.. pyLICORS documentation master file, created by
   sphinx-quickstart on Sat Jan 14 16:02:06 2012.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

pyLICORS Documentation
======================

pyLICORS is a `Python <http://www.python.org>`_ package estimates the predictive
state space of a spatio-temporal process given spatio-temporal data. 
Typically this is a 
video (2D random field) observed for :math:`T` time steps.

.. note::
  References are arxiv.org/abs/1211.3760 and arxiv.org/abs/1206.2398 .

pyLICORS can handle

#. :math:`(2+1)D` space-time random fields (aka as videos = 2D images in time (1D))

   * sequences of images (``bmp``, ``jpg``, or ``png``)

   * videos (``avi``, ``mpg``, or ``mov``)

   * fMRI data formats (``.gz``, ``.img``, ``nii.gz``) 

#. :math:`(1+1)D` space-time random fields 
   (e.g. `cellular automata <https://en.wikipedia.org/wiki/Cellular_automaton>`_. They are less common in practice, but good for simulations
   and visualization: think of an image where space is vertical and time goes from left to right).
  
   * comma separated ``txt`` or ``dat`` files, where each row is the time evolution of the system at space point :math:`r`; 
     column 1 is the entire system at time :math:`t=1`, column 2 the system at time :math:`t=2`, and so on.
   
   * images (``bmp``, ``jpg``, or ``png``)

.. note::
  Although libraries used in pyLICORS are available for most platforms that run Python, it was developed on
  a Windows installation of Python. It has also been successfully tested on Ubuntu 11.10 (only difference
  that on Ubuntu built-in `cv` library was used for OpenCV; on Windows `pyopencv`).
  
  These instruction may follow - sometimes unaware - a Windows style installation.
  In principle pyLICORS should not have any problems to run on Linux/MacOS.

  If you do encounter problems, please let me know.

Pre-release of software and documentation
-----------------------------------------

This is a very first planning release of the software: the main features are not available yet, 
it is just an initial draft. Core functions will be added over the course of the next months.

This means that the functionality and the documentation will change in the future. In 
particular, function names, class names, functionality of classes,
internal structures of the code, etc. **will** certainly **change** (so all follow the `Python PEP8
naming conventions <http://www.python.org/dev/peps/pep-0008/>`_ ). 

.. warning::
  Users that want to use individual functions in the package to run specific parts of the analysis
  must be aware that their scripts **will break** when run with future releases of pyLICORS.


Setup and Installation
======================

.. toctree::
   :maxdepth: 2
   
   installation.rst

Documentation
=============

.. toctree::
   :maxdepth: 2

   TODO.rst    
   
Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

