[scenes] Try to fix SOFA dashboard (#138)

* [scenes] Try to fix SOFA dashboard

* clean liver examples

* fix path for bouncingBall

* Fix caduceus reduced version

* Try to fix softrobots scenes...

* Update reduced_diamondRobotHyperElastic.py

* Update sofiaSixLegs.py

* Disable sofiaSixLegs on ci, too many errors

examples/.scene-tests

@@ -1,18 +1,16 @@
 # Scenes to reduce are too heavy and slow to be simulated, so compute only a few iterations
 
-# Organs
-iterations "organs/liver/liverFine.pyscn" "10"
-timeout "organs/liver/liverFine.pyscn" "120"
-
+# Organs/liver
+# Original scenes are tested with timout. Reduced versions and debug scenes are tested
 iterations "organs/liver/liverFineHyperElastic.pyscn" "10"
 timeout "organs/liver/liverFineHyperElastic.pyscn" "120"
 
-iterations "organs/liver/liverFine_rotationalActuation.py" "10"
-timeout "organs/liver/liverFine_rotationalActuation.py" "120"
-
 iterations "organs/liver/liverFine_gravity.py" "10"
 timeout "organs/liver/liverFine_gravity.py" "120"
 
+iterations "organs/liver/liverFine_rotationalActuation.py" "10"
+timeout "organs/liver/liverFine_rotationalActuation.py" "120"
+
 
 # Others
 iterations "others/caduceus/SphereOnAPlane.softSphereFalling.pyscn" "10"
@@ -31,3 +29,6 @@ timeout "softRobots/multiGait/reduced/reduced_multiGait.py" "120"
 
 ignore "softRobots/multiGait/reducedMultiGait-softRobot.pyscn" # TODO fix: MechanicalMatrixMapperMOR is missing 
 ignore "softRobots/multiGait/reduced/debug/debug_scene.py" # TODO fix: ODE solver is not copied during reduction process
+
+ignore "softRobots/sofiaLeg/sofiaComplete/sofiaSixLegs.py" # TODO fix: many errors in the scripts, methods signature changed, SOFA scene using old SofaPython API
+ignore "softRobots/sofiaLeg/sofiaComplete/DemoSofia.py" # TODO fix: depends on sofiaSixLegs.py . Should be fixed if sofiaSixLegs.py is working

examples/bouncingBall/softSphereFalling.py

@@ -5,14 +5,38 @@
 pathMesh = os.path.dirname(os.path.abspath(__file__))+'/'
 # Units: mm, kg, s.     Pressure in kPa = k (kg/(m.s^2)) = k (g/(mm.s^2) =  kg/(mm.s^2)
 
