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tensorpac

Phase-Amplitude Coupling under Python

https://github.com/etiennecmb/tensorpac

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 2 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 (12.2%) to scientific vocabulary

Keywords

amplitude coupling event-related filtering neuroscience oscillations pac parallel-computing phase phase-amplitude-coupling tensor
Last synced: 4 months ago · JSON representation ·

Repository

Phase-Amplitude Coupling under Python

Basic Info
Statistics
  • Stars: 112
  • Watchers: 9
  • Forks: 31
  • Open Issues: 9
  • Releases: 5
Topics
amplitude coupling event-related filtering neuroscience oscillations pac parallel-computing phase phase-amplitude-coupling tensor
Created over 8 years ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.rst 

=========
Tensorpac
=========

.. image:: https://github.com/EtienneCmb/tensorpac/workflows/Tensorpac/badge.svg
    :target: https://github.com/EtienneCmb/tensorpac/workflows/Tensorpac

.. image:: https://travis-ci.org/EtienneCmb/tensorpac.svg?branch=master
    :target: https://travis-ci.org/EtienneCmb/tensorpac

.. image:: https://circleci.com/gh/EtienneCmb/tensorpac/tree/master.svg?style=svg
    :target: https://circleci.com/gh/EtienneCmb/tensorpac/tree/master

.. image:: https://ci.appveyor.com/api/projects/status/0arxtw05583gc3e2/branch/master?svg=true
    :target: https://ci.appveyor.com/project/EtienneCmb/tensorpac/branch/master

.. image:: https://codecov.io/gh/EtienneCmb/tensorpac/branch/master/graph/badge.svg
  :target: https://codecov.io/gh/EtienneCmb/tensorpac

.. image:: https://badge.fury.io/py/tensorpac.svg
    :target: https://badge.fury.io/py/tensorpac

.. image:: https://pepy.tech/badge/tensorpac
    :target: https://pepy.tech/project/tensorpac

.. image:: https://badges.gitter.im/EtienneCmb/tensorpac.svg
    :target: https://gitter.im/EtienneCmb/tensorpac?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge

.. image:: https://zenodo.org/badge/93316276.svg
   :target: https://zenodo.org/badge/latestdoi/93316276


.. figure::  https://github.com/EtienneCmb/tensorpac/blob/master/docs/source/picture/tp.png
   :align:   center

Description
-----------

Tensorpac is an Python open-source toolbox for computing Phase-Amplitude Coupling (PAC) using tensors and parallel computing for an efficient, and highly flexible modular implementation of PAC metrics both known and novel. Check out our `documentation `_  for details.

Installation
------------

Tensorpac uses NumPy, SciPy and joblib for parallel computing. To get started, just open your terminal and run :


.. code-block:: console

    $ pip install tensorpac

Code snippet & illustration
---------------------------

.. code-block:: python

  from tensorpac import Pac
  from tensorpac.signals import pac_signals_tort

  # Dataset of signals artificially coupled between 10hz and 100hz :
  n_epochs = 20   # number of trials
  n_times = 4000  # number of time points
  sf = 512.       # sampling frequency

  # Create artificially coupled signals using Tort method :
  data, time = pac_signals_tort(f_pha=10, f_amp=100, noise=2, n_epochs=n_epochs,
                                dpha=10, damp=10, sf=sf, n_times=n_times)

  # Define a Pac object
  p = Pac(idpac=(6, 0, 0), f_pha='hres', f_amp='hres')
  # Filter the data and extract pac
  xpac = p.filterfit(sf, data)

  # plot your Phase-Amplitude Coupling :
  p.comodulogram(xpac.mean(-1), cmap='Spectral_r', plotas='contour', ncontours=5,
                 title=r'10hz phase$\Leftrightarrow$100Hz amplitude coupling',
                 fz_title=14, fz_labels=13)

  p.show()



.. figure::  https://github.com/EtienneCmb/tensorpac/blob/master/docs/source/picture/readme.png
   :align:   center

Cite Tensorpac
--------------

Tensorpac software has been published in `PLoS Computational Biology `_

Use the following Bibtex entry to cite it :

