Data

Tools

Indexes

Applications

Experiments

Open Source Science

actipy

Python Software Development Kit (SDK) to process wearable sensor data

https://github.com/oxwearables/actipy

Science Score: 67.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: plos.org, zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.7%) to scientific vocabulary

Keywords

actigraph activity-tracker axivity fitness-tracker geneactiv ukbiobank
Last synced: 6 months ago · JSON representation ·

Repository

Python Software Development Kit (SDK) to process wearable sensor data

Basic Info
Statistics
  • Stars: 24
  • Watchers: 3
  • Forks: 11
  • Open Issues: 3
  • Releases: 36
Topics
actigraph activity-tracker axivity fitness-tracker geneactiv ukbiobank
Created almost 5 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License Citation

README.md

actipy

Github all releases DOI

A Python package to process accelerometer data.

Axivity3 and Axivity6 (.cwa), Actigraph (.gt3x), GENEActiv (.bin), and Matrix (.bin) files are supported, as well as custom CSV files.

Axivity3 is the activity tracker watch used in the large-scale UK-Biobank accelerometer study.

Getting started

Prerequisite

  • Python 3.8 or greater console $ python --version # or python3 --version

  • Java 8 (1.8.0) or greater console $ java -version

Install

bash $ pip install actipy

Usage

```python import actipy

data, info = actipy.readdevice("sample.cwa.gz", # or "sample.gt3x.gz" or "sample.bin.gz" lowpasshz=20, calibrategravity=True, detectnonwear=True, resample_hz=50) ```

Output: ```console data [pandas.DataFrame] x y z temperature light time 2014-05-07 13:29:50.430 -0.513990 0.070390 1.671922 20.000000 78.420235 2014-05-07 13:29:50.440 -0.233940 -0.586568 0.082067 20.000000 78.420235 2014-05-07 13:29:50.450 -0.080319 -0.950817 -0.810613 20.000000 78.420235 2014-05-07 13:29:50.460 -0.067236 -0.975886 -0.865132 20.000000 78.420235 2014-05-07 13:29:50.470 -0.109636 -0.857004 -0.508666 20.000000 78.420235 ... ... ... ... ... ...

info [dict] Filename : data/sample.cwa.gz Filesize(MB) : 69.4 Device : Axivity DeviceID : 13110 ReadErrors : 0 SampleRate : 100.0 ReadOK : 1 StartTime : 2014-05-07 13:29:50 EndTime : 2014-05-13 09:50:33 NumTicks : 51391800 WearTime(days) : 5.847725231481482 NumInterrupts : 1 ResampleRate : 100.0 NumTicksAfterResample : 25262174 LowpassOK : 1 LowpassCutoff(Hz) : 20.0 CalibErrorBefore(mg) : 82.95806873592024 CalibErrorAfter(mg) : 4.434966371604519 CalibOK : 1 NonwearTime(days) : 0.0 NumNonwearEpisodes : 0 ...

``` Refer to the Data Dictionary for a comprehensive list of outputs.

