pyomeca
pyomeca: An Open-Source Framework for Biomechanical Analysis - Published in JOSS (2020)
Science Score: 95.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 13 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
Links to: joss.theoj.org -
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1 of 6 committers (16.7%) from academic institutions -
○Institutional organization owner
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✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Scientific Fields
Repository
Python toolbox for biomechanics analysis
Basic Info
- Host: GitHub
- Owner: pyomeca
- License: apache-2.0
- Language: Jupyter Notebook
- Default Branch: master
- Homepage: https://pyomeca.github.io/
- Size: 13.1 MB
Statistics
- Stars: 131
- Watchers: 8
- Forks: 33
- Open Issues: 4
- Releases: 11
Topics
Metadata Files
README.md
Pyomeca is a python library allowing you to carry out a complete biomechanical analysis; in a simple, logical and concise way.
Pyomeca documentation
See Pyomeca's documentation site.
Example
Pyomeca implements specialized functionalities commonly used in biomechanics.
As an example, let's process the electromyographic data contained in this c3d file.
You can follow along without installing anything by using our binder server: 
```python from pyomeca import Analogs
datapath = "../tests/data/markersanalogs.c3d" muscles = [ "Deltant", "Deltmed", "Deltpost", "Supra", "Infra", "Subscap", ] emg = Analogs.fromc3d(datapath, suffixdelimiter=".", usecols=muscles) emg.plot(x="time", col="channel", col_wrap=3) ```
```python emgprocessed = ( emg.meca.bandpass(order=2, cutoff=[10, 425]) .meca.center() .meca.abs() .meca.low_pass(order=4, cutoff=5, freq=emg.rate) .meca.normalize() )
emgprocessed.plot(x="time", col="channel", colwrap=3) ```
```python import matplotlib.pyplot as plt
fig, axes = plt.subplots(ncols=2, figsize=(10, 4))
emgprocessed.mean("channel").plot(ax=axes[0]) axes[0].settitle("Mean EMG activation")
emgprocessed.plot.hist(ax=axes[1], bins=50) axes[1].settitle("EMG activation distribution") ```
See the documentation for more details and examples.
Features
- Signal processing routine commonly used in biomechanics such as filters, normalization, onset detection, outliers detection, derivatives, etc.
- Common matrix manipulation routines implemented such as getting Euler angles to/from a rototranslation matrix, creating a system of axes, setting a rotation or translation, transpose or inverse, etc.
- Easy reading and writing interface to common files in biomechanics (
c3d,csv,xlsx,mat,trc,sto,mot) - All of xarray's awesome features
The following illustration shows all of pyomeca's public API. An interactive version is available in the documentation.
Installation
Pyomeca itself is a pure Python package, but its dependencies are not. The easiest way to get everything installed is to use conda.
To install pyomeca with its recommended dependencies using the conda command line tool:
bash
conda install -c conda-forge pyomeca
Now that you have installed pyomeca, you should be able to import it:
python
import pyomeca
Integration with other modules
Pyomeca is designed to work well with other libraries that we have developed:
- pyosim: interface between OpenSim and pyomeca to perform batch musculoskeletal analyses
- ezc3d: Easy to use C3D reader/writer in C++, Python and Matlab
- biorbd: C++ interface and add-ons to the Rigid Body Dynamics Library, with Python and Matlab binders.
Bug reports & questions
Pyomeca is Apache-licensed and the source code is available on GitHub. If any questions or issues come up as you use pyomeca, please get in touch via GitHub issues. We welcome any input, feedback, bug reports, and contributions.
Citing Pyomeca
If you use pyomeca in your academic work, please consider citing our paper as:
bibtex
@article{Martinez2020,
doi = {10.21105/joss.02431},
url = {https://doi.org/10.21105/joss.02431},
year = {2020},
publisher = {The Open Journal},
volume = {5},
number = {53},
pages = {2431},
author = {Romain Martinez and Benjamin Michaud and Mickael Begon},
title = {`pyomeca`: An Open-Source Framework for Biomechanical Analysis},
journal = {Journal of Open Source Software}
}
Please consider citing the xarray project, which pyomeca is based on:
bibtex
@article{jors-xarray,
title = {Xarray: N-D labeled arrays and datasets in Python},
author = {Joe Hamman and Stephan Hoyer},
year = {2017},
journal = {Journal of Open Research Software}
}
Contributors
Pyomeca is an open-source project created and supported by the S2M lab.
