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+.help aidpars Jan04 noao.onedspec
+.ih
+NAME
+aidpars -- Automatic line identification parameters and algorithm
+.ih
+SUMMARY
+The automatic line identification parameters and algorithm used in
+\fBautoidentify\fR, \fBidentify\fR, and \fBreidentify\fR are described.
+.ih
+USAGE
+aidpars
+.ih
+PARAMETERS
+.ls reflist = ""
+Optional reference coordinate list to use in the pattern matching algorithm
+in place of the task coordinate list.  This file is a simple text list of
+dispersion coordinates.  It would normally be a culled and limited list of
+lines for the specific data being identified.
+.le
+.ls refspec = ""
+Optional reference dispersion calibrated spectrum.  This template spectrum
+is used to select the prominent lines for the pattern matching algorithm.
+It need not have the same dispersion increment or dispersion coverage as
+the target spectrum.
+.le
+.ls crpix = "INDEF"
+Coordinate reference pixel for the coordinate reference value specified by
+the \fIcrval\fR parameter.  This may be specified as a pixel coordinate
+or an image header keyword name (with or without a '!' prefix).  In the
+latter case the value of the keyword in the image header of the spectrum
+being identified is used.  A value of INDEF translates to the middle of
+the target spectrum.
+.le
+.ls crquad = INDEF
+Quadratic correction to the detected pixel positions to "linearize" the
+pattern of line spacings.  The corrected positions x' are derived from
+the measured positions x by
+
+.nf
+    x' = x + crquad * (x - crpix)**2
+.fi
+
+where crpix is the pixel reference point as defined by the \fIcrpix\fR
+parameter.  The measured and corrected positions may be examined by
+using the 't' debug flag.  The value may be a number or a header
+keyword (with or without a '!' prefix).  The default of INDEF translates
+to zero; i.e. no quadratic correction.
+.le
+.ls cddir = "sign" (unknown|sign|increasing|decreasing)
+The sense of the dispersion increment with respect to the pixel coordinates
+in the input spectrum.  The possible values are "increasing" or
+"decreasing" if the dispersion coordinates increase or decrease with
+increasing pixel coordinates, "sign" to use the sign of the dispersion
+increment (positive is increasing and negative is decreasing), and
+"unknown" if the sense is unknown and to be determined by the algorithm.
+.le
+.ls crsearch = "INDEF"
+Coordinate reference value search radius.  The value may be specified
+as a numerical value or as an image header keyword (with or without
+a '!' prefix) whose value is to be used.  The algorithm will search
+for a final coordinate reference value within this amount of the value
+specified by \fIcrval\fR.  If the value is positive the search radius is
+the specified value.  If the value is negative it is the absolute value
+of this parameter times \fIcdelt\fR times the number of pixels in the
+input spectrum; i.e. it is the fraction of dispersion range covered by the
+target spectrum assuming a dispersion increment per pixel of \fIcdelt\fR.
+A value of INDEF translates to -0.1 which corresponds to a search radius
+of 10% of the estimated dispersion range.
+.le
+.ls cdsearch = "INDEF"
+Dispersion coordinate increment search radius.  The value may be specified
+as a numerical value or as an image header keyword (with or without
+a '!' prefix) whose value is to be used.  The algorithm will search
+for a dispersion coordinate increment within this amount of the value
+specified by \fIcdelt\fR.  If the value is positive the search radius is
+the specified value.  If the value is negative it is the absolute value of
+this parameter times \fIcdelt\fR; i.e.  it is a fraction of \fIcdelt\fR.
+A value of INDEF translates to -0.1 which corresponds to a search radius
+of 10% of \fIcdelt\fR.
+.le
+.ls ntarget = 100
+Number of spectral lines from the target spectrum to use in the pattern
+matching.
+.le
+.ls npattern = 5
+Initial number of spectral lines in patterns to be matched.  There is a
+minimum of 3 and a maximum of 10.  The algorithm starts with the specified
+number and if no solution is found with that number it is iteratively
+decreased by one to the minimum of 3.  A larger number yields fewer
+and more likely candidate matches and so will produce a result sooner.
+But in order to be thorough the algorithm will try smaller patterns to
+search more possiblities.
+.le
+.ls nneighbors = 10
+Number of neighbors to use in making patterns of lines.  This parameter
+restricts patterns to include lines which are near each other.
+.le
+.ls nbins = 6
+Maximum number of bins to divide the reference coordinate list or spectrum
+in searching for a solution.  When there are no weak dispersion constraints
+the algorithm subdivides the full range of the coordinate list or reference
+spectrum into one bin, two bins, etc. up to this maximum.  Each bin is
+searched for a solution.
+.le
+.ls ndmax = 1000
+Maximum number of candidate dispersions to examine.  The algorithm ranks
+candidate dispersions by how many candidate spectral lines are fit and the
+the weights assigned by the pattern matching algorithm.  Starting from
+the highest rank it tests each candidate dispersion to see if it is
+a satisfactory solution.  This parameter determines how many candidate
+dispersion in the ranked list are examined.
+.le
+.ls aidord = 3 (minimum of 2)
+The order of the dispersion function fit by the automatic identification
+algorithm.  This is the number of polynomial coefficients so
+a value of two is a linear function and a value of three is a quadratic
+function.  The order should be restricted to values of two or three.
+Higher orders can lead to incorrect solutions because of the increased
+degrees of freedom if finding incorrect line identifications.
+.le
+.ls maxnl = 0.02
+Maximum non-linearity allowed in any trial dispersion function.
+The definition of the non-linearity test is
+
+.nf
+    maxnl > (w(0.5) - w(0)) / (w(1) - w(0)) - 0.5
+.fi
+
+where w(x) is the dispersion function value (e.g. wavelength) of the fit
+and x is a normalized pixel positions where the endpoints of the spectrum
+are [0,1].  If the test fails on a trial dispersion fit then a linear
+function is determined.
+.le
+.ls nfound = 6
+Minimum number of identified spectral lines required in the final solution.
+If a candidate solution has fewer identified lines it is rejected.
+.le
+.ls sigma = 0.05
+Sigma (uncertainty) in the line center estimates specified in pixels.
+This is used to propagate uncertainties in the line spacings in
+the observed patterns of lines.
+.le
+.ls minratio = 0.1
+Minimum spacing ratio used.  Patterns of lines in which the ratio of
+spacings between consecutive lines is less than this amount are excluded.
+.le
+.ls rms = 0.1
+RMS goal for a correct dispersion solution.  This is the RMS in the
+measured spectral lines relative to the expected positions from the
+coordinate line list based on the coordinate dispersion solution.
+The parameter is specified in terms of the line centering parameter
+\fIfwidth\fR since for broader lines the pixel RMS would be expected
+to be larger.  A pixel-based RMS criterion is used to be independent of
+the dispersion.  The RMS will be small for a valid solution.
+.le
+.ls fmatch = 0.2
+Goal for the fraction of unidentified lines in a correct dispersion
+solution.  This is the fraction of the strong lines seen in the spectrum
+which are not identified and also the fraction of all lines in the
+coordinate line list, within the range of the dispersion solution, not
+identified.  Both fractions will be small for a valid solution.
+.le
+.ls debug = ""
+Print or display debugging information.  This is intended for the developer
+and not the user.  The parameter is specified as a string of characters
+where each character displays some information.  The characters are:
+
+.nf
+    a: Print candidate line assignments.
+    b: Print search limits.
+    c: Print list of line ratios.
+*   d: Graph dispersions.
+*   f: Print final result.
+*   l: Graph lines and spectra.
+    r: Print list of reference lines.
+*   s: Print search iterations.
+    t: Print list of target lines.
+    v: Print vote array.
+    w: Print wavelength bin limits.
+.fi
+
+The items with an asterisk are the most useful.  The graphs are exited
+with 'q' or 'Q'.
+.le
+.ih
+DESCRIPTION
+The \fBaidpars\fR parameter set contains the parameters for the automatic
+spectral line identification algorithm used in the task \fBautoidentify\fR,
+\fBidentify\fR, and \fBreidentify\fR.  These tasks include the parameter
+\fIaidpars\fR which links to this parameters set.  Typing \fBaidpars\fR
+allows these parameters to be edited.  When editing the parameters of the
+other tasks with \fBeparam\fR one can edit the \fBaidpars\fR parameters by
+type ":e" when pointing to the \fIaidpars\fR task parameter.  The values of
+the \fBaidpars\fR parameters may also be set on the command line for the
+task.  The discussion which follows describes the parameters and the
+algorithm.
+
+The goal of the automatic spectral line identification algorithm is to
+automate the identification of spectral lines so that given an observed
+spectrum of a spectral line source (called the target spectrum) and a file
+of known dispersion coordinates for the lines, the software will identify
+the spectral lines and use these identifications to determine a
+dispersion function.  This algorithm is quite general so that the correct
+identifications and dispersion function may be found even when there is
+limited or no knowledge of the dispersion coverage and resolution of the
+observation.
+
+However, when a general line list, including a large dispersion range and
+many weak lines, is used and the observation covers a much smaller portion
+of the coordinate list the algorithm may take a long to time or even fail
+to find a solution.  Thus, it is highly desirable to provide additional
+input giving approximate dispersion parameters and their uncertainties.
+When available, a dispersion calibrated reference spectrum (not necessarily
+of the same resolution or wavelength coverage) also aids the algorithm by
+indicating the relative strengths of the lines in the coordinate file.  The
+line strengths need not be very similar (due to different lamps or
+detectors) but will still help separate the inherently weak and strong
+lines.
+
+
+The Input
+
+The primary inputs to the algorithm are the observed one dimensional target
+spectrum in which the spectral lines are to be identified and a dispersion
+function determined and a file of reference dispersion coordinates.  These
+inputs are provided in the tasks using the automatic line identification
+algorithm.
+
+One way to limit the algorithm to a specific dispersion region and to the
+important spectral lines is to use a limited coordinate list.  One may do
+this with the task coordinate list parameter (\fIcoordlist\fR).  However,
+it is desirable to use a standard master line list that includes all the
+lines, both strong and weak.  Therefore, one may specify a limited line
+list with the parameter \fIreflist\fR.  The coordinates in this list will
+be used by the automatic identification algorithm to search for patterns
+while using the primary coordinate list for adding weaker lines during the
+dispersion function fitting.
+
+The tasks \fBautoidentify\fR and \fBidentify\fR also provide parameters to
+limit the search range.  These parameters specify a reference dispersion
+coordinate (\fIcrval\fR) and a dispersion increment per pixel (\fIcdelt\fR).
+When these parameters are INDEF this tells the algorithm to search for a
+solution over the entire range of possibilities covering the coordinate
+line list or reference spectrum.
+
+The reference dispersion coordinate refers to an approximate coordinate at
+the reference pixel coordinate specified by the parameter \fIcrpix\fR.
+The default value for the reference pixel coordinate is INDEF which
+translates to the central pixel of the target spectrum.
+
+The parameters \fIcrsearch\fR and \fIcdsearch\fR specify the expected range
+or uncertainty of the reference dispersion coordinate and dispersion
+increment per pixel respectively.  They may be specified as an absolute
+value or as a fraction.  When the values are positive they are used
+as an absolute value;
+
+.nf
+    crval(final) = \fIcrval\fR +/- \fIcrsearch\fR
+    cdelt(final) = \fIcdelt\fR +/- \fIcdsearch\fR.
+.fi
+
+When the values are negative they are used as a fraction of the dispersion
+range or fraction of the dispersion increment;
+
+.nf
+    crval(final) = \fIcrval\fR +/- abs (\fIcrsearch\fR * \fIcdelt\fR) * N_pix
+    cdelt(final) = \fIcdelt\fR +/- abs (\fIcdsearch\fR * \fIcdelt\fR)
+.fi
+
+where abs is the absolute value function and N_pix is the number of pixels
+in the target spectrum.  When the ranges are not given explicitly, that is
+they are specified as INDEF, default values of -0.1 are used.
+
+The parameters \fIcrval\fR, \fIcdelt\fR, \fIcrpix\fR, \fIcrsearch\fR,
+and \fIcdsearch\fR may be given explicit numerical values or may
+be image header keyword names.  In the latter case the values of the
+indicated keywords are used.  This feature allows the approximate
+dispersion range information to be provided by the data acquisition
+system; either by the instrumentation or by user input.
+
+Because sometimes only the approximate magnitude of the dispersion
+increment is known and not the sign (i.e. whether the dispersion
+coordinates increase or decrease with increasing pixel coordinates)
+the parameter \fIcdsign\fR specifies if the dispersion direction is
+"increasing", "decreasing", "unknown", or defined by the "sign" of the
+approximate dispersion increment parameter (sign of \fIcdelt\fR).
+
+The above parameters defining the approximate dispersion of the target
+spectrum apply to \fIautoidentify\fR and \fIidentify\fR.  The task
+\fBreidentify\fR does not use these parameters except that the \fIshift\fR
+parameter corresponds to \fIcrsearch\fR if it is non-zero.  This task
+assumes that spectra to be reidentified are the same as a reference
+spectrum except for a zero point dispersion offset; i.e. the approximate
+dispersion parameters are the same as the reference spectrum.  The
+dispersion increment search range is set to be 5% and the sign of the
+dispersion increment is the same as the reference spectrum.
+
+An optional input is a dispersion calibrated reference spectrum (referred to
+as the reference spectrum in the discussion).  This is specified either in
+the coordinate line list file or by the parameter \fIrefspec\fR.  To
+specify a spectrum in the line list file the comment "# Spectrum <image>"
+is included where <image> is the image filename of the reference spectrum.
+Some of the standard line lists in linelists$ may include a reference
+spectrum.  The reference spectrum is used to select the strongest lines for
+the pattern matching algorithm.
+
+
+The Algorithm
+
+First a list of the pixel positions for the strong spectral lines in the
+target spectrum is created.  This is accomplished by finding the local
+maxima, sorting them by pixel value, and then using a centering algorithm
+(\fIcenter1d\fR) to accurately find the centers of the line profiles.  Note
+that task parameters \fIftype\fR, \fIfwidth\fR, \fIcradius\fR,
+\fIthreshold\fR, and \fIminsep\fR are used for the centering.  The number
+of spectral lines selected is set by the parameter \fIntarget\fR.
+
+In order to insure that lines are selected across the entire spectrum
+when all the strong lines are concentrated in only a part of the
+spectrum, the spectrum is divided into five regions and approximately
+a fifth of the requested number of lines is found in each region.
+
+A list of reference dispersion coordinates is selected from the coordinate
+file (\fIcoordlist\fR or \fIreflist\fR).  The number of reference
+dispersion coordinates is set at twice the number of target lines found.
+The reference coordinates are either selected uniformly from the coordinate
+file or by locating the strong spectral lines (in the same way as for the
+target spectrum) in a reference spectrum if one is provided.  The selection
+is limited to the expected range of the dispersion as specified by the
+user.  If no approximate dispersion information is provided the range of
+the coordinate file or reference spectrum is used.
+
+The ratios of consecutive spacings (the lists are sorted in increasing
+order) for N-tuples of coordinates are computed from both lists.  The size
+of the N-tuple pattern is set by the \fInpattern\fR parameter.  Rather than
+considering all possible combinations of lines only patterns of lines with
+all members within \fInneighbors\fR in the lists are used; i.e. the first
+and last members of a pattern must be within \fInneighbors\fR of each other
+in the lists.  The default case is to find all sets of five lines which are
+within ten lines of each other and compute the three spacing ratios.
+Because very small spacing ratios become uncertain, the line patterns are
+limited to those with ratios greater than the minimum specified by the
+\fIminratio\fR parameter.  Note that if the direction of the dispersion is
+unknown then one computes the ratios in the reference coordinates in both
+directions.
+
+The basic idea is that similar patterns in the pixel list and the
+dispersion list will have matching spacing ratios to within a tolerance
+derived by the uncertainties in the line positions (\fIsigma\fR) from the
+target spectrum.  The reference dispersion coordinates are assumed to have
+no uncertainty.  All matches in the ratio space are found between patterns
+in the two lists.  When matches are made then the candidate identifications
+(pixel, reference dispersion coordinate) between the elements of the
+patterns are recorded.  After finding all the matches in ratio space a
+count is made of how often each possible candidate identification is
+found.  When there are a sufficient number of true pairs between the lists
+(of order 25% of the shorter list) then true identifications will appear in
+common in many different patterns.  Thus the highest counts of candidate
+identifications are the most likely to be true identifications.
+
+Because the relationship between the pixel positions of the lines in the
+target spectrum and the line positions in the reference coordinate space
+is generally non-linear the line spacing ratios are distorted and may
+reduce the pattern matching.  The line patterns are normally restricted
+to be somewhat near each other by the \fInneighbors\fR so some degree of
+distortion can be tolerated.  But in order to provide the ability to remove
+some of this distortion when it is known the parameter \fIcrquad\fR is
+provided.  This parameter applies a quadratic transformation to the measured
+pixel positions to another set of "linearized" positions  which are used
+in the line ratio pattern matching.  The form of the transformation is
+
+.nf
+    x' = x + crquad * (x - crpix)**2
+.fi
+
+where x is the measured position, x' is the transformed position,
+crquad is the value of the distortion parameter, and crpix is the value
+of the coordinate reference position.
+
+If approximate dispersion parameters and search ranges are defined then
+candidate identifications which fall outside the range of dispersion
+function possibilities are rejected.  From the remaining candidate
+identifications the highest vote getters are selected.  The number selected
+is three times the number of target lines.
+
+All linear dispersions functions, where dispersion and pixel coordinates
+are related by a zero point and slope, are found that pass within two
+pixels of two or more of the candidate identifications.  The dispersion
+functions are ranked primarily by the number of candidate identifications
+fitting the dispersion and secondarily by the total votes in the
+identifications.  Only the highest ranking candidate linear dispersion
+are kept.  The number of candidate dispersions kept is set by the
+parameter \fIndmax\fR.
+
+The candidate dispersions are evaluated in order of their ranking.  Each
+line in the coordinate file (\fIcoordlist\fR) is converted to a pixel
+coordinate based on the dispersion function.  The centering algorithm
+attempts to find a line profile near that position as defined by the
+\fImatch\fR parameter.  This may be specified in pixel or dispersion
+coordinates.  All the lines found are used to fit a polynomial dispersion
+function with \fIaidord\fR coefficients.  The order should be linear or
+quadratic because otherwise the increased degrees of freedom allow
+unrealistic dispersion functions to appear to give a good result.  A
+quadratic function (\fIaidord\fR = 3) is allowed since this is the
+approximate form of many dispersion functions.
+
+However, to avoid unrealistic dispersion functions a test is made that
+the maximum amplitude deviation from a linear function is less than
+an amount specified by the \fImaxnl\fR parameter.  The definition of
+the test is
+
+.nf
+    maxnl > (w(0.5) - w(0)) / (w(1) - w(0)) - 0.5
+.fi
+
+where w(x) is the dispersion function value (e.g. wavelength) of the fit
+and x is a normalized pixel positions where the endpoints of the spectrum
+are [0,1].  What this relation means is that the wavelength interval
+between one end and the center relative to the entire wavelength interval
+is within maxnl of one-half.  If the test fails then a linear function
+is fit.  The process of adding lines based on the last dispersion function
+and then refitting the dispersion function is iterated twice.  At the end
+of this step if fewer than the number of lines specified by the parameter
+\fInfound\fR have been identified the candidate dispersion is eliminated.
+
+The quality of the line identifications and dispersion solution is
+evaluated based on three criteria.  The first one is the root-mean-square
+of the residuals between the pixel coordinates derived from lines found
+from the dispersion coordinate file based on the dispersion function and
+the observed pixel coordinates.  This pixel RMS is normalized by the target
+RMS set with the \fIrms\fR parameter.  Note that the \fIrms\fR parameter
+is specified in units of the \fIfwidth\fR parameter.  This is because if
+the lines are broader, requiring a larger fwidth to obtain a centroid,
+then the expected uncertainty would be larger.  A good solution will have
+a normalized rms value less than one.  A pixel RMS criterion, as opposed
+to a dispersion coordinate RMS, is used since this is independent of the
+actual dispersion of the spectrum.
+
+The other two criteria are the fraction of strong lines from the target
+spectrum list which were not identified with lines in the coordinate file
+and the fraction of all the lines in the coordinate file (within the
+dispersion range covered by the candidate dispersion) which were not
+identified.  These are normalized to a target value given by \fIfmatch\fR.
+The default matching goal is 0.3 which means that less than 30% of
+the lines should be unidentified or greater than 70% should be identified.
+As with the RMS, a value of one or less corresponds to a good solution.
+
+The reason the fraction identified criteria are used is that the pixel RMS
+can be minimized by finding solutions with large dispersion increment per
+pixel.  This puts all the lines in the coordinate file into a small range
+of pixels and so (incorrect) lines with very small residuals can be found.
+The strong line identification criterion is clearly a requirement that
+humans use in evaluating a solution.  The fraction of all lines identified,
+as opposed to the number of lines identified, in the coordinate file is
+included to reduce the case of a large dispersion increment per pixel
+mapping a large number of lines (such as the entire list) into the range of
+pixels in the target spectrum.  This can give the appearance of finding a
+large number of lines from the coordinate file.  However, an incorrect
+dispersion will also find a large number which are not matched.  Hence the
+fraction not matched will be high.
+
+The three criteria, all of which are normalized so that values less
+than one are good, are combined to a single figure of merit by a weighted
+average.  Equal weights have been found to work well; i.e. each criterion
+is one-third of the figure of merit.  In testing it has been found that all
+correct solutions over a wide range of resolutions and dispersion coverage
+have figures of merit less than one and typically of order 0.2.  All
+incorrect candidate dispersion have values of order two to three.
+
+The search for the correct dispersion function terminates immediately,
+but after checking the first five most likely candidates, when
+a figure of merit less than one is found.  The order in which the candidate
+dispersions are tested, that is by rank, was chosen to try the most promising
+first so that often the correct solution is found on the first attempt.
+
+When the approximate dispersion is not known or is imprecise it is
+often the case that the pixel and coordinate lists will not overlap
+enough to have a sufficient number true coordinate pairs.  Thus, at a
+higher level the above steps are iterated by partitioning the dispersion
+space searched into bins of various sizes.  The largest size is the
+maximum dispersion range including allowance for the search radii.
+The smallest size bin is obtained by dividing the dispersion range by
+the number specified by the \fInbins\fR parameter.  The actual number
+of bins searched at each bin size is actually twice the number of
+bins minus one because the bins are overlapped by 50%.
+
+The search is done starting with bins in the middle of the size range and
+in the middle of the dispersion range and working outward towards larger
+and smaller bins and larger and smaller dispersion ranges.  This is done to
+improved the chances of finding the correction dispersion function in the
+smallest number of steps.
+
+Another iteration performed if no solution is found after trying all the
+candidate dispersion and bins is to reduce the number of lines in the
+pattern.  So the parameter \fInpattern\fR is an initial maximum pattern.
+A larger pattern gives fewer and higher quality candidate identifications
+and so converges faster.  However, if no solution is found the algorithm
+tries more possible matches produced by a lower number of lines in
+the pattern.  The pattern groups are reduced to a minimum of three lines.
+
+When a set of line identifications and dispersion solution satisfying the
+figure of merit criterion is found a final step is performed.
+Up to this point only linear dispersion functions are used since higher order
+function can be stretch in unrealistic ways to give good RMS values
+and fit all the lines.  The final step is to use the line identifications
+to fit a dispersion function using all the parameters specified by the
+user (such as function type, order, and rejection parameters).  This
+is iterated to add new lines from the coordinate list based on the
+more general dispersion function and then obtain a final dispersion
+function.  The line identifications and dispersion function are then
+returned to the task using this automatic line identification algorithm.
+
+If a satisfactory  solution is not found after searching all the
+possibilities the algorithm will inform the task using it and the task will
+report this appropriately.
+.ih
+EXAMPLES
+1. List the parameters.
+
+.nf
+    cl> lpar aidpars
+.fi
+
+2. Edit the parameters with \fBeparam\fR.
+
+.nf
+    cl> aidpars
+.fi
+
+3. Edit the \fBaidpars\fR parameters from within \fBautoidentify\fR.
+
+.nf
+    cl> epar autoid
+	[edit the parameters]
+	[move to the "aidpars" parameter and type :e]
+	[edit the aidpars parameters and type :q or EOF character]
+	[finish editing the autoidentify parameters]
+	[type :wq or the EOF character]
+.fi
+
+4. Set one of the parameters on the command line.
+
+.nf
+    cl> autoidentify spec002 5400 2.5 crpix=1
+.fi
+.ih
+REVISIONS
+.ls AIDPARS V2.12.2
+There were many changes made in the paramters and algorithm.  New parameters
+are "crquad" and "maxnl".  Changed definitions are for "rms".  Default
+value changes are for "cddir", "ntarget", "ndmax", and "fmatch".  The most
+significant changes in the algorithm are to allow for more non-linear
+dispersion with the "maxnl" parameter, to decrease the "npattern" value
+if no solution is found with the specified value, and to search a larger
+number of candidate dispersions.
+.le
+.ls AIDPARS V2.11
+This parameter set is new in this version.
+.le
+.ih
+SEE ALSO
+autoidentify, identify, reidentify, center1d
+.endhelp
diff --git a/noao/onedspec/doc/autoidentify.hlp b/noao/onedspec/doc/autoidentify.hlp
new file mode 100644
index 00000000..a344031a
--- /dev/null
+++ b/noao/onedspec/doc/autoidentify.hlp
@@ -0,0 +1,370 @@
+.help autoidentify Jan96 noao.onedspec
+.ih
+NAME
+autoidentify -- Automatically identify lines and fit dispersion
+.ih
+SUMMARY
+Spectral lines are automatically identified from a list of coordinates
+by pattern matching.  The identified lines are then used to fit a
+dispersion function which is written to a database for later use
+in dispersion calibration.  After a solution is found the identified
+lines and dispersion function may be examined interactively.
+.ih
+USAGE
+autoidentify images crval cdelt
+.ih
+PARAMETERS
+.ls images
+List of images containing one dimensional spectra in which to identify
+spectral lines and fit dispersion functions.  For two and three dimensional
+spectral and spatial data one may use an image section to select a one
+dimensional spectral vector or use the \fIsection\fR parameter.
+.le
+.ls crval, cdelt
+These parameters specify an approximate coordinate value and coordinate
+interval per pixel.  They may be specified as numerical values, INDEF, or
+image header keyword names whose values are to be used.  The coordinate
+reference value is for the pixel specified by the parameter
+\fIaidpars.crpix\fR.  The default reference pixel is INDEF which means the
+middle of the spectrum.  By default only the magnitude of the coordinate
+interval is used and the search will include both increasing and decreasing
+coordinate values with increasing pixel values.  If one or both of these
+parameters are specified as INDEF the search for a solution will be slower
+and more likely to fail.
+.le
+.ls coordlist = ""
+Coordinate list consisting of an list of spectral line coordinates.
+A comment line of the form "# units <units>", where <units> is one of the
+understood units names, defines the units of the coordinate list.  If no units
+are specified then Angstroms are assumed.
+The line list is used for both the final identifications and for the set of
+lines to use in the automatic search.  A restricted search list may be
+specified with the parameter \fIaidpars.reflist\fR.  The line list may
+contain a comment line of the form "# Spectrum <name>", where <name> is a
+filename containing a reference spectrum.  The reference spectrum will be
+used in selecting the strong lines for the automatic search.  A reference
+spectrum may also be specified with the parameter \fIaidpars.refspec\fR.
+
+Some standard line lists are available in the directory "linelists$".
+See the help topic \fIlinelists\fR for the available line lists.
+.le
+.ls units = ""
+The units to use if no database entry exists.  The units are specified as
+described in
+
+.nf
+    cl> help onedspec.package section=units
+.fi
+
+If no units are specified and a coordinate list is used then the units of
+the coordinate list are selected.  If a database entry exists then the
+units defined there override both this parameter and the coordinate list.
+.le
+.ls interactive = yes (no|yes|NO|YES)
+After automatically identifying the spectral lines and dispersion function
+review and modify the solution interactively?  If "yes" a query is given
+for each spectrum providing the choice of interactive review.  The
+query may be turned off during execution.  If "YES" the interactive review
+is entered automatically without a query.  The interactive, graphical
+review is the same as the task \fBidentify\fR with a few restriction.
+.le
+.ls aidpars = "" (parameter set)
+Parameter set for the automatic line identification algorithm.  The
+parameters are described in the help topic \fBaidpars\fR.
+.le
+
+For two and three dimensional spectral images the following parameters are
+used to select a one dimensional spectrum.
+.ls section = "middle line"
+If an image is not one dimensional or specified as a one dimensional image
+section then the image section given by this parameter is used.  The
+section defines a one dimensional spectrum.  The dispersion direction is
+derived from the vector direction.
+
+The section parameter may be specified directly as an image section or
+in one of the following forms
+
+.nf
+line|column|x|y|z first|middle|last|# [first|middle|last|#]]
+first|middle|last|# [first|middle|last|#] line|column|x|y|z
+.fi
+
+where each field can be one of the strings separated by | except for #
+which is an integer number.  The field in [] is a second designator which
+is used with three dimensional data.  Abbreviations are allowed though
+beware that 'l' is not a sufficient abbreviation.
+.le
+.ls nsum = "1"
+Number of lines, columns, or bands across the designated dispersion axis to
+be summed when the image is a two or three dimensional image.
+It does not apply to multispec format spectra.  If the image is three
+dimensional an optional second number can be specified for the higher
+dimensional axis  (the first number applies to the lower axis number and
+the second to the higher axis number).  If a second number is not specified
+the first number is used for both axes.
+.le
+
+The following parameters are used in finding spectral lines.
+.ls ftype = "emission"
+Type of spectral lines to be identified.  The possibly abbreviated choices are
+"emission" and "absorption".
+.le
+.ls fwidth = 4.
+Full-width at the base (in pixels) of the spectral lines to be identified.
+.le
+.ls cradius = 5.
+The maximum distance, in pixels, allowed between a line position
+and the initial estimate when defining a new line.
+.le
+.ls threshold = 0.
+In order for a line center to be determined the range of pixel intensities
+around the line must exceed this threshold.
+.le
+.ls minsep = 2.
+The minimum separation, in pixels, allowed between line positions
+when defining a new line.
+.le
+.ls match = -3.
+The maximum difference for a match between the line coordinate derived from
+the dispersion function and a coordinate in the coordinate list.  Positive
+values are in user coordinate units and negative values are in units of
+pixels.
+.le
+
+The following parameters are used to fit a dispersion function to the user
+coordinates.  The \fBicfit\fR routines are used and further descriptions
+about these parameters may be found under that topic.
+.ls function = "spline3"
+The function to be fit to user coordinates as a function of the pixel
+coordinates.  The choices are "chebyshev", "legendre", "spline1", or "spline3".
+.le
+.ls order = 1
+Order of the fitting function.  The order is the number of polynomial
+terms (coefficients) or the number of spline pieces.
+.le
+.ls sample = "*"
+Sample regions for fitting specified in pixel coordinates.
+.le
+.ls niterate = 10
+Number of rejection iterations.
+.le
+.ls low_reject = 3.0, high_reject = 3.0
+Lower and upper residual rejection in terms of the RMS of the fit.
+.le
+.ls grow = 0
+Distance from a rejected point in which additional points are automatically
+rejected regardless of their residuals.
+.le
+
+The following parameters control the input and output.
+.ls dbwrite = "yes"  (no|yes|NO|YES)
+Automatically write or update the database with the line identifications
+and dispersion function?  If "no" or "NO" then there is no database
+output.  If "YES" the results are automatically written to the database.
+If "yes" a query is made allowing the user to reply with "no", "yes", "NO"
+or "YES".  The negative responses do not write to the database and the
+affirmative ones do write to the database.  The upper-case responses
+suppress any further queries for any remaining spectra.
+.le
+.ls overwrite = yes
+Overwrite previous solutions in the database?  If there is a previous
+solution for the spectrum being identified this parameter selects whether
+to skip the spectrum ("no") or find a new solution ("yes").  In the later
+case saving the solution to the database will overwrite the previous
+solution.
+.le
+.ls database = "database"
+Database for reading and writing the line identifications and
+dispersion functions.
+.le
+.ls verbose = yes
+Print results of the identification on the standard output?
+.le
+.ls logfile = "logfile"
+Filename for recording log information about the identifications.
+The null string, "", may be specified to skip recording the log information.
+.le
+.ls plotfile = ""
+Filename for recording log plot information as IRAF metacode.  A
+null string, "", may be specified to skip recording the plot information.
+(Plot output is currently not implemented.)
+.le
+.ls graphics = "stdgraph"
+Graphics device for the interactive review.  The default is the standard
+graphics device which is generally a graphics terminal.
+.le
+.ls cursor = ""
+Cursor input file for the interactive review.  If a cursor file is not
+given then the standard graphics cursor is read.
+.le
+
+.ls query
+Parameter used by the program to query the user.
+.le
+.ih
+DESCRIPTION
+\fBAutoidentify\fR automatically identifies spectral lines from a list of
+spectral line coordinates (\fIcoordlist\fR) and determines a dispersion
+function.  The identified lines and the dispersion function may be reviewed
+interactively (\fIinteractive\fR) and the final results are recorded in a
+\fIdatabase\fR.
+
+Each image in the input list (\fIimages\fR) is considered in turn.  If the
+image is not one dimensional or a one dimensional section of an image then
+the parameter \fIsection\fR is used to select a one dimensional
+spectrum.  It defines the dispersion direction and central spatial
+coordinate(s).  If the image is not one dimensional or a set of one
+dimensional spectra n multispec format then the \fInsum\fR parameter
+selects the number of neighboring lines, columns, and bands to sum.
+
+This task is not intended to be used on all spectra in an image since in
+most cases the dispersion functions will be similar though possibly with a
+zero point shift.  Once one spectrum is identified the others may be
+reidentified with \fBreidentify\fR.
+
+The coordinate list of spectral lines often covers a much larger dispersion
+range than the spectra being identified.  This is true of the standard line
+lists available in the "linelists$" directory.  While the algorithm for
+identifying the lines will often succeed with a large line list it is not
+guaranteed nor will it find the solution quickly without additional
+information.  Thus it is highly desirable to provide the algorithm with
+approximate information about the spectra.  Generally this information is
+known by the observer or recorded in the image header.
+
+As implied in the previous paragraph, one may use a
+limited coordinate line list that matches the dispersion coverage of the
+spectra reasonably well (say within 100% of the dispersion range).
+This may be done with the \fIcoordlist\fR parameter or a second
+coordinate list used only for the automatic search may be specified
+with the parameter \fIaidpars.reflist\fR.  This allows using a smaller
+culled list of lines for finding the matching patterns and a large list
+with weaker lines for the final dispersion function fit.
+
+The alternative to a limited list is to use the parameters \fIcrval\fR and
+\fIcdelt\fR to specify the approximate coordinate range and dispersion
+interval per pixel.  These parameters may be given explicitly or by
+specifying image header keywords.  The pixel to which \fIcrval\fR refers is
+specified by the parameter \fIaidpars.crpix\fR.  By default this is INDEF
+which means use the center of the spectrum.  The direction in which the
+dispersion coordinates increase relative to the pixel coordinates may be
+specified by the \fIaidpars.cddir\fR parameter.  The default is "unknown"
+to search in either direction.
+
+The algorithm used to automatically identify the spectral lines and
+find a dispersion function is described under the help topic
+\fBaidpars\fR.  This topic also describes the various algorithm
+parameters.  The default parameters are adequate for most data.
+
+The characteristics of the spectral lines to be found and identified are
+set by several parameters.  The type of spectral lines, whether "emission"
+or "absorption", is set by the parameter \fIftype\fR.  For arc-line
+calibration spectra this parameter is set to "emission".  The full-width
+(in pixels) at the base of the spectral lines is set by the parameter
+\fIfwidth\fR.  This is used by the centering algorithm to define the extent
+of the line profile to be centered.  The \fIthreshold\fR parameter defines
+a minimum contrast (difference) between a line peak and the neighboring
+continuum.  This allows noise peaks to be ignored.  Finding the center of a
+possible line begins with an initial position estimate.  This may be an
+interactive cursor position or the expected position from the coordinate
+line list.  The centering algorithm then searches for a line of the
+specified type, width, and threshold within a given distance, specified by
+the \fIcradius\fR parameter.  These parameters and the centering algorithm
+are described by the help topic \fBcenter1d\fR.
+
+To avoid finding the same line multiple times, say when there are two lines
+in the line list which are blended into a single in the observation, the
+\fIminsep\fR parameter rejects any new line position found within that
+distance of a previously defined line.
+
+The automatic identification of lines includes matching a line position in
+the spectrum against the list of coordinates in the coordinate line list.
+The \fImatch\fR parameter defines how close the measured line position must
+be to a coordinate in the line list to be considered a possible
+identification.  This parameter may be specified either in user coordinate
+units (those used in the line list) by using a positive value or in pixels
+by using a negative value.  In the former case the line position is
+converted to user coordinates based on a dispersion function and in the
+latter the line list coordinate is converted to pixels using the inverse of
+the dispersion function.
+
+The dispersion function is determined by fitting a set of pixel positions
+and user coordinate identifications by least squares to a specified
+function type.  The fitting requires a function type, \fIfunction\fR, and
+the order (number of coefficients or spline pieces), \fIorder\fR.
+In addition the fitting can be limited to specified regions, \fIsample\fR,
+and provide for the rejection of points with large residuals.  These
+parameters are set in advance and used during the automatic dispersion
+function determination.  Later the fitting may be modified interactively.
+For additional discussion of these parameters see \fBicfit\fR.
+
+The output of this program consists of log information, plot information,
+and the line identifications and dispersion function.  The log information
+may be appended to the file specified by the \fIlogfile\fR parameter
+and printed to the standard output (normally the terminal) by
+setting the \fIverbose\fR parameter to yes.  This information consists
+of a banner line, a line of column labels, and results for each spectrum.
+For each spectrum the spectrum name, the number of spectral lines found,
+the dispersion coordinate at the middle of the spectrum, the dispersion
+increment per pixel, and the root-mean-square (RMS) of the residuals for
+the lines used in the dispersion function fit is recorded.  The units of
+the RMS are those of the user (line list) coordinates.  If a solution is
+not found the spectrum name and a message is printed.
+
+The line identifications and dispersion function are written to the
+specified \fIdatabase\fR.  The current format of the database is described
+in the help for \fIidentify\fR.  If a database entry is already present for
+a spectrum and the parameter \fIoverwrite\fR is "no" then the spectrum is
+skipped and a message is printed to the standard output.   After a solution
+is found and after any interactive review (see below) the results may be
+written to the database.  The \fIdbwrite\fR parameter may be specified as
+"no" or "NO" to disable writing to the database (and no queries will be
+made), as "yes" to query whether to or not to write to the database, or as
+"YES" to automatically write the results to the database with no queries.
+When a query is given the responses may be "no" or "yes" for an individual
+spectrum or "NO" or "YES" for all remaining spectra without further
+queries.
+
+After a solution is found one may review and modify the line
+identifications and dispersion function using the graphical functions of
+the \fBidentify\fR task (with the exception that a new spectrum may not be
+selected).  The review mode is selected with the \fIinteractive\fR
+parameter.  If the parameter is "no" or "NO" then no interactive review
+will be provided and there will be no queries either.  If the parameter is
+"YES" then the graphical review mode will be entered after each solution is
+found without any query.  If the parameter is "yes" then a query will be
+made after a solution is found and after any log information is written to
+the terminal.  One may respond to the query with "no" or "yes" for an
+individual spectrum or "NO" or "YES" for all remaining spectra without
+further queries.  For "yes" or "YES" the \fIidentify\fR review  mode is
+entered.  To exit type 'q'.
+.ih
+EXAMPLES
+1.  The following example finds a dispersion solution for the middle column
+of a long slit spectrum of a He-Ne-Ar arc spectrum using all the
+interactive options.
+
+.nf
+    cl> autoid arc0022 6000 6 coord=linelists$henear.dat sec="mid col"
+    AUTOIDENITFY: NOAO/IRAF IRAFX valdes@puppis Thu 15:50:31 25-Jan-96
+      Spectrum                # Found   Midpoint Dispersion        RMS
+      arc0022[50,*]                50      5790.       6.17      0.322
+    arc0022[50,*]: Examine identifications interactively?  (yes): 
+    arc0022[50,*]: Write results to database?  (yes): yes
+.fi
+
+2.  The next example shows a non-interactive mode with no queries for
+the middle fiber of an extracted multispec image.
+
+.nf
+    cl> autoid.coordlist="linelists$henear.dat"
+    cl> autoid a0003 5300 3.2 interactive- verbose- dbwrite=YES
+.fi
+.ih
+REVISIONS
+.ls AUTOIDENTIFY V2.11
+This task is new in this version.
+.le
+.ih
+SEE ALSO
+identify, reidentify, aidpars, linelists, center1d, icfit, gtools
+.endhelp
diff --git a/noao/onedspec/doc/bplot.hlp b/noao/onedspec/doc/bplot.hlp
new file mode 100644
index 00000000..f2214b94
--- /dev/null
+++ b/noao/onedspec/doc/bplot.hlp
@@ -0,0 +1,201 @@
+.help bplot Mar92 noao.onedspec
+.ih
+NAME
+bplot -- Plot spectra noninteractively using SPLOT
+.ih
+USAGE
+bplot images [records]
+.ih
+PARAMETERS
+.ls images
+List of images to be plotted.  These may be one dimensional, multiaperture,
+long slit, or nonspectral images.
+.le
+.ls records (imred.irs and imred.iids only)
+List of records to be appended to the input image root names when
+using record number extension format.  The syntax of this list is comma
+separated record numbers or ranges of record numbers.  A range consists of
+two numbers separated by a hyphen.  A null list may be used if no record
+number extensions are desired.
+.le
+.ls apertures = ""
+List of apertures/lines/columns to be plotted in each image.  If
+\fIapertures\fR is null all of the apertures/lines/columns will be plotted.
+.le
+.ls band = 1
+The band or plane of a three dimensional image to be plotted in each image.
+.le
+.ls graphics = "stdgraph"
+Output graphics device.  This may be one of "stdgraph", "stdplot",
+"stdvdm", or the actual device name.
+.le
+.ls cursor = "onedspec$gcurval.dat"
+File(s) containing cursor commands for the SPLOT task.
+The files will be cycled sequentially.  If there is more than one file
+usually the number of files will agree with the number of apertures
+for each image since otherwise different cursor/aperture pairings will
+occur.  The default is a file containing only the (q)uit command.
+.le
+
+The following parameters are used in response to particular keystrokes.
+In \fBsplot\fR they are query parameters but in \fBbplot\fR they are hidden
+parameters.
+.ls next_image = ""
+In response to 'g' (get next image) this parameter specifies the image.
+.le
+.ls new_image = ""
+In response to 'i' (write current spectrum) this parameter specifies the
+name of a new image to create or existing image to overwrite.
+.le
+.ls overwrite = yes
+Overwrite an existing output image?  If set to yes it is possible to write
+back into the input spectrum or to some other existing image.  Otherwise
+the user is queried again for a new image name.
+.le
+.ls spec2 = ""
+When adding, subtracting, multiplying, or dividing by a second spectrum
+('+', '-', '*', '/' keys in the 'f' mode) this parameter is used to get
+the name of the second spectrum.
+.le
+.ls constant = 0.
+When adding or multiplying by a constant ('p' or 'm' keys in the 'f' mode)
+the parameter is used to get the constant.
+.le
+.ls wavelength = 0.
+This parameter is used to get a dispersion coordinate value during deblending or
+when changing the dispersion coordinates with 'u'.
+.le
+.ls linelist = ""
+During deblending this parameter is used to get a list of line positions
+and widths.
+.le
+.ls wstart = 0., wend = 0., dw = 0.
+In response to 'p' (convert to a linear wavelength scale) these parameter
+specify the starting wavelength, ending wavelength, and wavelength per pixel.
+.le
+.ls boxsize = 2
+In response to 's' (smooth) this parameter specifies the box size in pixels
+to be used for the boxcar smooth
+.le
+.ih
+DESCRIPTION
+The spectra in the input image list are successively processed by the task
+\fBsplot\fR with input supplied by the cursor parameter and the output sent
+to the specified graphics device.  The range of apertures and bands
+specified by \fIapertures\fR and \fIbands\fR will be processed for each
+image.  In the \fBiids/irs\fR packages the record extension syntax is used
+with input root names and a record number list.  The hidden parameters from
+\fBsplot\fR apply to this task.
+
+The cursor file(s) consists of line(s) of the form:
+
+	[x y 1] key [command]
+
+where x and y are the position of the cursor (may be zero or absent if the
+cursor position is irrelevant) and key is one of the keystrokes understood
+by \fBsplot\fR.  If the key is ":" then the \fIcolon\fR command string follows.
+The default cursor file consists of the single line:
+
+	0 0 1 q
+
+If more than one cursor file is specified they are sequentially assigned to
+each aperture and the list is repeated as needed.  This allows the aperture
+to be manipulated in differing ways.
+.ih
+EXAMPLES
+1. To plot all of apertures of the multiaperture spectra indicated by the file
+"nite1.lst" on the default plotter and run in the background:
+
+.nf
+    cl> bplot @nite1.lst graphics=stdplot &
+.fi
+
+2. To preview the plots:
+
+.nf
+    cl> bplot @nite1.lst graphics=stdgraph
+.fi
+
+3.  To produce a histogram type plot about Balmer alpha for aperture 5 of
+each spectrum with the IRAF banner suppressed:
+
+.nf
+    cl> type curfile
+    6555 0 1 a
+    6570 0 1 a
+    q
+    cl> splot.options="auto hist nosysid"
+    cl> splot.xmin=6555
+    cl> splot.xmax=6570
+    cl> bplot @nite1.lst apertures=5 cursor=curfile
+.fi
+
+4. To produce plots with four spectra per page:
+
+.nf
+    cl> bplot @nite1.lst ... >G nite1.mc
+    cl> gkimosaic nite1.mc dev=stdplot
+.fi
+
+The first command redirects the output of the graphics to the metacode
+file nite1.mc.  The task \fBgkimosaic\fR is used to make multiple plots
+per page.  Other tasks in the \fBplot\fR package may be used to
+manipulate and redisplay the contents of the metacode file.
+
+5. To plot a list of apertures with a different cursor file for each aperture:
+
+.nf
+    cl> bplot @nite1.lst apertures=3,9,14 cursor=@nite1.cur
+.fi
+
+In this case the file "nite1.cur" is assumed to be a list of
+individual cursor file names, for instance:
+
+.nf
+	cur.03
+	cur.09
+	cur.14
+.fi
+
+that are in one to one correspondence with the range of apertures.
+.ih
+REVISIONS
+.ls BPLOT V2.10.3
+The query parameters from SPLOT were added as hidden parameters in BPLOT
+to allow use of those keys in a batch way.
+.le
+.ls BPLOT V2.10
+The \fIapertures\fR and \fIband\fR parameters been added to select
+apertures from multiple spectra and long slit images, and bands from 3D
+images.  Since the task is a script calling \fBsplot\fR, the many revisions
+to that task also apply.  The version in the \fBirs/iids\fR packages
+selects spectra using the record number extension syntax.
+.le
+.ih
+BUGS
+The cursor file command keystrokes cannot include any of the cursor
+mode (CAPITALIZED) keys.  This results from the implementation of
+the cursor mode commands as external to both BPLOT and SPLOT.
+
+When first entered, SPLOT will always display an initial plot.  BPLOT
+calls SPLOT once for each aperture in each image and thus produces
+N(apertures)*N(images) initial plots.  The plots are not optional because
+of the possible confusion a blank screen might cause an inexperienced
+user.  If the initial plots are unwanted they must be edited out of the
+graphics stream.  This can be done as follows, by directing the
+graphics output of BPLOT to a metacode file and then using GKIEXTRACT
+to remove only the desired plots from the metacode file:
+
+.nf
+    cl> bplot @nite1.lst cursor=curfile >G nite1.mc
+    cl> gkiextract nite1.mc 2x2 | gkimosaic dev=stdplot
+.fi
+
+This assumes that curfile is designed to produce only one plot in
+addition to the non-optional initial plot.  In this case there will be
+two plots per aperture per image and we extract every other plot starting
+with the second (as encoded in the range string:  "2x2").
+.ih
+SEE ALSO
+splot, specplot, slist, gkiextract, gkimosaic, implot, graph, ranges
+.endhelp
diff --git a/noao/onedspec/doc/calibrate.hlp b/noao/onedspec/doc/calibrate.hlp
new file mode 100644
index 00000000..cf68ac29
--- /dev/null
+++ b/noao/onedspec/doc/calibrate.hlp
@@ -0,0 +1,195 @@
+.help calibrate Mar93 noao.onedspec
+.ih
+NAME
+calibrate -- Apply extinction corrections and flux calibrations
+.ih
+USAGE
+calibrate input output [records]
+.ih
+PARAMETERS
+.ls input
+List of input spectra to be calibrated.  When using record format
+extensions the root names are specified, otherwise full image names
+are used.
+.le
+.ls output
+List of calibrated spectra.  If no output list is specified or if the
+output name is the same as the input name then the calibrated spectra
+replace the input spectra.  When using record format extensions the output
+names consist of root names to which the appropriate record number
+extension is added.  The record number extension will be the same as the
+input record number extension.  The output spectra are coerced to have
+real datatype pixels regardless of the  pixel type.
+.le
+.ls records (imred.irs and imred.iids only)
+The set of record number extensions to be applied to each input and output
+root name when using record number extension format.  The syntax consists
+of comma separated numbers or ranges of numbers.  A range consists of
+two numbers separated by a hyphen.  This parameter is not queried
+when record number formats are not used.
+.le
+.ls extinct = yes
+Apply extinction correction if a spectrum has not been previously
+corrected?  When applying an extinction correction, an extinction file
+is required.
+.le
+.ls flux = yes
+Apply a flux calibration if a spectrum has not been previously calibrated?
+When applying a flux calibration, sensitivity spectra are required.
+.le
+.ls extinction = <no default>
+Extinction file for the observation.  Standard extinction files
+are available in the "onedstds$" directory.
+.le
+.ls observatory = ")_.observatory"
+Observatory at which the spectra were obtained if not specified in the
+image header by the keyword OBSERVAT.  The default is a redirection to the
+package parameter of the same name.  The observatory may be one of the
+observatories in the observatory database, "observatory" to select the
+observatory defined by the environment variable "observatory" or the
+parameter \fBobservatory.observatory\fR, or "obspars" to select the current
+parameters in the \fBobservatory\fR task.  See \fBobservatory\fR for
+additional information.
+.le
+.ls ignoreaps = no
+Ignore aperture numbers and apply a single flux calibration to all
+apertures?  Normally multiaperture instruments have separate sensitivity
+functions for each aperture while long slit or Fabry-Perot data use a
+single sensitivity function where the apertures are to be ignored.  The
+sensitivity spectra are obtained by adding the aperture number as an
+extension to the sensitivity spectrum root name.  When apertures are
+ignored the specified sensitivity spectrum name is used without adding an
+extension and applied to all input apertures.
+.le
+.ls sensitivity = "sens"
+The root name for the sensitivity spectra produced by \fBsensfunc\fR.
+Normally with multiaperture instruments, \fBsensfunc\fR will produce a
+spectrum appropriate to each aperture with an aperture number extension.
+If the apertures are ignored (\fIignoreaps\fR = yes) then the sensitivity
+spectrum specified is used for all apertures and no aperture number is
+appended automatically.
+.le
+.ls fnu = no
+The default calibration is into units of flux per unit wavelength (F-lambda).
+If \fIfnu\fR = yes then the calibrated spectrum will be in units of
+flux per unit frequency (F-nu).
+.le
+.ls airmass, exptime
+If the airmass and exposure time are not in the header nor can they be
+determined from other keywords in the header then these query parameters
+are used to request the airmass and exposure time.  The values are updated
+in the input and output images.
+.le
+.ih
+DESCRIPTION
+The input spectra are corrected for extinction and calibrated to a flux
+scale using sensitivity spectra produced by the task \fBsensfunc\fR.
+One or both calibrations may be performed by selecting the appropriate
+parameter flags.  It is an error if no calibration is specified.  Normally
+the spectra should be extinction corrected if also flux calibrating.
+The image header keywords DC-FLAG (or the dispersion type field in the
+"multispec" world coordinate system), EX-FLAG, and CA-FLAG are checked for
+dispersion solution (required), previous extinction correction, and
+previous flux calibration.  If previously calibrated the spectrum is
+skipped and a new output image is not created.
+
+The input spectra are specified by a list of root names (when using record
+extension format) or full image names.  The output calibrated spectra may
+replace the input spectra if no output spectra list is specified or if the
+output name is the same as the input name.  When using record number
+extensions the output spectra will have the same extensions applied to the
+root names as those used for the input spectra.
+
+When applying an extinction correction the AIRMASS keyword is sought.
+If the keyword is not present then the airmass at the time defined
+by the other header keywords is computed using the
+latitude of the observatory and observation parameters in the image
+header.  The observatory is first determined from the image under the
+keyword OBSERVAT.  If absent the observatory specified by the task
+parameter "observatory" is used.  See \fBobservatory\fR for further
+details of the observatory database.  If the air mass cannot be
+determined an error results.  Currently a single airmass is used
+and no correction for changing extinction during the observation is
+made and adjustment to the middle of the exposure.  The task
+\fBsetairmass\fR provides a correction for the exposure time to compute
+an effective air mass.  Running this task before calibration is
+recommended.
+
+If the airmass is not in the header and cannot be computed then
+the user is queried for a value.  The value entered is then
+recorded in both the input and output image headers.  Also if
+the exposure time is not found then it is also queried and
+recorded in the image headers.
+
+The extinction correction is given by the factor
+
+		10. ** (0.4 * airmass * extinction)
+
+where the extinction is the value interpolated from the specified
+extinction file for the wavelength of each pixel.  After extinction
+correction the EX-FLAG is set to 0.
+
+When applying a flux calibration the spectra are divided by the
+aperture sensitivity which is represented by a spectrum produced by
+the task \fBsensfunc\fR.  The sensitivity spectrum is in units of:
+
+	2.5 * Log10 [counts/sec/Ang / ergs/cm2/sec/Ang].
+
+A new spectrum is created in "F-lambda" units - ergs/cm2/sec/Angstrom
+or "F-nu" units - ergs/cm2/sec/Hz.  The sensitivity must span the range of
+wavelengths in the spectrum and interpolation is used if the wavelength
+coordinates are not identical.  If some pixels in the spectrum being
+calibrated fall outside the wavelength range of the sensitivity function
+spectrum a warning message giving the number of pixels outside the
+range.  In this case the sensitivity value for the nearest wavelength
+in the sensitivity function is used.
+
+Multiaperture instruments typically have
+a separate aperture sensitivity function for each aperture.  The appropriate
+sensitivity function for each input spectrum is selected based on the
+spectrum's aperture by appending this number to the root sensitivity function
+spectrum name.  If the \fIignoreaps\fR flag is set, however, the aperture
+number relation is ignored and the single sensitivity spectrum (without
+extension) is applied.
+.ih
+EXAMPLES
+1.  To flux calibrates a series of spectra replacing the input spectra by
+the calibrated spectra:
+
+	cl> calibrate nite1 ""
+
+2.  To only extinction correct echelle spectra:
+
+	cl> calibrate ccd*.ec.imh new//ccd*.ec.imh flux-
+
+3. To flux calibrate a long slit spectrum:
+
+.nf
+	cl> dispaxis = 2
+	cl> calibrate obj.imh fcobj.imh
+.fi
+.ih
+REVISIONS
+.ls CALIBRATE V2.10.3
+This task was revised to operate on 2D and 3D spatial spectra; i.e. long
+slit and Fabry-Perot data cubes.  This task now includes the functionality
+previously found in \fBlongslit.extinction\fR and \fBlongslit.fluxcalib\fR.
+
+A query for the airmass and exposure time is now made if the information
+is not in the header and cannot be computed from other header keywords.
+.le
+.ls CALIBRATE V2.10
+This task was revised to operate on nonlinear dispersion corrected spectra
+and 3D images (the \fBapextract\fR "extras").  The aperture selection
+parameter was eliminated (since the header structure does not allow mixing
+calibrated and uncalibrated spectra) and the latitude parameter was
+replaced by the observatory parameter.  The observatory mechanism insures
+that if the observatory latitude is needed for computing an airmass and the
+observatory is specified in the image header the correct calibration will
+be applied.  The record format syntax is available in the \fBirs/iids\fR
+packages.  The output spectra are coerced to have real pixel datatype.
+.le
+.ih
+SEE ALSO
+setairmass, standard, sensfunc, observatory, continuum
+.endhelp
diff --git a/noao/onedspec/doc/continuum.hlp b/noao/onedspec/doc/continuum.hlp
new file mode 100644
index 00000000..6bb4e05e
--- /dev/null
+++ b/noao/onedspec/doc/continuum.hlp
@@ -0,0 +1,263 @@
+.help continuum Mar92 noao.onedspec
+.ih
+NAME
+continuum -- Continuum normalize spectra
+.ih
+USAGE	
+continuum input output
+.ih
+PARAMETERS
+.ls input
+Input spectra to be continuum normalized.  These may be any combination
+of echelle, multiaperture, one dimensional, long slit, and spectral
+cube images.
+.le
+.ls output
+Output continuum normalized spectra.  The number of output spectra must
+match the number of input spectra.  \fBOutput\fR may be omitted if
+\fBlistonly\fR is yes.
+.le
+.ls lines = "*", bands = "1"
+A range specifications for the image lines and bands to be fit.  Unspecified
+lines and bands will be copied from the original.  If the value is "*", all of
+the currently unprocessed lines or bands will be fit.  A range consists of
+a first line number and a last line number separated by a hyphen.  A
+single line number may also be a range and multiple ranges may be
+separated by commas.
+.le
+.ls type = "ratio"
+Type of output spectra.  The choices are "fit" for the fitted function,
+"ratio" for the ratio of the input spectra to the fit, "difference" for
+the difference between the input spectra and the fit, and "data" for
+the data minus any rejected points replaced by the fit.
+.le
+.ls replace = no
+Replace rejected points by the fit in the difference, ratio, and
+data output types?
+.le
+.ls wavescale = yes
+Wavelength scale the X axis of the plot?  This option requires that the
+spectra be wavelength calibrated.  If \fBwavescale\fR is no, the plots
+will be in "channel" (pixel) space.
+.le
+.ls logscale = no
+Take the log (base 10) of both axes?  This can be used when \fBlistonly\fR
+is yes to measure the exponent of the slope of the continuum.
+.le
+.ls override = no
+Override previously normalized spectra?  If \fBoverride\fR is yes and
+\fBinteractive\fR is yes, the user will be prompted before each order is
+refit.  If \fBoverride\fR is no, previously fit spectra are silently
+skipped.
+.le
+.ls listonly = no
+Don't modify any images?  If \fBlistonly\fR is yes, the \fBoutput\fR
+image list may be skipped.
+.le
+.ls logfiles = "logfile"
+List of log files to which to write the power series coefficients.  If
+\fBlogfiles\fR = NULL (""), the coefficients will not be calculated.
+.le
+.ls interactive = yes
+Perform the fit interactively using the icfit commands?  This will allow
+the parameters for each spectrum to be adjusted independently.  A separate
+set of the fit parameters (below) will be used for each spectrum and any
+interactive changes to the parameters for a specific spectrum will be
+remembered when that spectrum is fit in the next image.
+.le
+.ls sample = "*"
+The ranges of X values to be used in the continuum fits.  The units will vary
+depending on the setting of the \fBwavescale\fR and \fBlogscale\fR
+parameters.  The default units are in wavelength if the spectra have
+been dispersion corrected.
+.le
+.ls naverage = 1
+Number of sample points to combined to create a fitting point.
+A positive value specifies an average and a negative value specifies
+a median.
+.le
+.ls function = spline3
+Function to be fit to the spectra.  The functions are
+"legendre" (legendre polynomial), "chebyshev" (chebyshev polynomial),
+"spline1" (linear spline), and "spline3" (cubic spline).  The functions
+may be abbreviated.  The power series coefficients can only be
+calculated if \fBfunction\fR is "legendre" or "chebyshev".
+.le
+.ls order = 1
+The order of the polynomials or the number of spline pieces.
+.le
+.ls low_reject = 2., high_reject = 0.
+Rejection limits below and above the fit in units of the residual sigma.
+.le
+.ls niterate = 10
+Number of rejection iterations.
+.le
+.ls grow = 1.
+When a pixel is rejected, pixels within this distance of the rejected pixel
+are also rejected.
+.le
+.ls markrej = yes
+Mark rejected points?  If there are many rejected points it might be
+desired to not mark rejected points.
+.le
+.ls graphics = "stdgraph"
+Graphics output device for interactive graphics.
+.le
+.ls cursor = ""
+Graphics cursor input.
+.le
+.ih
+DESCRIPTION
+A one dimensional function is fit to the continuum of spectra in a list of
+echelle, multispec, or onedspec format images and then divided into the
+spectrum to produce continuum normalized spectra.  The first two formats
+will normalize the spectra or orders (i.e. the lines) in each image.  In
+this description the term "spectrum" will refer to a line (in whatever
+band) of an image while "image" will refer to all spectra in an image.  The
+parameters of the fit may vary from spectrum to spectrum within images and
+between images.  The fitted function may be a legendre polynomial,
+chebyshev polynomial, linear spline, or cubic spline of a given order or
+number of spline pieces.  The output image is of pixel type real.
+
+The line/band numbers (for two/three dimensional images) are written to a
+list of previously processed lines in the header keywords \fISFIT\fR and
+\fISFITB\fR of the output image.  A subsequent invocation of SFIT will only
+process those requested spectra that are not in this list.  This ensures
+that even if the output image is the same as the input image that no
+spectra will be processed twice and permits an easy exit from the task in
+the midst of processing many spectra without losing any work or requiring
+detailed notes.
+
+The points to be fit in each spectrum are determined by
+selecting a sample of X values specified by the parameter \fIsample\fR
+and taking either the average or median of the number of points
+specified by the parameter \fInaverage\fR.  The type of averaging is
+selected by the sign of the parameter with positive values indicating
+averaging, and the number of points is selected by the absolute value
+of the parameter.  The sample units will vary depending on the settings
+of the \fBwavescale\fR and the \fBlogscale\fR parameters.  Note that a
+sample that is specified in wavelength units may be entirely outside
+the domain of the data (in pixels) if some of the spectra are not
+dispersion corrected.  The syntax of the sample specification is a comma
+separated, colon delimited list similar to the image section notation.
+For example, the \fBsample\fR, "6550:6555,6570:6575" might be used to
+fit the continuum near H-alpha.
+
+If \fIlow_reject\fR and/or \fIhigh_reject\fR are greater than zero the
+sigma of the residuals between the fitted points and the fitted
+function is computed and those points whose residuals are less than
+\fI-low_reject\fR * sigma and greater than \fIhigh_reject\fR * sigma
+are excluded from the fit.  Points within a distance of \fIgrow\fR
+pixels of a rejected pixel are also excluded from the fit.  The
+function is then refit without the rejected points.  This rejection
+procedure may be iterated a number of times given by the parameter
+\fIniterate\fR.  This is how the continuum is determined.
+
+If \fIreplace\fR is set then any rejected points from the fitting
+are  replaced by the fit in the data before outputing the difference,
+ratio, or data.  For example with replacing the difference will
+be zero at the rejected points and the data output will be cleaned
+of deviant points.
+
+A range specification is used to select the \fIlines\fR and \fIbands\fR to be
+fit.  These parameters may either be specified with the same syntax as the
+\fBsample\fR parameter, or with the "hyphen" syntax used elsewhere in
+IRAF.  Note that a NULL range for \fBlines/bands\fR expands to \fBno\fR
+lines, not to all lines.  An asterisk (*) should be used to represent a
+range of all of the image lines/bands.  The fitting parameters (\fIsample,
+naverage, function, order, low_reject, high_reject, niterate, grow\fR)
+may be adjusted interactively if the parameter \fIinteractive\fR is
+yes.  The fitting is performed with the \fBicfit\fR package.  The
+cursor mode commands for this package are described in a separate help
+entry under "icfit".  Separate copies of the fitting parameters are
+maintained for each line so that interactive changes to the parameter
+defaults will be remembered from image to image.
+.ih
+PROMPTS
+If several images or lines/bands are specified, the user is asked whether
+to perform an interactive fit for each spectrum.  The response
+may be \fByes, no, skip, YES, NO\fR or \fBSKIP\fR.  The meaning of each
+response is:
+
+.nf
+	yes   - Fit the next spectrum interactively.
+	no    - Fit the next spectrum non-interactively.
+	skip  - Skip the next spectrum in this image.
+
+	YES   - Interactively fit all of the spectra of
+		all of the images with no further prompts.
+	NO   	Non-interactively fit all chosen spectra of all images.
+	SKIP  - This will produce a second prompt, "Skip what?",
+		with the choices:
+
+		spectrum - skip this spectrum in all images
+		image    - skip the rest of the current image
+		all      - \fBexit\fR the program
+		           This will \fBunlearn\fR the fit parameters
+			   for all spectra!
+		cancel  - return to the main prompt
+.fi
+.ih
+EXAMPLES
+1.  To normalize all orders of the echelle spectrum for hd221170
+
+	cl> continuum hd221170.ec nhd221170.ec type=ratio
+
+Each order of the spectrum is graphed and the interactive options for
+setting and fitting the continuum are available.  The important
+parameters are low_rejection (for an absorption spectrum), the function
+type, and the order of the function; these fit parameters are
+originally set to the defaults in the \fBcontinuum\fR parameter file.  A
+'?' will display a menu of cursor key options.  Exiting with 'q' will
+update the output normalized order for the current image and proceed to
+the next order or image.
+
+The parameters of the fit for each order are initialized to the current
+values the first time that the order is fit.  In subsequent images, the
+parameters for a order are set to the values from the previous image.
+The first time an order is fit, the sample region is reset to the
+entire order.  Deleted points are ALWAYS forgotten from order to order
+and image to image.
+
+2.  To do several images at the same time
+
+	cl> continuum spec*.imh c//spec*.imh
+
+Note how the image template concatenation operator is used to construct
+the output list of spectra.  Alternatively:
+
+	cl> continuum @inlist @outlist
+
+where the two list files could have been created with the sections
+command or by editing.
+
+3.  To measure the power law slope of the continuum (fluxed data)
+
+	cl> continuum uv.* type=ratio logscale+ listonly+ fun=leg order=2
+.ih
+REVISIONS
+.ls CONTINUUM V2.10.4
+The task was expanded to include fitting specified bands in 3D multispec
+spectra.
+
+The task was expanded to include long slit and spectral cube data.
+.le
+.ls CONTINUUM V2.10
+This task was changed from a script based on \fBimages.fit1d\fR to a
+task based on \fBsfit\fR.  This provides for individual independent
+continuum fitting in multiple spectra images and for additional
+flexibility and record keeping.  The parameters have been largely
+changed.
+.le
+.ih
+BUGS
+The errors are not listed for the power series coefficients.
+
+Spectra that are updated when \fBlogscale\fR is yes are written with a
+linear wavelength scale, but with a log normalized data value.
+
+Selection by aperture number is not supported.
+.ih
+SEE ALSO
+sfit, fit1d, icfit, ranges
+.endhelp
diff --git a/noao/onedspec/doc/deredden.hlp b/noao/onedspec/doc/deredden.hlp
new file mode 100644
index 00000000..862c441c
--- /dev/null
+++ b/noao/onedspec/doc/deredden.hlp
@@ -0,0 +1,201 @@
+.help deredden Feb94 noao.onedspec
+.ih
+NAME
+deredden -- Apply interstellar reddening correction
+.ih
+USAGE
+deredden input output [records] value
+.ih
+PARAMETERS
+.ls input
+List of input spectra to be dereddened.  When using record
+format extensions the root names are specified, otherwise full
+image names are used.
+.le
+.ls output
+List of derreddened spectra.  If no output list is specified then
+the input spectra are modified.  Also the output name may be
+the same as the input name to replace the input spectra by the
+calibrated spectra.  When using record format extensions the
+output names consist of root names to which the appropriate
+record number extension is added.  The record number extension
+will be the same as the input record number extension.
+.le
+.ls records (imred.irs and imred.iids only)
+The set of record number extensions to be applied to each input
+and output root name when using record number extension 
+format.  The syntax consists of comma separated numbers or
+ranges of numbers.  A range consists of two numbers separated
+by a hyphen.  This parameter is not queried when record number
+formats are not used.
+.le
+.ls value
+Extinction parameter value as selected by the type parameter.
+This value may be a visual extinction, A(V), the color excess between
+B and V, E(B-V), or the logarithmic H beta extinction.
+These quantities are discussed further below.
+.le
+.ls R = 3.1
+The ratio of extinction at V, A(V), to color excess between B and V, E(B-V).
+.le
+.ls type = "E(B-V)"
+The type of extinction parameter used.  The values may be:
+.ls A(V)
+The absolute extinction at the V band at 5550 Angstroms.
+.le       
+.ls E(B-V)
+The color excess between the B and V bands.
+.le
+.ls c     
+The logarithmic H beta extinction.
+.le
+.le
+.ls apertures = ""
+List of apertures to be selected from input one dimensional spectra
+to be calibrated.  If no list is specified then all apertures are
+corrected.  The syntax is the same as the record number
+extensions.  This parameter is ignored for N-dimensional spatial
+spectra such as calibrated long slit and Fabry-Perot data.
+.le
+.ls override = no, uncorrect = yes
+If a spectrum has been previously corrected it will contain the header
+parameter DEREDDEN.  If this parameter is present and the override
+parameter is no then a warning will be issued and no further correction
+will be applied.  The override parameter permits overriding this check.  If
+overriding a previous correction the \fIuncorrect\fR parameter determines
+whether the spectra are first uncorrected to the original values before
+applying the new correction.  If \fIuncorrect\fR is yes then the image
+header DEREDDEN parameter will refer to a correction from the original data
+while if it is no then the new correction is differential and the keyword
+will only reflect the last correction.  When correcting individual spectra
+separately in a multispectra image with different extinction parameters the
+uncorrect parameter should be no.
+.le
+.ih
+DESCRIPTION
+The input spectra are corrected for interstellar extinction, or
+reddening, using the empirical selective extinction function of
+Cardelli, Clayton, and Mathis, \fBApJ 345:245\fR, 1989, (CCM).
+The function is defined over the range 0.3-10 inverse microns
+or 100-3333 nanometers.  If the input data extend outside this
+range an error message will be produced.
+
+The extinction function requires two parameters, the absolute extinction at
+5550A, A(V), and the ratio, R(V), of this extinction to the color excess
+between 4350A and 5550A, E(B-V).
+
+One of the input task parameters is R(V).  If it is not known one
+may use the default value of 3.1 typical of the average 
+interstellar extinction.  The second input parameter is chosen by
+the parameter \fItype\fR which may take the values "A(V)", "E(B-V)", or
+"c".  The value of the parameter is specified by the parameter
+\fIvalue\fR.
+
+If A(V) is used then the CCM function can be directly evaluated.  If
+E(B-V) is used then A(V) is derived by:
+
+.nf
+(1)     A(V) = R(V) * E(B-V)
+.fi
+
+For planetary nebula studies the logarithmic extinction at H beta,
+denoted as c, is often determined instead of E(B-V).  If this type
+of input is chosen then A(V) is derived by:
+
+.nf
+(2)     A(V) = R(V) * c * (0.61 + 0.024 * c).
+.fi
+
+This relation is based on the relation betwen E(B-V) and c computed
+by Kaler and Lutz, \fBPASP 97:700\fR, 1985 to include corrections between
+the monochromatic parameter c and the broadband parameter E(B-V).
+In particular the function is a least squares fit to the values of
+c and E(B-V) in Table III of the form:
+
+.nf
+(3)     E(B-V) = c * (A + B * c)
+.fi
+
+The input spectra are specified by a list of root names (when using record
+extension format) or full image names.  They are required to be dispersion
+corrected (DC-FLAG >= 0) and not previously corrected (DEREDDEN absent).
+Spectra not satisfying these requirements are skipped with a warning.  The
+DEREDDEN flag may be overridden with the \fIoverride\fR parameter.  This
+may be done if different extinction parameters are required for different
+spectra in the same multiple spectrum image or if a new correction is
+to be applied.  The \fIuncorrect\fR parameter determines whether the
+previous correction is removed so that the final correction is relative
+to the original data or if the new correction is differential on the
+previous correction.  Note that if applying separate corrections to
+different spectra in a single multispectral image then override should
+be yes and uncorrect should be no.
+
+A subset of apertures to be corrected may be selected from one dimensional
+spectra with the \fIapertures\fR parameter.  Long slit or other higher
+dimensional spatially sampled spectra are treated as a unit.  The output
+calibrated spectra may replace the input spectra if no output spectra list
+is specified or if the output name is the same as the input name.  When
+using record number extensions the output spectra will have the same
+extensions applied to the root names as those used for the input spectra.
+
+Note that by specifying a negative extinction parameter this task may
+be used to add interstellar extinction.
+.ih
+EXAMPLES
+1.  To deredden a spectrum with an extinction of 1.2 magnitudes at V:
+    
+.nf
+	cl> deredden obj1.ms drobj1.ms 1.2 type=A
+.fi
+
+2.  To deredden a spectrum in place with a color excess of 0.65 and
+and R(V) value of 4.5:
+
+.nf
+	cl> deredden obj2.ms obj2.ms R=4.5
+	E(B-V): .65
+.fi
+
+3.  To deredden a series of IRS planetary nebula spectra using the
+H beta extinction in the irs package:
+
+.nf
+	cl> deredden pn12 drpn12 1-5,12-14 type=c
+	c: 1.05
+.fi
+
+4.  To redden a spectrum:
+
+.nf
+	cl> deredden artspec artspec -1.2 type=A
+.fi
+
+5. To deredden a long slit or Fabry-Perot spectrum either DISPAXIS
+must be in the image header or be specified in the package parameters.
+The summing parameters are ignored.
+    
+.nf
+	cl> deredden obj1 drobj1 1.2 type=A
+.fi
+.ih
+REVISIONS
+.ls DEREDDEN V2.10.3
+Extended to operate on two and three dimensional spatial spectra such as
+calibrated long slit and Fabry-Perot data.
+
+An option was added to allow a previous correction to be undone in order
+to keep the DEREDDEN information accurate relative to the original
+data.
+.le
+.ls DEREDDEN V2.10
+This task is new.
+.le
+.ih
+NOTES
+Since there can be only one deredding flag in multispectral images
+one needs to override the flag if different spectra require different
+corrections and then only the last correction will be recorded.
+.ih
+SEE ALSO
+calibrate
+.endhelp
diff --git a/noao/onedspec/doc/dispcor.hlp b/noao/onedspec/doc/dispcor.hlp
new file mode 100644
index 00000000..9e916e70
--- /dev/null
+++ b/noao/onedspec/doc/dispcor.hlp
@@ -0,0 +1,497 @@
+.help dispcor Oct92 noao.onedspec
+.ih
+NAME
+dispcor -- Dispersion correct and resample spectra
+.ih
+USAGE
+dispcor input output [records]
+.ih
+PARAMETERS
+.ls input
+List of input spectra or root names to be dispersion corrected.  These may
+be echelle or non-echelle spectra, the task will determine which from the
+database dispersion functions.  When using the record number extension
+format, record number extensions will be appended to each root name in the
+list.
+.le
+.ls output
+List of dispersion corrected output spectra or root names.  When using the
+record number extension format, record number extensions will be appended
+to each root name in the list.  The output extension will be the same as
+the input extension.  If "no" output list is specified then the output
+spectrum will replace the input spectrum after dispersion correction.
+.le
+.ls records (imred.irs and imred.iids only)
+List of records or ranges of records to be appended to the input and output
+root names when using record number extension format.  The syntax of this
+list is comma separated record numbers or ranges of record numbers.  A
+range consists of two numbers separated by a hyphen.  A null list may be
+used if no record number extensions are desired.  This is a positional
+query parameter only if the record format is specified.
+.le
+.ls linearize = yes
+Interpolate the spectra to a linear dispersion sampling?  If yes, the
+spectra will be interpolated to a linear or log linear sampling using
+the linear dispersion parameters specified by other parameters.  If
+no, the nonlinear dispersion function(s) from the dispersion function
+database are assigned to the input image world coordinate system
+and the spectral data are not interpolated.
+.le
+.ls database = "database"
+Database containing dispersion solutions created by \fBidentify\fR or
+\fBecidentify\fR.  If the spectra have been previous dispersion corrected
+this parameter is ignored unless a new reference spectra are defined.
+.le
+.ls table = ""
+Wavelength coordinate table or reference image.  Elements in this optional
+table or reference image override the wavelength coordinates given below
+for specified apertures.  See the DISCUSSION for additional information.
+.le
+.ls w1 = INDEF, w2 = INDEF, dw = INDEF, nw = INDEF
+The starting wavelength, ending wavelength, wavelength interval per pixel,
+and the number of pixels in the output spectra.  Any combination of these
+parameters may be used to restrict the wavelength coordinates of the output
+spectra.  If two or more have the value INDEF then suitable defaults based
+on the number of input pixels and the wavelength range of the reference
+dispersion solutions are used.  These defaults may either come from all
+spectra, all spectra of the same aperture, or individually for each
+spectrum depending on the values of the \fIglobal\fR and \fIsamedisp\fR
+parameters.  Note that these parameters are specified in linear units even
+if a logarithmic wavelength scale is selected.  The conversion between
+linear and logarithmic intervals between pixels is given below.  These
+values may be overridden for specified apertures by a wavelength table or
+reference image.  Otherwise these values apply to all apertures.
+.le
+.ls log = no
+Transform to linear logarithmic wavelength coordinates?  Linear logarithmic
+wavelength coordinates have wavelength intervals which are constant
+in the logarithm (base 10) of the wavelength.  Note that if conserving flux
+this will change the flux units to flux per log lambda interval.
+Note that if the input spectra are in log sampling then \fIlog\fR=no will
+resample back to linear sampling and \fIlog\fR=yes will resample keeping
+the output spectra in log sampling.
+.le
+.ls flux = yes
+Conserve the total flux during interpolation rather than the flux density?
+If "no", the output spectrum is average of the input spectrum across each
+output wavelength coordinate.  This conserves flux density.  If "yes" the
+input spectrum is integrated over the extent of each output pixel.  This
+conserves the total flux.  Note that in this case units of the flux will
+change; for example rebinning to logarithmic wavelengths will produce flux
+per log lambda.  For flux calibrated data you most likely would not want to
+conserve flux.
+.le
+.ls blank = 0.
+Output value corresponding to points outside the range of the input
+data.  In other words, the out of bounds value.  This only has an
+effect when linearizing and the output spectral coordinates extend
+beyond the input spectral range.
+.le
+.ls samedisp = no
+Use the same dispersion parameters for all apertures?  If yes then all
+apertures in a single image will have the same dispersion parameters.
+If the \fIglobal\fR parameter is all selected then all spectra in all
+images will have the same dispersion paramters.  This parameter
+would not normally be used with echelle spectra where each order
+has a different wavelength coverage.
+.le
+.ls global = no
+Apply global wavelength defaults?  Defaults for the INDEF wavelength
+coordinate parameters are determined if two or less of the wavelength
+parameters are specified.  The defaults are based on the number of
+pixels and the wavelengths of the first and last pixel as given by the
+dispersion solution.  If this parameter is "no" this is done
+independently for each input spectrum.  If this parameter is "yes"
+then the maximum number of pixels and the minimum and maximum
+wavelengths of all the input spectra or those of the same aperture are
+used to provide defaults for the spectra.  The parameter
+\fIsamedisp\fR determines whether the global coordinates are over all
+spectra or only those with the same aperture number.  The global option
+is used to have all the dispersion corrected spectra have the same
+wavelength coordinates without actually specifying the wavelength
+parameters.
+.le
+.ls ignoreaps = no
+If a reference dispersion solution is not found for an aperture
+use the first reference dispersion solution and ignore the aperture
+number?  If not ignoring the apertures all spectra must have a matching
+aperture for the dispersion solution and the task aborts if this is
+not the case.  Ignoring the apertures avoids this abort and instead
+the first dispersion solution is used.  Note this parameter does not
+mean ignore matches between reference and spectrum aperture numbers
+but only ignore the aperture number if no matching reference is
+found.
+
+Also if a reference table or image is given and \fIignoreaps\fR=yes
+then the default dispersion parameters for any aperture not defined
+by the table or image will be that of the first defined aperture.
+This can still be overridden by giving explicit values for
+\fIw1, w2, dw\fR and \fInw\fR.
+.le
+.ls confirm = no
+Confirm the wavelength parameters for each spectrum?  If \fIyes\fR
+the wavelength parameters will be printed and the user will be asked
+whether to accept them.  If the parameters are not acceptable the
+user will be queried for new values.  The confirmation and parameter
+changes are repeated until an acceptable set of parameters is obtained.
+When the \fIglobal\fR parameter is \fIyes\fR changes to the wavelength
+parameters will remain in effect until changed again.
+.le
+.ls listonly = no
+List the dispersion coordinates only?  If set then the dispersion coordinates
+are listed but the spectra are not dispersion corrected.  This may be used
+to determine what the default wavelengths would be based on the dispersion
+solutions.
+.le
+.ls verbose = yes
+Print the dispersion function and coordinate assignments?
+.le
+.ls logfile = ""
+Log file for recording the dispersion correction operations.  If no file
+name is given then no log information is recorded.
+.le
+.ih
+DESCRIPTION
+The dispersion coordinate systems of the input spectra are set or changed
+in the output spectra.  The output spectra may be the same as the input
+spectra if no output spectra are specified or the output name is the
+same as the input name.  The input and output spectra are specified
+by image templates or lists.  In the \fBirs/iids\fR packages the
+input and output spectra are specified as root names and the record
+numbers are specified by the \fIrecord\fR parameter.  The records are
+given as a set of comma separate single numbers or ranges of hyphen
+separated numbers.  If no records are specified then the input and output
+images are assumed to be full names.
+
+The dispersion coordinate system is defined either in the image header or
+by dispersion functions in the specified database.  To use reference
+spectra dispersion functions they must first be assigned to the image with
+\fBidentify (reidentify)\fR, \fBecidentify (ecreidentify)\fR,
+\fBrefspectra\fR, or \fBhedit\fR.  These tasks define the image header
+keywords REFSPEC1, REFSPEC2, REFSHFT1, and REFSHFT2.  The test which
+determines whether to use the current dispersion coordinate system or
+reference spectra dispersion solutions is the presence of the REFSPEC1
+keyword.  Since it is an error to apply a dispersion function to data which
+have already been dispersion corrected the any dispersion function keywords
+are deleted after use and a record of them entered in sequential image
+header keywords beginning with DCLOG.
+
+Dispersion functions are specified by one or both of the reference spectrum
+image header keywords REFSPEC1 and REFSPEC2 containing the name of
+calibration spectra with dispersion function solutions (either echelle
+dispersion functions from \fBecidentify\fR or non-echelle dispersion
+functions from \fBidentify\fR) in the database.  There must be a dispersion
+function for each aperture in the input spectrum unless the \fIignoreaps\fR
+flag is set.  If the flag is not set the task will abort if a matching
+aperture is not found while if it is set spectra without a matching
+aperture in the reference dispersion solutions will use the first
+dispersion solution.  Note that aperture number matching is done in both
+cases and the \fIignoreaps\fR parameter only applies to non-matching
+spectra.  The common situation for using the \fIignoreaps\fR option is when
+there is a single reference dispersion solution which is to be applied to a
+number of spectra with different aperture numbers; hence effectively
+ignoring the reference spectrum aperture number.
+
+If two reference spectra are specified the names may be followed by a
+weighting factor (assumed to be 1 if missing).  The wavelength of a pixel
+is then the weighted averge of the wavelengths of the two dispersion
+functions.  The task \fBrefspectra\fR provides a number of ways to assign
+reference spectra.  Note, however, that these assignments may be made
+directly using the task \fBhedit\fR or with some other task or script if
+none of the methods are suitable.  Also note that \fBidentify\fR and
+\fBreidentify\fR add the REFSPEC1 keyword refering to the image itself
+when a database entry is written.
+
+In addition to the one or two reference dispersion functions for each input
+aperture there may also be image header keywords REFSHFT1 and REFSHFT2
+specifying reference spectra whose dispersion function zero point shifts
+(the "shift" parameter in the database files) are to be applied to the
+reference dispersion functions.  The shifts from REFSHFT1 will be applied
+to the dispersion functions from REFSPEC1 and similarly for the second
+dispersion functions.  The reference shifts need not be present for every
+aperture in a multispectrum image.  By default the mean shift from all the
+reference apertures having a zero point shift is applied to all the
+reference dispersion functions.  If the REFSHFT keyword has the modifier
+word "nearest" following the spectrum name then the shift from the nearest
+aperture in spatial position (from the aperture extraction limits in the
+original 2D spectrum as recorded in the 6th and 7th fields of the APNUM
+keywords) is used for a particular input aperture.  If the modifier word is
+"interp" then the nearest two apertures are used to interpolate a zero
+point shift spatially.
+
+The purpose of the reference shift keywords is to apply a wavelength zero
+point correction to the reference dispersion functions determined from
+separate arc calibration observations using a few apertures taken at the
+same time as object observations.  For example, consider multifiber
+observations in which one or more fibers are assigned to arc lamps at the
+same time the other fibers are used to observe various objects.  The basic
+dispersion reference, the REFSPEC keywords, will come from arc observations
+taken through all the fibers.  The arc fibers used during an object
+observation are then calibrated against their corresponding fibers in the
+arc calibration observations to determine a zero point shift.  The REFSHFT
+keywords will contain the name of the object spectrum itself and the shifts
+from the simultaneous arc fibers will be interpolated spatially to the
+nonarc object fibers and applied to the dispersion functions from the arc
+calibrations for those fibers.
+
+The reference shift keywords are currently added with \fBhedit\fR and zero
+point shifts computed with \fBidentify/reidentify\fR.  The complexities of
+this have been hidden in the multifiber \fBimred\fR instrument reduction
+packages.  The reference shift correction feature was added primarily for
+use in those reduction packages.
+
+If the \fIlinearize\fR parameter is no the dispersion functions, weights,
+and shifts are transferred from the database to the world coordinate system
+keywords in the image header.  Except for printing processing information
+that is all that is done to the spectra.
+
+If the \fIlinearize\fR parameter is yes the spectra are interpolated to a
+linear wavelength scale and the dispersion coordinate system in the header
+is set apprpriately.  A linear wavelength coordinate system is defined by a
+starting wavelength, an ending wavelength, a wavelength interval per pixel,
+and the number of pixels.  These four parameters actually overspecify the
+coordinate system and only three of these values are needed to define it.
+The output coordinate system is specified by giving a set or subset of
+these parameters using the parameters \fIw1\fR, \fIw2\fR, \fIdw\fR, and
+\fInw\fR.
+
+When the \fIlog\fR option is used these parameters are still specified and
+computed in non-log units but the effective interval per pixel is
+
+.nf
+	dw_log = (log10(w2) - log10(w1)) / (nw - 1)
+	dw_log = (log10(w1+dw*(nw-1)) - log10(w1)) / (nw - 1)
+.fi
+
+In other words, the logarithmic interval divides the starting and ending
+wavelength into the required number of pixels in log step.  To avoid
+confusion in this case it is best to specify the starting and ending
+wavelengths (in non-log units) and the number of pixels.
+
+Note that if \fIlog\fR=yes the input spectra in either linear
+or log sampling will be resampled to produces an output spectrum in
+log sampling.  Similarly, if \fIlog\fR=no the input spectra will
+be resampled to linear sampling.  This means that log sampled input
+spectra will be resampled to linear sampling.
+
+Default values for any parameters which are not specified, by using the
+value INDEF, are supplied based on the wavelengths of the first and last
+pixel as given by the dispersion function and the number of pixels in the
+input image.  The defaults may either be determined separately for each
+spectrum (\fIglobal\fR = \fIno\fR), from all spectra with the same aperture
+(\fIglobal\fR = \fIyes\fR and \fIsamedisp\fR = \fIno\fR), or from all the
+spectra (\fIglobal\fR = \fIyes\fR and \fIsamedisp\fR = \fIyes\fR).  As
+indicated, the parameter \fIsamedisp\fR determines whether defaults are
+determined independently for each aperture or set the same for all
+apertures.
+
+Another way to specify the wavelengths when there are many apertures is to
+use a wavelength table or reference image.  If an spectrum image name is
+specified with the \fItable\fR parameter then the dispersion parameters for
+each apertures are set to be the same as the reference spectrum.
+Alternatively, a text file table consisting of lines containing an aperture
+number, the starting wavelength, the ending wavelength, the wavelength
+interval per pixel, and the number of output pixels may be specified.  Any
+of these values may be specified as INDEF (though usually the aperture
+number is not).  One way to view the wavelength table/reference spectrum is
+that an entry in the wavelength table/reference spectrum overrides the
+values of the parameters \fIw1\fR, \fIw2\fR, \fIdw\fR, and \fInw\fR, which
+normally apply to all apertures, for the specified aperture.  The
+wavelength table is used to specify explicit independent values for
+apertures.  The global mechanism can supply independent values for the
+INDEF parameters when the \fIsamedisp\fR parameter is no.
+
+If one wishes to verify and possibly change the defaults assigned,
+either globally or individually, the \fIconfirm\fR flag may be set.  The
+user is asked whether to accept these values.  By responding with no the
+user is given the chance to change each parameter value.  Then the new
+parameters are printed and the user is again asked to confirm the
+parameters.  This is repeated until the desired parameters are set.  When
+the defaults are not global the changed parameters will not be used for the
+next spectrum.  When the global option is used any changes made are
+retained (either for all apertures or independently for each aperture)
+until changed again.
+
+When adjusting the wavelengths the user should specify which parameter is
+free to change by entering INDEF.  If none of the parameters are specified
+as INDEF then those values which were not changed, i.e. by accepting the
+current value, are the first to be changed.
+
+Once the wavelength scale has been defined the input spectrum is
+interpolated for each output pixel.  Output wavelengths outside the range
+of the input spectrum are set to the value given by the \fIblank\fR parameter
+value.  The default interpolation function
+is a 5th order polynomial.  The choice of interpolation type is made
+with the package parameter "interp".  It may be set to "nearest",
+"linear", "spline3", "poly5", or "sinc".  Remember that this
+applies to all tasks which might need to interpolate spectra in the
+\fBonedspec\fR and associated packages.  For a discussion of interpolation
+types see \fBonedspec\fR.
+
+When it is desired to conserve total flux, particularly when the dispersion is
+significantly reduced, the parameter \fIflux\fR is set to yes and the
+output pixel value is obtained by integrating the interpolation function
+across the wavelength limits of the output pixel.  If it is set to no
+then the flux density is conserved by averaging across the output pixel
+limits.
+
+The input spectrum name, reference spectra, and the wavelength parameters
+will be printed on the standard output if the \fIverbose\fR parameter is
+set and printed to a log file if one is specified with the \fIlogfile\fR
+parameter.  If one wishes to only check what wavelengths will be determined
+for the defaults without actually dispersion correcting the spectra the
+\fIlistonly\fR flag may be set.
+
+Other tasks which may be used to change the dispersion coordinate system
+are \fBscopy\fR, \fBspecshift\fR, and \fBsapertures\fR.
+.ih
+EXAMPLES
+In the examples when the task is used in the IRS and IIDS packages,
+shown with the "ir>" prompt the spectra have a record number extension
+image name format and the records parameter must be specified.  In
+the other case shown with the "on>" prompt the records parameter is
+not used.
+
+1.  Dispersion correct spectra so that they have the same number of pixels
+and the wavelengths limits are set by the reference spectra.
+
+.nf
+ir> dispcor spec dcspec 9,10,447-448
+dcspec.0009: ap = 0, w1 = 5078.84, w2 = 6550.54, dw = 1.797, nw = 820
+dcspec.0010: ap = 1, w1 = 5078.71, w2 = 6552.81, dw = 1.800, nw = 820
+dcspec.0447: ap = 0, w1 = 5082.57, w2 = 6551.45, dw = 1.794, nw = 820
+dcspec.0448: ap = 1, w1 = 5082.03, w2 = 6553.66, dw = 1.797, nw = 820
+
+on> dispcor allspec.ms dcallspec.ms
+dcallspec.ms: ap = 1, w1 = 5078.84, w2 = 6550.54, dw = 1.797, nw = 820
+dcallspec.ms: ap = 2, w1 = 5078.71, w2 = 6552.81, dw = 1.800, nw = 820
+dcallspec.ms: ap = 3, w1 = 5082.57, w2 = 6551.45, dw = 1.794, nw = 820
+dcallspec.ms: ap = 4, w1 = 5082.03, w2 = 6553.66, dw = 1.797, nw = 820
+.fi
+
+2.  Confirm and change assignments.
+
+.nf
+on> dispcor spec* %spec%new%* confirm+
+new009: ap = 0, w1 = 5078.84, w2 = 6550.54, dw = 1.797, nw = 820
+  Change wavelength coordinate assignments? (yes):
+  Starting wavelength (5078.8421234): 5070
+  Ending wavelength (6550.535123):
+  Wavelength interval per pixel (1.79693812):
+  Number of output pixels (820): INDEF
+new009: ap = 0, w1 = 5070., w2 = 6550.53, dw = 1.795, nw = 826
+  Change wavelength coordinate assignments? (yes): no
+new010: ap = 1, w1 = 5078.71, w2 = 6552.81, dw = 1.800, nw = 820
+  Change wavelength coordinate assignments? (no): yes
+  Starting wavelength (5078.7071234): 5100
+  Ending wavelength (6550.805123): 6500
+  Wavelength interval per pixel (1.79987512): INDEF
+  Number of output pixels (820): INDEF
+new010: ap = 1, w1 = 5100., w2 = 6500., dw = 1.797, nw = 780
+  Change wavelength coordinate assignments? (yes): no
+new447: ap = 0, w1 = 5082.57, w2 = 6551.45, dw = 1.793, nw = 820
+  Change wavelength coordinate assignments? (yes): no
+new448: ap = 1, w1 = 5082.03, w2 = 6553.66, dw = 1.797, nw = 820
+  Change wavelength coordinate assignments? (no):
+.fi
+
+3. Confirm global assignments and do dispersion correction in place.
+record format.
+
+.nf
+ir> dispcor irs "" 9,10,447,448 confirm+ global+ samedisp+
+irs.0009: ap = 0, w1 = 5078.71, w2 = 6553.66, dw = 1.801, nw = 820
+  Change wavelength coordinate assignments? (yes):
+  Starting wavelength (5078.7071234): 5100
+  Ending wavelength (6553.664123): 6500
+  Wavelength interval per pixel (1.80092412):
+  Number of output pixels (820):
+irs.0009: ap = 0, w1 = 5100., w2 = 6500., dw = 1.799, nw = 779
+  Change wavelength coordinate assignments? (yes): no
+irs.0010: ap = 1, w1 = 5100., w2 = 6500., dw = 1.799, nw = 779
+  Change wavelength coordinate assignments? (no):
+irs.0447: ap = 0, w1 = 5100., w2 = 6500., dw = 1.799, nw = 779
+  Change wavelength coordinate assignments? (no):
+irs.0448: ap = 1, w1 = 5100., w2 = 6500., dw = 1.799, nw = 779
+  Change wavelength coordinate assignments? (no):
+.fi
+
+4. Make a nonlinear dispersion correction in place.
+
+.nf
+on> dispcor spec* ""  linearize=no verbose- logfile=logfile
+.fi
+
+5. Apply a single dispersion solution to a set of record number format
+images.
+
+ir> dispcor nite101 dcnite101 "1-10" ignore+ confirm-
+
+.ih
+REVISIONS
+.ls DISPCOR V2.12.3
+Added the blank parameter value.
+.le
+.ls DISPCOR V2.11.3
+Long slit and data cubes can be used with this task to either resample
+using the existing WCS or to use a single dispersion function from
+IDENTIFY.  It uses the first one found.
+.le
+.ls DISPCOR V2.10.3
+Provision was added for IDENTIFY dispersion solutions consisting of
+only a shift (as produced by the 'g' key in IDENTIFY or the refit=no
+flag in REIDENTIFY) to be applied to previously LINEARIZED spectra.
+Thus it is possible to use IDENIFY/REIDENTIFY to automatically
+compute a zero point shift based on 1 or more lines and then shift
+all the spectra to that zero point.
+
+DISPCOR will now allow multiple uses of IDENTIFY dispersion solutions
+in a simple way with but with continuing protection against accidental
+multiple uses of the same dispersion solutions.  When a spectrum is
+first dispersion corrected using one or more reference spectra keywords
+the dispersion flag is set and the reference spectra keywords are moved to
+DCLOGn keywords.  If DISPCOR is called again without setting new
+reference spectra keywords then the spectra are resampled (rebinned)
+using the current coordinate system.  If new reference spectra are set
+then DISPCOR will apply these new dispersion functions.  Thus the user
+now explicitly enables multiple dispersion functions by adding
+reference spectra keywords and DISPCOR eliminates accidental multiple
+uses of the same dispersion function by renaming the reference
+spectra.  The renamed keywords also provide a history.
+
+The flux conservation option now computes an average across the
+output pixel rather than interpolating to the middle of the output
+pixel when \fIflux\fR is no.  This preserves the flux density and
+includes all the data; i.e. a coarse resampling will not eliminate
+features which don't fall at the output pixel coordinates.
+
+Some additional log and verbose output was added to better inform the
+user about what is done.
+
+Better error information is now printed if a database dispersion function
+is not found.
+.le
+.ls DISPCOR V2.10
+This is a new version with many differences.  It replaces the previous
+three tasks \fBdispcor, ecdispcor\fR and \fBmsdispcor\fR.  It applies both
+one dimensional and echelle dispersion functions.  The new parameter
+\fIlinearize\fR selects whether to interpolate the spectra to a uniform
+linear dispersion (the only option available previously) or to assign a
+nonlinear dispersion function to the image without any interpolation.  The
+interpolation function parameter has been eliminated and the package
+parameter \fIinterp\fR is used to select the interpolation function.  The
+new interpolation type "sinc" may be used but care should be exercised.
+The new task supports applying a secondary zero point shift spectrum to a
+master dispersion function and a spatial interpolation of the shifts when
+calibration spectra are taken at the same time on a different region of the
+same 2D image.  The optional wavelength table may now also be an image to
+match dispersion parameters.  The \fIapertures\fR and \fIrebin\fR
+parameters have been eliminated.  If an input spectrum has been previously
+dispersion corrected it will be resampled as desired.  Verbose and log file
+parameters have been added to log the dispersion operations as desired.
+The record format syntax is available in the \fBirs/iids\fR packages.
+.le
+.ih
+SEE ALSO
+package, refspectra, scopy, specshift, sapertures
+.endhelp
diff --git a/noao/onedspec/doc/disptrans.hlp b/noao/onedspec/doc/disptrans.hlp
new file mode 100644
index 00000000..d73a4cb4
--- /dev/null
+++ b/noao/onedspec/doc/disptrans.hlp
@@ -0,0 +1,193 @@
+.help disptrans Aug94 noao.onedspec
+.ih
+NAME
+disptrans -- Transform dispersion units and apply air correction
+.ih
+USAGE
+disptrans input output units
+.ih
+PARAMETERS
+.ls input
+List of dispersion calibrated input spectra to be dispersion transformed.
+.le
+.ls output
+List of output dispersion transformed spectra.  If given the input names
+(or a null list), each input spectrum will be replaced by the transformed
+output spectrum.
+.le
+.ls units
+Output dispersion units.  A wide range of dispersion units may be
+specified and they are described in the UNITS section.
+.le
+.ls error = 0.01
+Maximum error allowed in the output dispersion transformation expressed
+as a pixel error; that is, the equivalent pixel shift in the output
+dispersion function corresponding to the maximum difference between
+the exact transformation and the dispersion function approximation.
+The smaller the allowed error the higher the order of dispersion
+function used.
+.le
+.ls linearize = no
+Resample the spectrum data to linear increments in the output dispersion
+system?  If no then the output dispersion function is stored in the
+spectrum header and if yes the spectrum is resampled into the same
+number of pixels over the same dispersion range but in even steps
+of the output dispersion units.
+.le
+.ls verbose = yes
+Print a log of each spectrum transformed to the standard output?
+.le
+
+.ls air = "none" (none|air2vac|vac2air)
+Apply an air to vacuum or vacuum to air conversion?  It is the
+responsibility of the user to know whether the input dispersion
+is in air or vacuum units and to select the appropriate conversion.
+The conversion types are "none" for no conversion, "air2vac" to
+convert from air to vacuum, and "vac2air" to convert from vacuum
+to air.
+.le
+.ls t = 15, p = 760, f = 4
+Temperature t in degrees C, pressure p in mmHg, and water vapour pressure f
+in mmHg for the air index of refraction.
+.le
+
+OTHER PARAMETERS
+
+.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
+.ih
+DESCRIPTION
+The dispersion function in the input spectra, y = f(x) where x is the
+pixel coordinate and y is the input dispersion coordinate, is
+transformed to y' = g(x) where y' is in the new dispersion units.  This is done
+by evaluating the input dispersion coordinate y at each pixel, applying an
+air to vacuum or vacuum to air conversion if desired, and applying the
+specified unit transformation y' = h(y).  Since the transformations are
+nonlinear functions and the output dispersion function must be expressed in
+polynomial form, the function g(x) is determined by fitting a cubic spline
+to the set of x and y' values.  The lowest number of spline pieces is used
+which satisfies the specified error.  Note that this error is not a random
+error but difference between the smooth fitted function and the smooth
+dispersion function in the header.  As a special case, the first
+fit tried is a linear function.  If this satisfies the error condition
+then a simpler dispersion description is possible.  Also this is
+appropriate for dispersion units which are simply related by a
+scale change such as Angstroms to nanometers or Hertz to Mev.
