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+.help dofibers Jul95 noao.imred.specred
+.ih
+NAME
+dofibers -- Multifiber data reduction task
+.ih
+USAGE
+dofibers objects
+.ih
+SUMMARY
+The \fBdofibers\fR reduction task is specialized for scattered light
+subtraction, extraction, flat
+fielding, fiber throughput correction, wavelength calibration, and sky
+subtraction of multifiber spectra.  It is a
+command language script which collects and combines the functions and
+parameters of many general purpose tasks to provide a single complete data
+reduction path.  The task provides a degree of guidance, automation, and
+record keeping necessary when dealing with the large amount of data
+generated by multifiber instruments.  Variants of this task are
+\fBdoargus\fR, \fBdofoe\fR, \fBdohydra\fR, and \fBdo3fiber\fR.
+.ih
+PARAMETERS
+.ls objects
+List of object spectra to be processed.  Previously processed spectra are
+ignored unless the \fIredo\fR flag is set or the \fIupdate\fR flag is set and
+dependent calibration data has changed.  Extracted spectra are ignored.
+.le
+.ls apref = ""
+Aperture reference spectrum.  This spectrum is used to define the basic
+extraction apertures and is typically a flat field spectrum.
+.le
+.ls flat = "" (optional)
+Flat field spectrum.  If specified the one dimensional flat field spectra
+are extracted and used to make flat field calibrations.  If a separate
+throughput file or image is not specified the flat field is also used
+for computing a fiber throughput correction.
+.le
+.ls throughput = "" (optional)
+Throughput file or image.  If an image is specified, typically a blank
+sky observation, the total flux through
+each fiber is used to correct for fiber throughput.  If a file consisting
+of lines with the aperture number and relative throughput is specified
+then the fiber throughput will be corrected by those values.  If neither
+is specified but a flat field image is given it is used to compute the
+throughput.  
+.le
+.ls arcs1 = "" (at least one if dispersion correcting)
+List of primary arc spectra.  These spectra are used to define the dispersion
+functions for each fiber apart from a possible zero point correction made
+with secondary shift spectra or arc calibration fibers in the object spectra.
+One fiber from the first spectrum is used to mark lines and set the dispersion
+function interactively and dispersion functions for all other fibers and
+arc spectra are derived from it.
+.le
+.ls arcs2 = "" (optional)
+List of optional shift arc spectra.  Features in these secondary observations
+are used to supply a wavelength zero point shift through the observing
+sequence.  One type of observation is dome lamps containing characteristic
+emission lines.
+.le
+.ls arctable = "" (optional) (refspectra)
+Table defining arc spectra to be assigned to object
+spectra (see \fBrefspectra\fR).  If not specified an assignment based
+on a header parameter, \fIparams.sort\fR, such as the observation time is made.
+.le
+
+.ls readnoise = "0." (apsum)
+Read out noise in photons.  This parameter defines the minimum noise
+sigma.  It is defined in terms of photons (or electrons) and scales
+to the data values through the gain parameter.  A image header keyword
+(case insensitive) may be specified to get the value from the image.
+.le
+.ls gain = "1." (apsum)
+Detector gain or conversion factor between photons/electrons and
+data values.  It is specified as the number of photons per data value.
+A image header keyword (case insensitive) may be specified to get the value
+from the image.
+.le
+.ls datamax = INDEF (apsum.saturation)
+The maximum data value which is not a cosmic ray.
+When cleaning cosmic rays and/or using variance weighted extraction
+very strong cosmic rays (pixel values much larger than the data) can
+cause these operations to behave poorly.  If a value other than INDEF
+is specified then all data pixels in excess of this value will be
+excluded and the algorithms will yield improved results.
+This applies only to the object spectra and not the flat field or
+arc spectra.  For more
+on this see the discussion of the saturation parameter in the
+\fBapextract\fR package.
+.le
+.ls fibers = 97 (apfind)
+Number of fibers.  This number is used during the automatic definition of
+the apertures from the aperture reference spectrum.  It is best if this
+reflects the actual number of fibers which may be found in the aperture
+reference image.  The interactive
+review of the aperture assignments allows verification and adjustments
+to the automatic aperture definitions.
+.le
+.ls width = 12. (apedit)
+Approximate base full width of the fiber profiles.  This parameter is used
+for the profile centering algorithm.
+.le
+.ls minsep = 8. (apfind)
+Minimum separation between fibers.  Weaker spectra or noise within this
+distance of a stronger spectrum are rejected.
+.le
+.ls maxsep = 15. (apfind)
+Maximum separation between adjacent fibers.  This parameter
+is used to identify missing fibers.  If two adjacent spectra exceed this
+separation then it is assumed that a fiber is missing and the aperture
+identification assignments will be adjusted accordingly.
+.le
+.ls apidtable = "" (apfind)
+Aperture identification table.  This may be either a text file or an
+image.  A text file contains the fiber number, beam number defining object
+(1), sky (0), and arc (2) fibers, and a object title.  An image contains
+the keywords SLFIBnnn with string value consisting of the fiber number,
+beam number, optional right ascension and declination, and an object
+title.  Unassigned and broken fibers (beam of -1) should be included in the
+identification information since they will automatically be excluded.
+.le
+.ls crval = INDEF, cdelt = INDEF (autoidentify)
+These parameters specify an approximate central wavelength and dispersion.
+They may be specified as numerical values, INDEF, or image header keyword
+names whose values are to be used.
+If both these parameters are INDEF then the automatic identification will
+not be done.
+.le
+.ls objaps = "", skyaps = "", arcaps = ""
+List of object, sky, and arc aperture numbers.  These are used to
+identify arc apertures for wavelength calibration and object and sky
+apertures for sky subtraction.  Note sky apertures may be identified as
+both object and sky if one wants to subtract the mean sky from the
+individual sky spectra.  Typically the different spectrum types are
+identified by their beam numbers and the default, null string,
+lists select all apertures.
+.le
+.ls objbeams = "0,1", skybeams = "0", arcbeams = 2
+List of object, sky, and arc beam numbers.  The convention is that sky
+fibers are given a beam number of 0, object fibers a beam number of 1, and
+arc fibers a beam number of 2.  The beam numbers are typically set in the
+\fIapidtable\fR.  Unassigned or broken fibers may be given a beam number of
+-1 in the aperture identification table since apertures with negative beam
+numbers are not extracted.  Note it is valid to identify sky fibers as both
+object and sky.
+.le
+
+.ls scattered = no (apscatter)
+Smooth and subtracted scattered light from the object and flat field
+images.  This operation consists of fitting independent smooth functions
+across the dispersion using data outside the fiber apertures and then
+smoothing the individual fits along the dispersion.  The initial
+flat field, or if none is given the aperture reference image, are
+done interactively to allow setting the fitting parameters.  All
+subsequent subtractions use the same fitting parameters.
+.le
+.ls fitflat = yes (flat1d)
+Fit the composite flat field spectrum by a smooth function and divide each
+flat field spectrum by this function?  This operation removes the average
+spectral signature of the flat field lamp from the sensitivity correction to
+avoid modifying the object fluxes.
+.le
+.ls clean = yes (apsum)
+Detect and correct for bad pixels during extraction?  This is the same
+as the clean option in the \fBapextract\fR package.  If yes this also
+implies variance weighted extraction and requires reasonably good values
+for the readout noise and gain.  In addition the datamax parameters
+can be useful.
+.le
+.ls dispcor = yes
+Dispersion correct spectra?  Depending on the \fIparams.linearize\fR
+parameter this may either resample the spectra or insert a dispersion
+function in the image header.
+.le
+.ls skyalign = no
+Align sky lines?  If yes then for the first object spectrum you are asked
+to mark one or more sky lines to use for alignment.  Then these lines will
+be found in all spectra and an average zeropoint shift computed and applied
+to the dispersion solution to align these lines.  Note that this assumes
+the sky lines are seen in all fibers.
+.le
+.ls savearcs = yes
+Save any simultaneous arc apertures?  If no then the arc apertures will
+be deleted after use.
+.le
+.ls skysubtract = yes
+Subtract sky from the object spectra?  If yes the sky spectra are combined
+and subtracted from the object spectra as defined by the object and sky
+aperture/beam parameters.
+.le
+.ls skyedit = yes
+Overplot all the sky spectra and allow contaminated sky spectra to be
+deleted?
+.le
+.ls saveskys = yes
+Save the combined sky spectrum?  If no then the sky spectrum will be
+deleted after sky subtraction is completed.
+.le
+.ls splot = no
+Plot the final spectra with the task \fBsplot\fR?
+.le
+.ls redo = no
+Redo operations previously done?  If no then previously processed spectra
+in the objects list will not be processed (unless they need to be updated).
+.le
+.ls update = yes
+Update processing of previously processed spectra if aperture, flat
+field, or dispersion reference definitions are changed?
+.le
+.ls batch = no
+Process spectra as a background or batch job provided there are no interactive
+options (\fIskyedit\fR and \fIsplot\fR) selected.
+.le
+.ls listonly = no
+List processing steps but don't process?
+.le
+
+.ls params = "" (pset)
+Name of parameter set containing additional processing parameters.  The
+default is parameter set \fBparams\fR.  The parameter set may be examined
+and modified in the usual ways (typically with "epar params" or ":e params"
+from the parameter editor).  Note that using a different parameter file
+is not allowed.  The parameters are described below.
+.le
+
+.ce
+-- PACKAGE PARAMETERS
+
+Package parameters are those which generally apply to all task in the
+package.  This is also true of \fBdofibers\fR.
+.ls dispaxis = 2
+Default dispersion axis.  The dispersion axis is 1 for dispersion
+running along image lines and 2 for dispersion running along image
+columns.  If the image header parameter DISPAXIS is defined it has
+precedence over this parameter.  The default value defers to the
+package parameter of the same name.
+.le
+.ls observatory = "observatory"
+Observatory at which the spectra were obtained if not specified in the
+image header by the keyword OBSERVAT.  See \fBobservatory\fR for more
+details.
+.le
+.ls interp = "poly5" (nearest|linear|poly3|poly5|spline3|sinc)
+Spectrum interpolation type used when spectra are resampled.  The choices are:
+
+.nf
+	nearest - nearest neighbor
+	 linear - linear
+	  poly3 - 3rd order polynomial
+	  poly5 - 5th order polynomial
+	spline3 - cubic spline
+	   sinc - sinc function
+.fi
+.le
+.ls database = "database"
+Database (directory) used for storing aperture and dispersion information.
+.le
+.ls verbose = no
+Print verbose information available with various tasks.
+.le
+.ls logfile = "logfile", plotfile = ""
+Text and plot log files.  If a filename is not specified then no log is
+kept.  The plot file contains IRAF graphics metacode which may be examined
+in various ways such as with \fBgkimosaic\fR.
+.le
+.ls records = ""
+Dummy parameter to be ignored.
+.le
+.ls version = "SPECRED: ..."
+Version of the package.
+.le
+
+.ce
+PARAMS PARAMETERS
+
+The following parameters are part of the \fBparams\fR parameter set and
+define various algorithm parameters for \fBdofibers\fR.
+
+.ce
+--  GENERAL PARAMETERS --
+.ls line = INDEF, nsum = 10
+The dispersion line (line or column perpendicular to the dispersion
+axis) and number of adjacent lines (half before and half after unless
+at the end of the image) used in finding, recentering, resizing,
+editing, and tracing operations.  A line of INDEF selects the middle of the
+image along the dispersion axis.
+.le
+.ls order = "decreasing" (apfind)
+When assigning aperture identifications order the spectra "increasing"
+or "decreasing" with increasing pixel position (left-to-right or
+right-to-left in a cross-section plot of the image).
+.le
+.ls extras = no (apsum)
+Include extra information in the output spectra?  When cleaning or using
+variance weighting the cleaned and weighted spectra are recorded in the
+first 2D plane of a 3D image, the raw, simple sum spectra are recorded in
+the second plane, and the estimated sigmas are recorded in the third plane.
+.le
+
+.ce
+-- DEFAULT APERTURE LIMITS --
+.ls lower = -5., upper = 5. (apdefault)
+Default lower and upper aperture limits relative to the aperture center.
+These limits are used when the apertures are first found and may be
+resized automatically or interactively.
+.le
+
+.ce
+-- AUTOMATIC APERTURE RESIZING PARAMETERS --
+.ls ylevel = 0.05 (apresize)
+Data level at which to set aperture limits during automatic resizing.
+It is a fraction of the peak relative to a local background.
+.le
+
+.ce
+-- TRACE PARAMETERS --
+.ls t_step = 10 (aptrace)
+Step along the dispersion axis between determination of the spectrum
+positions.  Note the \fInsum\fR parameter is also used to enhance the
+signal-to-noise at each step.
+.le
+.ls t_function = "spline3", t_order = 3 (aptrace)
+Default trace fitting function and order.  The fitting function types are
+"chebyshev" polynomial, "legendre" polynomial, "spline1" linear spline, and
+"spline3" cubic spline.  The order refers to the number of
+terms in the polynomial functions or the number of spline pieces in the spline
+functions.
+.le
+.ls t_niterate = 1, t_low = 3., t_high = 3. (aptrace)
+Default number of rejection iterations and rejection sigma thresholds.
+.le
+
+.ce
+-- SCATTERED LIGHT PARAMETERS --
+.ls buffer = 1. (apscatter)
+Buffer distance from the aperture edges to be excluded in selecting the
+scattered light pixels to be used.
+.le
+.ls apscat1 = "" (apscatter)
+Fitting parameters across the dispersion.  This references an additional
+set of parameters for the ICFIT package.  The default is the "apscat1"
+parameter set.
+.le
+.ls apscat2 = "" (apscatter)
+Fitting parameters along the dispersion.  This references an additional
+set of parameters for the ICFIT package.  The default is the "apscat2"
+parameter set.
+.le
+
+.ce
+-- APERTURE EXTRACTION PARAMETERS --
+.ls weights = "none" (apsum)
+Type of extraction weighting.  Note that if the \fIclean\fR parameter is
+set then the weights used are "variance" regardless of the weights
+specified by this parameter.  The choices are:
+.ls "none"
+The pixels are summed without weights except for partial pixels at the
+ends.
+.le
+.ls "variance"
+The extraction is weighted by the variance based on the data values
+and a poisson/ccd model using the \fIgain\fR and \fIreadnoise\fR
+parameters.
+.le
+.le
+.ls pfit = "fit1d" (apsum) (fit1d|fit2d)
+Profile fitting algorithm for cleaning and variance weighted extractions.
+The default is generally appropriate for multifiber data but users
+may try the other algorithm.  See \fBapprofiles\fR for further information.
+.le
+.ls lsigma = 3., usigma = 3. (apsum)
+Lower and upper rejection thresholds, given as a number of times the
+estimated sigma of a pixel, for cleaning.
+.le
+.ls nsubaps = 1 (apsum)
+During extraction it is possible to equally divide the apertures into
+this number of subapertures.
+.le
+
+.ce
+-- FLAT FIELD FUNCTION FITTING PARAMETERS --
+.ls f_interactive = yes (fit1d)
+Fit the composite one dimensional flat field spectrum interactively?
+This is used if \fIfitflat\fR is set and a two dimensional flat field
+spectrum is specified.
+.le
+.ls f_function = "spline3", f_order = 10 (fit1d)
+Function and order used to fit the composite one dimensional flat field
+spectrum.  The functions are "legendre", "chebyshev", "spline1", and
+"spline3".  The spline functions are linear and cubic splines with the
+order specifying the number of pieces.
+.le
+
+.ce
+-- ARC DISPERSION FUNCTION PARAMETERS --
+.ls threshold = 10. (autoidentify/identify/reidentify)
+In order for a feature center to be determined the range of pixel intensities
+around the feature must exceed this threshold.
+.le
+.ls coordlist = "linelists$idhenear.dat" (autoidentify/identify)
+Arc line list consisting of an ordered list of wavelengths.
+Some standard line lists are available in the directory "linelists$".
+.le
+.ls match = -3. (autoidentify/identify)
+The maximum difference for a match between the dispersion function prediction
+value and a wavelength in the coordinate list.
+.le
+.ls fwidth = 4. (autoidentify/identify)
+Approximate full base width (in pixels) of arc lines.
+.le
+.ls cradius = 10. (reidentify)
+Radius from previous position to reidentify arc line.
+.le
+.ls i_function = "spline3", i_order = 3 (autoidentify/identify)
+The default function and order to be fit to the arc wavelengths as a
+function of the pixel coordinate.  The functions choices are "chebyshev",
+"legendre", "spline1", or "spline3".
+.le
+.ls i_niterate = 2, i_low = 3.0, i_high = 3.0 (autoidentify/identify)
+Number of rejection iterations and sigma thresholds for rejecting arc
+lines from the dispersion function fits.
+.le
+.ls refit = yes (reidentify)
+Refit the dispersion function?  If yes and there is more than 1 line
+and a dispersion function was defined in the arc reference then a new
+dispersion function of the same type as in the reference image is fit
+using the new pixel positions.  Otherwise only a zero point shift is
+determined for the revised fitted coordinates without changing the
+form of the dispersion function.
+.le
+.ls addfeatures = no (reidentify)
+Add new features from a line list during each reidentification?
+This option can be used to compensate for lost features from the
+reference solution.  Care should be exercised that misidentified features
+are not introduced.
+.le
+
+.ce
+-- AUTOMATIC ARC ASSIGNMENT PARAMETERS --
+.ls select = "interp" (refspectra)
+Selection method for assigning wavelength calibration spectra.
+Note that an arc assignment table may be used to override the selection
+method and explicitly assign arc spectra to object spectra.
+The automatic selection methods are:
+.ls average
+Average two reference spectra without regard to any sort parameter.
+If only one reference spectrum is specified then it is assigned with a
+warning.  If more than two reference spectra are specified then only the
+first two are used and a warning is given.
+This option is used to assign two reference spectra, with equal weights,
+independent of any sorting parameter.
+.le
+.ls following
+Select the nearest following spectrum in the reference list based on the
+sorting parameter.  If there is no following spectrum use the nearest preceding
+spectrum.
+.le
+.ls interp
+Interpolate between the preceding and following spectra in the reference
+list based on the sorting parameter.  If there is no preceding and following
+spectrum use the nearest spectrum.  The interpolation is weighted by the
+relative distances of the sorting parameter.
+.le
+.ls match
+Match each input spectrum with the reference spectrum list in order.
+This overrides the reference aperture check.
+.le
+.ls nearest
+Select the nearest spectrum in the reference list based on the sorting
+parameter.
+.le
+.ls preceding
+Select the nearest preceding spectrum in the reference list based on the
+sorting parameter.  If there is no preceding spectrum use the nearest following
+spectrum.
+.le
+.le
+.ls sort = "jd", group = "ljd" (refspectra)
+Image header keywords to be used as the sorting parameter for selection
+based on order and to group spectra.
+A null string, "", or the word "none" may be use to disable the sorting
+or grouping parameters.
+The sorting parameter
+must be numeric but otherwise may be anything.  The grouping parameter
+may be a string or number and must simply be the same for all spectra within
+the same group (say a single night).
+Common sorting parameters are times or positions.
+In \fBdofibers\fR the Julian date (JD) and the local Julian day number (LJD)
+at the middle of the exposure are automatically computed from the universal
+time at the beginning of the exposure and the exposure time.  Also the
+parameter UTMIDDLE is computed.
+.le
+.ls time = no, timewrap = 17. (refspectra)
+Is the sorting parameter a 24 hour time?  If so then the time origin
+for the sorting is specified by the timewrap parameter.  This time
+should precede the first observation and follow the last observation
+in a 24 hour cycle.
+.le
+
+.ce
+-- DISPERSION  CORRECTION PARAMETERS --
+.ls linearize = yes (dispcor)
+Interpolate the spectra to a linear dispersion sampling?  If yes the
+spectra will be interpolated to a linear or log linear sampling
+If no the nonlinear dispersion function(s) from the dispersion function
+database are assigned to the input image world coordinate system
+and the spectral data are not interpolated.
+.le
+.ls log = no (dispcor)
+Use linear logarithmic wavelength coordinates?  Linear logarithmic
+wavelength coordinates have wavelength intervals which are constant
+in the logarithm of the wavelength.
+.le
+.ls flux = yes (dispcor)
+Conserve the total flux during interpolation?  If \fIno\fR the output
+spectrum is interpolated from the input spectrum at each output
+wavelength coordinate.  If \fIyes\fR the input spectrum is integrated
+over the extent of each output pixel.  This is slower than
+simple interpolation.
+.le
+
+.ce
+-- SKY SUBTRACTION PARAMETERS --
+.ls combine = "average" (scombine) (average|median)
+Option for combining sky pixels at the same dispersion coordinate after any
+rejection operation.  The options are to compute the  "average" or "median"
+of the pixels.  The median uses the average of the two central
+values when the number of pixels is even.
+.le
+.ls reject = "none" (scombine) (none|minmax|avsigclip)
+Type of rejection operation performed on the pixels which overlap at each
+dispersion coordinate.  The algorithms are discussed in the
+help for \fBscombine\fR.  The rejection choices are:
+
+.nf
+      none - No rejection
+    minmax - Reject the low and high pixels
+ avsigclip - Reject pixels using an averaged sigma clipping algorithm
+.fi
+
+.le
+.ls scale = "none" (none|mode|median|mean)
+Multiplicative scaling to be applied to each spectrum.  The choices are none
+or scale by the mode, median, or mean.  This should not be necessary if the
+flat field and throughput corrections have been properly made. 
+.le
+.ih
+ENVIRONMENT PARAMETERS
+The environment parameter \fIimtype\fR is used to determine the extension
+of the images to be processed and created.  This allows use with any
+supported image extension.  For STF images the extension has to be exact;
+for example "d1h".
+.ih
+DESCRIPTION
+The \fBdofibers\fR reduction task is specialized for scattered light
+subtraction, extraction, flat
+fielding, fiber throughput correction, wavelength calibration, and sky
+subtraction of multifiber spectra.  It is a command language script
+which collects and combines the functions and parameters of many general
+purpose tasks to provide a single complete data reduction path.  The task
+provides a degree of guidance, automation, and record keeping necessary
+when dealing with the large amount of data generated by multifiber
+instruments.  Variants of this task are \fBdoargus\fR, \fBdofoe\fR,
+\fBdohydra\fR, and \fBdo3fiber\fR.
+
+The general organization of the task is to do the interactive setup steps
+first using representative calibration data and then perform the majority
+of the reductions automatically, and possibly as a background process, with
+reference to the setup data.  In addition, the task determines which setup
+and processing operations have been completed in previous executions of the
+task and, contingent on the \fIredo\fR and \fIupdate\fR options, skip or
+repeat some or all the steps.
+
+The description is divided into a quick usage outline followed by details
+of the parameters and algorithms.  The usage outline is provided as a
+checklist and a refresher for those familiar with this task and the
+component tasks.  It presents only the default or recommended usage Since
+\fBdofibers\fR combines many separate, general purpose tasks the
+description given here refers to these tasks and leaves some of the details
+to their help documentation.
+
+\fBUsage Outline\fR
+
+.ls 6 [1]
+The images are first processed with \fBccdproc\fR for overscan,
+bias, and dark corrections.
+The \fBdofibers\fR task will abort if the image header keyword CCDPROC,
+which is added by \fBccdproc\fR, is missing.  If the data processed outside
+of the IRAF \fBccdred\fR package then a dummy CCDPROC keyword should be
+added to the image headers; say with \fBhedit\fR.
+.le
+.ls [2]
+Set the \fBdofibers\fR parameters with \fBeparam\fR.  Specify the object
+images to be processed, the flat field image as the aperture reference and
+the flat field, and one or more arc images.  A throughput file or image,
+such as a blank sky observation, may also be specified.  If there are many
+object or arc spectra per setup you might want to prepare "@ files".
+Specify the aperture identification table for the configuration
+if one has been created.  If the image headers contain the SLFIB keywords
+specify an image name; typically the same as the aperture reference
+image.
+You might wish to verify the geometry parameters,
+separations, dispersion direction, etc., which may
+change with different detector setups.  The processing parameters are set
+for complete reductions but for quicklook you might not use the clean
+option or dispersion calibration and sky subtraction.
+
+The parameters are set for a particular configuration and different
+configurations may use different flat fields, arcs, and aperture
+identification tables.
+.le
+.ls [3]
+Run the task.  This may be repeated multiple times with different
+observations and the task will generally only do the setup steps
+once and only process new images.  Queries presented during the
+execution for various interactive operations may be answered with
+"yes", "no", "YES", or "NO".  The lower case responses apply just
+to that query while the upper case responses apply to all further
+such queries during the execution and no further queries of that
+type will be made.
+.le
+.ls [4]
+The apertures are defined using the specified aperture reference image.
+The spectra are found automatically and apertures assigned based on
+task parameters and the aperture identification table.  Unassigned
+fibers may have a negative beam number and will be ignored in subsequent
+processing.  The resize option sets the aperture size to the widths of
+the profiles at a fixed fraction of the peak height.  The interactive
+review of the apertures is recommended.  If the identifications are off
+by a shift the 'o' key is used.  To exit the aperture review type 'q'.
+.le
+.ls [5]
+The fiber positions at a series of points along the dispersion are measured
+and a function is fit to these positions.  This may be done interactively to
+adjust the fitting parameters.  Not all fibers need be examined and the "NO"
+response will quit the interactive fitting.  To exit the interactive
+fitting type 'q'.
+.le
+.ls [6]
+If scattered light subtraction is to be done the flat field image is
+used to define the scattered light fitting parameters interactively.
+If one is not specified then the aperture reference image is used for
+this purpose.
+
+There are two queries for the interactive fitting.  A graph of the
+data between the defined reference apertures separated by a specified
+buffer distance is first shown.  The function order and type may be
+adjusted.  After quiting with 'q' the user has the option of changing
+the buffer value and returning to the fitting, changing the image line
+or column to check if the fit parameters are satisfactory at other points,
+or to quit and accept the fit parameters.  After fitting all points
+across the dispersion another graph showing the scattered light from
+the individual fits is shown and the smoothing parameters along the
+dispersion may be adjusted.  Upon quiting with 'q' you have the option
+of checking other cuts parallel to the dispersion or quiting and finishing
+the scattered light function smoothing and subtraction.
+
+If there is a throughput image then this is corrected for scattered light
+noninteractively using the previous fitting parameters.
+.le
+.ls [7]
+If flat fielding is to be done the flat field spectra are extracted.  The
+average spectrum over all fibers is determined and a function is fit
+interactively (exit with 'q').  This function is generally of sufficiently
+high order that the overall shape is well fit.  This function is then used
+to normalize the individual flat field spectra.  If a throughput image, a
+sky flat, is specified then the total sky counts through each fiber are
+used to correct the total flat field counts.  Alternatively, a separately
+derived throughput file can be used for specifying throughput corrections.
+If neither type of throughput is used the flat field also provides the
+throughput correction.  The final response spectra are normalized to a unit
+mean over all fibers.  The relative average throughput for each fiber is
+recorded in the log and possibly printed to the terminal.
+.le
+.ls [8]
+If dispersion correction is selected the first arc in the arc list is
+extracted.  The middle fiber is used to identify the arc lines and define
+the dispersion function using the task \fBautoidentify\fR.  The
+\fIcrval\fR and \fIcdelt\fR parameters are used in the automatic
+identification.  Whether or not the automatic identification is
+successful you will be shown the result of the arc line identification.
+If the automatic identification is not successful identify a few arc
+lines with 'm' and use the 'l' line list identification command to
+automatically add additional lines and fit the dispersion function.  Check
+the quality of the dispersion function fit with 'f'.  When satisfied exit
+with 'q'.
+.le
+.ls [9]
+The remaining fibers are automatically reidentified.  You have the option
+to review the line identifications and dispersion function for each fiber
+and interactively add or delete arc lines and change fitting parameters.
+This can be done selectively, such as when the reported RMS increases
+significantly.
+.le
+.ls [10]
+If the spectra are to be resampled to a linear dispersion system
+(which will be the same for all spectra) default dispersion parameters
+are printed and you are allowed to adjust these as desired.
+.le
+.ls [11]
+If the sky line alignment option is selected and the sky lines have not
+been identified for a particular aperture identification table then you are
+asked to mark one or more sky lines.  You may simply accept the wavelengths
+of these lines as defined by the dispersion solution for this spectrum and
+fiber or you may specify knowns wavelengths for the lines. These lines will
+be reidentified in all object spectra extracted and a mean zeropoint shift
+will be added to the dispersion solution.  This has the effect of aligning
+these lines to optimize sky subtraction.
+.le
+.ls [12]
+The object spectra are now automatically scattered light subtracted,
+ extracted, flat fielded, and dispersion corrected.
+.le
+.ls [13]
+When sky subtracting, the individual sky spectra may be reviewed and some
+spectra eliminated using the 'd' key.  The last deleted spectrum may be
+recovered with the 'e' key.  After exiting the review with 'q' you are
+asked for the combining option.  The type of combining is dictated by the
+number of sky fibers.
+.le
+.ls [14]
+The option to examine the final spectra with \fBsplot\fR may be given.
+To exit type 'q'.
+.le
+.ls [15]
+If scattered light is subtracted from the input data a copy of the
+original image is made by appending "noscat" to the image name.
+If the data are reprocessed with the \fIredo\fR flag the original
+image will be used again to allow modification of the scattered
+light parameters.
+
+The final spectra will have the same name as the original 2D images
+with a ".ms" extension added.  The flat field and arc spectra will
+also have part of the aperture identification table name added to
+allow different configurations to use the same 2D flat field and arcs
+but with different aperture definitions.  If using the sky alignment
+option an image "align" with the aperture identification table name
+applied will also be created.
+.le
+
+\fBSpectra and Data Files\fR
+
+The basic input consists of multifiber object and
+calibration spectra stored as IRAF images.
+The type of image format is defined by the
+environment parameter \fIimtype\fR.  Only images with that extension will
+be processed and created.
+The raw CCD images must
+be processed to remove overscan, bias, and dark count effects.  This
+is generally done using the \fBccdred\fR package.
+The \fBdofibers\fR task will abort if the image header keyword CCDPROC,
+which is added by \fBccdproc\fR, is missing.  If the data processed outside
+of the IRAF \fBccdred\fR package then a dummy CCDPROC keyword should be
+added to the image headers; say with \fBhedit\fR.
+Flat fielding is
+generally not done at this stage but as part of \fBdofibers\fR.
+If flat fielding is done as part of the basic CCD processing then
+a flattened flat field, blank sky observation, or throughput file
+should still be created for applying fiber throughput corrections.
+
+The task \fBdofibers\fR uses several types of calibration spectra.  These
+are flat fields, blank sky flat fields, comparison lamp spectra, auxiliary
+mercury line (from the dome lights) or sky line spectra, and simultaneous
+arc spectra taken during the object observation.  The flat field,
+throughput image or file, auxiliary emission line spectra, and simultaneous
+comparison fibers are optional.  If a flat field is used then the sky flat
+or throughput file is optional assuming the flat field has the same fiber
+iillumination.  It is legal to specify only a throughput image or file and
+leave the flat field blank in order to simply apply a throughput
+correction.  Because only the total counts through each fiber are used from
+a throughput image, sky flat exposures need not be of high signal per
+pixel.
+
+There are three types of arc calibration methods.  One is to take arc
+calibration exposures through all fibers periodically and apply the
+dispersion function derived from one or interpolated between pairs to the
+object fibers.  This is the most common method.  Another method is to
+use only one or two all-fiber arcs to define the shape of the dispersion
+function and track zero point wavelength shifts with \fIsimultaneous arc\fR
+fibers taken during the object exposure.  The simultaneous arcs may or may
+not be available at the instrument but \fBdofibers\fR can use this type of
+observation.  The arc fibers are identified by their beam or aperture
+numbers.  A related and mutually exclusive method is to use \fIauxiliary
+line spectra\fR such as lines in the dome lights or sky lines to monitor
+shifts relative to a few actual arc exposures.  The main reason to do this
+is if taking arc exposures through all fibers is inconvenient.
+
+The assignment of arc or auxiliary line calibration exposures to object
+exposures is generally done by selecting the nearest in time and
+interpolating.  There are other options possible which are described under
+the task \fBrefspectra\fR.  The most general option is to define a table
+giving the object image name and the one or two arc spectra to be assigned
+to that object.  That file is called an \fIarc assignment table\fR and it
+is one of the optional setup files which can used with \fBdofibers\fR.
+
+The first step in the processing is identifying the spectra in the images.
