The pyosim from pyomeca

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:

from pyomeca import Analogs

data_path = "../tests/data/markers_analogs.c3d"
muscles = [
    "Delt_ant",
    "Delt_med",
    "Delt_post",
    "Supra",
    "Infra",
    "Subscap",
]
emg = Analogs.from_c3d(data_path, suffix_delimiter=".", usecols=muscles)
emg.plot(x="time", col="channel", col_wrap=3)

emg_processed = (
    emg.meca.band_pass(order=2, cutoff=[10, 425])
    .meca.center()
    .meca.abs()
    .meca.low_pass(order=4, cutoff=5, freq=emg.rate)
    .meca.normalize()
)

emg_processed.plot(x="time", col="channel", col_wrap=3)

import matplotlib.pyplot as plt

fig, axes = plt.subplots(ncols=2, figsize=(10, 4))

emg_processed.mean("channel").plot(ax=axes[0])
axes[0].set_title("Mean EMG activation")

emg_processed.plot.hist(ax=axes[1], bins=50)
axes[1].set_title("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:

conda install -c conda-forge pyomeca

Now that you have installed pyomeca, you should be able to import it:

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:

@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:

@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.

Does not work with python 3.6

Hi,

When I try to install the package (using conda install -c pyomeca pyosim) in a conda environment with python 3.6 I get the following error:

Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: - 
Found conflicts! Looking for incompatible packages.                                                                                                                                                  failed                                                                                                                                                                                                   

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - pyosim -> python[version='>=3.7,<3.8.0a0']

Your python: python=3.6

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with each other:



Package libgcc-ng conflicts for:
python=3.6 -> libgcc-ng[version='>=7.2.0|>=7.3.0']
Package readline conflicts for:
python=3.6 -> readline[version='7.*|>=7.0,<8.0a0']
Package pyomeca conflicts for:
pyosim -> pyomeca
Package libffi conflicts for:
python=3.6 -> libffi[version='3.2.*|>=3.2.1,<4.0a0']
Package tk conflicts for:
python=3.6 -> tk[version='8.6.*|>=8.6.7,<8.7.0a0|>=8.6.8,<8.7.0a0']
Package xz conflicts for:
python=3.6 -> xz[version='>=5.2.3,<6.0a0|>=5.2.4,<6.0a0']
Package pip conflicts for:
python=3.6 -> pip
Package matplotlib conflicts for:
pyosim -> matplotlib
Package opensim conflicts for:
pyosim -> opensim
Package ncurses conflicts for:
python=3.6 -> ncurses[version='6.0.*|>=6.0,<7.0a0|>=6.1,<7.0a0']
Package zlib conflicts for:
python=3.6 -> zlib[version='>=1.2.11,<1.3.0a0']
Package pandas conflicts for:
pyosim -> pandas
Package openssl conflicts for:
python=3.6 -> openssl[version='1.0.*|1.0.*,>=1.0.2l,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1c,<1.1.2a']
Package sqlite conflicts for:
python=3.6 -> sqlite[version='>=3.20.1,<4.0a0|>=3.22.0,<4.0a0|>=3.23.1,<4.0a0|>=3.24.0,<4.0a0|>=3.25.2,<4.0a0|>=3.26.0,<4.0a0|>=3.29.0,<4.0a0']
Package libstdcxx-ng conflicts for:
python=3.6 -> libstdcxx-ng[version='>=7.2.0|>=7.3.0']
Package numpy conflicts for:
pyosim -> numpy

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pyosim's Introduction

Pyomeca documentation

Example

Features

Installation

Integration with other modules

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Citing Pyomeca

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