[SOLVED] TetrahedralCorotationalFEMForcefeild used with SurfaceRegistration

[Lujain]

Hi everyone,

I am using SurfaceRegistration in my mesh data,adding TriangleFEMForcefield. All seem to work fine. I can export the rest_position(after registration and deformation). I also want to know the status of internal points. The problem is that I used only surface mesh.
Can I use TetrahedralCorotationalFEMForcefeild together with SurfaceRegistration in one scene?
If i can, how to import volumetric mesh?

I am waiting for the idea. Thanks in advance.

[Hugo]

Hi Lujain,

What do you mean with SurfaceRegistration ? Is this a scene ? a component ?
I am not aware of it.

With a surface mesh, you cannot use the TetrahedralCorotationalFEMForcefield since tetrahedra are needed. Importing volumetric meshes is possible using VTKExporter for instance (or others like GmshLoader).

Hugo

[Lujain]

Hi Hugo,

Sorry for very late reply.

I did registration with two data sets of two surface. But I can only get the displacement.
I means that in this case how I can apply force field without tetra meshes?

Best!

[Hugo]

Hi Lujain,

Sorry but I really don’t get what you intend to do. Could you explain it more in details (why applying a force on your surface object)

For registration between datasets have a look at the examples in registration plugin.
Did you already build your own simulation ?

If you want to create forces, all you need to use is a forcefield (look at the ConstantForcefield which is very basic to have an idea).

HTH

Hugo

[Lujain]

Hi Hugo，

Sorry for late reply again!

For the first question, I extracted two surfaces from the volumetric mesh(before and after deformation) and did initial registration between them. Now I want to apply the effect of the registration into the volumetric mesh when it is deformed. But I have no idea how to achieve this. This is why I want to apply force filed on surface. I already build my own simulation and hope that i explained clearly.

Best,
Lujain

[Hugo]

Dear Lujain,

If I got you right, you want to register a 3D object. But to do it, you are registering its surface against the surface of the target. Is that correct ?

If so, then I would advise to have a scene looking as follows (just an example based on Registration/examples/ICPRegistration_ShapeMatching_Engine.scn):

<?xml version="1.0"?>
<Node name="Scene" gravity="0 0 0" dt="1"  >
    <RequiredPlugin name="Registration" pluginName="Registration" />
    
    <VisualStyle displayFlags="showForceFields showVisual" />
    
    <EulerImplicitSolver rayleighStiffness="0.5"  rayleighMass="0.5" />
    <CGLinearSolver template="GraphScattered" iterations="25"  threshold="1e-008" />

    <Node name="target">
            <OglModel name="Bone" fileMesh="data/femur_f.obj"  color="0.5 .4 1 1" />
    </Node>
            
    <Node name="PassiveVolumetricMesh">
        <MeshVTKLoader name="meshLoader" filename="yourVTKfile.vtk"/>
        <Mesh src="@loader" />
        <MechanicalObject src="@loader" dx="2.5" />
        <include href="Objects/TetrahedronSetTopology.xml" src="@loader" />
        <UniformMass totalmass="5" />
        <TetrahedronFEMForceField name="FEM" youngModulus="1000" poissonRatio="0.4" computeGlobalMatrix="false" method="large" />        

        <Node name="RegisteredTriangleSurface">
            <include href="Objects/TriangleSetTopology.xml" src="@" tags=" " />
            <Tetra2TriangleTopologicalMapping input="@../Container" output="@Container" />
            <MechanicalObject  name="PointSet"   />
            <UniformMass mass="10"/>
            
            <ClusteringEngine template="Vec3d" name="clustering" radius='0.4'  number='100' position="@meshLoader.position"/>
            <ShapeMatching template="Vec3d" name="shapeMatching" iterations='1' position="@PointSet.position" cluster="@clustering.cluster"/>
            <PositionBasedDynamicsConstraint template="Vec3d" stiffness = '1' position="@shapeMatching.targetPosition"/>        
                        
            <NormalsFromPoints name="NormalsFromPoints" template="Vec3d" position="@PointSet.position" triangles="@meshLoader.triangles" quads="@meshLoader.quads"/>

            <ClosestPointRegistrationForceField template="Vec3d"
                    sourceTriangles="@../meshLoader.triangles"                 
                    sourceNormals="@NormalsFromPoints.normals"                  
                    position="@../../target/Bone.position" 
                    triangles="@../../target/Bone.triangles"   
                    normals="@../../target/Bone.normal"                    
                    cacheSize="4"
                    stiffness="1" damping="0" />

            <Node name="Visu">
                <OglModel name="Visual" fileMesh="data/femur_m.obj" normals="0"   color="1 .4 0.5 1" />
                <BarycentricMapping input="@.." output="@Visual" />
            </Node>
        </Node>
    </Node>
</Node>

HTH

Hugo

[Lujain]

Hi Hugo,

You are right. THis is what i want. But when I use the example you gave, it reminds me to set tetrahedirc topology in TetrahedronFEMForceField. But it seems the mesh has already been the volumetric one.

