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