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ephyviewer

Simple viewers for ephys signals, events, video and more

https://github.com/neuralensemble/ephyviewer

Science Score: 39.0%

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 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.1%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Simple viewers for ephys signals, events, video and more

Basic Info
Statistics
  • Stars: 56
  • Watchers: 3
  • Forks: 13
  • Open Issues: 16
  • Releases: 9
Created almost 9 years ago · Last pushed about 1 year ago
Metadata Files
Readme License

README.rst 

ephyviewer
==========

*Simple viewers for ephys signals, events, video and more*

:Distributions: |pypi-badge| |anaconda-cloud-badge|
:Source Code:   |github-badge| |conda-forge-feedstock-badge|
:Tests Status:  |github-actions-badge| |conda-forge-azure-badge| |rtd-status-badge| |coveralls-badge|

Documentation_ | `Release Notes`_ | `Issue Tracker`_

**ephyviewer** is a Python library based on pyqtgraph_ for building custom
viewers for electrophysiological signals, video, events, epochs, spike trains,
data tables, and time-frequency representations of signals. It also provides an
epoch encoder for creating annotations.

|screenshot|

**ephyviewer** can be used at two levels: standalone app and library.

For an example of an application that utilizes **ephyviewer**'s capabilities as
a library, see the neurotic_ app and this paper:

    Gill, J. P., Garcia, S., Ting, L. H., Wu, M., & Chiel, H. J. (2020).
    *neurotic*: Neuroscience Tool for Interactive Characterization. eNeuro,
    7(3). https://doi.org/10.1523/ENEURO.0085-20.2020

Standalone application
----------------------

The standalone app works with file types supported by Neo_'s RawIO interface
(Axograph, Axon, Blackrock, BrainVision, Neuralynx, NeuroExplorer, Plexon,
Spike2, Tdt, etc.; see the documentation for neo.rawio_ for the full list).

Launch it from the console and use the menu to select a data file::

    ephyviewer

Alternatively, launch it from the console with a filename (and optionally the
format)::

    ephyviewer File_axon_1.abf
    ephyviewer File_axon_1.abf -f Axon

Library for designing custom viewers for ephys datasets
-------------------------------------------------------

Build viewers using code like this:

.. code:: python

    import ephyviewer
    import numpy as np

    app = ephyviewer.mkQApp()

    #signals
    sigs = np.random.rand(100000,16)
    sample_rate = 1000.
    t_start = 0.
    view1 = ephyviewer.TraceViewer.from_numpy(sigs, sample_rate, t_start, 'Signals')

    win = ephyviewer.MainViewer(debug=True, show_auto_scale=True)
    win.add_view(view1)
    win.show()

    app.exec()

Check the docs for more examples_.


.. |pypi-badge| image:: https://img.shields.io/pypi/v/ephyviewer.svg?logo=python&logoColor=white
    :target: pypi_
    :alt: PyPI

.. |anaconda-cloud-badge| image:: https://img.shields.io/conda/vn/conda-forge/ephyviewer.svg?label=anaconda&logo=anaconda&logoColor=white
    :target: anaconda-cloud_
    :alt: Anaconda Cloud

.. |github-badge| image:: https://img.shields.io/badge/github-source_code-blue.svg?logo=github&logoColor=white
    :target: github_
    :alt: GitHub

.. |conda-forge-feedstock-badge| image:: https://img.shields.io/badge/conda--forge-feedstock-blue.svg?logo=conda-forge&logoColor=white
    :target: conda-forge-feedstock_
    :alt: conda-forge Feedstock

.. |github-actions-badge| image:: https://img.shields.io/github/workflow/status/NeuralEnsemble/ephyviewer/tests/master?label=tests&logo=github&logoColor=white
    :target: github-actions_
    :alt: Tests Status

.. |conda-forge-azure-badge| image:: https://dev.azure.com/conda-forge/feedstock-builds/_apis/build/status/ephyviewer-feedstock?branchName=master
    :target: conda-forge-azure_
    :alt: conda-forge Build Status

.. |rtd-status-badge| image:: https://img.shields.io/readthedocs/ephyviewer/latest.svg?logo=read-the-docs&logoColor=white
    :target: rtd-status_
    :alt: Documentation Status

.. |coveralls-badge| image:: https://coveralls.io/repos/github/NeuralEnsemble/ephyviewer/badge.svg?branch=master
    :target: coveralls_
    :alt: Coverage status

.. |screenshot| image:: https://raw.githubusercontent.com/NeuralEnsemble/ephyviewer/master/doc/img/mixed_viewer_example.png
    :target: https://raw.githubusercontent.com/NeuralEnsemble/ephyviewer/master/doc/img/mixed_viewer_example.png
    :alt: Screenshot

