PACKAGE = ccdred
   TASK = ccdproc

images  =              ccd*.imh  List of CCD images to correct
(ccdtype=                     ) CCD image type to correct
(max_cac=                    0) Maximum image caching memory (in Mbytes)
(noproc =                   no) List processing steps only?

(fixpix =                   no) Fix bad CCD lines and columns?
(oversca=                  yes) Apply overscan strip correction?
(trim   =                  yes) Trim the image?
(zerocor=                   no) Apply zero level correction?
(darkcor=                   no) Apply dark count correction?
(flatcor=                   no) Apply flat field correction?
(illumco=                   no) Apply illumination correction?
(fringec=                   no) Apply fringe correction?
(readcor=                   no) Convert zero level image to readout correction?
(scancor=                   no) Convert flat field image to scan correction?

(readaxi=                 line) Read out axis (column|line)
(fixfile=                     ) File describing the bad lines and columns
(biassec=        [2033:2047,*]) Overscan strip image section
(trimsec=         [120:1940,*]) Trim data section
(zero   =                     ) Zero level calibration image
(dark   =                     ) Dark count calibration image
(flat   =                     ) Flat field images
(illum  =                     ) Illumination correction images
(fringe =                     ) Fringe correction images
(minrepl=                   1.) Minimum flat field value
(scantyp=            shortscan) Scan type (shortscan|longscan)
(nscan  =                    1) Number of short scan lines
(interac=                   no) Fit overscan interactively?
(functio=            chebyshev) Fitting function
(order  =                    1) Number of polynomial terms or spline pieces
(sample =                    *) Sample points to fit
(naverag=                 -100) Number of sample points to combine
(niterat=                    1) Number of rejection iterations
(low_rej=                   3.) Low sigma rejection factor
(high_re=                   3.) High sigma rejection factor
(grow   =                   0.) Rejection growing radius
(mode   =                   ql)

Imtransp ccd*.imh[*,-*] transp*.imh 

PACKAGE = longslit
   TASK = transform

        input = "@inp"          Input images
       output = "@out"          Output images
     fitnames = "cosmicdist"    Names of coordinate fits in the database
    (database = "database")     Identify database
  (interptype = "spline3")      Interpolation type
          (x1 = INDEF)          Output starting x coordinate
          (x2 = INDEF)          Output ending x coordinate
          (dx = INDEF)          Output X pixel interval
          (nx = INDEF)          Number of output x pixels
        (xlog = no)             Logarithmic x coordinate?
          (y1 = INDEF)          Output starting y coordinate
          (y2 = INDEF)          Output ending y coordinate
          (dy = INDEF)          Output Y pixel interval
          (ny = INDEF)          Number of output y pixels
        (ylog = no)             Logarithmic y coordinate?
        (flux = no)             Conserve flux per pixel?
    (logfiles = "STDOUT,logfile") List of log files
        (mode = "ql")           

Imtransp transf*.imh[*,-*] rot*.imh 

PACKAGE = immatch
   TASK = geotran

        input = "@out4"         Input data
       output = "@out3"         Output data
     database = "apinmap2.map"  Name of geomap database file
   transforms = "@transf.in"    Names of coordinate transforms in database file
    (geometry = "geometric")    Transformation type (linear,geometric)
         (xin = INDEF)          X origin of input image in pixels
         (yin = INDEF)          Y origin of input image in pixels
      (xshift = INDEF)          X origin shift in pixels
      (yshift = INDEF)          Y origin shift in pixels
        (xout = INDEF)          X origin of output image in reference units
        (yout = INDEF)          Y origin of output image in reference units
        (xmag = INDEF)          X scale of input image in pixels per reference 
        (ymag = INDEF)          Y scale of input image in pixels per reference 
   (xrotation = INDEF)          X rotation angle in degrees
   (yrotation = INDEF)          Y rotation angle in degrees
        (xmin = INDEF)          Minimum reference x value of output image
        (xmax = INDEF)          Maximum reference x value of output image
        (ymin = INDEF)          Minimum reference y value of output image
        (ymax = INDEF)          Maximum reference y value of output image
      (xscale = 1.)             X scale of output image in reference units per 
      (yscale = 1.)             Y scale of output image in reference units per 
       (ncols = 1789)           Number of columns in the output image
      (nlines = 2048)           Number of lines in the output image
     (xsample = 1.)             Coordinate surface sampling interval in x
     (ysample = 1.)             Coordinate surface sampling interval in y
 (interpolant = "linear")       Interpolant (nearest,linear,poly3,poly5,spline3
    (boundary = "nearest")      Boundary extension (nearest,constant,reflect,wr
    (constant = 0.)             Constant for constant boundary extension 
(fluxconserve = yes)            Preserve image flux ?
     (nxblock = 512)            X dimension of working block size in pixels
     (nyblock = 512)            Y dimension of working block size in pixels
     (verbose = yes)            Print messages about the progress of the task ?
        (mode = "ql")           

