Skip to content

[scene] A scene with haptics and insertion in a liver represented by a .msh tetrahedral mesh #42

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
th-skam merged 2 commits into from
Jul 30, 2025
Merged

[scene] A scene with haptics and insertion in a liver represented by a .msh tetrahedral mesh #42

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
e59829d
[Needle][scene] Starting point for a scene with geomagic
th-skam Jul 24, 2025
8ab4c91
[scene] Deactivated friction and showing mstate
th-skam Jul 29, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
208 changes: 208 additions & 0 deletions scenes/InsertionGeomagic.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,208 @@
import Sofa

g_needleLength=0.100 #(m)
g_needleNumberOfElems=20 #(# of edges)
g_needleBaseOffset=[0.15,0.04,0.04]
g_needleRadius = 0.001 #(m)
g_needleMechanicalParameters = {
"radius":g_needleRadius,
"youngModulus":1e11,
"poissonRatio":0.3
}
g_needleTotalMass=0.01

g_gelRegularGridParameters = {
"n":[8, 8, 8],
"min":[-0.125, -0.125, -0.350],
"max":[0.125, 0.125, -0.100]
} #Again all in mm
g_gelMechanicalParameters = {
"youngModulus":9e4,
"poissonRatio":0.45,
"method":"large"
}
g_gelTotalMass = 1
g_cubeColor=[0.8, 0.34, 0.34, 0.3]
g_gelFixedBoxROI=[-0.350, -0.280, -0.360, 0.130, 0.130, -0.200 ]

# Function called when the scene graph is being created
def createScene(root):
root.gravity=[0,0,0]
root.dt = 0.01

root.addObject("RequiredPlugin",pluginName=['Sofa.Component.AnimationLoop',
'Sofa.Component.Constraint.Lagrangian.Solver',
'Sofa.Component.ODESolver.Backward',
'Sofa.Component.Visual',
'Sofa.Component.Constraint.Lagrangian.Correction',
'Sofa.Component.Constraint.Lagrangian.Model',
'Sofa.Component.LinearSolver.Direct',
'Sofa.Component.Mapping.Linear',
'Sofa.Component.Mass',
'Sofa.Component.SolidMechanics.FEM.Elastic',
'Sofa.Component.StateContainer',
'Sofa.Component.Topology.Container.Dynamic',
'Sofa.Component.Topology.Mapping',
'Sofa.Component.Mapping.NonLinear',
'Sofa.Component.Topology.Container.Grid',
'Sofa.Component.Constraint.Projective',
'Sofa.Component.SolidMechanics.Spring',
'Sofa.GL.Component.Rendering3D',
'Sofa.GUI.Component',
'Sofa.Component.Engine.Select',
'MultiThreading',
'CollisionAlgorithm',
'ConstraintGeometry',
'Geomagic',
'Sofa.Component.Haptics',
'Sofa.Component.IO.Mesh'
])


root.addObject("ConstraintAttachButtonSetting")
root.addObject("VisualStyle", displayFlags="showVisualModels hideBehaviorModels showCollisionModels hideMappings hideForceFields showWireframe showInteractionForceFields" )
root.addObject("FreeMotionAnimationLoop")
root.addObject("GenericConstraintSolver", tolerance=0.00001, maxIt=5000, printLog=False, computeConstraintForces=True)
root.addObject("CollisionLoop")

root.addObject("GeomagicDriver"
, name='GeomagicDevice'
, deviceName='Default Device'
, scale='0.02'
, drawDeviceFrame='false'
, drawDevice='false'
, manualStart='0'
, positionBase='0.12 0 0'
, orientationBase='0 0.174 0 -0.985'
)

toolController = root.addChild("ToolController")
toolController.addObject("MechanicalObject", name="mstate_baseMaster", position="@GeomagicDevice.positionDevice", template="Rigid3d", showObjectScale=0.01, showObject="false", drawMode=1)

needle = root.addChild("Needle")
needle.addObject("EulerImplicitSolver", firstOrder=True)
needle.addObject("EigenSparseLU", name="LinearSolver", template="CompressedRowSparseMatrixd")
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)]
, edges=[[i, i+1] for i in range(g_needleNumberOfElems)])