+plugins=['SofaPython3',
+         'Sofa.Component.Collision.Detection.Algorithm',
+         'Sofa.Component.Visual',
+         'Sofa.Component.AnimationLoop',
+         'Sofa.Component.Collision.Detection.Intersection',
+         'Sofa.Component.Collision.Geometry',
+         'Sofa.Component.Collision.Response.Contact',
+         'Sofa.Component.Constraint.Lagrangian.Correction',
+         'Sofa.Component.Constraint.Lagrangian.Solver',
+         'Sofa.Component.IO.Mesh',
+         'Sofa.Component.LinearSolver.Direct',
+         'Sofa.Component.Mapping.Linear',
+         'Sofa.Component.Mass',
+         'Sofa.Component.ODESolver.Backward',
+         'Sofa.Component.SolidMechanics.FEM.Elastic',
+         'Sofa.Component.StateContainer',
+         'Sofa.Component.Topology.Container.Constant',
+         'Sofa.Component.Topology.Container.Dynamic',
+         'Sofa.Component.Visual',
+         'Sofa.GL.Component.Rendering3D'
+        ]
+
 def createScene(rootNode):
+                rootNode.addObject('RequiredPlugin', pluginName=plugins, printLog=False)
+
                 rootNode.addObject('VisualStyle', displayFlags='showVisualModels hideBehaviorModels showCollisionModels hideBoundingCollisionModels showForceFields showInteractionForceFields hideWireframe')
                 rootNode.gravity=[0,-9810, 0]
                 rootNode.dt = 0.0001
                 rootNode.addObject('FreeMotionAnimationLoop')
                 rootNode.addObject('GenericConstraintSolver', name='GSSolver', maxIterations='10000', tolerance='1e-15')
-                rootNode.addObject('CollisionPipeline', verbose="0")
-                rootNode.addObject('BruteForceBroadPhase', name="N2")
+                rootNode.addObject('CollisionPipeline', verbose='0')
+                rootNode.addObject('BruteForceBroadPhase', name='N2')
                 rootNode.addObject('BVHNarrowPhase')
                 rootNode.addObject('CollisionResponse', response="FrictionContactConstraint", responseParams="mu=0.0")
                 rootNode.addObject('LocalMinDistance', name="Proximity", alarmDistance="8.0", contactDistance="0.5", angleCone="0.01")
@@ -29,7 +53,7 @@ def createScene(rootNode):
                 sphereTranslation = [0,10,0]
                 model = solverNode.addChild('model')
                 model.addObject('MeshVTKLoader', name='loader', filename=pathMesh+'sphere.vtk', translation=sphereTranslation)
-                model.addObject('Mesh',src = '@loader')
+                model.addObject('MeshTopology',src = '@loader')
                 model.addObject('MechanicalObject', name='tetras', template='Vec3d', showIndices='false', showIndicesScale='4e-5', rx='0',printLog="0")
 #                model.addObject('WriteState', name="StateWriter", filename="fullBall.state",period="0.001", writeX=True, writeX0=True, writeV=False, writeF=False, time=0)
                 model.addObject('UniformMass', totalMass='0.2', printLog='0')
@@ -48,13 +72,14 @@ def createScene(rootNode):
                 rotation=[0,0,0]
                 #rotation=[30,0,0]
                 planeNode = rootNode.addChild('Plane')
-                planeNode.addObject('MeshObjLoader', name='loader', filename="mesh/floorFlat.obj", triangulate="true",rotation=rotation)
-                planeNode.addObject('Mesh', src="@loader")
+                planeNode.addObject('MeshOBJLoader', name='loader', filename="mesh/floorFlat.obj", triangulate="true", rotation=rotation)
+                planeNode.addObject('MeshTopology', src="@loader")
                 planeNode.addObject('MechanicalObject', src="@loader", rotation="0 0 0", translation="0 0 0", scale="1")
                 planeNode.addObject('TriangleCollisionModel',simulated="0", moving="0",group="1",name='TriPlane')
                 planeNode.addObject('LineCollisionModel',simulated="0", moving="0",group="1")
                 planeNode.addObject('PointCollisionModel',simulated="0", moving="0",group="1")
-                planeNode.addObject('OglModel',name="Visual", fileMesh="mesh/floorFlat.obj", color="1 0 0 1",rotation=rotation, translation="0 0 0", scale="1")
-                planeNode.addObject('UncoupledConstraintCorrection')
+                planeNode.addObject('OglModel',name="Visual", src="@loader", color="1 0 0 1", rotation=rotation, translation="0 0 0", scale="1")
 
