https://github.com/computationalphysiology/cardiac-geometries

Tool for creating idealised cardiac geometries and microstructure
https://github.com/computationalphysiology/cardiac-geometries

cardiac geometry mesh

Last synced: 2 months ago
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Tool for creating idealised cardiac geometries and microstructure

• Host: GitHub
• URL: https://github.com/computationalphysiology/cardiac-geometries
• Owner: ComputationalPhysiology
• License: mit
• Created: 2022-01-31T10:39:08.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2024-11-24T12:02:38.000Z (2 months ago)
• Last Synced: 2024-11-24T13:17:32.415Z (2 months ago)
• Topics: cardiac, geometry, mesh
• Language: Python
• Homepage: https://computationalphysiology.github.io/cardiac-geometries
• Size: 6.92 MB
• Stars: 6
• Watchers: 6
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Contributing: docs/CONTRIBUTING.md
  • License: LICENSE

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README

        
# 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](https://github.com/finsberg/ldrb) algorithm BiV geometries.

## Install

User are encourage to use the the [provided docker image](https://github.com/ComputationalPhysiology/cardiac_geometries/pkgs/container/cardiac-geometries)

```

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

```python

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