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 import ListSqueeze
from polpo.preprocessing.load.pregnancy import PregnancyPilotSegmentationsLoader
from polpo.preprocessing.mesh.conversion import PvFromData
from polpo.preprocessing.mesh.filter import PvSelectColor
from polpo.preprocessing.mri import (
    MeshExtractorFromSegmentedImage,
    MriImageLoader,
    segmtool2encoding,
)

[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

pipe = (
    PregnancyPilotSegmentationsLoader(subset=[SESSION_ID])
    + ListSqueeze()
    + MriImageLoader()
    + MeshExtractorFromSegmentedImage(encoding="ashs")
    + 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 encoded by colors. In this particular case, the encoding is generated by ASHS. We provide access to the encoding.

encoding = segmtool2encoding(tool="ashs")

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, color) in enumerate(encoding.structs2colors.items()):
    row, col = index // n_cols, index % n_cols
    pl.subplot(row, col)

    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.

NB: recall that a substructure can directly be extracted from the image, as shown here.