From 40e5a5811c6ffce9b0974e93cdd927cbcf60c157 Mon Sep 17 00:00:00 2001
From: Joe Hunkeler <jhunkeler@gmail.com>
Date: Tue, 11 Aug 2015 16:51:37 -0400
Subject: Repatch (from linux) of OSX IRAF

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+.help dofoe Feb93 noao.imred.echelle
+.ih
+NAME
+dofoe -- Fiber Optic Echelle (FOE) data reduction task
+.ih
+USAGE
+dofoe objects
+.ih
+SUMMARY
+The \fBdofoe\fR reduction task is specialized for scattered light
+subtraction, extraction, flat fielding, and wavelength calibration of Fiber
+Optic Echelle (FOE) spectra.  There may be one fiber or two fibers where
+the second fiber is illuminated by an arc calibration during arc and object
+exposures and a flat field during flat field exposures.  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.
+.ih
+PARAMETERS
+.ls objects
+List of object spectra to be processed.  Previously processed spectra are
+ignored unless the \fIredo\fR flag is set or the \fIupdate\fR flag is set and
+dependent calibration data has changed.  Extracted spectra are ignored.
+.le
+.ls apref = ""
+Aperture reference spectrum.  This spectrum is used to define the basic
+extraction apertures and is typically a flat field spectrum.
+.le
+.ls flat = "" (optional)
+Flat field spectrum.  If specified the one dimensional flat field spectrum
+is extracted and used to make flat field calibrations.
+.le
+.ls arcs = "" (at least one if dispersion correcting)
+List of arc spectra.  The first arc in the list is used to create a
+dispersion solution interactively.  All other arc spectra will be
+automatically reidentified.
+.le
+.ls arctable = "" (optional) (refspectra)
+Table defining arc spectra to be assigned to object spectra (see
+\fBrefspectra\fR).  If not specified an assignment based on a header
+parameter, \fIparams.sort\fR, such as the observation time is made.
+.le
+
+.ls readnoise = "0." (apsum)
+Read out noise in photons.  This parameter defines the minimum noise
+sigma.  It is defined in terms of photons (or electrons) and scales
+to the data values through the gain parameter.  A image header keyword
+(case insensitive) may be specified to get the value from the image.
+.le
+.ls gain = "1." (apsum)
+Detector gain or conversion factor between photons/electrons and
+data values.  It is specified as the number of photons per data value.
+A image header keyword (case insensitive) may be specified to get the value
+from the image.
+.le
+.ls datamax = INDEF (apsum.saturation)
+The maximum data value which is not a cosmic ray.
+When cleaning cosmic rays and/or using variance weighted extraction
+very strong cosmic rays (pixel values much larger than the data) can
+cause these operations to behave poorly.  If a value other than INDEF
+is specified then all data pixels in excess of this value will be
+excluded and the algorithms will yield improved results.
+This applies only to the object spectra and not the flat field or
+arc spectra.  For more
+on this see the discussion of the saturation parameter in the
+\fBapextract\fR package.
+.le
+.ls norders = 12 (apfind)
+Number of orders to be found.  This number is used during the automatic
+definition of the apertures from the aperture reference spectrum.  Note
+that when there is a second fiber for simultaneous arcs the specified
+number will be automatically doubled for finding both sets of orders.
+So in either case specify only the number of orders from a single fiber.
+The interactive review of the aperture assignments allows verification
+and adjustments to the automatic aperture definitions.
+.le
+.ls width = 4. (apedit)
+Approximate base full width of the fiber profiles.  This parameter is used
+for the profile centering algorithm.
+.le
+.ls arcaps = "2x2"
+When there is only a single fiber set this parameter to "".  When there is
+a second fiber used to create simultaneous arcs during the object exposures
+this parameter specifies a list of aperture numbers for the arc fibers.
+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
+
+.ls fitflat = yes (flat1d)
+Fit and divide the extracted flat 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
+.ls background = "none" (apsum, apscatter)
+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
+.ls clean = yes (apsum)
+Detect and correct for bad pixels during extraction?  This is the same
+as the clean option in the \fBapextract\fR package.  If yes this also
+implies variance weighted extraction and requires reasonably good values
+for the readout noise and gain.  In addition the datamax parameters
+can be useful.
