Mesh modifier

[LucaCarlini]

Hi,
I am trying to develop a simulator of a needle insertion procedure.
Up to now I have obtained a scene in which the needle collides with the membrane.
Now I need to perform the needle insertion by eliminating elements where the needle is cutting, but I don't have a clear idea about how to do it.
Is there any suggestion?
Thank you in advance

[hugtalbot]

Hi @lucac-crypto

Needle insertion is a pretty complex topic for simulation.
For needle insertion, I invite you to check what is done here in the Cosserat plugin : https://github.com/SofaDefrost/plugin.Cosserat/tree/master/python3/cosserat/needle

[hugtalbot]

The path C:\Users\lcarl\sofa\Sofa_bundle\plugins\CosseratPlugin\lib\python3\site-packages is not where the scene is located. It's a path to have in PYTHONPATH. However, the command python3 should point towards the sources of the plugin

The examples are indeed not shipped when compiling/installing Cosserat.

[LucaCarlini]

Yes, i have set that path in PYTHONPATH and started the scene from the folder 'needle' using runSofa.
Unfortunately I have just noticed that the comment written before wasn't complete and was indeed:

[SofaPython3::SceneLoader] Unable to completely load the scene from file 'C:/Users/lcarl/SOFA/Sofa_bundle/plugins/CosseratPlugin/lib/python3/site-pack                                                                               kages/cosserat/needle/needleTissueInteraction.py'.
Python exception:
  ModuleNotFoundError: No module named 'Sofa.CosseratPlugin'

I am really sorry but I can't still load the scene. Could you please tell me if there is something else I must do?

[hugtalbot]

Could you detail @lucac-crypto step by step the command / actions you do to launch runSofa and open the scene file ?

[LucaCarlini]

I simply open the command window and then type:

runSofa "C:\Users\lcarl\sofa\Sofa_bundle\plugins\CosseratPlugin\lib\python3\site-packages\cosserat\needle\needleTissueInteraction.py"

[hugtalbot]

@lucac-crypto Alright, this was my previous point: the repository does not contain the python scene ! You can check yourself.

What you need to do, is to make sure you have somewhere the needleTissueInteraction.py. To my best memory - as I wrote above - examples are indeed not shipped when compiling/installing Cosserat. So what you need is to download/clone the sources of Cosserat so that you have this needleTissueInteraction.py file which should be located in python3/cosserat/needle/.

Finally run runSofa giving the path of this needleTissueInteraction.py file.
Cheers

[LucaCarlini]

Ok, the procedure I have followed is this one:

1. downloaded and unzipped the plugin from github.
2. I have copied all the contents of the folder "Plugin.Cosserat-master" inside "CosseratPlugin" that is the folder containing the plugin already loaded in Sofa.
3. I have added C:\Users\lcarl\sofa\Sofa_bundle\plugins\CosseratPlugin\lib\python3\site-packages to PYTHONPATH
4. I have copied the folder "cosserat" containing all the examples inside the path "\plugins\CosseratPlugin\lib\python3\site-packages"
5. Then I have launched sofa using:
   runSofa "C:\Users\lcarl\sofa\Sofa_bundle\plugins\CosseratPlugin\lib\python3\site-packages\cosserat\needle\needleTissueInteraction.py"

But needleTissueInteraction.py still doesn't work while other examples work. Did I missed a step?

I am really sorry for this inconvenience and thank you again

[hugtalbot]

Hey @lucac-crypto

No worries ;)
I would have been clearer to unzip the sources else where than in the build of the CosseratPlugin.
But it should work fine anyway, could you share the error you get ?

[LucaCarlini]

I have reinstalled Sofa using the last release of DefrostSofaBundle, then I have substituted the 'cosserat' folder with the one of the plugin (https://github.com/SofaDefrost/plugin.Cosserat/tree/master/python3/cosserat). Then modifying the script NeedleController.py substituting import Sofa.CosseratPlugin with import CosseratPlugin. This have solved the precedent problem but now I have the following error:

[ERROR]   [SofaPython3::SceneLoader] Unable to completely load the scene from file 'C:\Users\lcarl\OneDrive\Desktop\DefrostSofaBundle\plugins\CosseratPlugin\lib                                                                               b\python3\site-packages\cosserat\needle\needleTissueInteraction.py'.
Python exception:
  ValueError: Object type PointsManager<> was not created
The object is not in the factory.


At:
  C:\Users/lcarl/OneDrive/Desktop/DefrostSofaBundle/plugins/CosseratPlugin/lib/python3/site-packages\cosserat\utils.py(38): addConstraintPoint
  C:\Users\lcarl\OneDrive\Desktop\DefrostSofaBundle\plugins\CosseratPlugin\lib\python3\site-packages\cosserat\needle\needleTissueInteraction.py(77): createScene

What it could be due to?

[hugtalbot]

Hmm this is a Cosserat issue @lucac-crypto
I think the scene file is more recent than the bundle. Could you please try another example scene from the same folder please?

[LucaCarlini]

I have just tried other scene from the same folder and they gave me some kind of error that are all different from each other. The following scenes give the following errors:

'NeedleInsertionWithConstraintPointsCreation.py' :

[ERROR]   [SofaPython3::SceneLoader] Unable to completely load the scene from file 'C:\Users\lcarl\OneDrive\Desktop\DefrostSofaBundle\plugins\CosseratPlugin\lib                                                                               b\python3\site-packages\cosserat\needle\NeedleInsertionWithConstraintPointsCreation.py'.
Python exception:
  TypeError: BuildCosseratGeometry() got an unexpected keyword argument 'nbSection'

At:
  C:\Users\lcarl\OneDrive\Desktop\DefrostSofaBundle\plugins\CosseratPlugin\lib\python3\site-packages\cosserat\needle\NeedleInsertionWithConstraintPointsCreation                                                                               n.py(127): createScene

'needleInteractionTest.py' :

[ERROR]   [CosseratNeedleSlidingConstraint(QPConstraint)] Indices at index 0 is too large regarding mechanicalState [position] size

########## SIG 11 - SIGSEGV: segfault ##########

'completDirectNeedleInsertion.py' does't give errors but as soon as the scene is animated the needle and the mesh disappear.

'CosserateLikeNeedle.py' on the other side is the only one working fine.

[hugtalbot]

Hey @lucac-crypto

Sorry for the long no-show, this thread disappeared from my radar
Have you succeeded using it and modeling needle insertion? Maybe using the v23.06 release? Soon the new v23.12 will be available as well.

My apologies again.

[github-actions[bot]]

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@lucac-crypto
Feedback has been given to you by the project reviewers, however we have not received a response from you. Without further news in the coming weeks, this discussion will be automatically closed in order to keep this forum clean and fresh 🌱 Thank you for your understanding

[github-actions[bot]]

⚠️ ⚠️ ⚠️
@lucac-crypto
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