.. LineAnalysisScripting documentation documentation master file, created by
   sphinx-quickstart on Mon Apr 22 18:16:10 2013.
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LineAnalysisScripting
=====================

:Last update: 
    23/07/14


.. Introduction                                                              {{{1
.. _introduction:

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

In addition to the graphical user interface, CASSIS allows its users to 
create their own scripts in Jython to analyze lines.

*LineAnalysisScripting.py* is a library allowing to simplify the search of the
best physical parameters for modelling an astrophysical source in CASSIS_
LineAnalysis_ by using a regular grid or a Markov Chain Monte Carlo method in
Local Thermodynamic Equilibrium or in RADEX models. 

The current documentation describes how to use this library and create your own scripts.
(Examples_ of scripts with their associated data are provided on the website.)


In order to determine the best set of parameters fitting a given observation,
you define the parameters and how they vary for a given component.
*LineAnalysisScripting.py* computes the :math:`\chi^{2}` between the simulated
and the observed data for each model and finds the minimal :math:`\chi^{2}`. 
The parameters that generated this value are the parameters modelling the best
the observation.

The steps below will explain you more in details how to use *LineAnalysisScripting.py*.


Setup
-----

.. toctree::
   :maxdepth: 2

   setup/user_inputs_creation
   setup/ranges
   setup/components_creation


Computation
-----------

.. toctree::
   :maxdepth: 2

   computation/rg_method
   computation/mcmc_method


Data analysis
-------------

.. toctree::
   :maxdepth: 2

   data_analysis/plot_results
   data_analysis/use_best_physical_models


Development
-----------

.. toctree::
   :maxdepth: 1

   CHANGELOG
   authors


.. _Examples: http://cassis.irap.omp.eu/download/mycassis.tar.gz
.. _CASSIS: http://cassis.irap.omp.eu/
.. _LTE documentation: http://cassis.irap.omp.eu/docs/RadiativeTransfer.pdf
.. _RADEX documentation: http://www.strw.leidenuniv.nl/~moldata/radex.html
.. _LineAnalysis: http://cassis.irap.omp.eu/help/?page=line_analysis