Applied reviewable comments and doc string

cocofest/examples/dynamics/minimize_fatigue/frequecy_optimization_minimize_fatigue.py

@@ -50,8 +50,8 @@
     pulse_apparition_dict={"time_min": 0.01, "time_max": 1, "time_bimapping": False},
     with_residual_torque=True,
     objective_dict={"custom_objective": objective_functions},
-    muscle_force_length_relationship=True,
-    muscle_force_velocity_relationship=False,
+    activate_force_length_relationship=True,
+    activate_force_velocity_relationship=False,
     minimize_muscle_fatigue=True,
 )
 

cocofest/examples/dynamics/minimize_fatigue/pulse_duration_optimization_minimize_fatigue.py

@@ -50,8 +50,8 @@
     },
     with_residual_torque=False,
     objective_dict={"custom_objective": objective_functions},
-    muscle_force_length_relationship=True,
-    muscle_force_velocity_relationship=False,
+    activate_force_length_relationship=True,
+    activate_force_velocity_relationship=False,
     minimize_muscle_fatigue=True,
 )
 

cocofest/examples/dynamics/minimize_fatigue/pulse_intensity_optimization_minimize_fatigue.py

@@ -52,8 +52,8 @@
     },
     with_residual_torque=False,
     objective_dict={"custom_objective": objective_functions},
-    muscle_force_length_relationship=True,
-    muscle_force_velocity_relationship=False,
+    activate_force_length_relationship=True,
+    activate_force_velocity_relationship=False,
     minimize_muscle_fatigue=True,
 )
 

cocofest/examples/dynamics/muscle_force_length_and_force_velocity_relationships_comparison.py

@@ -17,7 +17,7 @@
 
 sol_list = []
 sol_time = []
-muscle_force_length_relationship = [False, True]
+activate_force_length_relationship = [False, True]
 
 for i in range(2):
     ocp = OcpFesMsk.prepare_ocp(
@@ -30,8 +30,8 @@
         final_time=1,
         pulse_duration_dict={"pulse_duration": 0.00025},
         with_residual_torque=False,
-        muscle_force_length_relationship=muscle_force_length_relationship[i],
-        muscle_force_velocity_relationship=muscle_force_length_relationship[i],
+        activate_force_length_relationship=activate_force_length_relationship[i],
+        activate_force_velocity_relationship=activate_force_length_relationship[i],
         use_sx=False,
     )
     sol = ocp.solve(Solver.IPOPT(_max_iter=1000))

cocofest/examples/dynamics/reaching_task/reaching_task_frequency_optimization.py

@@ -92,8 +92,8 @@
         pulse_apparition_dict={"time_min": 0.01, "time_max": 0.1, "time_bimapping": False},
         with_residual_torque=False,
         custom_constraint=constraint,
-        muscle_force_length_relationship=True,
-        muscle_force_velocity_relationship=True,
+        activate_force_length_relationship=True,
+        activate_force_velocity_relationship=True,
         minimize_muscle_fatigue=True if pickle_file_list[i] == "minimize_muscle_fatigue.pkl" else False,
         minimize_muscle_force=True if pickle_file_list[i] == "minimize_muscle_force.pkl" else False,
         use_sx=False,

cocofest/examples/dynamics/reaching_task/reaching_task_intensity_optimization.py

@@ -99,8 +99,8 @@
         },
         with_residual_torque=False,
         custom_constraint=constraint,
-        muscle_force_length_relationship=True,
-        muscle_force_velocity_relationship=True,
+        activate_force_length_relationship=True,
+        activate_force_velocity_relationship=True,
         minimize_muscle_fatigue=True if pickle_file_list[i] == "minimize_muscle_fatigue.pkl" else False,
         minimize_muscle_force=True if pickle_file_list[i] == "minimize_muscle_force.pkl" else False,
         use_sx=False,

cocofest/examples/dynamics/reaching_task/reaching_task_pulse_duration_optimization.py

@@ -93,8 +93,8 @@
         },
         with_residual_torque=False,
         custom_constraint=constraint,
-        muscle_force_length_relationship=True,
-        muscle_force_velocity_relationship=True,
+        activate_force_length_relationship=True,
+        activate_force_velocity_relationship=True,
         minimize_muscle_fatigue=True if pickle_file_list[i] == "minimize_muscle_fatigue.pkl" else False,
         minimize_muscle_force=True if pickle_file_list[i] == "minimize_muscle_force.pkl" else False,
         use_sx=False,

cocofest/examples/getting_started/frequency_optimization_musculoskeletal_dynamic.py

