Removing mx_reduced by creating "biorbd wrapper"

.gitignore

@@ -86,9 +86,6 @@ venv.bak/
 # pycharm
 .idea
 
-# Personnal stuff
-Misc/
-
 # Remove symbolic links to bioptim in examples and tests folder
 examples/*/biorbd_optim
 examples/biorbd_optim

README.md

@@ -175,7 +175,6 @@ As a tour guide that uses this binder, you can watch the `bioptim` workshop that
     - [CostType](#enum-costtype)
     - [SolutionIntegrator](#enum-solutionintegrator)
     - [QuadratureRule](#enum-quadraturerule)
-    - [RigidBodyDynamics](#enum-rigidbodydynamics)
     - [SoftContactDynamics](#enum-softcontactdynamics)
     - [DefectType](#enum-defecttype)
 
@@ -1226,11 +1225,11 @@ This constraint assumes that the normal forces is positive (that is having an ad
 - **TRACK_COM_VELOCITY**  — Constraints the center of mass velocity toward a target. The extra parameter `axis_to_track: Axis = (Axis.X, Axis.Y, Axis.Z)` can be provided to specify the axes along which the velocity should be tracked.
 - **TRACK_CONTACT_FORCES**  — Tracks the non-acceleration point reaction forces toward a target.
 - **TRACK_LINEAR_MOMENTUM**  — Constraints the linear momentum toward a target. The extra parameter `axis_to_track: Axis = (Axis.X, Axis.Y, Axis.Z)` can be sent to specify the axes along which the momentum should be tracked.
-- **TRACK_MARKER_WITH_SEGMENT_AXIS**  — Tracks a marker using a segment, that is aligning an axis toward the marker. The extra parameters `marker_idx: int`, `segment_idx: int`, and `axis: Axis` must be passed to the `Constraint` constructor
+- **TRACK_MARKER_WITH_SEGMENT_AXIS**  — Tracks a marker using a segment, that is aligning an axis toward the marker. The extra parameters `marker_idx: int`, `segment_index: int`, and `axis: Axis` must be passed to the `Constraint` constructor
 - **TRACK_MARKERS_VELOCITY** — Tracks the skin marker velocities toward a target.
 - **TRACK_MARKERS** — Tracks the skin markers toward a target. The extra parameter `axis_to_track: Axis = (Axis.X, Axis.Y, Axis.Z)` can be provided to specify the axes along which the markers should be tracked.
 - **TRACK_MUSCLES_CONTROL**  — Tracks the muscles (part of the control variables) toward a target.
-- **TRACK_SEGMENT_WITH_CUSTOM_RT**  —Links a segment with an RT (for instance, an Inertial Measurement Unit). It does so by computing the homogenous transformation between the segment and the RT and then converting this to Euler angles. The extra parameters `segment_idx: int` and `rt_idx: int` must be passed to the `Constraint` constructor.
+- **TRACK_SEGMENT_WITH_CUSTOM_RT**  —Links a segment with an RT (for instance, an Inertial Measurement Unit). It does so by computing the homogenous transformation between the segment and the RT and then converting this to Euler angles. The extra parameters `segment_index: int` and `rt_index: int` must be passed to the `Constraint` constructor.
 - **TRACK_STATE** — Tracks the state's variable toward a target.
 - **TRACK_TORQUE**  — Tracks the generalized forces (part of the control variables) toward a target.
 - **CUSTOM**  — The user should not directly send CUSTOM, but the user should pass the custom_constraint function directly. You can look at Constraint and ConstraintList sections for more information about how to define custom constraints.
@@ -1322,11 +1321,11 @@ Here a list of objective function with its type (Lagrange and/or Mayer) in alpha
 - **SUPERIMPOSE_MARKERS** (Lagrange and Mayer) — Tracks one marker with another one. The extra parameters `first_marker_idx: int` and `second_marker_idx: int` informs which markers are to be superimposed
 - **TRACK_ALL_CONTROLS (Lagrange)** — Tracks all the control variables toward a target.
 - **TRACK_CONTACT_FORCES** (Lagrange) — Tracks the non-acceleration points of the reaction forces toward a target.
-- **TRACK_MARKER_WITH_SEGMENT_AXIS** (Lagrange and Mayer) — Minimizes the distance between a marker and an axis of a segment, that is aligning an axis toward the marker. The extra parameters `marker_idx: int`, `segment_idx: int` and `axis: Axis` must be passed to the `Objective` constructor
+- **TRACK_MARKER_WITH_SEGMENT_AXIS** (Lagrange and Mayer) — Minimizes the distance between a marker and an axis of a segment, that is aligning an axis toward the marker. The extra parameters `marker_idx: int`, `segment_index: int` and `axis: Axis` must be passed to the `Objective` constructor
 - **TRACK_MARKERS_VELOCITY or TRACK_MARKERS_ACCELERATION** (Lagrange and Mayer) —  Tracks the marker velocities or accelerations toward a target.
 - **TRACK_MARKERS** (Lagrange and Mayer) — Tracks the skin markers towards a target. The extra parameter `axis_to_track: Axis = (Axis.X, Axis.Y, Axis.Z)` can be sent to specify the axes along which the markers should be tracked.
 - **TRACK_MUSCLES_CONTROL** (Lagrange) — Tracks the muscles' controls (part of the control variables) toward a target.
-- **TRACK_SEGMENT_WITH_CUSTOM_RT** (Lagrange and Mayer)  — Minimizes the distance between a segment and an RT (for instance, an Inertial Measurement Unit). It does so by computing the homogenous transformation between the segment and the RT and then converting this to Euler angles. The extra parameters `segment_idx: int` and `rt_idx: int` must be passed to the `Objective` constructor.
+- **TRACK_SEGMENT_WITH_CUSTOM_RT** (Lagrange and Mayer)  — Minimizes the distance between a segment and an RT (for instance, an Inertial Measurement Unit). It does so by computing the homogenous transformation between the segment and the RT and then converting this to Euler angles. The extra parameters `segment_index: int` and `rt_index: int` must be passed to the `Objective` constructor.
 - **TRACK_SOFT_CONTACT_FORCES**  (Lagrange)  — Tracks the external forces induced by soft contacts toward a target.
 - **TRACK_STATE**  (Lagrange and Mayer) — Tracks the state variable toward a target.
 - **TRACK_TORQUE** (Lagrange — Tracks the generalized forces (part of the control variables) toward a target.
@@ -1746,14 +1745,6 @@ The type of integration used to integrate the cost function terms of Lagrange:
 - APPROXIMATE_TRAPEZOIDAL: The integral is approximated by a trapezoidal rule using the state at the beginning of the next interval.
 - TRAPEZOIDAL: The integral is approximated by a trapezoidal rule using the state at the end of the current interval.
 
