How to create a gif showing how the brain substructures change over time?

from pathlib import Path

import pyvista as pv

import polpo.preprocessing.dict as ppdict
import polpo.utils as putils
from polpo.plot.pyvista import RegisteredMeshesGifPlotter
from polpo.preprocessing import PartiallyInitializedStep
from polpo.preprocessing.load.fsl import get_all_first_structs
from polpo.preprocessing.load.pregnancy.jacobs import MeshLoader
from polpo.preprocessing.mesh.registration import PvAlign

[KeOps] Warning : cuda was detected, but driver API could not be initialized. Switching to cpu only.

STATIC_VIZ = True

if STATIC_VIZ:
    pv.set_jupyter_backend("static")

Loading meshes

NB: we perform rigid alignment on the meshes wrt the first mesh.

structs = get_all_first_structs(include_brstem=False, order=True)

subject_id = "01"

mesh_loader = (
    MeshLoader(
        subject_subset=[subject_id],
        struct_subset=structs,
        as_mesh=True,
    )
    + ppdict.ExtractUniqueKey()
    + ppdict.NestedDictSwapper()
)

prep_pipe = PartiallyInitializedStep(
    Step=lambda **kwargs: ppdict.DictMap(PvAlign(**kwargs)),
    _target=lambda meshes: meshes[list(meshes.keys())[0]],
    max_iterations=500,
)


pipe = mesh_loader + ppdict.DictMap(prep_pipe)

# prefixed_struct, time
meshes = pipe()

Create gif

gif_dir = Path("_images")
gif_dir.mkdir(exist_ok=True)

gif_name = gif_dir / f"{subject_id}_all_structs.gif"


pl = RegisteredMeshesGifPlotter(
    shape=putils.plot_shape_from_n_plots(len(meshes), n_axis=2, axis=0),
    rowise=False,
    gif_name=gif_name.as_posix(),
    fps=5,
    border=False,
    off_screen=True,
    notebook=False,
    window_size=(1920, 1080),
    subtitle=(
        lambda session_id, struct_name: f"{subject_id}, {struct_name}, {session_id}"
    ),
)

pl.add_meshes(ppdict.NestedDictSwapper()(meshes))
pl.close()

pl.show()