Marching Cubes

Generate a surface from a scalar field using the flying edges and marching cubes filters as provided by the contour filter.

Special thanks to GitHub user stla for providing examples.

import numpy as np

import pyvista as pv

Spider Cage

Use the marching cubes algorithm to extract the isosurface generated from the spider cage function.

a = 0.9


def spider_cage(x, y, z):
    x2 = x * x
    y2 = y * y
    x2_y2 = x2 + y2
    return (np.sqrt((x2 - y2) ** 2 / x2_y2 + 3 * (z * np.sin(a)) ** 2) - 3) ** 2 + 6 * (
        np.sqrt((x * y) ** 2 / x2_y2 + (z * np.cos(a)) ** 2) - 1.5
    ) ** 2


# create a uniform grid to sample the function with
n = 100
x_min, y_min, z_min = -5, -5, -3
grid = pv.ImageData(
    dimensions=(n, n, n),
    spacing=(abs(x_min) / n * 2, abs(y_min) / n * 2, abs(z_min) / n * 2),
    origin=(x_min, y_min, z_min),
)
x, y, z = grid.points.T

# sample and plot
values = spider_cage(x, y, z)
mesh = grid.contour([1], values, method='marching_cubes')
dist = np.linalg.norm(mesh.points, axis=1)
mesh.plot(scalars=dist, smooth_shading=True, cmap="plasma", show_scalar_bar=False)

Static Scene

Interactive Scene

Barth Sextic

Use the flying edges algorithm to extract the isosurface generated from the Barth sextic function.

phi = (1 + np.sqrt(5)) / 2
phi2 = phi * phi


def barth_sextic(x, y, z):
    x2 = x * x
    y2 = y * y
    z2 = z * z
    arr = (
        3 * (phi2 * x2 - y2) * (phi2 * y2 - z2) * (phi2 * z2 - x2)
        - (1 + 2 * phi) * (x2 + y2 + z2 - 1) ** 2
    )
    nan_mask = x2 + y2 + z2 > 3.1
    arr[nan_mask] = np.nan
    return arr


# create a uniform grid to sample the function with
n = 100
k = 2.0
x_min, y_min, z_min = -k, -k, -k
grid = pv.ImageData(
    dimensions=(n, n, n),
    spacing=(abs(x_min) / n * 2, abs(y_min) / n * 2, abs(z_min) / n * 2),
    origin=(x_min, y_min, z_min),
)
x, y, z = grid.points.T

# sample and plot
values = barth_sextic(x, y, z)
mesh = grid.contour([0], values, method='flying_edges')
dist = np.linalg.norm(mesh.points, axis=1)
mesh.plot(scalars=dist, smooth_shading=True, cmap="plasma", show_scalar_bar=False)

Static Scene

Interactive Scene

Animate Barth Sextic

Show 20 frames of various isocurves extracted from the Barth sextic function.

def angle_to_range(angle):
    return -2 * np.sin(angle)


pl = pv.Plotter(window_size=[800, 800], off_screen=True)

pl.open_gif('barth_sextic.gif')

for angle in np.linspace(0, np.pi, 20, endpoint=False):
    # clear the plotter before adding each frame's mesh
    pl.clear()
    pl.enable_lightkit()
    mesh = grid.contour([angle_to_range(angle)], values, method='flying_edges')
    dist = np.linalg.norm(mesh.points, axis=1)
    pl.add_mesh(
        mesh,
        scalars=dist,
        smooth_shading=True,
        rng=[0.5, 1.5],
        cmap="plasma",
        show_scalar_bar=False,
    )
    pl.write_frame()

pl.close()