+
+The error condition is that the maximum difference between the exact or
+analytic (the air/vacuum conversion is never exact) transformation and the
+fitted function value at any pixel be less than the equivalent shift in
+pixel coordinate evaluated at that point.  The reason for using an error
+condition in terms of pixels is that it is independent of the dispersion of
+the spectra and the resolution of spectra is ultimately limited by the
+pixel sampling.
+
+After the new dispersion function is determined the function is either
+stored in the coordinate system description for the spectrum or used to
+resample the pixels to linear increments in the output dispersion units.
+The resampling is not done if the new dispersion function is already linear
+as noted above.  The sampling uses the mean value over the input spectrum
+covered by an output spectrum pixel (it is flux per unit dispersion element
+preserving as opposed to flux/counts preserving).  The linear sampling
+parameters are limited to producing the same number of output pixels as
+input pixels over the same range of dispersion.  If one wants to have more
+control over the resampling then the \fIlinearize\fR parameter should be
+set to no and the task \fBdispcor\fR used on the output spectrum.
+
+Note that an alternative to using this task is to do the original
+dispersion calibration (based on calibration spectra) with IDENTIFY
+and DISPCOR in the desired units.  However, currently the standard
+lines lists are in Angstroms.  There are, however, linelists for
+He-Ne-Ar, Th-Ar, and Th in vacuum wavelengths.
+.ih
+UNITS
+The dispersion units are specified by strings having a unit type from the
+list below along with the possible preceding modifiers, "inverse", to
+select the inverse of the unit and "log" to select logarithmic units. For
+example "log angstroms" to select the logarithm of wavelength in Angstroms
+and "inv microns" to select inverse microns.  The various identifiers may
+be abbreviated as words but the syntax is not sophisticated enough to
+recognized standard scientific abbreviations except for those given
+explicitly below.
+
+.nf
+	   angstroms - Wavelength in Angstroms
+	  nanometers - Wavelength in nanometers
+	millimicrons - Wavelength in millimicrons
+	     microns - Wavelength in microns
+	 millimeters - Wavelength in millimeters
+	  centimeter - Wavelength in centimeters
+	      meters - Wavelength in meters
+	       hertz - Frequency in hertz (cycles per second)
+	   kilohertz - Frequency in kilohertz
+	   megahertz - Frequency in megahertz
+	    gigahertz - Frequency in gigahertz
+	         m/s - Velocity in meters per second
+	        km/s - Velocity in kilometers per second
+	          ev - Energy in electron volts
+	         kev - Energy in kilo electron volts
+	         mev - Energy in mega electron volts
+
+	          nm - Wavelength in nanometers
+	          mm - Wavelength in millimeters
+	          cm - Wavelength in centimeters
+	           m - Wavelength in meters
+	          Hz - Frequency in hertz (cycles per second)
+	         KHz - Frequency in kilohertz
+	         MHz - Frequency in megahertz
+	         GHz - Frequency in gigahertz
+		  wn - Wave number (inverse centimeters)
+.fi
+
+The velocity units require a trailing value and unit defining the
+velocity zero point.  For example to transform to velocity relative to
+a wavelength of 1 micron the unit string would be:
+
+.nf
+	km/s 1 micron
+.fi
+.ih
+AIR/VACUUM CONVERSION
+The air to vacuum and vacuum to air conversions are obtained by multiplying
+or dividing by the air index of refraction as computed from the
+formulas in Allen's Astrophysical Quantities (p. 124 in 1973 edition).
+These formulas include temperature, pressure, and water vapour terms
+with the default values being the standard ones.
+.ih
+EXAMPLES
+1. Convert a spectrum dispersion calibrated in Angstroms to electron
+volts and resample to a linear sampling.
+
+.nf
+    cl> disptrans spec1 evspec1 ev linear+
+    evspec1: Dispersion transformed to ev.
+.fi
+
+2. Apply an air to vacuum correction to an echelle spectrum using the
+default standard temperature and pressure.  Don't resample but rather use
+a nonlinear dispersion function.
+
+.nf
+    cl> disptrans highres.ec vac.ec angs air=air2vac
+    vac.ec: Dispersion transformed to angstroms in vacuum with
+      t = 15. C, p = 760. mmHg, f = 4. mmHg.
+.fi
+.ih
+REVISIONS
+.ls DISPTRANS V2.10.4
+New task with this release.
+.le
+.ih
+SEE ALSO
+dispcor, identify, scopy, dopcor
+.endhelp
diff --git a/noao/onedspec/doc/dopcor.hlp b/noao/onedspec/doc/dopcor.hlp
new file mode 100644
index 00000000..6bcd0992
--- /dev/null
+++ b/noao/onedspec/doc/dopcor.hlp
@@ -0,0 +1,184 @@
+.help dopcor Jun94 noao.onedspec
+.ih
+NAME
+dopcor -- Apply doppler correction
+.ih
+USAGE
+dopcor input output redshift
+.ih
+PARAMETERS
+.ls input
+List of input spectra to be doppler corrected.
+.le
+.ls output
+List of doppler corrected spectra.  If no output list is specified then
+the input spectra are modified.  Also the output name may be
+the same as the input name to replace the input spectra by the
+calibrated spectra.
+.le
+.ls redshift
+Redshift or radial velocity (km/s) to be removed?  The spectra are corrected so
+that the specified redshift is removed; i.e. spectra with a positive
+velocity are shifted to shorter wavelengths and vice-versa.  This parameter
+may be either a number or an image header keyword with the desired redshift
+or velocity value.  An image header keyword may also have an initial minus
+sign, '-', to specify the negative of a velocity or the redshift complement
+(1/(1+z)-1) of a redshift.  The choice between a redshift and a velocity is
+made with the \fIisvelocity\fR parameter.
+.le
+.ls isvelocity = no
+Is the value specified by the \fIredshift\fR parameter a velocity?  If
+no then the value is interpreted as a redshift and if it is yes then
+it is interpreted as a physical  velocity in kilometers per second.  Note that
+this is a relativistic velocity and not c*z!  For nearby cosmological
+velocities users should specify a redshift (z = v_cosmological / c).
+.le
+.ls add = no
+Add doppler correction to existing correction in "multispec" spectra?
+.le
+.ls dispersion = yes
+Apply a correction to the dispersion function?
+.le
+.ls flux = no
+Apply a flux correction?
+.le
+.ls factor = 3
+Flux correction factor as a power of 1+z when applying a flux correction.
+.le
+.ls apertures = ""
+List of apertures to be corrected.  If none are specified then all apertures
+are corrected.  An aperture list consists of comma separated aperture
+number or aperture number ranges.  A range is hypen separated and may
+include an interval step following the character 'x'.  See \fBranges\fR
+for further information.  For N-dimensional spatial spectra such as
+long slit and Fabry-Perot spectra this parameter is ignored.
+.le
+.ls verbose = no
+Print corrections performed?  The information includes the output image
+name, the apertures, the redshift, and the flux correction factor.
+.le
+.ih
+DESCRIPTION
+The input spectra (as specified by the input image list and apertures) are
+corrected by removing a specified doppler shift and written to the
+specified output images.  The correction is such that if the actual
+shift of the observed object is specified then the corrected spectra
+will be the rest spectra.  The opposite sign for a velocity or the
+redshift complement (1/(1+z)-1) may be used to add a doppler shift
+to a spectrum.
+
+There are two common usages.  One is to take spectra with high doppler
+velocities, such as cosmological sources, and correct them to rest with
+respect to the earth.  In this case the measured redshift or velocity is
+specified to "remove" this component.  The other usage is to correct
+spectra to heliocentric or local standard of rest.  The heliocentric or LSR
+velocities can be computed and entered in the image header with the task
+\fBrvcorrect\fR.  In this case it is tempting to again think you are
+"removing" the velocity so that you specify the velocity as given in the
+header.  But actually what is needed is to "add" the computed standard of
+rest velocity to the observed spectrum taken with respect to the telescope
+to place the dispersion in the desired center of rest.  Thus, in this case
+you specify the opposite of the computed heliocentric or LSR velocity; i.e.
+use a negative.
+
+The redshift or space velocity in km/s is specified either as a number or
+as an image header keyword containing the velocity or redshift.  If a
+number is given it applies to all the input spectra while an image header
+keyword may differ for each image.  The latter method of specifying a
+velocity is useful if velocity corrections are recorded in the image
+header.  See \fBrvcorrect\fR for example.
+
+The choice between a redshift and a space velocity for the \fIredshift\fR
+parameter is made using the \fIisvelocity\fR parameter. If isvelocity=yes
+then the header dispersion solution is modified according to the
+relativistic Doppler correction:
+
+	lambda_new = lamda_old * sqrt((1 + v/c)/(1 - v/c))
+
+where v is the value of "redshift".  If isvelocity=no, \fIredshift\fR is
+interpreted as a cosmological redshift and the header dispersion solution
+is modified to give:
+
+	lambda_new = lamda_old * z
+
+where z is the value of "redshift"
+
+If the \fIadd\fR parameter is used and the image uses a "multispec"
+format where the previous doppler factor is stored separately
+then the new doppler factor is:
+
+	znew = (1 + z) * (1 + zold) - 1 = z + zold + z * zold
+
+where z is the specified doppler factor, zold is the previous one,
+and znew is the final doppler factor.  If the \fIadd\fR parameter
+is no then the previous correction is replaced by the new correction.
+Note that for images using a linear or equispec coordinate system
+the corrections are always additive since a record is not kept of
+the previous correction.  Also any flux correction is made based
+on the specified doppler correction rather than znew.
+
+There are two corrections which may be made and the user selects one
+or both of these.  A correction to the dispersion function is selected
+with the \fIdispersion\fR parameter.  This correction is a term to be
+applied to the dispersion coordinates defined for the image.  \fIThe spectrum
+is not resampled, only the dispersion coordinate function is affected\fR.
+A correction to the flux, pixel values, is selected with the \fIflux\fR
+parameter.  This correction is only significant for cosmological redshifts.
+As such the correction is dependent on a cosmological model as well as
+whether a total flux or surface brightness is measured.  To provide the
+range of possible corrections the flux correction factor is defined by
+the \fIfactor\fR parameter as the power of 1+z (where z is the
+redshift) to be multiplied into the observed pixel values.
+
+A keyword DOPCORnn is added to the image header.  The index starts from
+01 and increments if multiple corrections are applied.  The value of
+the keywords gives the redshift applied, the flux factor if used, and
+the apertures which were corrected.
+.ih
+EXAMPLES
+1.  To dispersion and flux correct a quasar spectrum with redshift of
+3.2 to a rest frame:
+
+.nf
+	cl> dopcor qso001.ms qso001rest.ms 3.2 flux+
+.fi
+
+2.  To correct a set of spectra (in place) to heliocentric rest the task
+\fBrvcorrect\fR is used to set the VHELIO keyword using an observed
+velocity of 0.  Then:
+
+.nf
+	cl> dopcor *.imh "" -vhelio isvel+
+.fi
+
+3.  To artificially add a redshift of 3.2 to a spectrum the complementary
+redshift is computed:
+
+.nf
+	cl> = 1/(1+3.2)-1
+	-0.76190476190476
+	cl> dopcor artspec "" -0.762 flux+
+.fi
+.ih
+REVISIONS
+.ls DOPCOR V2.10.3
+This task was extended to work on two and three dimensional spatial spectra
+such as long slit and Fabry-Perot spectra.
+
+The \fIadd\fR parameter was added.
+.le
+.ls DOPCOR V2.10.3
+A keyword is added to log the correction applied.
+.le
+.ls DOPCOR V2.10.2
+A sign error in converting velocity to redshift was fixed.  A validity
+check on the velocities and redshifts was added.  The documentation
+was corrected and improved.
+.le
+.ls DOPCOR V2.10
+This task is new.
+.le
+.ih
+SEE ALSO
+ranges, rvcorrect
+.endhelp
diff --git a/noao/onedspec/doc/fitprofs.hlp b/noao/onedspec/doc/fitprofs.hlp
new file mode 100644
index 00000000..ed21e7b1
--- /dev/null
+++ b/noao/onedspec/doc/fitprofs.hlp
@@ -0,0 +1,403 @@
+.help fitprofs Mar92 noao.onedspec
+.ih
+NAME
+fitprofs -- Fit 1D profiles to features in image vectors
+.ih
+USAGE
+fitprofs input
+.ih
+PARAMETERS
+.ls input
+List of input images to be fit.  The images may be one dimensional
+spectra (one or more spectra per image) or long slit spectra.  Other
+types of nonspectral images may also be used and for two dimensional
+images the fitting direction will be determined from either the keyword
+DISPAXIS in the image header or the \fIdispaxis\fR parameter.
+.le
+.ls lines = ""
+List of lines, columns, or apertures to be selected from the input image
+format.  The default empty list, "", selects all vectors in the images.
+The syntax is a list of comma separated numbers or ranges, where a range
+is a pair of hyphen separated numbers.
+.le
+.ls bands = ""
+List of bands for 3D images.  The empty list, "", selects all bands.
+.le
+.ls dispaxis = ")_.dispaxis", nsum = ")_.nsum"
+Parameters for defining vectors in 2D and 3D images.  The
+dispersion axis is 1 for line vectors, 2 for column vectors, and 3 for band
+vectors.  A DISPAXIS parameter in the image header has precedence over the
+\fIdispaxis\fR parameter.  The default values defer to the package
+parameters of the same name.
+.le
+
+The following are the fitting parameters.
+.ls region = ""
+Region of the input vectors to be fit specified as a pair of space
+separated numbers.  The coordinates are defined in terms of the linear
+image header coordinate parameters.  For dispersion corrected spectra this
+is usually wavelength in Angstroms and for other data it is usually pixels.
+A fitting region must be specified.
+.le
+.ls positions = ""
+File of initial or fixed profile positions and (optional) peaks, profile
+types, and widths.  The
+format consists of lines with one or more whitespace separated fields.
+The fields are the position, peak relative to the continuum with
+negative values being absorption, profile type of gaussian, lorentzian,
+or voigt, and the gaussian and/or lorentzian full width at half maximum.
+Trailing fields may be missing and fields to be set from default parameters
+or the image data (the peak value) may be given as INDEF.
+Comments and any additional columns are ignored.  The positions and
+widths are specified in the coordinate units of the image, usually
+wavelength for dispersion corrected spectra and pixels otherwise.
+.le
+.ls background = ""
+Background values defining the linear background.  If not specified the
+single pixel values nearest the fitting region endpoints are used.
+Otherwise two whitespace separated values are expected.  If a value is
+a number then that is the background at the lower or upper end of the
+fitting region (ordered in pixel space not wavelength).  The special
+values "avg(w1,w2,z)" or "med(w1,w2,z)" (note that there can be no
+whitespace) may be specified, where w1 and w2 are dispersion values, and z
+is a multiplier.  This will take the average or median of pixels within the
+specified range and multiply the result by the third argument.  The
+dispersion point used for that value in computing the linear background is
+the average of the dispersion coordinates of the pixels used.
+.le
+.ls profile = "gaussian" (gaussian|lorentzian|voigt)
+Default profile type to be fit when a profile type is not specified in
+the positions file.  The type are "gaussian", "lorentzian", or "voigt".
+.le
+.ls gfwhm = 20., lfwhm = 20.
+Default gaussian and lorentzian full width at half maximum (FWHM).
+These values are used for the initial and/or fixed width when they are
+not specified in the position file.
+.le
+.ls fitbackground = yes
+Fit the background?  If "yes" a linear background across the fitting region
+will be fit simultaneously with the profiles.  If "no" the background will
+be fixed.
+.le
+.ls fitpositions = "all"
+Position fitting option.  This may be "fixed" to fix all positions at their
+initial values, "single" to fit a single shift to the positions while
+keeping their separations fixed, or "all" to independently fit all the
+positions.
+.le
+.ls fitgfwhm = "all", fitlfwhm = "all"
+Profile width fitting options.  These may be "fixed" to fix all widths
+at their initial values, "single" to fit a single scale factor to the initial
+widths, or "all" to independently fit all the widths.
+.le
+
+The following parameters are used for error estimates as described
+below in the ERROR ESTIMATES section.
+.ls nerrsample = 0
+Number of samples for the error computation.  A value less than 10 turns
+off the error computation.  A value of ~10 does a rough error analysis, a
+value of ~50 does a reasonable error analysis, and a value >100 does a
+detailed error analysis.  The larger this value the longer the analysis
+takes.
+.le
+.ls sigma0 = INDEF, invgain = INDEF
+The pixel sigmas are modeled by the formula:
+
+.nf
+    sigma**2 = sigma0**2 + invgain * I
+.fi
+
+where I is the pixel value and "**2" means the square of the quantity.  If
+either parameter is specified as INDEF or with a value less than zero then
+no sigma estimates are made and so no error estimates for the measured
+parameters is made.
+.le
+
+The following parameters determine the output of the task.
+.ls components = ""
+All profiles defined by the position file are simultaneously fit but only
+a subset of the fitted profiles may be selected for output.  A profile
+or component is identified by the order number in the position file;
+i.e. the first entry in the position file is 1, the second is 2, etc.
+The components to be output are specified by a range list.  The empty
+list, "", selects all profiles.
+.le
+.ls verbose = yes
+Print fitting results and record of output images created on the
+standard output (normally the terminal).
+The fitting information is printed to the logfile so there is normally
+no need to redirect this output.  The output may be turned off when
+the task is run as a background task.
+.le
+.ls logfile = "logfile"
+Logfile for fitting results.  If not specified the results will not be
+logged.
+.le
+.ls plotfile = "plotfile"
+File to contain plot output.  The plots show the image vector with
+overplots of the total fit, the individual components, and the residuals.
+The plotfile may be examined and manipulated later with tools such as
+\fBgkimosaic\fR.
+.le
+.ls output = ""
+List of output images.  If not specified then no output images are created.
+If images are specified the list is matched with the input list.
+.le
+.ls option = "fit" (fit|difference)
+Image output option.  The choices are "fit" to output the fitted image
+vector which is the sum of the fitted profiles (without a background),
+or "difference" to output the data with the profiles subtracted.
+.le
+.ls clobber = no, merge = no
+Clobber or modify any existing output images?  If clobbering is not
+enabled a warning is printed and any existing output images are not
+modified.  If clobbering is enabled then either new images are created
+if merge is "no" or the new fits are merged with the existing images.
+Merging is meaningful when only a subset of the input is fit such
+as selected lines or apertures.
+.le
+.ih
+DESCRIPTION
+\fBFitprofs\fR fits one dimensional profile functions to image vectors
+and outputs the fitting parameters, plots, and model or residual
+image vectors.  This is done noninteractively using a file of initial
+profile positions and widths.  Interactive profile fitting may be
+done with the deblending option of \fBsplot\fR or
+\fBstsdas.fitting.ngaussfit\fR.
+
+The input consists of images in a variety of formats.  These include
+all the spectral formats as well as standard images.  For two dimensional
+images (or the first 2D plane of higher dimensional images) either the
+lines or columns may be fit with possible summing of adjacent lines or
+columns to increase the signal-to-noise.  A subset of the image apertures,
+lines, or columns may be specified or all image vectors may be fit.
+
+The fitting parameters consist of a fitting region, a list of initial
+positions, peaks, and widths, initial background endpoints, the fitting
+function, and the parameters to be fit or constrained.  The coordinates and
+units used for the positions and widths are those defined by the standard
+linear coordinate header parameters.  For dispersion corrected spectra
+these are generally wavelengths in Angstroms and otherwise they are
+generally pixels.  A fitting region must be specified by a pair of
+numbers.
+
+The background parameter may be left empty to select the pixel values at
+the endpoints of the fitting region for defining the initial linear
+background.  Or values at the endpoints of the fitting region may be given
+explicitly in pixel space order (i.e. the first value is for the edge of
+the fitting region which has smaller pixel coordinate0 Values can also be
+computed from the data using the functions "avg(w1,w2)" or "med(w1,w2)"
+where w1 and w2 are dispersion coordinates.  The pixels in the specified
+range are average or medianed and the dispersion point for the linear
+background is the average of the dispersion coordinates of the pixels.
+
+The position list file consists of one or more columns.
+The format of this file has
+one or more columns.  The columns are the wavelength, the peak value
+(relative to the continuum with negative values being absorption),
+the profile type (gaussian, lorentzian, or voigt), and the
+gaussian and/or lorentzian FWHM.  End columns may be missing
+or INDEF values may be specified to use the default parameter
+values (the profile and widths) or determine the peak from the data.
+Below are examples of the file line formats
+
+.nf
+	wavelength
+	wavelength peak
+	wavelength peak (gaussian|lorenzian|voigt)
+	wavelength peak gaussian gfwhm
+	wavelength peak lorentzian lfwhm
+	wavelength peak voigt gfwhm
+	wavelength peak voigt gfwhm lfwhm
+
+	1234.5			<- Wavelength only
+	1234.5 -100		<- Wavelength and peak
+	1234.5 INDEF v		<- Wavelength and profile type
+	1234.5 INDEF g 12	<- Wavelength and gaussian FWHM
+.fi
+
+where peak is the peak value, gfwhm is the gaussian FWHM, and lfwhm is
+the lorentzian FWHM.  This format is the same as used by \fBsplot\fR
+and also by \fBartdata.mk1dspec\fR (except in the latter case the
+peak is normalized to a continuum of 1).
+
+The profile parameters fit are the central position, the peak amplitude,
+and the profile widths.  The fitting may be constrained in number of ways.
+The linear background may be fixed or simultaneously fit with the
+profiles.  The profile positions may be fixed, the relative separations
+fixed but a single zero point shift fit, or all positions may be fit
+simultaneously.  The profile widths may also be fixed, the relative ratios
+of the widths fixed while fitting a single scale factor, or all widths fit
+simultaneously.  The profile amplitudes are always fit.
+
+The fitting technique uses a nonlinear iterative Levenberg-Marquardt
+algorithm to reduce the Chi-square of the fit.  The execution time
+increases rapidly with the number of profiles fit so there is an
+effective limit to the number of profiles that can be fit at once.
+
+The output includes a number of formats.  The fitted parameters  are
+recorded in a logfile (if specified) and printed on the standard
+output (if the verbose flag is set).  This output includes the date,
+image vector, fitting parameters used, and a table of fitted or
+derived quantities.  The parameters included some quantities relevant to
+spectral lines but others apply to any image data.  The quantities are
+the profile center, the background or continuum at the center of the
+profile, the integral or flux of the profile (which is negative for
+profiles below the background), the equivalent width, the profile peak
+amplitude or core value, and the profile full width at half
+maximum.  Pure gaussian and lorentzian profiles will have one of
+the widths set to zero while voigt profiles will have both values.
+
+Summary plots are recored in a plotfile (if specified).  The plots
+show the data with the total fit, individual profiles, and residuals
+overplotted.  The plotfile may be examined and printed using the
+task \fBgkimosaic\fR as well as other tasks which interpret GKI metacode.
+
+The final output consists of images in the same format as the input.
+The images  may be of the total fit (sum of profiles without background)
+or of the difference (residuals) of the data minus the model.
+.ih
+ERROR ESTIMATES
+Error estimates may be computed for the fitted parameters.
+This requires a model for the pixel sigmas.  Currently this
+model is based on a Poisson statistics model of the data.  The model
+parameters are a constant Gaussian sigma and an "inverse gain" as specified
+by the parameters \fIsigma0\fR and \fIinvgain\fR.  These parameters are
+used to compute the pixel value sigma from the following formula:
+
+.nf
+    sigma**2 = sigma0**2 + invgain * I
+.fi
+
+where I is the pixel value and "**2" means the square of the quantity.
+
+If either the constant sigma or the inverse gain are specified as INDEF or
+with values less than zero then no noise model is applied and no error
+estimates are computed.  Also if the number of error samples is less than
+10 then no error estimates are computed.  Note that for processed spectra
+this noise model will not generally be the same as the detector readout
+noise and gain.  These parameters would need to be estimated in some way
+using the statistics of the spectrum.  The use of an inverse gain rather
+than a direct gain was choosed to allow a value of zero for this
+parameters.  This provides a model with constant uncertainties.
+
+The error estimates are computed by Monte-Carlo simulation.  The model is
+fit to the data (using the noise sigmas) and this model is used to describe
+the noise-free spectrum.  A number of simulations, given by the
+\fInerrsample\fR, are created in which random Gaussian noise is added to
+the noise-free spectrum based on the pixel sigmas from the noise model.
+The model fitting is done for each simulation and the absolute deviation of
+each fitted parameter to model parameter is recorded.  The error estimate
+for the each parameter is then the absolute deviation containing 68.3% of
+the parameter estimates.  This corresponds to one sigma if the distribution
+of parameter estimates is Gaussian though this method does not assume
+this.
+
+The Monte-Carlo technique automatically includes all effects of
+parameter correlations and does not depend on any approximations.
+However the computation of the errors does take a significant
+amount of time.  The amount of time and the accuracy of the
+error estimates depend on how many simulations are done.  A
+small number of samples (of order 10) is fast but gives crude
+estimates.  A large number (greater than 100) is slow but gives
+very good estimates.  A compromise value of 50 is recommended
+for many applications.
+
+.ih
+EXAMPLES
+1.  The following example creates an artificial spectrum and fits it.
+It requires the \fBartdata\fR and \fBproto\fR packages be loaded.
+
+.nf
+    cl> mk1dspec test slope=1 temp=0 lines=testlines nl=20
+    cl> mknoise test rdnoise=10 poisson=yes
+    cl> fields testlines fields=1,3 > fitlines
+    cl> fitprofs test reg="4000 8000" pos=fitlines
+    # Jul 27 17:49 test - Ap 1: 
+    # Nfit=20, background=YES, positions=all, gfwhm=all, lfwhm=all
+    #   center      cont      flux      eqw      core   gfwhm   lfwhm
+      6832.611  1363.188  -13461.8    9.875  -408.339   30.97      0.
+      7963.674  1507.641  -8193.58    5.435  -395.207   19.48      0.
+      5688.055   1217.01  -7075.11    5.814  -392.006   16.96      0.
+	6831.3   1363.02  -7102.01     5.21  -456.463   14.62      0.
+      7217.335  1412.323   -10110.    7.158  -427.797    22.2      0.
+      6709.286  1347.437  -4985.06      3.7  -225.346   20.78      0.
+      6434.317  1312.319  -7121.03    5.426  -342.849   19.51      0.
+      6130.415  1273.506    -6164.     4.84  -224.146   25.83      0.
+      4569.375  1074.138   -3904.6    3.635  -183.963   19.94      0.
+      5656.645  1212.999  -8202.81    6.762  -303.617   25.38      0.
+       4219.53  1029.458  -5161.64    5.014  -241.135   20.11      0.
+      4551.424  1071.845  -3802.61    3.548   -139.39   25.63      0.
+      4604.649  1078.643  -5539.15    5.135  -264.654   19.66      0.
+      6966.557  1380.294  -11717.5    8.489  -600.581   18.33      0.
+      4259.019  1034.501  -4280.38    4.138  -213.446   18.84      0.
+      5952.958  1250.843  -8006.98    6.401  -318.313   23.63      0.
+       4531.89  1069.351  -712.598   0.6664  -155.197   4.313      0.
+      7814.418  1488.579  -2926.49    1.966  -164.891   16.67      0.
+      5310.929  1168.846  -10132.2    8.669  -487.502   19.53      0.
+      5022.948  1132.066   -7532.8    6.654  -325.594   21.73      0.
+
+.fi
+
+2.  Suppose there is no obvious continuum level near the fitting
+region but you want to specify a flat continuum level as the average
+of pixels in a specified wavelength region.  The background region
+would be specified as
+
+.nf
+    background = "avg(4250,4425.3) avg(4250,4425.3)"
+.fi
+
+Note that the value must be given twice to get a flat continuum.
+.ih
+REVISIONS
+.ls FITPROFS V2.11.3
+Modified to allow a more general specification of the background.
+.le
+.ls FITPROFS V2.11
+Modified to include lorentzian and voigt profiles.  The parameters and
+positions file format have changed in this version.  A new parameter
+controls the number of Monte-Carlo samples used in the error estimates.
+.le
+.ls FITPROFS V2.10.3
+Error estimates based on a simple noise model are now computed.
+.le
+.ls FITPROFS V2.10
+This task is new.
+.le
+.ih
+TIME REQUIREMENTS
+The following CPU times were obtained with a Sun Sparcstation I.  The
+number of pixels in the fitting region and the number of lines fit
+were varied.   The worst case of fitting all parameters and a background
+was considered as well as the constrained case of  fitting line positions
+and a single width with fixed background.
+
+.nf
+	Npixels Nprofs Fitbkg Fitpos  Fitsig   CPU(sec)
+	  100	   5	 yes	all	all	  1.9
+	  100	  10	 yes	all	all	  3.3
+	  100	  15	 yes	all	all	  5.6
+	  100	  20	 yes	all	all	  9.0
+	  512	   5	 yes	all	all	  4.7
+	  512	  10	 yes	all	all	 10.0
+	  512	  15	 yes	all	all	 17.6
+	  512	  20	 yes	all	all	 27.8
+	 1000	   5	 yes	all	all	  8.0
+	 1000	  10	 yes	all	all	 18.0
+	 1000	  15	 yes	all	all	 31.8
+	 1000	  20	 yes	all	all	 50.2
+	 1000	  25	 yes	all	all	 72.8
+	 1000	  30	 yes	all	all	100.2
+	  512	   5	  no	all  single	  2.8
+	  512	  10	  no	all  single	  5.3
+	  512	  15	  no	all  single	  8.6
+	  512	  20	  no	all  single	 12.8
+.fi
+
+Crudely this implies CPU time goes as the 1.4 power of the number of profiles
+and the 0.75 power of the number of pixels.
+.ih
+SEE ALSO
+splot, stsdas.fitting.ngaussfit
+.endhelp
diff --git a/noao/onedspec/doc/identify.hlp b/noao/onedspec/doc/identify.hlp
new file mode 100644
index 00000000..fea7086c
--- /dev/null
+++ b/noao/onedspec/doc/identify.hlp
@@ -0,0 +1,810 @@
+.help identify Jan96 noao.onedspec
+.ih
+NAME
+identify -- Identify features in one dimensional image vectors
+.ih
+SUMMARY
+Features are interactively marked in one dimensional image vectors.
+The features may be spectral lines when the vector is a spectrum
+or profile positions when the vector is a spatial cut.  A function
+may be fit to the user coordinates as a function of pixel coordinates.
+This is primarily used to find dispersion functions for spectra
+such as arc-line calibration spectra.  The profile position measurements
+are generally used for geometric calibrations.
+.ih
+USAGE
+identify images
+.ih
+PARAMETERS
+.ls images
+List of images in which to identify features and fit coordinate functions.
+.le
+.ls section = "middle line"
+If an image is not one dimensional or specified as a one dimensional image
+section then the image section given by this parameter is used.  The
+section defines a one dimensional vector.  The image is still considered to
+be two or three dimensional.  It is possible to change the data vector
+within the program.
+
+The section parameter may be specified directly as an image section or
+in one of the following forms
+
+.nf
+line|column|x|y|z first|middle|last|# [first|middle|last|#]]
+first|middle|last|# [first|middle|last|#] line|column|x|y|z
+.fi
+
+where each field can be one of the strings separated by | except for #
+which is an integer number.  The field in [] is a second designator
+which is used with three dimensional data.  See the example section for
+examples of this syntax.  Abbreviations are allowed though beware that 'l'
+is not a sufficient abbreviation.
+.le
+.ls database = "database"
+Database in which the feature data and coordinate functions are recorded.
+.le
+.ls coordlist = "linelists$idhenear.dat"
+User coordinate list consisting of an list of line coordinates.  A
+comment line of the form "# units <units>", where <units> is one of the
+understood units names, defines the units of the line list.  If no units
+are specified then Angstroms are assumed.  Some standard line lists are
+available in the directory "linelists$".  The standard line lists are
+described under the topic \fIlinelists\fR.
+.le
+.ls units = ""
+The units to use if no database entry exists.  The units are specified as
+described in
+
+.nf
+    cl> help onedspec.package section=units
+.fi
+
+If no units are specified and a coordinate list is used then the units of
+the coordinate list are selected.  If a database entry exists then the
+units defined there override both this parameter and the coordinate list.
+.le
+.ls nsum = "10"
+Number of lines, columns, or bands across the designated vector axis to be
+summed when the image is a two or three dimensional spatial spectrum.
+It does not apply to multispec format spectra.  If the image is three
+dimensional an optional second number can be specified for the higher
+dimensional axis  (the first number applies to the lower axis number and
+the second to the higher axis number).  If a second number is not specified
+the first number is used for both axes.
+.le
+.ls match = -3.
+The maximum difference for a match between the feature coordinate function
+value and a coordinate in the coordinate list.  Positive values
+are in user coordinate units and negative values are in units of pixels.
+.le
+.ls maxfeatures = 50
+Maximum number of the strongest features to be selected automatically from
+the coordinate list (function 'l') or from the image data (function 'y').
+.le
+.ls zwidth = 100.
+Width of graphs, in user coordinates, when in zoom mode (function 'z').
+.le
+
+The following parameters are used in determining feature positions.
+.ls ftype = "emission"
+Type of features to be identified.  The possibly abbreviated choices are
+"emission" and "absorption".
+.le
+.ls fwidth = 4.
+Full-width at the base (in pixels) of features to be identified.
+.le
+.ls cradius = 5.
+The maximum distance, in pixels, allowed between a feature position
+and the initial estimate when defining a new feature.
+.le
+.ls threshold = 0.
+In order for a feature center to be determined the range of pixel intensities
+around the feature must exceed this threshold.
+.le
+.ls minsep = 2.
+The minimum separation, in pixels, allowed between feature positions
+when defining a new feature.
+.le
+
+The following parameters are used to fit a function to the user coordinates.
+The \fBicfit\fR package is used and further descriptions about these parameters
+may be found under that package.
+.ls function = "spline3"
+The function to be fit to the user coordinates as a function of the pixel
+coordinate.  The choices are "chebyshev", "legendre", "spline1", or "spline3".
+.le
+.ls order = 1
+Order of the fitting function.  The order is the number of polynomial terms
+or number of spline pieces.
+.le
+.ls sample = "*"
+Sample regions for fitting. This is in pixel coordinates and not the user
+coordinates.
+.le
+.ls niterate = 0
+Number of rejection iterations.
+.le
+.ls low_reject = 3.0, high_reject = 3.0
+Lower and upper residual rejection in terms of the RMS of the fit.
+.le
+.ls grow = 0
+Distance from a rejected point in which additional points are automatically
+rejected regardless of their residuals.
+.le
+
+The following parameters control the input and output.
+.ls autowrite = no
+Automatically write or update the database?  If "no" then when exiting the
+program a query is given if the feature data and fit have been modified.
+The query is answered with "yes" or "no" to save or not save the results.
+If \fIautowrite\fR is "yes" exiting the program automatically updates the
+database.
+.le
+.ls graphics = "stdgraph"
+Graphics device.  The default is the standard graphics device which is
+generally a graphics terminal.
+.le
+.ls cursor = ""
+Cursor input file.  If a cursor file is not given then the standard graphics
+cursor is read.
+.le
+
+The following parameters are queried when the 'b' key is used.
+.ls crval, cdelt
+These parameters specify an approximate coordinate value and coordinate
+interval per pixel when the automatic line identification
+algorithm ('b' key) is used.  The coordinate value is for the
+pixel specified by the \fIcrpix\fR parameter in the \fBaidpars\fR
+parameter set.  The default value of \fIcrpix\fR is INDEF which then
+refers the coordinate value to the middle of the spectrum.  By default
+only the magnitude of the coordinate interval is used.  Either value
+may be given as INDEF.  In this case the search for a solution will
+be slower and more likely to fail.  The values may also be given as
+keywords in the image header whose values are to be used.
+.le
+.ls aidpars = "" (parameter set)
+This parameter points to a parameter set for the automatic line
+identification algorithm.  See \fIaidpars\fR for further information.
+.le
+.ih
+CURSOR KEYS
+.ls ?
+Clear the screen and print a menu of options.
+.le
+.ls a
+Apply next (c)enter or (d)elete operation to (a)ll features
+.le
+.ls b
+Identify features and find a dispersion function automatically using
+the coordinate line list and approximate values for the dispersion.
+.le
+.ls c
+(C)enter the feature nearest the cursor.  Used when changing the position
+finding parameters or when features are defined from a previous feature list.
+.le
+.ls d
+(D)elete the feature nearest the cursor.  (D)elete all features when preceded
+by the (a)ll key.  This does not affect the dispersion function.
+.le
+.ls e
+Find features from a coordinate list without doing any fitting.  This is
+like the 'l' key without any fitting.
+.le
+.ls f
+(F)it a function of the pixel coordinates to the user coordinates.  This enters
+the interactive function fitting package.
+.le
+.ls g
+Fit a zero point shift to the user coordinates by minimizing the difference
+between the user and fitted coordinates.  The coordinate function is
+not changed.
+.le
+.ls i
+(I)nitialize (delete features and coordinate fit).
+.le
+.ls j
+Go to the preceding line, column, or band in a 2D/3D or multispec image.
+.le
+.ls k
+Go to the next line, column, or band in a 2D/3D or multispec image.
+.le
+.ls l
+(L)ocate features in the coordinate list.  A coordinate function must be
+defined or at least two features must have user coordinates from which a
+coordinate function can be determined.  If there are features an
+initial fit is done, then features are added from the coordinate list,
+and then a final fit is done.
+.le
+.ls m
+(M)ark a new feature using the cursor position as the initial position
+estimate.
+.le
+.ls n
+Move the cursor or zoom window to the (n)ext feature (same as +).
+.le
+.ls o
+Go to the specified line, column, or band in a 2D/3D or multispec image.
+For 3D images two numbers are specified.
+.le
+.ls p
+(P)an to the original window after (z)ooming on a feature.
+.le
+.ls q
+(Q)uit and continue with next image.
+.le
+.ls r
+(R)edraw the graph.
+.le
+.ls s
+(S)hift the fit coordinates relative to the pixel coordinates.  The
+user specifies the desired fit coordinate at the position of the cursor
+and a zero point shift to the fit coordinates is applied.  If features
+are defined then they are recentered and the shift is the average shift.
+The shift in pixels, user coordinates, and z (fractional shift) is printed.
+.le
+.ls t
+Reset the current feature to the position of the cursor.  The feature
+is \fInot\fR recentered.  This is used to mark an arbitrary position.
+.le
+.ls u
+Enter a new (u)ser coordinate for the current feature.
+When (m)arking a new feature the user coordinate is also requested.
+.le
+.ls v
+Modify the fitting weight of the current feature.  The weights are
+integers with the lowest weight being the default of 1.
+.le
+.ls w
+(W)indow the graph.  A window prompt is given and a number of windowing
+options may be given.  For more help type '?' to the window prompt or
+see help under \fIgtools\fR.
+.le
+.ls x
+Find a zero point shift for the current dispersion function.  This is used
+by starting with the dispersion solution and features from a different
+spectrum.  The mean shift in user coordinates, mean shift in pixels, and
+the fractional shift in user coordinates is printed.
+.le
+.ls y
+Up to \fImaxfeatures\fR emission peaks are found automatically (in order of
+peak intensity) and, if a dispersion solution is defined, the peaks are
+identified from the coordinate list.
+.le
+.ls z
+(Z)oom on the feature nearest the cursor.  The width of the zoom window
+is determined by the parameter \fIzwidth\fR.
+.le
+.ls .
+Move the cursor or zoom window to the feature nearest the cursor.
+.le
+.ls 4 +
+Move the cursor or zoom window to the (n)ext feature.
+.le
+.ls 4 -
+Move the cursor or zoom window to the previous feature.
+.le
+
+Parameters are shown or set with the following "colon commands", which may be
+abbreviated.  To show the value of a parameter type the parameter name alone
+and to set a new value follow the parameter name by the value.
+.ls :show file
+Show the values of all the parameters.  If a file name is given then the
+output is appended to that file.  If no file is given then the terminal
+is cleared and the output is sent to the terminal.
+.le
+.ls :features file
+Print the feature list and the fit rms.  If a file name is given then the
+output is appended to that file.  If no file is given then the terminal
+is cleared and the output is sent to the terminal.
+.le
+.ls :coordlist file
+Set or show the coordinate list file.
+.le
+.ls :cradius value
+Set or show the centering radius in pixels.
+.le
+.ls :threshold value
+Set or show the detection threshold for centering.
+.le
+.ls :database name
+Set or show the database for recording feature records.
+.le
+.ls :ftype value
+Set or show the feature type (emission or absorption).
+.le
+.ls :fwidth value
+Set or show the feature width in pixels.
+.le
+.ls :image imagename
+Set a new image or show the current image.
+.le
+.ls :labels value
+Set or show the feature label type (none, index, pixel, coord, user, or both).
+None produces no labeling, index labels the features sequentially in order
+of pixel position, pixel labels the features by their pixel coordinates,
+coord labels the features by their user coordinates (such as wavelength),
+user labels the features by the user or line list supplied string, and
+both labels the features by both the user coordinates and user strings.
+.le
+.ls :match value
+Set or show the coordinate list matching distance.
+.le
+.ls :maxfeatures value
+Set or show the maximum number of features automatically found.
+.le
+.ls :minsep value
+Set or show the minimum separation allowed between features.
+.le
+.ls :read name ap
+Read a record from the database.  The record name defaults to the image name
+and, for 1D spectra, the aperture number defaults to aperture of
+the current image.
+.le
+.ls :write name ap
+Write a record to the database.  The record name defaults to the image name
+and, for 1D spectra, the aperture number defaults to aperture of
+the current image.
+.le
+.ls :add name ap
+Add features from a database record.  The record name defaults to the image name
+and, for 1D spectra, the aperture number defaults to aperture of
+the current image.  Only the features are added to any existing list
+of features.  The dispersion function is not read.
+.le
+.ls :zwidth value
+Set or show the zoom width in user units.
+.le
+.ls :/help
+Print additional help for formatting graphs.  See help under "gtools".
+.le
+.ih
+DESCRIPTION
+Features in the input images are identified interactively and assigned
+user coordinates.  A "coordinate function" mapping pixel coordinates to
+user coordinates may be determined from the identified features.  A
+user coordinate list may be defined to automatically identify additional
+features.  This task is used to measure positions of features,
+determine dispersion solutions for spectra, and to identify features in
+two and three dimensional images for mapping a two or three dimensional
+coordinate transformation.  Because of this dual use the terms vector
+and feature are used rather than spectrum and spectral line.
+
+Each image in the input list is considered in turn.  If the image is
+not one dimensional or a one dimensional section of an image
+then the image section given by the parameter
+\fIsection\fR is used.  This parameter may be specified in several ways as
+described in the PARAMETERS and EXAMPLES sections.  The image section is used
+to select a starting vector and image axis.
+
+If the image is not one dimensional or in multispec format then the number
+of lines, columns, or bands given by the parameter \fInsum\fR are summed.
+The one dimensional image vector is graphed.  The initial feature list and
+coordinate function are read from the database if an entry exists.  The
+features are marked on the graph.  The image coordinates are in pixels
+unless a coordinate function is defined, in which case they are in user
+coordinate units.  The pixel coordinate, coordinate function value, and
+user coordinate for the current feature are printed.
+
+The graphics cursor is used to select features and perform various
+functions.  A menu of the keystroke options and functions is printed
+with the key '?'.  The cursor keys and their functions are defined in
+the CURSOR KEYS section and described further below.  The standard
+cursor mode keys are also available to window and redraw the graph and
+to produce hardcopy "snaps".
+
+There are a number of ways of defining features.  They fall into
+two categories; interactively defining features with the cursor
+and using automatic algorithms.
+
+The 'm' key is the principle interactive feature marking method.  Typing
+'m' near the position of a feature applies a feature centering algorithm
+(see \fBcenter1d\fR) and, if a center is found, the feature is entered in
+the feature list and marked on the spectrum.  If the new position is within
+a distance given by the parameter \fIminsep\fR of a previous feature it is
+considered to be the same feature and replaces the old feature.  Normally
+the position of a new feature will be exactly the same as the original
+feature.  The coordinate list is searched for a match between the
+coordinate function value (when defined) and a user coordinate in the
+list.  If a match is found it becomes the default user coordinate which the
+user may override.  The new feature is marked on the graph and it becomes
+the current feature.  The redefinition of a feature which is within the
+minimum separation may be used to set the user coordinate from the
+coordinate list.  The 't' key allows setting the position of a feature to
+other than that found by the centering algorithm.
+
+The principle automatic feature identification algorithm is executed
+with the 'b' key.  The user is queried for an approximate coordinate
+value and coordinate interval per pixel.  The coordinate value
+is for the center of the spectrum by default though this may be changed
+with the \fBaidpars\fR parameters.  Only the magnitude of the
+coordinate interval per pixel is used by default though this also
+may be changed.  Either value may be given as INDEF to do an unconstrained
+search, however, this will be much slower and more likely to fail.
+The algorithm searches for matches between the strong lines in the
+spectrum and lines in the coordinate list.  The algorithm is described
+in the documentation for \fBaidpars\fR.
+
+The 'b' key works with no predefined dispersion solution or features.  If
+two or more features are identified, with 'm', spanning the range of the
+data or if a coordinate function is defined, from a previous solution, then
+the 'e', 'l', and 'y' keys may be used to identify additional features from
+a coordinate list.  The 'e' key only adds features at the coordinates of
+the line lists if the centering algorithm finds a feature at that
+wavelength (as described below).  The 'y' key works in reverse by finding
+the prominent features using a peak finding algorithm and then looking in
+the coordinate list for entries near the estimated position.  Up to a
+maximum number of features (\fImaxfeatures\fR) will be selected.  If there
+are more peaks only the strongest are kept.  In either of these cases there
+is no automatic fitting and refitting of the dispersion function.
+
+The 'l' key combines automatic fits with locating lines from the coordinate
+list.  If two or more features are defined an initial fit is made.  Then
+for each coordinate value in the coordinate list the pixel coordinate is
+determined and a search for a feature at that point is made.  If a feature
+is found (based on the parameters \fIftype, fwidth\fR, \fIcradius\fR, and
+\fBthreshold\fR) its user coordinate value based on the coordinate function
+is determined.  If the coordinate function value matches the user
+coordinate from the coordinate list within the error limit set by the
+parameter \fImatch\fR then the new feature is entered in the feature list.
+Up to a maximum number of features, set by the parameter \fImaxfeatures\fR,
+may be defined in this way.  A new user coordinate function is fit to all
+the located features.  Finally, the graph is redrawn in user coordinates
+with the additional features found from the coordinate list marked.
+
+A minimum of two features must be defined for the 'l' key algorithm to
+work.  However, three or more features are preferable to determine changes
+in the dispersion as a function of position.
+
+The 'f' key fits a function of the pixel coordinates to the user
+coordinates.  The type of function, order and other fitting parameters
+are initially set with the parameters \fIfunction, order, sample,
+niterate, low_reject, high_reject\fR and \fIgrow\fR..  The value of the
+function for a particular pixel coordinate is called the function
+coordinate and each feature in the feature list has a function
+coordinate value.  The fitted function also is used to convert pixel
+coordinates to user coordinates in the graph.  The fitting is done
+within the interactive curve fitting package which has its own set of
+interactive commands.  For further information on this package see the
+help material under \fBicfit\fR.
+
+If a zero point shift is desired without changing the coordinate function
+the user may specify the coordinate of a point in the spectrum with
+the 's' key from which a shift is determined.  The 'g' key also
+determines a shift by minimizing the difference between the user
+coordinates and the fitted coordinates.  This is used when a previously
+determined coordinate function is applied to a new spectrum having
+fewer or poorer lines and only a zero point shift can reasonably be
+determined.  Note that the zero point shift is in user coordinates.
+This is only an approximate correction for shifts in the raw spectra
+since these shifts are in pixels and the coordinate function should
+also be appropriately shifted.
+
+One a set of features is defined one may select features for various
+operations.  To select feature as the current feature the keys '.', 'n',
+'+', and '-' are used.  The '.' selects the feature nearest the cursor, the
+'n' and '+' select the next feature, and the '-' selects the previous
+feature relative to the current feature in the feature list as ordered by
+pixel coordinate.  These keys are useful when redefining the user
+coordinate with the 'u' key, changing the fitting weight of a feature with
+'v', and when examining features in zoom mode.
+
+Features may be deleted with the key 'd'.  All features are deleted
+when the 'a' key immediately precedes the delete key.  Deleting the
+features does not delete the coordinate function.  Features deleted in the
+curve fitting package also are removed from the feature list upon
+exiting the curve fitting package.
+
+It is common to transfer the feature identifications and coordinate function
+from one image to another.  When a new image without a database entry
+is examined, such as when going to the next image in the input list,
+changing image lines or columns with 'j', 'k' and 'o', or selecting
+a new image with the ":image" command, the current feature list and coordinate
+function are kept.  Alternatively, a database record from a different
+image may be read with the ":read" command.  When transferring feature
+identifications between images the feature coordinates will not agree exactly
+with the new image feature positions and several options are available to
+reregister the feature positions.  The key 'c' centers the feature nearest
+the cursor using the current position as the starting point.  When preceded
+with the 'a' key all the features are recentered (the user must refit
+the coordinate function if desired).  As an aside, the recentering
+function is also useful when the parameters governing the feature
+centering algorithm are changed.  An additional options is the ":add"
+command to add features from a database record.  This does not overwrite
+previous features (or the fitting functions) as does ":read".
+
+The (c)entering function is applicable when the shift between the current
+and true feature positions is small.  Larger shifts may be determined
+automatically with the 's' or 'x' keys.
+
+A zero point shift is specified interactively with the 's' key by using the
+cursor to indicate the coordinate of a point in the spectrum.  If there are
+no features then the shift is exactly as marked by the cursor.  If there
+are features the specified shift is applied, the features are recentered,
+and the mean shift for all the features is determined.
+
+The 'x' key uses the automatic line identification algorithm (see
+\fBaidpars\fR) with the constraint that the dispersion is nearly the
+same and the is primarily a shift in the coordinate zero point.  If
+features are defined, normally by inheritance from another spectrum, then a
+first pass is done to identify those features in the spectrum.  Since this
+only works when the shifts are significantly less than the dispersion range
+of the spectrum (i.e. a significant number of features are in common) a
+second pass using the full coordinate line list is performed if a shift
+based on the features is not found.  After a shift is found any features
+remaining from the original list are recentered and a mean shift is
+computed.
+
+In addition to the single keystroke commands there are commands initiated
+by the key ':' (colon commands).  As with the keystroke commands there are
+a number of standard graphics features available beginning with ":."
+(type ":.help" for these commands).  The identify colon commands
+allow the task parameter values to be listed and to be reset
+within the task.  A parameter is listed by typing its name.  The colon command
+":show" lists all the parameters.  A parameter value is reset by
+typing the parameter name followed by the new value; for example
+":match 10".  Other colon commands display the feature list (:features),
+control reading and writing records to the database (:read and :write),
+and set the graph display format.
+
+The feature identification process for an image is completed by typing
+'q' to quit.  Attempting to quit an image without explicitly
+recording changes in the feature database produces a warning message
+unless the \fIautowrite\fR parameter is set.  If this parameter is
+not set a prompt is given asking whether to save the results otherwise
+the results are automatically saved.  Also
+the reference spectrum keyword REFSPEC is added to the image header at
+this time.  This is used by \fBrefspectra\fR and \fBdispcor\fR.
+As an immediate exit the 'I' interrupt key may be used.  This does not save
+the feature information and may leave the graphics in a confused state.
+.ih
+DATABASE RECORDS
+The database specified by the parameter \fIdatabase\fR is a directory of
+simple text files.  The text files have names beginning with 'id' followed
+by the entry name, usually the name of the image.  The database text files
+consist of a number of records.  A record begins with a line starting with the
+keyword "begin".  The rest of the line is the record identifier.  Records
+read and written by \fBidentify\fR have "identify" as the first word of the
+identifier.  Following this is a name which may be specified following the
+":read" or ":write" commands.  If no name is specified then the image name
+is used.  For 1D spectra the database entry includes the aperture number
+and so to read a solution from a aperture different than the current image
+and aperture number must be specified.  For 2D/3D images the entry name
+has the 1D image section which is what is specified to read the entry.
+The lines following the record identifier contain
+the feature information and dispersion function coefficients.
+
+The dispersion function is saved in the database as a series of
+coefficients.  The section containing the coefficients starts with the
+keyword "coefficients" and the number of coefficients.
+
+The first four coefficients define the type of function, the order
+or number of spline pieces, and the range of the independent variable
+(the line or column coordinate along the dispersion).  The first
+coefficient is the function type code with values:
+
+.nf
+	Code	Type
+	   1	Chebyshev polynomial
+	   2	Legendre polynomial
+	   3	Cubic spline
+	   4	Linear spline
+.fi
+
+The second coefficient is the order (actually the number of terms) of
+the polynomial or the number of pieces in the spline.
+
+The next two coefficients are the range of the independent variable over
+which the function is defined.  These values are used to normalize the
+input variable to the range -1 to 1 in the polynomial functions.  If the
+independent variable is x and the normalized variable is n, then
+
+.nf
+	n = (2 * x - (xmax + xmin)) / (xmax - xmin)
+.fi
+
+where xmin and xmax are the two coefficients.
+
+The spline functions divide the range into the specified number of
+pieces.  A spline coordinate s and the nearest integer below s,
+denoted as j, are defined by
+
+.nf
+	s = (x - xmin) / (xmax - xmin) * npieces
+	j = integer part of s
+.fi
+
+where npieces are the number of pieces.
+
+The remaining coefficients are those for the appropriate function.
+The number of coefficients is either the same as the function order
+for the polynomials, npieces+1 for the linear spline, or npieces + 3
+for the cubic spline.
+
+1. Chebyshev Polynomial
+
+The polynomial can be expressed as the sum
+
+.nf
+	y = sum from i=1 to order {c_i * z_i}
+.fi
+
+where the c_i are the coefficients and the z_i are defined
+interactively as:
+
+.nf
+	z_1 = 1
+	z_2 = n
+	z_i = 2 * n * z_{i-1} - z_{i-2}
+.fi
+
+2. Legendre Polynomial
+
+The polynomial can be expressed as the sum
+
+.nf
+	y = sum from i=1 to order {c_i * z_i}
+.fi
+
+where the c_i are the coefficients and the z_i are defined
+interactively as:
+
+.nf
+	z_1 = 1
+	z_2 = n
+	z_i = ((2*i-3) * n * z_{i-1} - (i-2) * z_{i-2}) / (i-1)
+.fi
+
+3. Linear Spline
+
+The linear spline is evaluated as
+
+.nf
+	y = c_j * a + c_{j+1} * b
+.fi
+
+where j is as defined earlier and a and b are fractional difference
+between s and the nearest integers above and below
+
+.nf
+	a = (j + 1) - s
+	b = s - j
+.fi
+
+4.  Cubic Spline
+
+The cubic spline is evaluated as
+
+.nf
+	y = sum from i=0 to 3 {c_{i+j} * z_i}
+.fi
+
+where j is as defined earlier.  The term z_i are computed from
+a and b, as defined earlier, as follows
+
+.nf
+	z_0 = a**3
+	z_1 = 1 + 3 * a * (1 + a * b)
+	z_2 = 1 + 3 * b * (1 + a * b)
+	z_3 = b**3
+.fi
+.ih
+EXAMPLES
+1.  Because this task is interactive and has many possible applications
+it is difficult to provide actual examples.  Instead some uses of the task
+are described.
+
+.ls o
+For defining distortions in the slit dimension as a function of
+wavelength the positions of objects are marked at some wavelength.
+The task \fBreidentify\fR is then used to trace the features to other
+wavelengths.
+.le
+.ls o
+For determining dispersion solutions in a one dimensional
+spectrum an arc calibration is used.  Three emission features are marked
+and the (l)ocate key is used to find additional features from a
+coordinate list of arc lines.  The dispersion solution is fit interactively
+and badly determined or misidentified lines are deleted.  The
+solution may be written to the database or transferred to the object
+spectrum by reading the object image and deleting all the features.
+Deleting the features does not delete the coordinate function.
+.le
+.ls o
+For determining a two or three dimensional coordinate transformation a
+dispersion solution is determined at one slit position in a long slit arc
+spectrum or one spatial position in a Fabry-Perot spectrum as in the
+previous example.  The features are then traced to other positions with the
+task \fBreidentify\fR.
+.le
+
+2.  For images which are two or three dimensional it is necessary to
+specify the image axis for the data vector and the number of pixels at each
+point across the vector direction to sum.  One way specify a vector is to
+use an image section to define a vector.  For example, to select column
+20:
+
+.nf
+    cl> identify obj[20,*]
+.fi
+
+The alternative is to use the section parameter.  Below are some examples
+of the section parameter syntax for an image "im2d" which is 100x200
+and "im3d" which is 100x200x50.  On the left is the section string syntax
+and on the right is the image section
+
+.nf
+    Section parameter |  Image section      |  Description
+    ------------------|---------------------|---------------------
+    first line        |  im2d[*,1]          |  First image line
+    middle column     |  im2d[50,*]         |  Middle image column
+    last z            |  im3d[100,200,*]    |  Last image z vector
+    middle last y     |  im3d[50,*,50]      |  Image y vector
+    line 20           |  im2d[*,20]         |  Line 20
+    column 20         |  im2d[20,*]         |  Column 20
+    x 20              |  im2d[*,20]         |  Line 20
+    y 20              |  im2d[20,*]         |  Column 20
+    y 20 30           |  im2d[20,*,30]      |  Column 20
+    z 20 30	      |  im3d[20,30,*]      |  Image z vector
+    x middle          |  im3d[*,100,25]     |  Middle of image
+    y middle          |  im3d[50,*,25]      |  Middle of image
+    z middle          |  im3d[50,100,*]     |  Middle of image
+.fi
+
+The most common usage should be "middle line", "middle column" or "middle z".
+
+The summing factors apply to the axes across the specified vector.  For
+3D images there may be one or two values.  The following shows which axes
+are summed, the second and third columns, when the vector axis is that shown
+in the first column.
+
+.nf
+    Vector axis       |   Sum axis in 2D    |  Sum axes in 3D
+    ------------------|---------------------|--------------------
+         1            |         2           |      2 3                 
+         2            |         1           |      1 3                 
+         3            |         -           |      1 2                 
+.fi
+
+.ih
+REVISIONS
+.ls IDENTIFY V2.11
+The dispersion units are now determined from a user parameter,
+the coordinate list, or the database entry.
+
+A new key, 'e', has been added to add features from a line list without
+doing any fits.  This is like the 'l' but without the automatic
+fitting before and after adding new features.
+
+A new key, 'b', has been added to apply an automatic line identification
+algorithm.
+
+The 'x' key has been changed to use the automatic line identification
+algorithm.  The allows finding much larger shifts.
+
+The match parameter may now be specified either in user coordinates or
+in pixels.  The default is now 3 pixels.
+
+The default threshold value has been changed to 0.
+.le
+.ls IDENTIFY V2.10.3
+The section and nsum parameter syntax was extended to apply to 3D
+images.  The previous values and defaults may still be used.
+
+The 'v' key was added to allow assigning weights to features.
+.le
+.ls IDENTIFY V2.10
+The principle revision is to allow multiple aperture images and long slit
+spectra to be treated as a unit.  New keystrokes allow jumping or scrolling
+within multiple spectra in a single image.  For aperture spectra the
+database entries are referenced by image name and aperture number and not
+with image sections.  Thus, IDENTIFY solutions are not tied to specific
+image lines in this case.  There is a new autowrite parameter which may
+be set to eliminate the save to database query upon exiting.  The new
+colon command "add" may be used to add features based on some other
+spectrum or arc type and then apply the fit to the combined set of features.
+.le
+.ih
+SEE ALSO
+autoidentify, reidentify, aidpars, center1d, linelists, fitcoords, icfit,
+gtools
+.endhelp
diff --git a/noao/onedspec/doc/lcalib.hlp b/noao/onedspec/doc/lcalib.hlp
new file mode 100644
index 00000000..cc327217
--- /dev/null
+++ b/noao/onedspec/doc/lcalib.hlp
@@ -0,0 +1,125 @@
+.help lcalib Mar92 noao.onedspec
+.ih
+NAME
+lcalib -- List information about the spectral calibration data
+.ih
+USAGE
+lcalib option star_name
+.ih
+PARAMETERS
+.ls option
+Chooses calibration data to be listed.  Option
+may be: "bands" to list the bandpasses at each wavelength, "ext" to
+list the extinction at each wavelength, "mags", "fnu", or "flam"
+to list the magnitude, or flux of
+the star (selected by the star_name parameter) at each wavelength, or
+"stars" to list the star names available in the calibration directory.
+.le
+.ls star_name
+Selects which star's magnitude list is chosen if the option parameter
+is "mags", "fnu", "flam", or "bands".  Also if '?' a list of available
+stars in the specified calibration directory is given.
+.le
+
+The following three queried parameters apply if the selected calibration
+file is for a blackbody.  See \fBstandard\fR for further details.
+.ls mag
+The magnitude of the observed star in the band given by the
+\fImagband\fR parameter.  If the magnitude is not in the same band as
+the blackbody calibration file then the magnitude may be converted to
+the calibration band provided the "params.dat" file containing relative
+magnitudes between the two bands is in the calibration directory
+.le
+.ls magband
+The standard band name for the input magnitude.  This should generally
+be the same band as the blackbody calibration file.  If it is
+not the magnitude will be converted to the calibration band.
+.le
+.ls teff
+The effective temperature (deg K) or the spectral type of the star being
+calibrated.  If a spectral type is specified a "params.dat" file must exist
+in the calibration directory.  The spectral types are specified in the same
+form as in the "params.dat" file.  For the standard blackbody calibration
+directory the spectral types are specified as A0I, A0III, or A0V, where A
+can be any letter OBAFGKM, the single digit subclass is between 0 and 9,
+and the luminousity class is one of I, III, or V.  If no luminousity class
+is given it defaults to dwarf.
+.le
+
+.ls extinction
+Extinction file.  The current standard extinction files:
+.nf
+	onedstds$kpnoextinct.dat - KPNO standard extinction
+	onedstds$ctioextinct.dat - CTIO standard extinction
+.fi
+.le
+.ls caldir
+Calibration directory containing standard star data.  The directory name
+must end with /.  The current calibration directories available in the
+onedstds$ may be listed with the command:
+
+.nf
+	cl> page onedstds$README
+.fi
+.le
+.ls fnuzero = 3.68e-20
+The absolute flux per unit frequency at a magnitude of zero.  This is used
+to convert the calibration  magnitudes to absolute flux by the formula
+
+	Flux = fnuzero * 10. ** (-0.4 * magnitude)
+
+The flux units are also determined by this parameter.  However, the
+frequency to wavelength interval conversion assumes frequency in hertz.
+The default value is based on a calibration of Vega at 5556 Angstroms of
+3.52e-20 ergs/cm2/s/hz for a magnitude of 0.048.  This default value
+is that used in earlier versions of this task which did not allow the
+user to change this calibration.
+.le
+.ih
+DESCRIPTION
+LCALIB provides a means of checking the flux calibration data.  The calibration
+data consists of extinction, bandpasses, and stellar magnitudes.
+
+The extinction is given in an extinction file consisting of lines with
+wavelength and extinction.  The wavelengths must be order in increasing
+wavelength and the wavelengths must be in Angstroms.  There are two
+standard extinction files currently available, "onedstds$kpnoextinct.dat",
+and "onedstds$ctioextinct.dat".
+
+The standard star data are in files in a calibration
+directory specified with the parameter \fIcaldir\fR.  A standard star
+file is selected by taking the star name given, by the parameter
+\fIstar_name\fR, removing blanks, +'s and -'s, appending ".dat", and converting
+to lower case.  This file name is appended to the specified calibration
+directory.  A calibration file consists of lines containing a wavelength,
+a stellar magnitude, and a bandpass full width.  The wavelengths are in
+Angstroms.  Comment lines beginning with # may be included in the file.
+The star names printed by this task are just the first line of each file
+in the calibration directory with the first character (#) removed.
+The calibration files may be typed, copied, and printed.  \fBLcalib\fR
+may also be used to list data from the calibration files.
+.ih
+EXAMPLES
+
+.nf
+	# List the extinction table
+	cl> lcalib ext
+	# Plot the extinction table
+	cl> lcalib ext | graph
+	# Plot the energy distribution
+	cl> lcalib mags "bd+28 4211" | graph
+	# List the names of all the stars
+	cl> lcalib stars caldir=onedstds$irscal/
+	# As above but for IIDS file
+	cl> lcalib stars calib_file=onedstds$iidscal/
+.fi
+.ih
+REVISIONS
+.ls LCALIB V2.10
+This task has a more compact listing for the "stars" option and allows
+paging a list of stars when the star name query is not recognized.
+.le
+.ih
+SEE ALSO
+standard, sensfunc, onedstds$README
+.endhelp
diff --git a/noao/onedspec/doc/mkspec.hlp b/noao/onedspec/doc/mkspec.hlp
new file mode 100644
index 00000000..96efd726
--- /dev/null
+++ b/noao/onedspec/doc/mkspec.hlp
@@ -0,0 +1,86 @@
+.help mkspec Mar92 noao.onedspec
+.ih
+NAME
+mkspec -- generate an artificial spectrum or image (obsolete)
+.ih
+USAGE
+mkspec image_name image_title ncols nlines function
+.ih
+PARAMETERS
+.ls image_name
+The name to be given to the image file
+.le
+.ls image_title
+A character string to be used to describe the image
+.le
+.ls ncols
+The number of pixels in the spectrum (the length of the image).
+.le
+.ls nlines
+The number or lines (rows) in the image.
+.le
+.ls function
+An indicator specifying the form of the spectrum: 1 - a constant,
+2 - a ramp running from start_level to end_level, 3 - a black body
+extending in wavelength (Angstroms) from start_wave to end_wave
+at a given temperature (in degrees K).
+.le
+.ls constant
+The value to be assigned to the spectrum if function=1 (constant).
+.le
+.ls start_level
+The starting value to be assigned to the spectrum at pixel 1 if
+function=2 (ramp).
+.le
+.ls end_level
+The ending value of the spectrum assigned at pixel=ncols if function=2.
+.le
+.ls start_wave
+The wavelength (Angstroms) assigned to pixel 1 if function=3 (Black Body).
+.le
+.ls end_wave
+The wavelength (Angstroms) assigned to the last pixel if function=3.
+.le
+.ls temperature
+The black body temperature (degrees K) for which the spectrum
+is to be created if function=3.
+.le
+.ih
+DESCRIPTION
+An artificial image is created with the specified name and length.
+The image may have a constant value (function=1), or may be a ramp
+with either positive or negative slope (function=2), or may be
+a black body curve (function=3).
+
+Only those parameters specific to the functional form of the image
+need be specified. In all cases the parameters image_name, image_title,
+ncols, nlines, and function are required. If function=1, parameter constant
+is required; if function=2, start_level and end_level are required;
+if function=3, start_wave, end_wave, and temperature are required.
+
+All black body functions are normalized to 1.0 at their peak
+intensity which may occur at a wavelength beyond the extent of
+the generated spectrum.
+
+NOTE THAT THIS TASK IS OBSOLETE AND ARTDATA.MK1DSPEC SHOULD BE USED.
+In particular this task does not set the header dispersion coordinate
+system.
+.ih
+EXAMPLES
+
+.nf
+	cl> mkspec allones "Spectrum of 1.0" 1024 1 1 constant=1.0
+	cl> mkspec ramp "From 100.0 to 0.0" 1024 64 2 start=100 \
+	>>> end=0.0
+	cl> mkspec bb5000 "5000 deg black body" 512 1 3 start=3000 \
+	>>> end=8000 temp=5000
+.fi
+.ih
+REVISIONS
+.ls MKSPEC V2.10
+This task is unchanged.
+.le
+.ih
+SEE ALSO
+artdata.mk1dspec, artdata.mk2dspec, artdata.mkechelle
+.endhelp
diff --git a/noao/onedspec/doc/names.hlp b/noao/onedspec/doc/names.hlp
new file mode 100644
index 00000000..9004b20e
--- /dev/null
+++ b/noao/onedspec/doc/names.hlp
@@ -0,0 +1,67 @@
+.help names Mar92 noao.onedspec
+.ih
+NAME
+names -- Generate image names from a root and a range descriptor
+.ih
+USAGE
+names input records
+.ih
+PARAMETERS
+.ls input
+The root file name for the input records to be calibrated.
+.le
+.ls records
+The range of spectra to be included in the calibration operation.
+Each range item will be appended to the root name to form an
+image file name.
+.le
+.ls append = ""
+If not a null string, this character string will be appended to
+all the generated image names. This allows for a specification of
+image sections.
+.le
+.ls check = no
+If set to yes, a check is made that each name implied by the range
+specification has at least an image header. The pixel file is not
+checked. If set to no, then all possible image names are generated
+even if no image exists.
+.le
+.ih
+DESCRIPTION
+A sequence of image names is generated from the input root file name
+and the range description by appending the possible range values to
+the root in the form "root.nnnn". At least four digits will follow the
+root.
+
+If an append string is specified, this is added to the image name as well.
+
+The generated image names are written to STDOUT, but may be redirected
+to a file for further use.
+.ih
+EXAMPLES
+The following will generate names of the form nite1.0001, nite1.0002 ...
+nite1.0010 and place the list in the file nite1.lst.
+
+.nf
+	cl> names nite1 1-10 >nite1.lst
+.fi
+
+The next example uses the append option to specify that only the
+first 512 pixels of each image (spectrum) are to used in the image name.
+
+.nf
+	cl> names nite1 1-10 append="[1:512]" >nite1.lst
+.fi
+.ih
+REVISIONS
+.ls NAMES V2.10
+This task is unchanged.
+.le
+.ih
+.ih
+BUGS
+The append option is only useful for adding image sections since it is
+added after the ONEDSPEC name is generated.  Appending other strings
+produces names such as root.0012str which are not recognized by
+the package.
+.endhelp
diff --git a/noao/onedspec/doc/ndprep.hlp b/noao/onedspec/doc/ndprep.hlp
new file mode 100644
index 00000000..6f59ba4b
--- /dev/null
+++ b/noao/onedspec/doc/ndprep.hlp
@@ -0,0 +1,115 @@
+.help ndprep Mar92 noao.onedspec
+.ih
+NAME
+ndprep -- Make a neutral density filter calibration image
+.ih
+USAGE
+ndprep filter_curve output
+.ih
+PARAMETERS
+.ls filter_curve
+Neutral density filter curve.  The directory specified by the parameter
+\fIdirectory\fR is prepended to this name so if a directory is specified
+then it should not be given here.  If '?' a list of filter curves
+in the specified directory is typed.
+.le
+.ls output
+Output neutral density filter image.
+.le
+.ls w0   
+Starting wavelength for the output image in Angstroms.
+.le
+.ls dw   
+Wavelength increment for the output image in Angstroms.
+.le
+.ls nw   
+Number of wavelength points for the output image (i.e. the size of the
+output image).
+.le
+.ls nspace = 0
+Number of spatial points for a two dimensional image.  If the value is
+zero then a one dimensional image is created.
+.le
+.ls logarithm = no
+Use logarithmic wavelengths and intervals?  If yes then the wavelengths
+will have the same starting and ending points and number of pixels but
+the wavelength intervals will be logarithmic.
+.le
+.ls flux = yes
+Conserve flux when rebinning to logarithmic wavelength intervals?
+.le
+.ls dispaxis = 1
+Dispersion axis for two dimensional images.  Dispersion along the lines
+is 1 and dispersion along the columns is 2.
+.le
+.ls directory = "onedstds$ctio/"
+Directory containing neutral density filter curves.  This directory is
+prepended to the specified fiter curve file (and so must end with '/'
+or '$').
+.le
+.ih
+DESCRIPTION
+A neutral density (ND) filter curve is converted to a calibration image
+with the same size and wavelength range as the images to be calibrated.
+A list of standard neutral density curves is typed if the filter
+curve name is given as '?'.  The ND curves are text files containing
+wavelength and filter transmission pairs.  Comments begin with '#'.
+A plot of the ND curve can be obtained using \fBgraph\fR.
+
+The ND curve is first interpolated to a one dimensional image of
+\fInw\fR wavelength points with starting wavelength \fIwO\fR and
+wavelength increment \fIdw\fR using the task \fBsinterp\fR.  The
+wavelength parameters must be in the same units as the filter curves
+(currently Angstroms) even if the final calibration image is to be in
+logarithmic wavelength intervals.  If logarithmic wavelength format
+is specified the image is rebinned over the same wavelength range with
+the same number of points using the task \fBdispcor\fR.  The rebinning
+may include flux conservation to account for the changing size of
+pixels or simply interpolate.  Note that flux conservation will
+change the apparent shape of the ND curve.
+
+If the number of points across the dispersion, \fInspace\fR is zero then
+the final calibration image is one dimensional.  If it is greater than
+zero the one dimensional ND image is expanded to the specified number
+of spatial points with the dispersion axis specified by the parameter
+\fIdispaxis\fR (1 = dispersion along the lines, 2 = dispersion along
+the columns).
+.ih
+EXAMPLES
+To get a list of standard ND filter curves:
+
+	cl> ndprep ?
+
+To graph the ND filter curve:
+
+	cl> graph onedstds$ctio/nd1m.100mag.dat
+
+Naturally, if a calibration image is made then the image plotting tasks
+such as \fBgraph\fR, \fBimplot\fR, and \fBsplot\fR may also be used.
+
+To make a one dimensional ND calibration spectrum:
+
+.nf
+	cl> ndprep w0=4000 dw=1.2 nw=512
+	Input ND filter curve:  onedstds$ctio/nd1m.100mag.dat
+	Output calibration image: NDimage
+.fi
+
+To make a two dimensional ND calibration spectrum in logarithmic wavelength:
+
+.nf
+	cl> ndprep w0=4000 dw=1.2 nw=512 nspace=200 log+
+	Input ND filter curve:  onedstds$ctio/nd4m.u000mag.dat
+	Output calibration image: NDimage
+.fi
+.ih
+REVISIONS
+.ls NDPREP V2.10
+This task was moved from the \fBproto\fR package.  It was originally
+written at CTIO for CTIO data.  It's functionality is largely unchanged
+though it has been updated for changes in the \fBonedspec\fR package.
+.le
+.ih
+SEE ALSO
+sinterp, dispcor
+.endhelp
diff --git a/noao/onedspec/doc/odcombine.hlp b/noao/onedspec/doc/odcombine.hlp
new file mode 100644
index 00000000..11ddffe5
--- /dev/null
+++ b/noao/onedspec/doc/odcombine.hlp
@@ -0,0 +1,480 @@
+.help odcombine Apr04 onedspec
+.ih
+NAME
+odcombine -- Combine spectra using various algorithms
+.ih
+USAGE	
+odcombine input output
+.ih
+PARAMETERS
+.ls input
+List of input images containing spectra to be combined.  The spectra
+in the images to be combined are selected with the \fIapertures\fR and
+\fIgroup\fR parameters.  Only the primary spectrum is combined and
+the associated band spectra are ignored.  This task does not work on
+higher dimensional spectra data.  To apply it first use a task to
+extract it to 1D spectra.  The simplest method is \fBscopy\fR.
+.le
+.ls output
+List of output images to be created containing the combined spectra.  If
+the grouping option is "all" then only one output image is created with the
+specified name.  If the grouping option is "images" then there will be one
+output image for each input image and the output list must match the input
+list in number.  If the grouping option is "apertures" then only one output
+root name is specified and there will be one output image for each selected
+aperture.  In this case the output images will have a name formed from the
+root name and a four digit aperture number extension.  In all cases the
+output images contain a single 1D spectrum.  Other tasks, such as
+\fBscopy\fR, may be used to pack the spectra into a single file.
+.le
+
+
+There are a number of additional optional output files that may be produced.
+The lists are handled in the same was as for the primary output; i.e.
+depending on the grouping a single name, root name, or a matching list
+is specified.
+.ls headers = "" (optional)
+Optional output multiextension FITS file(s).  The extensions are dataless
+headers from each input image.
+.le
+.ls bpmasks = "" (optional)
+Optional output bad pixel mask(s) with good values of 0 and bad values of
+1.  Output pixels are marked as bad when no input pixels contributed to the
+output pixel.  The file name is also added to the output image header under
+the keyword BPM.
+.le
+.ls rejmask = "" (optional)
+Optional output mask file(s) identifying rejected or excluded pixels.  The
+pixel mask is the size of the output image but there is one extra dimension
+with length equal to the number of input images.  Each element of the
+highest dimension is a mask corresponding to an input image with values of
+1 for rejected or excluded pixels and values of 0 for pixels which were
+used.  The order of the masks is the order of the input images and image
+header keywords, indexed by the pixel coordinate of the highest dimension
+identify the input images.  Note that the pixel positions are in the output
+pixel coordinate system.
+.le
+.ls nrejmasks = "" (optional)
+Optional output pixel mask(s) giving the number of input pixels rejected or
+excluded from the input images.
+.le
+.ls expmasks = "" (optional)
+Optional output exposure mask(s) giving the sum of the exposure values of
+the input images with non-zero weights that contributed to that pixel.
+Since masks are integer, the exposure values may be scaled to preserve
+dynamic range and fractional significance.  The scaling values are given in
+the header under the keywords MASKSCAL and MASKZERO.  Exposure values are
+computed from the mask values by scale * value + zero where scale is the
+value of the MASKSCAL keyword and zero is the value of the MASKZERO
+keyword.
+.le
+.ls sigma = "" (optional)
+Optional output sigma image(s).  The sigma is the standard deviation,
+corrected for a finite population, of the input pixel values (excluding
+rejected pixels) about the output combined pixel values.
+.le
+.ls logfile = "STDOUT" (optional)
+Optional output log file.  If no file is specified then no log information is
+produced.  The special filename "STDOUT" prints log information to the
+terminal.
+.le
+
+
+.ce
+Grouping Parameters
+.ls apertures = ""
+List of apertures to be selected for combining.  If none is specified
+then all apertures are selected.  The syntax is a blank or comma separated
+list of aperture numbers or hypen separated aperture ranges.
+.le
+.ls group = "apertures" (all|images|apertures)
+Option for grouping input spectra for combining (after selection by aperture)
+from one or more input images.  The options are:
+.ls "all"
+Combine all spectra from all images in the input list into a single output
+spectrum.
+.le
+.ls "images"
+Combine all spectra in each input image into a single spectrum in
+separate output images.
+.le
+.ls "apertures"
+Combine all spectra of the same aperture from all input images and put it
+into an output image with specified root name and a four digit aperture
+number extension.
+.le
+.le
+
+
+.ce
+Dispersion Matching Parameters
+.ls first = no
+Use the first input spectrum of each set to be combined to define the
+dispersion coordinates for combining and output?  If yes then all other
+spectra to be combined will be interpolated to the dispersion of this
+spectrum and that dispersion defines the dispersion of the
+output spectrum.  If no, then all the spectra are interpolated to a linear
+dispersion as determined by the following parameters.  The interpolation
+type is set by the package parameter \fIinterp\fR.
+.le
+.ls w1 = INDEF, w2=INDEF, dw = INDEF, nw = INDEF, log = no
+The output linear or log linear wavelength scale if the dispersion of the
+first spectrum is not used.  INDEF values are filled in from the maximum
+wavelength range and minimum dispersion of the spectra to be combined.  The
+parameters are aways specified in linear wavelength even when the log
+parameter is set to produce constant pixel increments in the log of the
+wavelength.  The dispersion is interpreted in that case as the difference
+in the log of the endpoints divided by the number of pixel.
+.le
+
+
+.ce
+Combining Parameters
+.ls combine = "average" (average|median|sum)
+Type of combining operation performed on the final set of pixels (after
+offsetting, masking, thresholding, and rejection).  The choices are
+"average", "median", or "sum".  The median uses the average of the two central
+values when the number of pixels is even.  For the average and sum, the
+pixel values are multiplied by the weights (1 if no weighting is used)
+and summed.  The average is computed by dividing by the sum of the weights.
+If the sum of the weights is zero then the unweighted average is used.
+.le
+.ls reject = "none" (none|minmax|ccdclip|crreject|sigclip|avsigclip|pclip)
+Type of rejection operation performed on the pixels remaining after offsetting,
+masking and thresholding.  The algorithms are described in the
+help page for \fBimcombine\fR.  The rejection choices are:
+
+.nf
+      none - No rejection
+    minmax - Reject the nlow and nhigh pixels
+   ccdclip - Reject pixels using CCD noise parameters
+  crreject - Reject only positive pixels using CCD noise parameters
+   sigclip - Reject pixels using a sigma clipping algorithm
+ avsigclip - Reject pixels using an averaged sigma clipping algorithm
+     pclip - Reject pixels using sigma based on percentiles
+.fi
+
+.le
+.ls outtype = "real" (none|short|ushort|integer|long|real|double)
+Output image pixel datatype.  The pixel datatypes are "double", "real",
+"long", "integer", unsigned short "ushort", and "short" with highest
+precedence first.  If "none" is specified then the highest precedence
+datatype of the input images is used.  When there is a mixture of
+short and unsigned short images the highest precedence become integer.
+The datatypes may be abbreviated to a single character.
+.le
+.ls outlimits = ""
+Output region limits specified as a pair of whitespace separated pixel
+values.
+.le
+
+
+.ce
+Masking Parameters
+.ls smaskformat = "bpmspectrum" (bpmspectrum|bpmpixel)
+When a mask is applied it must be matched to the input spectrum.  If the
+value of this parameter is "bpmspectrum" the mask file is assumed to have a
+spectral file structure with aperture and dispersion information.  The mask
+spectrum is matched to the input spectrum by aperture number and is
+rebinned from its dispersion to match the rebinned dispersion of the input
+spectrum.  If the value is "bpmpixel" the mask file is assumed to have
+minimal header information and the pixel information is matched to the
+input image pixels.  This means the mask pixels are extracted from the same
+line as the input spectrum and the mask pixels are resampled in the same
+way as the input spectrum pixels.
+.le
+.ls smasktype = "none" (none|goodvalue|badvalue|goodbits|badbit)
+Type of pixel masking to use.  If "none" or "" then no pixel masking is
+done even if an image has an associated  pixel mask.  The other choices are
+to select the value in the pixel mask to be treated as good (goodvalue) or
+bad (badvalue) or the bits (specified as a value) to be treated as good
+(goodbits) or bad (badbits).  The pixel mask filename is specified by the
+image header keyword "BPM".  Note that if the input image contains
+multiple spectra then the mask file must also contain at least the
+selected apertures if the mask format is "bpmspectrum" or matching
+image dimensions if the mask format is "bpmpixel".
+.le
+.ls maskvalue = 0
+Mask value used with the \fImasktype\fR parameter.  If the mask type
+selects good or bad bits the value may be specified using IRAF notation
+for decimal, octal, or hexadecimal; i.e 12, 14b, 0cx to select bits 3
+and 4.
+.le
+.ls blank = 0.
+Output value to be used when there are no pixels.
+.le
+
+
+.ce
+Scaling/Weighting Parameters
+
+The following scaling and weighting parameters have the following behavior
+and constraints, which are particularly relevant to multispec formats where
+multiple spectra are contained in an image with a single image header.
+When using image statistics these are calculated from the rebinned spectra
+being combined as expected.  When using header keywords the values will be
+the same for all spectra from the same input file.
+
+When using a file then the list will be applied repeatedly to each
+group being combined.  If the grouping is by aperture then the values will
+be matched in the order of the input images.  Note that if an image does
+not contain a specified aperture the ordering will be wrong.  If the
+grouping is by image then the file will be matched to the spectra in the
+order of the apertures in the image.  And if the grouping is "all" then the
+list is matched in the order of the images and apertures within the
+images with the apertures in an image varying first.
+
+.ls scale = "none" (none|mode|median|mean|exposure|@<file>|!<keyword>)
+Multiplicative image scaling to be applied.  The choices are none, multiply
+by the reciprocal of the mode, median, or mean of the specified statistics
+section, multiply by the reciprocal of the exposure time in the image header,
+multiply by the values in a specified file, or multiply by a specified
+image header keyword.  When specified in a file the scales must be one per
+line in the order of the input images.
+.le
+.ls zero = "none" (none|mode|median|mean|@<file>|!<keyword>)
+Additive zero level image shifts to be applied.  The choices are none, add
+the negative of the mode, median, or mean of the specified statistics
+section, add the values given in a file, or add the values given by an
+image header keyword.  When specified in a file the zero values must be one
+per line in the order of the input images.  File or keyword zero offset
+values do not allow a correction to the weights.
+.le
+.ls weight = "none" (none|mode|median|mean|exposure|@<file>|!<keyword>)
+Weights to be applied during the final averaging.  The choices are none,
+the mode, median, or mean of the specified statistics section, the exposure
+time, values given in a file, or values given by an image header keyword.
+When specified in a file the weights must be one per line in the order of
+the input images and the only adjustment made by the task is for the number of
+images previously combined.   In this case the weights should be those
+appropriate for the scaled images which would normally be the inverse
+of the variance in the scaled image.
+.le
+.ls statsec = ""
+Section of images to use in computing image statistics for scaling and
+weighting.  If no section is given then the entire region of the input is
+sampled (for efficiency the images are sampled if they are big enough).
+When the images are offset relative to each other one can precede the image
+section with one of the modifiers "input", "output", "overlap".  The first
+interprets the section relative to the input image (which is equivalent to
+not specifying a modifier), the second interprets the section relative to
+the output image, and the last selects the common overlap and any following
+section is ignored.
+.le
+.ls  expname = ""
+Image header keyword to be used with the exposure scaling and weighting
+options.  Also if an exposure keyword is specified that keyword will be
+added to the output image using a weighted average of the input exposure
+values.
+.le
+
+
+.ce
+Algorithm Parameters
+.ls lthreshold = INDEF, hthreshold = INDEF
+Low and high thresholds to be applied to the input pixels.  This is done
+before any scaling, rejection, and combining.  If INDEF the thresholds
+are not used.
+.le
+.ls nlow = 1,  nhigh = 1 (minmax)
+The number of low and high pixels to be rejected by the "minmax" algorithm.
+These numbers are converted to fractions of the total number of input images
+so that if no rejections have taken place the specified number of pixels
+are rejected while if pixels have been rejected by masking, thresholding,
+or nonoverlap, then the fraction of the remaining pixels, truncated
+to an integer, is used.
+.le
+.ls nkeep = 1
+The minimum number of pixels to retain or the maximum number to reject
+when using the clipping algorithms (ccdclip, crreject, sigclip,
+avsigclip, or pclip).  When given as a positive value this is the minimum
+number to keep.  When given as a negative value the absolute value is
+the maximum number to reject.  The latter is in addition to pixels
+missing due to non-overlapping offsets, bad pixel masks, or thresholds.
+.le
+.ls mclip = yes (ccdclip, crreject, sigclip, avsigcliip)
+Use the median as the estimate for the true intensity rather than the
+average with high and low values excluded in the "ccdclip", "crreject",
+"sigclip", and "avsigclip" algorithms?  The median is a better estimator
+in the presence of data which one wants to reject than the average.
+However, computing the median is slower than the average.
+.le
+.ls lsigma = 3., hsigma = 3. (ccdclip, crreject, sigclip, avsigclip, pclip)
+Low and high sigma clipping factors for the "ccdclip", "crreject", "sigclip",
+"avsigclip", and "pclip" algorithms.  They multiply a "sigma" factor
+produced by the algorithm to select a point below and above the average or
+median value for rejecting pixels.  The lower sigma is ignored for the
+"crreject" algorithm.
+.le
+.ls rdnoise = "0.", gain = "1.", snoise = "0." (ccdclip, crreject)
+CCD readout noise in electrons, gain in electrons/DN, and sensitivity noise
+as a fraction.  These parameters are used with the "ccdclip" and "crreject"
+algorithms.  The values may be either numeric or an image header keyword
+which contains the value.  The noise model for a pixel is:
+
+.nf
+    variance in DN = (rdnoise/gain)^2 + DN/gain + (snoise*DN)^2
+    variance in e- = (rdnoise)^2 + (gain*DN) + (snoise*(gain*DN))^2
+		   = rdnoise^2 + Ne + (snoise * Ne)^2
+.fi
+
+where DN is the data number and Ne is the number of electrons.  Sensitivity
+noise typically comes from noise introduced during flat fielding.
+.le
+.ls sigscale = 0.1 (ccdclip, crreject, sigclip, avsigclip)
+This parameter determines when poisson corrections are made to the
+computation of a sigma for images with different scale factors.  If all
+relative scales are within this value of unity and all relative zero level
+offsets are within this fraction of the mean then no correction is made.
+The idea is that if the images are all similarly though not identically
+scaled, the extra computations involved in making poisson corrections for
+variations in the sigmas can be skipped.  A value of zero will apply the
+corrections except in the case of equal images and a large value can be
+used if the sigmas of pixels in the images are independent of scale and
+zero level.
+.le
+.ls pclip = -0.5 (pclip)
+Percentile clipping algorithm parameter.  If greater than
+one in absolute value then it specifies a number of pixels above or
+below the median to use for computing the clipping sigma.  If less
+than one in absolute value then it specifies the fraction of the pixels
+above or below the median to use.  A positive value selects a point
+above the median and a negative value selects a point below the median.
+The default of -0.5 selects approximately the quartile point.
+See the DESCRIPTION section for further details.
+.le
+.ls grow = 0.
+Radius in pixels for additional pixel to be rejected in an image with a
+rejected pixel from one of the rejection algorithms.  This applies only to
+pixels rejected by one of the rejection algorithms and not the masked or
+threshold rejected pixels.
+.le
+
+The following parameters are internal to the task and not user parameters:
+
+.nf
+    offsets, masktype, maskvalue
+.fi
+
+.ce
+Environment Variables
+
+.ls <package>.interp
+When the spectra have to be interpolated to a common pixel sampling
+the "interp" parameter from the package from which ODCOMBINE is used
+will be used.
+.le
+.ih
+DESCRIPTION
+\fBOdcombine\fR combines input spectra by interpolating them (if necessary)
+to a common dispersion sampling, rejecting pixels exceeding specified low
+and high thresholds or identified as bad in a bad pixel mask, scaling them
+in various ways, applying a rejection algorithm based on known or empirical
+noise statistics, and computing the sum, weighted average, or median of the
+remaining pixels.  Note that the "sum" option is the direct summation of
+the pixels and does not perform any rejection or scaling of the data
+regardless of the parameter settings.
+
+The input spectra are specified using an image list in which each image
+may contain multiple spectra.  The set of spectra may be restricted
+by the \fIaperture\fR parameter to specific apertures.  The set of input
+spectra may then be grouped using the \fIgroup\fR parameter and each
+group combined separately into final output spectra.  The grouping
+options are to select all the input spectra regardless of the input
+image or aperture number, select all spectra of the same aperture,
+or select all the spectra from the same input image.
+
+The output consists of one image for each combined group.  The output
+images and combined spectra inherit the header parameters from the first
+spectrum in the combined group.  There are a number of additional optional
+outputs provided.  The optional logfile lists parameters, the spectra
+combined for each group, scaling, weights, etc., and the output names.
+
+The spectral combining is done using pixels at common dispersion
+coordinates rather than physical or logical pixel coordinates.  If the
+spectra to be combined do not have identical dispersion coordinates then
+the spectra are interpolated to a common dispersion sampling before
+combining.  The interpolation conserves pixel values rather pixel fluxes.
+This means that flux calibrated data is treated correctly and that
+spectra in counts are not corrected in the interpolation for changes in
+pixel widths.  The default interpolation function is a 5th order
+polynomial.  The choice of interpolation type is made with the package
+parameter "interp".  It may be set to "nearest", "linear", "spline3",
+"poly5", or "sinc".  Remember that this applies to all tasks which might
+need to interpolate spectra in the \fBonedspec\fR and associated packages.
+For a discussion of interpolation types see \fBonedspec\fR.
+
+There are two choices for the common dispersion coordinate sampling. If the
+\fIfirst\fR parameter is set then the dispersion sampling of the first
+spectrum is used.  If this dispersion is nonlinear then the end points and
+number of pixels are preserved and a linear dispersion is applied between
+the endpoints.  If the parameter is not set then the user specified linear
+or log linear dispersion system is used.  Any combination of starting
+wavelength, ending wavelength, wavelength per pixel, and number of output
+pixels may be specified.  Unspecified values will default to reasonable
+values based on the minimum or maximum wavelengths of all spectra, the
+minimum dispersion, and the number of pixels needed to satisfy the other
+parameters.  If the parameters overspecify the linear system then the
+ending wavelength is adjusted based on the other parameters.  Note that for
+a log linear system the wavelengths are still specified in nonlog units and
+the dispersion is finally recalculated using the difference of the log
+wavelength endpoints divided by the number pixel intervals (the number of
+pixels minus one).
+
+This task is layered on top of the \fBimcombine\fR task.  What happens
+is that the spectra for each group to be combined is extracted from
+the input, resampled to a common dispersion, and the resulting spectra
+written to temporary images, one per spectrum.  The temporary images
+are written to the current working directory with names begining with
+"tmp".  The same is done with any bad pixel masks.  Then the list of
+images are combined using the IMCOMBINE algorithms.  When the combining
+is completed the temporary images are removed.  If ODCOMBINE aborts
+for some reason these file may be left behind and the user may delete
+them.  Details of what IMCOMBINE does are presented separate under the
+help topic for the IMCOMBINE task.
+
+.ih
+EXAMPLES
+1.  Combine orders of echelle images.
+
+.nf
+	cl> odcombine *.ec *%.ec%% group=images combine=sum
+.fi
+
+2.  Combine all spectra using range syntax and scale by the exposure times.
+
+.nf
+	cl> names irs 10-42 > irs.dat
+	cl> odcombine @irs.dat irscombine group=all scale=exptime
+.fi
+
+3.  Combine spectra by apertures using exposure time scaling and weighting.
+
+.nf
+	cl> odcombine *.ms comb1d \\
+	>>> group=apertures scale=exptime weights=exptime
+	cl> scopy comb1d.* comb.ms format="multispec"
+	cl> imdel comb1d.*
+.fi
+.ih
+REVISIONS
+.ls ODCOMBINE V2.12.3
+This is a new version that incorporates most of the features of
+IMCOMBINE.
+
+In addition to the many new features, including application of pixel
+masks, the following functional differences from the old SCOMBINE
+are noted.
+
+.ls 1
+The output is always a single spectrum per image.
+.le
+.ls 2
+The "first" option does not allow rebinning to a non-linear dispersion.
+Instead, it rebins to the nearest linear dispersion matching the first
+spectrum.
+.le
+.ih
+SEE ALSO
+imcombine, scombine, scopy, sarith, lscombine
+.endhelp
diff --git a/noao/onedspec/doc/onedspec.hlp b/noao/onedspec/doc/onedspec.hlp
new file mode 100644
index 00000000..a1c06ab9
--- /dev/null
+++ b/noao/onedspec/doc/onedspec.hlp
@@ -0,0 +1,293 @@
+.help package Nov94 noao.onedspec
+.ih
+NAME
+onedspec -- generic 1D spectral reduction and analysis package
+.ih
+USAGE
+onedspec
+.ih
+PARAMETERS
+.ls observatory = "observatory"
+Observatory at which the spectra were obtained if not specified in the
+image header by the keyword OBSERVAT.  This parameter is used by several
+tasks in the package through parameter redirection so this parameter may be
+used to affect all these tasks at the same time.  The observatory may be
+one of the observatories in the observatory database, "observatory" to
+select the observatory defined by the environment variable "observatory" or
+the parameter \fBobservatory.observatory\fR, or "obspars" to select the
+current parameters set in the \fBobservatory\fR task.  See help for
+\fBobservatory\fR for additional information.
+.le
+.ls caldir = ""
+Calibration directory containing standard star data.  This parameter
+is used by several tasks in the package through redirection.  A list of
+standard calibration directories may be obtained by listing the file
+"onedstds$README"; for example:
+
+	cl> page onedstds$README
+
+The user may copy or create their own calibration files and specify
+the directory.  The directory "" refers to the current working directory.
+.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
+
+The following parameters apply to two and three dimensional images
+such as long slit or Fabry-Perot spectra.  They allow selection of
+a line or column as the spectrum "aperture" and summing of neighboring
+elements to form a one dimensional spectrum as the tasks in the
+ONEDSPEC package expect.
+
+.ls dispaxis = 1
+The image axis corresponding to the dispersion.  If there is an image
+header keyword DISPAXIS then the value of the keyword will be used
+otherwise this package parameter is used.  The dispersion coordinates
+are a function of column, line, or band when this parameter is 1, 2
+or 3.
+.le
+.ls nsum = "1"
+The number of neighboring elements to sum.  This is a string parameter
+that can have one or two numbers.  For two dimensional images only
+one number is needed and specifies the number of lines or columns
+to sum depending on the dispersion axis.  For three dimensional
+images two numbers may be given (if only one is given it defaults
+to the same value for both spatial axes) to specify the summing of
+the two spatial axes.  The order is the lower dimensional spatial
+axis first.
+
+For an even value the elements summed are the central specified
+"aperture", nsum / 2 - 1 below, and nsum /2 above; i.e the
+central value is closer to the lower element than the upper.
+For example, for nsum=4 and an aperture of 10 for a dispersion
+axis of 1 in a two dimensional image the spectrum used will be
+the sum of lines 9 to 12.
+.le
+
+.ls records = ""
+This is a dummy parameter.  It is applicable only in the \fBimred.irs\fR
+and \fBimred.iids\fR packages.
+.le
+.ls version = "ONEDSPEC V3: November 1991"
+Package version identification.
+.le
+.ih
+DESCRIPTION
+The \fBonedspec\fR package contains generic tasks for the reduction,
+analysis, and display of one dimensional spectra.  The specifics of
+individual tasks may be found in their IRAF "help" pages.  This document
+describes the general and common features of the tasks.
+
+The functions provided in the \fBonedspec\fR package with applicable tasks
+are summarized in Table 1.
+
+.ce
+Table 1:  Functions provided in the \fBonedspec\fR package
+
+.nf
+1.  Graphical display of spectra
+          bplot - Batch plots of spectra
+       identify - Identify features and fit dispersion functions
+       specplot - Stack and plot multiple spectra
+          splot - Interactive spectral plot/analysis
+
+2.  Determining and applying dispersion calibrations
+        dispcor - Dispersion correct spectra
+         dopcor - Apply doppler corrections
+       identify - Identify features and fit dispersion functions
+     refspectra - Assign reference spectra to other spectra
+     reidentify - Automatically identify features in spectra
+      specshift - Shift spectral dispersion coordinate system
+
+3.  Determining and applying flux calibrations
+      calibrate - Apply extinction and flux calibrations to spectra
+       deredden - Apply interstellar extinction correction
+         dopcor - Apply doppler corrections
+         lcalib - List calibration file data
+       sensfunc - Create sensitivity function
+       standard - Tabulate standard star data
+
+4.  Fitting spectral features and continua
+      continuum - Fit the continuum in spectra
+       fitprofs - Fit gaussian profiles
+           sfit - Fit spectra and output fit, ratio, or difference
+          splot - Interactive spectral plot/analysis
+
+5.  Arithmetic and combining of spectra
+         sarith - Spectrum arithmetic
+       scombine - Combine spectra
+          splot - Interactive spectral plot/analysis
+
+6.  Miscellaneous functions
+         mkspec - Generate an artificial spectrum
+          names - Generate a list of image names from a string
+     sapertures - Set or change aperture header information
+          scopy - Select and copy spectra
+        sinterp - Interpolate a table of x,y to create a spectrum
+          slist - List spectrum header parameters
+          splot - Interactive spectral plot/analysis
+.fi
+
+There are other packages which provide additional functions or specialized
+tasks for spectra.  Radial velocity measurements are available in the
+\fBnoao.rv\fR package.  The \fBnoao.imred\fR package contains a number
+of packages for specific types of data or instruments.  These packages
+are listed in Table 2.
+
+.ce
+Table 2:  \fBImred\fR spectroscopy packages
+
+.nf
+ 	  argus - CTIO ARGUS reduction package
+       ctioslit - CTIO spectrophotometric reduction package
+	echelle - Echelle spectral reductions (slit and FOE)
+ 	  hydra - KPNO HYDRA (and NESSIE) reduction package
+	   iids - KPNO IIDS spectral reductions
+	    irs - KPNO IRS spectral reductions
+      kpnocoude - KPNO coude reduction package (slit and 3 fiber)
+       kpnoslit - KPNO low/moderate dispersion slits (Goldcam, RCspec, Whitecam)
+        specred - Generic slit and fiber spectral reduction package
+.fi
+
+Finally, there are non-NOAO packages which may contain generally useful
+software for spectra.  Currently available packages are \fBstsdas\fR
+and \fBxray\fR.
+.ih
+SPECTRUM IMAGE FORMATS AND COORDINATE SYSTEMS
+See the separate help topic \fIspecwcs\fR.
+.ih
+INTERPOLATION
+Changing the dispersion sampling of spectra, such as when converting to a
+constant sampling interval per pixel or a common sampling for combining or
+doing arithmetic on spectra, requires interpolation.  The tasks which
+reinterpolate spectra, if needed, are \fBdispcor, sarith, scombine,\fR and
+\fBsplot\fR.