@@ -30,8 +30,8 @@
     pulse_apparition_dict={"time_min": 0.01, "time_max": 0.1, "time_bimapping": True},
     objective_dict={"custom_objective": objective_functions},
     with_residual_torque=True,
-    muscle_force_length_relationship=True,
-    muscle_force_velocity_relationship=True,
+    activate_force_length_relationship=True,
+    activate_force_velocity_relationship=True,
 )
 
 sol = ocp.solve(Solver.IPOPT(_max_iter=1000))

cocofest/examples/getting_started/pulse_duration_optimization_musculoskeletal_dynamic.py

@@ -36,8 +36,8 @@
     },
     objective_dict={"custom_objective": objective_functions},
     with_residual_torque=True,
-    muscle_force_length_relationship=True,
-    muscle_force_velocity_relationship=True,
+    activate_force_length_relationship=True,
+    activate_force_velocity_relationship=True,
 )
 
 sol = ocp.solve(Solver.IPOPT(_max_iter=2000))

cocofest/examples/getting_started/pulse_intensity_optimization_musculoskeletal_dynamic.py

@@ -35,8 +35,8 @@
     pulse_intensity_dict={"intensity_min": minimum_pulse_intensity, "intensity_max": 130, "intensity_bimapping": False},
     objective_dict={"custom_objective": objective_functions},
     with_residual_torque=True,
-    muscle_force_length_relationship=True,
-    muscle_force_velocity_relationship=True,
+    activate_force_length_relationship=True,
+    activate_force_velocity_relationship=True,
 )
 
 sol = ocp.solve(Solver.IPOPT(_max_iter=1000))

cocofest/integration/ivp_fes.py

@@ -29,27 +29,6 @@ class IvpFes:
     The main class to define an ivp. This class prepares the ivp and gives all
     the needed parameters to integrate a functional electrical stimulation problem.
 
-    Attributes
-    ----------
-    model: FesModel
-        The model type used for the ivp
-    n_stim: int
-        Number of stimulation that will occur during the ivp, it is as well refer as phases
-    n_shooting: int
-        Number of shooting point for each individual phases
-    final_time: float
-        Refers to the final time of the ivp
-    pulse_duration: int | float
-        Setting a chosen pulse duration among phases
-    pulse_intensity: int | float
-        Setting a chosen pulse intensity among phases
-    ode_solver: OdeSolver
-        The ode solver to use
-    use_sx: bool
-        The nature of the casadi variables. MX are used if False.
-    n_threads: int
-        The number of thread to use while solving (multi-threading if > 1)
-
     Methods
     -------
     from_frequency_and_final_time(self, frequency: int | float, final_time: float, round_down: bool)
@@ -70,10 +49,10 @@ def __init__(
         ----------
         fes_parameters: dict
             The parameters for the fes configuration including :
-            model, n_stim, pulse_duration, pulse_intensity, pulse_mode
+            model (FesModel type), n_stim (int type), pulse_duration (float type), pulse_intensity (int | float type), pulse_mode (str type)
         ivp_parameters: dict
             The parameters for the ivp problem including :
-            n_shooting, final_time, extend_last_phase, ode_solver, use_sx, n_threads
+            n_shooting (int type), final_time (int | float type), extend_last_phase (int | float type), ode_solver (OdeSolver type), use_sx (bool type), n_threads (int type)
         """
 
         self._fill_fes_dict(fes_parameters)

cocofest/models/dynamical_model.py

@@ -21,21 +21,36 @@ def __init__(
         self,
         name: str = None,
         biorbd_path: str = None,
-        muscles_model: DingModelFrequency() = None,
-        muscle_force_length_relationship: bool = False,
-        muscle_force_velocity_relationship: bool = False,
+        muscles_model: list[FesModel] = None,
+        activate_force_length_relationship: bool = False,
+        activate_force_velocity_relationship: bool = False,
     ):
+        """
+        The custom model that will be used in the optimal control program for the FES-MSK models
+
+        Parameters
+        ----------
+        name: str
+            The model name
+        biorbd_path: str
+            The path to the biorbd model
+        muscles_model: DingModelFrequency
+            The muscle model that will be used in the model
+        activate_force_length_relationship: bool
+            If the force-length relationship should be activated
+        activate_force_velocity_relationship: bool
+            If the force-velocity relationship should be activated
+        """
+
         super().__init__(biorbd_path)
         self._name = name
         self.bio_model = BiorbdModel(biorbd_path)
-        self.bounds_from_ranges_q = self.bio_model.bounds_from_ranges("q")
-        self.bounds_from_ranges_qdot = self.bio_model.bounds_from_ranges("qdot")
 
         self.muscles_dynamics_model = muscles_model
         self.bio_stim_model = [self.bio_model] + self.muscles_dynamics_model
 
