GMOS Spectral Reduction: Traditional Mode

For Nod and Shuffle Reductions, check here.

This is the method that worked best for our data; this may not be true for other data. When in doubt, e-mail the Gemini Help Desk.

This page has been prepared by Kelle Cruz and Anne Sweet. If you find this information useful for reducing data that later appears in publication, please consider acknowledging this page.

Also see the reduction method of Eduard Westra.

• Get all data prepared and organized

  1. Download data, sort it by type, gprepare it and move to working directory. see gemini_getfiles.txt.
  2. GPREPARE the data:

      
        - grepare @objects.lis rawpath=/datapath/rawdata outpref=/filepath/workingdirectory/gt fl_addm+ fl_vardq-
     

• Make biases, flats, and arcs

  3. Make bias. See gbias.txt - ONLY FOR OLD DATA WHERE BIAS WAS NOT PROVIDED (ex: S20070913S0213_bias.fits)

         - gbias @bias.lis bias.fits 
      
        => bias.fits
        cleanup: mv gb* proc_images/
     

  4. Make FLATS - gemini_flats.txt.

     
        - gsflat @flat_a.lis flat_a fl_answe+ fl_over+ fl_trim+ fl_bias+ fl_fixpix+ bias=gS20070913S0213_bias.fits 
          fl_inte+ fl_dete+  
        -  gsflat @flat_b.lis flat_b fl_answe+ fl_over+ fl_trim+ fl_bias+ fl_fixpix+ bias=gS20070913S0213_bias.fits 
          fl_inte+ fl_dete+
     
        -When prompted: fitline = 200-300 for standard reductions
         order for each chip:  1,1,6-9 for GS 
     		          1,3,6-9 for GN
     
     
     
        => flat_a, flat_b
        cleanup: mv gfgs*,gf*,flat*.lis into procimages/
     
     

  5. Make ARCS - gemini_arc.txt.

     
       - gsreduce @arcs.lis fl_trim+ fl_bias+ fl_gmosaic+ fl_gsappwave+ fl_cut+ bias=gS20070913S0213_bias.fits
       - gswavelength gsgaS20070913S0152.fits 
         gswavelength gsgaS20070913S0153.fits
     
       => 2 gsga (with two central wavelengths)
       cleanup: mv ga* proc_images/
     	

• Reduce targets, flux standards, and telluric

  6. Make lists of observations according to central wavelength

        - hselect > objects_a.lis
          images  = *.fits[0]
          select = $I
          expr = obstype ?= 'OBJECT' && grwlen == 810 
     
        - hselect > objects_b.lis
          images  = *.fits[0]
          select = $I
          expr    = obstype ?= 'OBJECT' && grwlen == 815
     
     

  7. GSREDUCE - gsreduce.txt.

         - reduce in steps:
             gsreduce @objects.lis fl_over+ fl_trim+ fl_bias+ ovs_fli+ bias=gS20070913S0213_bias.fits
             gsreduce @objects_a.lis fl_flat+ flat=flat_a
             gsreduce @objects_b.lis fl_flat+ flat=flat_b
             gsreduce @objects.lis fl_gmos+ fl_fixpix+ fl_gssap+ fl_cut+
       
             Don't forget to update prefixes in .lis each time!
     
        => gsgsgsgt*
        cleanup: mv gt*, gsgt*, gsgsgt*, flat_*.fits, bias to proc_images/
     
      

  8. FOR GEMINI SOUTH - FIX PIXELS (Optional, not well tested)

     EDIT HEADER so CCDPROC will work.
     hedit gsgt*[2],gsgt*[3] ccdsec delete+
     
     FIX BAD PIXELS on each extension
     ccdproc gsgtS20050810S0062[2] out=f2gsgtS20050810S0062 fixpix+ fixfile=gsfixfile2
     task $fix2=fix2.cl
     
     ccdproc gsgtS20050810S0062[3] out=f3gsgtS20050810S0062 fixpix+ fixfile=gsfixfile3
     task $fix3=fix3.cl
     
