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+.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 Fiber Optic Echelle Reduction Task DOFOE
+.AU
+Francisco Valdes
+.AI
+IRAF Group - Central Computer Services
+.K2
+.DY
+
+.AB
+The \fBdofoe\fR reduction task is specialized for scattered light
+subtraction, extraction, flat fielding, and wavelength calibration of Fiber
+Optic Echelle (FOE) 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 complexities of reducing this type of data.
+.AE
+.NH
+Introductions
+.LP
+The \fBdofoe\fR reduction task is specialized for scattered light
+subtraction, extraction, flat fielding, and wavelength calibration of Fiber
+Optic Echelle (FOE) 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 complexities of reducing this type of data.
+.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, 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
+\fBdofoe\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 must first be processed with \fBccdproc\fR for overscan,
+bias, and dark corrections.
+.IP [2]
+Set the \fBdofoe\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.  If there are many
+object or arc spectra per setup you might want to prepare "@ files".
+Verify and set the format parameters, particularly the number of orders to be
+extracted and processed.  The processing parameters are set
+for simple extraction and dispersion correction but dispersion correction
+can be turned off for quicklook or background subtraction and cleaning
+may be added.
+.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
+which is usually a flat field in which both the object and arc fibers are
+illuminated.  The specified number of orders are found automatically and
+sequential apertures assigned.  The resize option sets the aperture size to
+the widths of the profiles at a fixed fraction of the peak height.
+.IP [5]
+The automatic order identification and aperture assignment is based on peak
+height and may be incorrect.  The interactive aperture editor is entered
+with a plot of the apertures.  It is essential that the object and arc
+fiber orders are properly paired with the arc fibers having even aperture
+numbers and the object fibers having odd aperture numbers.  It is also
+required that no orders be skipped in the region of interest.  Missing
+orders are added with the 'm' key.  Once all orders have been marked the
+aperture numbers are resequenced with 'o'.  If local background subtraction
+is selected the background regions should be checked with the 'b' key.
+Preceding this with the 'a' key allows any changes to the background
+regions to be applied to all orders.  To exit type 'q'.
+.IP [6]
+The order 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 orders need be examined and the "NO"
+response will quit the interactive fitting.  To exit the interactive
+fitting type 'q'.
+.IP [7]
+If flat fielding is to be done the flat field spectra are extracted.  A
+smooth function is fit to each flat field spectrum to remove the large
+scale spectral signature.  The final response spectra are normalized to a
+unit mean over all fibers.
+.IP [8]
+If scattered light subtraction is selected the scattered light parameters
+are set using the aperture reference image and the task \fBapscatter\fR.
+The purpose of this is to interactively define the aperture buffer distance
+for the scattered light and the cross and parallel dispersion fitting
+parameters.  The fitting parameters are taken from and recorded in the
+parameter sets \fBapscat1\fR and \fBapscat2\fR.  All other scattered light
+subtractions are done noninteractively with these parameters.  Note that
+the scattered light correction modifies the input images.
+.IP [9]
+If dispersion correction is selected the first arc in the arc list is
+extracted.  One fiber is used to identify the arc lines and define the
+dispersion function using the task \fBecidentify\fR.  Identify a few arc
+lines in a few orders with 'm' and 'k' or 'o', 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 [10]
+The other fiber dispersion function is automatically determined using
+the task \fBecreidentify\fR.
+.IP [11]
+The arc reference spectrum is dispersion corrected.
+If the spectra are resampled to a linear dispersion system
+(which will be the same for all spectra) the dispersion parameters
+determined from the dispersion solution are printed.
+.IP [12]
+The object spectra are now automatically background subtracted (an
+alternative to scattered light subtraction), extracted, flat fielded,
+and dispersion corrected.  Any new dispersion function reference arcs
+assigned to the object images are automatically extracted and
+dispersion functions determined.  A zero point wavelength correction
+is computed from the simultaneous arc fiber spectrum and applied to
+the object spectrum.
+.IP [13]
+The final spectra will have the same name as the original 2D images
+with a ".ec" extension added.
+.NH
+Spectra and Data Files
+.LP
+The basic input consists of dual fiber FOE 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.  Flat fielding is generally not done at this stage
+but as part of \fBdofoe\fR.  The calibration spectra are
+flat field observations in both fibers, comparison arc lamp spectra
+in both fibers, and arc spectra in one fiber while the second
+fiber observes the object.  If for some reason the flat field or
+calibration arc spectra have separate exposures for the two fibers
+the separate exposures may simply be added.
