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Last modified: Wed Apr 26 19:41:01 2000.


List of Routines


Routine Descriptions

ARCFIT_GUESS

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 NAME:
   arcfit_guess

 PURPOSE:
   Determine initial wavelength solution by comparing spectrum to arc
spectrum

 CALLING SEQUENCE:
   wset = arcfit_guess( spec, loglam, intensity, color=color, $
    [ func=func, bestcorr=bestcorr ] )

 INPUTS:
   spec       - 1-D spectrum
   loglam     - Log-lambda of arc lines
   intensity  - Intensity of arc lines

 REQUIRED KEYWORDS:
   color      - 'red' or 'blue'

 OPTIONAL KEYWORDS:
   func       - Name of fitting function; default to 'legendre'

 OUTPUTS:
   wset       - traceset (pix - lambda)

 OPTIONAL OUTPUTS:
   bestcorr   - Correlation coefficient with simulated arc spectrum

 COMMENTS:

 EXAMPLES:

 BUGS:

 INTERNAL SUPPORT PROCEDURES:
   tset_struc()
   arcfit_iter()

 PROCEDURES CALLED:
   traceset2xy()
   xy2traceset

 REVISION HISTORY:
   18-Nov-1999  Written by D. Schlegel, Princeton.
                Excised code from FITARCIMAGE.

(See pro/spec2d//arcfit_guess.pro)


COMBINE2DOUT

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 NAME:
   combine2dout

 PURPOSE:
   Combine several reduced frames of the same objects

 CALLING SEQUENCE:
   combine2dout, filenames, outputroot, spectrographid, $
    binsz, zeropoint, nord=nord, wavemin=wavemin, $
    bkptbin=bkptbin, everyn=everyn, display=display, window=window, $
    individual=individual

 INPUTS:
   filenames      - Name(s) of files written by SPREDUCE
   outputroot     - Root name for all output files
   spectrographid - Spectrograph ID (1 or 2) for use in computing fiber
                    number for output file name; fibers from spectro-1
                    are numbered from 1, those from spectro-2 from 321.

 REQUIRED KEYWORDS:

 OPTIONAL KEYWORDS:

   display        - Show QA plot for each combined spectrum
   individual     - Append individual spectra in HDU's after combined spectra

 OUTPUTS:

 OPTIONAL OUTPUTS:

 COMMENTS:

       This routine also outputs original 2048 spectra with mask pixels
       replaced with their b-spline values.  Helpful for FFT



 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:
   djs_oplot
   djs_plot
   djs_maskinterp()
   mrdfits()
   writefits

 INTERNAL SUPPORT PROCEDURES:
   makelabel()

 REVISION HISTORY:
   ??-Sep-1999  Written by S. Burles
   02-Jan-2000  Modified by D. Schlegel, Princeton

(See pro/spec2d//combine2dout.pro)


DIVIDEFLAT

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 NAME:
   divideflat

 PURPOSE:
   Divide an extracted image with a fiber-flat

 CALLING SEQUENCE:
   divideflat, flux, fluxivar, fflat, [ fibermask=fibermask, minval=minval ]

 INPUTS:
   flux       - Array of extracted flux from a flat-field image [Nrow,Ntrace]
   fluxivar   - Inverse variance map for FLUX.
   fflat      - Array of flat-field flat-field vectors [Nrow,Ntrace]

 OPTIONAL KEYWORDS:
   fibermask  - Fiber status bits, set nonzero for bad status [NFIBER]
   minval     - Minimum value to consider good for flat-field;
                default to 0.03.

 OUTPUTS:

 OPTIONAL OUTPUTS:

 COMMENTS:
   Wherever the fiber is denoted bad in FIBERMASK, or wherever FFLAT is
   <= MINVAL, we set FLUX=FLUXIVAR=0.

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:
   splog

 REVISION HISTORY:
   17-Nov-1999  Written by S. Burles, Chicago
   23-Nov-1999  Modified by D. Schlegel, Princeton

(See pro/spec2d//divideflat.pro)


EXTRACT_BOXCAR

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 NAME:
   extract_boxcar

 PURPOSE:
   Extract the total flux within a boxcar window at many positions.

 CALLING SEQUENCE:
   fextract = extract_boxcar( fimage, xcen, ycen, [radius=radius] )

 INPUTS:
   fimage     - Image
   xcen       - Initial guesses for X centers
   ycen       - Y positions corresponding to "xcen" (expected as
integers)

 OPTIONAL KEYWORDS:
   radius     - Radius of extraction; default to 3.0

 OUTPUTS:
   fextract   - Extracted flux at each position specified by (xcen, ycen)

 OPTIONAL OUTPUTS:

 COMMENTS:

 EXAMPLES:

 PROCEDURES CALLED:
   Dynamic link to extract_boxcar.c

 REVISION HISTORY:
   24-Mar-1999  Written by David Schlegel, Princeton.

(See pro/spec2d//extract_boxcar.pro)


EXTRACT_IMAGE

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 NAME:
   extract_image

 PURPOSE:
   Extract the fiber profile flux for an entire image

 CALLING SEQUENCE:
   extract_image(fimage, invvar, xcen, sigma, flux, [finv, yrow=yrow,
              ymodel=ymodel, fscat=fscat,proftype =
proftype,ansimage=ansimage,
              wfixed=wfixed, mask=mask, pixelmask=,  reject=, wsigma=, 
              nPoly=nPoly, maxIter=maxIter, highrej=highrej, lowrej=lowrej,
              fitans=fitans, whopping=whopping,relative=relative])

 INPUTS:
   fimage     - Image[nCol, nRow]
   invvar     - Inverse Variance[nCol, nRow]
   xcen       - Initial guesses for X centers[nRow, nFibers]
   sigma      - sigma of gaussian profile; default to 1.0 
                  (scalar or [nFibers] or [nRow, nFibers])

 OPTIONAL KEYWORDS:
   yrow       - long array specifying which rows to extract, default is all
   proftype   - currently, one can only use 1: Gaussian (scalar)
              - or                          2: Exp Cubic
              - or                          3: Double Gaussian
              - or              4: Exp Cubic with doublewide Gaussian
   ansimage   - return the coefficients of fit for each row [nCoeff,nRow]
   wfixed     - array of 1's and zero's which set which parameters are fixed.
                e.g. [1] just gaussian's with fixed width sigma
                     [1, 1] fit gaussian + sigma correction
                     [1, 0, 1] fit gaussian + center correction
                     [1, 1, 1] fit gaussian + sigma and center
corrections.   
   mask       - byte mask: 1 is good and 0 is bad [nCol,nRow] 
   pixelmask  - bits set due to extraction rejection [nRow,nFiber]
   reject     - two elements array setting partial and full rejection
thresholds 
   nPoly      - order of chebyshev scattered light background; default to 4
   maxIter    - maximum number of profile fitting iterations; default to 20
   highrej    - positive sigma deviation to be rejected (default 10.0)
   lowrej     - negative sigma deviation to be rejected (default 10.0)
   fitans     - ratio of profiles to do in single profile fitting
   relative   - Scale rejection thresholds by reduced chi-squared (default 0)
   whopping   - traces which have WHOPPINGingly high counts, and need extra
                background terms
   wsigma     - sigma width of whopping profile (exponential, default 25)

 OUTPUTS:
   flux       - Total extracted flux in each profile [nRowExtract, nFibers]

 OPTIONAL OUTPUTS:
   mask       - modified by setting the values of bad pixels to 0
   finv       - Estimated inverse variance each profile [nRowExtract,
nFibers]
   ymodel     - model best fit of row[nCol, nRow]
   fscat      - scattered light contribution in each fiber[nRow, nFibers]

 COMMENTS:

 EXAMPLES:

 PROCEDURES CALLED:
    extract_row.pro

 REVISION HISTORY:
    8-Aug-1999  Version 0.0 Scott Burles, Chicago 

(See pro/spec2d//extract_image.pro)


EXTRACT_OBJECT

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 NAME:
   extract_object

 PURPOSE:

   Performs all object extraction tasks
      0) Locate bright fibers, and test image background
      1) 3 step Optimal extraction
      2) Tweak to sky lines
      3) Sky subtraction
      4) Flux calibration
      5) Telluric correction

 CALLING SEQUENCE:
   extract_object, outname, objhdr, image, invvar, plugsort, wset, $
    xarc, lambda, xtrace, fflat, fibermask, color=, [plottitle=]

 INPUTS:
   outname    - Name of outputs FITS file
   objhdr     - Header cards from object image
   image      - Object image [nx,ny]
   invvar     - Inverse Variance of object image [nx,ny]
   plugsort   - Plugmap structure for [ntrace] spectra
   wset       - wavelength solution from arc line spectra
   xarc       - centroids measured in arc line spectra
   lambda     - air wavelengths corresponding to xarc
   xtrace     - spatial traces from flat field
   fflat      - 1d flat field vectors
   fibermask  - Fiber status bits, set nonzero for bad status [NFIBER]

 REQUIRED KEYWORDS:
   color      - camera color (red or blue)

 OPTIONAL KEYWORDS:
   plottitle  - Prefix for titles in QA plots.

 OUTPUTS:
   A fits file is output in outname, which contains
      float flux [nx,ntrace]
      float flux_invvar [nx,ntrace]
      plugsort struct [ntrace]
      vacuum wavelength coefficients 
      integer pixelmask [nx,ntrace]
      byte    fibermask [ntrace]

 OPTIONAL OUTPUTS:

 COMMENTS:

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:
   djs_median()
   djs_oplot
   djs_plot
   extract_boxcar()
   extract_image
   fibermask_bits()
   fitansimage()
   fitvacset()
   fluxcorr()
   locateskylines
   mwrfits
   pixelmask_bits()
   qaplot_scatlight
   qaplot_skyline
   qaplot_skysub
   qaplot_skydev
   skysubtract
   splog
   telluric_corr
   tweaktrace

 INTERNAL SUPPORT ROUTINES:
   find_whopping()

 REVISION HISTORY:
   24-Jan-2000  Written by S. Burles, Chicago

(See pro/spec2d//extract_object.pro)


EXTRACT_PROFILE

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 NAME:
   extract_profile

 PURPOSE:
   Extract the flux with profile weighting at centroid positions.

 CALLING SEQUENCE:
   fextract = extract_profile( fimage, invvar, xcen, ycen, 
                  [ferror=ferror, fscattered=fscattered, fwidth=fwidth, 
                   sigma=sigma, nPoly=nPoly, maxIter=maxIter,
                   refit=refit, highrej=highrej, lowrej=lowrej, boxap=boxap])

 INPUTS:
   fimage     - Image[nCol,nRow]
   invvar     - Inverse Variance[nCol,nRow]
   xcen       - Initial guesses for X centers[nFibers,nRow]
   ycen       - Y positions corresponding to "xcen[nFibers]" [nRow]

 OPTIONAL KEYWORDS:
   ferror     - error array (-1 if bad pixel)
   fscattered - scattered light contribution 
   fwidth     - final profile width used

   sigma      - sigma of gaussian profile; default to 1.0
   nPoly      - order of chebyshev scattered light background; default to 5
   maxIter    - maximum number of profile fitting iterations; default to 5
   refit      - order of chebyshev to fit to profile widths vs. row,
                       default is 0, which does no refitting
   highrej    - positive sigma deviation to be rejected (default 5.0)
   lowrej     - negative sigma deviation to be rejected (default 5.0)
   boxap      - boxcar aperture size in pixels 
                       default is 0, which does no boxcar extraction

 OUTPUTS:
   fextract   -  Extracted flux at each position specified by (xcen, ycen)
                  [nFibers,nRow]
               2: Scattered light estimate
               3: Final profile width 
               4: Boxcar extracted flux

 OPTIONAL OUTPUTS:

 COMMENTS:

 EXAMPLES:

 PROCEDURES CALLED:
   Dynamic link to extract_profile.c

 REVISION HISTORY:
   24-Mar-1999  David Schlegel, Princeton.
   24-Jun-1999  Stolen and modified by Scott Burles, Chicago.