Imtransp geo*.imh[*,-*] georot*.imh 

       inlist = "rot117.1"      Image(s) for cosmic ray cleaning
      outlist = "foo.1"         Output image(s)
      (zboxsz = 3)              Box size for zapping
      (nsigma = 4.)             Number of sky sigma for zapping threshold
   (nnegsigma = 5.)             Number of sky sigma for negative zapping
      (nrings = 1)              Number of pixels to flag as buffer around
   (nobjsigma = 0.)             Number of sky sigma for object identifica
 (skyfiltsize = 1)                Median filter size for local sky evalua
(skysubsample = 1)                Block averaging factor before median fi
    (ngrowobj = 0)                Number of pixels to flag as buffer arou
     (statsec = "")             Image section to use for computing sky si
  (deletemask = no)             Delete CR mask after execution?
     (cleanpl = yes)            Delete other working .pl masks after exec
    (cleanimh = yes)            Delete working .imh images after executio
     (verbose = yes)            Verbose output?
       (unzap = no)             Unzap using objects from OBJmask files?
 (checklimits = yes)            Check min and max pix values before filte
        (zmin = 0.)             Minimum data value for fmedian
        (zmax = 32767.)         Minimum data value for fmedian
   (inimglist = "")             
  (outimglist = "")             
    (statlist = "")             
        (mode = "ql")           

Set background parameters:

        input = "rot118.1"      Input images to be background subtracted
       output = "foo1"          Output background subtracted images
        (axis = 1)              Axis along which background is fit and subtract
 (interactive = yes)            Set fitting parameters interactively?
      (sample = "*")            Sample of points to use in fit
    (naverage = -5)             Number of points in sample averaging
    (function = "chebyshev")    Fitting function
       (order = 1)              Order of fitting function
  (low_reject = 1.5)            Low rejection in sigma of fit
 (high_reject = 1.5)            High rejection in sigma of fit
    (niterate = 1)              Number of rejection iterations
        (grow = 1.)             Rejection growing radius
    (graphics = "stdgraph")     Graphics output device
      (cursor = "")             Graphics cursor input
        (mode = "ql")       

