evfuncs

Functions for working with files created by the EvTAF program and the evsonganaly GUI

https://github.com/nickledave/evfuncs

Science Score: 67.0%

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DOI references
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Links to: nature.com, zenodo.org
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Low similarity (15.8%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

Functions for working with files created by the EvTAF program and the evsonganaly GUI

Basic Info

Host: GitHub
Owner: NickleDave
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://github.com/NickleDave/evfuncs
Size: 52.5 MB

Statistics

Stars: 2
Watchers: 2
Forks: 1
Open Issues: 5
Releases: 14

Created over 7 years ago · Last pushed about 2 years ago

Metadata Files

Readme License Citation

This project is no longer actively maintained, although the code uses core, stable functions from Python, Numpy, and SciPy, so it is likely to work.
If you need to load cbin (audio) files from evsonganaly, there are maintained, updated versions of the functions in this package in the vocalpy library: https://vocalpy.readthedocs.io
If you need to load .not.mat (annotation) files from evsonganaly, there are maintained, updated versions of that function in crowsetta: https://crowsetta.readthedocs.io
(Note that if you install vocalpy, you will already have crowsetta installed.)

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evfuncs

Functions for working with files created by EvTAF and the evsonganaly GUI.
In case you need to work with those files in Python 😊😊😊 (see "Usage" below).

The first work published with data collected using EvTAF and evsonganaly is in this paper:
Tumer, Evren C., and Michael S. Brainard.
"Performance variability enables adaptive plasticity of ‘crystallized’adult birdsong."
Nature 450.7173 (2007): 1240.
https://www.nature.com/articles/nature06390

These functions are translations to Python of the original functions written in MATLAB (copyright Mathworks) by Evren Tumer (shown below).

Image of Evren

Installation

with `pip`

console $ pip install evfuncs

with `conda`

console $ conda install evfuncs -c conda-forge

Usage

The main purpose for developing these functions in Python was to work with files of Bengalese finch song in this data repository: https://figshare.com/articles/Bengalese_Finch_song_repository/4805749

Using evfuncs with that repository, you can load the .cbin audio files ... ```Python

import evfuncs

rawsong, sampfreq = evfuncs.loadcbin('gy6or6baseline230312_0808.138.cbin') ```

... and the annotation in the .not.mat files ... ```Python

notmatdict = evfuncs.loadnotmat('gy6or6baseline2303120808.138.cbin') (or, using the `.not.mat` filename directly)Python notmatdict = evfuncs.loadnotmat('gy6or6baseline2303120808.138.not.mat') ```