+
+The interpolation type is set by the package parameter \fIinterp\fR.
+The available interpolation types are:
+
+.nf
+	nearest - nearest neighbor
+	 linear - linear
+	  poly3 - 3rd order polynomial
+	  poly5 - 5th order polynomial
+	spline3 - cubic spline
+	   sinc - sinc function
+.fi
+
+The default interpolation type is a 5th order polynomial.
+
+The choice of interpolation type depends on the type of data, smooth
+verses strong, sharp, undersampled features, and the requirements of
+the user.  The "nearest" and "linear" interpolation are somewhat
+crude and simple but they avoid "ringing" near sharp features.  The
+polynomial interpolations are smoother but have noticible ringing
+near sharp features.  They are, unlike the sinc function described
+below, localized.
+
+In V2.10 a "sinc" interpolation option is available.  This function
+has advantages and disadvantages.  It is important to realize that
+there are disadvantages!  Sinc interpolation approximates applying a phase
+shift to the fourier transform of the spectrum.  Thus, repeated
+interpolations do not accumulate errors (or nearly so) and, in particular,
+a forward and reverse interpolation will recover the original spectrum
+much more closely than other interpolation types.  However, for
+undersampled, strong features, such as cosmic rays or narrow emission or
+absorption lines, the ringing can be more severe than the polynomial
+interpolations.  The ringing is especially a concern because it extends
+a long way from the feature causing the ringing; 30 pixels with the
+truncated algorithm used.  Note that it is not the truncation of the
+interpolation function which is at fault!
+
+Because of the problems seen with sinc interpolation it should be used with
+care.  Specifically, if there are no undersampled, narrow features it is a
+good choice but when there are such features the contamination of the
+spectrum by ringing is much more severe than with other interpolation
+types.
+.ih
+UNITS
+In versions of the NOAO spectroscopy packages prior to V2.10 the dispersion
+units used were restricted to Angstroms.  In V2.10 the first,
+experimental, step of generalizing to other units was taken by
+allowing the two principle spectral plotting tasks, \fBsplot\fR and
+\fBspecplot\fR, to plot in various units.  Dispersion functions are still
+assumed to be in Angstroms but in the future the generalization will be
+completed to all the NOAO spectroscopy tasks.
+
+The dispersion units capability of the plotting tasks allows specifying
+the units with the "units" task parameter and interactively changing the
+units with the ":units" command.  In addition the 'v' key allows plotting
+in velocity units with the zero point velocity defined by the cursor
+position.
+
+The units are specified by strings having a unit type from the list below
+along with the possible preceding modifiers, "inverse", to select the
+inverse of the unit and "log" to select logarithmic units. For example "log
+angstroms" to plot the logarithm of wavelength in Angstroms and "inv
+microns" to plot inverse microns.  The various identifiers may be
+abbreviated as words but the syntax is not sophisticated enough to
+recognized standard scientific abbreviations except as noted below.
+
+.nf
+		Table 1:  Unit Types
+
+	   angstroms - Wavelength in Angstroms
+	  nanometers - Wavelength in nanometers
+	millimicrons - Wavelength in millimicrons
+	     microns - Wavelength in microns
+	 millimeters - Wavelength in millimeters
+	  centimeter - Wavelength in centimeters
+	      meters - Wavelength in meters
+	       hertz - Frequency in hertz (cycles per second)
+	   kilohertz - Frequency in kilohertz
+	   megahertz - Frequency in megahertz
+	   gigahertz - Frequency in gigahertz
+	         m/s - Velocity in meters per second
+	        km/s - Velocity in kilometers per second
+	          ev - Energy in electron volts
+	         kev - Energy in kilo electron volts
+	         mev - Energy in mega electron volts
+		   z - Redshift
+
+	          nm - Wavelength in nanometers
+	          mm - Wavelength in millimeters
+	          cm - Wavelength in centimeters
+	           m - Wavelength in meters
+	          Hz - Frequency in hertz (cycles per second)
+	         KHz - Frequency in kilohertz
+	         MHz - Frequency in megahertz
+	         GHz - Frequency in gigahertz
+		  wn - Wave number (inverse centimeters)
+.fi
+
+The velocity and redshift units require a trailing value and unit defining the
+velocity zero point.  For example to plot velocity relative to
+a wavelength of 1 micron the unit string would be:
+
+.nf
+	km/s 1 micron
+.fi
+
+Some additional examples of units strings are:
+
+.nf
+	milliang
+	megahertz
+	inv mic
+	log hertz
+	m/s 3 inv mic
+	z 5015 ang
+.fi
+.ih
+SEE ALSO
+apextract, longslit, rv, imred, specwcs
+.endhelp
diff --git a/noao/onedspec/doc/refspectra.hlp b/noao/onedspec/doc/refspectra.hlp
new file mode 100644
index 00000000..01cfab30
--- /dev/null
+++ b/noao/onedspec/doc/refspectra.hlp
@@ -0,0 +1,413 @@
+.help refspectra Mar92 noao.onedspec
+.ih
+NAME
+refspectra -- Assign reference spectra
+.ih
+USAGE
+refspectra input [records]
+.ih
+PARAMETERS
+.ls input
+List of input spectra or root names to be assigned reference spectra.
+When using the record number extension format, record number extensions
+will be appended to each root name in the list.
+.le
+.ls records (imred.irs and imred.iids packages only)
+List of records or ranges of records to be appended to the input root
+names when using record number extension format.  The syntax of this
+list is comma separated record numbers or ranges of record numbers.  A
+range consists of two numbers separated by a hyphen. An example of this
+syntax is "1-5,13,17-19".  A null list ("") may
+be used if no record number extensions are desired.  This is a
+positional query parameter only if the record format is specified with
+the \fIrecformat\fR parameter.
+.le
+.ls references = "*.imh"
+List of reference spectra to be assigned or a "reference spectra assignment
+table" (see DESCRIPTION section).
+.le
+.ls apertures = ""
+List of apertures to be SELECTED from the input list of spectra.  If no list
+is specified then all apertures are selected.  The syntax is the same as the
+record number extensions.
+.le
+.ls refaps = ""
+List of reference spectra apertures to be SELECTED.  If no list is specified
+then all apertures are selected.  The syntax is the same as the record number
+extensions.
+.le
+.ls ignoreaps = yes
+Ignore the input and reference apertures when ASSIGNING reference spectra.
+If the aperture numbers are not ignored then only the reference spectra with
+the same aperture number as a particular input spectra are used when assigning
+reference spectra.  Otherwise all the reference spectra are used.  This does
+not apply to the "match" and "average" options which always ignore the aperture
+numbers.  Note that this parameter applies to relating reference spectra to
+input spectra and does not override the aperture selections on the input
+spectra and reference spectra.
+.le
+.ls select = "interp"
+Selection method for assigning reference spectra.  The methods are:
+.ls average
+Average two reference spectra without regard to any aperture,
+sort, or group parameters.
+If only one reference spectrum is specified then it is assigned with a
+warning.  If more than two reference spectra are specified then only the
+first two are used and a warning is given.  There is no checking of the
+aperture numbers or group values.
+.le
+.ls following
+Select the nearest following spectrum in the reference list based on the
+sort and group parameters.  If there is no following spectrum use the
+nearest preceding spectrum.
+.le
+.ls interp
+Interpolate between the preceding and following spectra in the reference
+list based on the sort and group parameters.  If there is no preceding and
+following spectrum use the nearest spectrum.  The interpolation is weighted
+by the relative distances of the sorting parameter (see cautions in
+DESCRIPTION section).
+.le
+.ls match
+Match each input spectrum with the reference spectrum list in order.
+This overrides any aperture or group values.
+.le
+.ls nearest
+Select the nearest spectrum in the reference list based on the sort and
+group parameters.
+.le
+.ls preceding
+Select the nearest preceding spectrum in the reference list based on the
+sort and group parameters.  If there is no preceding spectrum use the
+nearest following spectrum.
+.le
+.le
+.ls sort = "jd"
+Image header keyword to be used as the sorting parameter for selection
+based on order.  The header parameter must be numeric but otherwise may
+be anything.  Common sorting parameters are times or positions.
+A null string, "", or the word "none" may be use to disable the sorting
+parameter.
+.le
+.ls group = "ljd"
+Image header keyword to be used to group spectra.  For those selection
+methods which use the group parameter the reference and object spectra must
+have identical values for this keyword.  This can be anything but it must
+be constant within a group.  Common grouping parameters are the date of
+observation "date-obs" (provided it does not change over a night) or the
+local Julian day number.  A null string, "", or the word "none" may be use
+to disable the grouping parameter.
+.le
+.ls time = no, timewrap = 17.
+Is the sorting parameter a 24 hour time?  If so then the time orgin
+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
+.ls override = no
+Override previous assignments?  If an input spectrum has reference
+spectra assigned previously the assignment will not be changed unless
+this flag is set.
+.le
+.ls confirm = yes
+Confirm reference spectrum assignments?  If \fIyes\fR then the reference
+spectra assignments for each input spectrum are printed and the user may
+either accept the assignment or not.  Rejected assignments leave the
+input spectrum unchanged.
+.le
+.ls assign = yes
+Assign the reference spectrum by entering it in the image header?
+The input spectra are only modified if this parameter is \fIyes\fR.
+This parameter may be set to \fIno\fR to get a list of assignments
+without actually entering the assignments in the image headers.
+.le
+.ls logfiles = "STDOUT,logfile"
+List of log files for recording reference spectra assignments.
+The file STDOUT prints to the standard output.  If not specified ("")
+then no logs will be recorded.
+.le
+.ls verbose = yes
+Verbose log output?  This prints additional information about the input
+and reference spectra.  This is useful for diagnosing why certain spectra
+are ignored or not assigned as intended.
+.le
+.ih
+DESCRIPTION
+This task allows the user to define which reference spectra are to be 
+used in the calculation of the dispersion solution of object spectra.
+The assignment of reference spectra to object spectra is often
+a complex task because of the number of spectra, the use of many distinct
+apertures, and different modes of observing such as interspersed arc
+calibration spectra or just one calibration for a night.  This task
+provides a number of methods to cover many of the common cases.
+
+A reference spectrum is defined to be a spectrum that has been used to
+calculate a wavelength solution with the tasks IDENTIFY or REIDENTIFY.
+These tasks have set the keyword REFSPEC1 in the image header
+equal to the spectrum's own name.
+
+Wavelength reference spectra are assigned to input spectra by entering
+the reference spectrum name or pair of names in the image
+header under the keywords REFSPEC1 and REFSPEC2.  When two reference
+spectra are assigned, the spectrum names may be followed by a weighting
+factor (assumed to be 1 if missing).  The wavelength of a pixel is
+then the weighted average of the wavelengths from the reference
+spectra dispersion solutions.  The weighting factors are calculated
+by choosing an appropriate selection method, ie average, interpolation,
+etc. Note, however, that these assignments may be made directly using
+the task \fBhedit\fR or with some other task or script if none of the
+methods are suitable. 
+
+The spectra to be assigned references are specified by an input list.
+Optional numeric record format extensions may be appended to each name
+(used as a root name) in the input list in the \fBiids/irs\fR packages.
+The input spectra may be restricted to a particular set of aperture numbers
+by the parameter \fIapertures\fR; the spectra not in the list of apertures
+are skipped.  If the aperture list is null (i.e. specified as "") then all
+apertures are selected.  One further selection may be made on the input
+spectra.  If the parameter \fIoverride\fR is no then input spectra which
+have existing reference spectra assignments (which includes the reference
+spectra) are skipped.
+
+The reference spectra parameter \fIreferences\fR may take two forms.
+It may be an image list of spectra or a text file containing
+a "reference spectrum assignment table".  The table consists of pairs
+of strings/lists with the first string being a list of object spectra
+and the second string being a list of reference spectra.  If this
+table is used, then only those object spectra in the table that are also
+listed in the input parameter list are processed.  The example below
+illustrates the reference spectrum assignment table:
+
+.nf
+	spec1		spec2,spec3,spec4
+	spec5
+	spec6,spec7	spect8,spec9
+	spec10		spec11
+	spec12		spec13
+	spec14		spec15
+.fi
+
+As a convenience, if a reference list in the table is missing, the preceding
+reference list is implied. This table may be used to make arbitrary assignments.
+
+The reference spectra in the specified list may also be restricted to a
+subset of aperture numbers.  However, in the case of averaging, the
+reference aperture selection is ignored. In the case of matching, if
+a reference spectrum is not selected then the matching input spectrum
+is also skipped (in order to maintain a one-to-one correspondence).
+Spectra in the reference list which are not reference spectra (as
+defined earlier) are also ignored and a warning is printed.  Note that
+no check is made that a dispersion solution actually exists in the
+dispersion solution database.
+
+There may be cases where there are only reference spectra for some
+apertures and it is desired to apply these reference spectra to the
+other apertures.  The \fIignoreaps\fR flag may be used to force an
+assignment between reference and object spectra with different
+aperture numbers.  Note that this flag is applied after the input and
+reference list aperture number selections are made; in other words this
+applies only to the assignments and not the input selection process.
+
+Once the appropriate reference spectra from the reference list have been
+determined for an input spectrum they are assigned using one of the
+methods selected by the parameter \fIselect\fR.  The "match" method
+simply pairs each element of the input spectrum list with each element
+in the reference spectrum list.  If a reference assignment table
+is used with "match", then only the first spectrum in the reference
+list for each input spectrum is assigned.
+
+The "average" method assigns the first two spectra in the reference list
+ignoring aperture numbers or groups. The spectra are averaged by assigning
+equal weights.  There is no weighting based on any sort parameter.  If
+there are more than two spectra in the reference list then only the first
+two spectra are used and the remainder are ignored.  If a reference
+assignment table is used only the first two reference spectra listed for
+each object in the table are averaged.
+
+The remaining selection methods group the spectra using a header keyword
+which must be constant within a group.  If no group parameter is specfied
+(the null string "" or the word "none")
+then grouping does not occur.  Only reference spectra with the same
+group header value as the object are assigned to an object spectrum.
+One likely group parameter is the "date-obs" keyword.  This is usually
+constant over a night at CTIO and KPNO.  At other sites this may not
+be the case.  Therefore, the task \fBsetjd\fR may be used to set a
+local Julian day number which is constant over a night at any
+observatory.
+
+Within a group the spectra are ordered based on a numeric image header
+parameter specified by the \fIsort\fR parameter.  A null string "" or the
+word "null" may be used to select no sort parameter.  Parameters which are
+times, as indicated by the \fItime\fR parameter, are assumed to be cyclic
+with a period of 24 hours.  The time wrap parameter defines the origin of a
+cycle and should precede the first observation and follow the last
+observation in a 24 hour period; i.e. for nighttime observations this
+parameter value should bee sometime during the day.  Particularly with
+interpolating or choosing the nearest reference spectrum it is important
+that the sorting parameter refer to the middle of the exposure.  A Julian
+date at the middle of an exposure may be calculated with the task
+\fBsetjd\fR or a middle UT time may be computed with the task
+\fBsetairmass\fR.
+
+The selection methods may choose the "nearest", "preceding", or "following"
+reference spectrum.  Alternatively, the reference wavelengths may be
+interpolated between the preceding and following reference spectra with
+weights given by the relative distances measured by the sorting parameter.
+In the cases where a preceding or following spectrum is required and one is
+not found then the nearest reference spectrum is used.  These methods are
+used for observing sequences where the reference spectra are taken either
+nearby in time or space.
+
+The option "interp" should not be used without some thought as to the
+nature of the interpolation.  If the sorting parameter is a time (a 24 hour
+cyclic parameter as opposed to a continuous parameter such as a Julian
+date) then the user must be aware of when these times were recorded in the
+header.  For example, let us assume that the sort parameter is "ut" and
+that this time was recorded in the header at the beginning of the
+exposure.  If the object spectrum exposure time is longer than the
+reference spectra exposure times, then interpolation will weight the
+preceding reference spectrum too heavily.  This problem can be circumvented
+by using the "average" selection method along with the reference assignment
+table.  Or the sort time parameter in the headers of the spectra can be
+changes with \fIsetjd\fR or \fIsetairmass\fR or edited to reflect the
+values at mid-exposure (see EXAMPLES).
+
+Once the reference spectrum or spectra for a input spectrum have been 
+identified the user may also chose to override any previous reference
+assignments, to accept or not accept the current reference assignments
+(in the case of not accepting the reference assignment the image header
+is not updated), to only list the current reference assignments and not
+update any image headers, as well as to record the reference assignments
+to log files.  These options are separately controlled by the remaining
+task parameters. 
+.ih
+KEYWORDS
+This task uses the header keyword BEAM-NUM to sort the apertures.  It
+has an integer value.  If the keyword does not exist then all apertures
+are assumed to be 1.
+
+The keyword REFSPEC1 is used to search for reference spectra. This 
+keyword can be previously created by the tasks IDENTIFY and REIDENTIFY.
+
+The two keywords REFSPEC1 and optionally REFSPEC2 are created by the
+task when the assign parameter is set to yes.  They take the form:
+
+.nf
+           REFSPEC1='d1.0001'  or
+
+           REFSPEC1='d5.0001 0.756'
+           REFSPEC2='d5.0002 0.244'
+.fi
+
+.ih
+EXAMPLES
+1.  Compute a Julian date at the midpoint of the exposure for sorting
+and a local Julian day number for grouping and then assign spectra
+using interpolation.
+
+.nf
+    cl> setjd *.imh jd=jd ljd=ljd
+    cl> refspec *.imh sort=jd group=ljd select=interp
+.fi
+
+2.  Specifically assign reference spectra to input spectra.
+
+.nf
+    cl> refspectra spec1,spec3 refe=spec2,spec4 select=match
+.fi
+
+3.  Use a reference assignment table to assign reference spectra to input
+spectra using the "average" option.  First a table is created using an
+editor.
+
+.nf
+    cl> type reftable
+    spec1		spec2,spec3,spec4
+    spec5
+    spec6,spec7		spect8,spec9
+    spec10		spec11
+    spec12		spec13
+    spec14		spec15
+    cl> refspec spec*.imh recfor- select=average refe=reftable
+.fi
+
+4.  Assign the nearest reference spectrum in zenith distance using
+wildcard lists.  By default the aperture numbers must match.
+
+    cl> refspec *.imh "" sort=zd select=nearest time-
+
+5.  Assign a specific reference spectrum to all apertures.
+
+    cl> refspec *.imh "" refer=refnite1 ignoreaps+
+
+6.  Confirm assignments.
+
+.nf
+    cl> hselect irs.*.imh "$I,beam-num,ut,refspec1" yes
+    irs.0009.imh	0	0:22:55		irs.0009
+    irs.0010.imh	1	0:22:53		irs.0010
+    irs.0100.imh	0	8:22:55
+    irs.0101.imh	1	8:22:53
+    irs.0447.imh	0	13:00:07	irs.0447
+    irs.0448.imh	1	13:00:05	irs.0448
+    cl> refspec irs 100-101 refer=irs.*.imh conf+ ver+ select=nearest\
+       >>> ignoreaps-
+    [irs.0100] Not a reference spectrum
+    [irs.0101] Not a reference spectrum
+    [irs.0100] refspec1='irs.0447'   Accept assignment (yes)?
+    [irs.0101] refspec1='irs.0448'   Accept assignment (yes)?
+.fi
+
+Because the reference spectrum list includes all spectra the
+warning messages "Not a reference spectrum" are printed with verbose
+output.  Remember a reference spectrum is any spectrum which has a
+reference spectrum assigned which refers to itself.
+
+7.  Assign reference spectra with weights using interpolation.  In this
+example we want to sort by "ut" but this keyword value was 
+recorded at the beginning of the integration. So we first create an
+new keyword and then compute its value to be that of mid-exposure.  The
+new keyword is then used as the sorting parameter.
+
+.nf
+    cl> hedit *.imh utmid 0. add+ ver- show-     
+    cl> hedit *.imh utmid "(ut)" ver- show-
+    cl> hedit *.imh utmid "(mod(utmid+exptime/7200.,24.))" ver- show-
+    cl> refspec *.imh refer=*.imh recfor- select=interp sort=utmid
+.fi
+
+8.  Assign reference spectra using the "average" option and the reference
+assignment table with data with record number extensions.  First edit
+the file reftable:
+
+.nf
+     cl> type reftable
+            spec.0001     arc1.0001,arc2.0001
+            spec.0002     arc1.0002,arc2.0002
+            spec.0003     arc1.0003,arc2.0003
+            spec.0004     arc1.0004,arc2.0004
+     cl> refspec spec.*.imh recfor- refer=reftable select=average
+.fi
+
+9.  Assign a reference spectrum for aperture 1 to the object spectra
+for apertures 2 thru 5.
+
+.nf
+     cl> refspec spec 2-5 recfor+ refer=arc.*.imh refaps=1 ignoreaps+
+.fi
+.ih
+REVISIONS
+.ls REFSPECTRA V2.10.3
+If no reference spectrum is found in the interp, nearest, following,
+preceding methods then a list of the reference spectra is given
+showing why each was not acceptable.
+.le
+.ls REFSPECTRA V2.10
+A group parameter was added to allow restricting assignments by observing
+period; for example by night.  The record format option was removed and
+the record format syntax is available in the \fBirs/iids\fR packages.
+.le
+.ih
+SEE ALSO
+identify, reidentify, dispcor, setjd, setairmass
+.endhelp
diff --git a/noao/onedspec/doc/reidentify.hlp b/noao/onedspec/doc/reidentify.hlp
new file mode 100644
index 00000000..07eb2238
--- /dev/null
+++ b/noao/onedspec/doc/reidentify.hlp
@@ -0,0 +1,516 @@
+.help reidentify Jan96 noao.onedspec
+.ih
+NAME
+reidentify -- Reidentify features
+.ih
+SUMMARY
+Given a reference vector with identified features and (optionally) a
+coordinate function find the same features in other elements of the
+reference image and fit a new dispersion function or determine a
+zero point shift.  After all vectors of the reference image are
+reidentified use the reference vectors to reidentify corresponding
+vectors in other images.  This task is used for transferring dispersion
+solutions in arc calibration spectra and for mapping geometric and
+dispersion distortion in two and three dimensional images.
+.ih
+USAGE
+reidentify reference images
+.ih
+PARAMETERS
+.ls reference
+Image with previously identified features to be used as features reference for
+other images.  If there are multiple apertures, lines, or columns in the
+image a master reference is defined by the \fIsection\fR parameter.
+The other apertures in multispec images or other lines, or columns
+(selected by \fIstep\fR) are reidentified as needed.
+.le
+.ls images
+List of images in which the features in the reference image are to be
+reidentified.  In two and three dimensional images the reidentifications are
+done by matching apertures, lines, columns, or bands with those in the reference
+image.
+.le
+.ls interactive = no
+Examine and fit features interactively?  If the task is run interactively a
+query (which may be turned off during execution) will be given for each
+vector reidentified after printing the results of the automatic fit and the
+user may chose to enter the interactive \fBidentify\fR task.
+.le
+.ls section = "middle line"
+If the reference image is not one dimensional or specified as a one dimensional
+image section then this parameter selects the master reference image
+vector.  The master reference is used when reidentifying other vectors in
+the reference image or when other images contain apertures not present in
+the reference image.  This parameter also defines the direction
+(columns, lines, or z) of the image vectors to be reidentified.
+
+The section parameter may be specified directly as an image section or
+in one of the following forms
+
+.nf
+line|column|x|y|z first|middle|last|# [first|middle|last|#]]
+first|middle|last|# [first|middle|last|#] line|column|x|y|z
+.fi
+
+where each field can be one of the strings separated by | except for #
+which is an integer number.  The field in [] is a second designator which
+is used with three dimensional data.  See the example section for
+\fBidentify\fR for examples of this syntax.  Abbreviations are allowed
+though beware that 'l' is not a sufficient abbreviation.
+.le
+.ls newaps = yes
+Reidentify new apertures in the images which are not in the reference
+image?  If no, only apertures found in the reference image will be
+reidentified in the other images.  If yes, the master reference spectrum
+is used to reidentify features in the new aperture and then the
+new aperture solution will be added to the reference apertures.  All
+further identifications of the new aperture will then use this solution.
+.le
+.ls override = no
+Override previous solutions?  If there are previous solutions for a
+particular image vector being identified, because of a previous
+\fBidentify\fR or \fBreidentify\fR, this parameter selects whether
+to simply skip the reidentification or do a reidentification and
+overwrite the solution in the database.
+.le
+.ls refit = yes
+Refit the coordinate function?  If yes and there is more than one feature
+and a coordinate function was defined in the reference image database then a new
+coordinate function of the same type as in the reference is fit
+using the new pixel positions.  Otherwise only a zero point shift is
+determined for the revised coordinates without changing the
+form of the coordinate function.
+.le
+
+The following parameters are used for selecting and reidentifying additional
+lines, columns, or apertures in two dimensional formats.
+.ls trace = no
+There are two methods for defining additional reference lines, columns, or
+bands in two and three dimensional format images as selected by the
+\fIstep\fR parameter.  When \fItrace\fR is no the master reference line or
+column is used for each new reference vector.  When this parameter is yes
+then as the reidentifications step across the image the last reidentified
+features are used as the reference.  This "tracing" is useful if there is a
+coherent shift in the features such as with long slit spectra.  However,
+any features lost during the tracing will be lost for all subsequent lines
+or columns while not using tracing always starts with the initial set of
+reference features.
+.le
+.ls step = "10"
+The step from the reference line, column, or band used for selecting and/or
+reidentifying additional lines, columns, or bands in a two or three
+dimensional reference image.  For three dimensional images there may be two
+numbers to allow independent steps along different axes.  If the step is
+zero then only the reference aperture, line, column, or band is used.  For
+multiaperture images if the step is zero then only the requested aperture
+is reidentified and if it is non-zero (the value does not matter) then all
+spectra are reidentified.  For long slit or Fabry-Perot images the step is
+used to sample the image and the step should be large enough to map any
+significant changes in the feature positions.
+.le
+.ls nsum = "10"
+Number of lines, columns, or bands across the designated vector axis to be
+summed when the image is a two or three dimensional spatial spectrum.
+It does not apply to multispec format spectra.  If the image is three
+dimensional an optional second number can be specified for the higher
+dimensional axis  (the first number applies to the lower axis number and
+the second to the higher axis number).  If a second number is not specified
+the first number is used for both axes.  This parameter is not used for
+multispec type images.
+.le
+.ls shift = "0"
+Shift in user coordinates to be added to the reference features before
+centering.  If the image is three dimensional then two numbers may be
+specified for the two axes.  Generally no shift is used by setting the
+value to zero.  When stepping to other lines, columns, or bands in the
+reference image the shift is added to the primary reference spectrum if not
+tracing.  When tracing the shift is added to last spectrum when stepping to
+higher lines and subtracted when stepping to lower lines.  If a value
+if INDEF is specified then an automatic algorithm is applied to find
+a shift.
+.le
+.ls search = 0.
+If the \fIshift\fR parameter is specified as INDEF then an automatic
+search for a shift is made.  There are two algorithms.  If the search
+value is INDEF then a cross-correlation of line peaks is done.  Otherwise
+if a non-zero value is given then a pattern matching algorithm (see
+\fIautoidentify\fR) is used.  A positive value specifies the search radius in
+dispersion units and a negative value specifies a search radius as a
+fraction of the reference dispersion range.
+.le
+.ls nlost = 0
+When reidentifying features by tracing, if the number of features not found
+in the new image vector exceeds this number then the reidentification
+record is not written to the database and the trace is terminated.  A
+warning is printed in the log and in the verbose output.
+.le
+
+The following parameters define the finding and recentering of features.
+See also \fBcenter1d\fR.
+.ls cradius = 5.
+Centering radius in pixels.  If a reidentified feature falls further
+than this distance from the previous line or column when tracing or
+from the reference feature position when reidentifying a new image
+then the feature is not reidentified.
+.le
+.ls threshold = 0.
+In order for a feature center to be determined, the range of pixel
+intensities around the feature must exceed this threshold.  This parameter
+is used to exclude noise peaks and terminate tracing when the signal
+disappears.  However, failure to properly set this parameter, particularly
+when the data values are very small due to normalization or flux
+calibration, is a common error leading to failure of the task.
+.le
+
+The following parameters select and control the automatic addition of
+new features during reidentification.
+.ls addfeatures = no
+Add new features from a line list during each reidentification?  If
+yes then the following parameters are used.  This function can be used
+to compensate for lost features from the reference solution, particularly
+when tracing.  Care should be exercised that misidentified features
+are not introduced.
+.le
+.ls coordlist = "linelists$idhenear.dat"
+User coordinate list consisting of a list of line coordinates.
+Some standard line lists are available in the directory "linelists$".
+The standard line lists are described under the topic \fIlinelists\fR.
+.le
+.ls match = -3.
+The maximum difference for a match between the feature coordinate function
+value and a coordinate in the coordinate list.  Positive values
+are in user coordinate units and negative values are in units of pixels.
+.le
+.ls maxfeatures = 50
+Maximum number of the strongest features to be selected automatically from
+the coordinate list.
+.le
+.ls minsep = 2.
+The minimum separation, in pixels, allowed between feature positions
+when defining a new feature.
+.le
+
+The following parameters determine the input and output of the task.
+.ls database = "database"
+Database containing the feature data for the reference image and in which
+the features for the reidentified images are recorded.
+.le
+.ls logfiles = "logfile"
+List of files in which to keep a processing log.  If a null file, "",
+is given then no log is kept.
+.le
+.ls plotfile = ""
+Optional file to contain metacode plots of the residuals.
+.le
+.ls verbose = no
+Print reidentification information on the standard output?
+.le
+.ls graphics = "stdgraph"
+Graphics device.  The default is the standard graphics device which is
+generally a graphics terminal.
+.le
+.ls cursor = ""
+Cursor input file.  If a cursor file is not given then the standard graphics
+cursor is read.
+.le
+
+The following parameters are queried when the 'b' key is used in the
+interactive review.
+.ls crval, cdelt
+These parameters specify an approximate coordinate value and coordinate
+interval per pixel when the automatic line identification
+algorithm ('b' key) is used.  The coordinate value is for the
+pixel specified by the \fIcrpix\fR parameter in the \fBaidpars\fR
+parameter set.  The default value of \fIcrpix\fR is INDEF which then
+refers the coordinate value to the middle of the spectrum.  By default
+only the magnitude of the coordinate interval is used.  Either value
+may be given as INDEF.  In this case the search for a solution will
+be slower and more likely to fail.  The values may also be given as
+keywords in the image header whose values are to be used.
+.le
+.ls aidpars = "" (parameter set)
+This parameter points to a parameter set for the automatic line
+identification algorithm.  See \fIaidpars\fR for further information.
+.le
+.ih
+DESCRIPTION
+Features (spectral lines, cross-dispersion profiles, etc.) identified in a
+single reference vector (using the tasks \fBidentify\fR or
+\fBautoidentify\fR) are reidentified in other reference vectors and the set
+of reference vectors are reidentified in other images with the same type of
+vectors.  A vector may be a single one dimensional (1D) vector in a two or
+three dimensional (2D or 3D) image, the sum of neighboring vectors to form
+a 1D vector of higher signal, or 1D spectra in multiaperture images.  The
+number of vectors summed in 2D and 3D images is specified by the parameter
+\fInsum\fR.  This parameter does not apply to multiaperture images.
+
+As the previous paragraph indicates, there are two stages in this task.
+The first stage is to identify the same features from a single reference
+vector to a set of related reference vectors.  This generally consists
+of other vectors in the same reference image such as other lines or
+columns in a long slit spectrum or the set of 1D aperture spectra in
+a multiaperture image.  In these cases the vectors are identified by
+a line, column, band, or aperture number.  The second stage is to
+reidentify the features from the reference vectors in the matching
+vectors of other images.  For example the same lines in the reference
+image and another image or the same apertures in several multiaperture
+images.  For multiaperture images the reference vector and target vector
+will have the same aperture number but may be found in different image
+lines.  The first stage may be skipped if all the reference vectors
+have been identified.
+
+If the images are 2D or 3D or multiaperture format and a \fIstep\fR greater
+than zero is specified then additional vectors (lines/columns/bands) in the
+reference image will be reidentified from the initial master reference
+vector (as defined by an image section or \fIsection\fR parameter) provided
+they have not been reidentified previously or the \fIoverride\fR flag is
+set.  For multiple aperture spectral images, called multiaperture, a step
+size of zero means don't reidentify any other aperture and any other step
+size reidentifies all apertures.  For two and three dimensional images,
+such as long slit and Fabry-Perot spectra, the step(s) should be large
+enough to minimize execution time and storage requirements but small enough
+to follow shifts in the features (see the discussion below on tracing).
+
+The reidentification of features in other reference image vectors
+may be done in two ways selected by the parameter \fItrace\fR.  If not
+tracing, the initial reference vector is applied to the other selected
+vectors.  If tracing, the reidentifications are made with respect to the
+last set of identifications as successive steps away from the reference
+vector are made.  The tracing method is appropriate for two and three
+dimensional spatial images, such as long slit and Fabry-Perot spectra, in
+which the positions of features traced vary smoothly.  This allows
+following large displacements from the initial reference by using suitably
+small steps.  It has the disadvantage that features lost during the
+reidentifications will not propagate (unless the \fIaddfeatures\fR option
+is used).  By not tracing, the original set of features is used for every
+other vector in the reference image.
+
+When tracing, the parameter \fInlost\fR is used to terminate the
+tracing whenever this number of features has been lost.  This parameter,
+in conjunction with the other centering parameters which define
+when a feature is not found, may be useful for tracing features
+which disappear before reaching the limits of the image.
+
+When reidentifying features in other images, the reference
+features are those from the same aperture, line, column, or band of the
+reference image.  However, if the \fInewaps\fR parameter is set
+apertures in multiaperture spectra which are not in the reference
+image may be reidentified against the master reference aperture and
+added to the list of apertures to be reidentified in other images.
+This is useful when spectra with different aperture numbers are
+stored as one dimensional images.
+
+The reidentification of features between a reference vector and
+a target vector is done as follows.  First a mean shift between
+the two vectors is determined.  After correcting for the shift
+the estimated pixel position of each reference feature in the
+target vector is used as the starting point for determining
+a feature center near this position.  The centering fails the
+feature is dropped and a check against the \fInlost\fR is made.
+If it succeeds it is added to the list of features found in the
+target spectrum.  A zero point shift or new dispersion
+function may be determined.  New features may then be added from
+a coordinate list.  The details are given below.
+
+There may be a large shift between the two vectors such that the same
+feature in the target vector is many pixels away from the pixel position in
+the reference spectrum.  A shift must then be determined.   The \fIshift\fR
+parameter may be used to specify a shift.  The shift is in user coordinates
+and is added to the reference user coordinates before trying to center
+on a feature.  For example if the reference spectrum has a feature at
+5015A but in the new spectrum the feature is at 5025A when the reference
+dispersion function is applied then the shift would be +10.  Thus
+a reference feature at 5015A would have the shift added to get 5025A,
+then the centering would find the feature some pixel value and that
+pixel value would be used with the true user coordinate of 5015A in the
+new dispersion solution.
+
+When tracing a 2D/3D reference spectrum the shift is applied to the
+previous reidentified spectrum rather than the initial reference spectrum.
+The shift is added for increasing line or column values and subtracted for
+decreasing line or column values.  This allows "tracing" when there is a
+rotation or tilt of the 2D or 3D spectrum.  When not tracing the shift is
+always added to the reference spectrum features as described previously.
+
+When reidentify other images with the reference spectrum the shift
+parameter is always just added to the reference dispersion solution
+matching the aperture, line, or column being reidentified.
+
+If the \fIshift\fR parameter is given as INDEF then an automatic
+search algorithm is applied.  There are two algorithms that may be
+used.  If the \fIsearch\fR parameter is INDEF then a cross-correlation
+of the features list with the peaks found in the target spectrum is
+performed.  This algorithm can only find small shifts since otherwise
+many lines may be missing off either end of the spectrum relative to
+the reference spectrum.
+
+If the search parameter is non-zero then the pattern matching algorithm
+described in \fIaidpars\fR is used.  The search parameter specified a
+search radius from the reference solution.  If the value is positive the
+search radius is a distance in dispersion units.  If the value is negative
+then the absolute value is used as a fraction of the dispersion range in
+the reference solution.  For example, a value of -0.1 applied to reference
+dispersion solution with a range of 1000A would search for a new solution
+within 100A of the reference dispersion solution.
+
+The pattern matching algorithm has to stages.  First if there are
+more than 10 features in the reference the pattern matching tries
+to match the lines in the target spectrum to those features with
+a dispersion per pixel having the same sign and a value within 2%.
+If no solution is found then the \fIlinelist\fR is used to match
+against the lines in the target spectrum, again with the dispersion
+per pixel having the same sign and a value within 5%.  The first
+stage works when the set of features is nearly the same while the
+second stage works when the shifts are large enough that many features
+in the reference and target spectra are different.
+
+The centering algorithm is described under the topic \fIcenter1d\fR and
+also in \fBidentify\fR.  If a feature positions shifts by more than the
+amount set by the parameter \fIcradius\fR from the starting position
+(possibly after adding a shift) or the feature strength (peak to valley) is
+less than the detection \fIthreshold\fR then the new feature is discarded.
+The \fIcradius\fR parameter should be set large enough to find the correct
+peak in the presence of any shifts but small enough to minimize incorrect
+identifications.  The \fIthreshold\fR parameter is used to eliminate
+identifications with noise.  Failure to set this parameter properly for the
+data (say if data values are very small due to a calibration or
+normalization operation) is the most common source of problems in using
+this task.
+
+If a fitting function is defined for the features in the reference image,
+say a dispersion function in arc lamp spectra, then the function is refit
+at each reidentified line or column if the parameter \fIrefit\fR is yes.
+If refitting is not selected then a zero point shift in the user
+coordinates is determined without changing the form of the fitting
+function.  The latter may be desirable for tracking detector shifts through
+a sequence of observation using low quality calibration spectra.  When
+refitting, the fitting parameters from the reference are used including
+iterative rejection parameters to eliminate misidentifications.
+
+If the parameter \fIaddfeatures\fR is set additional features may be added
+from a line list.  If there are reference features then the new features
+are added AFTER the initial reidentification and function fit.  If the
+reference consists only of a dispersion function, that is it has no
+features, then new features will be added followed by a function fit and
+then another pass of adding new features.  A maximum number of added
+features, a matching distance in user coordinates, and a minimum separation
+from other features are additional parameters.  This option is similar to
+that available in \fBidentify\fR and is described more fully in the help
+for that task.
+
+A statistics line is generated for each reidentified vector.  The line
+contains the name of the image being reidentified (which for two
+dimensional images includes the image section and for multiaperture
+spectra includes the aperture number), the number of features found
+relative to the number of features in the reference, the number of
+features used in the function fit relative to the number found,  the
+mean pixel, user coordinate, and fractional user coordinate shifts
+relative to the reference coordinates, and the RMS relative to the
+final coordinate system (whether refit or simply shifted) excluding any
+iteratively rejected features from the calculation.
+
+If the task is run with the \fIinteractive\fR flag the statistics line
+is printed to the standard output (the terminal) and a query is
+made whether to examine and/or refit the features.  A response
+of yes or YES will put the user in the interactive graphical mode
+of \fBidentify\fR.  See the description of this task for more
+information.  The idea is that one can monitor the statistics information,
+particularly the RMS if refitting, and select only those which may be
+questionable to examine interactively.  A response of no or NO will
+continue on to the next reidentification.  The capitalized responses
+turn off the query and act as permanent response for all other
+reidentifications.
+
+This statistics line, including headers, is written to any specified
+log files.  The log information includes the image being
+reidentified and the reference image, and the initial shift.
+
+If an accessible file name is given for the plot file then a residual plot
+of the reidentified lines is recorded in this file.  The plot file can
+be viewed with \fBgkimosaic, stdgraph\fR or reading the file
+with ".read" when in cursor mode (for example with "=gcur").
+
+The reidentification results for this task are recorded in a
+\fIdatabase\fR.  Currently the database is a directory and entries
+in the database are text files with filenames formed by adding
+the prefix "id" to the image name without an image extension.
+.ih
+EXAMPLES
+1.  Arc lines and a dispersion solution were defined for the middle
+aperture in the multispec for arc spectrum a042.ms.  To reidentify the
+other apertures in the reference image and then another arc image:
+
+.nf
+  cl> reiden a042.ms a045.ms inter+ step=1 ver+
+  REIDENTIFY: NOAO/IRAF V2.9 valdes@puppis Fri 29-Jun-90
+    Reference image = a042.ms.imh, New image = a042.ms, Refit = yes
+     Image Data    Found     Fit Pix Shift  User Shift     RMS
+  a042.ms - Ap 24  48/48   47/48   -2.38E-4    -3.75E-6  0.699
+  Fit dispersion function interactively? (no|yes|NO|YES) (yes): y
+  a042.ms - Ap 24  48/48   47/48   -2.38E-4    -3.75E-6  0.699
+  a042.ms - Ap 23  48/48   47/48      0.216        1.32  0.754
+  Fit dispersion function interactively? (no|yes|NO|YES) (yes): n
+  a042.ms - Ap 22  48/48   47/48     0.0627       0.383  0.749
+  Fit dispersion function interactively? (no|yes|NO|YES) (yes): n
+  a042.ms - Ap 21  48/48   47/48      0.337        2.06  0.815
+  <etc>
+    Reference image = a042.ms.imh, New image = a045.ms, Refit = yes
+     Image Data    Found     Fit Pix Shift  User Shift     RMS
+  a045.ms - Ap 24  48/48   47/48   -2.38E-4    -3.75E-6  0.699
+  Fit dispersion function interactively? (no|yes|NO|YES) (yes): y
+  a045.ms - Ap 24  48/48   47/48   -2.38E-4    -3.75E-6  0.699
+  a045.ms - Ap 23  48/48   47/48      0.216        1.32  0.754
+  Fit dispersion function interactively? (no|yes|NO|YES) (yes): N
+  a045.ms - Ap 22  48/48   47/48     0.0627       0.383  0.749
+  a042.ms - Ap 21  48/48   47/48      0.337        2.06  0.815
+  a042.ms - Ap 20  48/48   47/48     -0.293       -1.79  0.726
+  a042.ms - Ap 19  48/48   48/48      0.472        2.88  0.912
+.fi
+
+This example is verbose and includes interactive review of reidentifications.
+The statistics lines have been shortened.
+
+2.  To trace a stellar profile and arc lines in long slit images for the
+purpose of making a distortion correction:
+
+.nf
+  cl> reiden rog022[135,*] "" trace+
+  cl> reiden rog023 "" sec="mid line" trace+
+.fi
+.ih
+REVISIONS
+.ls REIDENTIFY V2.11
+The \fIsearch\fR parameter and new searching algorithm has been added.
+
+The task will now work with only a warning if the reference image is absent;
+i.e. it is possible to reidentify given only the database.
+
+The \fIaddfeatures\fR function will now add features before a fit if there
+are no reference database features.  Previously features could only be
+added after an initial fit using the reference features and, so, required
+the reference database to contain features for reidentification.  This
+new feature is useful if one wants to uses a dispersion function from one
+type of calibration but wants to add features for a different kind of
+calibration.
+.le
+.ls REIDENTIFY V2.10.3
+The section, nsum, step, and shift parameter syntax was extended to apply to 3D
+images.  The previous values and defaults may still be used.
+
+For multiaperture data a step of zero selects only the reference aperture
+to be reidentified and any other step selects reidentifying all apertures.
+.le
+.ls REIDENTIFY V2.10
+This task is a new version with many new features.  The new features
+include an interactive options for reviewing identifications, iterative
+rejection of features during fitting, automatic addition of new features
+from a line list, and the choice of tracing or using a single master
+reference when reidentifying features in other vectors of a reference
+spectrum.  Reidentifications from a reference image to another image is
+done by matching apertures rather than tracing.  New apertures not present
+in the reference image may be added.
+.le
+.ih
+SEE ALSO
+autoidentify, identify, aidpars, center1d, linelists, fitcoords
+.endhelp
diff --git a/noao/onedspec/doc/rspectext.hlp b/noao/onedspec/doc/rspectext.hlp
new file mode 100644
index 00000000..2973f552
--- /dev/null
+++ b/noao/onedspec/doc/rspectext.hlp
@@ -0,0 +1,138 @@
+.help rspectext Oct93 onedspec
+.ih
+NAME
+rspectext -- convert 1D ascii text spectra to IRAF image spectra
+.ih
+USAGE
+rspectext input output
+.ih
+PARAMETERS
+.ls input
+Input list of ascii text spectra.  These may have a optional FITS header
+at the beginning and then two columns of wavelength and flux.
+.le
+.ls output
+Output list of IRAF spectra image names.  The list must match the
+input list.
+.le
+
+
+The following parameters are only used if there is no FITS header
+with the data.
+.ls title = ""
+Title to be assigned to the spectra.
+.le
+.ls flux = no
+Are the flux values flux calibrated?  If so then header keywords are
+inserted to identify this for the IRAF spectral software.
+.le
+.ls dtype = "linear" (none|linear|log|nonlinear|interp)
+Type of dispersion to assign to the spectra.  The options are:
+.ls none
+No dispersion function and nothing is added to the image header.
+.le
+.ls linear
+Store the linear dispersion parameters \fBcrval1\fR and \fBcdelt1\fR
+in the image header.  The wavelength values are ignored.  This may
+be used if the wavelength values are known to be linear but one wants
+to avoid possible roundoff and resampling errors introduced by the
+"interp" option.
+.le
+.ls log
+Store the log-linear dispersion parameters \fBcrval1\fR and \fBcdelt1\fR in
+the image header.  The wavelength values are ignored.  This may be used if
+the wavelength values are known to be linear in the log of the wavelength
+but one wants to avoid possible roundoff and resampling errors introduced
+by the "interp" option.
+.le
+.ls nonlinear
+Store the wavelength values in the image header as a lookup table.
+The flux values are not resampled.  The wavelength values need not
+be evenly sampled.
+.le
+.ls interp
+Use the wavelength values to resample to a linear dispersion between
+the first and last wavelength values.  The dispersion per pixel is
+determined by the number of pixels and the endpoint wavelengths.
+.le
+.le
+.ls crval1 = 1., cdelt1 = 1.
+The wavelength coordinate of the first pixel and the wavelength interval
+per pixel to be used with the linear and log dispersion types.
+.le
+.ih
+DESCRIPTION
+Ascii text files consisting of an optional FITS header (usually produced
+by \fBwspectext\fR) and a two column list of wavelengths and fluxes
+are converted to IRAF image spectra.  If a header is included then
+the header information is assumed to describe the spectra including
+any dispersion function.  If no header is given then the minimal
+information for describing spectra in IRAF is added.  The dispersion
+function can be set either a linear or log-linear based on two
+keywords (ignoring the wavelength values) or from the wavelength
+values.  The latter may be stored in the header as a lookup table
+allowing for nonlinear dispersions or resample to a linear dispersion.
+This task is a script based on \fBrtextimage\fR for the creating
+the image and entering the flux values, \fBhedit\fR to set some
+of the header keywords, and \fBdispcor\fR to handle the nonlinear
+or resampled dispersion functions.
+.ih
+EXAMPLES
+1.  Create spectrum from a text file originally produced by \fBwspectext\fR.
+
+.nf
+    cl> type text001
+    BITPIX  =                    8  /  8-bit ASCII characters
+    NAXIS   =                    1  /  Number of Image Dimensions
+    NAXIS1  =                  100  /  Length of axis
+    ORIGIN  = 'NOAO-IRAF: WTEXTIMAGE'  /
+    IRAF-MAX=                   0.  /  Max image pixel (out of date)
+    IRAF-MIN=                   0.  /  Min image pixel (out of date)
+    IRAF-B/P=                   32  /  Image bits per pixel
+    IRAFTYPE= 'REAL FLOATING     '  /  Image datatype
+    OBJECT  = 'TITLE             '  /
+    FILENAME= 'TEST              '  /  IRAF filename
+    FORMAT  = '5G14.7            '  /  Text line format
+    APNUM1  = '1 1     '
+    DC-FLAG =                    0
+    WCSDIM  =                    1
+    CTYPE1  = 'LINEAR  '
+    CRVAL1  =                4000.
+    CRPIX1  =                   1.
+    CDELT1  =     10.1010101010101
+    CD1_1   =     10.1010101010101
+    LTM1_1  =                   1.
+    WAT0_001= 'system=equispec                                 '
+    WAT1_001= 'wtype=linear label=Wavelength units=Angstroms   '
+    END
+										    
+    4000.00  1000.
+    4010.10  1005.54
+    4020.20  1011.05
+    ...
+    cl> rspectext text001 spec001
+.fi
+
+2.  Create a spectrum with a nonlinear dispersion using the wavelength
+values as a lookup table.
+
+.nf
+    cl> type text002
+    4000.00  1000.
+    4010.10  1005.54
+    4020.20  1011.05
+    ...
+    cl> rspectext text002 spec002 title="HH12" dtype=nonlinear
+.fi
+.ih
+REVISIONS
+.ls RSPECTEXT V2.11
+The task now automatically senses the presence of a header.
+.le
+.ls RSPECTEXT V2.10.3
+This is a new task with this version.
+.le
+.ih
+SEE ALSO
+wspectext, rtextimage, dispcor, mkms, imspec, sinterp
+.endhelp
diff --git a/noao/onedspec/doc/sapertures.hlp b/noao/onedspec/doc/sapertures.hlp
new file mode 100644
index 00000000..37398d6a
--- /dev/null
+++ b/noao/onedspec/doc/sapertures.hlp
@@ -0,0 +1,217 @@
+.help sapertures Jul95 noao.onedspec
+.ih
+NAME
+sapertures -- Set or change aperture header information
+.ih
+USAGE
+sapertures input
+.ih
+PARAMETERS
+.ls input
+List of spectral images to be modified.
+.le
+.ls apertures = ""
+List of apertures to be modified.  The null list
+selects all apertures.  A list consists of comma separated
+numbers and ranges of numbers.  A range is specified by a hyphen.  An
+optional step size may be given by using the 'x' followed by a number.
+See \fBxtools.ranges\fR for more information.
+.le
+.ls apidtable = ""
+Aperture table.  This may be either a text file or an image.
+A text file consisting of lines with an aperture number,
+beam number, dispersion type code, coordinate of the first physical
+pixel, coordinate interval per physical pixel, redshift factor,
+lower extraction aperture position, upper extraction aperture position,
+and aperture title or identification.  An image will contain the
+keywords SLFIBnnn with string value consisting of aperture number,
+beam number, optional right ascension and declination, and aperture title.
+Any field except the aperture number may be given the value INDEF to
+indicate that the value is not to be changed from the current value.  Any
+apertures not in this table are assigned the values given by the task
+parameters described below.
+
+As a special case a file having just the aperture number, beam number, and
+spectrum aperture identification may be used.  This file format as well as
+use of an image header is the same as that in the \fBapextract\fR package.
+.le
+.ls wcsreset = no
+Reset the world coordinate system (WCS) of the selected apertures to
+uncorrected pixels.  If this parameter is set the \fIapidtable\fR and task
+aperture parameters are ignored.  This option sets the dispersion type flag
+to -1, the starting coordinate value to 1, the interval per pixel to 1, and
+no redshift factor and leaves the other parameters unchanged.  The option
+is useful when it is desired to apply a second dispersion correction using
+\fBidentify\fR and \fBdispcor\fR.
+.le
+.ls verbose = no
+Print a record of each aperture modified?  Only those apertures 
+in which the beam number or label are changed are printed.
+.le
+
+If no aperture table is specified or if there is not an aperture
+entry in the table for a selected aperture the following parameter
+values are used.  A value of INDEF will leave the corresponding
+parameter unchanged.
+.ls beam = INDEF
+Beam number.
+.le
+.ls dtype = INDEF
+Dispersion type.  The dispersion types are:
+
+.nf
+	-1  Linear with dispersion correction flag off
+	 0  Linear with dispersion correction flag on
+	 1  Log-linear with dispersion correction flag on
+.fi
+
+.le
+.ls w1 = INDEF
+Coordinate of the first physical pixel.  Note that it is possible
+that the physical pixels are not the same as the logical pixels if
+an image section has been extracted.
+.le
+.ls dw = INDEF
+Coordinate interval per physical pixel.  Note that it is possible
+that the physical pixels intervals are not the same as the logical pixels
+intervals if an image section has been extracted.
+.le
+.ls z = INDEF
+Redshift factor.  This is usually set with the task \fBdopcor\fR.
+Coordinates are divided by one plus the redshift factor (1+z).
+.le
+.ls aplow = INDEF, aphigh = INDEF
+The aperture extraction limits.  These are set when the \fBapextract\fR
+package is used and it is unlikely that one would use this task to
+change them.
+.le
+.ls title = INDEF
+Aperture title or identification string.
+.le
+.ih
+DESCRIPTION
+This task sets or changes any of the aperture specific parameters except
+the aperture number and the number of  valid pixels.  It is particularly
+useful for images which use the "multispec" world coordinate system
+attribute strings which are not readily accessible with other header
+editors.  A list of images and a list of apertures is used to select which
+spectra are to be modified.  The default empty string for the apertures
+selects all apertures.  The new values are specified either in an aperture
+table file or with task parameters.  The aperture table is used to give
+different values to specific apertures.  If all apertures are to have the
+same values this file need not be used.
+
+The aperture parameters which may be modified are the beam number, the
+dispersion type, the coordinate of the first physical pixel, the coordinate
+interval per physical pixel, the redshift factor, the aperture extraction
+limits, and the title.  The task has parameters for each of these and the
+aperture table consists of lines starting with an aperture number followed
+by the above parameters in the list order and separated by whitespace.  As
+a special case the aperture table may be a file abbreviated to aperture
+number, beam number, and title or an image with keywords SLFIBnnn
+containing the aperture number, beam number, optional right ascension and
+declination, and title.  These special cases allow use of the same file
+orimage used in the \fBapextract\fR package.  If any of the parameters are
+specified as INDEF then the value will be unchanged.
+
+If the \fIwcsreset\fR parameter is set then the aperture table and
+task aperture parameters are ignored and the selected apertures are
+reset to have a dispersion type of -1, a starting coordinate of 1,
+a coordinate interval of 1, and a redshift factor of 0.  This other
+parameters are not changed.  These choice of parameters has the effect
+of resetting the spectrum to physical pixel coordinates and flagging
+the spectra as not being dispersion calibrated.  One use of this option
+is to allow the \fBdispcor\fR task to be reapplied to previously
+dispersion calibrated spectra.
+
+The \fIverbose\fR parameter lists the old and new values when there is
+a change.  If there are no changes there will be no output.
+.ih
+EXAMPLES
+1.  To add titles to a multifiber extraction and change one of the
+beam numbers:
+
+.nf
+	cl> type m33aps
+	36 2 Henear
+	37 0 Sky
+	38 1 New title
+	39 1 Another title
+	41 0 Sky
+	42 1 Yet another title
+	43 1 YAT
+	44 1 Was a sky but actually has an object
+	45 1 Wow
+	46 1 Important new discovery
+	47 0 Sky
+	48 2 Henear
+	cl> saper m33.ms apid=m33aps v+
+	demoobj1.ms:
+	  Aperture 37:  --> Sky
+	  Aperture 38:  --> New title
+	  Aperture 39:  --> Another title
+	  Aperture 41:  --> Sky
+	  Aperture 42:  --> Yet another title
+	  Aperture 43:  --> YAT
+	  Aperture 44: beam 0 --> beam 1
+	  Aperture 44:  --> Was a sky but actually has an object
+	  Aperture 45:  --> Wow
+	  Aperture 46:  --> Important new discovery
+	  Aperture 47:  --> Sky
+.fi
+
+2.  To reset a dispersion calibrated multifiber spectrum:
+
+.nf
+	cl> saper test.ms wcsreset+ verbose+
+	test.ms:
+	  Aperture 1:
+	    w1 4321. --> 1.
+	    dw 1.23 --> 1.
+	  Aperture 2:
+	    w1 4321. --> 1.
+	    dw 1.23 --> 1.
+	  <etc.>
+.fi
+
+3.  To set a constant wavelength length scale (with the default parameters):
+
+.nf
+	cl> saper test.ms dtype=0 w1=4321 dw=1.23 v+
+	test.ms:
+	  Aperture 1:
+	    w1 1. --> 4321.
+	    dw 1. --> 1.23
+	  Aperture 2:
+	    w1 1. --> 4321.
+	    dw 1. --> 1.23
+	  <etc.>
+.fi
+
+4. To reset the wavelengths and title of only aperture 3:
+
+.nf
+	cl> saper test.ms aper=3 w1=4325 dw=1.22 title=HD12345 v+
+	test.ms:
+	  Aperture 3:
+	    w1 4321. --> 4325.
+	    dw 1.23 --> 1.22
+	    apid  --> HD12345
+.fi
+.ih
+REVISIONS
+.ls SAPERTURES V2.11
+This task has been modified to allow use of image header keywords
+as done in the APEXTRACT package.
+.le
+.ls SAPERTURES V2.10.3
+This task has been greatly expanded to allow changing any of the WCS
+parameters as well as the beam number and aperture title.
+.le
+.ls SAPERTURES V2.10
+This task is new.
+.le
+.ih
+SEE ALSO
+specshift, imcoords.wcsreset, hedit, ranges, onedspec.package
+.endhelp
diff --git a/noao/onedspec/doc/sarith.hlp b/noao/onedspec/doc/sarith.hlp
new file mode 100644
index 00000000..a7e7cf87
--- /dev/null
+++ b/noao/onedspec/doc/sarith.hlp
@@ -0,0 +1,571 @@
+.help sarith Mar93 noao.onedspec
+.ih
+NAME
+sarith -- Spectrum arithmetic
+.ih
+USAGE	
+sarith input1 op input2 output
+.ih
+PARAMETERS
+.ls input1
+List of input images to be used as operands.
+.le
+.ls op    
+Operator to be applied to the first operand or to both operands.  The
+unary or single operand operators are:
+
+.nf
+	abs  - absolute value
+	copy - copy (see also \fBscopy\fR)
+	dex  - decimal exponentiation (antilog of base 10 logarithm)
+	exp  - base e exponentiation (antilog of natural logarithm)
+	flam - convert F-nu to F-lambda
+	fnu  - convert F-lambda to F-nu
+	inv  - inverse
+	ln   - natural logarithm
+	log  - base 10 logarithm
+	lum  - convert magnitude to luminosity
+	mag  - convert luminosity to magnitude
+	sqrt - square root
+.fi
+
+The binary or two operand operators are:
+
+.nf
+	replace - replace first operand values by second operand values
+	+       - addition
+	-       - subtraction
+	*       - multiplication
+	/       - division
+	^       - exponentiation
+.fi
+.le
+.ls input2
+Lists of input spectra or constants to be used as second operands for
+binary operations.  If a single value is specified it applies
+to all the first operand input images otherwise the list must match
+the first operand list in number.
+.le
+.ls output
+List of resultant output images or root names.  Image
+sections are ignored and if the output format is "onedspec" then any record
+extensions are stripped to form the root name.  If no output list is
+specified then the input list is used and the input images are replaced by
+the resultant spectra.  If a single output name is specified then all
+resultant spectra are written to the same output image or image root
+name.  This allows packing or merging multiple spectra and requires
+properly setting the \fIclobber\fR, \fImerge\fR, \fIrenumber\fR and
+\fIoffset\fR parameters to achieve the desired output.  If more than one
+output image is specified then it must match the input image list in
+number.
+.le
+.ls w1 = INDEF, w2 = INDEF
+Starting and ending wavelengths to be copied.  If \fIw1\fR is not specified
+then the wavelength of the starting edge of the first pixel is used
+(wavelength at pixel coordinate 0.5) and if \fIw2\fR is not specified then
+the wavelength of the ending edge of the last pixel is used (wavelength of
+the last pixel plus 0.5).  If both are not specified, that is set to INDEF,
+then the whole spectrum is copied and the \fIrebin\fR parameter is
+ignored.  Note that by specifying both endpoints the copied region can be
+set to have increasing or decreasing wavelength per pixel.  If the spectrum
+only partially covers the specified range only that portion of the spectrum
+within the range is copied.  It is an error if the range is entirely
+outside that of a spectrum.
+.le
+.ls apertures = "", beams = ""
+List of apertures and beams to be selected from the input spectra.  The
+logical intersection of the two lists is selected.  The null list
+selects all apertures or beams.  A list consists of comma separated
+numbers and ranges of numbers.  A range is specified by a hyphen.  An
+optional step size may be given by 'x' followed by a number.
+See \fBxtools.ranges\fR for more information.  If the first character
+is "!" then the apertures/beams not in the list are selected.  Note
+that a "!" in either of the lists complements the intersection of the
+two lists.
+For longslit input spectra the aperture numbers
+selects the lines or columns to be extracted.  For 3D Fabry-Perot
+spectra the aperture numbers select the first spatial axis.
+.le
+.ls bands = ""
+List of bands in 3D multispec.
+For 3D spatial spectra the band parameter applies to the second
+spatial axis.
+The null list selects all bands.  The syntax is as described above.
+.le
+.ls apmodulus = 0
+Modulus to be applied to the input aperture numbers before matching against
+the aperture list.  If zero then no modulus is used.  This is used to
+select apertures which are related by the same modulus, typically a
+factor of 10; for example, 10, 1010, and 2010 with a modulus of 1000 are
+related.
+.le
+.ls reverse = no
+Reverse the order of the operands in a binary operation?  Because the first
+operand is used as the image header template, dispersion coordinate
+template, and output image in the case of a null output list it  must be an
+image and not a constant.  To allow certain operations, for
+example subtracting a spectra from a constant or using the subtractand as
+the dispersion coordinate template, the reverse option is used to reverse
+the order of the operands in a binary operation.
+.le
+.ls ignoreaps = no
+Ignore aperture numbers in the second operand?  Normally, spectra in
+binary operations must have matching aperture numbers, otherwise an
+error is printed.  If this parameter is yes then the spectra are matched
+by line number with the last line being used if the second operand spectrum
+has fewer lines than the first operand spectrum.  This is generally
+used to allow using a single spectrum with multiple aperture spectra.
+.le
+.ls format = "multispec" (multispec|onedspec)
+Output image format and name syntax.  The "multispec" format consists of
+one or more spectra in the same image file.  The "onedspec" format consists
+of a single spectrum per image with names having a root name and a four
+digit aperture number extension.  Note that converting to "onedspec" format
+from three dimensional images where the third dimension contains associated
+spectra will not include data from the extra dimension.  Image sections may
+be used in this case.
+.le
+.ls renumber = no
+Renumber the output aperture numbers?  If set the output aperture
+numbers, including any preexisting spectra when merging, are renumbered
+beginning with 1.  The \fIoffset\fR parameter may be used to
+change the starting number.
+.le
+.ls offset = 0
+Offset to be added to the input or renumbered aperture number to form
+the final output aperture number.
+.le
+.ls clobber = no
+Modify an existing output image either by overwriting or merging?
+.le
+.ls merge = no
+Merge apertures into existing spectra?  This
+requires that the \fIclobber\fR parameter be set.  If not merging
+then the selected spectra entirely replace those in existing output images.
+If merging then the input spectra replace those in the output image
+with the same aperture number and new apertures are added if not present.
+.le
+.ls rebin = yes
+Rebin the spectrum to the exact wavelength range specified by the \fIw1\fR
+and \fIw2\fR parameters?  If the range is given as INDEF for both endpoints
+this parameter does not apply.  If a range is given and this parameter is
+not set then the pixels in the specified range (using the nearest pixels to
+the endpoint wavelengths) are copied without rebinning.  In this case the
+wavelength of the first pixel may not be exactly that specified by \fIw1\fR
+and the dispersion, including non-linear dispersions, is unchanged.  If
+this parameter is set the spectra are interpolated to have the first and
+last pixels at exactly the specified endpoint wavelengths while preserving
+the same number of pixels in the interval.  Linear and log-linear
+dispersion types are maintained while non-linear dispersions are
+linearized.
+.le
+.ls errval = 0.
+Value for resultant pixel if an arithmetic error occurs such as dividing
+by zero or the square root of a negative number.
+.le
+.ls verbose = no
+Print a record of each operation?
+.le
+.ih
+DESCRIPTION
+\fBSarith\fR performs arithmetic operations on spectra.  It is
+distinguished from \fBimarith\fR in that it includes unary operators, like
+\fBimfunction\fR but with some specific to astronomical spectra, and binary
+operations between two spectra are performed in dispersion coordinate space
+(typically wavelength) rather than logical pixel space.  In the latter case
+the spectra are checked for matching dispersion functions (which are not
+necessarily linear) and, if they don't match, the second operand is
+interpolated without flux conservation.  (If flux conservation is desired
+then the task \fBdispcor\fR should be used first.) Thus, the spectra may
+have different dispersion functions but the arithmetic is done at matching
+wavelengths.  The default interpolation function is a 5th order
+polynomial.  The choice of interpolation type is made with the package
+parameter "interp".  It may be set to "nearest", "linear", "spline3",
+"poly5", or "sinc".  Remember that this applies to all tasks which might
+need to interpolate spectra in the \fBonedspec\fR and associated packages.
+For a discussion of interpolation types see \fBonedspec\fR.
+
+The unary operators operate on the spectra in the first operand list to
+produce the specified output spectra, which may be the same as the
+input spectra.  The operators include:
+
+.nf
+	abs  - absolute value
+	copy - copy (see also \fBscopy\fR)
+	dex  - decimal exponentiation (antilog of base 10 logarithm)
+	exp  - base e exponentiation (antilog of natural logarithm)
+	flam - convert F-nu to F-lambda
+	fnu  - convert F-lambda to F-nu
+	inv  - inverse
+	ln   - natural logarithm
+	log  - base 10 logarithm
+	lum  - convert magnitude to luminosity
+	mag  - convert luminosity to magnitude
+	sqrt - square root
+.fi
+
+The luminosity to magnitude and magnitude to luminosity operators are
+based on the standard relation:
+
+.nf
+	mag = -2.5 * log (lum)
+.fi
+
+where the log is base 10.  The F-nu to F-lambda and F-lambda to F-nu
+operators are based on the relation:
+
+.nf
+	F-nu = F-lambda * lambda / nu
+.fi
+
+where lambda is wavelength and nu is frequency (currently the wavelength
+is assumed to be Angstroms and so F-lambda is in units of per Angstrom
+and F-nu is in units of per Hertz).  In all the operators it is the
+responsibility of user as to the appropriateness of the operator to
+the input.
+
+The binary operators operate on the spectra in the first operand list
+and the spectra or numerical constants in the second operand.  Numeric
+constants are equivalent to spectra having the specified value at all
+pixels.  The binary operators are the standard arithmetic ones plus
+exponentiation and replacement:
+
+.nf
+	replace - replace first operand values by second operand values
+	+       - addition
+	-       - subtraction
+	*       - multiplication
+	/       - division
+	^       - exponentiation
+.fi
+
+If the second operand is a spectrum, as mentioned previously, it is
+interpolated, without flux conservation, to the dispersion
+function of the first operand spectrum if necessary.
+
+There is a distinctions between the first operand and the second operand.
+The first operand must always be a spectrum.  It supplies the dispersion
+function to be matched by the second operand spectrum.  It also supplies
+a copy of it's image header when a new output spectrum is created.
+In cases where it is desired to have the second operand be the
+dispersion/header reference and/or the first operand be a constant
+the \fIreverse\fR parameter is used.  For example to subtract a
+spectrum from the constant 1:
+
+.nf
+	cl> sarith 1 - spec invspec reverse+
+.fi
+
+or to subtract two spectra using the subtractand as the dispersion
+reference:
+
+.nf
+	cl> sarith spec1 - spec2 diff reverse+
+.fi
+
+When a binary operation on a pair of spectra is performed the aperture
+numbers may be required to be the same if \fIignoreaps\fR is no.  For
+images containing multiple spectra the apertures need not be in the
+same order but only that matching apertures exist.  If this parameter
+is set to yes then aperture numbers are ignored when the operation is
+performed.  For multiple spectra images the second operand spectra
+are matched by image line number rather than by aperture.  If the
+second operand image has fewer lines, often just one line, then the
+last line is used repeatedly.  This feature allows multiple spectra
+in the primary operand list to be operated upon by a single spectrum;
+for example to subtract one spectrum from all spectra in the
+in a multiple spectrum image.
+
+If it is an error to perform an operation on certain data values, for
+example division by zero or the square root of a negative number,
+then the output value is given the value specified by the parameter
+\fIerrval\fR.
+
+A log of the operations performed may be printed to the standard
+output, which may then be redirected if desired, if the \fIverbose\fR
+parameter is set.  In the output the last bracketed number is the
+aperture number of the spectrum.
+
+INPUT/OUTPUT
+
+The arithmetic part of \fBsarith\fR is fairly straightforward and
+intuitive.  The selection of input spectra from input images and
+the placing of output spectra in output images can be more confusing
+because there are many possibilities.  This section concentrates
+on the topics of the input and output.  Since the concepts apply to all
+of the operators it simplifies things to think in terms of copying
+input spectra to output spectra; the "copy" operator.  Note that the
+task \fBscopy\fR is actually just this case of \fBsarith\fR with
+parameters set for copying.  While the discussion here is similar
+to that in the help for \fBscopy\fR, the examples for that task
+are more focused for illustrating this topic than the \fBsarith\fR
+examples which concentrate more on the arithmetic aspects of 
+the task.
+
+Input spectra are specified by an image list which may include explicit
+image names, wildcard templates and @files containing image names.
+The image names may also include image sections such as to select portions of
+the wavelength coverage.  The input images may be either one or two
+dimensional spectra.  One dimensional spectra may be stored in
+individual one dimensional images or as lines in two (or three)
+dimensional images.  The one dimensional spectra are identified by
+an aperture number, which must be unique within an image, and a beam number.
+Two dimensional long slit and three dimensional Fabry-Perot spectra are
+treated, for the purpose of this
+task, as a collection of spectra with dispersion either along any axis
+specified by the DISPAXIS image header parameter
+or the \fIdispaxis\fR package parameter.  The aperture and band
+parameters specify a spatial position.  A number of adjacent
+lines, columns, and bands, specified by the \fInsum\fR package parameter,
+will be summed to form an aperture spectrum.  If number is odd then the
+aperture/band number refers to the middle and if it is even it refers to the
+lower of the two middle lines or columns.
+
+In the case of many spectra each stored in separate one dimensional
+images, the image names may be such that they have a common root name
+and a four digit aperture number extension.  This name syntax is
+called "onedspec" format.  Including such spectra in an
+input list may be accomplished either with wildcard templates such as
+
+.nf
+	name*
+	name.????.imh
+.fi
+
+where the image type extension ".imh" must be given to complete the
+template but the actual extension could also be that for an STF type
+image, or using an @file prepared with the task \fBnames\fR.
+To generate this syntax for output images the \fIformat\fR parameter
+is set to "onedspec" (this will be discussed further later).
+
+From the input images one may select a range of wavelengths with the
+\fIw1\fR and \fIw2\fR parameters and a subset of spectra based on aperture and
+beam numbers using the \fIaperture\fR and \fIbeam\fR parameters.
+If the wavelength range is specified as INDEF the full spectra are
+used without any resampling.  If the aperture and beam lists are not
+specified, an empty list, then all apertures and beams are selected.  The
+lists may be those spectra desired or the complement obtained by prefixing
+the list with '!'.  Only the selected wavelength range and spectra will
+be operated upon and passed on to the output images.
+
+Specifying a wavelength range is fairly obvious except for the question
+of pixel sampling.  Either the pixels in the specified range are used
+without resampling or the pixels are resampled to correspond eactly
+to the requested range.  The choice is made with the \fIrebin\fR parameter.
+In the first case the nearest pixels to the specified wavelength
+endpoints are determined and those pixels and all those in between
+are used.  The dispersion relation is unchanged.  In the second case
+the spectra are reinterpolated to have the specified starting and
+ending wavelengths with the same number of pixels between those points
+as in the original spectrum.  The reinterpolation is done in either
+linear or log-linear dispersion.  The non-linear dispersion functions
+are interpolated to a linear dispersion.
+
+Using \fBsarith\fR with long slit and Fabry-Perot images provides a quick
+and simple type of extraction as opposed to using the \fBapextract\fR
+package.  When summing it is often desired to start each aperture after the
+number of lines summed.  To do this specify a step size in the aperture/band
+list.  For example to extract columns 3 to 23 summing every 5 columns you
+would use an aperture list of "3-23x5" and an \fInsum\fR of 5.  If you do
+not use the step in the aperture list you would extract the sum of columns
+1 to 5, then columns 2 to 6, and so on.
+
+In the special case of subapertures extracted by \fBapextract\fR, related
+apertures are numbered using a modulus; for example apertures
+5, 1005, 2005.  To allow selecting all related apertures using a single
+aperture number the \fIapmodulus\fR parameter is used to specify the
+modulus factor; 1000 in the above example.  This is a very specialized
+feature which should be ignored by most users.
+
+The output list of images may consist of an empty list, a single image,
+or a list of images matching the input list in number.  Note that it
+is the number of image names that matters and not the number of spectra
+since there may be any number of spectra in an image.  The empty list
+converts to the same list as the input and is shorthand for replacing
+the input image with the output image upon completion; therefore it
+is equivalent to the case of a matching list.  If the input
+consists of just one image then the distinction between a single
+output and a matching list is moot.  The interesting distinction is
+when there is an input list of two or more images.  The two cases
+are then a mapping of many-to-many or many-to-one.  Note that it is
+possible to have more complex mappings by repeating the same output
+name in a matching list provided clobbering, merging, and possibly
+renumbering is enabled.
+
+In the case of a matching list, spectra from different input images
+will go to different output images.  In the case of a single output
+image all spectra will go to the same output image.  Note that in
+this discussion an output image when "onedspec" format is specified
+is actually a root name for possibly many images.  However,
+it should be thought of as a single image from the point of view
+of image lists.
+
+When mapping many spectra to a single output image, which may have existing
+spectra if merging, there may be a conflict with repeated aperture
+numbers.  One option is to consecutively renumber the aperture numbers,
+including any previous spectra in the output image when merging and then
+continuing with the input spectra in the order in which they are selected.
+This is specified with the \fIrenumber\fR parameter which renumbers
+beginning with 1.
+
+Another options which may be used independently of renumbering or in
+conjunction with it is to add an offset as specified by the \fIoffset\fR
+parameter.  This is last step in determining the output aperture
+numbers so that if used with the renumber option the final aperture
+numbers begin with one plus the offset.
+
+It has been mentioned that it is possible to write and add to
+existing images.  If an output image exists an error will be
+printed unless the \fIclobber\fR parameter is set.  If clobbering
+is allowed then the existing output image will be replaced by the
+new output.  Rather than replacing an output image sometimes one
+wants to replace certain spectra or add new spectra.  This is
+done by selecting the \fImerge\fR option.  In this case if the output
+has a spectrum with the same aperture number as the input spectrum
+it is replaced by the input spectrum.  If the input spectrum aperture
+number is not in the output then the spectrum is added to the output
+image.  To add spectra with the same aperture number and not
+replace the one in the output use the \fIrenumber\fR or
+\fIoffset\fR options.
+.ih
+EXAMPLES
+In addition to the examples in this section there are many examples
+in the help for \fBscopy\fR which illustrate aspects of selecting
+input spectra and producing various types of output.  Those examples
+are equivalent to using the "copy" operator.  The same examples will
+also apply with other operators where the input spectra are modified
+arithmetically before being copied to the output images.
+
+I.  SIMPLE EXAMPLES
+
+The simple examples use only a single input image and create a new
+output image.
+
+1.  Examples of unary operations:
+
+.nf
+	cl> sarith example1 mag "" magexample
+	cl> sarith magexample lum "" example2
+	cl> sarith example1 log "" logexample
+.fi
+
+Note that a place holder for the second operand is required on the command
+line which will be ignored.
+
+2.  Examples of binary operations using constants:
+
+.nf
+	cl> sarith example1 + 1000 example2
+	cl> sarith example1 - 1000 example2 reverse+
+	cl> sarith example1 / 1000 example2
+	cl> sarith example1 ** 2 example2
+.fi
+
+3.  Examples of binary operations between spectra with matching apertures:
+
+.nf
+	cl> sarith example1 + example2 example3
+	cl> sarith example1 - example2 example3
+.fi
+
+4.  Example of binary operations between spectra with the second image
+consisting of a single spectrum:
+
+.nf
+	cl> sarith example1 / flatspec flatexample1 ignore+ errval=1
+.fi
+
+II.  MORE COMPLEX EXAMPLES
+
+5.  Unary and constant operations on a list of images:
+
+.nf
+	cl> sarith example* fnu "" %example%fnu%
+	cl> sarith example* + 1000 %example%fnu%
+.fi
+
+6.  Binary operations on a list of images using a single second operand
+with matching apertures:
+
+.nf
+	cl> sarith example* - skyspec %example%skysub%*
+.fi
+
+7.  Selecting apertures to operate upon:
+
+.nf
+	cl> sarith example* - skyspec %example%skysub%* aper=1,5,9
+.fi
+
+8.  Extract the sum of each 10 columns in a long slit spectrum and normalize
+by the central spectrum:
+
+.nf
+	cl> nsum = "10"
+	cl> sarith longslit copy "" longslit.ms aper=5-500x10
+	longslit[5]  -->  longslit.ms[5]
+	longslit[15]  -->  longslit.ms[15]
+	longslit[25]  -->  longslit.ms[25]
+	...
+	cl> sarith longslit.ms / longslit.ms[*,25] norm ignore+
+	longslit.ms[5]  /  longslit.ms[*,25][245]  -->  norm[5]
+	longslit.ms[15]  /  longslit.ms[*,25][245]  -->  norm[15]
+	longslit.ms[25]  /  longslit.ms[*,25][245]  -->  norm[25]
+	...
+.fi
+
+9.  In place operations:
+
+.nf
+	cl> sarith example* + 1000 example* clobber+
+	example1[1]  +  1000.  -->  example1[1]
+	example1[2]  +  1000.  -->  example1[2]
+	...
+	example2[1]  +  1000.  -->  example2[1]
+	example2[2]  +  1000.  -->  example2[2]
+	...
+	cl> sarith example* flam "" example* clobber+
+	example1[1]  -- flam -->  example1[1]
+	example1[2]  -- flam -->  example1[2]
+	...
+	example2[1]  -- flam -->  example2[1]
+	example2[2]  -- flam -->  example2[2]
+	...
+	cl> sarith example* - skyspec "" clobber+ ignore+
+	example1[1]  +  skyspec[1]  -->  example1[1]
+	example1[2]  +  skyspec[1]  -->  example1[2]
+	...
+	example2[1]  +  skyspec[1]  -->  example2[1]
+	example2[2]  +  skyspec[1]  -->  example2[2]
+	...
+.fi
+
+10.  Merging existing spectra with the results of operations:
+
+.nf
+	cl> sarith example* / flat "" clobber+ merge+ renum+ ignor+
+.fi
+.ih
+REVISIONS
+.ls SARITH V2.11
+Previously both w1 and w2 had to be specified to select a range to
+be used.  Now if only one is specified the second endpoint defaults
+to the first or last pixel.
+
+The noise band in multispec data is only copied from the primary
+spectrum and not modified.  This is a kludge until the noise is
+handled properly.
+.le
+.ls SARITH V2.10.3
+Additional support for 3D multispec/equispec or spatial spectra has been
+added.  The "bands" parameter allows selecting specific bands and
+the onedspec output format creates separate images for each selected
+aperture and band.
+.le
+.ls SARITH V2.10
+This task is new.
+.le
+.ih
+SEE ALSO
+scopy, splot, imarith, imfunction
+.endhelp
diff --git a/noao/onedspec/doc/sbands.hlp b/noao/onedspec/doc/sbands.hlp
new file mode 100644
index 00000000..0bde52ac
--- /dev/null
+++ b/noao/onedspec/doc/sbands.hlp
@@ -0,0 +1,209 @@
+.help sbands Nov93 onedspec
+.ih
+NAME
+sbands -- bandpass spectrophotometry of spectra
+.ih
+USAGE
+sbands input output bands
+.ih
+PARAMETERS
+.ls input
+Input list of spectra to be measured.  These may be one dimensional
+spectra in individual or "multispec" format or calibrated spatial spectra such
+as long slit or Fabry-Perot images.  The dispersion axis and summing
+parameters are specified by package parameters for the spatial spectra.
+.le
+.ls output
+Output file for the results.  This may be a filename or "STDOUT" to
+write to the terminal.
+.le
+.ls bands
+Bandpass file consisting of lines with one, two, or three bandpasses per
+line.  A bandpass is specified by an identification string (quoted if it is
+null or contains whitespace), the central wavelength, the width of the
+bandpass in wavelength, and a filter filename with the special value "none"
+if there is no filter (a flat unit response).  This format is described
+further in the description section.
+.le
+.ls apertures = ""
+List of apertures to select from the input spectra.  For one dimensional
+spectra this is the aperture number and for spatial spectra it is
+the column or line.  If the null string is specified all apertures are
+selected.  The aperture list syntax is a range list which includes
+intervals and steps (see \fBranges\fR).
+.le
+.ls normalize = yes
+Normalize the bandpass fluxes by the bandpass response?  If no then
+the results will depend on the bandpass widths and filter function
+values.  If yes then fluxes will be comparable to an average pixel
+value.  When computing indices and equivalent widths the flux must
+either be normalized or the bandpasses and filter response functions
+must be the same.
+.le
+.ls mag = no, magzero = 0.
+Output the bandpass fluxes as magnitudes with specified magnitude
+zero point?
+.le
+.ls verbose = yes
+Include a verbose header giving a banner, the parameters used,
+the bandpasses, and column headings?
+.le
+.ih
+DESCRIPTION
+\fBSbands\fR performs bandpass spectrophotometry with one or more bandpasses
+on one or more spectra.  A list of input spectra is specified.  The spectra
+may be of any type acceptable in the \fBnoao.onedspec\fR package including
+multispec format with nonlinear dispersion, long slit spectra, and even
+3D cubes with one dispersion axis.  The \fIapertures\fR parameter allows
+selecting a subset of the spectra by aperture number.
+
+The bandpasses are specified in a text file.  A bandpass consists of four
+fields; an identification name, the wavelength of the bandpass center, a
+bandpass width, and a filename for a filter.  The identification is a
+string which must be quoted if a null name or a name with whitespace is
+desired.  The identification could be given as the central wavelength if
+nothing else is appropriate.  The filter field is a filename for a text
+file containing the filter values.  A filter file consists of a wavelength
+ordered list of wavelength and relative response.  Extrapolation uses the
+end point values and interpolation is linear.  The special name "none" is
+used if there is no filter.  This is equivalent to unit response at all
+wavelengths.
+
+In the bandpass file there may be one, two, or three bandpasses on
+a line.  Below are some examples of the three cases:
+
+.nf
+   alpha 5000 10 myalpha.dat
+   beta1 4000 100 none	     beta2 4100 100 none
+   line  4500 100 none	     red   4000 200 none blue 5000 200 none
+.fi
+
+The flux in each bandpass is measured by summing each pixel in the interval
+multiplied by the interpolated filter response at that pixel.  At the edges
+of the bandpass the fraction of the pixel in the bandpass is used.  If the
+bandpass goes outside the range of the data an INDEF value will be reported.
+If the \fInormalize\fR option is yes then the total flux is divided by
+the sum of the filter response values.  If the \fImag\fR option is
+yes the flux will be converted to a magnitude (provided it is positive)
+using the formula
+
+.nf
+    magnitude = magzero - 2.5 * log10 (flux)
+.fi
+
+where \fImagzero\fR is a parameter for the zero point magnitude and log10
+is the base 10 logarithm.  Note that there is no attempt to deal with the
+pixel flux units.  This is the responsibility of the user.
+
+If there is only one bandpass (on one line of the band file) then only
+the band flux or magnitude is reported.  If there are two bandpasses
+the fluxes or magnitudes for the two bands are reported as well as a
+band index, the flux ratio or magnitude difference (depending on the \fImag\fR)
+flag, and an equivalent width using the second band as the continuum.
+If there are three bandpasses then a continuum bandpass flux is computed
+as the interpolation between the bandpass centers to the center of the
+first bandpass.  The special bandpass identification "cont" will
+be reported.
+
+The equivalent width is obtained from the two bandpasses by the
+formula
+
+.nf
+    eq. width = (1 - flux1 / flux2) * width1
+.fi
+
+where flux1 and flux2 are the two bandpass fluxes and width1 is the
+width of the first bandpass.  Note that for this to be meaningful
+the bandpasses should be normalized or have the same width/response.
+
+The results of measuring each bandpass in each spectrum are written
+to the specified output file.  This file may be given as "STDOUT" to
+write the results to the terminal.  The output file contains lines
+with the spectrum name and aperture, the band identifications and
+fluxes or magnitudes, and the band index and equivalent width (if
+appropriate).  The \fIverbose\fR option allows creating a more
+documented output by including a commented header with the task
+name and parameters, the bandpass definitions, and column labels.
+The examples below show the form of the output.
+.ih
+EXAMPLES
+The following examples use artificial data and arbitrary bands.
+
+1.  Show example results with one, two, and three bandpass entries in
+the bandpass file.
+
+.nf
+    cl> type bands
+    test 6125 50 none red 6025 100 none blue 6225 100 none
+    test 6125 50 none red 6025 100 none
+    test 6125 50 none blue 6225 100 none
+    test 6125 50 none
+    cl> sbands oned STDOUT bands
+
+    # SBANDS: NOAO/IRAF IRAFX valdes@puppis Mon 15:31:45 01-Nov-93
+    #   bands = bands, norm = yes, mag = no
+    #       band     filter wavelength      width
+    #       test       none      6125.        50.
+    #        red       none      6025.       100.
+    #       blue       none      6225.       100.
+    #       test       none      6125.        50.
+    #        red       none      6025.       100.
+    #       test       none      6125.        50.
+    #       blue       none      6225.       100.
+    #       test       none      6125.        50.
+    #
+    #       spectrum    band    flux    band    flux   index eqwidth
+	     oned(1)    test   44.33    cont   97.97    0.45   27.37
+	     oned(1)    test   44.33     red   95.89    0.46   26.89
+	     oned(1)    test   44.33    blue  100.04    0.44   27.84
+	     oned(1)    test   44.33
+.fi
+
+2.  This example shows measurements on a long slit spectrum with an
+aperture selection and magnitude output.
+
+.nf
+    cl> type lsbands.dat
+    band1 4500 40 none
+    band2 4600 40 none
+    band3 4700 40 none
+    cl> nsum=5
+    cl> sbands ls STDOUT lsbands.dat apertures=40-60x5 mag+ magzero=10.1
+
+    # SBANDS: NOAO/IRAF IRAFX valdes@puppis Mon 15:37:18 01-Nov-93
+    #   bands = lsbands.dat, norm = yes, mag = yes, magzero = 10.10
+    #       band     filter wavelength      width
+    #      band1       none      4500.        40.
+    #      band2       none      4600.        40.
+    #      band3       none      4700.        40.
+    #
+    #       spectrum    band     mag
+     ls[38:42,*](40)   band1    3.14
+     ls[38:42,*](40)   band2    3.19
+     ls[38:42,*](40)   band3    3.15
+     ls[43:47,*](45)   band1    3.13
+     ls[43:47,*](45)   band2    3.15
+     ls[43:47,*](45)   band3    3.14
+     ls[48:52,*](50)   band1    2.34
+     ls[48:52,*](50)   band2    2.43
+     ls[48:52,*](50)   band3    2.43
+     ls[53:57,*](55)   band1    3.10
+     ls[53:57,*](55)   band2    3.15
+     ls[53:57,*](55)   band3    3.12
+     ls[58:62,*](60)   band1    3.14
+     ls[58:62,*](60)   band2    3.19
+     ls[58:62,*](60)   band3    3.15
+.fi
+.ih
+REVISIONS
+.ls SBANDS V2.10.4
+The flux column is now printed to 6 digits of precision with possible
+exponential format to permit flux calibrated spectra to print properly.
+.le
+.ls SBANDS V2.10.3
+The task is new in this release
+.le
+.ih
+SEE ALSO
+splot
+.endhelp
diff --git a/noao/onedspec/doc/scombine.hlp b/noao/onedspec/doc/scombine.hlp
new file mode 100644
index 00000000..06e63003
--- /dev/null
+++ b/noao/onedspec/doc/scombine.hlp
@@ -0,0 +1,765 @@
+.help scombine Sep97 noao.onedspec
+.ih
+NAME
+scombine -- Combine spectra
+.ih
+USAGE
+scombine input output
+.ih
+PARAMETERS
+.ls input
+List of input images containing spectra to be combined.  The spectra
+in the images to be combined are selected with the \fIapertures\fR and
+\fIgroup\fR parameters.  Only the primary spectrum is combined and
+the associated band spectra are ignored.
+.le
+.ls output
+List of output images to be created containing the combined spectra.
+If the grouping option is "all"
+or "apertures" then only one output image will be created.  In the
+first case the image will contain only one spectrum and in the latter case
+there will be a spectrum for each selected aperture.
+If the grouping option is "images" then there will be one
+output spectrum per input spectrum.
+.le
+.ls noutput = ""
+List of output images to be created containing the number of spectra combined.
+The number of images required is the same as the \fIoutput\fR list.
+Any or all image names may be given as a null string, i.e. "", in which
+case no output image is created.
+.le
+.ls logfile = "STDOUT"
+File name for recording log information about the combining operation.
+The file name "STDOUT" is used to write the information to the terminal.
+If the null string is specified then no log information is printed or
+recorded.
+.le
+
+.ls apertures = ""
+List of apertures to be selected for combining.  If none is specified
+then all apertures are selected.  The syntax is a blank or comma separated
+list of aperture numbers or aperture ranges separated by a hyphen.
+.le
+.ls group = "apertures" (all|images|apertures)
+Option for grouping input spectra for combining (after selection by aperture)
+from one or more input images.  The options are:
+.ls "all"
+Combine all spectra from all images in the input list into a single output
+spectrum.
+.le
+.ls "images"
+Combine all spectra in each input image into a single spectrum in
+separate output images.
+.le
+.ls "apertures"
+Combine all spectra of the same aperture from all input images and put it
+into a single output image with the other selected apertures.
+.le
+.le
+.ls combine = "average" (average|median|sum)
+Option for combining pixels at the same dispersion coordinate.  after any
+rejection operation.  The options are to compute the  "average", "median",
+or "sum" of the pixels.  The first two are applied after any pixel
+rejection.  The sum option ignores the rejection and scaling parameters and
+no rejection is performed.  In other words, the "sum" option is simply the
+direct summation of the pixels.  The median uses the average of the two
+central values when the number of pixels is even.
+.le
+.ls reject = "none" (none|minmax|ccdclip|crreject|sigclip|avsigclip|pclip)
+Type of rejection operation performed on the pixels which overlap at each
+dispersion coordinate.  The algorithms are discussed in the
+DESCRIPTION section.  The rejection choices are:
+
+.nf
+      none - No rejection
+    minmax - Reject the nlow and nhigh pixels
+   sigclip - Reject pixels using a sigma clipping algorithm
+ avsigclip - Reject pixels using an averaged sigma clipping algorithm
+   ccdclip - Reject pixels using CCD noise parameters
+  crreject - Reject only positive pixels using CCD noise parameters
+     pclip - Reject pixels using sigma based on percentiles
+.fi
+
+.le
+
+.ls first = no
+Use the first input spectrum of each set to be combined to define the
+dispersion coordinates for combining and output?  If yes then all other
+spectra to be combined will be interpolated to the dispersion of this
+reference spectrum and that dispersion defines the dispersion of the
+output spectrum.  If no, then all the spectra are interpolated to a linear
+dispersion as determined by the following parameters.  The interpolation
+type is set by the package parameter \fIinterp\fR.
+.le
+.ls w1 = INDEF, w2=INDEF, dw = INDEF, nw = INDEF, log = no
+The output linear or log linear wavelength scale if the dispersion of the
+first spectrum is not used.  INDEF values are filled in from the maximum
+wavelength range and minimum dispersion of the spectra to be combined.  The
+parameters are aways specified in linear wavelength even when the log
+parameter is set to produce constant pixel increments in the log of the
+wavelength.  The dispersion is interpreted in that case as the difference
+in the log of the endpoints divided by the number of pixel increments.
+.le
+
+.ls scale = "none" (none|mode|median|mean|exposure|@<file>|!<keyword>)
+Multiplicative image scaling to be applied.  The choices are none,
+multiply by the reciprocal of the mode , median, or mean of the specified
+statistics section, scale by the exposure time in the image header, multiply
+by the values in a specified file, or multiply by a specified image header
+keyword.  When specified in a file the scales must be one per line in the
+order of the input spectra.
+.le
+.ls zero = "none" (none|mode|median|mean|@<file>|!<keyword>)
+Additive zero level image shifts to be applied.  The choices are none,
+add the negative of the mode, median, or mean of the specified statistics
+section, add the values given in a file, or add values given by an
+image header keyword.  When specified in a file the zero values must be one
+per line in the order of the input spectra. File or keyword zero offset
+values do not allow a correction to the weights.
+.le
+.ls weight = "none" (none|mode|median|mean|exposure|@<file>|!<keyword>)
+Weights to be applied during the final averaging.  The choices are none,
+the mode, median, or mean of the specified statistics section, the exposure
+time, values given in a file, or values given by an image header keyword.
+When specified in a file the weights must be one per line in the order of
+the input spectra.
+.le
+.ls sample = ""
+Wavelength sample regions to use in computing spectrum statistics for
+scaling and weighting.  If no sample regions are given then the entire
+input spectrum is used.  The syntax is colon separated wavelengths
+or a file containing colon separated wavelengths preceded by the
+@ character; i.e. @<file>.
+.le
+
+.ce
+Algorithm Parameters
+.ls lthreshold = INDEF, hthreshold = INDEF
+Low and high thresholds to be applied to the input pixels.  This is done
+before any scaling, rejection, and combining.  If INDEF the thresholds
+are not used.
+.le
+.ls nlow = 1,  nhigh = 1 (minmax)
+The number of low and high pixels to be rejected by the "minmax" algorithm.
+These numbers are converted to fractions of the total number of input spectra
+so that if no rejections have taken place the specified number of pixels
+are rejected while if pixels have been rejected by thresholding
+or nonoverlap, then the fraction of the remaining pixels, truncated
+to an integer, is used.
+.le
+.ls nkeep = 1
+The minimum number of pixels to retain or the maximum number to reject
+when using the clipping algorithms (ccdclip, crreject, sigclip,
+avsigclip, or pclip).  When given as a positive value this is the minimum
+number to keep.  When given as a negative value the absolute value is
+the maximum number to reject.  This is actually converted to a number
+to keep by adding it to the number of images.
+.le
+.ls mclip = yes (ccdclip, crreject, sigclip, avsigcliip)
+Use the median as the estimate for the true intensity rather than the
+average with high and low values excluded in the "ccdclip", "crreject",
+"sigclip", and "avsigclip" algorithms?  The median is a better estimator
+in the presence of data which one wants to reject than the average.
+However, computing the median is slower than the average.
+.le
+.ls lsigma = 3., hsigma = 3. (ccdclip, crreject, sigclip, avsigclip, pclip)
+Low and high sigma clipping factors for the "ccdclip", "crreject", "sigclip",
+"avsigclip", and "pclip" algorithms.  They multiply a "sigma" factor
+produced by the algorithm to select a point below and above the average or
+median value for rejecting pixels.  The lower sigma is ignored for the
+"crreject" algorithm.
+.le
+.ls rdnoise = "0.", gain = "1.", snoise = "0." (ccdclip, crreject)
+Effective CCD readout noise in electrons, gain in electrons/DN, and
+sensitivity noise as a fraction.  These parameters are used with the
+"ccdclip" and "crreject" algorithms.  The values may be either numeric or
+an image header keyword which contains the value.  Note that if the spectra
+have been extracted from a 2D CCD image then the noise parameters must be
+adjusted for background and the aperture summing.
+.le
+.ls sigscale = 0.1 (ccdclip, crreject, sigclip, avsigclip)
+This parameter determines when poisson corrections are made to the
+computation of a sigma for images with different scale factors.  If all
+relative scales are within this value of unity and all relative zero level
+offsets are within this fraction of the mean then no correction is made.
+The idea is that if the images are all similarly though not identically
+scaled, the extra computations involved in making poisson corrections for
+variations in the sigmas can be skipped.  A value of zero will apply the
+corrections except in the case of equal images and a large value can be
+used if the sigmas of pixels in the images are independent of scale and
+zero level.
+.le
+.ls pclip = -0.5 (pclip)
+Percentile clipping algorithm parameter.  If greater than
+one in absolute value then it specifies a number of pixels above or
+below the median to use for computing the clipping sigma.  If less
+than one in absolute value then it specifies the fraction of the pixels
+above or below the median to use.  A positive value selects a point
+above the median and a negative value selects a point below the median.
+The default of -0.5 selects approximately the quartile point.
+See the DESCRIPTION section for further details.
+.le
+.ls grow = 0
+Number of pixels to either side of a rejected pixel
+to also be rejected.  This applies only to pixels rejected by one of
+the rejection algorithms and not the threshold rejected pixels.
+.le
+.ls blank = 0.
+Value to use when there are no input pixels to combine for an output pixel.
+.le
+.ih
+DESCRIPTION
+\fBScombine\fR combines input spectra by interpolating them (if necessary)
+to a common dispersion sampling, rejecting pixels exceeding specified low
+and high thresholds, scaling them in various ways, applying a rejection
+algorithm based on known or empirical noise statistics, and computing the
+sum, weighted average, or median of the remaining pixels.  Note that
+the "sum" option is the direct summation of the pixels and does not
+perform any rejection or scaling of the data regardless of the parameter
+settings.
+
+The input spectra are specified using an image list in which each image
+may contain multiple spectra.  The set of spectra may be restricted
+by the \fIaperture\fR parameter to specific apertures.  The set of input
+spectra may then be grouped using the \fIgroup\fR parameter and each
+group combined separately into a final output spectrum.  The grouping
+options are to select all the input spectra regardless of the input
+image or aperture number, select all spectra of the same aperture,
+or select all the spectra from the same input image.
+
+The output consists of either a single image with one spectrum for each
+combined group or, when grouping by image, an image with the single
+combined spectra from each input image.  The output images and
+combined spectra inherit the header parameters from the first spectrum
+of the combined group.  In addition to the combined spectrum an associated
+integer spectrum containing the number of pixels combined
+and logfile listing the combined spectra, scaling, weights, etc, may
+be produced.
+
+The spectral combining is done using pixels at common dispersion
+coordinates rather than physical or logical pixel coordinates.  If the
+spectra to be combined do not have identical dispersion coordinates then
+the spectra are interpolated to a common dispersion sampling before
+combining.  The interpolation conserves pixel values rather pixel fluxes.
+This means that flux calibrated data is treated correctly and that
+spectra in counts are not corrected in the interpolation for changes
+in pixel widths.  
+The default interpolation function is a 5th order polynomial.  The
+choice of interpolation type is made with the package parameter "interp".
+It may be set to "nearest", "linear", "spline3", "poly5", or "sinc".
+Remember that this applies to all tasks which might need to interpolate
+spectra in the \fBonedspec\fR and associated packages.  For a discussion of
+interpolation types see \fBonedspec\fR.
+
+There are two choices for the common dispersion coordinate sampling. If the
+\fIfirst\fR parameter is set then the dispersion sampling of the first
+spectrum is used.  This dispersion system may be nonlinear.  If the
+parameter is not set then the user specified linear or log linear
+dispersion system is used.  Any combination of starting wavelength, ending
+wavelength, wavelength per pixel, and number of output pixels may be
+specified.  Unspecified values will default to reasonable values based on
+the minimum or maximum wavelengths of all spectra, the minimum dispersion,
+and the number of pixels needed to satisfy the other parameters.  If the
+parameters overspecify the linear system then the ending wavelength is
+adjusted based on the other parameters.  Note that for a log linear system
+the wavelengths are still specified in nonlog units and the dispersion is
+finally recalculated using the difference of the log wavelength endpoints
+divided by the number pixel intervals (the number of pixels minus one).
+
+There are several stages to combining a selected group of spectra.  The
+first is interpolation to a common dispersion sampling as discussed
+above.  The second stage is to eliminate any pixels outside the specified
+thresholds.  Note that the thresholds apply to the interpolated
+spectra.  Scaling and zero offset factors are computed and applied to the
+spectra if desire.  The computation of these factors as well as weights is
+discussed in the following section.  Next there is a choice of rejection
+algorithms to identify and eliminate deviant pixels.  Some of these are
+based on order statistics and some relative to the distance from an initial
+median or average using a noise model cutoff.  A growing factor may be
+applied to neighbors of rejected pixels to reject additional pixels.  The
+various algorithms are described in detail in a following section.
+Finally, the remaining pixels are combined by summing (which may not be
+appropriate when pixels are rejected), computing a median, or computing a
+weighted or unweighted average.  The combined spectrum is written to an
+output image as well the number of pixels used in the final combining.
+
+SCALES AND WEIGHTS
+
+In order to combine spectra with rejection of pixels based on deviations
+from some average or median they must be scaled to a common level.  There
+are two types of scaling available, a multiplicative intensity scale and an
+additive zero point shift.  The intensity scaling is defined by the
+\fIscale\fR parameter and the zero point shift by the \fIzero\fR
+parameter.  These parameters may take the values "none" for no scaling,
+"mode", "median", or "mean" to scale by statistics of the spectrum pixels,
+"exposure" (for intensity scaling only) to scale by the exposure time
+keyword in the image header, any other image header keyword specified by
+the keyword name prefixed by the character '!', and the name of a file
+containing the scale factors for the input image prefixed by the
+character '@'.
