[Prefabs] dataclasses to pydantic BaseModel

bindings/Sofa/src/SofaPython3/Sofa/Types/Binding_CompressedRowSparseMatrix.cpp

@@ -53,10 +53,18 @@ void bindCompressedRowSparseMatrixConstraint(pybind11::module& m)
 
     crsmc.def_property_readonly("value", [](sofa::Data<MatrixDeriv>& self)
     {
-        sofa::helper::ReadAccessor accessor(self);
+        sofa::helper::WriteAccessor accessor(self);
+        accessor.wref().compress();
         return toEigen(accessor.ref());
     });
 
+    crsmc.def("add", [](sofa::Data<MatrixDeriv>& self, sofa::Index row, sofa::Index col, const typename MatrixDeriv::Block value)
+    {
+        sofa::helper::WriteAccessor accessor(self);
+        auto line = accessor->writeLine(row);
+        line.addCol(col, value);
+    });
+
     PythonFactory::registerType(MatrixDeriv::Name(), [](sofa::core::BaseData* data) -> py::object {
         auto matrix = reinterpret_cast<sofa::Data<MatrixDeriv>*>(data);
         return py::cast(matrix);

examples/stlib/SofaScene.py

@@ -3,7 +3,7 @@
 from stlib.geometries.plane import PlaneParameters
 from stlib.geometries.file import FileParameters
 from stlib.geometries.extract import ExtractParameters
-from stlib.materials.deformable import DeformableBehaviorParameters
+from stlib.materials.deformable import DeformableMaterialParameters
 from stlib.collision import Collision, CollisionParameters
 from stlib.entities import Entity, EntityParameters
 from stlib.visual import Visual, VisualParameters
@@ -66,7 +66,7 @@ def createScene(root):
 
     LogoParams = EntityParameters(name = "Logo",
                                   geometry = FileParameters(filename="mesh/SofaScene/Logo.vtk"),
-                                  material = DeformableBehaviorParameters(),
+                                  material = DeformableMaterialParameters(),
                                   collision = CollisionParameters(geometry = FileParameters(filename="mesh/SofaScene/LogoColli.sph")),
                                   visual = VisualParameters(geometry = FileParameters(filename="mesh/SofaScene/LogoVisu.obj")))
 
@@ -94,12 +94,12 @@ def createScene(root):
     SParams.name = "S"
     SParams.geometry = FileParameters(filename="mesh/SofaScene/S.vtk")
     SParams.geometry.elementType = ElementType.TETRAHEDRA
-    SParams.material = DeformableBehaviorParameters()
+    SParams.material = DeformableMaterialParameters()
     SParams.material.constitutiveLawType = ConstitutiveLaw.ELASTIC
     SParams.material.parameters = [200, 0.45]
 
     def SAddMaterial(node):
-        DeformableBehaviorParameters.addDeformableMaterial(node)
+        DeformableMaterialParameters.addDeformableMaterial(node)
         #TODO deal with that is a more smooth way in the material directly
         node.addObject("LinearSolverConstraintCorrection", name="ConstraintCorrection", linearSolver=SNode.LinearSolver.linkpath, ODESolver=SNode.ODESolver.linkpath)
 

splib/core/utils.py

@@ -1,6 +1,7 @@
 from typing import List, Callable, Tuple, Dict
 from functools import wraps
 
+
 class defaultValueType():
     def __init__(self):
         pass
@@ -32,5 +33,24 @@ def wrapper(*args, **kwargs):
     return MapArg
 