+.le
+.ls dispcor = yes
+Dispersion correct spectra?  Depending on the \fIparams.linearize\fR
+parameter this may either resample the spectra or insert a dispersion
+function in the image header.
+.le
+.ls redo = no
+Redo operations previously done?  If no then previously processed spectra
+in the objects list will not be processed (unless they need to be updated).
+.le
+.ls update = no
+Update processing of previously processed spectra if aperture, flat
+field, or dispersion reference definitions are changed?
+.le
+.ls batch = no
+Process spectra as a background or batch job.
+.le
+.ls listonly = no
+List processing steps but don't process?
+.le
+
+.ls params = "" (pset)
+Name of parameter set containing additional processing parameters.  The
+default is parameter set \fBparams\fR.  The parameter set may be examined
+and modified in the usual ways (typically with "epar params" or ":e params"
+from the parameter editor).  Note that using a different parameter file
+is not allowed.  The parameters are described below.
+.le
+
+.ce
+-- PACKAGE PARAMETERS
+
+Package parameters are those which generally apply to all task in the
+package.  This is also true of \fBdofoe\fR.
+.ls observatory = "observatory"
+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
+.ls interp = "poly5" (nearest|linear|poly3|poly5|spline3|sinc)
+Spectrum interpolation type used when spectra are resampled.  The choices are:
+
+.nf
+	nearest - nearest neighbor
+	 linear - linear
+	  poly3 - 3rd order polynomial
+	  poly5 - 5th order polynomial
+	spline3 - cubic spline
+	   sinc - sinc function
+.fi
+.le
+.ls dispaxis = 2
+Default dispersion axis.  The dispersion axis is 1 for dispersion
+running along image lines and 2 for dispersion running along image
+columns.  If the image header parameter DISPAXIS is defined it has
+precedence over this parameter.
+.le
+.ls database = "database"
+Database (directory) used for storing aperture and dispersion information.
+.le
+.ls verbose = no
+Print verbose information available with various tasks.
+.le
+.ls logfile = "logfile", plotfile = ""
+Text and plot log files.  If a filename is not specified then no log is
+kept.  The plot file contains IRAF graphics metacode which may be examined
+in various ways such as with \fBgkimosaic\fR.
+.le
+.ls records = ""
+Dummy parameter to be ignored.
+.le
+.ls version = "ECHELLE: ..."
+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 --
+.ls line = INDEF, nsum = 10
+The dispersion line (line or column perpendicular to the dispersion
+axis) and number of adjacent lines (half before and half after unless
+at the end of the image) used in finding, recentering, resizing,
+editing, and tracing operations.  A line of INDEF selects the middle of the
+image along the dispersion axis.
+.le
+.ls extras = no (apsum)
+Include extra information in the output spectra?  When cleaning or using
+variance weighting the cleaned and weighted spectra are recorded in the
+first 2D plane of a 3D image, the raw, simple sum spectra are recorded in
+the second plane, and the estimated sigmas are recorded in the third plane.
+.le
+
+.ce
+-- DEFAULT APERTURE LIMITS --
+.ls lower = -3., upper = 3. (apdefault)
+Default lower and upper aperture limits relative to the aperture center.
+These limits are used when the apertures are first found and may be
+resized automatically or interactively.
+.le
+
+.ce
+-- AUTOMATIC APERTURE RESIZING PARAMETERS --
+.ls ylevel = 0.05 (apresize)
+Data level at which to set aperture limits during automatic resizing.
+It is a fraction of the peak relative to a local background.
+.le
+
+.ce
+-- TRACE PARAMETERS --
+.ls t_step = 10 (aptrace)
+Step along the dispersion axis between determination of the spectrum
+positions.  Note the \fInsum\fR parameter is also used to enhance the
+signal-to-noise at each step.
+.le
+.ls t_function = "spline3", t_order = 2 (aptrace)
+Default trace fitting function and order.  The fitting function types are
+"chebyshev" polynomial, "legendre" polynomial, "spline1" linear spline, and
+"spline3" cubic spline.  The order refers to the number of
+terms in the polynomial functions or the number of spline pieces in the spline
+functions.