+
+Examples of the possible parameter values are shown below where
+"myval" is the name of an image header keyword and "scales.dat" is
+a text file containing a list of scale factors.
+
+.nf
+	scale = none		No scaling
+	zero = mean		Intensity offset by the mean
+	scale = exposure	Scale by the exposure time
+	zero = !myval		Intensity offset by an image keyword
+	scale = @scales.dat	Scales specified in a file
+.fi
+
+The spectrum statistics factors are computed within specified sample
+regions given as a series of colon separated wavelengths.  If no
+regions are specified then all pixels are used.  If the
+wavelength sample list is too long the regions can be defined in a file and
+specified in the \fIsample\fR parameter using the syntax @<file> where file
+is the filename.
+
+The statistics are as indicated by their names.  In particular, the
+mode is a true mode using a bin size which is a fraction of the
+range of the pixels and is not based on a relationship between the
+mode, median, and mean.  Also thresholded pixels are excluded from the
+computations as well as during the rejection and combining operations.
+
+The "exposure" option in the intensity scaling uses the value of the image
+header keyword (EXPTIME, EXPOSURE, or ITIME).  Note that the exposure
+keyword is also updated in the final image as the weighted average of the
+input values.  If one wants to use a nonexposure time keyword and keep the
+exposure time updating feature the image header keyword syntax is
+available; i.e. !<keyword>.
+
+Scaling values may be defined as a list of values in a text file.  The file
+name is specified by the standard @file syntax.  The list consists of one
+value per line.  The order of the list is assumed to be the same as the
+order of the input spectra.  It is a fatal error if the list is incomplete
+and a warning if the list appears longer than the number of input spectra.
+Consideration of the grouping parameter must be included in
+generating this list since spectra may come from different images,
+some apertures may be missing, and, when there are multiple output spectra
+or images, the same list will be repeatedly used.
+
+If both an intensity scaling and zero point shift are selected the
+multiplicative scaling is done first.  Use of both makes sense for images
+if the intensity scaling is the exposure time to correct for
+different exposure times and with the zero point shift allowing for
+sky brightness changes.  This is less relevant for spectra but the option
+is available.
+
+The spectrum statistics and scale factors are recorded in the log file
+unless they are all equal, which is equivalent to no scaling.  The
+intensity scale factors are normalized to a unit mean and the zero
+point shifts are adjusted to a zero mean.  When scal factors
+or zero point shifts are specified by the user in an @file or by an
+image header keyword, no normalization is done.
+
+Scaling affects not only the mean values between spectra but also the
+relative pixel uncertainties.  For example scaling an spectrum by a
+factor of 0.5 will reduce the effective noise sigma of the spectrum
+at each pixel by the square root of 0.5.  Changes in the zero
+point also changes the noise sigma if the spectrum noise characteristics
+are Poissonian.  In the various rejection algorithms based on
+identifying a noise sigma and clipping large deviations relative to
+the scaled median or mean, one may need to account for the scaling induced
+changes in the spectrum noise characteristics.
+
+In those algorithms it is possible to eliminate the "sigma correction"
+while still using scaling.  The reasons this might be desirable are 1) if
+the scalings are similar the corrections in computing the mean or median
+are important but the sigma corrections may not be important and 2) the
+spectrum statistics may not be Poissonian, either inherently or because the
+spectra have been processed in some way that changes the statistics.  In the
+first case because computing square roots and making corrections to every
+pixel during the iterative rejection operation may be a significant
+computational speed limit the parameter \fIsigscale\fR selects how
+dissimilar the scalings must be to require the sigma corrections.  This
+parameter is a fractional deviation which, since the scale factors are
+normalized to unity, is the actual minimum deviation in the scale factors.
+For the zero point shifts the shifts are normalized by the mean shift
+before adjusting the shifts to a zero mean.  To always use sigma scaling
+corrections the parameter is set to zero and to eliminate the correction in
+all cases it is set to a very large number.
+
+If the final combining operation is "average" then the spectra may be
+weighted during the averaging.  The weights are specified in the same way
+as the scale factors.  The weights, scaled to a unit sum, are printed in
+the log output.
+
+The weights are only used for the final weighted average and sigma image
+output.  They are not used to form averages in the various rejection
+algorithms.  For weights in the case of no scaling or only multiplicative
+scaling the weights are used as given or determined so that images
+with lower signal levels will have lower weights.  However, for
+cases in which zero level scaling is used the weights are computed
+from the initial weights (the exposure time, image statistics, or
+input values) using the formula:
+
+.nf
+	weight_final = weight_initial / (scale * zero)
+.fi
+
+where the zero values are those before adjustment to zero mean over
+all images.  The reasoning is that if the zero level is high the sky
+brightness is high and so the S/N is lower and the weight should be lower.
+
+
+THRESHOLD REJECTION
+
+There is an initial threshold rejection step which may be applied.  The
+thresholds are given by the parameters \fIlthreshold\fR and
+\fIhthreshold\fR.  Values of INDEF mean that no threshold value is
+applied.  Threshold rejection may be used to exclude very bad pixel values
+or as a way of masking images.  The former case is useful to exclude very
+bright cosmic rays.  Some of the rejection algorithms, such as "avsigclip",
+can perform poorly if very strong cosmic rays are present.  For masking one
+can use a task like \fBimedit\fR or \fBimreplace\fR to set parts of the
+spectra to be excluded to some very low or high magic value.
+
+
+REJECTION ALGORITHMS
+
+The \fIreject\fR parameter selects a type of rejection operation to
+be applied to pixels not thresholded.  If no rejection
+operation is desired the value "none" is specified.  This task is
+closely related to the image combining task \fBimcombine\fR and, in
+particular, has the same rejection algorithms.
+Some the algorithms are more appropriate to images but are available
+in this task also for completeness.
+
+MINMAX
+.in 4
+A specified fraction of the highest and lowest pixels are rejected.
+The fraction is specified as the number of high and low pixels, the
+\fInhigh\fR and \fInlow\fR parameters, when data from all the input spectra
+are used.  If pixels are missing where there is no overlap or have been
+rejected by thresholding then a matching fraction of the remaining pixels,
+truncated to an integer, are used.  Thus,
+
+.nf
+	nl = n * nlow/nspectra + 0.001 
+	nh = n * nhigh/nspectra + 0.001 
+.fi
+
+where n is the number of pixels to be combined, nspectra is the number
+of input spectra, nlow and nhigh
+are task parameters and nl and nh are the final number of low and
+high pixels rejected by the algorithm.  The factor of 0.001 is to
+adjust for rounding of the ratio.
+
+As an example with 10 input spectra and specifying one low and two high
+pixels to be rejected the fractions to be rejected are 0.1 and 0.2
+and the number rejected as a function of n is:
+
+.nf
+	 n   0  1  2  3  4  5  6  7  8  9 10
+	 nl  0  0  0  0  0  1  1  1  1  1  2
+	 nh  0  0  0  0  0  0  0  0  0  0  1
+.fi
+.in -4
+CCDCLIP
+.in 4
+If the noise characteristics of the spectra can be described by fixed
+gaussian noise, a poissonian noise which scales with the square root of
+the intensity, and a sensitivity noise which scales with the intensity,
+the sigma in data values at a pixel with true value <I>,
+as approximated by the median or average with the lowest and highest value
+excluded, is given as:
+
+.nf
+	sigma = ((rn / g) ** 2 + <I> / g + (s * <I>) ** 2) ** 1/2
+.fi
+
+where rn is the read out noise in electrons, g is the gain in
+electrons per data value, s is a sensitivity noise given as a fraction,
+and ** is the exponentiation operator.  Often the sensitivity noise,
+due to uncertainties in the pixel sensitivities (for example from the
+flat field), is not known in which case a value of zero can be used.
+
+This model is typically valid for CCD images.  During extraction of 
+spectra from CCD images the noise parameters of the spectrum pixels
+will be changed from those of the CCD pixels.  Currently it is up to
+the user to determine the proper modifications of the CCD read noise
+gain, and sensitivity noise.
+
+The read out noise is specified by the \fIrdnoise\fR parameter.  The value
+may be a numeric value to be applied to all the input spectra or an image
+header keyword containing the value for spectra from each image.
+Similarly, the parameter \fIgain\fR specifies the gain as either a value or
+image header keyword and the parameter \fIsnoise\fR specifies the
+sensitivity noise parameter as either a value or image header keyword.
+
+The algorithm operates on each output pixel independently.  It starts by
+taking the median or unweighted average (excluding the minimum and maximum)
+of the unrejected pixels provided there are at least two input pixels.  The
+expected sigma is computed from the CCD noise parameters and pixels more
+that \fIlsigma\fR times this sigma below or \fIhsigma\fR times this sigma
+above the median or average are rejected.  The process is then iterated
+until no further pixels are rejected.  If the average is used as the
+estimator of the true value then after the first round of rejections the
+highest and lowest values are no longer excluded.  Note that it is possible
+to reject all pixels if the average is used and is sufficiently skewed by
+bad pixels such as cosmic rays.
+
+If there are different CCD noise parameters for the input images
+(as might occur using the image header keyword specification) then
+the sigmas are computed for each pixel from each image using the
+same estimated true value.
+
+If the images are scaled and shifted and the \fIsigscale\fR threshold
+is exceedd then a sigma is computed for each pixel based on the
+spectrum scale parameters; i.e. the median or average is scaled to that of the
+original image before computing the sigma and residuals.
+
+After rejection the number of retained pixels is checked against the
+\fInkeep\fR parameter.  If there are fewer pixels retained than specified
+by this parameter the pixels with the smallest residuals in absolute
+value are added back.  If there is more than one pixel with the same
+absolute residual (for example the two pixels about an average
+or median of two will have the same residuals) they are all added
+back even if this means more than \fInkeep\fR pixels are retained.
+Note that the \fInkeep\fR parameter only applies to the pixels used
+by the clipping rejection algorithm and does not apply to threshold
+or bad pixel mask rejection.
+
+This is the best clipping algorithm to use if the CCD noise parameters are
+adequately known.  The parameters affecting this algorithm are \fIreject\fR
+to select this algorithm, \fImclip\fR to select the median or average for
+the center of the clipping, \fInkeep\fR to limit the number of pixels
+rejected, the CCD noise parameters \fIrdnoise, gain\fR and \fIsnoise\fR,
+\fIlsigma\fR and \fIhsigma\fR to select the clipping thresholds,
+and \fIsigscale\fR to set the threshold for making corrections to the sigma
+calculation for different image scale factors.
+
+.in -4
+CRREJECT
+.in 4
+This algorithm is identical to "ccdclip" except that only pixels above
+the average are rejected based on the \fIhsigma\fR parameter.  This
+is appropriate for rejecting cosmic ray events and works even with
+two spectra.
+
+.in -4
+SIGCLIP
+.in 4
+The sigma clipping algorithm computes at each output pixel the median or
+average excluding the high and low values and the sigma about this
+estimate.  There must be at least three input pixels, though for this method
+to work well there should be at least 10 pixels.  Values deviating by more
+than the specified sigma threshold factors are rejected.  These steps are
+repeated, except that after the first time the average includes all values,
+until no further pixels are rejected or there are fewer than three pixels.
+
+After rejection the number of retained pixels is checked against the
+\fInkeep\fR parameter.  If there are fewer pixels retained than specified
+by this parameter the pixels with the smallest residuals in absolute
+value are added back.  If there is more than one pixel with the same
+absolute residual (for example the two pixels about an average
+or median of two will have the same residuals) they are all added
+back even if this means more than \fInkeep\fR pixels are retained.
+Note that the \fInkeep\fR parameter only applies to the pixels used
+by the clipping rejection algorithm and does not apply to threshold
+rejection.
+
+The  parameters affecting this algorithm are \fIreject\fR to select
+this algorithm, \fImclip\fR to select the median or average for the
+center of the clipping, \fInkeep\fR to limit the number of pixels
+rejected, \fIlsigma\fR and \fIhsigma\fR to select the
+clipping thresholds, and \fIsigscale\fR to set the threshold for
+making corrections to the sigma calculation for different spectrum scale
+factors.
+
+.in -4
+AVSIGCLIP
+.in 4
+The averaged sigma clipping algorithm assumes that the sigma about the
+median or mean (average excluding the low and high values) is proportional
+to the square root of the median or mean at each point.  This is
+described by the equation:
+
+.nf
+	sigma(column,line) = sqrt (gain(line) * signal(column,line))
+.fi
+
+where the \fIestimated\fR signal is the mean or median (hopefully excluding
+any bad pixels) and the gain is the \fIestimated\fR proportionality
+constant having units of photons/data number.
+
+This noise model is valid for spectra whose values are proportional to the
+number of photons recorded.  In effect this algorithm estimates a
+photon per data value gain for each spectrum.
+The gain proportionality factor is computed
+independently for each output spectrum by averaging the square of the residuals
+(at points having three or more input values) scaled by the median or
+mean.
+
+Once the proportionality factor is determined, deviant pixels exceeding the
+specified thresholds are rejected at each point by estimating the sigma
+from the median or mean.  If any values are rejected the median or mean
+(this time not excluding the extreme values) is recomputed and further
+values rejected.  This is repeated until there are no further pixels
+rejected or the number of remaining input values falls below three.  Note
+that the proportionality factor is not recomputed after rejections.
+
+If the spectra are scaled differently and the sigma scaling correction
+threshold is exceedd then a correction is made in the sigma
+calculations for these differences, again under the assumption that
+the noise in an spectra scales as the square root of the mean intensity.
+
+After rejection the number of retained pixels is checked against the
+\fInkeep\fR parameter.  If there are fewer pixels retained than specified
+by this parameter the pixels with the smallest residuals in absolute
+value are added back.  If there is more than one pixel with the same
+absolute residual (for example the two pixels about an average
+or median of two will have the same residuals) they are all added
+back even if this means more than \fInkeep\fR pixels are retained.
+Note that the \fInkeep\fR parameter only applies to the pixels used
+by the clipping rejection algorithm and does not apply to threshold
+rejection.
+
+This algorithm works well for even a few input spectra.  It works better if
+the median is used though this is slower than using the average.  Note that
+if the spectra have a known read out noise and gain (the proportionality
+factor above) then the "ccdclip" algorithm is superior.  However, currently
+the CCD noise characteristics are not well propagated during extraction so
+this empirical algorithm is the one most likely to be useful.  The two
+algorithms are related in that the average sigma proportionality factor is
+an estimate of the gain.
+
+The  parameters affecting this algorithm are \fIreject\fR to select
+this algorithm, \fImclip\fR to select the median or average for the
+center of the clipping, \fInkeep\fR to limit the number of pixels
+rejected, \fIlsigma\fR and \fIhsigma\fR to select the
+clipping thresholds, and \fIsigscale\fR to set the threshold for
+making corrections to the sigma calculation for different image scale
+factors.
+
+.in -4
+PCLIP
+.in 4
+The percentile clipping algorithm is similar to sigma clipping using the
+median as the center of the distribution except that, instead of computing
+the sigma of the pixels from the CCD noise parameters or from the data
+values, the width of the distribution is characterized by the difference
+between the median value and a specified "percentile" pixel value.  This
+width is then multipled by the scale factors \fIlsigma\fR and \fIhsigma\fR
+to define the clipping thresholds above and below the median.  The clipping
+is not iterated.
+
+The pixel values at each output point are ordered in magnitude and the
+median is determined.  In the case of an even number of pixels the average
+of the two middle values is used as the median value and the lower or upper
+of the two is the median pixel when counting from the median pixel to
+selecting the percentile pixel.  The parameter \fIpclip\fR selects the
+percentile pixel as the number (if the absolute value is greater
+than unity) or fraction of the pixels from the median in the ordered set.
+The direction of the percentile pixel from the median is set by the sign of
+the \fIpclip\fR parameter with a negative value signifying pixels with
+values less than the median.  Fractional values are internally converted to
+the appropriate number of pixels for the number of input spectra.  A minimum
+of one pixel and a maximum corresponding to the extreme pixels from the
+median are enforced.  The value used is reported in the log output.  Note
+that the same percentile pixel is used even if pixels have been rejected by
+nonoverlap or thresholding; for example, if the 3nd pixel below
+the median is specified then the 3rd pixel will be used whether there are
+10 pixels or 5 pixels remaining after the preliminary steps.
+
+After rejection the number of retained pixels is checked against the
+\fInkeep\fR parameter.  If there are fewer pixels retained than specified
+by this parameter the pixels with the smallest residuals in absolute
+value are added back.  If there is more than one pixel with the same
+absolute residual (for example the two pixels about an average
+or median of two will have the same residuals) they are all added
+back even if this means more than \fInkeep\fR pixels are retained.
+Note that the \fInkeep\fR parameter only applies to the pixels used
+by the clipping rejection algorithm and does not apply to threshold
+or bad pixel mask rejection.
+
+Some examples help clarify the definition of the percentile pixel.  In the
+examples assume 10 pixels.  The median is then the average of the
+5th and 6th pixels.  A \fIpclip\fR value of 2 selects the 2nd pixel
+above the median (6th) pixel which is the 8th pixel.  A \fIpclip\fR
+value of -0.5 selects the point halfway between the median and the
+lowest pixel.  In this case there are 4 pixels below the median,
+half of that is 2 pixels which makes the percentile pixel the 3rd pixel.
+
+The percentile clipping algorithm is most useful for clipping small
+excursions, such as the wings of bright lines when combining
+disregistered observations, that are missed when using
+the pixel values to compute a sigma.  It is not as powerful, however, as
+using the CCD noise parameters (provided they are accurately known) to clip
+about the median.  This algorithm is primarily used with direct images
+but remains available for spectra.
+
+The  parameters affecting this algorithm are \fIreject\fR to select this
+algorithm, \fIpclip\fR to select the percentile pixel, \fInkeep\fR to limit
+the number of pixels rejected, and \fIlsigma\fR and \fIhsigma\fR to select
+the clipping thresholds.
+
+
+.in -4
+GROW REJECTION
+
+Neighbors of pixels rejected by the rejection algorithms
+may also be rejected.  The number of neighbors to be rejected on either
+side is specified by the \fIgrow\fR parameter.
+
+This rejection step is also checked against the \fInkeep\fR parameter
+and only as many pixels as would not violate this parameter are
+rejected.  Unlike it's application in the rejection algorithms at
+this stage there is no checking on the magnitude of the residuals
+and the pixels retained which would otherwise be rejected are randomly
+selected.
+
+
+COMBINING
+
+After all the steps of offsetting the input images, masking pixels,
+threshold rejection, scaling, and applying a rejection algorithms the
+remaining pixels are combined and output.  The pixels may be combined
+by computing the median or by computing a weighted average.
+.ih
+EXAMPLES
+1.  Combine orders of echelle images.
+
+.nf
+	cl> scombine *.ec *%.ec%% group=images combine=sum
+.fi
+
+2.  Combine all spectra using range syntax and scale by the exposure times.
+
+.nf
+	cl> names irs 10-42 > irs.dat
+	cl> scombine @irs.dat irscombine group=all scale=exptime
+.fi
+
+3.  Combine spectra by apertures using exposure time scaling and weighting.
+
+.nf
+	cl> scombine *.ms combine.ms nout=ncombine.ms \\
+	>>> group=apertures scale=exptime weights=exptime
+.fi
+.ih
+REVISIONS
+.ls SCOMBINE V2.10.3
+The weighting was changed from using the square root of the exposure time
+or spectrum statistics to using the values directly.  This corresponds
+to variance weighting.  Other options for specifying the scaling and
+weighting factors were added; namely from a file or from a different
+image header keyword.  The \fInkeep\fR parameter was added to allow
+controlling the maximum number of pixels to be rejected by the clipping
+algorithms.  The \fIsnoise\fR parameter was added to include a sensitivity
+or scale noise component to the noise model.
+.le
+.ls SCOMBINE V2.10
+This task is new.
+.le
+.ih
+NOTES
+The pixel uncertainties and CCD noise model are not well propagated.  In
+particular it would be desirable to propagate the pixel uncertainties
+and CCD noise parameters from the initial CCD images.
+.ih
+SEE ALSO
+imcombine, odcombine, lscombine
+.endhelp
diff --git a/noao/onedspec/doc/scoords.hlp b/noao/onedspec/doc/scoords.hlp
new file mode 100644
index 00000000..9a529ffa
--- /dev/null
+++ b/noao/onedspec/doc/scoords.hlp
@@ -0,0 +1,83 @@
+.help scoords May97 onedspec
+.ih
+NAME
+scoords -- set spectrum coordinates from a pixel array (1D only)
+.ih
+USAGE
+scoords images coords
+.ih
+PARAMETERS
+.ls images
+List of one dimensional spectrum image names.
+.le
+.ls coords
+List of file names containing the coordinate values.  There may be
+one file which applies to all input images or a matching list
+of one coordinate file for each input image.  The coordinate files
+are a list of coordinate values with one coordinate per line.
+The coordinates must be ordered in increasing or decreasing value.
+The number of coordinates must match the number of pixels in the image.
+.le
+.ls label = ""
+Optional coordinate axis label.  A typical value is "Wavelength"
+for wavelength coordinates.
+.le
+.ls units = ""
+Optional coordinate axis units.  A typical value is "Angstroms".  In
+order to allow coordinate conversions by other IRAF spectra tasks
+the value should be specified as one of the known units
+(see units description in \fBonedspec.package\fR).
+.le
+.ls verbose = yes
+Print a line as each spectrum is processed?
+.le
+.ih
+DESCRIPTION
+\fBScoords\fR sets spectral coordinates in one dimensional spectral
+images as a list of coordinates in the image header.  The
+coordinate file(s) consists of coordinate values given one per line.
+Each coordinate value is assigned to an image pixel in the order given
+and so the number of coordinate values must match the number of pixels
+in the spectrum.  Also the coordinates must be monotonically increasing
+or decreasing.
+
+When multiple spectra are to be set a matching list of coordinates can
+be specified or a single coordinate file for all images may be used.
+
+The coordinate system set in the header is an example of the "multispec"
+world coordinate system.  This is understood by all the standard
+IRAF tasks.  It is described under the help topic "onedspec.specwcs".
+Once the coordinates are set one may resample the spectrum to a
+more compact linear description using the task \fBdispcor\fR.
+
+Since the coordinate values are stored in the header (double
+precision numbers) the header can become quite large if the spectrum
+is long.  Be sure the environment variable "min_lenuserarea" which
+defines the maximum size of the image header in number of characters
+is large enough to hold all the coordinates.
+.ih
+EXAMPLES
+1.  Set the coordinates for a spectrum.
+
+.nf
+    cl> type coords.dat
+    4000.
+    4010.123
+    4020.246
+    4031.7
+    <etc>
+    cl> scoords spec coords.dat label=Wavelength units=Angstroms
+    cl> listpix spec wcs=world
+    4000.  	124.
+    4010.123	543
+    <etc>
+.fi
+.ih
+REVISIONS
+.ls SCOORDS V2.11
+This is a new task with this version.
+.le
+.ih
+SEE ALSO
+rtextimage, dispcor, specwcs, onedspec.package
+.endhelp
diff --git a/noao/onedspec/doc/scopy.hlp b/noao/onedspec/doc/scopy.hlp
new file mode 100644
index 00000000..d0863687
--- /dev/null
+++ b/noao/onedspec/doc/scopy.hlp
@@ -0,0 +1,541 @@
+.help scopy Mar93 noao.onedspec
+.ih
+NAME
+scopy -- Select and copy spectra
+.ih
+USAGE
+scopy input output
+.ih
+PARAMETERS
+.ls input
+List of input images containing spectra to be copied.
+.le
+.ls output
+List of output image names or root names.  Image
+sections are ignored and if the output format is "onedspec" then any record
+extensions are stripped to form the root name.  If no output list is
+specified then the input list is used and the input images are replaced by
+the copied output spectra.  If a single output name is specified then all
+copied spectra are written to the same output image or image root
+name.  This allows packing or merging multiple spectra and requires
+properly setting the \fIclobber\fR, \fImerge\fR, \fIrenumber\fR and
+\fIoffset\fR parameters to achieve the desired output.  If more than one
+output image is specified then it must match the input image list in
+number.
+.le
+.ls w1 = INDEF, w2 = INDEF
+Starting and ending wavelengths to be copied.  If \fIw1\fR is not specified
+then the wavelength of the starting edge of the first pixel is used
+(wavelength at pixel coordinate 0.5) and if \fIw2\fR is not specified then
+the wavelength of the ending edge of the last pixel is used (wavelength of
+the last pixel plus 0.5).  If both are not specified, that is set to INDEF,
+then the whole spectrum is copied and the \fIrebin\fR parameter is
+ignored.  Note that by specifying both endpoints the copied region can be
+set to have increasing or decreasing wavelength per pixel.  If the spectrum
+only partially covers the specified range only that portion of the spectrum
+within the range is copied.  It is an error if the range is entirely
+outside that of a spectrum.
+.le
+.ls apertures = "", beams = ""
+List of apertures and beams to be selected from the input spectra.  The
+logical intersection of the two lists is selected.  The null list
+selects all apertures or beams.  A list consists of comma separated
+numbers and ranges of numbers.  A range is specified by a hyphen.  An
+optional step size may be given by 'x' followed by a number.
+See \fBxtools.ranges\fR for more information.  If the first character
+is "!" then the apertures/beams not in the list are selected.  Note
+that a "!" in either of the lists complements the intersection of the
+two lists.  For longslit input spectra the aperture numbers
+selects the lines or columns to be extracted.  For 3D Fabry-Perot
+spectra the aperture numbers select the first spatial axis.
+.le
+.ls bands = ""
+List of bands in 3D multispec.
+For 3D spatial spectra the band parameter applies to the second
+spatial axis.
+The null list selects all bands.  The syntax is as described above.
+.le
+.ls apmodulus = 0
+Modulus to be applied to the input aperture numbers before matching against
+the aperture list.  If zero then no modulus is used.  This is allows
+selecting apertures which are related by the same modulus, typically a
+factor of 10; for example, 10, 1010 and 2010 with a modulus of 1000 are
+related.
+.le
+.ls format = "multispec" (multispec|onedspec)
+Output image format and name syntax.  The "multispec" format consists of
+one or more spectra in the same image file.  The "onedspec" format consists
+of a single spectrum per image with names having a root name and a four
+digit aperture number extension.  Note that converting to "onedspec" format
+from three dimensional images where the third dimension contains associated
+spectra will not include data from the extra dimension.  Image sections may
+be used in that case.
+.le
+.ls renumber = no
+Renumber the output aperture numbers?  If set the output aperture
+numbers, including any preexisting spectra when merging, are renumbered
+beginning with 1.  The \fIoffset\fR parameter may be used to
+change the starting number.
+.le
+.ls offset = 0
+Offset to be added to the input or renumbered aperture number to form
+the final output aperture number.
+.le
+.ls clobber = no
+Modify an existing output image either by overwriting or merging?
+.le
+.ls merge = no
+Merge apertures into existing spectra?  This
+requires that the \fIclobber\fR parameter be set.  If not merging
+then the selected spectra entirely replace those in existing output images.
+If merging then the input spectra replace those in the output image
+with the same aperture number and new apertures are added if not present.
+.le
+.ls rebin = yes
+Rebin the spectrum to the exact wavelength range specified by the \fIw1\fR
+and \fIw2\fR parameters?  If the range is given as INDEF for both endpoints
+this parameter does not apply.  If a range is given and this parameter is
+not set then the pixels in the specified range (using the nearest pixels to
+the endpoint wavelengths) are copied without rebinning.  In this case the
+wavelength of the first pixel may not be exactly that specified by \fIw1\fR
+and the dispersion, including non-linear dispersions, is unchanged.  If
+this parameter is set the spectra are interpolated to have the first and
+last pixels at exactly the specified endpoint wavelengths while preserving
+the same number of pixels in the interval.  Linear and log-linear
+dispersion types are maintained while non-linear dispersions are
+linearized.
+.le
+.ls verbose = no
+Print a record of each aperture copied?
+.le
+.ih
+DESCRIPTION
+\fBScopy\fR selects regions of spectra from an input list of spectral
+images and copies them to output images.  This task can be used to extract
+aperture spectra from long slit and Fabry-Perot images and to select,
+reorganize, merge, renumber, pack, and unpack spectra in many ways.  Below
+is a list of some of the uses and many examples are given in the EXAMPLES
+section.
+
+.nf
+   o Pack many spectra into individual images into a single image
+   o Unpack images with multiple spectra into separate images
+   o Extract a set of lines or columns from long slit spectra
+   o Extract a set of spatial positions from Fabry-Perot spectra
+   o Extract specific wavelength regions
+   o Select a subset of spectra to create a new image
+   o Merge a subset of spectra into an existing image
+   o Combine spectra from different images into one image
+   o Renumber apertures
+.fi
+
+Input spectra are specified by an image list which may include explicit
+image names, wildcard templates and @files containing image names.
+The image names may also include image sections such as to select portions of
+the wavelength coverage.  The input images may be either one or two
+dimensional spectra.  One dimensional spectra may be stored in
+individual one dimensional images or as lines in two (or three)
+dimensional images.  The one dimensional spectra are identified by
+an aperture number, which must be unique within an image, and a beam number.
+Two dimensional long slit and three dimensional Fabry-Perot spectra are
+treated, for the purpose of this
+task, as a collection of spectra with dispersion either along any axis
+specified by the DISPAXIS image header parameter
+or the \fIdispaxis\fR package parameter.  The aperture and band
+parameters specify a spatial position.  A number of adjacent
+lines, columns, and bands, specified by the \fInsum\fR package parameter,
+will be summed to form an aperture spectrum.  If number is odd then the
+aperture/band number refers to the middle and if it is even it refers to the
+lower of the two middle lines or columns.
+
+In the case of many spectra each stored in separate one dimensional
+images, the image names may be such that they have a common root name
+and a four digit aperture number extension.  This name syntax is
+called "onedspec" format.  Including such spectra in an
+input list may be accomplished either with wildcard templates such as
+
+.nf
+	name*
+	name.????.imh
+.fi
+
+where the image type extension ".imh" must be given to complete the
+template but the actual extension could also be that for an STF type
+image, or using an @file prepared with the task \fBnames\fR.
+To generate this syntax for output images the \fIformat\fR parameter
+is set to "onedspec" (this will be discussed further later).
+
+From the input images one may select a range of wavelengths with the
+\fIw1\fR and \fIw2\fR parameters and a subset of spectra based on aperture and
+beam numbers using the \fIaperture\fR and \fIbeam\fR parameters.
+If the wavelength range is specified as INDEF the full spectra are
+copied without any resampling.  If the aperture and beam lists are not
+specified, an empty list, then all apertures and beams are selected.  The
+lists may be those spectra desired or the complement obtained by prefixing
+the list with '!'.  Only the selected wavelength range and spectra will
+be operated upon and passed on to the output images.
+
+Specifying a wavelength range is fairly obvious except for the question
+of pixel sampling.  Either the pixels in the specified range are copied
+without resampling or the pixels are resampled to correspond eactly
+to the requested range.  The choice is made with the \fIrebin\fR parameter.
+In the first case the nearest pixels to the specified wavelength
+endpoints are determined and those pixels and all those in between
+are copied.  The dispersion relation is unchanged.  In the second case
+the spectra are reinterpolated to have the specified starting and
+ending wavelengths with the same number of pixels between those points
+as in the original spectrum.  The reinterpolation is done in either
+linear or log-linear dispersion.  The non-linear dispersion functions
+are interpolated to a linear dispersion.
+
+Using \fBscopy\fR with long slit or Fabry-Perot images provides a quick and
+simple type of extraction as opposed to using the \fBapextract\fR package.
+When summing it is often desired to start each aperture after the number of
+lines summed.  To do this specify a step size in the aperture/band list.  For
+example to extract columns 3 to 23 summing every 5 columns you would use an
+aperture list of "3-23x5" and an \fInsum\fR of 5.  If you do not use the
+step in the aperture list you would extract the sum of columns 1 to 5, then
+columns 2 to 6, and so on.
+
+In the special case of subapertures extracted by \fBapextract\fR, related
+apertures are numbered using a modulus; for example apertures
+5, 1005, 2005.  To allow selecting all related apertures using a single
+aperture number the \fIapmodulus\fR parameter is used to specify the
+modulus factor; 1000 in the above example.  This is a very specialized
+feature which should be ignored by most users.
+
+The output list of images may consist of an empty list, a single image,
+or a list of images matching the input list in number.  Note that it
+is the number of image names that matters and not the number of spectra
+since there may be any number of spectra in an image.  The empty list
+converts to the same list as the input and is shorthand for replacing
+the input image with the output image upon completion; therefore it
+is equivalent to the case of a matching list.  If the input
+consists of just one image then the distinction between a single
+output and a matching list is moot.  The interesting distinction is
+when there is an input list of two or more images.  The two cases
+are then a mapping of many-to-many or many-to-one.  Note that it is
+possible to have more complex mappings by repeating the same output
+name in a matching list provided clobbering, merging, and possibly
+renumbering is enabled.
+
+In the case of a matching list, spectra from different input images
+will go to different output images.  In the case of a single output
+image all spectra will go to the same output image.  Note that in
+this discussion an output image when "onedspec" format is specified
+is actually a root name for possibly many images.  However,
+it should be thought of as a single image from the point of view
+of image lists.
+
+When mapping many spectra to a single output image, which may have existing
+spectra if merging, there may be a conflict with repeated aperture
+numbers.  One option is to consecutively renumber the aperture numbers,
+including any previous spectra in the output image when merging and then
+continuing with the input spectra in the order in which they are selected.
+This is specified with the \fIrenumber\fR parameter which renumbers
+beginning with 1.
+
+Another options which may be used independently of renumbering or in
+conjunction with it is to add an offset as specified by the \fIoffset\fR
+parameter.  This is last step in determining the output aperture
+numbers so that if used with the renumber option the final aperture
+numbers begin with one plus the offset.
+
+It has been mentioned that it is possible to write and add to
+existing images.  If an output image exists an error will be
+printed unless the \fIclobber\fR parameter is set.  If clobbering
+is allowed then the existing output image will be replaced by the
+new output.  Rather than replacing an output image sometimes one
+wants to replace certain spectra or add new spectra.  This is
+done by selecting the \fImerge\fR option.  In this case if the output
+has a spectrum with the same aperture number as the input spectrum
+it is replaced by the input spectrum.  If the input spectrum aperture
+number is not in the output then the spectrum is added to the output
+image.  To add spectra with the same aperture number and not
+replace the one in the output use the \fIrenumber\fR or
+\fIoffset\fR options.
+
+To print a record as each input spectrum is copied the \fIverbose\fR
+parameter may be set.  The syntax is the input image name followed
+by the aperture number in [].  An arrow then points to the output
+image name with the final aperture number also in [], except for
+"onedspec" format where the image name extension gives the aperture
+number.  It is important to remember that it is the aperture numbers
+which are shown and not the image lines; there is not necessarily any
+relation between image lines and aperture numbers though often they
+are the same.
+.ih
+EXAMPLES
+Because there are so many possiblities there are many examples.  To
+help find examples close to those of interest they are divided into
+three sections; examples involving standard multispec images only, examples
+with onedspec format images, and examples with long slit and Fabry-Perot
+images.  In the examples the verbose flag is set to yes and the output is
+shown.
+
+I.   MULTISPEC IMAGES
+
+The examples in this section deal with the default spectral format of
+one or more spectra in an image.  Note that the difference between
+a "onedspec" image and a "multispec" image with one spectrum is purely
+the image naming syntax.
+
+1.  Select a single spectrum (aperture 3):
+
+.nf
+	cl> scopy example1 ap3 aperture=3
+	example1[3]  -->  ap3[3]
+.fi
+
+2.  Select a wavelength region from a single spectrum:
+
+.nf
+	cl> scopy example1 ap3 aperture=3 w1=5500 w2=6500
+	example1[3]  -->  ap3[3]
+.fi
+
+3.  Select a subset of spectra (apertures 1, 2, 4, 6, and 9): 
+
+.nf
+	cl> scopy example1 subset apertures="1-2,4,6-9x3"
+	example1[1]  -->  subset[1]
+	example1[2]  -->  subset[2]
+	example1[4]  -->  subset[4]
+	example1[6]  -->  subset[6]
+	example1[9]  -->  subset[9]
+.fi
+
+This example shows various features of the aperture list syntax.
+
+4.  Select the same apertures (1 and 3) from multiple spectra and in the
+same wavelength region:
+
+.nf
+	cl> scopy example* %example%subset%* apertures=1,3 w1=5500 w2=6500
+	example1[1]  -->  subset1[1]
+	example1[3]  -->  subset1[3]
+	example2[1]  -->  subset2[1]
+	example2[3]  -->  subset2[3]
+	...
+.fi
+
+The output list uses the pattern substitution feature of image templates.
+
+5.  Select the same aperture from multiple spectra and pack them in a
+a single image:
+
+.nf
+	cl> scopy example* ap2 aperture=2 renumber+
+	example1[2]  -->  ap2[1]
+	example2[2]  -->  ap2[2]
+	example3[2]  -->  ap2[3]
+	...
+.fi
+
+6.  To renumber the apertures sequentially starting with 11:
+
+.nf
+	cl> scopy example1 renum renumber+
+	example1[1]  -->  renum[11]
+	example1[5]  -->  renum[12]
+	example1[9]  -->  renum[13]
+	...
+.fi
+
+7.  To replace apertures (2) in one image with that from another:
+
+.nf
+	cl> scopy example1 example2 aperture=2 clobber+ merge+
+	example1[2]  --> example2[2]
+.fi
+
+8.  To merge two sets of spectra with different aperture numbers into
+    one image:
+
+.nf
+	cl> scopy example![12]* merge
+	example1[1]  ->  merge[1]
+	example1[3]  ->  merge[3]
+	...
+	example2[2]  ->  merge[2]
+	example2[4]  ->  merge[4]
+	...
+.fi
+
+The input list uses the ![] character substitution syntax of image templates.
+
+9.  To merge a set of spectra with the same aperture numbers into another
+existing image:
+
+.nf
+	cl> scopy example2 example1 clobber+ merge+ renumber+
+	example1[5]  -->  example1[2]
+	example1[9]  -->  example1[3]
+	example2[1]  -->  example1[4]
+	example2[5]  -->  example1[5]
+	example2[9]  -->  example1[6]
+.fi
+
+Both images contained apertures 1, 5, and 9.  The listing does not show
+the renumbering of the aperture 1 from example1 since the aperture number
+was not changed.
+
+10.  Select parts of a 3D image where the first band is the
+variance weighted extraction, band 2 is nonweighted extraction,
+band 3 is the sky, and band 4 is the sigma:
+
+.nf
+	cl> scopy example3d.ms[*,*,1] var1.ms
+	example3d.ms[*,*,1][1]  -->  var1.ms[1]
+	example3d.ms[*,*,1][2]  -->  var1.ms[2]
+	...
+	cl> scopy example3d.ms[10:400,3,3] skyap3
+	example3d.ms[10:400,3,3][3]  -->  skyap3[3]
+	cl> scopy example3d.ms[*,*,1] "" clobber+
+	example3d.ms[*,*,1][1]  -->  example3d.ms[1]
+	example3d.ms[*,*,1][2]  -->  example3d.ms[2]
+	...
+.fi
+
+Note that this could also be done with \fBimcopy\fR.  The last example
+is done in place; i.e. replacing the input image by the output image
+with the other bands eliminatated; i.e. the output image is two dimensional.
+
+II.  ONEDSPEC IMAGES
+
+1.  Expand a multi-spectrum image to individual single spectrum images:
+
+.nf
+	cl> scopy example1 record format=onedspec
+	example1[1]  -->  record.0001
+	example1[5]  -->  record.0005
+	example1[9]  -->  record.0009
+	...
+.fi
+
+2.  Pack a set of individual 1D spectra into a single image:
+
+.nf
+	cl> scopy record.????.imh record.ms
+	record.0001[1]  -->  record.ms[1]
+	record.0005[5]  -->  record.ms[5]
+	record.0009[9]  -->  record.ms[9]
+	...
+.fi
+
+3.  Copy a set of record syntax spectra to a different rootname and renumber:
+
+.nf
+	cl> scopy record.????.imh newroot format=onedspec
+	record.0001[1]  -->  newroot.0001
+	record.0005[5]  -->  newroot.0002
+	record.0009[9]  -->  newroot.0003
+	...
+.fi
+
+III. LONG SLIT IMAGES
+
+To define the dispersion axis either the image header parameter DISPAXIS
+must be set (using HEDIT for example) or a the package \fIdispaxis\fR
+parameter must be set.  In these examples the output is the default
+multispec format.
+
+1.  To extract column 250 into a spectrum:
+
+.nf
+	cl> scopy longslit1 c250 aperture=250
+	longslit1[250]  -->  c250[250]
+.fi
+
+2.  To sum and extract every set of 10 columns:
+
+.nf
+	cl> nsum = 10  (or epar the package parameters)
+	cl> scopy longslit1 sum10 apertures=5-500x10
+	longslit1[5]  -->  sum10[5]
+	longslit1[15]  -->  sum10[15]
+	longslit1[25]  -->  sum10[25]
+	...
+.fi
+
+3.  To extract the sum of 10 columns centered on column 250 from a set
+of 2D images:
+
+.nf
+	cl> nsum = 10  (or epar the package parameters)
+	cl> scopy longslit* %longslit%c250.%* aperture=250
+	longslit1[250]  -->  c250.1[250]
+	longslit2[250]  -->  c250.2[250]
+	longslit3[250]  -->  c250.3[250]
+	...
+.fi
+
+4.  To extract the sum of 10 columns centered on column 250 from a set of
+2D images and merge them into a single, renumbered output image:
+
+.nf
+	cl> nsum = 10  (or epar the package parameters)
+	cl> scopy longslit* c250 aperture=250 renum+
+	longslit1[250]  -->  c250[1]
+	longslit2[250]  -->  c250[2]
+	longslit3[250]  -->  c250[3]
+	...
+.fi
+
+IV. FABRY-PEROT IMAGES
+
+To define the dispersion axis either the image header parameter DISPAXIS
+must be set (using HEDIT for example) or a the package \fIdispaxis\fR
+parameter must be set.  In these examples the output is the default
+multispec format.
+
+1.  To extract a spectrum from the spatial position (250,250) where
+dispaxis=3:
+
+.nf
+	cl> scopy fp1 a250 aperture=250 band=250
+	longslit1[250]  -->  a250[250]
+.fi
+
+2.  To sum and extract every set of 10 lines and bands (dispaxis=1):
+
+.nf
+	cl> nsum = "10"
+	cl> scopy fp1 sum10 apertures=5-500x10 bands=5-500x10
+	longslit1[5]  -->  sum10[5]
+	longslit1[15]  -->  sum10[15]
+	longslit1[25]  -->  sum10[25]
+	...
+.fi
+
+3.  To extract the sum of 10 columns and 20 lines centered on column 250 and
+line 100 from a set of 3D images with dispaxis=3:
+
+.nf
+	cl> nsum = "10 20"
+	cl> scopy longslit* %longslit%c250.%* aperture=250 band=100
+	longslit1[250]  -->  c250.1[250]
+	longslit2[250]  -->  c250.2[250]
+	longslit3[250]  -->  c250.3[250]
+	...
+.fi
+.ih
+REVISIONS
+.ls SCOPY V2.11
+Previously both w1 and w2 had to be specified to select a range to
+copy.  Now if only one is specified the second endpoint defaults
+to the first or last pixel.
+.le
+.ls SCOPY V2.10.3
+Additional support for 3D multispec/equispec or spatial spectra has been
+added.  The "bands" parameter allows selecting specific bands and
+the onedspec output format creates separate images for each selected
+aperture and band.
+.le
+.ls SCOPY V2.10
+This task is new.
+.le
+.ih
+SEE ALSO
+ranges, sarith, imcopy, dispcor, specshift
+.endhelp
diff --git a/noao/onedspec/doc/sensfunc.hlp b/noao/onedspec/doc/sensfunc.hlp
new file mode 100644
index 00000000..1ebd7e24
--- /dev/null
+++ b/noao/onedspec/doc/sensfunc.hlp
@@ -0,0 +1,447 @@
+.help sensfunc Mar93 noao.onedspec
+.ih
+NAME
+sensfunc -- Determine sensitivity and extinction functions
+.ih
+USAGE
+sensfunc standards sensitivity
+.ih
+PARAMETERS
+.ls standards = "std"
+Input standard star data file created by the task \fBstandard\fR.
+.le
+.ls sensitivity = "sens"
+Output sensitivity function image name or rootname.  Generally each
+aperture results in an independent sensitivity function with the
+aperture number appended to the rootname.  If the parameter \fIignoreaps\fR
+is set, however, the aperture numbers are ignored and a single sensitivity
+function is determined with the output image having the specified name
+with no extension.
+.le
+.ls apertures = ""
+List of apertures to be selected from the input file.  All other apertures
+are ignored.  If no list is specified then all apertures are selected.
+See \fBranges\fR for the syntax.
+.le
+.ls ignoreaps = no
+Ignore aperture numbers and create a single sensitivity function?  Normally
+each aperture produces an independent sensitivity function.  If the
+apertures are ignored then all the observations are combined into
+a single sensitivity function.
+.le
+.ls logfile = "logfile"
+Output log filename for statistical information about the stars used
+and the sensitivity function and extinction function.
+If no filename is given then no file is written.
+.le
+.ls extinction = <no default>
+Input extinction file.  Any extinction determination made will be
+relative to this extinction.  If no file is given then no extinction
+correction is applied and any extinction determination from the
+standard star data will be an absolute determination of the
+extinction.  The default value is redirected to the package parameter
+of the same name.  The extinction file is generally one of the standard
+extinctions in the calibration directory "onedstds$".
+
+If extinction corrected spectra were used as input to \fBstandard\fR
+then it is important that the same extinction file be used here.
+This includes using no extinction file in both tasks.
+.le
+.ls newextinction = "extinct.dat"
+Output revised extinction file.  If the extinction is revised and an
+output filename is given then a revised extinction file is written.  It
+has the same format as the standard extinction files.
+.le
+.ls observatory = ")_.observatory"
+Observatory at which the spectra were obtained if not specified in the
+image header by the keyword OBSERVAT.  The default is a redirection to look
+in the parameters for the parent package for a value.  This is only used
+when graphing flux calibrated data of spectra which do not include the
+airmass in the image header.  The observatory may be one of the
+observatories in the observatory database, "observatory" to select the
+observatory defined by the environment variable "observatory" or the
+parameter \fBobservatory.observatory\fR, or "obspars" to select the current
+parameters set in the \fBobservatory\fR task.  See help for
+\fBobservatory\fR for additional information.
+.le
+.ls function = "spline3"
+Function used to fit the sensitivity data.  The function types are
+"chebyshev" polynomial, "legendre" polynomial, "spline3" cubic spline,
+and "spline1" linear spline.  The default value may be changed interactively.
+.le
+.ls order = 6
+Order of the sensitivity fitting function.  The value corresponds to the
+number of polynomial terms or the number of spline pieces.  The default
+value may be changed interactively.
+.le
+.ls interactive = yes
+Determine the sensitivity function interactively?  If yes the user
+graphically interacts with the data, modifies data and parameters
+affecting the sensitivity function, and determines a residual extinction.
+.le
+.ls graphs = "sr"
+Graphs to be displayed per frame.  From one to four graphs may be displayed
+per frame.  The graph types are selected by single characters and are:
+
+.nf
+a - residual sensitivity vs airmass
+c - composite residual sensitivity and error bars vs wavelength
+e - input extinction and revised extinction vs wavelength
+i - Flux calibrated spectrum vs wavelength
+r - residual sensitivity vs wavelength
+s - sensitivity vs wavelength
+.fi
+
+All other characters including whitespace and commas are ignored.  The order
+and number of graphs determines the positions of the graphs.
+.le
+.ls marks = "plus cross box"
+Symbols used to mark included, deleted, and added data respectively.
+The available mark types are point, box, plus, cross, diamond, hline
+(horizontal line), vline (vertical line), hebar (horizontal error bar),
+vebar (vertical error bar), and circle.
+.le
+.ls colors = "2 1 3 4"
+Colors to use for "lines", "marks", "deleted" data, and "added" data.
+The colors associated with the numbers is graphics device dependent.
+For example in XGTERM they are defined by resources while on other
+devices that don't support colors only one color will appear.
+.le
+.ls cursor = ""
+Graphics cursor input list.  If not specified as a file then standard
+graphics cursor is read.
+.le
+.ls device = "stdgraph"
+Graphics output device.
+.le
+.ls answer
+Query parameter for selecting whether to fit apertures interactively.
+.le
+.ih
+CURSOR COMMANDS
+
+.nf
+?	Print help
+a	Add a point at the cursor position
+c	Toggle use of composite points
+d	Delete point, star, or wavelength nearest the cursor
+e	Toggle residual extinction correction
+f	Fit data with a sensitivity function and overplot
+g	Fit data with a sensitivity function and redraw the graph(s)
+i	Print information about point nearest the cursor
+m	Move point, star, wavelength nearest the cursor to new sensitivity
+o	Reset to original data
+q	Quit and write sensitivity function for current aperture
+r	Redraw graph(s)
+s	Toggle shift of standard stars to eliminate mean deviations
+u	Undelete point, star, or wavelength nearest the cursor
+w	Change weights of point, star, or wavelength nearest the cursor
+
+:flux [min] [max]  Limits for flux calibrated graphs (INDEF for autoscale)
+:function [type]   Function to be fit to sensitivity data:
+			chebyshev - Chebyshev polynomial
+			legendre  - Legendre polynomial
+			spline1   - Linear spline
+			spline3   - Cubic spline
+:graphs [types]    Graphs to be displayed (up to four):
+		a - Residual sensitivity vs airmass
+		c - Composite residuals and error bars vs wavelength
+		e - Extinction (and revised extinction) vs wavelength
+		i - Flux calibrated image vs wavelength
+		l - Log of flux calibrated image vs wavelength
+		r - Residual sensitivity vs wavelength
+		s - Sensitivity vs wavelength
+:images [images]   Images to flux calibrate and plot (up to four)
+:marks marks       Mark types to use for included, delete, and added points:
+			point, box, plus, cross, diamond, hline,
+			vline, hebar, vebar, circle
+:order [order]     Order of function
+:skys [images]     Sky images for flux calibration (up to four)
+:stats [file]      Statistics about stars and sensitivity fit
+:vstats [file]     Verbose statistics about sensitivity fit
+.fi
+.ih
+DESCRIPTION
+Standard star calibration measurements are used to determine the system
+sensitivity as a function of wavelength for each independent aperture.
+If the parameter \fIignoreaps\fR is set then the aperture numbers are
+ignored and a single sensitivity function is determined from all the
+observations.  Using measurements spanning a range of airmass it is
+also possible to derive an adjustment to the standard extinction curve
+or even an absolute determination.  Extinction determination requires
+that the observations span a good range of airmass during photometric
+conditions.  When conditions are poor and standard star observations
+are obtained during periods of variable transparency, the entire
+sensitivity curve may vary by a constant factor, assuming that the
+cause of the variations has no color effect.  This is often the case
+during periods of thin clouds.  In this case the mean sensitivity of
+each observation may be shifted to match the observation of greatest
+sensitivity.  This allows for the possibility of deriving correct
+absolute fluxes if one observation of a standard was obtained during a
+clear period.
+
+The input data is a file of calibration information produced by the
+task \fBstandard\fR.  The data consists of a spectrum identification
+line containing the spectrum image name, the sky image name if beam
+switching, the aperture number, the length of the spectrum, the
+exposure time, airmass, wavelength range, and title.  Following the
+identification line are calibration lines consisting of the central
+bandpass wavelengths, the tabulated fluxes in the bandpasses, the
+bandpass widths, and the observed counts in the bandpasses.  The
+spectrum identification and calibration lines repeat for each standard
+star observation.  The parameter \fIapertures\fR may be used to select
+only specific apertures from the input data.  This parameter is in the
+form of a range list (see help for \fBranges\fR) and if no list is
+given (specified by the null string "") then all apertures are selected.
+
+An input extinction file may also be specified.  Any extinction
+determinations are then residuals to this input extinction table.
+The format of this table is described in \fBlcalib\fR.
+
+The calibration factor at each point is computed as
+
+	(1) C = 2.5 log (O / (T B F)) + A E
+
+where O is the observed counts in a bandpass of an observation,
+T is the exposure time of the observation, B is the bandpass width,
+F is the flux per Angstrom at the bandpass for the standard star,
+A is the airmass of the observation, and E is the extinction
+at the bandpass.  Thus, C is the ratio of the observed count rate per
+Angstrom corrected to some extinction curve to the expected flux
+expressed in magnitudes.  The goal of the task is to fit the observations
+to the relation
+
+	(2) C = S(W) + AE(W)
+
+where W is wavelength, S(W) is the sensitivity function, and E(W) is
+a residual extinction function relative to the extinction used in (1).
+In later discussion we will also refer to the residual sensitivity which
+is defined by
+
+	(3) R = C - S(W) - AE(W)
+
+The sensitivity function S(W) is output as an one dimensional image
+much like the spectra.  The sensitivities are in magnitude units to
+better judge the variations and because the interpolation is smoother
+in the logarithmic space (mags = 2.5 log10[sensitivity]).  There is one
+sensitivity function for each aperture unless the parameter
+\fIignoreaps\fR is set.  In the first case the image names are formed
+from the specified rootname with the aperture number as a four digit
+numerical extension.  In the latter case a single sensitivity function
+is determined from all data, ignoring the aperture numbers, and the
+specified output image is created without an extension.  These images
+are used by \fBcalibrate\fR to correct observations to a relative of
+absolute flux scale.  If no sensitivity function image rootname is
+specified then the sensitivity curves are not output.
+
+If a revised extinction function E(W) has been determined for one or
+more of the apertures then the functions are averaged over all
+apertures, added to the original extinction, and written to the
+specified extinction table.  The format of this table is the same as
+the standard extinction tables and are, thus, interchangeable.  If no
+new extinction filename is specified then no extinction table is
+recorded.
+
+If a log filename is given then statistical information about the
+sensitivity function determinations are recorded.  This includes the
+names of the input standard star observations and the tabulated
+sensitivity, extinction, and error information.
+
+Some points to note are that if no input extinction is given then the
+E in (1) are zero and the E determined in (2) is the absolute extinction.
+If the data are not good enough to determine extinction then using one
+of the standard extinction curves the problem reduces to fitting
+
+	(4) C = S(W)
+
+The sensitivity and extinction functions are determined as fitted
+curves.  The curves are defined by a function type and order.  There
+are four function types and the order specifies either the number of
+terms in the polynomial or the number of pieces in the spline.  The
+order is automatically reduced to the largest
+value which produces a nonsingular result.  In this case the function
+will attempt to pass through every calibration point.  Lower orders
+provide for a smoother representation of the function.  The latter
+is generally more appropriate for a detector.  The initial function
+type and order for the sensitivity function is specified by the
+parameters \fIfunction\fR and \fIorder\fR.
+
+If the \fIinteractive\fR flag is no then the default function and order
+is fit to equation (4) (i.e. there is no residual extinction determination
+or manipulation of the data).  The sensitivity functions are output
+if an image rootname is given and the log information is output if a
+log filename is given.
+
+When the sensitivity is determined interactively a query is given for
+each aperture.  The responses "no" and "yes" select fitting the sensitivity
+interactively or not for the specified aperture.  The responses "NO" and
+"YES" apply to all apertures and no further queries will be given.
+When interactive fitting is selected the data are graphed
+on the specified graphics device and input is through the specified
+cursor list.  The graphics output consists of from one to four graphs.
+The user selects how many and which types of graphs to display.  The
+graph types and their single character code used to select them are:
+
+.nf
+   a - residual sensitivity vs airmass
+   c - composite residual sensitivity and error bars vs wavelength
+   e - input extinction and revised extinction vs wavelength
+   i - Flux calibrated spectrum vs wavelength
+   r - residual sensitivity vs wavelength
+   s - sensitivity vs wavelength
+.fi
+
+The initial graphs are selected with the parameter \fBgraphs\fR and changed
+interactively with the colon command ':graphs \fItypes\fR'.  The ability
+to view a variety of graphs allows evaluating the effects of the
+sensitivity curve and extinction in various ways.  The flux calibrated
+spectrum graph uses the current sensitivity function and checks for
+possible wiggles in the sensitivity curve which affect the shape of the
+continuum.  The choice of graphs also allows the
+user to trade off plotting speed and resolution against the amount of
+information available simultaneously.  Thus, with some graphics devices
+or over a slow line one can reduce the number of graphs for greater speed
+while on very fast devices with large screens one can look at more
+data.  The parameter \fImarks\fR and the associated colon command
+':marks \fItypes\fR' also let the user define the symbols used to mark
+included, deleted, and added data points.
+
+The list of interactive commands in given in the section on CURSOR COMMANDS.
+The commands include deleting, undeleting, adding, moving, and identifying
+individual data points, whole stars, or all points at the same wavelength.
+Some other commands include 'c' to create composite points by averaging
+all points at the same wavelength (this requires exact overlap in the
+bandpasses) which then replace the individual data points in the fit.
+This is different than the composite point graph which displays the
+residual in the mean sensitivity
+and error \fIin the mean\fR but uses the input data in the fitting.
+The 's' command shifts the data so that the mean sensitivity of each
+star is the same as the star with the greatest mean sensitivity.
+This compensates for variable grey extinction due to clouds.  Note
+that delete points are excluded from the shift calculation and a
+deleted star will not be used as the star of greatest sensitivity.
+Another useful command is 'o' to recover the original data.  This cancels
+all changes made due to shifting, extinction corrections, deleting points,
+creating composite points, etc.
+
+The 'e' command attempts to compute a residual extinction by finding
+correlations between the sensitivity points at different airmass.
+Note that this is not iterative so that repeating this after having
+added an extinction correction simply redetermines the correction.
+At each wavelength or wavelength regions having multiple observations at
+different airmass a slope with airmass is determined.  This slope is
+the residual extinction at that wavelength.  A plot of the residual
+extinctions at each wavelength is made using the ICFIT procedure.
+The user may then examine and fit a curve through the residual extinction
+estimates as a function of wavelength (see \fBicfit\fR for a description
+of the commands).  The user must decide how much wavelength dependence
+is derivable from the data.  In many cases only a constant fit
+to a "gray extinction" or possibly a linear fit is realistic.
+The fitting is exited by the key 'q'.
+
+To help evaluate how important the residual extinction determination
+is a t-statistic significance is computed.  This statistic is defined by
+
+	(5) t = sqrt (r**2 * (N - 2) / (1 - r**2))
+
+where the correlation coefficient
+
+	(6) r = RMS with correction / RMS without correction
+
+is the fractional improvement in the RMS due to the added extinction
+correction and N is the number of wavelength points.  For large
+N this approaches a gaussian sigma but a more precise significance
+requires the t-distribution for N-2 degrees of freedom.  Basically this
+asks, was the improvement in the RMS significantly more than would
+occur with random errors?  A value greater than 3 is good while
+a value less than 1 is not significant.  The user may then accept the
+revised extinction and apply it to the data.
+
+Note that when there are multiple apertures used each aperture has an
+independent system sensitivity but the residual extinction is the same.
+Therefore, the residual extinctions from each aperture are averaged at
+the end.  If one determines a new extinction then one may replace the
+original input extinction by the new extinction and rederive the
+sensitivity.
+.ih
+EXAMPLES
+1.  The following command generates sensitivity spectra
+
+	cl> sensfunc std sens
+
+This command uses the data from the \fBstandard\fR output
+file "std" to create sensitivity functions with rootname "sens".
+If not interactive the task will produce the output with some
+progress messages being printed.  If it is interactive the graphics
+device will be used to display the data and the fit and user can
+change the function and order of the fit, delete bad points, shift
+data to correct for clouds or bandpass errors, and possibly determine
+a revised extinction function.  The statistics of the
+sensitivity determination are written to the logfile ("logfile" by
+default).
+
+2. The following examples illustrate the colon command syntax.  Generally
+if no argument is given the current value is displayed.  For the statistics
+commands an optional output file may be given to record the information.
+
+.nf
+:flux 1e-12 INDEF    Set lower limit for flux plots
+:flux INDEF INDEF    Restore autoscaling in flux plots
+:func spline3	     Select cubic spline function
+:g srae		     Graph sensitivity, residuals, airmass,
+		     and extinction
+:g sii		     Graph sensitivity and two images
+:i n1.0004 n1.0008   Set first two images to graph (the defaults
+		     are taken from the standard star list)
+:skys n1.0005	     Subtract this sky image from first image
+		     for flux calibrated spectrum
+:m plus		     Change the mark type for included points and
+		     don't change the deleted or added point mark type
+:stats		     Print statistics to terminal
+:vstats stdstats     Print verbose statistics to file
+.fi
+.ih
+REVISIONS
+.ls SENSFUNC V2.10.3+
+Deleted points and stars are now ignored from the grey shift calculation.
+.le
+.ls SENSFUNC V2.10.3
+A color parameter was added for graphics terminals supporting color.
+.le
+.ls SENSFUNC V2.10
+The latitude parameter has been replaced by the observatory parameter.
+The 'i' flux calibrated graph type now shows flux in linear scaling 
+while the new graph type 'l' shows flux in log scaling.  A new colon
+command allows fixing the flux limits for the flux calibrated graphs.
+.le
+.ls SENSFUNC V2.8
+This task has been completely rewritten from that of versions 2.5 and
+earlier.
+
+.nf
+1. The input standard data format is different.
+2. Extinction corrections beyond a grey term are now supported.
+3. Weighting by the counts is not supported.
+4. Tabular input is not supported.
+5. The data which can be displayed is greatly improved.
+6. The fitting options have been greatly enhanced.
+7. The fitting function types available have been extended.
+8. One or more flux calibrated images may be displayed using the
+   current sensitivity function.
+9. Additional flexibility is provided for treating apertures.
+.fi
+.le
+.ih
+BUGS
+If the flux points do not span the wavelength range, set by the
+standard star observations, then the fitting may fail at some maximum
+order.  When it fails there is no message but the highest order which
+can be successfully fit is used.  To work around this one can either
+add fake points, truncate the wavelength range in the first line of each
+tabulated object in the file produced by \fBstandard\fR, or exclude the
+part of the image data which cannot be uncalibrated (using
+\fBscopy\fR or \fBdispcor\fR).
+.ih
+SEE ALSO
+standard, lcalib, calibrate, observatory, icfit, ranges, scopy, dispcor
+.endhelp
diff --git a/noao/onedspec/doc/sfit.hlp b/noao/onedspec/doc/sfit.hlp
new file mode 100644
index 00000000..0416c622
--- /dev/null
+++ b/noao/onedspec/doc/sfit.hlp
@@ -0,0 +1,262 @@
+.help sfit Mar92 noao.onedspec
+.ih
+NAME
+sfit -- Fit spectra
+.ih
+USAGE	
+sfit input output
+.ih
+PARAMETERS
+.ls input
+Input spectra to be fit.  These may be any combination of echelle,
+multispec, onedspec, long slit, and spectral cube format images.
+.le
+.ls output
+Output fitted spectra.  The number of output spectra must
+match the number of input spectra.  \fBOutput\fR may be omitted if
+\fBlistonly\fR is yes.
+.le
+.ls lines = "*", bands = "1"
+A range specifications for the image lines and bands to be fit.  Unspecified
+lines and bands will be copied from the original.  If the value is "*", all of
+the currently unprocessed lines or bands will be fit.  A range consists of
+a first line number and a last line number separated by a hyphen.  A
+single line number may also be a range and multiple ranges may be
+separated by commas.
+.le
+.ls type = "fit"
+Type of output spectra.  The choices are "fit" for the fitted function,
+"ratio" for the ratio of the input spectra to the fit, "difference" for
+the difference between the input spectra and the fit, and "data" for
+the data minus any rejected points replaced by the fit.
+.le
+.ls replace = no
+Replace rejected points by the fit in the difference, ratio, and
+data output types?
+.le
+.ls wavescale = yes
+Wavelength scale the X axis of the plot?  This option requires that the
+spectra be wavelength calibrated.  If \fBwavescale\fR is no, the plots
+will be in "channel" (pixel) space.
+.le
+.ls logscale = no
+Take the log (base 10) of both axes?  This can be used when \fBlistonly\fR
+is yes to measure the exponent of the slope of the continuum.
+.le
+.ls override = no
+Override previously fit spectra?  If \fBoverride\fR is yes and
+\fBinteractive\fR is yes, the user will be prompted before each order is
+refit.  If \fBoverride\fR is no, previously fit spectra are silently
+skipped.
+.le
+.ls listonly = no
+Don't modify any images?  If \fBlistonly\fR is yes, the \fBoutput\fR
+image list may be skipped.
+.le
+.ls logfiles = "logfile"
+List of log files to which to write the power series coefficients.  If
+\fBlogfiles\fR = NULL (""), the coefficients will not be calculated.
+.le
+.ls interactive = yes
+Perform the fit interactively using the icfit commands?  This will allow
+the parameters for each spectrum to be adjusted independently.  A separate
+set of the fit parameters (below) will be used for each spectrum and any
+interactive changes to the parameters for a specific spectrum will be
+remembered when that spectrum is fit in the next image.
+.le
+.ls sample = "*"
+The ranges of X values to be used in the fits.  The units will vary
+depending on the setting of the \fBwavescale\fR and \fBlogscale\fR
+parameters.  The default units are in wavelength if the spectra have
+been dispersion corrected.  The sample range syntax consists of
+pairs of values separated by colons and multiple ranges can be
+given separated by commas.
+.le
+.ls naverage = 1
+Number of sample points to combined to create a fitting point.
+A positive value specifies an average and a negative value specifies
+a median.
+.le
+.ls function = spline3
+Function to be fit to the spectra.  The functions are
+"legendre" (legendre polynomial), "chebyshev" (chebyshev polynomial),
+"spline1" (linear spline), and "spline3" (cubic spline).  The functions
+may be abbreviated.  The power series coefficients can only be
+calculated if \fBfunction\fR is "legendre" or "chebyshev".
+.le
+.ls order = 1
+The order of the polynomials or the number of spline pieces.
+.le
+.ls low_reject = 3., high_reject = 3.
+Rejection limits below and above the fit in units of the residual sigma.
+.le
+.ls niterate = 0
+Number of rejection iterations.
+.le
+.ls grow = 1.
+When a pixel is rejected, pixels within this distance of the rejected pixel
+are also rejected.
+.le
+.ls markrej = yes
+Mark rejected points?  If there are many rejected points it might be
+desired to not mark rejected points.
+.le
+.ls graphics = "stdgraph"
+Graphics output device for interactive graphics.
+.le
+.ls cursor = ""
+Graphics cursor input.
+.le
+.ih
+DESCRIPTION
+A one dimensional function is fit to spectra in a list of echelle,
+multispec, or onedspec format images.  The first two formats will
+fit the spectra or orders (i.e. the lines) in each image.
+In this description the term "spectrum" will refer to a line of
+an image while "image" will refer to all spectra in an image.
+The parameters of the fit may vary from spectrum to spectrum within
+images and between images.  The fitted function may
+be a legendre polynomial, chebyshev polynomial, linear spline, or cubic
+spline of a given order or number of spline pieces.  The output spectra
+are formed from the fit, the ratio between the pixel values and the fit,
+the difference of the spectra to the fit, and the original data with
+rejected points possibly replaced.  The output image is of pixel type real.
+
+The line/band numbers (for two/three dimensional images) are written to a
+list of previously processed lines in the header keywords \fISFIT\fR and
+\fISFITB\fR of the output image.  A subsequent invocation of SFIT will only
+process those requested spectra that are not in this list.  This ensures
+that even if the output image is the same as the input image that no
+spectra will be processed twice and permits an easy exit from the task in
+the midst of processing many spectra without losing any work or requiring
+detailed notes.
+
+The points to be fit in each spectrum are determined by
+selecting a sample of X values specified by the parameter \fIsample\fR
+and taking either the average or median of the number of points
+specified by the parameter \fInaverage\fR.  The type of averaging is
+selected by the sign of the parameter with positive values indicating
+averaging, and the number of points is selected by the absolute value
+of the parameter.  The sample units will vary depending on the settings
+of the \fBwavescale\fR and the \fBlogscale\fR parameters.  Note that a
+sample that is specified in wavelength units may be entirely outside
+the domain of the data (in pixels) if some of the spectra are not
+dispersion corrected.  The syntax of the sample specification is a comma
+separated, colon delimited list similar to the image section notation.
+For example, the \fBsample\fR, "6550:6555,6570:6575" might be used to
+fit the continuum near H-alpha.
+
+If \fIlow_reject\fR and/or \fIhigh_reject\fR are greater than zero the
+sigma of the residuals between the fitted points and the fitted
+function is computed and those points whose residuals are less than
+\fI-low_reject\fR * sigma and greater than \fIhigh_reject\fR * sigma
+are excluded from the fit.  Points within a distance of \fIgrow\fR
+pixels of a rejected pixel are also excluded from the fit.  The
+function is then refit without the rejected points.  This rejection
+procedure may be iterated a number of times given by the parameter
+\fIniterate\fR.
+
+If \fIreplace\fR is set then any rejected points from the fitting
+are  replaced by the fit in the data before outputing the difference,
+ratio, or data.  For example with replacing the difference will
+be zero at the rejected points and the data output will be cleaned
+of deviant points.
+
+A range specification is used to select the \fIlines\fR and \fIbands\fR to be
+fit.  These parameters may either be specified with the same syntax as the
+\fBsample\fR parameter, or with the "hyphen" syntax used elsewhere in
+IRAF.  Note that a NULL range for \fBlines/bands\fR expands to \fBno\fR
+lines, not to all lines.  An asterisk (*) should be used to represent a
+range of all of the image lines/bands.  The fitting parameters (\fIsample,
+naverage, function, order, low_reject, high_reject, niterate, grow\fR)
+may be adjusted interactively if the parameter \fIinteractive\fR is
+yes.  The fitting is performed with the \fBicfit\fR package.  The
+cursor mode commands for this package are described in a separate help
+entry under "icfit".  Separate copies of the fitting parameters are
+maintained for each line so that interactive changes to the parameter
+defaults will be remembered from image to image.
+.ih
+PROMPTS
+If several images or lines are specified, the user is asked whether
+to perform an interactive fit for each spectrum.  The response
+may be \fByes, no, skip, YES, NO\fR or \fBSKIP\fR.  The meaning of each
+response is:
+
+.nf
+	yes   - Fit the next spectrum interactively.
+	no    - Fit the next spectrum non-interactively.
+	skip  - Skip the next spectrum in this image.
+
+	YES   - Interactively fit all of the spectra of
+		all of the images with no further prompts.
+	NO   	Non-interactively fit all chosen spectra of all images.
+	SKIP  - This will produce a second prompt, "Skip what?",
+		with the choices:
+
+		spectrum - skip this spectrum in all images
+		image    - skip the rest of the current image
+		all      - \fBexit\fR the program
+		           This will \fBunlearn\fR the fit parameters
+			   for all spectra!
+		cancel  - return to the main prompt
+.fi
+.ih
+EXAMPLES
+1.  To normalize all orders of the echelle spectrum for hd221170
+
+	cl> sfit hd221170.ec nhd221170.ec type=ratio
+
+Each order of the spectrum is graphed and the interactive options for
+setting and fitting the continuum are available.  The important
+parameters are low_rejection (for an absorption spectrum), the function
+type, and the order of the function; these fit parameters are
+originally set to the defaults in the SFIT parameter file.  A
+'?' will display a menu of cursor key options.  Exiting with 'q' will
+update the output normalized order for the current image and proceed to
+the next order or image.
+
+The parameters of the fit for each order are initialized to the current
+values the first time that the order is fit.  In subsequent images, the
+parameters for a order are set to the values from the previous image.
+The first time an order is fit, the sample region is reset to the
+entire order.  Deleted points are ALWAYS forgotten from order to order
+and image to image.
+
+2.  To do several images at the same time
+
+	cl> sfit spec*.imh c//spec*.imh
+
+Note how the image template concatenation operator is used to construct
+the output list of spectra.  Alternatively:
+
+	cl> sfit @inlist @outlist
+
+where the two list files could have been created with the sections
+command or by editing.
+
+3.  To measure the power law slope of the continuum (fluxed data)
+
+	cl> sfit uv.* type=ratio logscale+ listonly+ fun=leg order=2
+.ih
+REVISIONS
+.ls SFIT V2.10.4
+The task was expanded to include fitting specified bands in 3D multispec
+spectra.
+
+The task was expanded to include long slit and spectral cube data.
+.le
+.ls SFIT V2.10
+This task is new.
+.le
+.ih
+BUGS
+The errors are not listed for the power series coefficients.
+
+Spectra that are updated when \fBlogscale\fR is yes are written with a
+linear wavelength scale, but with a log normalized data value.
+
+Selection by aperture number is not supported.
+.ih
+SEE ALSO
+continuum, fit1d, icfit, ranges
+.endhelp
diff --git a/noao/onedspec/doc/sflip.hlp b/noao/onedspec/doc/sflip.hlp
new file mode 100644
index 00000000..66790e4e
--- /dev/null
+++ b/noao/onedspec/doc/sflip.hlp
@@ -0,0 +1,114 @@
+.help sflip Jul94 noao.onedspec
+.ih
+NAME
+sflip -- Flip data and/or dispersion coordinates in spectra
+.ih
+USAGE
+sflip input output
+.ih
+PARAMETERS
+.ls input
+List of input images containing spectra to be flipped.
+.le
+.ls output
+Matching list of output image names for flipped spectra.
+If no list is specified then the flipped spectra will replace the input
+spectra.  If the output image name matching an input image name is the
+same then the flipped spectrum will replace the original spectrum.
+.le
+.ls coord_flip = no
+Flip the dispersion coordinates?  If yes then the relationship between the
+logical pixel coordinates and the dispersion coordinates will be reversed so
+that the dispersion coordinate of the first pixel of the output image will
+correspond to the coordinate of the last pixel in the input image and
+vice-versa for the other endpoint pixel.  The physical coordinates
+will also be flipped.  Only the coordinate system along the dispersion
+axis is flipped.
+.le
+.ls data_flip = yes
+Flip the order of the data pixels as they are stored in the image along
+the dispersion axis?  If yes then the first pixel in the input spectrum
+becomes the last pixel in the output spectrum along the dispersion
+axis of the image.
+.le
+.ih
+DESCRIPTION
+The dispersion coordinate system and/or the data in the spectra specified
+by the input list of images are flipped and stored in the matching output
+image given in the output list of images.  If the output image list is left
+blank or an output image name is the same as an input image name then the
+operation is done so that the flipped spectra in the image replace the
+original spectra.  All of the supported spectrum types are allowed; one
+dimensional images, collections of spectra in multispec format, and two and
+three dimensional spatial spectra in which one axis is dispersion.  In all
+cases the flipping affects only the dispersion axis of the image as
+specified by the DISPAXIS header keyword or the "dispaxis" parameter.  The
+parameters \fIcoord_flip\fR and \fIdata_flip\fR select whether the
+coordinate system and data are flipped.  If neither operation is selected
+then the output spectra will simply be copies of the input spectra.
+
+Flipping of the coordinate system means that the relation between
+"logical" pixel coordinates (the index system of the image array)
+and the dispersion and physical coordinate systems is reversed.
+The dispersion coordinate of the first pixel in the flipped spectrum
+will be the same as the dispersion coordinate of the last pixel
+in the original spectrum and vice-versa for the other endpoint.
+
+Flipping of the data means that the order in which the pixels are stored
+in the image file is reversed along the image axis corresponding to
+the dispersion.
+
+While flipping spectra seems simple there are some subtleties.  If
+both the coordinate system and the data are flipped then plots of
+the spectra in which the dispersion coordinates are shown will appear
+the same as in the original spectra.  In particular the coordinate
+of a feature in the spectrum will remain unchanged.  In contrast
+flipping either the coordinate system or the data will cause features
+in the spectrum to move to opposite ends of the spectrum relative
+to the dispersion coordinates.
+
+Since plotting programs often plot the dispersion axis in some standard way
+such as increasing from left to right, flipping both the dispersion
+coordinates and the data will produce plots that look identical even though
+the order of the points plotted will be reversed.  Only if the spectra are
+plotted against logical pixel coordinates will a change be evident.  Note
+also that the plotting programs themselves have options to reverse the
+displayed graph.  So if all one wants is to reverse the direction of
+increasing dispersion in a plot then physically flipping of the spectra is
+not generally necessary.
+
+Flipping of both the coordinate system and the data is also equivalent
+to using an image section with a reversed axis.  For example
+a one dimensional spectrum can be flipped in both dispersion coordinates
+and data pixel order by
+
+.nf
+    cl> imcopy spec1[-*] spec2
+.fi
+
+Higher dimensional spectra need appropriate dimensions in the image
+sections.  One advantage of \fBsflip\fR is that it will determine the
+appropriate dispersion axis itself.
+.ih
+EXAMPLES
+In the following the spectra can be one dimensional, multispec,
+long slit, or spectral data cubes.
+
+.nf
+    cl> sflip spec1 spec1f		# Flip data to new image
+    cl> sflip spec1 spec1		# Flip data to same image
+    cl> sflip spec1 spec1f coord+ data-	# Flip coordinates and not data
+    cl> sflip spec1 spec1f coord+ 	# Flip both coordinates and data
+    cl> sflip spec* f//spec*		# Flip a list of images
+.fi
+.ih
+REVISIONS
+.ls SFLIP V2.10.4
+New in this release.  Note that the V2.9 SFLIP was different in that
+it was script which simply flipped the data.  Coordinate systems were
+not handled in the same way.
+.le
+.ih
+SEE ALSO
+imcopy, scopy, dispcor, sapertures
+.endhelp
diff --git a/noao/onedspec/doc/sinterp.hlp b/noao/onedspec/doc/sinterp.hlp
new file mode 100644
index 00000000..b983beba
--- /dev/null
+++ b/noao/onedspec/doc/sinterp.hlp
@@ -0,0 +1,146 @@
+.help sinterp Mar92 noao.onedspec
+.ih
+NAME
+sinterp -- Interpolate a tables of x,y pairs to produce a spectrum
+.ih
+USAGE
+sinterp tbl_file
+.ih
+PARAMETERS
+.ls tbl_file
+The name of a file which contains the x,y pairs to be used as
+the basis for interpolation. The pairs must be in order of
+increasing x.
+.le
+
+The following parameters may or may not be necessary, depending
+on the options selected.
+
+.ls input
+If a few single elements are desired, rather than a full
+array of elements, the user may enter a sequence of x values
+from the terminal or a file to be used to interpolate into
+the x,y table (parameter curve_gen=no).
+.le
+.ls image
+If parameter make_image=yes, then an image file name is needed
+.le
+.ls order = 5
+If the interpolator is a polynomial fit or spline (interp_mode=
+chebyshev, legnedre, spline3, spline1), the order of the fit
+is required.
+.le
+.ls x1
+If parameter curve_gen=yes, this is the starting x value to
+begin the curve generation.
+.le
+
+Of the following three parameters, two must be specified, and the
+third will be derived.
+
+.ls x2 = 0.0
+As above, but x2 determines the endpoint of the curve.
+.le
+.ls dx = 0.0
+As above, but dx determines the pixel-to-pixel increment
+to be used during the curves generation.
+.le
+.ls npts = 0
+As above, but this determines the number of pixels to be generated.
+.le
+
+.ls curve_gen = no
+If this parameter is set to yes, then parameters x1, and two of
+the three x2, dx, npts are required. The output is in the form
+of new x,y pairs and may be redirected to a text file.
+But if parameter make_image is also yes, the output is
+in the form of an IRAF image file having the name given by
+the parameter image. If curve_gen=no, the user must supply
+a set of x values and interpolation is performed on those values.
+.le
+.ls make_image = no
+If set to yes, then curve_gen=yes is implied and an image file name
+is requied. A one dimensional IRAF image is created.
+.le
+.ls tbl_size = 1024
+This parameter defines the maximum size to be set aside for
+memory storage of the input x,y pairs.
+.le
+.ls interp_mode = "chebyshev"
+This parameter controls the method of interpolation. The linear
+and curve options are true interpolators, while chebyshev,
+legendre, spline3, and splin1 are fits to the data.
+.le
+.ih
+DESCRIPTION
+The specified file is read assuming it is a text file containing
+pairs of x,y values in the form: xxx yyy. The table is used
+to define the function y(x). The pairs must be entered in the file
+in increasing order of x.
+
+The user specifies either specific x values for which the function
+is to be evaluated, or specifies that a sequence of values beginning
+with x1 are to be generated. In the former case, the explicit x values
+may come either from the keyboard or from a file. In the latter case
+the user must also specify the sequence by defining the increment, dx,
+the endpoint, x2, and the number of points to generate in the sequence.
+Then y(x) is evaluated at x1, x1+dx, x1+2*dx, ...  , x1+(n-2)*dx, x2.
+Only 2 of the 3 parameters (x2, dx, npts) are needed to fully
+specify the sequence.
+
+The output of the function evaluation is either new x,y pairs written
+to STDOUT, or an IRAF image.
+
+The function used to evaluated the tabular data may be any of the following
+forms:
+
+.ls (1)
+Linear interpolation between points.
+.le
+.ls (2)
+Smooth interpolation between points.
+.le
+.ls (3)
+A polynomial fit of either Legendre or Chebyshev types.
+.le
+.ls (4)
+A cubic or linear spline.
+.le
+
+If the table of x,y pairs is very large, the parameter tbl_size
+should be set to the number of pairs. For example, if a spectrum
+is available as a text file of x,y pairs (such as might be
+obtained from IUE), and the number of pairs is 4096, then tbl_size
+should be set to 4096. This provides for sufficient memory to
+contain the table.
+
+.ih
+EXAMPLES
+The following shows how a text file may be used to generate a spectrum:
+
+.nf
+	cl> sinterp textfile make+ x1=4000 x2=5000 npts=1024 \
+	>>> image=testimage interp_mode=curve
+.fi
+
+The following sequence shows how to generate a spectrum of an IRS
+standard star using the calibration file data as the source.
+
+.nf
+	cl> lcalib flam feige34 caldir=onedstds$irscal/ >textfile
+	cl> sinterp textfile make+ x1=3550 dx=1.242 npts=1024 \
+	>>> interp_mode=linear image=feige34
+.fi
+.ih
+REVISIONS
+.ls SINTERP V2.10.3+
+The image header dispersion coordinate system has been updated to the
+current system.
+.le
+.ls SINTERP V2.10
+This task is unchanged.
+.le
+.ih
+SEE ALSO
+lcalib
+.endhelp
diff --git a/noao/onedspec/doc/skytweak.hlp b/noao/onedspec/doc/skytweak.hlp
new file mode 100644
index 00000000..857e4380
--- /dev/null
+++ b/noao/onedspec/doc/skytweak.hlp
@@ -0,0 +1,311 @@
+.help skytweak Mar97 noao.onedspec
+.ih
+NAME
+skytweak -- sky subtract 1D spectra after tweaking sky spectra
+.ih
+SUMMARY
+Sky spectra are shifted and scaled to best subtract sky features from data
+spectra.  This may be done non-interactively to minimize the RMS in some
+region or regions of the data spectra and interactively with a graphically
+search.
+.ih
+USAGE
+skytweak input output cal
+.ih
+PARAMETERS
+.ls input
+List of input data images containing one dimensional spectra to be
+corrected.  All spectra in each image are corrected. The spectra need not
+be wavelength calibrated.
+.le
+.ls output
+List of output corrected images.  The list must either match the input list
+or be an empty list.  If an empty list is specified the input spectra will
+be replaced by the corrected spectra.  The input spectra will also be
+replaced if the input and output image names are the same.  Any other image
+name must be for a new image otherwise a warning message will be given and
+the task will proceed to the next input image.
+.le
+.ls cal  
+List of sky calibration images.  If a single image is specified it
+will apply to all the input images.  Otherwise the list of calibration
+images must match the list of input images.
+.le
+.ls ignoreaps = no
+Ignore aperture numbers between the input spectra and the calibration
+spectra?  If "no" then the calibration image must contain a spectrum
+with the same aperture number as each spectrum in the input image.
+Otherwise the first spectrum in the calibration image will be used
+for all spectra in the input image.
+.le
+.ls xcorr = yes
+Cross-correlate each input spectrum with the calibration spectrum to
+determine an shift for the calibration spectrum?  Only regions specified by
+the sample regions parameter will be used in the cross-correlation.
+.le
+.ls tweakrms = yes
+Search for the minimum RMS in the corrected spectrum by adjusting the
+shifts and scales between the input spectrum and the calibration spectrum?
+The RMS is minimized in the specified sample regions.
+.le
+.ls interactive = yes
+Enter an interactive graphical mode to search for the best shift
+and scale between the input spectra and calibration spectra?  This
+is done after the optional automatic cross-correlation and RMS minimization
+step.  A query is made for each input spectrum so that the interactive
+step may be skipped during the execution of the task.
+.le
+.ls sample = "*"
+Sample regions to use for cross-correlation, automatic RMS minimization,
+and RMS values.  The sample regions are specified by a list of comma
+separated ranges.  The ranges are colon separate coordinate values.
+For dispersion calibrated spectra the coordinate values are in the
+dispersion units otherwise they are in pixel coordinates.  The string "*"
+selects the entire spectrum.  The sample regions may be changed
+interactively either with the cursor or with a colon command.
+.le
+.ls lag = 10
+The cross-correlation lag to use when \fIxcorr\fR = yes.  The lag
+is given in pixels.   This is the distance to either side of the
+initial shift over which the cross-correlation profile is computed.
+If a value of zero is given then the cross-correlation step is not done.
+.le
+.ls shift = 0., dshift = 1.
+The initial shift and shift step in pixels.  This initializes the shift
+search parameters for the first spectrum.  If \fIdshift\fR is zero then
+there will be no search for a new shift and the 'x' interactive function is
+disabled.  These parameters may be changed interactively.  After the
+first spectrum subsequent spectra begin with the values from the last
+spectrum.
+.le
+.ls scale = 1., dscale = 0.2
+The initial scale and scale step.  This initializes the scale
+search parameters for the first spectrum.  If \fIdscale\fR is zero then
+there will be no search for a new scale and the 'y' interactive function is
+disabled.  These parameters may be changed interactively.  After the
+first spectrum subsequent spectra begin with the values from the last
+spectrum.
+.le
+.ls offset = 1.
+The interactive search displays three candidate corrected spectra which
+have been normalized to a mean of one.  The offset is added and subtracted
+to separate the three candidates.  The value may be changed interactively.
+.le
+.ls smooth = 1
+The displayed candidate corrected spectra are smoothed by a moving
+boxcar average with a box size specified by this parameter.  The smoothing
+only applies to the displayed spectra and does not affect the measured
+RMS or the output corrected spectra.  The value may be changed interactively.
+.le
+.ls cursor = ""
+Input cursor for the interactive graphics.  A null value selects the
+graphics cursor otherwise a file of cursor values may be specified.
+.le
+.ls answer
+Query parameter for responding to the interactive question.  This parameter
+should not be specified on the command line.
+.le
+.ls interp = poly5
+The \fBpackage\fR parameter specifying the interpolation function for shifting
+the calibration spectra to match the input spectra.
+.le
+.ih
+DESCRIPTION
+Input one dimensional spectra are corrected to remove sky features by
+subtracting a shifted and scaled sky calibration spectra.
+The shifting
+allows for possible small shifts or errors in the dispersion zeropoints.
+
+The following describes the correction.  Let J(x_i) be the calibration
+spectrum at a set of pixels x_i.  An interpolation function is fit to this
+spectrum to give J(x).  The shifted and scaled calibration function
+is then
+
+.nf
+    (1)  J'(x) = J(x+dx) *scale
+.fi
+
+where dx is the pixel shift parameter and
+scale is the scale parameter.
+The output corrected spectrum is then computed as
+
+.nf
+    (2)  I'(x_i) = I(x_i) - J'(x_i)
+.fi
+
+where I' is the corrected spectrum and I is the input spectrum.  If the
+spectra are dispersion calibrated, possibly with different dispersion
+parameters, then the x values in (2) from the input spectrum are converted
+to matching pixels in the calibration spectrum using the dispersion
+functions of the two spectra.
+
+The purpose of this task is to determine the best values of the
+shift and scale parameters dx and scale.  There
+are automatic and interactive methods provided.  The automatic
+methods are cross-correlation of the calibration and input spectra
+to find a shift and an iterative search for the in both
+shift and scale that minimizes the RMS of I' in some region.
+The automatic methods are performed first, if selected, followed
+by the interactive, graphical step.  The following describes
+the steps in the order in which they occur.
+
+The initial values of the shift and scale are set by the parameters
+\fIshift\fR and \fIscale\fR for the first spectrum.  After that the values
+determined for the previous spectrum, those actually applied to correcting
+that spectrum, are used as the initial values for the next spectrum.  The
+search steps and sample regions are also initialized by task parameters but
+may be modified during the interactive step and the modified values apply
+to subsequent spectra.
+
+If the \fIxcorr\fR parameter is yes and the \fIlag\fR parameter is
+not zero the calibration spectrum is cross-correlated against the input
+spectrum.  Each spectrum is prepared as follows.  A large scale continuum
+is fit by a quadratic chebyshev using 5 iterations of sigma clipping with a
+clipping factor of 3 sigma below the fit and 1 sigma above the fit and
+rejecting the deviant points along with one pixel on either side.  This
+attempts to eliminate the effects of absorption lines.  The continuum fit
+is subtracted from the spectrum and the spectrum is extended and tapered by
+a cosine function of length given by the \fIlag\fR parameter.
+
+The prepared spectra are then cross-correlated by shifting the calibration
+spectrum plus and minus the specified \fIlag\fR amount about the current
+shift value.  Only the regions in the input spectrum specified by the
+sample regions parameter are used in the correlation.  This produces a
+correlation profile whose peak defines the relative shift between the two
+spectra.  The current shift value is updated.  This method assumes the
+common telluric features dominate within the specified sample regions.  The
+lag size should be roughly the profile widths of the telluric features.
+
+If the \fItweakrms\fR parameter is yes and \fIdshift\fR is greater than
+zero trial corrections at the current shift value and plus and minus one
+shift step with the scale value fixed at its current value are made and the
+RMS in the sample regions computed.  If the RMS is smallest at the current
+shift value the shift step is divided in half otherwise the current shift
+value is set to the shift with the lowest RMS.  The process is then
+repeated with the new shift and shift step values.  This continues until
+either the shift step is less than 0.01 pixels or the shift is more than
+two pixels from the initial shift.  In the latter case the final shift is
+reset to the original shift.
+
+The scale factor is then varied if \fIdscale\fR is greater than zero by the
+scale step at a fixed shift in the same way as above to search for a
+smaller RMS in the sample regions.  This search terminates when the scale
+step is less than 0.01 or if the scale value has departed by 100% of the
+initial value.  In the latter case the scale value is left unchanged.
+
+The search over the shifts and scales is repeated a second time after which
+the tweak algorithm terminates.
+
+After the optional cross-correlation and tweak steps the interactive search
+mode may be entered.  This occurs if \fIinteractive\fR = yes.  A query is
+asking whether to search interactively.  The answers may be "no", "yes",
+"NO", or "YES".  The lower case answers apply to the current spectrum and
+the upper case answers apply to all subsequent spectra.  This means that if
+an answer of "NO" or "YES" is given then there will be no further queries
+for the remaining input spectra.
+
+If the interactive step is selected a graph of three candidate corrections
+for the input spectrum is displayed.  There also may be a graph of the
+calibration or input spectrum shown for reference.  Initially the
+calibration spectrum is displayed.  The additional graph may be toggled off
+and on and between the input and calibration spectra with the 'c' and 'd'
+keys.  The three candidate corrected spectra will be with the current shift
+and scale in the middle and plus or minus one step in either the shift or
+scale.  Initially the spectra will be at different scale values.
+Information about the current shift and scale and the step used is given in
+the graph title.
+
+One may toggle between shift steps and scale steps with the 'x' (for shift)
+or 'y' (for scale) keys.  The RMS in the title is the RMS within the
+currently defined sample regions.  If one of the step values is zero then a
+display of different values of that parameter will not be selected.  The
+step size will need to be set with a colon command to search in that
+parameter.
+
+If 'x' is typed when the three spectra are at different shifts then the
+nearest spectrum to the y cursor at the x cursor position will be
+selected.  If the central spectrum is selected the step size is divided in
+half otherwise the current shift is changed and the  selected spectrum
+becomes the middle spectrum.  Three new spectra are then shown.  The same
+applies if 'y' is typed when the three spectra are at different scales.
+This allows an interactive search similar to the iterative tweakrms method
+described previously except the user can use whatever criteria is desired
+to search for the best scale and shift.
+
+There are additional keystrokes and colon commands to set or change sample
+regions, reset the current shift, scale, and step sizes, expand the step
+size in the current mode, adjust the offsets between the spectra, and
+get help.  The 'w' key and GTOOLS colon commands are available to window
+the graphs.  Any changes in the x limits apply to both graphs while y limit
+adjustments apply to the graph pointed to by the cursor.
+
+Two other commands require a short explanation.  The 'a' key may
+be used to run the tweakrms algorithm starting from the current
+shift, scale, and steps and the current sample regions.  This allows
+one to graphically set or reset the sample regions before doing
+the RMS minimization.  The ":smooth" command and associated
+\fIsmooth\fR task parameter allow the corrected spectra to be
+displayed with a boxcar smoothing to better see faint features in
+noise.  It is important to realize that the smoothing is only
+done on the displayed spectra.  The telluric correction and computed RMS
+are done in the unsmoothed data.
+
+After the interactive step is quit with 'q' or if the interactive
+step is not done then the final output spectrum is computed and
+written to the output image.  A brief log output is printed for
+each spectrum.
+.ih
+CURSOR KEYS AND COLON COMMANDS
+.nf
+? - print help
+a - automatic RMS minimization within sample regions
+c - toggle calibration spectrum display
+d - toggle data spectrum display
+e - expand (double) the step for the current selection
+q - quit
+r - redraw the graphs
+s - add or reset sample regions
+w - window commands (see :/help for additional information)
+x - graph and select from corrected shifted candidates
+y - graph and select from corrected scaled candidates
+
+:help           - print help
+:shift  [value] - print or reset the current shift
+:scale  [value] - print or reset the current scale
+:dshift [value] - print or reset the current shift step
+:dscale [value] - print or reset the current scale step
+:offset [value] - print or reset the current offset between spectra
+:sample [value] - print or reset the sample regions
+:smooth [value] - print or reset the smoothing box size
+.fi
+.ih
+EXAMPLES
+1.  To interactively search for a best correction with the default
+cross-correlation and tweak steps:
+
+.nf
+    cl> skytweak spec001.ms skyspec001.ms spec005.ms
+.fi
+
+2.  To search only for a scale factor:
+
+.nf
+    cl> skytweak spec001.ms skyspec001.ms spec005.ms xcorr- dshift=0.
+.fi
+
+3.  To processes a set of spectra non-interactively with the same calibration
+spectrum and to replace the input spectra with the corrected spectra and
+log the processing:
+
+.nf
+    cl> skytweak spec* "" skyspec inter- > log
+.fi
+.ih
+REVISIONS
+.ls SKYTWEAK V2.11
+This task is new in this version.
+.le
+.ih
+SEE ALSO
+telluric
+.endhelp
diff --git a/noao/onedspec/doc/skytweak.key b/noao/onedspec/doc/skytweak.key
new file mode 100644
index 00000000..a694ba36
--- /dev/null
+++ b/noao/onedspec/doc/skytweak.key
@@ -0,0 +1,35 @@
+		SKYTWEAK COMMAND SUMMARY
+
+? - print help
+a - automatic RMS minimization within sample regions
+c - toggle calibration spectrum display
+d - toggle data spectrum display
+e - expand (double) the step for the current selection
+q - quit
+r - redraw the graphs
+s - add or reset sample regions
+w - window commands (see :/help for additional information)
+x - graph and select from corrected shifted candidates
+y - graph and select from corrected scaled candidates
+
+:help           - print help
+:shift  [value] - print or reset the current shift
+:scale  [value] - print or reset the current scale
+:dshift [value] - print or reset the current shift step
+:dscale [value] - print or reset the current scale step
+:offset [value] - print or reset the current offset between spectra
+:sample [value] - print or reset the sample regions
+:smooth [value] - print or reset the smoothing box size
+
+
+The stacked display shows three corrected candidate spectra.  The center
+one is for the current shift and scale and the other two are one step
+higher or lower in the shift or scale.  The current values and the
+step is shown in the title.  Toggle between the shift and scale candidates
+with 'x' or 'y'.  Select the best spectrum with the cursor and typing
+'x' or 'y'.  Selecting the middle spectrum with 'x' in the shift display
+divides the shift step in half.  Selecting one of the other spectra
+changes the current shift.  Selecting the middle spectrum with 'y'
+in the scale display divides the scale step in half.  Selecting one of
+the other spectra changes the current scale.  When 'q' is typed the
+final shift and scale will be that of the middle spectrum.
diff --git a/noao/onedspec/doc/slist.hlp b/noao/onedspec/doc/slist.hlp
new file mode 100644
index 00000000..322914b0
--- /dev/null
+++ b/noao/onedspec/doc/slist.hlp
@@ -0,0 +1,142 @@
+.help slist Mar92 noao.onedspec
+.ih
+NAME
+slist -- List spectral header information
+.ih
+USAGE
+slist images
+.ih
+PARAMETERS
+.ls images
+List of images to be listed.
+.le
+.ls apertures = ""
+List of apertures to be selected from the images for listing.  A null
+list selects all apertures.  See \fBranges\fR for the syntax of
+this list.
+.le
+.ls long_header = no
+If set to yes, then a multiline listing of the header elements is given.
+If set to no, then a single line per spectrum is given.  The contents
+of the listing depend on the format.
+.le
+.ih
+DESCRIPTION
+This task lists header information from apertures in a list of input
+images.  There is a short one line per spectrum listing and a more
+extended listing selected by the \fIlong_header\fR parameter.
+
+In both short and long outputs the aperture information consists of
+lines with the following whitespace separated fields: the image line,
+the aperture number, the beam number, the dispersion type, the
+wavelength of the first pixel, the wavelength interval per pixel,
+the number of valid pixels, and the aperture title.  The dispersion
+type is an integer with a value of -1 if not dispersion corrected,
+0 if dispersion corrected to a linear wavelength sampling, 1 if
+dispersion corrected to a log wavelength sampling, and 2 if dispersion
+corrected to a nonlinear sampling.  The wavelength per pixel is
+an approximation based on the wavelength endpoints divided by the
+number of pixels in the case of a nonlinear dispersion function.
+Also the wavelengths refer to the actual pixels taking any image sections
+into account and so may differ from the coordinate system information in
+the header which is defined for the original physical coordinates.
+The aperture titles may be identical with the image title if individual
+aperture titles are not defined.
+
+In the short output format the image title is given first followed
+by the above described information.  This format is compact and
+suitable for easy use in other programs (see the example below).
+The long output format is blocked by image and gives the image name
+and title on the first line, the exposure time, universal time,
+and siderial time on the second line, the right ascention, declination,
+hour angle, and airmass on the third line, and then the individual
+aperture information on the remaining lines.  If some of the header
+information is missing a value of INDEF is printed.  The keywords used
+are EXPTIME/ITIME/EXPOSURE (in that order) for the exposure time,
+and UT, ST, RA, DEC, HA, and AIRMASS for the remaining values.
+
+    demoobj.ms: Hydra artificial image
+	EXPTIME = 2133.33 UT = 9:10:09.0    ST = 20:09:34.0
+	RA = 1:34:02.00   DEC = 30:37:03.0  HA = INDEF    AIRMASS = 2.3
+.ih
+EXAMPLES
+1.  List short header for an object and arc from a Hydra multifiber reduction
+for fibers 36 to 39.
+
+.nf
+    cl> slist demoobj.ms,demoarc1.ms ap=36-39
+    demoobj.ms 1 37 0 0 5785.85 6.140271 256 Sky fiber
+    demoobj.ms 2 38 1 0 5785.85 6.140271 256 SS313
+    demoobj.ms 3 39 1 0 5785.85 6.140271 256 SS444
+    demoarc1.ms 1 36 2 0 5785.85 6.140271 256 Arc fiber
+    demoarc1.ms 2 37 0 0 5785.85 6.140271 256 Sky fiber
+    demoarc1.ms 3 38 1 0 5785.85 6.140271 256 SS313
+    demoarc1.ms 4 39 1 0 5785.85 6.140271 256 SS444
+.fi
+
+Note that fiber 37 is the first image line in demoobj.ms and teh second image
+line in demoarc.ms.  The dispersion is the same in all fibers by design.
+
+2.  List long headers for the two images of example 1 but restricted to
+apertures 38 and 39.
+
+.nf
+    cl> slist demoobj.ms,demoarc1.ms ap=38,39 l+
+    demoobj.ms: Hydra artificial image
+	EXPTIME = 2133.33 UT = 9:10:09.0    ST = 20:09:34.0
+	RA = 1:34:02.00   DEC = 30:37:03.0  HA = INDEF    AIRMASS = 2.3
+        2 38 1 0 5785.85 6.140271 256 SS313
+	3 39 1 0 5785.85 6.140271 256 SS444
+    demoarc1.ms: Hydra artificial image
+	EXPTIME = 2133.33 UT = 9:10:09.0    ST = 20:09:34.0
+	RA = 1:34:02.00   DEC = 30:37:03.0  HA = INDEF    AIRMASS = 2.3
+        3 38 1 0 5785.85 6.140271 256 SS313
+	4 39 1 0 5785.85 6.140271 256 SS444
+.fi
+
+The other header parameters are the same because this is artificial
+data using the same template header.
