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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 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".