vip-hci 2.0.0
Package for astronomical high-contrast image processing.
Requires Python: >=3.10

VIP - Vortex Image Processing package
=====================================

|VIP| |Versions| |License| |ArXiV| |docs| |codecov| |DOI| |Zenodo| |EMAC|

.. |VIP| image:: https://badge.fury.io/py/vip-hci.svg
        :target: https://pypi.python.org/pypi/vip-hci

.. |Versions| image:: https://img.shields.io/badge/Python-3.10%2C%203.11%2C%203.12%2C%203.13-brightgreen.svg
             :target: https://pypi.python.org/pypi/vip-hci

.. |License| image:: https://img.shields.io/badge/license-MIT-blue.svg?style=flat
            :target: https://github.com/vortex-exoplanet/VIP/blob/master/LICENSE

.. |ArXiV| image:: https://img.shields.io/badge/arXiv-1705.06184%20-yellowgreen.svg
          :target: https://arxiv.org/abs/1705.06184

.. |docs| image:: https://readthedocs.org/projects/vip/badge/?version=latest
         :target: http://vip.readthedocs.io/en/latest/?badge=latest

.. |codecov| image:: https://codecov.io/gh/vortex-exoplanet/VIP/branch/master/graph/badge.svg?token=HydCFQqLRf
            :target: https://codecov.io/gh/vortex-exoplanet/VIP

.. |DOI| image:: https://joss.theoj.org/papers/10.21105/joss.04774/status.svg
        :target: https://doi.org/10.21105/joss.04774

.. |Zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.7499314.svg
           :target: https://doi.org/10.5281/zenodo.7499314

.. |EMAC| image:: https://img.shields.io/badge/EMAC-2207--116-blue
         :target: https://emac.gsfc.nasa.gov/?cid=2207-116

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             Vortex Image Processing package
    ---------------------------------------------------


Introduction
------------

VIP is a python package for high-contrast imaging of exoplanets and circumstellar disks.
VIP is compatible with Python 3.10 to 3.13 (Python 2 compatibility dropped with VIP 0.9.9, and Python 3.7 compatibility dropped with VIP 1.4.3).

The goal of VIP is to integrate open-source, efficient, easy-to-use and
well-documented implementations of high-contrast image processing algorithms to
the interested scientific community. The main repository of VIP resides on
`GitHub <https://github.com/vortex-exoplanet/VIP>`_, the standard for scientific
open source code distribution, using Git as a version control system.

Most of VIP's functionalities are mature but
it does not mean it is free from bugs. The code is continuously evolving and
therefore feedback/contributions are greatly appreciated. Please refer to `these instructions <https://vip.readthedocs.io/en/latest/Contact.html>`_ if you want to report
a bug, ask a question, suggest a new functionality or contribute to the code (the latter is particularly welcome)!

.. image:: https://github.com/carlgogo/carlgogo.github.io/blob/master/assets/images/vip.png?raw=true
    :alt: Mosaic of S/N maps

Documentation
-------------
The documentation for VIP can be found here: http://vip.readthedocs.io.


Jupyter notebook tutorial
-------------------------
Tutorials, in the form of Jupyter notebooks, showcasing VIP's usage and
other resources such as test datasets are available in the
``VIP-extras`` `repository <https://github.com/vortex-exoplanet/VIP_extras>`_.
**In order to execute the notebook tutorials, you will have to download or clone the VIP-extras repository, and open each tutorial locally with jupyter notebook.**
Alternatively, you can execute the notebooks directly on
`Binder <https://mybinder.org/v2/gh/vortex-exoplanet/VIP_extras/master>`_ (in
the tutorials directory). The first (quick-start) notebook can be visualized
online with `nbviewer
<http://nbviewer.jupyter.org/github/vortex-exoplanet/VIP_extras/blob/master/tutorials/01_quickstart.ipynb>`_.
If you are new to the Jupyter notebook application check out the `beginner's guide
<https://jupyter-notebook-beginner-guide.readthedocs.io/en/latest/what_is_jupyter.html>`_.


TL;DR setup guide
-----------------
.. code-block:: bash

   pip install vip_hci


Installation and dependencies
-----------------------------
The benefits of using a Python package manager (distribution), such as
(ana)conda, are many. Mainly, it brings easy and robust package
management and avoids messing up with your system's default python. An
alternative is to use package managers like apt-get for Ubuntu or
Homebrew/MacPorts/Fink for macOS. We recommend using
`Miniconda <https://conda.io/miniconda>`_.