-### Enum: RigidBodyDynamics
-The type of transcription of any dynamics (e.g., rigidbody_dynamics or soft_contact_dynamics):
-- ODE: the dynamics is handled explicitly in the continuity constraint of the ordinary differential equation of the Direct Multiple Shooting approach.
-- DAE_INVERSE_DYNAMICS: it adds an extra control *qddot* to respect inverse dynamics on nodes; this is a DAE-constrained OCP.
-- DAE_FORWARD_DYNAMICS: it adds an extra control *qddot* to respect forward dynamics on nodes; this is a DAE-constrained OCP.
-- DAE_INVERSE_DYNAMICS_JERK: it adds an extra control *qdddot* and an extra state *qddot* to respect inverse dynamics on nodes; this is a DAE-constrained OCP.
-- DAE_FORWARD_DYNAMICS_JERK: it adds an extra control *qdddot* and an extra state *qddot* to respect forward dynamics on nodes; this is a DAE-constrained OCP.
-
 ### Enum: SoftContactDynamics
 The type of transcription of any dynamics (e.g., rigidbody_dynamics or soft_contact_dynamics):
 - ODE: soft contact dynamics is handled explicitly.
@@ -1910,9 +1901,6 @@ example, a spring) can be found at 'examples/torque_driven_ocp/spring_load.py'
 `Bioptim` expects `external_forces` to be a np.ndarray [6 x n x n_shooting], where the six components are 
 [Mx, My, Mz, Fx, Fy, Fz], expressed at the origin of the global reference frame for each node.
 
-### The [example_implicit_dynamics.py](./bioptim/examples/getting_started/example_implicit_dynamics.py) file
-*#TODO*
-
 ### The [example_inequality_constraint.py](./bioptim/examples/getting_started/example_inequality_constraint.py) file
 This example mimics what a jumper does when maximizing the predicted height of the center of mass at the peak of an aerial phase. It does so with a simplistic two segments model.
 It is a clone of 'torque_driven_ocp/maximize_predicted_height_CoM.py' using
@@ -2366,7 +2354,7 @@ definition of the constraints of the problem:
 ```python
 constraints = ConstraintList()
 constraints.add(
-ConstraintFcn.TRACK_MARKER_WITH_SEGMENT_AXIS, node=Node.ALL, marker_idx=1, segment_idx=2, axis=Axis.X
+ConstraintFcn.TRACK_MARKER_WITH_SEGMENT_AXIS, node=Node.ALL, marker_idx=1, segment_index=2, axis=Axis.X
 )
 ```
 
@@ -2380,12 +2368,9 @@ the rest is fully optimized. It is designed to show how to use the tracking RT f
 any RT (for instance, Inertial Measurement Unit [IMU]) with a body segment.
 
