specdb Scripts¶

This file summarizes the specdb scripts which are executed outside a Python shell, but use Python code. These are installed within your standard Python script path (e.g. ~/anaconda/bin).

Notebooks¶

Simple Scripts

Download a Database¶

specdb includes a set of scripts for downloading its public databases. Here is a brief description of each.

specdb_get_igmspec¶

The download script for igmspec is named specdb_get_igmspec. Here is its usage:

wolverine-6.local> specdb_get_igmspec -h
usage: specdb_get_igmspec [-h] [-v VERSION]

Grab the IGMspec DB

optional arguments:
  -h, --help            show this help message and exit
  -v VERSION, --version VERSION
                        DB version to generate

The script uses a simple wget command to the URL of the igmspec database. It defaults to the most recent version of the database.

specdb_get_uvqs¶

The download script for UVQS is named specdb_get_uvqs. Here is its usage:

wolverine> specdb_get_uvqs -h
usage: specdb_get_uvqs [-h] [-v VERSION]

Grab the UVQS DB

optional arguments:
  -h, --help            show this help message and exit
  -v VERSION, --version VERSION
                        DB version to generate

The script uses a simple wget command to the URL of the UVQS database. It defaults to the most recent version of the database.

specdb_plot¶

Plot a spectrum at the given coordinate. One can restrict the database and/or surveys used and/or select the desired spectrum from the available list. By default, the XSpecGui gui from linetools is called to display the spectrum. Here is the usage:

wolverine-6.local> specdb_plot -h
 usage: specdb_plot [-h] [--tol TOL] [--meta] [-g GROUP] [--select SELECT]
                    [--mplot MPLOT] [--db_file DB_FILE]
                    coord dbase

 specdb_plot script v0.3

 positional arguments:
   coord                 Coordinates, e.g. J081240.7+320809 or 122.223,-23.2322
                         or 07:45:00.47,34:17:31.1
   dbase                 Database [igmspec,all,priv]

 optional arguments:
   -h, --help            show this help message and exit
   --tol TOL             Maximum offset in arcsec [default=5.]
   --meta                Show meta data? [default: True]
   -g GROUP, --group GROUP
                         Name of Group to use (e.g. BOSS_DR12)
   --select SELECT       Index of spectrum to plot (when multiple exist)
   --mplot MPLOT         Use simple matplotlib plot [default: False]
   --db_file DB_FILE     Full path of db_file

Here is an example or two:

specdb_plot J220248.31+123656.3 priv --db_file=qpq_optical.hdf5
specdb_plot J220248.31+123656.3 igmspec

specdb_cat¶

Query the main catalog by coordinate and return RA, DEC, zem, and flag_group. Here is the usage:

usage: specdb_cat [-h] [--tol TOL] [--db_file DB_FILE] coord dbase

specdb_cat script v0.1

positional arguments:
  coord              Coordinates, e.g. J081240.7+320809 or 122.223,-23.2322 or
                     07:45:00.47,34:17:31.1
  dbase              Database [igmspec,uvqs,qpq,priv]

optional arguments:
  -h, --help         show this help message and exit
  --tol TOL          Maximum offset in arcsec [default=5.]
  --db_file DB_FILE  Full path of db_file

specdb_meta¶

Show some meta data for all the sources within tolerance of a given coordinate and with meta data in one of the data groups. Sources that only appear in the main catalog will return nothing. You may wish to use spedb_cat instead.

One must specify the database and can restrict on Group. Here is the usage:

specdb_meta -h
usage: specdb_meta [-h] [--tol TOL] [-g GROUP] [--db_file DB_FILE] coord dbase

specdb_meta script v0.1

positional arguments:
  coord                 Coordinates, e.g. J081240.7+320809 or 122.223,-23.2322
                        or 07:45:00.47,34:17:31.1
  dbase                 Database [igmspec,uvqs,all,priv]

optional arguments:
  -h, --help            show this help message and exit
  --tol TOL             Maximum offset in arcsec [default=5.]
  -g GROUP, --group GROUP
                        Restrict on Group (e.g. BOSS_DR12)
  --db_file DB_FILE     Full path of db_file

sdss_spec¶

Grab data from the SDSS/BOSS survey with plate-fiber notation. Here is the help:

$specdb_sdss -h
 usage: specdb_sdss [-h] [-s SURVEY] [--select SELECT] [-p] plate fiberid dbase

 specdb_sdss script v0.1

 positional arguments:
   plate                 Plate
   fiberid               FiberID
   dbase                 Database [igmspec,all]

 optional arguments:
   -h, --help            show this help message and exit
   -s SURVEY, --survey SURVEY
                         Name of Survey to use (BOSS_DR12 or SDSS_DR7)
   --select SELECT       Index of spectrum to plot (when multiple exist)
   -p, --plot            Plot with lt_xspec

Here is an example:

specdb_sdss 377 321 igmspec

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