 
+REQUIRES_COLLISIONPIPELINE = "requiresCollisionPipeline"
+
+def setRequiresCollisionPipeline(rootnode):
+    if rootnode is not None: 
+        if rootnode.findData(REQUIRES_COLLISIONPIPELINE) is None:
+            rootnode.addData(name=REQUIRES_COLLISIONPIPELINE, type="bool", value=True, help="Some prefabs in the scene requires a collision pipeline.")
+        else:
+            rootnode.requiresCollisionPipeline.value = True
+
+
+REQUIRES_LAGRANGIANCONSTRAINTSOLVER = "requiresLagrangianConstraintSolver"
+
+def setRequiresLagrangianConstraintSolver(rootnode):
+    if rootnode is not None: 
+        if rootnode.findData(REQUIRES_LAGRANGIANCONSTRAINTSOLVER) is None:
+            rootnode.addData(name=REQUIRES_LAGRANGIANCONSTRAINTSOLVER, type="bool", value=True, help="Some prefabs in the scene requires a Lagrangian constraint solver.")
+        else:
+            rootnode.requiresLagrangianConstraintSolver.value = True
+
 
 

splib/mechanics/mass.py

@@ -3,21 +3,24 @@
 from splib.core.enum_types import ElementType
 
 
-# TODO : use the massDensity ONLY and deduce totalMass if necessary from it + volume
-
 @ReusableMethod
-def addMass(node, elem:ElementType, totalMass=DEFAULT_VALUE, massDensity=DEFAULT_VALUE, lumping=DEFAULT_VALUE, topology=DEFAULT_VALUE, **kwargs):
+def addMass(node, elementType:ElementType, totalMass=DEFAULT_VALUE, massDensity=DEFAULT_VALUE, lumping=DEFAULT_VALUE, topology=DEFAULT_VALUE, **kwargs):
     if (not isDefault(totalMass)) and (not isDefault(massDensity)) :
         print("[warning] You defined the totalMass and the massDensity in the same time, only taking massDensity into account")
         del kwargs["massDensity"]
 
-    if(elem !=ElementType.POINTS and elem !=ElementType.EDGES):
-        node.addObject("MeshMatrixMass",name="mass", totalMass=totalMass, massDensity=massDensity, lumping=lumping, topology=topology,  **kwargs)
+    if(elementType is not None and elementType !=ElementType.POINTS and elementType !=ElementType.EDGES):
+        node.addObject("MeshMatrixMass", 
+                       name="mass", 
+                       totalMass=totalMass, 
+                       massDensity=massDensity, 
+                       lumping=lumping, 
+                       topology=topology,  **kwargs)
     else:
         if (not isDefault(massDensity)) :
             print("[warning] mass density can only be used on a surface or volumetric topology. Please use totalMass instead")
         if (not isDefault(lumping)) :
             print("[warning] lumping can only be set for surface or volumetric topology")
 
-        node.addObject("UniformMass",name="mass", totalMass=totalMass, topology=topology,**kwargs)
+        node.addObject("UniformMass", name="mass", totalMass=totalMass, topology=topology,**kwargs)
 

stlib/__init__.py

@@ -1,4 +1,4 @@
-__all__ = ["core","entities","geometries","materials","collision","visual"]
+__all__ = ["core","entities","geometries","materials","collision","visual","prefabs"]
 
 import Sofa.Core
 from stlib.core.basePrefab import BasePrefab
@@ -48,6 +48,7 @@ def checkName(context : Sofa.Core.Node, name):
     else:
         params["name"] = checkName(self, params["name"])
 
+
     # Dispatch the creation to either addObject or addChild
     if isinstance(typeName, type) and issubclass(typeName, BasePrefab):
         pref = self.addChild(typeName(**params))

stlib/collision.py

@@ -1,34 +1,37 @@
 from stlib.core.basePrefab import BasePrefab
-from stlib.core.baseParameters import BaseParameters, Optional, dataclasses
+from stlib.core.baseParameters import BaseParameters, Optional
 from stlib.geometries import Geometry, GeometryParameters
 from stlib.geometries.file import FileParameters
 from splib.core.enum_types import CollisionPrimitive
 from splib.core.utils import DEFAULT_VALUE
 from splib.mechanics.collision_model import addCollisionModels
-from Sofa.Core import Object 
+from splib.core.utils import setRequiresCollisionPipeline
+
 
