======
perses
======
The Pre-EoR Signal Extraction Software (perses) package was designed to fit global 21-cm datasets, including various foregrounds, parameters of the instrument, and the cosmological signal itself.

A few papers on how it works:

- Original implementation: Harker et al. (2012) http://adsabs.harvard.edu/abs/2012MNRAS.419.1070H
- emcee implementation: Harker et al. (2015) http://adsabs.harvard.edu/abs/2015arXiv151000271H

Be warned: this code is still under active development -- use at your own risk! Correctness of results is not guaranteed.

Getting started
---------------------
To clone a copy and install:

    git clone https://github.com/CU-NESS/perses.git
    cd perses
    python setup.py develop

To download a few common sky maps:

    python remote.py

If something goes wrong or you'd just like new copies of the files, you can run:

    python remote.py fresh

It would be in your best interest to set an environment variable which points to the perses install directory, e.g. (in bash):

    export PERSES=/users/<yourusername>/perses

perses will look in $PERSES/input for lookup tables of various kinds, e.g., instrumental response, beam pattern, foreground models, etc.

Dependencies
--------------------
You will need:

- [numpy](http://www.numpy.org/)
- [scipy](http://www.scipy.org/)
- [matplotlib](http://matplotlib.org/)
- [ares](https://github.com/mirochaj/ares.git)
- [emcee](http://dan.iel.fm/emcee/current/)

and probably (but optionally), 

- [h5py](http://www.h5py.org/)
- [healpy](https://healpy.readthedocs.org/en/latest/)
- [mpi4py](http://mpi4py.scipy.org)
- [astropy](http://www.astropy.org/)
- [ephem](http://rhodesmill.org/pyephem/)
- [python-progressbar](https://code.google.com/p/python-progressbar/)
- [setuptools](https://pypi.python.org/pypi/setuptools)
- [multiprocess](https://pypi.python.org/pypi/multiprocess)

Quick Example
--------------
To make sure everything is working, read in the global sky model and plot it at 80 MHz:

    import perses
    gal = perses.foregrounds.HaslamGalaxy()
    gal.plot(80.)
    plt.show()

See the documentation for more examples.

Documentation
--------------
To generate the documentation locally,

    cd $PERSES/docs
    ./make_docs.sh

Contributors
------------

Primary developer: Keith Tauscher

Additional contributions / corrections / suggestions from:
    
- Geraint Harker http://zuserver2.star.ucl.ac.uk/~harkerg/  
- Jordan Mirocha https://sites.google.com/site/jordanmirocha/home
- Abhi Datta
- Neil Bassett
- David Rapetti
- Joshua Hibbard