+.LP
+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 the task \fBrefspectra\fR.
+.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
+".ec" extension.  Each line in the reduced image is a one dimensional
+spectrum (an echelle order) with associated aperture and wavelength
+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 tasks 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.  The task \fBscombine\fR is used to combine or merge orders into
+a single spectrum.
+.NH
+Package Parameters
+.LP
+The \fBechelle\fR package parameters, shown in Figure 1, set parameters
+affecting all the tasks in the package.  Some of the parameters are not
+applicable to the \fBdofoe\fR task.
+.KS
+.V1
+
+.ce
+Figure 1: Package Parameter Set for the ECHELLE Package
+
+                           I R A F
+            Image Reduction and Analysis Facility
+PACKAGE = imred
+   TASK = echelle
+
+(extinct= onedstds$kpnoextinct.dat) Extinction file
+(caldir = onedstds$spechayescal/) 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) Text log file
+(plotfil=             ) Plot file
+
+(records=                     ) Record number extensions
+(version= ECHELLE V3: July 1991)
+
+.KE
+.V2
+The observatory parameter is only required for data
+without an OBSERVAT header parameter (currently included in NOAO data).
+The spectrum interpolation type might be changed to "sinc" but with the
+cautions given in \fBonedspec.package\fR.  The dispersion axis parameter is
+only needed if a DISPAXIS image header parameter is not defined.  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 \fBdofoe\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 \fBdofoe\fR parameters are shown in Figure 2.
+.KS
+.V1
+
+.ce
+Figure 2: Parameters Set for DOFOE
+
+                           I R A F
+            Image Reduction and Analysis Facility
+PACKAGE = echelle
+   TASK = dofoe
+
+objects =               List of object spectra
+(apref  =             ) Aperture reference spectrum
+(flat   =             ) Flat field spectrum
+(arcs   =             ) List of 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
+(norders=           12) Number of orders
+(width  =           4.) Width of profiles (pixels)
+(arcaps =          2x2) Arc apertures
+
+(fitflat=          yes) Fit and ratio flat field spectrum?
+(backgro=         none) Background to subtract
+(clean  =           no) Detect and replace bad pixels?
+(dispcor=          yes) Dispersion correct spectra?
+(redo   =           no) Redo operations if previously done?
+(update =           no) 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 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.
+The aperture reference spectrum is used to find the orders and trace
+them.  Thus, this requires an image with good signal in both fibers
+which usually means a flat field spectrum.  It is recommended that
+flat field correction be done using one dimensional extracted spectra
+rather than as two dimensional images.  This is done if a flat field
+spectrum is specified.  The arc assignment table is used to specifically
+assign arc spectra to particular object spectra and the format
+of the file is described in \fBrefspectra\fR.
+.LP
+The detector read out noise and gain are used for cleaning and variance
+(optimal) extraction.  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 parameter (in pixels) is used for the profile
+centering algorithm (\fBcenter1d\fR).
+.LP
+The number of orders selects the number of "pairs" of object and arc
+fiber profiles to be automatically found based on the strongest peaks.
+Because it is important that both elements of a pair be found,
+no orders be skipped, and the aperture numbers be sequential with
+arc profiles having even aperture numbers and object profiles having
+odd numbers in the region of interest, the automatic identification is  
+just a starting point for the interactive review.  The even/odd
+relationship between object and arc profiles is set by the \f(CWarcaps\fR
+parameter and so may be reversed if desired.
+.LP
+The next set of parameters select the processing steps and options.  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, including the blaze function, and not introducing the reciprocal of
+the flat field spectrum into the object spectra.  If not selected the flat
+field will remove the blaze function from the observations and introduce
+some wavelength dependence from the flat field lamp spectrum.
+.LP
+The \f(CWbackground\fR option selects the type of correction for background or
+scattered light.  If the type is "scattered" a global scattered light is
+fit to the data between the apertures  and subtracted from the images.
+\fINote that the input images are modified by this operation\fR.  This
+option is slow.  Alternatively, a local background may be subtracted using
+background regions defined for each aperture.  The data in the regions may
+be averaged, medianed, or the minimum value used.  Another choice is to fit
+the data in the background regions by a function and interpolate to the
+object aperture.