...and you should be able to reproduce the segmentation of the raw audio files of birdsong into syllables and silent periods, using the segmenting parameters from a .not.mat file and the simple algorithm applied by the SegmentNotes.m function.

```Python

smooth = evfuncs.smoothdata(rawsong, sampfreq) threshold = notmatdict['threshold'] minsyldur = notmatdict['mindur'] / 1000 minsilentdur = notmatdict['minint'] / 1000 onsets, offsets = evfuncs.segmentsong(smooth, sampfreq, threshold, minsyldur, minsilentdur) import numpy as np np.allclose(onsets, notmatdict['onsets']) True ``(*Note that this test would returnFalse` if the onsets and offsets in the .not.mat annotation file had been modified, e.g., a user of the evsonganaly GUI had edited them, after they were originally computed by the SegmentNotes.m function.*)

evfuncs is used to load annotations by
'crowsetta', a data-munging tool for building datasets of vocalizations that can be used to train machine learning models. Two machine learning libraries that can use those datasets are: hybrid-vocal-classifier, and vak.

Getting Help

Please feel free to raise an issue here:
https://github.com/NickleDave/evfuncs/issues

License

BSD License.

Citation

Please cite this software as shown below. To get the most up-to-date, automatically-generated citation, please click "Cite this repository" on the upper right side of the page.

bibtex:
@software{Nicholson_evfuncs_2021, author = {Nicholson, David}, doi = {10.5281/zenodo.4584209}, license = {BSD-3-Clause}, month = {3}, title = {{evfuncs}}, url = {https://github.com/NickleDave/evfuncs}, version = {0.3.2.post1}, year = {2021}

APA:
Nicholson, D. (2021). evfuncs (Version 0.3.2.post1) [Computer software]. https://doi.org/10.5281/zenodo.4584209

Build Status

Owner

Name: David Nicholson
Login: NickleDave
Kind: user
Location: Charm City
Company: @vocalpy

Website: https://nicholdav.info/
Repositories: 15
Profile: https://github.com/NickleDave

ML, AI; behavior + cog + neuro. Open + inclusive science. Pythonista. He/him (they's ok too). Habla espanglish y baila salsa y bachata a medio tiempo.

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: evfuncs
message: >-
  If you use evfuncs, please cite it with these
  metadata
type: software
authors:
  - given-names: David
    email: nicholdav@gmail.com
    family-names: Nicholson
    orcid: 'https://orcid.org/0000-0002-4261-4719'
doi: 10.5281/zenodo.4584209
abstract: >-
  Functions for working with files created by the
  EvTAF program and the evsonganaly GUI
license: BSD-3-Clause
version: 0.3.5
commit: b1e6b942c19c3ab13f8aecbeab82a05ab47b2a83
date-released: '2022-05-14'
repository-code: 'https://github.com/NickleDave/evfuncs'
repository: 'https://pypi.org/project/evfuncs/'
identifiers:
  - type: doi
    value: 10.5281/zenodo.4584209
    description: >-
      This DOI represents all versions, and will
      always resolve to the latest one.

GitHub Events

Total

Last Year

Committers

Last synced: over 2 years ago

All Time

Total Commits: 108
Total Committers: 2
Avg Commits per committer: 54.0
Development Distribution Score (DDS): 0.12

Past Year

Commits: 6
Committers: 1
Avg Commits per committer: 6.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
David Nicholson	n**e@u**m	95
NickleDave	n**v@g**m	13

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 16
Total pull requests: 5
Average time to close issues: 9 days
Average time to close pull requests: 7 minutes
Total issue authors: 1
Total pull request authors: 1
Average comments per issue: 0.5
Average comments per pull request: 0.2
Merged pull requests: 5
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

NickleDave (16)

Pull Request Authors

NickleDave (5)

Top Labels

Issue Labels

bug (2) DEV: development (2) enhancement (1) CI: continuous integration (1)

Pull Request Labels

enhancement (1)

Packages

Total packages: 2
Total downloads:
- pypi 831 last-month

Total dependent packages: 5
(may contain duplicates)
Total dependent repositories: 1
(may contain duplicates)
Total versions: 17
Total maintainers: 1

pypi.org: evfuncs

Functions for working with files created by the EvTAF program and the evsonganaly GUI

Documentation: https://evfuncs.readthedocs.io/
License: BSD License
Latest release: 0.3.5
published almost 4 years ago

Versions: 14
Dependent Packages: 3
Dependent Repositories: 1
Downloads: 831 Last month

Rankings

Dependent packages count: 2.3%

Downloads: 18.0%

Average: 18.5%

Dependent repos count: 21.7%

Forks count: 22.6%

Stargazers count: 27.8%

Maintainers (1)

nicholdav

Last synced: 7 months ago

conda-forge.org: evfuncs

Homepage: https://pypi.org/project/evfuncs/
License: BSD-3-Clause
Latest release: 0.3.5
published almost 4 years ago

Versions: 3
Dependent Packages: 2
Dependent Repositories: 0

Rankings

Dependent packages count: 19.5%

Dependent repos count: 34.0%

Average: 41.5%

Forks count: 54.2%

Stargazers count: 58.4%

Last synced: 7 months ago

Dependencies

.github/workflows/ci.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

pyproject.toml pypi

numpy >=1.18.1
scipy >=1.2.0

evfuncs

Science Score: 67.0%

Repository

Basic Info

Statistics

Metadata Files

README.md

evfuncs

Installation

with pip

with conda

Usage

Getting Help

License

Citation

Build Status

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: evfuncs

Rankings

Maintainers (1)

conda-forge.org: evfuncs

Rankings

Dependencies

with `pip`

with `conda`