needle.addObject("EdgeSetTopologyModifier", name="modifier")
needle.addObject("PointSetTopologyModifier", name="modifier2")

needle.addObject("MechanicalObject", name="mstate", template="Rigid3d", showObjectScale=0.002, showObject="false", drawMode=1)

needle.addObject("UniformMass", totalMass=g_needleTotalMass)
needle.addObject("BeamFEMForceField", name="FEM", **g_needleMechanicalParameters)
# needle.addObject("FixedLagrangianConstraint", indices="0" )
needle.addObject("LinearSolverConstraintCorrection", printLog="false", linearSolver="@LinearSolver")
needle.addObject("LCPForceFeedback", activate='1', forceCoef='0.01')

needleBase = needle.addChild("needleBase")
needleBase.addObject("PointSetTopologyContainer", name="Container_base", position="@../mstate.position")#"@../../GeomagicDevice.positionBase")
needleBase.addObject("MechanicalObject",name="mstate_base", template="Rigid3d")
needleBase.addObject("RestShapeSpringsForceField",points=[0],stiffness=1e9, angularStiffness=1e9,external_points=[0],external_rest_shape="@/ToolController/mstate_baseMaster")
needleBase.addObject("SubsetMapping", indices="0")

needleBodyCollision = needle.addChild("bodyCollision")
needleBodyCollision.addObject("EdgeSetTopologyContainer", name="Container_body", src="@../Container")
needleBodyCollision.addObject("MechanicalObject",name="mstate_body", template="Vec3d", drawMode=0, showObject="false", showObjectScale="10")
needleBodyCollision.addObject("EdgeGeometry",name="geom_body",mstate="@mstate_body", topology="@Container_body")
needleBodyCollision.addObject("EdgeNormalHandler", name="NeedleBeams", geometry="@geom_body")

needleBodyCollision.addObject("IdentityMapping")

needleTipCollision = needle.addChild("tipCollision")
needleTipCollision.addObject("MechanicalObject",name="mstate_tip",position=[g_needleBaseOffset[0], g_needleBaseOffset[1], -(g_needleLength+g_needleBaseOffset[2])],template="Vec3d", showObject="false", showObjectScale=20)
needleTipCollision.addObject("PointGeometry",name="geom_tip",mstate="@mstate_tip")
needleTipCollision.addObject("RigidMapping",globalToLocalCoords=True,index=g_needleNumberOfElems)


needleVisual = needle.addChild("visual")
needleVisual.addObject("QuadSetTopologyContainer", name="Container_visu")
needleVisual.addObject("QuadSetTopologyModifier", name="Modifier")
needleVisual.addObject("Edge2QuadTopologicalMapping", nbPointsOnEachCircle=8, radius=g_needleRadius, input="@../Container", output="@Container_visu")

needleVisual.addObject("MechanicalObject", name="mstate_visu", showObjectScale="0.0002", showObject="false", drawMode="1")

needleVisual.addObject("TubularMapping", nbPointsOnEachCircle=8, radius=g_needleRadius, input="@../mstate", output="@mstate_visu")

needleOGL = needleVisual.addChild("OGL")
needleOGL.addObject("OglModel", position="@../Container_visu.position",
vertices="@../Container_visu.position",
quads="@../Container_visu.quads",
color="0.4 0.34 0.34",
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",
name="visualOgl")
needleOGL.addObject("IdentityMapping")



#gelTopo = root.addChild("GelGridTopo")
#gelTopo.addObject("RegularGridTopology", name="HexaTop", **g_gelRegularGridParameters)


volume = root.addChild("Volume")
volume.addObject("EulerImplicitSolver")
volume.addObject("EigenSimplicialLDLT", name="LinearSolver", template='CompressedRowSparseMatrixMat3x3d')
#volume.addObject("TetrahedronSetTopologyContainer", name="TetraContainer", position="@../GelGridTopo/HexaTop.position")
volume.addObject("MeshGmshLoader", name="meshLoader", filename="mesh/liver.msh", scale3d="0.08 0.08 0.08", translation="0 -0.3 -0.2")
volume.addObject("TetrahedronSetTopologyContainer", name="TetraContainer", position="@meshLoader.position", tetrahedra="@meshLoader.tetrahedra")
volume.addObject("TetrahedronSetTopologyModifier", name="TetraModifier")
#volume.addObject("Hexa2TetraTopologicalMapping", input="@../GelGridTopo/HexaTop", output="@TetraContainer", swapping="false")

