Network Morphology

Builds a pore network scene from a MAT file, coloring pores and throats by radius, with a solid overlay and axes.

example/network_morphology.py

import json
from pathlib import Path

from porescene import image, worker
from porescene.color.palette import Colormap, Palette
from porescene.config import PropertyConfiguration
from porescene.model import PoreNetwork
from porescene.scene import Scene
from porescene.utility import CompassDirection, Orientation

# =============================================================================
# Import Parameters

# data directory
pth_data = Path.cwd() / "data"

# temporary directory for rendered images
pth_tmp = Path.cwd() / "tmp"


# =============================================================================
# Scene configuration and rendering

# load variable mapping for variable import from .mat file
with open(pth_data / "map_vars.json") as f:
    map_vars = json.load(f)

# load pore network data from MAT file
pn = PoreNetwork.from_mat(pth_data / "pnm.mat", map_vars["data_network"])

# load PoreScene config from JSON file
sc = Scene.from_json(pn.extent, pth_data / "porescene.json")

# initialized PNM property "radius"
sc.config_scene.add_property(
    PropertyConfiguration(
        "radius",
        Palette.load(Colormap.LIPARI).all(),
        heading="Diameter [µm]",
        orientation=Orientation.VERTICAL,
        align=CompassDirection.WEST,
        precision=0,
        factor=2e6,  # converts radius in [m] to diameter in [µm]
    )
)

# add cylinders and spheres to the scene
worker.build_structure(sc, pn, top=True, bottom=True)

# add axes around the scene
sc.create_axes()

# add a solid object to the scene
sc.create_solid(pth_data / "solid.ply")

# render the scene and color pores and throat according to their radius
pth_img = worker.make_radius(pth_tmp, pn, sc)

# add padding of 10 %
image.img_pad(pth_img, 0.1, trim=False)