 To implement this tracking task, we use the `ConstraintFcn.TRACK_SEGMENT_WITH_CUSTOM_RT` constraint function, which 
-minimizes the distance between a segment and an RT. The extra parameters `segment_idx: int` and `rt_idx: int` must be 
+minimizes the distance between a segment and an RT. The extra parameters `segment_index: int` and `rt_index: int` must be 
 passed to the Objective constructor.
 
-### The [track_vector_orientation.py](./bioptim/examples/track/track_vector_orientation.py) file
-*#TODO*
-
 ## Moving estimation horizon (MHE)
 In this section, we perform MHE on the pendulum example.
 

bioptim/__init__.py

@@ -164,33 +164,50 @@
 
 """
 
-from .misc.__version__ import __version__
 from .dynamics.configure_problem import ConfigureProblem, DynamicsFcn, DynamicsList, Dynamics
-from .dynamics.dynamics_functions import DynamicsFunctions
+from .dynamics.configure_problem import ConfigureProblem, DynamicsFcn, DynamicsList, Dynamics
 from .dynamics.dynamics_evaluation import DynamicsEvaluation
+from .dynamics.dynamics_evaluation import DynamicsEvaluation
+from .dynamics.dynamics_functions import DynamicsFunctions
+from .dynamics.dynamics_functions import DynamicsFunctions
+from .dynamics.fatigue.effort_perception import EffortPerception, TauEffortPerception
+from .dynamics.fatigue.effort_perception import EffortPerception, TauEffortPerception
+from .dynamics.fatigue.fatigue_dynamics import FatigueList
 from .dynamics.fatigue.fatigue_dynamics import FatigueList
-from .dynamics.fatigue.xia_fatigue import XiaFatigue, XiaTauFatigue, XiaFatigueStabilized
 from .dynamics.fatigue.michaud_fatigue import MichaudFatigue, MichaudTauFatigue
-from .dynamics.fatigue.effort_perception import EffortPerception, TauEffortPerception
+from .dynamics.fatigue.michaud_fatigue import MichaudFatigue, MichaudTauFatigue
+from .dynamics.fatigue.xia_fatigue import XiaFatigue, XiaTauFatigue, XiaFatigueStabilized
+from .dynamics.fatigue.xia_fatigue import XiaFatigue, XiaTauFatigue, XiaFatigueStabilized
 from .dynamics.ode_solver import OdeSolver, OdeSolverBase
+from .dynamics.ode_solver import OdeSolver, OdeSolverBase
+from .gui.online_callback_server import PlottingServer
+from .gui.online_callback_server import PlottingServer
+from .gui.plot import CustomPlot
+from .gui.plot import CustomPlot
+from .interfaces import Solver
 from .interfaces import Solver
-from .models.biorbd.biorbd_model import BiorbdModel
-from .models.biorbd.multi_biorbd_model import MultiBiorbdModel
-from .models.biorbd.holonomic_biorbd_model import HolonomicBiorbdModel
-from .models.biorbd.variational_biorbd_model import VariationalBiorbdModel
-from .models.biorbd.stochastic_biorbd_model import StochasticBiorbdModel
-from .models.holonomic_constraints import HolonomicConstraintsFcn, HolonomicConstraintsList
-from .models.protocols.stochastic_biomodel import StochasticBioModel
-from .models.protocols.biomodel import BioModel
 from .limits.constraints import ConstraintFcn, ConstraintList, Constraint, ParameterConstraintList
-from .limits.phase_transition import PhaseTransitionFcn, PhaseTransitionList, PhaseTransition
+from .limits.constraints import ConstraintFcn, ConstraintList, Constraint, ParameterConstraintList
+from .limits.fatigue_path_conditions import FatigueBounds, FatigueInitialGuess
+from .limits.fatigue_path_conditions import FatigueBounds, FatigueInitialGuess
+from .limits.multinode_constraint import MultinodeConstraintFcn, MultinodeConstraintList, MultinodeConstraint
 from .limits.multinode_constraint import MultinodeConstraintFcn, MultinodeConstraintList, MultinodeConstraint
 from .limits.multinode_objective import MultinodeObjectiveFcn, MultinodeObjectiveList, MultinodeObjective
+from .limits.multinode_objective import MultinodeObjectiveFcn, MultinodeObjectiveList, MultinodeObjective
