[WIP] Walking penalties #921

EveCharbie · 2025-02-18T06:32:44Z

Added TRACK_GRF and TRACK_COP penalties (+ tested values)
Added a test for the configure variables
Did not add an example for the new penalties
Did not add the forces to the ExternalForceSetTimeSeries (which should be done in a future refactor, but it is not fast and simple)

This change is

codecov · 2025-02-18T06:44:57Z

Codecov Report

Attention: Patch coverage is 92.94118% with 6 lines in your changes missing coverage. Please review.

Project coverage is 77.88%. Comparing base (c194ef1) to head (5713f0f).
Report is 8 commits behind head on master.

Files with missing lines	Patch %	Lines
bioptim/limits/penalty.py	88.88%	4 Missing ⚠️
bioptim/models/biorbd/biorbd_model.py	95.83%	1 Missing ⚠️
bioptim/optimization/optimization_variable.py	66.66%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #921      +/-   ##
==========================================
+ Coverage   77.70%   77.88%   +0.18%     
==========================================
  Files         156      156              
  Lines       18011    18074      +63     
==========================================
+ Hits        13995    14077      +82     
+ Misses       4016     3997      -19

Flag	Coverage Δ
unittests	`77.88% <92.94%> (+0.18%)`	⬆️

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EveCharbie · 2025-02-18T14:39:25Z

@Ipuch this too ?

Ipuch

Reviewed 7 of 9 files at r1, 2 of 2 files at r2, all commit messages.
Reviewable status: all files reviewed, 13 unresolved discussions (waiting on @EveCharbie)

bioptim/models/biorbd/biorbd_model.py line 615 at r2 (raw file):

        return casadi_fun

    def ground_reaction_forces_and_positions(self, with_position, associated_marker_index: list = None) -> Function:

two separated functions ?

bioptim/models/biorbd/biorbd_model.py line 626 at r2 (raw file):

        tau_biorbd = GeneralizedTorque(self.tau)
        if self.external_force_set is None:
            contact_forces = self.model.ContactForcesFromForwardDynamicsConstraintsDirect(

try to use the method if is exist or create it.

bioptim/models/biorbd/biorbd_model.py line 631 at r2 (raw file):

        else:
            contact_forces = self.model.ContactForcesFromForwardDynamicsConstraintsDirect(
                q_biorbd, qdot_biorbd, tau_biorbd, self.biorbd_external_forces_set

Try to write a one-liner.
biorbd_external_forces_set = self.biorbd_external_forces_set if is not none else None

tests/shard4/test_penalty.py line 104 at r2 (raw file):

    if with_external_forces:
        if not with_contact:
            raise NotImplementedError("External forces must be used with contact")

This case make no sens to test.

bioptim/optimization/optimization_variable.py line 538 at r2 (raw file):

    def shape(self):
        if isinstance(self._unscaled, list) and len(self._unscaled) == 0:
            return 0

remove or raise that says it's empty

bioptim/dynamics/configure_problem.py line 1806 at r2 (raw file):

    @staticmethod
    def configure_contact_forces(ocp, nlp, as_states: bool, as_controls: bool, n_contacts: int = 1):

Translational ? More generic ?

bioptim/limits/penalty.py line 770 at r2 (raw file):

        @staticmethod
        def minimize_ground_reaction_forces(

total_contact_force ?
total_reaction_force ?

bioptim/limits/penalty.py line 771 at r2 (raw file):

        @staticmethod
        def minimize_ground_reaction_forces(
            penalty: PenaltyOption, controller: PenaltyController, contact_index: tuple | list | int | str = None

enlever int et str

bioptim/limits/penalty.py line 774 at r2 (raw file):

        ):
            """
            Simulate force plate data from the contact forces computed through the dynamics with contact

In the case of gait analysis, ...

bioptim/limits/penalty.py line 816 at r2 (raw file):

            controller: PenaltyController,
            associated_marker_index: tuple | list | int | str,
            contact_index: tuple | list | int | str = None,

remove int and str

bioptim/limits/penalty.py line 843 at r2 (raw file):

            penalty.quadratic = True if penalty.quadratic is None else penalty.quadratic

            if controller.external_forces.shape[0] == 0:

the "if case" doesn't make a consistent call of ground_reaction_forces_and_positions

bioptim/limits/penalty.py line 844 at r2 (raw file):

            if controller.external_forces.shape[0] == 0:
                forces_on_each_point, position_of_each_point = controller.model.ground_reaction_forces_and_positions(

C'est nouveau

Code quote:

ground_reaction_forces_and_positions

bioptim/limits/penalty.py line 862 at r2 (raw file):

            for i_component in range(3):
                center_of_pressure[i_component] = if_else(
                    total_force[i_component] < 1e-6, 0, val[i_component] / total_force[i_component]

barycenter = val[i_component] / total_force[i_component]
separate the physics from the numerical hack.

EveCharbie

Reviewable status: all files reviewed, 13 unresolved discussions (waiting on @Ipuch)

bioptim/dynamics/configure_problem.py line 1806 at r2 (raw file):