Accessing and mofiying array values with Context Managers in SofaPython3

[nicklj]

This question was previously asked in the SOFA forum as:
https://www.sofa-framework.org/community/forum/topic/accessing-and-mofiying-array-values-with-context-managers-in-sofapython3/

However, as there was no response, and I believe this is really a very important issue, so I post the problem here again for discussion.

The issue occurs when accessing numpy list values with context managers in SofaPython3. I think the nature of the problem is very similar to the question as in the thread as (Issue when changing object position via python scene.), but I’ll try to explain it more clearly.

The motivation is I’d like to move object with modifying the rest_position in the mechanicalObject and with the help of RestShapeSpringsForceField. This is very stratiforward in the previous SofaPython2 version. However, in the SofaPython3, it seems cannot directly modify the value. I’ve tried
self.rootNode.finger1.mechObj.rest_position.value = ****
But clearly it doens not work. I’ve checked many related topics in the forum, and one very clear explanation is as:
Data.value vs Data.writeable() with SP3

However, although I understand the motivation and common practice in modifying the values, I cannot successfully achieve it. The big issue is, the accessed numpy array is not the correct one after 2-3 time steps, and obviously it does not point to the correct memory address, which will yield segmentation fault if I modify it. Here I attached the sample scene file for your reference. The example is with rigid body, but the same problem occurs for deformable body.
https://www.dropbox.com/s/2exibu9m2vahlhs/simplegripper.zip?dl=0

Environment: Ubuntu 20.04 + compiled latest SOFA commit at github

Not sure whether this is because of my wrong usage, or some bugs in the program. Much appreciate if anyone may help to address this issue.

[hugtalbot]

Hey @nicklj
Sorry for keeping you waiting on both forums.
An example of this is given below:

import sys
import Sofa

class ManageParticles(Sofa.Core.Controller):

    def __init__(self, *args, **kwargs):
        # These are needed (and the normal way to override from a python class)
        Sofa.Core.Controller.__init__(self, *args, **kwargs)
        self.CFF = kwargs.get("ForceField")
        self.rootNode = kwargs.get("rootNode")
        self.iteration = 1

    def onKeypressedEvent(self, event):
        key = event['key']

        if key=="+" :
            with self.CFF.totalForce.writeableArray() as wa:
                wa[0] += 0.002

        if key=="-" :
            with self.CFF.totalForce.writeableArray() as wa:
                wa[0] -= 0.002

        if key=="A" :
            self.addParticle()

        if key=="M" :
            self.removeParticle()

        return 0;


    def addParticle(self):
        iteration_loc = self.iteration
        name = 'Particle'+str(iteration_loc)
        myParticleNode = self.rootNode.addChild(str(name))
        myParticleNode.addObject('EulerImplicitSolver')
        myParticleNode.addObject('CGLinearSolver', threshold='1e-09', tolerance='1e-09', iterations='200')
        myParticleNode.addObject('MechanicalObject', showObject='1', position='0 0 '+str(iteration_loc)+'    0 0 0 1', name='myParticle-'+str(iteration_loc), template='Rigid3d')

        myNewMass = myParticleNode.addObject('UniformMass', totalMass='1')
        myNewCFF  = myParticleNode.addObject('ConstantForceField', name="CFF", totalForce="0.05 0 0 0 0 0" )

        myNewMass.init()
        myNewCFF.init()

        self.iteration = iteration_loc +1

        return 0;

    def removeParticle(self):
        iteration_loc = self.iteration - 1
        
        if iteration_loc >= 0:
            name = 'Particle'+str(iteration_loc)
            nodeToDelete = self.rootNode.getChild(str(name))
            for obj in nodeToDelete.objects:
                nodeToDelete.removeObject(obj)

            myParticleNode = self.rootNode.removeChild(str(name))
            self.iteration = iteration_loc

        return 0;

def createScene(root):
    root.dt = 0.01
    root.gravity = [0,0,0]

    root.addObject('RequiredPlugin', name="SIOS-load", pluginName="SofaImplicitOdeSolver")
    root.addObject('RequiredPlugin', name="SBC-load",  pluginName="SofaBoundaryCondition")

    root.addObject('DefaultVisualManagerLoop')
    root.addObject('DefaultAnimationLoop')

    Particle = root.addChild('Particle0')
    Particle.addObject('EulerImplicitSolver')
    Particle.addObject('CGLinearSolver', threshold='1e-09', tolerance='1e-09', iterations='200')
    Particle.addObject('MechanicalObject', showObject='1', position='0 0 0    0 0 0 1', name='Particle-0', template='Rigid3d')
    Particle.addObject('UniformMass', totalMass='1')
    Particle.addObject('ConstantForceField', name="CFF", totalForce="0 0 0 0 0 0" )

    root.addObject( ManageParticles(name="MyParticlesController", ForceField=Particle.CFF, rootNode=root) )

    return 0;



def main():
    import SofaRuntime
    import Sofa.Gui
    # Make sure to load all SOFA libraries
    SofaRuntime.importPlugin("SofaBaseMechanics")
    SofaRuntime.importPlugin("SofaOpenglVisual")
    SofaRuntime.importPlugin("CImgPlugin")

    #Create the root node
    root = Sofa.Core.Node("root")
    # Call the below 'createScene' function to create the scene graph
    createScene(root)
    Sofa.Simulation.init(root)

    # Launch the GUI (qt or qglviewer)
    Sofa.Gui.GUIManager.Init("myscene", "qglviewer")
    Sofa.Gui.GUIManager.createGUI(root, __file__)
    Sofa.Gui.GUIManager.SetDimension(1080, 600)
    # Initialization of the scene will be done here
    Sofa.Gui.GUIManager.MainLoop(root)
    Sofa.Gui.GUIManager.closeGUI()

    print("Simulation is done.")



# Function used only if this script is called from a python environment
if __name__ == '__main__':
    main()

or an example on forcefield is given in the plugin examples

[hugtalbot]

Let us know whether you need more details on this!

[damienmarchal]

Hello @nicklj,

Thanks for reporting... I think this was related to a bug reported and fixed in PR: #243.
If this is still happening in recent version of Sofa please report.

[github-actions[bot]]

⚠️ ⚠️ ⚠️
@nicklj
We are setting a new forum management policy: topics like this one, in which the last reply is more than 4 months old, will automatically be closed. Without further news in the coming weeks, our bot will proceed to automatic closure, thus keeping this forum clean and fresh 🌱 Thank you for your understanding

[github-actions[bot]]

⚠️ ⚠️ ⚠️
@nicklj
In accordance with our forum management policy, the last reply is more than 4 months old and is therefore closed. Our objective is to keep the forum up to date and offer the best support experience.

Please feel free to reopen it if the topic is still active by providing us with an update. Please feel free to open a new thread at any time - we'll be happy to help where and when we can.

[github-actions[bot]]

⚠️ ⚠️ ⚠️
@nicklj
In accordance with our forum management policy, the last reply is more than 4 months old and is therefore closed. Our objective is to keep the forum up to date and offer the best support experience.

Please feel free to reopen it if the topic is still active by providing us with an update. Please feel free to open a new thread at any time - we'll be happy to help where and when we can.