Metadata-Version: 2.1
Name: neurotic
Version: 1.5.0
Summary: Curate, visualize, annotate, and share your behavioral ephys data using Python
Home-page: https://github.com/jpgill86/neurotic
Author: Jeffrey Gill
Author-email: jeffrey.p.gill@gmail.com
License: MIT
Project-URL: Documentation, https://neurotic.readthedocs.io
Project-URL: Source code, https://github.com/jpgill86/neurotic
Project-URL: Bug tracker, https://github.com/jpgill86/neurotic/issues
Project-URL: Change log, https://neurotic.readthedocs.io/en/latest/releasenotes.html
Description: |neurotic logo| *neurotic*: NEUROscience Tool for Interactive Characterization
        ==============================================================================
        
        *Curate, visualize, annotate, and share your behavioral ephys data using Python*
        
        :Distributions: |PyPI badge| |Anaconda badge| |Installers badge|
        :Source Code:   |GitHub badge| |Feedstock badge| |Constructor badge|
        :Tests Status:  |GitHub Actions badge| |Azure badge| |Docs badge| |Coverage badge|
        :Citing:        |Zenodo badge| |eNeuro badge|
        
        Documentation_ | `Release Notes`_ | `Issue Tracker`_
        
        *neurotic* is an app for Windows, macOS, and Linux that allows you to easily
        review and annotate your electrophysiology data and simultaneously captured
        video. It is an easy way to load your Neo_-compatible data (see neo.io_ for
        file formats) into ephyviewer_ without doing any programming. Share a single
        metadata file with your colleagues and they too will quickly be looking at the
        same datasets!
        
        To use the app, first organize your datasets in a *metadata file* like this
        (see `Configuring Metadata`_):
        
        .. code-block:: yaml
        
            my favorite dataset:
                description: This time it actually worked!
        
                data_dir:           C:\local_dir_containing_files
                remote_data_dir:    http://myserver/remote_dir_containing_downloadable_files  # optional
                data_file:          data.axgx
                video_file:         video.mp4
                # etc
        
                video_offset: -3.4  # seconds between start of video and data acq
                epoch_encoder_possible_labels:
                    - label01
                    - label02
                plots:
                    - channel: I2
                      ylim: [-30, 30]
                    - channel: RN
                      ylim: [-60, 60]
                    # etc
        
                filters:  # used only if fast loading is off (lazy=False)
                    - channel: Force
                      lowpass: 50
                    # etc
                amplitude_discriminators:  # used only if fast loading is off (lazy=False)
                    - name: B3 neuron
                      channel: BN2
                      units: uV
                      amplitude: [50, 100]
                    # etc
        
            another dataset:
                # etc
        
        Open your metadata file in *neurotic* and choose a dataset. If the data and
        video files aren't already on your local computer, the app can download them
        for you, even from a password-protected server or from Google Drive. Finally,
        click launch and the app will use a standard viewer layout to display your data
        to you using ephyviewer_.
        
        |Example screenshot|
        
        *In the screenshot above, the video frame shows a voracious sea slug* (Aplysia
        californica) *swallowing a strip of unbreakable seaweed attached to a force
        transducer. Implanted electrodes recorded from a muscle and the major nerves
        controlling feeding. The epoch encoder was used to mark the times when seaweed
        moved into the mouth. Spikes corresponding to activity of identified neurons
        were detected by* neurotic *using customizable parameters.*
        
        The viewers are easy and intuitive to navigate (see `User Interface`_):
        
        - Pressing the play button will scroll through your data and video in real
          time, or at a higher or lower rate if the speed parameter is changed.
        - The arrow/WASD keys allow you to step through time in variable increments.
        - Jump to a time by clicking on an event in the event list or a table entry in
          the epoch encoder.
        - To show more or less time at once, right-click and drag right or left to
          contract or expand time.
        - Scroll the mouse wheel in the trace viewer or video viewer to zoom.
        - The epoch encoder can be used to block out periods of time during which
          something interesting is happening for later review or further analysis
          (saved to a CSV file).
        - All panels can be hidden, undocked, stacked, or repositioned on the fly.
        
        Electrophysiologists will find this tool useful even if they don't need the
        video synchronization feature!
        
