[SOLVED] How to extract the surface of a volumeyric mesh

[Zahra]

Hi,
How can I extract the surface of a volumetric mesh?

Best,
Zahra

[Bruno Marques]

Hi Zahra,

You might want to look at the “Tetra2TriangleTopologicalMapping” component.
You can find an example in the scene “examples/Components/topology/Tetra2TriangleTopologicalMapping.scn”

[Zahra]

Hi Bruno,

Thank you for your help. I tried the Tetra2TriangleTopologicalMapping.scn, but when I add a meshexporter to the “T” node of the aforementioned example to extract the surface, it still extracts the triangles of the whole volume, not just the surface. DO you have any idea why?

[Binesh]

Hi @zahra
it is better to use ObjExporter component for export surface of volume

[jnbrunet]

Hi @Zahra

I’m not sure why you’re getting the whole volume’s triangle set. I just tried adding the mesh exporter to the “T” node and it works fine on my side. I disabled the edges export to really get only the positions and triangle indices:

<?xml version="1.0" ?>
<Node name="root" dt="0.05" showBoundingTree="0" gravity="0 0 0">
    <VisualStyle displayFlags="showBehaviorModels showVisual" />
    <CollisionPipeline verbose="0" />
    <BruteForceDetection name="N2" />
    <CollisionResponse response="default" />
    <MinProximityIntersection name="Proximity" alarmDistance="0.8" contactDistance="0.5" />
    <CollisionGroup />
    <Node name="TT">
        <EulerImplicit name="cg_odesolver" printLog="false"  rayleighStiffness="0.1" rayleighMass="0.1" />
        <CGLinearSolver iterations="25" name="linear solver" tolerance="1.0e-9" threshold="1.0e-9" />
        <MeshGmshLoader name="loader" filename="mesh/cylinder.msh" />
        <MechanicalObject src="@loader" name="Volume" />
        <include href="Objects/TetrahedronSetTopology.xml" src="@loader" tags=" " />
        <DiagonalMass massDensity="0.5" />
        <FixedPlaneConstraint direction="0 0 1" dmin="-0.1" dmax="0.1" />
        <FixedConstraint indices="0" />
        <TetrahedralCorotationalFEMForceField name="FEM" youngModulus="360" poissonRatio="0.3" method="large" />
        <Node name="T">
            <MeshExporter format="vtk" filename="cylinder_surface" exportAtBegin="true" edges="false"/>
            <include href="Objects/TriangleSetTopology.xml" src="@" tags=" " />
            <Tetra2TriangleTopologicalMapping input="@../Container" output="@Container" />
            <TriangularFEMForceField name="FEM" youngModulus="60" poissonRatio="0.3" method="large" />
            <TriangularBendingSprings name="FEM-Bend" stiffness="300" damping="1.0" />
            <TrianglePressureForceField normal="0 0 1" dmin="0.9" dmax="1.1" pressure="0.4 0 0" />
            <TriangleSet />
            <Node name="Visu">
                <OglModel name="Visual" color="blue" />
                <IdentityMapping input="@../../Volume" output="@Visual" />
            </Node>
        </Node>
    </Node>
</Node>

Let me know if you’re still having difficulties to get it right.

[Hugo]

Hi Zahra,

The Tetra2TriangleTopologicalMapping creates indeed a triangle topology from a tetrahedral one. Therefore is not supposed to remove the triangles within the volume. As Binesh suggested the ObjExporter does the job.

But a nice thing would be to create a new class Tetra2SurfaceTriangleTopologicalMapping inheriting from Tetra2TriangleTopologicalMapping and selecting only triangles on the border.

Hugo

[jnbrunet]

Hey @Hugo

Tetra2TriangleTopologicalMapping will be able to retrieve the surface mesh. In fact, it will retrieve the triangles that only got one tangent tetrahedron. If this is your case,
Tetra2TriangleTopologicalMapping is good enough to get the surface representation. The MeshExporter will then find the mesh topology in the context of the exporter’s object. You can then toggle which elements you want exported.

As for the ObjExporter, it will export the triangles only if a VisualModel can be found. I don’t think there is one better than the other, they both inherits from the same base exporter. It really depends on your application.

