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neuromechfly

Fly

Bases: NeuroMechFly

Deprecated alias for NeuroMechFly. Will be removed in a future release.

Source code in src/flygym/compose/fly/neuromechfly.py 
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class Fly(NeuroMechFly):
    """Deprecated alias for `NeuroMechFly`. Will be removed in a future release."""

    def __init__(self, *args: Any, **kwargs: Any) -> None:
        warnings.warn(
            "`Fly` is deprecated and will be removed in a future release; "
            "use `NeuroMechFly` instead.",
            DeprecationWarning,
            stacklevel=2,
        )
        super().__init__(*args, **kwargs)

NeuroMechFly

Bases: BaseFly

The NeuroMechFly body model for Drosophila melanogaster.

NeuroMechFly is derived from a micro-CT scan of a real fly. It is the default body model in FlyGym and supports all locomotion, sensorimotor, and vision experiments. For an alternative anatomically detailed model with wing and abdomen degrees of freedom, see FlyBody.

Both NeuroMechFly and FlyBody inherit from BaseFly and expose the same composition API, so they can be used interchangeably.

Parameters:

Name Type Description Default
name str

Identifier for this fly instance. Defaults to "nmf".

 'nmf'
rigging_config_path PathLike

Path to YAML file defining body segment positions, orientations, and masses.

 DEFAULT_RIGGING_CONFIG_PATH
mesh_basedir PathLike

Directory containing STL mesh files for body segments.

 DEFAULT_MESH_DIR
mujoco_globals_path PathLike

Path to YAML file with global MuJoCo parameters.

 DEFAULT_MUJOCO_GLOBALS_PATH
root_segment BodySegment | str

Root body segment for the kinematic tree.

 'c_thorax'
mirror_left2right bool

If True, mirror left-side meshes for the right side.

 True
mesh_type MeshType

Mesh resolution to use.

 SIMPLIFIED_MAX2000FACES
geom_fitting_option GeomFittingOption

How to fit collision geometries.

 UNMODIFIED
vision_config_path PathLike

Path to YAML file with vision sensor configuration.

 DEFAULT_VISION_CONFIG_PATH
Source code in src/flygym/compose/fly/neuromechfly.py 
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class NeuroMechFly(BaseFly):
    """The NeuroMechFly body model for *Drosophila melanogaster*.

    NeuroMechFly is derived from a micro-CT scan of a real fly. It is the
    default body model in FlyGym and supports all locomotion, sensorimotor,
    and vision experiments. For an alternative anatomically detailed model
    with wing and abdomen degrees of freedom, see `FlyBody`.

    Both `NeuroMechFly` and `FlyBody` inherit from `BaseFly` and expose the
    same composition API, so they can be used interchangeably.

    Args:
        name: Identifier for this fly instance. Defaults to ``"nmf"``.
        rigging_config_path: Path to YAML file defining body segment positions,
            orientations, and masses.
        mesh_basedir: Directory containing STL mesh files for body segments.
        mujoco_globals_path: Path to YAML file with global MuJoCo parameters.
        root_segment: Root body segment for the kinematic tree.
        mirror_left2right: If True, mirror left-side meshes for the right side.
        mesh_type: Mesh resolution to use.
        geom_fitting_option: How to fit collision geometries.
        vision_config_path: Path to YAML file with vision sensor configuration.
    """

    def __init__(
        self,
        name: str = "nmf",
        *,
        rigging_config_path: PathLike = DEFAULT_RIGGING_CONFIG_PATH,
        mesh_basedir: PathLike = DEFAULT_MESH_DIR,
        mujoco_globals_path: PathLike = DEFAULT_MUJOCO_GLOBALS_PATH,
        root_segment: BodySegment | str = "c_thorax",
        mirror_left2right: bool = True,
        mesh_type: MeshType = MeshType.SIMPLIFIED_MAX2000FACES,
        geom_fitting_option: GeomFittingOption = GeomFittingOption.UNMODIFIED,
        vision_config_path: PathLike = DEFAULT_VISION_CONFIG_PATH,
    ) -> None:
        super().__init__(
            name=name,
            rigging_config_path=rigging_config_path,
            mesh_basedir=mesh_basedir,
            mujoco_globals_path=mujoco_globals_path,
            root_segment=root_segment,
            mirror_left2right=mirror_left2right,
            mesh_type=mesh_type,
            geom_fitting_option=geom_fitting_option,
            vision_config_path=vision_config_path,
        )

    def _add_mesh_assets(
        self, mesh_basedir: PathLike, mirror_left2right: bool, mesh_type: MeshType
    ) -> None:
        # Simplified meshes are bundled with the package; fullsize meshes are
        # downloaded from S3 and cached on first use.
        if mesh_type == MeshType.FULLSIZE:
            mesh_dir = lazy_load_asset_dir(NEUROMECHFLY_FULLSIZE_MESH_DIR)
        else:
            mesh_dir = Path(mesh_basedir) / mesh_type.value

        for segment_name in ALL_SEGMENT_NAMES:
            if mirror_left2right and segment_name[0] == "r":
                mesh_to_use = f"l{segment_name[1:]}"
                y_sign = -1
            else:
                mesh_to_use = segment_name
                y_sign = 1

            mesh_path = (mesh_dir / f"{mesh_to_use}.stl").resolve()
            if not mesh_path.exists():
                raise FileNotFoundError(
                    f"Mesh file not found for segment {segment_name}: {mesh_path}"
                )

            self.bodyseg_to_mjcfmesh[segment_name] = self.mjcf_root.add_mesh(
                name=segment_name,
                file=str(mesh_path),
                scale=(self.SCALE, y_sign * self.SCALE, self.SCALE),
            )

    def colorize(
        self, visuals_config_path: PathLike = DEFAULT_VISUALS_CONFIG_PATH
    ) -> None:
        """Apply colors and textures to the NeuroMechFly model.

        Args:
            visuals_config_path: Path to the YAML file defining per-segment material
                and texture assignments. Defaults to the bundled NeuroMechFly visuals.
        """
        super().colorize(visuals_config_path)

colorize(visuals_config_path=DEFAULT_VISUALS_CONFIG_PATH)

Apply colors and textures to the NeuroMechFly model.

Parameters:

Name Type Description Default
visuals_config_path PathLike

Path to the YAML file defining per-segment material and texture assignments. Defaults to the bundled NeuroMechFly visuals.

 DEFAULT_VISUALS_CONFIG_PATH
Source code in src/flygym/compose/fly/neuromechfly.py 
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def colorize(
    self, visuals_config_path: PathLike = DEFAULT_VISUALS_CONFIG_PATH
) -> None:
    """Apply colors and textures to the NeuroMechFly model.

    Args:
        visuals_config_path: Path to the YAML file defining per-segment material
            and texture assignments. Defaults to the bundled NeuroMechFly visuals.
    """
    super().colorize(visuals_config_path)