autoreject

Automated rejection and repair of bad trials/sensors in M/EEG

https://github.com/autoreject/autoreject

Science Score: 46.0%

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Found 2 DOI reference(s) in README
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Links to: sciencedirect.com
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3 of 34 committers (8.8%) from academic institutions
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Low similarity (13.4%) to scientific vocabulary

Keywords

cross-validation electroencephalography magnetoencephalography meg mne-python preprocessing

Keywords from Contributors

neuroimaging eeg neuroscience ecog electrocorticography bids mne ieeg standards data-standards

Last synced: 6 months ago · JSON representation

Repository

Automated rejection and repair of bad trials/sensors in M/EEG

Basic Info

Host: GitHub
Owner: autoreject
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://autoreject.github.io
Size: 700 KB

Statistics

Stars: 145
Watchers: 11
Forks: 59
Open Issues: 36
Releases: 10

Topics

cross-validation electroencephalography magnetoencephalography meg mne-python preprocessing

Created almost 10 years ago · Last pushed 6 months ago

Metadata Files

Readme License

README.rst

autoreject
==========

|CircleCI|_ |GitHub Actions|_ |Codecov|_ |PyPI|_ |Conda-Forge|_

.. |CircleCI| image:: https://circleci.com/gh/autoreject/autoreject/tree/main.svg?style=shield&circle-token=:circle-token
.. _CircleCI: https://circleci.com/gh/autoreject/autoreject

.. |GitHub Actions| image:: https://github.com/autoreject/autoreject/actions/workflows/test.yml/badge.svg
.. _GitHub Actions: https://github.com/autoreject/autoreject/actions/workflows/test.yml

.. |Codecov| image:: http://codecov.io/github/autoreject/autoreject/coverage.svg?branch=main
.. _Codecov: http://codecov.io/github/autoreject/autoreject?branch=main

.. |PyPI| image:: https://badge.fury.io/py/autoreject.svg
.. _PyPI: https://badge.fury.io/py/autoreject

.. |Conda-Forge| image:: https://img.shields.io/conda/vn/conda-forge/autoreject.svg
.. _Conda-Forge: https://anaconda.org/conda-forge/autoreject/

This is a library to automatically reject bad trials and repair bad sensors in magneto-/electroencephalography (M/EEG) data.

.. image:: https://autoreject.github.io/stable/_images/sphx_glr_plot_auto_repair_001.png
   :width: 400


The documentation can be found under the following links:

- for the `stable release `_
- for the `latest (development) version `_

.. docs_readme_include_label

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

We recommend the `Anaconda Python distribution `_
and a **Python version >= 3.10**.
We furthermore recommend that you install ``autoreject`` into an isolated
Python environment.
To obtain the stable release of ``autoreject``, you can use ``pip``::

    pip install -U autoreject

Or ``conda``::

    conda install -c conda-forge autoreject

If you want the latest (development) version of ``autoreject``, use::

    pip install https://github.com/autoreject/autoreject/archive/refs/heads/main.zip

To check if everything worked fine, you can do::

    python -c 'import autoreject'

and it should not give any error messages.

Below, we list the dependencies for ``autoreject``.
All required dependencies are installed automatically when you install ``autoreject``.

* ``mne`` (>=1.5.0)
* ``numpy`` (>=1.21.2)
* ``scipy`` (>=1.7.1)
* ``scikit-learn`` (>=1.0.0)
* ``joblib``
* ``matplotlib`` (>=3.5.0)

Optional dependencies are:

* ``openneuro-py`` (>= 2021.10.1, for fetching data from `OpenNeuro.org `_)

Quickstart
==========

The easiest way to get started is to copy the following three lines of code
in your script:

.. code:: python

	>>> from autoreject import AutoReject
	>>> ar = AutoReject()
	>>> epochs_clean = ar.fit_transform(epochs)  # doctest: +SKIP

This will automatically clean an `epochs` object read in using MNE-Python. To get the
rejection dictionary, simply do:

.. code:: python

	>>> from autoreject import get_rejection_threshold
	>>> reject = get_rejection_threshold(epochs)  # doctest: +SKIP

We also implement RANSAC from the `PREP pipeline `_
(see `PyPREP `_ for a full implementation of the PREP pipeline).
The API is the same:

.. code:: python

	>>> from autoreject import Ransac
	>>> rsc = Ransac()
	>>> epochs_clean = rsc.fit_transform(epochs)  # doctest: +SKIP

For more details check out the example to
`automatically detect and repair bad epochs `_.

Bug reports
===========

Please use the `GitHub issue tracker `_ to report bugs.

Cite
====

[1] Mainak Jas, Denis Engemann, Federico Raimondo, Yousra Bekhti, and Alexandre Gramfort, "`Automated rejection and repair of bad trials in MEG/EEG `_."
In 6th International Workshop on Pattern Recognition in Neuroimaging (PRNI), 2016.

[2] Mainak Jas, Denis Engemann, Yousra Bekhti, Federico Raimondo, and Alexandre Gramfort. 2017.
"`Autoreject: Automated artifact rejection for MEG and EEG data `_".
NeuroImage, 159, 417-429.