VIP depends on existing packages from the Python ecosystem, such as
``numpy``, ``scipy``, ``matplotlib``, ``pandas``, ``astropy``, ``scikit-learn``,
``scikit-image``, ``photutils`` and others. There are different ways of
installing VIP suitable for different scenarios.

Before installing the package, it is **highly recommended to create a dedicated
conda environment** to not mess up with the package versions in your base
environment. This can be done easily with (replace ``vipenv`` by the name you want
for your environment):

.. code-block:: bash

   conda create -n vipenv python=3.10 ipython

.. note::
   Installing ipython while creating the environment, as in the example above, will
   avoid a commonly reported issue which stems from trying to import VIP from
   within a base python2.7 ipython console.


For users not planning to contribute:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Once within your new environment, the easiest way to install VIP is
through the Python Package Index, aka `PyPI <https://pypi.org/>`_, with
the ``pip`` package manager. Simply run:

.. code-block:: bash

  pip install vip_hci

With ``pip`` you can easily uninstall, upgrade or install a specific version of
VIP. For upgrading the package, run:

.. code-block:: bash

  pip install --upgrade vip_hci


For potential contributors:
^^^^^^^^^^^^^^^^^^^^^^^^^^^
If you plan to contribute or experiment with the code you need to make a
fork of the repository (click on the fork button in the top right corner) and
clone it:

.. code-block:: bash

   git clone https://github.com/<replace-by-your-username>/VIP.git

If you do not create a fork, you can still benefit from the ``git`` syncing
functionalities by cloning the repository (but will not be able to contribute):

.. code-block:: bash

   git clone https://github.com/vortex-exoplanet/VIP.git


To install VIP, then simply cd into your local VIP directory, and run the installation in editable mode pointing to developer requirements:

.. code-block:: bash

   cd VIP
   pip install -e . --group dev

If cloned from your fork, make sure to link your VIP directory to the upstream
source, to be able to easily update your local copy when a new version comes
out or a bug is fixed:

.. code-block:: bash

   git remote add upstream https://github.com/vortex-exoplanet/VIP.git

If you plan to develop VIP or use it intensively, it is highly recommended to
also install the optional dependencies listed below.


Optional dependencies
^^^^^^^^^^^^^^^^^^^^^
The following dependencies are not automatically installed upon installation of VIP but may significantly improve your experience:

- VIP contains a class ``vip_hci.vip_ds9`` that enables, through ``pyds9``, the interaction with a DS9 window (displaying numpy arrays, controlling the display options, etc). To enable this feature, ``pyds9`` must be installed from the latest development version: ``pip install git+git://github.com/ericmandel/pyds9.git#egg=pyds9``
- VIP image operations (e.g. shifts, rotations, scaling) can be performed using ``OpenCV`` instead of the default FFT-based methods. While flux are less well preserved, ``OpenCV`` offers a significant speed improvement (up to a factor 50x), in particular for image rotations, which can be useful to get quick results. Installation: ``pip install opencv-python``.
- Also, you can install the Intel Math Kernel Library (``mkl``) optimizations (provided that you have a recent version of ``conda``) or ``openblas`` libraries. Either of them can be installed with ``conda install``.
- VIP offers the possibility of computing SVDs on GPU by using ``CuPy`` (starting from version 0.8.0) or ``PyTorch`` (from version 0.9.2). These remain as optional requirements, to be installed by the user, as well as a proper CUDA environment (and a decent GPU card).
- Bad pixel correction routines can be optimised with ``Numba``, which  converts some Python code, particularly ``NumPy``, into fast machine code. A factor up to ~50x times speed improvement can be obtained on large images compared to NumPy. Numba can be installed with ``conda install numba``.
- Finally, robust contrast curves and contrast grids can be calculated with ``applefy`` (``pip install Applefy``). Example usage is provided in `VIP tutorial 4 <https://vip.readthedocs.io/en/latest/tutorials/04_metrics.html>`_. See more details in `Bonse et al. (2023) <https://ui.adsabs.harvard.edu/abs/2023AJ....166...71B/abstract>`_.