Jean-Nicolas

[Zahra]

Hi @jnbrunet,

Thank you for your comment. I ran your code, I am not that much familiar with vtk format (I use gmsh), however, I guess it still extracts the whole volume. I see the number of nodes are 510 which is the same number of nodes in the cylinderical volume. If it extract the surface, the number of the nodes should be less than that.

Best,

Zahra

[Zahra]

Hi @Binesh,

I tried ObjExporter, here is the .scn file:

https://gist.github.com/zbounik/d3bc51ade6b27f04fa38b38e6b8fcdf7

It causes this error which I can not figure out:

https://gist.github.com/zbounik/328f316a4e8616dd053f9a30b5f68ec5

Best,

Zahra

[Zahra]

Dear Hugo,

As I have mentioned to Binesh, ObjExporter causes an error.

The idea of creating a new class Tetra2SurfaceTriangleTopologicalMapping is appealing, however, I never accomplished such a code in SOFA before (my programming skill is to the level of MATLAB). I have recently learned python but I still have problems with python scripting in sofa

Is it possible that you kindly give me some guiding steps to know how to create Tetra2SurfaceTriangleTopologicalMapping class?

How only the triangles on the border should be selected?

I am sorry if I am asking too many questions 😐

Best,

Zahra

[Hugo]

Hi,

This scene is working fine for me. I am using the master branch of SOFA.
Which version of SOFA are you using Zahra ?

Jean Nico is right:
– Tetra2TriangleTopologicalMapping is good enough to get the surface representation
– ObjExporter must be carefully used since it uses the visual model and exports it, VTKExporter is always a good solution and works fine also in your case.

Hugo

[Zahra]

Hi Hugo,

I am using the stable branch of SOFA now v17.06.

Zahra

[Hugo]

Hi Zahra,

I guess you behavior has been fixed since the PR#372
That explains your problem. JeanNicolas and my advices might whatever help you in overcome this issue. Keep us updated.

Hugo

[Zahra]

Dear @Hugo and @jnbrunet,

Thank you for leading me to this point. You are right, by using Tetra2TriangleTopologicalMapping and MeshExporter I can get the surface mesh.

What misleaded me was that the number of nodes of both surface and volume meshes remained the same, however, I recognized that the inner nodes become disconnected (the number of elements are reduced in the surface mesh).

I really appreciate your time.

Best regards,

Zahra

[Binesh]

Hi @zahra
Try this scene :

