[Hugo]

Hi @hkomninos,

how did you solve your issue? what was the problem?

Regarding the PrecomputedConstraintCorrection, you can find some explanation in the updated doc.

I think the paper entitled “GPU-based real-time soft tissue deformation with cutting and haptic feedback” used it.

Best,

Hugo

[Hugo]

Thank you very much for you notice and for daring taking a look into the c++ code!
That’s brave and that’s a good reflex.

We noticed this week (on master branch) that some check of unity on the quaternion (for Rigid3Types) disappeared. However, the addition instead of multiplication might be an error. I need to check this part.

Thanks again for updating us: I created an issue to follow the prob here.

Best

Hugo

[Hugo]

Hi @hkomninos,

it appears that you are having an issue due to an wrong access in memory (un-initialized vector, or pointer). The creation of the FreeMotionAnimationLoop should not be an issue in cpp. Could you share with us you cpp scene ?

Best

Hugo

[Hugo]

Hi @hkomninos

Please do not double post your questions

Your question has already been submitted in the post : #12090 about the Geomagic plugin. It will be answered there. Thank you.

Best,

Hugo

[Hugo]

Hi Noura,

Thanks for your feedback.
The best would be to do your remarks on the GitHub doc so that I can more efficiently update.

Regarding the mapping, a dedicated doc page exists here now. Some pages remains at “todo” or “soon” since we would like to go even more into details for each class (of Mapping among others). But this will come a bit later on.

Best

Hugo

[Hugo]

Don’t be confused.
I close the topic then.

If you face the issue again, please just follow my instructions above, by specifying a bbox value to your root node.

Hugo

[Hugo]

Hi Zahra,

There is two possible ways to use SOFA:

• download the sources of SOFA: there you will need to clone (from GitHub using the command git clone -b v18.06 https://github.com/sofa-framework/sofa.git, configure (CMake) and compile (with your desired compiler gcc, clang ..) the code. After compilation, you will have an executable runSofa generated. Everything is detailed in the doc
• download the binaries: go on the download page, download the package corresponding to your OS and find runSofa in it

Best

Hugo

[Hugo]

Hi @fsharifi135

As a free forum, everyone here replies as fast as possible. However, if you need a specific support, do not hesitate to the SOFA Consortium that can provide you any service you want around SOFA.

For your issue, is there a reason to use the debug build mode?
If not, try first running SOFA in release mode.

Best,

Hugo

[Hugo]

Hi Fei

You should read carefully the error messages.
It explains that you can set the bbox="-1 -1 -1 1 1 1" in the root node to specify the bounding box. Bounding box is usually computed by visual model (OglModel), in this case the bbox is automatically computed. I guess you do not have an OglModel in your scene. That’s why you have this warning.

Let me know if this fixes your issue.
Best

Hugo

[Hugo]

Dear @suwan

You should have a look to the TetrahedronFEMForceField which includes elasto-plastic deformation. You can have a look in the Data of this class in the SOFA API.

Best

Hugo

[Hugo]

HI @jangirrishabh

You should have a look to my previous message, applying the same structure to your case will make the cloth controlled by a rigid object.

Best,

Hugi

[Hugo]

Hi @hkomninos,

When you say that you can’t write, what kind of error do you get?

Hugo

[Hugo]

Hi Eleonora,

I think the starting a common project around SOFA validation (against other solutions and analytical solutions when existing) would be a great idea. We have many interested partners for this.

Best

Hugo

[Hugo]

Dear @fsharifi135

The errors are pretty clear indeed: you need to have a version of SOFA with the metis option activated (flag SOFA_BUILD_METIS), with the plugin SofaPython activated (flag PLUGIN_SOFAPYTHON), with the module SofaSparseSolver activate (flag MODULE_SOFASPARSESOLVER) and your version of Qt appears to be undefined.

You should then rather use and compile the sources of SOFA instead of the binaries.

Best

Hugo

[Hugo]

Hi,

The release of SOFA v18.06 had these small errors appearing, but no worries nothing bad. It has been fixed since then in the master branch of the SOFA sources (see PR#758).

Best

Hugo

[Hugo]

Hi @jangirrishabh

Several components do have such a visualization option (MechanicalObject, SparseGrid, MeshTopology etc.). If you don’t find it, please post us your scene.

Hugo

[Hugo]

Nice to hear Wong,

Could you let us know how you solved your issue?
I close also this topic.

Best

Hugo

[Hugo]

Hi @outtt

When a topic is solved you can close it yourself.

Note for people facing the same question: you can activate in the Visualization Data of the TetrahedronSetGeometryAlgorithm with showPointIndices, showEdgeIndices etc.

A work is in progress to integrate it in a more easy way into a new GUI for SOFA.

Best regards

Hugo

[Hugo]

Alright, I close the topic then.
If you have any further question, as usual, do not hesitate to post it !

Hugo

[Hugo]

Hi @fsharifi135 @meldiwiny

@fsharifi135 : just to make sure you are attempting to compile SOFA with the binary version of SOFA (from the download page of SOFA). Is this correct?