(See pro/spec2d//extract_profile.pro)


EXTRACT_ROW[1]

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 NAME:
   extract_row

 PURPOSE:
   Fit the fiber profiles and background in a single row with least squares

 CALLING SEQUENCE:
   ans = extract_row( fimage, invvar, xcen, sigma, [ymodel=, fscat=, 
              proftype=, wfixed=, inputans=, iback=, bfixarr=, xvar=,
              mask=, relative=, diagonal=, fullcovar=, wfixarr=, npoly=,
              maxiter=, lowrej=, highrej=, niter=, squashprofile=,
              whopping=, wsigma=, pixelmask=, reject=, reducedChi= ])

 INPUTS:
   fimage     - Vector [nCol]
   invvar     - Inverse variance [nCol]
   xcen       - Initial guesses for X centers [nFiber]
   sigma      - Sigma of gaussian profile; (scalar or [nFiber])

 OPTIONAL KEYWORDS:
   proftype   - Select profile type:
                  1: Gaussian
                  2: (exponential)^3
                  3: (exponential)^2.5
                Default to 1.
   inputans   - Input fit, excluding background and whopping terms
                [ncoeff*nFiber]
                The array is sorted as follows:
                  [ncoeff] values for fiber #0
                   ...
                  [ncoeff] values for fiber #(nFiber-1)
   relative   - Set to use reduced chi-square to scale rejection threshold
   squashprofile - ???
   npoly      - Order of chebyshev scattered light background; default to 5
   maxiter    - Maximum number of profile fitting iterations; default to 10
   lowrej     - Negative sigma deviation to be rejected; default to 5
   highrej    - Positive sigma deviation to be rejected; default to 5
   whopping   - X locations to center additional "whopping"
terms to describe
                the exponentail tails of flux near bright fibers; default
                to -1, which means not to use any such terms.
   wsigma     - Sigma width for exponential whopping profiles; default to 25
   reject     - Three-element array setting partial and full rejection
                thresholds for profiles; default [0.2, 0.5, 0.8].
                What does this mean???
                When this was hardwired, it was [0.4, ??, 0.8].

 MODIFIED INPUTS (OPTIONAL):
   wfixed     - Array to describe which parameters to fix in the profile;
                0=fixed, 1=float; default to [1].
                The number of parameters to fit per fiber is determined
                this way; e.g. nCoeff = n_elements(wfixed), so the default
                is to fit only 1 parameter per fiber.  For the (default)
                Gaussian profile, this is the height of the Gaussian.
                Note that WFIXED is used to build the array WFIXARR.
   iback      - 1D array of input background coeff 
                (needed if fixed parameters are non-zero)
   bfixarr    - 1D integer array to specify which terms of the background
                coefficients to fix; 0=fixed, 1=float.
   wfixarr    - 1D integer array to specify which parameters in the full fit
                to fix; 0=fixed, 1=float.
                The array is sorted as follows:
                  [ncoeff] values for fiber #0
                   ...
                  [ncoeff] values for fiber #(nFiber-1)
                  [npoly] values for the background polynomial terms
                  [whoppingct] values for the whopping terms
   xvar       - X values of fimage and invvar; default is findgen(NX).
   mask       - Image mask: 1=good, 0=bad [NX]
   pixelmask  - Bits set for each fiber due to extraction rejection [nFiber]

 OUTPUTS:
   ans        - Output fit [ncoeff*nFiber+npoly+whoppingct]
                The array is sorted as follows:
                  [nFiber] values for coefficient #0
                   ...
                  [nFiber] values for coefficient #(nCoeff-1)
                  [npoly] values for the background polynomial terms
                  [whoppingct] values for the whopping terms
                Note this array is **not** sorted as INPUTANS or WFIXARR!

 OPTIONAL OUTPUTS:
   ymodel     - Evaluation of best fit [nCol]
   fscat      - Scattered light contribution in each fiber [nFiber]
   diagonal   - 1D diagonal of covariance matrix.  Currently, this is
                the diagonal from the Cholesky decompostion, which is
                1/error[j].  [ncoeff*nFiber+npoly+whoppingct]
   fullcovar  - 2D covariance matrix.  This is a symmetric matrix, and we
                only fill the lower triangle.  Computing this increases CPU
                time by a factor of 2 or 3.
   niter      - Number of rejection iterations performed
   reducedChi - Reduced chi ???

 COMMENTS:

 BUGS:
    Still need to do:
       limits on chebyshev polynomial are assumed to be 0.0 <-- nx
       these may need to be optional if only partial rows are being fit

       Error codes need to be returned, currently no such codes are returned

 EXAMPLES:

 PROCEDURES CALLED:
   Dynamic link to extract_row.c

 REVISION HISTORY:
    8-Aug-1999  Written by Scott Burles, Chicago 

(See pro/spec2d//extract_row.pro)


EXTRACT_ROW[2]

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 NAME:
   extract_row

 PURPOSE:
   Fit the fiber profiles and background in a single row with least squares
   Wrapper to extract row, which does extra testing

 CALLING SEQUENCE:
   ans = extract_row_safe( fimage, invvar, xcen, sigma, [ymodel=, fscat=, 
              proftype=, wfixed=, inputans=, iback=, bfixarr=, xvar=,
              mask=, relative=, diagonal=, fullcovar=, wfixarr=, npoly=,
              maxiter=, lowrej=, highrej=, niter=, squashprofile=,
              whopping=, wsigma=, pixelmask=, reject=, reducedChi= ])

 INPUTS:
   fimage     - Vector [nCol]
   invvar     - Inverse variance [nCol]
   xcen       - Initial guesses for X centers [nFiber]
   sigma      - Sigma of gaussian profile; (scalar or [nFiber])

 OPTIONAL KEYWORDS:
   proftype   - Select profile type:
                  1: Gaussian
                  2: (exponential)^3
                  3: (exponential)^2.5
                Default to 1.
   inputans   - Input fit, excluding background and whopping terms
                [ncoeff*nFiber]
                The array is sorted as follows:
                  [ncoeff] values for fiber #0
                   ...
                  [ncoeff] values for fiber #(nFiber-1)
   relative   - Set to use reduced chi-square to scale rejection threshold
   squashprofile - ???
   npoly      - Order of chebyshev scattered light background; default to 5
   maxiter    - Maximum number of profile fitting iterations; default to 10
   lowrej     - Negative sigma deviation to be rejected; default to 5
   highrej    - Positive sigma deviation to be rejected; default to 5
   whopping   - X locations to center additional "whopping"
terms to describe
                the exponentail tails of flux near bright fibers; default
                to -1, which means not to use any such terms.
   wsigma     - Sigma width for exponential whopping profiles; default to 25
   reject     - Two-element array setting partial and full rejection
                thresholds for profiles; default [0.8, 0.2].
                What does this mean???
                When this was hardwired, it was [0.8,0.4].

 MODIFIED INPUTS (OPTIONAL):
   wfixed     - Array to describe which parameters to fix in the profile;
                0=fixed, 1=float; default to [1].
                The number of parameters to fit per fiber is determined
                this way; e.g. nCoeff = n_elements(wfixed), so the default
                is to fit only 1 parameter per fiber.  For the (default)
                Gaussian profile, this is the height of the Gaussian.
                Note that WFIXED is used to build the array WFIXARR.
   iback      - 1D array of input background coeff 
                (needed if fixed parameters are non-zero)
   bfixarr    - 1D integer array to specify which terms of the background
                coefficients to fix; 0=fixed, 1=float.
   wfixarr    - 1D integer array to specify which parameters in the full fit
                to fix; 0=fixed, 1=float.
                The array is sorted as follows:
                  [ncoeff] values for fiber #0
                   ...
                  [ncoeff] values for fiber #(nFiber-1)
                  [npoly] values for the background polynomial terms
                  [whoppingct] values for the whopping terms
   xvar       - X values of fimage and invvar; default is findgen(NX).
   mask       - Image mask: 1=good, 0=bad [NX]
   pixelmask  - Bits set for each fiber due to extraction rejection [nFiber]

 OUTPUTS:
   ans        - Output fit [ncoeff*nFiber+npoly+whoppingct]
                The array is sorted as follows:
                  [nFiber] values for coefficient #0
                   ...
                  [nFiber] values for coefficient #(nCoeff-1)
                  [npoly] values for the background polynomial terms
                  [whoppingct] values for the whopping terms
                Note this array is **not** sorted as INPUTANS or WFIXARR!

 OPTIONAL OUTPUTS:
   ymodel     - Evaluation of best fit [nCol]
   fscat      - Scattered light contribution in each fiber [nFiber]
   diagonal   - 1D diagonal of covariance matrix.  Currently, this is
                the diagonal from the Cholesky decompostion, which is
                1/error[j].  [ncoeff*nFiber+npoly+whoppingct]
   fullcovar  - 2D covariance matrix.  This is a symmetric matrix, and we
                only fill the lower triangle.  Computing this increases CPU
                time by a factor of 2 or 3.
   niter      - Number of rejection iterations performed
   reducedChi - Reduced chi ???

 COMMENTS:

 BUGS:
    Still need to do:
       limits on chebyshev polynomial are assumed to be 0.0 <-- nx
       these may need to be optional if only partial rows are being fit

       Error codes need to be returned, currently no such codes are returned

 EXAMPLES:

 PROCEDURES CALLED:
   Dynamic link to extract_row.c

 REVISION HISTORY:
    4-Feb-1999  Written by Schlegel
        

(See pro/spec2d//extract_row_safe.pro)


FCHEBYSHEV

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 NAME:
        FCHEBYSHEV
 PURPOSE:
       Compute the first M terms in a CHEBYSHEV polynomial expansion.  
 EXPLANATION:
       Meant to be used as a supplied function to SVDFIT.

 CALLING SEQUENCE:
       result = FCHEBYSHEV( X, M, /halfintwo)

 INPUTS:
       X - the value of the independent variable, scalar or vector
       M - number of term of the CHEBYSHEV expansion to compute, integer
scalar 

 OUTPUTS:
       result - (N,M) array, where N is the number of elements in X and M
               is the order.   Contains the value of each CHEBYSHEV term for
               each value of X
 EXAMPLE:
       (1) If x = 2.88 and M = 3 then 
       IDL print, fchebyshev(x,3)   ==   [1.00, 2.88, 15.5888]

       (2) Find the coefficients to an M term Chebyshev polynomial that gives
               the best least-squares fit to a dataset (x,y)
               IDL coeff = SVDFIT( x,y,M,func='fchebyshev')
       
 METHOD:

 REVISION HISTORY:
       04-Aug-1999  Written by Scott Burles by hacking FLEGENDRE code
                    by Landsman in the Goddard libraries.

(See pro/spec2d//fchebyshev.pro)


FIBERFLAT

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 NAME:
   fiberflat

 PURPOSE:
   Construct the flat-field vectors from an extracted flat-field image.

 CALLING SEQUENCE:
   fflat = fiberflat( flux, fluxivar, wset, [ fibermask=fibermask, $
    minval=, ncoeff=, pixspace=, /dospline, nord=, lower=, upper=,
    /dospline, plottitle= ])

 INPUTS:
   flux       - Array of extracted flux from a flat-field image [Nrow,Ntrace]
   fluxivar   - Inverse variance map for FLUX.
   wset       - Wavelength solution

 OPTIONAL KEYWORDS:
   fibermask  - Mask of 0 for bad fibers and 1 for good fibers [NFIBER]
   minval     - Minimum value to use in fits to flat-field vectors;
                default to 3% of the median of FLUX.
   ncoeff     - Number of coefficients used in constructing FFLAT;
                default to 3 (cubic)
   pixspace   - Approximate spacing in pixels for break points in the
                spline fits to individual fibers; default to 10 pixels.
   dospline   - If this keyword is set, then fit the flat-field vectors
                to splines (using PIXSPACE) rather than to a Legendre
                polynomial (using NCOEFF).  This is **not** recommended.
   plottitle  - Prefix for titles in QA plots.

 PARAMETERS FOR SLATEC_SPLINEFIT:
   nord
   lower
   upper

 OUTPUTS:
   fflat      - Array of flat-field flat-field vectors for each fiber
                that remove relative flat-field variations as a function
                of wavelength between fibers [Nrow, Ntrace]

 OPTIONAL OUTPUTS:
   fibermask  - (Modified)

 COMMENTS:
   The user should first "flat-field" the input array to take out
   pixel-to-pixel variations.

   The parameters for SLATEC_SPLINEFIT are only used when generating the
   "superflat".

   The 'BADFLAT' bit is set in FIBERMASK if the mean throughput for
   a fiber is less than 0.7 times the median of all good-fiber throughputs.

   In any given fiber, set FFLAT=0 wherever there are at least 5 contiguous
   bad pixels.

