Data

Tools

Indexes

Applications

Experiments

Open Source Science

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

Tool for creating idealised cardiac geometries and microstructure

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

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.0%) to scientific vocabulary

Keywords

cardiac geometry mesh

Keywords from Contributors

image-analysis energy-system-model parallel
Last synced: 5 months ago · JSON representation

Repository

Tool for creating idealised cardiac geometries and microstructure

Basic Info
Statistics
  • Stars: 7
  • Watchers: 6
  • Forks: 2
  • Open Issues: 0
  • Releases: 5
Topics
cardiac geometry mesh
Created about 4 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License

README.md

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 ```python import cardiac_geometries

geo = cardiacgeometries.mesh.createlv_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

Owner

  • Name: Computational Physiology at Simula Research Laboratory
  • Login: ComputationalPhysiology
  • Kind: organization
  • Location: Fornebu, Norway

GitHub organization for the computational physiology department at Simula Research Laboratory

GitHub Events

Total
  • Watch event: 1
  • Push event: 52
  • Pull request event: 25
Last Year
  • Watch event: 1
  • Push event: 52
  • Pull request event: 25

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 171
  • Total Committers: 4
  • Avg Commits per committer: 42.75
  • Development Distribution Score (DDS): 0.193
Past Year
  • Commits: 47
  • Committers: 2
  • Avg Commits per committer: 23.5
  • Development Distribution Score (DDS): 0.17
Top Committers
Name Email Commits
Henrik Finsberg h****g@h****m 138
Henrik Finsberg h****f@s****o 23
pre-commit-ci[bot] 6****] 8
Reidmen r****n@g****m 2
Committer Domains (Top 20 + Academic)
simula.no: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 3
  • Total pull requests: 52
  • Average time to close issues: 3 days
  • Average time to close pull requests: 8 days
  • Total issue authors: 2
  • Total pull request authors: 3
  • Average comments per issue: 0.33
  • Average comments per pull request: 0.0
  • Merged pull requests: 47
  • Bot issues: 0
  • Bot pull requests: 29
Past Year
  • Issues: 0
  • Pull requests: 23
  • Average time to close issues: N/A
  • Average time to close pull requests: 19 days
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 18
  • Bot issues: 0
  • Bot pull requests: 23
View more stats
Top Authors
Issue Authors
  • finsberg (1)
  • Reidmen (1)
Pull Request Authors
  • pre-commit-ci[bot] (44)
  • finsberg (23)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

.github/workflows/build_docs.yml actions
  • actions/checkout v3 composite
  • peaceiris/actions-gh-pages v3 composite
.github/workflows/docker-image.yml actions
  • actions/checkout v3 composite
  • docker/build-push-action v3 composite
  • docker/login-action v2 composite
  • docker/metadata-action 98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 composite
  • docker/setup-buildx-action v2 composite
  • docker/setup-qemu-action v2 composite
.github/workflows/main.yml actions
  • actions/checkout v3 composite
.github/workflows/pypi.yml actions
  • actions/checkout v3 composite
  • pypa/gh-action-pypi-publish master composite
Dockerfile docker
  • finsberg/fenics-gmsh latest build
.github/workflows/mpi.yml actions
  • actions/checkout v3 composite
pyproject.toml pypi
  • cardiac-geometries-core >=0.2.1
  • meshio *
  • numpy *
  • rich-click *