feat: pinocchio x muscles

.gitignore

@@ -169,3 +169,7 @@ sandbox/
 
 .DS_Store
 .aider*
+
+examples/pinocchio/urdf (Copie)/
+
+examples/pinocchio/urdf (Copie).zip

pyorerun/model_components/mesh.py

@@ -84,17 +84,22 @@ def from_file(
             mesh = load(file_path)
             mesh.apply_scale(scale_factor)
 
-            # assume the first geometry if multiple are present
-            first_key = list(mesh.geometry.keys())[0]
-
-            real_mesh = Trimesh(
-                vertices=mesh.geometry[first_key].vertices,
-                faces=mesh.geometry[first_key].faces,
-                vertex_normals=mesh.geometry[first_key].vertex_normals,
-                metadata=dict(file_name=mesh.source.file_name),
-            )
-            if "file_name" not in mesh.metadata:
-                mesh.metadata["file_name"] = file_path.split("/")[-1].split(".")[0]
+            # Handle both Scene (multiple geometries) and single Trimesh
+            if hasattr(mesh, "geometry") and len(mesh.geometry) > 0:
+                # It's a Scene with multiple geometries - merge them properly
+                from trimesh.util import concatenate
+
+                geometries = list(mesh.geometry.values())
+                real_mesh = concatenate(geometries)
+                real_mesh.metadata = dict(
+                    file_name=mesh.source.file_name if hasattr(mesh, "source") else file_path.split("/")[-1]
+                )
+            else:
+                # It's already a single Trimesh
+                real_mesh = mesh
+                if "file_name" not in real_mesh.metadata:
+                    real_mesh.metadata["file_name"] = file_path.split("/")[-1].split(".")[0]
+
             return cls(name, real_mesh, transform_callable)
         else:
             raise ValueError(

pyorerun/model_interfaces/biorbd_model_interface.py

@@ -162,20 +162,20 @@ def ligament_strips(self, q: np.ndarray) -> list[list[np.ndarray]]:
     @cached_property
     def nb_muscles(self) -> int:
         """
-        Returns the number of ligaments
+        Returns the number of muscles
         """
         return self.model.nbMuscles()
 
     @cached_property
     def muscle_names(self) -> tuple[str, ...]:
         """
-        Returns the names of the ligaments
+        Returns the names of the muscles
         """
         return tuple([s.to_string() for s in self.model.muscleNames()])
 
     def muscle_strips(self, q: np.ndarray) -> list[list[np.ndarray]]:
         """
-        Returns the position of the ligaments in the global reference frame
+        Returns the position of the muscles in the global reference frame
         """
         muscles = []
         self.model.updateMuscles(q, True)

pyorerun/model_interfaces/pinocchio_model_interface.py

@@ -131,9 +131,10 @@ def __init__(self, path: str, options=None):
             raise ValueError(f"Unsupported file format for Pinocchio: {path}. Expected .urdf")
 
         self.data = self.model.createData()
+        self.muscles_names = []  # Pinocchio doesn't have native muscle support, so this will be empty
 
     @classmethod
-    def from_pinocchio_object(cls, model: pin.Model, path: str = None, options=None):
+    def from_pinocchio_object(cls, model: pin.Model, path: str = None, options=None, muscles_names: list[str] = None):
         """
         Create from an existing Pinocchio model object.
         """
@@ -144,8 +145,13 @@ def from_pinocchio_object(cls, model: pin.Model, path: str = None, options=None)
         instance.options = options if options is not None else DisplayModelOptions()
         instance._mesh_dir = Path(path).parent if path else Path.cwd()
         instance.visual_model = None
+        instance.muscles_names = muscles_names if muscles_names is not None else []
         return instance
 
+    @cached_property
+    def _frame_list_names(self) -> list[str]:
+        return [frame.name for frame in self.model.frames]
+
     @cached_property
     def name(self) -> str:
         return self.model.name if hasattr(self.model, "name") else Path(self.path).stem
@@ -355,20 +361,36 @@ def nb_muscles(self) -> int:
         """
         Pinocchio doesn't have native muscle support.
         """
-        return 0
+        return len(self.muscles_names)
 
     @cached_property
     def muscle_names(self) -> tuple[str, ...]:
         """
         Pinocchio doesn't have native muscle support.
         """
-        return tuple()
+        return tuple(self.muscles_names)
 
     def muscle_strips(self, q: np.ndarray) -> list[list[np.ndarray]]:
         """
         Pinocchio doesn't have native muscle support.
         """
-        return []
+        pin.forwardKinematics(self.model, self.data, q)
+        pin.updateFramePlacements(self.model, self.data)
+
+        muscles = []
+        for idx in range(self.nb_muscles):
+            muscle_name = self.muscle_names[idx]
+            muscle_frames = [
+                f_name for f_name in self._frame_list_names if muscle_name == f_name.split("-")[0]
+            ]  # assume muscle frames are named like "muscleName-1", "muscleName-2", etc.
+            muscle_strip = []
+            print(f"Muscle {muscle_name} frames: {muscle_frames}")
+            for i in range(len(muscle_frames)):
+                f1_id = self.model.getFrameId(muscle_frames[i])
+                frame_location = self.data.oMf[f1_id].translation
+                muscle_strip.append(frame_location)
+            muscles.append(muscle_strip)
+        return muscles
 
     @cached_property
     def gravity(self) -> np.ndarray:
@@ -443,6 +465,7 @@ def from_pinocchio_object(
         collision_model: pin.GeometryModel = None,
         path: str = None,
         options=None,
+        muscles_names: list[str] = None,
     ):
         """
         Create from existing Pinocchio objects.
@@ -455,6 +478,7 @@ def from_pinocchio_object(
         instance.path = path if path else "pinocchio_model"
         instance.options = options if options is not None else DisplayModelOptions()
         instance._mesh_dir = Path(path).parent if path else Path.cwd()
+        instance.muscles_names = muscles_names if muscles_names is not None else []
         return instance
 
     @cached_property

pyorerun/phase_rerun.py

@@ -243,7 +243,6 @@ def rerun_by_frame(
         if init:
             spawn = not notebook and os.environ.get("PYORERUN_HEADLESS", "0").lower() not in ("1", "true", "yes")
             rr.init(f"{name}_{self.phase}", spawn=spawn)
-            rr.init(f"{name}_{self.phase}", spawn=spawn)
             rr.log("/", rr.ViewCoordinates.RIGHT_HAND_Y_UP, static=True)
             rr.send_blueprint(
                 rrb.Blueprint(