Problems in Model Order Reduction

[kaihuang-ak]

Hello Community!
I am using the MOR plugin of SOFA to reduce the model. I am using the code called modelOrderReduction.py located in the folder ModelOrderReduction/tools. This is the code:

import os
import sys
path = os.path.dirname(os.path.abspath(__file__))
sys.path.append(path+'/../python3') # TO CHANGE
# MOR IMPORT
from mor.gui import utility
from mor.reduction import ReduceModel
from mor.reduction.container import ObjToAnimate
from PyQt5 import QtWidgets
app = QtWidgets.QApplication(sys.argv)

originalScene = utility.openFileName('Select the SOFA scene you want to reduce')
outputDir = utility.openDirName('Select the directory tha will contain all the results')

nodeToReduce = '/modelNode'
nord = ObjToAnimate("modelNode/nord", incr=5,incrPeriod=10,rangeOfAction=40)
sud = ObjToAnimate("modelNode/sud", incr=5,incrPeriod=10,rangeOfAction=40)
est = ObjToAnimate("modelNode/est", incr=5,incrPeriod=10,rangeOfAction=40)
ouest = ObjToAnimate("modelNode/ouest", incr=5,incrPeriod=10,rangeOfAction=40)
listObjToAnimate = [nord,ouest,sud,est]
addRigidBodyModes = [0,0,0]
# Tolerance
tolModes = 0.001
tolGIE =  0.05

# Optional
verbose = True
nbrCPU = 4

packageName = 'test'
addToLib = False

reduceMyModel = ReduceModel(    originalScene,  
                                nodeToReduce,
                                listObjToAnimate,
                                tolModes,tolGIE,
                                outputDir,
                                packageName = packageName,
                                addToLib = addToLib,
                                verbose = verbose,
                                addRigidBodyModes = addRigidBodyModes)
reduceMyModel.phase1()
reduceMyModel.phase2()
reduceMyModel.phase3()
reduceMyModel.phase4()

when run this command in .ipynb:

reduceMyModel.phase3()

I have a bug in the terminal:

I test all test scenes of the tools, all error in this phase. I use Sofa V23.06 and Sofapython3+pyqt5, I don't know if it is caused by python3?
Can anyone help me with this error? Thanks! @hugtalbot @VannesteFelix

[kaihuang-ak]

If anyone can help? I still have the same problem when running reduceMyModel.phase3()? thanks!

[hugtalbot]

Thanks for poking us @kaihuang-ak it helps detecting left-answered topics 👍

[hugtalbot]

Not being myself familiar with MOR I will need to ask other guys

[adagolodjo]

Hello,
Maybe, @olivier-goury can help, or @VannesteFelix if he is around.
However, I would like to suggest an idea: placing line 377 under the for loop for the purpose of debugging.

[kaihuang-ak]

Thanks for your reply! I will try it for debug. I found there was not .reduced.txt. And I don't know why?

[kaihuang-ak]

I still can't find what happened in the phase3()? for some reason there was not _reduce.txt. Maybe the scene has problems after adding MOR in phase3()? Could you help me? @olivier-goury @VannesteFelix

[datou1209]

Is your problem solved? I had a problem in phase4() and could not generate the meshFiles.txt file.

[alxbilger]

Just to be clear:

1. The code you execute is not the script tools/modelOrderReduction.py. It is the one you copied/pasted in this issue, right?
2. The script relies on a SOFA scene. Do you have one that you can share?

[kaihuang-ak]

Yeah. I run the tools/modelOrderReduction.py as belows.

import os
import sys
path = os.path.dirname(os.path.abspath(__file__))
sys.path.append(path+'/../python3') # TO CHANGE


# MOR IMPORT
from mor.gui import utility
from mor.reduction import ReduceModel
from mor.reduction.container import ObjToAnimate

from PyQt5 import QtWidgets
app = QtWidgets.QApplication(sys.argv)

originalScene = utility.openFileName('Select the SOFA scene you want to reduce')
outputDir = utility.openDirName('Select the directory tha will contain all the results')

nodeToReduce ='/liver'
actuator = ObjToAnimate("actuator/actuatorState","shakingLiver",incr=0.4,incrPeriod=2.5,rangeOfAction=6.2,dataToWorkOn="position",angle=0,rodRadius=0.4)
listObjToAnimate = [actuator]
addRigidBodyModes = [0,0,0]