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:
   fibermask_bits()
   slatec_bvalu()
   slatec_splinefit()
   splog
   superflat
   traceset2xy
   xy2traceset

 REVISION HISTORY:
   14-Oct-1999  Written by D. Schlegel, APO

(See pro/spec2d//fiberflat.pro)


FIBERMASK_BITS

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 NAME:
   fibermask_bits

 PURPOSE:
   Return a byte with a single bit set which matches bitlabel

 CALLING SEQUENCE:
   fibermask_bits(bitlabel)

 INPUTS:
   bitlabel   - String to match to corresponding bit

 OUTPUTS:
   One byte with 1 bit set 
   returns 0 if no label is matched

 OPTIONAL OUTPUTS:

 COMMENTS:

 EXAMPLES:
   fibermask[i] = fibermask_bits('BADARC') 

 BUGS:

 PROCEDURES CALLED:

 REVISION HISTORY:
   23-Jan-2000 Written by S. Burles, Chicago

(See pro/spec2d//fibermask_bits.pro)


FITANSIMAGE

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 NAME:
   fitansimage

 PURPOSE:
   Convert output from extract_image (ansimage) into a smooth
    function of fiber number and row

 CALLING SEQUENCE:
    fitans = fitansimage(ansimage, nterms, ntrace, npoly, nfirst, yrow, $
            tempflux, fluxm = [1,1,0], scatfit=scatfit, $
            smallflux, fluxm=fluxm, nord=nord, nscatbkpts=nscatbkpts, $
            ymin=ymin, ymax=ymax, fullrows=fullrows)

 INPUTS:
     ansimage  -  Keyword Output from extract_image
     nterms    -  number of profile terms
     ntrace    -  Number of fibers (currently hardwired to 320)
     npoly     -  Order of chebyshev polynomial in scattered light
     yrow      -  Array of rows extracted in first pass 
     smallflux -  Flux extracted in first pass

 OPTIONAL KEYWORDS:
     fluxm    -   Factor profile terms contribute to total flux
                   (asymmetric terms are set to zero)

 OUTPUTS:
    fitans    -  Smooth version of ansimage (expanded to 2048 rows)

 OPTIONAL OUTPUTS:
    scatfit   - Image of scattered light from smoothing polynomials

 COMMENTS:
       fitansimage takes the output from extract_image, and smooths
          the corresponding parameters of nfibers and npoly with
          functions of order nord 

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:

 REVISION HISTORY:
   ??-Oct-1999  Written by S. Burles, Chicago
   25-Feb-2000  Modified to be more robust (yeah!)
                  but requires exactly 320 fibers (boo)

(See pro/spec2d//fitansimage.pro)


FITARCIMAGE[1]

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 NAME:
   fitarcimage

 PURPOSE:
   Determine wavelength calibration from arclines

 CALLING SEQUENCE:
   fitarcimage, arc, arcivar, xcen, ycen, wset, [wfirst=, $
    color=color, lampfile=lampfile, fibermask=fibermask, $
    func=func, aset=aset, ncoeff=ncoeff, lambda=lambda, $
    thresh=thresh, row=row, nmed=nmed, /gauss, $
    xdif_tset=xdif_tset, bestcorr=bestcorr ]

 INPUTS:
   arc        - Extracted arc spectra with dimensions [NY,NFIBER]
   arcivar    - Inverse variance of ARC

 OPTIONAL KEYWORDS:
   color      - 'red' or 'blue'; not required if ANS is set
   lampfile   - Name of file describing arc lamp lines;
                default to the file 'lamphgcdne.dat' in $IDLSPEC2D_DIR/etc.
   fibermask  - Fiber status bits, set nonzero for bad status [NFIBER]
   func       - Name of fitting function; default to 'legendre'
   aset       - Trace set for initial wavelength solution in row number ROW.
   ncoeff     - Number of coefficients in fits.  This may be different than
                the number of coefficients in the initial guess ASET.
                Default to 5.
   thresh     - Threshhold counts for significant lines;
                default to 200 if COLOR='blue' or 500 if COLOR='red'
   row        - Row to use in initial guess of wavelength solution;
                default to (NFIBER-30)/2
   nmed       - Number of rows around ROW to median filter for initial
                wavelengths solution; default to 5
   gauss      - Use gaussian profile fitting for final centroid fit

 OUTPUTS:
   aset       - (Modified)
   xcen       - pixel position of lines [nfiber, nlambda]
   ycen       - fiber number [nfiber, nlambda]
   wset       - traceset (pix - lambda)

 OPTIONAL OUTPUTS:
   lampfile   - Modified from input to include full path name of file
   lambda     - Returns wavelengths of good lamp lines [Angstroms]
   fibermask  - (Modified)
   xdif_tset  - Fit residual of lamp lines to fit positions [pixels]
   bestcorr   - Correlation coefficient with simulated arc spectrum
   wfirst     - traceset from first iteration on arc fits

 COMMENTS:
   Return from routine after computing BESTCORR if XCEN, YCEN and WSET
   are not to be returned.

 EXAMPLES:

 BUGS:
   Not making sure that only the same lines are fit for each fiber.
      (Different lines can be rejected in xy2traceset.)
   THRESH is unused.
   TRACESET2PIX maybe returns the transpose of what is natural?
   Check QA stuff at end.
   FIBERMASK not yet modified if an arc is atrociously bad.


 PROCEDURES CALLED:
   arcfit_guess()
   djs_median
   djsig()
   finalarcfit
   trace_crude()
   trace_fweight()
   traceset2pix()
   traceset2xy()
   xy2traceset

 REVISION HISTORY:
   15-Oct-1999  Written by S. Burles, D. Finkbeiner, & D. Schlegel, APO.
   09-Nov-1999  Major modifications by D. Schlegel, Ringberg.
   20-Jan-2000  Gone back to very simple procedure: replacement (S. Burles)

(See pro/spec2d//fitarcimage.pro)


FITARCIMAGE[2]

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 NAME:
   fitarcimage

 PURPOSE:
   Determine wavelength calibration from arclines

 CALLING SEQUENCE:
   fitarcimage, arc, arcivar, xnew, ycen, wset, $
    [ color=color, lampfile=lampfile, fibermask=fibermask, $
    func=func, aset=aset, ncoeff=ncoeff, lambda=lambda, $
    thresh=thresh, row=row, nmed=nmed, $
    xdif_tset=xdif_tset, bestcorr=bestcorr ]

 INPUTS:
   arc        - Extracted arc spectra with dimensions [NY,NFIBER]
   arcivar    - Inverse variance of ARC

 OPTIONAL KEYWORDS:
   color      - 'red' or 'blue'; not required if ANS is set
   lampfile   - Name of file describing arc lamp lines;
                default to the file 'lamphgcdne.dat' in the IDL path.
   fibermask  - Fiber status bits, set nonzero for bad status [NFIBER]
   func       - Name of fitting function; default to 'legendre'
   aset       - Trace set for initial wavelength solution in row number ROW.
   ncoeff     - Number of coefficients in fits.  This may be different than
                the number of coefficients in the initial guess ASET.
                Default to 5.
   thresh     - Threshhold counts for significant lines;
                default to 200 if COLOR='blue' or 500 if COLOR='red'
   row        - Row to use in initial guess of wavelength solution;
                default to (NFIBER-30)/2
   nmed       - Number of rows around ROW to median filter for initial
                wavelengths solution; default to 5

 OUTPUTS:
   aset       - (Modified)
   xnew       - pixel position of lines [nfiber, nlambda]
   ycen       - fiber number [nfiber, nlambda]
   wset       - traceset (pix - lambda)

 OPTIONAL OUTPUTS:
   lampfile   - Modified from input to include full path name of file
   lambda     - Returns wavelengths of good lamp lines [Angstroms]
   fibermask  - (Modified)
   xdif_tset  - Fit residual of lamp lines to fit positions [pixels]
   bestcorr   - Correlation coefficient with simulated arc spectrum

 COMMENTS:
   Return from routine after computing BESTCORR if XCEN, YCEN and WSET
   are not to be returned.

   THIS IS REVISION 1.27 OF FITARCIMAGE, SINCE THE CURRENT VERSION
   APPEARS TO BE BUGGY!!!

 EXAMPLES:

 BUGS:
   Not making sure that only the same lines are fit for each fiber.
      (Different lines can be rejected in xy2traceset.)
   THRESH is unused.
   TRACESET2PIX maybe returns the transpose of what is natural?
   Check QA stuff at end.
   FIBERMASK not yet modified if an arc is atrociously bad.


 PROCEDURES CALLED:
   arcfit_guess()
   djs_median
   djsig()
   trace_crude()
   trace_fweight()
   traceset2pix()
   traceset2xy()
   xy2traceset

 REVISION HISTORY:
   15-Oct-1999  Written by S. Burles, D. Finkbeiner, & D. Schlegel, APO.
   09-Nov-1999  Major modifications by D. Schlegel, Ringberg.

(See pro/spec2d//fitarcimage_old.pro)


FITDISPERSION

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 NAME:
   fitdispersion

 PURPOSE:
   Fit polynomials to the line width (dispersion axis) for each fiber bundle

 CALLING SEQUENCE:
   dispset = fitdispersion(arc_flux, arc_fluxivar, xcen, $
             sigma=sigma, ncoeff=ncoeff, xmin=xmin, xmax=xmax)

 INPUTS:
   arc_flux     - arc image extracted flux
   arc_fluxivar - corresponding inverse variance
   xcen         - xpeaks of arc lines [ntrace,nlines]

 OPTIONAL KEYWORDS:
   ncoeff     - order of legendre polynomial to apply to width vs. row
   sigma      - The initial sigma (in pixels, 1.0 is a good guess)
   xmin, xmax - limits in traceset

 OUTPUTS:
   dispset   - a traceset structure containing fitted coefficients

 OPTIONAL OUTPUTS:

 COMMENTS:
    Used to fill arcstruct.dispset, which can then be applied
     to psf-corrected sky subtraction 

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:

 REVISION HISTORY:
   1-Mar-2000  Written by S. Burles, FNAL

(See pro/spec2d//fitdispersion.pro)


FITFLATWIDTH

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 NAME:
   fitflatwidth

 PURPOSE:
   Fit a traceset to the first-order corrected width of the flat field

 CALLING SEQUENCE:
   widthset = fitflatwidth(flux, fluxivar, ansimage, fibermask, $
        ncoeff=ncoeff, sigma=sigma)

 INPUTS:
   flux       - flat-field extracted flux
   fluxivar   - corresponding inverse variance
   ansimage   - output from extract image which contains parameter values
   fibermask  - nTrace bit mask, which marks bad fibers

 OPTIONAL KEYWORDS:
   ncoeff     - order of legendre polynomial to apply to width vs. row
   sigma      - The zeroth order sigma of extracted profile

 OUTPUTS:
   widthset   - a traceset structure containing fitted coefficients

 OPTIONAL OUTPUTS:

 COMMENTS:
    Used to fill flatstruct.widthset, which can then be applied
     to object extraction (known profile widths)

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:

 REVISION HISTORY:
   1-Mar-2000  Written by S. Burles, FNAL

(See pro/spec2d//fitflatwidth.pro)


FITMEANX

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 NAME:
   fitmeanx

 PURPOSE:
   Use fitans to tweak trace and sigma
   This just perturbs the input values of xcen and sigma

 CALLING SEQUENCE:
   xdiff = fitmeanx(wset, lambda, xpos, xinvvar, $
                      nord=nord, maxdev=maxdev, mx=mx)

 INPUTS:
   wset     - Initial wavelength solution
   lambda   - air wavelengths corresponding to xpos
   xpos     - centroids of sky lines in object image

 OPTIONAL KEYWORDS:
   nord     - order of fit to delta x positions
   maxdev   - max abs difference to reject outlying sky line positions

 OUTPUTS:
   xdiff    - smooth fit to difference between measured sky positions
                and those predicted from arc wavelength solution

 OPTIONAL OUTPUTS:
   xinvvar  - weights in xpos (mask)
   mx       - sky line positions predicted from arc line solution

 COMMENTS:
    LAMBDA = log10-wavelength

 EXAMPLES:

 PROCEDURES CALLED:

 REVISION HISTORY:
   19-Oct-1999  Written by S. Burles, Chicago

(See pro/spec2d//fitmeanx.pro)


FITVACSET

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 NAME:
   fitvacset

 PURPOSE:
   Use measured positions of arc lines and shift coefficients
    passed through xset to produce a final vacuum wavelength solution 

 CALLING SEQUENCE:
   vacset = fitvacset(xpeak, lambda, wset, xset, ncoeff=ncoeff)

 INPUTS:
   xpeak  - Arc line centroids 
   lambda - Corresponding wavelengths
   wset   - Initial arc line solution coefficients
   xset   - Coefficients specifying shift to coefficients 

 OPTIONAL KEYWORDS:
   ncoeff - Number of coefficients to fit final wavelength solution
(Default 5)

 OUTPUTS:
   vacset - output wavelength solution which includes shift to
                    sky lines and conversion to vacuum wavelengths

 OPTIONAL OUTPUTS:

 COMMENTS:

 EXAMPLES:

 PROCEDURES CALLED:
   traceset2xy
   xy2traceset

 REVISION HISTORY:
   20-Jan-2000  Written by S. Burles, Chicago

(See pro/spec2d//fitvacset.pro)


FLEGENDRE

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 NAME:
        FLEGENDRE
 PURPOSE:
       Compute the first M terms in a Legendre polynomial expansion.  
 EXPLANATION:
       Meant to be used as a supplied function to SVDFIT.