+The \fIaperture identification table\fR contains information about the fiber
+assignments.  The identification table is not mandatory, sequential numbering
+will be used, but it is highly recommended for keeping track of the objects
+assigned to the fibers.  The aperture identification table may be
+a file containing lines
+specifying an aperture number, a beam number, and an object
+identification.  It may also be an image whose header contains the keywords
+SLFIB with strings consisting of an aperture number, beam number, optional
+right ascension and declination, and a tile.  The file lines or keywords
+must be in the same order as the fibers in the
+image.  The aperture number may be any unique number but it is recommended
+that the fiber number be used.  The beam number is used to flag object,
+sky, arc, or other types of spectra.  The default beam numbers used by the
+task are 0 for sky, 1 for object, and 2 for arc.  The object
+identifications are optional but it is good practice to include them so
+that the data will contain the object information independent of other
+records.  Figure 1 shows an example identification file called M33Sch2.
+.nf
+
+    Figure 1: Example Aperture Identification File
+
+    cl> type m33sch2
+    1 1 143
+    2 1 254
+    3 0 sky
+    4 -1 Broken
+    5 2 arc
+       .
+       .
+       .
+    44 1 s92
+    45 -1 Unassigned
+    46 2 arc
+    47 0 sky
+    48 1 phil2
+
+.fi
+Note the identification of the sky fibers with beam number 0, the object
+fibers with 1, and the arc fibers with 2.
+The broken and unassigned fiber entries, given beam
+number -1, are optional but recommended to give the automatic spectrum
+finding operation the best chance to make the correct identifications.  The
+identification table will vary for each plugboard setup.  Additional
+information about the aperture identification table may be found in the
+description of the task \fBapfind\fR.
+
+An alternative to using an aperture identification table is to give no
+name, the "" empty string, and to explicitly give a range of
+aperture numbers for the skys and possibly for the sky subtraction
+object list in the parameters \fIobjaps, skyaps, arcaps, objbeams,
+skybeams,\fR and \fIarcbeams\fR.  This is reasonable if the fibers always
+have a fixed typed.  As an example the CTIO Argus instrument always
+alternates object and sky fibers so the object apertures can be given
+as 1x2 and the sky fibers as 2x2; i.e. objects are the odd numbered
+apertures and skys are the even numbered apertures.
+
+The final reduced spectra are recorded in two or three dimensional IRAF
+images.  The images have the same name as the original images with an added
+".ms" extension.  Each line in the reduced image is a one dimensional
+spectrum with associated aperture, wavelength, and identification
+information.  When the \fIextras\fR parameter is set the lines in the
+third dimension contain additional information (see
+\fBapsum\fR for further details).  These spectral formats are accepted by the
+one dimensional spectroscopy tools such as the plotting tasks \fBsplot\fR
+and \fBspecplot\fR.  The special task \fBscopy\fR may be used to extract
+specific apertures or to change format to individual one dimensional
+images.
+
+\fBPackage Parameters\fR
+
+The \fBspecred\fR package parameters set parameters affecting all the
+tasks in the package.
+The dispersion axis parameter defines the image axis along which the
+dispersion runs.  This is used if the image header doesn't define the
+dispersion axis with the DISPAXIS keyword.
+The observatory parameter is used if there is no
+OBSERVAT keyword in the image header (see \fBobservatory\fR for more
+details).  The spectrum interpolation type might be changed to "sinc" but
+with the cautions given in \fBonedspec.package\fR.
+The other parameters define the standard I/O functions.
+The verbose parameter selects whether to print everything which goes
+into the log file on the terminal.  It is useful for monitoring
+what the \fBdofibers\fR task does.  The log and plot files are useful for
+keeping a record of the processing.  A log file is highly recommended.
+A plot file provides a record of apertures, traces, and extracted spectra
+but can become quite large.
+The plotfile is most conveniently viewed and printed with \fBgkimosaic\fR.
+
+\fBProcessing Parameters\fR
+
+The list of objects and arcs can be @ files if desired.  The aperture
+reference spectrum is usually the same as the flat field spectrum though it
+could be any exposure with enough signal to accurately define the positions
+and trace the spectra.  The first list of arcs are the standard Th-Ar or
+HeNeAr comparison arc spectra (they must all be of the same type).  The
+second list of arcs are the auxiliary emission line exposures mentioned
+previously.
+
+The detector read out noise and gain are used for cleaning and variance
+(optimal) extraction.  This is specified either explicitly or by reference
+to an image header keyword.
+The dispersion axis defines the wavelength direction of spectra in
+the image if not defined in the image header by the keyword DISPAXIS.  The
+width and separation parameters define the dimensions (in pixels) of the
+spectra (fiber profile) across the dispersion.  The width parameter
+primarily affects the centering.  The maximum separation parameter is
+important if missing spectra from the aperture identification table are to
+be correctly skipped.  The number of fibers is either the actual number
+of fibers or the number in the aperture identification table.  An attempt
+is made to account for unassigned or missing fibers.  As a recommendation
+the actual number of fibers should be specified.
+
+The approximate central wavelength and dispersion are used for the
+automatic identification of the arc reference.  They may be specified
+as image header keywords or values.  The INDEF values search the
+entire range of the coordinate reference file but the automatic
+line identification algorithm works much better and faster if
+approximate values are given.
+
+The task needs to know which fibers are object, sky if sky subtraction is
+to be done, and simultaneous arcs if used.  One could explicitly give the
+aperture numbers but the recommended way, provided an aperture
+identification table is used, is to select the apertures based on the beam
+numbers.  The default values are recommended beam numbers.  Sky
+subtracted sky spectra are useful for evaluating the sky subtraction.
+Since only the spectra identified as objects are sky subtracted one can
+exclude fibers from the sky subtraction.  For example, if the
+\fIobjbeams\fR parameter is set to 1 then only those fibers with a beam of
+1 will be sky subtracted.  All other fibers will remain in the extracted
+spectra but will not be sky subtracted.
+
+The next set of parameters select the processing steps and options.  The
+scattered light option allows fitting and subtracting a scattered light
+surface from the input object and flat field.  If there is significant
+scattered light which is not subtracted the fiber throughput correction
+will not be accurate.  The
+flat fitting option allows fitting and removing the overall shape of the
+flat field spectra while preserving the pixel-to-pixel response
+corrections.  This is useful for maintaining the approximate object count
+levels and not introducing the reciprocal of the flat field spectrum into
+the object spectra.  The \fIclean\fR option invokes a profile fitting and
+deviant point rejection algorithm as well as a variance weighting of points
+in the aperture.  These options require knowing the effective (i.e.
+accounting for any image combining) read out noise and gain.  For a
+discussion of cleaning and variance weighted extraction see
+\fBapvariance\fR and \fBapprofiles\fR.
+
+The dispersion correction option selects whether to extract arc spectra,
+determine a dispersion function, assign them to the object spectra, and,
+possibly, resample the spectra to a linear (or log-linear) wavelength
+scale.  If simultaneous arc fibers are defined there is an option to delete
+them from the final spectra when they are no longer needed.
+
+The sky alignment option allows applying a zeropoint dispersion shift
+to all fibers based on one or more sky lines.  This requires all fibers
+to have the sky lines visible.  When there are sky lines this will
+improve the sky subtraction if there is a systematic error in the
+fiber iillumination between the sky and the arc calibration.
+
+The sky subtraction option selects whether to combine the sky fiber spectra
+and subtract this sky from the object fiber spectra.  \fIDispersion
+correction and sky subtraction are independent operations.\fR  This means
+that if dispersion correction is not done then the sky subtraction will be
+done with respect to pixel coordinates.  This might be desirable in some
+quick look cases though it is incorrect for final reductions.
+
+The sky subtraction option has two additional options.  The individual sky
+spectra may be examined and contaminated spectra deleted interactively
+before combining.  This can be a useful feature in crowded regions.  The
+final combined sky spectrum may be saved for later inspection in an image
+with the spectrum name prefixed by \fBsky\fR.
+
+After a spectrum has been processed it is possible to examine the results
+interactively using the \fBsplot\fR tasks.  This option has a query which
+may be turned off with "YES" or "NO" if there are multiple spectra to be
+processed.
+
+Generally once a spectrum has been processed it will not be reprocessed if
+specified as an input spectrum.  However, changes to the underlying
+calibration data can cause such spectra to be reprocessed if the
+\fIupdate\fR flag is set.  The changes which will cause an update are a new
+aperture identification table, a new reference image, new flat fields, and a
+new arc reference.  If all input spectra are to be processed regardless of
+previous processing the \fIredo\fR flag may be used.  Note that
+reprocessing clobbers the previously processed output spectra.
+
+The \fIbatch\fR processing option allows object spectra to be processed as
+a background or batch job.  This will only occur if sky spectra editing and
+\fBsplot\fR review (interactive operations) are turned off, either when the
+task is run or by responding with "NO" to the queries during processing.
+
+The \fIlistonly\fR option prints a summary of the processing steps which
+will be performed on the input spectra without actually doing anything.
+This is useful for verifying which spectra will be affected if the input
+list contains previously processed spectra.  The listing does not include
+any arc spectra which may be extracted to dispersion calibrate an object
+spectrum.
+
+The last parameter (excluding the task mode parameter) points to another
+parameter set for the algorithm parameters.  The way \fBdofibers\fR works
+this may not have any value and the parameter set \fBparams\fR is always
+used.  The algorithm parameters are discussed further in the next section.
+
+\fBAlgorithms and Algorithm Parameters\fR
+
+This section summarizes the various algorithms used by the \fBdofibers\fR
+task and the parameters which control and modify the algorithms.  The
+algorithm parameters available to the user are collected in the parameter
+set \fBparams\fR.  These parameters are taken from the various general
+purpose tasks used by the \fBdofibers\fR processing task.  Additional
+information about these parameters and algorithms may be found in the help
+for the actual task executed.  These tasks are identified in the parameter
+section listing in parenthesis.  The aim of this parameter set organization
+is to collect all the algorithm parameters in one place separate from the
+processing parameters and include only those which are relevant for
+multifiber data.  The parameter values can be changed from the
+defaults by using the parameter editor,
+.nf
+
+	cl> epar params
+
+.fi
+or simple typing \fIparams\fR.  The parameter editor can also be
+entered when editing the \fBdofibers\fR parameters by typing \fI:e
+params\fR or simply \fI:e\fR if positioned at the \fIparams\fR
+parameter.
+
+\fBExtraction\fR
+
+The identification of the spectra in the two dimensional images and their
+scattered light subtraction and extraction to one dimensional spectra
+in multispec format is accomplished
+using the tasks from the \fBapextract\fR package.  The first parameters
+through \fInsubaps\fR control the extractions.
+
+The dispersion line is that used for finding the spectra, for plotting in
+the aperture editor, and as the starting point for tracing.  The default
+value of \fBINDEF\fR selects the middle of the image.  The aperture
+finding, adjusting, editing, and tracing operations also allow summing a
+number of dispersion lines to improve the signal.  The number of lines is
+set by the \fInsum\fR parameter.
+
+The order parameter defines whether the order of the aperture
+identifications in the aperture identification table (or the default
+sequential numbers if no table is used) is in the same sense as the image
+coordinates (increasing) or the opposite sense (decreasing).  If the
+aperture identifications turn out to be opposite to what is desired when
+viewed in the aperture editing graph then simply change this parameter.
+
+The basic data output by the spectral extraction routines are the one
+dimensional spectra.  Additional information may be output when the
+\fIextras\fR option is selected and the cleaning or variance weighting
+options are also selected.  In this case a three dimensional image is
+produced with the first element of the third dimension being the cleaned
+and/or weighted spectra, the second element being the uncleaned and
+unweighted spectra, and the third element being an estimate of the sigma
+of each pixel in the extracted spectrum.  Currently the sigma data is not
+used by any other tasks and is only for reference.
+
+The initial step of finding the fiber spectra in the aperture reference
+image consists of identifying the peaks in a cut across the dispersion,
+eliminating those which are closer to each other than the \fIminsep\fR
+distance, and then keeping the specified \fInfibers\fR highest peaks.  The
+centers of the profiles are determined using the \fBcenter1d\fR algorithm
+which uses the \fIwidth\fR parameter.
+
+Apertures are then assigned to each spectrum.  The initial edges of the
+aperture relative to the center are defined by the \fIlower\fR and
+\fIupper\fR parameters.  The trickiest part of assigning the apertures is
+relating the aperture identification from the aperture identification table
+to automatically selected fiber profiles.  The first aperture id in the
+file is assigned to the first spectrum found using the \fIorder\fR parameter to
+select the assignment direction.  The numbering proceeds in this way except
+that if a gap greater than a multiple of the \fImaxsep\fR parameter is
+encountered then assignments in the file are skipped under the assumption
+that a fiber is missing (broken).  If unassigned fibers are still
+visible in a flat field, either by design or by scattered light, the
+unassigned fibers can be included in the number of fibers to find and
+then the unassigned (negative beam number) apertures are excluded from
+any extraction.  For more on the finding and
+assignment algorithms see \fBapfind\fR.
+
+The initial apertures are the same for all spectra but they can each be
+automatically resized.  The automatic resizing sets the aperture limits
+at a fraction of the peak relative to the interfiber minimum.
+The default \fIylevel\fR is to resize the apertures to 5% of the peak.
+See the description for the task \fBapresize\fR for further details.
+
+The user is given the opportunity to graphically review and adjust the
+aperture definitions.  This is recommended.  As mentioned previously, the
+correct identification of the fibers is tricky and it is fundamentally
+important that this be done correctly; otherwise the spectrum
+identifications will not be for the objects they say.  An important command in
+this regard is the 'o' key which allows reordering the identifications
+based on the aperture identification table.  This is required if the first
+fiber is actually missing since the initial assignment begins assigning the
+first spectrum found with the first entry in the aperture file.  The
+aperture editor is a very powerful tool and is described in detail as
+\fBapedit\fR.
+
+The next set of parameters control the tracing and function fitting of the
+aperture reference positions along the dispersion direction.  The position
+of a spectrum across the dispersion is determined by the centering
+algorithm (see \fBcenter1d\fR) at a series of evenly spaced steps, given by
+the parameter \fIt_step\fR, along the dispersion.  The step size should be
+fine enough to follow position changes but it is not necessary to measure
+every point.  The fitted points may jump around a little bit due to noise
+and cosmic rays even when summing a number of lines.  Thus, a smooth
+function is fit.  The function type, order, and iterative rejection of
+deviant points is controlled by the other trace parameters.  For more
+discussion consult the help pages for \fBaptrace\fR and \fBicfit\fR.  The
+default is to fit a cubic spline of three pieces with a single iteration of
+3 sigma rejection.
+
+The actual extraction of the spectra by summing across the aperture at each
+point along the dispersion is controlled by the next set of parameters.
+The default extraction simply sums the pixels using partial pixels at the
+ends.  The options allow selection of a weighted sum based on a Poisson
+variance model using the \fIreadnoise\fR and \fIgain\fR detector
+parameters.  Note that if the \fIclean\fR option is selected the variance
+weighted extraction is used regardless of the \fIweights\fR parameter.  The
+sigma thresholds for cleaning are also set in the \fBparams\fR parameters.
+For more on the variance weighted extraction and cleaning see
+\fBapvariance\fR and \fBapprofiles\fR as well as \fBapsum\fR.
+
+The last parameter, \fInsubaps\fR, is used only in special cases when it is
+desired to subdivide the fiber profiles into subapertures prior to
+dispersion correction.  After dispersion correction the subapertures are
+then added together.  The purpose of this is to correct for wavelength
+shifts across a fiber.
+
+\fBScattered Light Subtraction\fR
+
+Scattered light may be subtracted from the input two dimensional image as
+the first step.  This is done using the algorithm described in
+\fBapscatter\fR.  This can be important if there is significant scattered
+light since the flat field/throughput correction will otherwise be
+incorrect.  The algorithm consists of fitting a function to the data
+outside the defined apertures by a specified \fIbuffer\fR at each line or
+column across the dispersion.  The function fitting parameters are the same
+at each line.  Because the fitted functions are independent at each line or
+column a second set of one dimensional functions are fit parallel to the
+dispersion using the evaluated fit values from the cross-dispersion step.
+This produces a smooth scattered light surface which is finally subtracted
+from the input image.  Again the function fitting parameters are the
+same at each line or column though they may be different than the parameters
+used to fit across the dispersion.
+
+The first time the task is run with a particular flat field (or aperture
+reference image if no flat field is used) the scattered light fitting
+parameters are set interactively using that image.  The interactive step
+selects a particular line or column upon which the fitting is done
+interactively with the \fBicfit\fR commands.  A query is first issued
+which allows skipping this interactive stage.  Note that the interactive
+fitting is only for defining the fitting functions and orders.  When
+the graphical \fBicfit\fR fitting is exited (with 'q') there is a second prompt
+allowing you to change the buffer distance (in the first cross-dispersion
+stage) from the apertures, change the line/column, or finally quit.
+
+The initial fitting parameters and the final set parameters are recorded
+in the \fBapscat1\fR and \fBapscat2\fR hidden parameter sets.  These
+parameters are then used automatically for every subsequent image
+which is scattered light corrected.
+
+The scattered light subtraction modifies the input 2D images.  To preserve
+the original data a copy of the original image is made with the same
+root name and the word "noscat" appended.  The scattered light subtracted
+images will have the header keyword "APSCATTE" which is how the task
+avoids repeating the scattered light subtraction during any reprocessing.
+However if the \fIredo\fR option is selected the scattered light subtraction
+will also be redone by first restoring the "noscat" images to the original
+input names.
+
+\fBFlat Field and Fiber Throughput Corrections\fR
+
+Flat field corrections may be made during the basic CCD processing; i.e.
+direct division by the two dimensional flat field observation.  In that
+case do not specify a flat field spectrum; use the null string "".  The
+\fBdofibers\fR task provides an alternative flat field response correction
+based on division of the extracted object spectra by the extracted flat field
+spectra.  A discussion of the theory and merits of flat fielding directly
+verses using the extracted spectra will not be made here.  The
+\fBdofibers\fR flat fielding algorithm is the \fIrecommended\fR method for
+flat fielding since it works well and is not subject to the many problems
+involved in two dimensional flat fielding.
+
+In addition to correcting for pixel-to-pixel response the flat field step
+also corrects for differences in the fiber throughput.  Thus, even if the
+pixel-to-pixel flat field corrections have been made in some other way it
+is desirable to use a sky or dome flat observation for determining a fiber
+throughput correction.  Alternatively, a separately derived throughput
+file may be specified.  This file consists of the aperture numbers
+(the same as used for the aperture reference) and relative throughput
+numbers.
+
+The first step is extraction of the flat field spectrum, if specified,
+using the reference apertures.  Only one flat field is allowed so if
+multiple flat fields are required the data must be reduced in groups.
+After extraction one or more corrections are applied.  If the \fIfitflat\fR
+option is selected (the default) the extracted flat field spectra are
+averaged together and a smooth function is fit.  The default fitting
+function and order are given by the parameters \fIf_function\fR and
+\fIf_order\fR.  If the parameter \fIf_interactive\fR is "yes" then the
+fitting is done interactively using the \fBfit1d\fR task which uses the
+\fBicfit\fR interactive fitting commands.
+
+The fitted function is divided into the individual flat field spectra to
+remove the basic shape of the spectrum while maintaining the relative
+individual pixel responses and any fiber to fiber differences.  This step
+avoids introducing the flat field spectrum shape into the object spectra
+and closely preserves the object counts.
+
+If a throughput image is available (an observation of blank sky
+usually at twilight) it is extracted.  If no flat field is used the average
+signal through each fiber is computed and this becomes the response
+normalization function.  Note that a dome flat may be used in place of a
+sky in the sky flat field parameter for producing throughput only
+corrections.  If a flat field is specified then each sky spectrum is
+divided by the appropriate flat field spectrum.  The total counts through
+each fiber are multiplied into the flat field spectrum thus making the sky
+throughput of each fiber the same.  This correction is important if the
+iillumination of the fibers differs between the flat field source and the
+sky.  Since only the total counts are required the sky or dome flat field
+spectra need not be particularly strong though care must be taken to avoid
+objects.
+
+Instead of a sky flat or other throughput image a separately derived
+throughput file may be used.  It may be used with or without a
+flat field.
+
+The final step is to normalize the flat field spectra by the mean counts of
+all the fibers.  This normalization step is simply to preserve the average
+counts of the extracted object and arc spectra after division by the
+response spectra.  The final relative throughput values are recorded in the
+log and possibly printed on the terminal.
+
+These flat field response steps and algorithm are available as a separate
+task called \fBmsresp1d\fR.
+
+\fBDispersion Correction\fR
+
+Dispersion corrections are applied to the extracted spectra if the
+\fBdispcor\fR parameter is set.  This can be a complicated process which
+the \fBdofibers\fR task tries to simplify for you.  There are three basic
+steps involved; determining the dispersion functions relating pixel
+position to wavelength, assigning the appropriate dispersion function to a
+particular observation, and resampling the spectra to evenly spaced pixels
+in wavelength.
+
+The comparison arc spectra are used to define dispersion functions for the
+fibers using the tasks \fBautoidentify\fR and \fBreidentify\fR.  The
+interactive \fBautoidentify\fR task is only used on the central fiber of the
+first arc spectrum to define the basic reference dispersion solution from
+which all other fibers and arc spectra are automatically derived using
+\fBreidentify\fR. \fBAutoidentify\fR attempts to automatically identify
+the arc lines using the \fIcrval\fR and \fIcdelt\fR parameters.  Whether
+or not it is successful the user is presented with the interactive
+identification graph.  The automatic identifications can be reviewed and a
+new solution or corrections to the automatic solution may be performed.
+
+The set of arc dispersion function parameters are from \fBautoidentify\fR and
+\fBreidentify\fR.  The parameters define a line list for use in
+automatically assigning wavelengths to arc lines, a parameter controlling
+the width of the centering window (which should match the base line
+widths), the dispersion function type and order, parameters to exclude bad
+lines from function fits, and parameters defining whether to refit the
+dispersion function, as opposed to simply determining a zero point shift,
+and the addition of new lines from the line list when reidentifying
+additional arc spectra.  The defaults should generally be adequate and the
+dispersion function fitting parameters may be altered interactively.  One
+should consult the help for the two tasks for additional details of these
+parameters and the operation of \fBautoidentify\fR.
+
+Generally, taking a number of comparison arc lamp exposures interspersed
+with the program spectra is sufficient to accurately dispersion calibrate
+multifiber spectra.  However, there are some other calibration options
+which may be of interest.  These options apply additional calibration data
+consisting either of auxiliary line spectra, such as from dome lights or
+night sky lines, or simultaneous arc lamp spectra taken through a few
+fibers during the object exposure.  These options add complexity to the
+dispersion calibration process.
+
+When only arc comparison lamp spectra are used, dispersion functions are
+determined independently for each fiber of each arc image and then assigned
+to the matching fibers in the program object observations.  The assignment
+consists of selecting one or two arc images to calibrate each object
+image.  When two bracketing arc spectra are used the dispersion functions
+are linearly interpolated (usually based on the time of the observations).
+
+If taking comparison exposures is time-consuming, possibly requiring
+reconfiguration to illuminate the fibers, and the spectrograph is
+expected to be fairly stable apart from small shifts, there are two
+mutually exclusive methods for monitoring
+shifts in the dispersion zero point from the basic arc lamp spectra other
+than taking many arc lamp exposures.  One is to use some fibers to take a
+simultaneous arc spectrum while observing the program objects.  The fibers
+are identified by aperture or beam numbers.  The second method is to use
+\fIauxiliary line spectra\fR, such as mercury lines from the dome lights.
+These spectra are specified with an auxiliary shift arc list, \fIarc2\fR.
+
+When using auxiliary line spectra for monitoring zero point shifts one of
+these spectra is plotted interactively by \fBidentify\fR with the
+reference dispersion function from the reference arc spectrum.  The user
+marks one or more lines which will be used to compute zero point wavelength
+shifts in the dispersion functions automatically.  The actual wavelengths
+of the lines need not be known.  In this case accept the wavelength based
+on the reference dispersion function.  As other observations of the same
+features are made the changes in the positions of the features will be
+tracked as zero point wavelength changes such that wavelengths of the
+features remain constant.
+
+When using auxiliary line spectra the only arc lamp spectrum used is the
+initial arc reference spectrum (the first image in the \fIarcs1\fR list).
+The master dispersion functions are then shifted based on the spectra in
+the \fIarcs2\fR list (which must all be of the same type).  The dispersion
+function assignments made by \fBrefspectra\fR using either the arc
+assignment file or based on header keywords is done in the same way as
+described for the arc lamp images except using the auxiliary spectra.
+
+If simultaneous arcs are used the arc lines are reidentified to determine a
+zero point shift relative to the comparison lamp spectra selected, by
+\fBrefspectra\fR, of the same fiber.  A linear function of aperture
+position on the image across the dispersion verses the zero point shifts
+from the arc fibers is determined and applied to the dispersion functions
+from the assigned calibration arcs for the non-arc fibers.  Note that if
+there are two comparison lamp spectra (before and after the object
+exposure) then there will be two shifts applied to two dispersion functions
+which are then combined using the weights based on the header parameters
+(usually the observation time).
+
+The arc assignments may be done either explicitly with an arc assignment
+table (parameter \fIarctable\fR) or based on a header parameter.  The task
+used is \fBrefspectra\fR and the user should consult this task if the
+default behavior is not what is desired.  The default is to interpolate
+linearly between the nearest arcs based on the Julian date (corrected to
+the middle of the exposure).  The Julian date and a local Julian day number
+(the day number at local noon) are computed automatically by the task
+\fBsetjd\fR and recorded in the image headers under the keywords JD and
+LJD.  In addition the universal time at the middle of the exposure, keyword
+UTMIDDLE, is computed by the task \fBsetairmass\fR and this may also be used
+for ordering the arc and object observations.
+
+An optional step is to use sky lines in the spectra to compute a zeropoint
+dispersion shift that will align the sky lines.  This may improve sky
+subtraction if the iillumination is not the same between the arc calibration
+and the sky.  When selected the object spectrum is dispersion corrected
+using a non-linear dispersion function to avoid resampling the spectrum.
+The sky lines are then reidentified in wavelength space from a template
+list of sky lines.  The mean shift in the lines for each fiber relative to
+the template in that fiber is computed to give the zeropoint shift.  The
+database file is created when the first object is extracted.  You are asked
+to mark the sky lines in one fiber and then the lines are automatically
+reidentified in all other fibers.  Note that this technique requires the
+sky lines be found in all fibers.
+
+The last step of dispersion correction (resampling the spectrum to evenly
+spaced pixels in wavelength) is optional and relatively straightforward.
+If the \fIlinearize\fR parameter is no then the spectra are not resampled
+and the nonlinear dispersion information is recorded in the image header.
+Other IRAF tasks (the coordinate description is specific to IRAF) will use
+this information whenever wavelengths are needed.  If linearizing is
+selected a linear dispersion relation, either linear in the wavelength or
+the log of the wavelength, is defined once and applied to every extracted
+spectrum.  The resampling algorithm  parameters allow selecting the
+interpolation function type, whether to conserve flux per pixel by
+integrating across the extent of the final pixel, and whether to linearize
+to equal linear or logarithmic intervals.  The latter may be appropriate
+for radial velocity studies.  The default is to use a fifth order
+polynomial for interpolation, to conserve flux, and to not use logarithmic
+wavelength bins.  These parameters are described fully in the help for the
+task \fBdispcor\fR which performs the correction.  The interpolation
+function options and the nonlinear dispersion coordinate system is
+described in the help topic \fBonedspec.package\fR.
+
+\fBSky Subtraction\fR
+
+Sky subtraction is selected with the \fIskysubtract\fR processing option.
+The sky spectra are selected by their aperture and beam numbers and
+combined into a single master sky spectrum
+which is then subtracted from each object spectrum.  If the \fIskyedit\fR
+option is selected the sky spectra are plotted using the task
+\fBspecplot\fR.  By default they are superposed to allow identifying
+spectra with unusually high signal due to object contamination.  To
+eliminate a sky spectrum from consideration point at it with the cursor and
+type 'd'.  The last deleted spectrum may be undeleted with 'e'.  This
+allows recovery of incorrect or accidental deletions.
+
+The sky combining algorithm parameters define how the individual sky fiber
+spectra, after interactive editing, are combined before subtraction from
+the object fibers.  The goals of combining are to reduce noise, eliminate
+cosmic-rays, and eliminate fibers with inadvertent objects.  The common
+methods for doing this to use a median and/or a special sigma clipping
+algorithm (see \fBscombine\fR for details).  The scale
+parameter determines whether the individual skys are first scaled to a
+common mode.  The scaling should be used if the throughput is uncertain,
+but in that case you probably did the wrong thing in the throughput
+correction.  If the sky subtraction is done interactively, i.e. with the
+\fIskyedit\fR option selected, then after selecting the spectra to be
+combined a query is made for the combining algorithm.  This allows
+modifying the default algorithm based on the number of sky spectra
+selected since the "avsigclip" rejection algorithm requires at least
+three spectra.
+
+The combined sky spectrum is subtracted from only those spectra specified
+by the object aperture and beam numbers.  Other spectra, such as comparison
+arc spectra, are retained unchanged.  One may include the sky spectra as
+object spectra to produce residual sky spectra for analysis.  The combined
+master sky spectra may be saved if the \fIsaveskys\fR parameter is set.
+The saved sky is given the name of the object spectrum with the prefix
+"sky".
+.ih
+EXAMPLES
+1.  The following example uses artificial data and may be executed
+at the terminal (with IRAF V2.10).  This is also the sequence performed
+by the test procedure "demos dohydra" from the \fBhydra\fR package..
+
+.nf
+sp> hydra
+hy> demos mkhydra
+Creating image demoobj ...
+Creating image demoflat ...
+Creating image demoarc ...
+hy> bye
+sp> type demoapid
+===> demoapid <===
+36 1
+37 0
+38 1
+39 1
+41 0
+42 1
+43 1
+44 0
+45 1
+46 -1
+47 0
+48 1
+sp> specred.verbose = yes
+sp> dofibers demoobj apref=demoflat flat=demoflat arcs1=demoarc \
+>>> fib=12 apid=demoapid width=4. minsep=5. maxsep=7. clean- splot+
+Set reference apertures for demoflat
+Resize apertures for demoflat?  (yes):
+Edit apertures for demoflat?  (yes):
+<Exit with 'q'>
+Fit curve to aperture 36 of demoflat interactively  (yes):
+<Exit with 'q'>
+Fit curve to aperture 37 of demoflat interactively  (yes): N
+Create response function demoflatdemoad.ms
+Extract flat field demoflat
+Fit and ratio flat field demoflat
+<Exit with 'q'>
+Create the normalized response demoflatdemoad.ms
+demoflatdemoad.ms -> demoflatdemoad.ms  using bzero: 0.
+    and bscale: 1.000001
+    mean: 1.000001  median: 1.052665  mode: 1.273547
+    upper: INDEF  lower: INDEF
+Average fiber response:
+1.  1.151023
+2.  0.4519709
+3.  1.250614
+4.  1.287281
+5.  1.271358
+6.  0.6815334
+7.  1.164336
+8.  0.7499605
+9.  1.008654
+10.  1.053296
+11.  0.929967
+Extract arc reference image demoarc
+Determine dispersion solution for demoarc
+<A solution is found and presented.>
+<Type 'f' to look at fit.  Type 'q' to exit fit.>
+<Exit with 'q'>
+
+REIDENTIFY: NOAO/IRAF V2.10BETA valdes@puppis Tue 16:01:07 11-Feb-92
+  Reference image = d....ms.imh, New image = d....ms, Refit = yes
+     Image Data Found    Fit Pix Shift User Shift  Z Shift     RMS
+d....ms - Ap 41 16/20  16/16   0.00796     0.0682  8.09E-6    3.86
+Fit dispersion function interactively? (no|yes|NO|YES) (NO): y
+<Exit with 'q'>
+d....ms - Ap 41 16/20  16/16   0.00796     0.0682  8.09E-6    3.86
+d....ms - Ap 39 19/20  19/19     0.152        1.3  1.95E-4    3.89
+Fit dispersion function interactively? (no|yes|NO|YES) (yes): N
+d....ms - Ap 39 19/20  19/19     0.152        1.3  1.95E-4    3.89
+d....ms - Ap 38 18/20  18/18     0.082      0.697  9.66E-5    3.64
+d....ms - Ap 37 19/20  19/19    0.0632      0.553  1.09E-4    6.05
+d....ms - Ap 36 18/20  18/18    0.0112     0.0954  1.35E-5    4.12
+d....ms - Ap 43 17/20  17/17    0.0259      0.221  3.00E-5    3.69
+d....ms - Ap 44 19/20  19/19     0.168       1.44  2.22E-4    4.04
+d....ms - Ap 45 20/20  20/20      0.18       1.54  2.35E-4    3.95
+d....ms - Ap 47 18/20  18/18  -2.02E-4    0.00544  9.86E-6     4.4
+d....ms - Ap 48 16/20  16/16   0.00192     0.0183  1.44E-6    3.82
+
+Dispersion correct demoarc
+d....ms.imh: w1 = 5748.07..., w2 = 7924.62..., dw = 8.50..., nw = 257
+  Change wavelength coordinate assignments? (yes|no|NO): n
+Extract object spectrum demoobj
+Assign arc spectra for demoobj
+[demoobj] refspec1='demoarc'
+Dispersion correct demoobj
+demoobj.ms.imh: w1 = 5748.078, w2 = 7924.622, dw = 8.502127, nw = 257
+Sky subtract demoobj:  skybeams=0
+Edit the sky spectra? (yes):
+<Exit with 'q'>
+Sky rejection option (none|minmax|avsigclip) (avsigclip):
+demoobj.ms.imh:
+Splot spectrum? (no|yes|NO|YES) (yes):
+Image line/aperture to plot (1:) (1):
+<Look at spectra and change apertures with # key>
+<Exit with 'q'>
+.fi
+.ih
+REVISIONS
+.ls DOFIBERS V2.11
+A sky alignment option was added.
