Merge branch 'master' into update_python_prefabs

examples/python3/NeedleInsertion.py

@@ -9,7 +9,7 @@
 from cosserat.usefulFunctions import pluginList
 from cosserat.createFemRegularGrid import createFemCubeWithParams
 from cosserat.cosseratObject import Cosserat
-from cosserat.utils import addConstraintPoint
+from useful.utils import addConstraintPoint
 import sys
 
 # params = NeedleParameters()
@@ -57,10 +57,9 @@ def createScene(rootNode):
     solverNode.addObject('SparseLDLSolver', name='solver', template="CompressedRowSparseMatrixd")
     solverNode.addObject('GenericConstraintCorrection')
 
-    needle = solverNode.addChild(
-        Cosserat(parent=solverNode, cosseratGeometry=needleGeometryConfig, radius=GeometryParams.radius,
-                 name="needle", youngModulus=PhysicsParams.youngModulus, poissonRatio=PhysicsParams.poissonRatio,
-                 rayleighStiffness=PhysicsParams.rayleighStiffness))
+    needle = Cosserat(parent=solverNode, cosseratGeometry=needleGeometryConfig, radius=GeometryParams.radius,
+        name="needle", youngModulus=PhysicsParams.youngModulus, poissonRatio=PhysicsParams.poissonRatio,
+        rayleighStiffness=PhysicsParams.rayleighStiffness)
     needleCollisionModel = needle.addPointCollisionModel("needleCollision")
 
     # These state is mapped on the needle and used to compute the distance between the needle and the

examples/python3/PCS_Example2.py

@@ -52,11 +52,11 @@ def __init__(self, *args, **kwargs):
             position = self.frames.position[self.size]  # get the last rigid of the cosserat frame
             orientation = Quat(position[3], position[4], position[5], position[6])  # get the orientation
             # Get the force direction in order to remain orthogonal to the last section of beam
-            with self.forceNode.force.writeable() as force:
+            with self.forceNode.forces.writeable() as force:
                 vec = orientation.rotate([0., self.forceCoeff, 0.])
                 # print(f' The new vec is : {vec}')
                 for count in range(3):
-                    force[count] = vec[count]
+                    force[0][count] = vec[count]
             if self.forceCoeff < 13.1e4:
                 self.forceCoeff += 100
             else:
@@ -88,15 +88,14 @@ def createScene(rootNode):
     solverNode.addObject('SparseLDLSolver', name='solver', template="CompressedRowSparseMatrixd")
 
     needCollisionModel = 0  # use this if the collision model if the beam will interact with another object
-    PCS_Cosserat = solverNode.addChild(
-        Cosserat(parent=solverNode, cosseratGeometry=nonLinearConfig, useCollisionModel=needCollisionModel,
-                 inertialParams=inertialParams, name="cosserat", radius=Rb, youngModulus=YM))
+    PCS_Cosserat = Cosserat(parent=solverNode, cosseratGeometry=nonLinearConfig, useCollisionModel=needCollisionModel,
+                 inertialParams=inertialParams, name="cosserat", radius=Rb, youngModulus=YM, showObject="1")
 
     beamFrame = PCS_Cosserat.cosseratFrame
 
     constForce = beamFrame.addObject('ConstantForceField', name='constForce', showArrowSize=0.0,
-                        indices=nonLinearConfig['nbFramesF'], force=F1)
+                        indices=nonLinearConfig['nbFramesF'], forces=F1)
 
-    solverNode.addObject(ForceController(parent=solverNode, cosseratFrames=beamFrame.FramesMO, forceNode=constForce))
+    solverNode.addObject(ForceController(parent=solverNode, name='forceController', cosseratFrames=beamFrame.FramesMO, forceNode=constForce))
 
     return rootNode

examples/python3/wip/PCS_Example3.py → examples/python3/PCS_Example3.py

@@ -11,15 +11,13 @@
 
 import Sofa
 from cosserat.cosseratObject import Cosserat
-# from cosserat.nonLinearCosserat import NonLinearCosserat as nonCosserat
 from cosserat.usefulFunctions import buildEdges, pluginList, BuildCosseratGeometry
 from math import sqrt
 