        **Portability is easy with neurotic!** Use relative paths in your metadata file
        along with a remotely accessible data store such as GIN_ or a Shared Drive on
        Google Drive to make your metadata file fully portable. The same metadata file
        can be copied to a different computer, and downloaded files will automatically
        be saved to the right place. Data stores can be password protected and
        *neurotic* will prompt you for a user name and password. This makes it easy to
        share the *neurotic* experience with your colleagues! ðŸ¤ª
        
        Installing *neurotic*
        ---------------------
        
        *neurotic* requires Python 3.6 or later.
        
        Standalone Installers (recommended for beginners)
        .................................................
        
        Downloadable installers make installing *neurotic* easy for beginners. They can
        be downloaded from the GitHub Releases page:
        
            `ðŸ‘‰ Download installers here (listed under "Assets") ðŸ‘ˆ`__
        
            __ `GitHub Releases`_
        
        These installers are intended for users who do not want to independently
        install Python or conda just to use *neurotic*. They will install *neurotic*
        and everything it needs (including a fully contained Python environment) into a
        dedicated directory on your computer. On Windows, the installer will also
        create a Start Menu shortcut for launching the app.
        
        For developers, a recipe for building new installers using `conda constructor`_
        is maintained here: `constructor recipe`_.
        
        Alternate Method: conda (recommended for Pythonistas)
        .....................................................
        
        conda_ users can install *neurotic* and all of its dependencies with one
        command::
        
            conda install -c conda-forge neurotic
        
        On Windows, this will also create a Start Menu shortcut for launching the app.
        
        Alternate Method: pip
        .....................
        
        Install *neurotic* from PyPI_ using ::
        
            pip install neurotic
        
        Note that installation via ``pip`` skips one dependency: PyAV_, which is
        required for displaying videos, and without which *neurotic* will ignore
        videos. PyAV is not easily installed with ``pip`` on some systems, especially
        Windows. The easiest way to separately install PyAV is using conda_::
        
            conda install -c conda-forge av
        
        Updating *neurotic*
        -------------------
        
        The recommended method of updating *neurotic* depends on the original method of
        installation.
        
        If you are unsure what method you used, updating using ``conda`` or ``pip`` is
        likely to work. Standalone installers may be safe too, though this could lead
        to having multiple version installed simultaneously.
        
        Updating with Standalone Installers
        ...................................
        
        If you previously installed *neurotic* using a standalone installer, you may
        install a newer version using another installer, either into a different
        directory or by first uninstalling the old version. Installers can be
        downloaded from the GitHub Releases page:
        
            `ðŸ‘‰ Download installers here (listed under "Assets") ðŸ‘ˆ`__
        
            __ `GitHub Releases`_
        
        Alternatively, if a new installer is not currently available for your platform,
        or if you would just like a much faster method, you may use the command line
        tools provided by the installer (via the "Anaconda Prompt" on Windows, or the
        Terminal on macOS and Linux)::
        
            conda update -c conda-forge neurotic
        
        Updating with conda
        ...................
        
        If you installed *neurotic* with `conda`_, you can update to the latest release
        using ::
        
            conda update -c conda-forge neurotic
        
        Updating with pip
        .................
        
        If you installed *neurotic* using ``pip``, you can update to the latest release
        available on PyPI_ using ::
        
            pip install -U neurotic
        
        Development Version
        ...................
        
        If you are interested in trying new, unreleased features of *neurotic*, you may
        install the latest development version from GitHub_ using ::
        
            pip install -U git+https://github.com/jpgill86/neurotic.git
        
        Note that if you install the development version, you may also need the latest
        development version of ephyviewer_, which you can get using ::
        
            pip install -U git+https://github.com/NeuralEnsemble/ephyviewer.git
        
        Getting Started
        ---------------
        
        Windows users who installed using a standalone installer or conda_ should be
        able to launch *neurotic* from the Start Menu.
        