+
+The aperture identification can now be taken from image header keywords.
+
+The initial arc line identifications is done with the automatic line
+identification algorithm.
+.le
+.ls DOFIBERS V2.10.3
+The usual output WCS format is "equispec".  The image format type to be
+processed is selected with the \fIimtype\fR environment parameter.  The
+dispersion axis parameter is now a package parameter.  Images will only
+be processed if the have the CCDPROC keyword.  A \fIdatamax\fR parameter
+has been added to help improve cosmic ray rejection.  A scattered
+light subtraction processing option has been added.
+.le
+.ih
+SEE ALSO
+apedit, apfind, approfiles, aprecenter, apresize, apsum, aptrace,
+apvariance, ccdred, center1d, doargus, dohydra, dofoe, do3fiber, dispcor,
+fit1d, icfit, identify, msresp1d, observatory, onedspec.package,
+refspectra, reidentify, scombine, setairmass, setjd, specplot, splot
+.endhelp
diff --git a/noao/imred/specred/doc/dofibers.ms b/noao/imred/specred/doc/dofibers.ms
new file mode 100644
index 00000000..c0196563
--- /dev/null
+++ b/noao/imred/specred/doc/dofibers.ms
@@ -0,0 +1,1807 @@
+.nr PS 9
+.nr VS 11
+.de V1
+.ft CW
+.nf
+..
+.de V2
+.fi
+.ft R
+..
+.de LS
+.br
+.in +2
+..
+.de LE
+.br
+.sp .5v
+.in -2
+..
+.ND July 1995
+.TL
+Guide to the Multifiber Reduction Task DOFIBERS
+.AU
+Francisco Valdes
+.AI
+IRAF Group - Central Computer Services
+.K2
+.DY
+
+.AB
+The \fBdofibers\fR reduction task is specialized for scattered light
+subtraction, extraction, flat
+fielding, fiber throughput correction, wavelength calibration, and sky
+subtraction of multifiber spectra.  It is a
+command language script which collects and combines the functions and
+parameters of many general purpose tasks to provide a single complete data
+reduction path.  The task provides a degree of guidance, automation, and
+record keeping necessary when dealing with the large amount of data
+generated by multifiber instruments.  Variants of this task are
+\fBdoargus\fR, \fBdofoe\fR, \fBdohydra\fR, and \fBdo3fiber\fR.
+.AE
+.NH
+Introduction
+.LP
+The \fBdofibers\fR reduction task is specialized for scattered light
+subtraction, extraction, flat
+fielding, fiber throughput correction, wavelength calibration, and sky
+subtraction of multifiber spectra.  It is a command language script
+which collects and combines the functions and parameters of many general
+purpose tasks to provide a single complete data reduction path.  The task
+provides a degree of guidance, automation, and record keeping necessary
+when dealing with the large amount of data generated by multifiber
+instruments.  Variants of this task are \fBdoargus\fR, \fBdofoe\fR,
+\fBdohydra\fR, and \fBdo3fiber\fR.
+.LP
+The general organization of the task is to do the interactive setup steps
+first using representative calibration data and then perform the majority
+of the reductions automatically, and possibly as a background process, with
+reference to the setup data.  In addition, the task determines which setup
+and processing operations have been completed in previous executions of the
+task and, contingent on the \f(CWredo\fR and \f(CWupdate\fR options, skip or
+repeat some or all the steps.
+.LP
+The description is divided into a quick usage outline followed by details
+of the parameters and algorithms.  The usage outline is provided as a
+checklist and a refresher for those familiar with this task and the
+component tasks.  It presents only the default or recommended usage Since
+\fBdofibers\fR combines many separate, general purpose tasks the
+description given here refers to these tasks and leaves some of the details
+to their help documentation.
+.NH
+Usage Outline
+.LP
+.IP [1] 6
+The images are first processed with \fBccdproc\fR for overscan,
+bias, and dark corrections.
+The \fBdofibers\fR task will abort if the image header keyword CCDPROC,
+which is added by \fBccdproc\fR, is missing.  If the data processed outside
+of the IRAF \fBccdred\fR package then a dummy CCDPROC keyword should be
+added to the image headers; say with \fBhedit\fR.
+.IP [2]
+Set the \fBdofibers\fR parameters with \fBeparam\fR.  Specify the object
+images to be processed, the flat field image as the aperture reference and
+the flat field, and one or more arc images.  A throughput file or image,
+such as a blank sky observation, may also be specified.  If there are many
+object or arc spectra per setup you might want to prepare "@ files".
+Specify the aperture identification table for the configuration
+if one has been created.  If the image headers contain the SLFIB keywords
+specify an image name; typically the same as the aperture reference
+image.
+You might wish to verify the geometry parameters,
+separations, dispersion direction, etc., which may
+change with different detector setups.  The processing parameters are set
+for complete reductions but for quicklook you might not use the clean
+option or dispersion calibration and sky subtraction.
+
+The parameters are set for a particular configuration and different
+configurations may use different flat fields, arcs, and aperture
+identification tables.
+.IP [3]
+Run the task.  This may be repeated multiple times with different
+observations and the task will generally only do the setup steps
+once and only process new images.  Queries presented during the
+execution for various interactive operations may be answered with
+"yes", "no", "YES", or "NO".  The lower case responses apply just
+to that query while the upper case responses apply to all further
+such queries during the execution and no further queries of that
+type will be made.
+.IP [4]
+The apertures are defined using the specified aperture reference image.
+The spectra are found automatically and apertures assigned based on
+task parameters and the aperture identification table.  Unassigned
+fibers may have a negative beam number and will be ignored in subsequent
+processing.  The resize option sets the aperture size to the widths of
+the profiles at a fixed fraction of the peak height.  The interactive
+review of the apertures is recommended.  If the identifications are off
+by a shift the 'o' key is used.  To exit the aperture review type 'q'.
+.IP [5]
+The fiber positions at a series of points along the dispersion are measured
+and a function is fit to these positions.  This may be done interactively to
+adjust the fitting parameters.  Not all fibers need be examined and the "NO"
+response will quit the interactive fitting.  To exit the interactive
+fitting type 'q'.
+.IP [6]
+If scattered light subtraction is to be done the flat field image is
+used to define the scattered light fitting parameters interactively.
+If one is not specified then the aperture reference image is used for
+this purpose.
+
+There are two queries for the interactive fitting.  A graph of the
+data between the defined reference apertures separated by a specified
+buffer distance is first shown.  The function order and type may be
+adjusted.  After quiting with 'q' the user has the option of changing
+the buffer value and returning to the fitting, changing the image line
+or column to check if the fit parameters are satisfactory at other points,
+or to quit and accept the fit parameters.  After fitting all points
+across the dispersion another graph showing the scattered light from
+the individual fits is shown and the smoothing parameters along the
+dispersion may be adjusted.  Upon quiting with 'q' you have the option
+of checking other cuts parallel to the dispersion or quiting and finishing
+the scattered light function smoothing and subtraction.
+
+If there is a throughput image then this is corrected for scattered light
+noninteractively using the previous fitting parameters.
+.IP [7]
+If flat fielding is to be done the flat field spectra are extracted.  The
+average spectrum over all fibers is determined and a function is fit
+interactively (exit with 'q').  This function is generally of sufficiently
+high order that the overall shape is well fit.  This function is then used
+to normalize the individual flat field spectra.  If a throughput image, a
+sky flat, is specified then the total sky counts through each fiber are
+used to correct the total flat field counts.  Alternatively, a separately
+derived throughput file can be used for specifying throughput corrections.
+If neither type of throughput is used the flat field also provides the
+throughput correction.  The final response spectra are normalized to a unit
+mean over all fibers.  The relative average throughput for each fiber is
+recorded in the log and possibly printed to the terminal.
+.IP [8]
+If dispersion correction is selected the first arc in the arc list is
+extracted.  The middle fiber is used to identify the arc lines and define
+the dispersion function using the task \fBautoidentify\fR.  The
+\fIcrval\fR and \fIcdelt\fR parameters are used in the automatic
+identification.  Whether or not the automatic identification is
+successful you will be shown the result of the arc line identification.
+If the automatic identification is not successful identify a few arc
+lines with 'm' and use the 'l' line list identification command to
+automatically add additional lines and fit the dispersion function.  Check
+the quality of the dispersion function fit with 'f'.  When satisfied exit
+with 'q'.
+.IP [9]
+The remaining fibers are automatically reidentified.  You have the option
+to review the line identifications and dispersion function for each fiber
+and interactively add or delete arc lines and change fitting parameters.
+This can be done selectively, such as when the reported RMS increases
+significantly.
+.IP [10]
+If the spectra are to be resampled to a linear dispersion system
+(which will be the same for all spectra) default dispersion parameters
+are printed and you are allowed to adjust these as desired.
+.IP [11]
+If the sky line alignment option is selected and the sky lines have not
+been identified for a particular aperture identification table then you are
+asked to mark one or more sky lines.  You may simply accept the wavelengths
+of these lines as defined by the dispersion solution for this spectrum and
+fiber or you may specify knowns wavelengths for the lines. These lines will
+be reidentified in all object spectra extracted and a mean zeropoint shift
+will be added to the dispersion solution.  This has the effect of aligning
+these lines to optimize sky subtraction.
+.IP [12]
+The object spectra are now automatically scattered light subtracted,
+ extracted, flat fielded, and dispersion corrected.
+.IP [13]
+When sky subtracting, the individual sky spectra may be reviewed and some
+spectra eliminated using the 'd' key.  The last deleted spectrum may be
+recovered with the 'e' key.  After exiting the review with 'q' you are
+asked for the combining option.  The type of combining is dictated by the
+number of sky fibers.
+.IP [14]
+The option to examine the final spectra with \fBsplot\fR may be given.
+To exit type 'q'.
+.IP [15]
+If scattered light is subtracted from the input data a copy of the
+original image is made by appending "noscat" to the image name.
+If the data are reprocessed with the \fIredo\fR flag the original
+image will be used again to allow modification of the scattered
+light parameters.
+
+The final spectra will have the same name as the original 2D images
+with a ".ms" extension added.  The flat field and arc spectra will
+also have part of the aperture identification table name added to
+allow different configurations to use the same 2D flat field and arcs
+but with different aperture definitions.  If using the sky alignment
+option an image "align" with the aperture identification table name
+applied will also be created.
+.NH
+Spectra and Data Files
+.LP
+The basic input consists of multifiber object and
+calibration spectra stored as IRAF images.
+The type of image format is defined by the
+environment parameter \fIimtype\fR.  Only images with that extension will
+be processed and created.
+The raw CCD images must
+be processed to remove overscan, bias, and dark count effects.  This
+is generally done using the \fBccdred\fR package.
+The \fBdofibers\fR task will abort if the image header keyword CCDPROC,
+which is added by \fBccdproc\fR, is missing.  If the data processed outside
+of the IRAF \fBccdred\fR package then a dummy CCDPROC keyword should be
+added to the image headers; say with \fBhedit\fR.
+Flat fielding is
+generally not done at this stage but as part of \fBdofibers\fR.
+If flat fielding is done as part of the basic CCD processing then
+a flattened flat field, blank sky observation, or throughput file
+should still be created for applying fiber throughput corrections.
+.LP
+The task \fBdofibers\fR uses several types of calibration spectra.  These
+are flat fields, blank sky flat fields, comparison lamp spectra, auxiliary
+mercury line (from the dome lights) or sky line spectra, and simultaneous
+arc spectra taken during the object observation.  The flat field,
+throughput image or file, auxiliary emission line spectra, and simultaneous
+comparison fibers are optional.  If a flat field is used then the sky flat
+or throughput file is optional assuming the flat field has the same fiber
+illumination.  It is legal to specify only a throughput image or file and
+leave the flat field blank in order to simply apply a throughput
+correction.  Because only the total counts through each fiber are used from
+a throughput image, sky flat exposures need not be of high signal per
+pixel.
+.LP
+There are three types of arc calibration methods.  One is to take arc
+calibration exposures through all fibers periodically and apply the
+dispersion function derived from one or interpolated between pairs to the
+object fibers.  This is the most common method.  Another method is to
+use only one or two all-fiber arcs to define the shape of the dispersion
+function and track zero point wavelength shifts with \fIsimultaneous arc\fR
+fibers taken during the object exposure.  The simultaneous arcs may or may
+not be available at the instrument but \fBdofibers\fR can use this type of
+observation.  The arc fibers are identified by their beam or aperture
+numbers.  A related and mutually exclusive method is to use \fIauxiliary
+line spectra\fR such as lines in the dome lights or sky lines to monitor
+shifts relative to a few actual arc exposures.  The main reason to do this
+is if taking arc exposures through all fibers is inconvenient.
+.LP
+The assignment of arc or auxiliary line calibration exposures to object
+exposures is generally done by selecting the nearest in time and
+interpolating.  There are other options possible which are described under
+the task \fBrefspectra\fR.  The most general option is to define a table
+giving the object image name and the one or two arc spectra to be assigned
+to that object.  That file is called an \fIarc assignment table\fR and it
+is one of the optional setup files which can used with \fBdofibers\fR.
+.LP
+The first step in the processing is identifying the spectra in the images.
+The \fIaperture identification table\fR contains information about the fiber
+assignments.  The identification table is not mandatory, sequential numbering
+will be used, but it is highly recommended for keeping track of the objects
+assigned to the fibers.  The aperture identification table may be
+a file containing lines
+specifying an aperture number, a beam number, and an object
+identification.  It may also be an image whose header contains the keywords
+SLFIB with strings consisting of an aperture number, beam number, optional
+right ascension and declination, and a tile.  The file lines or keywords
+must be in the same order as the fibers in the
+image.  The aperture number may be any unique number but it is recommended
+that the fiber number be used.  The beam number is used to flag object,
+sky, arc, or other types of spectra.  The default beam numbers used by the
+task are 0 for sky, 1 for object, and 2 for arc.  The object
+identifications are optional but it is good practice to include them so
+that the data will contain the object information independent of other
+records.  Figure 1 shows an example aperture identification file
+called M33Sch2.
+.V1
+
+.ce
+Figure 1: Example Aperture Identification File
+
+    cl> type m33sch2
+    1 1 143
+    2 1 254
+    3 0 sky
+    4 -1 Broken
+    5 2 arc
+       .
+       .
+       .
+    44 1 s92
+    45 -1 Unassigned
+    46 2 arc
+    47 0 sky
+    48 1 phil2
+
+.V2
+Note the identification of the sky fibers with beam number 0, the object
+fibers with 1, and the arc fibers with 2.
+The broken and unassigned fiber entries, given beam
+number -1, are optional but recommended to give the automatic spectrum
+finding operation the best chance to make the correct identifications.  The
+identification table will vary for each plugboard setup.  Additional
+information about the aperture identification table may be found in the
+description of the task \fBapfind\fR.
+.LP
+An alternative to using an aperture identification table is to give no
+name, the "" empty string, and to explicitly give a range of
+aperture numbers for the skys and possibly for the sky subtraction
+object list in the parameters \f(CWobjaps, skyaps, arcaps, objbeams,
+skybeams,\fR and \f(CWarcbeams\fR.  This is reasonable if the fibers always
+have a fixed typed.  As an example the CTIO Argus instrument always
+alternates object and sky fibers so the object apertures can be given
+as 1x2 and the sky fibers as 2x2; i.e. objects are the odd numbered
+apertures and skys are the even numbered apertures.
+.LP
+The final reduced spectra are recorded in two or three dimensional IRAF
+images.  The images have the same name as the original images with an added
+".ms" extension.  Each line in the reduced image is a one dimensional
+spectrum with associated aperture, wavelength, and identification
+information.  When the \f(CWextras\fR parameter is set the lines in the
+third dimension contain additional information (see
+\fBapsum\fR for further details).  These spectral formats are accepted by the
+one dimensional spectroscopy tools such as the plotting tasks \fBsplot\fR
+and \fBspecplot\fR.  The special task \fBscopy\fR may be used to extract
+specific apertures or to change format to individual one dimensional
+images.
+.NH
+Package Parameters
+.LP
+The \fBspecred\fR package parameters, shown in Figure 2, set parameters
+affecting all the tasks in the package.
+.KS
+.V1
+
+.ce
+Figure 2: Package Parameter Set for SPECRED
+
+                           I R A F
+            Image Reduction and Analysis Facility
+PACKAGE = imred
+   TASK = specred
+
+(extinct= onedstds$kpnoextinct.dat) Extinction file
+(caldir = onedstds$spec16redcal/) Standard star calibration directory
+(observa=  observatory) Observatory of data
+(interp =        poly5) Interpolation type
+(dispaxi=            2) Image axis for 2D images
+(nsum   =            1) Number of lines/columns to sum for 2D images
+
+(databas=     database) Database
+(verbose=           no) Verbose output?
+(logfile=      logfile) Log file
+(plotfil=             ) Plot file
+
+(records=             ) Record number extensions
+(version= SPECRED V3: April 1992)
+
+.KE
+.V2
+The dispersion axis parameter defines the image axis along which the
+dispersion runs.  This is used if the image header doesn't define the
+dispersion axis with the DISPAXIS keyword.
+The observatory parameter is used if there is no
+OBSERVAT keyword in the image header (see \fBobservatory\fR for more
+details).  The spectrum interpolation type might be changed to "sinc" but
+with the cautions given in \fBonedspec.package\fR.
+The other parameters define the standard I/O functions.
+The verbose parameter selects whether to print everything which goes
+into the log file on the terminal.  It is useful for monitoring
+what the \fBdofibers\fR task does.  The log and plot files are useful for
+keeping a record of the processing.  A log file is highly recommended.
+A plot file provides a record of apertures, traces, and extracted spectra
+but can become quite large.
+The plotfile is most conveniently viewed and printed with \fBgkimosaic\fR.
+.NH
+Processing Parameters
+.LP
+The \fBdofibers\fR parameters are shown in Figure 3.
+.KS
+.V1
+
+.ce
+Figure 3: Parameter Set for DOFIBERS
+
+                           I R A F
+            Image Reduction and Analysis Facility
+PACKAGE = specred
+   TASK = dofibers
+
+objects =               List of object spectra
+(apref  =             ) Aperture reference spectrum
+(flat   =             ) Flat field spectrum
+(through=             ) Throughput file or image (optional)
+(arcs1  =             ) List of arc spectra
+(arcs2  =             ) List of shift arc spectra
+(arctabl=             ) Arc assignment table (optional)
+
+.KE
+.V1
+(readnoi=           0.) Read out noise sigma (photons)
+(gain   =           1.) Photon gain (photons/data number)
+(datamax=        INDEF) Max data value / cosmic ray threshold
+(fibers =           97) Number of fibers
+(width  =          12.) Width of profiles (pixels)
+(minsep =           8.) Minimum separation between fibers (pixels)
+(maxsep =          15.) Maximum separation between fibers (pixels)
+(apidtab=             ) Aperture identifications
+(crval  =        INDEF) Approximate wavelength
+(cdelt  =        INDEF) Approximate dispersion
+(objaps =             ) Object apertures
+(skyaps =             ) Sky apertures
+(arcaps =             ) Arc apertures
+(objbeam=          0,1) Object beam numbers
+(skybeam=            0) Sky beam numbers
+(arcbeam=             ) Arc beam numbers
+
+(scatter=           no) Subtract scattered light?
+(fitflat=          yes) Fit and ratio flat field spectrum?
+(clean  =          yes) Detect and replace bad pixels?
+(dispcor=          yes) Dispersion correct spectra?
+(savearc=          yes) Save simultaneous arc apertures?
+(skysubt=          yes) Subtract sky?
+(skyedit=          yes) Edit the sky spectra?
+(savesky=          yes) Save sky spectra?
+(splot  =           no) Plot the final spectrum?
+(redo   =           no) Redo operations if previously done?
+(update =          yes) Update spectra if cal data changes?
+(batch  =           no) Extract objects in batch?
+(listonl=           no) List steps but don't process?
+
+(params =             ) Algorithm parameters
+
+.V2
+The list of objects and arcs can be @ files if desired.  The aperture
+reference spectrum is usually the same as the flat field spectrum though it
+could be any exposure with enough signal to accurately define the positions
+and trace the spectra.  The first list of arcs are the standard Th-Ar or
+HeNeAr comparison arc spectra (they must all be of the same type).  The
+second list of arcs are the auxiliary emission line exposures mentioned
+previously.
+.LP
+The detector read out noise and gain are used for cleaning and variance
+(optimal) extraction.  This is specified either explicitly or by reference
+to an image header keyword.
+The variance
+weighting and cosmic-ray cleanning are sensitive to extremely strong
+cosmic-rays; ones which are hundreds of times brighter than the
+spectrum.  The \fIdatamax\fR is used to set an upper limit for any
+real data.  Any pixels above this value will be flagged as cosmic-rays
+and will not affect the extractions.
+The dispersion axis defines the wavelength direction of spectra in
+the image if not defined in the image header by the keyword DISPAXIS.  The
+width and separation parameters define the dimensions (in pixels) of the
+spectra (fiber profile) across the dispersion.  The width parameter
+primarily affects the centering.  The maximum separation parameter is
+important if missing spectra from the aperture identification table are to
+be correctly skipped.  The number of fibers is either the actual number
+of fibers or the number in the aperture identification table.  An attempt
+is made to account for unassigned or missing fibers.  As a recommendation
+the actual number of fibers should be specified.
+.LP
+The approximate central wavelength and dispersion are used for the
+automatic identification of the arc reference.  They may be specified
+as image header keywords or values.  The INDEF values search the
+entire range of the coordinate reference file but the automatic
+line identification algorithm works much better and faster if
+approximate values are given.
+.LP
+The task needs to know which fibers are object, sky if sky subtraction is
+to be done, and simultaneous arcs if used.  One could explicitly give the
+aperture numbers but the recommended way, provided an aperture
+identification table is used, is to select the apertures based on the beam
+numbers.  The default values are recommended beam numbers.  Sky
+subtracted sky spectra are useful for evaluating the sky subtraction.
+Since only the spectra identified as objects are sky subtracted one can
+exclude fibers from the sky subtraction.  For example, if the
+\f(CWobjbeams\fR parameter is set to 1 then only those fibers with a beam of
+1 will be sky subtracted.  All other fibers will remain in the extracted
+spectra but will not be sky subtracted.
+.LP
+The next set of parameters select the processing steps and options.  The
+scattered light option allows fitting and subtracting a scattered light
+surface from the input object and flat field.  If there is significant
+scattered light which is not subtracted the fiber throughput correction
+will not be accurate.  The
+flat fitting option allows fitting and removing the overall shape of the
+flat field spectra while preserving the pixel-to-pixel response
+corrections.  This is useful for maintaining the approximate object count
+levels and not introducing the reciprocal of the flat field spectrum into
+the object spectra.  The \f(CWclean\fR option invokes a profile fitting and
+deviant point rejection algorithm as well as a variance weighting of points
+in the aperture.  These options require knowing the effective (i.e.
+accounting for any image combining) read out noise and gain.  For a
+discussion of cleaning and variance weighted extraction see
+\fBapvariance\fR and \fBapprofiles\fR.
+.LP
+The dispersion correction option selects whether to extract arc spectra,
+determine a dispersion function, assign them to the object spectra, and,
+possibly, resample the spectra to a linear (or log-linear) wavelength
+scale.  If simultaneous arc fibers are defined there is an option to delete
+them from the final spectra when they are no longer needed.
+.LP
+The sky alignment option allows applying a zeropoint dispersion shift
+to all fibers based on one or more sky lines.  This requires all fibers
+to have the sky lines visible.  When there are sky lines this will
+improve the sky subtraction if there is a systematic error in the
+fiber illumination between the sky and the arc calibration.
+.LP
+The sky subtraction option selects whether to combine the sky fiber spectra
+and subtract this sky from the object fiber spectra.  \fIDispersion
+correction and sky subtraction are independent operations.\fR  This means
+that if dispersion correction is not done then the sky subtraction will be
+done with respect to pixel coordinates.  This might be desirable in some
+quick look cases though it is incorrect for final reductions.
+.LP
+The sky subtraction option has two additional options.  The individual sky
+spectra may be examined and contaminated spectra deleted interactively
+before combining.  This can be a useful feature in crowded regions.  The
+final combined sky spectrum may be saved for later inspection in an image
+with the spectrum name prefixed by \fBsky\fR.
+.LP
+After a spectrum has been processed it is possible to examine the results
+interactively using the \fBsplot\fR tasks.  This option has a query which
+may be turned off with "YES" or "NO" if there are multiple spectra to be
+processed.
+.LP
+Generally once a spectrum has been processed it will not be reprocessed if
+specified as an input spectrum.  However, changes to the underlying
+calibration data can cause such spectra to be reprocessed if the
+\f(CWupdate\fR flag is set.  The changes which will cause an update are a new
+aperture identification table, a new reference image, new flat fields, and a
+new arc reference.  If all input spectra are to be processed regardless of
+previous processing the \f(CWredo\fR flag may be used.  Note that
+reprocessing clobbers the previously processed output spectra.
+.LP
+The \f(CWbatch\fR processing option allows object spectra to be processed as
+a background or batch job.  This will only occur if sky spectra editing and
+\fBsplot\fR review (interactive operations) are turned off, either when the
+task is run or by responding with "NO" to the queries during processing.
+.LP
+The \f(CWlistonly\fR option prints a summary of the processing steps which
+will be performed on the input spectra without actually doing anything.
+This is useful for verifying which spectra will be affected if the input
+list contains previously processed spectra.  The listing does not include
+any arc spectra which may be extracted to dispersion calibrate an object
+spectrum.
+.LP
+The last parameter (excluding the task mode parameter) points to another
+parameter set for the algorithm parameters.  The way \fBdofibers\fR works
+this may not have any value and the parameter set \fBparams\fR is always
+used.  The algorithm parameters are discussed further in the next section.
+.NH
+Algorithms and Algorithm Parameters
+.LP
+This section summarizes the various algorithms used by the \fBdofibers\fR
+task and the parameters which control and modify the algorithms.  The
+algorithm parameters available to the user are collected in the parameter
+set \fBparams\fR.  These parameters are taken from the various general
+purpose tasks used by the \fBdofibers\fR processing task.  Additional
+information about these parameters and algorithms may be found in the help
+for the actual task executed.  These tasks are identified in the parameter
+section listing in parenthesis.  The aim of this parameter set organization
+is to collect all the algorithm parameters in one place separate from the
+processing parameters and include only those which are relevant for
+multifiber data.  The parameter values can be changed from the
+defaults by using the parameter editor,
+.V1
+
+	cl> epar params
+
+.V2
+or simple typing \f(CWparams\fR.  The parameter editor can also be
+entered when editing the \fBdofibers\fR parameters by typing \f(CW:e
+params\fR or simply \f(CW:e\fR if positioned at the \f(CWparams\fR
+parameter.  Figure 4 shows the parameter set.
+.KS
+.V1
+
+.ce
+Figure 4: Algorithm Parameter Set
+
+                           I R A F
+            Image Reduction and Analysis Facility
+PACKAGE = specred
+   TASK = params
+
+(line   =        INDEF) Default dispersion line
+(nsum   =           10) Number of dispersion lines to sum
+(order  =   decreasing) Order of apertures
+(extras =           no) Extract sky, sigma, etc.?
+
+                        -- DEFAULT APERTURE LIMITS --
+(lower  =          -5.) Lower aperture limit relative to center
+(upper  =           5.) Upper aperture limit relative to center
+
+                        -- AUTOMATIC APERTURE RESIZING PARAMETERS --
+(ylevel =         0.05) Fraction of peak or intensity for resizing
+
+.KE
+.KS
+.V1
+                        -- TRACE PARAMETERS --
+(t_step =           10) Tracing step
+(t_funct=      spline3) Trace fitting function
+(t_order=            3) Trace fitting function order
+(t_niter=            1) Trace rejection iterations
+(t_low  =           3.) Trace lower rejection sigma
+(t_high =           3.) Trace upper rejection sigma
+
+.KE
+.KS
+.V1
+                        -- SCATTERED LIGHT PARAMETERS --
+(buffer =           1.) Buffer distance from apertures
+(apscat1=             ) Fitting parameters across the dispersion
+(apscat2=             ) Fitting parameters along the dispersion
+
+.KE
+.KS
+.V1
+                        -- APERTURE EXTRACTION PARAMETERS --
+(weights=         none) Extraction weights (none|variance)
+(pfit   =        fit1d) Profile fitting algorithm (fit1d|fit2d)
+(weights=         none) Extraction weights (none|variance)
+(pfit   =        fit1d) Profile fitting algorithm (fit1d|fit2d)
+(lsigma =           3.) Lower rejection threshold
+(usigma =           3.) Upper rejection threshold
+(nsubaps=            1) Number of subapertures
+
+.KE
+.KS
+.V1
+                        -- FLAT FIELD FUNCTION FITTING PARAMETERS --
+(f_inter=          yes) Fit flat field interactively?
+(f_funct=      spline3) Fitting function
+(f_order=           10) Fitting function order
+
+.KE
+.KS
+.V1
+                        -- ARC DISPERSION FUNCTION PARAMETERS --
+(coordli=linelists$idhenear.dat) Line list
+(match  =          -3.) Line list matching limit in Angstroms
+(fwidth =           4.) Arc line widths in pixels
+(cradius=          10.) Centering radius in pixels
+(i_funct=      spline3) Coordinate function
+(i_order=            3) Order of dispersion function
+(i_niter=            2) Rejection iterations
+(i_low  =           3.) Lower rejection sigma
+(i_high =           3.) Upper rejection sigma
+(refit  =          yes) Refit coordinate function when reidentifying?
+(addfeat=           no) Add features when reidentifying?
+
+.KE
+.KS
+.V1
+                        -- AUTOMATIC ARC ASSIGNMENT PARAMETERS --
+(select =       interp) Selection method for reference spectra
+(sort   =           jd) Sort key
+(group  =          ljd) Group key
+(time   =           no) Is sort key a time?
+(timewra=          17.) Time wrap point for time sorting
+
+.KE
+.KS
+.V1
+                        -- DISPERSION CORRECTION PARAMETERS --
+(lineari=          yes) Linearize (interpolate) spectra?
+(log    =           no) Logarithmic wavelength scale?
+(flux   =          yes) Conserve flux?
+
+.KE
+.KS
+.V1
+                        -- SKY SUBTRACTION PARAMETERS --
+(combine=      average) Type of combine operation
+(reject =    avsigclip) Sky rejection option
+(scale  =         none) Sky scaling option
+
+.KE
+.V2
+.NH 2
+Extraction
+.LP
+The identification of the spectra in the two dimensional images and their
+scattered light subtraction and extraction to one dimensional spectra
+in multispec format is accomplished
+using the tasks from the \fBapextract\fR package.  The first parameters
+through \f(CWnsubaps\fR control the extractions.
+.LP
+The dispersion line is that used for finding the spectra, for plotting in
+the aperture editor, and as the starting point for tracing.  The default
+value of \fBINDEF\fR selects the middle of the image.  The aperture
+finding, adjusting, editing, and tracing operations also allow summing a
+number of dispersion lines to improve the signal.  The number of lines is
+set by the \f(CWnsum\fR parameter.
+.LP
+The order parameter defines whether the order of the aperture
+identifications in the aperture identification table (or the default
+sequential numbers if no file is used) is in the same sense as the image
+coordinates (increasing) or the opposite sense (decreasing).  If the
+aperture identifications turn out to be opposite to what is desired when
+viewed in the aperture editing graph then simply change this parameter.
+.LP
+The basic data output by the spectral extraction routines are the one
+dimensional spectra.  Additional information may be output when the
+\f(CWextras\fR option is selected and the cleaning or variance weighting
+options are also selected.  In this case a three dimensional image is
+produced with the first element of the third dimension being the cleaned
+and/or weighted spectra, the second element being the uncleaned and
+unweighted spectra, and the third element being an estimate of the sigma
+of each pixel in the extracted spectrum.  Currently the sigma data is not
+used by any other tasks and is only for reference.