 # @todo ================ Unit: N, m, Kg, Pa  ================
 from splib3.numerics import Quat
 
 LegendrePolyOrder = 5
-# initialStrain = [[0., 0., 0], [0., 0., 0], [0., 0., 0]]
 initialStrain = [[0., 0., 0], [0., 0., 0],
                  [0., 0., 0], [0., 0., 0], [0., 0., 0]]
 YM = 4.015e8
@@ -52,11 +50,10 @@ def onAnimateEndEvent(self, event):
             orientation = Quat(
                 position[3], position[4], position[5], position[6])
             # Get the force direction in order to remain orthogonal to the last section of beam
-            with self.forceNode.force.writeable() as force:
+            with self.forceNode.forces.writeable() as force:
                 vec = orientation.rotate([0., self.forceCoeff, 0.])
-                # print(f' The new vec is : {vec}')
                 for count in range(3):
-                    force[count] = vec[count]
+                    force[0][count] = vec[count]
 
     def onKeypressedEvent(self, event):
         key = event['key']
@@ -91,12 +88,12 @@ def createScene(rootNode):
         Cosserat(parent=solverNode, cosseratGeometry=nonLinearConfig, useCollisionModel=needCollisionModel,
                  inertialParams=inertialParams, name="cosserat", radius=Rb, youngModulus=YM))
 
-    beamFrame = nonLinearCosserat.cosseratFrame
+    beamFrame = PCS_Cosserat.cosseratFrame
 
     constForce = beamFrame.addObject('ConstantForceField', name='constForce', showArrowSize=0.02,
-                                     indices=nonLinearConfig['nbFramesF'], force=F1)
+                                     indices=nonLinearConfig['nbFramesF'], forces=F1)
 
-    nonLinearCosserat = solverNode.addObject(
+    solverNode.addObject(
         ForceController(parent=solverNode, cosseratFrames=beamFrame.FramesMO, forceNode=constForce))
 
     # ----------------

examples/python3/PNLS_Example1.py

@@ -52,10 +52,10 @@ def __init__(self, *args, **kwargs):
 
     def onAnimateEndEvent(self, event):
         if self.applyForce:
-            with self.forceNode.force.writeable() as force:
+            with self.forceNode.forces.writeable() as force:
                 vec = [0., 0., 0., 0., (self.forceCoeff * 1.) / sqrt(2), (self.forceCoeff * 1.) / sqrt(2)]
                 for i, v in enumerate(vec):
-                    force[i] = v
+                    force[0][i] = v
                 # print(f' The new force: {force}')
 
     def onKeypressedEvent(self, event):
@@ -85,18 +85,17 @@ def createScene(rootNode):
     solverNode.addObject('SparseLDLSolver', name='solver', template="CompressedRowSparseMatrixd")
 
     needCollisionModel = 0  # use this if the collision model if the beam will interact with another object
-    nonLinearCosserat = solverNode.addChild(
-        nonCosserat(parent=solverNode, cosseratGeometry=nonLinearConfig, inertialParams=inertialParams,
+    nonLinearCosserat = nonCosserat(parent=solverNode, cosseratGeometry=nonLinearConfig, inertialParams=inertialParams,
                     useCollisionModel=needCollisionModel, name="cosserat", radius=Rb, youngModulus=YM,
                     legendreControlPoints=initialStrain, poissonRatio=PR,order=LegendrePolyOrder,
                     rayleighStiffness=rayleighStiffness,
-                    activatedMMM=False))
+                    activatedMMM=False)
     cosseratNode = nonLinearCosserat.legendreControlPointsNode
 
     beamFrame = nonLinearCosserat.cosseratFrame
 
     constForce = beamFrame.addObject('ConstantForceField', name='constForce', showArrowSize=1.e-8,
-                        indices=nonLinearConfig['nbFramesF'], force=F1)
+                        indices=nonLinearConfig['nbFramesF'], forces=F1)
 
