pytessel 1.3.0

Python package for building isosurfaces from 3D scalar fields

PyTessel

Purpose

PyTessel is a Python package for constructing isosurfaces from 3D scalar fields using the marching cubes algorithm. It is designed for scientific visualization, computational geometry, and mesh generation workflows. While PyTessel was originally developed for rendering molecular orbitals, it is flexible enough to tessellate arbitrary scalar fields.

Installation

pip install pytessel

Getting started

The example below constructs an isosurface of a three-dimensional Gaussian function. The resulting surface is written to test.ply, which can be viewed using tools such as:

• ctmviewer (Linux)
• 3D Viewer (Windows, free via Microsoft Store)
• Blender, MeshLab, etc.

from pytessel import PyTessel
import numpy as np

def main():
    pytessel = PyTessel()

    # Generate a regular grid
    x = np.linspace(0, 10, 50)

    # Grid ordering:
    # z is the slowest-moving index, x is the fastest-moving index
    grid = np.flipud(
        np.vstack(np.meshgrid(x, x, x, indexing='ij')).reshape(3, -1)
    ).T

    R = [5, 5, 5]
    scalarfield = np.reshape(
        np.array([gaussian(r, R) for r in grid]),
        (len(x), len(x), len(x))
    )

    unitcell = np.diag(np.ones(3) * 10.0)

    vertices, normals, indices = pytessel.marching_cubes(
        scalarfield.flatten(),
        scalarfield.shape,
        unitcell.flatten(),
        0.1
    )

    pytessel.write_ply('test.ply', vertices, normals, indices)

def gaussian(r, R):
    return np.exp(-(r - R).dot(r - R))

if __name__ == '__main__':
    main()

Isosurface quality

The script below demonstrates how grid resolution affects surface quality. Six isosurfaces of an icosahedral metaball are generated using grids of:

• 10×10×10
• 20×20×20
• 25×25×25
• 50×50×50
• 100×100×100
• 200×200×200

Each surface is exported as a .ply file and rendered using Blender.

from pytessel import PyTessel
import numpy as np

def main():
    """
    Build 6 .ply files of increasing quality
    """
    pytessel = PyTessel()

    for nrpoints in [10, 20, 25, 50, 100, 200]:
        sz = 3

        x = np.linspace(-sz, sz, nrpoints)
        y = np.linspace(-sz, sz, nrpoints)
        z = np.linspace(-sz, sz, nrpoints)

        xx, yy, zz, field = icosahedron_field(x, y, z)

        unitcell = np.diag(np.ones(3) * sz * 2)
        isovalue = 3.75

        vertices, normals, indices = pytessel.marching_cubes(
            field.flatten(),
            field.shape,
            unitcell.flatten(),
            isovalue
        )

        pytessel.write_ply(
            f'icosahedron_{nrpoints:03d}.ply',
            vertices,
            normals,
            indices
        )

def icosahedron_field(x, y, z):
    """
    Produce a scalar field for icosahedral metaballs
    """
    phi = (1 + np.sqrt(5)) / 2
    vertices = [
        [0, 1, phi], [0, -1, -phi], [0, 1, -phi], [0, -1, phi],
        [1, phi, 0], [-1, -phi, 0], [1, -phi, 0], [-1, phi, 0],
        [phi, 0, 1], [-phi, 0, -1], [phi, 0, -1], [-phi, 0, 1]
    ]

    xx, yy, zz = np.meshgrid(x, y, z)
    field = np.zeros_like(xx)

    for v in vertices:
        field += metaball(xx, yy, zz, v[0], v[1], v[2])

    return xx, yy, zz, field

def metaball(x, y, z, X0, Y0, Z0):
    """
    Single metaball function
    """
    return 1 / ((x - X0)**2 + (y - Y0)**2 + (z - Z0)**2)

if __name__ == '__main__':
    main()

Gallery

Stanford Bunny

Gyroid surface