zCluster Commands

The zCluster package includes a number of command-line programs, each of which is described below.

zCluster

zCluster estimates galaxy cluster photometric redshifts for objects in a user-supplied cluster catalog.

usage: zCluster [-h] [-o OUTLABEL] [-w WEIGHTSTYPE] [-R MAXRMPC] [-m MASK]
                [-a ALGORITHM] [-i MAXITER] [-c CACHEDIR] [-F] [-M]
                [-e MAXMAGERROR] [-E ZPERROR] [-f] [-z ZPRIORMIN]
                [-Z ZPRIORMAX] [-b ABSMAGCUT] [-n NAME] [-t TEMPLATESDIR] [-d]
                [-W] [-P] [-X ADDEXTRAPHOTO]
                [--min-background-area-Mpc2 MINBACKGROUNDAREAMPC2]
                [-B BCKCATALOGFILENAME] [-A BCKAREADEG2]
                [-C CREDENTIALSFILENAME]
                catalogFileName database

Positional Arguments

catalogFileName: A .fits table or a .csv file with at least the columns ‘name’, ‘RADeg’, ‘decDeg’.
database: The photometric database to use. Options are ‘SDSSDR12’, ‘S82’ (for SDSS DR7 Stripe 82 co-add); ‘CFHTLenS’; ‘DESDR1’, ‘DESDR2’, ‘DESY3’ [experimental; requires access to proprietary DES data]; ‘PS1’ [experimental]; ‘DECaLSDR8’, ‘DECaLSDR9’; or the path to a .fits table with columns in the appropriate format (‘ID’, ‘RADeg’, ‘decDeg’, and magnitude column names in the form ‘u_MAG_AUTO’, ‘u_MAGERR_AUTO’ etc.).

Named Arguments

-o, --output-label

Label to use for outputs (default: catalogFileName_database, stripped of file extension). A redshift catalog called zCluster_outLabel.fits will be created. Cached results for each entry in the input cluster catalog and associated plots will be written into the directory outLabel/, together with a log file that records the arguments used for running zCluster.

-w, --weights-type

Radial weighting type. Options are ‘NFW’, ‘flat’, or ‘radial’ (default: NFW).

Default: “NFW”

-R, --max-radius-Mpc

Maximum radius in Mpc within which to calculate delta statistic for each cluster (default: 0.5).

Default: 0.5

-m, --mask

Path to mask image (FITS format with WCS) that defines valid survey area.

-a, --algorithm

Algorithm to use for the maximum likelihood redshift. Options are ‘max’ or ‘odds’ (default: odds).

Default: “odds”

-i, --max-iter

Maximum number of iterations for finding the cluster redshift and optical position based on projected density map (default: 1).

Default: 1

-c, --cachedir

Cache directory location (default: $HOME/.zCluster/cache). Downloaded photometric catalogs will be stored here.

-F, --fetch-only-and-cache

Only fetch and cache galaxy catalogs - i.e., do not run photo-z estimation. This is useful if you are running on a compute cluster where compute nodes do not have internet access (allows a first run with -F, followed by a second run under MPI to compute the photo-zs in parallel).

Default: False

-M, --mpi

Enable MPI. If you want to use this, run zCluster using something like: mpirun –np 4 zCluster …

Default: False

-e, --max-mag-error

Maximum acceptable photometric error (in magnitudes; default: 0.25).

Default: 0.25

-E, --photometric-zero-point-error

Global photometric zero point uncertainty in magnitudes, applied to all bands (default: 0). Added in quadrature to the photometric uncertainties in the catalog.

Default: 0.0

-f, --fit-for-zero-point-offsets

If the input catalog contains a z_spec column, use those galaxies to fit for magnitude zero point offsets. These will then be applied when estimating galaxy photometric redshifts.

Default: False

-z, --z-prior-min

Set minimum redshift of prior.

-Z, --z-prior-max

Set maximum redshift of prior.

-b, --absmag-cut

Set absolute (r-band) magnitude cut to use in magnitude-based prior. If a single number is given, p(z) for objects brighter than this limit will be set to 0. If a list of numbers is given (e.g., [-15,-24]), p(z) will be set to 0 for objects outside of the absolute magnitude range.

Default: -24.0

-n, --name

Find photo-z of only the named cluster in the catalog.

-t, --templates-directory

Specify a directory containing a custom set of spectral templates.

-d, --write-density-maps

Write out a .fits image projected density map (within delta z = +/- 0.1 of the best fit redshift) for each cluster.

Default: False

-W, --write-galaxy-catalogs

Write out a .fits format galaxy catalog and DS9 .reg file for each cluster.

Default: False

-P, --write-plots

Write out a .pdf plot of n(z) for each cluster.

Default: False

-X, --add-extra-photometry

If using a user-supplied FITS galaxy photometic catalog, add in additional photometry from the given database (e.g., SDSSDR12, DECaLS - see ‘database’), if available.