PACKAGE = ccdred
   TASK = slitredux
    
     imprefix = "georot"        Root ID for initial input images
      outroot = "proc"          Root for output images and files
      (images = "117")          Numbers of science images
       (flats = "134,135,136")  Numbers of flat images
        (arcs = "119")          Numbers of arc images
    (showmode = no)             Show processing steps only?
    (secsfile = "475.1a.1.secs") File with image sections and IDs, def=outroot.
     (offsets = "proc.offsets") File with image xy offsets, def=outroot.offsets
   (rotprefix = "rot")          Root ID for rotated images
    (szprefix = "sz")           Root ID for szapped images
    (bgprefix = "bg")           Root ID for sky subtracted images
        (flat = "flat")         Name of flat
       (rflat = "rflat")        Name of response-corrected flat
  (do_ccdproc = no)             Do ccdproc stage?
     (numamps = 1)              Number of amps used in readout
     (biassec = "[*,2032:2047]") Bias section for one amp ccdproc
     (trimsec = "[*,130:1918]") Trim section for one amp ccdproc
     (gainrat = 1.0695)         ratio of left gain to right, for two amp ccdpro
  (do_flatsum = yes)            Do flatsum stage?
 (do_response = yes)            Do response stage?
      (sample = "10:2038")      Sampling x range for response fitting
        (func = "spline3")      Function for fitting response
       (order = 30)             Order for response function fitting
    (dispaxis = 1)              Dispersion axis
(do_flatfield = yes)            Do flatfield stage?
    (do_cutup = yes)            Do cutup stage?
   (do_rotate = yes)            Do rotate stage?
   (delete_in = yes)            Delete old images after rotation?
     (do_szap = yes             Do szap stage?
     (szinter = no)             Interactive szapping?
     (szorder = 4)              Order for background fitting?
   (szlow_rej = 4.)             N sigma for low rejection threshold
  (szhigh_rej = 4.)             N sigma for high rejection threshold
     (szniter = 3)              Number of iterations for bad pixel rejection
      (szgrow = 1)              Grow radius for bad pixel rejection
      (sznavg = -5)             Naverage for background fitting
     (szboxsz = 5)              Zapping box size
    (sznsigma = 5.)             Number of sigma for positive zapping threshold
 (sznnegsigma = 5.)             Number of sigma for negative zapping threshold
    (sznrings = 1)              Growth radius around cosmic rays
     (do_bkgd = yes)            Do bkgd stage?
     (bginter = no)             Interactive background fitting?
  (bgfunction = "chebyshev")    Fitting function
      (bgaxis = 1)              Axis along which to fit & subtract sky
    (fitorder = 2)              Order for background fitting
   (bglow_rej = 1.)             N sigma for low rejection threshold
  (bghigh_rej = 1.4)            N sigma for high rejection threshold
     (bgniter = 2)              Number of iterations for bad pixel rejection
      (bggrow = 1)              Grow radius for bad pixel rejection
      (bgnavg = -3)             Naverage for background fitting
      (do_bpm = yes)            Do bpm stage?
      (do_sum = yes)            Sum science images?
   (do_arcsum = yes)            Sum arc image(s) correspondingly?
     (arcname = "")             Name for summed arc image, def=outrootarc
     (expname = "elaptime")     Header keyword for exposure times
  (do_smosaic = no)             Do smosaic stage?
      (tvfile = "")             Name of tvmark file to make, def=outroot.tvmark
     (reverse = no)             Reverse direction of mosaic?
      (ninter = 0)              Interval to skip (in pixels) between spectra
    (blankval = -50.)           Value for filling blank pixels
       (ifile = "")             
      (ifile2 = "")             
        (mode = "ql")

PACKAGE = apextract
   TASK = apall
 
input   =            @proclist  List of input images
(output =            @speclist) List of output spectra
(apertur=                     ) Apertures
(format =            multispec) Extracted spectra format
(referen=                     ) List of aperture reference images
(profile=                     ) List of aperture profile images

(interac=                  yes) Run task interactively?
(find   =                  yes) Find apertures?
(recente=                  yes) Recenter apertures?
(resize =                  yes) Resize apertures?
(edit   =                  yes) Edit apertures?
(trace  =                  yes) Trace apertures?
(fittrac=                  yes) Fit the traced points interactively?
(extract=                  yes) Extract spectra?
(extras =                  yes) Extract sky, sigma, etc.?
(review =                   no) Review extractions?

(line   =                INDEF) Dispersion line
(nsum   =                   10) Number of dispersion lines to sum or median

                                # DEFAULT APERTURE PARAMETERS

(lower  =                  -5.) Lower aperture limit relative to center
(upper  =                   5.) Upper aperture limit relative to center
(apidtab=                     ) Aperture ID table (optional)

                                # DEFAULT BACKGROUND PARAMETERS

(b_funct=            chebyshev) Background function
(b_order=                    1) Background function order
(b_sampl=          -10:-6,6:10) Background sample regions
(b_naver=                   -3) Background average or median
(b_niter=                    0) Background rejection iterations
(b_low_r=                   3.) Background lower rejection sigma
(b_high_=                   3.) Background upper rejection sigma
(b_grow =                   0.) Background rejection growing radius

                                # APERTURE CENTERING PARAMETERS

(width  =                   5.) Profile centering width
(radius =                  10.) Profile centering radius
(thresho=                   0.) Detection threshold for profile centering

                                # AUTOMATIC FINDING AND ORDERING PARAMETERS

nfind   =                    1  Number of apertures to be found automatically
(minsep =                   5.) Minimum separation between spectra
(maxsep =                1000.) Maximum separation between spectra
(order  =           increasing) Order of apertures

                                # RECENTERING PARAMETERS

(aprecen=                     ) Apertures for recentering calculation
(npeaks =                INDEF) Select brightest peaks

(shift  =                  yes) Use average shift instead of recentering?