     PASTE fixed extensions back into MEF
     imcopy f2gsgtS20050810S0062 gsgtS20050810S0062[2,overwrite] 
     task $copy2=copy2.cl
     
     imcopy f3gsgtS20050810S0062 gsgtS20050810S0062[3,overwrite] 
     task $copy3=copy3.cl
     
     FIX HEADERS 
     hedit gsgt*[2],gsgt*[3] extname sci add+
     hedit gsgt*[2] extver 2 add+
     hedit gsgt*[3] extver 3 add+
     hedit gsgt*[2],gsgt*[3] datasec [1:1024,1:2304] add+
     
     

  9. GSTRANSFORM - Wavelength Calibrate

        - gstransform @objects_a.lis wavtran=gsgaN20040817S0016
        - gstransform @objects_b.lis wavtran=gsgaN20040817S0017
     
        - note: to use the same arc in other folders to wavelength calibrate, create a 
          database/ folder in the new folder and copy over the id* and fc* 
          files.
     
        => tgsgsgsgt
        cleanup: mv gsgsgsgt* proc_images/
     
     

  10. GSSKYSUBTRACT

         - gsskysub @objects.lis long_sample = "100:200,300:400" fl_inter+
      
         - enter a column to see interactive fit.
         - use s to define new sample (just like in background fitting in apall)
          
         => stgsgsgsgt
         cleanup: mv tgsgsgsgt* proc_images/
      
      

  11. GEMCOMBINE (OPTIONAL)

         Note: Can combine 2-D spectra here if trace is difficult to follow when extracting.
      
         - gemcombine @objects_a.lis object_a_sum offsets=offset_file_a
         - gemcombine @objects_b.lis object_b_sum offsets=offset_file_b
      
         => object_a_sum, object_b_sum
         cleanup: mv stgsgsgsgt* proc_images/
      

  12. GSEXTRACT gemini_gsextract.txt.

         - gsextract stgsgtN20040911S0116, fl_inte+
      
         => estgsgsgsgt
         cleanup: mv stgsgsgsgt* proc_images/
      

  13. GSSTANDARD flux standard to determine flux calibration

          - gsstandard estgsgsgsgtS20070914S0117.fits sfunction=sens starname=eg21 graphs=srei
      
          => sens.fits
          cleanup: mv estgsgsgsgtS20070914S0117.fits procimages/
      
      

  14. GSCALIBRATE to flux calibrate. gscalibrate.txt

         - gscalibrate estgsgsgst* sens.fits
         
         => cestgsgsgsgt
         cleanup: mv estgsgsgsgt* proc_images/
      	

  15. Delete header information before extracting 1-D spectra

         - The wavelength calibration header keywords are in the SCI extension, but the pre-existing
           2-D ones remain in the the PHU extension. For splot to find the correct information ALL 
           wavelength info must be removed from the PHU.   
      
           hedit filename[0] CRPIX*,CRVAL*,CD* delete+ verify-
         	

  16. Separate 1D spectra from MEF file

         - imcopy @eobjects.lis @oeobjects.lis
              objects.lis:      cestgsgsgsgtobject.fits[2,inherit]						
              oobjects.lis:     ocestgsgsgsgtobject.fits
             
              Note: using the [2,inherit] preserves the SCI header info, otherwise it will be lost.
      
          => ocestgsgsgsgt*
          cleanup: mv c* proc_images/
      	

  17. SCOMBINE scombine.txt.

          - scombine @object.lis object.fits
      
         => object.fits
          cleanup: mv o* proc_images/
          

  18. Telluric Correct telluric.txt.

          - cp telluric.fits telluric_fixed.fits
          - splot and remove the telluric features and save:
          - sarith telluric.fits / telluric_fixed.fits telluric_mult.fits
          - splot telluric_mult.fits 
             => make sure the features are predominantly above one (edit if necessary).
          - sarith object.fits * telluric_mult.fits object_tellcor.fits
      
          => object_tellcor.fits
          cleanup: everything else
      
          
      
          

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