+.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.  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.
+.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
+reference image, new flat field, adding the scattered light option, and a
+new arc reference image.  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.  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 \fBdofoe\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 \fBdofoe\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 \fBdofoe\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
+FOE 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 \fBdofoe\fR parameters by typing \f(CW:e
+params\fR or simply \f(CW:e\fR if positioned at the \f(CWparams\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 = echelle
+   TASK = params
+
+(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=            2) 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
+                        -- DEFAULT BACKGROUND PARAMETERS --
+(buffer =           1.) Buffer distance from apertures
+(apscat1=             ) Fitting parameters across the dispersion
+(apscat2=             ) Fitting parameters along the dispersion
+(b_funct=     legendre) Background function
+(b_order=            2) Background function order
+(b_sampl=  -10:-6,6:10) Background sample regions
+(b_naver=           -3) Background average or median
+(b_niter=            0) Background rejection iterations
+(b_low  =           3.) Background lower rejection sigma
+(b_high =           3.) Background upper rejection sigma
+(b_grow =           0.) Background rejection growing radius
+(b_smoot=           10) Background smoothing length
+
+.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
+                        -- FLAT FIELD FUNCTION FITTING PARAMETERS --
+(f_inter=           no) Fit flat field interactively?
+(f_funct=      spline3) Fitting function
+(f_order=           20) Fitting function order
+
+.KE
+.KS
+.V1
+                        -- ARC DISPERSION FUNCTION PARAMETERS --
+(coordli= linelist$thar.dat) Line list
+(match  =           1.) Line list matching limit in Angstroms
+(fwidth =           4.) Arc line widths in pixels
+(cradius=           4.) Centering radius in pixels
+(i_funct=    chebyshev) Echelle coordinate function
+(i_xorde=            3) Order of coordinate function along dispersion
+(i_yorde=            3) Order of coordinate function across dispersion
+(i_niter=            3) Rejection iterations
+(i_low  =           3.) Lower rejection sigma
+(i_high =           3.) Upper rejection sigma
+(refit  =          yes) Refit coordinate function 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
+.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 object and arc orders of interest.  This is done
+on a reference spectrum which is usually a flat field taken through
+both fibers.  Other spectra will inherit the reference apertures and
+apply a correction for any shift of the orders across the dispersion.
+The reference apertures are defined only once unless the \f(CWredo\fR
+option is set.
+.LP
+The selected number of orders are found automatically by selecting the
+highest peaks in a cut across the dispersion.  Note that the specified
+number of orders is multiplied by two in defining the apertures.  Apertures
+are assigned with a limits set by the \f(CWlower\fR and
+\f(CWupper\fR parameter and numbered sequentially.  A query is then
+given allowing the aperture limits to be "resized" based on the profile
+itself (see \fBapresize\fR).
+.LP
+A cut across the orders is then shown with the apertures marked and
+an interactive aperture editing mode is entered (see \fBapedit\fR).
+For \fBdofoe\fR the aperture identifications and numbering is particularly
+critical.  All "pairs" of object and arc orders in the region of
+interest must be defined without skipping any orders.  The orders must
+also be numbered sequentially (though the direction does not matter)
+so that the arc apertures are either all even or all odd as defined
+by the \f(CWarcaps\fR parameter (the default is even numbers for the
+arc apertures).  The 'o' key will provide the necessary reordering.
+If local background subtraction is used the background regions should
+also be checked with the 'b' key.  Typically one adjusts all
+the background regions at the same time by selecting all apertures with
+the 'a' key first.  To exit the background and aperture editing steps type
+'q'.
+.LP
+Next the positions of the orders at various points along the dispersion are
+measured and "trace functions" are fit.  The user is asked whether to fit
+each trace function interactively.  This is selected to adjust the fitting
+parameters such as function type and order.  When interactively fitting a
+query is given for each aperture.  After the first aperture one may skip
+reviewing the other traces by responding with "NO".  Queries made by
+\fBdofoe\fR generally may be answered with either lower case "yes" or "no"
+or with upper case "YES" or "NO".  The upper case responses apply to all
+further queries and so are used to eliminate further queries of that kind.
