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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.