Fix python pipeline

python3/mor/reduction/reduceModel.py

@@ -374,9 +374,13 @@ def phase3(self,phasesToExecute=None,nbrOfModes=None):
 
         for fileName in self.reductionParam.savedElementsFilesNames :
             u.copyFileIntoAnother(results[self.phaseToSaveIndex]["directory"]+slash+fileName,self.packageBuilder.debugDir+fileName)
-        self.reductionParam.massName = glob.glob(results[self.phaseToSaveIndex]["directory"]+slash+"*_reduced.txt")[0]
-        # print("massName -----------------------> ",self.reductionParam.massName)
-        u.copy(self.reductionParam.massName,self.reductionParam.dataDir)
+
+        ### commented out waiting for change in c++ code
+        # optimization done in MMM but now removed
+        # self.reductionParam.massName = glob.glob(results[self.phaseToSaveIndex]["directory"]+slash+"*_reduced.txt")[0]
+        # # print("massName -----------------------> ",self.reductionParam.massName)
+        # u.copy(self.reductionParam.massName,self.reductionParam.dataDir)
+        #####
 
         files = glob.glob(results[self.phaseToSaveIndex]["directory"]+slash+"*_Gie.txt")
         if files: 
@@ -460,13 +464,12 @@ def phase4(self,nbrOfModes=None):
                     self.reductionParam.savedElementsFilesNames[j] = self.reductionParam.savedElementsFilesNames[i]
                     self.reductionParam.savedElementsFilesNames[i] = tmp
 
-        # print(self.reductionParam.savedElementsFilesNames)
-        # print(self.reductionParam.gieFilesNames)
-        tmp = glob.glob(self.packageBuilder.dataDir+"*_reduced.txt")[0]
-        tmp = os.path.normpath(tmp)
-        self.reductionParam.massName = tmp.split(slash)[-1]
-        # print("massName -----------------------> ",self.reductionParam.massName)
-
+        ### commented out waiting for change in c++ code
+        # optimization done in MMM but now removed
+        # tmp = glob.glob(self.packageBuilder.dataDir+"*_reduced.txt")[0]
+        # tmp = os.path.normpath(tmp)
+        # self.reductionParam.massName = tmp.split(slash)[-1]
+        ####
 
         self.reductionParam.RIDFilesNames = []
         self.reductionParam.weightsFilesNames = []

python3/mor/utility/sceneCreation.py

@@ -243,11 +243,8 @@ def modifyGraphScene(node,nbrOfModes,newParam):
                     modelMOR.addObject(obj)
                 modelMOR.addObject('MechanicalObject', **argMecha)
                 # print param['paramMappedMatrixMapping']
-                modelMOR.addObject('MechanicalMatrixMapperMOR', **param['paramMappedMatrixMapping'] )
-                # print 'Create MechanicalMatrixMapperMOR in modelMOR'
                 if save:
                     replaceAndSave.myMORModel.append(('MechanicalObject',argMecha))
-                    replaceAndSave.myMORModel.append(('MechanicalMatrixMapperMOR',param['paramMappedMatrixMapping']))
 
                 if 'paramMORMapping' in param:
                     #Find MechanicalObject name to be able to save to link it to the ModelOrderReductionMapping

python3/mor/utility/writeScene.py

@@ -181,7 +181,7 @@ def MyReducedModel(
                     parentNode = nodeName+"_MOR"
                 elif childName.find('/'+nodeName+'/') == -1:
                     print(childName,1)
-                    tmp = filter(None, childName.split('/'))
+                    tmp = list(filter(None, childName.split('/')))
                     if len(tmp) > 2: # Add all the parents that haven't been created yet 
                         for i, node in enumerate(tmp):
                             if i < len(tmp)-2:
@@ -194,7 +194,6 @@ def MyReducedModel(
                                     # print(toFind)
                                     logFile.write(toFind)
                         parentNode = childName.split('/')[-2]
-
                     else:
                         parentNode = 'modelRoot'
 
@@ -204,7 +203,7 @@ def MyReducedModel(
                     if childName.split('/')[-2] == nodeName:
                         parentNode = nodeName
                     else:
-                        tmp = filter(None, childName.split('/'))
+                        tmp = list(filter(None, childName.split('/')))
                         parentNode = tmp[-2]
                         if len(tmp) > 2:
                             for i, node in enumerate(tmp):
@@ -388,4 +387,4 @@ def buildArgStr(arg,translation=None):
                 myArgs += ", "+key+" = "+str(val)#+"'"
 
