Last update 20200323 Theo Pribulla

Reduction steps for echelle spectroscopy with IRAF:

1. Prepare master darks

   red12

2. Performe dark, flat correction, bad-pixel cleaning

   red34

   [Lists of dark and flat calibrated spectra for the same targets are produced 
    in the work directory, edit/remove the list if necessary]

3. Prepare blaze-function-correcting spectrum from the lamp flats:

   blaze

   [blaze correction is done by extracting and combining the lamp flat
    spectra which do not contain spectral lines. The blaze correction
    is applied to resulting fluxes *FL*]

4. Combine mutiple CCD frames 

   spoj

   [N.B.: resulting FITS file will have exposure-weighted average
    HJD, siderial time, airmass, and total exposure time updated.]

   [N.B.: if you need individual spectra separately 
   reduced, remove appropriate list file(s) in your working directory]

5. Extract aperture spectra, wavelength calibrate, normalize

   redsp

   if you want to avoid questions about the continuuum normalization,
   you should run:

   redsp y

   [N.B. parameter file cleredsp.par must contain:

   quiet,s,h,"y",,,
   mode,s,h,"ql",,,

5. Output files go to ~/IRAF/DATASP/G1_60cm_Eshl (eShel echelle in G1) or
                      ~/IRAF/DATASP/SP_1.3m_MUSI (MUSICOS echelle at SP)

   The following spectra are produced

   *FL* : 1-dimensional spectrum which contains fluxes compared to calibration lamp
   *n1D*: 1-dimensional rectified spectrum 
   [only if the normalization was performed manually]
   *2D* : 2-dimensional spectrum containing different products (see FITS header) 
   *SN* : 2-dimension spectrum giving the signal-to-noise ratio


############### Older reduction process using spectrum of Vega for #########
############### spectrophotometry ########################################## 

1. Prepare master darks

   red12

2. Performe dark, flat correction, bad-pixel cleaning

   red34

   [Lists of dark and flat calibrated spectra for the same targets are produced 
    in the work directory, edit/remove the list if necessary]

3. Combine mutiple CCD frames 

   spoj

   [N.B.: resulting FITS file will have exposure-weighted average
    HJD, siderial time, airmass, and total exposure time updated.]

   [N.B.: if you need individual spectra separately 
   reduced, remove appropriate list file(s) in your working directory]

4. Extract aperture spectra, wavelength calibrate, normalize

   redspvega

   [N.B. redspvega.cl must be defined in login.cl as
   task $redspvega = /iraf/iraf/local/scripts/redspvega.cl]

   [blaze correction is done using observed and tabulated Vega spectra
    using stand, sensf, and calib tasks]

############### Definition of orders and background ########################
############### Done only once for a given binning of the frames ###########

1) Set default aperture parameters

   apdefault

   lower    -12.
   upper     12.

   and then

   b_funct     chebyshev
   b_sampl   -30:-20,20:30
   b_order     2


2) Define apertures (picture "Apertures_marked.png") on spectrum
   of a bright target

    epar apedit

   [If "m" does not find the aperture, use "n" which uses cursor position]


3) Trace the apertures of the same spectrum. First use

   epar aptrace

   and set

   function chebyshev
   order    5
   (order 2 is linear function)

   then

   run aptrace

4) Extract aperture spectrum from a ThAr spectrum using bright star spectrum as
   a template, using epar apsum define reference as the bright spectrum or "last".

   apsum ThAr-001.fit

5) ThAr line identification

   run epar ecidentify

   and check if 

   coordlist = "linelists$thar.dat"
   xorder = 4
   yorder = 4

   [use plots with line identifications, mark at least 5 lines/order before fitting
    a model to lines and adding new lines]