cardiac-geometries

Cardiac Geometries

This is a library for creating idealized cardiac geometries in FEniCS using gmsh. Currently you can create bi-ventricular (BiV) and left-ventricular (LV) ellipsoidal geometries as well as slab geometries. There is also support for creating bi-ventricular and slab geometries embedded in a torso / bath.

This package can also output analytic fiber orientations for LV and Slab and integrated with the ldrb algorithm BiV geometries.

Install

User are encourage to use the the provided docker image

docker pull ghcr.io/computationalphysiology/cardiac_geometries:latest

which comes pre-installed with FEniCs and gmsh.

You can also install cardiac-geometries using pip

python3 -m pip install cardiac-geometries

but this requires FEniCS and gmsh to be installed in other ways. See more at https://computationalphysiology.github.io/cardiac_geometries/install.html

Getting started

cardiac-geometries comes with a command-line interface, and to e.g create an LV mesh you can do

cardiac-geometries create-lv-ellipsoid lv-mesh

The same functionality can be accessed through the Python API, e.g

import cardiac_geometries

geo = cardiac_geometries.mesh.create_lv_ellipsoid(outdir="lv-mesh")

See https://computationalphysiology.github.io/cardiac_geometries/quickstart.html for more info.

Documentation

Please read the documentation at http://computationalphysiology.github.io/cardiac_geometries for more info.

Contributing

See https://computationalphysiology.github.io/cardiac_geometries/CONTRIBUTING.html

License

MIT