Loading VIP
^^^^^^^^^^^
Finally, start Python (or IPython or a Jupyter notebook if you prefer) and check
that you are able to import VIP:

.. code-block:: python

   import vip_hci as vip

If everything went fine with the installation, you should not get any error message upon importation, and you can start finding exoplanets!


Conventions
-----------

Image Center
^^^^^^^^^^^^
By default, VIP routines are compatible with either even- or odd-dimension input frames. For VIP routines that require the star to be centered in the input images (e.g. post-processing routines involving (de)rotation or scaling), the code will assume that it is placed on (zero-based indexing):

- size/2-0.5 for odd-size input images;
- size/2 for even-size input images;

i.e. exactly on a pixel in either cases. The VIP recentering routines will place the star centroid at one of these locations accordingly.

Position angles
^^^^^^^^^^^^^^^
In VIP, all angles are measured counter-clockwise from the positive x axis (i.e. trigonometric angles), following the convention of most packages VIP leverages upon. This includes the position angles returned by algorithms in the forward modelling subpackage of VIP used to characterize directly imaged exoplanets (e.g. negative fake companion routines). This convention is different to the typical astronomical convention which measures angles east from north (for the conversion, simply subtract 90deg to angles returned by VIP).

4D IFS+ADI cubes
^^^^^^^^^^^^^^^^
For all routines compatible with 4D IFS+ADI cubes, the convention throughout VIP is to consider the zeroth axis to correspond to the spectral dimension, and the first axis to be the temporal (ADI) dimension.


Contact
-------

Answers to `frequently asked questions <https://vip.readthedocs.io/en/latest/faq.html>`_ are provided in the relevant section of the documentation.
If you have an issue with VIP, please first check it is not detailed in the FAQ.
If you find a bug or experience an unreported issue in VIP, it is recommended to post a new entry in the `Issues section <https://github.com/vortex-exoplanet/VIP/issues>`_ on GitHub. Feel free to propose a pull request if you have already identified the source of the bug/issue.

If you have a global comment, inquiry about how to solve a specific task using VIP, or suggestions to improve VIP, feel free to open a new thread in the `Discussions <https://github.com/vortex-exoplanet/VIP/discussions>`_ section. The 'Discussions' section is also used to post VIP-related announcements and discuss recent/on-going changes in VIP.
Envisioned future developments are listed in the `Projects <https://github.com/vortex-exoplanet/VIP/projects/1>`_ section. Contributions are very welcome!

If you wish to be kept informed about major VIP updates and on-going/future developments, feel free to click the 'watch' button at the top of the GitHub page.


Attribution
-----------

VIP started as the effort of `Carlos Alberto Gomez Gonzalez <https://github.com/carlos-gg>`_,
a former PhD student of `PSILab <https://sites.google.com/site/olivierabsil/psilab>`_
(ULiege, Belgium), who has led the development of VIP from 2015 to 2020.
Maintenance and current development is now led by `Valentin Christiaens <https://github.com/VChristiaens>`_.
VIP benefitted from contributions made by collaborators from several teams, including: Ralf Farkas, Julien Milli, Olivier Wertz, Henry Ngo, Alan Rainot, Gary Ruane, Corentin Doco, Miles Lucas, Gilles Orban de Xivry, Lewis Picker, Faustine Cantalloube, Iain Hammond, Christian Delacroix, Arthur Vigan, Dimitri Mawet and Olivier Absil.
More details about the respective contributions are available `here <https://github.com/vortex-exoplanet/VIP/graphs/contributors?from=2015-07-26&to=2022-03-29&type=a>`_.

Please cite `Gomez Gonzalez et al. (2017) <https://ui.adsabs.harvard.edu/abs/2017AJ....154....7G/abstract>`_ and `Christiaens et al. (2023) <https://ui.adsabs.harvard.edu/abs/2023JOSS....8.4774C/abstract>`_ whenever
you publish data reduced with VIP (Astrophysics Source Code Library reference `ascl:1603.003`).
In addition, please cite the relevant publication(s) for the algorithms you use within VIP (usually mentioned in the documentation, e.g. `Marois et al. 2006 <https://ui.adsabs.harvard.edu/abs/2006ApJ...641..556M/abstract>`_ for median-ADI).