Owner

Name: autoreject
Login: autoreject
Kind: organization

Repositories: 2
Profile: https://github.com/autoreject

GitHub Events

Total

Issues event: 3
Watch event: 6
Delete event: 1
Issue comment event: 2
Push event: 3
Pull request event: 3
Fork event: 2

Last Year

Issues event: 3
Watch event: 6
Delete event: 1
Issue comment event: 2
Push event: 3
Pull request event: 3
Fork event: 2

Committers

Last synced: about 2 years ago

All Time

Total Commits: 535
Total Committers: 34
Avg Commits per committer: 15.735
Development Distribution Score (DDS): 0.664

Past Year

Commits: 36
Committers: 8
Avg Commits per committer: 4.5
Development Distribution Score (DDS): 0.5

Top Committers

Name	Email	Commits
Mainak Jas	m**s@g**m	180
Stefan Appelhoff	s**f@m**g	84
dengemann	d**n@g**m	77
Alexandre Gramfort	a**t@m**g	34
Alex	a**l@m**g	19
Mainak Jas	m**s@t**r	17
Eric Larson	l**d@g**m	17
Mainak Jas	j****k	16
Marcin Koculak	k**n@g**m	15
Mathieu Scheltienne	m**e@g**m	15
pstetz	p**z@b**u	9
Robert Luke	7****e	6
“mattboggess”	“**s@p**”	5
Paul Bogdan	p**n@g**m	4
Carlos de la Torre	4****e	4
Fede Raimondo	f**o@g**m	3
Mathieu Scheltienne	7****e	3
dependabot[bot]	4****]	3
Nikolai M Chapochnikov	2****n	3
skjerns	1****s	3
Robert Luke	h**o@r**t	2
Richard Höchenberger	r**r@g**m	2
mattboggess	m**7@g**m	2
Adina Wagner	a**r@t**e	2
Stephen Zerfas	z**3@y**m	1
santopolskiy	s**y@c**m	1
Hubert Banville	h**e@g**m	1
callezenwaka	c**a@g**m	1
rugolotti	r**i@c**m	1
Raghav R V	r**3@g**m	1
and 4 more...

Committer Domains (Top 20 + Academic)

mailbox.org: 2 cyceron.fr: 1 visor.udg.edu: 1 tu-ilmenau.de: 1 camlingroup.com: 1 camlintechnologies.com: 1 t-online.de: 1 robertluke.net: 1 protonmail.com”: 1 berkeley.edu: 1 telecom-paristech.fr: 1 m4x.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 64
Total pull requests: 76
Average time to close issues: about 2 months
Average time to close pull requests: 14 days
Total issue authors: 35
Total pull request authors: 19
Average comments per issue: 5.5
Average comments per pull request: 4.75
Merged pull requests: 64
Bot issues: 0
Bot pull requests: 7

Past Year

Issues: 1
Pull requests: 2
Average time to close issues: N/A
Average time to close pull requests: about 18 hours
Issue authors: 1
Pull request authors: 1
Average comments per issue: 1.0
Average comments per pull request: 0.5
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 2

View more stats

Top Authors

Issue Authors

jasmainak (7)
sappelhoff (7)
hoechenberger (6)
adam2392 (4)
eort (3)
mscheltienne (3)
alexrockhill (3)
skjerns (2)
guishuyunye-lyw (2)
larsoner (2)
guiomar (1)
AlexLepauvre (1)
sab-d (1)
binarycache (1)
aaronjnewman (1)

Pull Request Authors

sappelhoff (21)
larsoner (13)
jasmainak (10)
dependabot[bot] (9)
alexrockhill (4)
hoechenberger (3)
agramfort (3)
c-torre (2)
mscheltienne (2)
chapochn (2)
skjerns (2)
ktavabi (2)
LegrandNico (1)
fraimondo (1)
callezenwaka (1)

Top Labels

Issue Labels

question (4) docs (4) maint (4) bug (2) enhancement (2)

Pull Request Labels

dependencies (9) maint (3) enhancement (2) hacktoberfest-accepted (1) docs (1) github_actions (1)

Packages

Total packages: 2
Total downloads:
- pypi 8,522 last-month
Total docker downloads: 12

Total dependent packages: 4
(may contain duplicates)
Total dependent repositories: 43
(may contain duplicates)
Total versions: 14
Total maintainers: 3

pypi.org: autoreject

Automated rejection and repair of epochs in M/EEG.

Homepage: http://autoreject.github.io/
Documentation: http://autoreject.github.io/
License: BSD-3-Clause
Latest release: 0.4.3
published over 2 years ago

Versions: 10
Dependent Packages: 4
Dependent Repositories: 41
Downloads: 8,522 Last month
Docker Downloads: 12

Rankings

Dependent packages count: 1.9%

Dependent repos count: 2.3%

Docker downloads count: 3.5%

Downloads: 3.6%

Average: 3.8%

Forks count: 5.5%

Stargazers count: 6.2%

Maintainers (3)

Eric89GXL mainakjas sappelhoff

Last synced: 6 months ago

conda-forge.org: autoreject

Homepage: https://autoreject.github.io
License: BSD-3-Clause
Latest release: 0.4.0
published over 3 years ago

Versions: 4
Dependent Packages: 0
Dependent Repositories: 2

Rankings

Dependent repos count: 20.2%

Forks count: 24.1%

Stargazers count: 31.0%

Average: 31.7%

Dependent packages count: 51.6%

Last synced: 6 months ago

Dependencies

setup.py pypi

mne *
numpy *
scipy *

.github/workflows/circle-artifacts.yml actions

larsoner/circleci-artifacts-redirector-action master composite

.github/workflows/python-publish.yml actions

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

.github/workflows/test.yml actions

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

doc/_static/versions.json meteor