fractal-tree

This code is to create a fractal tree over a surface discretized by triangles. It was developed to create a representation of the Purkinje network in the ventricles of the human heart.

Note that this is a rewrite of the original code found at https://github.com/fsahli/fractal-tree

The details of the algorithm are presented in this article. If you are going to use this code, please cite:

Generating Purkinje networks in the human heart. F. Sahli Costabal, D. Hurtado and E. Kuhl. Journal of Biomechanics, doi:10.1016/j.jbiomech.2015.12.025

• Source code: https://github.com/finsberg/fractal-tree
• Documentation: https://github.com/finsberg/fractal-tree

Install

You can install the library with pip

python3 -m pip install fractal-tree

Note that you also need a way to load the mesh from e.g gmsh or another meshing tool. For this we recommend to use meshio as it support the most common formats.

Getting started

The following illustrates a minimal example, assuming that you have surface mesh called sphere.obj in your current directory.

import meshio
import numpy as np
from fractal_tree import generate_fractal_tree, FractalTreeParameters, Mesh

msh = meshio.read("sphere.obj")
mesh = Mesh(verts=msh.points, connectivity=msh.cells[0].data)
param = FractalTreeParameters(
    filename="sphere-line",
    N_it=10,
)
branches, nodes = generate_fractal_tree(mesh, param)

For a more elaborate example you can checkout the gmsh example.

License

MIT

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