+.le
+.ls t_niterate = 1, t_low = 3., t_high = 3. (aptrace)
+Default number of rejection iterations and rejection sigma thresholds.
+.le
+
+.ce
+-- DEFAULT BACKGROUND PARAMETERS --
+.ls buffer = 1. (apscatter)
+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
+.ls apscat1 = "", apscat2 = "" (apscatter)
+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
+.ls b_function = "legendre", b_order = 1 (apsum)
+Default background fitting function and order.  The fitting function types are
+"chebyshev" polynomial, "legendre" polynomial, "spline1" linear spline, and
+"spline3" cubic spline.  The order refers to the number of
+terms in the polynomial functions or the number of spline pieces in the spline
+functions.
+.le
+.ls b_naverage = -100 (apsum)
+Default number of points to average or median.  Positive numbers
+average that number of sequential points to form a fitting point.
+Negative numbers median that number, in absolute value, of sequential
+points.  A value of 1 does no averaging and each data point is used in the
+fit.
+.le
+.ls b_niterate = 0 (apsum)
+Default number of rejection iterations.  If greater than zero the fit is
+used to detect deviant fitting points and reject them before repeating the
+fit.  The number of iterations of this process is given by this parameter.
+.le
+.ls b_low_reject = 3., b_high_reject = 3. (apsum)
+Default background lower and upper rejection sigmas.  If greater than zero
+points deviating from the fit below and above the fit by more than this
+number of times the sigma of the residuals are rejected before refitting.
+.le
+.ls b_smooth = 10 (apsum)
+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 background to improve the
+statistics.
+.le
+
+
+.ce
+-- APERTURE EXTRACTION PARAMETERS --
+.ls weights = "none" (apsum)
+Type of extraction weighting.  Note that if the \fIclean\fR parameter is
+set then the weights used are "variance" regardless of the weights
+specified by this parameter.  The choices are:
+.ls "none"
+The pixels are summed without weights except for partial pixels at the
+ends.
+.le
+.ls "variance"
+The extraction is weighted by the variance based on the data values
+and a poisson/ccd model using the \fIgain\fR and \fIreadnoise\fR
+parameters.
+.le
+.le
+.ls pfit = "fit1d" (apsum) (fit1d|fit2d)
+Profile fitting algorithm for cleaning and variance weighted extractions.
+The default is generally appropriate for FOE data but users
+may try the other algorithm.  See \fBapprofiles\fR for further information.
+.le
+.ls lsigma = 3., usigma = 3. (apsum)
+Lower and upper rejection thresholds, given as a number of times the
+estimated sigma of a pixel, for cleaning.
+.le
+
+.ce
+-- FLAT FIELD FUNCTION FITTING PARAMETERS --
+.ls f_interactive = no (fit1d)
+Fit the one dimensional flat field order spectra interactively?
+This is used if \fIfitflat\fR is set and a two dimensional flat field
+spectrum is specified.
+.le
+.ls f_function = "spline3", f_order = 20 (fit1d)
+Function and order used to fit the composite one dimensional flat field
+spectrum.  The functions are "legendre", "chebyshev", "spline1", and
+"spline3".  The spline functions are linear and cubic splines with the
+order specifying the number of pieces.
+.le
+
+.ce
+-- ARC DISPERSION FUNCTION PARAMETERS --
+.ls threshold = 10. (identify/reidentify)
+In order for a feature center to be determined the range of pixel intensities
+around the feature must exceed this threshold.
+.le
+.ls coordlist = "linelist$thar.dat" (ecidentify)
+Arc line list consisting of an ordered list of wavelengths.
+Some standard line lists are available in the directory "linelist$".
+.le
+.ls match = 1. (ecidentify)
+The maximum difference for a match between the dispersion function computed
+value and a wavelength in the coordinate list.
+.le
+.ls fwidth = 4. (ecidentify)
+Approximate full base width (in pixels) of arc lines.
+.le
+.ls cradius = 4. (reidentify)
+Radius from previous position to reidentify arc line.