-        self.muscle_force_length_relationship = muscle_force_length_relationship
-        self.muscle_force_velocity_relationship = muscle_force_velocity_relationship
+        self.activate_force_length_relationship = activate_force_length_relationship
+        self.activate_force_velocity_relationship = activate_force_velocity_relationship
 
     # ---- Absolutely needed methods ---- #
     def serialize(self, index: int = 0) -> tuple[Callable, dict]:
@@ -149,15 +164,15 @@ def muscles_joint_torque(
                 muscle_force_length_coefficient(
                     model=nlp.model.bio_model.model, muscle=nlp.model.bio_model.model.muscle(muscle_idx), q=q
                 )
-                if nlp.model.muscle_force_velocity_relationship
+                if nlp.model.activate_force_velocity_relationship
                 else 1
             )
 
             muscle_force_velocity_coeff = (
                 muscle_force_velocity_coefficient(
                     model=nlp.model.bio_model.model, muscle=nlp.model.bio_model.model.muscle(muscle_idx), q=q, qdot=qdot
                 )
-                if nlp.model.muscle_force_velocity_relationship
+                if nlp.model.activate_force_velocity_relationship
                 else 1
             )
 

cocofest/models/hmed2018.py

@@ -338,6 +338,6 @@ def min_pulse_intensity(self):
         """
         Returns
         -------
-        The minimum pulse intensity
+        The minimum pulse intensity threshold of the model
         """
         return (np.arctanh(-self.cr) / self.bs) + self.Is

cocofest/optimization/fes_ocp.py

@@ -367,7 +367,7 @@ def _sanity_check(
             if not isinstance(time_bimapping, bool):
                 raise TypeError("time_bimapping must be bool type")
 
-        if isinstance(model, DingModelPulseDurationFrequency):
+        if isinstance(model, DingModelPulseDurationFrequency | DingModelPulseDurationFrequencyWithFatigue):
             if pulse_duration is None and [pulse_duration_min, pulse_duration_max].count(None) != 0:
                 raise ValueError("pulse duration or pulse duration min max bounds need to be set for this model")
             if all([pulse_duration, pulse_duration_min, pulse_duration_max]):
@@ -412,7 +412,7 @@ def _sanity_check(
             if not isinstance(pulse_duration_bimapping, None | bool):
                 raise NotImplementedError("If added, pulse duration parameter mapping must be a bool type")
 
-        if isinstance(model, DingModelIntensityFrequency):
+        if isinstance(model, DingModelIntensityFrequency | DingModelIntensityFrequencyWithFatigue):
             if pulse_intensity is None and [pulse_intensity_min, pulse_intensity_max].count(None) != 0:
                 raise ValueError("Pulse intensity or pulse intensity min max bounds need to be set for this model")
             if all([pulse_intensity, pulse_intensity_min, pulse_intensity_max]):

