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
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.
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.
MIT
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