       This procedure became partially obsolete in IDL V5.0 with the 
       introduction of the /LEGENDRE keyword to SVDFIT and the associated 
       SVDLEG function.    However, note that, unlike SVDLEG, FLEGENDRE works
       on vector values of X.     
 CALLING SEQUENCE:
       result = FLEGENDRE( X, M)

 INPUTS:
       X - the value of the independent variable, scalar or vector
       M - number of term of the Legendre expansion to compute, integer
scalar 

 OUTPUTS:
       result - (N,M) array, where N is the number of elements in X and M
               is the order.   Contains the value of each Legendre term for
               each value of X
 EXAMPLE:
       (1) If x = 2.88 and M = 3 then 
       IDL print, flegendre(x,3)   ==   [1.00, 2.88, 11.9416]

       This result can be checked by explicity computing the first 3 Legendre
       terms, 1.0, x, 0.5*( 3*x^2 -1)

       (2) Find the coefficients to an M term Legendre polynomial that gives
               the best least-squares fit to a dataset (x,y)
               IDL coeff = SVDFIT( x,y,M,func='flegendre')
       
           The coefficients can then be supplied to the function POLYLEG to 
               compute the best YFIT values for any X. 
 METHOD:
       The recurrence relation for the Legendre polynomials is used to
compute
       each term.   Compare with the function FLEG in "Numerical
Recipes"
       by Press et al. (1992), p. 674

 REVISION HISTORY:
       Written     Wayne Landsman    Hughes STX      April 1995
    
       Converted to IDL V5.0   W. Landsman   September 1997

(See pro/spec2d//flegendre.pro)


FLUXCORR

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 NAME:
   fluxcorr

 PURPOSE:
   Use sky-subtracted SPECTROPHOTO_STD's to calculate flux correction
   as a function of wavelength.  We assume the correction is uniform
   for all fibers (This may change).

 CALLING SEQUENCE:
   ff = fluxcorr(flux, fluxivar, wset, plugsort, color=color, $
        spectrostd=spectrostd, bkptfile=bkptfile, lower=lower, upper=upper, $
        fibermask=fibermask)

 INPUTS:
   flux         - sky-subtracted extracted spectra [nx,ntrace]
   fluxivar     - corresponding inverse variance [nx,ntrace]
   wset         - wavelength coefficients as a trace set
   plugsort     - plugmap entries

 REQUIRED KEYWORDS:
   color        - 'red' or 'blue'

 OPTIONAL KEYWORDS:
   spectrostd   - file with spectrophoto continuum, set to 1.0 at 5556 Ang.
   bkptfile     - file with wavelengths of specific bkpts 
                     default is (red.bkpts or blue.bkpts)
   absfile      - file delineating regions of absorption to avoid in
                     in continuum fitting
   lower        - lower rejection threshold for continuum fitting
   upper        - upper rejection threshold for continuum fitting
   fibermask    - use to reject possible standards which have spectral
troubles
   
 OUTPUTS:
   ff           - Flux calibration to correct each pixel in flux array

 OPTIONAL OUTPUTS:

 COMMENTS:

 EXAMPLES:

 BUGS:
       !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
         What we really need is an accurate prediction of
         f-star continua as a function of u',g',r', and i'
         Right now, all we can do is estimate.
         Also need to rewrite to make use of all f-stars.
       !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

 PROCEDURES CALLED:

 REVISION HISTORY:
   19-Oct-1999  Written by S. Burles, Chicago

(See pro/spec2d//fluxcorr.pro)


FUNC_FIT

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 NAME:
   func_fit

 PURPOSE:
   Fit X, Y positions to a functional form.

 CALLING SEQUENCE:
   res = function func_fit( x, y, ncoeff, [invvar=, function_name=, $
    /halfintwo, yfit=, ia=, inputans= ]

 INPUTS:
   x          - X values (independent variable)
   y          - Y values (dependent variable)
   ncoeff     - Number of coefficients to fit
   invvar     - Weight values (inverse variance)

 OPTIONAL KEYWORDS:
   function_name - Function to fit; options are:
                'legendre'
                'chebyshev'
                Default to 'legendre'
   halfintwo  - Optional keyword for Chebyshev function, FCHEBYSHEV
   ia         - Array specifying free (1) and fixed (0) variables [NCOEFF]
   inputans   - If holding parameters fixed, set this array to those values
                [NCOEFF]

 OUTPUTS:
   res        - Fit coefficients [NCOEFF]

 OPTIONAL OUTPUTS:
   yfit       - Fit evaluated at the points X

 COMMENTS:

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:
   fchebyshev()
   flegendre()

 REVISION HISTORY:
   10-Sep-1999  Written by D. Finkbeiner, APO?
   16-Nov-1999  Modified by D. Schlegel to never fit more coefficients
                than there are data points.

(See pro/spec2d//func_fit.pro)


GENFLATMASK

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 NAME:
   genflatmask

 PURPOSE:
   Read or generate a mask for pixels to ignore when generating flat-fields.

 CALLING SEQUENCE:
   maskimg = genflatmask( [ flatname, spectrographid=, color=, indir=,
tmpdir= ] )

 OPTIONAL INPUTS:
   flatname   - Name of flat-field image
                Note that many flats from many nights can be combined.

 OPTIONAL KEYWORDS:
   spectrographid - Spectrograph ID (1 or 2); reqired if FLATNAME not set.
   color      - Spectrograph color ('red' or 'blue');
                reqired if FLATNAME not set.
   indir      - Input directory for FLATNAME; default to '.'
   tmpdir     - Temporary directory for uncompressing the mask image
                if FLATNAME is not specified; default to '.'

 OUTPUTS:
   maskimg    - Mask image with 0=good, 1=bad

 COMMENTS:
   If FLATNAME is specified, then a bad pixel mask is generated from
   that flat-field image assuming it has a mean value approximately equal
   to one.  If not, then read the mask from the distribution of IDLSPEC2D
   in the "etc" subdirectory.

   Mask values =0 for good pixels, =1 for bad.

   This routine spawns the Unix comments 'zcat' and 'rm'.

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:
   readfits()

 DATA FILES:
   $IDLSPEC2D/etc/flatmask-b1.fits.gz
   $IDLSPEC2D/etc/flatmask-b2.fits.gz
   $IDLSPEC2D/etc/flatmask-r1.fits.gz
   $IDLSPEC2D/etc/flatmask-r2.fits.gz

 REVISION HISTORY:
   16-Dec-1999  Written by D. Schlegel, Princeton

(See pro/spec2d//genflatmask.pro)


IDLSPEC2D_VERSION

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 NAME:
   idlspec2d_version

 PURPOSE:
   Return the version name for the product idlspec2d

 CALLING SEQUENCE:
   vers = idlspec2d_version()

 INPUTS:

 OUTPUTS:
   vers       - Version name for the product idlspec2d

 COMMENTS:
   If this version is not tagged by CVS, then we return 'NOCVS:TOPLEVEL'
   where TOPLEVEL is the last directory in the environment variable
   $IDLSPEC2D_DIR.  For example, if you are using a version of the code
   in the directory '/u/schlegel/idlspec2d/v0_0', then this returns
   'NOCVS:v0_0'.

 BUGS:

 PROCEDURES CALLED:

 REVISION HISTORY:
   01-Dec-1999  Written by D. Schlegel, Princeton.

(See pro/spec2d//idlspec2d_version.pro)


LOCATESKYLINES

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 NAME:
   locateskylines

 PURPOSE:
   Tweak wavelength calibration using skylines

 CALLING SEQUENCE:
   locateskylines, skylinefile, fimage, ivar, wset, xsky, ysky, skywaves, $
    lambda=lambda, xset=xset

 INPUTS:
   skylinefile - filename of skyline file
   fimage      - flattened image containing skylines (npix x nfiber)
   ivar        - inverse variance of fimage
   wset        - traceset (pix - lambda)

 OPTIONAL KEYWORDS:
   lambda      - override skyline file (log10 Angstroms)

 OUTPUTS:
   xsky        - pixel position of lines [nfiber, nline]
   ysky        - fiber number [nfiber, nline]
   skywaves    - wavelengths used (Angstroms)

 OPTIONAL OUTPUTS:
   errcode     - returns errcode (see below)

 COMMENTS:
   Error codes:
  -1 - <unknown error
   0 - Everything fine

 EXAMPLES:

 BUGS:
  I've now changed traceset2pix to use the forward trace set, but have
  not yet made any changes to this code.

 PROCEDURES CALLED:
  fitmeanx()         
  trace_gweight()
  traceset2pix()

 REVISION HISTORY:
   15-Oct-1999  Written by S. Burles, D. Finkbeiner, & D. Schlegel, APO
   18-Nov-1999  Moved skyline QA to fit_skyset (SMB)

(See pro/spec2d//locateskylines.pro)


LOGSHEET

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 NAME:
   logsheet

 PURPOSE:
   Make a summary of header keywords in a directory of raw SDSS spectro
files.
   Only look at files matching "*.fit"

 CALLING SEQUENCE:
   logsheet, [dir, outfile=]

 INPUTS:

 OPTIONAL INPUTS:
   dir        - Directory name; default to ''
   outfile    - Output file

 OUTPUTS:

 COMMENTS:

 EXAMPLES:

 PROCEDURES CALLED:
   headfits()
   sxpar()

 REVISION HISTORY:
   06-Oct-1999  Written by David Schlegel, Princeton.

(See pro/spec2d//logsheet.pro)


PIXELMASK_BITS

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 NAME:
   pixelmask_bits

 PURPOSE:
   Return mask value corresponding to a mask condition for PIXELMASK.

 CALLING SEQUENCE:
   mask = pixelmask_bits(bitlabel)

 INPUTS:
   bitlabel   - String name specifying bit

 OUTPUTS:
   mask       - Signed long set to 2^BIT, where BIT is the bit specified by
                BITLABEL, or set to 0 if no label is matched

 OPTIONAL OUTPUTS:

 COMMENTS:

 EXAMPLES:
   mask = pixelmask_bits('FULLREJECT') 

 BUGS:

 PROCEDURES CALLED:

 REVISION HISTORY:
   23-Jan-2000 Written by S. Burles, Chicago
   27-Jan-2000 Changed from signed int to signed long

(See pro/spec2d//pixelmask_bits.pro)


QAPLOT_ARCLINE

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 NAME:
   qaplot_arcline

 PURPOSE:
   Generate QA plot for arcline fits

 CALLING SEQUENCE:
   qaplot_arcline, xdif, lambda, [color=, fibermask=, title=]

 INPUTS:
   xdif       - Deviations in arc line fits in pixels, array [NFIBER, NLAMP]
   lambda     - Wavelength for each lamp in Angstroms, vector [NLAMP]

 OPTIONAL KEYWORDS:
   color      - Specify 'blue' or 'red' to fix plotting limits
   fibermask  - Fiber status bits, set nonzero for bad status [NFIBER]
   title      - TITLE of plot

 OUTPUTS:

 OPTIONAL OUTPUTS:

 COMMENTS:
   Skip over bad fibers in plots.

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:
   djs_iterstat
   djs_oplot
   djs_plot

 REVISION HISTORY:
   15-Oct-1999  Written by D. Finkbeiner, APO
   23-Nov-1999  Modified by D. Schlegel, Princeton

(See pro/spec2d//qaplot_arcline.pro)


QAPLOT_FFLAT

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 NAME:
   qaplot_fflat

 PURPOSE:
   Generate QA plot for fiber-flats

 CALLING SEQUENCE:
   qaplot_fflat, fflat, wset, [ fibermask=, dx=, title= ]

 INPUTS:
   fflat      - Array of flat-field flat-field vectors for each fiber
                that remove relative flat-field variations as a function
                of wavelength between fibers [Nrow, Ntrace]
   wset       - Wavelength solution

 OPTIONAL KEYWORDS:
   fibermask  - Fiber status bits, set nonzero for bad status [NFIBER]
   dx         - Bin log-lambda by this number; default to 1.e-3 (about 10
pix)
   title      - TITLE of plot

 OUTPUTS:

 OPTIONAL OUTPUTS:

 COMMENTS:
   Do not plot bad fibers or masked pixels in good fibers.