+.le
+.ls i_function = "chebyshev", i_xorder = 3, i_yorder = 3 (ecidentify)
+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
+.ls i_niterate = 3, i_low = 3.0, i_high = 3.0 (ecidentify)
+Number of rejection iterations and sigma thresholds for rejecting arc
+lines from the dispersion function fits.
+.le
+.ls refit = yes (ecreidentify)
+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 --
+.ls select = "interp" (refspectra)
+Selection method for assigning wavelength calibration spectra.
+Note that an arc assignment table may be used to override the selection
+method and explicitly assign arc spectra to object spectra.
+The automatic selection methods are:
+.ls average
+Average two reference spectra without regard to any sort parameter.
+If only one reference spectrum is specified then it is assigned with a
+warning.  If more than two reference spectra are specified then only the
+first two are used and a warning is given.
+This option is used to assign two reference spectra, with equal weights,
+independent of any sorting parameter.
+.le
+.ls following
+Select the nearest following spectrum in the reference list based on the
+sorting parameter.  If there is no following spectrum use the nearest preceding
+spectrum.
+.le
+.ls interp
+Interpolate between the preceding and following spectra in the reference
+list based on the sorting parameter.  If there is no preceding and following
+spectrum use the nearest spectrum.  The interpolation is weighted by the
+relative distances of the sorting parameter.
+.le
+.ls match
+Match each input spectrum with the reference spectrum list in order.
+This overrides the reference aperture check.
+.le
+.ls nearest
+Select the nearest spectrum in the reference list based on the sorting
+parameter.
+.le
+.ls preceding
+Select the nearest preceding spectrum in the reference list based on the
+sorting parameter.  If there is no preceding spectrum use the nearest following
+spectrum.
+.le
+.le
+.ls sort = "jd", group = "ljd" (refspectra)
+Image header keywords to be used as the sorting parameter for selection
+based on order and to group spectra.
+A null string, "", or the word "none" may be use to disable the sorting
+or grouping parameters.
+The sorting parameter
+must be numeric but otherwise may be anything.  The grouping parameter
+may be a string or number and must simply be the same for all spectra within
+the same group (say a single night).
+Common sorting parameters are times or positions.
+In \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
+.ls time = no, timewrap = 17. (refspectra)
+Is the sorting parameter a 24 hour time?  If so then the time origin
+for the sorting is specified by the timewrap parameter.  This time
+should precede the first observation and follow the last observation
+in a 24 hour cycle.
+.le
+
+.ce
+-- DISPERSION  CORRECTION PARAMETERS --
+.ls linearize = yes (dispcor)
+Interpolate the spectra to a linear dispersion sampling?  If yes the
+spectra will be interpolated to a linear or log linear sampling
+If no the nonlinear dispersion function(s) from the dispersion function
+database are assigned to the input image world coordinate system
+and the spectral data are not interpolated.
+.le
+.ls log = no (dispcor)
+Use linear logarithmic wavelength coordinates?  Linear logarithmic
+wavelength coordinates have wavelength intervals which are constant
+in the logarithm of the wavelength.
+.le
+.ls flux = yes (dispcor)
+Conserve the total flux during interpolation?  If \fIno\fR the output
+spectrum is interpolated from the input spectrum at each output
+wavelength coordinate.  If \fIyes\fR the input spectrum is integrated
+over the extent of each output pixel.  This is slower than
+simple interpolation.
+.le
+.ih
+ENVIRONMENT PARAMETERS
+The environment parameter \fIimtype\fR is used to determine the extension
+of the images to be processed and created.  This allows use with any
+supported image extension.  For STF images the extension has to be exact;
+for example "d1h".
+.ih
+DESCRIPTION
+The \fBdofoe\fR reduction task is specialized for scattered light
+subtraction, extraction, flat fielding, and wavelength calibration of Fiber
+Optic Echelle (FOE) spectra.  There may be one fiber or two fibers where
+the second fiber is illuminated by an arc calibration during arc and object
+exposures and a flat field during flat field exposures.  When there is
+just one fiber the parameter \fIarcaps\fR is set to "" and when there are
+two fibers the parameter is used to select which of the defined
+apertures are the orders from the simultaneous arc fiber.
