******
|logo|
******
``restoreio`` is a Python package to **Restore** **I**\ ncomplete **O**\ ceanographic dataset, with specific focus on ocean surface velocity data. This package can also generate data ensemble and perform statistical analysis, which allows uncertainty qualification of such datasets.
Links
=====
* `Online Gateway <https://restoreio.org>`__
* `Documentation <https://ameli.github.io/restoreio>`__
* `PyPI <https://pypi.org/project/restoreio/>`__
* `Anaconda Cloud <https://anaconda.org/s-ameli/restoreio>`__
* `Github <https://github.com/ameli/restoreio>`__
Install
=======
Install with ``pip``
--------------------
|pypi|
::
pip install restoreio
Install with ``conda``
----------------------
|conda-version|
::
conda install -c s-ameli restoreio
Supported Platforms
===================
Successful installation and tests performed on the following operating systems and Python versions:
.. |y| unicode:: U+2714
.. |n| unicode:: U+2716
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.. |build-linux| image:: https://img.shields.io/github/actions/workflow/status/ameli/restoreio/build-linux.yml
:target: https://github.com/ameli/restoreio/actions?query=workflow%3Abuild-linux
.. |build-macos| image:: https://img.shields.io/github/actions/workflow/status/ameli/restoreio/build-macos.yml
:target: https://github.com/ameli/restoreio/actions?query=workflow%3Abuild-macos
.. |build-windows| image:: https://img.shields.io/github/actions/workflow/status/ameli/restoreio/build-windows.yml
:target: https://github.com/ameli/restoreio/actions?query=workflow%3Abuild-windows
Documentation
=============
|deploy-docs|
See `documentation <https://ameli.github.io/restoreio/index.html>`__, including:
* `Installation Guide <https://ameli.github.io/restoreio/install.html>`__
* `User Guide <https://ameli.github.io/restoreio/user_guide/user_guide.html>`__
* `API Reference <https://ameli.github.io/restoreio/api.html>`__
* `Examples <https://ameli.github.io/restoreio/examples.html>`__
* `Publications <https://ameli.github.io/restoreio/cite.html>`__
Usage
=====
An installation of ``restoreio`` offers two interfaces: a Python interface and a command-line interface.
1. Python Interface
-------------------
You can import ``restoreio`` in python by ``import restoreio``. This package offers the following functions:
* `restoreio.restore <https://ameli.github.io/restoreio/generated/restoreio.restore.html#restoreio.restore>`__: This is the main function of the package which reconstructs incomplete velocity data, generates data ensemble, and performs statistical analysis. You can import this function by
::
from restoreio import restore
* `restoreio.scan <https://ameli.github.io/restoreio/generated/restoreio.scan.html#restoreio.scan>`__: This function performs a pre-scan of your NetCDF dataset and ensures your dataset is compatible as an input to ``restoreio.restore`` function. The scan also provides you basic information about the dataset such as the time span, spatial extent of the data. These information could be useful to configure the settings for ``restoreio.restore`` function. You can import this function by
::
from restoreio import scan
2. Command-Line Interface
-------------------------
Alternatively, you may use ``restoreio`` as a standalone application which can be executed in command line. When ``restoreio`` is installed, the following executables are available:
* `restore <https://ameli.github.io/restoreio/cli_restore.html>`__: This executable is equivalent to ``restoreio.restore`` function in the Python interface.
* `restore-scan <https://ameli.github.io/restoreio/cli_scan.html>`__: This executable is equivalent to ``restoreio.scan`` function in the Python interface.
To use these executables, make sure the ``/bin`` directory of your Python installation is set on your ``PATH`` environment variable. For instance, if your Python is installed on ``/opt/minicinda3/``, add this path ``/opt/miniconda3/bin`` directory to ``PATH`` by
::
export PATH=/opt/minicinda/bin:$PATH
You may place the above line in ``~/.bashrc`` to make the above change permanently.
Online Web-Based Interface
==========================
Alongside ``restoreio`` python package, we also offer an online service as a web-based interface for this software. This platform is available at: `https://restoreio.org <https://restoreio.org>`__.
This online gateway allows users to efficiently process both local and remote datasets. The computational tasks are executed on the server side, leveraging the parallel processing capabilities of a high-performance computing cluster. Moreover, the web-based interface seamlessly integrates an interactive globe map, empowering sophisticated visualization of the results within the online platform.
How to Contribute
=================
We welcome contributions via `GitHub's pull request <https://github.com/ameli/restoreio/pulls>`__. If you do not feel comfortable modifying the code, we also welcome feature requests and bug reports as `GitHub issues <https://github.com/ameli/restoreio/issues>`__.
How to Cite
===========
If you publish work that uses ``restoreio``, please consider citing the manuscripts available `here <https://ameli.github.io/restoreio/cite.html>`__.
License
=======
|license|
This project uses a `BSD 3-clause license <https://github.com/ameli/restoreio/blob/main/LICENSE.txt>`__, in hopes that it will be accessible to most projects. If you require a different license, please raise an `issue <https://github.com/ameli/restoreio/issues>`__ and we will consider a dual license.
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.. |binder| image:: https://mybinder.org/badge_logo.svg
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.. |codecov-devel| image:: https://img.shields.io/codecov/c/github/ameli/restoreio
:target: https://codecov.io/gh/ameli/restoreio
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You can import this function by\n\n ::\n\n from restoreio import scan\n\n2. Command-Line Interface\n-------------------------\n\nAlternatively, you may use ``restoreio`` as a standalone application which can be executed in command line. When ``restoreio`` is installed, the following executables are available:\n\n* `restore <https://ameli.github.io/restoreio/cli_restore.html>`__: This executable is equivalent to ``restoreio.restore`` function in the Python interface.\n* `restore-scan <https://ameli.github.io/restoreio/cli_scan.html>`__: This executable is equivalent to ``restoreio.scan`` function in the Python interface.\n\nTo use these executables, make sure the ``/bin`` directory of your Python installation is set on your ``PATH`` environment variable. 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