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:
   djs_oplot
   djs_plot

 REVISION HISTORY:
   23-Nov-1999  Written by D. Schlegel, Princeton

(See pro/spec2d//qaplot_fflat.pro)


QAPLOT_SCATLIGHT

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 NAME:
   qaplot_scatlight

 PURPOSE:
   Generate QA plots for scattered light

 CALLING SEQUENCE:
   qaplot_scatlight, scatfit, yrow, wset=, xcen=, [ fibermask=, title= ]

 INPUTS:
   scatfit    - Scattered light image after fitting [NX,NY/8]
   yrow       - extracted rows in scatfit 

 REQUIRED KEYWORDS:
   wset       - Wavelength solution
   xcen       - X positions corresponding to the extracted wavelength sol'n
                [NY,NTRACE]

 OPTIONAL KEYWORDS:
   fibermask  - Fiber status bits, set nonzero for bad status [NFIBER]
   title      - TITLE of plot

 OUTPUTS:

 OPTIONAL OUTPUTS:

 COMMENTS:

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:
   djs_median()
   djs_oploterr
   djs_plot
   traceset2xy

 REVISION HISTORY:
   13-Dec-1999  Written by D. Schlegel, Princeton
   22-Jan-2000  Trying to speed up, S. Burles

(See pro/spec2d//qaplot_scatlight.pro)


QAPLOT_SKYDEV

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 NAME:
   qaplot_skydev

 PURPOSE:
   Generate QA plot: scatter in sky line positions

 CALLING SEQUENCE:
   qaplot_skydev, flux, fluxivar, vacset, plugsort, color, $
    [fibermask=, title=]

 INPUTS:
   flux       - Pre-skysubtracted flux array [Nrow, Ntrace]
   fluxivar   - Associated inverse variance
   vacset     - Vacuum Wavelength solution
   plugsort   - Plugmap struct [Ntrace]
   color      - string specifying 'red' or 'blue' spectra

 OPTIONAL KEYWORDS:
   fibermask  - Fiber status bits, set nonzero for bad status [NFIBER]
   title      - TITLE of plot

 OUTPUTS:
   Output plots only

 OPTIONAL OUTPUTS:

 COMMENTS:

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:
   djs_oplot
   djs_plot
   trace_gweight
   traceset2xy
   traceset2pix
   djs_median

 REVISION HISTORY:
   22-Jan-2000 Written by S. Burles, Chicago

(See pro/spec2d//qaplot_skydev.pro)


QAPLOT_SKYLINE

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 NAME:
   qaplot_skyline

 PURPOSE:
   Generate QA plots for flux in particular skylines

 CALLING SEQUENCE:
   qaplot_skyline, lwave, obj, objivar, objsub, objsubivar, plugsort, wset, $
    [fibermask=, dwave=, title= ]

 INPUTS:
   lwave      -
   obj        - Image
   objivar    - Inverse variance for OBJ
   objsub     - Image after sky-subtraction
   objsubivar - Inverse variance for image after sky-subtraction
   plugsort   - Plugmap structure trimmed to one element per fiber
   wset       - Wavelength solution

 OPTIONAL KEYWORDS:
   fibermask  - Fiber status bits, set nonzero for bad status [NFIBER]
   dwave      - Half-width about LWAVE for fitting sky line;
                default to 5.0 Ang
   titel      - File name to use for TITLE of plot

 OUTPUTS:

 OPTIONAL OUTPUTS:

 COMMENTS:

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:
   djs_iterstat
   djs_median
   djs_oplot
   splog
   traceset2xy

 INTERNAL SUPPORT ROUTINES:

 REVISION HISTORY:
   01-Jan-2000  Written by D. Schlegel, Princeton

(See pro/spec2d//qaplot_skyline.pro)


QAPLOT_SKYSUB

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 NAME:
   qaplot_skysub

 PURPOSE:
   Generate QA plots for sky-subtraction

 CALLING SEQUENCE:
   qaplot_skysub, obj, objivar, objsub, objsubivar, wset, $
    iskies, [title= ]

 INPUTS:
   obj        - Image
   objivar    - Inverse variance for OBJ
   objsub     - Image after sky-subtraction
   objsubivar - Inverse variance for image after sky-subtraction
   wset       - Wavelength solution
   iskies     - List of good sky fibers

 OPTIONAL KEYWORDS:
   title      - TITLE of plot

 OUTPUTS:

 OPTIONAL OUTPUTS:

 COMMENTS:

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:
   djs_median
   djs_oplot
   djs_plot

 INTERNAL SUPPORT ROUTINES:
   skyplot

 REVISION HISTORY:
   30-Dec-1999  Written by D. Schlegel, Princeton

(See pro/spec2d//qaplot_skysub.pro)


QUICKPROC

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 NAME:
   quickproc

 PURPOSE:
   Read in Raw SDSS files, and keep as UINT, process with opConfig.par

 CALLING SEQUENCE:
   image = quickproc(infile, hdr=hdr, configfile=configfile)
    

 INPUTS:
   infile     - Raw SDSS frame

 OPTIONAL KEYWORDS:
   hdr        - Header returned in memory
   configfile - Default to "opConfig.par"

 OUTPUTS:
   image      - Processed 2d image (UINT) zero level 1000

 COMMENTS:

 BUGS:

 PROCEDURES CALLED:
   rdss_fits()
   yanny_free
   yanny_read

 REVISION HISTORY:
   10-Nov-1999  Written by Scott Burles, modified from sdssproc

(See pro/spec2d//quickproc.pro)


RDSS_FITS

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 NAME:
   rdss_fits

 PURPOSE:
   Read a FITS file into IDL data and header variables

 CALLING SEQUENCE:
   image = rdss_fits( filename, [ hdr, nofloat ] )

 INPUTS:
   filename   - Scalar string containing the name of the FITS file  
                (including extension) to be read.   If the filename has
                a *.gz extension, it will be treated as a gzip compressed
                file.   If it has a .Z extension, it will be treated as a
                Unix compressed file.

 OPTIONAL KEYWORDS:

 OUTPUTS:
   image      - FITS data array constructed from designated record.
                If the specified file was not found, then return -1.

 OPTIONAL OUTPUTS:
   hdr        - String array containing the header from the FITS file.

 COMMENTS:
   This routine will read a simple FITS image, or convert a non-standard
   SDSS image that uses unsigned 16-bit integers.  One can pass any other
   keywords expected by READFITS().

 EXAMPLES:

 PROCEDURES CALLED:
   readfits()
   sxpar()

 REVISION HISTORY:
   13-May-1999  Written by David Schlegel, Princeton.

(See pro/spec2d//rdss_fits.pro)


SDSSPROC

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 NAME:
   sdssproc

 PURPOSE:
   Read in Raw SDSS files, and process with opConfig, opECalib, opBC par
files.

 CALLING SEQUENCE:
   sdssproc, infile, [image, invvar, indir=, $
    outfile=, varfile=, nsatrow=, fbadpix=, $
    hdr=hdr, configfile=, ecalibfile=, bcfile=, $
    pixflatname=, minflat=, spectrographid=, color= ]

 INPUTS:
   infile     - Raw SDSS file name

 OPTIONAL KEYWORDS:
   indir      - Input directory for INFILE
   outfile    - Calibrated 2d frame, after processing
   varfile    - Inverse variance frame after processing
   nsatrow    - Number of saturated rows, assuming that a row is saturated
                if at least 20 of its pixels are above saturation level
   fbadpix    - Fraction of bad pixels, not including bad columns
   hdr        - Header returned in memory
   configfile - Default to "opConfig.par"
   ecalibfile - Default to "opECalib.par"
   bcfile     - Default to "opBC.par"
   minflat    - Minimum values allowed for pixflat
                   (lower values of pixflat are set to 0 invvar)
   pixflatname- Name of pixel-to-pixel flat, produced with SPFLATTEN.

 OUTPUTS:
   image      - Processed 2d image
   invvar     - Associated inverse variance
   spectrographid - Return spectrograph ID (1 or 2)
   color      - Return spectrograph color ('red' or 'blue')

 COMMENTS:
   Only the header is read from the image if IMAGE, INVVAR, OUTFILE and
   VARFILE are all not set.

   Required header keywords: EXPTIME.

 BUGS:
   The open-shutter correction SMEARIMG will include smeared data from
   any cosmic rays, which is wrong.  At the minimum, I could interpolate
   over A/D saturations (in ADMASK) before constructing SMEARIMG.

 PROCEDURES CALLED:
   djs_iterstat
   headfits()
   idlspec2d_version()
   idlutils_version()
   rdss_fits()
   readfits()
   splog
   sxaddpar
   sxpar()
   writefits
   yanny_free
   yanny_read

 REVISION HISTORY:
   13-May-1999  Written by Scott Burles & David Schlegel, Apache Point.
   08-Sep-1999  Modified to read Yanny param files instead of FITS
                versions of the same (DJS).
   01-Dec-1999  Added version stamping (DJS).
   07-Dec-1999  Mask neighbors of pixels that saturated the A/D converter.
                Identify blead trails and mask from that row up (DJS).
   10-Dec-1999  Test if the shutter was open during readout, and try
                to correct the light for that (DJS).
   04-Feb-2000  Declare that the shutter was open if it is a 640 sec
                exposure taken before MJD=51570 (DJS).

(See pro/spec2d//sdssproc.pro)


SELECT_ARC

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 NAME:
   select_arc

 PURPOSE:
   Select best arc from an arc structure produced with SPCALIB.

 CALLING SEQUENCE:
   bestarc = select_arc ( arcstruct )

 INPUTS:
   arcstruct  - Structure array with extracted arc calibration information

 OPTIONAL KEYWORDS:

 OUTPUTS:
   bestarc    - Structure with extracted arc calibration information
                for that arc selected from ARCSTRUCT

 OPTIONAL OUTPUTS:

 COMMENTS:

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:
   djsig()

 REVISION HISTORY:
   25-Jan-2000  Written by D. Schlegel, Princeton

(See pro/spec2d//select_arc.pro)


SELECT_FLAT

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 NAME:
   select_flat

 PURPOSE:
   Select best flat from a flat-field structure produced with SPCALIB.

 CALLING SEQUENCE:
   bestflat = select_flat( flatstruct, tai )

 INPUTS:
   flatstruct - Structure array with extracted flat calibration information
   tai        - Time of observation for object frame (from header card)

 OPTIONAL KEYWORDS:

 OUTPUTS:
   bestflat   - Structure array with extracted flat calibration information
                for best flat selected for the time specified by TAI.

 OPTIONAL OUTPUTS:

 COMMENTS:

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:

 REVISION HISTORY:
   25-Jan-2000  Written by D. Schlegel, Princeton

(See pro/spec2d//select_flat.pro)


SKYSUBTRACT

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 NAME:
   skysubtract

 PURPOSE:
   Sky-subtract an image and modify the variance

 CALLING SEQUENCE:
   skystruct = skysubtract(obj, objivar, plugsort, wset, objsub,
objsubivar, $
    [iskies= , fibermask=, nord=, upper=, lower=, maxiter=, pixelmask=, $
      relchi2struct= ])

 INPUTS:
   obj        - Image
   objivar    - Inverse variance for OBJ
   plugsort   - Plugmap structure trimmed to one element per fiber
   wset       - Wavelength solution

 OPTIONAL KEYWORDS:
   fibermask  - Fiber status bits, set nonzero for bad status [NFIBER]
   pixelmask  - Mask of 0 for good pixels [NPIX,NFIBER]
   relchi2struct  - Structure containing information of chi^2 fitting

 PARAMETERS FOR SLATEC_SPLINEFIT (for supersky fit):
   nord       -
   upper      -
   lower      -
   maxiter    -

 OUTPUTS:
   skystruct  - structure containing sorted sky wavelengths,flux,fluxivar
                      +  bkpts and coeffs from fitting
   objsub     - Image (OBJ) after sky-subtraction
   objsubivar - Inverse variance (OBJIVAR) after sky-subtraction

 OPTIONAL OUTPUTS:
   iskies=    - array of good sky fibers

 COMMENTS:
   Construct a "supersky" spectrum by spline-fitting the (good)
sky fibers,
   resampling this at every wavelength in the extracted image, then
   subtracting.  We then measure the variance of the sky-subtracted sky
   fibers in terms of chi^2.  Wherever chi^2  1, we increase the variance
   of all fibers such that chi^2=1 in the sky fibers.

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:
   djs_iterstat
   djs_oplot
   djs_oploterr
   djs_plot
   pixelmask_bits()
   slatec_splinefit()
   slatec_bvalue()

 REVISION HISTORY:
   16-Sep-1999  Written by S. Burles, APO
   30-Dec-1999  Modified by D. Schlegel, Princeton

(See pro/spec2d//skysubtract.pro)


SORTPLUGMAP

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 NAME:
   sortplugmap

 PURPOSE:
   Cull the nTrace plugmap entries which match the fibers in the
     current image

 CALLING SEQUENCE:
  plugsort = sortplugmap(plugmap, spectrographid, fibermask, nFibers=nFibers)

 INPUTS:
   plugmap         - The full Plug map structure read in from plPlugMapM
   spectrographid  - The spectrograph number

 OPTIONAL KEYWORDS:
   nFiebrs         - number of fibers to locate (default 320)

 OUTPUTS:
   plugsort        - culled plugmap structure matching current traces

 OPTIONAL OUTPUTS:
   fibermask       - returns an array of byte with bits set for unknown
fibers

 COMMENTS:

 EXAMPLES:

 PROCEDURES CALLED:
   fibermask_bits()

 REVISION HISTORY:
   19-Oct-1999  Written by S. Burles, Chicago

(See pro/spec2d//sortplugmap.pro)


SPALLFLAT

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 NAME:
   spallflat

 PURPOSE:
   Calling script for SPFLATTEN that generates pixel flats as specified in
   a plan file.

 CALLING SEQUENCE:
   spallflat, planfile=planfile

 INPUTS:

 OPTIONAL INPUTS:
   planfile   - Name of output plan file; default to 'spPlanFlat.par'

 OUTPUT:

 COMMENTS:

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:
   spflatten
   yanny_read

 INTERNAL SUPPORT ROUTINES:

 REVISION HISTORY:
   02-Nov-1999  Written by David Schlegel, Princeton.

(See pro/spec2d//spallflat.pro)


SPALLREDUCE

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 NAME:
   spallreduce

 PURPOSE:
   Calling script for SPREDUCE and COMBINE2DOUT that reduces a night
   of data according to a plan file.