     nonLinearCosserat = solverNode.addObject(
         ForceController(parent=solverNode, cosseratFrames=beamFrame.FramesMO, forceNode=constForce))

examples/python3/PNLS_Example2.py

@@ -52,11 +52,11 @@ def onAnimateEndEvent(self, event):
             position = self.frames.position[self.size]  # get the last rigid of the cosserat frame
             orientation = Quat(position[3], position[4], position[5], position[6])  # get the orientation
             # Get the force direction in order to remain orthogonal to the last section of beam
-            with self.forceNode.force.writeable() as force:
+            with self.forceNode.forces.writeable() as force:
                 vec = orientation.rotate([0., self.forceCoeff, 0.])
                 # print(f' The new vec is : {vec}')
                 for count in range(3):
-                    force[count] = vec[count]
+                    force[0][count] = vec[count]
             if self.forceCoeff < 13.1e4:
                 self.forceCoeff += 100
             else:
@@ -87,17 +87,16 @@ def createScene(rootNode):
     solverNode.addObject('SparseLDLSolver', name='solver', template="CompressedRowSparseMatrixd")
 
     needCollisionModel = 0  # use this if the collision model if the beam will interact with another object
-    nonLinearCosserat = solverNode.addChild(
-        nonCosserat(parent=solverNode, cosseratGeometry=nonLinearConfig, useCollisionModel=needCollisionModel,
+    nonLinearCosserat = nonCosserat(parent=solverNode, cosseratGeometry=nonLinearConfig, useCollisionModel=needCollisionModel,
                     name="cosserat", radius=Rb, youngModulus=YM, legendreControlPoints=initialStrain,
                     order=LegendrePolyOrder, inertialParams=inertialParams,
-                    activatedMMM=True))
+                    activatedMMM=True, showObject="1")
     cosseratNode = nonLinearCosserat.legendreControlPointsNode
 
     beamFrame = nonLinearCosserat.cosseratFrame
 
     constForce = beamFrame.addObject('ConstantForceField', name='constForce', showArrowSize=1.e-5,
-                                     indices=nonLinearConfig['nbFramesF'], force=F1)
+                                     indices=nonLinearConfig['nbFramesF'], forces=F1)
 
     nonLinearCosserat = solverNode.addObject(
         ForceController(parent=solverNode, cosseratFrames=beamFrame.FramesMO, forceNode=constForce))

examples/python3/PNLS_Example3.py

@@ -124,7 +124,7 @@ def createScene(rootNode):
     cosseratNode = nonLinearCosserat.legendreControlPointsNode
 
     constForce = beamFrame.addObject('ConstantForceField', name='constForce', showArrowSize=1.e-9,
-                        indices=nonLinearConfig['nbFramesF'], force=F1)
+                        indices=nonLinearConfig['nbFramesF'], forces=F1)
 
     nonLinearCosserat = solverNode.addObject(
         ForceController(parent=solverNode, cosseratFrames=beamFrame.FramesMO, controller=controlMo))

examples/python3/cosserat/cosseratObject.py

@@ -348,10 +348,7 @@ def createScene(rootNode):
     rootNode.addObject(
         "RequiredPlugin",
         name="plugins",
-        pluginName=[
-            pluginList,
-            ["SofaEngine", "SofaLoader", "SofaSimpleFem", "SofaExporter"],
-        ],
+        pluginName=pluginList,
     )
     rootNode.addObject(
         "VisualStyle",
@@ -376,13 +373,11 @@ def createScene(rootNode):
     )
     solverNode.addObject("GenericConstraintCorrection")
 
-    cosserat = solverNode.addChild(
-        Cosserat(
-            parent=solverNode,
-            cosseratGeometry=cosserat_config,
-            name="cosserat",
-            radius=0.15,
-        )
+    cosserat = Cosserat(
+        parent=solverNode,
+        cosseratGeometry=cosserat_config,
+        name="cosserat",
+        radius=0.15,
     )
 