+
+3.  Dump the set of image headers on a printer in long format.
+
+.nf
+    cl> slist *.ms.imh l+ | lprint
+.fi
+
+4.  The short form of SLIST may be used to get some of the aperture
+information for use in a script.  The following simply prints the
+image line corresponding to a specified aperture.  In a real application
+something more complex would be done.
+
+.nf
+	procedure example (images, aperture)
+
+	string	images		{prompt="List of images"}
+	int	aperture	{prompt="Aperture"}
+
+	begin
+		string temp, image
+		int	line
+
+		# Use SLIST to print to a temporary file.
+		temp = mktemp ("example")
+		slist (images, aperture=aperture, long=no, > temp)
+
+		# Scan each line and print the line number.
+		list = temp
+		while (fscan (list, image, line) != EOF)
+		    print (image, ": ", line)
+		list = ""
+		delete (temp, verify=no)
+	end
+.fi
+.ih
+REVISIONS
+.ls SLIST V2.10
+This task was revised to be relevant for the current spectral image
+formats.  The old version is still available in the IRS/IIDS package.
+.le
+.ih
+SEE ALSO
+imheader, hselect
+.endhelp
diff --git a/noao/onedspec/doc/specplot.hlp b/noao/onedspec/doc/specplot.hlp
new file mode 100644
index 00000000..222d77ff
--- /dev/null
+++ b/noao/onedspec/doc/specplot.hlp
@@ -0,0 +1,387 @@
+.help specplot Jan96 noao.onedspec
+.ih
+NAME
+specplot -- stack and plot multiple spectra
+.ih
+USAGE
+specplot spectra
+.ih
+PARAMETERS
+.ls spectra
+List of spectra to plot.  The spectra are assigned index numbers increasing
+from one in the order of the list.
+.le
+.ls apertures = ""
+List of apertures to plot.  An empty list selects all apertures.
+An aperture list consists of a comma separated list of aperture numbers or
+hyphen separated range of numbers.  A step size may also be specified preceded
+by 'x'.  See \fBranges\fR for more.
+.le
+.ls bands = "1"
+List of bands to plot if the image is three dimensional.  The list has
+the same syntax as for the apertures.
+.le
+.ls dispaxis = 1, nsum = 1
+Parameters for defining vectors in 2D images.  The
+dispersion axis is 1 for line vectors and 2 for column vectors.
+A DISPAXIS parameter in the image header has precedence over the
+\fIdispaxis\fR parameter.  These may be changed interactively.
+.le
+.ls autolayout = yes
+Automatically layout the spectra by shifting or scaling to a common mean
+and determining a separation step which does overlaps the spectra
+by the specified fraction?  The algorithm uses the following parameters.
+.ls autoscale = yes
+Scale the spectra to a common mean?  If no then the spectra are shifted
+to a common mean and if yes they are scaled to a common mean.
+.le
+.ls fraction = 1.
+The separation step which just avoids overlapping the spectra is multiplied
+by this number.  Numbers greater than 1 increase the separation while numbers
+less than 1 decrease the separation and provide some amount of overlap.
+.le
+.le
+.ls units = ""
+Dispersion coordinate units.  If the spectra have known units, currently
+this is generally Angstroms, the plotted units may be converted
+for plotting to other units as specified by this parameter.
+If this parameter is the null string then the units specified by the
+world coordinate system attribute "units_display" is used.  If neither
+is specified than the units of the coordinate system are used.
+The units
+may also be changed interactively.  See the units section of the
+\fBonedspec\fR help for a further description and available units.
+.le
+.ls transform = "none" (none|log)
+Transform for the input pixel values.  Currently only "log" is implemented.
+If all pixels are negative the spectrum values will be unchanged and if
+some pixels are negative they are mapped to the lowest non-negative value in
+the spectrum.  Note that this cannot be changed interactively or applied
+independently for each spectrum.  To change the setting one must exit
+the task and execute it with the new value.
+.le
+.ls scale = 1., offset = 0. (value, @file, keyword)
+The scale and offset to apply to each spectrum.  The value of the parameter
+may be a constant value applying to all spectra, a file containing the
+values specified as @<file> where <file> is the filename, or an image
+header keyword whose value is to be used.
+.le
+.ls step = 0
+The step separating spectra when not using the autolayout option.
+The value of this parameter depends on the range of the data.
+.le
+.ls ptype = "1"
+Default plotting type for the spectra.  A numeric value selects line plots
+while marker type strings select marker plots.  The sign of the line type
+number selects histogram style lines when negative or connected pixel
+values when positive.  The absolute value selects the line type with 0
+being an invisible line, 1 being a solid line, and higher integers
+different types of lines depending on the capabilities of the graphics
+device.  The marker type strings are "point", "box", "plus", "cross",
+"diamond", "hline", "vline", "hebar", "vebar", and "circle".
+The types for individual spectra may be changed interactively.
+.le
+.ls labels = "user"
+Spectrum labels to be used.  If the null string or the word "none" is
+given then the spectra are not labeled.  The word "imname" labels the
+spectra with the image name, the word "imtitle" labels them wih the
+image title, the word "index" labels them with the index number, and
+the word "user" labels them with user defined labels.  The user labels
+may be given in the file specified by the parameter \fIulabels\fR, which
+are matched with the list of spectra, and also added interactively.
+.le
+.ls ulabels = ""
+File containing user labels.
+.le
+.ls xlpos = 1.02, ylpos = 0.0
+The starting position for the spectrum labels in fractions of the
+graph limits.  The horizontal (x) position is measured from the left
+edge while the vertical position is measured from the mean value of the
+spectrum.  For vertical positions a negative value may be used to label
+below the spectrum.  The default is off the right edge of the graph at
+the mean level of the spectrum.
+.le
+.ls sysid = yes
+Include system banner and separation step label?  This may be changed
+interactively using ":/sysid".
+.le
+.ls yscale = no
+Draw a Y axis scale?  Since stacked plots are relative labeling the Y
+axes may not be useful.  This parameter allows adding the Y axis scale
+if desired.  The default is to not have a Y axis scale.
+.le
+.ls title = "", xlabel = "", ylabel = ""
+Title, x axis label, and y axis label for graphs.  These may be changed
+interactively using ":/title", ":/xlabel", and ":/ylabel".
+.le
+.ls xmin = INDEF, xmax = INDEF, ymin = INDEF, ymax = INDEF
+The default limits for the initial graph.  If INDEF then the limit is
+determined from the range of the data (autoscaling).  These values can
+be changed with 'w' cursor key or the cursor commands ":/xwindow" and
+":/ywindow".
+.le
+.ls logfile = ""
+Logfile to record the final set of spectra and scale factors displayed.
+.le
+.ls graphics = "stdgraph"
+Output graphics device.  One of "stdgraph", "stdplot", "stdvdm",
+@(enviroment variable), or actual device.
+.le
+.ls cursor = ""
+Graphics cursor input.  When null the standard cursor is used otherwise
+the specified file is used.
+.le
+.ih
+DESCRIPTION
+\fBSpecplot\fR plots multiple spectra with provisions for scaling them,
+separating them vertically, shifting them horizontally, and labeling them.
+The layout can be defined by an automatic algorithm or explicitly and
+adjusted noninteractively (with some limitations) or interactively.  The
+plotting units can be selected and the vertical axis scale can be shown or
+not as desired.  This task is used for compressing many spectra to a page
+for review, intercomparison of spectra, classification against standards,
+and final display.
+
+The input list of spectra consists of one, two, or three dimensional images.
+The set of spectra may be restricted to specific apertures using the
+\fIapertures\fR parameter.  Note that for true 2D images, such as long slit
+spectra, the aperture number corresponds to the line or column to be plotted
+and the dispersion axis and nsum parameter are determined either from the
+image header or the package parameters.  Spectra extracted
+with the \fBapextract\fR package may be three dimensional where the 3rd
+dimension corresponds to related data.  The higher dimensional data is
+also plotted though it may be restricted with the \fIbands\fR
+parameter.
+
+Each spectrum has a number of associated parameters which are initially
+assigned default values but which may be changed interactively.  First each
+spectrum is assigned an index number.  This is generally sequential
+starting from 1.  Spectra added interactively are assigned the next higher
+or lower index relative to the spectrum being appended or inserted.  The
+index is used for refering to parameters of a particular spectrum and for
+separating the spectra vertically.  The spectra are scaled and shifted by
+the equation
+
+	I = value * scale + offset + (index - 1) * step
+
+where "I" is the final plotted value, "value" is the pixel value, "scale"
+is a multiplicative scaling, "offset" is a additive offset, and "step" is
+an additive separation step used to stack spectra vertically.
+
+The default values of the vertical scaling parameters may be set by an
+automatic layout algorithm or with explicit constants (the same for all
+spectra).  The automatic mode is selected with the parameter
+\fIautolayout\fR and works as follows.  All spectra are scaled or shifted
+to a common mean (depending on the parameter \fIautoscale\fR) relative to
+the lowest indexed spectrum.  A step size is then computed to just avoid
+overlapping of the minimum of one spectrum with the maximum of another.
+Note that this may not yield a good layout if the spectra have large
+continuum slopes.  Finally, to add some extra space between the spectra or
+to allow some overlap, the minimum step is multiplied by a specified
+overlap factor, \fIfraction\fR.
+
+In nonautomatic mode the user specifies the intensity scale, offset,
+and separation step explicitly with the parameters, \fIscale, offset\fR
+and \fIstep\fR.  If the step is zero then spectra will be directly
+overplotted while a positive or negative value will separate the
+spectra either upward or downward with the index 1 spectrum having no
+offset.  The scale and offset parameters may be specified as either
+constant values, the name of file containing the values (one per line)
+preceded by the '@' character, or the name of an image header keyword.
+This parameter as well as the scale and offset may be set or
+changed interactively via colon commands and the "offset" may also be
+set using the cursor to shift a spectrum vertically.
+
+In addition to shifting spectra vertically they may also be shifted
+horizontally as a velocity/redshift or a zero point change with either
+cursor or colon commands.  The dispersion, inteval per pixel, may be
+modified, either with the 't' key or the "wpc" command, in which case if
+the dispersion is nonlinear the spectra will be linearized.
+
+Each spectrum may have a label associated with it.  The label type may
+be the image name, the image title, the index number, or a user defined
+label.  The default label type is specified by the parameter
+\fIlabels\fR.  For user labels the initial labels may be specified in a
+file.  Interactively the label type may be changed using the ":labels"
+command and the user assigned labels may be defined by a colon command
+or by using the cursor to mark the position for the label.  The label
+position is given relative to the range of the graph and the mean
+intensity.  The default values are set by the parameters \fIxlpos\fR
+and \fIylpos\fR.  The positions may be changed interactively for all
+the spectra or individually.  The latter may be done using the cursor
+to mark exactly where the label is to go.
+
+Each spectrum has an associated plotting type.  The default type which
+applies to all spectra initially is specified by the parameter
+\fIptype\fR.  This parameter specifies both whether line mode or
+marker mode is used and the line type, line style, or marker type to use.
+The line
+mode and types are given by a small integers with the style, connected
+pixel centers or histogram style, chosed by the sign of the integer.
+The type of lines produced depend on the capabilities of the terminal.  In most
+cases a zero line type is invisible.  (This may be used interactively
+to temporarily eliminate a spectrum from a plot instead of deleting the
+spectrum from the list of spectra).  A line type of 1 is a solid line
+and additional line types are specified by higher numbers.
+The marker types are given by name as described in the parameter
+section.  There is currently no combination of line and marker (such as
+connected points with vertical bars) or histogram type plotting.  The
+plotting type may be changed interactively for individual spectra or
+for all spectra using colon commands.
+
+The cursor and colon commands generally apply to the spectrum nearest
+the cursor.  This is determined by finding the nearest data point to
+the cursor.  For the colon commands the spectrum may also be specified
+explicitly by the index number using an optional suffix "[index]", where
+index is the index number for the spectrum.  Also the special index "*"
+may be specified to apply to all spectra.
+
+The operations of adding, deleting, moving, or shifting spectra affect
+the index numbers of the other spectra.  When deleting a spectrum the
+index numbers of all spectra with greater index numbers are decreased
+by one resulting in the plotted spectra moving down (positive step).
+When adding a spectrum the index numbers above the inserted spectrum
+are increased by one resulting in the spectra moving up.  Moving a
+spectrum to a new index number is equivalent to deleting the spectrum
+and then inserting it at the new index position.  Spectra may be
+shifted to insert gaps in the plotted spectra.  The specified value is
+added to all spectra above and including the one indicated if the value
+is positive to all spectra below and including the one indicated if the
+value is negative.
+.ih
+CURSOR COMMANDS
+
+The indicated spectrum is the one with a point closest to the cursor position.
+.nf
+
+? - Print help summary
+a - Append a new spectrum following the indicated spectrum
+i - Insert a new spectrum before the indicated spectrum
+d - Delete the indicated spectrum
+e - Insert last deleted spectrum before indicated spectrum
+f - Toggle between world coordinates and logical pixel coordinates
+l - Define the user label at the indicated position
+p - Define the label position at the indicated position
+o - Reorder the spectra to eliminate gaps
+q - Quit
+r - Redraw the plot
+s - Repeatedly shift the indicated spectrum position with the cursor
+     q - Quit shift                      x - Shift horizontally in velocity
+     s - Shift vertically in scale       y - Shift vertically in offset
+     t - Shift horizontally in velocity  z - Shift horizontally in velocity
+         and vertically in scale             and vertically in offset
+t - Set a wavelength scale using the cursor
+u - Set a wavelength point using the cursor
+v - Set velocity plot with zero point at cursor
+w - Window the plot
+x - Cancel all scales and offsets
+y - Automatically layout the spectra with offsets to common mean
+z - Automatically layout the spectra scaled to common mean
+.fi
+.ih
+COLON COMMANDS
+
+A command without a value generally shows the current value of the
+parameter while with a value it sets the value of the parameter.  The show
+commands print to the terminal unless a file is given.  For the spectrum
+parameters the index specification, "[index]", is optional.  If absent the
+nearest spectrum to the cursor when the command is given is selected except
+for the "units" command which selects all spectra.  The index is either a
+number or the character *.  The latter applies the command to all the
+spectra.
+
+.nf
+:show <file>		   Show spectrum parameters (file optional)
+:vshow <file>		   Show verbose parameters (file optional)
+:step <value>		   Set or show step
+:fraction <value>	   Set or show autolayout fraction
+:label <value>		   Set or show label type
+				(none|imtitle|imname|index|user)
+
+:move[index] <to_index>	   Move spectrum to new index position
+:shift[index|*] <value>	   Shift spectra by adding to index
+:w0[index|*] <value>	   Set or show zero point wavelength
+:wpc[index|*] <value>	   Set or show wavelength per channel
+:velocity[index|*] <value> Set or show radial velocity (km/s)
+:redshift[index|*] <value> Set or show redshift
+:offset[index|*] <value>   Set or show intensity offset
+:scale[index|*] <value>	   Set or show intensity scale
+:xlpos[index|*] <value>	   Set or show X label position
+:ylpos[index|*] <value>	   Set or show Y label position
+:ptype[index|*] <value>	   Set or show plotting type
+:color[index|*] <value>    Set or show color (1-9)
+:ulabel[index|*] <value>   Set or show user labels
+:units[index|*] <value>	   Change coordinate units
+
+:/title <value>		   Set the title of the graph
+:/xlabel <value>	   Set the X label of the graph
+:/ylabel <value>	   Set the Y label of the graph
+:/xwindow <min max>	   Set the X graph range
+				(use INDEF for autoscaling)
+:/ywindow <min max>	   Set the X graph range
+				(use INDEF for autoscaling)
+ 
+
+Examples:
+    w0		  Print value of wavelength zero point
+    w0 4010	  Set wavelength zero point of spectrum nearest the cursor
+    w0[3] 4010	  Set wavelength zero point of spectrum with index 3
+    w0[*] 4010	  Set wavelength zero point of all spectra
+.fi
+.ih
+EXAMPLES
+1. To make a nice plot of a set of spectra with the default layout:
+
+	cl> specplot spec*
+
+2.  To set the colors or line types for multiple spectra in a batch
+mode application create a cursor file like:
+
+	cl> type cursor.dat
+	:color[1] 2
+	:color[2] 3
+	:color[3] 4
+	r
+	cl> specplot im1,im2,im3 cursor=cursor.dat
+
+Note that the 'r' key is necessary redraw the graph with the changed
+attributes.
+.ih
+REVISIONS
+.ls SPECPLOT V2.11
+The scale and offset parameters may now be a value, a filename, or
+and image header keyword.
+
+The 'f' key was added to toggle between world and logical pixel coordinates.
+.le
+.ls SPECPLOT V2.10.3
+A color parameter was added for graphics terminals supporting color.
+
+The :units command was extended to have an optional spectrum specifier.
+This is primarily intended to plot different (or the same) spectra in
+velocity but with different velocity zeros.
+
+The default task units parameter has been changed to "" to allow picking
+up a "units_display" WCS attribute if defined.
+.le
+.ls SPECPLOT V2.10
+New parameters were added to select apertures and bands, plot
+additional dimensions (for example the additional output from the extras
+option in \fBapextract\fR), suppress the system ID banner, suppress the Y
+axis scale, output a logfile, and specify the plotting units.  The \fIptype\fR
+parameter now allows negative numbers to select histogram style lines.
+Interactively, the plotting units may be changed and the 'v' key allows
+setting a velocity scale zero point with the cursor.  The new version
+supports the new spectral WCS features including nonlinear dispersion
+functions.
+.le
+.ih
+NOTES
+The automatic layout algorithm is relatively simple and may not
+provide visually satisfactory results in all cases.  The fonts and Y axis
+scale capabilities are not as good as might be desired for publication
+quality plots.
+.ih
+SEE ALSO
+bplot, splot, onedspec, gtools, ranges
+.endhelp
diff --git a/noao/onedspec/doc/specshift.hlp b/noao/onedspec/doc/specshift.hlp
new file mode 100644
index 00000000..c72ebd0a
--- /dev/null
+++ b/noao/onedspec/doc/specshift.hlp
@@ -0,0 +1,67 @@
+.help specshift Oct92 noao.onedspec
+.ih
+NAME
+specshift -- Shift dispersion coordinate systems
+.ih
+USAGE
+specshift spectra shift
+.ih
+PARAMETERS
+.ls spectra
+List of spectra to be modified.
+.le
+.ls shift
+Dispersion coordinate shift to be added to the current dispersion coordinate
+system.
+.le
+.ls apertures = ""
+List of apertures to be modified.  The null list
+selects all apertures.  A list consists of comma separated
+numbers and ranges of numbers.  A range is specified by a hyphen.  An
+optional step size may be given by using the 'x' followed by a number.
+See \fBxtools.ranges\fR for more information.  This parameter is ignored
+for N-dimensional spatial spectra such as long slit and Fabry-Perot.
+.le
+.ls verbose = no
+Print a record of each aperture modified?
+.le
+.ih
+DESCRIPTION
+This task applies a shift to the dispersion coordinate system of selected
+spectra.  The image data is not modified as with \fBimshift\fR but rather
+the coordinate system is shifted relative to the data.  The spectra to be
+modified are selected by specifying a list of images and apertures.  If no
+aperture list is specified then all apertures in the images are modified.
+For N-dimensional spatial spectra such as long slit and Fabry-Perot the
+aperture list is ignored.
+
+The specified shift is added to the existing world coordinates.  For linear
+coordinate systems this has the effect of modifying CRVAL1, for linear
+"multispec" coordinate systems this modifies the dispersion coordinate of
+the first physical pixel, and for nonlinear "multispec" coordinate systems
+this modifies the shift coefficient(s).
+
+It is also possible to shift the linearized coordinate systems (but not the
+nonlinear coordinate systems) with \fBsapertures\fR or possibly with
+\fBwcsedit\fR or \fBhedit\fR if the coordinate system is stored with a
+global linear system.
+
+The \fIverbose\fR parameter lists the images, the apertures, the shift, and
+the old and new values for the first physical pixel are printed.
+.ih
+EXAMPLES
+1.  To add 1.23 Angstroms to the coordinates of all apertures in the
+image "ngc456.ms":
+
+.nf
+	cl> specshift ngc456.ms 1.23
+.fi
+.ih
+REVISIONS
+.ls SPECSHIFT V2.10.3
+First version.
+.le
+.ih
+SEE ALSO
+sapertures, dopcor, imcoords.wcsreset, hedit, ranges, onedspec.package
+.endhelp
diff --git a/noao/onedspec/doc/specwcs.hlp b/noao/onedspec/doc/specwcs.hlp
new file mode 100644
index 00000000..ed8852e3
--- /dev/null
+++ b/noao/onedspec/doc/specwcs.hlp
@@ -0,0 +1,586 @@
+.help specwcs Mar93 noao.onedspec
+
+.ce
+\fBThe IRAF/NOAO Spectral World Coordinate Systems\fR
+
+
+.sh
+1. Types of Spectral Data
+
+Spectra are stored as one, two, or three dimensional images with one axis
+being the dispersion axis.  A pixel value is the flux over
+some interval of wavelength and position.  The simplest example of a
+spectrum is a one dimensional image which has pixel values as a
+function of wavelength.
+
+There are two types of higher dimensional spectral image formats.  One type
+has spatial axes for the other dimensions and the dispersion axis may be
+along any of the image axes.  Typically this type of format is used for
+long slit (two dimensional) and Fabry-Perot (three dimensional) spectra.
+This type of spectra is referred to as \fIspatial\fR spectra and the
+world coordinate system (WCS) format is called \fIndspec\fR.
+The details of the world coordinate systems are discussed later.
+
+The second type of higher dimensional spectral image consists of multiple,
+independent, one dimensional spectra stored in the higher dimensions with
+the first image axis being the dispersion axis; i.e. each line is a
+spectrum.  This format allows associating many spectra and related
+parameters in a single data object.  This type of spectra is referred to
+as \fImultispec\fR and the there are two coordinate system formats,
+\fIequispec\fR and \fImultispec\fR.  The \fIequispec\fR format applies
+to the common case where all spectra have the same linear dispersion
+relation.  The \fImultispec\fR format applies to the general case of spectra
+with differing dispersion relations or non-linear dispersion functions.
+These multi-spectrum formats are important since maintaining large numbers
+of spectra as individual one dimensional images is very unwieldy for the
+user and inefficient for the software.
+
+Examples of multispec spectral images are spectra extracted from a
+multi-fiber or multi-aperture spectrograph or orders from an echelle
+spectrum.  The second axis is some arbitrary indexing of the spectra,
+called \fIapertures\fR, and the third dimension is used for
+associated quantities.  The IRAF \fBapextract\fR package may produce
+multiple spectra from a CCD image in successive image lines with an
+optimally weighted spectrum, a simple aperture sum spectrum, a background
+spectrum, and sigma spectrum as the associated quantities along the third
+dimension of the image.
+
+Many \fBonedspec\fR package tasks which are designed to operate on
+individual one dimensional spectra may operate on spatial spectra by
+summing a number of neighboring spectra across the dispersion axis.  This
+eliminates the need to "extract" one dimensional spectra from the natural
+format of this type of data in order to use tasks oriented towards the
+display and analysis of one dimensional spectra.  The dispersion axis is
+either given in the image header by the keyword DISPAXIS or the package
+\fIdispaxis\fR parameter.  The summing factors across the
+dispersion are specified by the \fInsum\fR package parameter.
+See "help onedspec.package" for information on these parmaeters.
+
+One dimensional spectra, whether from multispec spatial spectra, have
+several associated quantities which may appear in the image header as part
+of the coordinate system description.  The primary identification of a
+spectrum is an integer aperture number.  This number must be unique within
+a single image.  There is also an integer beam number used for various
+purposes such as discriminating object, sky, and arc spectra in
+multi-fiber/multi-aperture data or to identifying the order number in
+echelle data.  For spectra summed from spatial spectra the aperture number
+is the central line, column, or band.  In 3D images the aperture index
+wraps around the lowest non-dispersion axis.  Since most one dimensional
+spectra are derived from an integration over one or more spatial axes, two
+additional aperture parameters record the aperture limits.  These limits
+refer to the original pixel limits along the spatial axis.  This
+information is primarily for record keeping but in some cases it is used
+for spatial interpolation during dispersion calibration.  These values are
+set either by the \fBapextract\fR tasks or when summing neighboring vectors
+in spatial spectra.
+
+An important task to be aware of for manipulating spectra between image
+formats is \fBscopy\fR.  This task allows selecting spectra from multispec
+images and grouping them in various ways and also "extracts" apertures from
+long slit and 3D spectra simply and without resort to the more general
+\fBapextract\fR package.
+.sh
+2. World Coordinate Systems
+
+IRAF images have three types of coordinate systems.  The pixel array
+coordinates of an image or image section, i.e. the lines and
+columns, are called the \fIlogical\fR coordinates.  The logical coordinates of
+individual pixels change as sections of the image are used or extracted.
+Pixel coordinates are tied to the data, i.e. are fixed to features
+in the image, are called \fIphysical\fR coordinates.  Initially the logical
+and physical coordinates are the equivalent but differ when image sections
+or other tasks which modify the sampling of the pixels are applied.
+
+The last type of coordinate system is called the \fIworld\fR coordinate
+system.  Like the physical coordinates, the world coordinates are tied to
+the features in the image and remain unchanged when sections of the image
+are used or extracted.  If a world coordinate system is not defined for an
+image, the physical coordinate system is considered to be the world
+coordinate system.  In spectral images the world coordinate system includes
+dispersion coordinates such as wavelengths.  In many tasks outside the
+spectroscopy packages, for example the \fBplot\fR, \fBtv\fR and
+\fBimages\fR packages, one may select the type of coordinate system to be
+used.  To make plots and get coordinates in dispersion units for spectra
+with these tasks one selects the "world" system.  The spectral tasks always
+use world coordinates.
+
+The coordinate systems are defined in the image headers using a set of
+reserved keywords which are set, changed, and updated by various tasks.
+Some of the keywords consist of simple single values following the FITS
+convention.  Others, the WAT keywords, encode long strings of information,
+one for each coordinate axis and one applying to all axes, into a set of
+sequential keywords.  The values of these keywords must then be pasted
+together to recover the string.  The long strings contain multiple pieces
+called WCS \fIattributes\fR.  In general the WCS keywords should be left to
+IRAF tasks to modify.  However, if one wants modify them directly some
+tasks which may be used are \fBhedit\fR, \fBhfix\fR, \fBwcsedit\fR,
+\fBwcsreset\fR, \fBspecshift\fR, \fBdopcor\fR, and \fBsapertures\fR.  The
+first two are useful for the simple keywords, the two  "wcs" tasks are
+useful for the linear ndspec and equispec formats, the next two are for the
+common cases of shifting the coordinate zero point or applying a doppler
+correction, and the last one is the one to use for the more complex
+multispec format attributes.
+.sh
+3. Physical Coordinate System
+
+The physical coordinate system is used by the spectral tasks when there is
+no dispersion coordinate information (such as before dispersion
+calibration), to map the physical dispersion axis to the logical dispersion
+axis, and in the multispec world coordinate system dispersion functions
+which are defined in terms of physical coordinates.
+
+The transformation between logical and physical coordinates is defined by
+the header keywords LTVi, LTMi_j (where i and j are axis numbers) through
+the vector equation
+
+.nf
+    l = |m| * p + v
+.fi
+
+where l is a logical coordinate vector, p is a physical
+coordinate vector, v is the origin translation vector specified by
+the LTV keywords and |m| is the scale/rotation matrix
+specified by the LTM keywords.  For spectra rotation terms (nondiagonal
+matrix elements) generally do not make sense (in fact many tasks will not
+work if there is a rotation) so the transformations along each axis are
+given by the linear equation
+
+where l is a logical coordinate vector, p is a physical coordinate vector,
+v is the origin translation vector specified by the LTV keywords and |m| is
+the scale/rotation matrix specified by the LTM keywords.  For spectra a
+rotation term (nondiagonal matrix elements) generally does not make sense
+(in fact many tasks will not work if there is a rotation) so the
+transformations along each axis are given by the linear equation
+
+.nf
+    li = LTMi_i * pi + LTVi.
+.fi
+
+If all the LTM/LTV keywords are missing they are assumed to have zero
+values except that the diagonal matrix terms, LTMi_i, are assumed to be 1.
+Note that if some of the keywords are present then a missing LTMi_i will
+take the value zero which generally causes an arithmetic or matrix
+inversion error in the IRAF tasks.
+
+The dimensional mapping between logical and physical axes is given by the
+keywords WCSDIM and WAXMAP01.  The WCSDIM keyword gives the dimensionality
+of the physical and world coordinate system.  There must be coordinate
+information for that many axes in the header (though some may be missing
+and take their default values).  If the WCSDIM keyword is missing it is
+assumed to be the same as the logical image dimensionality.
+
+The syntax of the WAXMAP keyword are pairs of integer values,
+one for each physical axis.  The first number of each pair indicates which
+current \fIlogical\fR axis corresponds to the original \fIphysical\fR axis
+(in order) or zero if that axis is missing.   When the first number is zero
+the second number gives the offset to the element of the original axis
+which is missing.  As an example consider a three dimensional image in
+which the second plane is extracted (an IRAF image section of [*,2,*]).
+The keyword would then appear as WAXMAP01 = '1 0 0 1 2 0'.  If this keyword
+is missing the mapping is 1:1; i.e. the dimensionality and order of the
+axes are the same.
+
+The dimensional mapping is important because the dispersion axis for
+the nspec spatial spectra as specified by the DISPAXIS keyword or task
+parameter, or the axis definitions for the equispec and or multispec
+formats are always in terms of the original physical axes.
+.sh
+4. Linear Spectral World Coordinate Systems
+
+When there is a linear or logarithmic relation between pixels and
+dispersion coordinates which is the same for all spectra the WCS header
+format is simple and uses the FITS convention (with the CD matrix keywords
+proposed by Hanisch and Wells 1992) for the logical pixel to world
+coordinate transformation.  This format applies to one, two, and three
+dimensional data.  The higher dimensional data may have either linear
+spatial axes or the equispec format where each one dimensional spectrum
+stored along the lines of the image has the same dispersion.
+
+The FITS image header keywords describing the spectral world coordinates
+are CTYPEi, CRPIXi, CRVALi, and CDi_j where i and j are axis numbers.  As
+with the physical coordinate transformation the nondiagonal or rotation
+terms are not expected in the spectral WCS and may cause problems if they
+are not zero.  The CTYPEi keywords will have the value LINEAR to identify
+the type of coordinate system.  The transformation between dispersion
+coordinate, wi, and logical pixel coordinate, li, along axis i is given by
+
+.nf
+    wi = CRVALi + CDi_i * (li - CRPIXi)
+.fi
+
+If the keywords are missing then the values are assumed to be zero except
+for the diagonal elements of the scale/rotation matrix, the CDi_i, which
+are assumed to be 1.  If only some of the keywords are present then any
+missing CDi_i keywords will take the value 0 which will cause IRAF tasks to
+fail with arithmetic or matrix inversion errors.  If the CTYPEi keyword is
+missing it is assumed to be "LINEAR".
+
+If the pixel sampling is logarithmic in the dispersion coordinate, as
+required for radial velocity cross-correlations, the WCS coordinate values
+are logarithmic and wi (above) is the logarithm of the dispersion
+coordinate.  The spectral tasks (though not other tasks) will recognize
+this case and automatically apply the anti-log.  The two types of pixel
+sampling are identified by the value of the keyword DC-FLAG.  A value of 0
+defines a linear sampling of the dispersion and a value of 1 defines a
+logarithmic sampling of the dispersion.  Thus, in all cases the spectral
+tasks will display and analyze the spectra in the same dispersion units
+regardless of the pixel sampling.
+
+Other keywords which may be present are DISPAXIS for 2 and 3 dimensional
+spatial spectra, and the WCS attributes "system", "wtype", "label", and
+"units".  The system attribute will usually have the value "world" for
+spatial spectra and "equispec" for equispec spectra.  The wtype attribute
+will have the value "linear".  Currently the label will be either "Pixel"
+or "Wavelength" and the units will be "Angstroms" for dispersion corrected
+spectra.  In the future there will be more generality in the units
+for dispersion calibrated spectra.
+
+Figure 1 shows the WCS keywords for a two dimensional long slit spectrum.
+The coordinate system is defined to be a generic "world" system and the
+wtype attributes and CTYPE keywords define the axes to be linear.  The
+other attributes define a label and unit for the second axis, which is the
+dispersion axis as indicated by the DISPAXIS keyword.  The LTM/LTV keywords
+in this example show that a subsection of the original image has been
+extracted with a factor of 2 block averaging along the dispersion axis.
+The dispersion coordinates are given in terms of the \fIlogical\fR pixel
+coordinates by the FITS keywords as defined previously.
+
+.ce
+Figure 1: Long Slit Spectrum
+
+.nf
+    WAT0_001= 'system=world'
+    WAT1_001= 'wtype=linear'
+    WAT2_001= 'wtype=linear label=Wavelength units=Angstroms'
+    WCSDIM  =                    2
+    DISPAXIS=                    2
+    DC-FLAG =                    0
+
+    CTYPE1  = 'LINEAR  '
+    LTV1    =                 -10.
+    LTM1_1  =                   1.
+    CRPIX1  =                  -9.
+    CRVAL1  =     19.5743865966797
+    CD1_1   =     1.01503419876099
+
+    CTYPE2  = 'LINEAR  '
+    LTV2    =                -49.5
+    LTM2_2  =                  0.5
+    CRPIX2  =                 -49.
+    CRVAL2  =       4204.462890625
+    CD2_2   =     12.3337936401367
+.fi
+
+Figure 2 shows the WCS keywords for a three dimensional image where each
+line is an independent spectrum or associated data but where all spectra
+have the same linear dispersion.  This type of coordinate system has the
+system name "equispec".  The ancillary information about each aperture is
+found in the APNUM keywords.  These give the aperture number, beam number,
+and extraction limits.  In this example the LTM/LTV keywords have their
+default values; i.e. the logical and physical coordinates are the same.
+
+.ce
+Figure 2: Equispec Spectrum
+
+.nf
+    WAT0_001= 'system=equispec'
+    WAT1_001= 'wtype=linear label=Wavelength units=Angstroms'
+    WAT2_001= 'wtype=linear'
+    WAT3_001= 'wtype=linear'
+    WCSDIM  =                    3
+    DC-FLAG =                    0
+    APNUM1  = '41 3 7.37 13.48'
+    APNUM2  = '15 1 28.04 34.15'
+    APNUM3  = '33 2 43.20 49.32'
+
+    CTYPE1  = 'LINEAR  '
+    LTM1_1  =                   1.
+    CRPIX1  =                   1.
+    CRVAL1  =             4204.463
+    CD1_1   =     6.16689700000001
+
+    CTYPE2  = 'LINEAR  '
+    LTM2_2  =                   1.
+    CD2_2   =                   1.
+
+    CTYPE3  = 'LINEAR  '
+    LTM3_3  =                   1.
+    CD3_3   =                   1.
+.fi
+.sh
+5. Multispec Spectral World Coordinate System
+
+The \fImultispec\fR spectral world coordinate system applies only to one
+dimensional spectra; i.e. there is no analog for the spatial type spectra.
+It is used either when there are multiple 1D spectra with differing
+dispersion functions in a single image or when the dispersion functions are
+nonlinear.
+
+The multispec coordinate system is always two dimensional though there may
+be an independent third axis.  The two axes are coupled and they both have
+axis type "multispec".  When the image is one dimensional the physical line
+is given by the dimensional reduction keyword WAXMAP.  The second, line
+axis, has world coordinates of aperture number.  The aperture numbers are
+integer values and need not be in any particular order but do need to be
+unique.  This aspect of the WCS is not of particular user interest but
+applications use the inverse world to physical transformation to select a
+spectrum line given a specified aperture.
+
+The dispersion functions are specified by attribute strings with the
+identifier \fIspecN\fR where N is the \fIphysical\fR image line.  The
+attribute strings contain a series of numeric fields.  The fields are
+indicated symbolically as follows.
+
+.nf
+         specN = ap beam dtype w1 dw nw z aplow aphigh [functions_i]
+.fi
+
+where there are zero or more functions having the following fields,
+
+.nf
+    function_i =  wt_i w0_i ftype_i [parameters] [coefficients]
+.fi
+
+The first nine fields in the attribute are common to all the dispersion
+functions.  The first field of the WCS attribute is the aperture number,
+the second field is the beam number, and the third field is the dispersion
+type with the same function as DC-FLAG in the \fInspec\fR and
+\fIequispec\fR formats.  A value of -1 indicates the coordinates are not
+dispersion coordinates (the spectrum is not dispersion calibrated), a value
+of 0 indicates linear dispersion sampling, a value of 1 indicates
+log-linear dispersion sampling, and a value of 2 indicates a nonlinear
+dispersion.
+
+The next two fields are the dispersion coordinate of the first
+\fIphysical\fR pixel and the average dispersion interval per \fIphysical\fR
+pixel.  For linear and log-linear dispersion types the dispersion
+parameters are exact while for the nonlinear dispersion functions they are
+approximate.  The next field is the number of valid pixels, hence it is
+possible to have spectra with varying lengths in the same image.  In that
+case the image is as big as the biggest spectrum and the number of pixels
+selects the actual data in each image line.  The next (seventh) field is a
+doppler factor.  This doppler factor is applied to all dispersion
+coordinates by multiplying by 1/(1+z) (assuming wavelength dispersion
+units).  Thus a value of 0 is no doppler correction.  The last two fields
+are extraction aperture limits as discussed previously.
+
+Following these fields are zero or more function descriptions.  For linear
+or log-linear dispersion coordinate systems there are no function fields.
+For the nonlinear dispersion systems the function fields specify a weight,
+a zero point offset, the type of dispersion function, and the parameters
+and coefficients describing it.  The function type codes, ftype_i,
+are 1 for a chebyshev polynomial, 2 for a legendre polynomial, 3 for a
+cubic spline, 4 for a linear spline, 5 for a pixel coordinate array, and 6
+for a sampled coordinate array.  The number of fields before the next
+function and the number of functions are determined from the parameters of
+the preceding function until the end of the attribute is reached.
+
+The equation below shows how the final wavelength is computed based on
+the nfunc individual dispersion functions W_i(p).  Note that this
+is completely general in that different function types may be combined.
+However, in practice when multiple functions are used they are generally of
+the same type and represent a calibration before and after the actual
+object observation with the weights based on the relative time difference
+between the calibration dispersion functions and the object observation.
+
+.nf
+    w = sum from i=1 to nfunc {wt_i * (w0_i + W_i(p)) / (1 + z)}
+.fi
+
+The multispec coordinate systems define a transformation between physical
+pixel, p, and world coordinates, w.  Generally there is an intermediate
+coordinate system used.  The following equations define these coordinates.
+The first one shows the transformation between logical, l, and physical,
+p, coordinates based on the LTM/LTV keywords.  The polynomial functions
+are defined in terms of a normalized coordinate, n, as shown in the
+second equation.  The normalized coordinates run between -1 and 1 over the
+range of physical coordinates, pmin and pmax which are
+parameters of the function, upon which the coefficients were defined.  The
+spline functions map the physical range into an index over the number of
+evenly divided spline pieces, npieces, which is a parameter of the
+function.  This mapping is shown in the third and fourth equations where
+s is the continuous spline coordinate and j is the nearest integer less
+than or equal to s.
+
+.nf
+    p = (l - LTV1) / LTM1_1
+    n = (p - pmiddle) / (prange / 2)
+      = (p - (pmax+pmin)/2) / ((pmax-pmin) / 2)
+    s = (p - pmin) / (pmax - pmin) * npieces
+    j = int(s)
+.fi
+.sh
+5.1 Linear and Log Linear Dispersion Function
+
+The linear and log-linear dispersion functions are described by a
+wavelength at the first \fIphysical\fR pixel and a wavelength increment per
+\fIphysical\fR pixel.  A doppler correction may also be applied.  The
+equations below show the two forms.  Note that the coordinates returned are
+always wavelength even though the pixel sampling and the dispersion
+parameters may be log-linear.
+
+.nf
+    w = (w1 + dw * (p - 1)) / (1 + z)
+    w = 10 ** {(w1 + dw * (p - 1)) / (1 + z)}
+.fi
+
+Figure 3 shows an example from a multispec image with
+independent linear dispersion coordinates.  This is a linearized echelle
+spectrum where each order (identified by the beam number) is stored as a
+separate image line.
+
+.ce
+Figure 3: Echelle Spectrum with Linear Dispersion Function
+
+.nf
+    WAT0_001= 'system=multispec'
+    WAT1_001= 'wtype=multispec label=Wavelength units=Angstroms'
+    WAT2_001= 'wtype=multispec spec1 = "1 113 0 4955.44287109375 0.05...
+    WAT2_002= '5 256 0. 23.22 31.27" spec2 = "2 112 0 4999.0810546875...
+    WAT2_003= '58854293 256 0. 46.09 58.44" spec3 = "3 111 0 5043.505...
+    WAT2_004= '928358078002 256 0. 69.28 77.89"
+    WCSDIM  =                    2
+
+    CTYPE1  = 'MULTISPE'
+    LTM1_1  =                   1.
+    CD1_1   =                   1.
+
+    CTYPE2  = 'MULTISPE'
+    LTM2_2  =                   1.
+    CD2_2   =                   1.
+.fi
+.sh
+5.2 Chebyshev Polynomial Dispersion Function
+
+The parameters for the chebyshev polynomial dispersion function are the
+order (number of coefficients) and the normalizing range of physical
+coordinates, pmin and pmax, over which the function is
+defined and which are used to compute n.  Following the parameters are
+the order coefficients, ci.  The equation below shows how to
+evaluate the function using an iterative definition where x_1 = 1,
+x_2 = n, and x_i = 2 * n * x_{i-1} - x_{i-2}.
+
+The parameters for the chebyshev polynomial dispersion function are the
+order (number of coefficients) and the normalizing range of physical
+coordinates, pmin and pmax, over which the function is defined
+and which are used to compute n.  Following the parameters are the
+order coefficients, c_i.  The equation below shows how to evaluate the
+function using an iterative definition
+where x_1 = 1, x_2 = n, and x_i = 2 * n * x_{i-1} - x_{i-2}.
+
+.nf
+    W = sum from i=1 to order {c_i * x_i}
+.fi
+.sh
+5.3 Legendre Polynomial Dispersion Function
+
+The parameters for the legendre polynomial dispersion function are the
+order (number of coefficients) and the normalizing range of physical
+coordinates, pmin and pmax, over which the function is defined
+and which are used to compute n.  Following the parameters are the
+order coefficients, c_i.  The equation below shows how to evaluate the
+function using an iterative definition where x_1 = 1, x_2 = n, and
+x_i = ((2i-3)*n*x_{i-1}-(i-2)*x_{i-2})/(i-1).
+
+.nf
+    W = sum from i=1 to order {c_i * x_i}
+.fi
+
+Figure 4 shows an example from a multispec image with independent nonlinear
+dispersion coordinates.  This is again from an echelle spectrum.  Note that
+the IRAF \fBechelle\fR package determines a two dimensional dispersion
+function, in this case a bidimensional legendre polynomial, with the
+independent variables being the order number and the extracted pixel
+coordinate.  To assign and store this function in the image is simply a
+matter of collapsing the two dimensional dispersion function by fixing the
+order number and combining all the terms with the same order.
+
+.ce
+Figure 4: Echelle Spectrum with Legendre Polynomial Function
+
+.nf
+    WAT0_001= 'system=multispec'
+    WAT1_001= 'wtype=multispec label=Wavelength units=Angstroms'
+    WAT2_001= 'wtype=multispec spec1 = "1 113 2 4955.442888635351 0.05...
+    WAT2_002= '83 256 0. 23.22 31.27 1. 0. 2 4 1. 256. 4963.0163112090...
+    WAT2_003= '976664 -0.3191636898579552 -0.8169352858733255" spec2 =...
+    WAT2_004= '9.081188912082 0.06387049476832223 256 0. 46.09 58.44 1...
+    WAT2_005= '56. 5007.401409453303 8.555959076467951 -0.176732458267...
+    WAT2_006= '09935064388" spec3 = "3 111 2 5043.505764869474 0.07097...
+    WAT2_007= '256 0. 69.28 77.89 1. 0. 2 4 1. 256. 5052.586239197408 ...
+    WAT2_008= '271 -0.03173489817897474 -7.190562320405975E-4"
+    WCSDIM  =                    2
+
+    CTYPE1  = 'MULTISPE'
+    LTM1_1  =                   1.
+    CD1_1   =                   1.
+
+    CTYPE2  = 'MULTISPE'
+    LTM2_2  =                   1.
+    CD2_2   =                   1.
+.fi
+.sh
+5.4 Linear Spline Dispersion Function
+
+The parameters for the linear spline dispersion function are the number of
+spline pieces, npieces, and the range of physical coordinates, pmin
+and pmax, over which the function is defined and which are used to
+compute the spline coordinate s.  Following the parameters are the
+npieces+1 coefficients, c_i.  The two coefficients used in a linear
+combination are selected based on the spline coordinate, where a and b
+are the fractions of the interval in the spline piece between the spline
+knots, a=(j+1)-s, b=s-j, and x_0=a, and x_1=b.
+
+.nf
+    W = sum from i=0 to 1 {c_(i+j) * x_i}
+.fi
+.sh
+5.5 Cubic Spline Dispersion Function
+
+The parameters for the cubic spline dispersion function are the number of
+spline pieces, npieces, and the range of physical coordinates, pmin
+and pmax, over which the function is defined and which are used
+to compute the spline coordinate s.  Following the parameters are the
+npieces+3 coefficients, c_i.  The four coefficients used are
+selected based on the spline coordinate.  The fractions of the interval
+between the integer spline knots are given by a and b, a=(j+1)-s,
+b=s-j, and x_0 =a sup 3, x_1 =(1+3*a*(1+a*b)),
+x_2 =(1+3*b*(1+a*b)), and x_3 =b**3.
+
+The parameters for the cubic spline dispersion function are the number of
+spline pieces, npieces, and the range of physical coordinates, pmin
+and pmax, over which the function is defined and which are used to
+compute the spline coordinate s.  Following the parameters are the
+npieces+3 coefficients, c_i.  The four coefficients used are selected
+based on the spline coordinate.  The fractions of the interval between the
+integer spline knots are given by a and b, a=(j+1)-s, b=s-j,
+and x_0=a**3, x_1=(1+3*a*(1+a*b)), x_2=(1+3*b*(1+a*b)), and x_3=b**3.
+
+.nf
+    W = sum from i=0 to 3 {c_(i+j) * x_i}
+.fi
+.sh
+5.6 Pixel Array Dispersion Function
+
+The parameters for the pixel array dispersion function consists of just the
+number of coordinates ncoords.  Following this are the wavelengths at
+integer physical pixel coordinates starting with 1.  To evaluate a
+wavelength at some physical coordinate, not necessarily an integer, a
+linear interpolation is used between the nearest integer physical coordinates
+and the desired physical coordinate where a and b are the usual
+fractional intervals k=int(p), a=(k+1)-p, b=p-k,
+and x_0=a, and x_1=b.
+
+.nf
+    W = sum from i=0 to 1 {c_(i+j) * x_i}
+.fi
+.sh
+5.7 Sampled Array Dispersion Function
+
+The parameters for the sampled array dispersion function consists of
+the number of coordinate pairs, ncoords, and a dummy field.
+Following these are the physical coordinate and wavelength pairs
+which are in increasing order.  The nearest physical coordinates to the
+desired physical coordinate are located and a linear interpolation
+is computed between the two sample points.
+.endhelp
diff --git a/noao/onedspec/doc/splot.hlp b/noao/onedspec/doc/splot.hlp
new file mode 100644
index 00000000..a5bc3b96
--- /dev/null
+++ b/noao/onedspec/doc/splot.hlp
@@ -0,0 +1,1118 @@
+.help splot Jul95 noao.onedspec
+.ih
+NAME
+splot -- plot and analyze spectra
+.ih
+USAGE
+splot images [line [band]]
+.ih
+PARAMETERS
+.ls images
+List of images (spectra) to plot.  If the image is 2D or 3D the line
+and band parameters are used.  Successive images are plotted
+following each 'q' cursor command.  One may use an image section
+to select a desired column, line, or band but the full image will
+be in memory and any updates to the spectrum will be part of the
+full image.
+.le
+.ls line, band
+The image line/aperture and band to plot in two or three dimensional
+images.  For multiaperture spectra the aperture specified by the line
+parameter is first sought and if not found the specified image line is
+selected.  For other two dimensional images, such as long slit spectra, the
+line parameter specifies a line or column.  Note that if
+the line and band parameters are specified on the command line it will not
+be possible to change them interactively.
+.le
+.ls units = ""
+Dispersion coordinate units for the plot.  If the spectra have known units,
+currently this is generally Angstroms, the units may be converted
+to other units for plotting as specified by this task parameter.
+If this parameter is the null string and the world coordinate system
+attribute "units_display" is defined then that will
+be used.  If both this task parameters and "units_display" are not
+given then the spectrum dispersion units will be used.
+The units
+may also be changed interactively.  See the units section of the
+\fBpackage\fR help for a further description and available units.
+.le
+.ls options = "auto" [auto,zero,xydraw,histogram,nosysid,wcreset,flip,overplot]
+A list of zero or more, possibly abbreviated, options.  The options can
+also be toggled with colon commands.  The currently defined options are
+"auto", "zero", "xydraw", "histogram", "nosysid", "wreset", "flip", and
+"overplot".  Option "auto" automatically replots the graph whenever changes
+are made.  Otherwise the graph is replotted with keystrokes 'c' or 'r'.
+Option "zero" makes the initial minimum y of the graphs occur at zero.
+Otherwise the limits are set automatically from the range of the data or
+the \fIymin\fR parameter.  Option "xydraw" changes the 'x' draw key to use
+both x and y cursor values for drawing rather than the nearest pixel value
+for the y value.  Option "histogram" plots the spectra in a histogram style
+rather than connecting the pixel centers.  Option "nosysid" excludes the
+system banner from the graph title.  Option "wreset" resets the graph
+limits to those specified by the \fIxmin, xmax, ymin, ymax\fR parameters
+whenever a new spectrum is plotted.  The "flip" option selects that
+initially the spectra be plotted with decreasing wavelengths.  The options
+may be queried and changed interactively.  The "overplot" options overplots
+all graphs and a screen erase only occurs with the redraw key.
+.le
+.ls xmin = INDEF, xmax = INDEF, ymin = INDEF, ymax = INDEF
+The default limits for the initial graph.  If INDEF then the limit is
+determined from the range of the data (autoscaling).  These values can
+be changed interactively with 'w' window key options or the cursor commands
+":/xwindow" and ":/ywindow" (see \fBgtools\fR).
+.le
+.ls save_file = "splot.log"
+The file to contain any results generated by the equivalent width or
+deblending functions.  Results are added to this file until the file is
+deleted.  If the filename is null (""), then no results are saved.
+.le
+.ls graphics = "stdgraph"
+Output graphics device: one of "stdgraph", "stdplot", "stdvdm", or device
+name.
+.le
+.ls cursor = ""
+Graphics cursor input.  When null the standard cursor is used otherwise
+the specified file is used.
+.le
+
+The following parameters are used for error estimates in the 'd',
+'k', and 'e' key measurements.  See the ERROR ESTIMATES section for a
+discussion of the error estimates.
+.ls nerrsample = 0
+Number of samples for the error computation.  A value less than 10 turns
+off the error computation.  A value of ~10 does a rough error analysis, a
+value of ~50 does a reasonable error analysis, and a value >100 does a
+detailed error analysis.  The larger this value the longer the analysis
+takes.
+.le
+.ls sigma0 = INDEF, invgain = INDEF
+The pixel sigmas are modeled by the formula:
+
+.nf
+    sigma**2 = sigma0**2 + invgain * I
+.fi
+
+where I is the pixel value and "**2" means the square of the quantity.  If
+either parameter is specified as INDEF or with a value less than zero then
+no sigma estimates are made and so no error estimates for the measured
+parameters are made.
+.le
+
+The following parameters are for the interactive curve fitting function
+entered with the 't' key.  This function is usually used for continuum
+fitting.  The values of these parameters are updated during the fitting.
+See \fBicfit\fR for additional details on interactive curve fitting.
+.ls function = "spline3"
+Function to be fit to the spectra.  The functions are
+"legendre" (legendre polynomial), "chebyshev" (chebyshev polynomial),
+"spline1" (linear spline), and "spline3" (cubic spline).  The functions
+may be abbreviated.
+.le
+.ls order = 1
+The order of the polynomials or the number of spline pieces.
+.le
+.ls low_reject = 2., high_reject = 4.
+Rejection limits below and above the fit in units of the residual sigma.
+Unequal limits are used to reject spectral lines on one side of the continuum
+during continuum fitting.
+.le
+.ls niterate = 10
+Number of rejection iterations.
+.le
+.ls grow = 1.
+When a pixel is rejected, pixels within this distance of the rejected pixel
+are also rejected.
+.le
+.ls markrej = yes
+Mark rejected points?  If there are many rejected points it might be
+desired to not mark rejected points.
+.le
+
+The following parameters are used to overplot standard star fluxes with
+the 'y' key.  See \fBstandard\fR for more information about these parameters.
+.ls star_name
+Query parameter for the standard star fluxes to be overplotted.
+Unrecognized names or a "?" will print a list of the available stars
+in the specified calibration directory.
+.le
+.ls mag
+The magnitude of the observed star in the band given by the
+\fImagband\fR parameter.  If the magnitude is not in the same band as
+the blackbody calibration file then the magnitude may be converted to
+the calibration band provided the "params.dat" file containing relative
+magnitudes between the two bands is in the calibration directory
+.le
+.ls magband
+The standard band name for the input magnitude.  This should generally
+be the same band as the blackbody calibration file.  If it is
+not the magnitude will be converted to the calibration band.
+.le
+.ls teff
+The effective temperature (deg K) or the spectral type of the star being
+calibrated.  If a spectral type is specified a "params.dat" file must exist
+in the calibration directory.  The spectral types are specified in the same
+form as in the "params.dat" file.  For the standard blackbody calibration
+directory the spectral types are specified as A0I, A0III, or A0V, where A
+can be any letter OBAFGKM, the single digit subclass is between 0 and 9,
+and the luminousity class is one of I, III, or V.  If no luminousity class
+is given it defaults to dwarf.
+.le
+.ls caldir = ")_.caldir"
+The standard star calibration directory.  The default value redirects the
+value to the parameter of the same name in the package parameters.
+.le
+.ls fnuzero = 3.68e-20
+The absolute flux per unit frequency at a magnitude of zero used to
+to convert the calibration magnitudes to absolute flux.
+.le
+
+The following parameters are used for queries in response to particular
+keystrokes.
+.ls next_image
+In response to 'g' (get next image) this parameter specifies the image.
+.le
+.ls new_image
+In response to 'i' (write current spectrum) this parameter specifies the
+name of a new image to create or existing image to overwrite.
+.le
+.ls overwrite = no
+Overwrite an existing output image?  If set to yes it is possible to write
+back into the input spectrum or to some other existing image.  Otherwise
+the user is queried again for a new image name.
+.le
+.ls spec2
+When adding, subtracting, multiplying, or dividing by a second spectrum
+('+', '-', '*', '/' keys in the 'f' mode) this parameter is used to get
+the name of the second spectrum.
+.le
+.ls constant
+When adding or multiplying by a constant ('p' or 'm' keys in the 'f' mode)
+the parameter is used to get the constant.
+.le
+.ls wavelength
+This parameter is used to get a dispersion coordinate value during deblending or
+when changing the dispersion coordinates with 'u'.
+.le
+.ls linelist
+During deblending this parameter is used to get a list of line positions,
+peak values, profile types, and widths.
+.le
+.ls wstart, wend, dw
+In response to 'p' (convert to a linear wavelength scale) these parameters
+specify the starting wavelength, ending wavelength, and wavelength per pixel.
+.le
+.ls boxsize
+In response to 's' (smooth) this parameter specifies the box size in pixels
+to be used for the boxcar smooth.  The value must be odd.  If an even
+value is specified the next larger odd value is actually used.
+.le
+.ih
+DESCRIPTION
+\fBSplot\fR provides an interactive facility to display and analyze
+spectra.  See also \fBbplot\fR for a version of this task useful for making
+many plots noninteractively.  Each spectrum in the image list is displayed
+successively.  To quit the current image and go on to the next the 'q'
+cursor command is used.  If an image is two-dimensional, such as with
+multiple aperture or long slit spectra, the aperture or image column/line
+to be displayed is needed.  If the image is three-dimensional, such as with
+the extra information produced by \fBapextract\fR, the band is needed.
+These parameters are queried unless specified on the command line.  If
+given on the command line it will not be possible to change them
+interactively.
+
+The plots are made on the specfied graphics device which is usually to
+the graphics terminal.  The initial plot limits are set with the parameters
+\fIxmin, xmax, ymin\fR, and \fIymax\fR.  If a limit is INDEF then that limit
+is determined from the range of the data.  The "zero" option may also
+be set in the \fIoptions\fR parameter to set the lower intensity limit
+to zero.  Other options that may be set to control the initial plot
+are to exclude the system identification banner, and to select a
+histogram line type instead of connecting the pixel centers.
+The dispersion units used in the plot are set by the \fIunits\fR
+parameter.  This allows converting to units other than those in which the
+dispersion coordinates are defined in the spectra.
+
+The \fIoption\fR parameter, mentioned in the previous paragraph, is a
+a list of zero or more options.  As previously noted, some of the options
+control the initial appearance of the plots.  The "auto" option determines
+how frequently plots are redrawn.  For slow terminals or via modems one
+might wish to minimize the redrawing.  The default, however, is to redraw
+when changes are made.  The "xydraw" parameter is specific to the 'x'
+key.
+
+After the initial graph is made an interactive cursor loop is entered.
+The \fIcursor\fR parameter may be reset to read from a file but generally
+the graphics device cursor is read.  The cursor loop takes single
+keystroke commands and typed in commands begun with a colon, called
+colon commands.  These commands are described below and a summary of
+the commands may be produced interactively with the '?' key or
+a scrolling help on the status line with the '/' key.
+
+Modifications to the spectra being analyzed may be saved using the 'i' key
+in a new, the current, or other existing spectra.  A new image is created
+as a new copy of the current spectrum and so if the current spectrum is
+part of a multiple spectrum image (including a long slit spectrum) the
+other spectra are copied.  If other spectra in the same image are then
+modified and saved use the overwrite option to replace then in the new
+output image.  If the output spectrum already exists then the
+\fIoverwrite\fR flag must be set to allow modifying the data.  This
+includes the case when the output spectrum is the same as the input
+spectrum.  The only odd case here is when the input spectrum is one
+dimensional and the output spectrum is two dimensional.  In this case the
+user is queried for the line to be written.
+
+The other form of output, apart from that produced on the terminal, are
+measurements of equivalent widths, and other analysis functions.  This
+information will be recorded in the \fIsave_file\fR if specified.
+
+The following keystrokes are active in addition to the normal IRAF
+cursor facilities (available with ":.help"):
+
+.ls ?
+Page help information.
+.le
+.ls /
+Cycle through short status line help.
+.le
+.ls <space>
+The space bar prints the cursor position and value of the nearest
+pixel.
+.le
+.ls a
+Expand and autoscale to the data range between two cursor positions.
+See also 'w', and 'z'.  Selecting no range, that is the two
+cursor positions the same, produces an autoscale of the whole spectrum.
+.le
+.ls b
+Set the plot base level to zero rather than autoscaling.
+.le
+.ls c
+Clear all windowing and redraw the full current spectrum.  This redraws the
+spectrum and cancels any effects of the 'a', 'z', and 'w' keys.  The 'r'
+key is used to redraw the spectrum with the current windowing.
+.le
+.ls d
+Mark two continuum points and fit (deblend) multiple line profiles.
+The center, continuum at the center, core intensity, integrated flux,
+equivalent width, FWHMs for each profile are printed and saved
+in the log file.  See 'k' for fitting a single profile and
+'-' to subtract the fitted profiles.
+.le
+.ls e
+Measure equivalent width by marking two continuum points around the line
+to be measured.  The linear continuum is subtracted and the flux is
+determined by simply summing the pixels with partial pixels at the ends.
+Returned values are the line center, continuum at the region center,
+flux above or below the continuum, and the equivalent width.
+.le
+.ls f
+Enter arithmetic function mode. This mode allows arithmetic functions to be
+applied to the spectrum. The pixel values are modified according to the
+function request and may be saved as a new spectrum with the 'i'
+command.  Operations with a second spectrum are done in wavelength
+space and the second spectrum is automatically resampled if necessary.
+If one spectrum is longer than the other, only the smaller number of
+pixels are affected.  To exit this mode type 'q'.
+
+The following keystrokes are available in the function mode.  Binary
+operations with a constant or a second spectrum produce a query for the
+constant value or spectrum name.
+.ls a
+Absolute value
+.le
+.ls d
+Power of base 10 (inverse log base 10)
+.le
+.ls e
+Power of base e (inverse log base e)
+.le
+.ls i
+Inverse/reciprocal (values equal to zero are set to 0.0 in the inverse)
+.le
+.ls l
+Log base 10 (values less than or equal to 0.0 are set to -0.5)
+.le
+.ls m
+Multiply by a constant (constant is queried)
+.le
+.ls n
+Log base e (values less than or equal to 0.0 are set to -0.5)
+.le
+.ls p
+Add by a constant (constant is queried)
+.le
+.ls q
+Quit Function mode
+.le
+.ls s
+Square root (values less than 0.0 are set to 0.0)
+.le
+.ls +
+Add another spectrum
+.le
+.ls -3 -
+Subtract another spectrum
+.le
+.ls *
+Multiply by another spectrum
+.le
+.ls /
+Divide by another spectrum
+.le
+.le
+.ls g
+Get another spectrum. The current spectrum is replaced by the new spectrum.
+The aperture/line and band are queried is necessary.
+.le
+.ls h
+Measure equivalent widths assuming a gaussian profile with the width
+measured at a specified point.  Note that this is not a gaussian fit (see
+'k' to fit a gaussian)!  The gaussian profile determined here may be
+subtracted with the '-' key.  A second cursor key is requested with one of
+the following values:
+.ls a
+Mark the continuum level at the line center and use the LEFT half width
+at the half flux point.
+.le
+.ls b
+Mark the continuum level at the line center and use the RIGHT half width
+at the half flux point.
+.le
+.ls c
+Mark the continuum level at the line center and use the FULL width
+at the half flux point.
+.le
+.ls l
+Mark a flux level at the line center relative to a normalized continuum
+and use the LEFT width at that flux point.
+.le
+.ls r
+Mark a flux level at the line center relative to a normalized continuum
+and use the RIGHT width at that flux point.
+.le
+.ls k
+Mark a flux level at the line center relative to a normalized continuum
+and use the FULL width at that flux point.
+.le
+.le
+.ls i
+Write the current spectrum out to a new or existing image.  The image
+name is queried and overwriting must be confirmed.
+.le
+.ls j
+Set the value of the nearest pixel to the x cursor to the y cursor position.
+.le
+.ls k + (g, l or v)
+Mark two continuum points and fit a single line profile.  The second key
+selects the type of profile: g for gaussian, l for lorentzian, and v for
+voigt.  Any other second key defaults to gaussian.  The center, continuum
+at the center, core intensity, integrated flux, equivalent width, and FWHMs
+are printed and saved in the log file.  See 'd' for fitting multiple
+profiles and '-' to subtract the fit.
+.le
+.ls l
+Convert to flux per unit wavelength (f-lambda). The spectrum is assumed
+to be flux calibrated in flux per unit frequency (f-nu).  See also 'n'.
+.le
+.ls m
+Compute the mean, RMS, and signal-to-noise over a region marked with two
+x cursor positions.
+.le
+.ls n
+Convert to flux per unit frequency (f-nu). The spectrum is assumed
+to be flux calibrated in flux per unit wavelength (f-lambda).  See also 'l'.
+.le
+.ls o
+Set overplot flag.  The next plot will overplot the current plot.
+Normally this key is immediately followed by one of 'g', '#', '%', '(', or ')'.
+The ":overplot" colon command and overplot parameter option may be
+used to set overplotting to be permanently on.
+.le
+.ls p
+Define a linear wavelength scale.  The user is queried for a starting
+wavelength and an ending wavelength.  If either (though not both)
+are specified as INDEF a dispersion is queried for and used to compute
+an endpoint.  A wavelength scale set this way will be used for
+other spectra which are not dispersion corrected.
+.le
+.ls q
+Quit and go on to next input spectrum.  After the last spectrum exit.
+.le
+.ls r
+Redraw the spectrum with the current windowing.  To redraw the full
+spectrum and cancel any windowing use the 'c' key.
+.le
+.ls s
+Smooth via a boxcar.  The user is prompted for the box size.
+.le
+.ls t
+Fit a function to the spectrum using the ICFIT mode.  Typically
+interactive rejection is used to exclude spectra lines from the fit
+in order to fit a smooth continuum.  A second keystroke
+selects what to do with the fit.
+.ls /
+Normalize by the fit.  When fitting the continuum this continuum
+normalizes the spectrum.
+.le
+.ls -3 -
+Subtract the fit.  When fitting the continuum this continuum subtracts
+the spectrum.
+.le
+.ls f
+Replace the spectrum by the fit.
+.le
+.ls c
+Clean the spectrum by replacing any rejected points by the fit.
+.le
+.ls n
+Do the fitting but leave the spectrum unchanged (a NOP on the spectrum).
+This is useful to play with the spectrum using the capabilities of ICFIT.
+.le
+.ls q
+Quit and don't do any fitting.  The spectrum is not modified.
+.le
+.le
+.ls u
+Adjust the user coordinate scale.  There are three options, 'd' mark a
+position with the cursor and doppler shift it to a specified value,
+'z' mark a position with the cursor and zeropoint shift it to a specified
+value, or 'l' mark two postions and enter two values to define a linear
+(in wavelength) dispersion scale.  The units used for input are those
+currently displayed.  A wavelength scale set this way will be used for
+other spectra which are not dispersion corrected.
+.le
+.ls v
+Toggle to a velocity scale using the position of the cursor as the
+velocity origin and back.
+.le
+.ls w
+Window the graph.  For further help type '?' to the "window:" prompt or
+see help under \fBgtools\fR.  To cancel the windowing use 'a'.
+.le
+.ls x
+"Etch-a-sketch" mode. Straight lines are drawn between successive
+positions of the cursor. Requires 2 cursor settings in x.  The nearest pixels
+are used as the endpoints.  To draw a line between arbitrary y values first
+use 'j' to adjust the endpoints or set the "xydraw" option.
+.le
+.ls y
+Overplot standard star values from a calibration file.
+.le
+.ls z
+Zoom the graph by a factor of 2 in x.
+.le
+.ls (
+In multiaperture spectra go to the spectrum in the preceding image line.
+If there is only one line go to the spectrum in the preceding band.
+.le
+.ls )
+In multiaperture spectra go to the spectrum in the following image line.
+If there is only one line go to the spectrum in the following band.
+.le
+.ls #
+Get a different line in multiaperture spectra or two dimensional images.
+The aperture/line/column is queried.
+.le
+.ls %
+Get a different band in a three dimensional image.
+.le
+.ls $
+Switch between physical pixel coordinates and world (dispersion) coordinates.
+.le
+.ls -4 -
+Subtract the fits generated by the 'd' (deblend), 'k' (single profile fit),
+and 'h' (gaussian of specified width).  The region to be subtracted is
+marked with two cursor positions.
+.le
+.ls -4 ','
+Shift the graph window to the left.
+.le
+.ls .
+Shift the graph window to the right.
+.le
+.ls I
+Force a fatal error interupt to leave the graph.  This is used because
+the normal interupt character is ignored in graphics mode.
+.le
+
+.ls :show
+Page the full output of the previous deblend and equivalent width
+measurements.
+.le
+.ls :log
+Enable logging of measurements to the file specified by the parameter
+\fIsave_file\fR.  When the program is first entered logging is enabled
+(provided a log file is specified).  There is no way to change the file
+name from within the program.
+.le
+.ls :nolog
+Disable logging of measurements.
+.le
+.ls :dispaxis <val>
+Show or change dispersion axis for 2D images.
+.le
+.ls :nsum <val>
+Show or change summing for 2D images.
+.le
+.ls :units <value>
+Change the coordinate units in the plot.  See below for more information.
+.le
+.ls :# <comment>
+Add comment to logfile.
+.le
+.ls Labels:
+.ls :label <label> <format>
+Add a label at the cursor position.
+.le
+.ls :mabove <label> <format>
+Add a tick mark and label above the spectrum at the cursor position.
+.le
+.ls :mbelow <label> <format>
+Add a tick mark and label below the spectrum at the cursor position.
+.le
+
+The label must be quoted if it contains blanks.  A label beginning
+with % (i.e. %.2f) is treated as a format for the x cursor position.
+The optional format is a gtext string (see help on "cursors").
+The labels are not remembered between redraws.
+.le
+
+.ls :auto [yes|no]
+Enable/disable autodraw option
+.le
+.ls :zero [yes|no]
+Enable/disable zero baseline option
+.le
+.ls :xydraw [yes|no]
+Enable/disable xydraw option
+.le
+.ls :hist [yes|no]
+Enable/disable histogram line type option
+.le
+.ls :nosysid [yes|no]
+Enable/disable system ID option
+.le
+.ls :wreset [yes|no]
+Enable/disable window reset for new spectra option
+.le
+.ls :flip [yes|no]
+Enable/disable the flipped coordinates option
+.le
+.ls :overplot [yes|no]
+Enable/disable the permanent overplot option
+.le
+
+
+.ls :/help
+Get help on GTOOLS options.
+.le
+.ls :.help
+Get help on standard cursor mode options
+.le
+.ih
+PROFILE FITTING AND DEBLENDING
+The single profile ('k') and multiple profile deblending ('d') commands fit
+gaussian, lorentzian, and voigt line profiles with a linear background.
+The single profile fit, 'k' key, is a special case of the multiple profile
+fitting designed to be simple to use.  Two cursor positions define the
+region to be fit and a fixed linear continuum.  The second key is used to
+select the type of profile to fit with 'g' for gaussian, 'l' for
+lorentzian, and 'v' for voigt.  Any other second key will default to a
+gaussian profile.  The profile center, peak strength, and width(s) are then
+determined and the results are printed on the status line and in the log
+file.  The meaning of these quantities is described later.  The fit is also
+overplotted and may be subtracted from the spectrum subsequently with
+the '-' key.
+
+The more complex deblending function, 'd' key, defines the fitting region
+and initial linear continuum in the same way with two cursor positions.
+The continuum may be included in the fitting as an option.  The lines to be
+fit are entered with the cursor near the line center ('g' for gaussian, 'l'
+for lorentzian, 'v' for voigt), by typing the wavelengths ('t'), or read
+from a file ('f').  The latter two methods are useful if the wavelengths of
+the lines are known accurately and if fits restricting the absolute or
+relative positions of the lines will be used.  The 't' key is
+restricted to gaussian fits only.
+
+The 'f' key asks for a line list file.  The format of this file has
+one or more columns.  The columns are the wavelength, the peak value
+(relative to the continuum with negative values being absorption),
+the profile type (gaussian, lorentzian, or voigt), and the
+gaussian and/or lorentzian FWHM.  End columns may be missing
+or INDEF values may be used to have values be approximated.
+Below are examples of the file line formats
+
+.nf
+	wavelength
+	wavelength peak
+	wavelength peak (gaussian|lorenzian|voigt)
+	wavelength peak gaussian gfwhm
+	wavelength peak lorentzian lfwhm
+	wavelength peak voigt gfwhm
+	wavelength peak voigt gfwhm lfwhm
+
+	1234.5			<- Wavelength only
+	1234.5 -100		<- Wavelength and peak
+	1234.5 INDEF v		<- Wavelength and profile type
+	1234.5 INDEF g 12	<- Wavelength and gaussian FWHM
+.fi
+
+where peak is the peak value, gfwhm is the gaussian FWHM, and lfwhm is
+the lorentzian FWHM.  This format is the same as used by \fBfitprofs\fR
+and also by \fBartdata.mk1dspec\fR (except in the latter case the
+peak is normalized to a continuum of 1).
+
+There are four queries made to define the set of parameters to be fit or
+constrained.  The positions may be held "fixed" at their input values,
+allowed to shift by a "single" offset from the input values, or "all"
+positions may be fit independently.  The widths may be
+constrained to a "single" value or "all" fit independently.  The linear
+background may be included in the fit or kept fixed at that input using the
+cursor.
+
+As noted above, sometimes the absolute or relative wavelengths of the lines
+are known a priori and this information may be entered by typing the
+wavelengths explicitly using the 't' option or read from a file using the
+'f' option during marking.  In this case one should fix or fit a single
+shift for the position.  The latter may be useful if the lines are known
+but there is a measurable doppler shift.
+
+After the fit, the modeled lines are overplotted.  The line center,
+flux, equivalent width, and full width half maxima are printed on the
+status line for the first line.  The values for the other lines and
+the RMS of the fit may be examined by scrolling the status line
+using the '+', '-', and 'r' keys.  To continue enter 'q'.
+
+The fitting may be repeated with different options until exited with 'q'.
+For each line in the blend the line center, continuum intensity at the
+line center, the core intensity above or below the continuum, the
+FWHM for the gaussian and lorentzian parts, the flux above or below the continuum, and the
+equivalent width are recorded in the log file.  All these parameters
+except the continuum are based on the fitted analytic profiles.
+Thus, even though the fitted region may not extend into the wings of a line
+the equivalent width measurements include the wings in the fitted profile.
+For direct integration of the flux use the 'e' key.
+
+The fitted model may be subtracted from the data (after exiting the
+deblending function) using the '-' (minus) keystroke to delimit the region
+for which the subtraction is to be performed. This allows you to fit a
+portion of a line which may be contaminated by a blend and then subtract
+away the entire line to examine the remaining components.
+
+The fitting uses an interactive algorithm based on the Levenberg-Marquardt
+method.  The iterations attempt to improve the fit by varying the parameters
+along the gradient of improvement in the chi square.  This method requires
+that the initial values for the parameters be close enough that the
+gradient leads to the correct solution rather than an incorrect local
+minimum in the chi square.  The initial values are determined as follows:
+
+.nf
+    1.  If the lines are input from a data file then those values
+	in the file are used.  Missing information is determined
+	as below.
+    2.  The line centers are those specified by the user
+	either by marking with the cursor, entering the wavelenths,
+	for read from a file.
+    3.  The initial widths are obtained by dividing the width of
+	the marked fitting region by the number of lines and then
+	dividing this width by a factor depending on the profile
+	type.
+    4.  The initial peak intensities are the data values at the
+	given line centers with the marked continuum subtracted.
+.fi
+
+Note that each time a new fitting option is specified the initial parameters
+are those from the previous fits.
+Thus the results do depend on the history of previous fits until the
+fitting is exited.
+Within each fit an iteration of parameters is performed as
+described next.
+
+The iteration is more likely to fail if one initially attempts to fit too
+many parameters simultaneously.  A constrained approach to the solution
+is obtained by iterating starting with a few parameters and then adding
+more parameters as the solution approaches the true chi square minimum.
+This is done by using the solutions from the more constrained options
+as the starting point for the less constrained options.  In particular,
+the positions and a single width are fit first with fixed background.
+Then multiple widths and the background are added.
+
+To conclude, here are some general comments.  The most restrictive
+(fixed positions and single width(s)) will give odd results if the initial
+positions are not close to the true centers.  The most general
+(simultaneous positions, widths, and background) can also lead to
+incorrect results by using unphysically different widths to make one
+line very narrow and another very broad in an attempt to fit very
+blended lines.  The algorithm works well when the lines are not
+severely blended and the shapes of the lines are close to the profile
+type.
+.ih
+CENTROID, FLUX, AND EQUIVALENT WIDTH DETERMINATIONS
+There are currently five techniques in SPLOT to measure equivalent widths
+and other line profile parameters. The simplest (conceptually) is by
+integration of the pixel values between two marked pixels. This is
+invoked  with the 'e' keystroke.  The user marks the two edges of the line
+at the continuum.  The measured line center, contiuum value, line flux, and
+equivalent width are given by:
+
+.nf
+	center = sum (w(i) * (I(i)-C(i))**3/2) / sum ((I(i)-C(i))**3/2)
+	continuum = C(midpoint)
+	flux = sum ((I(i)-C(i)) * (w(i2) - w(i1)) / (i2 - i2)
+	eq. width = sum (1 - I(i)/C(i))
+.fi
+
+where w(i) is the wavelength of pixel i,  i1 and i2 are the nearest integer
+pixel limits of the integrated wavelength range, I(i) is the data value of
+pixel i, C(i) is the continuum at pixel (i), and the sum is over the marked
+range of pixels.  The continuum is a linear function between the two points
+marked.  The factor mulitplying the continuum subtracted pixel values
+in the flux calculation is the wavelength interval per pixel so that
+the flux integration is done in wavelength units.  (See the discussion
+at the end of this section concerning flux units).
+
+The most complex method for computing line profile parameters is performed
+by the profile fitting and deblending commands which compute a non-linear
+least-squares fit to the line(s).  These are invoked with the 'd' or 'k'
+keystroke.  These were described in detail previously.
+
+The fourth and fifth methods, selected with the 'h' key, determine the
+equivalent width from a gaussian profile defined by a constant continuum
+level "cont", a core depth "core", and the width of the line "dw" at some
+intermediate level "Iw".
+
+.nf
+     I(w) = cont + core * exp (-0.5*((w-center)/sigma)**2)
+     sigma = dw / 2 / sqrt (2 * ln (core/Iw))
+     fwhm = 2.355 * sigma
+     flux = core * sigma * sqrt (2*pi)
+     eq. width = abs (flux) / cont
+.fi
+
+where w is wavelength.
+
+For ease of use with a large number of lines only one cursor position is
+used to mark the center of the line and one flux level.  Note that both
+the x any y cursor positions are read simultaneously.  From the x cursor
+position the line center and core intensity are determined.  The region around
+the specified line position is searched for a minimum or maximum and a
+parabola is fit to better define the extremum.
+
+The two methods based on the simple gaussian profile model differ in how
+they use the y cursor position and what part of the line is used.  After
+typing 'h' one selects the method and whether to use the left, right, or
+both sides of the line by a second keystroke.  The 'l', 'r', and 'k' keys
+require a continuum level of one.  The y cursor position defines where the
+width of the line is determined.  The 'a', 'b', and 'c' keys use the y
+cursor position to define the continuum and the line width is determined at
+the point half way between the line core and the continuum.  In both cases
+the width at the appropriate level is determined by the interception of the
+y level with the data using linear interpolation between pixels.  The
+one-sided measurements use the half-width on the appropriate side and
+the two-sided measurements use the full-width.
+
+The adopted gaussian line profile is drawn over the spectrum and the
+horizontal and vertical lines show the measured line width and the depth of
+the line center from the continuum.  This model may also be subtracted
+from the spectrum using the '-' key.
+
+The major advantages of these methods are that only a single cursor setting
+(both the x and y positions are used) is required and they are fast.  The
+'l', 'r', and 'k' keys give more flexibility in adjusting the width of the
+gaussian line at the expense or requiring that the spectrum be normalized
+to a unit continuum.  The 'a', 'b', and 'c' keys allow measurements at any
+continuum level at the expense of only using the half flux level to
+determine the gaussian line width.
+
+All these methods print and record in the log file the line center,
+continuum intensity at the line center, the flux, and the equivalent
+width.  For the 'e' key the flux is directly integrated while for the other
+methods the fitted gaussian is integrated.  In addition, for the profile
+fitting methods the core intensity above or below the continuum, and the
+FWHMs are also printed.  A zero value is record for the gaussian or
+lorentzian width if the value is not determined by profile fit.  A brief
+line of data for each measurement is printed on the graphics status line.
+To get the full output and the output from previous measurements use the
+command ":show".  This pages the output on the text output which may
+involve erasing the graphics.
+
+The integrated fluxes for all the methods  are in the same units as the
+intensities and the integration is done in the same units as the
+plotted scale.  It is the user's responsibility to keep track of the flux
+units.  As a caution, if the data is in flux per unit frequency, say
+ergs/cm2/sec/hz, and the dispersion in Angstroms then the integrated
+flux will not be in the usual units but will be A-ergs/cm2/sec/hz.
+For flux in wavelength units, ergs/cm2/sec/A and the dispersion scale
+in Angstroms the integrated flux will be correct; i.e. ergs/cm2/sec.
+
+Note that one can compute integrated flux in pixel units  by using the '$'
+to plot in pixels.  This is appropriate if the pixel values are in
+data numbers or photon counts to get total data number or photons.
+.ih
+ERROR ESTIMATES
+The deblending ('d'), single profile fitting ('k'), and profile integration and
+equivalent width ('e') functions provide error estimates for the measured
+parameters.  This requires a model for the pixel sigmas.  Currently this
+model is based on a Poisson statistics model of the data.  The model
+parameters are a constant gaussian sigma and an "inverse gain" as specified
+by the parameters \fIsigma0\fR and \fIinvgain\fR.  These parameters are
+used to compute the pixel value sigma from the following formula:
+
+.nf
+    sigma**2 = sigma0**2 + invgain * I
+.fi
+
+where I is the pixel value and "**2" means the square of the quantity.
+
+If either the constant sigma or the inverse gain are specified as INDEF or
+with values less than zero then no noise model is applied and no error
+estimates are computed.  Also if the number of error samples is less than
+10 then no error estimates are computed.  Note that for processed spectra
+this noise model will not generally be the same as the detector readout
+noise and gain.  These parameters would need to be estimated in some way
+using the statistics of the spectrum.  The use of an inverse gain rather
+than a direct gain was choosed to allow a value of zero for this
+parameters.  This provides a model with constant uncertainties.
+
+The direct profile integration error estimates are computed by error
+propagation assuming independent pixel sigmas.  Also it is assumed that the
+marked linear background has no errors.  The error estimates are one sigma
+estimates.  They are given in the log output (which may also be view
+without exiting the program using the :show command) below the value to
+which they apply and in parenthesis.
+
+The deblending and profile fit error estimates are computed by Monte-Carlo
+simulation.  The model is fit to the data (using the sigmas) and this model
+is used to describe the noise-free spectrum.  A number of simulations,
+given by the \fInerrsample\fR parameter, are created in which random
+gaussian noise is added to the noise-free spectrum using the pixel
+sigmas from the noise model.  The model fitting is done for each simulation
+and the absolute deviation of each fitted parameter to model parameter is
+recorded.  The error estimate for the each parameter is then the absolute
+deviation containing 68.3% of the parameter estimates.  This corresponds to
+one sigma if the distribution of parameter estimates is gaussian though
+this method does not assume this.
+
+The Monte-Carlo technique automatically includes all effects of
+parameter correlations and does not depend on any approximations.
+However the computation of the errors does take a significant
+amount of time.  The amount of time and the accuracy of the
+error estimates depend on how many simulations are done.  A
+small number of samples (of order 10) is fast but gives crude
+estimates.  A large number (greater than 100) is slow but gives
+good estimates.  A compromise value of 50 is recommended
+for many applications.
+.ih
+UNITS
+The dispersion units capability of \fBsplot\fR allows specifying the
+units with the \fIunits\fR parameter and interactively changing the units
+with the ":units" command.  In addition the 'v' key allows plotting in
+velocity units with the zero point velocity defined by the cursor
+position.
+
+The units are specified by strings having a unit type from the list below
+along with the possible preceding modifiers, "inverse", to select the
+inverse of the unit and "log" to select logarithmic units. For example "log
+angstroms" to plot the logarithm of wavelength in Angstroms and "inv
+microns" to plot inverse microns.  The various identifiers may be
+abbreviated as words but the syntax is not sophisticated enough to
+recognized standard scientific abbreviations except as noted below.
+
+.nf
+	   angstroms - Wavelength in Angstroms
+	  nanometers - Wavelength in nanometers
+	millimicrons - Wavelength in millimicrons
+	     microns - Wavelength in microns
+	 millimeters - Wavelength in millimeters
+	  centimeter - Wavelength in centimeters
+	      meters - Wavelength in meters
+	       hertz - Frequency in hertz (cycles per second)
+	   kilohertz - Frequency in kilohertz
+	   megahertz - Frequency in megahertz
+	    gigahertz - Frequency in gigahertz
+	         m/s - Velocity in meters per second
+	        km/s - Velocity in kilometers per second
+	          ev - Energy in electron volts
+	         kev - Energy in kilo electron volts
+	         mev - Energy in mega electron volts
+
+	          nm - Wavelength in nanometers
+	          mm - Wavelength in millimeters
+	          cm - Wavelength in centimeters
+	           m - Wavelength in meters
+	          Hz - Frequency in hertz (cycles per second)
+	         KHz - Frequency in kilohertz
+	         MHz - Frequency in megahertz
+	         GHz - Frequency in gigahertz
+		  wn - Wave number (inverse centimeters)
+.fi
+
+The velocity units require a trailing value and unit defining the
+velocity zero point.  For example to plot velocity relative to
+a wavelength of 1 micron the unit string would be:
+
+.nf
+	km/s 1 micron
+.fi
+
+Some additional examples of units strings are:
+
+.nf
+	milliang
+	megahertz
+	inv mic
+	log hertz
+	m/s 3 inv mic
+.fi
+.ih
+EXAMPLES
+This task has a very large number of commands and capabilities which
+are interactive and  graphical.  Therefore it these examples are
+fairly superficial.  The user is encouraged to simply experiment with
+the task.  To get some help use the '?' or '/' keys.
+
+1.  To plot a single spectrum and record any measurements in the file
+'ngc7662':
+
+	cl> splot spectrum save_file=ngc7662
+
+2.  To force all plots to display zero as the minimum y value:
+
+	cl> splot spectrum options="auto, zero"
+
+Note that the options auto and zero can be abbreviated to one character.
+
+3.  To successively display graphs for a set of spectra with the wavelength
+limits set to 3000 to 6000 angstroms:
+
+	cl> splot spec* xmin=3000 xmax=6000
+
+4.  To make batch plots create a file containing the simple cursor command
+
+	0 0 0 q
+
+or an empty file and then execute one of the following:
+
+.nf
+	cl> splot spec* graphics=stdplot cursor=curfile
+	cl> set stdvdm=splot.mc
+	cl> splot spec* graphics=stdvdm cursor=curfile
+	cl> splot spec* cursor=curfile >G splot.mc
+.fi
+
+The first example sends the plots to the standard plot device specified
+by the environment variable "stdplot".  The next example sends the plots
+to the standard virtual display metacode file specified by the
+environment variable "stdvdm".  The last example redirects the
+standard graphics to the metacode file splot.mc.  To spool the metacode
+file the tasks \fBstdplot\fR and \fBgkimosaic\fR may be used.
+For a large number of plots \fBgkimosaic\fR is prefered since it places
+many plots on one page instead of one plot per page.
+The other GKI tasks in the \fBplot\fR package may be used to examine
+the contents of a metacode file.  A simple script call \fBbplot\fR is provided
+which has the default cursor file given above and default device of "stdplot".
+
+5.  More complex plots may be produced both interactively using the
+'=' key or the ":.snap"  or ":.write" commands or by preparing a script
+of cursor commands.
+.ih
+REVISIONS
+.ls SPLOT V2.11
+The profile fitting and deblending was expanded to include lorentzian
+and voigt profiles.  A new parameter controls the number of Monte-Carlo
+samples used in the error estimates.
+
+Added colon commands for labeling.
+.le
+.ls SPLOT V2.10.3
+The 'u' key now allows three ways to adjust the dispersion scale.  The
+old method of setting a linear dispersion scale is retained as well
+as adding a doppler and zeropoint adjustment.  The coordinates are
+input in the currently displayed units.
+
+If a wavelength scale is set with either 'p' or 'u' then any other
+spectra which are not dispersion corrected will adopt this wavelength
+scale.
+
+The '(' and ')' keys cycle through bands if there is only one spectrum.
+
+A new option, "flip", has been added to the options parameter to select
+that the spectra are plotted in decreasing wavelength.
+
+A new options "overplot" has been added to the options parameters and
+colon commands to permanently set overplotting.  This allows quickly
+overplotting many spectra.
+
+This task will now write out the current display units in the "units_display"
+WCS attribute.  The default task units have been changed to "" to allow
+picking up the "units_display" units if defined.
+
+The deblending and gaussian fitting code now subsamples the profile by
+a factor of 3 and fits the data pixels to the sum of the three
+subsamples.  This accounts for finite sampling of the data.
+
+Error estimates are provided for the deblending ('d'), gaussian fitting
+('k'), and profile integration ('e') results.
+.le
+.ls SPLOT V2.10
+This is a new version with a significant number of changes.  In addition to
+the task changes the other general changes to the spectroscopy packages
+also apply.  In particular, long slit spectra and spectra with nonlinear
+dispersion functions may be used with this task.  The image header or
+package dispaxis and nsum parameters allow automatically extracting spectra
+from 2D image.  The task parameters have been modified primarily to obtain
+the desired initial graph without needing to do it interactively.  In
+particular, the new band parameter selects the band in 3D images, the units
+parameter selects the dispersion units, and the new histogram, nosysid, and
+xydraw options select histogram line type, whether to include a system ID
+banner, and allow editing a spectrum using different endpoint criteria.
+
+Because nearly every key is used there has been some shuffling,
+consolidating, or elimination of keys.  One needs to check the run time '?'
+help or the help to determine the key changes.
+
+Deblending may now use any number of components and simultaneous fitting of
+a linear background.  A new simplified version of Gaussian fitting for a
+single line has been added in the 'k' key.  The old 'k', 'h', and 'v'
+equivalent width commands are all part of the single 'h' command using a
+second key to select a specific option.  The Gaussian line model from these
+modes may now be subtracted from the spectrum in the same way as the
+Gaussian fitting.  The one-sided options, in particular, are interesting in
+this regard as a new capability.
+
+The arithmetic functions between two spectra are now done in wavelength
+with resampling to a common dispersion done automatically.  The 't' key now
+provides for the full power of the ICFIT package to be used on a spectrum
+for continuum normalization, subtraction, or line and cosmic ray removal.
+The 'x' editing key may now use the nearest pixel values rather than only
+the y cursor position to replace regions by straight line segments.  The
+mode is selected by the task option parameter "xydraw".
+
+Control over the graph window (plotting limits) is better integrated so
+that redrawing, zooming, shifting, and the GTOOLS window commands all work
+well together.  The new 'c' key resets the window to the full spectrum
+allowing the 'r' redraw key to redraw the current window to clean up
+overplots from the Gaussian fits or spectrum editing.
+
+The dispersion units may now be selected and changed to be from hertz to
+Mev and the log or inverse (for wave numbers) of units taken.  As part of
+the units package the 'v' key or colon commands may be used to plot in
+velocity relative to some origin.  The $ key now easily toggles between the
+dispersion units (whatever they may be) and pixels coordinates.
+
+Selection of spectra has become more complex with multiaperture and long
+slit spectra.  New keys allow selecting apertures, lines, columns, and
+bands as well as quickly scrolling through the lines in multiaperture
+spectra.  Overplotting is also more general and consistent with other tasks
+by using the 'o' key to toggle the next plot to be overplotted.  Overplots,
+including those of the Gaussian line models, are now done in a different
+line type.
+
+There are new colon commands to change the dispersion axis and summing
+parameters for 2D image, to toggle logging, and also to put comments
+into the log file.  All the options may also be set with colon commands.
+.le
+.ih
+SEE ALSO
+bplot, gtools, icfit, standard, package, specplot, graph, implot, fitprofs
+.endhelp
diff --git a/noao/onedspec/doc/standard.hlp b/noao/onedspec/doc/standard.hlp
new file mode 100644
index 00000000..d0c84aef
--- /dev/null
+++ b/noao/onedspec/doc/standard.hlp
@@ -0,0 +1,551 @@
+.help standard Jan00 noao.onedspec
+.ih
+NAME
+standard -- Add standard stars to sensitivity file
+.ih
+USAGE
+standard input [records] output
+.ih
+PARAMETERS
+.ls input
+List of input standard star spectra or root names if using the record number
+extension format.  All spectra of the same aperture must be of the same
+standard star.  In beam switch mode or when the same star parameter is set
+all spectra must be of the same standard star regardless of aperture number.
+Normally the spectra will not be extinction corrected but if they are
+then the extinction file should also be given and the same extinction
+file should be used with \fBsensfunc\fR.
+.le
+.ls records (imred.irs and imred.iids only)
+List of records or ranges of records to be appended to the input spectra
+names when using record number extension format.  The
+syntax of this list is comma separated record numbers or ranges of record
+numbers.  A range consists of two numbers separated by a hyphen.
+A null list may be used if no record number extensions are
+desired.  This is a positional query parameter only if the record
+format is specified.
+.le
+.ls output
+The name of a text file which will contain the output from \fBstandard\fR.
+Each execution of \fBstandard\fR appends to this file information about the
+standard stars, the calibration bandpasses, and observed counts (see the
+DESCRIPTION section for more details).  The output must be explicitly
+deleted by the user if the filename is to be reused.
+.le
+.ls samestar = yes
+Is the same star in all apertures?  If set to no then each aperture may
+contain a different standard star.  The standard star name is queried
+each time a new aperture is encountered.  Note that this occurs only
+once per aperture and multiple spectra with the same aperture number
+must be of the same star.  If set to yes the standard star name is only
+queried once.  When in beam switch mode this parameter is ignored since
+all apertures must contain the same star.
+.le
+.ls beam_switch = no
+Beam switch the spectra?  If yes then a beam switch mode is used for the spectra
+in which successive pairs of object and sky observations from the same aperture
+are sky subtracted.  This requires that the object type flag OFLAG be present
+and that the spectra are appropriately ordered.  All object observations must be
+of the same standard star and the \fIsamestar\fR parameter is ignored.
+.le
+.ls apertures = ""
+List of apertures to be selected from the input list of spectra.  If no list
+is specified then all apertures are selected.  The syntax is the same as the
+record number extensions.
+.le
+.ls bandwidth = INDEF, bandsep = INDEF
+Bandpass widths and separations in wavelength units.  If INDEF then the
+default bandpasses are those given in the standard star calibration
+file.  If values for these parameters are specified then a default set
+of bandpasses of equal width and separation are defined over the range
+of the input spectrum.  In both cases the default bandpasses can be
+changed interactively if desired.
+.le
+.ls fnuzero = 3.68e-20
+The absolute flux per unit frequency at an AB magnitude of zero.  This is used
+to convert the calibration  AB magnitudes to absolute flux by the formula
+
+.nf
+    f_nu = fnuzero * 10. ** (-0.4 * m_AB)
+.fi
+
+The flux units are also determined by this parameter.  However, the
+frequency to wavelength interval conversion assumes frequency in hertz.
+The default value is based on a calibration of Vega at 5556 Angstroms of
+3.52e-20 ergs/cm2/s/Hz for an AB magnitude of 0.0336.  This default value
+is that used in earlier versions of this task which did not allow the
+user to change this calibration.
+.le
+.ls extinction = <no default>
+Extinction file used to make second order extinction corrections across
+the bandpasses.  The default value is  redirected to the package
+parameter of the same name.  See \fBlcalib\fR for a list of standard
+extinction files.  Normally the input spectra will not be extinction
+corrected.  But if they are this file will be used to remove the
+extinction and then the same file should be specified in \fBsensfunc\fR.
+Note that one can choose to use a null extinction file in both.
+.le
+.ls caldir = ")_.caldir"
+Calibration directory containing standard star data.  The
+default value of ")_.caldir" means to use the package parameter "caldir".
+A list of standard calibration directories may be obtained by listing the
+file "onedstds$README"; for example:
+
+.nf
+    cl> page onedstds$README
+.fi
+
+The user may copy or create their own calibration files and specify the
+directory.  The directory "" refers to the current working directory.  The
+standard calibration directory for blackbody curves is
+"onedstds$blackbody/".
+.le
+.ls observatory = ")_.observatory"
+Observatory at which the spectra were obtained if not specified in the
+image header by the keyword OBSERVAT.  The default is a redirection to look
+in the parameters for the parent package for a value.  The observatory may
+be one of the observatories in the observatory database, "observatory" to
+select the observatory defined by the environment variable "observatory" or
+the parameter \fBobservatory.observatory\fR, or "obspars" to select the
+current parameters set in the \fBobservatory\fR task.  See help for
+\fBobservatory\fR for additional information.
+.le
+.ls interact = no
+If set to no, then the default wavelength set (either that from the star
+calibration file or the set given by the \fIbandwidth\fR and \fIbandsep\fR
+parameters) is used to select wavelength points along the spectrum where the
+sensitivity is measured. If set to yes, the spectra may be plotted
+and the bandpasses adjusted.
+.le
+.ls graphics = "stdgraph"
+Graphics output device for use with the interactive mode.  Normally this is
+the user's graphics terminal.
+.le
+.ls cursor = ""
+Graphics cursor input for use with the interactive mode.  When null the
+standard graphics cursor is used otherwise the specified file is used.
+.le
+.ls star_name
+The name of the star observed in the current series of spectra.  Calibration
+data for the star must be in the specified calibration directory "caldir".
+This is normally a interactive query parameter and should not be specified on
+the command line unless all spectra are of the same standard star.
+.le
+
+The following three queried parameters apply if the selected calibration
+file is for a blackbody.
+.ls mag
+The magnitude of the observed star in the band given by the
+\fImagband\fR parameter.  If the magnitude is not in the same band as
+the blackbody calibration file then the magnitude may be converted to
+the calibration band provided the "params.dat" file containing relative
+magnitudes between the two bands is in the calibration directory
+.le
+.ls magband
+The standard band name for the input magnitude.  This should generally
+be the same band as the blackbody calibration file.  If it is
+not the magnitude will be converted to the calibration band.
+.le
+.ls teff
+The effective temperature (deg K) or the spectral type of the star being
+calibrated.  If a spectral type is specified a "params.dat" file must exist
+in the calibration directory.  The spectral types are specified in the same
+form as in the "params.dat" file.  For the standard blackbody calibration
+directory the spectral types are specified as A0I, A0III, or A0V, where A
+can be any letter OBAFGKM, the single digit subclass is between 0 and 9,
+and the luminousity class is one of I, III, or V.  If no luminousity class
+is given it defaults to dwarf.
+.le
+
+The following two parameters are queried if the image does not contain
+the information.
+.ls airmass, exptime
+If the airmass and exposure time are not in the header nor can they be
+determined from other keywords in the header then these query parameters
+are used to request the airmass and exposure time.  The values are updated
+in the image.
+.le
+
+The following parameter is for the task to make queries.
+.ls answer
+Interactive query parameter.
+.le
+.ih
+CURSOR KEYS
+.nf
+?  Display help page
+a  Add a new band by marking the endpoints
+d  Delete band nearest the cursor in wavelength
+r  Redraw current plot
+q  Quit with current bandpass definitions
+w  Window plot  (follow with '?' for help)
+I  Interrupt task immediately
+
+:show	Show current bandpass data
+.fi
+.ih
+DESCRIPTION
+Observations of standard stars are integrated over calibration bandpasses
+and written to an output file along with the associated calibration
+fluxes.  The fluxes are obtained from tabulated standard star calibration
+files or a model flux distribution (currently just a blackbody) based on
+the magnitude and spectral type of the star.  The output data is used by
+the task \fBsensfunc\fR to determine the detector sensitivity function and
+possibly the extinction.  The spectra are required to be dispersion
+corrected.  The input spectra may be in either "onedspec" or "echelle"
+format and may have many different observation apertures.  The spectra may
+also be beam switched and use the a record number extension format.
+
+The input spectra are specified by a list of names or root names if using
+the record number extension format.  In the latter case each name in the
+list has each of the specified record numbers appended.  A subset of the
+input spectra may be selected by their aperture numbers using the parameter
+\fIapertures\fR.  The spectrum name, aperture number, and title are printed
+to the standard output.  The airmass is required but if absent from the image
+header it may be computed from the observation header parameters and the
+latitude task parameter (normally obtained from the \fBobservatory\fR task).
+If the airmass cannot be computed, due to missing keywords, then a
+query is made for the airmass.  The airmass is then updated in the header.
+
+The name of the standard star or blackbody curve is obtained by querying
+the user.  If the parameter \fIsamestar\fR is yes or beam switch mode is
+selected then all spectra are assumed to be of the same standard star and
+the query is made once.  If the parameter is no then a query is made for
+each aperture.  This allows each aperture to contain a different standard
+star.  Note however that multiple observations with the same aperture
+number must be of the same standard star.
+
+The standard star name is either the name of an actual standard star or of
+a blackbody calibration.  The latter generally have a star name consisting
+of just the standard bandpass identifier.  If the standard star name is not
+recognized a menu of the available standard stars in the calibration
+directory, the file "standards.men", is printed and then the query is
+repeated.  Thus, to get a list you can type ?  or help.
+
+The standard star names must map to a file containing tabulated
+calibration data.  The calibration filename is formed from the star
+name with blanks, "+", and "-" removed, converted to lower case, and
+the extension ".dat" added.  This name is appended to a calibration
+directory, so the directory name must have an appropriate directory
+delimiter such as "$" or "/".  Generally one of the system calibration
+directories is used but one may copy and modify or create new
+calibration files in a personal directory.  For the current working
+directory the calibration directory is either null or "./".
