Merge pull request #358 from EveCharbie/model_creation_update

Model creation (BIS)

.github/workflows/run_casadi_tests.yml

@@ -130,7 +130,8 @@ jobs:
       - name: Run python binder tests 
         run: |
           BIORBD_FOLDER=`pwd`
-          cd $BIORBD_FOLDER/$BUILD_FOLDER/test/binding/Python3
+          cd $BIORBD_FOLDER/$BUILD_FOLDER/test/binding/python3
+          export CI_MAIN_EXAMPLES_FOLDER=$BIORBD_FOLDER/$EXAMPLES_FOLDER
           pytest .
           cd $BIORBD_FOLDER
 

.github/workflows/run_eigen_tests.yml

@@ -161,7 +161,8 @@ jobs:
       - name: Run python binder tests 
         run: |
           BIORBD_FOLDER=`pwd`
-          cd $BIORBD_FOLDER/$BUILD_FOLDER/test/binding/Python3
+          cd $BIORBD_FOLDER/$BUILD_FOLDER/test/binding/python3
+          export CI_MAIN_EXAMPLES_FOLDER=$BIORBD_FOLDER/$EXAMPLES_FOLDER
           pytest .
           cd $BIORBD_FOLDER
 

binding/python3/model_creation/__init__.py

@@ -5,9 +5,15 @@
 from .axis import Axis
 from .inertia_parameters import InertiaParameters
 from .marker import Marker
+from .contact import Contact
+from .muscle import Muscle
+from .muscle_group import MuscleGroup
+from .via_point import ViaPoint
 from .mesh import Mesh
+from .mesh_file import MeshFile
 from .protocols import Data, GenericDynamicModel
 from .rotations import Rotations
+from .range_of_motion import RangeOfMotion, Ranges
 from .segment import Segment
 from .segment_coordinate_system import SegmentCoordinateSystem
 from .translations import Translations
@@ -16,7 +22,11 @@
 from .biomechanical_model_real import BiomechanicalModelReal
 from .axis_real import AxisReal
 from .marker_real import MarkerReal
+from .contact_real import ContactReal
+from .muscle_real import MuscleReal, MuscleType, MuscleStateType
+from .via_point_real import ViaPointReal
 from .mesh_real import MeshReal
+from .mesh_file_real import MeshFileReal
 from .segment_real import SegmentReal
 from .segment_coordinate_system_real import SegmentCoordinateSystemReal
 from .inertia_parameters_real import InertiaParametersReal

binding/python3/model_creation/biomechanical_model.py

@@ -1,29 +1,22 @@
 from .protocols import Data
 from .segment_real import SegmentReal
-from .segment import Segment
+from .muscle_group import MuscleGroup
+from .muscle_real import MuscleReal
 from .segment_coordinate_system_real import SegmentCoordinateSystemReal
 from .biomechanical_model_real import BiomechanicalModelReal
 
 
 class BiomechanicalModel:
     def __init__(self, bio_sym_path: str = None):
         self.segments = {}
+        self.muscle_groups = {}
+        self.muscles = {}
+        self.via_points = {}
 
         if bio_sym_path is None:
             return
         raise NotImplementedError("bioMod files are not readable yet")
 
-    def __getitem__(self, name: str):
-        return self.segments[name]
-
-    def __setitem__(self, name: str, segment: Segment):
-        if segment.name is not None and segment.name != name:
-            raise ValueError(
-                "The segment name should be the same as the 'key'. Alternatively, segment.name can be left undefined"
-            )
-        segment.name = name  # Make sure the name of the segment fits the internal one
-        self.segments[name] = segment
-
     def to_real(self, data: Data) -> BiomechanicalModelReal:
         """
         Collapse the model to an actual personalized biomechanical model based on the generic model and the data
@@ -54,19 +47,63 @@ def to_real(self, data: Data) -> BiomechanicalModelReal:
             if s.mesh is not None:
                 mesh = s.mesh.to_mesh(data, model, scs)
 
-            model[s.name] = SegmentReal(
+            mesh_file = None
+            if s.mesh_file is not None:
+                mesh_file = s.mesh_file.to_mesh_file(data)
+
+            model.segments[s.name] = SegmentReal(
                 name=s.name,
                 parent_name=s.parent_name,
                 segment_coordinate_system=scs,
                 translations=s.translations,
                 rotations=s.rotations,
+                q_ranges=s.q_ranges,
+                qdot_ranges=s.qdot_ranges,
                 inertia_parameters=inertia_parameters,
                 mesh=mesh,
+                mesh_file=mesh_file,
             )
 
             for marker in s.markers:
                 model.segments[name].add_marker(marker.to_marker(data, model, scs))
 