+
+This task is a command language script which collects and combines the
+functions and parameters of many general purpose tasks to provide a single
+complete data reduction path.  The task provides a degree of guidance,
+automation, and record keeping necessary when dealing with the complexities
+of reducing this type of data.
+
+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 \fIredo\fR and \fIupdate\fR options, skip or
+repeat some or all the steps.
+
+The description is divided into a quick usage outline followed by details
+of the parameters and algorithms.  The usage outline is provided as a
+checklist and a refresher for those familiar with this task and the
+component tasks.  It presents only the default or recommended usage.  Since
+\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.
+
+\fBUsage Outline\fR
+
+.ls 6 [1]
+The images must first be processed with \fBccdproc\fR for overscan,
+bias, and dark corrections.
+.le
+.ls [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.
+.le
+.ls [3]
+Run the task.  This may be repeated multiple times with different
+observations and the task will generally only do the setup steps
+once and only process new images.  Queries presented during the
+execution for various interactive operations may be answered with
+"yes", "no", "YES", or "NO".  The lower case responses apply just
+to that query while the upper case responses apply to all further
+such queries during the execution and no further queries of that
+type will be made.
+.le
+.ls [4]
+The apertures are defined using the specified aperture reference image
+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.
+.le
+.ls [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.  When there is a second simultaneous arc
+fiber 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'.
+.le
+.ls [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'.
+.le
+.ls [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.
+.le
+.ls [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.
+.le
+.ls [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'.
+.le
+.ls [10]
+If there is a second fiber the dispersion function is automatically
+determined using the task \fBecreidentify\fR.
+.le
+.ls [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.
+.le
+.ls [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 if orders from the second fiber have been identified
+with the \fIarcaps\fR parameter.
+.le
+.ls [13]
+The final spectra will have the same name as the original 2D images
+with a ".ec" extension added.
+.le
+
+\fBSpectra and Data Files\fR
+
+The basic input consists of single or dual fiber FOE object and calibration
+spectra stored as IRAF images.  The \fIarcaps\fR parameter is used to
+discriminate between the two cases.  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 all fibers, comparison arc lamp spectra in all
+fibers, and, for dual fiber model, 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.
+
+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.
+
+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 \fIextras\fR parameter is set the lines in the
+third dimension contain additional information (see
+\fBapsum\fR for further details).  These spectral formats are accepted by the
+one dimensional spectroscopy 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.
+
+\fBPackage Parameters\fR
+
+The \fBechelle\fR package parameters set parameters affecting all the tasks
+in the package.  Some of the parameters are not applicable to the
+\fBdofoe\fR task.  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.
+
+\fBProcessing Parameters\fR
+
+The input images are specified by image lists.  The lists may be
+a list of explicit, comma separate image names, @ files, or image
+templates using pattern matching against file names in the directory.
+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.
+
+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).
+
+The number of orders selects the number of orders for a single
+fiber and "pairs" of object and arc
+fiber profiles for dual fibers.   The number specified will be
+automatically found based on the strongest peaks.
+In the  dual fiber case it is important that both elements of a pair be found,
+so no orders be skipped, and the aperture numbers must 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 \fIarcaps\fR
+parameter and so may be reversed if desired.
+
+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.
+
+The \fIbackground\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.
+
+The \fIclean\fR option invokes a profile fitting and deviant point rejection
+algorithm as well as a variance weighting of points in the aperture.  These
+options require knowing the effective (i.e. accounting for any image
+combining) read out noise and gain.  For a discussion of cleaning and
+variance weighted extraction see \fBapvariance\fR and \fBapprofiles\fR.
+
+The dispersion correction option selects whether to extract arc spectra,
+determine a dispersion function, assign them to the object spectra, and,
+possibly, resample the spectra to a linear (or log-linear) wavelength
+scale.
+
+Generally once a spectrum has been processed it will not be reprocessed if
+specified as an input spectrum.  However, changes to the underlying
+calibration data can cause such spectra to be reprocessed if the
+\fIupdate\fR flag is set.  The changes which will cause an update are a new
+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 \fIredo\fR flag may be used.  Note
+that reprocessing clobbers the previously processed output spectra.