+
+The calibration files may include comment parameter information consisting
+of the comment character '#', a parameter name, and the parameter value.
+These elements are separated by whitespace.  Any other comment where the
+first word does not match one of the allowed parameter names is ignored by
+the program.  The parameter names are "type" identifying the type of
+calibration file, "units" identifying wavelength units, "band" identifying
+the band for magnitudes, and "weff" identifying the effective wavelength of
+the band.
+
+There are two types of standard star calibration files as described
+below.
+
+.ls STANDARD STAR CALIBRATION FILES
+This type of file is any file that does not contain the parameter "type"
+with a value of "blackbody".  The only other parameter used by this type of
+calibration file is the "units" parameter for the wavelength units.  If the
+units are not specified then the wavelengths default to Angstroms.  All
+older calibration files will have no parameter information so they are
+interpreted as standard star calibration files with wavelengths in
+Angstroms.
+
+The calibration files consist of lines with wavelengths, calibration
+magnitudes, and bandpass widths.  The magnitudes are m_AB defined as
+
+.nf
+    m_AB(star) = -2.5 * log10 (f_nu) - 48.60
+.fi
+
+where f_nu is in erg/cm^2/s/Hz.  The m_AB calibration magnitudes
+are converted to absolute flux per unit frequency using the
+parameter \fIfnuzero\fR defined by
+
+.nf
+    f_nu = fnuzero * 10. ** (-0.4 * m_AB)
+.fi
+
+Thus, \fIfnuzero\fR is the flux at m_AB of zero.  The flux units are
+determined by this number.  The default value was chosen such that Vega
+at 5556 Angstroms has an AB magnitude of 0.0336 and a flux of 3.52e-20
+ergs/cm2/s/Hz.  This is the same value that was used by all previous
+versions of this task.
+.le
+
+.ls BLACKBODY CALIBRATION FILES
+This type of file has the comment parameter "type" with a value of
+"blackbody".  It must also include the "band" and "weff"
+comment parameters.  If no "units" comment parameter is given then
+the default units are Angstroms.
+
+The rest of the file consists of lines with wavelengths, m_AB of a zero
+magnitude star (in that band magnitude system), and the bandpass widths.
+The m_AB are defined as described previously.  Normally all the m_AB values
+will be the same though it is possible to adjust them to produce a
+departure from a pure blackbody flux distribution.
+
+The actual m_AB calibration magnitudes for the star are obtained by
+the relation
+
+.nf
+    m_AB(star) = mag + m_AB(m=0) -
+        2.5 * log10 (B(weff,teff)/B(w,teff))
+.fi
+
+where m is the magnitude of the star in the calibration band, m_AB(m=0) is
+the calibration value in the calibration file representing the magnitude of
+a m=0 star (basically the m_AB of Vega), weff is the effective wavelength
+for the calibration file, and teff is the effective temperature of the
+star.  The function B(w,T) is the blackbody function in f_nu that provides
+the shape of the calibration.  Note how the normalization is such that at
+weff the last term is zero and m_AB(star) = m + m_AB(m=0).
+
+The m_AB(star) computed using the calibration values and the blackbody
+function are then in the same units and form as for the standard
+star files.  The conversion to f_nu and the remaining processing
+proceeds in the same way as for standard star calibration data.
+
+The parameters \Imag\fR and \fIteff\fR are specified by the user for each
+star as described in the section BLACKBODY PARAMETERS.  These parameters
+are queried by the task for each star (unless forced to a value on the
+command line).
+.le
+
+The beam switch mode is selected with the \fIbeam_switch\fR parameter.
+This mode requires that all apertures are of the same star, the header
+keyword OFLAG be present to identify object and sky spectra, and that
+the sequence of spectra specified are paired such that if an object
+spectrum is encountered first the next spectrum for that aperture
+(spectra from other apertures may appear in between) is a sky spectrum
+or the reverse.  These restrictions are not fundamental but are made so
+that this mode behaves the same as with the previous version of this
+task.  The sky spectrum is subtracted from the object spectrum and the
+result is then used in generating the observed intensities in the calibration
+bandpasses.
+
+If the spectra have been extinction corrected (EX-FLAG = 0) the
+extinction correction is removed.  The specified extinction file is
+used for this operation and so must be the same as that used when the
+extinction correction was made.  The airmass is also required in this step
+and, if needed to compute the airmass, the observatory specified in the
+image or observatory parameter is used.  The
+treatment of extinction in this task is subtle.  The aim of this task
+is to produce observed integrated instrumental intensities without
+extinction correction.  Thus, the extinction correction is removed from
+extinction corrected spectra.  However, a correction is made for an
+extinction gradient across the bandpasses.  This is done by applying an
+extinction correction, integrating across the bandpass, and then
+correcting the integrated intensity for the extinction at the center of
+the bandpass.  An alternative way to look at this is that the integral
+is weighted by the ratio of the extinction correction at each pixel to
+the extinction correction at the center of the bandpass.  This
+correction or weighting is why the extinction file and latitude are
+parameters in this task even though for nonextinction corrected spectra
+they appear not to be needed.
+
+The observed instrumental intensities are integrated within a set of
+bandpasses by summing the pixels using partial pixels at the bandpass
+edges.  Initial bandpasses are defined in one of two ways.  A set of
+evenly spaced bandpasses of constant width covering the range of the
+input spectrum may be specified using the parameters \fIbandwidth\fR
+and \fIbandsep\fR in the same units as the spectrum dispersion.  If
+these parameters have the value INDEF then the bandpasses from the
+calibration file which are entirely within the spectrum are selected.
+Generally these bandpasses are the actual measured bandpasses though
+one is free to make calibration files using estimated points.  The
+calibration bandpasses are preferable because they have been directly
+measured and they have been placed to avoid troubles with spectral
+lines.  However, when the coverage or resolution is such that these
+bandpasses do not allow a good determination of the instrumental
+response the evenly spaced bandpasses may be needed.  The calibration
+fluxes are linearly interpolated (or extrapolated) from the calibration
+data points to the defined bandpasses.
+
+Each spectrum adds a line to the output file containing the spectrum image
+name, the sky spectrum image name if beam switching, the aperture or beam
+number, the number of points in the spectrum, the exposure time, airmass,
+wavelength range, and title.  If the airmass is not found in the image
+header it is computed using the latitude parameter and observation
+information from the header.  If the airmass cannot be computed, due to
+missing keywords, then a query is made for the airmass.
+
+Following the spectrum information, calibration data is added for each
+bandpass.  The bandpass wavelength, absolute flux (per Angstrom),
+bandpass width, and observed instrumental intensity in the bandpass are
+added to the output file.  As discussed above, the observed intensity
+does not include an extinction term but does apply a small correction
+or weighting for the variation of the extinction across the bandpass.
+
+The setting and editing of the bandpasses may be performed
+interactively if the \fIinteract\fR flag is set.  In this case the user
+is queried for each spectrum.  The answers to this query may be "no" or
+"yes" to skip editing or edit the bandpasses for this spectrum, "NO" or
+"YES" to skip or not skip editing all spectra of the same aperture with
+no further queries for this aperture, and "NO!" or "YES!" to skip
+editing or edit all spectra with no further queries.
+
+When editing the bandpasses a graph of the spectrum is made with the
+bandpasses plotted at the computed intensity per pixel.  The cursor and
+colon commands available are summarized in the section CURSOR KEYS.
+Basically bandpasses may be added or deleted and the current bandpass
+data may be examined.  Additional keys allow the usual windowing and
+cursor mode operations.  When satisfied with the bandpasses exit with
+'q'.  The edited bandpasses for that aperture remain in effect until
+changed again by the user.  Thus if there are many spectra from the
+same aperture one may reply with "NO" to queries for the next spectra
+to accept the current bandpasses for all other spectra of the same
+aperture.
+
+BLACKBODY PARAMETERS
+
+When a blackbody calibration is selected (the calibration file selected by
+the \fIstar_name\fR parameter has "# type blackbody") there are two
+quantities needed to scale the blackbody to the observation.  These are the
+magnitude of the star in the same band as the observation and the effective
+temperature.  The magnitude is used for the flux scaling and the effective
+temperature for the shape of the flux distribution.  The values are
+obtained or derived from the user specified parameters \fImag\fR,
+\fImagband\fR, and \fIteff\fR.  This section describes how the the
+values are derived from other parameters using the data file "params.dat"
+in the calibration directory.
+
+The effective temperature in degrees Kelvin may be specified directly or it
+may be derived from a spectral type for the star.  In the latter case the
+file "params.dat" is searched for the effective temperature.  The file
+consists of lines with the first value being the spectral type and the
+second the effective temperature.  Other columns are described later.  The
+spectral type can be any string without whitespace that matches what is in
+the file.  However, the program finds the last spectral type that matches
+the first two characters when there is no complete match.  This scheme is
+intended for the case where the spectral types are of the form A0I, A0III,
+or A0V, where A can be any spectral type letter OBAFGKM, the single digit
+subtype is between 0 and 9, and the luminousity class is one of I, III, or
+V.  The two character match selects the last spectral type independent of
+the luminosity class.  The standard file "onedstds$blackbody/params.dat"
+uses these spectral type identifiers with the dwarf class acting as the
+default.
+
+The magnitude band is specified along with the input magnitude.  If the
+band is the same as the calibration band given in the calibration file then
+no further transformation is required.  However if the magnitude is
+specified in a different band, a conversion is performed using information
+from the "params.dat" file based on the spectral type of the star.
+
+When an effective temperature is specified rather and a spectral type then
+the nearest tabulated temperature for the spectral types that have "V" as
+the third character is used.  For the standard spectral type designations
+this means that when an effective temperature is specified the dwarf
+spectral type is used for the magnitude transformation.
+
+As mentioned previously, the "params.dat" data file has additional columns
+following the spectral type and effective temperature.  These columns are
+relative magnitudes in various bands.  The standard file has V magnitudes
+of zero so in this case the columns are also the X-V colors (where X is the
+appropriate magnitude).  Given the spectral type the relative magnitudes
+for the calibration band, m_1, and the input magnitude band, m_2, are found
+and the calibration magnitude for the star is given by
+
+.nf
+    m_calibration = m_input + m_1 - m_2
+.fi
+
+If one of the magnitudes is missing,  given as "INDEF" because the
+transformation is not available for the spectral type, the last spectral
+type matching the first two characters which does specify the two
+magnitudes will be used.  For example if there is no information for a
+B3III star for a M-J color then the spectral type B3V might be used.
+
+In order for the program to determine the bands for each column in the data
+file there must be a comment before the data with the column names.  It must
+begin with "# Type Teff" and then be followed by the same band identifiers
+used in the blackbody calibration files and as specified by the
+\fImagband\fR parameter.  Any amount whitespace (space or tab) is used to
+separate the various fields in the comment and in the fields of the table.
+For example the file might have the comment
+
+.nf
+    # Type    Teff     V      J      H      K      L   Lprime    M
+.fi
+
+identifying the third column of the file as the V magnitude and the
+ninth file as the M magnitude.
+.ih
+EXAMPLES
+1.  To compile observations of three standard stars using a beam
+switched instrument like the IIDS:
+
+.nf
+    cl> standard.recformat=yes
+    cl> standard nite1 1001-1008 std beam_switch+ interact-
+    [nite1.1001][0]: HZ 44 - Night 1
+    [nite1.1004][0]: HZ 44 - Night 1
+    [nite1.1005][0]: HZ 44 - Night 1
+    [nite1.1008][0]: HZ 44 - Night 1
+    Star name in calibration list: hz 44
+    cl> standard nite1 1009-1016 std beam_switch+ interact-
+    	...
+    cl> standard nite1 1017-1024 std beam_switch+ interact-
+    	...
+.fi
+
+This will create a file "std" which will contain sensitivity measurements
+from the beam-switched observations of the three standard stars given.
+Note that \fBstandard\fR is run separately for each standard star.
+
+The spectra will be from the images: nite1.1001, nite.1002 ... nite1.1024,
+and the default calibration file, "onedstds$irscal.dat" will be used.
+
+2.  For echelle spectra all apertures, the orders, are of the same star and
+so the samestar parameter is set.  Usually the resolution is much higher than
+the calibration data so in order to get sufficient coverage bandpasses must
+be interpolated from the calibration data.  Therefore the evenly spaced
+bandpasses are used.
+
+.nf
+    cl> standard.recformat=no
+    cl> standard.samestar=yes
+    cl> standard ech001.ec std bandwidth=10 bandsep=15
+    [ech001.ec][0]: Feige 110
+    Star name in calibration list: feige 110
+    [ech001.ec][0]: Edit bandpasses? (no|yes|NO|YES|NO!|YES!): yes
+    [ech001.ec][1]: Edit bandpasses? (no|yes|NO|YES|NO!|YES!): yes
+    [ech001.ec][2]: Edit bandpasses? (no|yes|NO|YES|NO!|YES!): NO!
+.fi
+
+3. To use a blackbody infrared calibration where the V magnitude of
+the star is known.
+
+.nf
+    cl> standard std1.ms std caldir=onedstds$blackbody/
+    std1.ms(1): Standard Star
+    Star name in calibration list: J
+    Magnitude of star: 10.3
+    Magnitude type (|V|J|H|K|L|Lprime|M|): V
+    Effective temperature or spectral type: B3III
+    WARNING: Effective temperature for B3III not found - using B3V
+    Blackbody: V = 10.30, J = 10.32, Teff = 19000
+    std1[1]: Edit bandpasses? (no|yes|NO|YES|NO!|YES!) (yes): 
+.fi
+
+Note the warning message and the confirmation information.
+.ih
+REVISIONS
+.ls STANDARD V2.10.4
+The calibration files can be defined to compute blackbody values.
+.le
+.ls STANDARD V2.10.3
+A query for the airmass and exposure time is now made if the information
+is not in the header and cannot be computed from other header keywords.
+.le
+.ls STANDARD V2.10
+Giving an unrecognized standard star name will page a list of standard
+stars available in the calibration directory and then repeat the
+query.
+.le
+.ih
+SEE ALSO
+observatory, lcalib, sensfunc
+.endhelp
diff --git a/noao/onedspec/doc/sys/1and2dspec.hlp b/noao/onedspec/doc/sys/1and2dspec.hlp
new file mode 100644
index 00000000..01f01763
--- /dev/null
+++ b/noao/onedspec/doc/sys/1and2dspec.hlp
@@ -0,0 +1,66 @@
+.help onedspec (Oct84) "Spectral Reductions"
+.ce
+Relationship Between Onedspec and Twodspec
+.ce
+Discussion
+.ce
+October 24, 1984
+.sp 3
+Two types of interactions between one dimensional and two dimensional
+spectra may be defined:
+
+.ls (1)
+Perform a one dimensional operation on the average or sum of a set
+of lines in a two dimensional image.
+.le
+.ls (2)
+Perform a one dimensional operation successively on a set of lines
+in a two dimensional image.
+.le
+
+The two functions might be combined as:
+
+.ls (3)
+Perform a one dimensional operation on the average or sum of a set
+of lines in a two dimensional image and apply the one dimensional
+result successively on a set of lines in a two dimensional image.
+.le
+
+Examples of this are dispersion solutions and flux calibrations for
+longslit spectra.
+
+     Some choices for implementation are:
+
+.ls (1)
+Use a 2-D to 1-D operator to create a 1-D spectrum by averaging or summing
+lines.
+.le
+.ls (2)
+Use an apply a 1-D arithmetic correction to a 2-D image operator.
+Alternatively, expand a 1-D correction to a 2-D correction.
+.le
+.ls (3)
+Convert the 2-D image to a group of 1-D images and provide the 1-D operators
+with the ability to perform averaging or summation.
+.le
+.ls (4)
+To perform a one dimensional operation successively on
+a set of lines first convert the two dimensional image into a group
+of one dimensional spectra.  Perform the 1-D operation on the desired
+elements of the group and then reconstruct the 2-D image from the group
+of 1-D images.
+.le
+.ls (5)
+Built separate operators for 2-D images using the 1-D subroutines.
+.le
+.ls (6)
+Provide the ability in the 1-D operators to perform the desired 2-D
+operations directly.
+.le
+
+     Options (1) and (2) are essentially what is done on the IPPS.  Option (5)
+would lessen the amount of development but increase the number of tasks
+to be written.  I find option (6) desirable because of its
+increased generality but it would require a
+further definition of the data structures allowed and the syntax.
+.endhelp
diff --git a/noao/onedspec/doc/sys/Headers.hlp b/noao/onedspec/doc/sys/Headers.hlp
new file mode 100644
index 00000000..9bb394b7
--- /dev/null
+++ b/noao/onedspec/doc/sys/Headers.hlp
@@ -0,0 +1,189 @@
+.LP
+.SH
+Image Header Parameters
+.PP
+The ONEDSPEC package uses the extended image header to extract
+information required to direct processing of spectra. If the
+header information were to be ignored, the user would need to
+enter observing parameters to the program at the risk of
+typographical errors, and with the burden of supplying the
+data. For more than a few spectra this is a tedious job,
+and the image header information provides the means to eliminate
+almost all the effort and streamline the processing.
+.PP
+However, this requires that the header information be present,
+correct, and in a recognizable format. To meet the goal of
+providing a functional package in May 1985, the first iteration
+of the header format was to simply adopt the IIDS/IRS headers.
+This allowed for processing of the data which would be first
+used heavily on the system, but would need to be augmented at
+a later date. The header elements may be present in any order,
+but must be in a FITS-like format and have the following names
+and formats for the value fields:
+.sp 1
+.TS
+l c l
+l l l.
+Parameter	Value Type	Definition
+
+HA	SX	Hour angle (+ for west, - for east)
+RA	SX	Right Ascension
+DEC	SX	Declination
+UT	SX	Universal time
+ST	SX	Sidereal time
+AIRMASS	R	Observing airmass  (effective)
+W0	R	Wavelength at center of pixel 1
+WPC	R	Pixel-to-pixel wavelength difference
+NP1	I	Index to first pixel containing good data (actually first-1)
+NP2	I	Index to last pixel containing good data (last really)
+EXPOSURE	I	Exposure time in seconds (ITIME is an accepted alias)
+BEAM-NUM	I	Instrument aperture used for this data (0-49)
+SMODE	I	Number of apertures in instrument - 1 (IIDS only)
+OFLAG	I	Object or sky flag (0=sky, 1=object)
+DF-FLAG	I	Dispersion fit made on this spectrum (I=nr coefs in fit)
+SM-FLAG	I	Smoothing operation performed on this spectrum (I=box size)
+QF-FLAG	I	Flat field fit performed on this spectrum (0=yes)
+DC-FLAG	I	Spectrum has been dispersion corrected (0=linear, 1=logarithmic)
+QD-FLAG	I	Spectrum has been flat fielded (0=yes)
+EX-FLAG	I	Spectrum has been extinction corrected (0=yes)
+BS-FLAG	I	Spectrum is derived from a beam-switch operation (0=yes)
+CA-FLAG	I	Spectrum has been calibrated to a flux scale (0=yes)
+CO-FLAG	I	Spectrum has been coincidence corrected (0=yes)
+DF1	I	If DF-FLAG is set, then coefficients DF1-DFn (n <= 25) exist
+.TE
+.PP
+The values for the parameters follow the guidelines adopted for
+FITS format tapes. All keywords occupy 8 columns and contain
+trailing blanks. Column 9 is an "=" followed by a space. The value field
+begins in column 11. Comments to the parameter may follow a "/" after
+the value field.  The value type code is as follows:
+.RS
+.IP SX
+This is a sexagesimal string of the form '12:34:56   ' where the first
+quote appears in column 11 and the last in column 30.
+.IP R
+This is a floating point ("real") value beginning in column 11 and
+extending to column 30 with leading blanks.
+.IP I
+This is an integer value beginning in column 11 and extending to
+column 30 with leading blanks.
+.RE
+.sp 1
+.PP
+The parameters having FLAG designations all default to -1 to indicate
+that an operation has not been performed.
+The ONEDSPEC subroutines "load_ids_hdr" and "store_keywords" follow
+these rules when reading and writing spectral header fields.
+If not present in a header, load_ids_hdr will assume a value of zero
+except that all flags are set to -1, and the object flag parameter
+defaults to object.
+.PP
+When writing an image, only the above parameters are stored by store_keywords.
+Other header information is lost. This needs to be improved.
+.PP
+Not all programs need all the header elements. The following table
+indicates who needs what. Tasks not listed generally do not require
+any header information. Header elements not listed are not used.
+The task SLIST requires all the elements listed above.
+The task WIDTAPE requires almost all (except NP1 and NP2).
+The headings are abbreviated task names as follows:
+.sp 1
+.nr PS 8
+.ps 8
+.TS
+center;
+l l | l l | l l.
+ADD	addsets	COE	coefs	FIT	flatfit
+BSW	bswitch	COM	combine	REB	rebin
+CAL	calibrate	DIS	dispcor	SPL	splot
+COI	coincor	FDV	flatdiv	STA	standard
+.TE
+.sp 1
+.TS
+center, tab(/);
+l | l | l | l | l | l | l | l | l | l | l | l | l.
+Key/ADD/BSW/CAL/COI/COE/COM/DIS/FDV/FIT/REB/SPL/STA
+_
+HA// X////////// X/
+RA// X////////// X/
+DEC// X////////// X/
+ST// X////////// X/
+UT// X////////// X/
+AIRMASS// X////////// X/
+W0// X/ X/// X//// X/ X/ X/
+WPC// X/ X/// X//// X/ X/ X/
+NP1/////////// X///
+NP2/////////// X///
+EXPOSURE/ X/ X/// X/ X///// X///
+BEAM-NUM// X/ X//// X/ X/ X// X/ X//
+OFLAG// X////////// X/
+DF-FLAG//// X
+DC-FLAG// X//// X//// X/ X/ X/
+QD-FLAG//////// X/
+EX-FLAG// X/
+BS-FLAG// X/
+CA-FLAG/ X// X//////// X/
+CO-FLAG///// X//
+DFn//// X/
+.TE
+.nr PS 10
+.ps 10
+.bp
+.SH
+Headers From Other Instruments
+.PP
+The header elements listed above are currently created only when reading
+IIDS and IRS data from one of the specific readers: RIDSMTN and RIDSFILE.
+The time-like parameters, (RA, DEC, UT, ST, HA), are created in a
+compatible fashion by RCAMERA and RFITS (when the FITS tape is written
+by the KPNO CCD systems).
+.PP
+For any other header information, the ONEDSPEC package is at a loss
+unless the necessary information is edited into the headers with
+an editing task such as HEDIT. This is not an acceptable long term
+mode of operation, and the following suggestion is one approach to
+the header problem.
+.PP
+A translation table can be created as a text file which outlines
+the mapping of existing header elements to those required by the
+ONEDSPEC package. A mapping line is needed for each parameter
+and may take the form:
+.sp 1
+.RS
+.DC
+1D_param    default    hdr_param    key_start   value_start   type   conversion
+.DE
+.RE
+where the elements of an entry have the following definitions:
+.TS
+center;
+l l.
+1D_param	T{The name of the parameter expected by the ONEDSPEC package,
+such as EXPOSURE, OFLAG, BEAM-NUM.  T}
+
+default	T{A value to be used if no entry is found for this parameter.T}
+
+hdr_param	T{The string actually present in the existing image header to be
+associated with the ONEDSPEC parameter. T}
+
+key_start	T{The starting column number at which the string starts 
+in the header. T}
+
+value_start	T{The starting column number at which the string describing the
+value of the parameter starts in the header. T}
+
+type	T{The format type of the parameter: integer, real, string, boolean,
+sexagesimal. T}
+
+conversion	T{If the format type is string, a further conversion may 
+optionally be made to one of the formats listed under type. T}
+.TE
+.sp 1
+.PP
+A translation file can be built for each instrument and its
+peculiar header formats, and the file name associated with a
+package parameter. The two subroutines in ONEDSPEC dealing
+directly with the headers (load_ids_hdr and store_keywords)
+can be modified or replaced to access this file and
+translate the header elements.
+.endhelp
diff --git a/noao/onedspec/doc/sys/Onedspec.hlp b/noao/onedspec/doc/sys/Onedspec.hlp
new file mode 100644
index 00000000..85a3f20e
--- /dev/null
+++ b/noao/onedspec/doc/sys/Onedspec.hlp
@@ -0,0 +1,2219 @@
+.help spbasic
+.sh
+One Dimensional Package - Basic Operators
+
+.sh
+INTRODUCTION
+
+     The IRAF One Dimensional Package is intended to provide the basic
+tools required to reduce, analyze, and display data having a
+single dimension. This primarily refers to spectra, but may have
+applicability to time series photometry, or any other
+source of data which can be considered a simple vector.
+All such data will be referred to as spectra in the following discussion.
+Furthermore, the spectrum vector is assumed to be equally spaced
+along the independent variable (wavelength, channel, frequency,
+wavenumber,...). For the purposes of discussion, the independent
+variable will be referred to as wavelength but may be any of the
+possible physical transformations.
+
+     Spectra are to be stored as 2 dimensional IRAF floating point images
+having a single line
+and are therefore limited to lengths smaller than or equal to the
+largest representable positive integer. For 32 bit machines, this
+is about 2 billion points, so that disk space will likely be the
+operational limit.  The precision and dynamic range  for each pixel
+will be determined by the local machine.
+The second dimension of the spectrum is spatial, and therefore
+represents a special case of the long slit spectroscopic mode.
+
+     Each spectrum will, by default, be stored as a separate image
+file.  Alternatively, an association
+can be declared for a related set of spectra
+through a "data group" mechanism. A data group can be defined to
+contain any number of related spectra so that an operation can
+be specified for the group. For example, one can group a single
+night of IIDS spectra into a group labeled JAN28, and then
+wavelength linearize JAN28. This helps minimize
+the user interaction which would otherwise be repetitive, and
+also reduces the user bookkeeping required.
+
+     Data input to the package is provided through the DATAIO
+package. Tape readers will be provided for FITS, IIDS and IRS mountain
+formats, Text ("card-image"),  REDUCER and PDS. The descriptor fields
+included in these formats will be mapped into standard IRAF
+image header fields when possible. Special fields will be
+added to the image header to represent instrument
+related parameters.
+
+     Data output to tape (for visitor take home) will be
+either in FITS or text format.
+
+     A variety of graphics display options will be provided
+for both interactive use and for hardcopy generation.
+Scale expansion and contraction, labeling, multiple spectra
+plots, and axis limit specification are to be included in the
+options.
+
+     Specific reduction scripts will be provided to efficiently
+process raw data from the Kitt Peak instruments IIDS and IRS.
+
+
+.sh
+SCOPE OF SPECIFICATIONS
+
+This paper specifies the command format, parameters, and
+operations for the Basic contents of the One Dimensional
+Spectral Package. The Basic functions are those comprising the
+minimum set to reduce a large variety of spectra.
+More complicated operators and analysis functions
+are described in a companion paper on Intermediate Functions.
+Major projects in spectral analysis will be considered at
+a later date in the Advanced function set.
+
+The primary functions within the Basic operator set are:
+
+.ls 4 Transport
+Primarily magtape readers for the common tape formats. Included
+are FITS, IIDS/IRS, REDUCER, PDS, and Card-image formats.
+Tape writers will be initially limited to FITS and Card-image.
+.le
+.ls 4 Mathematical
+Add, subtract, multiply, divide spectra by spectra or constants.
+Apply functional operators such as log, exp, sqrt, sin, cos.
+Weighted sums and averages of spectra.
+.le
+.ls 4 Reduction operators
+Line identification, dispersion solution, flux calibration,
+coincidence correction, atmospheric extinction correction,
+flat fielding.
+.le
+.ls 4 Plotting
+Terminal package to expand, overplot, annotate plots. Hard
+copy package for printer/plotters.
+.le
+.ls 4 Utilities
+Header examination and modification. List, copy, delete spectra.
+Define, add, delete entries in a data group.
+.le
+.ls 4 Artificial spectra
+Generate ramps, Gaussian and Voigt lines, noise.
+.le
+
+These functions will be considered in detail in the following
+discussion.
+
+.ks
+A summary of the commands is given below:
+
+.nf
+rfits       -- Convert FITS data files to IRAF data files
+riids       -- Convert IIDS mountain tape format to IRAF data files
+rreducer    -- Convert Reducer format tape to IRAF data files
+rpds        -- Convert a PDS format tape to IRAF data files
+rtext       -- Convert a card-image text file to an IRAF image file
+wfits       -- Convert IRAF data files to FITS data format
+wtext       -- Convert an IRAF image file to a card-image text file
+.sp 1
+coin_cor    -- Correct specified spectra for photon coincidence
+line_list   -- Create a new line list, or modify an existing one
+mlinid      -- Manually identify line features in a spectrum
+alinid      -- Automatically locate spectral features in a spectrum
+disp_sol    -- Determine the dispersion relation for a set of spectra
+disp_cor    -- Linearize spectra having dispersion relation coefficients
+cr_flat     -- Create a flat field spectrum
+flt_field   -- Correct spectra for pixel-to-pixel variations
+std_star    -- Define the standard stars to be used for solving the 
+               extinction and system sensitivity functions
+crext_func  -- Create an extinction function from a set of observations
+crsens_func -- Create system sensitivity function
+ext_cor     -- Extinction correct specified spectra
+sens_cor    -- Correct the specified spectra for system sensitivity
+.fi
+.ju
+.ke
+
+.bp
+.sh
+TRANSPORT - INPUT
+
+Although the primary data input source for the near future
+will be magtape, direct links from other computers will
+be a likely source of input. The IRAF DATAIO package
+treats magtape as simple bit streams so that alternate
+input devices (e.g. disk, ethernet, phone lines) can also
+be accommodated with no programming modifications.
+
+This section describes the different formats to be made
+available in the initial release of the Spectroscopic
+package. Additional formats may be added if needed.
+
+In general, the following information will be copied to
+the standard image header: length of spectrum, title, 
+abscissa units, brightness units, reference pixel
+abscissa value and increment, right ascension and declination
+of telescope.
+
+Non-standard header parameters include but are not limited to:
+integration time, UT and LST of the observation, airmass (or 
+zenith distance), processing history, and comments.
+
+.sh
+FITS
+.ih
+NAME
+rfits -- Convert FITS data files to IRAF data files
+.ih
+USAGE
+rfits [source, filename, files]
+.ih
+DESCRIPTION
+FITS data is read from the specified source.
+The FITS header may optionally be printed on the standard
+output as either a full listing or a short description.  Image data may
+optionally be converted to an IRAF image of specified data type.
+
+Eventually all data from the mountain will be in FITS format,
+with the exception of time-critical data transfer projects
+and special applications. The IRAF FITS reader will
+copy the data to disk for most applications.
+
+.ih
+PARAMETERS
+.ls 4 fits_source
+The FITS data source.  If the data source is a disk file or an explicit tape file
+specification of the form mt*[n] where n is a file number then only that file
+is converted.  If the general tape device name is given, i.e. mta, mtb800, etc,
+then the files specified by the files parameter will be read from the tape.
+.le
+.ls filename
+The IRAF file which will receive the FITS data if the make_image parameter
+switch set.  For tape files specified by the files parameter the filename
+will be used as a prefix and the file number will be appended.   Otherwise,
+the file will be named as specified.  Thus,
+reading files 1 and 3 from a FITS tape with a filename of data will produce
+the files data1 and data3.  It is legal to use a null filename.  However,
+converting a source without a file number and with a null filename will cause
+a default file fits to be created.
+.le
+.ls files
+The files to be read from a tape are specified by the files string.  The
+string can consist of any sequence of file numbers separated by
+at least one of whitespace, comma, or dash.
+A dash specifies a range of files.  For example the string
+
+1 2, 3 - 5,8-6
+
+will convert the files 1 through 8.
+.le
+.ls print_header
+If this switch is set header information is printed on the standard output
+output. (default = yes)
+.le
+.ls short_header
+This switch controls the format of the header information printed when the
+print_header switch is set.
+When the short_header switch is set only the output filename,
+the FITS OBJECT string, and the image dimensions are printed.
+Otherwise, the output filename is followed by the full FITS header.
+(default = yes)
+.le
+.ls bytes_per_record
+The FITS standard record size is 2880 bytes which is the default for this
+parameter.  However, non-standard FITS tapes with different record sizes can
+be read by setting the appropriate size.
+.le
+.ls make_image
+This switch determines whether FITS image data is converted to an IRAF image
+file.  This switch is set to no to obtain just header information with the
+print_header switch. (default = yes)
+.le
+.ls data_type
+The IRAF image file may be of a different data type than the FITS image data.
+The data type may be specified as s for short, l for long, and r for real.
+The user must beware of truncation problems if an inappropriate data type is
+specified.  If the FITS keywords BSCALE and BZERO are found then the image
+data is scaled appropriately.  In this case the real data type may be most
+appropriate.
+.le
+.sh
+For spectroscopic applications, the parameter data_type would be
+specified as r for real, and the filename would probably be assigned
+as the "group" name as well. (see section on data groups.)
+
+
+.sh
+IIDS/IRS
+.ih
+NAME
+riids -- Convert IIDS mountain tape format to IRAF data files
+.ih
+USAGE
+riids [source, filename, form, records]
+.ih
+DESCRIPTION
+IIDS/IRS mountain format data is read from the specified source.
+The header may be printed
+on the standard output either in short form, label only, or a long
+form containing telescope and time information, processing flags,
+and wavelength solution values.
+
+Either raw or "mountain reduced" tapes can be specified with the
+parameter form.
+
+The IIDS format is destined for extinction. A FITS format will
+replace the current tape format, but an interim period will exist
+for which this tape reader must exist.
+.ih
+PARAMETERS
+.ls 4 iids_source
+The data source, either magtape or a data stream (e.g. disk file).
+The current IIDS tape format produces tapes having only a single
+file. If the source is a magtape, the general tape specification
+mt*[n], should either have n specified as 1, or [n] should not be present.
+.le
+.ls 4 filename
+The IRAF file which will contain the data if the make_image parameter
+is set. The filename will be used as a prefix and the record number
+will be used as the suffix. Thus reading records 1 through 100 from
+an IIDS tape with a file name of 'blue' will produce 100 files having
+names blue1, blue2, ..., blue100. A null filename will default to 'iids'.
+.le
+.ls 4 form
+This string parameter defines the tape to be either 'new' or 'red'.
+The 'new' designation refers to tapes made after January 1977, and
+'red' refers to mountain reduced tapes. (default = 'red')
+.le
+.ls 4 records
+The records specified by this string parameter will be copied to disk.
+The syntax is identical to that for the files parameter of the FITS reader.
+.le
+.ls 4 print_header
+If this switch is set, header information is printed on the standard
+output. (default = yes)
+.le
+.ls 4 short_header
+If this switch is set, only the filename and label information will be printed
+if the print_header switch is also set. If set to 'no', the long form
+will be printed. (default = yes)
+.le
+.ls 4 make_image
+See definition of this parameter under FITS.
+.le
+
+
+.sh
+REDUCER
+
+REDUCER tapes require several considerations beyond the
+previous simple formats. The spectra actually consist of
+many spectra having lengths of 4096 but slightly different
+spectral sampling. Thus, the reader can create many small
+independent spectra, or interpolate the data onto a common
+spectral scale to create a single large spectrum.
+The latter alternative seems to be more generally useful,
+unless the interpolation process introduces significant errors.
+Probably the initial reader will provide both options.
+   
+A second consideration is the 60 bit word length conversion.
+The IRAF images are limited to 32 bit reals on most 32 bit machines.
+Some loss of precision and dynamic range will result while reading REDUCER
+format data.
+   
+Also, there may be a considerable number (~100) of non-standard header
+elements. These can be handled in a normal fashion, and tools
+will be provided to extract or modify these elements as needed.
+New elements may be added as well.
+
+.ih
+NAME
+rreducer -- Convert Reducer format tape to IRAF data files
+.ih
+USAGE
+rreducer [source, filename, files]
+.ih
+DESCRIPTION
+REDUCER format data is read from the specified source.
+The header may be printed on the standard output either in short form
+consisting of the 80 character ID field, or a long form containing some
+selection (to be agreed upon) of the many header elements.
+
+Either a single long spectrum requiring interpolation
+to match the spectral characteristics of the first data block, or
+multiple short spectra having individual spectral parameters can
+be specified with the hidden parameter, interp.
+Interpolation is performed via a fifth order polynomial.
+
+Subsets of the spectrum can be selected with the blocks string
+parameter. This specifies which blocks in the file are to be extracted.
+
+.ih
+PARAMETERS
+.ls 4 reducer_source
+The data source, either magnetic tape or a data stream (e.g. disk
+file). See the definition of fits_source above for a description
+of how this parameter interacts with the files parameter.
+.le
+.ls 4 filename
+The filename which will contain the data.
+See the definition of this parameter under FITS.
+If no name is given, the default of 'reducer' will be used.
+.le
+.ls 4 files
+The files to be read from tape are given by the files string. See
+the description of this parameter under FITS.
+.le
+.ls 4 print_header
+If this switch is set header information will be printed on the
+standard output. (default = yes)
+.le
+.ls 4 short_header
+If this switch is set only the filename and the first 60 characters
+of the 80 character ID field will be printed if the print_header
+switch is also set. If set to no, the long form of the header
+will be printed, containing selected elements of the 100 word
+header record. (default = yes)
+.le
+.ls 4 make_image
+See the definition of this parameter under FITS.
+.le
+.ls 4 interp
+If this switch is set, a single long spectrum is produced. If
+set to no, multiple spectra will be generated, one for each
+header-data block. The resulting filenames will have suffixes
+of '.1' , '.2' ... '.n'. For example, if the given filename is
+fts and the tape file is 2, the resulting spectrum will be
+fts2 if interp is set to yes, but will be fts2.1, fts2.2, and
+fts2.3 if there are 3 header-data block sets and interp is set
+to no. (default = yes).
+.le
+.ls 4 blocks
+This string parameter allows selected extraction of the
+specified header-block sets, rather than the entire spectrum.
+Thus subsets of the spectrum may be extracted. The parameter
+specifies the starting block and ending block within a tape file.
+If an end-of-file is found prior to exhaustion of the
+specification, reading is terminated.
+For example, the string '12 19' specifies that the eight sets
+starting with the twelfth block are to be extracted to
+form the spectrum. (default = '1 32767', or all)
+.le
+
+
+.sh
+PDS
+
+Tapes from the new PDS 11/23 system will be either FITS or
+old format PDS 9 track tapes. This reader will accept the
+old format tapes which are based on the PDP 8 character set
+and either 10 or 12 bit format.
+
+.ih
+NAME
+rpds -- Convert a PDS format tape to IRAF data files
+.ih
+USAGE
+rpds [source, filename, files]
+.ih
+DESCRIPTION
+PDS format data is read from the specified source. The header
+may be printed on the standard output either in short form
+consisting of the 40 character ID field, filename, and size,
+or in long form including raster parameters and origin.
+
+Because PDS data is limited to no more than 12 bit data, the output image
+will be short integers if the number of lines ("scans") implies
+two dimensional data. If one dimensional data is implied, the
+output image will be converted to reals.
+.ih
+PARAMETERS
+.ls 4 pds_source
+The data source, either magtape or a data stream. See the definition
+of fits_source above for a description of how this parameter interacts
+with the files parameter.
+.le
+.ls 4 filename
+If no filename is given, the default of 'pds' will be used.
+.le
+.ls 4 files
+See the definition of this parameter under FITS.
+.le
+.ls 4 print_header
+If this switch is set, header information will be printed on the
+standard output. (default = yes).
+.le
+.ls 4 short_header
+If this switch is set, only the filename, size, and the 40 character ID
+field will be printed if the print_header switch is also set.
+If set to no, the long form of the header will be printed
+containing the full information block (delta X, delta Y, scan type,
+speed, origin, corner, travel). (default = yes)
+.le
+.ls 4 make_image
+See the definition of this parameter under FITS. (default = yes)
+.le
+.ls 4 data_type
+Specifies the IRAF image file output data type. Normally one
+dimensional PDS data (NSCANS=1) will be stored as real and
+two dimensional PDS data (NSCANS>1) will be stored as short.
+The data type may be specified as s (short), l (long), or r
+(real).
+.le
+
+
+.sh
+TEXT (Read Card-Image)
+
+Card-image tapes are probably the most portable form of data transport.
+Unlike FITS, there is no standard for internally documenting the
+contents of the text file. Header information is essentially
+lost. This makes card-image data transfer a relatively unattractive
+format.
+
+
+.ih
+NAME
+rtext -- Convert a card-image text file to an IRAF image file.
+.ih
+USAGE
+rtext [source, filename, files, ncols, nlines, label]
+.ih
+DESCRIPTION
+The card-image text file specified by the source parameter is 
+converted to an IRAF image file. The file is read in a free form
+mode (values separated by spaces) converting data along lines (1-ncols) first.
+No header information is stored except for the image size and
+the label.
+
+If additional header information is to be stored, the standard
+image header utility must be used.
+
+Pixel values exactly equal to some constant will be assumed to be blanks
+if the blank switch is set to yes. The flag value for blanks can be
+set with the blank_value parameter.
+
+.ih
+PARAMETERS
+.ls 4 text_source
+The input data source. See the definition of this parameter under FITS.
+.le
+.ls 4 filename
+The IRAF file which will contain the image data if the make_image
+switch is set. If no filename is given, the default of 'text'
+will be used.
+.le
+.ls 4 files
+See the definition of this parameter under FITS.
+.le
+.ls 4 ncols
+The number of columns of data which describe the image extent.
+.le
+.ls 4 nlines
+The number of lines (or 'rows') of data which describe the image extent.
+For one dimensional spectra, this parameter will be 1.
+.le
+.ls 4 label
+This string parameter becomes the image identification label.
+Up to 80 characters may be stored.
+.le
+.ls 4 print_header
+If this switch is set, header information consisting of the filename,
+image label, and image size will be printed on the standard output.
+(default = yes)
+.le
+.ls 4 make_image
+If this switch is set, an IRAF image will be created. (default = yes)
+.le
+.ls 4 data_type
+The IRAF image may be either s (short), l (long), or r (real).
+(default = r)
+.le
+.ls 4 card_length
+The number of columns on the "card" in the card-image file.
+(default = 80)
+.le
+.ls 4 blank_value
+The value used to flag blank pixels if the blank switch is set to yes.
+(default = -32767)
+.le
+.ls 4 blank
+If this switch is set to yes, any pixel having exactly the value
+specified by the parameter blank_value will be flagged as a blank
+pixel. If set to no, all pixel values are assumed to be valid.
+.le
+
+
+.bp
+.sh
+TRANSPORT - OUTPUT
+
+The primary format for take away tapes will eventually be FITS.
+Because many facilities currently cannot read FITS format,
+the card-image format will also be provided.
+
+.sh
+FITS
+.ih
+NAME
+wfits -- Convert IRAF data files to FITS data format
+.ih
+USAGE
+wfits [destination, filename, files]
+.ih
+DESCRIPTION
+Data is read from the specified filename(s) and written to the
+destination, usually a magnetic tape specification. 
+A short header consisting of the filename, size, and label
+may optionally be printed on the standard output.
+
+The data will be automatically scaled to either 16 or 32 bit integer format
+(BITPIX = 16 or 32) depending on the number of bits per pixel in the
+image data, unless the bitpix parameter is specified
+otherwise. The scaling parameters may be forced to
+exactly represent the original data (BSCALE = 1.0, BZERO = 0.0)
+by setting the scale switch to no.
+
+If only the header information is to be copied to the destination,
+the write_image parameter can be set to no. If this is the case,
+then the NAXIS FITS keyword will be assigned the value of 0;
+otherwise the value for
+NAXIS will be taken from the IRAF image header.
+
+Each non-standard header element will be written into the FITS file
+in a form to be determined. These elements may be entered as FITS
+COMMENT records, or perhaps added to the file as FITS "special
+records".
+
+Other keywords will be written following standard FITS specifications.
+A few special cases will be set as follows:
+
+.ls 4 NAXISn
+The NAXIS1, NAXIS2, ... NAXISn values will be taken from the
+image header
+.le
+.ls 4 OBJECT
+The first 60 characters of the image label will be used.
+.le
+.ls 4 BLANK
+Blank pixels will be written to tape having the IRAF value for
+indefinite appropriate to 8, 16, or 32 bit integers.
+.le
+.ls 4 ORIGIN = 'KPNO IRAF'
+.le
+
+.ih
+PARAMETERS
+.ls 4 fits_destination
+The data destination, usually a magnetic tape, but may be a disk
+file or STDOUT. If magtape,
+the tape should be specified with a file number of either 1
+or "eot". The file number refers to the file which will be written.
+Thus a file number of 2 would overwrite file 2. If the tape already
+has data written on it, the safest specification would be "eot".
+This forces the tape to be positioned between the double end-of-tape
+marks prior to writing.
+.le
+.ls 4 filename
+The IRAF filename providing the root for the source name. The files
+string, if given, will be used as the suffix for the file names
+to be written to tape. For example, if the filename is given as
+"image", and the files string is "1 -5", then files image1, image2,
+image3, image4, and image5 will be written to the destination
+in FITS format. If the files string is empty, only the specified
+filename will be converted.
+.le
+.ls 4 files
+See the definition of this parameter under the FITS reader.
+.le
+.ls 4 print_header
+If this switch is set, a short header will be printed on the
+standard output for each image converted. (default = yes)
+.le
+.ls 4 write_image
+If this switch is set to no, only header information will be
+written to the destination, but no image data.
+By using this parameter,
+one can generate a FITS tape containing header information only
+and may be used as a means for examining the IRAF image header
+or for generating a table of contents on a tape prior to writing
+the data. (default = yes)
+.le
+.ls 4 bitpix
+This parameter must be either 8, 16, or 32 to specify the
+allowable FITS pixel sizes.
+.le
+.ls 4 scale
+If this switch parameter is set to no, the FITS scaling
+parameters BSCALE and BZERO will be set to 1.0 and 0.0
+respectively. The data will be copied as it appears in the
+original data, with possible loss of dynamic range.
+Values exceeding the maximum value implied by the bitpix
+parameter will be set to the maximum representable value.
+(default = yes)
+.le
+
+
+.sh
+TEXT (Write Card-Image)
+
+Although this format is easily readable by the destination
+machine, there is no real standard for encoding information,
+neither the image data itself nor the descriptive parameters.
+
+.ih
+NAME
+wtext -- Convert an IRAF image file to a card-image text file
+.ih
+USAGE
+wtext [destination, filename, files]
+.ih
+DESCRIPTION
+Data is read from the specified filename(s) and written to
+the destination, usually a magnetic tape. The data will be
+blank padded, ASCII in a format consistent with the data type
+of the image pixels, (integer or floating point).
+A short header description, consisting of the filename
+being converted and the image label, may optionally be printed
+on the standard output.
+
+The column length of the "card" may be changed from the default
+of 80 using the card_length parameter, and the field width
+to be allocated for each data element may be changed from the
+default of 10 columns by setting the field_width parameter.
+
+If the data are integers, the equivalent of the FORTRAN format
+I<field_width> will be used;
+if the data are reals, the equivalent of the FORTRAN format
+1P<n>E<field_width>.3
+will be used, where n is the number of elements which can
+be output into one card length. For the default values of
+card_length = 80, and field_width = 10, n will be 8. (1P8E10.3).
+
+Several cards may be written as a single "block" for
+improving the efficiency on magtape. Reasonable efficiency (80 percent)
+is attained with a blocking factor of 50, but this value
+may be modified by changing the parameter blocking_factor.
+If the last block is unfilled, it will be truncated to the
+minimum number of card images required to flush the data.
+
+A legitimate value must be defined to represent blank pixels.
+The parameter blank_value is used to define this value and
+defaults to -32767.
+
+.ih
+PARAMETERS
+.ls 4 text_destination
+See the definition for fits_destination for a description of this
+parameter.
+.le
+.ls 4 filename
+See the definition of this parameter under RFITS.
+.le
+.ls 4 files
+See the definition of this parameter under RFITS.
+.le
+.ls 4 print_header
+If this switch is set, a short header is printed for each
+file converted. (default = yes)
+.le
+.ls 4 card_length
+The number of columns on the "card" to be generated. (default = 80)
+.le
+.ls 4 field_width
+The number of columns on the "card" to be allocated for each pixel value.
+(default = 10)
+.le
+.ls 4 blocking_factor
+The number of card images to be written as a single blocked record.
+(default = 50)
+.le
+.ls 4 blank_value
+The value to be assigned to blank pixels for the purpose of
+representing them on the card image. (default = -32767)
+.le
+.bp
+
+
+.sh
+MATHEMATICAL OPERATORS
+
+Because spectra are stored as IRAF images, the standard image
+calculator utility provides the basic arithmetic services.
+For example, to create a spectrum (called spavg) which is the average of two
+other spectra (sp1 and sp2), one can enter the command:
+.ls 8 cl>imcalc "spavg = (sp1 + sp2) / 2"
+.le
+
+Other arithmetic operations are performed in a similar fashion.
+The general form of the command string is
+output_image = expression where "expression" may consist of:
+.ls 8 1. Spectra or segments of spectra
+A segment of a spectrum is specified by the notation spectrum[x1:x2]
+where x1 and x2 are pixel indices along the spectrum. For example,
+to create a spectrum which is the difference of the first 100
+pixels of two other spectra, the following command would be used:
+.ls 16 cl> imcalc "spdiff = sp1[1:100] - sp2[1:100]"
+.le
+An option to specify wavelength delineated segments may be added
+if this appears generally feasible.
+.le
+.ls 8 2. Numeric constants
+.le
+.ls 8 3. Data group names
+If an operation is performed on a data group, the output
+will be a new data group containing spectra which have been
+individually treated by the specified calculation.
+For example, if JAN28 is a group containing 100 congruent spectra
+and response is the instrumental response as a function of
+wavelength as determined from a set of standards, then
+the after the following command is entered:
+.ls 16 cl> imcalc "JAN28X = JAN28 * response"
+.le
+
+a new data group will be generated containing 100 spectra which
+have been calibrated for the instrument response. The new spectra will
+be given names JAN28X1 through JAN28X100.
+.le
+.ls 8 4. Intrinsic functions
+.ks
+The following intrinsic functions are to be provided:
+
+.nf
+    abs      atan2    cos      int      min      sin       
+    acos     ceil     cosh     log      mod      sinh      
+    aimag    char     double   log10    nint     sqrt      
+    asin     complex  exp      long     real     tan       
+    atan     conjug   floor    max      short    tanh      
+.fi
+.ke
+.le
+
+Expression elements are to be
+separated by arithmetic and boolean operators (+,-,*,/,**,<,>,<=,=>,==,!,!=). 
+The boolean operators provide a means to generate masks.
+
+Rules governing operations on non-congruent spectra are not yet fully defined.
+.bp
+
+.sh
+REDUCTION OPERATORS
+
+Most of the reduction operators discussed in this section are
+intended for spectra of the IIDS/IRS class, although they
+are sufficiently general to accommodate data obtained with
+the CryoCam (either multi-aperture or long-slit mode), Echelle,
+Coude Feed, and photographic (PDS) instruments. Some 
+application to FTS data is also feasible.
+
+It is intended that many of these operators will never be
+directly executed by users, but that they will be driven by
+CL command scripts tuned for individual instruments.
+In some cases the scripts will be fairly elaborate and extensive
+to lead new users through the reduction phase along a reliable
+path.
+
+It will no doubt be necessary to either modify some
+of these operators, or create more specific operators for
+certain other instruments. These operators should be considered
+a sample of what will eventually be available in this package. 
+
+The basic path which most spectroscopic data follows is:
+
+.ls 4 1.
+Coincidence Correction.
+.ls
+Many detectors can respond to incoming photevents at a limited
+rate. Once an event occurs, the detector cannot respond for some
+instrument dependent period, or dead-time. If events occur during
+this period, they will not be counted. If the event rate
+does not greatly exceed the detector limits, the uncounted events
+can be corrected for statistically.
+
+For many detectors, the coincidence correction is a well
+determined function and can be applied to the raw data
+to produce a reasonably corrected spectrum.
+.le
+.le
+.ls 4 2.
+Wavelength linearization.
+.ls
+Few instruments produce spectra having pixel to pixel wavelength
+differences which are constant across the entire spectrum.
+For subsequent reduction and analysis purposes, it is
+desirable to rectify the spectra. This is done by mapping the spectrum
+from the non-linear wavelength coordinate to a linear one.
+It is also desirable to provide a means of forcing the mapping
+to a grid which is common to many observations, and in some cases,
+to observations acquired with other instruments as well.
+
+The processes required for the mapping are outlined below.
+
+.le
+.ls 4 a.
+Manually identify a small number of spectral features having
+known wavelengths thereby creating a table of wavelength as
+a function of pixel number.
+.le
+.ls 4 b.
+Compute estimated relationship between wavelength and pixel number
+.le
+.ls 4 c.
+Automatically locate many features found in a user definable line list.
+Optionally locate additional features from other spectra using an alternate
+line list. (This allows spectra from several different sources to be used
+for the wavelength calibration, such as arc lamps, night/day sky.)
+.le
+.ls 4 d.
+Compute improved relationship between wavelength and pixel number.
+.le
+.ls 4 e.
+Perform 2.c. and 2.d. for all other spectral entries in the wavelength
+calibration data group.
+.le
+.ls 4 f.
+Compute relationship for wavelength as a function of pixel number and time (or
+zenith distance, or some other flexure parameter) as deduced from 2.e.
+.le
+.ls 4 g.
+Apply inverse of wavelength function to a data group. This requires
+interpolation of the data at pixels having fixed steps in wavelength.
+The start wavelength and the step size must be user definable.
+The interpolation may be via a polynomial of a user specified order (typically
+1 to 5), or a more sophisticated interpolator. The linearization
+in wavelength may also be a simple rebinning of the data to exactly preserve
+photon statistics.
+.le
+.le
+.ls 4 3.
+Field flattening.
+.ls
+Pixel to pixel sensitivity variations and other small scale
+fluctuations are removed by dividing the object spectra by the spectrum of
+a continuum source. The latter spectrum should have a very high
+signal-to-noise ratio so as not to introduce additional uncertainties
+into the data.
+
+If the spectrum of the continuum source has much low frequency
+modulation,
+it may be necessary to filter these variations before the division is performed.
+Otherwise fluctuations not characteristic
+of the instrument response may be introduced, and may be difficult to remove
+during the subsequent flux calibration process.
+.le
+.le
+.ls 4 4.
+Sky Subtraction
+.ls
+Except for extremely bright sources, all spectra require that the
+spectrum of the night sky be removed. In some cases, sky will
+be the dominant contributor to the raw spectrum.
+Sky subtraction is a simple subtraction operation and can be
+accomplished with the image calculator tools.
+.le
+.le
+.ls 4 5.
+Extinction Correction
+.ls
+The effects of the Earth's atmosphere produce a wavelength dependent
+reduction of flux across the spectrum. The extinction function
+is approximately known from extensive photometric measurements
+obtained at the observatory over a period of many years. But on
+any given night this function may deviate from the average, sometimes
+significantly. If the spectroscopic observer has acquired the necessary
+data, it is possible to solve for the extinction function directly.
+
+Therefore, it should be possible for the user to either derive the
+extinction function, input a user-defined function, or use the
+standard average function and subsequently correct spectra for the
+effects of the atmosphere as described by that function and the effective
+observing airmass. (Note that because  exposures may be quite long, the
+effective airmass must be calculated as a function
+of position on the sky.)
+.le
+.le
+.ls 4 6.
+Flux Calibration (Correction for Instrument Response)
+.ls
+By observing objects having known wavelength dependent flux
+distributions, it is possible to determine the sensitivity
+variations of the instrument as a function of wavelength.
+Usually several standards are observed for each group of data
+and these must be averaged together after corrections for
+"grey shift" variations (wavelength independent flux reductions
+such as those introduced by thin clouds).
+
+Although the actual flux of the standards is generally known only
+for a limited selection of wavelengths, the instrument response
+usually varies smoothly between those wavelengths and a smooth
+interpolator generally provides satisfactory calibration values
+at intermediate wavelengths.
+
+In some cases, the system sensitivity response may be known
+from other observations, and the user will be allowed to directly
+enter the sensitivity function.
+.le
+.le
+
+The above reduction path is primarily tuned to IIDS/IRS style data.
+Other instruments may require additional or alternate steps.
+It may be necessary for multiaperture Cryocam spectra, for example,
+to undergo an additional hole to hole sensitivity correction
+based on the total sky flux through each hole.
+
+The tasks performing the procedures outlined above will be described
+in more detail in the following discussion.
+
+.sh
+COINCIDENCE CORRECTION
+.ih
+NAME
+coin_cor -- Correct specified spectra for photon coincidence
+.ih
+USAGE
+coin_cor [filename, files, destination, dead_time]
+.ih
+DESCRIPTION
+The spectra specified by the root filename and the files parameter
+are corrected for photon counting losses due to detector dead-time.
+The corrected spectra are written to filenames having the root
+specified by the destination.
+
+The correction, if typical of photomultiplier discriminators,
+is usually of the form:
+
+.br
+         Co(i) = C(i) exp[C(i) dt],
+.br
+         dt = t/T,
+.br
+
+where Co(i) is the corrected count at pixel i, C(i) is the raw count,
+t is the detector/discriminator dead-time, and T is the
+exposure time at pixel i.
+
+Clearly, the correction factor can become extremely large when the
+count rate, C(i)/T, is large compared with the dead-time, t.
+The above formula cannot be expected to
+exactly remove the effects of undetected photo-events when
+large corrections are required.
+
+The exposure time will be read from the image header.
+If no value exists, or if the value is less than or equal to
+zero, a request from standard input will be issued for this parameter.
+
+Because each detector may have unique coincidence properties,
+this routine may be package dependent.
+.ih
+PARAMETERS
+.ls 4 filename
+See the definition of this parameter under RFITS.
+.le
+.ls 4 files
+See the definition of this parameter under RFITS.
+.le
+.ls 4 destination
+The IRAF filename providing the root for the name of the result
+spectra. The files parameter, if specified, will be used for the
+suffix. If the filename parameter is actually a data group name,
+the destination name will be used to create a new data group
+containing spectra having IRAF filenames with the destination
+group name as a root and a suffix starting with 1 and incremented for
+each converted spectrum.
+.le
+.ls 4 dead_time
+The value of this parameter, in seconds, represents the detector
+dead-time.
+.le
+.ls 4 print_header
+If this switch is set, a short header will be printed on the
+standard output for each spectrum corrected. (default = yes)
+.le
+.ls 4 exposure
+This parameter should be entered into the image header. If not
+present or not realistic, a request is made from standard input.
+.le
+
+.sh
+WAVELENGTH LINEARIZATION
+
+A package of routines is required to perform the operations
+leading to linearized data. These include:
+.ls 4 1. Spectral line list definition and editing facility
+.le
+.ls 4 2. Manual line identifier using graphics cursor.
+.le
+.ls 4 3. Automatic line identifier using preliminary identifications
+from manual identifier and locating lines from the predefined list.
+.le
+.ls 4 4. Computation of dispersion relationship as a function of
+pixel coordinate and a flexure parameter, probably zenith distance.
+.le
+.ls 4 5. Linearization of spectra according to dispersion relation.
+Correction can be to either a linear or logarithmic dispersion in
+the pixel coordinate.
+.le
+
+Perhaps the most critical aspect of determining the dispersion
+relation is the algorithm for locating spectral line centers.
+A variety of techniques are available, and some testing will
+be required before adopting a standard scheme. Probably several
+algorithms will be available and switch selectable at the command
+level.
+
+.sh
+LINE LIST PREPARATION
+.ih
+NAME
+line_list -- Create a new line list, or modify an existing one
+.ih
+USAGE
+line_list [filename, option]
+.ih
+DESCRIPTION
+The line list specified by the IRAF filename parameter will be
+either created, listed, or modified according to the option
+given. The IRAF database facility will be used to manage the
+line list file.
+
+Each entry within the list will contain an identification tag (e.g. HeII)
+a reference value (e.g. wavelength, frequency, wavenumber), and a weighting
+value such as 1.0 or 2.0 to be used later in the least-squares fitting.
+An optional descriptive header may be associated with the line list.
+(e.g. "HeII arc from 3500 to 11,000A")
+
+Either the header, entry identifier or value may be changed
+if the modify option is specified. Deletion or addition of
+entries is also possible with the appropriate option flags
+specifications.
+.ih
+PARAMETERS
+
+.ls 4 filename
+The IRAF filename to be assigned to the line list. The list will
+referenced by this name thereafter.
+.le
+.ls 4 option
+This string parameter determines the action of the line list task.
+If no option is specified, the default action is to list the
+specified line list on the standard output if the line list
+exists; if it does not exist, a new line list will be created
+with the given name.
+.ls 4 = create
+The identifications and values for the line list are read from
+the standard input on a record by record basis. Each input
+record contains data for one line according to the format:
+.br
+.ls 4 identification value
+.le
+.le
+.ls 4 = header
+A descriptive header is read from the standard input.
+.le
+.ls 4 = list (default)
+The line list is listed on the standard output.
+.le
+.ls 4 = add
+Additional entries to the list are read from the standard input.
+.le
+.ls 4 = delete
+The entries defined by the values read from the standard input
+are deleted from the line list. The entries deleted will be those
+having values nearest the entered value, unless the absolute
+difference from the listed value is too large. For example, one
+can enter 5015 to delete the helium line at 5015.675, but entering
+5014 would result in an error message that no match could be found.
+.le
+.ls 4 = id
+The entries defined by values entered as for delete will be modified.
+Input is expected in the format:
+.br
+approxvalue  newidentifier
+.le
+.ls 4 = value
+As for option = id except that the input format contains
+the newvalue instead of the newidentifier.
+.le
+.ls 4 = weight
+As for option = id except that the nput format contains the newweight
+instead of the newidentifier.
+.le
+.le
+
+.sh
+MANUAL LINE IDENTIFICATION
+
+This routine provides the option of manually identifying the locations
+of spectral features by either setting a graphics cursor interactively,
+or by entering a list of feature positions.
+
+The primary uses for this routine are to identify features of known
+wavelength in preparation for a dispersion solution, and also to
+identify features in linearized spectra for velocity measurements.
+
+.ih
+NAME
+mlinid -- Manually identify line features in a spectrum
+.ih
+USAGE
+mlinid [filename, files]
+.ih
+DESCRIPTION
+A list file is created for each of
+the spectra specified by the IRAF filename parameter and files string
+containing the locations of spectral features and their associated
+reference value (e.g. wavelength, frequency, wavenumber).
+If invoked as an interactive task from a graphics terminal,
+the spectra will be displayed and cursor input requested to ascertain
+the approximate position of the feature. An improved position will
+be obtained via one of the line centering algorithms, and
+a request will be made for the reference value of the feature.
+The requests continue until EOF is detected.
+The name of the created list file is added to the spectral image
+header.
+
+Positions of features are given in the coordinate system defined
+by the standard image header entries CRPIX and CDELT
+defining the reference pixel and the
+pixel to pixel distance. For raw spectra these values simply define
+the pixel position of the feature. For dispersion corrected spectra
+these values define the position of the feature in wavelength units.
+
+If invoked as a background task, or from a non-graphics terminal,
+additional requests for the cursor x-coordinate  and intensity
+will be made from the standard input.
+
+The procedure is repeated for all specified spectra.
+
+Because the dispersion solution may be a function of an additional
+instrument dependent parameter (e.g. zenith distance),
+the driving package script can indicate the header entry to be
+used as the second parameter. Values for this parameter, if present,
+will be written to the output list file.
+.ih
+PARAMETERS
+
+.ls 4 filename
+See the definition of this parameter under RFITS.
+.le
+.ls 4 files
+See the definition of this parameter under RFITS.
+.le
+.ls 4 cur (x,y)
+This is a list structured parameter of type "graphics cursor".
+The list contains the approximate values of the pixel
+coordinate for the spectral features to be identified
+and the intensity value of the continuum at the feature. If the
+task is invoked from a graphics terminal in an interactive mode,
+values for this parameter will be read from the terminal's
+graphics cursor.
+.le
+.ls 4 value
+This is a list structured parameter containing the reference values
+for the spectral features to be identified. If the task is invoked in
+an interactive mode, the user will be prompted for these values.
+.le
+.ls 4 center_option
+This string parameter controls which algorithm is to be used during
+the improved centering phase of the process. (default = cg)
+.ls 4 = cg
+This specifies a center of gravity algorithm defined as the
+first moment of the intensity above the continuum level
+across the spectral feature.
+The integrals are evaluated using the trapezoidal rule and
+the intensity will be weighted by the square root of the intensity
+if the switch parameter cgweight is set to yes. The integral
+is evaluated from the approximate position defined by x cursor position
+plus and minus the number of pixels specified by the parameter
+cgextent.
+.ls 4 cgweight
+This switch defines whether a weighted moment is used in the
+center of gravity centering algorithm. (default = yes)
+.le
+.ls 4 cgextent
+This integer parameter defines the limits of the integrals in the
+center of gravity centering algorithm. The integral extends from
+the approximate position minus the extent to the approximate position
+plus the extent in units of pixels. (default = 5).
+.le
+.le
+.ls 4 = parabola
+This specifies that the centering algorithm is to be a parabolic
+fit to the central 3 pixels. The improved center is taken as the
+center of the parabola. The central 3 pixels are defined as the
+most extreme local pixel plus and minus one pixel. The most extreme
+local pixel is that pixel nearest the approximate center having the
+greatest deviation from the local average value of the spectrum. The
+extent of "local" is taken as plus and minus the parameter parextent.
+.ls 4 parextent
+This integer parameter defines the extent in units of pixels
+of the search for a local extreme pixel. (default = 3)
+.le
+.le
+.ls 4 = gauss
+(This algorithm will not be implemented in the initial system release.)
+This specifies that the centering algorithm is to be a Gaussian
+fit to the region near the approximate center. The fit is
+made to a region specified by the parameter gextent. Because
+this is a three parameter non-linear least-squares fit
+(center, width, peak intensity), it is likely to
+be slow. It may also produce poor results with noisy data
+although centering on high signal to noise data should be
+excellent.
+.ls 4 gextent
+This integer parameter specifies the extent in pixels of the Gaussian fit.
+It may be necessary to include a significant region of continuum.
+(default = 9)
+.le
+.le
+.ls 4 = none
+If this option is chosen, no improvement to the approximate center
+will be made. This may be useful for asymmetric and weak features
+where the other techniques can be systematically incorrect.
+.le
+.ls 4 second_order
+This string parameter defines the name of the image header entry to be
+used as the second order correction parameter in the dispersion
+solution. Values for this parameter, if present, are read from the image header
+and written to the output list file. Examples of values are zenith_distance,
+sidereal_time, instr_temp. (default = none)
+.le
+
+.sh
+AUTOMATIC LINE IDENTIFICATION
+
+This task allows a user to locate a set of spectral features defined
+in a previously prepared list.
+
+.ih
+NAME
+alinid -- Automatically locate spectral features in a spectrum
+.ih
+USAGE
+alinid [filename, files, mfilename, mfiles, list]
+.ih
+DESCRIPTION
+A list file is created for each of the spectra specified by the
+IRAF filename and files parameters. The file will contain
+the positions of the features defined in the line list file
+specified by the list parameter. The name of the list file
+will be added to the spectral image header.
+
+A preliminary estimate of the
+relationship of feature position as a function of feature
+wavelength is obtained from the list file(s) created by the
+task MLINID and defined by the parameters mfilename and mfiles. 
+A single preliminary estimate may be applied to a number of
+spectra by specifying a null mfiles string. Otherwise,
+a one-to-one correspondence is assumed between preliminary
+list files and spectra. If the entry for mfilename is also null,
+the linear dispersion relation for the pixel coordinate contained
+in the image header will be used. This provides the option
+of locating features in linearized spectra.
+
+The initial position estimate is improved using one of the centering
+algorithms defined by the center_option parameter and then
+written to a list file. Also written to the list file will be
+the feature's reference value (e.g. wavelength), weight,
+identification string, and the acceptability of the line.
+Acceptibility is noted as either accepted, set, deleted, or not
+found (see below).
+
+If the task is invoked from a graphics terminal as an interactive
+task, the interact switches may be set to yes.
+Then each spectrum will
+be displayed in segments expanded about each feature with the
+automatically defined center marked. The user can then accept
+the given position, mark a new center, or declare the line
+unacceptable.
+
+If the display switch is set, the spectrum is displayed
+and the features marked.
+
+If the task is invoked as a background task, or if the
+user terminal is non-graphics, then the display and interact
+switches cannot assume values of yes.
+.ih
+PARAMETERS
+.ls 4 filename
+See the definition of this parameter under RFITS
+.le
+.ls 4 files
+See the definition of this parameter under RFITS
+.le
+.ls 4 mfilename
+The root for the spectra names used to define the preliminary
+relationship between spectral feature coordinate and reference
+value. The mfiles string parameter is used to define the
+suffix of the spectral name. If this parameter is null, the
+preliminary relationship is assumed to be linear and defined
+by the standard image header entries CRPIX and CDELT.
+.le
+.ls 4 mfiles
+This string parameter serves the same purpose for mfilename
+as the files parameter serves for filename. Note that if this
+parameter is null, the single spectrum defined by mfilename
+is used to define the preliminary relationship for all
+spectra defined by filename and files.
+.le
+.ls 4 list
+This parameter specifies the IRAF file name containing the
+spectral line list to be scanned for features. (See the
+task LINE_LIST)
+.le
+.ls 4 interact
+If this switch is set to yes and the task is invoked interactively
+from a graphics terminal, the spectrum will be displayed on the
+terminal. Each feature will be marked with its computed center
+and the user can type one of the following single keystrokes:
+.ls 4 a
+to accept the displayed position
+.le
+.ls 4 s
+to set the cursor to the desired position
+.le
+.ls 4 d
+to delete the displayed feature from the line list during this
+invocation of the task
+.le
+.ls 4 b
+to reset the operational mode to a "batch" environment where
+no display or interaction is desired
+.le
+.ls 4 p
+to reset the operational mode to a "passive" environment where
+the spectra are displayed and marked, but no interaction is desired
+.le
+.le
+.ls 4 display
+If this switch is set to yes, and the task is invoked from
+a graphics terminal, the spectrum will be displayed and the
+identified lines marked for the user's inspection. No
+interaction is allowed unless the interact switch is also set to yes.
+(default = yes)
+.le
+.ls 4 center_option
+See the description of this parameter under MLINID.
+.le
+.ls 4 second_order
+See the description of this parameter under MLINID.
+.le
+
+.sh
+DISPERSION SOLUTION
+
+After several spectral features have been identified, either
+manually with MLINID or automatically with ALINID, the relationship
+between feature reference value and pixel coordinate can be calculated.
+The dispersion relation may require a second order correction
+to account for variations as a function of some additional
+parameter, such as zenith distance or time of day.
+
+.ih
+NAME
+disp_sol -- Determine the dispersion relation for a set of spectra.
+.ih
+USAGE
+disp_sol [filename, files, order, global]
+.ih
+DESCRIPTION
+The list files containing the postions and reference values for
+features in the specified spectra are combined to solve for the
+dispersion relation by a polynomial least-squares fit to the lists.
+The solution can include a second order
+correction parameter which is also contained in the list file.
+
+The solution takes the form of a polynomial in the pixel
+coordinate having the specified order. The second order
+is also fit by a polynomial. (The choice of a polynomial
+applies to the initial release. Additional forms, selectable by
+parameter, of the solution may be available later.)
+The polynomial coefficients are stored in the spectral image header
+if the store_coeffs switch is set to yes and the spectrum does not already
+contain a solution. If a solution already exists, the user is
+asked for confirmation to overwrite the solution, unless the overwrite
+switch is set to yes.
+
+If filename is the name of a data group, all line list files for
+spectra in that data group are combined into the solution.
+
+If invoked as an interactive task from a graphics terminal,
+a representation of the solution will be displayed and the user
+will be allowed to alter the weights of the line entries.
+If invoked from a non-graphics terminal, the representation
+will be in a tabular format (also available at a graphics terminal)
+for inspection and alteration. If invoked as a background task,
+an attempt will be made to reject discrepant points.
+
+The solution is made using all available line lists combined
+into a single data set if the global switch is set to yes.
+If global is set to no, each spectrum is treated as an
+independent data set.
+.ih
+PARAMETERS
+.ls 4 filename
+See the definition of this parameter under RFITS.
+.le
+.ls 4 files
+See the definition of this parameter under RFITS.
+.le
+.ls 4 order
+The order of the polynomial for a least-squares fit to the
+dispersion solution. If the specified order exceeds the number
+of free parameters, the order will be reset to the maximum
+allowable. (default = 1 --> linear).
+.le
+.ls 4 global
+This switch determines if the data from all the specified spectra are
+to be treated as a single large data set. This is appropriate if the
+data represent a single congruent "setup". But if the data represent
+several different configurations, such as for multiaperture data,
+the global switch should be set to no. Note that if global is no, then
+no second order parameter solution is possible.
+.le
+.ls second_order
+This parameter specifies the order for the fit to the second
+order parameter. The limit described for the order parameter
+applies. (default = 0 --> no second parameter solution).
+.le
+.ls 4 interact
+If this switch is set to yes and the task is invoked interactively
+from a graphics terminal, the residuals of the solution will be displayed
+on the terminal. The user can type one of the following keystrokes:
+.ls 4 a
+to accept the current solution. The parameters of the fit
+are written into the headers of the spectra contributing to the fit.
+.le
+.ls 4 e
+to exit without saving the solution
+.le
+.ls 4 w
+to reset the weight of the point near the cursor positioned by the user.
+The user is then prompted for the new weight which may be set to zero
+to delete the point from the solution.
+.le
+.ls 4 t
+to display the solution parameters in tabular form
+.le
+.ls 4 o
+to specify a new order for the solution
+.le
+.ls 4 s
+to specify a new order for the second order parameter solution
+.le
+.ls 4 b
+to revert to batch mode to process the remainder of the solutions.
+This is only meaningful if the global switch is set to no.
+.le
+.ls 4 p
+to revert to passive mode as for ALINID. This is only meaningful
+if the global switch is set to no
+.le
+.le
+.ls 4 store_coeffs
+If this switch is set to yes, the dispersion solution polynomial
+coefficients will be written into the image header as special
+header elements. Otherwise, the solution is discarded. (default = yes)
+.le
+.ls 4 overwrite
+If this switch is set to yes, any existing dispersion solution contained
+in the image header will be overwritten without any request for confirmation
+from the user. If set to no, the user is asked if overwriting of the solution
+is acceptable. If no prior solution exists, this switch has no meaning.
+(default = no)
+.le
+
+.sh
+DISPERSION CORRECTION
+
+After the dispersion relation has been determined, the spectra
+are usually re-binned to create spectra having a linear
+relationship with wavelength. Although this is not always
+done, nor is it always desirable, subsequent processing
+is often simplified greatly by having to deal with only
+linearized data.
+
+.ih
+NAME
+disp_cor -- Linearize spectra having dispersion relation coefficients
+.ih
+USAGE
+disp_cor [filename, files, destination, option]
+.ih
+DESCRIPTION
+The spectra specified by the root filename and the files parameter
+are corrected for deviations from a linear wavelength relationship.
+The corrected spectra are written to filenames having the root
+specified by the destination parameter.
+
+The correction is performed by solving for the inverse relationship
+of pixel number as a function of equal increments in the wavelength.
+The new starting wavelength and increment are optionally specified
+by the parameters start and increment. If not specified, the current
+wavelength of the first pixel will be taken as the starting wavelength
+and the increment will be chosen to exactly fill the length of the
+current spectrum. The spectrum will be padded with INDEF on either
+end if the specified parameters request a larger spectral window than
+actually exists.
+
+The actual re-binning can be performed using one of several algorithms.
+The most efficient minimally smoothing algorithm to be available in the
+initial release is the fifth order polynomial interpolation.
+The most efficient count preserving algorithm is the simple partial-pixel
+summer.
+
+The interpolation can be either linear in wavelength or in the logarithm
+of wavelength. The latter is useful for subsequent radial velocity
+analyses. The choice is specified by the logarithm switch.
+.ih
+PARAMETERS
+.ls 4 filename
+See the definition of this parameter under RFITS.
+.le
+.ls 4 files
+See the definition of this parameter under RFITS
+.le
+.ls 4 destination
+See the definition of this parameter under COIN_COR.
+.le
+.ls 4 option
+This parameter specifies the algorithm to be used for the
+re-binning operation. The initial release will contain the
+following options:
+.ls 4 = linear
+to use a linear interpolation
+.le
+.ls 4 = poly
+to use a fifth order polynomial
+.le
+.ls 4 = sinc
+to use a sinc function interpolator
+.le
+.ls 4 = sum
+to use partial pixel summation
+.le
+.le
+.ls 4 start
+This parameter specifies the wavelength at which the corrected
+spectrum is to begin. The wavelength of the first pixel will
+be assigned this value. This parameter, combined with the increment
+parameter, allows data taken on different nights
+or with different instruments to be forced to be congruent.
+(default = value at first pixel)
+.le
+.ls 4 increment
+This parameter specifies the pixel to pixel wavelength (or logarithm of
+wavelength) increment
+that is to be used during the linearization process.
+(default = [wavelength at last pixel minus wavelength at first pixel]
+divided by [number of points in spectrum - 1])
+.le
+.ls 4 logarithm
+If this switch is set to yes, the linearization occurs with equal
+increments in the logarithm of wavelength. Otherwise, equal
+increments of wavelength are used. (default = no)
+.le
+.ls 4 print_header
+See the definition of this parameter for COIN_COR.
+.le
+
+.sh
+FIELD FLATTENING
+
+Most detectors exhibit variations in sensitivity across the field
+of interest. These are removed by dividing all observations by
+the spectrum of a smooth continuous source, such as an incandescant
+lamp. In order that these lamps, which usually have a low color
+temperature, produce sufficient energy in the blue and ultraviolet,
+they are often enclosed in a quartz rather than a glass bulb.
+Thus, the field flattening operation is often referred to as
+"quartz division".
+
+The operation is of marginal value unless the continuum source is
+observed properly. First, a very high signal-to-noise ratio per
+pixel is required. For certain detectors and applications this
+may not be possible in a reasonable amount of time. Second, the
+continuum source should not have any significant variations
+across small regions of the spectrum (high frequency "bumps").
+Otherwise the division will add these variations into the spectrum.
+
+There are basically two aspects to flat fielding spectra. The first
+is the removal of pixel-to-pixel sensitivity variations. The second
+is a more global pattern due to non-uniform iillumination and
+spatial and wavelength sensitivity variations across the detector.
+
+The very high frequency pixel-to-pixel variations are easily handled
+by a straightforward division of the observations by the continuum
+spectrum.
+
+The second problem is usually postponed in one-dimensional data
+reductions and included in the
+solution for the system sensitivity by observing standard stars.
+This aspect of the problem is adequately handled in this fashion
+and no special operators are provided in this package.
+
+If the continuum source exhibits large low frequency variations
+across the spectrum, it may be desirable to filter these.
+This is most easily done by fitting a moderately high order
+polynomial through the spectrum, and then dividing the polynomial
+representation into the original continuum spectrum. The result
+is a flat spectrum having an average value of unity and
+containing only the pixel-to-pixel sensitivity variations.
+
+Finally, it should be noted that the field flattening operation
+is most properly performed prior to the wavelength linearization
+of the spectra because the linearization process can smooth
+pixel-to-pixel variations.
+
+Flat fielding consists of two logical operations. The first
+is the solution for a continuum spectrum with the low frequency
+variations removed (CR_FLAT). It is assumed that multiple observations
+of the continuum source have been already averaged (using the
+image calculator program, for example).
+
+The second operation is the actual field flattening of the object
+spectra (FLT_FIELD).
+
+.ih
+NAME
+cr_flat -- Create a flat field spectrum
+.ih
+USAGE
+cr_flat [filename, destination]
+.ih
+DESCRIPTION
+The continuum spectrum specified by filename is corrected for
+low frequency spectral variations. Several algorithms may be
+available. The initial release will contain only a polynomial
+fitting technique. A fourier filtering algorithm may be added
+at a later date.
+
+The spectrum is fit by a polynomial in the pixel coordinate
+and the polynomial is divided into the original spectrum.
+Discrepant pixels may be rejected and the solution re-iterated.
+
+If invoked as an interactive task from a graphics terminal, the
+resultant spectrum is displayed and the user may alter the
+solution parameters if the interact switch is set to yes.
+If invoked from a non-graphics terminal, sufficient information
+concerning the fit is written to the terminal to allow
+the user to judge the quality of the fit and then alter the
+solution parameters.
+
+If invoked as a background task, or if the interact switch is set
+to no, default parameters will be assumed.
+
+The parameters of the fit are added to the image header for
+the corrected spectra.
+.ih
+PARAMETERS
+.ls 4 filename
+The IRAF filename containing the spectrum of the continuum
+source. If this is a data group name, then all spectra
+in the group will be corrected.
+.le
+.ls 4 destination
+The IRAF filename into which the resultant corrected
+spectrum is written. If the source filename is a data group,
+then the destination will be a new data group containing
+the names of the corrected spectra. The names will be
+assigned using the destination as a root name, and the
+ordinal of the spectrum in the list as a suffix.
+.le
+.ls 4 option
+This string parameter specifies the algorithm to be used
+in the correction process. Currently only option = poly
+is recognized.
+.le
+.ls 4 order
+This integer parameter specifies the initial order of the
+polynomial fit. (default = 8)
+.le
+.ls 4 reject
+This parameter specifies the number of standard deviations
+beyond which pixels are to be rejected. If the task
+is interactive, pixel rejection is performed only on command.
+If invoked as a background task, rejection is iterated 
+until no further pixels are rejected, or until the iteration
+count has been attained (see parameter niter). (default = 2.2)
+.le
+.ls 4 niter
+This integer parameter specifies the number of iterations
+to be performed in background mode. It may be set to 0 to
+specify no pixel rejection. (default = 2).
+.le
+.ls 4 interact
+If this switch is set to yes and the task is invoked as
+an interactive task, the user can alter the fit parameters
+order, reject, and niter. If at a graphics terminal, the resultant
+spectrum is displayed and the user can command the operation
+with the following single keystrokes:
+.ls 4 a
+to accept the solution
+.le
+.ls 4 o
+to change the order of the fit
+.le
+.ls 4 r
+to reset the reject parameter
+.le
+.ls 4 n
+to reset the niter parameter
+.le
+.ls 4 b
+to reset the operational mode to a batch environment
+.le
+.ls 4 p
+to reset the operational mode to a passive environment
+.le
+.le
+
+If at a non-graphics terminal, the fit parameters are
+written to the terminal so that the user may assess the quality
+of the fit. A request for one of the interactive commands
+is then issued and the user may proceed as if on a graphics
+terminal.
+.le
+
+.ih
+NAME
+flt_field -- Correct spectra for pixel-to-pixel variations
+.ih
+USAGE
+flt_field [filename, files, flatname, destination]
+.ih
+DESCRIPTION
+The spectra specified by the IRAF filename parameter and the files
+string are divided by the flat field spectra specified by
+the parameter flatname. If filename and flatname are data group names,
+the division is performed on a one-for-one basis.
+
+This operation is little more than a simple division. An image
+header entry is added indicating that flattening by the
+appropriate spectrum has been performed.
+.ih
+PARAMETERS
+.ls 4 filename
+See the definition of this parameter under RFITS.
+.le
+.ls 4 files
+See the definition of this parameter under RFITS.
+.le
+.ls 4 flatname
+This string parameter sepcifies the name of the flat field
+spectrum, or spectra if a data group name.
+It is not necessary that the flat field spectra be corrected
+for low frequency spectral variations.
+It is required that the spectra be congruent with the spectra
+to be flattened; that is, all spectra must have the same
+length, reference pixel, and pixel-to-pixel increment.
+.le
+.ls 4 destination
+See the definition of this parameter under COIN_COR.
+.le
+.ls 4 print_header
+See the definition of this parameter under COIN_COR.
+.le
+
+.sh
+EXTINCTION CORRECTION/FLUX CALIBRATION
+
+At each wavelength (lambda) along the spectrum, the observed
+flux (fobs) must be corrected for extinction (k) due to the
+Earth's atmosphere and the system sensitivity (S) to obtain
+a true flux (f) above the atmosphere.
+.sp 1
+fobs(lambda) = f(lambda) * exp{-z[k(lambda)+C]} * S(lambda)
+.sp 1
+where z is the path through the Earth's atmosphere during the
+observation and C is an optional "grey" opacity term.
+
+For most observations, the standard extinction function is adequate,
+but occasionally the additive term is beneficial. In rare cases,
+the observer has acquired sufficient high quality data to
+determine the extinction function across the spectral region
+of interest. And in other cases, the user may have a priori
+knowledge of the extinction function.
+
+Observations of standard stars are used to determine
+either the additive constant or a new extinction function,
+and the system sensitivity.
+The two operations, determining the extinction parameters
+and the system sensitivity curve, are therefore intimately
+related.
+
+The process breaks down into four basic operations:
+.ls 4 1.
+Define the standard stars and their observations. (STD_STAR)
+.le
+.ls 4 2.
+Define the extinction solution option and solve for the extinction
+additive term or complete function if necessary. (CREXT_FUNC)
+.le
+.ls 4 3.
+Determine the system sensitivity function. (CRSENS_FUNC)
+.le
+.ls 4 4.
+Remove the effects of the extinction and the system sensitivity
+from the observations. (EXT_COR, SENS_COR)
+.le
+
+These will be described below in more detail.
+
+.ih
+NAME
+std_star -- Define the standard stars to be used for solving the extinction and
+system sensitivity functions.
+.ih
+USAGE
+std_star [fnamelist, filelist, namelist, std_file]
+.ih
+DESCRIPTION
+The spectra defined by the list of filenames and associated files
+contained in the string list parameters fnamelist and filelist
+are compared with the standard flux measurements for the stars
+listed in the string list parameter namelist. The resultant
+table of ratios as a function of wavelength are saved in the
+IRAF file specified by the std_file parameter.
+
+All spectra must be wavelength linearized. The star names given
+in namelist must be in a form similar to that in the IIDS Reduction
+manual. If a star name cannot be matched to the standards contained
+in a calibration file, the user is prompted for additional
+information. The calibration file containing the list of reference
+flux values is specified by the calib_file parameter.
+.ih
+PARAMETERS
+.ls 4 fnamelist
+This is a list structured parameter containing the IRAF filenames
+associated with the spectra for each of the standard stars contained
+in the list of starnames defined by the list structured parameter
+namelist. Both these parameters must have the same number of elements.
+The filename specifications are defined as in RFITS.
+.le
+.ls 4 fileslist
+This is also a list structured parameter having the same number of
+elements as fnamelist although some may be null.
+The entries are defined as in RFITS.
+.le
+.ls 4 namelist
+This is also a list structured parameter having the same number
+of elements as fnamelist. All elements must exist and have a
+form to be decided on, but probably similar to that given in the IIDS
+Reduction manual, page 36. For example, a typical star name might
+be BD+8 2015, or HILTNER 102. Case will not be significant.
+.le
+.ls 4 std_file
+This string parameter defines the IRAF filename in which the
+results from the standard star observations are stored.
+This file will be used to contain further calibration information
+such as the extinction and sensitivity function for the
+current set of observations.
+.le
+.ls 4 calib_file
+This string parameter defines which of several calibration
+data files are to be accessed for the comparison of the
+observational data to the standard fluxes. Separate tools
+to examine, modify, and create these files are available
+in the utilities package. (default = onedspec$iids.cal)
+.le
+.ls 4 print_header
+If this parameter is set to yes, an informative header
+is listed on the standard output as the standard stars are processed
+(default = yes).
+.le
+
+.ih
+NAME
+crext_func -- Create an extinction function from a set of observations
+.ih
+USAGE
+crext_func [std_file, option]
+.ih
+DESCRIPTION
+The user may specify via the option parameter which of the four
+extinction solutions is to be used. These are:
+.sp 1
+.ls 4 1.
+Adopt standard extinction function (option = standard).
+.le
+.ls 4 2.
+Solve for an additive constant (option = additive).
+.le
+.ls 4 3.
+Solve for extinction function (option = new_function).
+.le
+.ls 4 4.
+Input a tabular extinction function consisting of extinction
+values at specified wavelengths (option = input).
+.le
+.sp 1
+If the first or last options are chosen, the std_file may be empty.
+If the second option is chosen, several observations at
+differing air masses must be included in the file specified by std_file.
+If the third option is chosen,
+at least two standard stars must be included in the list of observations.
+
+The derived extinction function is added to the IRAF file specified
+by the std_file parameter by creating a new spectrum containing the
+function and adding the spectrum name to the std_file.
+The new spectrum will adopt a name having a root from the
+name std_file and a suffix of ".ext". The spectrum is created by
+a spline interpolation through the extinction values.
+
+If invoked as an interactive task from a graphics terminal, the
+derived extinction function  is displayed. The user may interactively
+alter the derived extinction values using the graphics cursor.
+If invoked from a non-graphics terminal, the user may alter the
+values by specifying the wavelength and new extinction value
+from the standard input. Interaction may be suppressed by setting the
+interact switch to no.
+
+.ih
+PARAMETERS
+.ls 4 std_file
+See the definition of this parameter under STD_STAR.
+.le
+.ls 4 option
+This parameter specifies which aspects of the extinction solution
+are to be computed. See description section for CREXT_FUNC.
+.le
+.ls 4 interact
+If this switch is set the user may alter the derived extinction values.
+If invoked from a graphics terminal and interact is set to yes, the
+following single keystroke commands may be typed:
+.ls 4 a
+to accept the current solution
+.le
+.ls 4 m
+to modify the extinction value at the cursor wavelength position (cursor-x)
+to the cursor extinction value position (cursor-y).
+.le
+.ls 4 i
+to insert a new wavelength-extinction value pair at the current
+crosshair position.
+.le
+.ls 4 d
+to delete the wavelength-extinction value pair at the current
+cursor wavelength position.
+.le
+.le
+
+.ih
+NAME
+crsens_func -- Create system sensitivity function.
+.ih
+USAGE
+crsens_func [std_file, option]
+.ih
+DESCRIPTION
+The standard star data and extinction function contained in the
+IRAF file specified by the std_file parameter are used to
+compute the system sensitivity as a function of wavelength.
+The derived function is written to the file specified by
+std_file.
+
+There must be at least one standard star observation contained
+in the std_file, unless the parameter option = input.
+This allows the user to enter any function in the
+form of wavelength-sensitivity pairs.
+
+If option = shift, a "grey" shift is applied to all observations
+necessary to bring relatively faint values up to the brightest
+to account for possible cloud variations.
+
+If invoked as an interactive task from a graphics terminal,
+and the interact switch is set to yes, the sensitivity values
+from each standard are plotted with any "grey" shift correction
+added. The user may delete or add new points as desired using
+the cursor. If invoked from a non-graphics terminal, a tabular
+list of the solution is presented and additions or deletions
+may be entered through the standard input.
+
+The final function written to the std_file is simply the name of a new
+spectrum derived from a spline fit to the sensitivity
+if the spline switch is set to yes. If spline = no, a linear
+interpolation between sensitivity points will be used.
+The sensitivity spectrum name will be taken from the file name
+given to std_file and with the suffix ".sen".
+.ih
+PARAMETERS
+.ls 4 std_file
+See the definition of this parameter under STD_STAR.
+.le
+.ls 4 option
+This parameter can assume the following string values:
+.ls 4 = input
+to indicate that the sensitivity function is to be entered as
+wavelength-sensitivity pairs. 
+.le
+.ls 4 = shift
+to force a "grey" shift between all standard star spectra to
+account for clouds. This is actually a multiplicative factor
+across each of the affected spectra.
+.le
+.le
+.ls 4 spline
+This switch parameter determines if a spline fit is to be made
+between the sensitivity points (spline = yes), or a linear
+fit (spline = no). (default = yes).
+.le
+.ls 4 interact
+If invoked as an interactive task, the user may alter the sensitivity
+function values. If at a graphics terminal, the sensitivity curve
+is displayed first for each star in the solution. The user may
+add or delete values for any or all stars at a given wavelength.
+Subsequently, the derived average curve is displayed and the user
+may further modify the solution. The following keystrokes are
+available from the graphics terminal:
+.ls 4 a
+to accept the current displayed data (solution).
+.le
+.ls 4 d
+to delete the value at the cross-hairs. If several values
+are very close together, an expanded display is presented.
+.le
+.ls 4 i
+to insert the sensitivity value of the y-cursor at the wavelength position.
+.le
+.ls 4 c
+to "create" new sensitivity values at the wavelength position of the
+x-cursor. Normally sensitivity values are computed only at pre-defined
+wavelengths specified in the calib_file. Additional values
+may be computed by interpolation of the standard star fluxes
+from the calib_file. The name of the calib_file and the spectra
+in the current solution are taken from the std_file.
+.le
+.le
+
+.ih
+NAME
+ext_cor -- Extinction correct specified spectra
+.ih
+USAGE
+ext_cor [filename, files, std_file, destination]
+.ih
+DESCRIPTION
+The spectra specified by the filename and files parameters
+are corrected for atmospheric extinction according to the
+extinction correction function pointed to by the function
+name in std_file. The resulting new spectra are created with the
+root of the destination parameter and having suffixes of
+1 through n corresponding to the n spectra corrected.
+If filename is a data group name, a new data group will be created having
+the name given by the destination parameter.
+
+The correction has the form:
+.sp 1
+f(lambda) = fobs(lambda) / 10**{-z[a(lambda) + C]}
+.sp 1
+where:
+.ls 4 f(lambda) = the flux at wavelength lambda above the Earth's atmosphere.
+.le
+.ls 4 fobs(lambda) = the flux observed through the atmosphere
+.le
+.ls 4 z = the path length through the atmosphere is units of air masses
+(= 1 at the zenith)
+.le
+.ls 4 a(lambda) = the extinction function at wavelength lambda
+in magnitudes per airmass.
+.le
+.ls 4 C = the additive constant, if any, in magnitudes per airmass.
+.le
+.sp 1
+For each spectrum, the zenith distance must be present in the image header.
+This is assumed to be correct for the beginning of the observation.
+For short exposures, this is adequate for the correction, but for
+long exposures, an effective air mass must be calculated over the
+integration. To do so requires knowledge of the altitude and azimuth
+of the telescope (or equivalantly RA, Dec, and sidereal time).
+If these are not present, the approximate air mass calculation will be used
+based solely on the available zenith distance. If the zenith distance
+is not present, user input is requested.
+
+The air mass is calculated according to the following equation for a given
+telescope position (based on Allen p.125,133):
+.sp 1
+z = sqrt{[q sin (alt)]**2 + 2q + 1} - q sin(alt)
+.sp 1
+where:
+.ls 4 q
+= atmospheric scale height (approx = 750).
+.le
+.ls 4 alt
+= telescope altitude
+.le
+.sp 1
+If the telescope traverses a significant distance in elevation during
+the integration, an effective correction can be computed as:
+.sp 1
+f(lambda)a = f(lambda)obs*T / integral{10**[-z(t)(a(lambda) + c)]}dt
+.sp 1
+where the integral is over the integration time, T.
+
+This expression can then be evaluated numerically at each wavelength.
+Because this is a time-consuming operation, the switch effective_cor
+can be set to no and then a simplified correction scheme will be used.
+This will be to compute a midpoint airmass if sufficient information
+is available, or simply to use the header airmass otherwise.
+.ih
+PARAMETERS
+.ls 4 filename
+See the definition of this parameter under RFITS.
+.le
+.ls 4 files
+See the definition of this parameter under RFITS.
+.le
+.ls 4 std_file
+See the definition of this parameter under STD_STAR.
+.le
+.ls 4 destination
+See the definition of this parameter under COIN_COR.
+.le
+.ls 4 effective_cor
+If this switch is set to yes, the procedure to compute an effective
+corrective term averaged over the integration time will be used.
+Although a slow process, this method is more accurate than
+simply using the correction at any given time of the integration
+such as the midpoint. If set to no, a midpoint zenith distance
+will be computed and used if sufficient header information
+exists. (default = no).
+.le
+.ls 4 print_header
+See the definition of this parameter for COIN_COR.
+.le
+
+.ih
+NAME
+sens_cor -- Correct the specified spectra for system sensitivity
+variations across the spectrum.
+.ih
+USAGE
+sens_cor [filename, files, std_file, destination]
+.ih
+DESCRIPTION
+The spectra specified by the filename and files parameters are
+corrected for instrumental sensitivity by the 
+function pointed to by the spectrum name contained in std_file.
+The resulting spectra are stored according to the destination parameter.
+Filename may be a data group name. If so, then destination will be
+a new data group containing the names of the corrected spectra.
+
+This correction is a simple vector multiplcation.
+.ih
+PARAMETERS
+.ls 4 filename
+See the definition of this parameter under RFITS.
+.le
+.ls 4 files
+See the definition of this parameter under RFITS.
+.le
+.ls 4 std_file
+See the definition of this parameter under STD_STAR.
+.le
+.ls 4 destination
+See the definition of this parameter under COIN_COR.
+.le
+.ls 4 print_header
+See the definition of this parameter under COIN_COR.
+.le
+.endhelp
diff --git a/noao/onedspec/doc/sys/Review.hlp b/noao/onedspec/doc/sys/Review.hlp
new file mode 100644
index 00000000..5139f630
--- /dev/null
+++ b/noao/onedspec/doc/sys/Review.hlp
@@ -0,0 +1,512 @@
+.help onedspec Sep84 "Spectral Reductions"
+.ce
+\fBOne Dimensional Spectral Reductions\fR
+.ce
+Analysis and Discussion
+.ce
+September 4, 1984
+.sp 3
+.nh
+Introduction
+
+    The \fBonedspec\fR package is a collection of programs for the reduction
+and analysis of one dimensional spectral data.  The more general problem of
+operations upon one dimensional images or vectors shall be dealt with elsewhere,
+primarily in the \fBimages\fR and \fBplot\fR packages.  The problems of getting
+data in and out of the system are handled by the \fBdataio\fR package, at least
+for the standard data formats such as FITS.
+
+The operators provided in \fBonedspec\fR shall be general purpose and, as far
+as possible, independent of the instrument which produced the data.  Instrument
+dependent reductions tailored for specific instruments will be implemented as
+subpackages of the \fBimred\fR (image reductions) package.  For example,
+the subpackages \fBiids\fR and \fBirs\fR will be provided in \fBimred\fR for
+reducing data from the KPNO instruments of the same name.  The \fBimred\fR
+packages shall call upon the basic operators in \fBonedspec\fR, \fBimages\fR,
+and other packages to reduce the data for a specific instrument.
+
+
+.ks
+.nf
+	iids(etc)
+		imred
+		imredtools
+		onedspec
+			plot
+			tv
+				dataio
+				images
+					dbms
+					lists
+					system
+					language
+
+.fi
+.ce
+Relationship of \fBOnedspec\fR to other IRAF Packages
+.ke
+
+
+The relationship of the \fBonedspec\fR packages to other related packages in
+the IRAF system is shown above.  A program (CL script) in a package at one
+level in the hierarchy may only call programs in packages at lower levels.
+The system will load packages as necessary if not already loaded by the
+user.  The user is expected to be familiar with the standard system packages.
+
+.nh
+Basic Functions Required for One-Dimensional Spectral Reductions
+
+    The following classes of functions have been identified (in the preliminary
+specifications document for \fBonedspec\fR) as necessary to perform basic one
+dimensional spectral reductions.  Only a fraction of the functionality
+required is specific to the reduction of spectral data and is therefore
+provided by the \fBonedspec\fR package itself.
+
+.ls Transport
+Provided by the \fBdataio\fR package, although we do not currently have a
+reader for REDUCER format data tapes.  Readers for all standard format
+tapes are either available or planned.
+.le
+.ls Mathematical
+Standard system functions provided by \fBimages\fR (arithmetic, forward and
+inverse FFT, filtering, etc.).
+.le
+.ls Reduction Operators
+The heart of \fBonedspec\fR.  Operators are required (at a minimum) for
+coincidence correction, dispersion determination and correction, flat
+fielding, sky subtraction, extinction correction, and flux calibration.
+Operators for flat fielding and sky subtraction are already available elsewhere
+in IRAF.  Basic continuum fitting and subtraction is possible with existing
+software but additional algorithms designed for spectral data are desirable.
+.le
+.ls Plotting
+Standard system functions provided by the \fBplot\fR package.
+.le
+.ls Utilities
+Standard system functions provided by the \fBdbms\fR package.
+.le
+.ls Artificial Spectra
+These functions belong in the \fBartdata\fR package, but it is expected that
+prototype operators will be built as part of the initial \fBonedspec\fR
+development.
+.le
+
+.nh
+Data Structures
+
+    Spectra will be stored as one or two dimensional IRAF images embedded in
+database format files.  A free format header is associated with each image.
+Spectra may be grouped together as lines of a two dimensional image provided
+all can share the same header, but more commonly each image will contain a
+single spectrum.  The second image dimension, if used, will contain vectors
+directly associated with the images, such as a signal to noise vector.
+If the image is two dimensional the spectrum must be the first image line.
+The database facilities will allow images to be grouped together in a single
+file if desired.