+.LP
+The initial step of finding the fiber spectra in the aperture reference
+image consists of identifying the peaks in a cut across the dispersion,
+eliminating those which are closer to each other than the \f(CWminsep\fR
+distance, and then keeping the specified \f(CWnfibers\fR highest peaks.  The
+centers of the profiles are determined using the \fBcenter1d\fR algorithm
+which uses the \f(CWwidth\fR parameter.
+.LP
+Apertures are then assigned to each spectrum.  The initial edges of the
+aperture relative to the center are defined by the \f(CWlower\fR and
+\f(CWupper\fR parameters.  The trickiest part of assigning the apertures is
+relating the aperture identification from the aperture identification table
+to automatically selected fiber profiles.  The first aperture id in the
+file is assigned to the first spectrum found using the \f(CWorder\fR
+parameter to select the assignment direction.  The numbering proceeds in
+this way except that if a gap greater than a multiple of the \f(CWmaxsep\fR
+parameter is encountered then assignments in the file are skipped under the
+assumption that a fiber is missing (broken).  If unassigned fibers are
+still visible in a flat field, either by design or by scattered light, the
+unassigned fibers can be included in the number of fibers to find and then
+the unassigned (negative beam number) apertures are excluded from any
+extraction.  For more on the finding and assignment algorithms see
+\fBapfind\fR.
+.LP
+The initial apertures are the same for all spectra but they can each be
+automatically resized.  The automatic resizing sets the aperture limits
+at a fraction of the peak relative to the interfiber minimum.
+The default \f(CWylevel\fR is to resize the apertures to 5% of the peak.
+See the description for the task \fBapresize\fR for further details.
+.LP
+The user is given the opportunity to graphically review and adjust the
+aperture definitions.  This is recommended.  As mentioned previously, the
+correct identification of the fibers is tricky and it is fundamentally
+important that this be done correctly; otherwise the spectrum
+identifications will not be for the objects they say.  An important command in
+this regard is the 'o' key which allows reordering the identifications
+based on the aperture identification table.  This is required if the first
+fiber is actually missing since the initial assignment begins assigning the
+first spectrum found with the first entry in the aperture file.  The
+aperture editor is a very powerful tool and is described in detail as
+\fBapedit\fR.
+.LP
+The next set of parameters control the tracing and function fitting of the
+aperture reference positions along the dispersion direction.  The position
+of a spectrum across the dispersion is determined by the centering
+algorithm (see \fBcenter1d\fR) at a series of evenly spaced steps, given by
+the parameter \f(CWt_step\fR, along the dispersion.  The step size should be
+fine enough to follow position changes but it is not necessary to measure
+every point.  The fitted points may jump around a little bit due to noise
+and cosmic rays even when summing a number of lines.  Thus, a smooth
+function is fit.  The function type, order, and iterative rejection of
+deviant points is controlled by the other trace parameters.  For more
+discussion consult the help pages for \fBaptrace\fR and \fBicfit\fR.  The
+default is to fit a cubic spline of three pieces with a single iteration of
+3 sigma rejection.
+.LP
+The actual extraction of the spectra by summing across the aperture at each
+point along the dispersion is controlled by the next set of parameters.
+The default extraction simply sums the pixels using partial pixels at the
+ends.  The options allow selection of a weighted sum based on a Poisson
+variance model using the \f(CWreadnoise\fR and \f(CWgain\fR detector
+parameters.  Note that if the \f(CWclean\fR option is selected the variance
+weighted extraction is used regardless of the \f(CWweights\fR parameter.  The
+sigma thresholds for cleaning are also set in the \fBparams\fR parameters.
+For more on the variance weighted extraction and cleaning see
+\fBapvariance\fR and \fBapprofiles\fR as well as \fBapsum\fR.
+.LP
+The last parameter, \f(CWnsubaps\fR, is used only in special cases when it is
+desired to subdivide the fiber profiles into subapertures prior to
+dispersion correction.  After dispersion correction the subapertures are
+then added together.  The purpose of this is to correct for wavelength
+shifts across a fiber.
+.NH 2
+Scattered Light Subtraction
+.LP
+Scattered light may be subtracted from the input two dimensional image as
+the first step.  This is done using the algorithm described in
+\fBapscatter\fR.  This can be important if there is significant scattered
+light since the flat field/throughput correction will otherwise be
+incorrect.  The algorithm consists of fitting a function to the data
+outside the defined apertures by a specified \fIbuffer\fR at each line or
+column across the dispersion.  The function fitting parameters are the same
+at each line.  Because the fitted functions are independent at each line or
+column a second set of one dimensional functions are fit parallel to the
+dispersion using the evaluated fit values from the cross-dispersion step.
+This produces a smooth scattered light surface which is finally subtracted
+from the input image.  Again the function fitting parameters are the
+same at each line or column though they may be different than the parameters
+used to fit across the dispersion.
+.LP
+The first time the task is run with a particular flat field (or aperture
+reference image if no flat field is used) the scattered light fitting
+parameters are set interactively using that image.  The interactive step
+selects a particular line or column upon which the fitting is done
+interactively with the \fBicfit\fR commands.  A query is first issued
+which allows skipping this interactive stage.  Note that the interactive
+fitting is only for defining the fitting functions and orders.  When
+the graphical \fBicfit\fR fitting is exited (with 'q') there is a second prompt
+allowing you to change the buffer distance (in the first cross-dispersion
+stage) from the apertures, change the line/column, or finally quit.
+.LP
+The initial fitting parameters and the final set parameters are recorded
+in the \fBapscat1\fR and \fBapscat2\fR hidden parameter sets.  These
+parameters are then used automatically for every subsequent image
+which is scattered light corrected.
+.LP
+The scattered light subtraction modifies the input 2D images.  To preserve
+the original data a copy of the original image is made with the same
+root name and the word "noscat" appended.  The scattered light subtracted
+images will have the header keyword "APSCATTE" which is how the task
+avoids repeating the scattered light subtraction during any reprocessing.
+However if the \fIredo\fR option is selected the scattered light subtraction
+will also be redone by first restoring the "noscat" images to the original
+input names.
+.NH 2
+Flat Field and Fiber Throughput Corrections
+.LP
+Flat field corrections may be made during the basic CCD processing; i.e.
+direct division by the two dimensional flat field observation.  In that
+case do not specify a flat field spectrum; use the null string "".  The
+\fBdofibers\fR task provides an alternative flat field response correction
+based on division of the extracted object spectra by the extracted flat field
+spectra.  A discussion of the theory and merits of flat fielding directly
+verses using the extracted spectra will not be made here.  The
+\fBdofibers\fR flat fielding algorithm is the \fIrecommended\fR method for
+flat fielding since it works well and is not subject to the many problems
+involved in two dimensional flat fielding.
+.LP
+In addition to correcting for pixel-to-pixel response the flat field step
+also corrects for differences in the fiber throughput.  Thus, even if the
+pixel-to-pixel flat field corrections have been made in some other way it
+is desirable to use a sky or dome flat observation for determining a fiber
+throughput correction.  Alternatively, a separately derived throughput
+file may be specified.  This file consists of the aperture numbers
+(the same as used for the aperture reference) and relative throughput
+numbers.
+.LP
+The first step is extraction of the flat field spectrum, if specified,
+using the reference apertures.  Only one flat field is allowed so if
+multiple flat fields are required the data must be reduced in groups.
+After extraction one or more corrections are applied.  If the \f(CWfitflat\fR
+option is selected (the default) the extracted flat field spectra are
+averaged together and a smooth function is fit.  The default fitting
+function and order are given by the parameters \f(CWf_function\fR and
+\f(CWf_order\fR.  If the parameter \f(CWf_interactive\fR is "yes" then the
+fitting is done interactively using the \fBfit1d\fR task which uses the
+\fBicfit\fR interactive fitting commands.
+.LP
+The fitted function is divided into the individual flat field spectra to
+remove the basic shape of the spectrum while maintaining the relative
+individual pixel responses and any fiber to fiber differences.  This step
+avoids introducing the flat field spectrum shape into the object spectra
+and closely preserves the object counts.
+.LP
+If a throughput image is available (an observation of blank sky
+usually at twilight) it is extracted.  If no flat field is used the average
+signal through each fiber is computed and this becomes the response
+normalization function.  Note that a dome flat may be used in place of a
+sky in the sky flat field parameter for producing throughput only
+corrections.  If a flat field is specified then each sky spectrum is
+divided by the appropriate flat field spectrum.  The total counts through
+each fiber are multiplied into the flat field spectrum thus making the sky
+throughput of each fiber the same.  This correction is important if the
+illumination of the fibers differs between the flat field source and the
+sky.  Since only the total counts are required the sky or dome flat field
+spectra need not be particularly strong though care must be taken to avoid
+objects.
+.LP
+Instead of a sky flat or other throughput image a separately derived
+throughput file may be used.  It may be used with or without a
+flat field.
+.LP
+The final step is to normalize the flat field spectra by the mean counts of
+all the fibers.  This normalization step is simply to preserve the average
+counts of the extracted object and arc spectra after division by the
+response spectra.  The final relative throughput values are recorded in the
+log and possibly printed on the terminal.
+.LP
+These flat field response steps and algorithm are available as a separate
+task called \fBmsresp1d\fR.
+.NH
+Dispersion Correction
+.LP
+Dispersion corrections are applied to the extracted spectra if the
+\fBdispcor\fR parameter is set.  This can be a complicated process which
+the \fBdofibers\fR task tries to simplify for you.  There are three basic
+steps involved; determining the dispersion functions relating pixel
+position to wavelength, assigning the appropriate dispersion function to a
+particular observation, and resampling the spectra to evenly spaced pixels
+in wavelength.
+.LP
+The comparison arc spectra are used to define dispersion functions for the
+fibers using the tasks \fBautoidentify\fR and \fBreidentify\fR.  The
+interactive \fBautoidentify\fR task is only used on the central fiber of the
+first arc spectrum to define the basic reference dispersion solution from
+which all other fibers and arc spectra are automatically derived using
+\fBreidentify\fR. \fBAutoidentify\fR attempts to automatically identify
+the arc lines using the \fIcrval\fR and \fIcdelt\fR parameters.  Whether
+or not it is successful the user is presented with the interactive
+identification graph.  The automatic identifications can be reviewed and a
+new solution or corrections to the automatic solution may be performed.
+.LP
+The set of arc dispersion function parameters are from \fBautoidentify\fR and
+\fBreidentify\fR.  The parameters define a line list for use in
+automatically assigning wavelengths to arc lines, a parameter controlling
+the width of the centering window (which should match the base line
+widths), the dispersion function type and order, parameters to exclude bad
+lines from function fits, and parameters defining whether to refit the
+dispersion function, as opposed to simply determining a zero point shift,
+and the addition of new lines from the line list when reidentifying
+additional arc spectra.  The defaults should generally be adequate and the
+dispersion function fitting parameters may be altered interactively.  One
+should consult the help for the two tasks for additional details of these
+parameters and the operation of \fBautoidentify\fR.
+.LP
+Generally, taking a number of comparison arc lamp exposures interspersed
+with the program spectra is sufficient to accurately dispersion calibrate
+multifiber spectra.  However, there are some other calibration options
+which may be of interest.  These options apply additional calibration data
+consisting either of auxiliary line spectra, such as from dome lights or
+night sky lines, or simultaneous arc lamp spectra taken through a few
+fibers during the object exposure.  These options add complexity to the
+dispersion calibration process.
+.LP
+When only arc comparison lamp spectra are used, dispersion functions are
+determined independently for each fiber of each arc image and then assigned
+to the matching fibers in the program object observations.  The assignment
+consists of selecting one or two arc images to calibrate each object
+image.  When two bracketing arc spectra are used the dispersion functions
+are linearly interpolated (usually based on the time of the observations).
+.LP
+If taking comparison exposures is time-consuming, possibly requiring
+reconfiguration to illuminate the fibers, and the spectrograph is
+expected to be fairly stable apart from small shifts, there are two
+mutually exclusive methods for monitoring
+shifts in the dispersion zero point from the basic arc lamp spectra other
+than taking many arc lamp exposures.  One is to use some fibers to take a
+simultaneous arc spectrum while observing the program objects.  The fibers
+are identified by aperture or beam numbers.  The second method is to use
+\fIauxiliary line spectra\fR, such as mercury lines from the dome lights.
+These spectra are specified with an auxiliary shift arc list, \f(CWarc2\fR.
+.LP
+When using auxiliary line spectra for monitoring zero point shifts one of
+these spectra is plotted interactively by \fBidentify\fR with the
+reference dispersion function from the reference arc spectrum.  The user
+marks one or more lines which will be used to compute zero point wavelength
+shifts in the dispersion functions automatically.  The actual wavelengths
+of the lines need not be known.  In this case accept the wavelength based
+on the reference dispersion function.  As other observations of the same
+features are made the changes in the positions of the features will be
+tracked as zero point wavelength changes such that wavelengths of the
+features remain constant.
+.LP
+When using auxiliary line spectra the only arc lamp spectrum used is the
+initial arc reference spectrum (the first image in the \f(CWarcs1\fR list).
+The master dispersion functions are then shifted based on the spectra in
+the \f(CWarcs2\fR list (which must all be of the same type).  The dispersion
+function assignments made by \fBrefspectra\fR using either the arc
+assignment file or based on header keywords is done in the same way as
+described for the arc lamp images except using the auxiliary spectra.
+.LP
+If simultaneous arcs are used the arc lines are reidentified to determine a
+zero point shift relative to the comparison lamp spectra selected, by
+\fBrefspectra\fR, of the same fiber.  A linear function of aperture
+position on the image across the dispersion verses the zero point shifts
+from the arc fibers is determined and applied to the dispersion functions
+from the assigned calibration arcs for the non-arc fibers.  Note that if
+there are two comparison lamp spectra (before and after the object
+exposure) then there will be two shifts applied to two dispersion functions
+which are then combined using the weights based on the header parameters
+(usually the observation time).
+.LP
+The arc assignments may be done either explicitly with an arc assignment
+table (parameter \f(CWarctable\fR) or based on a header parameter.  The task
+used is \fBrefspectra\fR and the user should consult this task if the
+default behavior is not what is desired.  The default is to interpolate
+linearly between the nearest arcs based on the Julian date (corrected to
+the middle of the exposure).  The Julian date and a local Julian day number
+(the day number at local noon) are computed automatically by the task
+\fBsetjd\fR and recorded in the image headers under the keywords JD and
+LJD.  In addition the universal time at the middle of the exposure, keyword
+UTMIDDLE, is computed by the task \fBsetairmass\fR and this may also be used
+for ordering the arc and object observations.
+.LP
+.LP
+An optional step is to use sky lines in the spectra to compute a zeropoint
+dispersion shift that will align the sky lines.  This may improve sky
+subtraction if the illumination is not the same between the arc calibration
+and the sky.  When selected the object spectrum is dispersion corrected
+using a non-linear dispersion function to avoid resampling the spectrum.
+The sky lines are then reidentified in wavelength space from a template
+list of sky lines.  The mean shift in the lines for each fiber relative to
+the template in that fiber is computed to give the zeropoint shift.  The
+database file is created when the first object is extracted.  You are asked
+to mark the sky lines in one fiber and then the lines are automatically
+reidentified in all other fibers.  Note that this technique requires the
+sky lines be found in all fibers.
+.LP
+The last step of dispersion correction (resampling the spectrum to evenly
+spaced pixels in wavelength) is optional and relatively straightforward.
+If the \f(CWlinearize\fR parameter is no then the spectra are not resampled
+and the nonlinear dispersion information is recorded in the image header.
+Other IRAF tasks (the coordinate description is specific to IRAF) will use
+this information whenever wavelengths are needed.  If linearizing is
+selected a linear dispersion relation, either linear in the wavelength or
+the log of the wavelength, is defined once and applied to every extracted
+spectrum.  The resampling algorithm  parameters allow selecting the
+interpolation function type, whether to conserve flux per pixel by
+integrating across the extent of the final pixel, and whether to linearize
+to equal linear or logarithmic intervals.  The latter may be appropriate
+for radial velocity studies.  The default is to use a fifth order
+polynomial for interpolation, to conserve flux, and to not use logarithmic
+wavelength bins.  These parameters are described fully in the help for the
+task \fBdispcor\fR which performs the correction.  The interpolation
+function options and the nonlinear dispersion coordinate system is
+described in the help topic \fBonedspec.package\fR.
+.NH
+Sky Subtraction
+.LP
+Sky subtraction is selected with the \f(CWskysubtract\fR processing option.
+The sky spectra are selected by their aperture and beam numbers and
+combined into a single master sky spectrum
+which is then subtracted from each object spectrum.  If the \f(CWskyedit\fR
+option is selected the sky spectra are plotted using the task
+\fBspecplot\fR.  By default they are superposed to allow identifying
+spectra with unusually high signal due to object contamination.  To
+eliminate a sky spectrum from consideration point at it with the cursor and
+type 'd'.  The last deleted spectrum may be undeleted with 'e'.  This
+allows recovery of incorrect or accidental deletions.
+.LP
+The sky combining algorithm parameters define how the individual sky fiber
+spectra, after interactive editing, are combined before subtraction from
+the object fibers.  The goals of combining are to reduce noise, eliminate
+cosmic-rays, and eliminate fibers with inadvertent objects.  The common
+methods for doing this to use a median and/or a special sigma clipping
+algorithm (see \fBscombine\fR for details).  The scale
+parameter determines whether the individual skys are first scaled to a
+common mode.  The scaling should be used if the throughput is uncertain,
+but in that case you probably did the wrong thing in the throughput
+correction.  If the sky subtraction is done interactively, i.e. with the
+\f(CWskyedit\fR option selected, then after selecting the spectra to be
+combined a query is made for the combining algorithm.  This allows
+modifying the default algorithm based on the number of sky spectra
+selected since the "avsigclip" rejection algorithm requires at least
+three spectra.
+.LP
+The combined sky spectrum is subtracted from only those spectra specified
+by the object aperture and beam numbers.  Other spectra, such as comparison
+arc spectra, are retained unchanged.  One may include the sky spectra as
+object spectra to produce residual sky spectra for analysis.  The combined
+master sky spectra may be saved if the \f(CWsaveskys\fR parameter is set.
+The saved sky is given the name of the object spectrum with the prefix
+"sky".
+.NH
+References
+.NH 2
+IRAF Introductory References
+.LP
+Work is underway on a new introductory guide to IRAF.  Currently, the
+work below is the primary introduction.
+.IP
+P. Shames and D. Tody, \fIA User's Introduction to the IRAF Command
+Language\fR, Central Computer Services, NOAO, 1986.
+.NH 2
+CCD Reductions
+.IP
+F. Valdes, \fIThe IRAF CCD Reduction Package -- CCDRED\fR, Central
+Computer Services, NOAO, 1987.
+.IP
+F. Valdes, \fIUser's Guide to the CCDRED Package\fR, Central
+Computer Services, NOAO, 1988.  Also on-line as \f(CWhelp ccdred.guide\fR.
+.IP
+P. Massey, \fIA User's Guide to CCD Reductions with IRAF\fR, Central
+Computer Services, NOAO, 1989.
+.NH 2
+Aperture Extraction Package
+.IP
+F. Valdes, \fIThe IRAF APEXTRACT Package\fR, Central Computer Services,
+NOAO, 1987 (out-of-date).
+.NH 2
+Task Help References
+.LP
+Each task in the \fBspecred\fR packages and tasks used by \fBdofibers\fR have
+help pages describing the parameters and task in some detail.  To get
+on-line help type
+.V1
+
+cl> help \fItaskname\fR
+
+.V2
+The output of this command can be piped to \fBlprint\fR to make a printed
+copy.
+
+.V1
+      apall - Extract 1D spectra (all parameters in one task)
+  apdefault - Set the default aperture parameters and apidtable
+     apedit - Edit apertures interactively
+     apfind - Automatically find spectra and define apertures
+      apfit - Fit 2D spectra and output the fit, difference, or ratio
+  apflatten - Remove overall spectral and profile shapes from flat fields
+     apmask - Create and IRAF pixel list mask of the apertures
+apnormalize - Normalize 2D apertures by 1D functions
+ aprecenter - Recenter apertures
+   apresize - Resize apertures
+  apscatter - Fit and subtract scattered light
+      apsum - Extract 1D spectra
+    aptrace - Trace positions of spectra
+
+      bplot - Batch plot of spectra with SPLOT
+  calibrate - Extinction and flux calibrate spectra
+  continuum - Fit the continuum in spectra
+   deredden - Apply interstellar extinction correction
+    dispcor - Dispersion correct spectra
+     dopcor - Doppler correct spectra
+   fitprofs - Fit gaussian profiles
+   identify - Identify features in spectrum for dispersion solution
+   msresp1d - Create 1D response spectra from flat field and sky spectra
+ refspectra - Assign wavelength reference spectra to other spectra
+ reidentify - Automatically reidentify features in spectra
+ sapertures - Set or change aperture header information
+     sarith - Spectrum arithmetic
+   scombine - Combine spectra
+      scopy - Select and copy apertures in different spectral formats
+   sensfunc - Compute instrumental sensitivity from standard stars
+ setairmass - Compute effective airmass and middle UT for an exposure
+      setjd - Compute and set Julian dates in images
+       sfit - Fit spectra and output fit, ratio, or difference
+     skysub - Sky subtract extracted multispec spectra
+      slist - List spectrum header parameters
+   specplot - Scale, stack, and plot multiple spectra
+      splot - Preliminary spectral plot/analysis
+   standard - Tabulate standard star counts and fluxes
+
+   dofibers - Process multifiber spectra
+      demos - Demonstrations and tests
+
+	    Additional help topics
+
+   onedspec.package - Package parameters and general description of package
+  apextract.package - Package parameters and general description of package
+ approfiles - Profile determination algorithms
+ apvariance - Extractions, variance weighting, cleaning, and noise model
+   center1d - One dimensional centering algorithm
+      icfit - Interactive one dimensional curve fitting
+.V2
+.SH
+Appendix A: DOFIBERS Parameters
+.LP
+.nr PS 8
+.nr VS 10
+objects
+.LS
+List of object spectra to be processed.  Previously processed spectra are
+ignored unless the \fIredo\fR flag is set or the \fIupdate\fR flag is set and
+dependent calibration data has changed.  Extracted spectra are ignored.
+.LE
+apref = ""
+.LS
+Aperture reference spectrum.  This spectrum is used to define the basic
+extraction apertures and is typically a flat field spectrum.
+.LE
+flat = "" (optional)
+.LS
+Flat field spectrum.  If specified the one dimensional flat field spectra
+are extracted and used to make flat field calibrations.  If a separate
+throughput file or image is not specified the flat field is also used
+for computing a fiber throughput correction.
+.LE
+throughput = "" (optional)
+.LS
+Throughput file or image.  If an image is specified, typically a blank
+sky observation, the total flux through
+each fiber is used to correct for fiber throughput.  If a file consisting
+of lines with the aperture number and relative throughput is specified
+then the fiber throughput will be corrected by those values.  If neither
+is specified but a flat field image is given it is used to compute the
+throughput.  
+.LE
+arcs1 = "" (at least one if dispersion correcting)
+.LS
+List of primary arc spectra.  These spectra are used to define the dispersion
+functions for each fiber apart from a possible zero point correction made
+with secondary shift spectra or arc calibration fibers in the object spectra.
+One fiber from the first spectrum is used to mark lines and set the dispersion
+function interactively and dispersion functions for all other fibers and
+arc spectra are derived from it.
+.LE
+arcs2 = "" (optional)
+.LS
+List of optional shift arc spectra.  Features in these secondary observations
+are used to supply a wavelength zero point shift through the observing
+sequence.  One type of observation is dome lamps containing characteristic
+emission lines.
+.LE
+arctable = "" (optional) (refspectra)
+.LS
+Table defining arc spectra to be assigned to object
+spectra (see \fBrefspectra\fR).  If not specified an assignment based
+on a header parameter, \fIparams.sort\fR, such as the observation time is made.
+.LE
+
+readnoise = "0." (apsum)
+.LS
+Read out noise in photons.  This parameter defines the minimum noise
+sigma.  It is defined in terms of photons (or electrons) and scales
+to the data values through the gain parameter.  A image header keyword
+(case insensitive) may be specified to get the value from the image.
+.LE
+gain = "1." (apsum)
+.LS
+Detector gain or conversion factor between photons/electrons and
+data values.  It is specified as the number of photons per data value.
+A image header keyword (case insensitive) may be specified to get the value
+from the image.
+.LE
+datamax = INDEF (apsum.saturation)
+.LS
+The maximum data value which is not a cosmic ray.
+When cleaning cosmic rays and/or using variance weighted extraction
+very strong cosmic rays (pixel values much larger than the data) can
+cause these operations to behave poorly.  If a value other than INDEF
+is specified then all data pixels in excess of this value will be
+excluded and the algorithms will yield improved results.
+This applies only to the object spectra and not the flat field or
+arc spectra.  For more
+on this see the discussion of the saturation parameter in the
+\fBapextract\fR package.
+.LE
+fibers = 97 (apfind)
+.LS
+Number of fibers.  This number is used during the automatic definition of
+the apertures from the aperture reference spectrum.  It is best if this
+reflects the actual number of fibers which may be found in the aperture
+reference image.  The interactive
+review of the aperture assignments allows verification and adjustments
+to the automatic aperture definitions.
+.LE
+width = 12. (apedit)
+.LS
+Approximate base full width of the fiber profiles.  This parameter is used
+for the profile centering algorithm.
+.LE
+minsep = 8. (apfind)
+.LS
+Minimum separation between fibers.  Weaker spectra or noise within this
+distance of a stronger spectrum are rejected.
+.LE
+maxsep = 15. (apfind)
+.LS
+Maximum separation between adjacent fibers.  This parameter
+is used to identify missing fibers.  If two adjacent spectra exceed this
+separation then it is assumed that a fiber is missing and the aperture
+identification assignments will be adjusted accordingly.
+.LE
+apidtable = "" (apfind)
+.LS
+Aperture identification table.  This may be either a text file or an
+image.  A text file contains the fiber number, beam number defining object
+(1), sky (0), and arc (2) fibers, and a object title.  An image contains
+the keywords SLFIBnnn with string value consisting of the fiber number,
+beam number, optional right ascension and declination, and an object
+title.  Unassigned and broken fibers (beam of -1) should be included in the
+identification information since they will automatically be excluded.
+.LE
+crval = INDEF, cdelt = INDEF (autoidentify)
+.LS
+These parameters specify an approximate central wavelength and dispersion.
+They may be specified as numerical values, INDEF, or image header keyword
+names whose values are to be used.
+If both these parameters are INDEF then the automatic identification will
+not be done.
+.LE
+objaps = "", skyaps = "", arcaps = ""
+.LS
+List of object, sky, and arc aperture numbers.  These are used to
+identify arc apertures for wavelength calibration and object and sky
+apertures for sky subtraction.  Note sky apertures may be identified as
+both object and sky if one wants to subtract the mean sky from the
+individual sky spectra.  Typically the different spectrum types are
+identified by their beam numbers and the default, null string,
+lists select all apertures.
+.LE
+objbeams = "0,1", skybeams = "0", arcbeams = 2
+.LS
+List of object, sky, and arc beam numbers.  The convention is that sky
+fibers are given a beam number of 0, object fibers a beam number of 1, and
+arc fibers a beam number of 2.  The beam numbers are typically set in the
+\fIapidtable\fR.  Unassigned or broken fibers may be given a beam number of
+-1 in the aperture identification table since apertures with negative beam
+numbers are not extracted.  Note it is valid to identify sky fibers as both
+object and sky.
+.LE
+
+scattered = no (apscatter)
+.LS
+Smooth and subtracted scattered light from the object and flat field
+images.  This operation consists of fitting independent smooth functions
+across the dispersion using data outside the fiber apertures and then
+smoothing the individual fits along the dispersion.  The initial
+flat field, or if none is given the aperture reference image, are
+done interactively to allow setting the fitting parameters.  All
+subsequent subtractions use the same fitting parameters.
+.LE
+fitflat = yes (flat1d)
+.LS
+Fit the composite flat field spectrum by a smooth function and divide each
+flat field spectrum by this function?  This operation removes the average
+spectral signature of the flat field lamp from the sensitivity correction to
+avoid modifying the object fluxes.
+.LE
+clean = yes (apsum)
+.LS
+Detect and correct for bad pixels during extraction?  This is the same
+as the clean option in the \fBapextract\fR package.  If yes this also
+implies variance weighted extraction and requires reasonably good values
+for the readout noise and gain.  In addition the datamax parameters
+can be useful.
+.LE
+dispcor = yes
+.LS
+Dispersion correct spectra?  Depending on the \fIparams.linearize\fR
+parameter this may either resample the spectra or insert a dispersion
+function in the image header.
+.LE
+skyalign = no
+.LS
+Align sky lines?  If yes then for the first object spectrum you are asked
+to mark one or more sky lines to use for alignment.  Then these lines will
+be found in all spectra and an average zeropoint shift computed and applied
+to the dispersion solution to align these lines.  Note that this assumes
+the sky lines are seen in all fibers.
+.LE
+savearcs = yes
+.LS
+Save any simultaneous arc apertures?  If no then the arc apertures will
+be deleted after use.
+.LE
+skysubtract = yes
+.LS
+Subtract sky from the object spectra?  If yes the sky spectra are combined
+and subtracted from the object spectra as defined by the object and sky
+aperture/beam parameters.
+.LE
+skyedit = yes
+.LS
+Overplot all the sky spectra and allow contaminated sky spectra to be
+deleted?
+.LE
+saveskys = yes
+.LS
+Save the combined sky spectrum?  If no then the sky spectrum will be
+deleted after sky subtraction is completed.
+.LE
+splot = no
+.LS
+Plot the final spectra with the task \fBsplot\fR?
+.LE
+redo = no
+.LS
+Redo operations previously done?  If no then previously processed spectra
+in the objects list will not be processed (unless they need to be updated).
+.LE
+update = yes
+.LS
+Update processing of previously processed spectra if aperture, flat
+field, or dispersion reference definitions are changed?
+.LE
+batch = no
+.LS
+Process spectra as a background or batch job provided there are no interactive
+options (\fIskyedit\fR and \fIsplot\fR) selected.
+.LE
+listonly = no
+.LS
+List processing steps but don't process?
+.LE
+
+params = "" (pset)
+.LS
+Name of parameter set containing additional processing parameters.  The
+default is parameter set \fBparams\fR.  The parameter set may be examined
+and modified in the usual ways (typically with "epar params" or ":e params"
+from the parameter editor).  Note that using a different parameter file
+is not allowed.  The parameters are described below.
+.LE
+
+.ce
+-- PACKAGE PARAMETERS
+
+Package parameters are those which generally apply to all task in the
+package.  This is also true of \fBdofibers\fR.
+
+dispaxis = 2
+.LS
+Default dispersion axis.  The dispersion axis is 1 for dispersion
+running along image lines and 2 for dispersion running along image
+columns.  If the image header parameter DISPAXIS is defined it has
+precedence over this parameter.  The default value defers to the
+package parameter of the same name.
+.LE
+observatory = "observatory"
+.LS
+Observatory at which the spectra were obtained if not specified in the
+image header by the keyword OBSERVAT.  See \fBobservatory\fR for more
+details.
+.LE
+interp = "poly5" (nearest|linear|poly3|poly5|spline3|sinc)
+.LS
+Spectrum interpolation type used when spectra are resampled.  The choices are:
+
+.nf
+	nearest - nearest neighbor
+	 linear - linear
+	  poly3 - 3rd order polynomial
+	  poly5 - 5th order polynomial
+	spline3 - cubic spline
+	   sinc - sinc function
+.fi
+.LE
+database = "database"
+.LS
+Database (directory) used for storing aperture and dispersion information.
+.LE
+verbose = no
+.LS
+Print verbose information available with various tasks.
+.LE
+logfile = "logfile", plotfile = ""
+.LS
+Text and plot log files.  If a filename is not specified then no log is
+kept.  The plot file contains IRAF graphics metacode which may be examined
+in various ways such as with \fBgkimosaic\fR.
+.LE
+records = ""
+.LS
+Dummy parameter to be ignored.
+.LE
+version = "SPECRED: ..."
+.LS
+Version of the package.
+.LE
+
+.ce
+PARAMS PARAMETERS
+
+The following parameters are part of the \fBparams\fR parameter set and
+define various algorithm parameters for \fBdofibers\fR.
+
+.ce
+--  GENERAL PARAMETERS --
+
+line = INDEF, nsum = 10
+.LS
+The dispersion line (line or column perpendicular to the dispersion
+axis) and number of adjacent lines (half before and half after unless
+at the end of the image) used in finding, recentering, resizing,
+editing, and tracing operations.  A line of INDEF selects the middle of the
+image along the dispersion axis.
