How to select a mesh subset?

This notebook shows how to select a subset of a mesh that is encoded by a color.

import pyvista as pv

from polpo.preprocessing.load.pregnancy import FigsharePregnancyDataLoader
from polpo.preprocessing.mesh.conversion import PvFromData
from polpo.preprocessing.mesh.filter import PvSelectColor
from polpo.preprocessing.mri import (
    BRAINSTRUCT2COLOR,
    MeshExtractorFromSegmentedImage,
    MriImageLoader,
)
from polpo.preprocessing.path import FileFinder, FileRule

[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")

Mesh from MRI

Following How to get a mesh from an MRI image?, we get a pv.PolyData object representing the hippocampus.

SESSION_ID = 1

folder_name = f"BB{str(SESSION_ID).zfill(2)}"

loader = FigsharePregnancyDataLoader(
    data_dir="~/.herbrain/data/pregnancy/Segmentations",
    remote_path=f"Segmentations/{folder_name}",
)

finder = FileFinder(
    rules=[
        FileRule(value="left", func="startswith"),
        FileRule(value=".nii.gz", func="endswith"),
    ]
)

pipe = (
    loader
    + finder
    + MriImageLoader()
    + MeshExtractorFromSegmentedImage()
    + PvFromData()
)

mesh = pipe()

INFO: Data has already been downloaded... using cached file ('/home/luisfpereira/.herbrain/data/pregnancy/Segmentations/BB01').

pl = pv.Plotter(border=False)

pl.show_axes()
pl.add_mesh(mesh, show_edges=True)
pl.show()

Select a substructure

Substructures are endoded by colors. BRAINSTRUCT2COLOR maps their name to the corresponding color.

We now create a preprocessing step that selects the cells of the mesh with the given color.

struct_selector = PvSelectColor(extract_surface=True)

n_cols = 3
pl = pv.Plotter(shape=(3, n_cols), border=False)

for index, struct_name in enumerate(BRAINSTRUCT2COLOR):
    row, col = index // n_cols, index % n_cols
    pl.subplot(row, col)

    color = BRAINSTRUCT2COLOR[struct_name]

    substructure = struct_selector((mesh, color))

    pl.show_axes()
    substructure.clear_data()
    pl.add_mesh(substructure, show_edges=True)
    pl.add_title(struct_name, font_size=10)

pl.show()

Any mesh preprocessing step can now be applied to the substructure.