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Crowsetta

Crowsetta: A Python tool to work with any format for annotating animal vocalizations and bioacoustics data. - Published in JOSS (2023)

https://github.com/vocalpy/crowsetta

Science Score: 93.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 5 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: wiley.com, joss.theoj.org, zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

animal-communication animal-vocalizations annotation annotation-format bioacoustic-analysis bioacoustics birdsong csv dataset python python3

Scientific Fields

Mathematics Computer Science - 84% confidence
Last synced: 4 months ago · JSON representation

Repository

A tool to work with any format for annotating animal sounds

Basic Info
Statistics
  • Stars: 57
  • Watchers: 1
  • Forks: 4
  • Open Issues: 41
  • Releases: 35
Topics
animal-communication animal-vocalizations annotation annotation-format bioacoustic-analysis bioacoustics birdsong csv dataset python python3
Created about 7 years ago · Last pushed 5 months ago
Metadata Files
Readme Contributing License Code of conduct Citation

README.md


A Python tool to work with any format for annotating animal sounds and bioacoustics data

Project Status: Active The project has reached a stable, usable state and is being actively developed. pyOpenSci DOI Build Status Documentation Status DOI PyPI version PyPI Python versions codecov <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section --> All Contributors <!-- ALL-CONTRIBUTORS-BADGE:END -->

crowsetta provides a Pythonic way to work with annotation formats for animal sounds and bioacoustics data. These formats are used, for example, by applications that enable users to annotate audio and/or spectrograms. Such annotations typically include the times when sound events start and stop, and labels that assign each sound to some set of classes chosen by the annotator. crowsetta has built-in support for many widely used formats, such as Audacity label tracks, Praat .TextGrid files, and Raven .txt files.

example spectrogram showing Bengalese finch song with Praat TextGrid annotations indicated as segments underneath

Spectrogram of the song of a Bengalese finch with syllables annotated as segments underneath. Annotations parsed by crowsetta from a file in the Praat .TextGrid format. Example song from Bengalese finch song dataset, Tachibana and Morita 2021, adapted under CC-By-4.0 License.



example spectrogram from field recording with Raven annotations of birdsong indicated as rectangular bounding boxes

Spectrogram of a field recording with annotations of songs of different bird species indicated as bounding boxes. Annotations parsed by crowsetta from a file in the Raven Selection Table format. Example song from "An annotated set of audio recordings of Eastern North American birds containing frequency, time, and species information", Chronister et al., 2021, adapted under CC0 1.0 License.

Who would want to use crowsetta? Anyone that works with animal sounds or other bioacoustics data that is annotated in some way. Maybe you are a neuroscientist trying to figure out how songbirds learn their song, or why mice emit ultrasonic calls. Or maybe you're an ecologist studying dialects of finches distributed across Asia, or maybe you are a linguist studying accents in the Caribbean, or a speech pathologist looking for phonetic changes that indicate early onset Alzheimer's disease. crowsetta makes it easier for you to work with your annotations in Python, regardless of the format.

Features

  • take advantage of built-in support for many widely used formats, such as Audacity label tracks, Praat .TextGrid files, and Raven .txt files.
  • work with any format by remembering just one class:
    annot = crowsetta.Transcriber(format='format').from_file('annotations.ext')
    • no need to remember different functions for different formats
  • when needed, use classes that represent the formats to write readable scripts and libraries
  • convert annotations to common file formats like .csv that anyone can work with
  • work with custom formats that are not built in to crowsetta by writing simple classes, leveraging abstractions that can represent a wide array of annotation formats

For examples of these features, please see: https://crowsetta.readthedocs.io/en/latest/index.html#features

Getting Started

Installation

with pip

console $ pip install crowsetta

with conda

console $ conda install crowsetta -c conda-forge

Usage

If you are new to crowsetta, start with tutorial.

For vignettes showing how to use crowsetta for various tasks, such as working with your own annotation format, please see the how-to section.

Project Information

Background

crowsetta was developed for two libraries: - hybrid-vocal-classifier https://github.com/vocalpy/hybrid-vocal-classifier - vak https://github.com/vocalpy/vak

Support

To report a bug or request a feature (such as a new annotation format), please use the issue tracker on GitHub:
https://github.com/vocalpy/crowsetta/issues

To ask a question about crowsetta, discuss its development, or share how you are using it, please start a new topic on the VocalPy forum with the crowsetta tag:
https://forum.vocalpy.org/

Contribute

Code of conduct

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Contributing Guidelines

Below we provide some quick links, but you can learn more about how you can help and give feedback
by reading our Contributing Guide.