+.LE
+order = "decreasing" (apfind)
+.LS
+When assigning aperture identifications order the spectra "increasing"
+or "decreasing" with increasing pixel position (left-to-right or
+right-to-left in a cross-section plot of the image).
+.LE
+extras = no (apsum)
+.LS
+Include extra information in the output spectra?  When cleaning or using
+variance weighting the cleaned and weighted spectra are recorded in the
+first 2D plane of a 3D image, the raw, simple sum spectra are recorded in
+the second plane, and the estimated sigmas are recorded in the third plane.
+.LE
+
+.ce
+-- DEFAULT APERTURE LIMITS --
+
+lower = -5., upper = 5. (apdefault)
+.LS
+Default lower and upper aperture limits relative to the aperture center.
+These limits are used when the apertures are first found and may be
+resized automatically or interactively.
+.LE
+
+.ce
+-- AUTOMATIC APERTURE RESIZING PARAMETERS --
+
+ylevel = 0.05 (apresize)
+.LS
+Data level at which to set aperture limits during automatic resizing.
+It is a fraction of the peak relative to a local background.
+.LE
+
+.ce
+-- TRACE PARAMETERS --
+
+t_step = 10 (aptrace)
+.LS
+Step along the dispersion axis between determination of the spectrum
+positions.  Note the \fInsum\fR parameter is also used to enhance the
+signal-to-noise at each step.
+.LE
+t_function = "spline3", t_order = 3 (aptrace)
+.LS
+Default trace fitting function and order.  The fitting function types are
+"chebyshev" polynomial, "legendre" polynomial, "spline1" linear spline, and
+"spline3" cubic spline.  The order refers to the number of
+terms in the polynomial functions or the number of spline pieces in the spline
+functions.
+.LE
+t_niterate = 1, t_low = 3., t_high = 3. (aptrace)
+.LS
+Default number of rejection iterations and rejection sigma thresholds.
+
+.ce
+-- SCATTERED LIGHT PARAMETERS --
+
+buffer = 1. (apscatter)
+.LS
+Buffer distance from the aperture edges to be excluded in selecting the
+scattered light pixels to be used.
+.LE
+apscat1 = "" (apscatter)
+.LS
+Fitting parameters across the dispersion.  This references an additional
+set of parameters for the ICFIT package.  The default is the "apscat1"
+parameter set.
+.LE
+apscat2 = "" (apscatter)
+.LS
+Fitting parameters along the dispersion.  This references an additional
+set of parameters for the ICFIT package.  The default is the "apscat2"
+parameter set.
+.LE
+.LE
+
+.ce
+-- APERTURE EXTRACTION PARAMETERS --
+
+weights = "none" (apsum)
+.LS
+Type of extraction weighting.  Note that if the \fIclean\fR parameter is
+set then the weights used are "variance" regardless of the weights
+specified by this parameter.  The choices are:
+
+"none"
+.LS
+The pixels are summed without weights except for partial pixels at the
+ends.
+.LE
+"variance"
+.LS
+The extraction is weighted by the variance based on the data values
+and a poisson/ccd model using the \fIgain\fR and \fIreadnoise\fR
+parameters.
+.LE
+.LE
+pfit = "fit1d" (apsum) (fit1d|fit2d)
+.LS
+Profile fitting algorithm for cleaning and variance weighted extractions.
+The default is generally appropriate for multifiber data but users
+may try the other algorithm.  See \fBapprofiles\fR for further information.
+.LE
+lsigma = 3., usigma = 3. (apsum)
+.LS
+Lower and upper rejection thresholds, given as a number of times the
+estimated sigma of a pixel, for cleaning.
+.LE
+nsubaps = 1 (apsum)
+.LS
+During extraction it is possible to equally divide the apertures into
+this number of subapertures.
+.LE
+
+.ce
+-- FLAT FIELD FUNCTION FITTING PARAMETERS --
+
+f_interactive = yes (fit1d)
+.LS
+Fit the composite one dimensional flat field spectrum interactively?
+This is used if \fIfitflat\fR is set and a two dimensional flat field
+spectrum is specified.
+.LE
+f_function = "spline3", f_order = 10 (fit1d)
+.LS
+Function and order used to fit the composite one dimensional flat field
+spectrum.  The functions are "legendre", "chebyshev", "spline1", and
+"spline3".  The spline functions are linear and cubic splines with the
+order specifying the number of pieces.
+.LE
+
+.ce
+-- ARC DISPERSION FUNCTION PARAMETERS --
+
+threshold = 10. (autoidentify/identify/reidentify)
+.LS
+In order for a feature center to be determined the range of pixel intensities
+around the feature must exceed this threshold.
+.LE
+coordlist = "linelists$idhenear.dat" (autoidentify/identify)
+.LS
+Arc line list consisting of an ordered list of wavelengths.
+Some standard line lists are available in the directory "linelists$".
+.LE
+match = -3. (autoidentify/identify)
+.LS
+The maximum difference for a match between the dispersion function prediction
+value and a wavelength in the coordinate list.
+.LE
+fwidth = 4. (autoidentify/identify)
+.LS
+Approximate full base width (in pixels) of arc lines.
+.LE
+cradius = 10. (reidentify)
+.LS
+Radius from previous position to reidentify arc line.
+.LE
+i_function = "spline3", i_order = 3 (autoidentify/identify)
+.LS
+The default function and order to be fit to the arc wavelengths as a
+function of the pixel coordinate.  The functions choices are "chebyshev",
+"legendre", "spline1", or "spline3".
+.LE
+i_niterate = 2, i_low = 3.0, i_high = 3.0 (autoidentify/identify)
+.LS
+Number of rejection iterations and sigma thresholds for rejecting arc
+lines from the dispersion function fits.
+.LE
+refit = yes (reidentify)
+.LS
+Refit the dispersion function?  If yes and there is more than 1 line
+and a dispersion function was defined in the arc reference then a new
+dispersion function of the same type as in the reference image is fit
+using the new pixel positions.  Otherwise only a zero point shift is
+determined for the revised fitted coordinates without changing the
+form of the dispersion function.
+.LE
+addfeatures = no (reidentify)
+.LS
+Add new features from a line list during each reidentification?
+This option can be used to compensate for lost features from the
+reference solution.  Care should be exercised that misidentified features
+are not introduced.
+.LE
+
+.ce
+-- AUTOMATIC ARC ASSIGNMENT PARAMETERS --
+
+select = "interp" (refspectra)
+.LS
+Selection method for assigning wavelength calibration spectra.
+Note that an arc assignment table may be used to override the selection
+method and explicitly assign arc spectra to object spectra.
+The automatic selection methods are:
+
+average
+.LS
+Average two reference spectra without regard to any sort parameter.
+If only one reference spectrum is specified then it is assigned with a
+warning.  If more than two reference spectra are specified then only the
+first two are used and a warning is given.
+This option is used to assign two reference spectra, with equal weights,
+independent of any sorting parameter.
+.LE
+following
+.LS
+Select the nearest following spectrum in the reference list based on the
+sorting parameter.  If there is no following spectrum use the nearest preceding
+spectrum.
+.LE
+interp
+.LS
+Interpolate between the preceding and following spectra in the reference
+list based on the sorting parameter.  If there is no preceding and following
+spectrum use the nearest spectrum.  The interpolation is weighted by the
+relative distances of the sorting parameter.
+.LE
+match
+.LS
+Match each input spectrum with the reference spectrum list in order.
+This overrides the reference aperture check.
+.LE
+nearest
+.LS
+Select the nearest spectrum in the reference list based on the sorting
+parameter.
+.LE
+preceding
+.LS
+Select the nearest preceding spectrum in the reference list based on the
+sorting parameter.  If there is no preceding spectrum use the nearest following
+spectrum.
+.LE
+.LE
+sort = "jd", group = "ljd" (refspectra)
+.LS
+Image header keywords to be used as the sorting parameter for selection
+based on order and to group spectra.
+A null string, "", or the word "none" may be use to disable the sorting
+or grouping parameters.
+The sorting parameter
+must be numeric but otherwise may be anything.  The grouping parameter
+may be a string or number and must simply be the same for all spectra within
+the same group (say a single night).
+Common sorting parameters are times or positions.
+In \fBdofibers\fR the Julian date (JD) and the local Julian day number (LJD)
+at the middle of the exposure are automatically computed from the universal
+time at the beginning of the exposure and the exposure time.  Also the
+parameter UTMIDDLE is computed.
+.LE
+time = no, timewrap = 17. (refspectra)
+.LS
+Is the sorting parameter a 24 hour time?  If so then the time origin
+for the sorting is specified by the timewrap parameter.  This time
+should precede the first observation and follow the last observation
+in a 24 hour cycle.
+.LE
+
+.ce
+-- DISPERSION  CORRECTION PARAMETERS --
+
+linearize = yes (dispcor)
+.LS
+Interpolate the spectra to a linear dispersion sampling?  If yes the
+spectra will be interpolated to a linear or log linear sampling
+If no the nonlinear dispersion function(s) from the dispersion function
+database are assigned to the input image world coordinate system
+and the spectral data are not interpolated.
+.LE
+log = no (dispcor)
+.LS
+Use linear logarithmic wavelength coordinates?  Linear logarithmic
+wavelength coordinates have wavelength intervals which are constant
+in the logarithm of the wavelength.
+.LE
+flux = yes (dispcor)
+.LS
+Conserve the total flux during interpolation?  If \fIno\fR the output
+spectrum is interpolated from the input spectrum at each output
+wavelength coordinate.  If \fIyes\fR the input spectrum is integrated
+over the extent of each output pixel.  This is slower than
+simple interpolation.
+.LE
+
+.ce
+-- SKY SUBTRACTION PARAMETERS --
+
+combine = "average" (scombine) (average|median)
+.LS
+Option for combining sky pixels at the same dispersion coordinate after any
+rejection operation.  The options are to compute the  "average" or "median"
+of the pixels.  The median uses the average of the two central
+values when the number of pixels is even.
+.LE
+reject = "none" (scombine) (none|minmax|avsigclip)
+.LS
+Type of rejection operation performed on the pixels which overlap at each
+dispersion coordinate.  The algorithms are discussed in the
+help for \fBscombine\fR.  The rejection choices are:
+
+.nf
+      none - No rejection
+    minmax - Reject the low and high pixels
+ avsigclip - Reject pixels using an averaged sigma clipping algorithm
+.fi
+
+.LE
+scale = "none" (none|mode|median|mean)
+.LS
+Multiplicative scaling to be applied to each spectrum.  The choices are none
+or scale by the mode, median, or mean.  This should not be necessary if the
+flat field and throughput corrections have been properly made. 
+.LE
+
+.ce
+ENVIRONMENT PARAMETERS
+.LP
+The environment parameter \fIimtype\fR is used to determine the extension
+of the images to be processed and created.  This allows use with any
+supported image extension.  For STF images the extension has to be exact;
+for example "d1h".
diff --git a/noao/imred/specred/doc/doslit.hlp b/noao/imred/specred/doc/doslit.hlp
new file mode 100644
index 00000000..2bcf7294
--- /dev/null
+++ b/noao/imred/specred/doc/doslit.hlp
@@ -0,0 +1,1201 @@
+.help doslit Feb93 noao.imred.specred
+.ih
+NAME
+doslit -- Slit spectra data reduction task
+.ih
+USAGE
+doslit objects
+.ih
+SUMMARY
+\fBDoslit\fR extracts, sky subtracts, wavelength calibrates, and flux
+calibrates simple two dimensional slit spectra which have been processed to
+remove the detector characteristics; i.e. CCD images have been bias, dark
+count, and flat field corrected.  It is primarily intended for
+spectrophotometry or radial velocities of stellar spectra with the spectra
+aligned with one of the image axes; i.e. the assumption is that extractions
+can be done by summing along image lines or columns.  The alignment does
+not have to be precise but only close enough that the wavelength difference
+across the spectrum profiles is insignificant.  The task is available
+in the \fBctioslit\fR, \fBkpnoslit\fR, \fBkpnocoude\fR, and \fBspecred\fR
+packages.
+.ih
+PARAMETERS
+.ls objects
+List of object images to be processed.  Previously processed spectra are
+ignored unless the \fIredo\fR flag is set or the \fIupdate\fR flag is set
+and dependent calibration data has changed.  If the images contain the
+keyword IMAGETYP then only those with a value of "object" or "OBJECT"
+are used and those with a value of "comp" or "COMPARISON" are added
+to the list of arcs.  Extracted spectra are ignored.
+.le
+.ls arcs = "" (at least one if dispersion correcting)
+List of arc calibration spectra.  These spectra are used to define
+the dispersion functions.  The first spectrum is used to mark lines
+and set the dispersion function interactively and dispersion functions
+for all other arc spectra are derived from it.  If the images contain
+the keyword IMAGETYP then only those with a value of "comp" or
+"COMPARISON" are used.  All others are ignored as are extracted spectra.
+.le
+.ls arctable = "" (optional) (refspectra)
+Table defining which arc spectra are to be assigned to which object
+spectra (see \fBrefspectra\fR).  If not specified an assignment based
+on a header parameter, \fIsparams.sort\fR, such as the Julian date
+is made.
+.le
+.ls standards = "" (at least one if flux calibrating)
+List of standard star spectra.  The standard stars must have entries in
+the calibration database (package parameter \fIcaldir\fR).
+.le
+
+.ls readnoise = "rdnoise", gain = "gain" (apsum)
+Read out noise in photons and detector gain in photons per data value.
+This parameter defines the minimum noise sigma and the conversion between
+photon Poisson statistics and the data number statistics.  Image header
+keywords (case insensitive) may be specified to obtain the values from the
+image header.
+.le
+.ls datamax = INDEF (apsum.saturation)
+The maximum data value which is not a cosmic ray.
+When cleaning cosmic rays and/or using variance weighted extraction
+very strong cosmic rays (pixel values much larger than the data) can
+cause these operations to behave poorly.  If a value other than INDEF
+is specified then all data pixels in excess of this value will be
+excluded and the algorithms will yield improved results.
+This applies only to the object spectra and not the standard star or
+arc spectra.  For more
+on this see the discussion of the saturation parameter in the
+\fBapextract\fR package.
+.le
+.ls width = 5. (apedit)
+Approximate full width of the spectrum profiles.  This parameter is used
+to define a width and error radius for the profile centering algorithm.
+.le
+.ls crval = INDEF, cdelt = INDEF (autoidentify)
+These parameters specify an approximate central wavelength and dispersion.
+They may be specified as numerical values, INDEF, or image header keyword
+names whose values are to be used.
+If both these parameters are INDEF then the automatic identification will
+not be done.
+.le
+
+.ls dispcor = yes
+Dispersion correct spectra?  This may involve either defining a nonlinear
+dispersion coordinate system in the image header or resampling the
+spectra to uniform linear wavelength coordinates as selected by
+the parameter \fIsparams.linearize\fR.
+.le
+.ls extcor = no
+Extinction correct the spectra?
+.le
+.ls fluxcal = no
+Flux calibrate the spectra using standard star observations?
+.le
+.ls resize = no (apresize)
+Resize the default aperture for each object based on the spectrum profile?
+.le
+.ls clean = no (apsum)
+Detect and correct for bad pixels during extraction?  This is the same
+as the clean option in the \fBapextract\fR package.  If yes this also
+implies variance weighted extraction.  In addition the datamax parameters
+can be useful.
+.le
+.ls splot = no
+Plot the final spectra with the task \fBsplot\fR?  In quicklook mode
+this is automatic and in non-quicklook mode it is queried.
+.le
+.ls redo = no
+Redo operations previously done?  If no then previously processed spectra
+in the object list will not be processed unless required by the
+update option.
+.le
+.ls update = no
+Update processing of previously processed spectra if the
+dispersion reference image or standard star calibration data are changed?
+.le
+.ls quicklook = no
+Extract and calibrate spectra with minimal interaction?  In quicklook mode
+only the initial dispersion function solution and standard star setup are
+done interactively.  Normally the \fIsplot\fR option is set in this mode to
+produce an automatic final spectrum plot for each object.  It is
+recommended that this mode not be used for final reductions.
+.le
+.ls batch = yes
+Process spectra as a background or batch job provided there are no interactive
+steps remaining.
+.le
+.ls listonly = no
+List processing steps but don't process?
+.le
+
+.ls sparams = "" (pset)
+Name of parameter set containing additional processing parameters.  This
+parameter is only for indicating the link to the parameter set
+\fBsparams\fR and should not be given a value.  The parameter set may be
+examined and modified in the usual ways (typically with "epar sparams"
+or ":e sparams" from the parameter editor).  The parameters are
+described below.
+.le
+
+.ce
+-- GENERAL PARAMETERS --
+.ls line = INDEF, nsum = 10
+The dispersion line (line or column perpendicular to the dispersion
+axis) and number of adjacent lines (half before and half after unless
+at the end of the image) used in finding, resizing,
+editing, and tracing operations.  A line of INDEF selects the middle of the
+image along the dispersion axis.
+.le
+.ls extras = no (apsum)
+Include raw unweighted and uncleaned spectra, the background spectra, and
+the estimated sigmas in a three dimensional output image format.
+See the discussion in the \fBapextract\fR package for further information.
+.le
+
+.ce
+-- DEFAULT APERTURE LIMITS --
+.ls lower = -3., upper = 3. (apdefault)
+Default lower and upper aperture limits relative to the aperture center.
+These limits are used when the apertures are first defined.
+.le
+
+.ce
+-- AUTOMATIC APERTURE RESIZING PARAMETERS --
+.ls ylevel = 0.05 (apresize)
+Fraction of the peak to set aperture limits during automatic resizing.
+.le
+
+.ce
+-- TRACE PARAMETERS --
+.ls t_step = 10 (aptrace)
+Step along the dispersion axis between determination of the spectrum
+positions.  Note the \fInsum\fR parameter is also used to enhance the
+signal-to-noise at each step.
+.le
+.ls t_function = "spline3", t_order = 1 (aptrace)
+Default trace fitting function and order.  The fitting function types are
+"chebyshev" polynomial, "legendre" polynomial, "spline1" linear spline, and
+"spline3" cubic spline.  The order refers to the number of terms in the
+polynomial functions or the number of spline pieces in the spline
+functions.
+.le
+.ls t_niterate = 1, t_low = 3., t_high = 3. (aptrace)
+Default number of rejection iterations and rejection sigma thresholds.
+.le
+
+.ce
+-- APERTURE EXTRACTION PARAMETERS --
+.ls weights = "none" (apsum) (none|variance)
+Type of extraction weighting.  Note that if the \fIclean\fR parameter is
+set then the weights used are "variance" regardless of the weights
+specified by this parameter.  The choices are:
+.ls "none"
+The pixels are summed without weights except for partial pixels at the
+ends.
+.le
+.ls "variance"
+The extraction is weighted by the variance based on the data values
+and a poisson/ccd model using the \fIgain\fR and \fIreadnoise\fR
+parameters.
+.le
+.le
+.ls pfit = "fit1d" (apsum and approfile) (fit1d|fit2d)
+Type of profile fitting algorithm to use.  The "fit1d" algorithm is
+preferred except in cases of extreme tilt.
+.le
+.ls lsigma = 3., usigma = 3. (apsum)
+Lower and upper rejection thresholds, given as a number of times the
+estimated sigma of a pixel, for cleaning.
+.le
+
+.ce
+-- DEFAULT BACKGROUND PARAMETERS --
+.ls background = "fit" (apsum) (none|average|median|minimum|fit)
+Type of background subtraction.  The choices are "none" for no background
+subtraction, "average" to average the background within the background
+regions, "median" to use the median in the background regions, "minimum" to
+use the minimum in the background regions, or "fit" to fit across the
+dispersion using the background within the background regions.  Note that
+the "average" option does not do any medianing or bad pixel checking,
+something which is recommended.  The fitting option is slower than the
+other options and requires additional fitting parameter.
+.le
+.ls b_function = "legendre", b_order = 1 (apsum)
+Default background fitting function and order.  The fitting function types are
+"chebyshev" polynomial, "legendre" polynomial, "spline1" linear spline, and
+"spline3" cubic spline.  The order refers to the number of
+terms in the polynomial functions or the number of spline pieces in the spline
+functions.
+.le
+.ls b_sample = "-10:-6,6:10" (apsum)
+Default background sample.  The sample is given by a set of colon separated
+ranges each separated by either whitespace or commas.  The string "*" refers
+to all points.  Note that the background coordinates are relative to the
+aperture center and not image pixel coordinates so the endpoints need not
+be integer.  It is recommended that the background regions be examined
+and set interactively with the 'b' key in the interactive aperture
+definition mode.  This requires \fIquicklook\fR to be no.
+.le
+.ls b_naverage = -100 (apsum)
+Default number of points to average or median.  Positive numbers
+average that number of sequential points to form a fitting point.
+Negative numbers median that number, in absolute value, of sequential
+points.  A value of 1 does no averaging and each data point is used in the
+fit.
+.le
+.ls b_niterate = 1 (apsum)
+Default number of rejection iterations.  If greater than zero the fit is
+used to detect deviant fitting points and reject them before repeating the
+fit.  The number of iterations of this process is given by this parameter.
+.le
+.ls b_low_reject = 3., b_high_reject = 3. (apsum)
+Default background lower and upper rejection sigmas.  If greater than zero
+points deviating from the fit below and above the fit by more than this
+number of times the sigma of the residuals are rejected before refitting.
+.le
+
+.ce
+-- ARC DISPERSION FUNCTION PARAMETERS --
+.ls threshold = 10. (autoidentify/identify/reidentify)
+In order for a feature center to be determined the range of pixel intensities
+around the feature must exceed this threshold.
+.le
+.ls coordlist = "linelists$idhenear.dat" (autoidentify/identify)
+Arc line list consisting of an ordered list of wavelengths.
+Some standard line lists are available in the directory "linelists$".
+.le
+.ls match = -3. (autoidentify/identify)
+The maximum difference for a match between the dispersion function computed
+value and a wavelength in the coordinate list.
+.le
+.ls fwidth = 4. (autoidentify/identify)
+Approximate full base width (in pixels) of arc lines.
+.le
+.ls cradius = 10. (reidentify)
+Radius from previous position to reidentify arc line.
+.le
+.ls i_function = "spline3", i_order = 1 (autoidentify/identify)
+The default function and order to be fit to the arc wavelengths as a
+function of the pixel coordinate.  The functions choices are "chebyshev",
+"legendre", "spline1", or "spline3".
+.le
+.ls i_niterate = 0, i_low = 3.0, i_high = 3.0 (autoidentify/identify)
+Number of rejection iterations and sigma thresholds for rejecting arc
+lines from the dispersion function fits.
+.le
+.ls refit = yes (reidentify)
+Refit the dispersion function?  If yes and there is more than 1 line
+and a dispersion function was defined in the initial arc reference then a new
+dispersion function of the same type as in the reference image is fit
+using the new pixel positions.  Otherwise only a zero point shift is
+determined for the revised fitted coordinates without changing the
+form of the dispersion function.
+.le
+.ls addfeatures = no (reidentify)
+Add new features from a line list during each reidentification?
+This option can be used to compensate for lost features from the
+reference solution.  Care should be exercised that misidentified features
+are not introduced.
+.le
+
+.ce
+-- AUTOMATIC ARC ASSIGNMENT PARAMETERS --
+.ls select = "interp" (refspectra)
+Selection method for assigning wavelength calibration spectra.
+Note that an arc assignment table may be used to override the selection
+method and explicitly assign arc spectra to object spectra.
+The automatic selection methods are:
+.ls average
+Average two reference spectra without regard to any
+sort or group parameters.
+If only one reference spectrum is specified then it is assigned with a
+warning.  If more than two reference spectra are specified then only the
+first two are used and a warning is given.  There is no checking of the
+group values.
+.le
+.ls following
+Select the nearest following spectrum in the reference list based on the
+sort and group parameters.  If there is no following spectrum use the
+nearest preceding spectrum.
+.le
+.ls interp
+Interpolate between the preceding and following spectra in the reference
+list based on the sort and group parameters.  If there is no preceding and
+following spectrum use the nearest spectrum.  The interpolation is weighted
+by the relative distances of the sorting parameter (see cautions in
+DESCRIPTION section).
+.le
+.ls match
+Match each input spectrum with the reference spectrum list in order.
+This overrides any group values.
+.le
+.ls nearest
+Select the nearest spectrum in the reference list based on the sort and
+group parameters.
+.le
+.ls preceding
+Select the nearest preceding spectrum in the reference list based on the
+sort and group parameters.  If there is no preceding spectrum use the
+nearest following spectrum.
+.le
+.le
+.ls sort = "jd" (setjd and refspectra)
+Image header keyword to be used as the sorting parameter for selection
+based on order.  The header parameter must be numeric but otherwise may
+be anything.  Common sorting parameters are times or positions.
+.le
+.ls group = "ljd" (setjd and refspectra)
+Image header keyword to be used to group spectra.  For those selection
+methods which use the group parameter the reference and object
+spectra must have identical values for this keyword.  This can
+be anything but it must be constant within a group.  Common grouping
+parameters are the date of observation "date-obs" (provided it does not
+change over a night) or the local Julian day number.
+.le
+.ls time = no, timewrap = 17. (refspectra)
+Is the sorting parameter a 24 hour time?  If so then the time origin
+for the sorting is specified by the timewrap parameter.  This time
+should precede the first observation and follow the last observation
+in a 24 hour cycle.
+.le
+
+.ce
+-- DISPERSION  CORRECTION PARAMETERS --
+.ls linearize = yes (dispcor)
+Interpolate the spectra to a linear dispersion sampling?  If yes the
+spectra will be interpolated to a linear or log linear sampling using
+the linear dispersion parameters specified by other parameters.  If
+no the nonlinear dispersion function(s) from the dispersion function
+database are assigned to the input image world coordinate system
+and the spectral data is not interpolated.  Note the interpolation
+function type is set by the package parameter \fIinterp\fR.
+.le
+.ls log = no (dispcor)
+Use linear logarithmic wavelength coordinates?  Linear logarithmic
+wavelength coordinates have wavelength intervals which are constant
+in the logarithm of the wavelength.
+.le
+.ls flux = yes (dispcor)
+Conserve the total flux during interpolation?  If \fIno\fR the output
+spectrum is interpolated from the input spectrum at each output
+wavelength coordinate.  If \fIyes\fR the input spectrum is integrated
+over the extent of each output pixel.  This is slower than
+simple interpolation.
+.le
+
+.ce
+-- SENSITIVITY CALIBRATION PARAMETERS --
+.ls s_function = "spline3", s_order = 1 (sensfunc)
+Function and order used to fit the sensitivity data.  The function types
+are "chebyshev" polynomial, "legendre" polynomial, "spline3" cubic spline,
+and "spline1" linear spline.  Order of the sensitivity fitting function.
+The value corresponds to the number of polynomial terms or the number of
+spline pieces.  The default values may be changed interactively.
+.le
+.ls fnu = no (calibrate)
+The default calibration is into units of F-lambda. If \fIfnu\fR = yes then
+the calibrated spectrum will be in units of F-nu.
+.le
+
+.ce
+PACKAGE PARAMETERS
+
+The following package parameters are used by this task.  The default values
+may vary depending on the package.
+.ls dispaxis = 2
+Default dispersion axis.  The dispersion axis is 1 for dispersion
+running along image lines and 2 for dispersion running along image
+columns.  If the image header parameter DISPAXIS is defined it has
+precedence over this parameter.  The default value defers to the
+package parameter of the same name.
+.le
+.ls extinction (standard, sensfunc, calibrate)
+Extinction file for a site.  There are two extinction files in the
+NOAO standards library, onedstds$, for KPNO and CTIO.  These extinction
+files are used for extinction and flux calibration.
+.le
+.ls caldir (standard)
+Standard star calibration directory.  A directory containing standard
+star data files.  Note that the directory name must end with '/'.
+There are a number of standard star calibrations directories in the NOAO
+standards library, onedstds$.
+.le
+.ls observatory = "observatory" (observatory)
+The default observatory to use for latitude dependent computations.
+If the OBSERVAT keyword in the image header it takes precedence over
+this parameter.
+.le
+.ls interp = "poly5" (nearest|linear|poly3|poly5|spline3|sinc) (dispcor)
+Spectrum interpolation type used when spectra are resampled.  The choices are:
+
+.nf
+	nearest - nearest neighbor
+	 linear - linear
+	  poly3 - 3rd order polynomial
+	  poly5 - 5th order polynomial
+	spline3 - cubic spline
+	   sinc - sinc function
+.fi
+.le
+.ls database = "database"
+Database name used by various tasks.  This is a directory which is created
+if necessary.
+.le
+.ls verbose = no
+Verbose output?  If set then almost all the information written to the
+logfile is also written to the terminal except when the task is a
+background or batch process.
+.le
+.ls logfile = "logfile"
+If specified detailed text log information is written to this file.
+.le
+.ls plotfile = ""
+If specified metacode plots are recorded in this file for later review.
+Since plot information can become large this should be used only if
+really desired.
+.le
+.ih
+ENVIRONMENT PARAMETERS
+The environment parameter \fIimtype\fR is used to determine the extension
+of the images to be processed and created.  This allows use with any
+supported image extension.  For STF images the extension has to be exact;
+for example "d1h".
+.ih
+DESCRIPTION
+\fBDoslit\fR extracts, sky subtracts, wavelength calibrates, and flux
+calibrates simple two dimensional slit spectra which have been processed to
+remove the detector characteristics; i.e. CCD images have been bias, dark
+count, and flat field corrected.  It is primarily intended for
+spectrophotometry or radial velocities of stellar spectra with the spectra
+aligned with one of the image axes; i.e. the assumption is that extractions
+can be done by summing along image lines or columns.  The alignment does
+not have to be precise but only close enough that the wavelength difference
+across the spectrum profiles is insignificant.  Extended objects requiring
+accurate geometric alignment over many pixels are reduced using the
+\fBlongslit\fR package.
+
+The task is a command language script which collects and combines the
+functions and parameters of many general purpose tasks to provide a single,
+complete data reduction path and a degree of guidance, automation, and
+record keeping.  In the following description and in the parameter section
+the various general tasks used are identified.  Further
+information about those tasks and their parameters may be found in their
+documentation.  \fBDoslit\fR also simplifies and consolidates parameters
+from those tasks and keeps track of previous processing to avoid
+duplications.
+
+The general organization of the task is to do the interactive setup steps,
+such as the reference dispersion function
+determination, first using representative calibration data and then perform
+the majority of the reductions automatically, possibly as a background
+process, with reference to the setup data.  In addition, the task
+determines which setup and processing operations have been completed in
+previous executions of the task and, contingent on the \fIredo\fR and
+\fIupdate\fR options, skip or repeat some or all the steps.
+
+The description is divided into a quick usage outline followed by details
+of the parameters and algorithms.  The usage outline is provided as a
+checklist and a refresher for those familiar with this task and the
+component tasks.  It presents only the default or recommended usage
+since there are many variations possible.
+
+\fBUsage Outline\fR
+
+.ls 6 [1]
+The images are first processed with \fBccdproc\fR for overscan,
+zero level, dark count, and flat field corrections.
+.le
+.ls [2]
+Set the \fBdoslit\fR parameters with \fBeparam\fR.  Specify the object
+images to be processed,
+one or more arc images, and one or more standard
+star images.  If there are many object, arc, or standard star images
+you might prepare "@ files".  Set the detector and data
+specific parameters.  Select the processing options desired.
+Finally you might wish to review the \fIsparams\fR algorithm parameters
+though the defaults are probably adequate.
+.le
+.ls [3]
+Run the task.  This may be repeated multiple times with different
+observations and the task will generally only do the setup steps
+once and only process new images.  Queries presented during the
+execution for various interactive operations may be answered with
+"yes", "no", "YES", or "NO".  The lower case responses apply just
+to that query while the upper case responses apply to all further
+such queries during the current execution and no further queries of that
+type will be made.
+.le
+.ls [4]
+Apertures are defined for all the standard and object images.  This is only
+done if there are no previous aperture definitions for the image.
+The highest peak is found and centered and the default aperture limits
+are set.  If the resize option is set the aperture is resized by finding
+the level which  is 5% (the default) of the peak above local background.
+If not using the quicklook option you now have the option
+of entering the aperture editing loop to check the aperture position,
+size, and background fitting parameters, and possibly add additional
+apertures.  This is step is highly recommended.
+It is important to check the background regions with the 'b'
+key.  To exit the background mode and then
+to exit the review mode use 'q'.
+
+The spectrum positions at a series of points along the dispersion are
+measured and a function is fit to these positions.  If not using the
+quicklook option the traced positions may be examined interactively and the
+fitting parameters adjusted.  To exit the interactive fitting type 'q'.
+.le
+.ls [5]
+If dispersion correction is selected the first arc in the arc list is
+extracted.  The dispersion function is defined using the task
+\fBautoidentify\fR.  The \fIcrval\fR and \fIcdelt\fR parameters are used in
+the automatic identification.  Whether or not the automatic identification
+is successful you will be shown the result of the arc line identification.