+            for contact in s.contacts:
+                model.segments[name].add_contact(contact.to_contact(data))
+
+        for name in self.muscle_groups:
+            mg = self.muscle_groups[name]
+
+            model.muscle_groups[mg.name] = MuscleGroup(
+                name=mg.name,
+                origin_parent_name=mg.origin_parent_name,
+                insertion_parent_name=mg.insertion_parent_name,
+            )
+
+        for name in self.muscles:
+            m = self.muscles[name]
+
+            if m.muscle_group not in model.muscle_groups:
+                raise RuntimeError(
+                    f"Please create the muscle group {m.muscle_group} before putting the muscle {m.name} in it."
+                )
+
+            model.muscles[m.name] = m.to_muscle(model, data)
+
+        for name in self.via_points:
+            vp = self.via_points[name]
+
+            if vp.muscle_name not in model.muscles:
+                raise RuntimeError(
+                    f"Please create the muscle {vp.muscle_name} before putting the via point {vp.name} in it."
+                )
+
+            if vp.muscle_group not in model.muscle_groups:
+                raise RuntimeError(
+                    f"Please create the muscle group {vp.muscle_group} before putting the via point {vp.name} in it."
+                )
+
+            model.via_points[vp.name] = vp.to_via_point(data)
+
         return model
 
     def write(self, save_path: str, data: Data):

binding/python3/model_creation/biomechanical_model_real.py

@@ -1,23 +1,49 @@
 class BiomechanicalModelReal:
     def __init__(self):
         from .segment_real import SegmentReal  # Imported here to prevent from circular imports
+        from .muscle_group import MuscleGroup
+        from .muscle_real import MuscleReal
+        from .via_point_real import ViaPointReal
 
         self.segments: dict[str:SegmentReal, ...] = {}
         # From Pythom 3.7 the insertion order in a dict is preserved. This is important because when writing a new
         # .bioMod file, the order of the segment matters
-
-    def __getitem__(self, name: str):
-        return self.segments[name]
-
-    def __setitem__(self, name: str, segment: "SegmentReal"):
-        segment.name = name  # Make sure the name of the segment fits the internal one
-        self.segments[name] = segment
+        self.muscle_groups: dict[str:MuscleGroup, ...] = {}
+        self.muscles: dict[str:MuscleReal, ...] = {}
+        self.via_points: dict[str:ViaPointReal, ...] = {}
 
     def __str__(self):
         out_string = "version 4\n\n"
+
+        out_string += "// --------------------------------------------------------------\n"
+        out_string += "// SEGMENTS\n"
+        out_string += "// --------------------------------------------------------------\n\n"
         for name in self.segments:
             out_string += str(self.segments[name])
             out_string += "\n\n\n"  # Give some space between segments
+
+        out_string += "// --------------------------------------------------------------\n"
+        out_string += "// MUSCLE GROUPS\n"
+        out_string += "// --------------------------------------------------------------\n\n"
+        for name in self.muscle_groups:
+            out_string += str(self.muscle_groups[name])
+            out_string += "\n"
+        out_string += "\n\n\n"  # Give some space after muscle groups
+
+        out_string += "// --------------------------------------------------------------\n"
+        out_string += "// MUSCLES\n"
+        out_string += "// --------------------------------------------------------------\n\n"
+        for name in self.muscles:
+            out_string += str(self.muscles[name])
+            out_string += "\n\n\n"  # Give some space between muscles
+
+        out_string += "// --------------------------------------------------------------\n"
+        out_string += "// MUSCLES VIA POINTS\n"
+        out_string += "// --------------------------------------------------------------\n\n"
+        for name in self.via_points:
+            out_string += str(self.via_points[name])
+            out_string += "\n\n\n"  # Give some space between via points
+
         return out_string
 
     def write(self, file_path: str):

binding/python3/model_creation/contact.py

@@ -0,0 +1,41 @@
+from typing import Callable
+
+from .protocols import Data
+from .translations import Translations
+from .contact_real import ContactReal
+
+
+class Contact:
+    def __init__(
+        self,
+        name: str,
+        function: Callable | str = None,
+        parent_name: str = None,
+        axis: Translations = None,
+    ):
+        """
+        Parameters
+        ----------
+        name
+            The name of the new contact
+        function
+            The function (f(m) -> np.ndarray, where m is a dict of markers) that defines the contact with.
+        parent_name
+            The name of the parent the contact is attached to
+        axis
+            The axis of the contact
+        """
+        self.name = name
+        function = function if function is not None else self.name
+        self.function = (lambda m, bio: m[function]) if isinstance(function, str) else function
+        self.parent_name = parent_name
+        self.axis = axis
+
+    def to_contact(self, data: Data) -> ContactReal:
+        return ContactReal.from_data(
+            data,
+            self.name,
+            self.function,
+            self.parent_name,
+            self.axis,
+        )