     # use this to add the collision if the beam will interact with another object

examples/python3/cosserat/needle/needleController.py

@@ -10,7 +10,7 @@
 import Sofa
 import Cosserat
 from cosserat.needle.params import ConstraintsParams
-from cosserat.utils import computePositiveAlongXDistanceBetweenPoints, computeNegativeAlongXDistanceBetweenPoints
+from useful.utils import computePositiveAlongXDistanceBetweenPoints, computeNegativeAlongXDistanceBetweenPoints
 
 
 class Animation(Sofa.Core.Controller):

examples/python3/cosserat/nonLinearCosserat.py

@@ -51,7 +51,7 @@ class NonLinearCosserat(Sofa.Prefab):
                     Cosserat Mapping  //  it allow the transfer from the local to the global frame
             }
     """
-    properties = [
+    prefabParameters = [
         {'name': 'name', 'type': 'string', 'help': 'Node name', 'default': 'Cosserat'},
         {'name': 'position', 'type': 'Rigid3d::VecCoord', 'help': 'Cosserat base position',
          'default': [[0., 0., 0., 0, 0, 0, 1.]]},
@@ -67,7 +67,7 @@ class NonLinearCosserat(Sofa.Prefab):
          'default': 0.0},
         {'name': 'attachingToLink', 'type': 'string', 'help': 'a rest shape force field will constraint the object '
                                                               'to follow arm position', 'default': '1'},
-        {'name': 'showObject', 'type': 'string', 'help': ' Draw object arrow ', 'default': '0'}]
+        {'name': 'showObject', 'type': 'string', 'help': ' Draw object arrow ', 'default': '1'}]
 
     def __init__(self, *args, **kwargs):
         Sofa.Prefab.__init__(self, *args, **kwargs)
@@ -193,11 +193,11 @@ def addCosseratFrame(self, framesF, curv_abs_inputS, curv_abs_outputF):
 
 def createScene(rootNode):
     rootNode.addObject('RequiredPlugin', name='plugins', pluginName=[pluginList,
-                                                                     ['SofaEngine', 'SofaLoader', 'SofaSimpleFem',
-                                                                      'SofaExporter']])
+                                                                     ['Sofa.Component.Visual']])
     rootNode.addObject('VisualStyle', displayFlags='showVisualModels showBehaviorModels hideCollisionModels '
-                                                   'hideBoundingCollisionModels hireForceFields '
+                                                   'hideBoundingCollisionModels hideForceFields '
                                                    'hideInteractionForceFields hideWireframe')
+    rootNode.addObject('DefaultAnimationLoop')
     rootNode.findData('dt').value = 0.01
     # rootNode.findData('gravity').value = [0., -9.81, 0.]
     rootNode.findData('gravity').value = [0., 0., 0.]
@@ -213,12 +213,11 @@ def createScene(rootNode):
     # solverNode.addObject('CGLinearSolver', tolerance=1.e-12, iterations=1000, threshold=1.e-18)
 
     needCollisionModel = 0  # use this if the collision model if the beam will interact with another object
-    nonLinearCosserat = solverNode.addChild(
-        NonLinearCosserat(parent=solverNode, cosseratGeometry=nonLinearConfig, useCollisionModel=needCollisionModel,
-                          name="cosserat", radius=0.1, legendreControlPoints=initialStrain, order=3))
+    nonLinearCosserat = NonLinearCosserat(parent=solverNode, cosseratGeometry=nonLinearConfig,
+        useCollisionModel=needCollisionModel, name="cosserat", radius=0.1, legendreControlPoints=initialStrain, order=3)
 
     beamFrame = nonLinearCosserat.cosseratFrame
     beamFrame.addObject('ConstantForceField', name='constForce', showArrowSize=1.e-8, indices=12,
-                        force=[0., 0., 0., 0., 0., 450.])
+                        forces=[0., 0., 0., 0., 0., 450.])
 