Processing a custom CSV file

You can also use the routines in actipy.processing to process custom CSV files, or for more fine-grained control:

```python import actipy.processing as P

data, infolowpass = P.lowpass(data, 100, 20) data, infocalib = P.calibrategravity(data) data, infononwear = P.flagnonwear(data) data, inforesample = P.resample(data, sample_rate) ```

See the documentation for more.

Processing from the command line

We also provide a command-line tool to process a device file (currently, only AX3 and AX6 are supported) and output to CSV: bash $ read_cwa sample.cwa.gz -o outputs --lowpass-hz 20 --resample-hz 50 --calibrate-gravity --detect-nonwear

Outputs: - "outputs/sample/sample.csv.gz" - "outputs/sample/sample-Info.json"

Contributing

If you would like to contribute to this repository, please check out CONTRIBUTING.md. We welcome contributions in the form of bug reports, feature requests, and pull requests.

License

See LICENSE.md.

Owner

  • Name: Oxford Wearables Group
  • Login: OxWearables
  • Kind: organization
  • Location: United Kingdom

Citation (CITATION.cff) 

cff-version: 1.0.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Chan"
  given-names: "Shing"
  orcid: "https://orcid.org/0000-0001-9600-5575"
- family-names: "Doherty"
  given-names: "Aiden"
  orcid: "https://orcid.org/0000-0003-1840-0451"
title: "actipy: Python toolkit to process wearable sensor data"
doi: 10.5281/zenodo.14514488
date-released: 2021-10-13
url: "https://github.com/OxWearables/actipy"

GitHub Events

Total
  • Create event: 27
  • Issues event: 6
  • Release event: 10
  • Watch event: 4
  • Delete event: 17
  • Issue comment event: 4
  • Push event: 37
  • Pull request event: 30
  • Fork event: 3
Last Year
  • Create event: 27
  • Issues event: 6
  • Release event: 10
  • Watch event: 4
  • Delete event: 17
  • Issue comment event: 4
  • Push event: 37
  • Pull request event: 30
  • Fork event: 3

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 137
  • Total Committers: 1
  • Avg Commits per committer: 137.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Shing Chan c****m@g****m 137

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 22
  • Total pull requests: 41
  • Average time to close issues: 4 months
  • Average time to close pull requests: 3 days
  • Total issue authors: 8
  • Total pull request authors: 4
  • Average comments per issue: 1.36
  • Average comments per pull request: 0.24
  • Merged pull requests: 38
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 16
  • Average time to close issues: 14 days
  • Average time to close pull requests: 34 minutes
  • Issue authors: 3
  • Pull request authors: 1
  • Average comments per issue: 0.67
  • Average comments per pull request: 0.0
  • Merged pull requests: 15
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • chanshing (7)
  • angerhang (6)
  • aidanacquah (3)
  • muschellij2 (2)
  • rmndrs89 (1)
  • claaslendt (1)
  • spiousas (1)
  • abramschon (1)
Pull Request Authors
  • chanshing (50)
  • aidanacquah (6)
  • angerhang (3)
  • aidendoherty (1)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 4,645 last-month
  • Total dependent packages: 5
  • Total dependent repositories: 1
  • Total versions: 37
  • Total maintainers: 1
pypi.org: actipy

Python package to process wearable accelerometer data

  • Versions: 37
  • Dependent Packages: 5
  • Dependent Repositories: 1
  • Downloads: 4,645 Last month
Rankings
Dependent packages count: 3.1%
Downloads: 6.6%
Average: 12.0%
Forks count: 13.3%
Stargazers count: 15.2%
Dependent repos count: 21.6%
Maintainers (1)
chanshing
Last synced: 6 months ago

Dependencies

docs/requirements.txt pypi
  • docutils <0.18
  • readthedocs-sphinx-search ==0.1.1
  • sphinx ==4.2.0
  • sphinx_rtd_theme ==1.0.0
setup.py pypi
  • Jpype1 ==1.3.0
  • numpy ==1.21.6
  • pandas ==1.3.5
  • scipy ==1.7.3
  • statsmodels ==0.13.2
.github/workflows/cwa.yaml actions
  • actions/checkout v3 composite
  • actions/setup-java v1 composite
  • actions/setup-python v4 composite
.github/workflows/flake8.yaml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.github/workflows/install.yaml actions
  • actions/checkout v3 composite
  • actions/setup-java v1 composite
  • actions/setup-python v4 composite
.github/workflows/cwa-windows.yaml actions
  • actions/checkout v3 composite
  • actions/setup-java v3 composite
  • actions/setup-python v4 composite
.github/workflows/release.yaml actions
  • actions/checkout v3 composite
  • actions/setup-java v3 composite
  • actions/setup-python v4 composite
  • pypa/gh-action-pypi-publish release/v1 composite
pyproject.toml pypi