Mesh 3D (TPTBox.mesh3D)

3D surface mesh generation from segmentation NIfTI volumes and rendering of 3D snapshots. Requires pyvista and vtk (included in the dev extras).

Key symbols

Symbol	Module	Description
Mesh	mesh.py	Generates a surface mesh from a segmentation label using marching cubes
create_snapshot3D	snapshot3D.py	Renders a 3D snapshot from a list of meshes to a PNG file
LABEL_COLORS	mesh_colors.py	Default colour mapping for anatomical label IDs
label_to_color(label_id)	mesh_colors.py	Look up the RGB colour for a given label
create_html_preview(meshes)	html_preview.py	Generate an interactive HTML file with an embedded 3D viewer

Example

from TPTBox import NII
from TPTBox.mesh3D.mesh import Mesh
from TPTBox.mesh3D.snapshot3D import create_snapshot3D

seg = NII.load("seg.nii.gz", seg=True)

# Build meshes for all labels and render
meshes = [Mesh(seg, label=lbl) for lbl in seg.unique_labels()]
create_snapshot3D(meshes, to="snapshot3D.png")

Installation

pip install pyvista vtk
# or via the dev extras:
poetry install --with dev