+If the automatic identification is not successful identify a few arc lines
+with with 'm' and use the 'l' line list identification command to
+automatically add additional lines and fit the dispersion function.  Check
+the quality of the dispersion function fit with 'f'.  When satisfied exit
+with 'q'.
+.le
+.ls [6]
+If the flux calibration option is selected the standard star spectra are
+processed (if not done previously).  The images are
+extracted and wavelength calibrated.  The appropriate arc
+calibration spectra are extracted and the dispersion function refit
+using the arc reference spectrum as a starting point.  The standard star
+fluxes through the calibration bandpasses are compiled.  You are queried
+for the name of the standard star calibration data file.
+
+After all the standard stars are processed a sensitivity function is
+determined using the interactive task \fBsensfunc\fR.  Finally, the
+standard star spectra are extinction corrected and flux calibrated
+using the derived sensitivity function.
+.le
+.ls [7]
+The object spectra are now automatically
+extracted, wavelength calibrated, and flux calibrated.
+.le
+.ls [8]
+The option to examine the final spectra with \fBsplot\fR may be given.
+To exit type 'q'.  In quicklook mode the spectra are plotted
+noninteractively with \fBbplot\fR.
+.le
+.ls [9]
+The final spectra will have the same name as the original 2D images
+with a ".ms" extension added.
+.le
+
+\fBSpectra and Data Files\fR
+
+The basic input consists of two dimensional slit object, standard star, and
+arc calibration spectra stored as IRAF images.
+The type of image format is defined by the
+environment parameter \fIimtype\fR.  Only images with that extension will
+be processed and created.
+The raw CCD images must be
+processed to remove overscan, bias, dark count, and flat field effects.
+This is generally done using the \fBccdred\fR package.  Lines of constant
+wavelength should be closely aligned with one of the image axes though a
+small amount of misalignment only causes a small loss of resolution.  For
+large misalignments one may use the \fBrotate\fR task.  More complex
+geometric problems and observations of extended objects should be handled
+by the \fBlongslit\fR package.
+
+The arc
+spectra are comparison arc lamp observations (they must all be of the same
+type).  The assignment of arc calibration exposures to object exposures is
+generally done by selecting the nearest in time and interpolating.
+However, the optional \fIarc assignment table\fR may be used to explicitly
+assign arc images to specific objects.  The format of this file is
+described in task \fBrefspectra\fR.
+
+The final reduced spectra are recorded in one, two or three dimensional IRAF
+images.  The images have the same name as the original images with an added
+".ms" extension.  Each line in the reduced image is a one dimensional
+spectrum with associated aperture, wavelength, and identification
+information.  With a single aperture the image will be one dimensional
+and with multiple apertures the image will be two dimensional.
+When the \fIextras\fR parameter is set the images will be three
+dimensional (regardless of the number of apertures) and the lines in the
+third dimension contain additional information (see
+\fBapsum\fR for further details).  These spectral formats are accepted by the
+one dimensional spectroscopy tasks such as the plotting tasks \fBsplot\fR
+and \fBspecplot\fR.
+
+\fBPackage Parameters\fR
+
+The package parameters set parameters which change
+infrequently and set the standard I/O functions.  The extinction file
+is used for making extinction corrections and the standard star
+calibration directory is used for determining flux calibrations from
+standard star observations.  The calibration directories contain data files
+with standard star fluxes and band passes.  The available extinction
+files and flux calibration directories may be listed using the command:
+.nf
+
+	cl> help onedstds
+
+.fi
+
+The extinction correction requires computation of an air mass using the
+task \fBsetairmass\fR.  The air mass computation needs information
+about the observation and, in particular, the latitude of the observatory.
+This is determined using the OBSERVAT image header keyword.  If this
+keyword is not present the observatory parameter is used.  See the
+task \fBobservatory\fR for more on defining the observatory parameters.
+
+The spectrum interpolation type is used whenever a spectrum needs to be
+resampled for linearization or performing operations between spectra
+with different sampling.  The "sinc" interpolation may be of interest
+as an alternative but see the cautions given in \fBonedspec.package\fR.
+
+The general direction in which the spectra run is specified by the
+dispersion axis parameter.  Recall that ideally it is the direction
+of constant wavelength which should be aligned with an image axis and
+the dispersion direction may not be exactly aligned because atmospheric
+dispersion.
+
+The verbose parameter selects whether to print everything which goes
+into the log file on the terminal.  It is useful for monitoring
+what the \fBdoslit\fR task does.  The log and plot files are useful for
+keeping a record of the processing.  A log file is highly recommended.
+A plot file provides a record of the apertures, traces, and extracted
+spectra but can become quite large.
+The plotfile is most conveniently viewed and printed with \fBgkimosaic\fR.
+
+\fBProcessing Parameters\fR
+
+The input images are specified by image lists.  The lists may be
+a list of explicit comma separate image names, @ files, or image
+templates using pattern matching against file names in the directory.
+To allow wildcard image lists to be used safely and conveniently the
+image lists are checked to remove extracted images (the .ms images)
+and to automatically identify object and arc spectra.  Object and arc
+images are identified by the keyword IMAGETYP with values of "object",
+"OBJECT", "comp", or "COMPARISON" (the current practice at NOAO).
+If arc images are found in the object list they are transferred to the
+arc list while if object images are found in the arc list they are ignored.
+All other image types, such as biases, darks, or flat fields, are
+ignored.  This behavior allows simply specifying all images with a wildcard
+in the object list with automatic selections of arc spectra or a
+wildcard in the arc list to automatically find the arc spectra.
+If the data lack the identifying information it is up to the user
+to explicitly set the proper lists.
+
+The arc assignment table is a file which may be used to assign
+specific arc spectra to specific object and standard star spectra.
+For more on this option see \fBrefspectra\fR.
+
+The next set of parameters describe the noise characteristics and
+spectrum characteristics.  The read out noise and gain are used when
+"cleaning" cosmic rays and when using variance or optimal weighting.  These
+parameters must be fairly accurate.  Note that these are the effective
+parameters and must be adjusted if previous processing has modified the
+pixel values; such as with an unnormalized flat field.
+The variance
+weighting and cosmic-ray cleanning are sensitive to extremely strong
+cosmic-rays; ones which are hundreds of times brighter than the
+spectrum.  The \fIdatamax\fR is used to set an upper limit for any
+real data.  Any pixels above this value will be flagged as cosmic-rays
+and will not affect the extractions.
+
+The profile width should be approximately the full width
+at the profile base.  This parameter is used for centering and tracing
+of the spectrum profiles.
+
+The approximate central wavelength and dispersion are used for the
+automatic identification of the arc reference.  They may be specified
+as image header keywords or values.  The INDEF values search the
+entire range of the coordinate reference file but the automatic
+line identification algorithm works much better and faster if
+approximate values are given.
+
+The next set of parameters select the processing steps and options.  The
+various calibration steps may be done simultaneously, that is at the same
+time as the basic extractions, or in separate executions of the task.
+Typically, all the desired operations are done at the same time.
+Dispersion correction requires at least one arc spectrum and flux
+calibration requires dispersion correction and at least one standard star
+observation.
+
+The \fIresize\fR option resets the edges of the extraction aperture based
+on the profile for each object and standard star image.  The default
+resizing is to the 5% point relative to the peak measured above the
+background.  This allows following changes in the seeing.  However, one
+should consider the consequences of this if attempting to flux calibrate
+the observations.  Except in quicklook mode, the apertures for each object
+and standard star observation may be reviewed graphically and
+adjustments made to the aperture width and background regions.
+
+The \fIclean\fR option invokes a profile
+fitting and deviant point rejection algorithm as well as a variance weighting
+of points in the aperture.  See the next section for more about
+requirements to use this option.
+
+Generally once a spectrum has been processed it will not be reprocessed if
+specified as an input spectrum.  However, changes to the underlying
+calibration data can cause such spectra to be reprocessed if the
+\fIupdate\fR flag is set.  The changes which will cause an update are a
+new arc reference image and new standard stars.  If all input spectra are to be
+processed regardless of previous processing the \fIredo\fR flag may be
+used.  Note that reprocessing clobbers the previously processed output
+spectra.
+
+The final step is to plot the spectra if the \fIsplot\fR option is
+selected.  In non-quicklook mode there is a query which may be
+answered either in lower or upper case.  The plotting uses the interactive
+task \fBsplot\fR.  In quicklook mode the plot appears noninteractively
+using the task \fBbplot\fR.  
+
+The \fIquicklook\fR option provides a simpler, less interactive, mode.
+In quicklook mode a single aperture is defined using default parameters
+without interactive aperture review or trace fitting and
+the \fIsplot\fR option selects a noninteractive plot to be
+shown at the end of processing of each object and standard star
+spectrum.  While the algorithms used in quicklook mode are nearly the same
+as in non-quicklook mode and the final results may be the same it is
+recommended that the greater degree of monitoring and review in
+non-quicklook mode be used for careful final reductions.
+
+The batch processing option allows object spectra to be processed as a
+background or batch job.  This will occur only if the interactive
+\fIsplot\fR option is not active; either not set, turned off during
+processing with "NO", or in quicklook mode.  In batch processing the
+terminal output is suppressed.
+
+The \fIlistonly\fR option prints a summary of the processing steps
+which will be performed on the input spectra without actually doing
+anything.  This is useful for verifying which spectra will be affected
+if the input list contains previously processed spectra.  The listing
+does not include any arc spectra which may be extracted to dispersion
+calibrate an object spectrum.
+
+The last parameter (excluding the task mode parameter) points to
+another parameter set for the algorithm parameters.  The default
+parameter set is called \fIsparams\fR.  The algorithm parameters are
+discussed further in the next section.
+
+\fBAlgorithms and Algorithm Parameters\fR
+
+This section summarizes the various algorithms used by the
+\fBdoslit\fR task and the parameters which control and modify the
+algorithms.  The algorithm parameters available to you are
+collected in the parameter set \fBsparams\fR.  These parameters are
+taken from the various general purpose tasks used by the \fBdoslit\fR
+processing task.  Additional information about these parameters and
+algorithms may be found in the help for the actual
+task executed.  These tasks are identified below.  The aim of this
+parameter set organization is to collect all the algorithm parameters
+in one place separate from the processing parameters and include only
+those which are relevant for slit data.  The parameter values
+can be changed from the defaults by using the parameter editor,
+.nf
+
+cl> epar sparams
+
+.fi
+or simple typing \fIsparams\fR.
+The parameter editor can also be entered when editing the \fBdoslit\fR
+parameters by typing \fI:e\fR when positioned at the \fIsparams\fR
+parameter.
+
+\fBAperture Definitions\fR
+
+The first operation is to define the extraction apertures, which include the
+aperture width, background regions, and position dependence with
+wavelength, for the input slit spectra and, if flux calibration is
+selected, the standard star spectra.  This is done only for spectra which
+do not have previously defined apertures unless the \fIredo\fR option is
+set to force all definitions to be redone.  Thus, apertures may be
+defined separately using the \fBapextract\fR tasks.  This is particularly
+useful if one needs to use reference images to define apertures for very
+weak spectra which are not well centered or traced by themselves.
+
+Initially a single spectrum is found and a default aperture defined
+automatically.  If the \fIresize\fR parameter is set the aperture width is
+adjusted to a specified point on the spectrum profile (see
+\fBapresize\fR).  If not in "quicklook" mode (set by the \fIquicklook\fR
+parameter) a query is printed to select whether to inspect and modify the
+aperture and background aperture definitions using the commands described
+for \fBapedit\fR.  This option allows adding
+apertures for other objects on the slit and adjusting
+background regions to avoid contaminating objects.  The query may be
+answered in lower case for a single spectrum or in upper case to
+permanently set the response for the duration of the task execution.  This
+convention for query responses is used throughout the task.  It is
+recommended that quicklook only be used for initial quick extractions and
+calibration and that for final reductions one at least review the aperture
+definitions and traces.
+
+The initial spectrum finding and aperture definitions are done at a specified
+line or column.  The positions of the spectrum at a set of other lines or
+columns is done next and a smooth function is fit to define the aperture
+centers at all points in the image.  In non-quicklook mode the user has the
+option to review and adjust the function fitting parameters and delete bad
+position determinations.  As with the initial aperture review there is a
+query which may be answered either in lower or upper case.
+
+The above steps are all performed using tasks from the \fBapextract\fR
+package and parameters from the \fBsparams\fR parameters.  As a quick
+summary, the dispersion direction of the spectra are determined from the
+package \fBdispaxis\fR parameter if not defined in the image header.  The default
+line or column for finding the object position on the slit and the number
+of image lines or columns to sum are set by the \fIline\fR and \fInsum\fR
+parameters.  A line of INDEF (the default) selects the middle of the image.
+The automatic finding algorithm is described for the task
+\fBapfind\fR and is basically finds the strongest peak.  The default
+aperture size, background parameters, and resizing are described in
+the tasks \fBapdefault\fR and \fBapresize\fR and the
+parameters used are also described there.
+The tracing is done as described in \fBaptrace\fR and consists of
+stepping along the image using the specified \fIt_step\fR parameter.  The
+function fitting uses the \fBicfit\fR commands with the other parameters
+from the tracing section.
+
+\fBExtraction\fR
+
+The actual extraction of the spectra is done by summing across the
+fixed width apertures at each point along the dispersion.
+The default is to simply sum the pixels using
+partial pixels at the ends.  There is an option to weight the
+sum based on a Poisson variance model using the \fIreadnoise\fR and
+\fIgain\fR detector parameters.  Note that if the \fIclean\fR
+option is selected the variance weighted extraction is used regardless
+of the \fIweights\fR parameter.  The sigma thresholds for cleaning
+are also set in the \fBsparams\fR parameters.
+
+The cleaning and variance weighting options require knowing the effective
+(i.e. accounting for any image combining) read out noise and gain.  These
+numbers need to be adjusted if the image has been processed such that the
+intensity scale has a different origin (such as applying a separate
+background subtraction operation) or scaling (such as caused by
+unnormalized flat fielding).  These options also require using background
+subtraction if the profile does not go to zero.  For optimal extraction and
+cleaning to work it is recommended that any flat fielding be done using
+normalized flat fields (as is done in \fBccdproc\fR) and using background
+subtraction if there is any appreciable sky.  For further discussion of
+cleaning and variance weighted extraction see \fBapvariance\fR and
+\fBapprofiles\fR as well as  \fBapsum\fR.
+
+Background sky subtraction is done during the extraction based on
+background regions and parameters defined by the default parameters or
+changed during the interactive setting of the apertures.  The background
+subtraction options are to do no background subtraction, subtract the
+average, median, or minimum of the pixels in the background regions, or to
+fit a function and subtract the function from under the extracted object
+pixels.  The background regions are specified in pixels from
+the aperture center and follow changes in center of the spectrum along the
+dispersion.  The syntax is colon separated ranges with multiple ranges
+separated by a comma or space.  The background fitting uses the \fBicfit\fR
+routines which include medians, iterative rejection of deviant points, and
+a choice of function types and orders.  Note that it is important to use a
+method which rejects cosmic rays such as using either medians over all the
+background regions (\fIbackground\fR = "median") or median samples during
+fitting (\fIb_naverage\fR < -1).  The background subtraction algorithm and
+options are described in greater detail in \fBapsum\fR and
+\fBapbackground\fR.
+
+\fBDispersion Correction\fR
+
+If dispersion correction is not selected, \fIdispcor\fR=no, then the object
+spectra are simply extracted.  The extracted spectra may be plotted
+by setting the \fIsplot\fR option.  This produces a query and uses
+the interactive \fBsplot\fR task in non-quicklook mode and uses the
+noninteractive \fBbplot\fR task in quicklook mode.
+
+Dispersion corrections are applied to the extracted spectra if the
+\fIdispcor\fR processing parameter is set.  There are three basic steps
+involved; determining the dispersion functions relating pixel position to
+wavelength, assigning the appropriate dispersion function to a particular
+observation, and either storing the nonlinear dispersion function in the
+image headers or resampling the spectra to evenly spaced pixels in
+wavelength.
+
+The first arc spectrum in the arc list is used to define the reference
+dispersion solution.  It is extracted at middle of the image with no
+tracing.  Note extractions of arc spectra are not background subtracted.
+The task \fBautoidentify\fR is attempts to define the dispersion function
+automatically using the \fIcrval\fR and \fIcdelt\fR parameters.  Whether or
+not it is successful the user is presented with the interactive
+identification graph.  The automatic identifications can be reviewed and a
+new solution or corrections to the automatic solution may be performed.
+
+The arc dispersion function parameters are for \fBautoidentify\fR and it's
+related partner \fBreidentify\fR.  The parameters define a line list for
+use in automatically assigning wavelengths to arc lines, a centering width
+(which should match the line widths at the base of the lines), the
+dispersion function type and orders, parameters to exclude bad lines from
+function fits, and defining whether to refit the dispersion function as
+opposed to simply determining a zero point shift.  The defaults should
+generally be adequate and the dispersion function fitting parameters may be
+altered interactively.  One should consult the help for the two tasks for
+additional details of these parameters and the interactive operation of
+\fBautoidentify\fR.
+
+The extracted reference arc spectrum is then dispersion corrected.
+If the spectra are to be linearized, as set by the \fIlinearize\fR
+parameter, the default linear wavelength parameters are printed and
+you have the option to adjust them.  The dispersion system defined at
+this point will be applied automatically to all other spectra as they
+are dispersion corrected.
+
+Once the reference dispersion function is defined other arc spectra are
+extracted as required by the object spectra.  The assignment of arcs is
+done either explicitly with an arc assignment table (parameter
+\fIarctable\fR) or based on a header parameter such as a time.
+This assignments are made by the task
+\fBrefspectra\fR.  When two arcs are assigned to an object spectrum an
+interpolation is done between the two dispersion functions.  This makes an
+approximate correction for steady drifts in the dispersion.
+
+The tasks \fBsetjd\fR and \fBsetairmass\fR are automatically run on all
+spectra.  This computes and adds the header parameters for the Julian date
+(JD), the local Julian day number (LJD), the universal time (UTMIDDLE), and
+the air mass at the middle of the exposure.  The default arc assignment is
+to use the Julian date grouped by the local Julian day number.  The
+grouping allows multiple nights of data to be correctly assigned at the
+same time.
+
+The assigned arc spectra are then extracted using the object aperture
+definitions (but without background subtraction or cleaning) so that the
+same pixels on the detector are used.  The extracted arc spectra are then
+reidentified automatically against the reference arc spectrum.  Some
+statistics of the reidentification are printed (if not in batch mode) and
+the user has the option of examining the lines and fits interactively if
+not in quicklook mode.  The task which does the reidentification is called
+\fBreidentify\fR.
+
+The last step of dispersion correction is setting the dispersion
+of the object image from the arc images.  There are two choices here.
+If the \fIlinearize\fR parameter is not set the nonlinear dispersion
+function is stored in the image header.  Other IRAF tasks interpret
+this information when dispersion coordinates are needed for plotting
+or analysis.  This has the advantage of not requiring the spectra
+to be interpolated and the disadvantage that the dispersion
+information is only understood by IRAF tasks and cannot be readily
+exported to other analysis software.
+
+If the \fIlinearize\fR parameter is set then the spectra are resampled to a
+linear dispersion relation either in wavelength or the log of the
+wavelength using the dispersion coordinate system defined previously
+for the arc reference spectrum.
+
+The linearization algorithm parameters allow selecting the interpolation
+function type, whether to conserve flux per pixel by integrating across the
+extent of the final pixel, and whether to linearize to equal linear or
+logarithmic intervals.  The latter may be appropriate for radial velocity
+studies.  The default is to use a fifth order polynomial for interpolation,
+to conserve flux, and to not use logarithmic wavelength bins.  These
+parameters are described fully in the help for the task \fBdispcor\fR which
+performs the correction.
+
+\fBFlux Calibration\fR
+
+Flux calibration consists of an extinction correction and an instrumental
+sensitivity calibration.  The extinction correction only depends on the
+extinction function defined by the package parameter \fIextinct\fR and
+determination of the airmass from the header parameters (the air mass is
+computed by \fBsetairmass\fR as mentioned earlier).  The sensitivity
+calibration depends on a sensitivity calibration spectrum determined from
+standard star observations for which there are tabulated absolute fluxes.
+The task that applies both the extinction correction and sensitivity
+calibration to each extracted object spectrum is \fBcalibrate\fR.  Consult
+the manual page for this task for more information.
+
+Generation of the sensitivity calibration spectrum is done before
+processing any object spectra since it has two interactive steps and
+requires all the standard star observations.  The first step is tabulating
+the observed fluxes over the same bandpasses as the calibrated absolute
+fluxes.  The standard star tabulations are done after each standard star is
+extracted and dispersion corrected.  You are asked for the name of the
+standard star as tabulated in the absolute flux data files in the directory
+\fIcaldir\fR defined by the package parameters.
+The tabulation of the standard star
+observations over the standard bandpasses is done by the task
+\fBstandard\fR.  The tabulated data is stored in the file \fIstd\fR.  Note
+that if the \fIredo\fR flag is not set any new standard stars specified in
+subsequent executions of \fBdoslit\fR are added to the previous data in
+the data file, otherwise the file is first deleted.  Modification of the
+tabulated standard star data, such as by adding new stars, will cause any
+spectra in the input list which have been previously calibrated to be
+reprocessed if the \fIupdate\fR flag is set.
+
+After the standard star calibration bandpass fluxes are tabulated the
+information from all the standard stars is combined to produce a
+sensitivity function for use by \fBcalibrate\fR.  The sensitivity function
+determination is interactive and uses the task \fBsensfunc\fR.  This task
+allows fitting a smooth sensitivity function to the ratio of the observed
+to calibrated fluxes verses wavelength.  The types of manipulations one
+needs to do include deleting bad observations, possibly removing variable
+extinction (for poor data), and possibly deriving a revised extinction
+function.  This is a complex operation and one should consult the manual
+page for \fBsensfunc\fR.  The sensitivity function is saved as a one
+dimensional spectrum with the name \fIsens\fR.  Deletion of this image
+will also cause reprocessing to occur if the \fIupdate\fR flag is set.
+.ih
+EXAMPLES
+1.  The following example uses artificial data and may be executed
+at the terminal (with IRAF V2.10).  This is similar to the sequence
+performed by the test procedure "demos doslit".  The output is with
+the verbose package parameter set.  Normally users use \fBeparam\fR
+rather than the long command line.  All parameters not shown
+for \fBsparams\fR and \fBdoslit\fR are the default.
+
+.nf
+cl> demos mkdoslit
+Creating example longslit in image demoarc1 ...
+Creating example longslit in image demoobj1 ...
+Creating example longslit in image demostd1 ...
+Creating example longslit in image demoarc2 ...
+cl> doslit demoobj1 arcs=demoarc1,demoarc2 stand=demostd1 \
+>>> extcor=yes, fluxcal=yes resize=yes
+Searching aperture database ...
+Finding apertures ...
+Jan 17 15:52: FIND - 1 apertures found for demoobj1
+Resizing apertures ...
+Jan 17 15:52: APRESIZE  - 1 apertures resized for demoobj1 (-3.50, 3.49)
+Edit apertures for demostd1?  (yes):
+<Check aperture and background definitions ('b').  Exit with 'q'>
+Fit traced positions for demostd1 interactively?  (yes):  
+Tracing apertures ...
+Fit curve to aperture 1 of demostd1 interactively  (yes):
+<Exit with 'q'>
+Searching aperture database ...
+Finding apertures ...
+Jan 17 15:54: FIND - 1 apertures found for demostd1
+Resizing apertures ...
+Jan 17 15:54: APRESIZE  - 1 apertures resized for demostd1 (-3.35, 3.79)
+Edit apertures for demostd1?  (yes):
+<Exit with 'q'>
+Fit traced positions for demostd1 interactively?  (yes): n
+Tracing apertures ...
+Jan 17 15:55: TRACE - 1 apertures traced in demostd1.
+Jan 17 15:55: DATABASE - 1 apertures for demostd1 written to database
+Extract arc reference image demoarc1
+Searching aperture database ...
+Finding apertures ...
+Jan 17 15:55: FIND - 1 apertures found for demoarc1
+Jan 17 15:55: DATABASE - 1 apertures for demoarc1 written to database
+Extracting apertures ...
+Jan 17 15:55: EXTRACT - Aperture 1 from demoarc1 --> demoarc1.ms
+Determine dispersion solution for demoarc1
+<A dispersion function is automatically determined.>
+<Type 'f' to see the fit residuals>
+<Type 'd' to delete the two deviant lines>
+<Type 'f' to refit with the bad points deleted>
+<Type 'q' to quit fit and then 'q' to exit>
+demoarc1.ms.imh: w1 = 4204.18..., w2 = 7355.37..., dw = 6.16..., nw = 512
+  Change wavelength coordinate assignments? (yes|no|NO) (no): n
+Extract standard star spectrum demostd1
+Searching aperture database ...
+Jan 17 15:59: DATABASE  - 1 apertures read for demostd1 from database
+Extracting apertures ...
+Jan 17 15:59: EXTRACT - Aperture 1 from demostd1 --> demostd1.ms
+Assign arc spectra for demostd1
+[demostd1] refspec1='demoarc1 0.403'
+[demostd1] refspec2='demoarc2 0.597'
+Extract and reidentify arc spectrum demoarc1
+Searching aperture database ...
+Jan 17 15:59: DATABASE  - 1 apertures read for demostd1 from database
+Jan 17 15:59: DATABASE - 1 apertures for demoarc1 written to database
+Extracting apertures ...
+Jan 17 15:59: EXTRACT - Aperture 1 from demoarc1 --> demostd1demoarc1.ms
+
+REIDENTIFY: NOAO/IRAF V2.10BETA valdes@puppis Fri 15:59:21 17-Jan-92
+  Reference image = demoarc1.ms, New image = demostd1..., Refit = yes
+Image Data    Found     Fit Pix Shift  User Shift  Z Shift      RMS
+demo...       48/48   48/48    2.22E-4     0.00184  5.09E-7    0.225
+Fit dispersion function interactively? (no|yes|NO|YES) (yes):
+demoarc1.ms: w1 = 4211.81, w2 = 7353.58, dw = 6.148, nw = 512, log = no
+  Change wavelength coordinate assignments? (yes|no|NO): N
+demo... 48/48   48/48    2.22E-4     0.00184  5.09E-7    0.225
+Extract and reidentify arc spectrum demoarc2
+Searching aperture database ...
+Jan 17 16:01: DATABASE  - 1 apertures read for demostd1 from database
+Jan 17 16:01: DATABASE - 1 apertures for demoarc2 written to database
+Extracting apertures ...
+Jan 17 16:01: EXTRACT - Aperture 1 from demoarc2 --> demostd1demoarc2.ms
+
+REIDENTIFY: NOAO/IRAF V2.10BETA valdes@puppis Fri 16:01:54 17-Jan-92
+  Reference image = demoarc1.ms, New image = demostd1..., Refit = yes
+Image Data    Found     Fit Pix Shift  User Shift  Z Shift      RMS
+demo...       48/48   48/48    0.00302      0.0191  3.82E-6    0.244
+Dispersion correct demostd1
+demostd1.ms: ap = 1, w1 = 4204.181, w2 = 7355.375, dw = 6.16..., nw = 512
+Compile standard star fluxes for demostd1
+Star name in calibration list: hz2 <in kpnoslit package>
+demostd1.ms.imh[1]: Example artificial long slit image
+Compute sensitivity function
+Fit aperture 1 interactively? (no|yes|NO|YES) (no|yes|NO|YES) (yes):
+<Exit with 'q'>
+Sensitivity function for all apertures --> sens
+Flux and/or extinction calibrate standard stars
+[demostd1.ms.imh][1]: Example artificial long slit image
+  Extinction correction applied
+  Flux calibration applied
+Extract object spectrum demoobj1
+Searching aperture database ...
+Jan 17 16:05: DATABASE  - 1 apertures read for demoobj1 from database
+Extracting apertures ...
+Jan 17 16:05: EXTRACT - Aperture 1 from demoobj1 --> demoobj1.ms
+Assign arc spectra for demoobj1
+[demoobj1] refspec1='demoarc1 0.403'
+[demoobj1] refspec2='demoarc2 0.597'
+Extract and reidentify arc spectrum demoarc1
+Searching aperture database ...
+Jan 17 16:05: DATABASE  - 1 apertures read for demoobj1 from database
+Jan 17 16:05: DATABASE - 1 apertures for demoarc1 written to database
+Extracting apertures ...
+Jan 17 16:05: EXTRACT - Aperture 1 from demoarc1 --> demoobj1demoarc1.ms
+
+REIDENTIFY: NOAO/IRAF V2.10BETA valdes@puppis Fri 16:05:39 17-Jan-92
+  Reference image = demoarc1.ms, New image = demoobj1..., Refit = yes
+Image Data    Found     Fit Pix Shift  User Shift  Z Shift      RMS
+demo...       48/48   48/48   -2.49E-4    -0.00109  -1.1E-7    0.227
+Extract and reidentify arc spectrum demoarc2
+Searching aperture database ...
+Jan 17 16:05: DATABASE  - 1 apertures read for demoobj1 from database
+Jan 17 16:05: DATABASE - 1 apertures for demoarc2 written to database
+Extracting apertures ...
+Jan 17 16:05: EXTRACT - Aperture 1 from demoarc2 --> demoobj1demoarc2.ms
+
+REIDENTIFY: NOAO/IRAF V2.10BETA valdes@puppis Fri 16:05:42 17-Jan-92
+  Reference image = demoarc1.ms, New image = demoobj1..., Refit = yes
+Image Data    Found     Fit Pix Shift  User Shift  Z Shift      RMS
+demo...       48/48   48/48    0.00266      0.0169  3.46E-6     0.24
+Dispersion correct demoobj1
+demoobj1.ms: ap = 1, w1 = 4204.181, w2 = 7355.375, dw = 6.16..., nw = 512
+Extinction correct demoobj1
+Flux calibrate demoobj1
+[demoobj1.ms.imh][1]: Example artificial long slit image
+  Extinction correction applied
+  Flux calibration applied
+.fi
+
+2.  To redo the above:
+
+.nf
+cl> doslit demoobj1 arcs=demoarc1,demoarc2 stand=demostd1 \
+>>> extcor=yes, fluxcal=yes resize=yes redo+
+.fi
+.ih
+REVISIONS
+.ls DOSLIT V2.11
+The initial arc line identifications is done with the automatic line
+identification algorithm.
+.le
+.ls DOSLIT V2.10.3
+The usual output WCS format is "equispec".  The image format type to be
+processed is selected with the \fIimtype\fR environment parameter.  The
+dispersion axis parameter is now a package parameter.  Images will only
+be processed if the have the CCDPROC keyword.  A \fIdatamax\fR parameter
+has been added to help improve cosmic ray rejection.  The arc reference
+is no longer taken from the center of the image but using the first object
+aperture.  A bug which alphabetized the arc list was fixed.
+.le
+.ih
+SEE ALSO
+apbackground, apedit, apfind, approfiles, aprecenter, apresize, apsum,
+aptrace, apvariance, calibrate, ccdred, center1d, ctioslit, dispcor,
+echelle.doecslit, icfit, autoidentify, identify, kpnocoude, kpnoslit,
+specred, observatory, onedspec.package, refspectra, reidentify, sensfunc,
+setairmass, setjd, splot, standard
+.endhelp
diff --git a/noao/imred/specred/doc/doslit.ms b/noao/imred/specred/doc/doslit.ms
new file mode 100644
index 00000000..03ad0ab5
--- /dev/null
+++ b/noao/imred/specred/doc/doslit.ms
@@ -0,0 +1,1401 @@
+.nr PS 9
+.nr VS 11
+.de V1
+.ft CW
+.nf
+..
+.de V2
+.fi
+.ft R
+..
+.de LS
+.br
+.in +2
+..
+.de LE
+.br
+.sp .5v
+.in -2
+..
+.ND February 1993
+.TL
+Guide to the Slit Spectra Reduction Task DOSLIT
+.AU
+Francisco Valdes
+.AI
+IRAF Group - Central Computer Services
+.K2
+.DY
+
+.AB
+\fBDoslit\fR extracts, sky subtracts, wavelength calibrates, and flux
+calibrates simple two dimensional slit spectra which have been processed to
+remove the detector characteristics; i.e. CCD images have been bias, dark
+count, and flat field corrected.  It is primarily intended for
+spectrophotometry or radial velocities of stellar spectra with the spectra
+aligned with one of the image axes; i.e. the assumption is that extractions
+can be done by summing along image lines or columns.  The alignment does
+not have to be precise but only close enough that the wavelength difference
+across the spectrum profiles is insignificant.  The task is available
+in the \fBctioslit\fR, \fBkpnoslit\fR, \fBkpnocoude\fR, and \fBspecred\fR
+packages.