-@dataclasses.dataclass
 class CollisionParameters(BaseParameters):
     name : str = "Collision"
 
-    primitives : list[CollisionPrimitive] = dataclasses.field(default_factory = lambda :[CollisionPrimitive.TRIANGLES])
+    primitives : list[CollisionPrimitive] = [CollisionPrimitive.TRIANGLES]
 
     selfCollision : Optional[bool] = DEFAULT_VALUE
     bothSide : Optional[bool] = DEFAULT_VALUE
     group : Optional[int] = DEFAULT_VALUE
     contactDistance : Optional[float] = DEFAULT_VALUE
 
-    geometry : GeometryParameters = dataclasses.field(default_factory = lambda : GeometryParameters())
+    geometry : GeometryParameters = GeometryParameters()
 
 
 class Collision(BasePrefab):
+
     def __init__(self, parameters: CollisionParameters):
         BasePrefab.__init__(self, parameters)
 
     def init(self):
 
         geom = self.add(Geometry, parameters = self.parameters.geometry)
 
+        setRequiresCollisionPipeline(rootnode=self.getRoot())
+
         self.addObject("MechanicalObject", template="Vec3", position=f"@{self.parameters.geometry.name}/container.position")
         for primitive in self.parameters.primitives:
             addCollisionModels(self, primitive,

stlib/core/baseParameters.py

@@ -1,13 +1,34 @@
-import dataclasses
 from splib.core.utils import DEFAULT_VALUE
 
-import dataclasses
+from pydantic import BaseModel, ValidationError
+from dynapydantic import SubclassTrackingModel
 from typing import Callable, Optional, Any
+import Sofa
+
+class BaseParameters(SubclassTrackingModel,
+                     discriminator_field="type",
+                     discriminator_value_generator=lambda t: t.__name__,): 
 
-@dataclasses.dataclass
-class BaseParameters(object): 
     name : str = "Object"
-    kwargs : dict = dataclasses.field(default_factory=dict)
+    kwargs : dict = {}
+
+    @classmethod
+    def fromYaml(self, data: str):
+        import yaml
+        dataDict = yaml.safe_load(data)
+        return self.fromDict(dataDict)
+
+    @classmethod
+    def fromDict(self, data: dict):
+        try:
+            return self.model_validate(data, strict=True)
+        except ValidationError as exc:
+            for error in exc.errors():
+                loc = error.get("loc")
+                message = ""
+                for locPart in loc:
+                    message += locPart.__str__() + ": "
+                message += error.get("msg") 
+                Sofa.msg_error(self.__name__, message)
+
 
-    def toDict(self):
-        return dataclasses.asdict(self)

stlib/core/basePrefabParameters.py

@@ -1,15 +1,12 @@
-import dataclasses
+from stlib.core.baseParameters import BaseParameters
 
-@dataclasses.dataclass
-class BasePrefabParameters(object): 
+class BasePrefabParameters(BaseParameters): 
     name : str = "object"
-    kwargs : dict = dataclasses.field(default_factory=dict)
+    kwargs : dict = {}
 
     # Transformation information
     # TODO: these data are going to be added in Node in SOFA (C++ implementation)
-    translation : list[float] = dataclasses.field(default_factory = lambda : [0., 0., 0.])
-    rotation : list[float] = dataclasses.field(default_factory = lambda : [0., 0., 0.])
-    scale : list[float] = dataclasses.field(default_factory = lambda : [1., 1., 1.])
-
-    def toDict(self):
-        return dataclasses.asdict(self)
+    translation : list[float] = [0., 0., 0.]
+    rotation : list[float] = [0., 0., 0.]
+    scale : list[float] = [1., 1., 1.]
+

stlib/entities/__entity__.py

@@ -3,27 +3,30 @@
 from stlib.visual import VisualParameters, Visual
 from stlib.materials import Material, MaterialParameters
 from stlib.geometries import Geometry
-import dataclasses
 from typing import Callable, Optional
-from stlib.geometries import GeometryParameters
+from stlib.geometries import GeometryParameters, InternalDataProvider
 from splib.core.enum_types import StateType
 from stlib.core.basePrefab import BasePrefab
 
