[Hugo]

What do you mean by modifying the boundaries of the collision model ?
You want to edit the mesh ?

[Hugo]

Hi Zahra,

You are using v16.08, right ?
There has been changes with CImg since then.

Did you activate the image plugin as well?

Cheers,

Hugo

[Hugo]

Hi Sen,

You can have a look at the SofaCarving plugin.
I never used it personally (I never worked on cutting) but it could help.
Otherwise you can have a look at the follow discussion:

• Incise without mouse
• how to incise 3d object

Hope this helps.
Cheers,

Hugo

[Hugo]

Hi Sen,

Sorry I did not notice this thread.
Geomagic deals with the latest version of Geomagic omnis.
Did you succeed to use it ?

Hugo

[Hugo]

Hi Bruno,

As far as I know, it works this way:

• runSofa reads the scene file, and create the components (in the order 1,2,3,4)
• then, all the steps of the simulation (init(), step(), handleEvent()) are launched through visitors and follow the scene graph (3,4,1,2), i.e. the components in the root node, then in its first child and so on.

To change this behavior, you need to write your own AnimationLoop (see below in the SceneGraph page). Using the tag mechanism, you can define a custom order.

About the DataTracker, it is the right mechanism to use. It has been recently introduced in SOFA V16.12. You can use this DataTracker and the build-in callback function.

Let us know about your progress.
Cheers,

Hugo

[Hugo]

If you wish, you can try to pull-request it.

[Hugo]

Hi Elek,

The scene examples/Components/forcefield/TetrahedralCorotationalFEMForceField.scn produces a warning, but works fine for me. A TetrahedronSetGeometryAlgorithms should indeed be added to remove the warning.

Cheers

Hugo

[Hugo]

Dear Jason and octotod,

About the LM Constraint, to my best knowledge, it is not intensively used anymore. There was a discussion about constraints here (reply #6800).

The difference between the intersection methods is given in the documentation here.

When collision is working, but interpenetration persists:

• you can check the time step of your simulation, it could be due to a fast collision not detected due to a too-large time step,
• you can tune the proximity alarm distance and contact distance (increase it a bit),
• refine and smooth your mesh used for collision

About the DefaultCollisionGroupManager, I am no expert but from the code it looks responsible for gathering colliding objects in the same group, for consistent time integration.

Hope this helps. Best regards,

Hugo

[Hugo]

Hi Luigi,

Then, it can be due to the fact no BoundingBox is computed in the scene.
Two solutions:

• set the option showObject=”1″ in any of your MechanicalObject(s)
• or simply create an OglModel allowing for visualization of your object: it will compute the Bbox and should solve the problem

Let us know if it solves your issue.
Best,

Hugo

[Hugo]

Hi Lujain,

Here are my advices for such a pipeline:

• segment your organ (liver) from the medical images: you can do this using the image plugin in SOFA or any external tool like itkSnap. As output you can get either a labeled image or a surface mesh (using itkSnap)
• if you have a labeled image, use the CGAL plugin of SOFA to mesh this segmented image (see this reply from Alex in a forum discussion for detail); if you have a surface mesh, you can use the MeshTetraStuffing or the CGAL plugin to mesh it in the volume
• finally, create your SOFA scene in which you will load the above created mesh

To load and visualise medical images in SOFA, just use the image plugin.
These are the basic steps for generating a mesh from medical images.
Hope this helps,

Hugo

[Hugo]

Hey Juan,

Can you tell us more about how you solved this error?
Cheers,

Hugo

[Hugo]

Hi Toan,

Did my previous reply help?
If yes, I would close this topic.

Best regards,

Hugo

[Hugo]

Hey Luigi,

Do you have any OglModel in your scene ?
If not then, it’s normal that no visual model appears.
Did you activate the Collision>Collision Models in the SOFA gui ?

Best,

Hugo

[Hugo]

Hi Elek,

Would you not rather use one single mesh with heterogeneous material properties?
This would be more coherent and easy to simulate.

About the xml file you wrote: be careful with the quote you use. Only the regular one (“) are recognized. Another user recently got an issue due to this.

Hope this helps.

Hugo

[Hugo]

yes, nice to hear!
Good job Erik, and thank you for always sharing it with us.

H

[Hugo]

Hi Max(s),

The PR #168 has just been merged. Checkout the latest version of SOFA master branch. It should work now. Using sys.exit(0) you will get the following exception message from SOFA:

[FATAL]   [SofaPython] SP_CALL_MODULEFUNC_BOOL

Thank you max !

[Hugo]

Hi Erik,

Did you try to clean the build dir between your x86 and x64 builds ?

[Hugo]

If you bring new fixes, do not hesitate to pull-request them on GitHub, right?
We are warmly welcoming external contributions!

Check out the contribution guidelines.

Best,

Hugo

[Hugo]

Hi Sen,

This is no real SOFA specific question.
To answer you point by point:

• to generate msh files you can use Gmsh or Blender
• look here, there is discussions about how to generate a ,msh file from .obj
• for topological changes, I advise you to get inspiration from the examples available in sofa/examples/Components/topology/TopologicalModifiers/

Hope this helps.
Cheers,

Hugo

[Hugo]

Hi Ahmet,

After discussions the freePosition vector is initialized by the FreeMotionAnimationLoop (used for simulation involving collisions). So if you’re not using this, this explains the crash (accessor on a non-existing vector). However, this shows the problem of vector initialization depending on the animation loop.

We will discuss this at the dev meeting. It this appears to be a real problem, we will create an issue on Github.

Shall I close the forum topic ?

Hugo

[Hugo]

Hi Juan,

All you messages are always welcome !
Flexible is a plugin of SOFA. This plugin is a specific implementation of the physics (especially mechanics): Flexible decomposes the modeling approach.

Let’s take an example: the TetrahedronFEMForceField. In SOFA, this component defines:

• the mechanical constitutive law (linear elasticity),
• the finite element type : tetrahedron,
• the order of the tetrahedron (linear tetra), i.e. shape function,

All in one.
Flexible decomposes each of these modeling choices: you will have one component for the mechanical law, one for the shape function, one for the quadrature etc.

It is still maintained and used.
It is (a bit) slower than the all-in-one implementation but more intelligible.
Reusable yes and very flexible.
However, everyone is not expert of this plugin.

Hope this helps.

Hugo

[Hugo]

Hi Ahmet,

Nice to hear that it fixes your issue!
But, strange indeed. I will see if freePosition makes sense for rigid bodies and let you know if I find anything about it.

Cheers,

Hugo

[Hugo]

Hi Maxime (Moge),

The hint of Max (Tournier) was good for pausing the animation. But if you want to end it, then you need to send an exit command in python.

At each step of the simulation, you can check with a step counter how many steps have been computed. And when you want to quit, just do something like:
sys.exit(0) (need to import sys)

Hope this helps.

Hugo

[Hugo]

Hi Erdermir,

I doubt the problem is caused by the timer, it would be weird.
Don’t you think it comes from the the lines just below the Timer ?

[Hugo]

Hi pun,

I just looked at your file cube.scn
The only trouble with your file is located line 1.
When you write the scene file yourself, make sure of using the right quotes !

Line 1:

<Node name="root" dt="0.01" gravity="0 0 -9.81”>
                                              |--> here 

You should use the following quotes everywhere: mydata=”value”

Best,

Hugo

[Author]

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