+.AE
+.NH
+Introduction
+.LP
+\fBDoslit\fR extracts, sky subtracts, wavelength calibrates, and flux
+calibrates simple two dimensional slit spectra which have been processed to
+remove the detector characteristics; i.e. CCD images have been bias, dark
+count, and flat field corrected.  It is primarily intended for
+spectrophotometry or radial velocities of stellar spectra with the spectra
+aligned with one of the image axes; i.e. the assumption is that extractions
+can be done by summing along image lines or columns.  The alignment does
+not have to be precise but only close enough that the wavelength difference
+across the spectrum profiles is insignificant.  Extended objects requiring
+accurate geometric alignment over many pixels are reduced using the
+\fBlongslit\fR package.
+.LP
+The task is a command language script which collects and combines the
+functions and parameters of many general purpose tasks to provide a single,
+complete data reduction path and a degree of guidance, automation, and
+record keeping.  In the following description and in the parameter section
+the various general tasks used are identified.  Further
+information about those tasks and their parameters may be found in their
+documentation.  \fBDoslit\fR also simplifies and consolidates parameters
+from those tasks and keeps track of previous processing to avoid
+duplications.
+.LP
+The general organization of the task is to do the interactive setup steps,
+such as the reference dispersion function
+determination, first using representative calibration data and then perform
+the majority of the reductions automatically, possibly as a background
+process, with reference to the setup data.  In addition, the task
+determines which setup and processing operations have been completed in
+previous executions of the task and, contingent on the \f(CWredo\fR and
+\f(CWupdate\fR options, skip or repeat some or all the steps.
+.LP
+The description is divided into a quick usage outline followed by details
+of the parameters and algorithms.  The usage outline is provided as a
+checklist and a refresher for those familiar with this task and the
+component tasks.  It presents only the default or recommended usage
+since there are many variations possible.
+.NH
+Usage Outline
+.LP
+.IP [1] 6
+The images are first processed with \fBccdproc\fR for overscan,
+zero level, dark count, and flat field corrections.
+.IP [2]
+Set the \fBdoslit\fR parameters with \fBeparam\fR.  Specify the object
+images to be processed,
+one or more arc images, and one or more standard
+star images.  If there are many object, arc, or standard star images
+you might prepare "@ files".  Set the detector and data
+specific parameters.  Select the processing options desired.
+Finally you might wish to review the \f(CWsparams\fR algorithm parameters
+though the defaults are probably adequate.
+.IP [3]
+Run the task.  This may be repeated multiple times with different
+observations and the task will generally only do the setup steps
+once and only process new images.  Queries presented during the
+execution for various interactive operations may be answered with
+"yes", "no", "YES", or "NO".  The lower case responses apply just
+to that query while the upper case responses apply to all further
+such queries during the current execution and no further queries of that
+type will be made.
+.IP [4]
+Apertures are defined for all the standard and object images.  This is only
+done if there are no previous aperture definitions for the image.
+The highest peak is found and centered and the default aperture limits
+are set.  If the resize option is set the aperture is resized by finding
+the level which  is 5% (the default) of the peak above local background.
+If not using the quicklook option you now have the option
+of entering the aperture editing loop to check the aperture position,
+size, and background fitting parameters, and possibly add additional
+apertures.  This is step is highly recommended.
+It is important to check the background regions with the 'b'
+key.  To exit the background mode and then
+to exit the review mode use 'q'.
+.IP
+The spectrum positions at a series of points along the dispersion are
+measured and a function is fit to these positions.  If not using the
+quicklook option the traced positions may be examined interactively and the
+fitting parameters adjusted.  To exit the interactive fitting type 'q'.
+.IP [5]
+If dispersion correction is selected the first arc in the arc list is
+extracted.  The dispersion function is defined using the task
+\fBautoidentify\fR.  The \fIcrval\fR and \fIcdelt\fR parameters are used in
+the automatic identification.  Whether or not the automatic identification
+is successful you will be shown the result of the arc line identification.
+If the automatic identification is not successful identify a few arc lines
+with with 'm' and and use the 'l' line list identification command to
+automatically add additional lines and fit the dispersion function.  Check
+the quality of the dispersion function fit with 'f'.  When satisfied exit
+with 'q'.
+.IP [6]
+If the flux calibration option is selected the standard star spectra are
+processed (if not done previously).  The images are
+extracted and wavelength calibrated.  The appropriate arc
+calibration spectra are extracted and the dispersion function refit
+using the arc reference spectrum as a starting point.  The standard star
+fluxes through the calibration bandpasses are compiled.  You are queried
+for the name of the standard star calibration data file.
+.IP
+After all the standard stars are processed a sensitivity function is
+determined using the interactive task \fBsensfunc\fR.  Finally, the
+standard star spectra are extinction corrected and flux calibrated
+using the derived sensitivity function.
+.IP [7]
+The object spectra are now automatically
+extracted, wavelength calibrated, and flux calibrated.
+.IP [8]
+The option to examine the final spectra with \fBsplot\fR may be given.
+To exit type 'q'.  In quicklook mode the spectra are plotted
+noninteractively with \fBbplot\fR.
+.IP [9]
+The final spectra will have the same name as the original 2D images
+with a ".ms" extension added.
+.NH
+Spectra and Data Files
+.LP
+The basic input consists of two dimensional slit object, standard star, and
+arc calibration spectra stored as IRAF images.
+The type of image format is defined by the
+environment parameter \fIimtype\fR.  Only images with that extension will
+be processed and created.
+The raw CCD images must be
+processed to remove overscan, bias, dark count, and flat field effects.
+This is generally done using the \fBccdred\fR package.  Lines of constant
+wavelength should be closely aligned with one of the image axes though a
+small amount of misalignment only causes a small loss of resolution.  For
+large misalignments one may use the \fBrotate\fR task.  More complex
+geometric problems and observations of extended objects should be handled
+by the \fBlongslit\fR package.
+.LP
+The arc
+spectra are comparison arc lamp observations (they must all be of the same
+type).  The assignment of arc calibration exposures to object exposures is
+generally done by selecting the nearest in time and interpolating.
+However, the optional \fIarc assignment table\fR may be used to explicitly
+assign arc images to specific objects.  The format of this file is
+described in task \fBrefspectra\fR.
+.LP
+The final reduced spectra are recorded in one, two or three dimensional IRAF
+images.  The images have the same name as the original images with an added
+".ms" extension.  Each line in the reduced image is a one dimensional
+spectrum with associated aperture, wavelength, and identification
+information.  With a single aperture the image will be one dimensional
+and with multiple apertures the image will be two dimensional.
+When the \f(CWextras\fR parameter is set the images will be three
+dimensional (regardless of the number of apertures) and the lines in the
+third dimension contain additional information (see
+\fBapsum\fR for further details).  These spectral formats are accepted by the
+one dimensional spectroscopy tasks such as the plotting tasks \fBsplot\fR
+and \fBspecplot\fR.
+.NH
+Package Parameters
+.LP
+The package parameters, shown in Figure 1 for the \fBspecred\fR package,
+set parameters which change infrequently and define the standard I/O functions.
+.KS
+.V1
+
+.ce
+Figure 1: Package Parameter Set for DOSLIT Packages
+
+                           I R A F
+            Image Reduction and Analysis Facility
+PACKAGE = imred
+   TASK = specred
+
+(extinct= onedstds$kpnoextinct.dat) Extinction file
+(caldir = onedstds$spec16redcal/) Standard star calibration directory
+(observa=  observatory) Observatory of data
+(interp =        poly5) Interpolation type
+(dispaxi=            2) Image axis for 2D images
+(nsum   =            1) Number of lines/columns to sum for 2D images
+
+(databas=     database) Database
+(verbose=           no) Verbose output?
+(logfile=      logfile) Log file
+(plotfil=             ) Plot file
+
+(records=             ) Record number extensions
+(version= SPECRED V3: April 1992)
+
+.KE
+.V2
+The extinction file
+is used for making extinction corrections and the standard star
+calibration directory is used for determining flux calibrations from
+standard star observations.  The calibration directories contain data files
+with standard star fluxes and band passes.  The available extinction
+files and flux calibration directories may be listed using the command:
+.V1
+
+	cl> help onedstds
+
+.V2
+The extinction correction requires computation of an air mass using the
+task \fBsetairmass\fR.  The air mass computation needs information
+about the observation and, in particular, the latitude of the observatory.
+This is determined using the OBSERVAT image header keyword.  If this
+keyword is not present the observatory parameter is used.  See the
+task \fBobservatory\fR for more on defining the observatory parameters.
+.LP
+The spectrum interpolation type is used whenever a spectrum needs to be
+resampled for linearization or performing operations between spectra
+with different sampling.  The "sinc" interpolation may be of interest
+as an alternative but see the cautions given in \fBonedspec.package\fR.
+.LP
+The general direction in which the spectra run is specified by the
+dispersion axis parameter.  Recall that ideally it is the direction
+of constant wavelength which should be aligned with an image axis and
+the dispersion direction may not be exactly aligned because atmospheric
+dispersion.
+.LP
+The verbose parameter selects whether to print everything which goes
+into the log file on the terminal.  It is useful for monitoring
+what the \fBdoslit\fR task does.  The log and plot files are useful for
+keeping a record of the processing.  A log file is highly recommended.
+A plot file provides a record of the apertures, traces, and extracted
+spectra but can become quite large.
+The plotfile is most conveniently viewed and printed with \fBgkimosaic\fR.
+.NH
+Processing Parameters
+.LP
+The \fBdoslit\fR parameters are shown in Figure 2.
+.KS
+.V1
+
+.ce
+Figure 2: Parameter Set for DOSLIT
+
+                           I R A F
+            Image Reduction and Analysis Facility
+PACKAGE = specred
+   TASK = doslit
+
+objects =               List of object spectra
+(arcs   =             ) List of arc spectra
+(arctabl=             ) Arc assignment table (optional)
+(standar=             ) List of standard star spectra
+
+.KE
+.V1
+(readnoi=      rdnoise) Read out noise sigma (photons)
+(gain   =         gain) Photon gain (photons/data number)
+(datamax=        INDEF) Max data value / cosmic ray threshold
+(width  =           5.) Width of profiles (pixels)
+(crval  =        INDEF) Approximate wavelength
+(cdelt  =        INDEF) Approximate dispersion
+
+(dispcor=          yes) Dispersion correct spectra?
+(extcor =           no) Extinction correct spectra?
+(fluxcal=           no) Flux calibrate spectra?
+(resize =           no) Automatically resize apertures?
+(clean  =           no) Detect and replace bad pixels?
+(splot  =           no) Plot the final spectrum?
+(redo   =           no) Redo operations if previously done?
+(update =           no) Update spectra if cal data changes?
+(quicklo=           no) Minimally interactive quick-look?
+(batch  =           no) Extract objects in batch?
+(listonl=           no) List steps but don't process?
+
+(sparams=             ) Algorithm parameters
+
+.V2
+The input images are specified by image lists.  The lists may be
+explicit comma separate image names, @ files, or image
+templates using pattern matching against file names in the directory.
+To allow wildcard image lists to be used safely and conveniently the
+image lists are checked to remove extracted images (the .ms images)
+and to automatically identify object and arc spectra.  Object and arc
+images are identified by the keyword IMAGETYP with values of "object",
+"OBJECT", "comp", or "COMPARISON" (the current practice at NOAO).
+If arc images are found in the object list they are transferred to the
+arc list while if object images are found in the arc list they are ignored.
+All other image types, such as biases, darks, or flat fields, are
+ignored.  This behavior allows simply specifying all images with a wildcard
+in the object list with automatic selections of arc spectra or a
+wildcard in the arc list to automatically find the arc spectra.
+If the data lack the identifying information it is up to the user
+to explicitly set the proper lists.
+.LP
+The arc assignment table is a file which may be used to assign
+specific arc spectra to specific object and standard star spectra.
+For more on this option see \fBrefspectra\fR.
+.LP
+The next set of parameters describe the noise characteristics and
+spectrum characteristics.  The read out noise and gain are used when
+"cleaning" cosmic rays and when using variance or optimal weighting.  These
+parameters must be fairly accurate.  Note that these are the effective
+parameters and must be adjusted if previous processing has modified the
+pixel values; such as with an unnormalized flat field.
+The variance
+weighting and cosmic-ray cleanning are sensitive to extremely strong
+cosmic-rays; ones which are hundreds of times brighter than the
+spectrum.  The \fIdatamax\fR is used to set an upper limit for any
+real data.  Any pixels above this value will be flagged as cosmic-rays
+and will not affect the extractions.
+.LP
+The profile width should be approximately the full width
+at the profile base.  This parameter is used for centering and tracing
+of the spectrum profiles.
+.LP
+The approximate central wavelength and dispersion are used for the
+automatic identification of the arc reference.  They may be specified
+as image header keywords or values.  The INDEF values search the
+entire range of the coordinate reference file but the automatic
+line identification algorithm works much better and faster if
+approximate values are given.
+.LP
+The next set of parameters select the processing steps and options.  The
+various calibration steps may be done simultaneously, that is at the same
+time as the basic extractions, or in separate executions of the task.
+Typically, all the desired operations are done at the same time.
+Dispersion correction requires at least one arc spectrum and flux
+calibration requires dispersion correction and at least one standard star
+observation.
+.LP
+The \f(CWresize\fR option resets the edges of the extraction aperture based
+on the profile for each object and standard star image.  The default
+resizing is to the 5% point relative to the peak measured above the
+background.  This allows following changes in the seeing.  However, one
+should consider the consequences of this if attempting to flux calibrate
+the observations.  Except in quicklook mode, the apertures for each object
+and standard star observation may be reviewed graphically and
+adjustments made to the aperture width and background regions.
+.LP
+The \f(CWclean\fR option invokes a profile
+fitting and deviant point rejection algorithm as well as a variance weighting
+of points in the aperture.  See the next section for more about
+requirements to use this option.
+.LP
+Generally once a spectrum has been processed it will not be reprocessed if
+specified as an input spectrum.  However, changes to the underlying
+calibration data can cause such spectra to be reprocessed if the
+\f(CWupdate\fR flag is set.  The changes which will cause an update are a
+new arc reference image and new standard stars.  If all input spectra are to be
+processed regardless of previous processing the \f(CWredo\fR flag may be
+used.  Note that reprocessing clobbers the previously processed output
+spectra.
+.LP
+The final step is to plot the spectra if the \f(CWsplot\fR option is
+selected.  In non-quicklook mode there is a query which may be
+answered either in lower or upper case.  The plotting uses the interactive
+task \fBsplot\fR.  In quicklook mode the plot appears noninteractively
+using the task \fBbplot\fR.  
+.LP
+The \f(CWquicklook\fR option provides a simpler, less interactive, mode.
+In quicklook mode a single aperture is defined using default parameters
+without interactive aperture review or trace fitting and
+the \f(CWsplot\fR option selects a noninteractive plot to be
+shown at the end of processing of each object and standard star
+spectrum.  While the algorithms used in quicklook mode are nearly the same
+as in non-quicklook mode and the final results may be the same it is
+recommended that the greater degree of monitoring and review in
+non-quicklook mode be used for careful final reductions.
+.LP
+The batch processing option allows object spectra to be processed as a
+background or batch job.  This will occur only if the interactive
+\f(CWsplot\fR option is not active; either not set, turned off during
+processing with "NO", or in quicklook mode.  In batch processing the
+terminal output is suppressed.
+.LP
+The \f(CWlistonly\fR option prints a summary of the processing steps
+which will be performed on the input spectra without actually doing
+anything.  This is useful for verifying which spectra will be affected
+if the input list contains previously processed spectra.  The listing
+does not include any arc spectra which may be extracted to dispersion
+calibrate an object spectrum.
+.LP
+The last parameter (excluding the task mode parameter) points to
+another parameter set for the algorithm parameters.  The default
+parameter set is called \f(CWsparams\fR.  The algorithm parameters are
+discussed further in the next section.
+.NH
+Algorithms and Algorithm Parameters
+.LP
+This section summarizes the various algorithms used by the
+\fBdoslit\fR task and the parameters which control and modify the
+algorithms.  The algorithm parameters available to you are
+collected in the parameter set \fBsparams\fR.  These parameters are
+taken from the various general purpose tasks used by the \fBdoslit\fR
+processing task.  Additional information about these parameters and
+algorithms may be found in the help for the actual
+task executed.  These tasks are identified below.  The aim of this
+parameter set organization is to collect all the algorithm parameters
+in one place separate from the processing parameters and include only
+those which are relevant for slit data.  The parameter values
+can be changed from the defaults by using the parameter editor,
+.V1
+
+cl> epar sparams
+
+.V2
+or simple typing \f(CWsparams\fR.
+The parameter editor can also be entered when editing the \fBdoslit\fR
+parameters by typing \f(CW:e\fR when positioned at the \f(CWsparams\fR
+parameter.  Figure 3 shows the parameter set.
+.KS
+.V1
+
+.ce
+Figure 3: Algorithm Parameter Set
+
+                           I R A F
+            Image Reduction and Analysis Facility
+PACKAGE = specred
+   TASK = sparams
+
+(line   =        INDEF) Default dispersion line
+(nsum   =           10) Number of dispersion lines to sum
+(extras =           no) Extract sky, sigma, etc.?
+
+                        -- DEFAULT APERTURE LIMITS --
+(lower  =          -3.) Lower aperture limit relative to center
+(upper  =           3.) Upper aperture limit relative to center
+
+                        -- AUTOMATIC APERTURE RESIZING PARAMETERS --
+(ylevel =         0.05) Fraction of peak or intensity for resizing
+
+.KE
+.KS
+.V1
+                        -- TRACE PARAMETERS --
+(t_step =           10) Tracing step
+(t_funct=      spline3) Trace fitting function
+(t_order=            1) Trace fitting function order
+(t_niter=            1) Trace rejection iterations
+(t_low  =           3.) Trace lower rejection sigma
+(t_high =           3.) Trace upper rejection sigma
+
+.KE
+.KS
+.V1
+                        -- APERTURE EXTRACTION PARAMETERS --
+(weights=         none) Extraction weights (none|variance)
+(pfit   =        fit1d) Profile fitting algorithm (fit1d|fit2d)
+(lsigma =           3.) Lower rejection threshold
+(usigma =           3.) Upper rejection threshold
+
+.KE
+.KS
+.V1
+                        -- BACKGROUND SUBTRACTION PARAMETERS --
+(backgro=          fit) Background to subtract
+(b_funct=     legendre) Background function
+(b_order=            1) Background function order
+(b_sampl=  -10:-6,6:10) Background sample regions
+(b_naver=         -100) Background average or median
+(b_niter=            1) Background rejection iterations
+(b_low  =           3.) Background lower rejection sigma
+(b_high =           3.) Background upper rejection sigma
+
+.KE
+.KS
+.V1
+                        -- ARC DISPERSION FUNCTION PARAMETERS --
+(coordli=linelists$idhenear.dat) Line list
+(match  =          -3.) Line list matching limit in Angstroms
+(fwidth =           4.) Arc line widths in pixels
+(cradius=          10.) Centering radius in pixels
+(i_funct=      spline3) Coordinate function
+(i_order=            1) Order of dispersion function
+(i_niter=            0) Rejection iterations
+(i_low  =           3.) Lower rejection sigma
+(i_high =           3.) Upper rejection sigma
+(refit  =          yes) Refit coordinate function when reidentifying?
+(addfeat=           no) Add features when reidentifying?
+
+.KE
+.KS
+.V1
+                        -- AUTOMATIC ARC ASSIGNMENT PARAMETERS --
+(select =       interp) Selection method for reference spectra
+(sort   =           jd) Sort key
+(group  =          ljd) Group key
+(time   =           no) Is sort key a time?
+(timewra=          17.) Time wrap point for time sorting
+
+.KE
+.KS
+.V1
+                        -- DISPERSION CORRECTION PARAMETERS --
+(lineari=          yes) Linearize (interpolate) spectra?
+(log    =           no) Logarithmic wavelength scale?
+(flux   =          yes) Conserve flux?
+
+.KE
+.KS
+.V1
+                        -- SENSITIVITY CALIBRATION PARAMETERS --
+(s_funct=      spline3) Fitting function
+(s_order=            1) Order of sensitivity function
+(fnu    =           no) Create spectra having units of FNU?
+
+.KE
+.V2
+.NH 2
+Aperture Definitions
+.LP
+The first operation is to define the extraction apertures, which include the
+aperture width, background regions, and position dependence with
+wavelength, for the input slit spectra and, if flux calibration is
+selected, the standard star spectra.  This is done only for spectra which
+do not have previously defined apertures unless the \f(CWredo\fR option is
+set to force all definitions to be redone.  Thus, apertures may be
+defined separately using the \fBapextract\fR tasks.  This is particularly
+useful if one needs to use reference images to define apertures for very
+weak spectra which are not well centered or traced by themselves.
+.LP
+Initially a single spectrum is found and a default aperture defined
+automatically.  If the \f(CWresize\fR parameter is set the aperture width is
+adjusted to a specified point on the spectrum profile (see
+\fBapresize\fR).  If not in "quicklook" mode (set by the \f(CWquicklook\fR
+parameter) a query is printed to select whether to inspect and modify the
+aperture and background aperture definitions using the commands described
+for \fBapedit\fR.  This option allows adding
+apertures for other objects on the slit and adjusting
+background regions to avoid contaminating objects.  The query may be
+answered in lower case for a single spectrum or in upper case to
+permanently set the response for the duration of the task execution.  This
+convention for query responses is used throughout the task.  It is
+recommended that quicklook only be used for initial quick extractions and
+calibration and that for final reductions one at least review the aperture
+definitions and traces.
+.LP
+The initial spectrum finding and aperture definitions are done at a specified
+line or column.  The positions of the spectrum at a set of other lines or
+columns is done next and a smooth function is fit to define the aperture
+centers at all points in the image.  In non-quicklook mode the user has the
+option to review and adjust the function fitting parameters and delete bad
+position determinations.  As with the initial aperture review there is a
+query which may be answered either in lower or upper case.
+.LP
+The above steps are all performed using tasks from the \fBapextract\fR
+package and parameters from the \fBsparams\fR parameters.  As a quick
+summary, the dispersion direction of the spectra are determined from the
+package \fBdispaxis\fR parameter if not defined in the image header.  The default
+line or column for finding the object position on the slit and the number
+of image lines or columns to sum are set by the \f(CWline\fR and \f(CWnsum\fR
+parameters.  A line of INDEF (the default) selects the middle of the image.
+The automatic finding algorithm is described for the task
+\fBapfind\fR and is basically finds the strongest peak.  The default
+aperture size, background parameters, and resizing are described in
+the tasks \fBapdefault\fR and \fBapresize\fR and the
+parameters used are also described there.
+The tracing is done as described in \fBaptrace\fR and consists of
+stepping along the image using the specified \f(CWt_step\fR parameter.  The
+function fitting uses the \fBicfit\fR commands with the other parameters
+from the tracing section.
+.NH 2
+Extraction
+.LP
+The actual extraction of the spectra is done by summing across the
+fixed width apertures at each point along the dispersion.
+The default is to simply sum the pixels using
+partial pixels at the ends.  There is an option to weight the
+sum based on a Poisson variance model using the \f(CWreadnoise\fR and
+\f(CWgain\fR detector parameters.  Note that if the \f(CWclean\fR
+option is selected the variance weighted extraction is used regardless
+of the \f(CWweights\fR parameter.  The sigma thresholds for cleaning
+are also set in the \fBsparams\fR parameters.
+.LP
+The cleaning and variance weighting options require knowing the effective
+(i.e. accounting for any image combining) read out noise and gain.  These
+numbers need to be adjusted if the image has been processed such that the
+intensity scale has a different origin (such as applying a separate
+background subtraction operation) or scaling (such as caused by
+unnormalized flat fielding).  These options also require using background
+subtraction if the profile does not go to zero.  For optimal extraction and
+cleaning to work it is recommended that any flat fielding be done using
+normalized flat fields (as is done in \fBccdproc\fR) and using background
+subtraction if there is any appreciable sky.  For further discussion of
+cleaning and variance weighted extraction see \fBapvariance\fR and
+\fBapprofiles\fR as well as  \fBapsum\fR.
+.LP
+Background sky subtraction is done during the extraction based on
+background regions and parameters defined by the default parameters or
+changed during the interactive setting of the apertures.  The background
+subtraction options are to do no background subtraction, subtract the
+average, median, or minimum of the pixels in the background regions, or to
+fit a function and subtract the function from under the extracted object
+pixels.  The background regions are specified in pixels from
+the aperture center and follow changes in center of the spectrum along the
+dispersion.  The syntax is colon separated ranges with multiple ranges
+separated by a comma or space.  The background fitting uses the \fBicfit\fR
+routines which include medians, iterative rejection of deviant points, and
+a choice of function types and orders.  Note that it is important to use a
+method which rejects cosmic rays such as using either medians over all the
+background regions (\f(CWbackground\fR = "median") or median samples during
+fitting (\f(CWb_naverage\fR < -1).  The background subtraction algorithm and
+options are described in greater detail in \fBapsum\fR and
+\fBapbackground\fR.
+.NH 2
+Dispersion Correction
+.LP
+If dispersion correction is not selected, \f(CWdispcor\fR=no, then the object
+spectra are simply extracted.  The extracted spectra may be plotted
+by setting the \f(CWsplot\fR option.  This produces a query and uses
+the interactive \fBsplot\fR task in non-quicklook mode and uses the
+noninteractive \fBbplot\fR task in quicklook mode.
+.LP
+Dispersion corrections are applied to the extracted spectra if the
+\f(CWdispcor\fR processing parameter is set.  There are three basic steps
+involved; determining the dispersion functions relating pixel position to
+wavelength, assigning the appropriate dispersion function to a particular
+observation, and either storing the nonlinear dispersion function in the
+image headers or resampling the spectra to evenly spaced pixels in
+wavelength.
+.LP
+The first arc spectrum in the arc list is used to define the reference
+dispersion solution.  It is extracted at middle of the image with no
+tracing.  Note extractions of arc spectra are not background subtracted.
+The task \fBautoidentify\fR is attempts to define the dispersion function
+automatically using the \fIcrval\fR and \fIcdelt\fR parameters.  Whether or
+not it is successful the user is presented with the interactive
+identification graph.  The automatic identifications can be reviewed and a
+new solution or corrections to the automatic solution may be performed.
+.LP
+The arc dispersion function parameters are for \fBautoidentify\fR and it's
+related partner \fBreidentify\fR.  The parameters define a line list for
+use in automatically assigning wavelengths to arc lines, a centering width
+(which should match the line widths at the base of the lines), the
+dispersion function type and orders, parameters to exclude bad lines from
+function fits, and defining whether to refit the dispersion function as
+opposed to simply determining a zero point shift.  The defaults should
+generally be adequate and the dispersion function fitting parameters may be
+altered interactively.  One should consult the help for the two tasks for
+additional details of these parameters and the interactive operation of
+\fBautoidentify\fR.
+.LP
+The extracted reference arc spectrum is then dispersion corrected.
+If the spectra are to be linearized, as set by the \f(CWlinearize\fR
+parameter, the default linear wavelength parameters are printed and
+you have the option to adjust them.  The dispersion system defined at
+this point will be applied automatically to all other spectra as they
+are dispersion corrected.
+.LP
+Once the reference dispersion function is defined other arc spectra are
+extracted as required by the object spectra.  The assignment of arcs is
+done either explicitly with an arc assignment table (parameter
+\f(CWarctable\fR) or based on a header parameter such as a time.
+This assignments are made by the task
+\fBrefspectra\fR.  When two arcs are assigned to an object spectrum an
+interpolation is done between the two dispersion functions.  This makes an
+approximate correction for steady drifts in the dispersion.
+.LP
+The tasks \fBsetjd\fR and \fBsetairmass\fR are automatically run on all
+spectra.  This computes and adds the header parameters for the Julian date
+(JD), the local Julian day number (LJD), the universal time (UTMIDDLE), and
+the air mass at the middle of the exposure.  The default arc assignment is
+to use the Julian date grouped by the local Julian day number.  The
+grouping allows multiple nights of data to be correctly assigned at the
+same time.
+.LP
+The assigned arc spectra are then extracted using the object aperture
+definitions (but without background subtraction or cleaning) so that the
+same pixels on the detector are used.  The extracted arc spectra are then
+reidentified automatically against the reference arc spectrum.  Some
+statistics of the reidentification are printed (if not in batch mode) and
+the user has the option of examining the lines and fits interactively if
+not in quicklook mode.  The task which does the reidentification is called
+\fBreidentify\fR.
+.LP
+The last step of dispersion correction is setting the dispersion
+of the object image from the arc images.  There are two choices here.
+If the \f(CWlinearize\fR parameter is not set the nonlinear dispersion
+function is stored in the image header.  Other IRAF tasks interpret
+this information when dispersion coordinates are needed for plotting
+or analysis.  This has the advantage of not requiring the spectra
+to be interpolated and the disadvantage that the dispersion
+information is only understood by IRAF tasks and cannot be readily
+exported to other analysis software.
+.LP
+If the \f(CWlinearize\fR parameter is set then the spectra are resampled to a
+linear dispersion relation either in wavelength or the log of the
+wavelength using the dispersion coordinate system defined previously
+for the arc reference spectrum.
+.LP
+The linearization algorithm parameters allow selecting the interpolation
+function type, whether to conserve flux per pixel by integrating across the
+extent of the final pixel, and whether to linearize to equal linear or
+logarithmic intervals.  The latter may be appropriate for radial velocity
+studies.  The default is to use a fifth order polynomial for interpolation,
+to conserve flux, and to not use logarithmic wavelength bins.  These
+parameters are described fully in the help for the task \fBdispcor\fR which
+performs the correction.
+.NH 2
+Flux Calibration
+.LP
+Flux calibration consists of an extinction correction and an instrumental
+sensitivity calibration.  The extinction correction only depends on the
+extinction function defined by the package parameter \f(CWextinct\fR and
+determination of the airmass from the header parameters (the air mass is
+computed by \fBsetairmass\fR as mentioned earlier).  The sensitivity
+calibration depends on a sensitivity calibration spectrum determined from
+standard star observations for which there are tabulated absolute fluxes.
+The task that applies both the extinction correction and sensitivity
+calibration to each extracted object spectrum is \fBcalibrate\fR.  Consult
+the manual page for this task for more information.
+.LP
+Generation of the sensitivity calibration spectrum is done before
+processing any object spectra since it has two interactive steps and
+requires all the standard star observations.  The first step is tabulating
+the observed fluxes over the same bandpasses as the calibrated absolute
+fluxes.  The standard star tabulations are done after each standard star is
+extracted and dispersion corrected.  You are asked for the name of the
+standard star as tabulated in the absolute flux data files in the directory
+\f(CWcaldir\fR defined by the package parameters.
+The tabulation of the standard star
+observations over the standard bandpasses is done by the task
+\fBstandard\fR.  The tabulated data is stored in the file \f(CWstd\fR.  Note
+that if the \f(CWredo\fR flag is not set any new standard stars specified in
+subsequent executions of \fBdoslit\fR are added to the previous data in
+the data file, otherwise the file is first deleted.  Modification of the
+tabulated standard star data, such as by adding new stars, will cause any
+spectra in the input list which have been previously calibrated to be
+reprocessed if the \f(CWupdate\fR flag is set.
+.LP
+After the standard star calibration bandpass fluxes are tabulated the
+information from all the standard stars is combined to produce a
+sensitivity function for use by \fBcalibrate\fR.  The sensitivity function
+determination is interactive and uses the task \fBsensfunc\fR.  This task
+allows fitting a smooth sensitivity function to the ratio of the observed
+to calibrated fluxes verses wavelength.  The types of manipulations one
+needs to do include deleting bad observations, possibly removing variable
+extinction (for poor data), and possibly deriving a revised extinction
+function.  This is a complex operation and one should consult the manual
+page for \fBsensfunc\fR.  The sensitivity function is saved as a one
+dimensional spectrum with the name \f(CWsens\fR.  Deletion of this image
+will also cause reprocessing to occur if the \f(CWupdate\fR flag is set.
+.NH
+References
+.NH 2
+IRAF Introductory References
+.LP
+Work is underway on a new introductory guide to IRAF.  Currently, the
+work below is the primary introduction.
+.IP
+P. Shames and D. Tody, \fIA User's Introduction to the IRAF Command
+Language\fR, Central Computer Services, NOAO, 1986.
+.NH 2
+CCD Reductions
+.IP
+F. Valdes, \fIThe IRAF CCD Reduction Package -- CCDRED\fR, Central
+Computer Services, NOAO, 1987.
+.IP
+F. Valdes, \fIUser's Guide to the CCDRED Package\fR, Central
+Computer Services, NOAO, 1988.  Also on-line as \f(CWhelp ccdred.guide\fR.