To ask a question about crowsetta, discuss its development, or share how you are using it, please start a new "Q&A" topic on the VocalPy forum with the crowsetta tag:
https://forum.vocalpy.org/

To report a bug, or to request a feature, please use the issue tracker on GitHub:
https://github.com/vocalpy/crowsetta/issues

CHANGELOG

You can see project history and work in progress in the CHANGELOG

License

The project is licensed under the BSD license.

Citation

If you use crowsetta, please cite the DOI: DOI

Contributors

Thanks goes to these wonderful people (emoji key):

Tessa Rhinehart
Tessa Rhinehart
 Sylvain HAUPERT
Sylvain HAUPERT
 Yannick Jadoul
Yannick Jadoul
 sammlapp
sammlapp

This project follows the all-contributors specification. Contributions of any kind welcome!

Owner

  • Name: VocalPy
  • Login: vocalpy
  • Kind: organization

JOSS Publication

Crowsetta: A Python tool to work with any format for annotating animal vocalizations and bioacoustics data.
Published
April 13, 2023
DOI
Volume 8, Issue 84, Page 5338
Authors
David Nicholson ORCID
Independent Research, USA
Editor
Olivia Guest ORCID
Tags
animal acoustic communication bioacoustics
View PDF Review Thread Software Archive

GitHub Events

Total
  • Issues event: 6
  • Watch event: 6
  • Delete event: 3
  • Issue comment event: 2
  • Push event: 8
  • Pull request event: 4
  • Fork event: 1
  • Create event: 6
Last Year
  • Issues event: 6
  • Watch event: 6
  • Delete event: 3
  • Issue comment event: 2
  • Push event: 8
  • Pull request event: 4
  • Fork event: 1
  • Create event: 6

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 893
  • Total Committers: 3
  • Avg Commits per committer: 297.667
  • Development Distribution Score (DDS): 0.253
Past Year
  • Commits: 14
  • Committers: 1
  • Avg Commits per committer: 14.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
David Nicholson n****e 667
nickledave n****v@g****m 214
allcontributors[bot] 4****] 12

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 87
  • Total pull requests: 51
  • Average time to close issues: 7 months
  • Average time to close pull requests: 5 days
  • Total issue authors: 6
  • Total pull request authors: 2
  • Average comments per issue: 1.05
  • Average comments per pull request: 0.63
  • Merged pull requests: 48
  • Bot issues: 0
  • Bot pull requests: 6
Past Year
  • Issues: 17
  • Pull requests: 3
  • Average time to close issues: about 15 hours
  • Average time to close pull requests: about 6 hours
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 0.35
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • NickleDave (81)
  • shaupert (2)
  • rhine3 (2)
  • yangzheng-121 (1)
  • sfcooke96 (1)
  • sammlapp (1)
Pull Request Authors
  • NickleDave (52)
  • allcontributors[bot] (6)
Top Labels
Issue Labels
ENH: enhancement (27) DOC: documentation (15) annotation format (11) DEV: development (8) CLN: clean/refactor (4) TST: testing (3) BUG: bug (2) dependencies (1)
Pull Request Labels
DOC: documentation (1) CLN: clean/refactor (1) BUG: bug (1)

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 2,094 last-month
  • Total dependent packages: 5
    (may contain duplicates)
  • Total dependent repositories: 5
    (may contain duplicates)
  • Total versions: 41
  • Total maintainers: 1
pypi.org: crowsetta

A Python tool to work with any format for annotating animal sounds and bioacoustics data

  • Versions: 36
  • Dependent Packages: 4
  • Dependent Repositories: 5
  • Downloads: 2,094 Last month
Rankings
Dependent packages count: 1.9%
Dependent repos count: 6.6%
Average: 9.6%
Stargazers count: 10.4%
Downloads: 12.3%
Forks count: 16.9%
Maintainers (1)
nicholdav
Last synced: 4 months ago
conda-forge.org: crowsetta
  • Versions: 5
  • Dependent Packages: 1
  • Dependent Repositories: 0
Rankings
Dependent packages count: 28.8%
Dependent repos count: 34.0%
Average: 43.5%
Stargazers count: 50.2%
Forks count: 61.1%
Last synced: 5 months ago

Dependencies

.github/workflows/ci.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • codecov/codecov-action v3 composite
pyproject.toml pypi
  • SoundFile >=0.10.3
  • appdirs >=1.4.4
  • attrs >=19.3.0
  • birdsong-recognition-dataset >=0.3.2
  • evfuncs >=0.3.5
  • importlib-resources >=5.7.1
  • numpy >=1.18.1
  • pandas >= 1.3.5
  • pandera >= 0.9.0
  • scipy >=1.4.1
.github/workflows/lint.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • isort/isort-action master composite
  • psf/black stable composite
  • py-actions/flake8 v2 composite