        Mac and Linux users, as well as Windows users, can use the Terminal, command
        line, or Anaconda Prompt to start the app:
        
        1. Depending on your operating system, installation method, and environment
           settings, you may be able to just launch the app from the command line by
           invoking its name::
        
            neurotic
        
        2. If the command is not recognized, you likely need to first activate the
           conda environment into which the app was installed::
        
            conda activate <environment name>
        
           If you used a standalone installer, the environment name may be
           "``neurotic``", so you would use ::
        
            conda activate neurotic
        
           You can then try again invoking the app name::
        
            neurotic
        
        Several examples are provided. Select one, download the associated data using
        the "Download data" menu action, and then click "Launch". See `User Interface`_
        for help with navigation.
        
        Disabling "Fast loading" before launch will enable additional features
        including amplitude-threshold spike detection and signal filtering.
        
        To inspect the metadata file associated with the examples or to make changes to
        it, click "Edit metadata". See `Configuring Metadata`_ for details about the
        format.
        
        If you like working with Jupyter notebooks, you can launch an example notebook
        that includes a tutorial for using *neurotic*'s API::
        
            neurotic --launch-example-notebook
        
        The command line interface accepts other arguments too:
        
        .. code-block::
        
            usage: neurotic [-h] [-V] [--debug | --no-debug] [--lazy | --no-lazy]
                            [--thick-traces | --no-thick-traces]
                            [--show-datetime | --no-show-datetime]
                            [--ui-scale {tiny,small,medium,large,huge}]
                            [--theme {light,dark,original,printer-friendly}]
                            [--use-factory-defaults] [--launch-example-notebook]
                            [file] [dataset]
        
            neurotic lets you curate, visualize, annotate, and share your behavioral ephys
            data.
        
            positional arguments:
              file                  the path to a metadata YAML file (default: an example
                                    file)
              dataset               the name of a dataset in the metadata file to select
                                    initially (default: the first entry in the metadata
                                    file)
        
            optional arguments:
              -h, --help            show this help message and exit
              -V, --version         show program's version number and exit
              --debug               enable detailed log messages for debugging
              --no-debug            disable detailed log messages for debugging (default)
              --lazy                enable fast loading (default)
              --no-lazy             disable fast loading
              --thick-traces        enable support for traces with thick lines, which has
                                    a performance cost
              --no-thick-traces     disable support for traces with thick lines (default)
              --show-datetime       display the real-world date and time, which may be
                                    inaccurate depending on file type and acquisition
                                    software
              --no-show-datetime    do not display the real-world date and time (default)
              --ui-scale {tiny,small,medium,large,huge}
                                    the scale of user interface elements, such as text
                                    (default: medium)
              --theme {light,dark,original,printer-friendly}
                                    a color theme for the GUI (default: light)
              --use-factory-defaults
                                    start with "factory default" settings, ignoring other
                                    args and your global config file
        
            alternative modes:
              --launch-example-notebook
                                    launch Jupyter with an example notebook instead of
                                    starting the standalone app (other args will be
                                    ignored)
        
            Defaults for arguments and options can be changed in a global config file,
            .neurotic\neurotic-config.txt, located in your home directory.
        
        Citing *neurotic*
        -----------------
        
        To cite *neurotic* in your publication, please refer to:
        
            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
        
        Specific versions of the software can be cited from archives at Zenodo_.
        
        Documentation
        -------------
        
        For detailed information on configuring metadata, working examples, the API
        reference guide, release notes, and more, see the Documentation_.
        
        
        .. |neurotic logo| image:: https://raw.githubusercontent.com/jpgill86/neurotic/master/neurotic/gui/icons/img/neurotic-logo-30.png
            :alt: Project logo
        
        .. |PyPI badge| image:: https://img.shields.io/pypi/v/neurotic.svg?logo=python&logoColor=white
            :target: PyPI_
            :alt: PyPI project
        
        .. |Anaconda badge| image:: https://img.shields.io/conda/vn/conda-forge/neurotic.svg?label=anaconda&logo=anaconda&logoColor=white
            :target: `Anaconda Cloud`_
            :alt: Anaconda Cloud project
        
        .. |Installers badge| image:: https://img.shields.io/github/v/release/jpgill86/neurotic?label=installers&logo=github&logoColor=white&sort=semver
            :target: `GitHub Releases`_
            :alt: Installers
        