cocofest/optimization/fes_ocp_dynamics.py

@@ -46,8 +46,8 @@ def prepare_ocp(
         objective_dict: dict = None,
         custom_constraint: ConstraintList = None,
         with_residual_torque: bool = False,
-        muscle_force_length_relationship: bool = False,
-        muscle_force_velocity_relationship: bool = False,
+        activate_force_length_relationship: bool = False,
+        activate_force_velocity_relationship: bool = False,
         minimize_muscle_fatigue: bool = False,
         minimize_muscle_force: bool = False,
         use_sx: bool = True,
@@ -87,25 +87,25 @@ def prepare_ocp(
             Optional if not using the Hmed2018 models
         objective_dict : dict
             Dictionary containing parameters related to the objective of the optimization.
-        custom_constraint : ConstraintList, optional
+        custom_constraint : ConstraintList,
             Custom constraints for the OCP.
-        with_residual_torque : bool, optional
+        with_residual_torque : bool
             If residual torque is used.
-        muscle_force_length_relationship : bool, optional
+        activate_force_length_relationship : bool
             If the force length relationship is used.
-        muscle_force_velocity_relationship : bool, optional
+        activate_force_velocity_relationship : bool
             If the force velocity relationship is used.
-        minimize_muscle_fatigue : bool, optional
+        minimize_muscle_fatigue : bool
             Minimize the muscle fatigue.
-        minimize_muscle_force : bool, optional
+        minimize_muscle_force : bool
             Minimize the muscle force.
-        use_sx : bool, optional
+        use_sx : bool
             The nature of the CasADi variables. MX are used if False.
-        ode_solver : OdeSolverBase, optional
+        ode_solver : OdeSolverBase
             The ODE solver to use.
-        control_type : ControlType, optional
+        control_type : ControlType
             The type of control to use.
-        n_threads : int, optional
+        n_threads : int
             The number of threads to use while solving (multi-threading if > 1).
 
         Returns
@@ -182,8 +182,8 @@ def prepare_ocp(
             end_node_tracking=end_node_tracking,
             q_tracking=q_tracking,
             with_residual_torque=with_residual_torque,
-            muscle_force_length_relationship=muscle_force_length_relationship,
-            muscle_force_velocity_relationship=muscle_force_velocity_relationship,
+            activate_force_length_relationship=activate_force_length_relationship,
+            activate_force_velocity_relationship=activate_force_velocity_relationship,
             minimize_muscle_fatigue=minimize_muscle_fatigue,
             minimize_muscle_force=minimize_muscle_force,
         )
@@ -252,8 +252,8 @@ def prepare_ocp(
                 name=None,
                 biorbd_path=biorbd_model_path,
                 muscles_model=fes_muscle_models,
-                muscle_force_length_relationship=muscle_force_length_relationship,
-                muscle_force_velocity_relationship=muscle_force_velocity_relationship,
+                activate_force_length_relationship=activate_force_length_relationship,
+                activate_force_velocity_relationship=activate_force_velocity_relationship,
             )
             for i in range(n_stim)
         ]
@@ -754,8 +754,8 @@ def _sanity_check_fes_models_inputs(
         end_node_tracking,
         q_tracking,
         with_residual_torque,
-        muscle_force_length_relationship,
-        muscle_force_velocity_relationship,
+        activate_force_length_relationship,
+        activate_force_velocity_relationship,
         minimize_muscle_fatigue,
         minimize_muscle_force,
     ):
@@ -832,16 +832,16 @@ def _sanity_check_fes_models_inputs(
 
         list_to_check = [
             with_residual_torque,
-            muscle_force_length_relationship,
-            muscle_force_velocity_relationship,
+            activate_force_length_relationship,
+            activate_force_velocity_relationship,
             minimize_muscle_fatigue,
             minimize_muscle_force,
         ]
 
         list_to_check_name = [
             "with_residual_torque",
-            "muscle_force_length_relationship",
-            "muscle_force_velocity_relationship",
+            "activate_force_length_relationship",
+            "activate_force_velocity_relationship",
             "minimize_muscle_fatigue",
             "minimize_muscle_force",
         ]

tests/shard2/test_fes_dynamics.py

@@ -43,8 +43,8 @@ def test_pulse_duration_multi_muscle_fes_dynamics():
         pulse_duration_dict={"pulse_duration_min": minimum_pulse_duration, "pulse_duration_max": 0.0006, "pulse_duration_bimapping": False},
         objective_dict={"custom_objective": objective_functions},
         with_residual_torque=True,
-        muscle_force_length_relationship=True,
-        muscle_force_velocity_relationship=True,
+        activate_force_length_relationship=True,
+        activate_force_velocity_relationship=True,
         use_sx=False,
     )
 
@@ -119,8 +119,8 @@ def test_pulse_intensity_multi_muscle_fes_dynamics():
         pulse_intensity_dict={"pulse_intensity_min": minimum_pulse_intensity, "pulse_intensity_max": 130, "pulse_intensity_bimapping": False},
         objective_dict={"force_tracking": track_forces},
         with_residual_torque=False,
-        muscle_force_length_relationship=True,
-        muscle_force_velocity_relationship=True,
+        activate_force_length_relationship=True,
+        activate_force_velocity_relationship=True,
         use_sx=False,
     )