopo/HexaTop.position")
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volume.addObject("MeshGmshLoader", name="meshLoader", filename="mesh/liver.msh", scale3d="0.08 0.08 0.08", translation="0 -0.3 -0.2")
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volume.addObject("TetrahedronSetTopologyContainer", name="TetraContainer", position="@meshLoader.position", tetrahedra="@meshLoader.tetrahedra")
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volume.addObject("TetrahedronSetTopologyModifier", name="TetraModifier")
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#volume.addObject("Hexa2TetraTopologicalMapping", input="@../GelGridTopo/HexaTop", output="@TetraContainer", swapping="false")
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volume.addObject("MechanicalObject", name="mstate_gel", template="Vec3d")
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volume.addObject("TetrahedronGeometry", name="geom_tetra", mstate="@mstate_gel", topology="@TetraContainer", draw=False)
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#volume.addObject("TriangleGeometry", name="tri_geom", mstate="@mstate_gel", topology="@TetraContainer",draw=True)
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volume.addObject("PhongTriangleNormalHandler", name="InternalTriangles", geometry="@geom_tetra")
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volume.addObject("AABBBroadPhase",name="AABBTetra",geometry="@geom_tetra",nbox=[3,3,3],thread=1)
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#volume.addObject("ParallelTetrahedronFEMForceField", name="FF",**g_gelMechanicalParameters)
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volume.addObject("TetrahedronFEMForceField", name="FF",**g_gelMechanicalParameters)
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volume.addObject("MeshMatrixMass", name="Mass",totalMass=g_gelTotalMass)
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volume.addObject("BoxROI",name="BoxROI",box=g_gelFixedBoxROI)
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volume.addObject("RestShapeSpringsForceField", stiffness='1e6',points="@BoxROI.indices" )
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volume.addObject("LinearSolverConstraintCorrection", printLog="false", linearSolver="@LinearSolver")
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volumeCollision = volume.addChild("collision")
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volumeCollision.addObject("TriangleSetTopologyContainer", name="TriContainer")
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volumeCollision.addObject("TriangleSetTopologyModifier", name="TriModifier")
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volumeCollision.addObject("Tetra2TriangleTopologicalMapping", name="mapping", input="@../TetraContainer", output="@TriContainer", flipNormals=False)
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volumeCollision.addObject("MechanicalObject", name="mstate_gelColi",position="@../TetraContainer.position")
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volumeCollision.addObject("TriangleGeometry", name="geom_tri", mstate="@mstate_gelColi", topology="@TriContainer",draw=False)
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volumeCollision.addObject("PhongTriangleNormalHandler", name="SurfaceTriangles", geometry="@geom_tri")
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volumeCollision.addObject("AABBBroadPhase",name="AABBTriangles",thread=1,nbox=[2,2,3])
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volumeCollision.addObject("IdentityMapping", name="identityMappingToCollision", input="@../mstate_gel", output="@mstate_gelColi", isMechanical=True)
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volumeVisu = volumeCollision.addChild("visu")
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volumeVisu.addObject("OglModel", position="@../TriContainer.position",
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vertices="@../TriContainer.position",
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triangles="@../TriContainer.triangles",
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color=g_cubeColor,name="volume_visu",template="Vec3d")
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volumeVisu.addObject("IdentityMapping")
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volumeVisuWire = volume.addChild("visu_wire")
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volumeVisuWire.addObject("OglModel", position="@../TetraContainer.position",
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vertices="@../TetraContainer.position",
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triangles="@../TetraContainer.triangles",
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color=[1, 0, 1, 1],name="volume_visu",template="Vec3d")
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volumeVisuWire.addObject("IdentityMapping")
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root.addObject("InsertionAlgorithm", name="InsertionAlgo",
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fromGeom="@Needle/tipCollision/geom_tip",
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destGeom="@Volume/collision/geom_tri",
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fromVol="@Needle/bodyCollision/geom_body",
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destVol="@Volume/geom_tetra",
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punctureThreshold=2.,
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slideDistance=0.003,
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drawcollision=True,
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sphereRadius=0.0001
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#projective=True
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)
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root.addObject("DistanceFilter",algo="@InsertionAlgo",distance=0.01)
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root.addObject("SecondDirection",name="punctureDirection",handler="@Volume/collision/SurfaceTriangles")
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root.addObject("ConstraintUnilateral",input="@InsertionAlgo.output",directions="@punctureDirection",draw_scale="0.001")#, mu="0.001")
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root.addObject("FirstDirection",name="bindDirection", handler="@Needle/bodyCollision/NeedleBeams")
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root.addObject("ConstraintInsertion",input="@InsertionAlgo.outputList", directions="@bindDirection",draw_scale="0.01", frictionCoeff=0.000)

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