     return rootNode

examples/python3/tutorial/formation/chiba/Actuator.py

@@ -2,8 +2,6 @@
 from fingerController import FingerController #for keyboard controlling
 #from timerreset import FingerController   #Uncomment to perform timed measurements(increases of 5kPa every 2 seconds)
 from loopstest_function_param3 import looptest #algorithm for generating the fiber loops
-import gmsh
-
 
 
 def createScene(rootNode):
@@ -83,7 +81,7 @@ def createScene(rootNode):
         fiber.addObject('MeshTopology', name='lines', lines=[[i, i + 1] for i in range(loopnum)])
 
         #fiber.addObject("FixedConstraint", name="FixedConstragetLinkPathint", indices=[0])
-        fiber.addObject("StiffSpringForceField", template="Vec3d", name="springs", showArrowSize=0.5, drawMode=1,
+        fiber.addObject("SpringForceField", template="Vec3d", name="springs", showArrowSize=0.5, drawMode=1,
                         stiffness=Ks, damping=Kd, indices1=indices1, indices2=indices2, lengths=lengths)
 
         # Mapping 

examples/python3/tutorial/formation/chiba/actuator_v1.py

@@ -1,7 +1,6 @@
 import Sofa
 from fingerController import FingerController  # for keyboard controlling
 from loopstest_function_param3 import looptest  # algorithm for generating the fiber loops
-import gmsh
 
 from useful.header import addHeader, addSolverNode
 
@@ -73,7 +72,7 @@ def createScene(root_node):
                        showObject=True, showObjectScale=1)
     hitching.addObject('MeshTopology', name='lines',
                        lines=[[i, i + 1] for i in range(num_loops - 1)])
-    hitching.addObject("StiffSpringForceField", template="Vec3d", name="springs", showArrowSize=0.5, drawMode=1,
+    hitching.addObject("SpringForceField", template="Vec3d", name="springs", showArrowSize=0.5, drawMode=1,
                        stiffness=Ks, damping=Kd, indices1=[0, 1, 2, 3, 4, 5, 6], indices2=[1, 2, 3, 4, 5, 6, 7],
                        lengths=loop_distance)
     hitching.addObject('BarycentricMapping', name='mapping')

src/Cosserat/mapping/LegendrePolynomialsMapping.inl

@@ -42,14 +42,12 @@ namespace sofa::component::mapping {
         m_matOfCoeffs.clear();
         auto curvAbs = d_vectorOfCurvilinearAbscissa.getValue();
         auto  sz = curvAbs.size();
-        // std::cout << " curvAbs :" << curvAbs << std::endl;
         for (unsigned int i = 1; i < sz; i++){
             type::vector<double> coeffsOf_i;
             coeffsOf_i.clear();
             for (unsigned int order = 0; order < d_order.getValue(); order++)
                 coeffsOf_i.push_back(legendrePoly(order, curvAbs[i]));
 
-            // std::cout << " = = = >coeffsOf_i: " << coeffsOf_i << std::endl;
             m_matOfCoeffs.push_back(coeffsOf_i);
         }
     }
@@ -58,10 +56,10 @@ namespace sofa::component::mapping {
     template <class TIn, class TOut>
     void LegendrePolynomialsMapping<TIn, TOut>::init()
     {
-        Inherit1::init();
-
         //Compute the coefficients for each curv_abs at all orders of the polynomials
         reinit();
+
+        Inherit1::init();
     }
 
 
@@ -73,16 +71,13 @@ namespace sofa::component::mapping {
         const auto sz = d_vectorOfCurvilinearAbscissa.getValue().size();
         out.resize(sz-1);
 
-        // std::cout<< "Apply :  in " << in[0] <<std::endl;
         for (unsigned int i = 0; i < sz-1; i++){
             type::Vec3 Xi ;
             for (unsigned int j = 0; j < in.size(); j++)
                 Xi += m_matOfCoeffs[i][j] * in[j];
 
-            // std::cout << "   Xi : "<< Xi << std::endl;
             out[i] = Xi;
         }
-        // std::cout<< " " << std::endl;
     }
 
     template <class TIn, class TOut>