                 return rootNode
+
+

examples/bouncingBall/softSphereFalling_reduced.py

@@ -5,12 +5,17 @@
 pathMesh = os.path.dirname(os.path.abspath(__file__))+'/'
 nbrOfModes = 15
 # Units: mm, kg, s.     Pressure in kPa = k (kg/(m.s^2)) = k (g/(mm.s^2) =  kg/(mm.s^2)
-plugins=["SofaPython3","SoftRobots","ModelOrderReduction","STLIB",
+plugins=['SofaPython3','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.Visual',
+         'Sofa.Component.AnimationLoop',
+         'Sofa.GL.Component.Rendering3D',
+         'Sofa.Component.Constraint.Lagrangian.Solver',
+         'Sofa.Component.Collision.Detection.Algorithm',
+         'Sofa.Component.Collision.Detection.Intersection',
+         'Sofa.Component.Collision.Geometry',
+         'Sofa.Component.Collision.Response.Contact',
+         'Sofa.Component.Topology.Container.Constant',
          'Sofa.Component.IO.Mesh',
          'Sofa.Component.Playback',
          'Sofa.Component.Constraint.Lagrangian.Correction', # Needed to use components [GenericConstraintCorrection]
@@ -24,6 +29,7 @@
          'Sofa.Component.StateContainer', # Needed to use components [MechanicalObject]
          'Sofa.Component.Topology.Container.Dynamic'] # Needed to use components [TetrahedronSetTopologyContainer]
 
+
 def createScene(rootNode):
 
                 rootNode.addObject('RequiredPlugin', pluginName=plugins, printLog=False)
@@ -54,15 +60,15 @@ def createScene(rootNode):
 
                 model = modesNode.addChild('model')
                 model.addObject('MeshVTKLoader', name='loader', filename=pathMesh+'sphere.vtk', translation=sphereTranslation)
-                model.addObject('Mesh',src = '@loader')
+                model.addObject('MeshTopology',src = '@loader')
                 model.addObject('MechanicalObject', name='tetras', template='Vec3d', showIndices='false', showIndicesScale='4e-5', rx='0',printLog="0")
 #                model.addObject('WriteState', name="StateWriter", filename="fullBall.state",period="0.001", writeX=True, writeX0=True, writeV=False, writeF=False, time=0)
                 model.addObject('UniformMass', totalMass='0.2', printLog='0')
 #                model.addObject('TetrahedronFEMForceField', template='Vec3d',youngModulus=1.0e3,poissonRatio=0.45)
 #                model.addObject('HyperReducedTetrahedronFEMForceField' , template = 'Vec3', method = 'large', name = 'reducedFF_modelNode_0', poissonRatio = 0.45, youngModulus = 1.0e3, nbModes = nbrOfModes, prepareECSW = True, performECSW = False, modesPath = 'modes.txt',nbTrainingSet=100,periodSaveGIE=10)
-                model.addObject('HyperReducedTetrahedronFEMForceField' , template = 'Vec3', method = 'large', name = 'reducedFF_modelNode_0', poissonRatio = 0.45, youngModulus = 1.0e3, nbModes = nbrOfModes, prepareECSW = False, performECSW = True, modesPath = 'modes.txt', RIDPath='RID.txt',weightsPath='weights.txt')
+                model.addObject('HyperReducedTetrahedronFEMForceField' , template = 'Vec3', method = 'large', name = 'reducedFF_modelNode_0', poissonRatio = 0.45, youngModulus = 1.0e3, nbModes = nbrOfModes, prepareECSW = False, performECSW = True, modesPath = pathMesh + 'modes.txt', RIDPath = pathMesh + 'RID.txt', weightsPath = pathMesh + 'weights.txt')
 
-                model.addObject('ModelOrderReductionMapping' , input = '@../modes', modesPath = 'modes.txt', output = '@./tetras')
+                model.addObject('ModelOrderReductionMapping' , input = '@../modes', modesPath = pathMesh + 'modes.txt', output = '@./tetras')
 