<?xml version="1.0"?>
<Node 	 name="root"  gravity="0 0 0"  dt="0.05"  >
	<VisualStyle name="visualStyle1"  displayFlags="showVisual showBehaviorModels" />
	<DefaultPipeline name="defaultPipeline1"  verbose="0" />
	<BruteForceDetection name="N2" />
	<DefaultContactManager name="defaultContactManager1"  response="default" />
	<MinProximityIntersection name="Proximity"  alarmDistance="0.8"  contactDistance="0.5" />
	<DefaultCollisionGroupManager name="defaultCollisionGroupManager1" />
	<Node 	 name="TT"  >
		<EulerImplicitSolver name="cg_odesolver"  printLog="0" />
		<CGLinearSolver template="GraphScattered" name="linear solver"  iterations="25"  tolerance="1e-09"  threshold="1e-09" />
		<MeshGmshLoader name="loader"  filename="mesh/cylinder.msh"  tetrahedraGroups="  -1 0 2430" />
		<MechanicalObject template="Vec3d" name="Volume"  position="@loader.position"  velocity="0 0 0"  force="0 0 0"  externalForce="0 0 0"  restScale="1"  size="1" />
		<TetrahedronSetTopologyContainer name="Container"  position="@loader.position"  edges="@loader.edges"  triangles="@loader.triangles"  tetrahedra="@loader.tetras" />
		<TetrahedronSetTopologyModifier name="Modifier" />
		<TetrahedronSetTopologyAlgorithms template="Vec3d" name="TopoAlgo" />
		<TetrahedronSetGeometryAlgorithms template="Vec3d" name="GeomAlgo" />
		<DiagonalMass template="Vec3d" name="diagonalMass1"  massDensity="0.5" />
		<FixedPlaneConstraint template="Vec3d" name="fixedPlaneConstraint1"  direction="0 0 1"  dmin="-0.1"  dmax="0.1" />
		<FixedConstraint template="Vec3d" name="fixedConstraint1"  indices="0" />
		<TetrahedralCorotationalFEMForceField template="Vec3d" name="FEM"  method="large"  poissonRatio="0.3"  youngModulus="360" />
		<Node 	 name="T"  >
			<TriangleSetTopologyContainer name="Container"  position="@.position"  nbPoints="@.nbPoints"  edges="@.edges"  checkConnexity="@.checkConnexity"  triangles="@.triangles" />
			<TriangleSetTopologyModifier name="Modifier" />
			<TriangleSetTopologyAlgorithms template="Vec3d" name="TopoAlgo" />
			<TriangleSetGeometryAlgorithms template="Vec3d" name="GeomAlgo" />
			<Tetra2TriangleTopologicalMapping name="tetra2TriangleTopologicalMapping1"  input="@../Container"  output="@Container" />
			<TriangularFEMForceField template="Vec3d" name="FEM"  method="large"  poissonRatio="0.3"  youngModulus="60" />
			<TriangularBendingSprings template="Vec3d" name="FEM-Bend"  stiffness="300"  damping="1" />
			<TrianglePressureForceField template="Vec3d" name="trianglePressureFF1"  pressure="0.4 0 0"  normal="0 0 1"  dmin="0.9"  dmax="1.1" />
			<TTriangleModel template="Vec3d" name="tTriangleModel1" />
			<OBJExporter name="oBJExporter0"  listening="1"  filename="/home/behnam/Export/Surface"  exportEveryNumberOfSteps="1"  exportAtBegin="0"  exportAtEnd="0" />
			<Node 	 name="Visu"  >
				<OglModel template="ExtVec3f" name="Visual"  material="Default Diffuse 1 0 0 1 1 Ambient 1 0 0 0.2 1 Specular 0 0 0 1 1 Emissive 0 0 0 1 1 Shininess 0 45 "  primitiveType="DEFAULT"  blendEquation="GL_FUNC_ADD"  sfactor="GL_SRC_ALPHA"  dfactor="GL_ONE_MINUS_SRC_ALPHA" />
				<IdentityMapping template="Vec3d,ExtVec3f" name="identityMap1"  input="@../../Volume"  output="@Visual" />
			</Node>
		</Node>
	</Node>
</Node>

[Binesh]

@Hugo @jnbrunet @zahra
Mesh Exporter component get positions from mechanical object and all positions declare volume not surface , but “Tetra2SurfaceTriangleMapping” is a good idea and implementation of this component is easy.
I’ll do it if I have the opportunity

‌Best,

Behnam Binesh

[Hugo]

Good to hear Zahra!
Binesh, it appears that Tetra2TriangleTopologicalMapping will indeed be able to retrieve the surface mesh. So there might not be a need for the Tetra2SurfaceTriangleMapping

Thanks you all for the collaboration!

[Zahra]

Hi @Binesh,

Thank you for your explanation. As Hugo mentioned, I think there is no need for implementing “Tetra2SurfaceTriangleMapping”.

Regarding the scene you have mentioned, I tried it: No .Obj file is created, and finally I receive this error:

FROM SOFA [ERR] >>
########## SIG 11 – SIGSEGV: segfault ##########

Best,

Zahra

[Binesh]

@zahra
you must change “filename” of obj exporter

[Zahra]

Hi @Binesh,

I know, I have changed it and I got that error.

BTW, as I have mentioned, my problem with extracting the surface has been resolved. I am now trying to figure out why the same code works for others and gives me the “SIG 11 – SIGSEGV: segfault” error. I encountered this error previously and I have thought it is because of my code. I may start a new topic about it as soon as I collect more evidences.

Best,

Zahra

[Binesh]

Hi @zahra
I knew that your problem is solved , But my target is to fix SIG error

[Zahra]

Thank you @Binesh, I have started a new topic regarding this error:

SIG 11 – SIGSEGV: segfault Segmentation fault (core dumped)

I appreciate your help and deeply wish you have a good luck with this error 🙂

[Author]

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