+from stlib.geometries.file import FileParameters
+from stlib.materials.rigid import RigidMaterialParameters
+from splib.core.enum_types import ElementType
+
+from dynapydantic import Polymorphic
+import Sofa
+
 
-@dataclasses.dataclass
 class EntityParameters(BaseParameters): 
     name : str = "Entity"
 
-    stateType : StateType = StateType.VEC3
-
     ### QUID 
-    addCollision : Optional[Callable] = lambda x : Collision(CollisionParameters())
-    addVisual : Optional[Callable] = lambda x : Visual(VisualParameters()) 
+    addCollision : Optional[Callable] = Collision(CollisionParameters())
+    addVisual : Optional[Callable] = Visual(VisualParameters()) 
 
-    geometry : GeometryParameters = None
-    material : MaterialParameters = None
+    geometry : Polymorphic[GeometryParameters] = GeometryParameters(elementType = ElementType.POINTS, data = InternalDataProvider(position = [[0., 0., 0.]]))
+    material : Polymorphic[MaterialParameters] = RigidMaterialParameters()
     collision : Optional[CollisionParameters] = None
-    visual : Optional[VisualParameters] = None
+    visual : Optional[VisualParameters] = VisualParameters(geometry = FileParameters(filename="mesh/cube.obj"))
 
 
 
@@ -38,21 +41,16 @@ class Entity(BasePrefab):
     parameters : EntityParameters
 
 
-    def __init__(self, parameters=EntityParameters(), **kwargs):
+    def __init__(self, parameters: EntityParameters):
         BasePrefab.__init__(self, parameters)
 
 
     def init(self):
         self.geometry = self.add(Geometry, parameters=self.parameters.geometry)
 
-        ### Check compatilibility of Material
-        if self.parameters.material.stateType != self.parameters.stateType:
-            print("WARNING: imcompatibility between templates of both the entity and the material")
-            self.parameters.material.stateType = self.parameters.stateType
-
         self.material = self.add(Material, parameters=self.parameters.material)
-        self.material.States.position.parent = self.geometry.container.position.linkpath
-        
+        self.material.getMechanicalState().topology = self.geometry.container.linkpath
+
         if self.parameters.collision is not None:
             self.collision = self.add(Collision, parameters=self.parameters.collision)
             self.addMapping(self.collision)
@@ -64,18 +62,18 @@ def init(self):
 
     def addMapping(self, destinationPrefab):
 
-        template = f'{self.parameters.stateType},Vec3' # TODO: check that it is always true
+        template = f'{self.parameters.material.stateType},Vec3' # TODO: check that it is always true
 
         #TODO: all paths are expecting Geometry to be called Geomtry and so on. We need to robustify this by using the name parameter somehow
-        if( self.parameters.stateType == StateType.VEC3):
+        if( self.parameters.material.stateType == StateType.VEC3):
             destinationPrefab.addObject("BarycentricMapping", 
                                         output=destinationPrefab.linkpath, 
-                                        output_topology=destinationPrefab.Geometry.container.linkpath,
-                                        input=self.Material.linkpath,
-                                        input_topology=self.Geometry.container.linkpath,
+                                        output_topology=destinationPrefab.geometry.container.linkpath,
+                                        input=self.material.linkpath,
+                                        input_topology=self.geometry.container.linkpath,
                                         template=template)
         else:
             destinationPrefab.addObject("RigidMapping", 
                                          output=destinationPrefab.linkpath, 
-                                        input=self.Material.linkpath,
+                                        input=self.material.linkpath,
                                         template=template)