Skip to main content

Analysis package for actigraphy data

Project description

https://img.shields.io/badge/License-GPL%20v3-blue.svg https://gitlab.com/ghammad/pyActigraphy/badges/master/pipeline.svg?key_text=CI+tests https://img.shields.io/pypi/v/pyActigraphy.svg https://zenodo.org/badge/DOI/10.5281/zenodo.2537920.svg

pyActigraphy

Open-source python package for actigraphy data visualization and analysis.

This package is meant to provide a comprehensive set of tools to:

  • read native actigraphy data files with various formats:
    • Actigraph: wGT3X-BT
    • CamNtech: Actiwatch 4 and MotionWatch 8
    • Condor Instrument: ActTrust 2
    • Daqtix: Daqtometer
    • Respironics: Actiwatch 2 and Actiwatch Spectrum (plus)
    • Tempatilumi (CE Brasil)
  • clean the raw data and mask spurious periods of inactivity
  • produce activity profile plots
  • visualize sleep agendas and compute summary statistics
  • calculate typical wake/sleep cycle-related variables:
    • Non-parametric rest-activity variables: IS(m), IV(m), RA
    • Activity or Rest fragmentation: kRA, kAR
    • Sleep regularity index (SRI)
  • automatically detect rest periods using various algorithms (Cole-Kripke, Sadeh, …, Crespo, Roenneberg)
  • perform complex analyses:
    • Cosinor analysis
    • Detrended Fluctuation Analysis (DFA)
    • Functional Linear Modelling (FLM)
    • Locomotor Inactivity During Sleep (LIDS)
    • Singular Spectrum Analysis (SSA)
    • and much more…

Code and documentation

The pyActigraphy package is open-source and its source code is accessible online.

An online documentation of the package is also available here. It contains notebooks illustrating various functionalities of the package.

Installation

In a (bash) shell, simply type:

  • For users:
pip3 install pyActigraphy

To update the package:

pip3 install -U pyActigraphy
  • For developers:
git clone git@github.com:ghammad/pyActigraphy.git
cd pyActigraphy/
git checkout develop
pip3 install -e .

Quick start

The following example illustrates how to calculate the interdaily stability with the pyActigraphy package:

>>> import pyActigraphy
>>> rawAWD = pyActigraphy.io.read_raw_awd('/path/to/your/favourite/file.AWD')
>>> rawAWD.IS()
0.6900175913031027
>>> rawAWD.IS(freq='30min', binarize=True, threshold=4)
0.6245582891144925
>>> rawAWD.IS(freq='1H', binarize=False)
0.5257020914453097

Contributing

There are plenty of ways to contribute to this package, including (but not limiting to):

  • report bugs (and, ideally, how to reproduce the bug)
  • suggest improvements
  • improve the documentation

Authors

See also the list of contributors who participated in this project.

License

This project is licensed under the GNU GPL-3.0 License - see the LICENSE file for details

Acknowledgments

  • Aubin Ardois @aardoi developed the first version of the MTN class during his internship at the CRC, in May-August 2018.
  • The CRC colleagues for their support, ideas, etc.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for pyActigraphy, version 1.0
Filename, size File type Python version Upload date Hashes
Filename, size pyActigraphy-1.0-py3-none-any.whl (897.7 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size pyActigraphy-1.0.tar.gz (845.5 kB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page