     # print(myArgs)
-    return myArgs
+    return myArgs

python3/mor/wrapper/replaceAndSave.py

@@ -174,7 +174,7 @@ def MORreplace(node,type,newParam,initialParam):
     currentPath = node.getPathName()
     # print('NODE : '+node.name.value)
     # print('TYPE : '+str(type))
-    #print('PARAM  :'+str(newParam[0][0]) )
+    # print('PARAM  :'+str(newParam[0][0]) )
     save = False
     if 'save' in newParam[1]:
         save = True

tools/sofa_test_scene/diamondRobot.py

@@ -1,13 +1,11 @@
 # -*- coding: utf-8 -*-
-
-import os
 import sys
+import os
 
 #   STLIB IMPORT
-from stlib3.scene import MainHeader
-from stlib3.solver import DefaultSolver
-from stlib3.physics.deformable import ElasticMaterialObject
 from stlib3.physics.constraints import FixedBox
+from stlib3.visuals import VisualModel
+from stlib3.physics.deformable import ElasticMaterialObject
 
 # SOFTROBOTS IMPORT
 from softrobots.actuators import PullingCable
@@ -31,51 +29,90 @@
         }
     ]
 
+plugins=["SofaPython3","SoftRobots","ModelOrderReduction","STLIB",
+         # normally plugin Sofa.Component is enough but still warning
+         "Sofa.Component.Visual",
+         "Sofa.Component.AnimationLoop",
+         "Sofa.GL.Component.Rendering3D",
+         "Sofa.Component.Constraint.Lagrangian.Solver",
+         'Sofa.Component.IO.Mesh',
+         'Sofa.Component.Playback',
+         'Sofa.Component.Constraint.Lagrangian.Correction', # Needed to use components [GenericConstraintCorrection]
+         'Sofa.Component.Engine.Select', # Needed to use components [BoxROI]
+         'Sofa.Component.LinearSolver.Direct', # Needed to use components [SparseLDLSolver]
+         'Sofa.Component.Mapping.Linear', # Needed to use components [BarycentricMapping]
+         'Sofa.Component.Mass', # Needed to use components [UniformMass]
+         'Sofa.Component.ODESolver.Backward', # Needed to use components [EulerImplicitSolver]
+         'Sofa.Component.SolidMechanics.FEM.Elastic', # Needed to use components [TetrahedronFEMForceField]
+         'Sofa.Component.SolidMechanics.Spring', # Needed to use components [RestShapeSpringsForceField]
+         'Sofa.Component.StateContainer', # Needed to use components [MechanicalObject]
+         'Sofa.Component.Topology.Container.Dynamic'] # Needed to use components [TetrahedronSetTopologyContainer]
+
 meshPath = os.path.dirname(os.path.abspath(__file__))+'/mesh/'
 
 def createScene(rootNode):
 
+    rootNode.addObject('FreeMotionAnimationLoop')
+    rootNode.addObject('GenericConstraintSolver', tolerance="1e-6", maxIterations="1000")
+    rootNode.addObject('OglSceneFrame', style="Arrows", alignment="TopRight")
     rootNode.addObject('VisualStyle', displayFlags='showVisualModels showForceFields')
+    rootNode.addObject('RequiredPlugin', pluginName=plugins, printLog=False)
 
     rootNode.findData('gravity').value=[0.0,0.0,-9810];
     rootNode.findData('dt').value=1
 
-    plugins=["SofaPython","SoftRobots","ModelOrderReduction"]
-    for name in plugins:
-        rootNode.addObject('RequiredPlugin', name=name, printLog=False)
-
-    rootNode.addObject('OglSceneFrame', style="Arrows", alignment="TopRight")
 
