purkinje-uv 0.4.0

Utilities to generate Purkinje networks from fractal trees and mesh surfaces

PurkinjeUV

PurkinjeUV is a modular Python package for constructing, simulating, and exporting fractal-based Purkinje networks over anatomical or idealized cardiac surface meshes. It offers a flexible architecture for working with geometries via OBJ, VTK, and GMSH, and supports UV mapping, eikonal solvers, and export utilities.

Table of Contents

• Features
• Installation
• Getting Started
• Examples
• Requirements
• Attributions and Credits
• Citation
• License
• Contributing

Features

• Fractal-based generation of Purkinje networks constrained to 3D surface meshes
• Fast Iterative Method (FIM)-based eikonal solver for activation time simulation
• Surface processing tools, including Laplacian-based UV mapping
• VTK and IGB utilities for visualization and interoperability with scientific tools
• Fully modular and scriptable, suitable for both research and reproducible simulation pipelines

Installation

Install the latest release from PyPI:

pip install purkinje-uv

Documentation

The full documentation is available at:

https://ricardogr07.github.io/purkinje-uv/main

Getting Started

See Getting Started Guide for full documentation.

# Generate a fractal tree and save it to VTU (no activation required)

from pathlib import Path
import numpy as np

from purkinje_uv import FractalTreeParameters, FractalTree, PurkinjeTree

# Parameters: FractalTree reads the mesh from p.meshfile
p = FractalTreeParameters(
    meshfile="data/sphere.obj",
    init_node_id=0,
    second_node_id=1,
    l_segment=0.01,   # step size on the surface
    init_length=0.1,
    length=0.1,
    branch_angle=0.15,
    w=0.1,
    N_it=10,
)

# Grow the tree on the surface (UV domain)
ft = FractalTree(params=p)
ft.grow_tree()

# Wrap as a PurkinjeTree and save
out = Path("output")
out.mkdir(parents=True, exist_ok=True)

purk = PurkinjeTree(
    nodes=np.asarray(ft.nodes_xyz),
    connectivity=np.asarray(ft.connectivity),
    end_nodes=np.asarray(ft.end_nodes),
)

purk.save(str(out / "fractal_tree.vtu"))

Visualization:

import pyvista as pv

tree = pv.read("output/fractal_tree.vtu")
tree.plot()

Runnable notebooks:

• examples/demo_obj/demo_obj_fractal_tree.ipynb
• examples/demo_gmsh/demo_fractal_tree_biventricular.ipynb

Requirements

• Python ≥ 3.10
• Optional:
  • pyvista for visualization
  • cupy for GPU acceleration (used in FIM solver)
  • gmsh and cardiac-geometries for realistic biventricular geometries

Attributions and Credits

Based on the work by Francisco Sahli:

• fractal-tree: https://github.com/fsahli/fractal-tree
• purkinje-learning: https://github.com/fsahli/purkinje-learning

References: Sahli Costabal, F., Yao, J., & Kuhl, E. (2016). Predicting the cardiac toxicity of drugs using a hybrid multiscale model of the heart. Journal of the Mechanical Behavior of Biomedical Materials, 62, 217–231. DOI: 10.1016/j.jmbbm.2016.05.004

Maintained by Ricardo García Ramírez (July 2025)

Citation

@article{sahli2016hybrid,
  title={Predicting the cardiac toxicity of drugs using a hybrid multiscale model of the heart},
  author={Sahli Costabal, Feras and Yao, Jiajian and Kuhl, Ellen},
  journal={Journal of the Mechanical Behavior of Biomedical Materials},
  volume={62},
  pages={217--231},
  year={2016},
  publisher={Elsevier}
}

@misc{purkinjeuv2025,
  author = {Ricardo García Ramírez},
  title = {PurkinjeUV: Modular Fractal Purkinje Generator on Surface Meshes},
  year = {2025},
  howpublished = {\url{https://github.com/ricardogr07/purkinje-uv}}
}

License

Released under the MIT License. See LICENSE.

Contributing

See CONTRIBUTING.md for guidelines.