--min-background-area-Mpc2

The minimum area of the background region in square Mpc. Candidate redshifts that have less than this minimum background area will be filtered out of the output catalog (default: 11, which corresponds to 50% of the background area for the standard 3-4 Mpc annulus used).

Default: 11

-B, --background-catalog

A .fits table with columns in the appropriate format (‘ID’, ‘RADeg’, ‘decDeg’, and magnitude column names in the form ‘u_MAG_AUTO’, ‘u_MAGERR_AUTO’ etc.) to be used as the background sample for delta estimates. If this is given, the area covered by the background catalog must be given also (-A flag)

-A, --background-area-deg2

The area, in square degrees, covered by the background galaxy catalog given using the -B flag.

-C, --credentials-filename

The location of a file containing username (first line), password (second line), for login to e.g., ESO Portal (this option is only currently used for the KIDSDR3 database option).

zField

zField estimates galaxy photometric redshifts for objects in a user-supplied direction on the sky.

usage: zField [-h] [-r MAXRDEG] [-D DATABASE] [-c CACHEDIR] [-o OUTDIR]
              [-l LABEL] [-t TEMPLATESDIR] [-e MAXMAGERROR] [-E ZPERROR] [-f]
              [-b ABSMAGCUT] [-d] [-z Z] [-dz DZ] [-DS9] [-ErrMap] [-MC MC]
              [-S STELLARMASSMODELDIR] [-p]
              RADeg decDeg

Positional Arguments

RADeg: RA (in decimal degrees) of the centre of the field to fetch.
decDeg: Dec (in decimal degrees) of the centre of the field to fetch.

Named Arguments

-r, --max-radius-deg

Radius in degrees around the given RA, Dec. coordinates within which galaxy photo-zs will be estimated (default = 0.2).

Default: 0.2

-D, --database

The photometric database to use. Options are ‘SDSSDR12’, ‘S82’ (for SDSS DR7 Stripe 82 co-add); ‘CFHTLenS’; ‘DESDR1’, ‘DESDR2’, ‘DESY3’ [experimental; requires access to proprietary DES data]; ‘PS1’ [experimental]; ‘DECaLSDR8’, ‘DECaLSDR9’; or the path to a .fits table with columns in the appropriate format (‘ID’, ‘RADeg’, ‘decDeg’, and magnitude column names in the form ‘u_MAG_AUTO’, ‘u_MAGERR_AUTO’ etc.).

Default: “DECaLSDR8”

-c, --cachedir

Cache directory location (default: $HOME/.zCluster/cache). Downloaded photometric catalogs will be stored here.

-o, --output-directory

Name of the output directory (default: zFieldOutput).

Default: “zFieldOutput”

-l, --label

Optional label to use for output files (default is to use the given RA, Dec coordinates in the output file names).

-t, --templates-directory

Specify a directory containing a custom set of spectral templates.

-e, --max-mag-error

Maximum acceptable photometric error (in magnitudes; default: 0.25).

Default: 0.25

-E, --photometric-zero-point-error

Global photometric zero point uncertainty in magnitudes, applied to all bands (default: 0). Added in quadrature to the photometric uncertainties in the catalog.

Default: 0.0

-f, --fit-for-zero-point-offsets

If the input catalog contains a z_spec column, use those galaxies to fit for magnitude zero point offsets. These will then be applied when estimating galaxy photometric redshifts.

Default: False

-b, --brighter-absmag-cut

Set bright absolute magnitude cut.

Default: -24.0

-d, --write-density-maps

Write out a .fits image projected density map (within –delta-z of the value specified using –redshift).

Default: False

-z, --redshift

Redshift at which to make the density map.

-dz, --delta-z

When making a projected density map, galaxy p(z) distributions are integrated within +/- dz of the given redshift (default: 0.1).

Default: 0.1

-DS9, --write-ds9-regions

Write out a DS9 .reg file corresponding to the fetched photometric catalog.

Default: False

-ErrMap, --make-error-map

Estimate and output uncertainties on the projected density map and associated summary statistics (warning: extremely slow).

Default: False

-MC, --monte-carlo-samples

Number of Monte Carlo samples to use when estimating uncertainties on the projected galaxy density map

Default: 1000

-S, --stellar-mass-model-dir

If given, estimate stellar masses for galaxies using the (for now) BC03-format stellar population models in the given directory. If -z (–redshift) is given, stellar masses will be estimated at the given redshift. Otherwise, the stellar masses will be estimated at the maximum likelihood redshift of each galaxy (although that isn’t actually implemented yet).

-p, --pickle-galaxy-catalog

If given, pickle the galaxy catalog after estimating photo-zs. Use this if you want to e.g. read p(z) for each galaxy from disk for some other analysis.

Default: False