        .. |GitHub badge| image:: https://img.shields.io/badge/github-source_code-blue.svg?logo=github&logoColor=white
            :target: GitHub_
            :alt: GitHub source code
        
        .. |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
        
        .. |Constructor badge| image:: https://img.shields.io/badge/constructor-recipe-blue.svg
            :target: `constructor recipe`_
            :alt: constructor recipe
        
        .. |GitHub Actions badge| image:: https://img.shields.io/github/workflow/status/jpgill86/neurotic/tests/master?label=tests&logo=github&logoColor=white
            :target: `GitHub Actions`_
            :alt: Tests status
        
        .. |Azure badge| image:: https://dev.azure.com/conda-forge/feedstock-builds/_apis/build/status/neurotic-feedstock?branchName=master
            :target: `conda-forge CI`_
            :alt: conda-forge build status
        
        .. |Docs badge| image:: https://img.shields.io/readthedocs/neurotic/latest.svg?logo=read-the-docs&logoColor=white
            :target: ReadTheDocs_
            :alt: Documentation status
        
        .. |Coverage badge| image:: https://coveralls.io/repos/github/jpgill86/neurotic/badge.svg?branch=master
            :target: Coveralls_
            :alt: Coverage status
        
        .. |Zenodo badge| image:: https://img.shields.io/badge/DOI-10.5281/zenodo.3564990-blue.svg
            :target: Zenodo_
            :alt: Zenodo archive
        
        .. |eNeuro badge| image:: https://img.shields.io/badge/DOI-10.1523/ENEURO.0085--20.2020-blue.svg
            :target: eNeuro_
            :alt: eNeuro article
        
        .. |Example screenshot| image:: https://raw.githubusercontent.com/jpgill86/neurotic/master/docs/_static/example-screenshot.png
            :target: https://raw.githubusercontent.com/jpgill86/neurotic/master/docs/_static/example-screenshot.png
            :alt: Screenshot
        
        .. _Anaconda Cloud: https://anaconda.org/conda-forge/neurotic
        .. _conda:          https://docs.conda.io/projects/conda/en/latest/user-guide/install/
        .. _conda constructor: https://github.com/conda/constructor
        .. _constructor recipe: https://github.com/jpgill86/neurotic-constructor
        .. _conda-forge CI: https://dev.azure.com/conda-forge/feedstock-builds/_build/latest?definitionId=8417&branchName=master
        .. _conda-forge feedstock: https://github.com/conda-forge/neurotic-feedstock
        .. _Configuring Metadata: https://neurotic.readthedocs.io/en/latest/metadata.html
        .. _Coveralls:      https://coveralls.io/github/jpgill86/neurotic?branch=master
        .. _Documentation:  https://neurotic.readthedocs.io/en/latest
        .. _eNeuro:         https://doi.org/10.1523/ENEURO.0085-20.2020
        .. _ephyviewer:     https://ephyviewer.readthedocs.io/en/latest
        .. _GIN:            https://gin.g-node.org
        .. _GitHub:         https://github.com/jpgill86/neurotic
        .. _GitHub Actions: https://github.com/jpgill86/neurotic/actions?query=workflow%3Atests
        .. _GitHub Releases: https://github.com/jpgill86/neurotic/releases
        .. _Issue Tracker:  https://github.com/jpgill86/neurotic/issues
        .. _Neo:            https://neo.readthedocs.io/en/latest
        .. _neo.io:         https://neo.readthedocs.io/en/latest/io.html#module-neo.io
        .. _PyAV:           https://docs.mikeboers.com/pyav/develop/overview/installation.html
        .. _PyPI:           https://pypi.org/project/neurotic
        .. _ReadTheDocs:    https://readthedocs.org/projects/neurotic
        .. _Release Notes:  https://neurotic.readthedocs.io/en/latest/releasenotes.html
        .. _User Interface: https://ephyviewer.readthedocs.io/en/latest/interface.html
        .. _Zenodo:         https://doi.org/10.5281/zenodo.3564990
        
Keywords: neuroscience,electrophysiology,visualization,video-sync,data-management,data-sharing,download-manager,annotation-tool,open-science,python-neo
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering
Provides-Extra: docs
Provides-Extra: notebook
Provides-Extra: tests
