DR11 Lyman-alpha MockExpander Tutorial

This page describes the Lyman-alpha MockExpander package required to use the DR11 Lyman-alpha mock catalogs . More details on the mock catalogs can be found in Bautista et al. (2015).

The last version of the Lyman-alpha MockExpander can be downloaded from the BOSS svn repository.

This package transforms raw absorption fields (mockrawShort files) into realistic spectra (mock-PLATE-MJD-FIBER.fits) with quasar continua, and BOSS characteristics such as noise, resolution and flux calibration errors.


JAVA version needed
at least 1.6.0_*
spec files containing individual exposures organized in the per-plate structure as in the data.sdss3.org
Raw files
mockrawShort files containing all realizations of raw forests, also organized in a per-plate structure of folders. You can find these files in gzipped tarballs here


Edit the "Run.sh" file, setting paths for the mock and data folders, and other options. Execute the Run.sh script:

$ ./Run.sh

The code will search for all available "mockrawShort" and "spec" files. The expansion will be performed only for spectra having both files.

Failed expansions will be reported on: FailedExpandedMocks.txt

All suggestions and/or corrections are welcome. Please report problems or bugs to: bautista [at] astro.utah.edu

Expansion Options

 Initial_Realization and Final_Realization
The mockrawShort files contain the absorption field for many realizations. These options allows the choice of the range of realizations to be expanded.
Allows the choice between continuing from to expand mocks from the last point where it stopped (for some reason), or to start from the beginning eventually re-writing a previous version of expanded mocks.
The cooking formula that sets what physical features are included in the final spectra.

  • "f*cpca+n" = Lyman-alpha forests with PCA continua and noise
  • "fdla*cpca+n" = same as above, but including high column density systems and metals associated with these systems
  • "fmet*cpca+n" = same as the first one, but including IGM metal absorption lines correlated with all lyman-alpha absorption
  • "fdlamet*cpca+n" = mix of the last two.
Select the columns that will be written in the output expanded mock files. The available columns are described in the "Run.sh" file.