VaMPy
VaMPy: An Automated and Objective Pipeline for Modeling Vascular Geometries - Published in JOSS (2023)
Science Score: 98.0%
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✓CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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✓DOI references
Found 7 DOI reference(s) in README and JOSS metadata -
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Links to: joss.theoj.org, zenodo.org -
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✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Keywords from Contributors
Repository
A collection of tools for pre-processing, simulating, and post-processing vascular morphologies.
Basic Info
- Host: GitHub
- Owner: KVSlab
- License: other
- Language: Python
- Default Branch: master
- Homepage: https://kvslab.github.io/VaMPy
- Size: 153 MB
Statistics
- Stars: 17
- Watchers: 7
- Forks: 9
- Open Issues: 10
- Releases: 8
Topics
Metadata Files
README.md
VaMPy - Vascular Modeling Pypeline
Pre-processed and simulated artery model. From left to right: A variable density volumetric mesh, zoomed in view of an outlet showing the four boundary layers, corresponding inlet flow rate, outlet flow split, and probes for velocity and pressure sampling. From the simulation results, we have shown the velocity field represented by vectors, and the time averaged wall shear stress (TAWSS) as one of the many hemodynamic indices computed by the post-processing scripts.
Description
The Vascular Modeling Pypeline (VaMPy) is a collection of fully automated scripts used to prepare, run, and analyze cardiac and atrial morphologies. This includes pre-processing scripts for meshing and probe sampling, two Oasis problem files for simulating flow in the internal carotid artery and the left atrium, and a variety of post-processing scripts for computing WSS-based metrics, more advanced turbulence metrics, and a variety of morphological parameters in patient-specific geometries.
Installation
VaMPy is a Python package for Python >= 3.8, with main dependencies to morphMan and Oasis. VaMPy and its dependencies can be installed with conda on n Linux and
macOS using the following command:
conda create -n your_environment -c conda-forge vampy
More details on installation via conda can be found here. The package can also be installed and run through its latest Docker image supported by Windows, Linux, and macOS, and explained here.
Documentation
VaMPy's documentation is hosted here. This includes two tutorials, meant to guide the user through the basic steps of performing a computational fluid dynamic simulation in a vascular body.
Licence
VaMPy is licensed under the GNU GPL, version 3 or (at your option) any later version.
VaMPy is Copyright (2018-2023) by the authors.
Authors
VaMPy has been developed by
Issues
Please report bugs and other issues through the issue tracker at:
https://github.com/KVSlab/VaMPy/issues
Owner
- Name: KVSlab
- Login: KVSlab
- Kind: organization
- Repositories: 6
- Profile: https://github.com/KVSlab
JOSS Publication
VaMPy: An Automated and Objective Pipeline for Modeling Vascular Geometries
Authors
Department of Computational Physiology, Simula Research Laboratory, Oslo, Norway
Department of Computational Physiology, Simula Research Laboratory, Oslo, Norway
Department of Computational Physiology, Simula Research Laboratory, Oslo, Norway
Editor
Kevin M. Moerman
Tags
pre-processing computational fluid dynamics post-processing vascular modeling automated objective pipelineCitation (CITATION.cff)
cff-version: "1.2.0"
authors:
- family-names: Kjeldsberg
given-names: Henrik A.
orcid: "https://orcid.org/0000-0002-7764-4248"
- family-names: Bergersen
given-names: Aslak W.
orcid: "https://orcid.org/0000-0001-5063-3680"
- family-names: Valen-Sendstad
given-names: Kristian
orcid: "https://orcid.org/0000-0002-2907-0171"
doi: 10.5281/zenodo.7950605
message: If you use this software, please cite our article in the
Journal of Open Source Software.
preferred-citation:
authors:
- family-names: Kjeldsberg
given-names: Henrik A.
orcid: "https://orcid.org/0000-0002-7764-4248"
- family-names: Bergersen
given-names: Aslak W.
orcid: "https://orcid.org/0000-0001-5063-3680"
- family-names: Valen-Sendstad
given-names: Kristian
orcid: "https://orcid.org/0000-0002-2907-0171"
date-published: 2023-05-19
doi: 10.21105/joss.05278
issn: 2475-9066
issue: 85
journal: Journal of Open Source Software
publisher:
name: Open Journals
start: 5278
title: "VaMPy: An Automated and Objective Pipeline for Modeling
Vascular Geometries"
type: article
url: "https://joss.theoj.org/papers/10.21105/joss.05278"
volume: 8
title: "VaMPy: An Automated and Objective Pipeline for Modeling Vascular
Geometries"
GitHub Events
Total
- Watch event: 2
- Delete event: 1
- Issue comment event: 2
- Push event: 2
- Pull request review event: 3
- Pull request event: 6
- Fork event: 1
- Create event: 1
Last Year
- Watch event: 2
- Delete event: 1
- Issue comment event: 2
- Push event: 2
- Pull request review event: 3
- Pull request event: 6
- Fork event: 1
- Create event: 1
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Henrik Kjedsberg | h****g@l****o | 553 |
| Kei | w****5@g****m | 28 |
| Aslak Bergersen | a****n@g****m | 25 |
| Ehsan Khalili | e****n@s****o | 7 |
| Jørgen S. Dokken | d****n@s****o | 6 |
| cardioFluid | 4****d | 4 |
| Johannes Ring | j****g@g****m | 2 |
| Stef Smeets | s****s | 2 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 24
- Total pull requests: 79
- Average time to close issues: 5 months
- Average time to close pull requests: 7 days
- Total issue authors: 10
- Total pull request authors: 5
- Average comments per issue: 2.96
- Average comments per pull request: 0.82
- Merged pull requests: 70
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 6
- Average time to close issues: N/A
- Average time to close pull requests: 5 days
- Issue authors: 0
- Pull request authors: 2
- Average comments per issue: 0
- Average comments per pull request: 0.67
- Merged pull requests: 6
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- keiyamamo (11)
- hkjeldsberg (2)
- johannesring (2)
- stefsmeets (2)
- lshahid (2)
- michaelbernini (1)
- perolope (1)
- Owais-Khan (1)
- yewalenikhil65 (1)
- perezrmaria (1)
Pull Request Authors
- hkjeldsberg (65)
- keiyamamo (16)
- johannesring (3)
- jorgensd (2)
- stefsmeets (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/cache v2 composite
- actions/checkout v3 composite
- codecov/codecov-action v3 composite
- conda-incubator/setup-miniconda v2 composite
- actions/cache v2 composite
- actions/checkout v3 composite
- conda-incubator/setup-miniconda v2 composite
- peaceiris/actions-gh-pages v3.6.1 composite
- actions/checkout v3 composite
- docker/build-push-action v3 composite
- docker/login-action v2 composite
- docker/metadata-action v4 composite
- docker/setup-buildx-action v2 composite
- docker/setup-qemu-action v2 composite
- condaforge/mambaforge latest build
- cppimport *
- matplotlib *
- numpy *
- ghp-import *
- jupyter-book *
- matplotlib *
- numpy *