binding/python3/model_creation/contact_real.py

@@ -0,0 +1,80 @@
+from typing import Callable
+
+import numpy as np
+
+from .protocols import Data
+from .translations import Translations
+
+
+class ContactReal:
+    def __init__(
+        self,
+        name: str,
+        parent_name: str,
+        position: tuple[int | float, int | float, int | float] | np.ndarray = None,
+        axis: Translations = None,
+    ):
+        """
+        Parameters
+        ----------
+        name
+            The name of the new contact
+        parent_name
+            The name of the parent the contact is attached to
+        position
+            The 3d position of the contact
+        axis
+            The axis of the contact
+        """
+        self.name = name
+        self.parent_name = parent_name
+        if position is None:
+            position = np.array((0, 0, 0, 1))
+        self.position = position if isinstance(position, np.ndarray) else np.array(position)
+        self.axis = axis
+
+    @staticmethod
+    def from_data(
+        data: Data,
+        name: str,
+        function: Callable,
+        parent_name: str,
+        axis: Translations = None,
+    ):
+        """
+        This is a constructor for the Contact class. It evaluates the function that defines the contact to get an
+        actual position
+
+        Parameters
+        ----------
+        data
+            The data to pick the data from
+        name
+            The name of the new contact
+        function
+            The function (f(m) -> np.ndarray, where m is a dict of markers (XYZ1 x time)) that defines the contacts in the local joint coordinates.
+        parent_name
+            The name of the parent the contact is attached to
+        axis
+            The axis of the contact
+        """
+
+        # Get the position of the contact points and do some sanity checks
+        p: np.ndarray = function(data.values)
+        if not isinstance(p, np.ndarray):
+            raise RuntimeError(f"The function {function} must return a np.ndarray of dimension 3xT (XYZ x time)")
+        if p.shape == (3, 1):
+            p = p.reshape((3,))
+        elif p.shape != (3,):
+            raise RuntimeError(f"The function {function} must return a vector of dimension 3 (XYZ)")
+
+        return ContactReal(name, parent_name, p, axis)
+
+    def __str__(self):
+        # Define the print function, so it automatically formats things in the file properly
+        out_string = f"contact\t{self.name}\n"
+        out_string += f"\tparent\t{self.parent_name}\n"
+        out_string += f"\tposition\t{np.round(self.position[0], 4)}\t{np.round(self.position[1], 4)}\t{np.round(self.position[2], 4)}\n"
+        out_string += f"\taxis\t{self.axis.value}\n"
+        out_string += "endcontact\n"
+        return out_string

binding/python3/model_creation/inertia_parameters_real.py

@@ -81,7 +81,7 @@ def __str__(self):
         # Define the print function, so it automatically formats things in the file properly
         com = np.nanmean(self.center_of_mass, axis=1)[:3]
 
-        out_string = f"\tmass {self.mass}\n"
-        out_string += f"\tCenterOfMass {com[0]:0.5f} {com[1]:0.5f} {com[2]:0.5f}\n"
-        out_string += f"\tinertia_xxyyzz {self.inertia[0]} {self.inertia[1]} {self.inertia[2]}\n"
+        out_string = f"\tmass\t{self.mass}\n"
+        out_string += f"\tCenterOfMass\t{com[0]:0.5f}\t{com[1]:0.5f}\t{com[2]:0.5f}\n"
+        out_string += f"\tinertia_xxyyzz\t{self.inertia[0]}\t{self.inertia[1]}\t{self.inertia[2]}\n"
         return out_string

binding/python3/model_creation/marker_real.py

@@ -101,13 +101,13 @@ def mean_position(self) -> np.ndarray:
 
     def __str__(self):
         # Define the print function, so it automatically formats things in the file properly
-        out_string = f"marker {self.name}\n"
-        out_string += f"\tparent {self.parent_name}\n"
+        out_string = f"marker\t{self.name}\n"
+        out_string += f"\tparent\t{self.parent_name}\n"
 
         p = self.mean_position
-        out_string += f"\tposition {p[0]:0.4f} {p[1]:0.4f} {p[2]:0.4f}\n"
-        out_string += f"\ttechnical {1 if self.is_technical else 0}\n"
-        out_string += f"\tanatomical {1 if self.is_anatomical else 0}\n"
+        out_string += f"\tposition\t{p[0]:0.4f}\t{p[1]:0.4f}\t{p[2]:0.4f}\n"
+        out_string += f"\ttechnical\t{1 if self.is_technical else 0}\n"
+        out_string += f"\tanatomical\t{1 if self.is_anatomical else 0}\n"
         out_string += "endmarker\n"
         return out_string