If so, you need to download the SoftRobot plugin in a separate repository. Let’s call it “SoftRobotPlugin/src/“.
Then you need to build the plugin by:
– first creating a build/ directory for the plugin like “SoftRobotPlugin/build/”
– run cmake using the src and build directory of the plugin
– configure, generate
– and finally compile

Let me know if this helps.
Best

Hugo

[Hugo]

Hi Zahra

Indeed I can reproduce the problem.
Just after import Sofa you can add:

def createScene(rootNode):
    rootNode.createObject('RequiredPlugin', name='SofaPython')
    mySimulation = Ttest(rootNode,[])
    return 0;

and define all your scene in the initGraph function instead of the createGraph function.

Resulting in:

"""
TtestPython
is based on the scene 
/home/zahra/sofa/Work/test/Ttest.scn
but it uses the SofaPython plugin. 
Further informations on the usage of the plugin can be found in 
sofa/applications/plugins/SofaPython/doc/SofaPython.pdf
To lance the scene, type 
runSofa /home/zahra/sofa/Work/test/TtestPython.scn

The current file has been written by the python script
/home/zahra/sofa/Sofa17.06/src/applications/plugins/SofaPython/scn2python.py
Author of scn2python.py: Christoph PAULUS, christoph.paulus@inria.fr
"""

import Sofa

def createScene(rootNode):
    rootNode.createObject('RequiredPlugin', name='SofaPython')
    mySimulation = Ttest(rootNode,[])
    return 0;

class Ttest (Sofa.PythonScriptController):

    def initGraph(self,rootNode):

        # rootNode
        rootNode.createObject('DefaultPipeline', name='CollisionPipeline', verbose='0')
        rootNode.createObject('BruteForceDetection', name='N2')
        rootNode.createObject('DefaultContactManager', name='collision response', response='default')
        rootNode.createObject('DiscreteIntersection', name='discreteIntersection1')

        # rootNode/Liver
        Liver = rootNode.createChild('Liver')
        Liver.depend = 'topo dofs'
        Liver.createObject('EulerImplicitSolver', name='cg_odesolver', printLog='0')
        Liver.createObject('CGLinearSolver', threshold='1e-09', tolerance='1e-09', name='linear solver', iterations='25', template='GraphScattered')
        Liver.createObject('MeshGmshLoader', tetrahedraGroups='  -1 0 38144', name='loader', filename='/home/zahra/sofa/Work/testbygmsh/livertetra7509.msh')
        Liver.createObject('TetrahedronSetTopologyContainer', triangles='@loader.triangles', position='@loader.position', edges='@loader.edges', name='topo', tetrahedra='@loader.tetras')
        Liver.createObject('MechanicalObject', force='0 0 0', name='dofs', template='Vec3d', position='@loader.position', velocity='0 0 0', externalForce='0 0 0', restScale='1')
        Liver.createObject('TetrahedronSetGeometryAlgorithms', drawColorEdges='0.4 1 0.298039 1', showIndicesScale='0.01', name='GeomAlgo', showPointIndices='0', template='Vec3d')
        Liver.createObject('DiagonalMass', massDensity='1', name='computed using mass density', template='Vec3d')
        Liver.createObject('TetrahedralCorotationalFEMForceField', poissonRatio='0.3', name='FEM', computeGlobalMatrix='0', method='large', template='Vec3d', youngModulus='12000')
        Liver.createObject('PlaneForceField', name='planeFF0', template='Vec3d', normal='0 1 0')
        Liver.createObject('ConstantForceField', indices='111', name='constantFF0', template='Vec3d', forces='0 -120 0')
        Liver.createObject('FixedConstraint', indices='11 17 16 15 14 4 3 0 45 95 42 40 38 39 53 62 61 60 4 63 59 125 24 20 19 9', drawSize='0', name='fixedConstraint0', template='Vec3d')
        Liver.createObject('MeshExporter', exportEveryNumberOfSteps='1', quads='0', name='meshExporter3', format='gmsh', exportAtEnd='1', filename='/home/zahra/sofa/Work/Exported/Fine/LiverFine_111_0_-120_0', exportAtBegin='1', hexas='0', edges='0', listening='0', triangles='0')
        Liver.createObject('TetrahedronSetTopologyModifier', name='tetrahedronSetTopologyModifier9')
        Liver.createObject('TetrahedronSetTopologyAlgorithms', name='tetrahedronSetTopologyAlgorithms10', template='Vec3d')

        # rootNode/Liver/Visu-fine
        Visu_fine = Liver.createChild('Visu-fine')
        Visu_fine.createObject('OglModel', sfactor='GL_SRC_ALPHA', blendEquation='GL_FUNC_ADD', name='oglModel0', template='ExtVec3f', dfactor='GL_ONE_MINUS_SRC_ALPHA', material='Default Diffuse 1 0.666667 0 0 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')
        Visu_fine.createObject('IdentityMapping', input='@../', name='identityMap1', template='Vec3d,ExtVec3f', output='@./')

