[SOLVED] Problems generating mesh with CGALPlugin and TetrahedronSetTopologyContainer

[Anonymous]

Hi,
I’ve been trying to generate a mesh from a stl or obj file and when I try to open it in runSofa, it stops running and exits because of a “segment fault (core)”. I’m using the master version (because I needed the SoftRobotics plugin that follows this version) on Ubuntu 16.04.

The first option I tried to get the mesh was with TetrahedronSetTopologyContainer asi it follows:

<?xml version="1.0"?>
<Node 	 name="Root"  dt="0.02"  >
	<VisualStyle name="visualStyle1"  displayFlags="showAll" />
	<RequiredPlugin name="requiredPlugin8"  printLog="1"  pluginName="requiredPlugin8" />
	<FreeMotionAnimationLoop name="freeMotionAnimationLoop9" />
	<GenericConstraintSolver name="genericConstraintSolver10" />
	<DefaultVisualManagerLoop name="defaultVisualManagerLoop11" />
	<Node 	 name="objeto"  >
		<EulerImplicitSolver name="eulerImplicitSolver12" />
		<SparseLDLSolver template="CompressedRowSparseMatrix3f" name="sparseLDLSolver13" />
		<MeshSTLLoader name="loader"  filename="/home/montse/sofa/#TFG/kyma/disco.stl" />
		<TetrahedronSetTopologyContainer name="container"  position="@loader.position"  edges="@loader.edges"  triangles="@loader.triangles"  tetrahedra="@loader.tetras" />
		<MechanicalObject template="Vec3d" name="tetras"  position="0 0 0"  velocity="0 0 0"  force="0 0 0"  externalForce="0 0 0"  size="1" />
		<UniformMass template="Vec3d" name="uniformMass17"  filename="unused" />
		<TetrahedronFEMForceField template="Vec3d" name="tetrahedronFEMFF18"  gatherPt=" "  gatherBsize=" " />
		<BoxROI template="Vec3d" name="ROI1"  box="0 0 0 1 1 1"  position="@tetras.rest_position"  indices="0"  drawBoxes="1" />
		<RestShapeSpringsForceField template="Vec3d" name="restShapeSpringsFF20"  points="@ROI1.indices"  springColor="0 1 0 1" />
		<LinearSolverConstraintCorrection template="Vec3d" name="linearSolverConstraintCorrection21" />
		<Node 	 name="visu"  >
			<OglModel template="ExtVec3f" name="oglModel22"  fileMesh="/home/montse/sofa/#TFG/kyma/disco.stl"  material="Default Diffuse 1 0.74902 0.74902 0.74902 1 Ambient 1 0.2 0.2 0.2 1 Specular 0 1 1 1 1 Emissive 0 0 0 0 0 Shininess 0 45 "  primitiveType="DEFAULT"  blendEquation="GL_FUNC_ADD"  sfactor="GL_SRC_ALPHA"  dfactor="GL_ONE_MINUS_SRC_ALPHA" />
			<BarycentricMapping template="Vec3d,ExtVec3f" name="barycentricMap23"  input="@../"  output="@./" />
		</Node>
	</Node>
</Node>

I don’t know what is wrong with this code in order to do a “segment fault”.

My next option was using the CGALPlugin as described here:

Volumetric Mesh Generation Using CGAL plugin

But instead of python I used the Modeler and got this xml code:

<?xml version="1.0"?>
<Node 	 name="Root"  dt="0.02"  >
	<VisualStyle name="visualStyle1"  displayFlags="showAll" />
	<DefaultPipeline name="DefaultCollisionPipeline"  verbose="0"  draw="0"  depth="6" />
	<BruteForceDetection name="Detection" />
	<MinProximityIntersection name="Proximity"  alarmDistance="0.3"  contactDistance="0.2" />
	<DefaultContactManager name="Response"  response="default" />
	<RequiredPlugin name="requiredPlugin0"  printLog="1"  pluginName="CGALPlugin" />
	<Node 	 name="node3"  >
		<MeshSTLLoader name="mesh"  filename="/home/montse/sofa/src/share/mesh/dragon.stl" />
		<MeshGenerationFromPolyhedron template="Vec3d" name="gen"  inputPoints="@mesh.position"  inputTriangles="@mesh.triangles"  facetAngle="30"  facetSize="4"  facetApproximation="1"  cellRatio="2"  cellSize="10"  drawTetras="1" />
		<MeshTopology name="MeshTop"  position="@gen.outputPoints"  tetrahedra="@gen.outputTetras" />
		<OglModel template="ExtVec3f" name="oglModel4"  fileMesh="/home/montse/sofa/src/share/mesh/dragon.stl"  material="Default Diffuse 1 0.74902 0.74902 0.74902 1 Ambient 1 0.2 0.2 0.2 1 Specular 0 1 1 1 1 Emissive 0 0 0 0 0 Shininess 0 45 "  primitiveType="DEFAULT"  blendEquation="GL_FUNC_ADD"  sfactor="GL_SRC_ALPHA"  dfactor="GL_ONE_MINUS_SRC_ALPHA" />
	</Node>
</Node>

However, I get the same error (segment fault) and I don’t know why this happens.

[Hugo]

Hey @montsediaz !

Thank you for joining the SOFA forum!
Is there any way for you to share the mesh with us ? I always prefer to run the scenes locally.

For the first scene case, try to change the Uniform mass with:

<UniformMass template="Vec3d" name="uniformMass17" totalmass="1" />

(set the value of total mass that you want instead of 1)

For the example using CGAL did you downloaded and installed CGAL and then compiled the CGAL SOFA plugin ?