+
+The \fIbatch\fR processing option allows object spectra to be processed as
+a background or batch job.  The \fIlistonly\fR option prints a summary of
+the processing steps which will be performed on the input spectra without
+actually doing anything.  This is useful for verifying which spectra will
+be affected if the input list contains previously processed spectra.  The
+listing does not include any arc spectra which may be extracted to
+dispersion calibrate an object spectrum.
+
+The last parameter (excluding the task mode parameter) points to another
+parameter set for the algorithm parameters.  The way \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.
+
+\fBAlgorithms and Algorithm Parameters\fR
+
+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,
+.nf
+
+	cl> epar params
+
+.fi
+or simple typing \fIparams\fR.  The parameter editor can also be
+entered when editing the \fBdofoe\fR parameters by typing \fI:e
+params\fR or simply \fI:e\fR if positioned at the \fIparams\fR
+parameter.
+
+\fBAperture Definitions\fR
+
+The first operation is to define the extraction apertures, which include the
+aperture width, background regions, and position dependence with
+wavelength, for the object and arc orders of interest.  This is done
+on a reference spectrum which is usually a flat field taken through
+all 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 \fIredo\fR
+option is set.
+
+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 when
+there is a second fiber.  Apertures
+are assigned with a limits set by the \fIlower\fR and
+\fIupper\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).
+
+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.  When there is a single fiber the aperture numbers must
+be sequential with the order numbers.  If an order is skipped then the
+aperture number must also be skipped.
+
+For dual fibers 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 \fIarcaps\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'.
+
+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.
+
+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 \fIline\fR and \fInsum\fR parameters.  A
+line of INDEF (the default) selects the middle of the image.  The automatic
+finding algorithm is described for the task \fBapfind\fR and 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
+\fIt_step\fR parameter.  The function fitting uses the \fBicfit\fR commands
+with the other parameters from the tracing section.
+
+\fBBackground or Scattered Light Subtraction\fR
+
+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.
+
+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.
+
+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 \fIapscat1\fR and
+\fIapscat2\fR.  The scattered light algorithm is described more fully in
+\fBapscatter\fR.  This algorithm is relatively slow.
+
+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 (\fIbackground\fR =
+"median") or median samples during fitting (\fIb_naverage\fR < -1).
+The background smoothing parameter \fIb_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.
+
+\fBExtraction\fR
+
+The actual extraction of the spectra is done by summing across the fixed
+width apertures at each point along the dispersion.  The default is to
+simply sum the pixels using partial pixels at the ends.  There is an
+option to weight the sum based on a Poisson noise model using the
+\fIreadnoise\fR and \fIgain\fR detector parameters.  Note that if the
+\fIclean\fR option is selected the variance weighted extraction is used
+regardless of the \fIweights\fR parameter.  The sigma threshold for
+cleaning are also set in the \fBparams\fR parameters.
+
+The cleaning and variance weighting options require knowing the effective
+(i.e. accounting for any image combining) read out noise and gain.  These
+numbers need to be adjusted if the image has been processed such that the
+intensity scale has a different origin (such as 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
+\fIfitflat\fR option be used.  The \fIb_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.
+
+\fBFlat Field Correction\fR
+
+Flat field corrections may be made during the basic CCD processing; i.e.
+direct division by the two dimensional flat field observation.  In that
+case do not specify a flat field spectrum; use the null string "".  The
+\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.
+
+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 \fIfitflat\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 \fIf_function\fR and
+\fIf_order\fR.  If the parameter \fIf_interactive\fR is "yes" then the
+fitting is done interactively using the \fBfit1d\fR task which uses the
+\fBicfit\fR interactive fitting commands.
+
+If the \fIfitflat\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.
+
+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.
+
+\fBDispersion Correction\fR
+
+If dispersion correction is not selected, \fIdispcor\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 three steps involved;
+determining the dispersion functions relating pixel position to wavelength,
+assigning the appropriate dispersion function to a particular observation,
+and either storing the nonlinear
+dispersion function in the image headers or resampling the spectra to
+evenly spaced pixels in wavelength.  When there are two fibers there is
+also a step of applying a zero point correction to the object fiber based
+on the arc fiber.