volume.addObject("MechanicalObject", name="mstate_gel", template="Vec3d")
volume.addObject("TetrahedronGeometry", name="geom_tetra", mstate="@mstate_gel", topology="@TetraContainer", draw=False)
#volume.addObject("TriangleGeometry", name="tri_geom", mstate="@mstate_gel", topology="@TetraContainer",draw=True)
volume.addObject("PhongTriangleNormalHandler", name="InternalTriangles", geometry="@geom_tetra")
volume.addObject("AABBBroadPhase",name="AABBTetra",geometry="@geom_tetra",nbox=[3,3,3],thread=1)
#volume.addObject("ParallelTetrahedronFEMForceField", name="FF",**g_gelMechanicalParameters)
volume.addObject("TetrahedronFEMForceField", name="FF",**g_gelMechanicalParameters)
volume.addObject("MeshMatrixMass", name="Mass",totalMass=g_gelTotalMass)

volume.addObject("BoxROI",name="BoxROI",box=g_gelFixedBoxROI)
volume.addObject("RestShapeSpringsForceField", stiffness='1e6',points="@BoxROI.indices" )

volume.addObject("LinearSolverConstraintCorrection", printLog="false", linearSolver="@LinearSolver")

volumeCollision = volume.addChild("collision")
volumeCollision.addObject("TriangleSetTopologyContainer", name="TriContainer")
volumeCollision.addObject("TriangleSetTopologyModifier", name="TriModifier")
volumeCollision.addObject("Tetra2TriangleTopologicalMapping", name="mapping", input="@../TetraContainer", output="@TriContainer", flipNormals=False)
volumeCollision.addObject("MechanicalObject", name="mstate_gelColi",position="@../TetraContainer.position")
volumeCollision.addObject("TriangleGeometry", name="geom_tri", mstate="@mstate_gelColi", topology="@TriContainer",draw=False)
volumeCollision.addObject("PhongTriangleNormalHandler", name="SurfaceTriangles", geometry="@geom_tri")
volumeCollision.addObject("AABBBroadPhase",name="AABBTriangles",thread=1,nbox=[2,2,3])

volumeCollision.addObject("IdentityMapping", name="identityMappingToCollision", input="@../mstate_gel", output="@mstate_gelColi", isMechanical=True)

volumeVisu = volumeCollision.addChild("visu")
volumeVisu.addObject("OglModel", position="@../TriContainer.position",
vertices="@../TriContainer.position",
triangles="@../TriContainer.triangles",
color=g_cubeColor,name="volume_visu",template="Vec3d")
volumeVisu.addObject("IdentityMapping")

volumeVisuWire = volume.addChild("visu_wire")
volumeVisuWire.addObject("OglModel", position="@../TetraContainer.position",
vertices="@../TetraContainer.position",
triangles="@../TetraContainer.triangles",
color=[1, 0, 1, 1],name="volume_visu",template="Vec3d")
volumeVisuWire.addObject("IdentityMapping")


root.addObject("InsertionAlgorithm", name="InsertionAlgo",
fromGeom="@Needle/tipCollision/geom_tip",
destGeom="@Volume/collision/geom_tri",
fromVol="@Needle/bodyCollision/geom_body",
destVol="@Volume/geom_tetra",
punctureThreshold=2.,
slideDistance=0.003,
drawcollision=True,
sphereRadius=0.0001
#projective=True
)
root.addObject("DistanceFilter",algo="@InsertionAlgo",distance=0.01)
root.addObject("SecondDirection",name="punctureDirection",handler="@Volume/collision/SurfaceTriangles")
root.addObject("ConstraintUnilateral",input="@InsertionAlgo.output",directions="@punctureDirection",draw_scale="0.001")#, mu="0.001")

root.addObject("FirstDirection",name="bindDirection", handler="@Needle/bodyCollision/NeedleBeams")
root.addObject("ConstraintInsertion",input="@InsertionAlgo.outputList", directions="@bindDirection",draw_scale="0.01", frictionCoeff=0.000)