How to visualize meshes with overlay?

import pyvista as pv

from polpo.preprocessing import Map
from polpo.preprocessing.load import FigsharePregnancyDataLoader
from polpo.preprocessing.mesh.conversion import PvFromData
from polpo.preprocessing.mesh.io import PvReader
from polpo.preprocessing.mesh.transform import MeshCenterer, MeshScaler
from polpo.preprocessing.mri import (
    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")

Following How to get a mesh from an MRI image?, we download a segmented MRI and get a mesh out of it.

SESSION_ID = 2

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"),
    ]
)

loading_pipe = loader + finder + MriImageLoader()
img2mesh_pipe = MeshExtractorFromSegmentedImage() + PvFromData()

pipe = loading_pipe + img2mesh_pipe

raw_mesh = pipe()

INFO: Data has already been downloaded... using cached file ('/home/luisfpereira/.herbrain/data/pregnancy/Segmentations/BB02').

We also load a registered version of the same mesh (NB: there’s more registrations at figshare).

loader = (
    FigsharePregnancyDataLoader(
        data_dir="~/.herbrain/data/pregnancy/registration",
        remote_path="registration/elastic_20250106_80",
    )
    + FileFinder(
        rules=[
            FileRule(value=f"left_{str(SESSION_ID).zfill(2)}", func="startswith"),
            FileRule(value=".ply", func="endswith"),
        ],
    )
    + PvReader()
)

registered_mesh = loader()

INFO: Data has already been downloaded... using cached file ('/home/luisfpereira/.herbrain/data/pregnancy/registration/elastic_20250106_80').

The registered mesh was preprocessed before registration. Let’s apply the same preprocessing in order to have an overlayable representation.

processing_pipe = Map(
    [MeshCenterer(attr="points"), MeshScaler(attr="points")],
    force_iter=True,
)

raw_mesh = processing_pipe(raw_mesh)

Visualization.

pl = pv.Plotter(shape=(1, 2), border=False)

pl.subplot(0, 0)
pl.add_mesh(raw_mesh, show_edges=True)
pl.add_mesh(registered_mesh, opacity=0.25)
pl.remove_scalar_bar()

pl.subplot(0, 1)
pl.add_mesh(registered_mesh, show_edges=True)
pl.add_mesh(raw_mesh, opacity=0.25)
pl.remove_scalar_bar()

pl.link_views()

pl.show()

Notice the meshes fully overlap even though they have a very different combinatorial structure.

(
    raw_mesh.faces.shape[0] // 3,
    registered_mesh.faces.shape[0] // 3,
)

(27680, 6032)