+.LP
+The above steps are all performed using tasks from the \fBapextract\fR
+package and parameters from the \fBparams\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 orders 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 basically
+finds the strongest peaks.  The resizing is described in the task
+\fBapresize\fR and the parameters used are also described there and
+identified in the PARAMETERS section.  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
+Background or Scattered Light Subtraction
+.LP
+In addition to not subtracting any background scattered light there are two
+approaches to subtracting this light.  The first is to determine a smooth
+global scattered light component.  The second is to subtract a locally
+determined background at each point along the dispersion and for each
+aperture.  Note that background subtraction is only done for object images
+and not for arc images.
+.LP
+The global scattered light fitting and subtraction is done with the task
+\fBapscatter\fR.  The function fitting parameters are set interactively
+using the aperture reference spectrum.  All other subtractions are done
+noninteractively with the same set of parameters.  The scattered light is
+subtracted from the input images, thus modifying them, and one might wish
+to first make backups of the original images.
+.LP
+The scattered light is measured between the apertures using a specified
+buffer distance from the aperture edges.  The scattered light pixels are
+fit by a series of one dimensional functions across the dispersion.  The
+independent fits are then smoothed along the dispersion by again fitting
+low order functions.  These fits then define the smooth scattered light
+surface to be subtracted from the image.  The fitting parameters are
+defined and recorded in the two parameter sets \f(CWapscat1\fR and
+\f(CWapscat2\fR.  The scattered light algorithm is described more fully in
+\fBapscatter\fR.  This algorithm is relatively slow.
+.LP
+Local background subtraction is done during extraction based on background
+regions and parameters defined by the default background parameters or
+changed during interactive review of the apertures.  The background
+subtraction options are to 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 smoothing parameter \f(CWb_smooth\fR is may be used
+to provide some additional local smoothing of the background light.
+The background subtraction algorithm and options are described in greater
+detail in \fBapsum\fR and \fBapbackground\fR.
+.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 noise 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 threshold for
+cleaning are also set in the \fBparams\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 a scattered light
+subtraction) 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 scattered light be accounted for by local background
+subtraction rather than with the scattered light subtraction and the
+\f(CWfitflat\fR option be used.  The \f(CWb_smooth\fR parameter is also
+appropriate in this application and improves the optimal extraction results
+by reducing noise in the background signal.  For further discussion of
+cleaning and variance weighted extraction see \fBapvariance\fR and
+\fBapprofiles\fR as well as  \fBapsum\fR.
+.NH 2
+Flat Field Correction
+.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
+\fBdofoe\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
+\fBdofoe\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
+The first step is extraction of the flat field spectrum, if one is 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.  When
+the \f(CWfitflat\fR option is selected (the default) the extracted flat field
+spectra are fit by smooth functions and the ratio of the flat field spectra
+to the smooth functions define the response spectra.  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
+If the \f(CWfitflat\fR option is not selected the extracted and globally
+normalized flat field spectra are directly divided in the object spectra.
+This removes the blaze function, thus altering the data counts, and
+introduces the reciprocal of the flat field spectrum in the object
+spectra.
+.LP
+The final step is to normalize the flat field spectra by the mean counts over
+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.
+.NH 2
+Dispersion Correction
+.LP
+If dispersion correction is not selected, \f(CWdispcor\fR=no, then the object
+spectra are simply extracted.  If it is selected the arc spectra are used
+to dispersion calibrate the object spectra.  There are four steps involved;
+determining the dispersion functions relating pixel position to wavelength,
+assigning the appropriate dispersion function to a particular observation,
+determining a zero point wavelength shift from the arc fiber to be applied
+to the object fiber dispersion function, 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 using the reference aperture
+definitions.  Note extractions of arc spectra are not background or
+scattered light subtracted.  The interactive task \fBecidentify\fR is used
+to define the dispersion function in one fiber.  The idea is to mark some
+lines in a few orders whose wavelengths are known (with the line list used
+to supply additional lines after the first few identifications define the
+approximate wavelengths) and to fit a function giving the wavelength from
+the aperture number and pixel position.  The dispersion function for
+the second fiber is then determined automatically by reference to the first
+fiber using the task \fBecreidentify\fR.
+.LP
+The arc dispersion function parameters are for \fBecidentify\fR and it's
+related partner \fBecreidentify\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
+\fBecidentify\fR.
+.LP
+Once the reference dispersion functions are defined other arc spectra are
+extracted as they are assign to 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.
