Using object files

In this demo we will generate Purkinje networks on a Sphere from an .obj-file. This mesh is from the original repository at fsahli/fractal-tree

First we make the necessary imports. Note that we will import meshio for loading the .obj. You can install meshio with pip install meshio.

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

We set the log level to INFO, which will makes sure that we don’t pollute the console with output. To see more output, you can set the log level to DEBUG.

logging.basicConfig(level=logging.INFO)

Next, we will load the mesh using meshio

fname = "sphere.obj"
msh = meshio.read(fname)

This mesh is a surface mesh of triangles. We create a Mesh object by passing the points as the vertices and the cells as the connectivity array

mesh = Mesh(verts=msh.points, connectivity=msh.cells[0].data)

We can also specify some parameters for for the fractal tree. Here we specify an output filename, the number of generations to run.

param = FractalTreeParameters(
    filename="sphere-line",
    N_it=10,
)

Finally we run the fractal tree algorithm. Here are also set a seed for the random number generator in order to make the results reproducible.

np.random.seed(1)
generate_fractal_tree(mesh, param)

  0%|          | 0/10 [00:00<?, ?it/s]

 30%|███       | 3/10 [00:00<00:00, 15.35it/s]

 50%|█████     | 5/10 [00:00<00:00,  7.57it/s]

 60%|██████    | 6/10 [00:01<00:00,  4.78it/s]

 70%|███████   | 7/10 [00:01<00:01,  2.94it/s]

 80%|████████  | 8/10 [00:02<00:01,  1.89it/s]

 90%|█████████ | 9/10 [00:04<00:00,  1.27it/s]

100%|██████████| 10/10 [00:06<00:00,  1.21s/it]

100%|██████████| 10/10 [00:06<00:00,  1.55it/s]

INFO:fractal_tree.tree:Finished growing, writing paraview file

FractalTreeResult(branches={0: <fractal_tree.branch.Branch object at 0x7f45f0622a40>, 1: <fractal_tree.branch.Branch object at 0x7f45f0622b30>, 2: <fractal_tree.branch.Branch object at 0x7f45f0623ee0>, 3: <fractal_tree.branch.Branch object at 0x7f45cc6f5bd0>, 4: <fractal_tree.branch.Branch object at 0x7f45cc6f5a20>, 5: <fractal_tree.branch.Branch object at 0x7f45cc6f5c30>, 6: <fractal_tree.branch.Branch object at 0x7f45cc6f59f0>, 7: <fractal_tree.branch.Branch object at 0x7f45cc6f5990>, 8: <fractal_tree.branch.Branch object at 0x7f45cc6f5a80>, 9: <fractal_tree.branch.Branch object at 0x7f45cc6f5a50>, 10: <fractal_tree.branch.Branch object at 0x7f45cc6f5ae0>, 11: <fractal_tree.branch.Branch object at 0x7f45cc6f5ba0>, 12: <fractal_tree.branch.Branch object at 0x7f45cc6f5d20>, 13: <fractal_tree.branch.Branch object at 0x7f45cc6f5cc0>, 14: <fractal_tree.branch.Branch object at 0x7f45cc6f5d80>, 15: <fractal_tree.branch.Branch object at 0x7f45cc6f5d50>, 16: <fractal_tree.branch.Branch object at 0x7f45cc6f5db0>, 17: <fractal_tree.branch.Branch object at 0x7f45cc6f5cf0>, 18: <fractal_tree.branch.Branch object at 0x7f45cc6f5e10>, 19: <fractal_tree.branch.Branch object at 0x7f45cc6f5de0>, 20: <fractal_tree.branch.Branch object at 0x7f45cc6f5e40>, 21: <fractal_tree.branch.Branch object at 0x7f45cc6f5e70>, 22: <fractal_tree.branch.Branch object at 0x7f45cc6f5f00>, 23: <fractal_tree.branch.Branch object at 0x7f45cc6f5ea0>, 24: <fractal_tree.branch.Branch object at 0x7f45cc6f5f30>, 25: <fractal_tree.branch.Branch object at 0x7f45cc6f5f90>, 26: <fractal_tree.branch.Branch object at 0x7f45cc6f5fc0>, 27: <fractal_tree.branch.Branch object at 0x7f45cc6f60b0>, 28: <fractal_tree.branch.Branch object at 0x7f45cc6f5c90>, 29: <fractal_tree.branch.Branch object at 0x7f45cc6f5c60>, 30: <fractal_tree.branch.Branch object at 0x7f45cc6f6050>, 31: <fractal_tree.branch.Branch object at 0x7f45cc6f5ff0>, 32: <fractal_tree.branch.Branch object at 0x7f45cc6f5900>, 33: <fractal_tree.branch.Branch 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Fig. 1 The sphere coming from the object file with the generated Purkinje networks visualized in Paraview