 CALLING SEQUENCE:
   spallreduce, [ planfile, docams=, /nocombine, /xdisplay ]

 INPUTS:

 OPTIONAL INPUTS:
   planfile   - Name(s) of output plan file; default to reducing all
                plan files matching 'spPlan2d*.par'
   docams     - Cameras to reduce; default to ['b1', 'b2', 'r1', 'r2'];
                set to 0 or '' to disable running SPREDUCE and to only
                combine files.
   nocombine  - Only run SPREDUCE, not COMBINE2DOUT.
   xdisplay   - Send plots to X display rather than to plot file

 OUTPUT:

 COMMENTS:

 EXAMPLES:

 BUGS:
   Try to avoid using SPAWN.
   How do I just combine files? and not re-run spreduce?

   What happens when the gain has changed?
   We need to list opECalib.par in spPlan file.
   Use default opECalib if not found...

 PROCEDURES CALLED:
   combine2dout
   idlspec2d_version()
   idlutils_version()
   splog
   spreduce
   yanny_free
   yanny_read

 INTERNAL SUPPORT ROUTINES:

 REVISION HISTORY:
   02-Nov-1999  Written by David Schlegel, Princeton.

(See pro/spec2d//spallreduce.pro)


SPCALIB

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 NAME:
   spcalib

 PURPOSE:
   Extract calibration frames.

 CALLING SEQUENCE:
   spcalib, flatname, arcname, [pixflatname=, fibermask=, $
    lampfile=, indir=, timesep=, ecalibfile=, plottitle=, $
    arcinfoname=, flatinfoname=, arcstruct=, flatstruct=]

 INPUTS:
   flatname   - Name(s) of flat-field SDSS image(s)
   arcname    - Name(s) of arc SDSS image(s)

 OPTIONAL KEYWORDS:
   pixflatname- Name of pixel-to-pixel flat, produced with SPFLATTEN.
   fibermask  - Fiber status bits, set nonzero for bad status [NFIBER].
                Note this is not modified, but modified copies appear
                in the returned structures ARCSTRUCT and FLATSTRUCT.
   lampfile   - Name of file describing arc lamp lines;
                default to the file 'lamphgcdne.dat' in the IDL path.
   indir      - Input directory for FLATNAME, ARCNAME, OBJNAME;
                default to '.'
   timesep    - Maximum time separation between flats and arcs to pair them;
                set to zero to disable this test; default to 7200 sec.
   ecalibfile - opECalib file to pass to SDSSPROC
   plottitle  - Prefix for titles in QA plots.
   arcinfoname- File name (with path) to output arc extraction and fitting
                information
   flatinfoname-File name (with path) to output flat field extraction and
                fitting information

 OUTPUTS:
   arcstruct  - Structure array with extracted arc calibration information
   flatstruct - Structure array with extracted flat calibration information

 OPTIONAL OUTPUTS:

 COMMENTS:
   Always pair arcs to the nearest good flat, and flats to the nearest good
   arc (nearest in time, as defined by the TAI keyword in the FITS headers).

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:
   extract_image
   fiberflat()
   fitarcimage
   fitarcimage_old
   sdssproc
   shift_trace()
   splog
   trace320crude()
   traceset2xy
   xy2traceset

 INTERNAL SUPPORT ROUTINES:
   create_arcstruct()
   create_flatstruct()

 REVISION HISTORY:
   24-Jan-2000  Written by D. Schlegel, Princeton

(See pro/spec2d//spcalib.pro)


SPFLATTEN

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 NAME:
   spflatten

 PURPOSE:
   Create pixel-to-pixel flat-field from a stack of SDSS spectral flats.

 CALLING SEQUENCE:
   spflatten, flatname, [ pixflat, sigrej=, maxiter=, $
    outfile=, indir=, outdir=, tmpdir=, $
    bkspace=, nord=, lower=, upper= ]

 INPUTS:
   flatname   - Name(s) of raw SDSS flat-field image(s).
                Note that many flats from many nights can be combined.

 OPTIONAL INPUTS:
   sigrej     - Sigma rejection level; default to 1, 1, 1.1, 1.3, 1.6 or 1.9
                for 1,2,3,4,5 or 6 flats.  For more then 6 flats, default
                to 2.0.
   maxiter    - Number of rejection iterations; default to 2.
   outfile    - Write the image PIXFLAT to this file.
   indir      - Input directory for FLATNAME; default to './'
   outdir     - Output directory for OUTFILE; default to './'
   tmpdir     - Directory for temporary files; default to same as OUTDIR

 PARAMETERS FOR SLATEC_SPLINEFIT:
   bkspace
   nord
   lower
   upper

 OUTPUTS:

 OPTIONAL OUTPUTS:
   pixflat    - Image containing all the information about pixel-to-pixel
                variations.  Illumination variations are removed.

 COMMENTS:
   This program writes 2*nflat temporary files to disk to save internal
memory.
   But it still creates an two arrays (FLATARR (float) and OUTMASK (byte))
   that is as large as all of the input flats.
   Thus, if you are using ten 16 MB flat images,
   that array will be 10*(16+4)=200 MB (in addition to a few other images).

 EXAMPLES:

 BUGS:
   Not sure what to do if exactly 2 frames are passed.

 PROCEDURES CALLED:
   djs_avsigclip()
   extract_image
   readfits()
   slatec_bvalu()
   slatec_splinefit()
   sdssproc
   writefits

 REVISION HISTORY:
   13-Oct-1999  Written by D. Schlegel, APO

(See pro/spec2d//spflatten.pro)


SPFLATTEN2

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 NAME:
   spflatten2

 PURPOSE:
   Create pixel-to-pixel flat-field from a stack of SDSS spectral flats.

 CALLING SEQUENCE:
   spflatten2, flatname, arcname, allflats, [ pixflat, sigrej=, maxiter=, $
    oldflat=, outfile=, indir=, outdir=, tmpdir=, $
    pixspace=, nord=, lower=, upper= ]

 INPUTS:
   flatname   - Name of flat image for tracing arc
   arcname    - Name of arc image
   allflats   - Name(s) of raw SDSS flat-field image(s).
                Note that many flats from many nights can be combined.

 OPTIONAL INPUTS:
   sigrej     - Sigma rejection level; default to 1, 1, 1.1, 1.3, 1.6 or 1.9
                for 1,2,3,4,5 or 6 flats.  For more then 6 flats, default
                to 2.0.
   maxiter    - Number of rejection iterations; default to 2.
   oldflat    - Name of old flat-field from which to select pixels to mask;
                if not set, then read the masks in this source distribution.
   outfile    - Write the image PIXFLAT to this file.
   indir      - Input directory for FLATNAME; default to './'
   outdir     - Output directory for OUTFILE; default to './'
   tmpdir     - Directory for temporary files; default to same as OUTDIR
   pixspace   - Approximate spacing in pixels for break points in the
                spline fits to individual fibers; default to 50 pixels.
                Note that this spacing need be small enough to fit out
                the flux variations of multiple fibers crossing a single
                column, but it need not fit out the actual flat-field
                variations.

 PARAMETERS FOR SLATEC_SPLINEFIT:
   nord       - Default to 4
   lower      - Default to 2
   upper      - Default to 2

 OUTPUTS:

 OPTIONAL OUTPUTS:
   pixflat    - Image containing all the information about pixel-to-pixel
                variations.  Illumination variations are removed.

 COMMENTS:
   This program writes 2*nflat temporary files to disk to save internal
memory.
   But it still creates an two arrays (FLATARR (float) and OUTMASK (byte))
   that is as large as all of the input flats.
   Thus, if you are using ten 16 MB flat images,
   that array will be 10*(16+4)=200 MB (in addition to a few other images).

 EXAMPLES:

 BUGS:
   Not sure what to do if exactly 2 frames are passed.
   Pass UPPER and LOWER.
   Look for bad fibers or outlier fibers to exclude from superflat.
   Right now, we can get bad spline fits across the large hole in the
     b1 flat-field if the break points fall too close to the edges of
     that hole.  Try to keep more data points between the last break point
     and the beginning of the hole, or do a linear interpolation across
     the hole.

 PROCEDURES CALLED:
   djs_avsigclip()
   extract_image
   genflatmask()
   readfits()
   slatec_bvalu()
   slatec_splinefit()
   sdssproc
   superflat
   trace320crude()
   traceset2xy
   writefits
   xy2traceset

 REVISION HISTORY:
   13-Oct-1999  Written by D. Schlegel, APO

(See pro/spec2d//spflatten2.pro)


SPGAIN

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 NAME:
   spgain

 PURPOSE:
   Measure the gain + read noise for SDSS spectroscopic images

 CALLING SEQUENCE:
   spgain, flatfile1, flatfile2, [ biasfile1, biasfile2, indir=indir, $
    xskip=xskip, yave=yave, gain=gain, rnoise=rnoise ]

 INPUTS:
   flatfile1  - File name for flat #1
   flatfile2  - File name for flat #2
   biasfile1  - File name for bias #1
   biasfile2  - File name for bias #2

 OPTIONAL KEYWORDS:
   indir      - Input directory for all files
   xskip      - Number of columns to ignore at beginning and end of each
                amplifier; default to 50
   yave       - Number of rows to analyze for each calculation of gain and
                read noise; default to 15

 OUTPUTS:
   gain       - Gain in electrons/ADU for each amplifier (array)
   rnoise     - Read noise in electrons for each amplifier (array)

 COMMENTS:

 BUGS:;

 PROCEDURES CALLED:
   djs_iterstat
   sdssproc

 REVISION HISTORY:
   21-Nov-1999  Written by D. Schlegel, Princeton.

(See pro/spec2d//spgain.pro)


SPLOG

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 NAME:
   splog

 PURPOSE:
   Logging routine for spectroscopic pipeline.

 CALLING SEQUENCE:
   splog, v1, v2 ..., [, _EXTRA=extra, /noname, prelog=, filename=, $
    /append, /close ]

 INPUTS:
   v1, v2 ... - The expressions to be passed to PRINT or PRINTF

 OPTIONAL KEYWORDS:
   _EXTRA     - Any keywords for PRINT or PRINTF, such as FORMAT
   noname     - If set, then suppress printing name of calling routine
   prelog     - If set, then print this string immediately after the
                name of the calling routine on each line, i.e. 'b1'
   filename   - If specified, then open this file for text output
   append     - If set at the same time as FILENAME, then append to this
file;
                default is to overwrite file
   close      - If set, then close the output file

 OUTPUTS:

 OPTIONAL OUTPUTS:

 COMMENTS:

 EXAMPLES:
   Open a file for text output, write to it, then close it:
     splog, filename='test.log'
     splog, 'This is a test', 123.4, format='(a,f8.2)'
     splog, /close
   Alternatively, this can all be done on one line
     splog, filename='test.log', /close, $
      'This is a test', 123.4, format='(a,f8.2)'

 BUGS:

 PROCEDURES CALLED:

 REVISION HISTORY:
   17-Nov-1999  Written by D. Schlegel, Princeton

(See pro/spec2d//splog.pro)


SPPLAN

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 NAME:
   spplan

 PURPOSE:
   Create plan file(s) for running the Spectro-2D pipeline.

 CALLING SEQUENCE:
   spplan, [ rawdir, astrolog=, mjd=, flatdir=, minexp= ]

 INPUTS:

 OPTIONAL INPUTS:
   rawdir     - Search for raw data files in RAWDIR/MJD/*.
                This should be an absolute file path, and we default to
                '/usr/sdss/data05/spectro/rawdata'.
   astrolog   - Search for plug-map files in PLUGDIR/MJD/*.
                This should be an absolute file path, and we default to
                '/usr/sdss/data05/spectro/astrolog'.
   mjd        - Look for raw data files in RAWDIR/MJD; default to '*' to
                search all subdirectories.  Note that this need not be
                integer-valued, but could be for example '51441_test'.
   flatdir    - Directory for pixel flat files.  For now, default
                to 'pixflat'.
   minexp     - Minimum exposure time for science frames; default to 300 sec.

 OUTPUT:

 COMMENTS:
   Look for the input files in:
     RAWDIR/MJD/sdR-cs-eeeeeeee.fit          - Raw frames, c=color, s=spec #
     RAWDIR/MJD/plPlugMapM-pppp-mmmmm-aa.par - Plug map files, aa=mapper

   The top-level of the output directory structure, TOPDIR, is 2d_VERSION,
   where we read the version with IDLSPEC2d_VERSION().  If this is not a CVS-
   declared version of the code, then the output directory is '2d_test'.
   The files created are:
     TOPDIR/PLATE/spPlan2d-mmmmm-pppp.par    - 2D plan file (could be
several)

   If an output plan file already exists, this procedure will crash rather
   than overwrite that file.

   Note we assume Unix directory names and we SPAWN the Unix 'ls' command.

