xspec Documentation (v1.1.2)

This ipython Notebook is intended to provide documentation for the xastropy GUI named XSpecGUI.

Enjoy and feel free to suggest edits/additions, etc.

Python Dependencies

Here are the list of Python dependencies that I know of:

numpy
astropy (latest release; best to clone from github)
specutils (latest release; best to clone from github)
PyQt4
xastropy (duh; unfortunately this might have some extra dependencies..)
- Download from github. I'd suggest you fork me
- https://github.com/profxj/xastropy

Spectral File

The module readwrite.py reads in many formats into a Spectrum1D Class. This includes:

LowRedux output
HIRedux 1D output
HST formats
MagE, ESI, etc.

gzipped files are perfectly fine

Generically, the following data formats (all FITS files) are supported:

Flux in f.fits or F.fits file
- Wavelengths are parsed from the header
- A neighboring e.fits (or E.fits) file is searched for and input as Error if found
Flux, Error, Wavelength in multi-extension FITS file
Flux, Error, Wavelength in a Binary Table (extension=1)
- Supported Flux tags: ['SPEC', 'FLUX','FLAM','FX', 'FLUXSTIS', 'FLUX_OPT', 'fl']
- Supported Error tags: ['ERROR','ERR','SIGMA_FLUX','FLAM_SIG', 'SIGMA_UP', 'ERRSTIS', 'FLUXERR', 'er']
- Supported Ivar tags: ['IVAR', 'IVAR_OPT']
- Supported Wavelength tags: ['WAVE','WAVELENGTH','LAMBDA','LOGLAM', 'WAVESTIS', 'WAVE_OPT', 'wa']

The spectrum file used below is part of the xastropy documentation.



In [1]:

    
import imp
xa_path = imp.find_module('xastropy')[1]
spec_fil = xa_path+'/../docs/data/UM669_nF.fits.gz'

Launching the GUI

I recommend the command line approach, but you can launch from ipython too.

From within ipython or equivalent

from xastropy.xguis import spec_guis as xxsg

reload(xxsg)
xxsg.run_xspec(spec_fil)

From the command line (recommended)

I recommend you generate an alias like this:

alias xspec 'python ~/xastropy/xastropy/xguis/spec_guis.py 1'

Then it is as simple as:

> xspec filename

Here are the current command-line options:

> xspec -h
usage: spec_guis.py [-h] [-zsys ZSYS] [--un_norm] flag file

Parse for XSpec

positional arguments:
  flag        GUI flag (ignored)
  file        Spectral file

optional arguments:
  -h, --help  show this help message and exit
  -zsys ZSYS  System Redshift
  --un_norm   Spectrum is NOT normalized

Navigating - These key strokes help you explore the documenation (be sure to click in the spectrum first!)

Setting the window edges (mouse+keystroke)

l -- Set left edge of window
r -- Set right edge of window
t -- Set top edge of window
b -- Set bottom edge of window
Z -- Set bottom edge to 0.
W -- View full spectrum
s,s -- Set a zoom-in window at 2 mouse positions

Zoom in/out Wavelength

i -- Zoom in on cursor
I -- Zoom in extra fast
o -- Zoom out
O -- Zoom out extra fast

Zoom out Flux

Y -- Zoom out

Pan

[ -- Pan left
{ -- Pan left extra
] -- Pan right
} -- Pan right extra

Overlaying Line Lists

You can overlay a series of vertical lines at standard spectral lines at any given redshift.

Setting the Line List

You must choose a line-list by clicking one.

Setting the redshift

Type one in
RMB on a spectral feature (Ctrl-click on Emulated 3-button)
- Choose the rest wavelength

Marking Doublets

C -- CIV
M -- MgII
X -- OVI
4 -- SiIV
8 -- NeVIII
B -- Lyb/Lya

Velocity plot

Once a line list and redshift are set, type 'v' to launch a Velocity Plot GUI.

Simple Analysis

Equivalent Width

You can measure the rest EW of a spectral feature as follows:

Click "E" at the continuum at one edge of the feature
And then another "E" at the other edge (also at the continuum)
A simple boxcar integration is performed and reported

Apparent Column Density

You can measure the apparent column via AODM as follows:

Click "N" at the continuum at one edge of the feature
And then another "EN" at the other edge (also at the continuum)
A simple AODM integration is performed and reported

Ly$\alpha$ Lines

"D" - Plot a DLA with $N_{\rm HI} = 10^{20.3} \rm cm^{-2}$
"R" - Plot a SLLS with $N_{\rm HI} = 10^{19} \rm cm^{-2}$



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