+
+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, if one is present, is then determined automatically by
+reference to the first fiber using the task \fBecreidentify\fR.
+
+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.
+
+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
+\fIarctable\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.
+
+When a second 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.
+
+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.
+
+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.
+
+When there are two fibers there are two full dispersion function from the
+single or pair of arc spectra, 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 (\fIrefit\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.
+
+The last step of dispersion correction is setting the dispersion
+of the object spectrum.  There are two choices here.
+If the \fIlinearize\fR parameter is not set the nonlinear dispersion
+function is stored in the image header.  Other IRAF tasks interpret
+this information when dispersion coordinates are needed for plotting
+or analysis.  This has the advantage of not requiring the spectra
+to be interpolated and the disadvantage that the dispersion
+information is only understood by IRAF tasks and cannot be readily
+exported to other analysis software.
+
+If the \fIlinearize\fR parameter is set then the spectra are resampled to a
+linear dispersion relation either in wavelength or the log of the
+wavelength.  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.
+
+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.
+.ih
+EXAMPLES
+1.  The following example uses artificial data and may be executed
+at the terminal (with IRAF V2.10).  This is also the sequence performed
+by the test procedure "demos dofoe".  Because the images are small the
+dispersion solution is somewhat simplistic.
+
+.nf
+ec> demos mkdofoe
+Creating image demoobj ...
+Creating image demoflat ...
+Creating image demoarc ...
+ec> echelle.verbose = yes
+ec> dofoe demoobj apref=demoflat flat=demoflat arcs=demoarc \
+>>> norders=3 width=5.
+Set reference apertures for demoflat
+Searching aperture database ...
+Finding apertures ...
+Mar  4  9:39: FIND - 6 apertures found for demoflat
+Resize apertures for demoflat?  (yes):
+Resizing apertures ...
+Mar  4  9:39: RESIZE - 6 apertures resized for demoflat
+<Review aperture assignments.  Exit with 'q'>
+Fit traced positions for demoflat interactively?  (yes):
+Tracing apertures ...
+Fit curve to aperture 1 of demoflat interactively  (yes):
+<Review trace and fit. Exit with 'q'>
+Fit curve to aperture 2 of demoflat interactively  (yes): N
+Mar  4  9:39: TRACE - 6 apertures traced in demoflat.
+Mar  4  9:39: DATABASE - 6 apertures for demoflat written to database
+Create response function demoflatnorm.ec
+Extract flat field demoflat
+Searching aperture database ...
+Mar  4  9:39: DATABASE  - 6 apertures read for demoflat from database
+Extracting apertures ...
+Mar  4  9:39: EXTRACT - Aperture 1 from demoflat --> demoflat.ec
+Mar  4  9:39: EXTRACT - Aperture 2 from demoflat --> demoflat.ec
+Mar  4  9:39: EXTRACT - Aperture 3 from demoflat --> demoflat.ec
+Mar  4  9:39: EXTRACT - Aperture 4 from demoflat --> demoflat.ec
+Mar  4  9:39: EXTRACT - Aperture 5 from demoflat --> demoflat.ec
+Mar  4  9:40: EXTRACT - Aperture 6 from demoflat --> demoflat.ec
+Fit and ratio flat field demoflat
+Create the normalized response demoflatnorm.ec
+demoflatnorm.ec -> demoflatnorm.ec  using bzero: 0.  and bscale: 1.
+    mean: 1.  median: 0.9990048  mode: 0.9876572
+    upper: INDEF  lower: INDEF
+Extract arc reference image demoarc
+Mar  4  9:40: DATABASE  - 6 apertures read for demoflat from database
+Mar  4  9:40: DATABASE - 6 apertures for demoarc written to database
+Mar  4  9:40: EXTRACT - Aperture 1 from demoarc --> demoarc.ec
+Mar  4  9:40: EXTRACT - Aperture 2 from demoarc --> demoarc.ec
+Mar  4  9:40: EXTRACT - Aperture 3 from demoarc --> demoarc.ec
+Mar  4  9:40: EXTRACT - Aperture 4 from demoarc --> demoarc.ec
+Mar  4  9:40: EXTRACT - Aperture 5 from demoarc --> demoarc.ec
+Mar  4  9:40: EXTRACT - Aperture 6 from demoarc --> demoarc.ec
+Determine dispersion solution for demoarc
+<Mark lines with 'm' and change orders with 'k'
+<'m' line at pixel 78 and assign 4965.