-    rootNode.addObject('FreeMotionAnimationLoop')
-    rootNode.addObject('GenericConstraintSolver', tolerance="1e-6", maxIterations="1000")
+    volumeMeshFileName=meshPath+'siliconeV0.vtu'
+    rotation=[90, 0.0, 0.0]
+    translation=[0.0, 0.0, 35]
+    totalMass=0.5
+    surfaceMeshFileName=meshPath+'surface.stl'
+    surfaceColor=[0.7, 0.7, 0.7, 0.7]
+    poissonRatio=0.45
+    youngModulus=450
+    scale=[1., 1., 1.]
+
+
+    modelNode = rootNode.addChild('modelNode')
+    modelNode.addObject('EulerImplicitSolver', name='integration')
+    modelNode.addObject('SparseLDLSolver', name="solver", template='CompressedRowSparseMatrixMat3x3d')
+    loader = modelNode.addObject('MeshVTKLoader', name='loader', filename=volumeMeshFileName,
+                                 rotation=list(rotation), translation=list(translation),
+                                 scale3d=list(scale))
+
+    # loader.tetras.getLinkPath() AND loader.position.getLinkPath() ---> DO NOT WORK
+    # When you change the scene for the HyperReduction, seems to update the link path to correct new path
+    # BUT does not load the loader data anymore
+    modelNode.addObject('TetrahedronSetTopologyContainer', position='@loader.position',
+                                    tetras='@loader.tetrahedra', name='container')
+    modelNode.addObject('MechanicalObject', template='Vec3', name='dofs')
+    modelNode.addObject('UniformMass', totalMass=totalMass, name='mass')
+    modelNode.addObject('TetrahedronFEMForceField', template='Vec3',
+                                     method='large', name='forcefield',
+                                     poissonRatio=poissonRatio, youngModulus=youngModulus)
 
+    visualmodel = modelNode.addChild('visualmodel')
+    visualmodel.addObject('MeshSTLLoader', name='loader', filename=surfaceMeshFileName)
+    visualmodel.addObject('OglModel', name="OglModel", src="@loader",
+                   rotation=list(rotation),
+                   translation=list(translation),
+                   scale3d=list(scale),
+                   color=list(surfaceColor), updateNormals=False)
+    visualmodel.addObject('BarycentricMapping', name='mapping')
 
-    modelNode = ElasticMaterialObject(
-        attachedTo=rootNode,
-        volumeMeshFileName=meshPath+'siliconeV0.vtu',
-        name='modelNode',
-        rotation=[90, 0.0, 0.0],
-        translation=[0.0, 0.0, 35],
-        totalMass=0.5,
-        withConstrain=False,
-        surfaceMeshFileName=meshPath+'surface.stl',
-        surfaceColor=[0.7, 0.7, 0.7, 0.7],
-        poissonRatio=0.45,
-        youngModulus=450)
-
-    modelNode.addObject('GenericConstraintCorrection', solverName='solver')
+    modelNode.addObject('GenericConstraintCorrection', linearSolver='@solver')
 
     FixedBox(
         atPositions=[-15, -15, -40,  15, 15, 10],
         applyTo=modelNode,
-        doVisualization=True)       
+        doVisualization=True)
 
     for i in range(len(actuatorsParam)):
-        cable = PullingCable(
-                    attachedTo=modelNode,
-                    name=actuatorsParam[i]['withName'],
-                    cableGeometry=actuatorsParam[i]['withCableGeometry'],
-                    pullPointLocation=actuatorsParam[i]['withAPullPointLocation'],
-                    valueType="displacement")
+        PullingCable(
+            attachedTo=modelNode,
+            name=actuatorsParam[i]['withName'],
+            cableGeometry=actuatorsParam[i]['withCableGeometry'],
+            pullPointLocation=actuatorsParam[i]['withAPullPointLocation'],
+            valueType="displacement")
 
