create_model.py

"""
This example shows how to add different components to a model from scratch.
"""

import os
from pathlib import Path

import numpy as np
import biorbd
from biobuddy import (
    BiomechanicalModel,
    MeshFile,
    Segment,
    Contact,
    MuscleGroup,
    Muscle,
    MuscleType,
    MuscleStateType,
    Translations,
    Rotations,
    RangeOfMotion,
    Ranges,
    ViaPoint,
)


def complex_model_from_scratch(mesh_path, remove_temporary: bool = True):
    """
    We define a new model by feeding in the actual dimension and position of the model.
    Please note that this model is not a human, it is only used to show the functionalities of the model creation module.
    """

    kinematic_model_filepath = "temporary_complex.bioMod"

    # Create a model holder
    bio_model = BiomechanicalModel()

    # The ground segment
    bio_model.add_segment(Segment(name="GROUND"))

    # The pendulum segment
    bio_model.add_segment(
        Segment(
            name="PENDULUM",
            translations=Translations.XYZ,
            rotations=Rotations.X,
            q_ranges=RangeOfMotion(range_type=Ranges.Q, min_bound=[-1, -1, -1, -np.pi], max_bound=[1, 1, 1, np.pi]),
            qdot_ranges=RangeOfMotion(
                range_type=Ranges.Qdot, min_bound=[-10, -10, -10, -np.pi * 10], max_bound=[10, 10, 10, np.pi * 10]
            ),
            mesh_file=MeshFile(
                mesh_file_name="pendulum.STL",
                mesh_file_directory=mesh_path,
                mesh_color=np.array([0, 0, 1]),
                scaling_function=lambda m, model: np.array([1, 1, 10]),
                rotation_function=lambda m, model: np.array([np.pi / 2, 0, 0]),
                translation_function=lambda m, model: np.array([0.1, 0, 0]),
            ),
        )
    )
    # The pendulum segment contact point
    bio_model.segments["PENDULUM"].add_contact(
        Contact(
            name="PENDULUM_CONTACT",
            function=lambda m, model: np.array([0, 0, 0]),
            parent_name="PENDULUM",
            axis=Translations.XYZ,
        )
    )

    # The pendulum muscle group
    bio_model.add_muscle_group(
        MuscleGroup(name="PENDULUM_MUSCLE_GROUP", origin_parent_name="GROUND", insertion_parent_name="PENDULUM")
    )

    # The pendulum muscle
    bio_model.muscle_groups["PENDULUM_MUSCLE_GROUP"].add_muscle(
        Muscle(
            "PENDULUM_MUSCLE",
            muscle_type=MuscleType.HILL_THELEN,
            state_type=MuscleStateType.DEGROOTE,
            muscle_group="PENDULUM_MUSCLE_GROUP",
            origin_position=ViaPoint(
                name="PENDULUM_ORIGIN",
                parent_name="GROUND",
                muscle_name="PENDULUM_MUSCLE",
                muscle_group="PENDULUM_MUSCLE_GROUP",
                position_function=lambda m, model: np.array([0, 0, 0]),
            ),
            insertion_position=ViaPoint(
                name="PENDULUM_ORIGIN",
                parent_name="PENDULUM",
                muscle_name="PENDULUM_MUSCLE",
                muscle_group="PENDULUM_MUSCLE_GROUP",
                position_function=lambda m, model: np.array([0, 0, 1]),
            ),
            optimal_length_function=lambda m, model: 0.1,
            maximal_force_function=lambda m, model: 100.0,
            tendon_slack_length_function=lambda m, model: 0.05,
            pennation_angle_function=lambda m, model: 0.05,
            maximal_velocity_function=lambda m, model: 10.0,
            maximal_excitation=1,
        )
    )
    bio_model.muscle_groups["PENDULUM_MUSCLE_GROUP"].muscles["PENDULUM_MUSCLE"].add_via_point(
        ViaPoint(
            "PENDULUM_MUSCLE",
            parent_name="PENDULUM",
            muscle_name="PENDULUM_MUSCLE",
            muscle_group="PENDULUM_MUSCLE_GROUP",
            position_function=lambda m, model: np.array([0, 0, 0.5]),
        )
    )

    # Put the model together
    real_model = bio_model.to_real({}, None)

    # Print it to a bioMod file
    real_model.to_biomod(kinematic_model_filepath)

    model = biorbd.Model(kinematic_model_filepath)
    assert model.nbQ() == 4
    assert model.nbSegment() == 3
    assert model.nbMarkers() == 0
    assert model.nbMuscles() == 1
    assert model.nbMuscleGroups() == 1
    assert model.nbContacts() == 3

    if remove_temporary:
        os.remove(kinematic_model_filepath)

    return real_model


def main():
    current_path_file = Path(__file__).parent
    complex_model_from_scratch(mesh_path=f"{current_path_file}/meshFiles")


if __name__ == "__main__":
    main()