+.IP
+P. Massey, \fIA User's Guide to CCD Reductions with IRAF\fR, Central
+Computer Services, NOAO, 1989.
+.NH 2
+Aperture Extraction Package
+.IP
+F. Valdes, \fIThe IRAF APEXTRACT Package\fR, Central Computer Services,
+NOAO, 1987 (out-of-date).
+.NH 2
+DOSLIT Task
+.IP
+P. Massey, \fIUser's Guide to Slit Spectra Reductions\fR,
+Central Computer Services, NOAO, 1992.
+.NH 2
+Task Help References
+.LP
+Each task in the \fBspecred\fR packages and tasks used by \fBdoslit\fR have
+help pages describing the parameters and task in some detail.  To get
+on-line help type
+.V1
+
+cl> help \fItaskname\fR
+
+.V2
+The output of this command can be piped to \fBlprint\fR to make a printed
+copy.
+
+.V1
+       apall - Extract 1D spectra (all parameters in one task)
+   apdefault - Set the default aperture parameters and apidtable
+      apedit - Edit apertures interactively
+      apfind - Automatically find spectra and define apertures
+       apfit - Fit 2D spectra and output the fit, difference, or ratio
+   apflatten - Remove overall spectral and profile shapes from flat fields
+      apmask - Create and IRAF pixel list mask of the apertures
+ apnormalize - Normalize 2D apertures by 1D functions
+  aprecenter - Recenter apertures
+    apresize - Resize apertures
+   apscatter - Fit and subtract scattered light
+       apsum - Extract 1D spectra
+     aptrace - Trace positions of spectra
+ 
+autoidentify - Automatically identify arc lines and a dispersion function
+       bplot - Batch plot of spectra with SPLOT
+   calibrate - Extinction and flux calibrate spectra
+   continuum - Fit the continuum in spectra
+    deredden - Apply interstellar extinction correction
+     dispcor - Dispersion correct spectra
+      dopcor - Doppler correct spectra
+    fitprofs - Fit gaussian profiles
+    identify - Identify features in spectrum for dispersion solution
+    msresp1d - Create 1D response spectra from flat field and sky spectra
+  refspectra - Assign wavelength reference spectra to other spectra
+  reidentify - Automatically reidentify features in spectra
+  sapertures - Set or change aperture header information
+      sarith - Spectrum arithmetic
+    scombine - Combine spectra
+       scopy - Select and copy apertures in different spectral formats
+    sensfunc - Compute instrumental sensitivity from standard stars
+  setairmass - Compute effective airmass and middle UT for an exposure
+       setjd - Compute and set Julian dates in images
+        sfit - Fit spectra and output fit, ratio, or difference
+      skysub - Sky subtract extracted multispec spectra
+       slist - List spectrum header parameters
+    specplot - Scale, stack, and plot multiple spectra
+       splot - Preliminary spectral plot/analysis
+    standard - Tabulate standard star counts and fluxes
+ 
+      doslit - Process slit spectra
+       demos - Demonstrations and tests
+
+	    Additional help topics
+
+   onedspec.package - Package parameters and general description of package
+  apextract.package - Package parameters and general description of package
+ approfiles - Profile determination algorithms
+ apvariance - Extractions, variance weighting, cleaning, and noise model
+   center1d - One dimensional centering algorithm
+      icfit - Interactive one dimensional curve fitting
+.V2
+.SH
+Appendix A: DOSLIT Parameters
+.LP
+.nr PS 8
+.nr VS 10
+objects
+.LS
+List of object images to be processed.  Previously processed spectra are
+ignored unless the \f(CWredo\fR flag is set or the \f(CWupdate\fR flag is set
+and dependent calibration data has changed.  If the images contain the
+keyword IMAGETYP then only those with a value of "object" or "OBJECT"
+are used and those with a value of "comp" or "COMPARISON" are added
+to the list of arcs.  Extracted spectra are ignored.
+.LE
+arcs = "" (at least one if dispersion correcting)
+.LS
+List of arc calibration spectra.  These spectra are used to define
+the dispersion functions.  The first spectrum is used to mark lines
+and set the dispersion function interactively and dispersion functions
+for all other arc spectra are derived from it.  If the images contain
+the keyword IMAGETYP then only those with a value of "comp" or
+"COMPARISON" are used.  All others are ignored as are extracted spectra.
+.LE
+arctable = "" (optional) (refspectra)
+.LS
+Table defining which arc spectra are to be assigned to which object
+spectra (see \fBrefspectra\fR).  If not specified an assignment based
+on a header parameter, \f(CWsparams.sort\fR, such as the Julian date
+is made.
+.LE
+standards = "" (at least one if flux calibrating)
+.LS
+List of standard star spectra.  The standard stars must have entries in
+the calibration database (package parameter \f(CWcaldir\fR).
+.LE
+
+readnoise = "rdnoise", gain = "gain" (apsum)
+.LS
+Read out noise in photons and detector gain in photons per data value.
+This parameter defines the minimum noise sigma and the conversion between
+photon Poisson statistics and the data number statistics.  Image header
+keywords (case insensitive) may be specified to obtain the values from the
+image header.
+.LE
+datamax = INDEF (apsum.saturation)
+.LS
+The maximum data value which is not a cosmic ray.
+When cleaning cosmic rays and/or using variance weighted extraction
+very strong cosmic rays (pixel values much larger than the data) can
+cause these operations to behave poorly.  If a value other than INDEF
+is specified then all data pixels in excess of this value will be
+excluded and the algorithms will yield improved results.
+This applies only to the object spectra and not the standard star or
+arc spectra.  For more
+on this see the discussion of the saturation parameter in the
+\fBapextract\fR package.
+.LE
+width = 5. (apedit)
+.LS
+Approximate full width of the spectrum profiles.  This parameter is used
+to define a width and error radius for the profile centering algorithm.
+.LE
+crval = INDEF, cdelt = INDEF (autoidentify)
+.LS
+These parameters specify an approximate central wavelength and dispersion.
+They may be specified as numerical values, INDEF, or image header keyword
+names whose values are to be used.
+If both these parameters are INDEF then the automatic identification will
+not be done.
+.LE
+
+dispcor = yes
+.LS
+Dispersion correct spectra?  This may involve either defining a nonlinear
+dispersion coordinate system in the image header or resampling the
+spectra to uniform linear wavelength coordinates as selected by
+the parameter \f(CWsparams.linearize\fR.
+.LE
+extcor = no
+.LS
+Extinction correct the spectra?
+.LE
+fluxcal = no
+.LS
+Flux calibrate the spectra using standard star observations?
+.LE
+resize = no (apresize)
+.LS
+Resize the default aperture for each object based on the spectrum profile?
+.LE
+clean = no (apsum)
+.LS
+Detect and correct for bad pixels during extraction?  This is the same
+as the clean option in the \fBapextract\fR package.  If yes this also
+implies variance weighted extraction.  In addition the datamax parameters
+can be useful.
+.LE
+splot = no
+.LS
+Plot the final spectra with the task \fBsplot\fR?  In quicklook mode
+this is automatic and in non-quicklook mode it is queried.
+.LE
+redo = no
+.LS
+Redo operations previously done?  If no then previously processed spectra
+in the object list will not be processed unless required by the
+update option.
+.LE
+update = no
+.LS
+Update processing of previously processed spectra if the
+dispersion reference image or standard star calibration data are changed?
+.LE
+quicklook = no
+.LS
+Extract and calibrate spectra with minimal interaction?  In quicklook mode
+only the initial dispersion function solution and standard star setup are
+done interactively.  Normally the \f(CWsplot\fR option is set in this mode to
+produce an automatic final spectrum plot for each object.  It is
+recommended that this mode not be used for final reductions.
+.LE
+batch = yes
+.LS
+Process spectra as a background or batch job provided there are no interactive
+steps remaining.
+.LE
+listonly = no
+.LS
+List processing steps but don't process?
+.LE
+
+sparams = "" (pset)
+.LS
+Name of parameter set containing additional processing parameters.  This
+parameter is only for indicating the link to the parameter set
+\fBsparams\fR and should not be given a value.  The parameter set may be
+examined and modified in the usual ways (typically with "eparam sparams"
+or ":e sparams" from the parameter editor).  The parameters are
+described below.
+.LE
+
+.ce
+-- GENERAL PARAMETERS --
+
+line = INDEF, nsum = 10
+.LS
+The dispersion line (line or column perpendicular to the dispersion
+axis) and number of adjacent lines (half before and half after unless
+at the end of the image) used in finding, resizing,
+editing, and tracing operations.  A line of INDEF selects the middle of the
+image along the dispersion axis.
+.LE
+extras = no (apsum)
+.LS
+Include raw unweighted and uncleaned spectra, the background spectra, and
+the estimated sigmas in a three dimensional output image format.
+See the discussion in the \fBapextract\fR package for further information.
+.LE
+
+.ce
+-- DEFAULT APERTURE LIMITS --
+
+lower = -3., upper = 3. (apdefault)
+.LS
+Default lower and upper aperture limits relative to the aperture center.
+These limits are used when the apertures are first defined.
+.LE
+
+.ce
+-- AUTOMATIC APERTURE RESIZING PARAMETERS --
+
+ylevel = 0.05 (apresize)
+.LS
+Fraction of the peak to set aperture limits during automatic resizing.
+.LE
+
+.ce
+-- TRACE PARAMETERS --
+
+t_step = 10 (aptrace)
+.LS
+Step along the dispersion axis between determination of the spectrum
+positions.  Note the \f(CWnsum\fR parameter is also used to enhance the
+signal-to-noise at each step.
+.LE
+t_function = "spline3", t_order = 1 (aptrace)
+.LS
+Default trace fitting function and order.  The fitting function types are
+"chebyshev" polynomial, "legendre" polynomial, "spline1" linear spline, and
+"spline3" cubic spline.  The order refers to the number of terms in the
+polynomial functions or the number of spline pieces in the spline
+functions.
+.LE
+t_niterate = 1, t_low = 3., t_high = 3. (aptrace)
+.LS
+Default number of rejection iterations and rejection sigma thresholds.
+.LE
+
+.ce
+-- APERTURE EXTRACTION PARAMETERS --
+
+weights = "none" (apsum) (none|variance)
+.LS
+Type of extraction weighting.  Note that if the \f(CWclean\fR parameter is
+set then the weights used are "variance" regardless of the weights
+specified by this parameter.  The choices are:
+
+"none"
+.LS
+The pixels are summed without weights except for partial pixels at the
+ends.
+.LE
+"variance"
+.LS
+The extraction is weighted by the variance based on the data values
+and a poisson/ccd model using the \f(CWgain\fR and \f(CWreadnoise\fR
+parameters.
+.LE
+.LE
+pfit = "fit1d" (apsum and approfile) (fit1d|fit2d)
+.LS
+Type of profile fitting algorithm to use.  The "fit1d" algorithm is
+preferred except in cases of extreme tilt.
+.LE
+lsigma = 3., usigma = 3. (apsum)
+.LS
+Lower and upper rejection thresholds, given as a number of times the
+estimated sigma of a pixel, for cleaning.
+.LE
+
+.ce
+-- DEFAULT BACKGROUND PARAMETERS --
+
+background = "fit" (apsum) (none|average|median|minimum|fit)
+.LS
+Type of background subtraction.  The choices are "none" for no background
+subtraction, "average" to average the background within the background
+regions, "median" to use the median in the background regions, "minimum" to
+use the minimum in the background regions, or "fit" to fit across the
+dispersion using the background within the background regions.  Note that
+the "average" option does not do any medianing or bad pixel checking,
+something which is recommended.  The fitting option is slower than the
+other options and requires additional fitting parameter.
+.LE
+b_function = "legendre", b_order = 1 (apsum)
+.LS
+Default background fitting function and order.  The fitting function types are
+"chebyshev" polynomial, "legendre" polynomial, "spline1" linear spline, and
+"spline3" cubic spline.  The order refers to the number of
+terms in the polynomial functions or the number of spline pieces in the spline
+functions.
+.LE
+b_sample = "-10:-6,6:10" (apsum)
+.LS
+Default background sample.  The sample is given by a set of colon separated
+ranges each separated by either whitespace or commas.  The string "*" refers
+to all points.  Note that the background coordinates are relative to the
+aperture center and not image pixel coordinates so the endpoints need not
+be integer.  It is recommended that the background regions be examined
+and set interactively with the 'b' key in the interactive aperture
+definition mode.  This requires \f(CWquicklook\fR to be no.
+.LE
+b_naverage = -100 (apsum)
+.LS
+Default number of points to average or median.  Positive numbers
+average that number of sequential points to form a fitting point.
+Negative numbers median that number, in absolute value, of sequential
+points.  A value of 1 does no averaging and each data point is used in the
+fit.
+.LE
+b_niterate = 1 (apsum)
+.LS
+Default number of rejection iterations.  If greater than zero the fit is
+used to detect deviant fitting points and reject them before repeating the
+fit.  The number of iterations of this process is given by this parameter.
+.LE
+b_low_reject = 3., b_high_reject = 3. (apsum)
+.LS
+Default background lower and upper rejection sigmas.  If greater than zero
+points deviating from the fit below and above the fit by more than this
+number of times the sigma of the residuals are rejected before refitting.
+.LE
+
+.ce
+-- ARC DISPERSION FUNCTION PARAMETERS --
+
+threshold = 10. (autoidentify/reidentify)
+.LS
+In order for a feature center to be determined the range of pixel intensities
+around the feature must exceed this threshold.
+.LE
+coordlist = "linelists$idhenear.dat" (autoidentify)
+.LS
+Arc line list consisting of an ordered list of wavelengths.
+Some standard line lists are available in the directory "linelists$".
+.LE
+match = -3. (autoidentify)
+.LS
+The maximum difference for a match between the dispersion function computed
+value and a wavelength in the coordinate list.
+.LE
+fwidth = 4. (autoidentify)
+.LS
+Approximate full base width (in pixels) of arc lines.
+.LE
+cradius = 10. (reidentify)
+.LS
+Radius from previous position to reidentify arc line.
+.LE
+i_function = "spline3", i_order = 1 (autoidentify)
+.LS
+The default function and order to be fit to the arc wavelengths as a
+function of the pixel coordinate.  The functions choices are "chebyshev",
+"legendre", "spline1", or "spline3".
+.LE
+i_niterate = 0, i_low = 3.0, i_high = 3.0 (autoidentify)
+.LS
+Number of rejection iterations and sigma thresholds for rejecting arc
+lines from the dispersion function fits.
+.LE
+refit = yes (reidentify)
+.LS
+Refit the dispersion function?  If yes and there is more than 1 line
+and a dispersion function was defined in the initial arc reference then a new
+dispersion function of the same type as in the reference image is fit
+using the new pixel positions.  Otherwise only a zero point shift is
+determined for the revised fitted coordinates without changing the
+form of the dispersion function.
+.LE
+addfeatures = no (reidentify)
+.LS
+Add new features from a line list during each reidentification?
+This option can be used to compensate for lost features from the
+reference solution.  Care should be exercised that misidentified features
+are not introduced.
+.LE
+
+.ce
+-- AUTOMATIC ARC ASSIGNMENT PARAMETERS --
+
+select = "interp" (refspectra)
+.LS
+Selection method for assigning wavelength calibration spectra.
+Note that an arc assignment table may be used to override the selection
+method and explicitly assign arc spectra to object spectra.
+The automatic selection methods are:
+
+average
+.LS
+Average two reference spectra without regard to any
+sort or group parameters.
+If only one reference spectrum is specified then it is assigned with a
+warning.  If more than two reference spectra are specified then only the
+first two are used and a warning is given.  There is no checking of the
+group values.
+.LE
+following
+.LS
+Select the nearest following spectrum in the reference list based on the
+sort and group parameters.  If there is no following spectrum use the
+nearest preceding spectrum.
+.LE
+interp
+.LS
+Interpolate between the preceding and following spectra in the reference
+list based on the sort and group parameters.  If there is no preceding and
+following spectrum use the nearest spectrum.  The interpolation is weighted
+by the relative distances of the sorting parameter (see cautions in
+DESCRIPTION section).
+.LE
+match
+.LS
+Match each input spectrum with the reference spectrum list in order.
+This overrides any group values.
+.LE
+nearest
+.LS
+Select the nearest spectrum in the reference list based on the sort and
+group parameters.
+.LE
+preceding
+.LS
+Select the nearest preceding spectrum in the reference list based on the
+sort and group parameters.  If there is no preceding spectrum use the
+nearest following spectrum.
+.LE
+.LE
+sort = "jd" (setjd and refspectra)
+.LS
+Image header keyword to be used as the sorting parameter for selection
+based on order.  The header parameter must be numeric but otherwise may
+be anything.  Common sorting parameters are times or positions.
+.LE
+group = "ljd" (setjd and refspectra)
+.LS
+Image header keyword to be used to group spectra.  For those selection
+methods which use the group parameter the reference and object
+spectra must have identical values for this keyword.  This can
+be anything but it must be constant within a group.  Common grouping
+parameters are the date of observation "date-obs" (provided it does not
+change over a night) or the local Julian day number.
+.LE
+time = no, timewrap = 17. (refspectra)
+.LS
+Is the sorting parameter a 24 hour time?  If so then the time origin
+for the sorting is specified by the timewrap parameter.  This time
+should precede the first observation and follow the last observation
+in a 24 hour cycle.
+.LE
+
+.ce
+-- DISPERSION  CORRECTION PARAMETERS --
+
+linearize = yes (dispcor)
+.LS
+Interpolate the spectra to a linear dispersion sampling?  If yes the
+spectra will be interpolated to a linear or log linear sampling using
+the linear dispersion parameters specified by other parameters.  If
+no the nonlinear dispersion function(s) from the dispersion function
+database are assigned to the input image world coordinate system
+and the spectral data is not interpolated.  Note the interpolation
+function type is set by the package parameter \f(CWinterp\fR.
+.LE
+log = no (dispcor)
+.LS
+Use linear logarithmic wavelength coordinates?  Linear logarithmic
+wavelength coordinates have wavelength intervals which are constant
+in the logarithm of the wavelength.
+.LE
+flux = yes (dispcor)
+.LS
+Conserve the total flux during interpolation?  If \f(CWno\fR the output
+spectrum is interpolated from the input spectrum at each output
+wavelength coordinate.  If \f(CWyes\fR the input spectrum is integrated
+over the extent of each output pixel.  This is slower than
+simple interpolation.
+.LE
+
+.ce
+-- SENSITIVITY CALIBRATION PARAMETERS --
+
+s_function = "spline3", s_order = 1 (sensfunc)
+.LS
+Function and order used to fit the sensitivity data.  The function types
+are "chebyshev" polynomial, "legendre" polynomial, "spline3" cubic spline,
+and "spline1" linear spline.  Order of the sensitivity fitting function.
+The value corresponds to the number of polynomial terms or the number of
+spline pieces.  The default values may be changed interactively.
+.LE
+fnu = no (calibrate)
+.LS
+The default calibration is into units of F-lambda. If \f(CWfnu\fR = yes then
+the calibrated spectrum will be in units of F-nu.
+.LE
+
+.ce
+PACKAGE PARAMETERS
+
+The following package parameters are used by this task.  The default values
+may vary depending on the package.
+
+dispaxis = 2
+.LS
+Default dispersion axis.  The dispersion axis is 1 for dispersion
+running along image lines and 2 for dispersion running along image
+columns.  If the image header parameter DISPAXIS is defined it has
+precedence over this parameter.  The default value defers to the
+package parameter of the same name.
+.LE
+extinction (standard, sensfunc, calibrate)
+.LS
+Extinction file for a site.  There are two extinction files in the
+NOAO standards library, onedstds$, for KPNO and CTIO.  These extinction
+files are used for extinction and flux calibration.
+.LE
+caldir (standard)
+.LS
+Standard star calibration directory.  A directory containing standard
+star data files.  Note that the directory name must end with '/'.
+There are a number of standard star calibrations directories in the NOAO
+standards library, onedstds$.
+.LE
+observatory = "observatory" (observatory)
+.LS
+The default observatory to use for latitude dependent computations.
+If the OBSERVAT keyword in the image header it takes precedence over
+this parameter.
+.LE
+interp = "poly5" (nearest|linear|poly3|poly5|spline3|sinc) (dispcor)
+.LS
+Spectrum interpolation type used when spectra are resampled.  The choices are:
+
+.V1
+	nearest - nearest neighbor
+	 linear - linear
+	  poly3 - 3rd order polynomial
+	  poly5 - 5th order polynomial
+	spline3 - cubic spline
+	   sinc - sinc function
+.V2
+.LE
+database = "database"
+.LS
+Database name used by various tasks.  This is a directory which is created
+if necessary.
+.LE
+verbose = no
+.LS
+Verbose output?  If set then almost all the information written to the
+logfile is also written to the terminal except when the task is a
+background or batch process.
+.LE
+logfile = "logfile"
+.LS
+If specified detailed text log information is written to this file.
+.LE
+plotfile = ""
+.LS
+If specified metacode plots are recorded in this file for later review.
+Since plot information can become large this should be used only if
+really desired.
+.LE
+
+.ce
+ENVIRONMENT PARAMETERS
+.LP
+The environment parameter \fIimtype\fR is used to determine the extension
+of the images to be processed and created.  This allows use with any
+supported image extension.  For STF images the extension has to be exact;
+for example "d1h".
diff --git a/noao/imred/specred/doc/msresp1d.hlp b/noao/imred/specred/doc/msresp1d.hlp
new file mode 100644
index 00000000..cc3dfed2
--- /dev/null
+++ b/noao/imred/specred/doc/msresp1d.hlp
@@ -0,0 +1,191 @@
+.help msresp1d Feb92 noao.imred.specred
+.ih
+NAME
+msresp1d -- Create 1D aperture response from flat and throughput data
+.ih
+USAGE
+msresp1d flat throughput apreference response
+.ih
+PARAMETERS
+.ls flat
+Flat field image to extract and normalize to create a one dimensional
+aperture response image.  If no flat field is specified then a throughput
+image or file must be specified and only a throughput correction will be
+created.  Note that the two dimensional unextracted image is specified.
+If an extracted image of the same name with the ".ms" extension is present
+it is used without reextraction though the unextracted image must also
+be present.
+.le
+.ls throughput
+Throughput file or image.  If an image is specified, typically a blank sky
+observation, the total flux through each aperture is used to correct for
+the aperture throughput.  If a file consisting of lines with the aperture
+number and relative throughput is specified then the aperture throughput
+will be generated by those values.  If neither is specified but a flat
+field image is given the flat field is used to compute the throughput.
+Note that the image is a two dimensional unextracted image.  If an
+extracted image of the same name with the ".ms" extension is present
+it is used without reextraction though the unextracted image must also
+be present.
+.le
+.ls apreference
+Aperture reference spectrum.  If not specified the apertures are defined
+using the flat field or throughput images.  If only a throughput file
+is used then an aperture reference spectrum must be specified to define
+the apertures and dimensions of the final response image.
+.le
+.ls response
+Response spectrum to be created.
+.le
+
+.ls recenter = no
+Recenter throughput image apertures?
+.le
+.ls edit = yes
+Edit and review apertures?
+.le
+.ls trace = no
+Trace spectra?
+.le
+.ls clean = no
+Detect and replace bad pixels?
+.le
+.ls fitflat = yes
+Fit and ratio flat field spectrum?
+.le
+.ls interactive = yes
+Interactive flat field fit?
+.le
+.ls function = "spline3", order = 20
+Flat field fitting function and order.  The functions may be one of
+"chebyshev", "legendre", "spline1" (linear spline), or "spline3" (cubic spline).
+The order is either the number of polynomial terms or the number of spline
+pieces.
+.le
+.ih
+OTHER PARAMETERS
+The package parameters control logging of the operations performed and
+the verbose option allows printing of some progress information.  The
+graphics use the device defined by the STDGRAPH variable and cursor
+input is with the parameter \fIcl.gcur\fR.
+
+Aperture extraction is done using the task \fBapall\fR and any parameters
+not overridden by task parameters will be used; for example the detector
+noise parameters.
+.ih
+DESCRIPTION
+For multiaperture or multifiber spectra a throughput aperture correction 
+must be applied to extracted object spectra.  Also it is often better to
+divide by a one dimensional flat field than a two dimensional one.  This
+is valid provided the pixels sampled by the flat field and object are
+essentially the same.  The advantages are that interspectrum pixels where
+there is little signal are not used and small shifts (fractions of a pixel)
+can be tolerated.  The task \fBmsresp1d\fR creates a multiaperture image
+containing one dimensional flat field and throughput corrections which
+can be directly divided into extracted object spectra.
+
+If a one dimensional flat field is to be determined the flat field spectra
+are extracted unless an extracted image having the specified flat field
+name with the ".ms" extension is present.  If the \fIfitflat\fR parameter
+is set then all the spectra are averaged and a smooth function is fit to
+this composite flat field spectrum.  The smooth fit is divided into the
+individual flat field spectra.  This removes the mean flat field spectrum
+shape, thus avoiding introducing the inverse of the flat field spectrum
+into the object spectra and changing the approximate count levels in the
+object.  This procedure is recommended.  Note that it does not matter if
+the individual fibers have differing spectral shapes (such as might happen
+with a combination of fibers with differing spectral throughput) because
+only a common function is used.  The fitting is done using the \fBfit1d\fR
+task based on the \fBicfit\fR function fitting routines.  When the
+\fIinteractive\fR flag is set the fitting may be done interactively
+allowing iteration on the fitting function and other fitting parameters.
+Note that the function fit should follow the overall shape using a fairly
+high order.
+
+If no throughput image or file is specified the relative strengths
+of the flat field spectra define a throughput correction.  If a
+separate throughput image or file is given then the individual
+flat field spectra are normalized to unity and then scaled by the
+throughput determined from the image or file.
+
+If a throughput image, such as a blank sky observation, is specified it is
+extracted if needed.  The extracted sky spectra are divided by the flat
+field which is not yet corrected for throughput variations.  The total flux
+through each aperture is then found to define the relative throughputs of
+the apertures.  If a flat field was also specified the throughput values
+are multiplied into the normalized flat field otherwise the response image
+will consist of constant spectra with the relative throughputs derived from
+the image.
+
+If a throughput file is specified the throughput values for each aperture
+are defined from this file.  The file consists of lines with two columns,
+the aperture number and the relative throughput.  All apertures should
+be represented.  If a flat field was also specified the throughput values
+are multiplied into the normalized flat field.  If no flat field
+is given then the aperture reference image must be specified and it
+will be extracted, if necessary, to provide the template for the response
+image having constant values for each aperture spectrum.
+
+It is an error unless one or both of the flat field and throughput
+are specified.
+
+The last stage is to normalize of the response spectra over
+all apertures to a global unit mean.  Because of this step the throughput
+values derived from the flat field, throughput image, or throughput
+file need only be relative.  Log information is recorded and printed
+which includes the final relative throughputs values.
+
+Aperture extraction is done using the task \fBapall\fR and any parameters
+not overridden by task parameters will be used; for example the detector
+noise parameters.  Task parmeters control whether recentering,
+aperture review, and tracing are done.  If no aperture reference is
+specified the apertures will be defined as the task is run.
+The aperture reference, if defined, is often the same as the flat field.
+.ih
+EXAMPLES
+1.  To make a flat field response and apply it to an extracted object:
+
+.nf
+    ms> msred.verbose=yes
+    ms> msresp1d flat005 "" "" resp005.ms
+    Extract flat field flat005
+    Searching aperture database ...
+    Sep  7 14:36: DATABASE  - 44 apertures read for flat005.
+    Resize apertures for flat005?  (yes): n
+    Edit apertures for flat005?  (yes): n
+    Extract aperture spectra for flat005?  (yes): 
+    Review extracted spectra from flat005?  (yes): n
+    Extracting apertures ...
+    Sep  7 14:37: EXTRACT - Aperture 1 from flat005 --> flat005.ms
+    Sep  7 14:37: EXTRACT - Aperture 2 from flat005 --> flat005.ms
+    Sep  7 14:37: EXTRACT - Aperture 3 from flat005 --> flat005.ms
+    Sep  7 14:37: EXTRACT - Aperture 4 from flat005 --> flat005.ms
+    Sep  7 14:37: EXTRACT - Aperture 5 from flat005 --> flat005.ms
+    <etc>
+    Fit and ratio flat field flat005
+    <Interactive fitting of average extracted flat field>
+    Create the normalized response resp005.ms
+    Sep  7 14:38 BSCALE: image = resp005.ms
+      bzero=0.  bscale=1.0  mean=1.0  median=1.02386  mode=1.07141
+    Average fiber response:
+      1  0.8049859
+      2  0.6428247
+      3  0.9014022
+      4  0.7955039
+      5  0.9898984
+      <etc>
+    ms> imarith obj006.ms / resp005.ms obj006.ms
+.fi
+
+Of course the extracted object spectra must be the same in terms of apertures,
+wavelength coverage, etc.
+
+2.  To make only a throughput correction:
+
+.nf
+    ms> msresp1d "" obj005 "" resp005
+.fi
+.ih
+SEE ALSO
+icfit, fit1d, apflatten, apnormalize, dofibers
+.endhelp
diff --git a/noao/imred/specred/doc/skysub.hlp b/noao/imred/specred/doc/skysub.hlp
new file mode 100644
index 00000000..75392822
--- /dev/null
+++ b/noao/imred/specred/doc/skysub.hlp
@@ -0,0 +1,98 @@
+.help skysub Mar94 noao.imred.specred
+.ih
+NAME
+skysub -- Sky subtract extracted multispec spectra
+.ih
+USAGE
+skysub input
+.ih
+PARAMETERS
+.ls input
+List of input multispec spectra to sky subtract.
+.le
+.ls output = ""
+List of output sky subtracted spectra.  If no output is specified then
+the output replaces the input spectra.
+.le
+.ls objaps = "", objbeams = ""
+Object aperture and beam numbers.  An empty list selects all aperture
+or beam numbers.  Only the selected apertures are sky subtracted.
+Other apertures are left unmodified.  Note that it is valid to include
+the sky apertures in the object selection which results in residual
+sky spectra after subtraction by a mean sky.
+.le
+.ls skyaps = "", skybeams = ""
+Sky aperture and beam numbers.  An empty list selects all aperture or
+beam numbers.
+.le
+.ls skyedit = yes
+Edit the sky spectra?  If yes the sky spectra are graphed using the
+task \fBspecplot\fR and the user may delete contaminated sky spectra with
+the 'd' key and exit with 'q'.
+.le
+.ls combine = "average" (average|median|sum)
+Option for combining pixels at the same dispersion coordinate after any
+rejection operation.  The options are to compute the  "average", "median",
+or "sum" of the pixels.  The median uses the average of the two central
+values when the number of pixels is even.
+.le
+.ls reject = "none" (none|minmax|avsigclip)
+Type of rejection operation performed on the pixels which overlap at each
+dispersion coordinate.  The algorithms are discussed in the
+DESCRIPTION section.  The rejection choices are:
+
+.nf
+      none - No rejection
+    minmax - Reject the nlow and nhigh pixels
+ avsigclip - Reject pixels using an averaged sigma clipping algorithm
+.fi
+
+.le
+.ls scale = no
+Scale the sky spectra by the mode?
+.le
+.ls saveskys = yes
+Save the sky spectra?  If no then the mean sky spectra will be deleted after
+sky subtraction is completed.  Otherwise a one dimensional image with
+the prefix "sky" and then the output name is created.
+.le
+.ls logfile = ""
+Logfile for making a record of the sky subtraction operation.
+.le
+.ih
+DESCRIPTION
+This task selects a subset of aperture spectra from a multispec
+format image, called sky spectra though they could be anything,
+and combines them into a master spectrum which is subtracted
+from another subset of spectra called the objects.  Options include
+saving the master sky spectrum and reviewing the selected sky spectra
+graphically and deleting some of them.
+
+The sky apertures are selected using the aperture and beam numbers
+defined during extraction (see the \fBapextract\fR package).  In
+some applications the beam numbers are used to code object and sky
+apertures and selection by beam number is quite easy.  Otherwise one
+must list the aperture numbers explicitly.
+
+The object apertures are also selected using an aperture and beam
+number list.  Spectra not selected to be objects are not modified
+by the sky subtraction.  Note that it is perfectly valid to include
+the sky spectra in the object list to produce residual sky spectra.
+
+When interactively editing the sky spectra the task \fBspecplot\fR
+is used.  To delete a spectrum type 'd'.  To undelete the last deleted
+spectrum type 'e'.  When finished type 'e'.
+
+The sky spectra are combined using one of combining and rejection options from
+the task \fBscombine\fR except for the option "none".
+.ih
+EXAMPLES
+1.  To median and subtract apertures 1,10,15,20 from all apertures:
+
+.nf
+    ms> skysub obj010.ms out=skysub010.ms skyaps="1,10,15,20"
+.fi
+.ih
+SEE ALSO
+specplot, scombine
+.endhelp