Best

Hugo

[Anonymous]

Hi! Thanks for the quick answer.

I set the total mass to 1 in the first example and it does the same thing. The stl I’m using is: this one. I was trying also with some of the files in the sofa/src/share/mesh and getting the same result.

For the second one, yes, I did install and compile CGAL. When compiling the SOFA plugin it gave me an error with “mesh generation from image” but it compiled anyway so I don’t think there’s any problems with the rest of the elements (like mesh generation from polyhedron).

Thank you again!

[Hugo]

OK @montsediaz

I am looking at your first scene.
Several things are missing:

• 5first of all your mesh is a surface mesh, therefore no tetrahedron are available and the FEM component cannot work properly. You need to create a 3D volumetric mesh (including triangles AND tetrahedra) from your surface mesh.
• moreover, you are missing a TetrahedronSetGeometryAlgorithms

Here is a fixed scene:

<?xml version="1.0"?>
<Node    name="Root"  dt="0.02"  >
    <VisualStyle name="visualStyle1"  displayFlags="showVisualModel" />
    <RequiredPlugin name="requiredPlugin8"  printLog="1"  pluginName="requiredPlugin8" />
    <FreeMotionAnimationLoop name="freeMotionAnimationLoop9" />
    <GenericConstraintSolver name="genericConstraintSolver10" maxIterations="1000" tolerance="0.001"/>
    <DefaultVisualManagerLoop name="defaultVisualManagerLoop11" />
    <Node name="fromSurfaceToVolumetricMesh" >
        <MeshSTLLoader name="surface"  filename="Kyma.stl" />
        <MeshTetraStuffing name="stuffing" snapPoints="true" splitTetras="true" draw="false" size="3" alphaLong="0.25" alphaShort="0.4" inputPoints="@surface.position" inputTriangles="@surface.triangles" />
    </Node>
    <Node    name="objeto"  >
        <EulerImplicitSolver name="eulerImplicitSolver12" />
        <SparseLDLSolver template="CompressedRowSparseMatrix3f" name="sparseLDLSolver13" />
        <TetrahedronSetTopologyContainer name="container"  position="@../fromSurfaceToVolumetricMesh/stuffing.outputPoints" tetrahedra="@../fromSurfaceToVolumetricMesh/stuffing.outputTetras" />
        <MechanicalObject template="Vec3d" name="tetras"  position="0 0 0"  velocity="0 0 0"  force="0 0 0"  externalForce="0 0 0"  size="1" showObject="1" />
        <TetrahedronSetGeometryAlgorithms template="Vec3d" name="GeomAlgo" />
        <UniformMass template="Vec3d" name="uniformMass17"  totalmass="1"/>
        <TetrahedronFEMForceField template="Vec3d" name="tetrahedronFEMFF18"  poissonRatio="0.45" youngModulus="5000"/>
        <BoxROI template="Vec3d" name="ROI1"  box="0 0 0 1 1 1"  position="@tetras.rest_position"  indices="0"  drawBoxes="0" />
        <RestShapeSpringsForceField template="Vec3d" name="restShapeSpringsFF20"  points="@ROI1.indices"  springColor="0 1 0 1" />
        <LinearSolverConstraintCorrection template="Vec3d" name="linearSolverConstraintCorrection21" />
        <Node    name="NewMeshVisualization"  >
            <OglModel template="ExtVec3f" name="oglModel22"  color="green" />
            <IdentityMapping template="Vec3d,ExtVec3f" name="barycentricMap23"  input="@../"  output="@./" />
        </Node>
    </Node>

    <Node    name="visuOriginalMesh"  >
        <OglModel template="ExtVec3f" name="oglModel22"  fileMesh="Kyma.stl"  material="Default Diffuse 1 0.74902 0.74902 0.74902 1 Ambient 1 0.2 0.2 0.2 1 Specular 0 1 1 1 1 Emissive 0 0 0 0 0 Shininess 0 45 "  primitiveType="DEFAULT"  blendEquation="GL_FUNC_ADD"  sfactor="GL_SRC_ALPHA"  dfactor="GL_ONE_MINUS_SRC_ALPHA" />
    </Node>
</Node>

But you should really find a way to create your volumetric mesh in a proper meshing software (CGAL or other like MeshLab). The MeshTetraStuffing does only roughly the job.

I hope this helps

Hugo

[Anonymous]

So the problem is with the file? Does this happens with all STLs? I understand I need to generate the file with a special software like MeshLab so when I import it to Sofa it’s not “empty”, is that right?

The CGAL plugin converts the file I’m trying to model into a mesh, I imagine. So I imagine I can import the stl to Sofa and then CGAL does the work OR I can generate the mesh file with MeshLab and then import it to Sofa. I don’t know much about this topic so excuse me if I’m making some obvious mistake.

Thank you!

[Hugo]

Hey,

I think I was not perfectly clear.
STL format is a format dedicated to surface (only) mesh. You can’t therefore have a volumetric mesh, in other words a STL file never defines tetrahedron or hexahedron information.

From your STL file, you need to generate a volumetric mesh (VTK, gmsh …). CGAL does this step surface -> to volumetric mesh. The process that you describe with CGAL works.

Best regards,

Hugo

[Anonymous]

That explains so much of what I’ve been having trouble with. Thank you once again for your help.

[Hugo]

You’re very welcome @montsediaz

[Author]

Posts