lyacorr

This is a set of programs for calculating the autocorrelation of Lyman-α forests from SDSS BOSS data.

Installation

Note that deployment is not very user friendly.

• Some tinkering with configuration files and scripts may be required.

Hardware Requirements

• 500GB of storage space
• 32GB of RAM (preferrably more)
• 100GB of fast local storage (RAM or SSD)
• 16 CPU cores or more (recommended)

Software Requirements

• Python 2, or Python 3

Required python packages:

• Cython
• matplotlib
• lmfit
• h5py
• healpy
• astropy
• scipy
• numpy
• mpi4py

Cython module

To build and install the cython module run:

cd cython_helper
python setup.py install --user

Required data files:

• SDSS BOSS DR12 spPlate fits files, with the original directory structure
• QSO table from a CasJobs query, saved as a FITS file, for example:

  SELECT S.specObjID,S.mjd,S.plate,S.fiberID,S.ra,S.dec,
         S.zOffset,S.z,S.zErr,S.zWarning,S.class,S.subClass,P.extinction_g
  INTO mydb.QSOs FROM SpecObj AS S
  JOIN SpecPhotoAll AS P ON S.specObjID=P.specObjID
  WHERE S.instrument='BOSS' AND (S.zwarning | 0x10) = 0x10 AND
         S.class='QSO' AND (S.boss_target1 & 0x1FF) = 0 AND
         (S.z>2.1) AND (S.z<3.5) AND (S.plate>3523)

• PCA continuum fit tables from Suzuki et al. 2005 and Paris et al. 2011.
• Broard Absorption Line catalog DR12Q_BAL.fits
• DLA catalog from Garnett et al. 2016

Configuration

There is an annotated configuration file at example_config/.

The default configuration file is lyacorr.rc at the current directory.
The configuration file path can be overridden using the LYACORR_CONF_FILE environment variable, e.g.:

export LYACORR_CONF_FILE=/path/to/config_file.rc

Running

There is an annotated script file at example_config/.

The output files are in native numpy format (.npy,.npz). They can be viewed using matplotlib in a Jupyter notebook.