 EXAMPLES:
   Create the plan file(s) for reducing the data for MJD=51441, with that
   raw data in the directory '/u/schlegel/rawdata/51441'
     spplan, '/u/schlegel/rawdata', mjd=51441

 BUGS:

 PROCEDURES CALLED:
   headfits()
   idlspec2d_version()
   splog
   sxpar()
   yanny_read
   yanny_write

 INTERNAL SUPPORT ROUTINES:
   spplan_create_exp
   spplan_create_plug
   spplan_create_pixflats

 REVISION HISTORY:
   02-Nov-1999  Written by David Schlegel, Princeton.
   10-Nov-1999  SMB added checkstats to verify flavors.
   18-Jan-2000  Re-written to conform to new file names + directory
structure.
                Not using CHECKSTATS any more at the moment.

(See pro/spec2d//spplan.pro)


SPREDUCE

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 NAME:
   spreduce

 PURPOSE:
   Extract, wavelength-calibrate, and flatten SDSS spectral frame(s).

 CALLING SEQUENCE:
   spreduce, flatname, arcname, objname, pixflatname=pixflatname, $
    plugfile=plugfile, lampfile=lampfile, $
    indir=indir, plugdir=plugdir, outdir=outdir, $
    ecalibfile=ecalibfile, plottitle=plottitle, summarystruct=summarystruct

 INPUTS:
   flatname   - Name(s) of flat-field SDSS image(s)
   arcname    - Name(s) of arc SDSS image(s)
   objname    - Name(s) of object SDSS image(s)

 REQUIRED KEYWORDS:
   plugfile   - Name of plugmap file (Yanny parameter file)

 OPTIONAL KEYWORDS:
   pixflatname- Name of pixel-to-pixel flat, produced with SPFLATTEN.
   lampfile   - Name of file describing arc lamp lines;
                default to the file 'lamphgcdne.dat' in the IDL path.
   indir      - Input directory for FLATNAME, ARCNAME, OBJNAME;
                default to '.'
   plugdir    - Input directory for PLUGFILE; default to '.'
   outdir     - Directory for output files; default to '.'
   ecalibfile - opECalib.par file for SDSSPROC
   plottitle  - Prefix for titles in QA plots.
   summarystruct - Good intentions ???

 OUTPUTS:

 OPTIONAL OUTPUTS:

 COMMENTS:

 EXAMPLES:

 BUGS:
   Should test that arcs and flats are valid images with CHECKFLAVOR.

 PROCEDURES CALLED:
   extract_object
   qaplot_arcline
   qaplot_fflat
   select_arc()
   select_flat()
   sortplugmap
   sdssproc
   spcalib
   splog
   yanny_free
   yanny_read

 REVISION HISTORY:
   12-Oct-1999  Written by D. Schlegel & S. Burles, APO

(See pro/spec2d//spreduce.pro)


SSHIFT

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 NAME:
       sshift
 PURPOSE: (one line)
       Shift data using a damped sinc function for fractional part.
 DESCRIPTION:

       This function will shift an array of data pointed to by x and
       extending for n points.  The amount of the shift is given by shift.
       The result of the operation is placed at xp.  A shift that is within
       0.0001 of a whole number is treated to be that of the whole number.  If
       the shift is by an integral number of pixels then the shift involves
       reindexing the data, no interpolation is done.  If the shift is some
       non-integral amount then the data is resampled using a damped sinc
       function.

       The sense of the shift is as follows: think of the array plotted on a
       fixed scale.  A shift of 1 corresponds to shifting the data by one data
       point to the right relative to the fixed scale, ie. x[3]=xp[4].

       The data will fall off one end or another of the output vector as a
       result of the shift.  However, this is not as significant as the edge
       effect, the convolution is not complete for any data point within 10
       points of the edge, so those points cannot be trusted.  The missing
       points in the convolution are assumed to be equal to the end points.

 CATEGORY:
       Numerical
 CALLING SEQUENCE:
       xp = sshift(x,shift)
 INPUTS:
       x     - Input data array to be shifted.
       shift - Amount to shift (negative to left).
 OPTIONAL INPUT PARAMETERS:
 KEYWORD PARAMETERS:
 OUTPUTS:
       Return value is the shifted array.
 COMMON BLOCKS:
 SIDE EFFECTS:
 RESTRICTIONS:
       The input and output arrays cannot be the same.
 PROCEDURE:
 MODIFICATION HISTORY:
       Adapted from Zodiac routine: shiftc/sshift
         Marc W. Buie, Lowell Observatory, 1992 October 2

(See pro/spec2d//sshift.pro)


SSHIFT2D

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 NAME:
    sshift2d
 PURPOSE: (one line)
    Shift a 2-D array using a damped sinc function for the fractional part.
 DESCRIPTION:

 CATEGORY:
    Mathematical
 CALLING SEQUENCE:
    result = sshift2d( array, shiftvec )
 INPUTS:
    array    : Array to be shifted.
    shiftvec : Vector of two elements: [ xshift, yshift ].
 OPTIONAL INPUT PARAMETERS:

 KEYWORD PARAMETERS:

 OUTPUTS:
    The shifted array is returned as the function value.
 COMMON BLOCKS:

 SIDE EFFECTS:

 RESTRICTIONS:

 PROCEDURE:

 MODIFICATION HISTORY:
    February, 1993:
    Copied from "sincshift.pro" written by John Spencer, Lowell
Observatory.
    Very minor modifications by Doug Loucks, Lowell Observatory.

(See pro/spec2d//sshift2d.pro)


SSHIFTVEC

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 NAME:
   sshiftvec

 PURPOSE:
   Shift vector or image (line-at-a-time) using a damped sinc function.

 CALLING SEQUENCE:
   simage = sshiftvec( fimage, shift, [ sincrad=sincrad, dampfac=dampfac, $
    eps=eps ] )

 INPUTS:
   fimage     - Input vector (1D) or image (2D)
   shift      - Distance to shift

 OPTIONAL KEYWORDS:
   sincrad    - Half-width of sinc convolution kernal; default to 10 pixels
   dampfac    - Damping factor for gaussian; default to 3.25
   eps        - Smallest fractional shift allowed; default to 1.0e-5

 OUTPUTS:
   simage     - Shifted image

 OPTIONAL OUTPUTS:

 COMMENTS:
   This routine is based upon the IDL routine SSHIFT from Marc Buie,
   which in turn is based upon the Zodiac routine shiftc/sshift.

 EXAMPLES:

 PROCEDURES CALLED:
   Dynamic link to sshiftvec.c

 REVISION HISTORY:
   14-Apr-1999  Written by David Schlegel, Princeton.

(See pro/spec2d//sshiftvec.pro)


SUPERFLAT

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 NAME:
   superflat

 PURPOSE:
   Create a "superflat" from an extracted flat-field image

 CALLING SEQUENCE:
   superflat, flux, fluxivar, wset, fullbkpt, coeff, $
    [ fibermask=, minval=, lower=, upper=, medval=, title= ]

 INPUTS:
   flux       - Array of extracted flux from a flat-field image [Nrow,Ntrace]
   fluxivar   - Inverse variance map for FLUX.
   wset       - Wavelength solution

 OPTIONAL KEYWORDS:
   fibermask  - Fiber status bits, set nonzero for bad status [NFIBER]
   minval     - Minimum value to use in fits to flat-field vectors;
                default to 0.
   title      - TITLE of plot

 PARAMETERS FOR SLATEC_SPLINEFIT:
   lower      -
   upper      -

 OUTPUTS:
   fullbkpt   - Breakpoints describing spline fit to superflat
   coeff      - Coefficients describing spline fit to superflat

 OPTIONAL OUTPUTS:
   medval     - Median value of each fiber [NFIBER]
   fibermask  - (Modified)

 COMMENTS:

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:
   djs_maskinterp()
   djs_mean()
   djs_oplot
   djs_plot
   slatec_bvalu()
   slatec_splinefit()
   traceset2xy

 REVISION HISTORY:
   02-Jan-2000  Excised code from SPFLATTEN2 (DJS).

(See pro/spec2d//superflat.pro)


TELLURIC_CORR

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 NAME:
   telluric_corr

 PURPOSE:
   Use SPECTROPHOTO and REDDEN_STD's to fit telluric features
   between wavelengths 10^minw and 10^maxw

 CALLING SEQUENCE:
   telluric_factor = telluric_corr(flux, fluxivar, wset, plugsort, $
       contwave=contwave, contflux=contflux, contivar=contivar,    $
       telluricbkpt=telluricbkpt, telluriccoeff=telluriccoeff, $
       minw=minw, maxw=maxw, lower=lower, upper=upper, $
       ncontbkpts = ncontbkpts, fibermask=fibermask)

 INPUTS:
   flux         - sky-subtracted extracted spectra [nx,ntrace]
   fluxivar     - corresponding inverse variance [nx,ntrace]
   wset         - wavelength coefficients as a trace set
   plugsort     - plugmap entries

 OPTIONAL KEYWORDS:
   minw         - minimum wavelength to fit (Default 3.82)
   maxw         - maximum wavelength to fit (Default 3.92)
   ncontbkpts   - Number of bkpts to fit continuum in telluric region (5)
   lower        - lower rejection threshold for telluric fitting
   upper        - upper rejection threshold for telluric fitting
   fibermask    - use to reject possible standards which have spectral
troubles
   
 OUTPUTS:
   telluric_factor - Telluric correction for each pixel in flux array

 OPTIONAL OUTPUTS:
   contflux     - Normalized flux of stars used in telluric fitting
   contivar     - Corresponding inverse variance
   contwave     - Corresponding wavelengths  (log lambda)
   telluricbkpt - bkpts used in telluric absorption fit
   telluriccoeff- best fit b-spline coefficients for telluric absorption

 COMMENTS:

 EXAMPLES:

 BUGS:
   There is still some low order residual from flux correction
     (I think due to telluric absorption), which is in turned
   removed by the telluric_correction.  Although there is not
   a clean break between the two steps, used together they seem
   to correct the spectra properly

 PROCEDURES CALLED:

 REVISION HISTORY:
   19-Oct-1999  Written by S. Burles, Chicago

(See pro/spec2d//telluric_corr.pro)


TRACE320CEN

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 NAME:
   trace320cen

 PURPOSE:
   Find the 320 fiber positions for the central row of an image.

 CALLING SEQUENCE:
   xfiber = trace320cen( fimage, [mthresh=, ystart=, nmed=, xgood= ] )

 INPUTS:
   fimage     - Image

 OPTIONAL INPUTS:
   mthresh    - Threshold for peak-finding in convolved row; default to 0.5
                times the dispersion (found with djs_iterstat).
   ystart     - Y position in image to search for initial X centers; default
                to the central row
   nmed       - Number of rows to median filter around YSTART; default to 21

 OUTPUTS:
   xfiber     - Vector of 320 X centers

 OPTIONAL OUTPUTS:
   xgood      - Set to 1 for fibers that were actually found, 0 otherwise

 COMMENTS:

 EXAMPLES:

 PROCEDURES CALLED:
   djs_iterstat

 REVISION HISTORY:
   13-Sep-1999  Written by David Schlegel, Princeton.

(See pro/spec2d//trace320cen.pro)


TRACE320CRUDE

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 NAME:
   trace320crude

 PURPOSE:
   Calling script to return 320 full traces using TRACE_CRUDE.

 CALLING SEQUENCE:
   xset = trace320crude( fimage, invvar, [mthresh=, ystart=, nmed=, $
    xmask=, yset=, maxerr=, maxshifte=, maxshift0=, xerr=, maxdev=, ngrow=, $
    fibermask=  ] )

 INPUTS:
   fimage     - Image

 OPTIONAL INPUTS FOR TRACE320CEN:
   mthresh    - Threshold for peak-finding in convolved row; default to 0.5
                times the dispersion (found with djs_iterstat).
   ystart     - Y position in image to search for initial X centers; default
                to the central row
   nmed       - Number of rows to median filter around YSTART; default to 21

 OPTIONAL INPUTS FOR TRACE_CRUDE:
   invvar     - Inverse variance (weight) image
   radius     - Radius for centroiding; default to 3.0
   maxerr     - Maximum error in centroid allowed for valid recentering;
                default to 0.2
   maxshifte  - Maximum shift in centroid allowed for valid recentering;
                default to 0.1
   maxshift0  - Maximum shift in centroid allowed for initial row;
                default to 0.5

 OPTIONAL INPUTS:
   maxdev     - Maximum deviation of X in pixels; default to rejecting any
                XPOS positions that deviate by more than 1.0 pixels from
                a polynomial remapping of the centroids from other rows.
   ngrow      - For each trace, replace all centroids within NGROW rows
                of a bad centroid with the predicted centroid locations.
                Default to 5.
   fibermask  - Fiber status bits, set nonzero for bad status [NFIBER]

 OUTPUTS:
   xset       - X centers for all traces

 OPTIONAL OUTPUTS:
   yset       - Y centers for all traces
   xerr       - Errors for XSET
   xmask      - Mask set to 1 for good fiber centers, 0 for bad;
                same dimensions as XSET.
   fibermask  - (Modified.)