     return rootNode

tools/sofa_test_scene/diamondRobotWithPrefab.py

@@ -0,0 +1,91 @@
+# -*- coding: utf-8 -*-
+import sys
+import os
+
+#   STLIB IMPORT
+from stlib3.scene import MainHeader
+from stlib3.physics.constraints import FixedBox
+from stlib3.physics.deformable import ElasticMaterialObject
+
+# SOFTROBOTS IMPORT
+from softrobots.actuators import PullingCable
+
+actuatorsParam = [
+        {'withName' : 'nord',
+         'withCableGeometry' : [[0, 97, 45]],
+         'withAPullPointLocation' : [0, 10, 30]
+        },
+        {'withName' : 'ouest',
+         'withCableGeometry' : [[-97, 0, 45]],
+         'withAPullPointLocation' : [-10, 0, 30]
+        },
+        {'withName' : 'sud',
+         'withCableGeometry' : [[0, -97, 45]],
+         'withAPullPointLocation' : [0, -10, 30]
+        },
+        {'withName' : 'est',
+         'withCableGeometry' : [[97, 0, 45]],
+         'withAPullPointLocation' : [10, 0, 30]
+        }
+    ]
+
+plugins=["SofaPython3","SoftRobots","ModelOrderReduction","STLIB",
+         # normally plugin Sofa.Component is enough but still warning
+         "Sofa.Component.Visual",
+         "Sofa.Component.AnimationLoop",
+         "Sofa.GL.Component.Rendering3D",
+         "Sofa.Component.Constraint.Lagrangian.Solver",
+         'Sofa.Component.IO.Mesh',
+         'Sofa.Component.Playback',
+         'Sofa.Component.Constraint.Lagrangian.Correction', # Needed to use components [GenericConstraintCorrection]
+         'Sofa.Component.Engine.Select', # Needed to use components [BoxROI]
+         'Sofa.Component.LinearSolver.Direct', # Needed to use components [SparseLDLSolver]
+         'Sofa.Component.Mapping.Linear', # Needed to use components [BarycentricMapping]
+         'Sofa.Component.Mass', # Needed to use components [UniformMass]
+         'Sofa.Component.ODESolver.Backward', # Needed to use components [EulerImplicitSolver]
+         'Sofa.Component.SolidMechanics.FEM.Elastic', # Needed to use components [TetrahedronFEMForceField]
+         'Sofa.Component.SolidMechanics.Spring', # Needed to use components [RestShapeSpringsForceField]
+         'Sofa.Component.StateContainer', # Needed to use components [MechanicalObject]
+         'Sofa.Component.Topology.Container.Dynamic'] # Needed to use components [TetrahedronSetTopologyContainer]
+
+meshPath = os.path.dirname(os.path.abspath(__file__))+'/mesh/'
+
+def createScene(rootNode):
+
+    MainHeader(rootNode,plugins=plugins,
+               dt=1.0,
+               gravity=[0.0, 0.0, -9810.0])
+
+    # not in Mainheader anymore, need some update
+    rootNode.addObject('FreeMotionAnimationLoop')
+    rootNode.addObject('GenericConstraintSolver', tolerance="1e-6", maxIterations="1000")
+    rootNode.VisualStyle.displayFlags = 'showVisualModels showForceFields'
+    # -------------------------------------------
+
+    modelNode = ElasticMaterialObject(
+        parent=rootNode,
+        volumeMeshFileName=meshPath+'siliconeV0.vtu',
+        name='modelNode',
+        rotation=[90, 0.0, 0.0],
+        translation=[0.0, 0.0, 35],
+        totalMass=0.5,
+        withConstrain=False,
+        surfaceMeshFileName=meshPath+'surface.stl',
+        surfaceColor=[0.7, 0.7, 0.7, 0.7],
+        poissonRatio=0.45,
+        youngModulus=450)
+
+    FixedBox(
+        atPositions=[-15, -15, -40,  15, 15, 10],
+        applyTo=modelNode,
+        doVisualization=True)
+
+    for i in range(len(actuatorsParam)):
+        PullingCable(
+            attachedTo=modelNode,
+            name=actuatorsParam[i]['withName'],
+            cableGeometry=actuatorsParam[i]['withCableGeometry'],
+            pullPointLocation=actuatorsParam[i]['withAPullPointLocation'],
+            valueType="displacement")
+
+    return rootNode

tools/sofa_test_scene/quadruped.py

@@ -63,7 +63,7 @@ def createScene(rootNode):
     model.addObject('BoxROI', name='boxROISubTopo', box='0 0 0 150 -100 1', drawBoxes='true')
     model.addObject('BoxROI', name='membraneROISubTopo', box='0 0 -0.1 150 -100 0.1', computeTetrahedra="false",
                        drawBoxes='true')
-    model.addObject('GenericConstraintCorrection', solverName='preconditioner')
+    model.addObject('GenericConstraintCorrection', linearSolver='@preconditioner')
     ##########################################
     # Sub topology
     modelSubTopo = model.addChild('modelSubTopo')