[SOLVED] BUG-Visualising VTK Mesh in SOFA

[MA]

Hello,

I am trying to visualize the VTK mesh of the bunny mesh.It gives the following error

[INFO]    [SceneCheckerVisitor] Finished validating node "root".
[INFO]    [SofaViewer] QtViewer::keyPressEvent, CONTROL pressed
[ERROR]   [MeshVTKLoader] Error while parsing XML

The code for visualizing the VTK is

import Sofa

import os
path = os.path.dirname(os.path.abspath(__file__))+'/mesh/'

def createScene(rootNode):

        rootNode.createObject('VisualStyle', displayFlags='showForceFields showBehaviorModels')
        rootNode.createObject('RequiredPlugin', pluginName='CGALPlugin')
        rootNode.createObject('RequiredPlugin', pluginName='SofaExporter')
       
        
        
        rootNode.findData('gravity').value='-9810 0 0';
        
        node = rootNode.createChild('node')
     
        node.createObject('MeshVTKLoader',name='mesh',filename=path+'bunny0.vtu')
      
        
       
        
        node.createObject('MeshGenerationFromPolyhedron', name='gen',inputPoints='@mesh.position', inputTriangles='@mesh.triangles', drawTetras='1')
        
        node.createObject('Mesh', position='@gen.outputPoints', tetrahedra='@gen.outputTetras')
        
        return rootNode

I dont know wether this is a bug,I just simply reproduced the same code of bunny example.

[Hugo]

Hi @ma1991

Are you sure of your path?
could you also try doing filename=str(path)+’bunny0.vtu’ ?

[ERROR] [MeshVTKLoader] Error while parsing XML
this sounds like something wrong is passed as argument to the MeshVTKLoader and can not be parsed.

Best

Hugo

[MA]

Hi @Hugo,

Thanks for the help. the error was due to the path in the tutorial page is missing https://project.inria.fr/softrobot/documentation/volumetric-mesh-generation-using-cgal-plugin/

Now the problem is the generated VTK mesh has a problem, I check my mesh and has no error, however, I don’t know why when I am exporting the generated VTK mesh using MeshVTKLoader it gives me the following error:

[ERROR] [TetrahedronFEMForceField(TetrahedronFEMForceField)] object must have a tetrahedric topology. The component is inactivated. To remove this error message please add a tetrahedric topology component to your scene.

What does that mean?in the scene example of soft robots plugin, they have this component included

I am attaching my OBJ file as I am concerned that I am not getting an accurate VTK mesh and maybe it would cause that error

the. file:
https://gofile.io/?c=H65JiD

[Hugo]

Hi @ma1991

Here the error is clear: the TetrahedronFEMForceField can not work properly without a tetrahedral topology on which to compute the integration of the linear elasticitic constitutive law.

Could you share the generated VTK mesh? I would guess that something went wrong with your meshing step.

Best,

Hugo

[MA]

Hi @hugo,

Thanks! I think the problem from my mesh since it didn’t conform for FEM, I tried a new simple one

Here is the OBJ file:https://gofile.io/?c=X0Hm6U

Here the VTK file: https://gofile.io/?c=gFZfJ0

I tried to reconstruct the vtu mesh in ParaView, but the same issue.

Thanks so much for your help.

[Hugo]

Hi Marwa @ma1991

Indeed, your vtu mesh is only a surface and do not include any volumetric element (no tetrahedron). Have a look at the screenshot (crop in the volume of the mesh, only the surface appears):

Best

Hugo

[MA]

Hi Hugo,

This issue is solved, it was a mistake at the skin of the mesh and also because of the inverted normals I was trying to create faces manually.

Thanks for the help:)

[MA]

I still have a question when you convert from ObJ to vtk mesh, I am pressing ctr+E to export, the file I get is vtu and I have to reconstruct the mesh at Paraview as follows here:https://www.sofa-framework.org/community/doc/using-sofa/components/misc/vtkexport/

While I struggle to know whether I have to wait until simulations end to exports vtu file or just press ctr+E to export.

[Hugo]

Hi @ma1991

You have two options: you can either export at begin (exportAtBegin=”1″) or at end (exportAtEnd=”1″)

Note that obj are surface-only format, while vtk is a format for both surface and volume meshed.

Best wishes

Hugo

[MA]

Thanks, it could be a dumb question, it would be a difference if we select at the begin or end. Yes, I know obj is surface-format, but I don’t know why SOFA doesn’t accept transforming from STL to vtk?

[Hugo]

Hi @ma1991

No dumb question here.
When things are misunderstood, it means it can be better explained.

You can actually load or export both STL and VTK. So the transformation of one into the other should be not prob.

Hugo

[MA]

Thanks so much Hugo @Hugo for clarification 🙂

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