+from .limits.objective_functions import ObjectiveFcn, ObjectiveList, Objective, ParameterObjectiveList
 from .limits.objective_functions import ObjectiveFcn, ObjectiveList, Objective, ParameterObjectiveList
 from .limits.path_conditions import BoundsList, InitialGuessList, Bounds, InitialGuess
-from .limits.fatigue_path_conditions import FatigueBounds, FatigueInitialGuess
+from .limits.path_conditions import BoundsList, InitialGuessList, Bounds, InitialGuess
+from .limits.penalty_controller import PenaltyController
 from .limits.penalty_controller import PenaltyController
 from .limits.penalty_helpers import PenaltyHelpers
+from .limits.penalty_helpers import PenaltyHelpers
+from .limits.phase_transition import PhaseTransitionFcn, PhaseTransitionList, PhaseTransition
+from .limits.phase_transition import PhaseTransitionFcn, PhaseTransitionList, PhaseTransition
+from .misc.__version__ import __version__
+from .misc.__version__ import __version__
+from .misc.casadi_expand import lt, le, gt, ge, if_else, if_else_zero
+from .misc.casadi_expand import lt, le, gt, ge, if_else, if_else_zero
 from .misc.enums import (
     Axis,
     Node,
@@ -202,7 +219,6 @@
     VariableType,
     SolutionIntegrator,
     QuadratureRule,
-    RigidBodyDynamics,
     SoftContactDynamics,
     DefectType,
     MagnitudeType,
@@ -211,25 +227,30 @@
     OnlineOptim,
 )
 from .misc.mapping import BiMappingList, BiMapping, Mapping, NodeMapping, NodeMappingList, SelectionMapping, Dependency
+from .misc.mapping import BiMappingList, BiMapping, Mapping, NodeMapping, NodeMappingList, SelectionMapping, Dependency
+from .models.biorbd.biorbd_model import BiorbdModel
+from .models.biorbd.external_forces import ExternalForceSetTimeSeries
+from .models.biorbd.holonomic_biorbd_model import HolonomicBiorbdModel
+from .models.biorbd.multi_biorbd_model import MultiBiorbdModel
+from .models.biorbd.stochastic_biorbd_model import StochasticBiorbdModel
+from .models.biorbd.variational_biorbd_model import VariationalBiorbdModel
+from .models.holonomic_constraints import HolonomicConstraintsFcn, HolonomicConstraintsList
+from .models.protocols.biomodel import BioModel
+from .models.protocols.stochastic_biomodel import StochasticBioModel
 from .optimization.multi_start import MultiStart
 from .optimization.non_linear_program import NonLinearProgram
 from .optimization.optimal_control_program import OptimalControlProgram
-from .optimization.receding_horizon_optimization import MovingHorizonEstimator, NonlinearModelPredictiveControl
+from .optimization.optimization_variable import OptimizationVariableList
+from .optimization.parameters import ParameterList, ParameterContainer
+from .optimization.problem_type import SocpType
 from .optimization.receding_horizon_optimization import (
     CyclicNonlinearModelPredictiveControl,
     CyclicMovingHorizonEstimator,
     MultiCyclicNonlinearModelPredictiveControl,
 )
-from .optimization.parameters import ParameterList, ParameterContainer
+from .optimization.receding_horizon_optimization import MovingHorizonEstimator, NonlinearModelPredictiveControl
 from .optimization.solution.solution import Solution
 from .optimization.solution.solution_data import SolutionMerge, TimeAlignment
-from .optimization.optimization_variable import OptimizationVariableList
+from .optimization.stochastic_optimal_control_program import StochasticOptimalControlProgram
 from .optimization.variable_scaling import VariableScalingList, VariableScaling
 from .optimization.variational_optimal_control_program import VariationalOptimalControlProgram
-
-from .optimization.stochastic_optimal_control_program import StochasticOptimalControlProgram
-from .optimization.problem_type import SocpType
-from .misc.casadi_expand import lt, le, gt, ge, if_else, if_else_zero
-
-from .gui.plot import CustomPlot
-from .gui.online_callback_server import PlottingServer