+
+While most or all \fBonedspec\fR operators will expect a one dimensional
+image as input, image sections may be used to operate on vector subsections
+of higher dimensioned images if desired.  The datatype of an image is
+arbitrary, but all pixel data will be single precision real within
+\fBonedspec\fR.  While the IRAF image format does not impose any restrictions on
+the size of an image or image line, not all spectral operators may be usable
+on very large images.  In general, pointwise and local operations may easily
+be performed on images of any size with modest memory requirements, and
+most of the \fBonedspec\fR operations appear to fall into this class.
+
+.nh 2
+The IRAF Database Faciltities
+
+    An understanding of the IRAF database facilities is necessary to visualize
+how data will be treated by operators in \fBonedspec\fR and other packages.
+The database facilities will be used not just for image storage but also for
+program intercommunication, program output, and the storage of large
+astronomical catalogs (e.g. the SAO catalog).  Access to both small and
+large databases will be quite efficient; achieving this requires little
+innovation since database technology is already highly developed.  We begin by
+defining some important terms.
+
+.ls
+.ls DBIO
+The database i/o package, used by compiled programs to access a database.
+.le
+.ls DBMS
+The database management package, a CL level package used by the user to
+inspect, analyze, and manipulate the contents of a database.
+.le
+.ls database
+A set of one or more "relations" or tables (DBIO is a conventional relational
+database).  A convenient way to think of an IRAF database is as a directory.
+The relations appear as distinct files in the directory.
+.le
+.ls relation
+A relation is a set of \fBrecords\fR.  Each record consists of a set of
+\fBfields\fR, each characterized by a name and a datatype.  All the records
+in a relation have the same set of fields.  Perhaps the easiest way to
+visualize a relation is as a \fBtable\fR.  The rows and columns of the table
+correspond to the records and fields of the relation.
+.le
+.ls field
+A field of a record is characterized by an alphanumeric name, datatype, and
+size.  Fields may be one dimensional arrays of variable size.  Fields may be
+added to a relation dynamically at run time.  When a new field is added to
+a relation it is added to all records in the relation, but the value of the
+field in a particular record is undefined (and consumes no storage) until
+explicitly written into.
+.le
+.ls key
+.br
+A function of the values of one or more fields, used to select a subset of
+rows from a table.  Technically, a valid key will permit selection of any
+single row from a table, but we often use the term is a less strict sense.
+.le
+.le
+
+
+An \fBimage\fR appears in the database as a record.  The record is really
+just the image header; the pixels are stored external to the database in a
+separate file, storing only the name of the pixel storage file in the record
+itself (for very small images we are considering storing the pixels directly
+in the database file).  Note that the record is a simple flat structure;
+this simple structure places restrictions on the complexity of objects which
+can be stored in the database.
+
+The records in a relation form a set, not an array.  Records are referred to
+by a user-defined key.  A simple key might be a single field containing a
+unique number (like an array index), or a unique name.  More complex keys
+might involve pattern matching over one or more fields, selection of records
+with fields within a certain range of values, and so on.
+
+From the viewpoint of \fBonedspec\fR, a relation can be considered a
+\fBdata group\fR, consisting of a set of \fBspectra\fR.
+
+.nh 2
+Image Templates
+
+    The user specifies the set of spectra to be operated upon by means of an
+image template.  Image templates are much like the filename templates commonly
+used in operating systems.  The most simple template is the filename of
+a single data group; this template matches all spectra in the group.  If there
+is only one spectrum in a file, then only one spectrum is operated upon.
+A slightly more complex template is a list of filenames of data groups.
+More complex templates will permit use of expressions referencing the values
+of specific fields to select a subset of the spectra in a group.  The syntax
+of such expressions has not yet been defined (examples are given below
+nonetheless), but the function performed by an image template will be the same
+regardless of the syntax.  In all cases the image template will be a single
+string valued parameter at the CL level.
+
+.nh 2
+Standard Calling Sequence
+
+    The standard calling sequence for a unary image operator is shown below
+The calling sequence for a binary operator would be the same with a second input
+parameter added as the second argument.  In general, any data dependent
+control parameters should be implemented as positional arguments following
+the primary operands, and data independent or optional (rarely used) parameters
+should be implemented as hidden parameters.
+
+
+.ks
+.nf
+	imop (input, output, data_dependent_control_params)
+
+	imop	image operator name
+	input	image template specifying set of input images
+	output	filename of output datagroup
+
+	data_dependent_control_parameters
+	(hidden parameters)
+
+for example,
+
+	coincor (spectra, newgroup, dead_time)
+.fi
+.ke
+
+
+If a series of spectra are to be processed it seems reasonable to add the
+processed spectra to a new or existing data group (possibly the same as an
+input datagroup).  If the operation is to be performed in place a special
+notation (e.g. the null string) can be given as the output filename.
+At the \fBonedspec\fR level output filenames will not be defaulted.
+
+.nh 2
+Examples
+
+    Some examples of image templates might be useful to give a more concrete
+idea of the functionality which will be available.  Bear in mind that what we
+are describing here is really the usage of one of the fundamental IRAF system
+interfaces, the DBMS database management subsystem, albeit from the point of
+view of \fBonedspec\fR.  The same facilities will be available in any program
+which operates upon images, and in some non-image applications as well (e.g.
+the new \fBfinder\fR).  Our philosopy, as always, is to make standard usage
+simple, with considerable sophistication available for those with time to
+learn more about the system.
+
+The simplest case occurs when there is one spectrum per data group (file).
+For example, assuming that the file "a" contains a single spectrum, the
+command
+
+	cl> coincor a, b, .2
+
+would perform coincidence correction for spectrum A, placing the result in
+B, using a dead time parameter of .2.  For a more complex example, consider
+the following command:
+
+	cl> coincor "a.type=obj&coincor=no,b", a, .2
+
+This would perform coincidence correction for all spectra in group B plus all
+object spectra in group A which have not already been coincidence corrected,
+adding the corrected spectra to group A (notation approximate only).  If the
+user does not trust the database explicit record numbers may be used and
+referenced via range list expressions, e.g.,
+
+	cl> coincor "a.recnum=(1,5,7:11),b", a, .2
+
+would select records 1, 5, and 7 through 11 from data group A.  Alternatively
+the database utilities could be used to list the spectra matching the selection
+criteria prior to the operation if desired.  For example,
+
+	cl> db.select "a.type=obj"
+
+would write a table on the standard output (the terminal) wherein each spectrum
+in data group A is shown as a row of field values.  If one wanted to generate
+an explicit list of records to be processed with help from the database
+utilities, a set of records could be selected from a data group and selected
+fields from each record written into a text file:
+
+	cl> db.select "a.type=obj", "recnum, history" > reclistfile
+
+The output file "reclistfile" produced by this command would contain the
+fields "recnum" (record number) and "history" (description of processing
+performed to generate the record).  The editor could be used to delete
+unwanted records, producing a list of record numbers suitable for use as
+an image template:
+
+	cl> coincor "a.recnum=@reclistfile", a, .2
+
+.nh
+Reduction Operators
+
+.nh 2
+Line List Preparation
+
+    I suggest maintaining the line lists as text files so that the user can
+edit them with the text editor, or process them with the \fBlists\fR operators.
+A master line list might be maintained in a database and the DBMS \fBselect\fR
+operator used to extract ASCII linelists in the wavelength region of interest,
+but this would only be necessary if the linelist is quite large or if a linelist
+record contains many fields.  I don't think we need the \fBline_list\fR task.
+
+.nh 2
+Dispersion Solution
+
+    The problem with selecting a line list and doing the dispersion solution
+in separate operations is that the dispersion solution is invaluable as an aid
+for identifying lines and for rejecting lines.  Having a routine which merely
+tweaks up the positions of lines in an existing lineset (e.g., \fBalinid\fR)
+is not all that useful.  I would like to suggest the following alternate
+procedure for performing the dispersion solution for a set of calibration
+spectra which have roughly the same dispersion.
+
+.ls
+.ls [1] Generate Lineset [and fit dispersion]
+.sp
+Interactively determine the lineset to be used, i.e., wavelength (or whatever)
+and approximate line position in pixel units for N lines.  Input is one or more
+comparison spectra and optionally a list of candidate lines in the region
+of interest.  Output is the order for the dispersion curve and a linelist of
+the following (basic) form:
+
+	L#  X  Wavelength [Weight]
+
+It would be very useful if the program, given a rough guess at the dispersion,
+could match the standard linelist with the spectra and attempt to automatically
+identify the lines thus detected.  The user would then interactively edit the
+resultant line set using plots of the fitted dispersion curve to reject
+misidentified or blended lines and to adjust weights until a final lineset
+is produced.
+.le
+
+.ls [2] Fit Dispersion
+.sp
+Given the order and functional type of the curve to be fitted and a lineset
+determined in step [1] (or a lineset produced some any other means, e.g. with
+the editor), for each spectrum in the input data group tweak the center of
+each line in the lineset via an automatic centering algorithm, fit the
+dispersion curve, and save the coefficients of the fitted curve in the
+image header.  The approximate line positions would be used to find and measure
+the positions of the actual lines, and the dispersion curve would be fitted and
+saved in the image header of each calibration spectrum.
+
+While this operator would be intended to be used noninteractively, the default
+textual and graphics output devices could be the terminal.  To use the program
+in batch mode the user would redirect both the standard output and the graphics
+output (if any), e.g.,
+
+.nf
+	cl> dispsol "night1.type=comp", linelistfile, order,
+	>>> device=stdplot, > dispsol.spool &
+.fi
+
+Line shifts, correlation functions, statistical errors, the computed residuals
+in the fitted dispersion curves, plots of various terms of the dispersion
+curves, etc. may be generated to provide a means for later checking for
+erroneous solutions to the individual spectra.  There is considerable room for
+innovation in this area.
+.le
+
+.ls [3] Second Order Correction
+.sp
+If it is desired to interpolate the dispersion curve in some additional
+dimension such as time or hour angle, fit the individual dispersion solutions
+produced by [1] or [2] as a group to one or more additional dimensions,
+generating a dispersion solution of one, two or more dimensions as output.
+If the output is another one dimensional dispersion solution, the input
+solutions are simply averaged with optional weights.  This "second order"
+correction to a group of dispersion solutions is probably best performed by
+a separate program, rather than building it into \fBalineid\fR, \fBdispsol\fR,
+etc.  This makes the other programs simpler and makes it possible to exclude
+spectra from the higher dimensional fit without repeating the dispersion
+solutions.
+.le
+.le
+
+If the batch run [2] fails for selected spectra the dispersion solution for
+those spectra can be repeated interactively with operator [1].
+The curve fitting package should be used to fit the dispersion curve (we can
+extend the package to support \fBonedspec\fR if necessary).
+
+.nh 2
+Dispersion Correction
+
+    This function of this procedure is to change the dispersion of a
+spectrum or group of spectra from one functional form to another.
+At a mimimum it must be possible to produce spectra linear in wavelength or
+log wavelength (as specified), but it might also be useful to be able
+to match the dispersion of a spectrum to that of a second spectrum, e.g., to
+minimize the amount of interpolation required to register spectra, or
+to introduce a nonlinear dispersion for testing purposes.  This might be
+implemented at the CL parameter level by having a string parameter which
+takes on the values "linear" (default), "log", or the name of a record
+defining the dispersion solution to be matched.
+
+It should be possible for the output spectrum to be a different size than
+the input spectrum, e.g., since we are already interpolating the data,
+it might be nice to produce an output spectrum of length 2**N if fourier
+analysis is to be performed subsequently.  It should be possible to
+extract only a portion of a spectrum (perform subraster extraction) in the
+process of correcting the dispersion, producing an output spectrum of a
+user-definable size.  It should be possible for an output pixel to lie at
+a point outside the bounds of the input spectrum, setting the value of the
+output pixel to INDEF or to an artificially generated value.  Note that
+this kind of generality can be implemented at the \fBonedspec\fR level
+without compromising the simplicity of dispersion correction for a particular
+instrument at the \fBimred\fR level.
+
+.nh 3
+Line Centering Algorithms
+
+    For most data, the best algorithm in the set described is probably the
+parabola algorithm.  To reject nearby lines and avoid degradation of the
+signal to noise the centering should be performed within a small aperture,
+but the aperture should be allowed to move several pixels in either direction
+to find the peak of the line.
+
+The parabola algorithm described has these features,
+but as described it finds the extrema within a window about the
+initial position.  It might be preferable to simply walk up the peak nearest
+to the initial center.  This has the advantage that it is possible to center
+on a line which has a nearby, stronger neighbor which cannot itself be used
+for some reason, but which might fall within \fBparextent\fR pixels of the
+starting center.  The parabola algorithm as described also finds a local extrema
+rather than a local maximum; probably not what is desired for a dispersion
+solution.  The restriction to 3 pixels in the final center determination is
+bad; the width of the centering function must be a variable to accommodate
+the wide range of samplings expected.
+
+The parabola algorithm described is basically a grid search over
+2*\fIparextent\fR pixels for the local extrema.  What I am suggesting is
+an iterative gradient search for the local maximum.  The properties of the
+two algorithms are probably sufficiently different to warrant implementation
+of both as an option (the running times are comparable).  I suspect that
+everyone else who has done this will have their own favorite algorithm as
+well; probably we should study half a dozen but implement only one or two.
+
+.nh 2
+Field Flattening
+
+    It is not clear that we need special flat fielding operators for
+\fBonedspec\fR.  We have a two-dimensional operator which fits image lines
+independently which might already do the job.  Probably we should experiment
+with both the smoothing spline and possibly fourier filtering for removing
+the difficult medium frequency fluctuations.  The current \fBimred\fR flat field
+operator implements the cubic smoothing spline (along with the Chebyshev and
+Legendre polynomials), and is available for experimentation.
+
+Building interactive graphics into the operator which fits a smooth curve to
+the continuum is probably not necessary.  If a noninteractive \fBimred\fR or
+\fBimages\fR operator is used to fit the continuum the interactive graphics
+can still be available, but might better reside in a higher level CL script.
+The basic operator should behave like a subroutine and not write any output
+to the terminal unless enabled by a hidden parameter (we have been calling
+this parameter \fIverbose\fR in other programs).
+
+.nh 3
+Extinction Correction and Flux Calibration
+
+    I did not have time to review any of this.
+
+.nh
+Standard Library Packages
+
+    The following standard IRAF math library packages should be used in
+\fBonedspec\fR.  The packages are very briefly described here but are
+fully documented under \fBhelp\fR on the online (kpnob:xcl) system.
+
+.nh 2
+Curve Fitting
+
+    The curve fitting package (\fBcurfit\fR) is currently capable of fitting
+the Chebyshev and Legendre polynomials and the cubic smoothing spline.
+Weighting is supported as an option.
+We need to add a piecewise linear function to support the
+dispersion curves for the high resolution FTS spectra.  We may have to add a
+double precision version of the package to provide the 8-10 digits of
+precision needed for typical comparison line wavelength values, but
+normalization of the wavelength values may make this unnecessary for moderate
+resolution spectra.
+
+Ordinary polynomials are not supported because their numerical properties are
+very much inferior to those of orthogonal polynomials (the ls matrix can have
+a disastrously high condition number, and lacking normalization the function
+begin fitted is not invariant with respect to scale changes and translations
+in the input data).  For low order fits the Chebyshev polynomials are
+considered to have the best properties from an approximation theoretic point
+of view, and for high order fits the smoothing spline is probably best because
+it can follow arbitrary trends in the data.
+
+.nh 2
+Interpolation
+
+    The image interpolation package (\fBiminterp\fR) currently supports the
+nearest neighbor, linear, third and fifth order divided differences,
+cubic interpolating spline, and sinc function interpolators.
+We should add the zeroth and first order partial pixel ("flux conserving")
+interpolants because they offer unique properties not provided by any
+of the other interpolants.
+
+.nh 2
+Interactive Graphics
+
+    We will define a standard interactive graphics utility package for
+interactive operations upon data vectors (to be available in a system library
+in object form).  It should be possible to define a general package which
+can be used anywhere a data vector is to be plotted and
+examined interactively (not just in \fBonedspec\fR).  Standard keystrokes
+should be defined for common operations such as expanding a region of
+the plot and restoring the original scale.  This will not be attempted
+until an interactive version of the GIO interface is available later this
+fall.
+.endhelp
diff --git a/noao/onedspec/doc/sys/TODO b/noao/onedspec/doc/sys/TODO
new file mode 100644
index 00000000..0dfa136b
--- /dev/null
+++ b/noao/onedspec/doc/sys/TODO
@@ -0,0 +1,28 @@
+scombine:
+    1.  Combine with weights:
+	    By signal level
+	    By sigma spectrum
+
+doc:
+    Install SENSFUNC memo in the doc directory. (8/14)
+
+calibrate:
+    Have calibrate apply neutral density filter function.  This may also
+    have to be included in STANDARD and SENSFUNC. (2/25/87)
+
+splot:
+    Add a deblend option for PCYGNI profiles. (Tyson, 3/19/87)
+
+Tim Heckman (U. Maryland) came by with questions and requests
+concerning deblending in SPLOT.  Tim's comments are indicated in
+quotations.
+
+2. "The deblending should allow additional constraints if known.
+Specifically fixing the ratios of lines based on atomic physics."
+
+3.  "The deblending should provide some uncertainty estimates."  I added
+that there has also been a request to use known statistics in the
+pixel data themselves to generate uncertainty estimates.
+
+4.  "It would be useful to provide other choices for the profile rather
+than just gaussians."
diff --git a/noao/onedspec/doc/sys/coincor.ms b/noao/onedspec/doc/sys/coincor.ms
new file mode 100644
index 00000000..1b4d29cc
--- /dev/null
+++ b/noao/onedspec/doc/sys/coincor.ms
@@ -0,0 +1,46 @@
+.EQ
+delim $$
+.EN
+.OM
+.TO
+IIDS Users
+.FR
+F. Valdes
+.SU
+IIDS count rate corrections
+.PP
+The IRAF task \fBcoincor\fR transforms the observed count rates to
+something proportional to the input count rate.  The correction applied
+to the observed count rates depends upon the count rate and is instrument
+dependent.  One correction common to photomultiplier detectors and the
+IIDS is for coincident events, which is the origin of the task name.  
+The parameter \fIccmode\fR selects a particular type of correction.
+The value \fIccmode\fR = "iids" applies the following transformation to
+observed IIDS count rates.
+
+.EQ (1)
+	C sup ' ~=~(- ln (1- deadtime C)/ deadtime ) sup power
+.EN
+
+where $C$ is the orginal count rate, $C sup '$ is the corrected count
+rate, and $deadtime$ and $power$ are \fBcoincor\fR parameters.  The term
+inside the parenthesis is the correction for dead-time in the counting
+of coincident events on the back phospher of the image tube.  The power
+law correction is due to the non-linearity of the IIDS image tube chain.
+.PP
+The correction applied with the Mountain Reduction Code is only for
+coincidences, i.e. equation (1) with $power = 1$.  To obtain just this
+correction with \fBcoincor\fR set $power = 1$.  To take mountain reduced
+data and correct only for the non-linearity set \fIccmode\fR = "power".
+With raw IIDS data use \fBcoincor\fR with the default
+parameters.
+
+.LP
+References:
+.IP (1)
+L. Goad, \fBSPIE 172\fR, 1979, p. 86.
+.IP (2)
+G. Jacoby, Some Notes on the ONEDSPEC Package, \fBIRAF Handbook\fR
+.IP (3)
+P. Massey and J. De Veny, How Linear is the IIDS, \fBNOAO Newsletter\fR,
+#6, June 1986.
diff --git a/noao/onedspec/doc/sys/identify.ms b/noao/onedspec/doc/sys/identify.ms
new file mode 100644
index 00000000..6a69204b
--- /dev/null
+++ b/noao/onedspec/doc/sys/identify.ms
@@ -0,0 +1,347 @@
+.RP
+.TL
+Radial Velocity Measurements with IDENTIFY
+.AU
+Francisco Valdes
+.AI
+IRAF Group - Central Computer Services
+.K2
+P.O. Box 26732, Tucson, Arizona 85726
+August 1986
+Revised August 1990
+.AB
+The IRAF task \fBidentify\fP may be used to measure radial velocities.  
+This is done using the classical method of determining 
+the doppler shifted wavelengths of emission and absorption lines.  
+This paper covers many of the features and techniques available 
+through this powerful and versatile task which are not immediately 
+evident to a new user.
+.AE
+.sp 3
+.NH
+\fBIntroduction\fP
+.PP
+The task \fBidentify\fP is very powerful and versatile.  It can 
+be used to measure wavelengths and wavelength shifts for 
+doing radial velocity measurements from emission and 
+absorption lines.  When combined with the CL's ability 
+to redirect input and output both from the standard text 
+streams and the cursor and graphics streams virtually 
+anything may be accomplished either interactively or 
+automatically.  This, of course, requires quite a bit of 
+expertise and experience with \fBidentify\fP and with 
+the CL which a new user is not expected to be aware of initially.  
+This paper attempts to convey some of the possibilities.  
+There are many variations on these methods which the user 
+will learn through experience.
+.PP
+I want to make a caveat about the suggestions made in 
+this paper.  I wrote the \fBidentify\fP task and so I am 
+an expert in its use.  However, I am not a spectroscopist, 
+I have not been directly involved in the science of 
+measuring astronomical radial velocities, and I am not 
+very familiar with the literature.  Thus, the suggestions 
+contained in this paper are based on my understanding of 
+the basic principles and the abilities of the \fBidentify\fP 
+task.
+.PP
+The task \fBidentify\fP is used to measure radial velocities 
+by determining the wavelengths of individual emission 
+and absorption lines.  The user must compute the 
+radial velocities separately by relating the observed 
+wavelengths to the known rest wavelengths via the Doppler 
+formula.  This is a good method when the lines are 
+strong, when there are only one or two features, and 
+when there are many, possibly, weaker lines.  The 
+accuracy of this method is determined by the accuracy 
+of the line centering algorithm.
+.PP
+The alternative method is to compare an observed spectrum 
+to a template spectrum of known radial velocity.  This 
+is done by correlation or fourier ratio methods.  These 
+methods have the advantage of using all of the spectrum 
+and are good when there are many very weak and possibly 
+broad features.  Their disadvantages are confusion 
+with telluric lines, they don't work well with just a 
+few real features, and they require a fair amount of 
+preliminary manipulation of the spectrum to remove 
+continuum and interpolate the spectrum in logarithmic 
+wavelength intervals. IRAF tasks for correlation 
+and fourier ratio methods are under development at 
+this time.  Many people assume that these more abstract 
+methods are inherently better than the classical method.  
+This is not true, it depends on the quality and type of 
+data.
+.PP
+Wavelength measurements are best done on the original 
+data rather than after linearizing the wavelength 
+intervals. This is because 1) it is not necessary as 
+will be shown below and 2) the interpolation used to 
+linearize the wavelength scale can change the shape 
+of the lines, particularly strong, narrow emission 
+lines which are the best ones for determining radial 
+velocities.
+.PP
+This paper is specifically about \fBidentify\fP but one 
+should be aware of the task \fBsplot\fP which also may 
+be used to measure radial velocities.  It differs in 
+several respects from \fBidentify\fP.  \fBSplot\fP works 
+only on linearized data; the wavelength and pixel 
+coordinates are related by a zero point and wavelength 
+interval.  The line centering algorithms are different; 
+the line centering is generally less robust (tolerant 
+of error) and often less accurate.  It has many nice 
+features but is not designed for the specific purpose 
+of measuring positions of lines and, thus, is not as 
+easy to use for this purpose.
+.PP
+There are a number of sources of additional information 
+relating to the use of the task \fBidentify\fP.  The 
+primary source is the manual pages for the task.  As 
+with all manual pages it is available online with the 
+\fBhelp\fP command and in the \fIIRAF User Handbook\fP.  
+The NOAO reduction guides or cookbooks for the echelle 
+and IIDS/IRS include additional examples and discussion.  
+The line centering algorithm is the most critical 
+factor in determining dispersion solutions and radial 
+velocities.  It is described in more detail under the 
+help topic \fBcenter1d\fP online or in the handbook.
+.NH
+Method 1
+.PP
+In this method, arc calibration images are used to determine 
+a wavelength scale.  The dispersion solution is then transferred 
+to the object spectrum and the wavelengths of emission and 
+absorption lines are measured and recorded.  This is 
+relatively straightforward but some tricks will make this easier 
+and more accurate.
+.NH 2
+Transferring Dispersion Solutions
+.PP
+There are several ways to transfer the dispersion solution 
+from an arc spectrum to an object spectrum differing in the 
+order in which things are done.
+.IP (1)
+One way is to determine the dispersion solution for all the arc images
+first.  To do this interactively specify all the arc images as the
+input to \fBidentify\fP.  After determining the dispersion solution for
+the first arc and quitting (\fIq\fP key) the next arc will be displayed
+with the previous dispersion solution and lines retained.  Then use the
+cursor commands \fIa\fP and \fIc\fP (all center) to recenter and
+\fIf\fP (fit) to recompute the dispersion solution.  If large shifts
+are present use \fIs\fP (shift) or \fIx\fR (correlate peaks) to shift,
+recenter, and compute a wavelength zero point shift to the dispersion
+function.  A new dispersion function should then be fit with \fIf\fP.
+These commands are relatively fast and simple.
+.IP
+An important reason for doing all the arc images first 
+is that the same procedure can be done mostly noninteractively 
+with the task \fBreidentify\fP.  After determining a 
+dispersion solution for one arc image \fBreidentify\fP 
+does the recenter (\fIa\fP and \fIc\fP), shift and 
+recenter (\fIs\fP), or correlation features, shift, and 
+recenter (\fIx\fP) to transfer the dispersion solutions 
+between arcs.  This is usually done as a background task.
+.IP
+To transfer the solution to the object spectra specify 
+the list of object spectra as input to \fBidentify\fP.  
+For each image begin by entering the colon command 
+\fI:read arc\fP where arc is the name of the arc image 
+whose dispersion solution is to be applied; normally 
+the one taken at the same time and telescope position as 
+the object.  This will read the dispersion solution and arc 
+line positions.  Delete the arc line positions with the 
+\fIa\fP and \fId\fP (all delete) cursor keys.  You 
+can now measure the wavelengths of lines in the spectrum.
+.IP (2)
+An alternative method is to interactively alternate between 
+arc and object spectra either in the input image list or 
+with the \fI:image name\fP colon command.
+.NH 2
+Measuring Wavelengths
+.IP (1)
+To record the feature positions at any time use the \fI:features 
+file\fP colon command where \fIfile\fP is where the feature 
+information will be written.  Repeating this with the same 
+file appends to the file.  Writing to the database with the 
+\fI:write\fP colon command also records this information.  
+Without an argument the results are put in a file with 
+the same name as the image and a prefix of "id".  You 
+can use any name you like, however, with \fI:write 
+name\fP.  The \fI:features\fP command is probably preferable 
+because it only records the line information while the 
+database format includes the dispersion solution and 
+other information not needed for computing radial 
+velocities.
+.IP (2)
+Remember that when shifting between emission and absorption 
+lines the parameter \fIftype\fP must be changed.  This may be done 
+interactively with the \fI:ftype emission\fP and \fI:ftype 
+absorption\fP commands.  This parameter does not need to be 
+set except when changing between types of lines.
+.IP (3)
+Since the centering of the emission or absorption line is the 
+most critical factor, one should experiment with the parameter 
+\fIfwidth\fP.  To change this parameter type \fI:fwidth value\fP.  
+The positions of the marked features are not changed until a 
+center command (\fIc\fP) command is given.
+.IP
+A narrow \fIfwidth\fP is less influenced by blends and wings but 
+has a larger uncertainty.  A broad \fIfwidth\fP uses all of the 
+line profile and is thus stable but may be systematically influenced 
+by blending and wings.  One possible approach is to measure 
+the positions at several values of \fIfwidth\fP and decide which 
+value to use or use some weighting of the various measurements.  
+You can record each set of measurements with the \fI:fe 
+file\fP command.
+.IP (4)
+For calibration of systematic effects from the centering one should 
+obtain the spectrum of a similar object with a known radial 
+velocity.  The systematic effect is due to the fact that the 
+centering algorithm is measuring a weighted function of the 
+line profile which may not be the true center of the line as 
+tabulated in the laboratory or in a velocity standard.  By 
+using the same centering method on an object with the same line 
+profiles and known velocity this effect can be eliminated.
+.IP (5)
+Since the arcs are not obtained at precisely the same time 
+as the object exposures, there may be a wavelength shift relative 
+to the arc dispersion solution.  This may be calibrated from 
+night sky lines in the object itself (the night sky lines are 
+"good" in this case and should not be subtracted away).  There are 
+generally not enough night sky lines to act as the primary 
+dispersion calibrator but just one can determine a possible 
+wavelength zero point shift.  Measure the night sky line 
+positions at the same time the object lines are measured.  
+Determine a zero point shift from the night sky to be 
+taken out of the object lines.
+.NH
+Method 2
+.PP
+This method is similar to the correlation method in that a 
+template spectrum is used and the average shift relative 
+to the template measures the radial velocity. This has the 
+advantage of not requiring the user to do a lot of calculations 
+(the averaging of the line shifts is done by identify) but is 
+otherwise no better than method 1.  The template spectrum must 
+have the same features as the object spectrum.
+.IP (1)
+Determine a dispersion solution for the template spectrum 
+either from the lines in the spectrum or from an arc calibration.
+.IP (2)
+Mark the features to be correlated in the template spectrum.
+.IP (3)
+Transfer the template dispersion solution and line positions 
+to an object spectrum using one of the methods described 
+earlier.  Then, for the current feature, point the cursor near 
+the same feature in the object spectrum and type \fIs\fP.  The 
+mean shift in pixels, wavelength, and fractional wavelength (like 
+a radial velocity without the factor of the speed of light) 
+for the object is determined and printed.  A new dispersion 
+solution is determined but you may ignore this.
+.IP (4)
+When doing additional object spectra, remember to start over 
+again with the template spectrum (using \fI:read template\fP) 
+and not the solution from the last object spectrum.
+.IP (5)
+This procedure assumes that the dispersion solution between 
+the template and object are the same.  Checks for zero point
+shifts with night sky lines, as discussed earlier, should be 
+made if possible.  The systematic centering bias, however, is 
+accounted for by using the same lines from the template radial 
+velocity standard.
+.IP (6)
+One possible source of error is attempting to use very weak 
+lines.  The recentering may find the wrong lines and affect 
+the results.  The protections against this are the \fIthreshold\fP 
+parameter and setting the centering error radius to be relatively small.
+.NH
+Method 3
+.PP
+This method uses only strong emission lines and works with 
+linearized data without an \fBidentify\fP dispersion 
+solution; though remember the caveats about rebinning the
+spectra.  The recipe involves measuring 
+the positions of emission lines.  The 
+strongest emission lines may be found automatically using 
+the \fIy\fP cursor key.  The number of emission lines to 
+be identified is set by the \fImaxfeatures\fP parameter.  
+The emission line positions are then written to a data file 
+using the \fI:features file\fP colon command.  This may 
+be done interactively and takes only a few moments per 
+spectrum.  If done interactively, the images may be chained 
+by specifying an image template. The only trick required 
+is that when proceeding to the next spectrum the previous 
+features are deleted using the cursor key combination \fIa\fP 
+and \fId\fP (all delete).
+.PP
+For a large number of images, on the order of hundreds, this 
+may be automated as follows.  A file containing the cursor 
+commands is prepared.  The cursor command format consists 
+of the x and y positions, the window (usually window 1), and 
+the key stroke or colon command.  Because each new image from 
+an image template does not restart the cursor command file, 
+the commands would have to be repeated for each image in 
+the list.  Thus, a CL loop calling the task each time with 
+only one image is preferable.  Besides redirecting the 
+cursor input from a command file, we must also redirect the 
+standard input for the response to the database save query, the 
+standard output to discard the status line information, and , 
+possibly, the graphics to a metacode file which can then be 
+reviewed later. The following steps indicate what is to be 
+done.
+.IP (1)
+Prepare a file containing the images to be measured (one per line).
+This can usually be done using the sections command to expand 
+a template and directing the output into a file.
+.IP (2)
+Prepare a cursor command file (let's call it cmdfile) 
+containing the following two lines.
+.RS
+.IP
+.nf
+.ft CW
+1 1 1 y
+1 1 1 :fe positions.dat
+.ft P
+.fi
+.RE
+.IP (3)
+Enter the following commands.
+.RS
+.IP
+.nf
+.ft CW
+list="file"
+while (fscan (list,s1) !=EOF){
+print ("no") \(or identify (sl,maxfeatures=2, cursor="cmdfile",
+>"dev$null", >G "plotfile")
+}
+.ft P
+.fi
+.RE
+.LP
+Note that these commands could be put in a CL script and executed 
+using the command
+.sp
+.IP
+.ft CW
+on> cl <script.cl
+.ft P
+.sp
+.PP
+The commands do the following.  The first command initializes the 
+image list for the loop.  The second command is the loop to 
+be run until the end of the image file is reached.  The 
+command in the loop directs the string "no" to the standard 
+input of identify which will be the response to the database save 
+query.  The identify command uses the image name obtained from the list 
+by the fscan procedure, sets the maximum number of features to be 
+found to be 2 (this can be set using \fBeparam\fP instead), the 
+cursor input is taken from the cursor command file, the standard 
+output is discarded to the null device, and the STDGRAPH output 
+is redirected to a plot file.  If the plot file redirection is 
+not used, the graphs will appear on the specified graphics 
+device (usually the graphics terminal).  The plot file can then 
+be disposed of using the \fBgkimosaic\fP task to either the  
+graphics terminal or a hardcopy device.
diff --git a/noao/onedspec/doc/sys/onedproto.ms b/noao/onedspec/doc/sys/onedproto.ms
new file mode 100644
index 00000000..b1b05201
--- /dev/null
+++ b/noao/onedspec/doc/sys/onedproto.ms
@@ -0,0 +1,1673 @@
+.RP
+.ND
+.TL
+Some Notes on the ONEDSPEC Package
+.AU
+G. Jacoby
+.AI
+.K2 "" "" "*"
+June 1985
+.AB
+The first phase of the ONEDSPEC prototype package is complete.
+Comments and some internal description is presented for each task 
+in the package. Also presented are some more global descriptions
+of strategies used in the package and considerations for future
+improvements.
+.AE
+.SH
+1. Why is ONEDSPEC Different?
+.PP
+This section describes some of the ways in which the ONEDSPEC
+package diverges from other IRAF package strategies.
+A few of these should someday be modified to more closely
+adhere to IRAF conventions, but in other cases, restrictions
+or limitations in the IRAF system are revealed.
+.sp 1
+.SH
+Quantity
+.PP
+One of the major differences between a two dimensional image processing
+package and a one dimensional package is that spectra 
+frequently congregate in groups of hundreds to thousands while two-dimensional
+images live in groups of tens to hundreds. What this means is that spectral
+processing must be somewhat more automated and streamlined - the software cannot
+rely on user input to provide assistance and it cannot afford
+excessive overhead; otherwise  a large fraction of the processing time will be
+spent where it is least useful.
+.PP
+To process large volumes of spectra in a reasonably automated fashion,
+the software must be smart enough to know what to do with a variety
+of similar but different spectra. The way adopted here is to key
+off header parameters which define the type of spectrum and the
+processing required. In fact, most of the ONEDSPEC package will not
+work smoothly without some header parameter information.
+.PP
+It is also important that each task be self-reliant so that the
+overhead of task stop and restart is avoided. For many operations,
+the actual computation time is a fraction of a second, yet no
+operation in the ONEDSPEC package is faster than one second per spectrum
+due to task overhead. If task startup and stop were required for each
+spectrum, then the overhead would be much worse.
+.PP
+So the philosophy is one in which each task uses as much information
+as it can reasonably expect from the spectral image header.
+Usually this is not more than three or four elements.
+The strategy of using header information should not be limited to
+ONEDSPEC. Many image processing problems can be automated
+to a large degree if header information is used. The success of
+the KPNO CCD Mountain reduction system emphasizes this point.
+It would seem prudent that other IRAF applications make use of
+such information when possible.
+[See section 3 for a more detailed discussion of headers.]
+.sp 1
+.SH
+Spectral Image Names
+.PP
+One implication of the quantity problem is that it must be easy for the user to
+specify the names of large numbers of spectra.  The approach taken for ONEDSPEC
+was to assign a root name to a group of spectra and then
+append an index number of 4 or more digits starting with 0000.
+So spectra, by default, have the form root.0000, root.0001, ...
+To specify the spectra, the user types only the root name and the range
+of indices such as "root" and "0-99,112-113,105-108".
+The range decoder accesses the spectral indices in the order given
+as opposed to access in ascending order, so that the spectrum root.0112
+will be processed before root.0105 in the example specification above.
+Spectra having more general names may be specified using the
+standard IRAF filename expansion methods if the 
+the range specification is given as null.
+.PP
+The specification of large numbers of images is an area where
+most IRAF applications are weak. Resorting to odd combinations
+of bracket and backslash characters in filename specifications 
+is obscure to new users and still fails to
+meet the general need. The range specification adopted for ONEDSPEC
+comes closer but introduces a fixed image name format.
+.sp 1
+.SH
+Apertures -- A way to group data
+.PP
+Many spectrographs generate multiple spectra simultaneously by
+placing more than one slit or aperture in the focal plane.
+Examples include the IIDS, IRS, and Cryogenic Camera in use
+at Kitt Peak. The Echelle may be considered a multi-aperture
+instrument for purposes of reductions by associating each order
+with an "aperture" number. 
+.PP
+The concept of aperture can be generalized to indicate a set of
+spectral data having common group properties such as
+wavelength coverage. Most tasks in ONEDSPEC will key off
+an aperture number in the image header and treat those
+common aperture spectra uniformly.
+Defining data groups which are to be processed in this fashion
+is a technique not generally exploited by reduction programs.
+This is  due in part to the problem of image header usage.
+.PP
+For programming convenience and to avoid an additional level
+of indirectness, in ONEDSPEC the aperture number is used directly as an
+index in many static arrays. The current implementation has
+a declaration for 50 apertures and due to the IIDS/IRS
+notation of apertures 0 and 1, the apertures are zero-indexed, contrary
+to standard IRAF nomenclature,
+from 0-49. It would certainly be better to map the aperture numbers
+to the allowable index range, but the added complexity of another
+level of indirectness seemed distracting. Actually the mapping
+can still be done by the header reader, "load_ids_hdr", and
+unmapped by the header writer, "store_keywords".
+.sp 1
+.SH
+Static versus dynamic arrays
+.PP
+Although dynamic storage would alleviate some of the memory
+requirements in the package, the use of static arrays aids
+readability and accounts for only about 10 percent of the total
+task memory space. Many of the arrays are arrays of pointers.
+For example, in the task BSWITCH, there is an array (called "imnames") 
+of pointers for the names of spectral images, several for each aperture.
+The actual space for the names is dynamically allocated,
+so first we allocate an array of pointers for each
+aperture:
+.sp 1
+.DS
+     call salloc (imnames[aperture], nr_names, TY_POINT)
+.DE
+.sp 1
+Then, for each of these pointers, space must be allocated for the
+character arrays:
+.sp 1
+.DS
+     do i = 1, nr_names
+         call salloc (Memp[imnames[aperture]+i-1], SZ_LINE, TY_CHAR)
+.DE
+.sp 1
+Later to access the character strings, a name is specified as:
+.sp 1
+.DS
+     Memc[Memp[imnames[aperture]+nr_of_this_spectrum-1]]
+.DE
+.sp 1
+If the "imnames" array was also dynamically allocated, the
+above access would be even less readable.
+If memory requirements become a serious problem, then these ONEDSPEC
+tasks should be modified.
+.sp 1
+.SH
+Output image names
+.PP
+To retain the consistent usage of root names and ranges, output
+spectra also have the form root.nnnn. For user convenience,
+the current output root name and next suffix are maintained as
+package parameters onedspec.output and onedspec.next_rec.
+The latter parameter is automatically updated each time a
+new spectrum is written. This is done by the individual tasks
+which directly access this package parameter.
+.PP
+There is an interesting side effect when using indirect parameters
+(e.g. )onedspec.output) for input. In the local task parameter
+file, the mode of the parameter must be declared hidden. So when the user
+does an "lpar task", those parameters appear to be unnecessary
+(that is, they are enclosed in parenthesis). When run,
+prompts appear because the parameter is an automatic mode
+parameter in the package parameter file.
+If run as a background task, this is more annoying.
+Unfortunately, any other choice of parameter modes produces
+less desirable actions.
+.sp 1
+.SH
+ONEDUTIL
+.PP
+As the number of tasks in ONEDSPEC started growing, the
+need for a subdivision of the package became clear.
+The first cut was made at the utility level, and a number
+of task names (not necessarily physical tasks) were
+moved out into the ONEDUTIL submenu. In the future,
+additional tasks will eventually require another subpackage.
+.PP
+Actually, many of the tasks in ONEDUTIL may be more at home
+in some other package, but a conscious effort was made to
+avoid contaminating other IRAF packages with tasks written for
+the ONEDSPEC project.  If all the following tasks are relocated, 
+then the need for ONEDUTIL is reduced.
+.PP
+Two of the entries in ONEDUTIL may be considered as more appropriate
+to DATAIO - RIDSMTN and WIDSTAPE. In fact RIDSMTN can
+replace the version currently in DATAIO. WIDSTAPE may replace the
+DATAIO task WIDSOUT if the usage of header parameters does not
+present a problem.
+.PP
+The task MKSPEC may be a candidate for the ARTDATA package.
+It should be enhanced to include optional noise generation.
+Also, it may be appropriate for SINTERP to replace INTERP
+in the UTILITY package.
+.PP
+I suppose one could argue that SPLOT belongs in the PLOT package.
+Certainly, the kludge script BPLOT should be replaced by a more
+general batch plot utility in PLOT.
+Also, the two task names, IDENTIFY and REIDENTIFY are present
+in the ONEDSPEC menu for user convenience, but the task declarations
+in ONEDSPEC.CL refer to tasks in the LONGSLIT package.
+.PP
+Because ONEDUTIL is a logical separation of the tasks, not
+a complete physical task breakup, there is no subdirectory
+for ONEDUTIL as there is in other packages. This is a bit messy
+and it may be best to completely disentangle the tasks in the
+subpackage into a true package having all the implications.
+.LP
+.SH
+2. Task Information
+.PP
+There are currently about 30 tasks in the ONEDSPEC package.
+These are summarized in the menu listing below and
+a brief description of some less obvious aspects of each follows.
+.sp 1
+.DS L
+   ONEDSPEC
+
+	addsets   - Add subsets of strings of spectra
+	batchred  - Batch processing of IIDS/IRS spectra
+	bswitch   - Beam-switch strings of spectra to make obj-sky pairs
+	calibrate - Apply sensitivity correction to spectra
+	coincor   - Correct spectra for photon coincidence
+	dispcor   - Dispersion correct spectra
+	extinct   - Correct data for atmospheric extinction
+	flatfit   - Sum and normalize flat field spectra
+	flatdiv   - Divide spectra by flat field
+	identify  - Identify features in spectrum for dispersion solution
+	iids	  - Set reduction parameters for IIDS
+	irs	  - Set reduction parameters for IRS
+	onedutil  - Enter ONEDSPEC Utility package
+	process   - A task generated by BATCHRED
+	reidentify- Automatically identify features in spectra
+	sensfunc  - Create sensitivity function
+	slist     - List spectral header elements
+	splot     - Preliminary spectral plot/analysis
+	standard  - Identify standard stars to be used in sensitivity calc
+	subsets   - Substract pairs in strings of spectra
+
+   ONEDUTIL
+
+	bplot	  - Batch plots of spectra
+	coefs     - Extract mtn reduced ceofficients from henear scans
+	combine   - Combine spectra having different wavelength ranges
+	lcalib	  - List calibration file data
+	mkspec    - Generate an artificial spectrum
+	names     - Generate a list of image names from a string
+	rebin     - Rebin spectra to new dispersion parameters
+	ridsmtn   - Read IIDS/IRS mountain format tapes
+	sinterp   - Interpolate a table of x,y pairs to create a spectrum
+	widstape  - Write Cyber format IDSOUT tapes
+.DE
+.sp 1
+.SH
+ADDSETS
+.PP
+Spectra for a given object may have been observed through more than
+one instrument aperture. For the IIDS and IRS, this is the most common
+mode of operation. Both apertures are used to alternately observe
+the program objects. 
+.PP
+Each instrument aperture may be considered an
+independent instrument having unique calibration properties, and
+the observations may then be processed completely independently
+until fully calibrated. At that point the data may be combined to
+improve signal-to-noise and reduce systematic errors associated
+with the alternating observing technique. Because the data are
+obtained in pairs for IIDS and IRS (but may be obtained in groups
+of larger sizes from other instruments), ADDSETS provides a way 
+to combine the pairs of observations.
+.PP
+Each pair in the input string is added to produce a single output
+spectrum. Although the word "pair" is used here, the parameter
+"subset" defines the number of elements in a "pair" (default=2).
+The input string is broken down into groups where each group
+consists of the pair of spectra defined in order of the input
+list of image names.
+.PP
+"Add" in ADDSETS means:
+.RS
+.IP 1.
+Average the pairs if the data are calibrated to flux (CA_FLAG=0)
+optionally weighted by the integration time.
+.IP 2.
+Add the pairs if uncalibrated (CA_FLAG=-1).
+.RE
+.sp 1
+.SH
+BATCHRED
+.PP
+This is a script task which allows spectra from dual aperture instruments
+to be processed completely in a batch mode after the initial wavelength
+calibration and correction has been performed. The processes which
+may be applied and the tasks referenced are:
+.RS
+.IP 1.
+Declaring observations as standard stars for flux calibration (STANDARD).
+.IP 2.
+Solving for the sensitivity function based on the standard stars (SENSFUNC).
+.IP 3.
+Generating object minus sky differences and summing individual
+observations if several were made (BSWITCH).
+.IP 4.
+Correcting for atmospheric extinction (BSWITCH).
+.IP 5.
+Applying the system sensitivity function to generate flux calibrated
+data (CALIBRATE).
+.IP 6.
+Adding pairs of spectra obtained through the dual apertures (ADDSETS).
+.RE
+Any or all of these operations may be selected through the task
+parameters.
+.PP
+BATCHRED generates a secondary script task called PROCESS.CL
+which is a text file containing  constructed commands to the
+ONEDSPEC package. This file may be edited by the user if an
+entry to BATCHRED is incorrect. It may also be saved, or appended
+by further executions of BATCHRED.
+.PP
+BATCHRED also generates a log file of the output generated by the
+ONEDSPEC tasks it calls.
+.sp 1
+.SH
+BSWITCH
+.PP
+This task combines multiple observations of a single object
+or multiple objects taken through a multiaperture instrument.
+Object minus sky differences are generated as pairs of
+spectra are accumulated, then optionally corrected for
+atmospheric extinction, and the differences added together
+with optional weighting using counting statistics.
+Each instrument aperture is considered an independent
+device.
+.PP
+Despite the apparently simple goal of this task, it is probably
+the most complicated in the ONEDSPEC package due to the
+bookkeeping load associated with automated handling of large data sets
+having a number of properties associated with each spectrum (e.g
+object or sky, aperture number, exposure times).
+.PP
+There are several modes in which BSWITCH can operate. The mode
+appropriate to the IIDS and IRS assumes that the spectra
+are input in an order such that after 2N (N=number of
+instrument apertures) spectra have been
+accumulated, an equal number of object and sky spectra have been
+encountered in each aperture. 
+When in this mode, a check is made after 2N spectra
+have been processed, and the optional extinction correction is
+applied to the differences of the object minus sky, and then
+(optionally weighted and) added into an accumulator for the aperture.
+.PP
+If the IIDS mode is switched off, then no guarantee can be
+made that sky and object spectra pair off. If extinction
+correction is required, it is performed on each spectrum
+as it arrives, including sky spectra if any. The spectra are
+then added into separate accumulators for object and sky for
+each aperture after optional weighting is applied.
+.PP
+If after all spectra have been processed, there are no sky
+spectra, the object spectrum is written out. If there is no
+object spectrum, the sky spectrum is written out after
+multiplying by -1. (This allows adding an object later on with
+addsets, but the -1 multiply is probably a mistake.)
+If at least one of each, object and sky spectra were encountered,
+then the difference is computed and written out. Since
+all accumulations are performed in count rates and later converted
+back to counts, the object and sky spectra may have different
+exposure times (non IIDS mode only).
+.PP
+A statistics file is maintained to provide an indication of the
+quality of the individual spectra going into the sum. The
+statistics information is maintained internally and only
+written out after the sums have been generated.
+The basic data in the file is the count rate of the spectrum
+having the largest count rate, and the ratios of the count rates from
+all other spectra to that one.
+.PP
+If weighting is selected, the weights are taken as proportional to
+the count rate (prior to extinction correction) over a wavelength 
+delimited region of the spectrum. (Perhaps the weight
+should be proportional to counts, not count rate.)
+The default wavelength region is the entire spectrum.
+If the total count rate is negative, the weight is assigned
+a value of 0.0 and will be disregarded in the sum. (The counts
+may be negative if the object minus sky difference approaches zero
+on a bright and cloudy night.)
+.PP
+If extinction is selected, an extinction table is read from the
+package calibration file. An optional additive term may be applied
+as computed by the system sensitivity task SENSFUNC which is placed
+in the parameter sensfunc.add_const. A revision to the standard
+extinction table (delta extinction as a function of wavelength)
+may be read from a text file whose name is specified by the parameter
+sensfunc.rev_ext_file. The file format is that of a text file
+having pairs of (wavelength, delta extinction) on each line.
+[The option to solve for this function in SENSFUNC has not yet been
+implemented, but BSWITCH can read the file that would be generated.
+Thus, one can experiment with revisions, although this has never been
+tested.] BSWITCH will interpolate the values given in the file
+so that a course estimate of the revision may be entered, say if the
+deltas at U, B, V, R, and I are known.
+.PP
+BEWARE that the extinction correction is performed assuming the
+header parameters used for airmass refer to a "mean" airmass value
+for the exposure. In general the header value is wrong! It usually
+refers to the beginning, middle, or end of the exposure. I have
+never seen a header airmass value which was an equivalent airmass
+for the duration of the exposure. This is partly because there is
+no way to compute a single effective airmass; it is a function
+of wavelength, telescope position as a function of time, and
+the extinction function. Fortunately, for most observations
+this is not very significant. But anyone taking a one hour exposure near 
+3500 Angstroms at airmass values greater than 2, should not complain
+when the fluxes look a bit odd.
+.sp 1
+.SH
+CALIBRATE
+.PP
+Having a system sensitivity function allows the data to be
+placed on an absolute flux scale. CALIBRATE performs this
+correction using the output sensitivity function from SENSFUNC. Operations are
+keyed to the instrument aperture, and a system sensitivity
+function is required for each observing aperture, although
+this requirement may be overriden.
+.PP
+A valid exposure time is required (a value of 1.0 should
+probably be assumed if not present) to compute the observed
+count rate. Input counts are transformed to units of
+ergs/cm2/sec/Angstrom (or optionally ergs/cm2/sec/Hz).
+CALIBRATE will calibrate two dimensional images as well, applying the
+sensitivity function to all image lines.
+.PP
+The operation is performed on a pixel-by-pixel basis so that
+the defined sensitivity function should overlap precisely
+with data in terms of wavelength.
+.sp 1
+.SH
+COINCOR
+.PP
+This task applies a statistical correction to each pixel
+to account for undetected photoevents as a result of
+coincidental arrival of photons. This is a detector
+specific correcton, although the photoelectric detector
+model provides a reasonable correction for many detectors
+when a judicious value for the deadtime parameter is chosen.
+This model assumes that the correction follows the
+typical procedures applied to photoelectric photometer data:
+.sp 1
+.DS L
+     Ic = Io * exp [Io * dt / T]
+.DE
+.sp 1
+where Ic is the corrected count rate in a pixel, Io is the
+observed count rate in that pixel, dt is the detector deadtime,
+and T is the observation integration time.
+.PP
+In addition to the photoelectric model, a more accurate model
+is available for the IIDS and is included in COINCOR. This
+model is taken from Goad (1979, SPIE Vol 172, 86.) and the correction
+is applied as:
+.sp 1
+.DS L
+     Ic = ln [1 - Io * t] / t
+.DE
+.sp 1
+where t is sweep time between pixel samples (t=1.424 msec).
+The IIDS differs from a photomultiplier detector, in that
+there is a fixed rate at which each pixel is sampled due to
+time required for the dissector to sweep across the image tube
+phospher whether a photoevent has occurred in a pixel or not. 
+The photomultiplier plus discriminator system
+assumes that once a photoevent has been recorded, the detector is
+dead until a fixed interval has elapsed.
+.sp 1
+.SH
+DISPCOR
+.PP
+If a relation is known linking pixel coordinate to user coordinate
+(i.e. wavelength as a function of pixel number), then any non-linearities
+can be removed by remapping the pixels to a linear wavelength coordinate.
+This procedure, dispersion correction, is complicated by the
+lack of a wavelength-pixel solution which is derived from data simultaneously
+obtained with the object data. Any drifts in the detector then require
+an interpolation among solutions for the solution appropriate to
+the object observations. Depending on the detector, this interpolation
+may be a function of the time of observation, temperature, or some telescope
+parameter such as airmass.
+When multiple solutions are available, DISPCOR will linearly interpolate
+the solution in any available header parameter known to ONEDSPEC (see
+section 3).
+.PP
+Each solution is read from the database file created by the IDENTIFY
+task (in TWODSPEC$LONGSLIT), and the image name leading to that solution
+is also read from the database file. The image is opened to extract
+the header parameter to be used in the above interpolation.
+A null name for the interpolation parameter indicates that none
+is to be used. In this case, one of the options on the "guide"
+parameter should be set to indicate what solution should be used.
+The guide may be "precede", "follow", or "nearest" to select
+the most appropriate choice for each spectrum.
+.PP
+If an explicit wavelength solution is to be used, the parameter
+"reference" may be used to specify the image name of a comparison
+spectrum to be used as the reference for the wavelength solution.
+In this case all spectra will be corrected using a single solution - 
+no flexure correction will be applied.
+.PP
+If the parameter to be used for interpolation is a "time-like"
+variable, such as RA, UT, ST, then the variable is discontinuous
+at 24|0 hours. If UT is the chosen parameter (as has been the
+case for IIDS and IRS spectra), the discontinuity occurs at
+5 PM local Kitt Peak time. A comparison spectrum taken at 4:59PM
+(=23:59h UT, =just before dinner), will be treated as an "end of
+the night" observation rather than a beginning of the night
+observation. To circumvent this error, the parameter, "time_wrap",
+can be specified to a time at which a true zero should be assigned.
+For UT at Kitt Peak, a choice like 17h UT (=10AM local, =asleep),
+is an unlikely hour for nighttime observations to be made. Then for
+a given night's observations, 17h UT becomes the new zero point in time.
+.PP
+Each solution in the database may be any of the forms legal 
+to IDENTIFY: legendre, chebyshev, spline3, or spline1 - the form 
+is encoded in the database and will automatically be recalled.
+The interpolation in the solution is performed by locating the
+pixel location for each required wavelength for the two
+solutions bounding each observation and linearly interpolating
+for the appropriate pixel location. One cannot simply interpolate
+across the coefficients of the solutions to derive a new
+single solution because the solutions may have different forms
+or orders, so that the coefficients may have quite different
+meanings.
+.PP
+Dispersion correction requires that there be equal intervals
+of wavelength between pixels. The wavelength solution
+is of a form describing the wavelength for a given pixel location,
+not a pixel location for a given wavelength. So the solution
+must be inverted.
+.PP
+The inversion to pixel location for wavelength is done in the
+following way: The pixel coordinate in the solution is incremented
+until the desired wavelength is bounded. The pixel value for the
+desired wavelength is obtained by linearly interpolating across these
+two bounding pixel locations. A linear approximation appears to be
+very good for typical solutions, providing proper pixel locations to
+better than 0.01 pixels. An improvement may be obtained by
+increasing the order of the interpolation, but the improvement
+is generally not warranted because the wavelength solutions
+are rarely known to this accuracy. [Note that the use of real
+and not double precision limits the precision of this technique!
+For spectra longer than 50,000 pixels, the errors due to
+the precision of reals can be serious.]
+.PP
+Note that a transformation to
+a wavelength coordinate which is linear in the logarithm of
+wavelength only requires that the inversion occur at wavelengths
+selected by equal increments in the logarithm of wavelength.
+.PP
+During the actual remapping, 5 possible techniques are available.
+Actually there are only two techniques: re-interpolation in 4 flavors,
+and rebinning by partial pixel summation. The re-interpolation
+may be performed with polynomials of order 1 (=linear), 3, or 5,
+or by a cubic spline. The 3rd and 5th order polynomials may introduce
+some ringing in the wings of strong, sharp, features, but the 5th order
+is good at preserving the high frequency component of the data.
+The linear and spline interpolators introduce significant smoothing.
+The rebinning algorithm offers conservation of flux but also smooths
+the data. In fact, rebinning to a course grid offers a good smoothing
+algorithm.
+.PP
+At some future date, it would be a good idea to include a "synch"
+function interpolator in the image interpolator package. This would
+be a little slower to process, but results in very good frequency
+response.
+.PP
+Other options in DISPCOR include "ids_mode" which forces spectra
+from all apertures to a single output mapping (starting wavelength
+and pixel-to-pixel increment), and "cols_out" forces the output spectra
+to a specified length, zero-filling if necessary.
+.PP
+DISPCOR will correct two-dimensional data by applying the
+remapping to all lines in the image. If the input two-dimensional
+spectrum has only one line, the output spectrum will be written as
+a one-dimensional spectrum.
+.sp 1
+.SH
+EXTINCT
+.PP
+Extinction is currently only available as a script file which drives
+BSWITCH. This is possible by suppressing all options: weighting,
+ids_mode, statistics file, and setting the subset pair size to the
+number of instrument apertures.
+.sp 1
+.SH
+FLATDIV
+.PP
+This task divides the specified spectra by their flat field spectra.
+This is not much more than an "en mass" spectrum divider, with the
+exceptions that the header elements are used to key on the
+aperture number so that the appropriate flat field spectrum is used,
+and that the header processing flags are checked to prevent
+double divisions and subsequently set after the division. Also,
+division by zero is guarded by setting any zeroes in the flat field
+spectrum to 1.0 prior to the division.
+.sp 1
+.SH
+FLATFIT
+.PP
+Pixel-to-pixel variations in the detector response can be removed
+by dividing all observations by a flat field spectrum.
+Flat field spectra are generally obtained by observing a source
+having a continuous energy distribution, such as a tungsten filament
+lamp. This is sometimes called a "quartz" lamp when the enclosing
+glass bulb is made with quartz rather than silicon. The quartz
+enclosure transmits ultraviolet light much better than glass.
+.PP
+If the color temperature of the source is very low (or very high, though
+this is extremely unlikely), then a color term would be introduced
+into the data when the flat is divided into the data.
+Large scale variations in the system sensitivity also introduce a
+color term into the flat - the same variations that are introduced into
+any spectrum taken with the system. [Large scale variations are 
+evaluated by STANDARD and SENSFUNC, and removed by CALIBRATE.]
+This is not of any particular importance except that counting
+statistics are destroyed by the division.
+.PP
+To preserve the statistics, many find it desirable to divide by a flat
+field spectrum which has been filtered to remove any large scale variations
+but in which the pixel-to-pixel variations have been retained.
+A filtered flat can be obtained by fitting a low order polynomial
+through the spectrum and dividing the spectrum by the polynomial.
+The result is a spectrum normalized to 1.0 and having high frequency
+variations only. If one does not care to preserve the statistics,
+then this procedure is not required. In fact, for certain instruments
+(the IRS), the fitting and normalizing procedure is not recommended
+because some intermediate order curvature can be introduced.
+.PP
+The purpose of FLATFIT is to find the combination of parameters
+which produces a well flattened flat with a minimum of wiggles.
+The usual curve fitting package is used to fit a function (chebyshev,
+legendre, spline3, spline1) to the flats. Pixel rejection is
+user selectable by a choice of cutoff sigmas, both above and below
+the mean, and an optional growing region [A growing region is the number
+of pixels on either side of one rejected which will also be rejected - 
+Growing regions are not recommended for most spectral applications].
+Any number of iterations may be used to further reject discrepant
+pixels. The fitting may be performed interactively and controlled by cursor
+keystrokes to select the fitting order, and other fit parameters.
+.PP
+Prior to the fit, the specified spectra are read, optionally corrected
+for coincidence losses, and added to accumulators appropriate to
+their instrument apertures. Each aperture is treated independently,
+except that, the interactive fitting mode may be selected to operate
+on the first aperture only, and then apply the same fitting parameters
+to all other aperture accumulations. Or the interactive procedure
+may be selected to operate on all apertures or none.
+.PP
+After the fit has been done, the fit is divided into the accumulation
+and written as a new spectrum having a specified root name and a trailing
+index indicating the aperture.
+.sp 1
+.SH
+IDENTIFY
+.PP
+This task (written by Frank Valdes) is used to identify features
+in the comparison arcs to be used in the solution for a wavelength calibration.
+The solution is performed interactively for at least one spectrum
+and then optionally in a batch mode using REIDENTIFY.
+IDENTIFY writes to a database file which will contain the solutions
+generated from each input comparison spectrum. The database is
+later used by DISPCOR to correct spectra according to the solution.
+.sp 1
+.SH
+IIDS
+.PP
+This script file initializes several hidden parameters in a
+variety of tasks to values appropriate to the IIDS instrument.
+There is also a script for the IRS. There should probably be
+a script for resetting the parameters to a default instrument.
+These parameters are:
+.RS
+.IP 1.
+onedspec.calib_file - the package parameter indicating which file
+should be used for standard star calibration data and the atmospheric
+extinction table (=onedspec$iids.cl.)
+.IP 2.
+addsets.subset - the number of instrument apertures (=2).
+.IP 3.
+bswitch.ids_mode - assume and check for data taken in beam-switched
+quadruple mode (=yes).
+.IP 4.
+coincor.ccmode - coincidence correction model (=iids).
+.IP 5.
+coincor.deadtime - detector deadtime (=1.424e-3 seconds)
+.IP 6.
+dispcor.flex_par - the name of the parameter to be used as the
+guide to removing flexure during the observations (=ut).
+.IP 7.
+dispcor.time_wrap - the zero point to be adopted for the
+flexure parameter if it is a time-like variable having a discontinuity
+at 0/24 hours (=17).
+.IP 8.
+dispcor.idsmode - should data from all instrument apertures be dispersion
+corrected to a uniform wavelength scale? (=yes).
+.IP 9.
+dispcor.cols_out - the number of columns (row length of the spectrum)
+to which the output corrected spectrum should be forced during
+mapping (=1024).
+.IP 10.
+extinct.nr_aps - the number of instrument apertures (=2).
+.IP 11.
+flatfit.order - the order of the fit to be used when fitting to
+the flat field spectra (=6).
+.IP 12.
+flatfit.coincor - apply coincidence correction to the flat field
+spectra during accumulations (=yes).
+.IP 13.
+flatdiv.coincor - apply coincidence correction to all spectra during
+the flat field division process (=yes).
+.IP 14.
+identify.function - the fitting function to be used during the wavelength
+solution process (=chebyshev).
+.IP 15.
+identify.order - the order of the fit to be used during the wavelength
+solution process (=6).
+.RE
+.sp 1
+.SH
+IRS
+.PP
+This script file initializes several hidden parameters in a
+variety of tasks to values appropriate to the IRS instrument.
+These parameters are:
+.RS
+.IP 1.
+onedspec.calib_file - the package parameter indicating which file
+should be used for standard star calibration data and the atmospheric
+extinction table (=onedspec$irs.cl.)
+.IP 2.
+addsets.subset - the number of instrument apertures (=2).
+.IP 3.
+bswitch.ids_mode - assume and check for data taken in beam-switched
+quadruple mode (=yes).
+.IP 4.
+coincor.ccmode - coincidence correction model (=iids).
+.IP 5.
+coincor.deadtime - detector deadtime (=1.424e-3 seconds)
+.IP 6.
+dispcor.flex_par - the name of the parameter to be used as the
+guide to removing flexure during the observations (=ut).
+.IP 7.
+dispcor.time_wrap - the zero point to be adopted for the
+flexure parameter if it is a time-like variable having a discontinuity
+at 0/24 hours (=17).
+.IP 8.
+dispcor.idsmode - should data from all instrument apertures be dispersion
+corrected to a uniform wavelength scale? (=yes).
+.IP 9.
+dispcor.cols_out - the number of columns (row length of the spectrum)
+to which the output corrected spectrum should be forced during
+mapping (=1024).
+.IP 10.
+extinct.nr_aps - the number of instrument apertures (=2).
+.IP 11.
+flatfit.order - the order of the fit to be used when fitting to
+the flat field spectra. IRS users have frequently found that
+any curvature in the fit introduces wiggles in the resulting
+calibrations and a straight divide by the flat normalized to the
+mean works best (=1).
+.IP 12.
+flatfit.coincor - apply coincidence correction to the flat field
+spectra during accumulations (=no).
+.IP 13.
+flatdiv.coincor - apply coincidence correction to all spectra during
+the flat field division process (=no).
+.IP 14.
+identify.function - the fitting function to be used during the wavelength
+solution process (=chebyshev).
+.IP 15.
+identify.order - the order of the fit to be used during the wavelength
+solution process. The IRS has strong deviations from linearity
+in the dispersion and a fairly high order is required to correct
+the dispersion solution (=8).
+.RE
+.sp 1
+.SH
+ONEDUTIL
+.PP
+This is a group of utility operators for the ONEDSPEC package. They
+are documented separately after the ONEDSPEC operators. ONEDUTIL
+is a "pseudo-package" - it acts like a package under ONEDSPEC, but
+many of its logical tasks are physically a part of ONEDSPEC. This
+is done to minimize disk storage requirements, and to logically
+separate some of the functions from the main ONEDSPEC menu which
+was getting too large to visually handle.
+.sp 1
+.SH
+PROCESS
+.PP
+This task generally does not exist until the user executes the
+script task BATCHRED which creates PROCESS.CL, a secondary script
+file containing a CL command stream to batch process spectra.
+The task is defined so that the CL is aware of its potential
+existence. It is not declared as a hidden task so that the
+user is also aware of its existence and may execute PROCESS
+in the foreground or background.
+.sp 1
+.SH
+REIDENTIFY
+.PP
+This task (written b Frank Valdes) is intended to be used after
+IDENTIFY has been executed. Once a wavelength solution has been
+found for one comparison spectrum, it may be used as a starting point
+for subsequent spectra having similar wavelength characteristics.
+REIDENTIFY provides a batch-like means of performing wavelength solutions
+for many spectra. The output solution is directed to a database text file
+used by DISPCOR.
+.sp 1
+.SH
+SENSFUNC
+.PP
+This task solves for the system sensitivity function across
+the wavelength region of the spectra by comparison of observations
+of standard stars to their (assumed) known energy distribution.
+Each instrument aperture is treated completely independently
+with one exception discussed later. SENSFUNC is probably the
+largest task in the ONEDSPEC package due to heavy use of
+interactive graphics which represents more than half of the
+actual coding.
+.PP
+Input to SENFUNC is the "std" text file produced by STANDARD 
+containing the ratio of the count rate adjusted for atmospheric extinction 
+to the flux of the star in ergs/cm2/s/Angstrom. Both the count rates and
+fluxes are the average values in the pre-defined bandpasses tabulated
+in the calibration file (indicated by the parameter onedspec.calib_file).
+.PP
+Each entry is the "std" file may have an independent set of wavelength sampling
+points. After all entries have been loaded, a table containing all sampled
+wavelengths is built (a "composite" wavelength table) and all sensitivity
+values are reinterpolated onto this sampling grid. This allows the inclusion
+of standards in which the observational samples are not uniform.
+.PP
+When multiple measurements are available, one of two corrections may
+be applied to the data to account for either clouds or an additive extinction
+term. The effect of clouds is assumed to be grey. Each contributing
+observation is compared to the one producing the highest count rate ratio
+at each wavelength sample. The deviation averaged over all wavelengths
+for a given observation is derived and added back to
+each wavelength sample for that observation. This produces a shift
+(in magnitudes) which, on the average across the spectrum, accounts
+for an extinction due to clouds. This process is called "fudge"
+primarily for historical reasons (from the IPPS, R.I.P.) and also
+because there is questionable justification to apply this correction.
+One reason is so that one can better assess the errors
+in the data after a zero-point correction has been made.
+Another is that the sensitivity function is that closest to a cloud-free
+sky so that claibrations may approach a true flux system if one
+standard was observed during relatively clear conditions.
+Alsom there are claims that the "color solution" is improved by "fudging", but
+I admit that I don't fully understand this argument.
+.PP
+[Perhaps it goes as follows: 
+Although a grey scale correction is applied to each observation,
+a color term is introduced in the overall solution. Consider the
+case where 5 magnitudes of cloud extinction obscure one standard
+relative to another. This star generates a sensitivity curve which
+is a factor of 100 smaller. When averaged with the other curve,
+any variations are lost, and the net curve will be
+very similar to the first curve divided by 2. Now apply a "fudge"
+of 5 magnitudes to the second curve. On the average, both curves have
+similar amplitudes, so variations in the second now influence the
+average. The net curve then has color dependent variations not
+in the "un-fudged" net curve. If we assume that the variations in
+the individual observations are not systematic, then "fudge" will 
+improve the net color solution. Amazing, isn't it?
+End of hypothesis.]
+.PP
+The second form of correction is much more justifiable. In ONEDSPEC
+it is referred to as a "grey shift" and accounts for possible
+changes in the standard atmospheric extinction model due to
+a constant offset. SENSFUNC will optionally solve for this constant
+provided the observations sample a range of airmass values.
+The constant is computed in terms of magnitudes per airmass, so
+if the airmass range is small, then a large error is likely.
+To solve for this value, a list of pairs of delta magnitude (from the
+observation having the greatest sensitivity) as a function of
+delta airmass (relative to the same observation) is generated 
+for all observations. The list is fit using a least squares solution 
+of the form:
+.sp 1
+.DS L
+     delta_mag = delta_airmass * grey_shift
+.DE
+.sp 1
+Note that this is a restricted least-squares in the sense that there
+is no zero-point term. The standard curve fit package in IRAF
+does not support this option and the code to perform this is included
+in SENSFUNC.
+.PP
+Because the atmosphere is likely to be the same one for observations
+with each instrument aperture, it is not appropriate to limit
+the least-squares solution to the individual apertures, but rather
+to combine all the data to improve the solution. This would mean
+that the user could not view the effects of applying the grey term
+until all apertures had been analyzed. So, although each aperture is
+solved independently to derive a preliminary value, a final value is
+computed at the end when all data have been reviewed. This is the
+one exception to the independent aperture equals independent
+instrument philosophy.
+.PP
+When "fudging" is applied, the sensitivity function that is generated
+is altered to account for the shifts to the observations. But when
+the "grey shift" is computed, it cannot be directly applied to
+the sensitivity function because it must be modified by the
+observing airmass for each individual object. So the grey shift
+constant is written into the image headers of the generated
+sensitivity functions (which are IRAF images), and also placed
+into the task parameter "add_const" to be used later by BSWITCH.
+.PP
+SENSFUNC can be run in an interactive mode to allow editing
+of the sensitivity data. There are two phases of interaction:
+(1) a review of the individual observations in which every data
+element can be considered and edited, and (2) a review of the
+composite sensitivity table and the calculated fit to the table.
+In the interactive mode, both phases are executed for every instrument
+aperture.
+.PP
+At both phases of the interactive modes there will be a plot of the
+error in the input values for each wavelength. This is an RMS
+error. [The IPPS plotted standard error which is always a smaller number
+and represents the error in the mean; the RMS represents the error
+in the sample. I'm not sure which is better to use, but RMS is easier
+to understand. RMS is the same as the standard deviation.]
+During phase one, the rms is computed as the standard deviation of
+the sensitivity in magnitudes; but during phase two, it is computed
+as the standard deviation in raw numbers
+and then converted to a magnitude equivalent. The latter is more
+correct but both converge for small errors.
+.PP
+There is one option in SENSFUNC which has never been tried and it won't
+work - the option to enter a predefined table of sensitivities as
+a function of wavelength as a simple text file. This option may
+be useful a some time and should probably be fixed. I think the
+only problem with it is a lack of consistency in the units.
+.PP
+An additional option has been requested but it is not clear that it
+is a high priority item - the ability to compute the extinction
+function. There may be instances when the mean extinction table
+is not appropriate, or is not known. If sufficient data are
+available (many observations of high precision over a range of airmasses
+during a photometric night), then the extinction function is
+calculable. Presently SENSFUNC can only compute a constant offset to
+the extinction function, but the same algorithm used may be applied
+at each wavelength for which observations are made to compute a
+correction to an adopted extinction function (which may be zero),
+and the correction can then be written out to the revised extinction
+table file. This file will then be read by BSWITCH during the
+extinction correction process.
+So at each wavelength, pairs of delta magnitude as a function of
+delta airmass are tabulated and fit as above:
+.sp 1
+.DS L
+     delta_mag[lambda] = delta_airmass * delta_extinction[lambda]
+.DE
+.sp 1
+Because the data have been heavily subdivided into wavelength bins,
+there are only a few measurements available for solving this
+least-squares problem and the uncertainties are large unless many
+observations have been taken. Experience has shown that at least
+7-8 measurements are needed to come close, and 15 measurements are
+about the minimum to get a good solution. Unless the data are of
+high quality, the uncertainty in the solution is comparable to
+the error in assuming a constant offset to the mean extinction function.
+Nevertheless, the option should be installed at some time since
+some observers do obtain the necessary data. 
+.sp 1
+.SH
+SLIST
+.PP
+The spectrum specific header elements are listed in either a short
+or long form. See the discussion on headers (section 3) for an explanation
+of the terms. Values for airmass are printed if present in the header;
+otherwise, the value is given as the string "?????" to indicate no
+value present (even if one can be calculated from the telescope
+pointing information elsewhere in the header).
+.PP
+The short form header lists only the image name, whether it is
+an object or sky observation, the spectrum length, and the title.
+.sp 1
+.SH
+SPLOT
+.PP
+This is probably the second largest task in the ONEDSPEC package. It continues
+to grow as users provide suggestions for enhancement, although
+the growth rate appears to be slowing. SPLOT is an interactive
+plot program with spectroscopy in mind, although it can be used
+to plot two dimensional images as well.
+.PP
+SPLOT should still be considered a prototype - many of the algortihms
+used in the analysis functions are crude, provided as interim
+software to get results from the data until a more elaborate package
+is written. It would probably be best to create an analysis specific
+package - SPLOT is reasonably general, and to enhance it further
+would complicate the keystroke sequences.
+.PP
+Ideally it should be possible to do anything to a spectrum with
+a single keystroke. In reality, several keystrokes are required.
+And after 15 or 20 functions have been installed, the keystroke
+nomenclature becomes obscure - all the best keys are used up, and
+you have to resort to things like '(' which is rather less
+mneumonic than a letter. So some of the functionality in SPLOT
+has been assigned to the "function" submenu invoked by 'f' and
+exited by 'q' keystrokes. These include the arithmetic  operators:
+add, multiply by a constant, add, subtract, multiply, divide by
+a spectrum, and logarithms, square root, inverse, and absolute
+value of a spectrum.
+.PP
+Some of the analysis functions include: equivalent width, line centers,
+flux integration under a line, smoothing, spectrum flattening,
+and deblending of lines.
+.PP
+The deblender  has serious limitations but handles about half the
+cases that IIDS/IRS users are interested in. It fits only
+Gaussian models to the blends, and only a single width parameter.
+The fit is a non-linear least-squares problem, so starting values
+present some difficulties. All starting values are initialized to 1.0 -
+this includes the width, relative strengths of the lines, and deviation
+from intial marked centers. The iterative solution usually converges
+for high signal-to-noise data, but may go astray, resulting in
+a numerical abort for noisy data. If this occurs, it is often
+possible to find a solution by fitting to a single strong line
+to force a better approximation to the starting values, and then refit
+the blend of interest.
+.PP
+The non-linear least-squares routine is one obtained from an industrial
+source. The code is very poorly written and in FORTRAN. No one should
+attempt to understand it. The basic algorithm is an unconstrained simplex
+minization search combined with a parabolic linear least-squares approximation
+when in the region of a local minimum.
+A test was made comparing this to the algorithm in Bevington, and the
+Bevington algorithm appeared less likely to converge on noisy data.
+Only one test case was used, so this is hardly a fair benchmark.
+.PP
+The problem with non-convergence is that a floating point error is
+almost surely to arise. This is usually a floating point over/under
+flow while computing an exponential (as required for a Gaussian).
+In UNIX, there is apparently no easy way to discriminate from
+FORTRAN which floating point exception has occurred, and so there
+is no easy way to execute a fix up and continue. This is most
+unfortunate because the nature of these non-linear techniques is
+that given a chance, they will often recover from searching
+down the wrong alley. A VMS version of the same routines seems to
+survive the worst data because the error recovery is handled
+somewhat better. [The VMS version also seems to run much faster,
+presumably because the floating point library support is better
+optimized.]
+.PP
+The net result of all this, is that a weird undocumented subroutine
+is used which provides no error estimate. The Bevington routines
+do provide an error estimate which is why I wanted to use them.
+[In fact, there is no way to exactly compute the errors in the
+fit of a non-linear least-squares fit. One can however apply
+an approximation theory which assumes the hypersurface can be
+treated locally as a linear function.]
+.PP
+There are several methods for computing equivalent widths in SPLOT.
+The first method for measuring equivalent width is simply to integrate the
+flux above/under a user defined continuum level. Partial pixels
+are considered at the marked endpoints. A correction for the pixel size, 
+in Angstroms, is applied because the units of equivalent width are Angstroms.
+You will probably get a different answer when doing equivalent
+width measurements in channel mode ('$' keystroke) as compared to
+wavelength mode ('p').
+.PP
+Centering is performed as a weighted first moment of the region:
+.sp 1
+.DS L
+     int1 = integral [ (I-Ic) * sqrt (I-Ic) * w]
+     int2 = integral [ (I-Ic) * sqrt (I-Ic)    ]
+     xc = int1 / int2
+.DE
+.sp 1
+where I is the intensity at the pixel at wavelength w, and Ic is
+the estimated continuum intensity. The square root term provides
+the weighting assuming photon statistics [sigma = sqrt(I)], and xc
+is the derived center of the region.
+.PP
+An alternative method for equivalent widths was supplied by Caty
+Pilachowski and is described in some detail in the help file for
+SPLOT. This method is fast and insensitive to cursor settings, so
+the user can really zip through a spectrum quickly.
+.PP
+Smoothing is performed using a simple boxcar smooth of user specified
+size (in pixels). To handle edge effects, the boxcar size is
+dynamically reduced as the edge is approached, thereby reducing
+the smoothing size in those regions.
+.PP
+The flattening operator is a preliminary one, written before the
+curve fitting package was available in IRAF. This operator
+should probably be re-written to include the interactive
+style used in FLATFIT. Currently the flattening is done
+using classic polynomial least-squares with pixel rejection
+chosen to preferentially reject absorption lines and strong
+emission lines. The rejection process is repeated through
+a number of iterations specifiable as a hidden parameter to SPLOT.
+This is poorly done - the order of the fit and the number of
+iterations should be controllable while in SPLOT. However,
+experimentation has shown that for a given series of spectra,
+the combination of rejection criteria, order, and iteration count
+which works well on one spectrum will generally work well
+on the other spectra. Note that the flatten operator attempts to
+find a continuum level and normalize to that continuum, not to the
+average value of the spectrum.
+.PP
+There are also the usual host of support operators - expansion,
+overplotting, and so forth. There is also a pixel modifer mode
+which connects two cursor positions. This forces a replot of the entire
+spectrum after each pair of points has been entered. This should
+probably be changed to inhibit auto-replot.
+.PP
+Some users have requested that all two cursor operators allow
+an option to escape from the second setting in case the wrong
+key was typed. I think this is a good idea, and might be implemented
+using the "esc" key (although I could not seem to get this keystroke
+through the GIO interface).
+.PP
+Another user request is the option to overplot many spectra with
+autoscaling operational on the entire range. This is also a good
+idea. Yet another improvement could be made by allowing the user
+to specify the x and y range of the plot, rather than autoscaling.
+.PP
+There is one serious problem with respect to plotting spectra
+corrected to a logarithmic wavelength scale. It would be nice to
+plot these spectra using the logarithmic axis option, but this
+option in GIO requires that at least one entire decade of x axis
+be plotted. So for optical data, the x axis runs from 1000 Angstroms
+to 10,000 Angstroms. Imagine a high dispersion plot having only 100
+Angstroms of coverage - the plot will look like a delta function!
+The current version of SPLOT uses a linear axis but plots in
+the log10 of wavelength. Not very good, is it.
+.sp 1
+.SH
+STANDARD
+.PP
+This task computes the sensitivity factor of the instrument
+at each wavelength for which an a priori measured flux value is known
+and within the wavelength range of the observations.
+Sensitivity is defined as
+[average counts/sec/Angstrom]/[average ergs/cm2/sec/Angstrom]
+over the specified bandpass for which the star has been measured.
+Both numerator and denominator refer to quantities above the
+Earth's atmosphere and so the count rates must be corrected for
+extinction.
+The wavelengths of known measurements, the bandpasses, the
+fluxes (in magnitudes), and the mean extinction table
+are read from a calibration file whose name is specified
+by the calib_file parameter (see LCALIB for a description of this
+file). If a magnitude is exactly 0.0, it is assumed 
+that no magnitude is known for this star at the wavelength
+having a 0.0 magnitude. This allows entries having incomplete
+information.
+.PP
+As each observation is read, it is added into an accumulator for
+its aperture. Or subtracted if it is a sky measurement. After
+a pair of object and sky observations have been added, the
+difference is corrected for extinction (as in BSWITCH), converted
+to counts per second, and integrations performed over the bandpasses
+for which flux measures are known. The bandpasses must be completely
+contained within the spectrum - partial coverage of a bandpass
+disqualifies it from consideration. The integrations are compared
+with the known flux values and the ratio is written to a text
+file (the "std" file) along with the wavelength of the measurement
+and the total counts in the bandpass. The total counts value may
+be used by SENSFUNC for weighting the measurements during averaging.
+.PP
+Many users are surprised by the order of the spectral names
+printed out as STANDARD executes since the order is not necessarily
+ascending through the spectrum list. This is because the name
+printed is the name of the object spectrum most recently associated
+with an object-sky pair. So if a sky pair is several spectra down the
+list, an intervening object-sky pair taken through a different
+instrument aperture may be processed in the meantime.
+For example, say spectra 1-8 are taken so that object spectra
+numbers 1 and 7 and sky spectra 3 and 5 are taken through aperture 0, 
+object spectra 4 and 6  and sky spectra 2 and 8 are taken through
+aperture 1. [This is a very common pattern for IIDS/IRS users.]
+Then spectrum 1 and 3 will pair up and be processed first (spectrum
+name 1 will be printed). Then 4 and 2 (name 4 printed), then 
+7 and 5 (name 7 printed), and then 6 and 8 (name 6 printed).
+So the order of names printed will be 1,4,7,6.  Simple, isn't it?
+.PP
+If the input spectra are not taken in a beam-switched mode
+then the parameter "beam_switch" should be set to no.
+Then no sky subtraction will be attempted.
+.PP
+The user may enter sensitivity values directly into a file and use
+it as the "std" file for a correction.
+See the help file for STANDARD for a description of the entries in
+the file, and see a typical file.
+.PP
+STANDARD offers a limited interactive mode. The first sky subtracted
+spectrum is displayed and the bandpasses at which sensitivity
+measurements are made will be shown as boxes. This provides a means
+to see where the measurements are falling on the observational
+data and to assess whether a bandpass may be including some
+absorption edge which may be affecting the measurement. While it
+is true that the wavelengths of the reference measurements should
+fall in the same place, the effects of instrument resolution and
+inaccuracies in the wavelength calibration may shift the positions
+of the apparent bandpasses. The samples may then be biased.
+.PP
+The second purpose of the interactive mode is to allow the user
+to artificially create new bandpasses on the fly. By placing the
+cursor to bound a new wavelength region, STANDARD will interpolate
+in the magnitude table of the reference star to estimate the magnitude
+of the star at the bounded wavelength. The sensitivity will be calculated
+at that wavelength just as if the bandpass had come from the calibration
+file. This option should be exercised with care. Obviously, points
+should not be generated between reference wavelengths falling on
+strong absorption lines, or on a line either. This option is most useful
+when at a high dispersion and few samples happen to fall in the
+limited wavelength region. Sufficient space is allocated for 10
+artificial samples to be inserted. Once the artificial bandpasses
+have been designated, they are applied to the entire sequence of
+spectra for the current invocation of STANDARD. Once STANDARD
+completes, the added bandpasses are forgotten. This prevents
+an accidental usage of newly created bandpasses on stars of different
+spectral types where a bandpass may fall in a region of continuum
+for one star, but on an absorption line in another.
+.sp 1
+.SH
+SUBSETS
+.PP
+This is a simple task to subtract the second spectrum from the
+first in a series of spectra. So if spectra 1-10 are input,
+5 new spectra will be created from 1 minus 2, 3 minus 4, and so on.
+This is a straight subtraction, pixel for pixel, with no
+compensation for exposure time differences.
+The header from the first spectrum of the pair is applied to the
+output spectrum.
+.sp 1
+.SH
+The ONEDUTIL tasks
+.PP
+These utility tasks are logically separated from the ONEDSPEC
+package.
+.sp 1
+.SH
+COEFS
+.PP
+This task reads the header parameters contained in comparison arc spectra
+describing the wavelength solution generated by the mountain reduction
+program and re-writes the solution parameters into a database
+text file for use by DISPCOR. Otherwise those solutions would be
+lost. COEFS assumes that the coefficients represent a Legendre
+polynomial which is what the mountain reduction programs use.
+.sp 1
+.SH 
+COMBINE
+.PP
+When an object has been observed over a wide range of wavelength
+coverage by using more than one instrumental setup (such as
+a blue and a red setting) or with different instruments (such
+as IUE and the IRS), it is often desirable to combine the 
+spectra into a single spectrum. COMBINE will rebin a group of
+spectra to new spectra having a single dispersion and average the
+new spectra to create a single long spectrum.
+If there are gaps in the composite spectrum, zeroes are used
+as fillers. Ideally those pixels which have no known value
+should be considered blank pixels. IRAF does not currently
+support blank pixels, so zeroes are used for now. [One
+might suggest using INDEF, but then all other routines will
+have to check for this value.]
+A side effect of choosing 0.0 is that during the averaging
+of overlapping spectra, a true 0.0 will be ignored by COMBINE.
+The basic rebinning algorithms used in DISPCOR are used in COMBINE
+(and also REBIN).
+.PP
+The averaging can be weighted by exposure time, or by user assigned weights. 
+It would be better if each spectrum had an associated vector of
+weights (one weight at each wavelength) so that the weighted averaging
+could be done on a pixel basis. This is very expensive in terms
+of both storage and file access overhead since each spectrum would 
+require twice the storage and number of files. 
+[Actually weights could be small 4 bit integers and take up very little space.]
+.PP
+A less ideal alternative would be to place a small number 
+(about 16) of weight parameters
+in the header file which represent the approximate weights of that many
+regions of the spectrum, and then one could interpolate in these parameters
+for a weight appropriate to the pixel of interest.
+.PP
+A third solution (and even less ideal)
+is to place a single parameter in the header which
+represents an average weight of the entire spectrum. For the latter two cases,
+the header weights could be derived from the average counts per 
+wavelength region - the region being the entire spectrum in the last case.
+The weights must be entered into the header during the BSWITCH operation
+since that is the last time that true counts are seen. [An implicit
+assumption is that counts are proportional to photons. If data from
+two different instruments are to be averaged, then the weights should be
+expressed in photons because the ratio of counts to photons is highly
+instrument dependent.]
+.PP
+COMBINE suffers from a partial pixel problem at the end points.
+Interpolation at the ends can lead to an underestimate of the flux
+in the last pixels because the final pixel is not filled. When averaging
+in data from another spectrum or instrument, these pixels show up
+as sharp drops in the spectrum. The problem appears due to the
+rebinning algorithm and should be corrected someday (also in DISPCOR
+and REBIN).
+.sp 1
+.SH
+LCALIB
+.PP
+This utility provides a means of checking the calibration files
+containing the standard star fluxes and extinction table. 
+Any of the entries in the file may be listed out - the bandpasses,
+extinction, standard star names, standard star fluxes in either
+magnitudes, flambda, or fnu. For a description of the calibration
+file format, see the help documentation for LCALIB.
+.PP
+The primary uses for LCALIB are to verify that new entries in
+the tables are correct, to generate a list of standard star names
+in a calibration file, and to produce a table of fluxes for a given standard
+star. The table may then be used to generate a spectrum over a specified
+wavelength region using SINTERP and overplotted with observational
+data to check the accuracy of the reductions.
+.sp 1
+.SH
+MKSPEC
+.PP
+MKSPEC provides a way to generate a limited set of artificial
+spectra. Noise generation is not available. The current options
+are to generate a spectrum which is either a constant, a ramp,
+or a black body. The spectrum may be two dimensional, but
+all image lines will be the same.
+.sp 1
+.SH
+NAMES
+.PP
+This is the simplest task in the ONEDSPEC package. It
+generates the image file names which are implied by a
+root name and record string. The primary use for this
+task is to generate a list of image names to be used
+as input for some other program such as WFITS.
+The output from NAMES can be redirected to file
+and that file used with the "@file" notation for image
+name input. An optional parameter allows an additional
+string to be appended to the generated file name 
+to allow a subraster specification.
+.sp 1
+.SH
+REBIN
+.PP
+Spectra are rebinned to the wavelength parameters specified
+by either matching to a reference spectrum or by user input.
+The algorithms are those used by DISPCOR and the same options
+for the interpolation method are available. REBIN is useful
+when data are obtained with different instruments or setups
+producing roughly comparable wavelength ranges and possibly
+different dispersions, and the data are to be compared.
+REBIN may also be used as a shift operator by specifying a
+new starting wavelength. Or it may be used as a smoothing operator
+by specifying a course dispersion. It may also be used
+to convert between the two formats - linear in wavelength and 
+linear in the logarithm of wavelength. This latter option has
+not been thoroughly exercised - proceed with caution.
+.sp 1
+.SH
+RIDSMTN
+.PP
+This task was stolen from the DATAIO package to make the following
+modification: IIDS and IRS data are both written as 1024 pixel
+spectra at the mountain. But the detectors do not produce a full
+1024 pixels of acceptable data. In fact the IRS only has 936 pixels.
+The data are written this way to conform to the IIDS ideal spectrum
+which does have 1024 pixels, but the first few (about 6) are not usable.
+To signal the good pixels, the IIDS/IRS header words NP1 and NP2 are
+set to the beginning and ending good pixels. Actually NP1 points to
+the first good pixel minus one. [Really actually NP1 and NP2 may be reversed,
+but one is big and the other small so you can tell them apart.]
+.PP
+The version of RIDSMTN in ONEDUTIL keys off these parameters and writes
+images containing only good pixels which means that the images will be
+smaller than 1024 pixels. The user has the option of overriding the
+header values with the task parameters "np1" and "np2". These may be
+specified as 1 and 1024 to capture the entire set of pixels written to
+tape or any other subset. Beware that np1 and np2 as task parameters
+refer to the starting pixel and ending pixel respectively. None of this
+nonsense about possible role reversals or "first good minus one" is
+perpetuated.
+.sp 1
+.SH
+SINTERP
+.PP
+I think this is a handy little program. It provides a way to make
+an IRAF spectral image from a table of values in a text file.
+The table is interpolated out to any length and at any sampling
+rate. A user can create a table of corrections to be applied to
+a set of spectra, for example, use SINTERP to build a spectrum,
+and run CALIBRATE to multiply a group of spectra by the correction.
+.PP
+The original raison d'etre for SINTERP was to create spectra of
+standard stars from the listing of fluxes generated by LCALIB.
+Using SPLOT the created spectrum can be overplotted with calibrated
+observations to compare the true tabulated fluxes with the observed
+fluxes.
+.PP
+SINTERP grew out of the task INTERP in the UTILITIES package
+and works pretty much the same way. One major change is that
+the table containing the x-y pairs is now stored in a dynamically
+allocated array and can be as large as the user requests. The
+default size is 1024 pairs, but the parameter tbl_size can
+be set to a larger value. This then allows one to create a spectrum
+from its tabulated values of wavelength and flux even if the
+the table is several thousand elements long.
+Note that the option to route the output from INTERP to
+STDOUT has been retained if a new table is to be generated rather
+than an IRAF image.
+.PP
+Another major change from INTERP is the use of the IRAF curve fitting
+routines as an option. These were not originally available.
+The choices now include linear or curvey interpolators, Legendre
+or Chebyshev polynomial fits, and cubic or linear splines.
+.sp 1
+.SH
+WIDSTAPE
+.PP
+This task has vague origins in the DATAIO task WIDSOUT which writes
+a tape having the format of the IDSOUT package which ran on the
+CYBER (R.I.P.). For convenience to users this format has been
+maintained for spectra having lengths up to 1024 pixels.
+The version in DATAIO requires that the user enter all the header
+parameters as task parameters. For several hundred spectra, this
+approach is unwieldy. Because the ONEDSPEC package uses the header
+parameters heavily, it is able to read them directly and write the
+values to the tape file without user intervention.
+.PP
+The output tape (or diskfile) may be in either ASCII or EBCDIC format.
+Spectra shorter than 1024 are zero filled. Each invocation of
+the task write a new tape file followed by a tape mark (EOF).
+.LP
+.SH
+3. Image Header Parameters
+.PP
+The ONEDSPEC package uses the extended image header to extract
+information required to direct processing of spectra. If the
+header information were to be ignored, the user would need to
+enter observing parameters to the program at the risk of
+typographical errors, and with the burden of supplying the
+data. For more than a few spectra this is a tedious job,
+and the image header information provides the means to eliminate
+almost all the effort and streamline the processing.
+.PP
+However, this requires that the header information be present,
+correct, and in a recognizable format. To meet the goal of
+providing a functional package in May 1985, the first iteration
+of the header format was to simply adopt the IIDS/IRS headers.
+This allowed for processing of the data which would be first
+used heavily on the system, but would need to be augmented at
+a later date. The header elements may be present in any order,
+but must be in a FITS-like format and have the following names
+and formats for the value fields:
+.sp 1
+.TS
+l c l
+l l l.
+Parameter	Value Type	Definition
+
+HA	SX	Hour angle (+ for west, - for east)
+RA	SX	Right Ascension
+DEC	SX	Declination
+UT	SX	Universal time
+ST	SX	Sidereal time
+AIRMASS	R	Observing airmass  (effective)
+W0	R	Wavelength at center of pixel 1
+WPC	R	Pixel-to-pixel wavelength difference
+NP1	I	Index to first pixel containing good data (actually first-1)
+NP2	I	Index to last pixel containing good data (last really)
+EXPOSURE	I	Exposure time in seconds (ITIME is an accepted alias)
+BEAM-NUM	I	Instrument aperture used for this data (0-49)
+SMODE	I	Number of apertures in instrument minus one (IIDS only)
+OFLAG	I	Object or sky flag (0=sky, 1=object)
+DF-FLAG	I	Dispersion fit made on this spectrum (I=nr coefs in fit)
+SM-FLAG	I	Smoothing operation performed on this spectrum (I=box size)
+QF-FLAG	I	Flat field fit performed on this spectrum (0=yes)
+DC-FLAG	I	Spectrum has been dispersion corrected (0=linear, 1=logarithmic)
+QD-FLAG	I	Spectrum has been flat fielded (0=yes)
+EX-FLAG	I	Spectrum has been extinction corrected (0=yes)
+BS-FLAG	I	Spectrum is derived from a beam-switch operation (0=yes)
+CA-FLAG	I	Spectrum has been calibrated to a flux scale (0=yes)
+CO-FLAG	I	Spectrum has been coincidence corrected (0=yes)
+DF1	I	If DF-FLAG is set, then coefficients DF1-DFn (n <= 25) exist
+.TE
+.PP
+The values for the parameters follow the guidelines adopted for
+FITS format tapes. All keywords occupy 8 columns and contain
+trailing blanks. Column 9 is an "=" followed by a space. The value field
+begins in column 11. Comments to the parameter may follow a "/" after
+the value field.  The value type code is as follows:
+.RS
+.IP SX
+This is a sexigesimal string of the form '12:34:56   ' where the first
+quote appears in column 11 and the last in column 30.
+.IP R
+This is a floating point ("real") value beginning in column 11 and
+extending to column 30 with leading blanks.
+.IP I
+This is an integer value beginning in column 11 and extending to
+column 30 with leading blanks.
+.RE
+.sp 1
+.PP
+The parameters having FLAG designations all default to -1 to indicate
+that an operation has not been performed.
+The ONEDSPEC subroutines "load_ids_hdr" and "store_keywords" follow
+these rules when reading and writing spectral header fields.
+If not present in a header, load_ids_hdr will assume a value of zero
+except that all flags are set to -1, and the object flag parameter
+defaults to object.
+.PP
+When writing an image, only the above parameters are stored by store_keywords.
+Other header information is lost. This needs to be improved.
+.PP
+Not all programs need all the header elements. The following table
+indicates who needs what. Tasks not listed generally do not require
+any header information. Header elements not listed are not used.
+The task SLIST requires all the elements listed above.
+The task WIDTAPE requires almost all (except NP1 and NP2).
+The headings are abbreviated task names as follows:
+.sp 1
+.nr PS 8
+.ps 8
+.TS
+center;
+l l | l l | l l.
+ADD	addsets	COI	coincor	FIT	flatfit
+BSW	bswitch	COM	combine	REB	rebin
+CAL	calibrate	DIS	dispcor	SPL	splot
+COE	coefs	FDV	flatdiv	STA	standard
+.TE
+.sp 1
+.TS
+center, tab(/);
+l | l | l | l | l | l | l | l | l | l | l | l | l.
+Key/ADD/BSW/CAL/COE/COI/COM/DIS/FDV/FIT/REB/SPL/STA
+_
+HA// X////////// X/
+RA// X////////// X/
+DEC// X////////// X/
+ST// X////////// X/
+UT// X////////// X/
+AIRMASS// X////////// X/
+W0// X/ X/// X//// X/ X/ X/
+WPC// X/ X/// X//// X/ X/ X/
+NP1/////////// X///
+NP2/////////// X///
+EXPOSURE/ X/ X/// X/ X///// X///
+BEAM-NUM// X/ X//// X/ X/ X// X/ X//
+OFLAG// X////////// X/
+DF-FLAG//// X
+DC-FLAG// X//// X//// X/ X/ X/
+QD-FLAG//////// X/
+EX-FLAG// X/
+BS-FLAG// X/
+CA-FLAG/ X// X//////// X/
+CO-FLAG///// X//
+DFn//// X/
+.TE
+.nr PS 11
+.ps 11
+.bp
+.SH
+Headers From Other Instruments
+.PP
+The header elements listed above are currently created only when reading
+IIDS and IRS data from one of the specific readers: RIDSMTN and RIDSFILE.
+The time-like parameters, (RA, DEC, UT, ST, HA), are created in a
+compatible fashion by RCAMERA and RFITS (when the FITS tape is written
+by the KPNO CCD systems).
+.PP
+For any other header information, the ONEDSPEC package is at a loss
+unless the necessary information is edited into the headers with
+an editing task such as HEDIT. This is not an acceptable long term
+mode of operation, and the following suggestion is one approach to
+the header problem.
+.PP
+A translation table can be created as a text file which outlines
+the mapping of existing header elements to those required by the
+ONEDSPEC package. A mapping line is needed for each parameter
+and may take the form:
+.sp 1
+.RS
+.DC
+1D_param    default    hdr_param    key_start   value_start   type   conversion
+.DE
+.RE
+.sp 1
+where the elements of an entry have the following definitions:
+.sp 1
+.TS
+center, tab(	);
+l lw(5i).
+1D_param	T{
+The name of the parameter expected by the ONEDSPEC package,
+such as EXPOSURE, OFLAG, BEAM-NUM.  
+T}
+
+default	T{
+A value to be used if no entry is found for this parameter or if
+no mapping exists.
+T}
+
+hdr_param	T{
+The string actually present in the existing image header to be
+associated with the ONEDSPEC parameter. 
+T}
+
+key_start	T{
+The starting column number at which the string starts 
+in the header. 
+T}
+
+value_start	T{
+The starting column number at which the string describing the
+value of the parameter starts in the header. 
+T}
+
+type	T{
+The format type of the parameter: integer, real, string, boolean,
+sexigesimal. 
+T}
+
+conversion	T{
+If the format type is string, a further conversion may 
+optionally be made to one of the formats listed under type. 
+The conversion may requires some expression evaluation.
+T}
+.TE
+.sp 1
+.PP
+Consider the example where the starting wavelength of a
+spectrum is contained in a FITS-like comment and the object-
+sky flag in a similar fashion:
+.sp 1
+.DS
+     COMMENT = START-WAVE  4102.345   / Starting wavelength
+     COMMENT = OBJECT/SKY  'SKY      '/ Object or Sky observation
+.DE
+.sp 1
+The translation file entries for this would be:
+.sp 1
+.DS
+     W0  0.0  START-WAVE  12  24  R
+     OFLAG 0  OBJECT/SKY  12  25  S  SKY=0;OBJECT=1
+.DE
+.sp 1
+The first entry is fairly simple. The second requires an expression
+evaluation and second conversion.