.. code-block:: latex

    @article{combrisson_tensorpac_2020,
        title = {Tensorpac: {An} open-source {Python} toolbox for tensor-based phase-amplitude coupling measurement in electrophysiological brain signals},
        volume = {16},
        issn = {1553-7358},
        shorttitle = {Tensorpac},
        doi = {10.1371/journal.pcbi.1008302},
        language = {eng},
        number = {10},
        journal = {PLoS computational biology},
        author = {Combrisson, Etienne and Nest, Timothy and Brovelli, Andrea and Ince, Robin A. A. and Soto, Juan L. P. and Guillot, Aymeric and Jerbi, Karim},
        month = oct,
        year = {2020},
        pmid = {33119593},
        pmcid = {PMC7654762},
        pages = {e1008302},
    }

Owner

  • Name: Etienne Combrisson
  • Login: EtienneCmb
  • Kind: user
  • Location: Marseille
  • Company: INT

Postdoc

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "Please cite the following works when using this software."
authors:  
  - family-names: "Combrisson"
    given-names: "Etienne"
    orcid: "https://orcid.org/0000-0002-7362-3247"
  - family-names: "Nest"
    given-names: "Timothy"
  - family-names: "Brovelli"
    given-names: "Andrea"
  - family-names: "Ince"
    given-names: "Robin A A"
  - family-names: "Soto"
    given-names: "Juan L P"
  - family-names: "Guillot"
    given-names: "Aymeric"
  - family-names: "Jerbi"
    given-names: "Karim"
doi: 10.5281/zenodo.5141481
url: "https://github.com/EtienneCmb/tensorpac"
title: "Tensorpac: An open-source Python toolbox for tensor-based phase-amplitude coupling measurement in electrophysiological brain signals"

GitHub Events

Total
  • Issues event: 2
  • Watch event: 20
  • Fork event: 5
Last Year
  • Issues event: 2
  • Watch event: 20
  • Fork event: 5

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 356
  • Total Committers: 7
  • Avg Commits per committer: 50.857
  • Development Distribution Score (DDS): 0.045
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
EtienneCmb e****n@g****m 340
Raphael Vallat r****9@g****m 6
Tim t****t@g****m 6
Todd t****8@g****m 1
Jordan O'Byrne j****e 1
Daniel Garcia Moreno d****a@s****m 1
tylerbrunette t****e@p****m 1
Committer Domains (Top 20 + Academic)
packetdigital.com: 1 suse.com: 1

Issues and Pull Requests

Last synced: 5 months ago

All Time
  • Total issues: 13
  • Total pull requests: 10
  • Average time to close issues: 8 months
  • Average time to close pull requests: 29 days
  • Total issue authors: 12
  • Total pull request authors: 7
  • Average comments per issue: 1.69
  • Average comments per pull request: 1.5
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • guoyongjian111 (2)
  • m-bellv (1)
  • KareemShalabi (1)
  • tylerbrunette (1)
  • raphaelvallat (1)
  • alirezamahdavi571 (1)
  • agramfort (1)
  • bonokat (1)
  • NikVard (1)
  • SynapticSage (1)
  • toddrme2178 (1)
  • scott-huberty (1)
Pull Request Authors
  • raphaelvallat (4)
  • SquadHenri (2)
  • toddrme2178 (1)
  • danigm (1)
  • tonoplast (1)
  • tylerbrunette (1)
  • jnobyrne (1)
Top Labels
Issue Labels
bug (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 7,602 last-month
  • Total dependent packages: 6
    (may contain duplicates)
  • Total dependent repositories: 8
    (may contain duplicates)
  • Total versions: 14
  • Total maintainers: 1
pypi.org: tensorpac

Tensor-based Phase-Amplitude Coupling

  • Versions: 13
  • Dependent Packages: 5
  • Dependent Repositories: 8
  • Downloads: 7,602 Last month
Rankings
Dependent packages count: 4.7%
Dependent repos count: 5.2%
Downloads: 5.8%
Average: 6.4%
Stargazers count: 8.1%
Forks count: 8.1%
Maintainers (1)
EtienneCmb
Last synced: 5 months ago
conda-forge.org: tensorpac
  • Versions: 1
  • Dependent Packages: 1
  • Dependent Repositories: 0
Rankings
Dependent packages count: 28.8%
Average: 33.6%
Dependent repos count: 34.0%
Stargazers count: 35.3%
Forks count: 36.1%
Last synced: 4 months ago

Dependencies

setup.py pypi
  • joblib *
  • numpy *
  • scipy *
.github/workflows/tensorpac.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite