NeuroDSP

NeuroDSP: A package for neural digital signal processing - Published in JOSS (2019)

https://github.com/neurodsp-tools/neurodsp

Science Score: 100.0%

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 9 DOI reference(s) in README and JOSS metadata
✓
Academic publication links
Links to: joss.theoj.org
✓
Committers with academic emails
7 of 15 committers (46.7%) from academic institutions
○
Institutional organization owner
✓
JOSS paper metadata
Published in Journal of Open Source Software

Scientific Fields

Medicine Life Sciences - 84% confidence

Mathematics Computer Science - 84% confidence

Last synced: 4 months ago · JSON representation ·

Repository

Digital signal processing for neural time series.

Basic Info

Host: GitHub
Owner: neurodsp-tools
License: apache-2.0
Language: Python
Default Branch: main
Homepage: https://neurodsp-tools.github.io/
Size: 67.4 MB

Statistics

Stars: 319
Watchers: 16
Forks: 66
Open Issues: 13
Releases: 11

Created over 8 years ago · Last pushed 7 months ago

Metadata Files

Readme Contributing License Code of conduct Citation

README.rst

========================================
 Neuro Digital Signal Processing Toolbox
========================================

|ProjectStatus| |Version| |BuildStatus| |Coverage| |License| |PythonVersions| |Publication|

.. |ProjectStatus| image:: https://www.repostatus.org/badges/latest/active.svg
   :target: https://www.repostatus.org/#active
   :alt: build status

.. |Version| image:: https://img.shields.io/pypi/v/neurodsp.svg
   :target: https://pypi.org/project/neurodsp/
   :alt: version

.. |BuildStatus| image:: https://github.com/neurodsp-tools/neurodsp/actions/workflows/build.yml/badge.svg
   :target: https://github.com/neurodsp-tools/neurodsp/actions/workflows/build.yml
   :alt: build status

.. |Coverage| image:: https://codecov.io/gh/neurodsp-tools/neurodsp/branch/main/graph/badge.svg
   :target: https://codecov.io/gh/neurodsp-tools/neurodsp
   :alt: coverage

.. |License| image:: https://img.shields.io/pypi/l/neurodsp.svg
   :target: https://opensource.org/license/apache-2-0
   :alt: license

.. |PythonVersions| image:: https://img.shields.io/pypi/pyversions/neurodsp.svg
   :target: https://pypi.org/project/neurodsp/
   :alt: python versions

.. |Publication| image:: https://joss.theoj.org/papers/10.21105/joss.01272/status.svg
   :target: https://doi.org/10.21105/joss.01272
   :alt: publication

Tools to analyze and simulate neural time series, using digital signal processing.

Overview
--------

`neurodsp` is a collection of approaches for applying digital signal processing, and
related algorithms, to neural time series. It also includes simulation tools for generating
plausible simulations of neural time series.

Available modules in ``NeuroDSP`` include:

- ``filt`` : Filter data with bandpass, highpass, lowpass, or notch filters
- ``timefrequency`` : Estimate instantaneous measures of oscillatory activity
- ``spectral`` : Compute freqeuncy domain features such as power spectra
- ``burst`` : Detect bursting oscillations in neural signals
- ``rhythm`` : Find and analyze rhythmic and recurrent patterns in time series
- ``aperiodic`` : Analyze aperiodic features of neural time series
- ``sim`` : Simulate time series, including periodic and aperiodic signal components
- ``plts`` : Plot neural time series and derived measures
- ``utils`` : Additional utilities for managing time series data

Documentation
-------------

Documentation for the ``NeuroDSP`` module is available `here `_.

The documentation includes:

- `Tutorials `_: which describe and work through each module in NeuroDSP
- `Examples `_: demonstrating example applications and workflows
- `API List `_: which lists and describes all the code and functionality available in the module
- `Glossary `_: which defines all the key terms used in the module

If you have a question about using NeuroDSP that doesn't seem to be covered by the documentation, feel free to
open an `issue `_ and ask!

Dependencies
------------

``NeuroDSP`` is written in Python, and requires Python >= 3.7 to run.

It has the following dependencies:

- `numpy `_
- `scipy `_
- `matplotlib `_

Optional dependencies:

- `pytest `_ is needed if you want to run the test suite locally

Install
-------

The current major release of NeuroDSP is the 2.X.X series.

See the `changelog `_ for notes on major version releases.

**Stable Release Version**

To install the latest stable release, you can use pip:

.. code-block:: shell

    $ pip install neurodsp

NeuroDSP can also be installed with conda, from the conda-forge channel:

.. code-block:: shell

    $ conda install -c conda-forge neurodsp

**Development Version**

To get the current development version, first clone this repository:

.. code-block:: shell

    $ git clone https://github.com/neurodsp-tools/neurodsp

To install this cloned copy, move into the directory you just cloned, and run:

.. code-block:: shell

    $ pip install .

**Editable Version**

To install an editable version, download the development version as above, and run:

.. code-block:: shell

    $ pip install -e .

Contribute
----------

This project welcomes and encourages contributions from the community!

To file bug reports and/or ask questions about this project, please use the
`Github issue tracker `_.

To see and get involved in discussions about the module, check out:

- the `issues board `_ for topics relating to code updates, bugs, and fixes
- the `development page `_ for discussion of potential major updates to the module

When interacting with this project, please use the
`contribution guidelines `_
and follow the
`code of conduct `_.

Reference
---------

If you use this code in your project, please cite:

.. code-block:: text

    Cole, S., Donoghue, T., Gao, R., & Voytek, B. (2019). NeuroDSP: A package for
    neural digital signal processing. Journal of Open Source Software, 4(36), 1272.
    DOI: 10.21105/joss.01272

Direct Link: https://doi.org/10.21105/joss.01272

Bibtex:

.. code-block:: text

    @article{cole_neurodsp:_2019,
        title = {NeuroDSP: A package for neural digital signal processing},
        author = {Cole, Scott and Donoghue, Thomas and Gao, Richard and Voytek, Bradley},
        journal = {Journal of Open Source Software},
        year = {2019},
        volume = {4},
        number = {36},
        issn = {2475-9066},
        url = {https://joss.theoj.org/papers/10.21105/joss.01272},
        doi = {10.21105/joss.01272},
    }

Funding
-------

Supported by NIH award R01 GM134363 from the
`NIGMS `_.

.. image:: https://www.nih.gov/sites/all/themes/nih/images/nih-logo-color.png
  :width: 400

|

Owner

Name: NeuroDSP
Login: neurodsp-tools
Kind: organization

Website: https://neurodsp-tools.github.io/
Repositories: 1
Profile: https://github.com/neurodsp-tools

Digital signal processing for neuroscience.

JOSS Publication

NeuroDSP: A package for neural digital signal processing

Published

April 17, 2019

DOI

10.21105/joss.01272

Volume 4, Issue 36, Page 1272

Authors

Scott Cole

Neurosciences Graduate Program, UC San Diego

Thomas Donoghue

Department of Cognitive Science, UC San Diego

Richard Gao

Department of Cognitive Science, UC San Diego

Bradley Voytek

Neurosciences Graduate Program, UC San Diego, Department of Cognitive Science, UC San Diego, Halıcıoğlu Data Science Institute, UC San Diego, Kavli Institute for Brain and Mind, UC San Diego

Editor

Ariel Rokem

Citation (CITATION.cff)

cff-version: 1.2.0
message: >-
  If you use this software, please cite it using the metadata from this file.
type: software
title: 'neurodsp: neuro digital signal processing'
authors:
- given-names: 'Thomas'
  family-names: 'Donoghue'
  orcid: 'https://orcid.org/0000-0001-5911-0472'
- given-names: 'Ryan'
  family-names: 'Hammonds'
  orcid: 'https://orcid.org/0000-0002-5032-3241'
- given-names: 'Scott'
  family-names: 'Cole'
  orcid: 'https://orcid.org/0000-0002-6168-9951'
- given-names: 'Richard'
  family-names: 'Gao'
  orcid: 'https://orcid.org/0000-0001-5916-6433'
- given-names: 'Bradley'
  family-names: 'Voytek'
  orcid: 'https://orcid.org/0000-0003-1640-2525'
repository-code: 'https://github.com/neurodsp-tools/neurodsp'
url: 'https://neurodsp-tools.github.io/'
license: Apache-2.0
preferred-citation:
  type: article
  authors:
  - given-names: 'Scott'
    family-names: 'Cole'
    orcid: 'https://orcid.org/0000-0002-6168-9951'
  - given-names: 'Thomas'
    family-names: 'Donoghue'
    orcid: 'https://orcid.org/0000-0001-5911-0472'
  - given-names: 'Richard'
    family-names: 'Gao'
    orcid: 'https://orcid.org/0000-0001-5916-6433'
  - given-names: 'Bradley'
    family-names: 'Voytek'
    orcid: 'https://orcid.org/0000-0003-1640-2525'
  doi: '10.21105/joss.01272'
  journal: 'Journal of Open Source Software'
  month: 4
  title: 'NeuroDSP: A package for neural digital signal processing'
  issue: 36
  volume: 4
  year: 2019
  start: 1272

GitHub Events

Total

Create event: 8
Release event: 1
Issues event: 13
Watch event: 34
Delete event: 10
Issue comment event: 46
Push event: 34
Pull request review comment event: 10
Pull request review event: 21
Pull request event: 21
Fork event: 5

Last Year

Create event: 8
Release event: 1
Issues event: 13
Watch event: 34
Delete event: 10
Issue comment event: 46
Push event: 34
Pull request review comment event: 10
Pull request review event: 21
Pull request event: 21
Fork event: 5

Committers

Last synced: 5 months ago

All Time

Total Commits: 1,227
Total Committers: 15
Avg Commits per committer: 81.8
Development Distribution Score (DDS): 0.372

Past Year

Commits: 109
Committers: 2
Avg Commits per committer: 54.5
Development Distribution Score (DDS): 0.009

Top Committers

Name	Email	Commits
TomDonoghue	t**e@u**u	770
Scott Cole	s**0@g**m	161
ryanhammonds	r**s@u**u	131
rdgao	r**o@g**m	75
Eric Lybrand	e**d@u**u	27
Andrew Washington	a**7@g**m	26
Bradley Voytek	b**k@g**m	14
Michael	m**n@u**u	10
Grant R. Vousden-Dishington	G**D@g**m	3
SM-Figueroa	s**r@u**u	3
JohnDoenut	j**r@g**m	2
Meredith McCarty	m**y@u**u	2
Alex	a**l@m**g	1
Aniket Pradhan	a**3@i**n	1
agquinn	6****n	1

Committer Domains (Top 20 + Academic)

ucsd.edu: 4 iiitd.ac.in: 1 mailbox.org: 1 uth.tmc.edu: 1 utexas.edu: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 34
Total pull requests: 115
Average time to close issues: 7 months
Average time to close pull requests: about 1 month
Total issue authors: 13
Total pull request authors: 9
Average comments per issue: 2.15
Average comments per pull request: 2.28
Merged pull requests: 98
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 7
Pull requests: 17
Average time to close issues: 25 days
Average time to close pull requests: 17 days
Issue authors: 7
Pull request authors: 4
Average comments per issue: 2.29
Average comments per pull request: 0.71
Merged pull requests: 12
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

TomDonoghue (15)
ryanhammonds (7)
SM-Figueroa (1)
anthropikos (1)
danieltomasz (1)
AngCamp (1)
noortasnim (1)
apoorva6262 (1)
SusanL82 (1)
neuropil (1)
mwprestonjr (1)
fuqixiu (1)
larsoner (1)

Pull Request Authors

TomDonoghue (84)
ryanhammonds (31)
elybrand (6)
penguinpee (2)
SM-Figueroa (2)
kguarian (2)
blazyy (1)
JanCBrammer (1)
agquinn (1)

Top Labels

Issue Labels

2.3 (4) enhancement (4) 2.2 (3) bug (2) question (2) discussion (2) documentation (1)

Pull Request Labels

2.2 (35) 2.3 (22) 2.1 (13) maintenance (4) documentation (4) bug (3)

Packages

Total packages: 2
Total downloads:
- pypi 1,843 last-month
Total docker downloads: 131

Total dependent packages: 4
(may contain duplicates)
Total dependent repositories: 12
(may contain duplicates)
Total versions: 15
Total maintainers: 3

pypi.org: neurodsp

Digital signal processing for neural time series.

Homepage: https://github.com/neurodsp-tools/neurodsp
Documentation: https://neurodsp-tools.github.io/
License: Apache License, 2.0
Latest release: 2.3.0
published 11 months ago

Versions: 12
Dependent Packages: 3
Dependent Repositories: 11
Downloads: 1,843 Last month
Docker Downloads: 131

Rankings

Docker downloads count: 2.6%

Dependent packages count: 3.1%

Stargazers count: 3.9%

Average: 4.0%

Dependent repos count: 4.4%

Downloads: 4.6%

Forks count: 5.6%

Maintainers (3)

ryanhammonds voytekresearch tdonoghue

Last synced: 4 months ago

conda-forge.org: neurodsp

Homepage: https://github.com/neurodsp-tools/neurodsp
License: Apache-2.0
Latest release: 2.2.0
published over 3 years ago

Versions: 3
Dependent Packages: 1
Dependent Repositories: 1

Rankings

Dependent repos count: 24.3%

Forks count: 24.5%

Stargazers count: 24.7%

Average: 25.6%

Dependent packages count: 29.0%

Last synced: 4 months ago

Dependencies

requirements-docs.txt pypi

mne *
numpydoc *
pillow *
sphinx *
sphinx-copybutton *
sphinx_bootstrap_theme *
sphinx_gallery *

requirements.txt pypi

matplotlib *
numpy *
scipy *

.github/workflows/build.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite
codecov/codecov-action v3 composite

setup.py pypi

NeuroDSP

Science Score: 100.0%

Scientific Fields

Repository

Basic Info

Statistics

Metadata Files

README.rst

Owner

JOSS Publication

NeuroDSP: A package for neural digital signal processing

Authors

Editor

Tags

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

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: neurodsp

Rankings

Maintainers (3)

conda-forge.org: neurodsp

Rankings

Dependencies