xspec Documentation (v1.0)

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 a list of Python dependencies that I am aware of:

• numpy
• astropy (latest release)
• specutils (latest release)
• 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:

1. 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
2. Flux, Error, Wavelength in multi-extension FITS file
3. 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.

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

• 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

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

Simple Analysis

Equivalent Width

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

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

Apparent Column Density

You can measure the apparent column via AODM as follows:

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