+<'k' to order 2
+<'m' line at pixel 78 and assign 5009
+<'m' line at pixel 78 and assign 5020
+<'k' to order 3
+<'m' line at pixel 78 and assign 5049.8
+<'m' line at pixel 78 and assign 5050.8
+<'m' line at pixel 78 and assign 5055.3
+<'m' line at pixel 78 and assign 5062
+<'m' line at pixel 78 and assign 5064.9
+<'f' to fit
+<'q' to quit fit and 'q' to quit ECIDENTIFY
+
+ECREIDENTIFY: NOAO/IRAF V2.10BETA valdes@puppis Wed 09:54:16 04-Mar-92
+  Reference image = demoarc.ec, Refit = yes
+   Image    Found     Fit Pix Shift  User Shift  Z Shift      RMS
+  d...ec    8/8     8/8        1.48        7.06  2.11E-5  0.00879
+d...ec: ap = 1, w1 = 4959.1, w2 = 4978.5, dw = 0.076, nw = 256
+d...ec: ap = 2, w1 = 5003.4, w2 = 5022.1, dw = 0.073, nw = 256
+d...ec: ap = 3, w1 = 5049.0, w2 = 5067.0, dw = 0.070, nw = 256
+Extract object spectrum demoobj
+Searching aperture database ...
+Mar  4  9:54: DATABASE  - 6 apertures read for demoflat from database
+Recentering apertures ...
+Mar  4  9:54: RECENTER  - 6 apertures shifted by -0.03 for demoobj.
+Mar  4  9:54: DATABASE - 6 apertures for demoobj written to database
+Extracting apertures ...
+Mar  4  9:54: EXTRACT - Aperture 1 from demoobj --> demoobj.ec
+Mar  4  9:54: EXTRACT - Aperture 2 from demoobj --> demoobj.ec
+Mar  4  9:54: EXTRACT - Aperture 3 from demoobj --> demoobj.ec
+Mar  4  9:54: EXTRACT - Aperture 4 from demoobj --> demoobj.ec
+Mar  4  9:54: EXTRACT - Aperture 5 from demoobj --> demoobj.ec
+Mar  4  9:54: EXTRACT - Aperture 6 from demoobj --> demoobj.ec
+Assign arc spectra for demoobj
+[demoobj] refspec1='demoarc'
+Reidentify arc fibers in demoobj with respect to demoarc
+
+ECREIDENTIFY: NOAO/IRAF V2.10BETA valdes@puppis Wed 09:54:28 04-Mar-92
+  Reference image = demoarcarc.ec, Refit = no
+   Image    Found     Fit Pix Shift  User Shift  Z Shift      RMS
+  d...ec    8/8     8/8       0.119       0.566  1.69E-6  0.00834
+Dispersion correct demoobj
+d...ec.imh: ap = 1, w1 = 4959.1, w2 = 4978.5, dw = 0.076, nw = 256
+d...ec.imh: ap = 2, w1 = 5003.4, w2 = 5022.1, dw = 0.073, nw = 256
+d...ec.imh: ap = 3, w1 = 5049.0, w2 = 5067.0, dw = 0.070, nw = 256
+.fi
+.ih
+REVISIONS
+.ls DOFOE V2.10.3
+The image format type to be
+processed is selected with the \fIimtype\fR environment parameter.  The
+dispersion axis parameter is now a package parameter.  Images will only
+be processed if the have the CCDPROC keyword.  A \fIdatamax\fR parameter
+has been added to help improve cosmic ray rejection.  A scattered
+light subtraction processing option has been added.
+.le
+.ih
+SEE ALSO
+apedit, apfind, approfiles, aprecenter, apresize, apsum, aptrace, apvariance,
+ccdred, center1d, dispcor, fit1d, icfit, ecidentify, observatory,
+onedspec.package, refspectra, ecreidentify, setairmass, setjd
+.endhelp
-- 
cgit 