# Tolerance
tolModes = 0.001
tolGIE =  0.05

# Optional
verbose = True
nbrCPU = 4

packageName = 'test'
addToLib = False

#######################################################################
####################      INITIALIZATION     ##########################
reduceMyModel = ReduceModel(    originalScene,  
                                nodeToReduce,
                                listObjToAnimate,
                                tolModes,tolGIE,
                                outputDir,
                                packageName = packageName,
                                addToLib = addToLib,
                                verbose = verbose,
                                addRigidBodyModes = addRigidBodyModes)
reduceMyModel.phase1()
reduceMyModel.phase2()
reduceMyModel.phase3()
reduceMyModel.phase4()

The scene I used is in sofa_test_scene/liverFine.pyscn as below:

import Sofa
import Sofa.Core
import os

meshPath = os.path.dirname(os.path.abspath(__file__))+'/mesh/'

def createScene(rootNode):
    
    rootNode.addObject('RequiredPlugin', name='ModelOrderReduction', pluginName='ModelOrderReduction')
    rootNode.addObject('RequiredPlugin', name='SofaPython3', pluginName='SofaPython3')

    rootNode.addObject('VisualStyle', displayFlags='showCollision showVisualModels showForceFields showInteractionForceFields hideCollisionModels hideBoundingCollisionModels hideWireframe')
    rootNode.findData('dt').value=0.01
    rootNode.findData('gravity').value=[0, -981, 0]
    liver = rootNode.addChild('liver')
    liver.addObject('EulerImplicitSolver', rayleighStiffness = 0.0, rayleighMass = 0.0)
    liver.addObject('SparseLDLSolver',template="CompressedRowSparseMatrixMat3x3d")
    liver.addObject('MeshVTKLoader', name="loader", filename=meshPath+'liverFine.vtu')
    liver.addObject('TetrahedronSetTopologyContainer', src="@loader")
    liver.addObject('MechanicalObject')
    liver.addObject('BoxROI', name='ROI1', box='0 3 -1 2 5 2', drawBoxes='true')
    liver.addObject('BoxROI', name='boxROIactuation', box='-5 0 -0.5 -4 0.5 0.5', drawBoxes='true')

    liver.addObject('UniformMass', totalMass=0.3)
    liver.addObject('TetrahedronFEMForceField', poissonRatio="0.3", youngModulus="5000")
    liver.addObject('RestShapeSpringsForceField', points='@ROI1.indices', stiffness = '1e8')
    liver.addObject('RestShapeSpringsForceField' , external_points = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10], points = '@boxROIactuation.indices', name = 'actuatorSpring', stiffness = '1e8', external_rest_shape = '@actuator/actuatorState')
    
    visu = liver.addChild('visu')
    visu.addObject(  'MeshOBJLoader', name= 'loader', filename=meshPath+'liver-smoothUV.obj')
    visu.addObject('OglModel',src='@loader')
    visu.addObject('BarycentricMapping')

    

    actuator = rootNode.addChild('actuator')
    actuator.addObject('MechanicalObject', name = 'actuatorState', position = '@../liver/boxROIactuation.pointsInROI', template = 'Vec3d')

When I run the modelOrderReduction.py with SOFA V23.06.00 in ubuntu. It still have the problem:

[VannesteFelix]

Hello @kaihuang-ak,
The issue is resolved and merged into master. Try again and tell me what you got !

[hugtalbot]

For your information @kaihuang-ak we might have late September a training session on the Model Order Reduction plugin.
Let us know if you are interested: https://www.sofa-framework.org/sofa-events/sofa-training-sessions/

[hugtalbot]

Since you are back @VannesteFelix , your insight is already needed :) if you have some time 🙏

[VannesteFelix]

Hi @kaihuang-ak sorry for the issue and wait.

At first glance I would say that it searches for the file _reduced.txt and it does not find it.
Normally this file is generated on the previous step: phase2.
To troubleshoot this you can check the log/debug of phase2 to see why.

Most probably it's because the plugin is broken and it does not comes from your SOFA scene.
I am currently working on fixing the plugin with the current SOFA version and will keep you up to date !

[hugtalbot]

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@kaihuang-ak
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[github-actions[bot]]

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@kaihuang-ak
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[github-actions[bot]]

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@kaihuang-ak
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