+The 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.  Because the arc fiber monitors any zero point
+shifts in the dispersion functions it is probably only necessary to have
+one or two arc spectra, one at the beginning and/or one at the end of the
+night.
+.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
+Defining the dispersion function for a new arc extraction is done with
+the task \fBecreidentify\fR.  This is done noninteractively with log
+information recorded about the line reidentifications and the fit.
+.LP
+From the one or two arc spectra come two full dispersion function,
+one for the object fiber and one for the arc fiber.  When an object
+spectrum is extracted so is the simultaneous arc spectrum.  A zero point
+shift of the arc spectrum relative to the dispersion solution of the
+dual arc observation is computed using \fBecreidentify\fR
+(\f(CWrefit\fR=no).  This zero point shift is assumed to be the same for the
+object fiber and it is added to the dispersion function of the dual arc
+observation for the object fiber.  Note that this does not assume that the
+object and arc fiber dispersion functions are the same or have the same
+wavelength origin, but only that the same shift in wavelength zero point
+applies to both fibers.  Once the dispersion function correction is
+determined from the extracted arc fiber spectrum it is deleted leaving only
+the object spectrum.
+.LP
+The last step of dispersion correction is setting the dispersion
+of the object spectrum.  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.  For echelle spectra each order is linearized independently so
+that the wavelength interval per pixel is different in different orders.
+This preserves most of the resolution and avoids over or under sampling of
+the highest or lowest dispersion orders.  The wavelength limits are
+taken from the limits determined from the arc reference spectrum and
+the number of pixels is the same as the original images.  The dispersion
+per pixel is then derived from these constraints.
+.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
+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 plots of spectra
+  calibrate - Apply extinction and flux calibrations to spectra
+  continuum - Fit the continuum in spectra
+   deredden - Apply interstellar extinction corrections
+    dispcor - Dispersion correct spectra
+     dopcor - Doppler correct spectra
+ ecidentify - Identify features in spectrum for dispersion solution
+ecreidentify - Automatically identify features in spectra
+ refspectra - Assign wavelength reference spectra to other spectra
+     sarith - Spectrum arithmetic
+   scombine - Combine spectra
+      scopy - Select and copy apertures in different spectral formats
+   sensfunc - Create sensitivity function
+ setairmass - Compute effective airmass and middle UT for an exposure
+      setjd - Compute and set Julian dates in images
+      slist - List spectrum header parameters
+   specplot - Stack and plot multiple spectra
+      splot - Preliminary spectral plot/analysis
+   standard - Identify standard stars to be used in sensitivity calc
+
+      dofoe - Process Fiber Optic Echelle 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: DOFOE Parameters
+.LP
+.nr PS 8
+.nr VS 10
+objects
+.LS
+List of object spectra 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.  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 spectrum
+is extracted and used to make flat field calibrations.
+.LE
+arcs = "" (at least one if dispersion correcting)
+.LS
+List of arc spectra in which both fibers have arc spectra.  These spectra
+are used to define the dispersion functions for each fiber apart from a
+zero point correction made with the arc fiber during an observation.  One
+fiber from the first spectrum is used to mark lines and set the dispersion
+function interactively and dispersion functions for the other fiber and arc
+spectra are derived from it.
+.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, \f(CWparams.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
+norders = 12 (apfind)
+.LS
+Number of orders to be found.  This number is used during the automatic
+definition of the apertures from the aperture reference spectrum.  Note
+that the number of apertures defined is twice this number, one set for
+the object fiber orders and one set for the arc fiber orders.
+The interactive review of the aperture assignments allows verification
+and adjustments to the automatic aperture definitions.
+.LE
+width = 4. (apedit)
+.LS
+Approximate base full width of the fiber profiles.  This parameter is used
+for the profile centering algorithm.
+.LE
+arcaps = "2x2"
+.LS
+List of arc fiber aperture numbers.
+Since the object and arc fiber orders are paired the default setting
+expects the even number apertures to be the are apertures.  This should
+be checked interactively.
+.LE
+
+fitflat = yes (flat1d)
+.LS
+Fit and divide the extracted flat field field orders by a smooth function
+in order to normalize the wavelength response?  If not done the flat field
+spectral shape (which includes the blaze function) will be divided
+out of the object spectra, thus altering the object data values.