 COMMENTS:

 EXAMPLES:

 PROCEDURES CALLED:
   fibermask_bits()
   trace_crude()
   trace_fweight()
   trace320cen()

 REVISION HISTORY:
   13-Sep-1999  Written by David Schlegel, Princeton.

(See pro/spec2d//trace320crude.pro)


TRACESET2PIX

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 NAME:
   traceset2pix

 PURPOSE:
   Use a traceset to find the pixel numbers corresponding to a certain
postion

 CALLING SEQUENCE:
   pixpos = traceset2pix(tset, lambda, [nicoeff=nicoeff] )

 INPUTS:
   tset       - Structure containing trace set
   lambda     - Wavelengths at which to find X pixel position

 OPTIONAL KEYWORDS:
   nicoeff    - Number of coefficients to use in inversion; default to using
                2 more coefficients than for the forward trace set
                (e.g., TSET.NCOEFF+2)

 OUTPUTS:
   pixpos     - Pixel positions corresponding to LAMBDA as
                an [Nlambda,Ntrace] array

 OPTIONAL OUTPUTS:

 COMMENTS:

 EXAMPLES:

 BUGS:

 PROCEDURES CALLED:
   djs_laxisgen()
   flegendre()
   traceset2xy
   xy2traceset

 REVISION HISTORY:
   09-Nov-1999  Written by David Schlegel, Ringberg.

(See pro/spec2d//traceset2pix.pro)


TRACESET2XY

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 NAME:
   traceset2xy

 PURPOSE:
   Convert from a trace set to an array of x,y positions

 CALLING SEQUENCE:
   traceset2xy, tset, xpos, ypos

 INPUTS:
   tset       - Structure containing trace set

 OPTIONAL KEYWORDS:

 OUTPUTS:
   xpos       - X positions corresponding to YPOS as an [nx,Ntrace] array
   ypos       - Y centers as an [nx,nTrace] array

 OPTIONAL OUTPUTS:

 COMMENTS:

 EXAMPLES:

 PROCEDURES CALLED:
   djs_laxisgen()
   flegendre()

 REVISION HISTORY:
   19-May-1999  Written by David Schlegel, Princeton.

(See pro/spec2d//traceset2xy.pro)


TRACE_CRUDE

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 NAME:
   trace_crude

 PURPOSE:
   Create a crude trace set given one position (eg, a center) in each trace.

 CALLING SEQUENCE:
   xset = trace_crude( fimage, invvar, [xstart=, ystart=, radius=, yset=, $
    nave=, nmed=, thresh=, maxerr=, maxshifte=, maxshift0=, xerr= ] )

 INPUTS:
   fimage     - Image

 OPTIONAL INPUTS:
   invvar     - Inverse variance (weight) image
   xstart     - Initial guesses for X centers (one for each trace).
                If not set, then this code searches for all peaks at YSTART.
   ystart     - Y positions corresponding to "xstart" (expected
as integers).
                There are three options for this parameter:
                (1) One element of YSTART for each value of XSTART,
                (2) A scalar value that is used for every XSTART, or
                (3) Not set, in which case the center row is used.
   radius     - Radius for centroiding; default to 3.0
   nmed       - Median filtering size down columns before performing trace;
                default to 1
   nave       - Averaging size down columns before performing trace;
                default to 5
   thresh     - Threshold for initial peak finding; if not set, then use
                1.0 times the median of the row(s) used for the initial
peaks.
   maxerr     - Maximum error in centroid allowed for valid recentering;
                default to 0.2
   maxshifte  - Maximum shift in centroid allowed for valid recentering;
                default to 0.1
   maxshift0  - Maximum shift in centroid allowed for initial row;
                default to 0.5

 OUTPUTS:
   xset       - X centers for all traces

 OPTIONAL OUTPUTS:
   yset       - Y centers for all traces
   xerr       - Errors for XSET

 COMMENTS:

 EXAMPLES:

 PROCEDURES CALLED:
   djs_laxisgen()

   Dynamic link to trace_crude.c

 REVISION HISTORY:
   14-May-1999  Written by David Schlegel, Princeton.
   12-Jul-1999  Added optional output YSET (DJS).
   06-Aug-1999  Added optional outpust XERR (DJS).

(See pro/spec2d//trace_crude.pro)


TRACE_FIX

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 NAME:
   trace_fix

 PURPOSE:
   Fix a set of trace centers by replacing traces that converge.

 CALLING SEQUENCE:
   xnew = trace_fix( xcen, [minsep= , ngrow=, ycen=, xerr=])

 INPUTS:
   xcen       - X centers for all traces [ny,nTrace]

 OPTIONAL INPUTS:
   minsep     - Minimum separation between adjacent traces.  Smaller
                separations are regarded as bad traces.  Default to 5.5.
   ngrow      - Replace all pixels within MINSEP of its adjacent trace,
                plus NGROW of its neighboring pixels.  Default to 20.
   ycen       - Y centers corresponding to XCEN.
   xerr       - X errors corresponding to XCEN.

 OUTPUTS:
   xnew       - Modified XCEN; traces may be removed or shifted.
   ycen       - Modified YCEN; columns may be removed.
   xerr       - Modified XERR; columns may be removed.

 COMMENTS:

 EXAMPLES:

 PROCEDURES CALLED:

 INTERNAL PROCEDURES:
   remove_column

 REVISION HISTORY:
   13-Aug-1999  Written by David Schlegel, Princeton.

(See pro/spec2d//trace_fix.pro)


TRACE_FWEIGHT

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 NAME:
   trace_fweight

 PURPOSE:
   Recenter a trace using flux-weighting centers.

 CALLING SEQUENCE:
   xnew = trace_fweight( fimage, xcen, ycen, [radius=radius, xerr=xerr, 
    invvar=invvar] )

 INPUTS:
   fimage     - Image
   xcen       - Initial guesses for X centers
   ycen       - Y positions corresponding to "xcen" (expected as
integers)

 OPTIONAL KEYWORDS:
   radius     - Radius for centroiding; default to 3.0
   invvar     - Inverse variance of image used only in computing errors XERR.
                If not set, then INVVAR=1 is used.

 OUTPUTS:
   xnew       - New X centers

 OPTIONAL OUTPUTS:
   xerr       - Formal errors for XNEW; set equal to 999.0 if there are any
                masked pixels in a centroiding region (e.g., if INVVAR=0)

 COMMENTS:

 EXAMPLES:

 PROCEDURES CALLED:
   Dynamic link to trace_fweight.c

 REVISION HISTORY:
   24-Mar-1999  Written by David Schlegel, Princeton.

(See pro/spec2d//trace_fweight.pro)


TRACE_GWEIGHT

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 NAME:
   trace_gweight

 PURPOSE:
   Recenter a trace using gaussian-weighted centers.

 CALLING SEQUENCE:
   xnew = trace_fweight( fimage, xcen, ycen, [sigma=sigma, xerr=xerr, 
    invvar=invvar] )

 INPUTS:
   fimage     - Image
   xcen       - Initial guesses for X centers
   ycen       - Y positions corresponding to "xcen" (expected as
integers)

 OPTIONAL KEYWORDS:
   radius     - Sigma in pixels; default to 1.0
   invvar     - Inverse variance of image used only in computing errors XERR.
                If not set, then INVVAR=1 is used.

 OUTPUTS:
   xnew       - New X centers

 OPTIONAL OUTPUTS:
   xerr       - Formal errors for XNEW; set equal to 999.0 if there are any
                masked pixels in a centroiding region (e.g., if INVVAR=0)

 COMMENTS:

 EXAMPLES:

 REVISION HISTORY:
   17-Jan-2000  Written by Scott Burles, Chicago

(See pro/spec2d//trace_gweight.pro)


TWEAKTRACE

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 NAME:
   tweaktrace

 PURPOSE:
   Use fitans to tweak trace and sigma
   This just perturbs the input values of xcen and sigma

 CALLING SEQUENCE:
   tweaktrace, x, sigma, centershift, sigmashift, maxshift=maxshift

 INPUTS:
   x            - the input trace positions
   sigma        - the input sigma widths of profiles
   centershift  - the pixel shift in x
   sigmashift   - the fractional change of sigma

 OPTIONAL KEYWORDS:
   maxshift     - the absolute allowed shift in x (default = 1.0)

 OUTPUTS:

 OPTIONAL OUTPUTS:

 COMMENTS:

 EXAMPLES:

 PROCEDURES CALLED:

 REVISION HISTORY:
   19-Oct-1999  Written by S. Burles, Chicago

(See pro/spec2d//tweaktrace.pro)


USHIFT

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 NAME:
       ushift
 PURPOSE: (one line)
       Shift data using a damped sinc onto slightly non-linear x values
       
 DESCRIPTION:

       This function will shift an array of data pointed to by x and
       extending for n points.  The amount of the shift is given by shift.
       The result of the operation is placed at xp.  A shift that is within
       0.0001 of a whole number is treated to be that of the whole number.  If
       the shift is by an integral number of pixels then the shift involves
       reindexing the data, no interpolation is done.  If the shift is some
       non-integral amount then the data is resampled using a damped sinc
       function.

       The sense of the shift is as follows: think of the array plotted on a
       fixed scale.  A shift of 1 corresponds to shifting the data by one data
       point to the right relative to the fixed scale, ie. x[3]=xp[4].

       The data will fall off one end or another of the output vector as a
       result of the shift.  However, this is not as significant as the edge
       effect, the convolution is not complete for any data point within 10
       points of the edge, so those points cannot be trusted.  The missing
       points in the convolution are assumed to be equal to the end points.

 CATEGORY:
       Numerical
 CALLING SEQUENCE:
       yp = ushift(y, invset, xp)
 INPUTS:
       y     - Input data array to be shifted.
       invset - Structure which contains coefficients to map xin to pixels
       xin    - The x-axis values for the requested yp
 OPTIONAL INPUT PARAMETERS:
 KEYWORD PARAMETERS:
 OUTPUTS:
       Return value is the shifted array.
 COMMON BLOCKS:
 SIDE EFFECTS:
 RESTRICTIONS:
       The input and output arrays cannot be the same.
 PROCEDURE:
 MODIFICATION HISTORY:
       Adapted from Zodiac routine: shiftc/sshift
         Marc W. Buie, Lowell Observatory, 1992 October 2

(See pro/spec2d//ushift.pro)


XY2TRACESET

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 NAME:
   xy2traceset

 PURPOSE:
   Convert from an array of x,y positions to a trace set

 CALLING SEQUENCE:
   xy2traceset, xpos, ypos, tset, [ func=func, ncoeff=ncoeff, $
    xmin=xmin, xmax=xmax, maxdev=maxdev, maxsig=maxsig, maxiter=maxiter, $
    singlerej=singlerej, xmask=xmask, yfit=yfit, inputans=inputans, $
    invvar=invvar, _EXTRA=KeywordsForFuncFit ]

 INPUTS:
   xpos       - X positions corresponding to YPOS as an [nx,Ntrace] array
   ypos       - Y centers as an [nx,ntrace] array

 OPTIONAL KEYWORDS:
   func       - Function for trace set; options are:
                'legendre'
                'chebyshev'
                Default to 'legendre'
   ncoeff     - Number of coefficients in fit; default to 3
   ncoeff     - Inverse variance for weighted func_fit
   xmin       - Explicitly set XMIN for trace set rather than using minimum
                in XPOS
   xmax       - Explicitly set XMAX for trace set rather than using maximum
                in XPOS
   maxdev     - Maximum deviation in the fit to YPOS; set to 0 for no reject;
                default to 0.
   maxsig     - Maximum deviation in the fit to YPOS in terms of the 1-sigma
                dispersion of the residuals; set to 0 for no reject;
                default to 0.
   maxiter    - Maximum number of rejection iterations; set to 0 for no
                rejection; default to 10 if either MAXDEV or MAXSIG are set.
                Rejection iterations continues until convergence
                (actually, until the number of rejected pixels is unchanged).
   singlerej  - If set, then reject at most one deviant point per iteration,
                rejecting the worst one each time.  In this case, MAXITER
                represents the maximum number of points that can be rejected
                per trace.
   inputans   - ???

 OUTPUTS:
   tset       - Structure containing trace set

 OPTIONAL OUTPUTS:
   xmask      - Mask set to 1 for good points and 0 for rejected points;
                same dimensions as XPOS, YPOS.
   yfit       - Fit values at each XPOS.

 COMMENTS:
   Note that both MAXDEV and MAXSIG can be set for applying both rejection
   schemes at once.

   The HALFINTWO keyword can be passed to FCHEBYSHEV by this procedure.

 EXAMPLES:

 BUGS:
   Should probably change default to no rejection.

 PROCEDURES CALLED:
   fchebyshev()
   flegendre()
   func_fit()

 REVISION HISTORY:
   19-May-1999  Written by David Schlegel, Princeton.
   04-Aug-1999  Added chebyshev option (DJS).

(See pro/spec2d//xy2traceset.pro)




 
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