Owner
- Name: pyomeca
- Login: pyomeca
- Kind: organization
- Location: Montréal
- Repositories: 21
- Profile: https://github.com/pyomeca
Biomechanics library
JOSS Publication
pyomeca: An Open-Source Framework for Biomechanical Analysis
Authors
School of Kinesiology and Exercise Science, Faculty of Medicine, University of Montreal, Canada
School of Kinesiology and Exercise Science, Faculty of Medicine, University of Montreal, Canada
School of Kinesiology and Exercise Science, Faculty of Medicine, University of Montreal, Canada
Editor
Kevin M. Moerman
Tags
python biomechanics electromyography kinematics dynamicsGitHub Events
Total
- Create event: 1
- Release event: 1
- Issues event: 2
- Watch event: 13
- Issue comment event: 6
- Push event: 3
- Pull request review event: 2
- Pull request event: 3
- Fork event: 1
Last Year
- Create event: 1
- Release event: 1
- Issues event: 2
- Watch event: 13
- Issue comment event: 6
- Push event: 3
- Pull request review event: 2
- Pull request event: 3
- Fork event: 1
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Romain Martinez | m****s@g****m | 310 |
| Pariterre | p****e@h****m | 113 |
| bernikr | g****t@b****r | 4 |
| eve-mac | e****1@u****a | 3 |
| d.kilic | d****c@f****e | 1 |
| Kristen Thyng | k****g@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 48
- Total pull requests: 60
- Average time to close issues: 3 months
- Average time to close pull requests: 7 days
- Total issue authors: 22
- Total pull request authors: 6
- Average comments per issue: 2.81
- Average comments per pull request: 2.07
- Merged pull requests: 55
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 4
- Average time to close issues: 1 day
- Average time to close pull requests: 22 days
- Issue authors: 1
- Pull request authors: 3
- Average comments per issue: 2.0
- Average comments per pull request: 1.25
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- romainmartinez (13)
- pariterre (6)
- Dareczin (5)
- jrdunga (2)
- BKillen05 (2)
- hasnaaouadoudibelabzioui (2)
- SebastienCordillet (2)
- mitkof6 (2)
- mrrezaie (1)
- marnunez (1)
- Arevis13 (1)
- anboen (1)
- SoniaSong826 (1)
- steakerlife (1)
- bernikr (1)
Pull Request Authors
- romainmartinez (33)
- pariterre (23)
- EveCharbie (3)
- bernikr (2)
- kthyng (1)
- Kilidsch (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 198 last-month
- Total docker downloads: 75
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Total dependent packages: 2
(may contain duplicates) -
Total dependent repositories: 6
(may contain duplicates) - Total versions: 11
- Total maintainers: 1
pypi.org: pyomeca
pyomeca is a python library allowing to carry out a complete biomechanical analysis; in a simple, logical and concise way
- Documentation: https://pyomeca.readthedocs.io/
- License: Apache 2.0
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Latest release: 2024.0.2
published about 1 year ago
Rankings
Maintainers (1)
conda-forge.org: pyomeca
Python toolbox for biomechanics analysis
- Homepage: http://github.com/pyomeca/pyomeca
- License: Apache-2.0
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Latest release: 2021.0.1
published almost 5 years ago
Rankings
Dependencies
- autoflake * development
- black * development
- bs4 * development
- isort * development
- jupyter * development
- mkdocs * development
- mkdocs-material * development
- mkdocs-minify-plugin * development
- mkdocstrings * development
- pytest * development
- pytest-cov * development
- requests * development
- actions/checkout master composite
- s-weigand/setup-conda v1 composite
- actions/checkout v4 composite
- actions/download-artifact v4 composite
- actions/setup-python v5 composite
- actions/upload-artifact v4 composite
- pypa/gh-action-pypi-publish release/v1 composite
- bottleneck *
- ezc3d >= 1.3.2
- matplotlib *
- numpy *
- openpyxl *
- scipy *
- xarray *