linetool Scripts

There are a number of scripts, many of which are GUIs, provided with linetools. As regards the GUIs we warn again that Mac users will need to set their matplotlib to something other than MacOSX. See backends.

lt_xspec

Launch a QT Gui to examine an input spectrum.

For example:

lt_xspec filename.fits
lt_xspec filename.fits#1#   -- Specifies extension 1 for a multi-extension FITS file of binary tables

You can explore the data, perform simple analysis (e.g. EW measurements) and more. See the Notebook for more.

Here is the full usage:

usage: lt_xspec [-h] [-z ZSYS] [--norm] [--air] [--exten EXTEN]
                [--splice SPLICE] [--scale SCALE]
                file

Parser for lt_xspec v1.2; Note: Extra arguments are passed to read_spec (e.g.
--flux_tag=FX)

positional arguments:
  file                  Spectral file; specify extension by appending #exten#

optional arguments:
  -h, --help            show this help message and exit
  -z ZSYS, --zsys ZSYS  System Redshift
  --norm                Show spectrum continuum normalized (if continuum is
                        provided)
  --air                 Convert input spectrum wavelengths from air to vacuum
  --exten EXTEN         FITS extension
  --splice SPLICE       Splice with the input file; extension convention
                        applies
  --scale SCALE         Scale factor for GUI size [1. is default]

lt_plot

Plot one or more spectra. This has fewer features than lt_xspec above, but is faster.

For example:

lt_plot filename1 filename2

A plot of the spectrum in filename1 appears, and you can navigate around it using the same commands as in lt_xspec. Move to the next or previous spectrum with the right or left arrow key.

To list all the command line options available, use:

lt_plot -h

lt_absline

This plots a single absorption line, given a transition rest wavelength (Angstroms) or name (e.g. CIV1548), log10 column density, and Doppler parameter (km/s).

For example:

lt_absline 1215.6701 14.0 30
lt_absline HI1215 14.0 30

plots a Hydrogen Ly-a line with column density of 1014 cm-2 and b=30 km/s. A plot will appear and the line info and EW as well, i.e.

[AbsLine: HI 1215, wrest=1215.6700 Angstrom]
EW = 0.268851 Angstrom

Try:

lt_absline -h

for the full set of options.

lt_radec

Input coordinates in one format and print them out in several formats:

lt_radec 152.25900,7.22885
lt_radec J100902.16+071343.86
lt_radec 10:09:02.16,+07:13:43.8

lt_line

Print the atomic data for an input ion, transition or for an entire linelist.:

lt_line -h
lt_line HI
lt_line HI -z 3.0
lt_line HI1215
lt_line 1215
lt_line --all

Here is the usage:

beast> lt_line -h
usage: lt_line [-h] [-a] [--llist LLIST] [-t TOLER] [-z REDSHIFT] [inp]

Print spectral line data of a line or lines.

positional arguments:
  inp                   Ion, transition name, or Rest wavelength (e.g. HI,
                        HI1215 or 1215)

optional arguments:
  -h, --help            show this help message and exit
  -a, --all             Print all lines
  --llist LLIST         Name of LineList: ISM, HI, H2, CO, etc.
  -t TOLER, --toler TOLER
                        Matching tolerance (in Ang) on input wavelength
  -z REDSHIFT, --redshift REDSHIFT
                        Matching tolerance (in Ang) on input wavelength

lt_solabnd

Print the solar abundances by number relative to Hydrogen on the traditional log scale of 12, e.g. e(Fe) = 7.55:

lt_solabnd Fe
lt_solabnd -a
lt_solabnd -a --sortZ

Here is the usage:

beast> lt_solabnd -h
usage: lt_solabnd [-h] [-a] [--sortZ] [inp]

Print Solar abundance data for an element or all elements.

positional arguments:
  inp         Elm (e.g. H, Fe)

optional arguments:
  -h, --help  show this help message and exit
  -a, --all   Print all values
  --sortZ     Sort on Atomic Number

lt_continuumfit

Launch the GUI to continuum fit a spectrum. If a redshift is supplied by zsys, then the script assumes this is a QSO.:

lt_continuumfit input_file output_filename --redshift 0.867

Here is the current usage message:

usage: lt_continuumfit [-h] [--redshift REDSHIFT] [--wchunk WCHUNK]
                       file outfil

GUI to fit a continuum to a spectrum

positional arguments:
  file                 Input spectral file (FITS, ASCII, etc.)
  outfil               Output, normalized spectrum filename; FITS [can be the
                       same]

optional arguments:
  -h, --help           show this help message and exit
  --redshift REDSHIFT  Redshift of the Source
  --wchunk WCHUNK      Width of a 'chunk' (Ang)