                 modelCollis = model.addChild('modelCollis')
                 modelCollis.addObject('MeshSTLLoader', name='loader', filename=pathMesh+'sphere.stl', rotation="0 0 0", translation=sphereTranslation)
@@ -77,13 +83,12 @@ def createScene(rootNode):
                 rotation=[0,0,0]
                 #rotation=[30,0,0]
                 planeNode = rootNode.addChild('Plane')
-                planeNode.addObject('MeshObjLoader', name='loader', filename="mesh/floorFlat.obj", triangulate="true",rotation=rotation)
-                planeNode.addObject('Mesh', src="@loader")
+                planeNode.addObject('MeshOBJLoader', name='loader', filename="mesh/floorFlat.obj", triangulate="true", rotation=rotation)
+                planeNode.addObject('MeshTopology', src="@loader")
                 planeNode.addObject('MechanicalObject', src="@loader", rotation="0 0 0", translation="0 0 0", scale="1")
                 planeNode.addObject('TriangleCollisionModel',simulated="0", moving="0",group="1",name='TriPlane')
                 planeNode.addObject('LineCollisionModel',simulated="0", moving="0",group="1")
                 planeNode.addObject('PointCollisionModel',simulated="0", moving="0",group="1")
-                planeNode.addObject('OglModel',name="Visual", fileMesh="mesh/floorFlat.obj", color="1 0 0 1",rotation=rotation, translation="0 0 0", scale="1")
-                planeNode.addObject('UncoupledConstraintCorrection')
+                planeNode.addObject('OglModel',name="Visual", src="@loader", color="1 0 0 1", rotation=rotation, translation="0 0 0", scale="1")
 
                 return rootNode

examples/organs/liver/liverFine_gravity.py

@@ -4,7 +4,7 @@
 
 meshPath = os.path.dirname(os.path.abspath(__file__))+'/mesh/'
 
-plugins=["SofaPython3","SoftRobots","ModelOrderReduction","STLIB",
+plugins=["SofaPython3","ModelOrderReduction","STLIB",
 
          "Sofa.Component.Visual",
          "Sofa.Component.AnimationLoop",

examples/organs/liver/liverFine_rotationalActuation.py

@@ -4,7 +4,7 @@
 
 meshPath = os.path.dirname(os.path.abspath(__file__))+'/mesh/'
 
-plugins=["SofaPython3","SoftRobots","ModelOrderReduction","STLIB",
+plugins=["SofaPython3","ModelOrderReduction","STLIB",
 
          "Sofa.Component.Visual",
          "Sofa.Component.AnimationLoop",

examples/organs/liver/reduced/liver/debug/debug_scene.py

@@ -19,7 +19,7 @@
     slash = "\\"
 
 # Our Original Scene IMPORT
-originalScene = os.path.dirname(os.path.abspath(__file__)) + "/../../../liverFine.pyscn"
+originalScene = os.path.dirname(os.path.abspath(__file__)) + "/../../../liverFine_gravity.py"
 originalScene = os.path.normpath(originalScene)
 originalScene = imp.load_source(originalScene.split(slash)[-1], originalScene)
 

examples/organs/liver/reduced/liver/reduced_liverFine.py

@@ -99,7 +99,7 @@ def Reduced_test(
 def createScene(rootNode):
     surfaceMeshFileName = False
 
-    MainHeader(rootNode,plugins=["SoftRobots","ModelOrderReduction"],
+    MainHeader(rootNode,plugins=["ModelOrderReduction"],
                         dt=0.01,
                         gravity=[0.0, -981.0, 0.0])
     rootNode.VisualStyle.displayFlags="showForceFields"

examples/organs/liver/reduced/liver_hyperElastic/reduced_liverFineHyperElastic.py

@@ -99,7 +99,7 @@ def Reduced_test(
 def createScene(rootNode):
     surfaceMeshFileName = False
 
-    MainHeader(rootNode,plugins=["SoftRobots","ModelOrderReduction"],
+    MainHeader(rootNode,plugins=["ModelOrderReduction"],
                         dt=0.01,
                         gravity=[0.0, -981.0, 0.0])
     rootNode.VisualStyle.displayFlags="showForceFields"

examples/others/caduceus/caduceusNG.pyscn

@@ -11,7 +11,6 @@ def createScene(rootNode):
     rootNode.addObject('VisualStyle', displayFlags='showBehaviorModels showForceFields')
 
