biomesh 0.4.1

Create meshes from segmented imaging data for finite element simulations using Gmsh.

biomesh

Installation

biomesh can be installed via pip as

pip install biomesh

If you want to generate a mesh with Gmsh, you also need to install the gmsh python library as

pip install gmsh

Usage

To generate a finite element mesh from multiple colored stl-files, you simply need to do

import biomesh

# note, this requires gmsh to be installed (pip install gmsh)
mesh = biomesh.mesh_colored_stl_files(
    "path/to/part1.stl",
    "path/to/part2.stl",
    "path/to/part3.stl",
    mesh_size=2.0
)
# alternatively, you can also just use meshio to load a mesh: mesh = meshio.read("path/to/mesh.vtu")

# make all elements quadratic
mesh = biomesh.lin_to_quad(mesh)

# reorder nodes to reduce bandwidth of matrix
mesh = biomesh.reorder(mesh)

The nodes of all stl-files are matched. Each stl-file will be considered as an own volume.