+If done only the small scale response variations are included in the
+flat field and the object spectra will retain their observed flux
+levels and blaze function.
+.LE
+background = "none" (apsum, apscatter)
+.LS
+Type of background light subtraction.  The choices are "none" for no
+background subtraction, "scattered" for a global scattered light
+subtraction, "average" to average the background within background regions,
+"median" to use the median in background regions, "minimum" to use the
+minimum in background regions, or "fit" to fit across the dispersion using
+the background within background regions.  The scattered light option fits
+and subtracts a smooth global background and modifies the input images.
+This is a slow operation and so is NOT performed in quicklook mode.  The
+other background options are local to each aperture at each point along the
+dispersion.  The "fit" option uses additional fitting parameters from
+\fBparams\fR and the "scattered" option uses parameters from \fBapscat1\fR
+and \fBapscat2\fR.
+.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 \f(CWparams.linearize\fR
+parameter this may either resample the spectra or insert a dispersion
+function in the image header.
+.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 = no
+.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.
+.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 \fBdofoe\fR.
+
+observatory = "observatory"
+.LS
+Observatory at which the spectra were obtained if not specified in the
+image header by the keyword OBSERVAT.  For FOE data the image headers
+identify the observatory as "kpno" so this parameter is not used.
+For data from other observatories this parameter may be used
+as describe in \fBobservatory\fR.
+.LE
+interp = "poly5" (nearest|linear|poly3|poly5|spline3|sinc)
+.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
+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.
+.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 = "ECHELLE: ..."
+.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 \fBdofoe\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
+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 = -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 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 \f(CWnsum\fR parameter is also used to enhance the
+signal-to-noise at each step.
+.LE
+t_function = "spline3", t_order = 2 (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
+-- DEFAULT BACKGROUND PARAMETERS --
+
+buffer = 1. (apscatter)
+.LS
+Buffer distance from the edge of any aperture for data to be included
+in the scattered light determination.  This parameter may be modified
+interactively.
+.LE
+apscat1 = "", apscat2 = "" (apscatter)
+.LS
+Parameter sets for the fitting functions across and along the dispersion.
+These parameters are those used by \fBicfit\fR.  These parameters are
+usually set interactively.
+.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_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 = 0 (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
+b_smooth = 10 (apsum)
+.LS
+Box car smoothing length for background when using background
+subtraction.  Since the background noise is often the limiting factor
+for good extraction one may box car smooth the the background to improve the
+statistics.
+.LE
+
+
+.ce
+-- APERTURE EXTRACTION PARAMETERS --
+
+weights = "none" (apsum)
+.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) (fit1d|fit2d)
+.LS
+Profile fitting algorithm for cleaning and variance weighted extractions.
+The default is generally appropriate for FOE 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
+
+.ce
+-- FLAT FIELD FUNCTION FITTING PARAMETERS --
+
+f_interactive = no (fit1d)
+.LS
+Fit the one dimensional flat field order spectra interactively?
+This is used if \f(CWfitflat\fR is set and a two dimensional flat field
+spectrum is specified.
+.LE
+f_function = "spline3", f_order = 20 (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. (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 = "linelist$thar.dat" (ecidentify)
+.LS
+Arc line list consisting of an ordered list of wavelengths.
+Some standard line lists are available in the directory "linelist$".
+.LE
+match = 1. (ecidentify)
+.LS
+The maximum difference for a match between the dispersion function computed
+value and a wavelength in the coordinate list.
+.LE
+fwidth = 4. (ecidentify)
+.LS
+Approximate full base width (in pixels) of arc lines.
+.LE
+cradius = 4. (reidentify)
+.LS
+Radius from previous position to reidentify arc line.
+.LE
+i_function = "chebyshev", i_xorder = 3, i_yorder = 3 (ecidentify)
+.LS
+The default function, function order for the pixel position dependence, and
+function order for the aperture number dependence to be fit to the arc
+wavelengths.  The functions choices are "chebyshev" or "legendre".
+.LE
+i_niterate = 3, i_low = 3.0, i_high = 3.0 (ecidentify)
+.LS
+Number of rejection iterations and sigma thresholds for rejecting arc
+lines from the dispersion function fits.
+.LE
+refit = yes (ecreidentify)
+.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
+
+.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 \fBdofoe\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 \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
+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".