     rootNode.addObject('RequiredPlugin', name='ModelOrderReduction')
-    rootNode.addObject('RequiredPlugin', name='SoftRobots')
     rootNode.addObject('RequiredPlugin', name='Sofa.Component.AnimationLoop') # Needed to use components [FreeMotionAnimationLoop]  
     rootNode.addObject('RequiredPlugin', name='Sofa.Component.Collision.Detection.Algorithm') # Needed to use components [BVHNarrowPhase,BruteForceBroadPhase,CollisionPipeline]  
     rootNode.addObject('RequiredPlugin', name='Sofa.Component.Collision.Detection.Intersection') # Needed to use components [LocalMinDistance]  

examples/others/caduceus/reduced/reduced_caduceusNG.py

@@ -106,6 +106,36 @@ def Reduced_test(
     VisualEye.addObject('OglModel' , name = 'VisualEye', src = '@loader', translation = [0, 5, 0])
     VisualEye.addObject('BarycentricMapping')
 
+
+    base = modelRoot.addChild("base")
+
+    stick = base.addChild("stick")
+    stick.addObject('MeshOBJLoader',name="loader", filename="mesh/collision_batons.obj")
+    stick.addObject('MeshTopology', src='@loader', name='topo')
+    stick.addObject('MechanicalObject', name='stickCollisModel')
+    stick.addObject('LineCollisionModel',simulated="false", moving="false")
+    stick.addObject('PointCollisionModel',simulated="false", moving="false")
+
+    blobs = base.addChild("blobs")
+    blobs.addObject('MeshOBJLoader',name="loader", filename="mesh/collision_boules_V3.obj")
+    blobs.addObject('MeshTopology', src='@loader', name='topo')
+    blobs.addObject('MechanicalObject', name='blobsCollisModel')
+    blobs.addObject('TriangleCollisionModel',simulated="false", moving="false")
+    blobs.addObject('LineCollisionModel',simulated="false", moving="false")
+    blobs.addObject('PointCollisionModel',simulated="false", moving="false")
+
+    foot = base.addChild("foot")
+    foot.addObject('MeshOBJLoader',name="loader", filename="mesh/collision_pied.obj")
+    foot.addObject('MeshTopology', src='@loader', name='topo')
+    foot.addObject('MechanicalObject', name='footCollisModel')
+    foot.addObject('TriangleCollisionModel',simulated="false", moving="false")
+    foot.addObject('LineCollisionModel',simulated="false", moving="false")
+    foot.addObject('PointCollisionModel',simulated="false", moving="false")
+
+    visu = base.addChild("visu")
+    visu.addObject('MeshOBJLoader', name="SOFA_pod", filename="mesh/SOFA_pod.obj", handleSeams="1" )
+    visu.addObject('OglModel' , src = '@SOFA_pod', name = 'VisuPOD',color=[1,69.0/255.0,0])
+
     return Snake
 
 
@@ -114,11 +144,19 @@ def Reduced_test(
 def createScene(rootNode):
     surfaceMeshFileName = False
 
-    MainHeader(rootNode,plugins=["SoftRobots","ModelOrderReduction"],
+    MainHeader(rootNode,plugins=["ModelOrderReduction"],
                         dt=0.02,
                         gravity=[0.0, -981.0, 0.0])
     rootNode.VisualStyle.displayFlags="showForceFields"
 
+    rootNode.addObject('FreeMotionAnimationLoop')
+    rootNode.addObject('GenericConstraintSolver', printLog='0', tolerance="1e-6", maxIterations="500")
+    rootNode.addObject('CollisionPipeline', verbose="0")
+    rootNode.addObject('BruteForceBroadPhase', name="N2")
+    rootNode.addObject('BVHNarrowPhase')
+    rootNode.addObject('CollisionResponse', response="FrictionContactConstraint", responseParams="mu=0.7")
+    rootNode.addObject('LocalMinDistance', name="Proximity", alarmDistance="2.5", contactDistance="0.1", angleCone="0.05")
+
     Reduced_test(rootNode,
                         name="Reduced_test",
                         surfaceMeshFileName=surfaceMeshFileName)