.. _anaconda-cloud:         https://anaconda.org/conda-forge/ephyviewer
.. _conda-forge-azure:      https://dev.azure.com/conda-forge/feedstock-builds/_build/latest?definitionId=8410&branchName=master
.. _conda-forge-feedstock:  https://github.com/conda-forge/ephyviewer-feedstock
.. _coveralls:              https://coveralls.io/github/NeuralEnsemble/ephyviewer?branch=master
.. _Documentation:          https://ephyviewer.readthedocs.io/en/latest
.. _examples:               https://ephyviewer.readthedocs.io/en/latest/examples.html
.. _github:                 https://github.com/NeuralEnsemble/ephyviewer
.. _github-actions:         https://github.com/NeuralEnsemble/ephyviewer/actions?query=workflow%3Atests
.. _Issue Tracker:          https://github.com/NeuralEnsemble/ephyviewer/issues
.. _Neo:                    https://neo.readthedocs.io/en/latest
.. _neo.rawio:              https://neo.readthedocs.io/en/latest/rawio.html#module-neo.rawio
.. _neurotic:               https://neurotic.readthedocs.io/en/latest
.. _pypi:                   https://pypi.org/project/ephyviewer
.. _pyqtgraph:              http://www.pyqtgraph.org
.. _Release Notes:          https://ephyviewer.readthedocs.io/en/latest/releasenotes.html
.. _rtd-status:             https://readthedocs.org/projects/ephyviewer

Owner

  • Name: NeuralEnsemble
  • Login: NeuralEnsemble
  • Kind: organization

GitHub Events

Total
  • Issues event: 2
  • Watch event: 3
  • Issue comment event: 5
  • Push event: 2
  • Pull request event: 5
  • Fork event: 1
Last Year
  • Issues event: 2
  • Watch event: 3
  • Issue comment event: 5
  • Push event: 2
  • Pull request event: 5
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 411
  • Total Committers: 4
  • Avg Commits per committer: 102.75
  • Development Distribution Score (DDS): 0.363
Past Year
  • Commits: 3
  • Committers: 1
  • Avg Commits per committer: 3.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Jeffrey Gill j****l@g****m 262
Samuel Garcia s****e@g****m 103
Samuel Garcia s****e@g****m 44
Peter N. Steinmetz P****z@s****g 2
Committer Domains (Top 20 + Academic)
steinmetz.org: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 24
  • Total pull requests: 88
  • Average time to close issues: 3 months
  • Average time to close pull requests: 13 days
  • Total issue authors: 11
  • Total pull request authors: 6
  • Average comments per issue: 2.21
  • Average comments per pull request: 1.7
  • Merged pull requests: 82
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 3
  • Average time to close issues: 8 days
  • Average time to close pull requests: about 5 hours
  • Issue authors: 1
  • Pull request authors: 3
  • Average comments per issue: 3.0
  • Average comments per pull request: 0.67
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jpgill86 (14)
  • pplenck (1)
  • flareno (1)
  • LazySheep7 (1)
  • sanjayankur31 (1)
  • ELGarulli (1)
  • tfoutz99 (1)
  • samuelgarcia (1)
  • lfrank (1)
  • QuLogic (1)
Pull Request Authors
  • jpgill86 (63)
  • samuelgarcia (22)
  • PeterNSteinmetz (4)
  • melodieborel (3)
  • penguinpee (2)
  • grahamfindlay (1)
Top Labels
Issue Labels
bug (6) tests (2) documentation (2) enhancement (1)
Pull Request Labels
enhancement (21) bug (16) documentation (9) tests (7)

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 359 last-month
  • Total dependent packages: 1
    (may contain duplicates)
  • Total dependent repositories: 3
    (may contain duplicates)
  • Total versions: 23
  • Total maintainers: 2
pypi.org: ephyviewer

Simple viewers for ephys signals, events, video and more

  • Versions: 15
  • Dependent Packages: 0
  • Dependent Repositories: 3
  • Downloads: 359 Last month
Rankings
Dependent repos count: 9.0%
Dependent packages count: 10.0%
Stargazers count: 10.2%
Average: 10.6%
Forks count: 11.4%
Downloads: 12.5%
Maintainers (2)
sgarcia jpgill86
Last synced: 11 months ago
conda-forge.org: ephyviewer

ephyviewer is a Python library based on pyqtgraph for building custom viewers for electrophysiological signals, video, events, epochs, spike trains, data tables, and time-frequency representations of signals. It also provides an epoch encoder for creating annotations.

  • Versions: 8
  • Dependent Packages: 1
  • Dependent Repositories: 0
Rankings
Dependent packages count: 28.8%
Dependent repos count: 34.0%
Average: 37.0%
Stargazers count: 40.5%
Forks count: 44.7%
Last synced: 10 months ago

Dependencies

requirements-docs.txt pypi
  • jinja2 <3.1.0
  • sphinx <2
requirements-tests.txt pypi
  • av * test
  • coveralls * test
  • neo >=0.10.0 test
  • pandas * test
  • pytest * test
  • pytest-cov * test
  • spikeinterface >=0.90.1 test
requirements.txt pypi
  • matplotlib >=2.0
  • numpy *
  • pyqtgraph >=0.10.0
  • scipy *