So I think it may be casued by the line <Mesh src=”@loader” />. After I changed the loader into meshLoader, it reminds me the following errors:

`[ERROR] [Mat] invertMatrix finds too small determinant, matrix = [0 0 0,0 0 0,0 0 0]
[ERROR] [Mat] invertMatrix finds too small determinant, matrix = [0 0 0,0 0 0,0 0 0]
[ERROR] [Mat] invertMatrix finds too small determinant, matrix = [0 0 0,0 0 0,0 0 0]
[ERROR] [Mat] invertMatrix finds too small determinant, matrix = [0 0 0,0 0 0,0 0 0]
[ERROR] [Mat] invertMatrix finds too small determinant, matrix = [0 0 0,0 0 0,0 0 0]

I have no idea about how to deal with these kind errors, and you? Thanks very much!

Best,
Lujain

[Hugo]

Hey Lujain

Have you tried to replace:

<include href="Objects/TetrahedronSetTopology.xml" src="@loader" />

by :

  <TetrahedronSetTopologyContainer  name="Container" src="@loader"/>
  <TetrahedronSetTopologyModifier   name="Modifier" />
  <TetrahedronSetGeometryAlgorithms name="GeomAlgo"  template="Vec3d" />

Cheers

Hugo

[Lujain]

Hi Hugo,

Yes i also tried but it didn’t work.
The error seems strange?

[Lujain]

Hi Hugo,

Here are the data and the scene file that I used.
Can u help me to have a test? The error makes me so confused.

Thanks in advance.
Best,
Lujain

[Hugo]

Your transfer is no longer available Lujain, could you resend it, please?

[Lujain]

Hi,

Here are the scene and data.
Thanks!

[Hugo]

Hey Lujain

You have a MechanicalObject that shouldn’t exist:

<Node name="Scene" gravity="0 0 0" dt="0.05"  >
  
    <RequiredPlugin name="Registration" pluginName="Registration" />
    <VisualStyle displayFlags="showForceFields showVisual" />
    <EulerImplicitSolver rayleighStiffness="0.5"  rayleighMass="0.5" />
    <CGLinearSolver template="GraphScattered" iterations="25"  threshold="1e-008" />

    <Node name="target">
			<OglModel name="Liver" fileMesh="output_liver_1_deformation.obj"  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" />
	</Node>
            
    <Node name="PassiveVolumetricMesh">
        <MeshVTKLoader name="meshLoader" filename="output_liver_1.vtu"/>
        <Mesh src="@meshLoader" />
        <MechanicalObject src="@meshLoader" dx="2.5" />
        
		<TetrahedronSetTopologyContainer  name="topo" src="@meshLoader"/>
        <TetrahedronSetTopologyModifier   name="Modifier" />
        <TetrahedronSetGeometryAlgorithms name="GeomAlgo"  template="Vec3d" />
  
        <UniformMass totalmass="5" />
        <TetrahedronFEMForceField name="FEM" youngModulus="1000" poissonRatio="0.4" computeGlobalMatrix="false" method="large" />        

        <Node name="RegisteredTriangleSurface">
            <TriangleSetTopologyContainer name="Container"/>
			<TriangleSetTopologyModifier   name="Modifier" />
            <TriangleSetTopologyAlgorithms name="TopoAlgo"  template="Vec3d" />
            <TriangleSetGeometryAlgorithms name="GeomAlgo"  template="Vec3d" />
			
            <Tetra2TriangleTopologicalMapping input="@../topo" output="@Container" />
            <UniformMass mass="10"/>
            <ClusteringEngine template="Vec3d" name="clustering" radius='0.01'  number='100' position="@meshLoader.position"/>
            <PositionBasedDynamicsConstraint template="Vec3d" stiffness ='0.1' position="@shapeMatching.targetPosition"/> -->
            <ClosestPointRegistrationForceField template="Vec3d"
                    sourceTriangles="@../meshLoader.triangles"                 
                    sourceNormals="@NormalsFromPoints.normals"                  
                    position="@../../target/Liver.position" 
                    triangles="@../../target/Liver.triangles"   
                    normals="@../../target/Liver.normal"                    
                    cacheSize="4"
                    stiffness="200" damping="0" theCloserTheStiffer="1" />
		    <Node name="Visu">
				<OglModel template="ExtVec3f" name="VisualModel" fileMesh="output_liver_1.obj" material="Default Diffuse 1 1 0 0 1 Ambient 1 0 0 0.2 1 Specular 0 1 0 0 1 Emissive 0 1 0 0 1 Shininess 0 45"  primitiveType="DEFAULT"  blendEquation="GL_FUNC_ADD"  sfactor="GL_SRC_ALPHA"  dfactor="GL_ONE_MINUS_SRC_ALPHA"/>
				<BarycentricMapping input="@.." output="@VisualModel" />
			</Node>
        </Node>
    </Node>
</Node>

On top of this, you can increase the stiffness in ClosestPointRegistrationForceField during the simulation. Here is what I get:

Please, do not forget to cite the plugin & SOFA in your work.
Best regards,

Hugo

[Lujain]

Hi Hugo,

Ok I will. And thank you very much!

Best,
Lujain

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