.. ACID documentation master file, created by
   sphinx-quickstart on Tue Oct 31 11:39:06 2023.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

A.C.I.D v2 (Accurate Continuum fItting and Deconvolution)
---------------------------------------------------------------

GitHub link: https://github.com/Benjamin-Cadell/ACID_v2

ACID_v2 is a fork of ACID (https://github.com/ldolan05/ACID) from the work of Lucy Dolan for her PhD. ACID_v2 improves on ACID by:
    - Updating packages and code to work with newer and stable versions of python.
    - Improving memory management so that ACID can be run on MacOS without crashes (ie extending compatibility to all POSIX systems)
    - Adding additional kwargs to ACID to tailor output, including verbosity settings, MCMC number of steps, multiprocessing switch, and more.
    - Utilising classes for both ACID and the result of ACID, allowing for analysis methods that can be found in the documentation.
    - Methods to extract fits formats for common instruments (e.g. ESPRESSO, HARPS, UVES) and to load them directly into ACID.
    - Updated documentation and examples

The mathematical functions and method remain the same as ACID and are outlined in Dolan et al. 2024 (https://academic.oup.com/mnras/article/529/3/2071/7624678).

The documentation will be kept up to date with the latest function descriptions until at least 2029.

ACID is a technique that builds on traditional Least-Squares Deconvolution (LSD) by simultaneously fitting the stellar continuum and stellar line profile and performing LSD in effective optical depth. 

In a basic sense, ACID simulatenously fits the stellar continuum and profile using a combination of LSD and MCMC techniques (MCMC implementation through emcee_). The spectra are then continuum corrected using this continuum fit. LSD is then run on the continuum corrected spectra to return high-resolution line profiles for each spectrum.

For a full outline of ACID's algorithm and implementation, see the paper_ or view the package on GitHub_.

Please note that ACID v2 now functions as a class, and so the usage is slightly different to ACID v1. Please see the User Guide and the Using ACID page for more information.

.. _emcee: https://emcee.readthedocs.io/en/
.. _paper: https://academic.oup.com/mnras/article/529/3/2071/7624678
.. _GitHub: https://github.com/Benjamin-Cadell/ACID_v2

User Guide
----------

.. toctree::
   :maxdepth: 2

   Installation and Setup <_installation>
   Tutorial - Using ACID <_tutorial>
   Results and Plotting <_results>
   Multiprocessing <_multiprocessing>
   Using the Data class <_data>
   The DataList and loading FITS files <_datalist>
   Analysing the Final Profiles <_profiles>
   Other ACID Functions <_other>
   ACID API <_API>

License and Attribution
-----------------------

Copyright 2025, Benjamin Cadell.

ACID is free software made available under the MIT License.

If you make use of ACID or ACID_v2 in your work please cite the original work by L.Dolan (L.Dolan et al, 2024): https://academic.oup.com/mnras/article/529/3/2071/7624678.