                                # RESIZING PARAMETERS

(llimit =                INDEF) Lower aperture limit relative to center
(ulimit =                INDEF) Upper aperture limit relative to center
(ylevel =                  0.1) Fraction of peak or intensity for automatic widt
(peak   =                  yes) Is ylevel a fraction of the peak?
(bkg    =                  yes) Subtract background in automatic width?
(r_grow =                   0.) Grow limits by this factor
(avglimi=                   no) Average limits over all apertures?

                                # TRACING PARAMETERS

(t_nsum =                   10) Number of dispersion lines to sum
(t_step =                   10) Tracing step
(t_nlost=                    3) Number of consecutive times profile is lost befo
(t_funct=             legendre) Trace fitting function
(t_order=                    5) Trace fitting function order
(t_sampl=                    *) Trace sample regions
(t_naver=                    1) Trace average or median
(t_niter=                    2) Trace rejection iterations
(t_low_r=                   2.) Trace lower rejection sigma
(t_high_=                   2.) Trace upper rejection sigma
(t_grow =                   0.) Trace rejection growing radius

                                # EXTRACTION PARAMETERS

(backgro=                  fit) Background to subtract
(skybox =                    1) Box car smoothing length for sky
(weights=                 none) Extraction weights (none|variance)
(pfit   =                fit1d) Profile fitting type (fit1d|fit2d)
(clean  =                   no) Detect and replace bad pixels?
(saturat=                INDEF) Saturation level
(readnoi=                  6.1) Read out noise sigma (photons)
(gain   =                 1.53) Photon gain (photons/data number)
(lsigma =                   4.) Lower rejection threshold
(usigma =                   4.) Upper rejection threshold
(nsubaps=                    1) Number of subapertures per aperture
(mode   =                   ql)

PACKAGE = apextract
   TASK = apall
    
input   =         @procarclist  List of input images
(output =         @specarclist) List of output spectra
(apertur=                     ) Apertures
(format =            multispec) Extracted spectra format
(referen=            @proclist) List of aperture reference images
(profile=                     ) List of aperture profile images

(interac=                   no) Run task interactively?
(find   =                   no) Find apertures?
(recente=                   no) Recenter apertures?
(resize =                   no) Resize apertures?
(edit   =                   no) Edit apertures?
(trace  =                   no) Trace apertures?
(fittrac=                   no) Fit the traced points interactively?
(extract=                  yes) Extract spectra?
(extras =                   no) Extract sky, sigma, etc.?
(review =                   no) Review extractions?

(line   =                INDEF) Dispersion line
...
(backgro=                 none) Background to subtract

PACKAGE = onedspec
   TASK = identify

images  =           specarc.29  Images containing features to be identified
(section=          middle line) Section to apply to two dimensional images
(databas=             database) Database in which to record feature data
(coordli= scripts$cosmic.300lmm.arcHgAr.table) User coordinate list
(units  =                     ) Coordinate units
(nsum   =                   10) Number of lines/columns/bands to sum in 2D image
(match  =                  10.) Coordinate list matching limit
(maxfeat=                   50) Maximum number of features for automatic identif
(zwidth =                 100.) Zoom graph width in user units
(ftype  =             emission) Feature type
(fwidth =                   4.) Feature width in pixels
(cradius=                   5.) Centering radius in pixels
(thresho=                  10.) Feature threshold for centering
(minsep =                   2.) Minimum pixel separation
(functio=              spline3) Coordinate function
(order  =                    1) Order of coordinate function
(sample =                    *) Coordinate sample regions
(niterat=                    1) Rejection iterations
(low_rej=                   3.) Lower rejection sigma
(high_re=                   3.) Upper rejection sigma
(grow   =                   0.) Rejection growing radius
(autowri=                   no) Automatically write to database
(graphic=             stdgraph) Graphics output device
(cursor =                     ) Graphics cursor input
crval   =                       Approximate coordinate (at reference pixel)
cdelt   =                       Approximate dispersion
(aidpars=                     ) Automatic identification algorithm parameters
(mode   =                   ql)