        # rootNode/Liver/coarse
        coarse = Liver.createChild('coarse')
        coarse.createObject('MeshGmshLoader', tetrahedraGroups='  -1 0 596', name='meshGmshLoader1', filename='/home/zahra/sofa/Work/testbygmsh/livertetra181.gmsh')
        coarse.createObject('TetrahedronSetTopologyContainer', triangles='@meshGmshLoader1.triangles', position='@meshGmshLoader1.position', edges='@meshGmshLoader1.edges', name='tetrahedronSetTopologyContainer2', tetrahedra='@meshGmshLoader1.tetras')
        coarse.createObject('MechanicalObject', force='0 0 0', name='mObject0', template='Vec3d', position='@meshGmshLoader1.position', velocity='0 0 0', externalForce='0 0 0', restScale='1')
        coarse.createObject('TetrahedronSetTopologyModifier', name='tetrahedronSetTopologyModifier3')
        coarse.createObject('TetrahedronSetGeometryAlgorithms', drawColorEdges='0.4 1 0.298039 1', recomputeTrianglesOrientation='0', name='tetrahedronSetGeometryAlgorithms0', showPointIndices='1', flipNormals='1', showIndicesScale='0.01', template='Vec3d')
        coarse.createObject('TetrahedronSetTopologyAlgorithms', name='tetrahedronSetTopologyAlgorithms1', template='Vec3d')
        coarse.createObject('MeshExporter', exportEveryNumberOfSteps='1', quads='0', name='meshExporter13', format='gmsh', exportAtEnd='1', filename='/home/zahra/sofa/Work/Exported/Coarse/LiverCoarse_111_0_-120_0', exportAtBegin='1', hexas='0', edges='0', listening='0', triangles='0')
        coarse.createObject('EulerImplicitSolver', name='eulerImplicitSolver0')
        coarse.createObject('CGLinearSolver', name='cGLinearSolver1', template='GraphScattered')
        coarse.createObject('DiagonalMass', name='diagonalMass2', template='Vec3d')
        coarse.createObject('FixedConstraint', indices='0', name='fixedConstraint3', template='Vec3d')
        coarse.createObject('PlaneForceField', name='planeFF4', template='Vec3d', normal='0 1 0')
        coarse.createObject('TetrahedralCorotationalFEMForceField', youngModulus='12000', name='tetrahedralCorotationalFEMFF5', poissonRatio='0.3', template='Vec3d')

        # rootNode/Liver/coarse/Visu-coarse
        Visu_coarse = coarse.createChild('Visu-coarse')
        Visu_coarse.createObject('OglModel', sfactor='GL_SRC_ALPHA', name='oglModel1', 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 ', primitiveType='DEFAULT', template='ExtVec3f', translation='0 0 0', dfactor='GL_ONE_MINUS_SRC_ALPHA', blendEquation='GL_FUNC_ADD')
        Visu_coarse.createObject('IdentityMapping', input='@../', name='identityMap2', template='Vec3d,ExtVec3f', output='@./')

        return 0;

    def onKeyPressed(self, c):
        return 0;

    def onKeyReleased(self, c):
        return 0;

    def onLoaded(self, node):
        return 0;

    def onMouseButtonLeft(self, mouseX,mouseY,isPressed):
        return 0;

    def onMouseButtonRight(self, mouseX,mouseY,isPressed):
        return 0;

    def onMouseButtonMiddle(self, mouseX,mouseY,isPressed):
        return 0;

    def onMouseWheel(self, mouseX,mouseY,wheelDelta):
        return 0;

    def onGUIEvent(self, strControlID,valueName,strValue):
        return 0;

    def onBeginAnimationStep(self, deltaTime):
        return 0;

    def onEndAnimationStep(self, deltaTime):
        return 0;

    def onScriptEvent(self, senderNode, eventName,data):
        return 0;

    def bwdInitGraph(self, node):
        return 0;

    def storeResetState(self):
        return 0;

    def reset(self):
        return 0;

    def cleanup(self):
        return 0;

Best

Hugo

[Hugo]

It’s merged in SOFA master branch.
Best

Hugo

[Hugo]

Hi @djoumessirenethierry

You can have a look to the examples in examples/Components/loader/MeshVTKLoader.scn
If it doesn’t help, could you post your error?

Best,

Hugo

[Hugo]

Hi Harris,

As Erik wrote you privately, it might be related to a current issue with the Geomagic plugin. A PR will be done within the week. Stay tuned, you’ll be able to test the fix very soon.

Cheers

Hugo

[Hugo]

Hi Harris

You mean that you add in the simulation created in runSofa, new components like the GeomagicDriver?

And what do you mean exactly by “I did the same for the SofaCarving and I did not had a problem”. Could you show the corresponding lines of code?

Instead of overwriting runSofa, I would rather advise you later to create your own plugin/applications separately from SOFA. See the doc.

Cheers

Hugo

[Author]

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