+.PP
+A translation file can be built for each instrument and its
+special header format, and the file name can be associated with a
+ONEDSPEC package parameter. The two subroutines in ONEDSPEC dealing
+directly with the headers (load_ids_hdr and store_keywords)
+can be modified or replaced to access this file and
+translate the header elements.
diff --git a/noao/onedspec/doc/sys/onedv210.ms b/noao/onedspec/doc/sys/onedv210.ms
new file mode 100644
index 00000000..431c84f5
--- /dev/null
+++ b/noao/onedspec/doc/sys/onedv210.ms
@@ -0,0 +1,680 @@
+.nr PS 9
+.nr VS 11
+.de LS
+.RT
+.if \\n(1T .sp \\n(PDu
+.ne 1.1
+.if !\\n(IP .nr IP +1
+.if \\n(.$-1 .nr I\\n(IR \\$2n
+.in +\\n(I\\n(IRu
+.ta \\n(I\\n(IRu
+.if \\n(.$ \{\
+.ds HT \&\\$1
+.ti -\\n(I\\n(IRu
+\\*(HT
+.br
+..
+.ND
+.TL
+ONEDSPEC/IMRED Package Revisions Summary: IRAF Version 2.10
+.AU
+Francisco Valdes
+.AI
+IRAF Group - Central Computer Services
+.K2
+P.O. Box 26732, Tucson, Arizona 85726
+May 1992
+.NH
+Introduction
+.LP
+The IRAF NOAO spectroscopy software, except for the \fBlongslit\fR
+package, has undergone major revisions.  The revisions to the aperture
+extraction package, \fBapextract\fR, are described in a separate
+document.  This paper addresses the revisions in the \fBonedspec\fR
+package and the spectroscopic image reduction packages in the
+\fBimred\fR package.  In addition to the revisions summary given here
+there is a new help topic covering general aspects of the new
+\fBonedspec\fR package such as image formats, coordinate systems, and
+units.  This help topic is referenced under the name
+"onedspec.package".
+.LP
+There are a large number of revisions both minor and major.  To avoid
+obscuring the basic themes and the major revisions in a wealth of minor
+detail, this document is organized into sections of increasing detail.  The
+most important aspects of the revisions are described in a major highlight
+section followed by a minor highlight section.  Then a reorganization chart
+for the \fBonedspec\fR package is presented showing where various
+tasks have been moved, which have been deleted, and which are new.
+Finally, a summary of the revisions to each task is presented.
+.LP
+I hope that the many new capabilities, particularly as presented in the
+highlight section, will outweigh any disruption in accomodating to so
+many changes.
+.NH
+Major Highlights
+.LP
+The major highlights of the revisions to the NOAO spectroscopy software
+are listed and then discussed below.
+
+.DS
+\(bu Non-linear dispersion calibration
+\(bu Integration of dispersion coordinates with the core system 
+\(bu Sinc interpolation
+\(bu Plotting in user selected units including velocity
+\(bu Integration of long slit spectra and 1D formats
+\(bu New \fBimred\fR packages featuring streamlined reductions
+.DE
+
+Possibly the most significant revision is the generalization allowing
+non-linear dispersion calibration.  What this means is that spectra do
+not need to be interpolated to a uniform sampling in wavelength or
+logarithmic wavelength.  The dispersion functions determined from
+calibration arc lines by \fBidentify\fR, \fBreidentify\fR,
+\fBecidentify\fR, or \fBecreidentify\fR can be simply assigned to the
+spectra and used throughout the package.  It is also possible to assign
+a dispersion table or vector giving the wavelengths at some or all of
+the pixels.  Note, however, that it is still perfectly acceptible to
+resample spectra to a uniform linear or log-linear dispersion as was
+done previously.
+.LP
+For data which does not require geometric corrections, combining, or
+separate sky subtraction the observed sampling need never be changed
+from the original detector sampling, thus avoiding any concerns over
+interpolation errors.  In other cases it is possible to just
+interpolate one spectrum, say a sky spectrum, to the dispersion of
+another spectrum, say an object spectrum, before operating on the two
+spectra.  There are several new tasks that perform interpolations to a
+common dispersion, not necessarily linear, when operating on more than
+one spectrum.  In particular, the new task \fBsarith\fR and the older
+task \fBsplot\fR now do arithmetic on spectra in wavelength space.
+Thus, one no longer need be concerned about having all spectra
+interpolated to the same sampling before doing arithmetic operations as
+was the case  previously.
+.LP
+The trade-off in using non-linear dispersion functions is a more complex
+image header structure.  This will make it difficult to import to non-IRAF
+software or to pre-V2.10 IRAF systems.  However, one may resample to a
+linear coordinate system in those cases before transfering the spectra as
+FITS images having standard linear coordinate keywords.
+.LP
+On the subject of interpolation, another important addition is the
+implementation of sinc interpolation.  This is generally considered
+the best interpolation method for spectra, however, it must be used
+with care as described below.
+Sinc interpolation approximates applying a phase shift to the fourier
+transform of the spectrum.  Thus, repeated interpolations do not accumulate
+errors (or nearly so) and, in particular, a forward and reverse
+interpolation will recover the original spectrum much more closely than
+other interpolation methods.  However, for undersampled (where the fourier
+transform is no longer completely represented), strong features, such as
+cosmic rays or narrow emission or absorption lines, the ringing can be much
+more severe than the polynomial interpolations.  The ringing is especially
+a concern because it extends a long way from the feature causing the
+ringing; 30 pixels with the truncated algorithm that has been added.  Note
+that it is not the truncation of the interpolation function which is at
+fault but the undersampling of the narrow features!
+.LP
+Because of the problems seen with sinc interpolation it should be used with
+care.  Specifically, if there are no undersampled, narrow features it is a
+good choice but when there are such features the contamination of the
+spectrum by ringing is more severe, corrupting more of the spectrum,
+than with other interpolation types.
+.LP
+The dispersion coordinates are now interfaced through the IRAF WCS
+(world coordinate system) interface.  This is important to users for
+two reasons.  First, operations performed on spectral images by IRAF
+core system tasks and the IRAF image I/O system will have access to the
+dispersion coordinates and will properly modify them as necessary.  The
+most common such operation is applying an image section to a spectrum
+either during an image copy or as input to another task.  In this case
+the relation between the pixels in the image section and their
+wavelengths is preserved.  For example one may \fBsplot\fR a section of
+a large spectrum and get the correct wavelengths.  The second reason is
+to allow use of proper dispersion coordinates in such IRAF tasks as
+\fBlistpixels\fR, \fBimplot\fR, and \fBgraph\fR.
+.LP
+The new package supports a variety of spectral image formats.  The
+older formats are understood when reading them.  In particular the one
+dimensional "onedspec" and the two dimensional "multispec" format will
+still be acceptable as input.  Note that the image naming syntax for
+the "onedspec" format using record number extensions is a separate
+issue and is still provided but only in the \fBimred.iids\fR and
+\fBimred.irs\fR packages.  Any new spectra created are either a one
+dimensional format using relatively simple keywords and a two or three
+dimensional format which treats each line of the image as a separate
+spectrum and uses a more complex world coordinate system and keywords.
+For the sake of discussion the two formats are still called "onedspec"
+and "multispec" though they are not equivalent to the earlier formats.
+.LP
+In addition, the one dimensional spectral tasks may also now operate on
+two dimensional images directly.  This is done by using the DISPAXIS
+keyword in the image header or a package dispaxis parameter if the
+keyword is missing to define the dispersion axis.  In addition there is
+a summing parameter in the packages to allow summing a number of lines
+or columns.  If the spectra are wavelength calibrated long slit
+spectra, the product of the \fBlongslit.transform\fR task, the
+wavelength information will also be properly handled.  Thus, one may
+use \fBsplot\fR or \fBspecplot\fR for plotting such data without having
+to extract them to another format.  If one wants to extract one
+dimensional spectra by summing columns or lines, as opposed to using
+the more complex \fBapextract\fR package, then one can simply use
+\fBscopy\fR (this effectively replaces \fBproto.toonedspec\fR).
+.LP
+The tasks \fBsplot\fR and \fBspecplot\fR allow use of and changes
+between various dispersion units.  Spectra may be plotted in units all
+the way from Hertz to Mev.  The units may also be inverted to plot in
+wavenumbers, such as inverse centimeters, and the decimal log may be
+applied, to plot something like log wavelength or log frequency.  One
+special "unit" which is available is a velocity computed about a
+specified wavelength/frequency.  The multiple unit capability was one
+of the last major changes made before the V2.10 release so the complete
+generalization to arbitrary units has not been completed.  Dispersion
+calibration and image world coordinate system generally must still be
+done in Angstroms, particularly if flux calibration is to be done.  The
+generalization to other units throughout the package is planned for a
+later release.
+.LP
+The last of the changes catagorized as a major highlight is the
+addition of a number of special packages for generic or specific
+types of instruments and data in the \fBimred\fR package.  Most of these
+package include a highly streamlined reduction task that combines
+all of the reduction operations into a single task.  For example,
+the \fBspectred.doslit\fR task can extract object, standard star, and
+arc spectra from long slit images, apply a consistent dispersion
+function based on only a single interactively performed dispersion
+solution, compute a sensitivity function and end up with flux
+calibrated spectra.  Another example, is \fBhydra.dohydra\fR for
+extracting, flatfielding, dispersion calibrating, and sky subtracting
+spectra from the NOAO Hydra multifiber spectrograph.  There are user's
+guides for each of these new reduction tasks.
+.NH
+Minor Highlights
+.LP
+There are some further highlights which are also quite important
+but which are secondary to the previous highlights.  These are listed
+and discussed below.
+
+.DS
+\(bu Greater use of package parameters
+\(bu An observatory database
+\(bu A more flexible \fBidentify/reidentify\fR
+\(bu Only one \fBdispcor\fR
+\(bu Spatial interpolation of dispersion solutions
+\(bu Deblending of arbitrary number of gaussian components
+\(bu Manipulating spectral formats
+\(bu Improved fitting of the continuum and related features
+\(bu Various new tasks
+.DE
+
+There is an even greater use of package parameters than in the previous
+release.  Package parameters are those which are common to many of the
+the tasks in the package and which one usually wants to change in
+one place.  The new package parameters are the default observatory for
+the data if the observatory is not identified in the image header
+(discussed further below), the interpolation type used
+when spectra need to be resampled either for dispersion calibration
+or when operating on pairs of spectra with different wavelength
+calibration, and the default dispersion axis and summing parameters
+for long slit and general 2D images (as discussed in the last section).
+You will find these parameters not only in the \fBonedspec\fR package but in
+all the spectroscopic packages in the \fBimred\fR package.
+.LP
+A number of spectroscopic tasks require information about the location
+of the observation.  Typically this is the observatory latitude for
+computing air masses if not defined in the header.  Radial velocity
+tasks, and possible future tasks, may require additional information
+such as longitude and altitude.  The difficulty is that if such
+parameters are specified in parameter files the default may well be
+inappropriate and even if the users set then once, they may forget to
+update them in later reductions of data from a different observatory.
+In other words this approach is prone to error.
+.LP
+To address this concern observatory parameters are now obtained from an
+observatory database keyed by an observatory identifier.  If the image data
+contains an observatory keyword, OBSERVAT, the tasks will look up the
+required parameters from the observatory database.  Thus, if the images
+contain the observatory identifier, as does data from the NOAO
+observatories, they will always be correctly reduced regardless of the
+setting of any parameters.  Of course one has to deal with data from
+observatories which may not include the observatory identifier and may not
+have an entry in the observatory database.  There are provisions for sites
+and individual users to define local database files and to set the default
+observatory parameters.  This is all discussed in the help for the
+\fBobservatory\fR task.
+.LP
+The dispersion function fitting tasks \fBidentify\fR and
+\fBreidentify\fR have been improved in a number of important ways.
+These tasks now treat the input images as units.  So for long slit and
+multispectrum images one can move about the image with a few
+keystrokes, transfer solutions, and so on.  When transfering solutions
+between a multispectrum reference image and another multispectrum image
+with the same apertures using \fBreidentify\fR, the features and
+dispersion solutions are transfered aperture by aperture.  This avoids
+problems encountered by having to trace successively between apertures
+and having the apertures be in the same order.
+.LP
+On the subject of tracing in \fBreidentify\fR, in some cases it is
+desirable to use the same reference spectrum with all other sampled
+lines or columns in a long slit spectrum or apertures in a
+multispectrum image rather than propagating solutions across the
+image.  The latter method is necessary if there is a continuous and
+progress shift in the features.  But if this is not the situation then
+the loss of features when tracing can be a problem.  In this case the
+alternative of reidentifying against the same starting reference is now
+possible and there will not be the problem of an increasing loss of
+features.  On the other hand, the problem of lost features, whether
+tracing or not, can also be addressed using another new feature of
+\fBreidentify\fR, the ability to add features from a line list.  For
+both tracing and nontracing reidentifications, another useful new
+feature is automatic iterative rejection of poorly fitting lines in
+determining a new dispersion function noninteractively.
+.LP
+The nontracing reidentifications, the automatic addition of new lines, and
+the iterative rejection of poorly fitting lines in determining a new
+dispersion function are all responses to make the reidentification process
+work better without intervention.  However, as a last resort there is also
+a new interactive feature of \fBreidentify\fR.  By monitoring the log output of
+the reidentification process one can have a query be made after the
+automatic reidentification and function fitting to allow selectively
+entering the interactive feature identification and dispersion function
+fitting based on the logged output.  Thus if a fit has a particularly large
+RMS or a large number of features are not found one can chose to intervene
+in the reidentification process.
+.LP
+Dispersion calibration is now done exclusively by the task
+\fBdispcor\fR regardless of the spectrum format or dispersion solution
+type; i.e. solutions from \fBidentify\fR or \fBecidentify\fR.  In addition to
+allowing assignment of non-linear dispersion functions, as described
+earlier, \fBdispcor\fR has other new features.  One is that, in
+addition to interpolating dispersion solutions between two calibration
+images (usually weighted by time), it is now possible to interpolate
+zero point shifts spatially when multiple spectra taken simultaneously
+include arc spectra.  This is mostly intended for the new generation of
+multifiber spectrographs which include some fibers assigned to an arc
+lamp source.  However, it can be used for the classic photographic case
+of calibration spectra on the same plate.
+.LP
+The limitation to four lines on the number of gaussian components which
+can be deblended by the deblending option in \fBsplot\fR has been removed.
+A new feature is that line positions may be input from a line list as 
+well as the original cursor marking or terminal input.
+In addition an option to simultaneously determine a linear background
+has been added.  As a spinoff of the deblending option a new, noninteractive
+task, called FITPROFS, has been added.  This task takes a list of initial
+line positions and sigmas and simultaneously fits gaussians with a
+linear background.  One can constrain various combination of parameters
+and output various parameters of the fitting.  While it can be used to
+fit an entire spectrum it becomes prohibitively slow beyond a number like
+30.  A banded matrix approach is required in that case.
+.LP
+As mentioned earlier there is a new task called \fBscopy\fR for manipulating
+spectra.  It allows changing between various formats such as producing
+the separate, simple keyword structure, one dimensional images from multispec
+format images, combining multiple one dimensional spectra into the
+more compact multispec format, and extracting line or column averaged one
+dimensional spectra from two dimensional images.  It can also be
+used to select any subset of apertures from a multispec format,
+merge multiple multispec format spectra, and extract regions of spectra
+by wavelength.
+.LP
+The \fBcontinuum\fR task has been revised to allow independent
+continuum fits for each aperture, order, line, or column in images
+containing multiple spectra.  Instead of being based on the
+\fBimages.fit1d\fR task it is based on the new task \fBsfit\fR.
+\fBSfit\fR allows fitting the \fBicfit\fR functions to spectra and
+outputing the results in several ways such as the ratio (continuum
+normalization), difference (continuum subtraction), and the actual
+function fit.  In addition it allows outputing the input data with
+points found to be deviant by the iterative rejection algorithm of
+\fBicfit\fR replaced by the fitted value.  This is similar to
+\fBimages.lineclean\fR.  In all cases, this is may be done
+independently and interactively or noninteractively when there are
+multiple spectra in an image.
+.LP
+A number of useful new tasks have already been mentioned:
+\fBfitprofs\fR, \fBsarith\fR, \fBscombine\fR, \fBscopy\fR, and
+\fBsfit\fR.  There are two more new tasks of interest.  The task \fBdopcor\fR
+applies doppler shifts to spectra.  It applies the shift purely to the
+dispersion coordinates by adding a redshift factor which is applied by
+the coordinate system interface.  This eliminates reinterpolation and
+preserves both the shift applied and the original observed dispersion
+function (either linear or nonlinear).  The task can also modify the
+pixel values for various relativistic and geometric factors.  This task
+is primarily useful for shifting spectra at high redshifts to the local
+rest frame.  The second new task is called \fBderedden\fR.  It applies
+corrections for interstellar reddening given some measure of the
+extinction along the line of site.
+.NH
+ONEDSPEC Package Task Reorganization
+.LP
+The \fBonedspec\fR package dates back to the earliest versions of IRAF.  Some of
+its heritage is tied to the reduction of IRS and IIDS spectra.  One of
+the revisions made for this release has been to reorganize the various
+tasks and packages.  A few tasks have been obsoleted by new tasks or
+the functionality of the new dispersion coordinate system, a number
+of new tasks have been added, and a number of IRS and IIDS specific
+tasks have been moved to the \fBimred\fR packages for those instruments.
+While these packages are organized for those particular instruments they may
+also be used by data having similar characteristics of beam switching,
+coincidence corrections, and the requirement of sequential numeric
+extensions.
+.LP
+The table below provides the road map to the reorganization showing
+tasks which have disappeared, been moved, been replaced, or are new.
+
+.DS
+.TS
+center;
+r l l l r l l.
+V2.9	V2.10	ALTERNATIVE	V2.9	V2.10	ALTERNATIVE
+
+addsets		irs/iids	process		irs/iids
+batchred		irs/iids	rebin		scopy/dispcor
+bplot	bplot		refspectra	refspectra
+bswitch		irs/iids	reidentify	reidentify
+calibrate	calibrate		sapertures
+coincor		iids	sarith
+combine		scombine	scombine
+continuum	continuum		scopy
+	deredden		sensfunc	sensfunc
+dispcor	dispcor		setdisp		hedit
+	dopcor		sextract	scopy
+	fitprofs		sfit
+flatdiv		irs/iids	sflip		scopy/imcopy [-*,*]
+flatfit		irs/iids	shedit		hedit
+identify	identify		sinterp	sinterp
+lcalib	lcalib		slist	slist
+mkspec	mkspec		specplot	specplot
+names	names		splot	splot
+	ndprep		standard	standard
+observatory		noao	subsets		irs/iids
+powercor		iids	sums		irs/iids
+.TE
+.DE
+.NH
+IMRED Packages
+.LP
+Many of the \fBonedspec\fR tasks from the previous release have been
+moved to the \fBiids\fR and \fBirs\fR packages, as indicated above,
+since they were applicable only to these and similar instruments.
+.LP
+A number of new specialized spectroscopic instrument reduction packages
+have been added to the \fBimred\fR package.  Many of these have been in
+use in somewhat earlier forms in the IRAF external package called
+\fBnewimred\fR.  In addition the other spectroscopic package have been
+updated based on the revisions to the \fBonedspec\fR and
+\fBapextract\fR packages.  Below is a table showing the changes between
+the two version and describing the purpose of the spectroscopic
+packages.  Note that while many of these package are named for and
+specialized for various NOAO instruments these packages may be applied
+fairly straightforwardly to similar instruments from other
+observatories.  In addition the same tools for multifiber and slit
+spectra are collected in a generic package called \fBspecred\fR.
+
+.DS
+.TS
+center;
+r l l s
+r l l l.
+V2.9	V2.10	SPECTROSCOPY PACKAGE
+	argus	Fiber:	CTIO Argus Reductions
+specphot	ctioslit	Slit:	CTIO Slit Instruments
+echelle	echelle	Fiber Slit:	Generic Echelle
+	hydra	Fiber:	KPNO Hydra (and Nessie) Reductions
+iids	iids	Scanner:	KPNO IIDS Reductions
+irs	irs	Scanner:	KPNO IRS Reductions
+coude	kpnocoude	Fiber/Slit:	KPNO Coude (High Res.) Reductions
+	kpnoslit	Slit:	KPNO Slit Instruments
+msred	specred	Fiber/Slit:	Generic fiber and slit reductions
+observatory	-> noao
+setairmass
+.TE
+.DE
+.LP
+An important feature of most of the spectroscopic packages are specialized
+routines for combining and streamlining the different reduction operations
+for a particular instrument or type of instrument.  These tasks are:
+
+.DS
+.TS
+center;
+r r r.
+argus.doargus	ctioslit.doslit	echelle.doecslit
+echelle.dofoe	hydra.dohydra	iids.batchred
+irs.batchred	kpnocoude.do3fiber	kpnocoude.doslit
+kpnoslit.doslit	specred.dofibers	specred.doslit
+.TE
+.DE
+.NH
+ONEDSPEC Task Revisions in V2.10
+.LS ADDSETS 2
+Moved to the \fBiids/irs\fR packages.
+.LS BATCHRED
+Moved to the \fBiids/irs\fR packages.
+.LS BPLOT
+The APERTURES and BAND parameters been added to select 
+apertures from multiple spectra and long slit images, and bands
+from 3D images. Since the task is a script calling \fBsplot\fR, the
+many revisions to that task also apply. The version in the
+\fBiids/irs\fR packages selects spectra using the record number 
+extension syntax.
+.LS BSWITCH
+Moved to the \fBiids/irs\fR packages.
+.LS CALIBRATE
+This task was revised to operate on nonlinear dispersion 
+corrected spectra and 3D images (the \fBapextract\fR "extras"). The
+aperture selection parameter was eliminated (since the header
+structure does not allow mixing calibrated and uncalibrated
+spectra) and the latitude parameter was replaced by  the 
+observatory parameter. The observatory mechanism insures that
+if the observatory latitude is needed for computing an airmass
+and the observatory is specified in the image header the
+correct calibration will be applied. The record format syntax
+is available in the \fBiids/irs\fR packages. The output spectra are
+coerced to have real pixel datatype.
+.LS COINCOR
+Moved to the \fBiids\fR package.
+.LS COMBINE
+Replaced by \fBscombine\fR.
+.LS CONTINUUM
+This task was changed from a script based on \fBimages.fit1d\fR to a
+script based on \fBsfit\fR. This provides for individual independent
+continuum fitting in multiple spectra images and for additional
+flexibility and record keeping.  The parameters have been 
+largely changed.
+.LS DEREDDEN
+This task is new.
+.LS DISPCOR
+This is a new version with many differences. It replaces the
+previous three tasks \fBdispcor\fR, \fBecdispcor\fR and \fBmsdispcor\fR. It
+applies both one dimensional and echelle dispersion functions.
+The new parameter LINEARIZE selects whether to interpolate the
+spectra to a uniform linear dispersion (the only  option 
+available previously) or to assign a nonlinear dispersion 
+function to the image  without  any  interpolation.  The 
+interpolation function parameter has been eliminated and the
+package parameter INTERP is used to select the interpolation
+function. The new interpolation type "sinc" may be used but
+care should be exercised. The new task supports applying a
+secondary zero point shift spectrum to a master dispersion
+function and a spatial interpolation of the shifts  when 
+calibration spectra are taken at the same time on a different
+region of the same 2D image. The optional wavelength table may
+now also be an image to match dispersion parameters. The
+APERTURES and REBIN parameters have been eliminated.  If an
+input spectrum has been previously dispersion corrected it will
+be resampled as desired. Verbose and log file parameters have
+been added to log the dispersion operations as desired. The
+record format syntax is available in the \fBiids/irs\fR packages.
+.LS DOPCOR
+This task is new.
+.LS FITPROFS
+This task is new.
+.LS FLATDIV
+Moved to the \fBiids/irs\fR packages.
+.LS FLATFIT
+Moved to the \fBiids/irs\fR packages.
+.LS IDENTIFY
+The principle revision is to allow multiple aperture images and
+long slit spectra to be treated as a unit. New keystrokes
+allow jumping or scrolling within multiple spectra in a single
+image. For  aperture  spectra  the database entries are 
+referenced by image name and aperture number and not with image
+sections. Thus, \fBidentify\fR solutions are not tied to specific
+image lines in this case. There is a new autowrite parameter
+which may be set to eliminate the save to database query upon
+exiting. The new colon command "add" may be used to add
+features based on some other spectrum or arc type and then
+apply the fit to the combined set of features.
+.LS LCALIB
+This task has a more compact listing for the "stars" option and
+allows paging a list of stars when the star name query is not
+recognized.
+.LS MKSPEC
+This task is unchanged.
+.LS NAMES
+This task is unchanged.
+.LS NDPREP
+This task was moved from the \fBproto\fR package. It was originally
+written at CTIO for CTIO data. It's functionality is largely
+unchanged though it has been updated for changes in the 
+\fBonedspec\fR package.
+.LS OBSERVATORY
+New version of this task moved to \fBnoao\fR root package.
+.LS POWERCOR
+Moved to the \fBiids\fR package.
+.LS PROCESS
+Moved to the \fBiids/irs\fR package.
+.LS REBIN
+This task has been eliminated. Use \fBscopy\fR or \fBdispcor\fR.
+.LS REFSPECTRA
+A group parameter was added to allow restricting assignments by
+observing period; for example by night.  The record format
+option was removed and the record format syntax is available in
+the \fBiids/irs\fR packages.
+.LS REIDENTIFY
+This task is a new version with many new features.  The new
+features include  an  interactive  options  for reviewing 
+identifications, iterative rejection  of  features  during 
+fitting, automatic addition of new features from a line list,
+and the choice of tracing or using a single master reference
+when reidentifying features in other vectors of a reference
+spectrum. Reidentifications from a reference image to another
+image is done by matching apertures rather than tracing. New
+apertures not present in the reference image may be added.
+.LS SAPERTURES
+This task is new.
+.LS SARITH
+This task is new.
+.LS SCOMBINE
+This task is new.
+.LS SCOPY
+This task is new.
+.LS SENSFUNC
+The latitude parameter has been replaced by the observatory
+parameter. The 'i' flux calibrated graph type now shows flux
+in linear scaling while the new graph type 'l' shows flux in
+log scaling. A new colon command allows fixing the flux limits
+for the flux calibrated graphs.
+.LS SETDISP
+This task has been eliminated.  Use \fBhedit\fR or the package
+DISPAXIS parameter.
+.LS SEXTRACT
+Replaced by \fBscopy\fR.
+.LS SFIT
+This task is new.
+.LS SFLIP
+This task has been eliminated. Use image sections.
+.LS SHEDIT
+This task has been eliminated. Use \fBhedit\fR if needed.
+.LS SINTERP
+This task is unchanged.
+.LS SLIST
+This task was revised to be relevant for the current spectral
+image formats. The old version is still available in the
+\fBiids/irs\fR package.
+.LS SPECPLOT
+New parameters were added to select apertures and bands, plot
+additional dimensions (for example the additional output from
+the extras option in \fBapextract\fR), suppress the system ID banner,
+suppress the Y axis scale, output a logfile, and specify the
+plotting units.  The PTYPE parameter now allows negative 
+numbers to select histogram style lines.  Interactively, the
+plotting units may be changed and the 'v' key allows setting a
+velocity scale zero point with the cursor.  The new version
+supports the new spectral WCS features including nonlinear
+dispersion functions.
+.LS SPLOT
+This is a new version with a significant number of changes. In
+addition to the task changes the other general changes to the
+spectroscopy packages also apply. In particular, long slit
+spectra and spectra with nonlinear dispersion functions may be
+used with this task. The image header or package dispaxis and
+nsum parameters allow automatically extracting spectra from 2D
+image. The task parameters have been modified primarily to
+obtain the desired initial graph without needing to do it
+interactively. In particular, the new band parameter selects
+the band in 3D images, the units parameter selects the 
+dispersion units, and the new histogram, nosysid, and xydraw
+options select histogram line type, whether to include a system
+ID banner, and allow editing a spectrum using  different 
+endpoint criteria.
+.LS
+Because nearly every key is used there has been some shuffling,
+consolidating, or elimination of keys. One needs to check the
+run time '?' help or the help to determine the key changes.
+.LS
+Deblending may  now  use  any  number of components and 
+simultaneous fitting of a linear background. A new simplified
+version of gaussian fitting for a single line has been added in
+the 'k' key. The old 'k', 'h', and 'v' equivalent width
+commands are all part of the single 'h' command using a second
+key to select a specific option. The gaussian line model from
+these modes may now be subtracted from the spectrum in the same
+way as the gaussian fitting.  The one-sided options,  in 
+particular, are interesting in this regard as a new capability.
+.LS
+The arithmetic functions between two spectra are now done in
+wavelength with resampling to a  common  dispersion  done 
+automatically. The 't' key now provides for the full power of
+the ICFIT package to be used on a spectrum for continuum
+normalization, subtraction, or line and cosmic ray removal.
+The 'x' editing key may now use the nearest pixel values rather
+than only the y cursor position to replace regions by straight
+line segments. The mode is selected by the task option 
+parameter "xydraw".
+.LS
+Control over the graph window (plotting limits) is better
+integrated so that redrawing, zooming, shifting, and the \fBgtools\fR
+window commands all work well together. The new 'c' key resets
+the window to the full spectrum allowing the 'r' redraw key to
+redraw the current window to clean up overplots from the
+gaussian fits or spectrum editing.
+.LS
+The dispersion units may now be selected and changed to be from
+hertz to Mev and the log or inverse (for wave numbers) of units
+taken. As part of the units package the 'v' key or colon
+commands may be used to plot in velocity relative to some
+origin. The $ key now easily toggles between the dispersion
+units (whatever they may be) and pixels coordinates.
+.LS
+Selection of spectra has become more complex with multiaperture
+and long slit spectra. New keys allow selecting apertures,
+lines, columns, and bands as well as quickly scrolling through
+the lines in multiaperture spectra. Overplotting is also more
+general and consistent with other tasks by using the 'o' key to
+toggle the next plot to be overplotted. Overplots, including
+those of the gaussian line models, are now done in a different
+line type.
+.LS
+There are new colon commands to change the dispersion axis and
+summing parameters for 2D image, to toggle logging, and also to
+put comments into the log file.
+.LS STANDARD
+Giving an unrecognized standard star name will page a list of
+standard stars available in the calibration directory and then
+repeat the query.
+.LS SUBSETS
+Moved to the \fBiids/irs\fR packages.
+.LS SUMS
+Moved to the \fBiids/irs\fR packages.
diff --git a/noao/onedspec/doc/sys/revisions.v3.ms b/noao/onedspec/doc/sys/revisions.v3.ms
new file mode 100644
index 00000000..1c3da8be
--- /dev/null
+++ b/noao/onedspec/doc/sys/revisions.v3.ms
@@ -0,0 +1,382 @@
+.nr PS 9
+.nr VS 11
+.RP
+.ND
+.TL
+ONEDSPEC Package Revisions Summary: IRAF Version 2.10
+.AU
+Francisco Valdes
+.AI
+IRAF Group - Central Computer Services
+.K2
+P.O. Box 26732, Tucson, Arizona 85726
+July 1990
+.AB
+This paper summarizes the changes in Version 3 of the IRAF \fBonedspec\fR
+package which is part of IRAF Version 2.10.  The major new features and
+changes are:
+
+.IP \(bu
+\fBIdentify\fR and \fBreidentify\fR now treat multispec format spectra
+and two dimensional images as a unit.
+.IP \(bu
+\fBReidentify\fR supports both tracing (the old method) and always starting
+with the primary reference vector when reidentifying other vectors in a
+two dimensional reference image.
+.IP \(bu
+\fBReidentify\fR matches reference lines or apertures when reidentifying
+those vectors in different images rather than tracing.
+.IP \(bu
+\fBReidentify\fR has an interactive capability to review
+suspect reidentifications.
+.IP \(bu
+\fBReidentify\fR provides the capability to add new features.
+.IP \(bu
+The task \fBmsdispcor\fR provides for spatial interpolation of wavelength
+zero point shifts from simultaneous arc spectra.
+.IP \(bu
+The new task \fBscopy\fR copies subsets of apertures and does format
+conversions between the different spectrum formats.
+.IP \(bu
+The new task \fBsapertures\fR adds or modifies beam numbers and
+aperture titles for selected apertures based on an aperture
+identification file.
+.IP \(bu
+The new task \fBsfit\fR fits spectra and outputs the fits in various ways.
+Apertures in  multispec and echelle format are fit independently.
+.IP \(bu
+The task \fBcontinuum\fR now does independent fits for multispec and
+echelle format spectra.
+.IP \(bu
+\fBSplot\fR now allows deblending of any number of components and
+allows simultaneous fitting of a linear background.
+.IP \(bu
+The new task \fBfitprofs\fR fits 1D gaussian profiles in images.
+.AE
+.NH
+Introduction
+.PP
+Though  most of the ONEDSPEC package is unchanged there have been
+significant changes to a number of the commonly used tasks in IRAF
+Version 2.10.  The changes will be made available as part of an
+external package prior to the release of V2.10.  This paper summarizes
+the changes and new features.  The changes primarily apply to multispec
+or echelle format spectra.
+.PP
+Tables 1 and 2 summarize most of the major and minor changes in the package.
+
+.ce
+TABLE 1:  Summary of Major New Features and Changes
+
+.IP \(bu
+\fBIdentify\fR and \fBreidentify\fR now treat multispec format spectra
+and two dimensional images as a unit allowing easy movement between
+different image lines or columns.  The database is only updated upon
+exiting the image.
+.IP \(bu
+\fBReidentify\fR supports both tracing (the old method) and always starting
+with the primary reference vector when reidentifying other vectors in a
+two dimensional reference image.
+.IP \(bu
+\fBReidentify\fR matches reference lines or apertures when reidentifying
+those vectors in different images rather than tracing.
+.IP \(bu
+\fBReidentify\fR has an interactive capability to review
+suspect reidentifications.
+.IP \(bu
+\fBReidentify\fR provides the capability to add new features.
+.IP \(bu
+The task \fBmsdispcor\fR allows using
+auxilary reference spectra to provide a shift in the wavelength
+zero point to the primary dispersion functions.  This includes
+spatial interpolation of simultaneous arc spectra in multifiber
+spectrographs.
+.IP \(bu
+The new task \fBscopy\fR copies subsets of apertures and does format
+conversions between the different spectrum formats.
+.IP \(bu
+The new task \fBsapertures\fR adds or modifies beam numbers and
+aperture titles for selected apertures based on an aperture
+identification file.
+.IP \(bu
+The new task \fBsfit\fR fits spectra and outputs the fits in various ways.
+This includes a new feature to replace deviant points by the fit.
+Apertures in  multispec and echelle format are fit independently.
+.IP \(bu
+The task \fBcontinuum\fR now does independent fits for multispec and
+echelle format spectra.
+.IP \(bu
+\fBSplot\fR now allows deblending of any number of components and
+allows simultaneous fitting of a linear background.
+.IP \(bu
+The new task \fBfitprofs\fR fits 1D gaussian profiles to spectral lines or
+features in an image line or column.  This is done noniteractively and
+driven by an input list of feature positions.
+.bp
+.LP
+.ce
+TABLE 2:  Summary of Other New Features and Changes
+
+.IP \(bu
+The \fBidentify\fR database format uses aperture numbers rather than
+image sections for multispec format spectra.
+.IP \(bu
+The apertures in multispec format images need not be in the same order
+or even the same number of apertures as the reference image in
+\fBreidentify\fR or \fBmsdispcor\fR.
+.IP \(bu
+An automatic write parameter has been added to \fBidentify\fR.
+.IP \(bu
+The tasks \fBmsdispcor\fR and \fBspecplot\fR support the extra information
+in the third dimension of multispec format spectra which is optionally
+output by the \fBapextract\fR package.
+.IP \(bu
+\fBMsdispcor\fR and \fBspecplot\fR now include a logfile.
+.IP \(bu
+\fBSplot\fR selects spectra from multispec or echelle format by their
+aperture number.  Also a new keystroke was added to select a new
+line/aperture without having to enter the image name again.
+.IP \(bu
+The task \fBspecplot\fR may select apertures from a multispec or
+echelle format spectrum.
+.IP \(bu
+The aperture identification in multispec format is used, if present,
+for labeling in \fBsplot\fR, \fBspecplot\fR, and \fBstandard\fR.
+.NH
+IDENTIFY and REIDENTIFY
+.PP
+These tasks have been modified for greater flexibility when dealing with
+two dimensional images and multispec format spectra in particular.  These
+tasks were initially designed primarily to work on one dimensional images
+with provisions for two dimensional images through image sections and
+tracing to other parts of the image.  Now these tasks treat such images
+as a unit.
+.PP
+The task \fBidentify\fR has three added keystrokes, 'j', 'k', and 'o'.
+These provide for moving between lines and columns of a two dimensional
+image and different apertures in a multispec format spectrum.  When
+changing vectors the last set of features and fit are recalled, if they
+have been previously defined, or the last set of features and fit are
+inherited.  For efficiency and to minimize queries, the feature
+information from all the lines or apertures is not written to the
+database until you quit the image (or explicitly write it) rather than
+one at a time.  A new parameter was also added, \fIautowrite\fR, which
+may be set to automatically write the results to the database rather
+than querying as is currently done.
+.PP
+The format of the database entries have also been slightly modified in
+the case of multispec format images.  Instead of using image sections
+as part of the image name to define different vectors in the image
+(this is still the case for regular two dimensional images) the aperture
+number is recorded.  This decouples the solutions for an aperture from
+the specific image line allowing reference images to have a different
+aperture order and additional or missing apertures.
+.PP
+While the changes to \fBidentify\fR are minor as far as usage, the task
+\fBreidentify\fR is quite different and is essentially a new program.
+Much of the complexity in this task relates to two dimensional images.
+Two additions that apply to both one and two dimensional images is the
+capability to add features from a coordinate list and to interactively
+review the reidentifications using \fBidentify\fR.  The addition of new
+features may be useful in cases where the signal-to-noise varies or to
+compensate for lost features when tracing across an image.  The review
+capability first prints the statistical results and then ask the user if
+they want to examine the results interactively .  This allows
+basing the decision to interactively examine the features and fit based
+on this information.  Ideally, only a few of the worst cases need be
+examined interactively.
+.PP
+There are two phases of reidentifications which apply to two
+dimensional and multispec format images.  In the first phase, one needs
+to expand the identifications in the reference image from an initial,
+interactively defined line, column, or aperture to other parts of the
+reference image.  A very important change is that there are now two
+ways to transfer the features list; by successive steps (tracing) using
+the previous results as a starting point (the only method provided in
+the previous version) or always starting from the original reference
+list.  The first method is suitable for long slit spectra which have
+significant positional trends across the image.  If a feature is lost,
+however, the feature remains missing (barring automatic addition as
+mentioned above) for all following lines or columns.  The latter method
+is best if there are only small variations relative to the initial
+reference or in multispec format spectra where there is no inherent
+relation between apertures.
+.PP
+The second phase of reidentifications is between the reference image
+and other images.  In the previous version the primary reference vector
+was transferred to the new image and then tracing would be applied
+again.  This compounds the problem with losing features during tracing
+and prevents any possible reidentifications from multispec images in
+which the wavelength range may vary greatly.  In the new version there
+is a direct reidentification from the same line, column, or aperture in
+the reference to that of the next image.  In the case where different
+apertures may have significantly different wavelength coverage, as
+occurs with aperture masks, it will at least be possible to
+interactively identify features and coordinate functions for each
+aperture, using the scrolling capability in the new \fBidentify\fR, in
+just a single image and then correctly transfer the features to
+additional images.
+.PP
+For multispec format spectra the database information is organized by
+aperture number independent of image line number.  Thus, it is possible
+to reidentify features in multispec format spectra even if the aperture
+order is different.  If there is only a partial overlap in the aperture
+set only those apertures having an entry in the reference image will be
+done.
+.NH
+MSDISPCOR
+.PP
+The task \fBmsdispcor\fR dispersion corrects (rebins to a linear
+dispersion function) multispec format spectra.  It was introduced in
+V2.8 of IRAF in the prototype \fBimred.msred\fR package.  A number of
+changes have been made in this task as summarized here.
+.PP
+The most fundamental change is support for spatial interpolation of
+reference dispersion functions from a subset of apertures to other
+apertures originating at different positions in a two dimensional
+image.  This is primarily intended for the case of comparison arc
+spectra which are interspersed with object spectra in multifiber
+spectrographs.  It would also be useful in digitized photographic
+spectra having calibration spectra exposed next to the object
+spectrum.  While usable directly, this feature is intended for the
+processing scripts in the new \fBimred\fR fiber instrument packages.
+.PP
+The interpolation is only for a wavelength zero point shift, as determined
+by \fBreidentify\fR with \fIrefit\fR=no.  The full dispersion function
+is still provided by a calibration image covering all apertures.  Thus,
+the simultaneous arc apertures are used to monitor shifts in the
+detector relative to the full calibration which includes the relative
+differences between each aperture and the arc monitoring apertures.
+.PP
+The multispec spectra containing the apertures used for the spatial
+wavelength zero point corrections are specified in the image header
+using the keywords REFSHFT1 and REFSHFT2.  These are analogous to
+the REFSPEC keywords used to define the reference dispersion functions
+for the apertures.
+.PP
+As part of the general theme of multispec format support the
+multispec dispersion reference spectra may have additional spectra and
+need not be in the same order.  However, all aperture in the
+images being dispersion corrected must have dispersion relations
+in the database.  Multispec format spectra may include additional
+data in the 3rd image dimension produced by the new
+\fBapextract\fR package.  \fBMsdispcor\fR rebins this information
+in the same way as the spectra, thus, preserving the information
+but now in linear wavelength sampling.
+.PP
+A new parameter, \fIlogfile\fR, has been added to capture information
+about the dispersion correction process.
+.NH
+SCOPY and SAPERTURES
+.PP
+The task \fBscopy\fR is intended to bridge the gap between the various
+spectrum formats and provide a tool to flexibly manipulate multispec
+format spectra.  It replaces the more primitve tasks
+\fBmsred.msselect\fR and \fBechelle.ecselect\fR.  Basically, this task
+copies all or selected spectra from one format to a new image or images
+of the same or different format.  The typical uses are:
+
+.IP \(bu
+Extract selected spectra from a multispec format image.
+.IP \(bu
+Allow converting the voluminous onedspec format from previous reductions
+done before the multispec format was introduced into the more compact
+multispec format.
+.IP \(bu
+Splice selected apertures from different multispec images into a new
+multispec image.
+.IP \(bu
+Provide a quick way to convert lines or columns from two dimensional
+long slit images into one dimensional spectra.  This replaces
+the task \fBproto.toonedspec\fR.
+.PP
+Because \fBscopy\fR can easily change the number and order of apertures
+in the multispec image format it is important that the other tasks which
+use the multispec format have been modified to be insensitive to which
+line a spectrum is in and generally key off the aperture number.
+.PP
+The task \fBsapertures\fR is a simple way to set the aperture identifications,
+APID keyword, and beam number, second field of APNUM keyword, based on
+the aperture number and a simple text file.  The text file contains lines
+with aperture number, beam number, and (optional) title.  This file is
+used by the \fBapextract\fR package as well.  Its likely usage is
+to change image titles which might be wrong because of being inherited
+from an aperture reference image during extraction.
+.NH
+SFIT, CONTINUUM, and ECCONTINUUM
+.PP
+The original version of \fBcontinuum\fR was a simple script based on
+the task \fBfit1d\fR.  The problem is that \fBfit1d\fR is intended to
+process all the lines or columns in a two dimensional image
+noninteractively.  To do this it applies the same fitting parameters to
+every line or column.  The interactive step in this task is simply to
+adjust fitting parameters.  For spectra, particularly multispec and
+echelle format spectra, one often needs to fit each spectrum
+interactively and independently.  When this problem was encountered for
+the \fBechelle\fR package Rob Seaman wrote a nice program,
+\fBeccontinuum\fR, which allows fitting a set of orders and keeps track
+of which orders have been fit.
+.PP
+The general feature of the continuum fitting tasks is that they fit
+spectra using the \fBicfit\fR interactive function fitting interface.
+The results of the fit may be output as the fit itself, the difference
+or residuals, the ratio, or the input data with rejected points replaced
+by the fitted values.  The last feature is new an provides a useful
+spectrum cleaning option.  The general equivalent to \fBfit1d\fR is
+the new task \fBsfit\fR which provides the same independent fitting and
+image line selection capabilites as \fBeccontinuum\fR.  Note this task
+is line oriented and does not select by aperture or order number.  The
+revised version of \fBcontinuum\fR is now based on \fBsfit\fR and
+provides the independent continuum fitting capability for onedspec and
+multispec format spectra that \fBeccontinuum\fR provides for echelle
+format spectra.  Technically what has been done is that \fBsfit\fR,
+\fBcontinuum\fR, and \fBeccontinuum\fR are the same task; essentially
+the task written by Seaman for echelle data.  They differ in the
+default parameters with the continuum fitting task having default
+parameters providing continuum normalization (ratio) output and
+iterative rejection values for excluding lines.
+.NH
+SPLOT, FITPROFS, and SPECPLOT
+.PP
+\fBSplot\fR has been modified to better support multispec and echelle
+format images.  The line selection for multispec and echelle format
+spectra is now in terms of the aperture number rather than the image
+line.  The aperture title is used in place of the image title
+if present.
+.PP
+The restriction to a maximum of four lines in the gaussian fitting and
+deblending option of \fBsplot\fR has been lifted.  Any number of
+lines may be fit simultaneously, though execution time will become
+long for a large number.  In addition the fitting allows determining
+a simultaneous linear background as well as using the cursor defined
+points.  The positions of the lines to be fit may be marked with
+the cursor, typed in, or read from a file.  The last choice is a new
+feature.
+.PP
+In the past many people have used \fBsplot\fR for bulk, noninteractive
+gaussian fitting by going through the trouble of redirecting the cursor
+input, ukey input, text output, and graphics output.  The main reason
+this has been done is the lack of a one dimensional gaussian fitting
+task.  The task \fBfitprofs\fR has been added to provide simultaneous
+gaussian fitting.  This task takes a list of positions and optional
+sigmas and fits gaussians to a list of images or spectra.  The lines,
+columns, or apertures may be selected.  In addition a linear
+background may be specified or included in the fitting.  The output
+consists of any combination of text similiar to the \fBsplot\fR
+logfile, plots showing the data and fit, and image output of the fit or
+the difference.  This task is noninteractive; the interactive version
+is the deblend command of \fBsplot\fR.  The multiparameter, nonlinear
+fitting software is the same as used in \fBsplot\fR.
+.PP
+\fBFitprofs\fR complements the task \fBstsdas.fitting.ngaussfit\fR from
+the \fBstsdas\fR package (available from the Space Telescope Science
+Institute).  This task is similar in character to \fBfit1d\fR and has
+an interactive one dimensional nonlinear function fitting interface
+similar to \fBicfit\fR.
+.PP
+The task \fBspecplot\fR has a new parameter to select apertures to
+plot.  Previously there was no way to limit the apertures plotted other
+than with image sections.  All associated lines of a multispec
+spectrum (those in the third dimension) are also plotted for the
+selected apertures.  This extra information is a new option of the
+\fBapextract\fR package.
diff --git a/noao/onedspec/doc/sys/revisions.v31.ms b/noao/onedspec/doc/sys/revisions.v31.ms
new file mode 100644
index 00000000..f9d6c24f
--- /dev/null
+++ b/noao/onedspec/doc/sys/revisions.v31.ms
@@ -0,0 +1,329 @@
+.nr PS 10
+.nr VS 12
+.RP
+.ND
+.TL
+NOAO Spectroscopy Packages Revisions: IRAF Version 2.10.3
+.AU
+Francisco Valdes
+.AI
+IRAF Group - Central Computer Services
+.K2
+P.O. Box 26732, Tucson, Arizona 85726
+March 1993
+.AB
+This paper summarizes the changes in Version 3.1 of the IRAF/NOAO
+spectroscopy packages, \fBonedspec\fR, \fBlongslit\fR, \fBapextract\fR, and
+those in \fBimred\fR.  These changes are part of IRAF Version 2.10.3.  A
+list of the revisions is:
+
+.in +2
+.nf
+\(bu A simplified \fIequispec\fR image header format
+\(bu \fIEquispec\fR format allows a larger number of apertures in an image
+\(bu Extensions to allow tasks to work on 3D images
+\(bu New task \fBspecshift\fR for applying a zeropoint dispersion shift
+\(bu Revised \fBsapertures\fR to edit spectrum coordinate parameters
+\(bu Revised \fBdispcor\fR to easily apply multiple dispersion corrections
+\(bu Revised \fBscombine\fR weighting and scaling options
+\(bu Revised \fBscopy\fR to better handle bands in 3D images
+\(bu Revised \fBcalibrate, deredden, dopcor\fR, and \fBspecshift\fR to work on 2D/3D images
+\(bu Extended \fBidentify\fR and \fBreidentify\fR to work on 3D images
+\(bu New color graphics capabilities in \fBsplot, specplot, sensfunc\fR, and \fBidentify\fR
+\(bu All spectral tasks use a common package dispersion axis parameter
+\(bu A more complete suite of tasks in the \fBlongslit\fR package
+\(bu The \fBimred\fR reductions scripts can now be used with any image format
+\(bu A \fIdatamax\fR parameter in the \fBimred\fR reduction scripts for better cleaning
+\(bu Revised the \fBimred\fR reduction scripts to abort on non-CCD processed data
+\(bu Revised fiber reduction tasks to include a scattered light subtraction option
+\(bu Revised fiber reduction tasks to allow as many sky apertures as desired
+\(bu Revised \fBdoslit\fR to take the reference arc aperture from the first object
+\(bu Bug fixes
+.fi
+.in -2
+.AE
+.NH
+Spectral Image Formats and Dispersion World Coordinate Systems
+.LP
+As with the original release of V2.10 IRAF, the primary changes in the
+NOAO spectroscopy
+software in V2.10.3 are in the area of spectral image formats and dispersion
+world coordinate systems (WCS).  A great deal was learned from experience
+with the first release and the changes in this release attempt to
+address problems encountered by users.  The main revisions are:
+
+.in +2
+.nf
+\(bu A new WCS format called \fIequispec\fR.
+\(bu Extensions to allow use of 3D images with arbitrary dispersion axis.
+\(bu Elimination of limits on the number of apertures in an image under certain conditions.
+\(bu Improved tools for manipulating the spectral coordinate systems.
+\(bu Bug fixes and solutions to problems found in the previous release.
+.fi
+.in -2
+
+In the previous version all images with multiple spectra used a coordinate
+system called \fImultispec\fR.  This type of WCS is complex and difficult
+to manipulate by image header editing tools.  Only the case of a single
+linearized spectrum per image, sometimes called \fIonedspec\fR format,
+provided a simple header format.  However, the \fBapextract\fR package
+used the \fImultispec\fR format even in the case of extracting a single
+spectrum so to get to the simple format required use of \fBscopy\fR.
+.LP
+In many cases all the spectra in a multispectrum image have the same linear
+dispersion function.  The new \fIequispec\fR format uses a simple linear
+coordinate system for the entire image.  This format is produced by the
+spectral software whenever possible.  In addition to being simple and
+compatible with the standard FITS coordinate representation, the
+\fIequispec\fR format also avoids a limitation of the \fImultispec\fR WCS
+on the number of spectra in a single image.  This has specific application
+to multifiber spectrographs with more than 250 fibers.
+.LP
+For multiple spectrum data in which the spectra have differing
+dispersion functions (such as echelle orders) or when the spectra are
+not linearized but use nonlinear dispersion functions, the \fImultispec\fR
+format is still used.  It is the most general WCS representation.
+The difficulties with modifying this coordinate system, \fBhedit\fR
+cannot be used, are addressed by enhancing the \fBsapertures\fR task
+and by the new task \fBspecshift\fR which covers the common case of
+modifying the dispersion zeropoint.
+.LP
+A feature of the spectral tasks which operate on one dimensional spectra
+is that they can operate on two dimensional long slit spectra by
+specifying a dispersion axis and a summing factor.  This feature has
+been extended to three dimensional spectra such as occur with
+Fabry-Perot and multichannel radio synthesis instruments.  The
+dispersion axis may be along any axis as specified by the DISPAXIS
+image header keyword or by the \fIdispaxis\fR package parameter.  The
+summing factor parameter \fInsum\fR is now a string which may have
+one or two values to allow separate summing factors along two spatial
+axes.  Also, some additional tasks which previously did not support this
+feature are \fBcalibrate\fR, \fBderedden\fR, \fBdopcor\fR, and \fBspecshift\fR.
+.LP
+The gory details of the spectral image formats and world coordinate
+systems are laid out in the new help topic \fIspecwcs\fR (also
+available in a postscript version in the IRAF network documentation
+archive as iraf/docs/specwcs.ps.Z).
+.LP
+Some of the bug fixes and solutions to problems found in the previous
+release concerning the image formats and WCS are a problem with the WCS
+dimensionality (WCSDIM keyword) with 3D images and problems reading various
+imported nonstandard formats.  It is hoped that all such formats, including
+previous IRAF spectral formats will all be allowed by the software in the
+latest release.
+.NH
+DISPCOR
+.LP
+The previous versions of \fBdispcor\fR, the dispersion correction task, was
+designed to prevent accidental repeated application; it is incorrect to
+apply the dispersion function from the original data to a linearized
+spectrum.  However, it is valid to determine a new dispersion solution, say
+from a dispersion calibrated arc, and apply that as a second correction.
+\fBDispcor\fR would not use a new dispersion function, as specified by the
+REFSPEC keywords, if the dispersion calibration flag was set.  In order to
+override this the user needed to manually change this flag to indicate the
+spectrum was uncorrected.  The problem was that it was difficult to do this
+with \fImultispec\fR format spectra because the flag is part of the complex
+WCS attribute strings.
+.LP
+\fBDispcor\fR was revised to use a different logic to prevent accidental
+recalibration using an unintended dispersion function.  The logic is as
+follows.  Previously \fBdispcor\fR would simply change the dispersion
+calibration flag after correcting a spectrum while leaving the dispersion
+function reference spectrum keywords alone as a record.  The revised
+\fBdispcor\fR keeps this useful record but moves this it to a new keyword
+DCLOGn (where n is a sequential integer).  Because the REFSPEC keyword is
+removed after each application of \fBdispcor\fR it now takes an explicit
+act by the user to assign another dispersion function to a spectrum and so
+it is not possible to accidentally reapply the same dispersion function
+twice.  Thus this version will apply additional dispersion functions by
+simply adding new REFSPEC keywords.  If they are absent the task resamples
+the spectra based on the current dispersion relation as was the case
+before.
+.LP
+The new version can also tell whether the data was calibrated by the
+previous version.  In this case the check on the dispersion calibration
+flag is still used so that during the transition users are still protected
+against accidentally applying the same reference dispersion function
+twice.  The new task \fBsapertures\fR can now be used to change the
+dispersion calibration flag to override this checking more easily than was
+the case previously.
+.NH
+New Tasks
+.LP
+In this release there is only one completely new task and one task which
+was significantly redesigned.  The new task is \fBspecshift\fR.  It is
+relatively simple, it adds a zero point shift to the dispersion coordinates
+of spectra.  This was the most common request for manipulating the spectral
+world coordinate system.  In this regard there was a common confusion about
+the distinction between shifting the coordinate system and shifting the
+pixel data.  Generally what people want is to apply a shift such that
+features in the spectrum move to the desired wavelength.  One thought is to
+apply the tasks \fBimshift\fR or \fBshiftlines\fR.  The surprise is that
+this does not to work.  The pixels are actually shifted in the image array,
+but these tasks also apply the same shift to the coordinate system so that
+features in the spectrum remain at the same wavelength.  What is really
+required is to leave the pixel data alone and shift only the coordinate
+system.  That is what \fBspecshift\fR does.
+.LP
+While one hopefully does not need to directly manipulate the image header
+keywords describing the coordinate system or other aspects of the spectra,
+instead using such tasks as \fBspecshift\fR, there always seem to be cases
+where this is needed or desired.  In the V2.10 release of the spectral
+software this was difficult because the general \fImultispec\fR format was
+the norm and it has information encoded in the complex WCS attribute
+strings.  As mentioned previously several changes have been made reduce the
+complexity.  Now \fIequispec\fR format will generally be the rule and this
+format has keywords which are more easily manipulated with \fBhedit\fR and
+\fBwcsedit\fR.  However, the task \fBsapertures\fR was revised to provide
+an editing capability specifically for spectral images, in either
+\fImultispec\fR or \fIequispec\fR format, with options to change various
+parameters globally or aperture-by-aperture.
+.NH
+New Features
+.LP
+There were a number of miscellaneous minor revisions and bug fixes.  One of
+the major new capabilities available with V2.10.3 is support for color
+graphics if the graphics device supports it.  \fBXgterm\fR supports color
+on X-window systems with color monitors.  Several of the spectral tasks
+were modified to use different colors for marks and overplots.  These tasks
+include \fBsplot\fR, \fBspecplot\fR, \fBidentify\fR, and \fBsensfunc\fR.
+In the case of \fBsensfunc\fR the user controls the various color
+assignments with a task parameter or \fBgtools\fR colon command while in
+other cases the next available color is used.
+.LP
+There were several changes to \fBscombine\fR equivalent to those in
+\fBimcombine\fR.  The weighting, when selected, was changed from the square
+root of the exposure time or spectrum statistics to the value with no
+square root.  This corresponds to the more commonly used variance
+weighting.  Other options were added to specify the scaling and weighting
+factors.  These allow specifying an image header keyword or a file
+containing the scale or weighting factors.  A new parameter, "nkeep" has
+been added to allow controlling the maximum number of pixels rejected by the
+clipping algorithms.  Previously it was possible to reject all pixels even
+when some of the data was good though with a higher scatter than estimated;
+i.e. all pixels might be greater than 3 sigma from the mean without being
+cosmic rays or other bad values.  Finally a parameter \fIsnoise\fR was
+added to include a sensitivity or scale noise component to a Poisson noise
+model.
+.LP
+In \fBsplot\fR the 'p' and 'u' keys which assign and modify the dispersion
+coordinates now include options for applying a zero point shift or a
+doppler shift in addition to defining an absolute wavelength for a feature
+or starting and ending wavelengths.  There are also bug fixes to the
+equivalent width calculations, it did not handle flux calibrated data, and
+the scroll keys '(' and ')'.
+.LP
+There were several changes to make it easier to deal with with three
+dimensional \fImultispec\fR and \fIequispec\fR data; that is the additional
+data from the "extras" option in the \fBapextract\fR tasks.  One was to fix
+problems associated with an incorrect WCSDIM keyword.  This allows use of
+image sections or \fBimcopy\fR for extracting specific bands and
+apertures.  Another was to add a "bands" parameter in \fBscopy/sarith\fR to
+allow selection of bands.  Also the "onedspec" output format in \fBscopy\fR
+copies any selected bands to separate one dimensional images.
+.LP
+As mentioned earlier, many of the \fBonedspec\fR tasks have been extended
+to work on 2D and 3D spatial spectra.  Some tasks which now have this
+capability in this version and not the previous one are \fBcalibrate\fR and
+\fBdopcor\fR.  \fBIdentify\fR and \fBredentify\fR were extended to operate
+on 3D images.  This involved extending the syntax for the section parameter
+selecting the image vector and the parameter specifying any summing
+across the vector direction.
+.NH
+LONGSLIT
+.LP
+With the applicability of more \fBonedspec\fR tasks to long slit data
+the \fBlongslit\fR package was modified to add many new tasks.
+This required adding additional package parameters.  One new task
+to point out is \fBcalibrate\fR.  This task is now the preferred one
+to use for extinction and flux calibration of long slit spectra
+rather than the obsolete \fBextinction\fR and \fBfluxcalib\fR.
+The obsolete tasks are still present in this release.
+.NH
+APEXTRACT
+.LP
+The \fBapextract\fR package had a few, mostly transparent, changes.  In
+the previous version the output image header format was always \fImultispec\fR
+even when there was a single spectrum, either because only one aperture
+was defined or because the output format parameter was "onedspec".
+In this release the default WCS format is the simpler \fIequispec\fR.
+.LP
+In the \fBonedspec\fR and \fBimred\fR spectral reduction packages there is
+a dispersion axis package parameter which is used to defined the dispersion
+axis for images without a DISPAXIS keyword.  This applies to all tasks.
+However, the \fBapextract\fR tasks had the dispersion axis defined by their
+own task parameters resulting in some confusion.  To make things consistent
+the dispersion axis parameter in \fBapextract\fR has been moved from the
+tasks to a package parameter.  Now in the \fBimred\fR spectral reduction
+packages, there is just one dispaxis parameter in the package parameters
+which applies to all tasks in those packages, both those from
+\fBonedspec\fR and those from \fBapextract\fR.
+.LP
+Some hidden algorithm parameters were adjusted so that the cleaning and
+variance weighting options perform better in some problem cases without
+requiring a great deal of knowledge about things to tweak.
+.NH
+IMRED Spectroscopic Reduction Tasks
+.LP
+The various spectroscopic reductions tasks, those beginning with "do", have
+had some minor revisions and enhancements in addition to those which apply
+to the individual tasks which make up these scripts.  In the latter class
+is the output WCS format is \fBequispec\fR except for the echelle tasks and
+when dispersion linearization is not done.  Related to this is that the
+multifiber tasks can operate on data with more than 250 fibers which was a
+limitation of the \fBmultispec\fR format.
+.LP
+In the previous version only the OIF format images were allowed (the ".imh"
+extensions).  This has been generalized to allow selecting the image format
+by setting the environment parameter \fIimtype\fR.  Only images with the
+specified extension will be processed and created.
+.LP
+The dispersion axis parameter in the reduction tasks and in the other tasks
+in the \fBimred\fR spectroscopy packages, such as the \fBapextract\fR
+tasks, is now solely a package parameter.
+.LP
+All the scripts now check the input spectra for the presence of the CCDPROC
+keyword and abort if it is not found.  This keyword indicates that the data
+have been processed for basic CCD calibrations, though it does not check
+the operations themselves.  For data reduced using \fBccdproc\fR this
+keyword will be present.  If these tasks are used on data not processed by
+\fBccdproc\fR then it is a simple matter to add this keyword with
+\fBhedit\fR.  Obviously, the purpose of this change is to avoid
+inadvertently operating on raw data.
+.LP
+All the "do" tasks now have a parameter "datamax".  This minimizes the
+effects of very strong cosmic rays during the extraction of object spectra;
+it does not apply to flat field or arc spectra.  When there is a very large
+difference between data pixel values and cosmic ray pixel values,
+especially true for very weak spectra, the cosmic ray cleaning operation
+does not always work well.  If it is possible to specify a threshold value
+between the maximum real data value and cosmic rays then the cosmic ray
+cleaning can be significantly improved by immediately rejecting those
+pixels above the threshold.  Of course the user must be careful that real
+data does not exceed this value since such data will be excluded.
+.LP
+The fiber reduction tasks, \fBdoargus, dohydra, dofibers, dofoe\fR, and
+\fBdo3fiber\fR have a new processing option for subtracting scattered
+light.  This is particularly useful if there is significant scattered light
+in producing uniform sky spectra for sky subtraction since the fiber
+throughput calibration does not generally correct for this.
+.LP
+The fiber reduction tasks also had a limit on the number of sky fibers
+which could be used with the interactive sky editing.  This limit has
+been eliminated so that it is possible, for example, to have one object
+fiber and 99 sky fibers.
+.LP
+The slit reduction task \fBdoslit\fR previously required that the spectrum
+for the reference arc cover the middle of the input data images.  There
+were cases of instrument configurations  where this was not true requiring
+additional manipulation to use this task.  This requirement has been
+eliminated.  Instead when the reference arc needs to be extracted it uses
+the aperture definition from one of the input object spectra since
+definition of the object apertures occurs prior to setting up the
+dispersion calibration.
+.LP
+In addition the task \fBdoslit\fR and \fBdoecslit\fR had a bug in which
+the order of the arcs specified by the user was ignored and alphabetical
+order was used instead.  This has been fixes so that the first arc
+specified by the use is the reference arc.
diff --git a/noao/onedspec/doc/sys/revisions.v31.ms.bak b/noao/onedspec/doc/sys/revisions.v31.ms.bak
new file mode 100644
index 00000000..1c7c3b31
--- /dev/null
+++ b/noao/onedspec/doc/sys/revisions.v31.ms.bak
@@ -0,0 +1,307 @@
+.nr PS 9
+.nr VS 11
+.RP
+.ND
+.TL
+NOAO Spectroscopy Packages Revision Summary: IRAF Version 2.10.3
+.AU
+Francisco Valdes
+.AI
+IRAF Group - Central Computer Services
+.K2
+P.O. Box 26732, Tucson, Arizona 85726
+March 1993
+.AB
+This paper summarizes the changes in Version 3.1 of the IRAF/NOAO
+spectroscopy packages, \fBonedspec\fR, \fBlongslit\fR, \fBapextract\fR,
+and those in \fBimred\fR.  These changes are part of
+part of IRAF Version 2.10.3.  A list of the revisions is:
+
+.nf
+\(bu A simplified \fIequispec\fR image header format
+\(bu \fIEquispec\fR format allows a larger number of apertures in an image
+\(bu Extensions to allow tasks to work on 3D images
+\(bu New task \fBspecshift\fR for applying a zeropoint dispersion shift
+\(bu Revised \fBsapertures\fR to edit spectrum coordinate parameters
+\(bu Revised \fBdispcor\fR to easily apply multiple dispersion corrections
+\(bu Revised \fBscombine\fR weighting and scaling options
+\(bu Revised \fBscopy\fR to better handle bands in 3D images
+\(bu Revised \fBcalibrate, dopcor\fR, and \fBspecshift\fR to work on 2D/3D images
+\(bu New color graphics capabilities in \fBsplot, specplot, sensfunc\fR, and \fBidentify\fR
+\(bu All spectral tasks use a common package dispersion axis parameter
+\(bu A more complete suite of tasks in the \fBlongslit\fR package
+\(bu A \fIdatamax\fR parameter in the \fBimred\fR reduction scripts for better cleaning
+\(bu Revised the \fBimred\fR reduction scripts to abort on non-CCD processed data
+\(bu Revised fiber reduction tasks to include a scattered light subtraction option
+\(bu Revised \fBdoslit\fR to take the reference arc aperture from the first object
+\(bu Bug fixes
+.fi
+.AE
+.NH
+Spectral Image Formats and Dispersion World Coordinate Systems
+.LP
+As with the original release of V2.10 IRAF, the primary changes in the
+NOAO spectroscopy
+software in V2.10.3 are in the area of spectral image formats and dispersion
+world coordinate systems (WCS).  A great deal was learned from experience
+with the first release and the changes in this release attempt to
+address problems encountered by users.  The main revisions are:
+
+.in +4
+.nf
+\(bu A new WCS format called \fIequispec\fR.
+\(bu Extensions to allow use of 3D images with arbitrary dispersion axis.
+\(bu Elimination of limits on the number of apertures in an image under certain conditions.
+\(bu Improved tools for manipulating the spectral coordinate systems.
+\(bu Bug fixes and solutions to problems found in the previous release.
+.fi
+.in - 4
+
+In the previous version all images with multiple spectra used a coordinate
+system called \fImultispec\fR.  This type of WCS is complex and difficult
+to manipulate by image header editting tools.  Only the case of a single
+linearized spectrum per image, sometimes called \fIonedspec\fR format,
+provided a simple header format.  However, the \fBapextract\fR package
+used the \fImultispec\fR format even in the case of extracting a single
+spectrum so to get to the simple format required use of \fBscopy\fR.
+.LP
+In many cases all the spectra in a multispectrum image have the same linear
+dispersion function.  The new \fIequispec\fR format uses a simple linear
+coordinate system for the entire image.  This format is produced by the
+spectral software whenever possible.  In addition to being simple and
+compatible with the standard FITS coordinate representation, the
+\fIequispec\fR format also avoids a limitation of the \fImultispec\fR WCS
+on the number of spectra in a single image.  This has specific application
+to multifiber spectrographs with more than 250 fibers.
+.LP
+For multiple spectrum data in which the spectra have differing
+dispersion functions (such as echelle orders) or when the spectra are
+not linearized but use nonlinear dispersion functions, the \fImultispec\fR
+format is still used.  It is the most general WCS representation.
+The difficulties with modifying this coordinate system, \fBhedit\fR
+cannot be used, are addressed by enhancing the \fBsapertures\fR task
+and by the new task \fBspecshift\fR which covers the common case of
+modifying the dispersion zeropoint.
+.LP
+A feature of the spectral tasks which operate on one dimensional spectra
+is that they can operate on two dimensional long slit spectra by
+specifying a dispersion axis and a summing factor.  This feature has
+been extended to three dimensional spectra such as occur with
+Fabry-Perot and multichannel radio synthesis instruments.  The
+dispersion axis may be along any axis as specified by the DISPAXIS
+image header keyword or by the \fIdispaxis\fR package parameter.  The
+summing factor parameter \fInsum\fR is now a string which may have
+one or two values to allow separate summing factors along two spatial
+axes.  Also, some additional tasks which previously did not support this
+feature are \fBcalibrate\fR, \fBdopcor\fR, and \fBspecshift\fR.
+.LP
+The gory details of the spectral image formats and world coordinate
+systems are laid out in the new help topic \fIspecwcs\fR (also
+available in a postscript version in the IRAF network documentation
+archive as iraf/docs/specwcs.ps.Z).
+.LP
+Some of the bug fixes and solutions to problems found in the previous
+release concerning the image formats and WCS are a problem with the WCS
+dimensionality (WCSDIM keyword) with 3D images and problems reading various
+imported nonstandard formats.  It is hoped that all such formats, including
+previous IRAF spectral formats will all be allowed by the software in the
+latest release.
+.NH
+DISPCOR
+.LP
+The previous versions of \fBdispcor\fR, the dispersion correction task, was
+designed to prevent accidental repeated application; it is incorrect to
+apply the dispersion function from the original data to a linearized
+spectrum.  However, it is valid to determine a new dispersion solution, say
+from a dispersion calibrated arc, and apply that as a second correction.
+\fBDispcor\fR would not use a new dispersion function, as specified by the
+REFSPEC keywords, if the dispersion calibration flag was set.  In order to
+override this the user needed to manually change this flag to indicate the
+spectrum was uncorrected.  The problem was that it was difficult to do this
+with \fImultispec\fR format spectra because the flag is part of the complex
+WCS attribute strings.
+.LP
+\fBDispcor\fR was revised to use a different logic to prevent accidental
+recalibration using an unintended dispersion function.  The logic is as
+follows.  Previously \fBdispcor\fR would simply change the dispersion
+calibration flag after correcting a spectrum while leaving the dispersion
+function reference spectrum keywords alone as a record.  The revised
+\fBdispcor\fR keeps this useful record but moves this it to a new keyword
+DCLOGn (where n is a sequential integer).  Because the REFSPEC keyword is
+removed after each application of \fBdispcor\fR it now takes an explicit
+act by the user to assign another dispersion function to a spectrum and so
+it is not possible to accidentally reapply the same dispersion function
+twice.  Thus this version will apply additional dispersion functions by
+simply adding new REFSPEC keywords.  If they are absent the task resamples
+the spectra based on the current dispersion relation as was the case
+before.
+.LP
+The new version can also tell whether the data was calibrated by the
+previous version.  In this case the check on the dispersion calibration
+flag is still used so that during the transition users are still protected
+against accidentally applying the same reference dispersion function
+twice.  The new task \fBsapertures\fR can now be used to change the
+dispersion calibration flag to override this checking more easily than was
+the case previously.
+.NH
+New Tasks
+.LP
+In this release there is only one completely new task and one task which
+was significantly redesigned.  The new task is \fBspecshift\fR.  It is
+relatively simple, it adds a zero point shift to the dispersion coordinates
+of spectra.  This was the most common request for manipulating the spectral
+world coordinate system.  In this regard there was a common confusion about
+the distinction between shifting the coordinate system and shifting the
+pixel data.  Generally what people want is to apply a shift such that
+features in the spectrum move to the desired wavelength.  One thought is to
+apply the tasks \fBimshift\fR or \fBshiftlines\fR.  The surprise is that
+this does not to work.  The pixels are actually shifted in the image array,
+but these tasks also apply the same shift to the coordinate system so that
+features in the spectrum remain at the same wavelength.  What is really
+required is to leave the pixel data alone and shift only the coordinate
+system.  That is what \fBspecshift\fR does.
+.LP
+While one hopefully does not need to directly manipulate the image header
+keywords describing the coordinate system or other aspects of the spectra,
+instead using such tasks as \fBspecshift\fR, there always seem to be cases
+where this is needed or desired.  In the V2.10 release of the spectral
+software this was difficult because the general \fImultispec\fR format was
+the norm and it has information encoded in the complex WCS attribute
+strings.  As mentioned previously several changes have been made reduce the
+complexity.  Now \fIequispec\fR format will generally be the rule and this
+format has keywords which are more easily manipulated with \fBhedit\fR and
+\fBwcsedit\fR.  However, the task \fBsapertures\fR was revised to provide
+an editing cabability specifically for spectral images, in either
+\fImultispec\fR or \fIequispec\fR format, with options to change various
+parameters globally or aperture-by-aperture.
+.NH
+New Features
+.LP
+There were a number of miscellaneous minor revisions and bug fixes.  One of
+the major new capabilities available with V2.10.3 is support for color
+graphics if the graphics device supports it.  \fBXgterm\fR supports color
+on X-window systems with color monitors.  Several of the spectral tasks
+were modified to use different colors for marks and overplots.  These tasks
+include \fBsplot\fR, \fBspecplot\fR, \fBidentify\fR, and \fBsensfunc\fR.
+In the case of \fBsensfunc\fR the user controls the various color
+assignments with a task parameter or \fBgtools\fR colon command while in
+other cases the next available color is used.
+.LP
+There were several changes to \fBscombine\fR equivalent to those in
+\fBimcombine\fR.  The weighting, when selected, was changed from the square
+root of the exposure time or spectrum statistics to the value with no
+square root.  This corresponds to the more commonly used variance
+weighting.  Other options were added to specify the scaling and weighting
+factors.  These allow specifying an image header keyword or a file
+containing the scale or weighting factors.  A new parameter, "nkeep" has
+been added to allow controling the maximum number of pixels rejected by the
+clipping algorithms.  Previously it was possible to reject all pixels even
+when some of the data was good though with a higher scatter than estimated;
+i.e. all pixels might be greater than 3 sigma from the mean without being
+cosmic rays or other bad values.  Finally a parameter \fIsnoise\fR was
+added to include a sensitivity or scale noise component to a Poisson noise
+model.
+.LP
+In \fBsplot\fR the 'p' and 'u' keys which assign and modify the dispersion
+coordinates now include options for applying a zero point shift or a
+doppler shift in addition to defining an absolute wavelength for a feature
+or starting and ending wavelengths.  There are also bug fixes to the
+equivalent width calculations, it did not handle flux calibrated data, and
+the scroll keys '(' and ')'.
+.LP
+There were several changes to make it easier to deal with with three
+dimensional \fImultispec\fR and \fIequispec\fR data; that is the additional
+data from the "extras" option in the \fBapextract\fR tasks.  One was to fix
+problems associated with an incorrect WCSDIM keyword.  This allows use of
+image sections or \fBimcopy\fR for extracting specific bands and
+apertures.  Another was to add a "bands" parameter in \fBscopy/sarith\fR to
+allow selection of bands.  Also the "onedspec" output format in \fBscopy\fR
+copies any selected bands to separate one dimensional images.
+.LP
+As mentioned earlier, many of the \fBonedspec\fR tasks have been extended
+to work on 2D and 3D spatial spectra.  Some tasks which now have this
+capability in this version and not the previous one are \fBcalibrate\fR and
+\fBdopcor\fR.  \fBIdentify\fR and \fBredentify\fR were extended to operate
+on 3D images.
+.NH
+LONGSLIT
+.LP
+With the applicablity of more \fBonedspec\fR tasks to long slit data
+the \fBlongslit\fR package was modified to add many new tasks.
+This required adding additional package parameters.  One new task
+to point out is \fBcalibrate\fR.  This task is now the prefered one
+to use for extinction and flux calibration of long slit spectra
+rather than the obsolete \fBextinction\fR and \fBfluxcalib\fR.
+The obsolete tasks are still present in this release.
+.NH
+APEXTRACT
+.LP
+The \fBapextract\fR package had a few, mostly transparent, changes.  In
+the previous version the output image header format was always \fImultispec\fR
+even when there was a single spectrum, either because only one aperture
+was defined or because the output format parameter was "onedspec".
+In this release the default WCS format is the simpler \fIequispec\fR.
+.LP
+In the \fBonedspec\fR and \fBimred\fR spectral reduction packages there is
+a dispersion axis package parameter which is used to defined the dispersion
+axis for images without a DISPAXIS keyword.  This applies to all tasks.
+However, the \fBapextract\fR tasks had the dispersion axis defined by their
+own task parameters resulting in some confusion.  To make things consistent
+the dispersion axis parameter in \fBapextract\fR has been moved from the
+tasks to a package parameter.  Now in the \fBimred\fR spectral reduction
+packages, there is just one dispaxis parameter in the package parameters
+which applies to all tasks in those packages, both those from
+\fBonedspec\fR and those from \fBapextract\fR.
+.LP
+Some hidden algorithm parameters were adjusted so that the cleaning and
+variance weighting options perform better in some problem cases without
+requiring a great deal of knowledge about things to tweak.
+.NH
+IMRED Spectroscopic Reduction Tasks
+.LP
+The various spectroscopic reductions tasks, those beginning with "do", have
+had some minor revisions and enhancements in addition to those which apply
+to the individual tasks which make up these scripts.  In the latter class
+is the output WCS format is \fBequispec\fR except for the echelle tasks and
+when dispersion linearization is not done.  Related to this is that the
+multifiber tasks can operate on data with more than 250 fibers which was a
+limitation of the \fBmultispec\fR format.
+.LP
+The dispersion axis parameter in the reduction tasks and in the other tasks
+in the \fBimred\fR spectroscopy packages, such as the \fBapextract\fR
+tasks, is now solely a package parameter.
+.LP
+All the scripts now check the input spectra for the presence of the CCDPROC
+keyword and abort if it is not found.  This keyword indicates that the data
+have been processed for basic CCD calibrations, though it does not check
+the operations themselves.  For data reduced using \fBccdproc\fR this
+keyword will be present.  If these tasks are used on data not processed by
+\fBccdproc\fR then it is a simple matter to add this keyword with
+\fBhedit\fR.  Obviously, the purpose of this change is to avoid
+inadvertently operating on raw data.
+.LP
+All the "do" tasks now have a parameter "datamax".  This minimizes the
+effects of very strong cosmic rays during the extraction of object spectra;
+it does not apply to flat field or arc spectra.  When there is a very large
+difference between data pixel values and cosmic ray pixel values,
+especially true for very weak spectra, the cosmic ray cleanning operation
+does not always work well.  If it is possible to specify a threshold value
+between the maximum real data value and cosmic rays then the cosmic ray
+cleanning can be significantly improved by immediately rejecting those
+pixels above the threshold.  Of course the user must be careful that real
+data does not exceed this value since such data will be excluded.
+.LP
+The fiber reduction tasks, \fBdoargus, dohydra, dofibers, dofoe\fR, and
+\fBdo3fiber\fR have a new processing option for subtracting scattered
+light.  This is particularly useful if there is significant scattered light
+in producing uniform sky spectra for sky subtraction since the fiber
+throughput calibration does not generally correct for this.
+.LP
+The slit reduction task \fBdoslit\fR previously required that the spectrum
+for the reference arc cover the middle of the input data images.  There
+were cases of instrument configurations  where this was not true requiring
+additional manipulation to use this task.  This requirement has been
+eliminated.  Instead when the reference arc needs to be extracted it uses
+the aperture definition from one of the input object spectra since
+definition of the object apertures occurs prior to setting up the
+dispersion calibration.
diff --git a/noao/onedspec/doc/sys/rvidentify.ms b/noao/onedspec/doc/sys/rvidentify.ms
new file mode 100644
index 00000000..dadab882
--- /dev/null
+++ b/noao/onedspec/doc/sys/rvidentify.ms
@@ -0,0 +1,304 @@
+.RP
+.TL
+Radial Velocity Measurements with IDENTIFY
+.AU
+Francisco Valdes
+.AI
+IRAF Group - Central Computer Services
+.K2
+P.O. Box 26732, Tucson, Arizona 85726
+.AB
+The IRAF task \fBidentify\fR may be used to measure radial velocities.
+This is done using the classical method of determining the doppler shifted
+wavelengths of emission and absorption lines.  This paper covers many of
+the features and techniques available through this powerful and versatile
+task which are not immediately evident to a new user.
+.AE
+.NH
+Introduction
+.PP
+The task \fBidentify\fR is very powerful and versatile.  It can be used
+to measure wavelengths and wavelength shifts for doing radial velocity
+measurements from emission and absorption lines.  When combined with
+the CL's ability to redirect input and output both from the standard
+text streams and the cursor and graphics streams virtually anything may
+be accomplished either interactively or automatically.  This, of
+course, requires quite a bit of expertise and experience with
+\fBidentify\fR and with the CL which a new user is not expected to be
+aware of initially.  This paper attempts to convey some of the
+possibilities.  There are many variations on these methods which the
+user will learn through experience.
+.PP
+I want to make a caveat about the suggestions made in this paper.  I wrote
+the \fBidentify\fR task and so I am an expert in its use.  However, I am not
+a spectroscopist, I have not been directly involved in the science of
+measuring astronomical radial velocities, and I am not very familiar with
+the literature.  Thus, the suggestions contained in this paper are based
+on my understanding of the basic principles and the abilities of the
+\fBidentify\fR task.
+.PP
+The task \fBidentify\fR is used to measure radial velocities by
+determining the wavelengths of individual emission and absorption
+lines.  The user must compute the radial velocities separately by
+relating the observed wavelengths to the known rest wavelengths via the
+Doppler formula.  This is a good method when the lines are strong, when
+there are only one or two features, and when there are many, possibly,
+weaker lines.  The accuracy of this method is determined by the
+accuracy of the line centering algorithm.
+.PP
+The alternative method is to compare an observed
+spectrum to a template spectrum of known radial velocity.  This is done
+by correlation or fourier ratio methods.  These methods have the
+advantage of using all of the spectrum and are good when there are many
+very weak and possibly broad features.  Their disadvantages are
+confusion with telluric lines, they don't work well with just a few
+real features, and they require a fair amount of preliminary
+manipulation of the spectrum to remove continuum and interpolate the
+spectrum in logarithmic wavelength intervals.  IRAF tasks for
+correlation and fourier ratio methods are under development at this
+time.  Many people assume that these more abstract methods are inherently
+better than the classical method.  This is not true, it depends on the
+quality and type of data.
+.PP
+Wavelength measurements are best done on the original data rather than
+after linearizing the wavelength intervals.  This is because 1) it is
+not necessary as will be shown below and 2) the interpolation used to
+linearize the wavelength scale can change the shape of the lines,
+particularly strong, narrow emission lines which are the best ones for
+determining radial velocities.  A second reason is that
+\fBidentify\fR currently does not recognize the linear wavelength parameters
+produced during linearization.  This will be fixed soon but
+in the mean time the lines must be measured in pixels and converted
+later by the user.  Alternatively one can determine a linear dispersion solution
+with \fBidentify\fR but this is more work than needed.
+.PP
+This paper is specifically about \fBidentify\fR but one should be aware of the
+task \fBsplot\fR which also may be used to measure radial velocities.  It
+differs in several respects from \fBidentify\fR.  \fBSplot\fR works only on linearized
+data; the wavelength and pixel coordinates are related by a zero point and
+wavelength interval.  The line centering algorithms are different;
+the line centering is generally less robust (tolerant
+of error) and often less accurate.  It has many nice features but is
+not designed for the specific purpose of measuring positions of lines
+and, thus, is not as easy to use for this purpose.
+.PP
+There are a number of sources of additional information relating to the
+use of the task \fBidentify\fR.  The primary source is the manual pages for
+the task.  As with all manual pages it is available online with the
+\fBhelp\fR command and in the \fIIRAF User Handbook\fR.  The NOAO
+reduction guides or cookbooks for the echelle and IIDS/IRS include
+additional examples and discussion.  The line centering algorithm
+is the most critical factor in determining dispersion solutions and
+radial velocities.  It is described in more detail under the help
+topic \fBcenter1d\fR online or in the handbook.
+.NH
+Method 1
+.PP
+In this method arc calibration images are used to determine a wavelength
+scale.  The dispersion solution is then transferred to the object spectrum
+and the wavelengths of emission and absorption lines are measured and
+recorded.  This is relatively straightforward but some tricks will make
+this easier and more accurate.
+.NH 2
+Transferring Dispersion Solutions
+.PP
+There are several ways to transfer the dispersion solution from an arc
+spectrum to an object spectrum differing in the order in which things are
+done.
+.IP (1)
+One way is to determine the dispersion solution for all the arc images
+first.  To do this interactively specify all the arc images as the
+input to \fBidentify\fR.  After determining the dispersion solution for
+the first arc and quitting (\fIq\fR key) the next arc will be displayed
+with the previous dispersion solution and lines retained.  Then use the
+cursor commands \fIa\fR and \fIc\fR (all center) to recenter and
+recompute the dispersion solution, \fIs\fR to shift to the cursor
+position, recenter, and recompute the dispersion solution, or \fIx\fR
+to correlate features, shift, recenter, and recompute the dispersion
+solution.  These commands are relatively fast and simple.
+.IP
+A important reason for doing all the arc images first is that this same
+procedure can be done mostly noninteractively with the task
+\fBreidentify\fR.  After determining a dispersion solution for one arc
+image \fBreidentify\fR does the recenter (\fIa\fR and \fIc\fR), shift
+and recenter (\fIs\fR), or correlation features, shift, and recenter
+(\fIx\fR) to transfer the dispersion solutions between arcs.  This is
+usually done as a background task.
+.IP
+To transfer the solution to the object spectra specify the list of
+object spectra as input to \fBidentify\fR.  For each image begin by
+entering the colon command \fI:read arc\fR where arc is the name of the
+arc image whose dispersion solution is to be applied; normally the one
+taken at the same time and telescope position as the object.  This will
+read the dispersion solution and arc line positions.  Delete the arc
+line positions with the \fIa\fR and \fId\fR (all delete) cursor keys.
+You can now measure the wavelengths of lines in the spectrum.
+.IP (2)
+An alternative method is to interactively alternate between arc and
+object spectra either in the input image list or with the \fI:image
+name\fR colon command.
+.NH 2
+Measuring Wavelengths
+.PP
+.IP (1)
+To record the feature positions at any time use the \fI:features file\fR
+colon command where file is where the feature information will be written.
+Repeating this with the same file appends to the file.  Writing to 
+the database with the \fI:write\fR colon command also records this information.
+Without an argument the results are put in a file with the same name as the
+image and a prefix of "id".  You can use any name you like, however,
+with \fI:write name\fR.  The \fI:features\fR command is probably preferable
+because it only records the line information while the database format
+includes the dispersion solution and other information not needed for
+computing radial velocities.
+.IP (2)
+Remember that when shifting between emission and absorption lines the
+parameter \fIftype\fR must be changed.  This may be done interactively with
+the \fI:ftype emission\fR and \fI:ftype absorption\fR commands.  This parameter
+does not need to be set except when changing between types of lines.
+.IP (3)
+Since the centering of the emission or absorption line is the most
+critical factor one should experiment with the parameter \fIfwidth\fR.
+To change this parameter type \fI:fwidth value\fR.  The positions of the
+marked features are not changed until a center command (\fIc\fR) command
+is given.  \fIWarning: The all center (\fIa\fR and \fIc') command automatically
+refits the dispersion solution to the lines which will lose your
+arc dispersion solution.\fR
+.IP
+A narrow \fIfwidth\fR is less influenced by blends and wings but has a larger
+uncertainty.  A broad \fIfwidth\fR uses all of the line profile and is thus
+stable but may be systematically influenced by blending and wings.  One
+possible approach is to measure the positions at several values of
+\fIfwidth\fR and decide which value to use or use some weighting of the
+various measurements.  You can record each set of measurements with
+the \fI:fe file\fR command.
+.IP (4)
+For calibration of systematic effects from the centering one should obtain
+the spectrum of a similar object with a known radial velocity.  The systematic
+effect is due to the fact that the centering algorithm is measuring a
+weighted function of the line profile which may not be the true center of
+the line as tabulated in the laboratory or in a velocity standard.
+By using the same centering method on an object with the same line profiles
+and known velocity this effect can be eliminated.
+.IP (5)
+Since the arcs are not obtained at precisely the same time as the object
+exposures there may be a wavelength shift relative to the arc dispersion
+solution.  This may be calibrated from night sky lines in the object
+itself (the night sky lines are "good" in this case and should not be
+subtracted away).  There are generally not enough night sky lines to act
+as the primary dispersion calibrator but just one can determine a possible
+wavelength zero point shift.  Measure the night sky line positions at the same
+time the object lines are measured.  Determine a zero point shift from
+the night sky to be taken out of the object lines.
+.NH
+Method 2
+.PP
+This method is similar to the correlation method in that a template
+spectrum is used and the average shift relative to the template measures the
+radial velocity.  This has the advantage of not requiring the user to
+do a lot of calculations (the averaging of the line shifts is done by
+\fRidentify\fR) but is otherwise no better than method 1.
+The template spectrum must have the same features as the object spectrum.
+.IP (1)
+Determine a dispersion solution for the template spectrum either from 
+the lines in the spectrum or from an arc calibration.
+.IP (2)
+Mark the features to be correlated in the template spectrum.
+.IP (3)
+Transfer the template dispersion solution and line positions to an object
+spectrum using one of the methods described earlier.  Then for the
+current feature point the cursor near the same feature in the object
+spectrum and type \fIs\fR.  The mean shift in pixels, wavelength, and
+fractional wavelength (like a radial velocity without the factor of
+the speed of light) for the object is determined and printed.  A new
+dispersion solution is determined but you may ignore this.
+.IP (4)
+When doing additional object spectra remember to start over again with
+the template spectrum (using \fI:read template\fR) and not the solution
+from the last object spectrum.
+.IP (5)
+This procedure assumes that the dispersion solution between the template
+and object are the same.  Checks for zero point shifts with night sky
+lines, as discussed earlier, should be made if possible.  The systematic
+centering bias, however, is accounted for by using the same lines from
+the template radial velocity standard.
+.IP (6)
+One possible source of error is attempting to use very weak lines.  The
+recentering may find the wrong lines and affect the results.  The protections
+against this are the \fIthreshold\fR parameter (in Version 2.4 IRAF) and
+setting the centering error radius to be relatively small.
+.NH
+Method 3
+.PP
+This method uses only strong emission lines and works with linearized
+data without an \fBidentify\fR dispersion solution.  \fBIdentify\fR has
+a failing when used with linearized data; it does not know about the
+wavelength parameters in the image header.  This will eventually be
+fixed.  However, if you have already linearized your spectra and wish
+to use them instead of the nonlinear spectra the following method will
+work.  The recipe involves measuring the positions of emission lines in
+pixels which must then be converted to wavelength using the header
+information.  The strongest emission lines are found automatically
+using the \fIy\fR cursor key.  The number of emission lines to be
+identified is set by the \fImaxfeatures\fR parameter.  The emission
+line positions are then written to a data file using the \fI:features
+file\fR colon command.  This may be done interactively and takes only a
+few moments per spectrum.  If done interactively the images may be
+chained by specifying an image template.  The only trick required is
+than when proceeding to the next spectrum the previous features are
+deleted using the cursor key combination \fIa\fR and \fId\fR (all
+delete).
+.PP
+For a large number of images, on the order of hundreds, this may be automated
+as follows.  A file containing the cursor commands is prepared.
+The cursor command format consists of the x and y positions, the window
+(usually window 1), and the key stroke or colon command.  Because each new
+image form an image template does not restart the cursor command file the
+commands would have to be repeated for each image in the list.  Thus, a CL
+loop calling the
+task each time with only one image is preferable.  Besides redirecting
+the cursor input from a command file we must also redirect the standard
+input for the response to the database save query, the standard output
+to discard the status line information, and, possibly, the graphics
+to a metacode file which can then be reviewed later.  The following
+steps indicate what is to be done.
+.IP (1)
+Prepare a file containing the images to be measured (one per line).
+This can usually be done using the sections command to expand a template
+and directing the output into a file.
+.IP (2)
+Prepare the a cursor command file (let's call it cmdfile) containing the
+following two lines.
+.nf
+	1 1 1 y
+	1 1 1 :fe positions.dat
+.fi
+.IP (3)
+Enter the following commands.
+.nf
+	list="file"
+	while (fscan (list, s1) != EOF) {
+	print ("no") | identify (s1, maxfeatures=2, cursor="cmdfile",
+		>"dev$null", >G "plotfile")
+	}
+.fi
+.LP
+Note that these commands could be put in a CL script and executed using the
+command
+
+	on> cl <script.cl
+
+.PP
+The commands do the following.  The first command initializes the image list
+for the loop.  The second command is the loop to be run until the end of
+the image file is reached.  The command in the loop directs the string
+"no" to the standard input of identify which will be the response to the
+database save query.  The identify command uses the image name obtained
+from the list by the fscan procedure, sets the maximum number of features
+to be found to be 2 (this can be set using \fBeparam\fR instead), the cursor
+input is taken from the cursor command file, the standard output is
+discarded to the null device, and the STDGRAPH output is redirected to
+a plot file.  If the plot file redirection is not used then the graphs
+will appear on the specified graphics device (usually the graphics terminal).
+The plot file can then be disposed of using the \fBgkimosaic\fR task to either
+the graphics terminal or a hardcopy device.
diff --git a/noao/onedspec/doc/sys/sensfunc.ms b/noao/onedspec/doc/sys/sensfunc.ms
new file mode 100644
index 00000000..67b6532d
--- /dev/null
+++ b/noao/onedspec/doc/sys/sensfunc.ms
@@ -0,0 +1,83 @@
+.EQ
+delim	$$
+.EN
+.OM
+.TO
+IRAF ONEDSPEC Users
+.FR
+Frank Valdes
+.SU
+SENSFUNC Corrections
+.LP
+This memorandum describes the meaning of the corrections
+computed by the \fBonedspec\fR task \fBsensfunc\fR.
+The basic equation is
+
+.EQ (1)
+I( lambda )~=~I sub obs ( lambda )~10 sup {0.4~(s( lambda )~+
+~A~e( lambda )~+~roman {fudge~terms})}
+.EN
+
+where $I sub obs$ is the observed spectrum corrected to counts per second,
+$I$ is the flux calibrated spectrum, $s( lambda )$ is the sensitivity
+correction needed to produce
+flux calibrated intensities, $A$ is the air mass at the time of the
+observation, $e( lambda )$ is a standard extinction function, and,
+finally, additional terms appropriately called \fIfudge\fR terms.  Expressed
+as a magnitude correction this equation is
+
+.EQ (2)
+DELTA m( lambda )~=s( lambda )~+~A~e( lambda )~+~roman {fudge~terms}
+.EN
+
+In \fBsensfunc\fR the standard extinction function is applied so that ideally
+the $DELTA m$ curves (defining the sensitivity function) obtained from
+observations of different stars and at different air masses are identical.
+However, at times this is not the case because the observations were taken
+through non-constant or nonstandard extinction.
+
+There are two types of fudge terms used in \fBsensfunc\fR, called \fIfudge\fR
+and \fIgrey\fR.  The \fIfudge\fR correction is a separate constant,
+independent of wavelength or air mass, applied to each observation to shift
+the sensitivity curves to the same level on average.  This is done to
+determine the shape of the sensitivity curve only.
+The fudge correction for each observation is obtained by determining
+the average magnitude shift over all wavelenths relative to the observation
+with the smallest sensitivity correction.  A composite sensitivity curve
+is then determined from the average of all the fudged observations.
+The fudge terms are not incorporated in the sensitivity or extinction
+corrections applied to calibrate the spectra.  Thus, after applying the
+sensitivity and extinction corrections to the standard star spectra there
+will be absolute flux scale errors due to the observing conditions.
+
+If the observer believes that there is an actual calibratible error in
+the standard extinction then \fBsensfunc\fR can be used to determine a
+correction which is a linear function of the air mass.  This is done by
+relating the fudge values (the magnitude shifts needed to bring observations
+to the same sensitivity level) to the air mass of the observations.
+The \fIgrey\fR term is obtained by the least square fit to 
+
+.EQ (3)
+f sub i~=~G~DELTA A sub i~=~G~A sub i~+~C
+.EN
+
+where the $f sub i$ are the fudge values relative to the observation with
+the smallest sensitivity correction and the $DELTA A sub i$ are the
+air mass differences relative to this same observation.  The slope constant
+$G$ is what is refered to as the \fIgrey\fR term.  The constant term,
+related to the air mass of the reference observation to which the other
+spectra are shifted, is absorbed in the sensitivity function.
+The modified equation (2) is
+
+.EQ (4)
+DELTA m( lambda )~=~s ( lambda ) + A~(e( lambda )~+~G)
+.EN
+
+It is important to realize that equation (3) can lead to erroneous results
+if there is no real relation to the air mass or the air mass range is
+too small.  In other words applying the grey term correction will produce
+some number for $G$ but it may be worse than no correction.  A plot of
+the individual fudge constants, $f sub i$, and the air mass or
+air mass differences would be useful to evaluate the validity of the
+grey correction.  The actual magnitude of the correction is not $G$
+but $DELTA A~G$ where $DELTA A$ is the range of observed air mass.
diff --git a/noao/onedspec/doc/sys/specwcs.ms b/noao/onedspec/doc/sys/specwcs.ms
new file mode 100644
index 00000000..a9d90a41
--- /dev/null
+++ b/noao/onedspec/doc/sys/specwcs.ms
@@ -0,0 +1,612 @@
+.EQ
+delim $$
+gsize 10
+.EN
+.nr PS 11
+.nr VS 13
+.de V1
+.ft CW
+.ps -2
+.nf
+..
+.de V2
+.fi
+.ft R
+.ps +2
+..
+.ND March 1993
+.TL
+The IRAF/NOAO Spectral World Coordinate Systems
+.AU
+Francisco Valdes
+.AI
+IRAF Group - Central Computer Services
+.K2
+.DY
+
+.AB
+The image formats and world coordinate systems for dispersion calibrated
+spectra used in the IRAF/NOAO spectroscopy packages are described; in
+particular, the image header keywords defining the coordinates are given.
+These keywords appear both as part of the IRAF image structure and map
+directly to FITS format.  The types of spectra include multidimensional
+images with one or more spatial axes and a linear or log-linear dispersion
+axis and special \fIequispec\fR and \fImultispec\fR formats having multiple
+independent one dimensional spectra in a single multidimensional image.
+The \fImultispec\fR format also includes general nonlinear dispersion
+coordinate systems using polynomial, spline, sampled table, and look-up
+table functions.
+.AE
+
+.NH
+Types of Spectral Data
+.LP
+Spectra are stored as one, two, or three dimensional images with one axis
+being the dispersion axis.  A pixel value is the flux over
+some interval of wavelength and position.  The simplest example of a
+spectrum is a one dimensional image which has pixel values as a
+function of wavelength.
+.LP
+There are two types of higher dimensional spectral image formats.  One type
+has spatial axes for the other dimensions and the dispersion axis may be
+along any of the image axes.  Typically this type of format is used for
+long slit (two dimensional) and Fabry-Perot (three dimensional) spectra.
+This type of spectra is referred to as \fIspatial\fR spectra and the
+world coordinate system (WCS) format is called \fIndspec\fR.
+The details of the world coordinate systems are discussed later.
+.LP
+The second type of higher dimensional spectral image consists of multiple,
+independent, one dimensional spectra stored in the higher dimensions with
+the first image axis being the dispersion axis; i.e. each line is a
+spectrum.  This format allows associating many spectra and related
+parameters in a single data object.  This type of spectra is referred to
+as \fImultispec\fR and the there are two coordinate system formats,
+\fIequispec\fR and \fImultispec\fR.  The \fIequispec\fR format applies
+to the common case where all spectra have the same linear dispersion
+relation.  The \fImultispec\fR format applies to the general case of spectra
+with differing dispersion relations or non-linear dispersion functions.
+These multi-spectrum formats are important since maintaining large numbers
+of spectra as individual one dimensional images is very unwieldy for the
+user and inefficient for the software.
+.LP
+Examples of multispec spectral images are spectra extracted from a
+multi-fiber or multi-aperture spectrograph or orders from an echelle
+spectrum.  The second axis is some arbitrary indexing of the spectra,
+called \fIapertures\fR, and the third dimension is used for
+associated quantities.  The IRAF \fBapextract\fR package may produce
+multiple spectra from a CCD image in successive image lines with an
+optimally weighted spectrum, a simple aperture sum spectrum, a background
+spectrum, and sigma spectrum as the associated quantities along the third
+dimension of the image.
+.LP
+Many \fBonedspec\fR package tasks which are designed to operate on
+individual one dimensional spectra may operate on spatial spectra by
+summing a number of neighboring spectra across the dispersion axis.  This
+eliminates the need to "extract" one dimensional spectra from the natural
+format of this type of data in order to use tasks oriented towards the
+display and analysis of one dimensional spectra.  The dispersion axis is
+either given in the image header by the keyword DISPAXIS or the package
+\fIdispaxis\fR parameter.  The summing factors across the
+dispersion are specified by the \fInsum\fR package parameter.
+.LP
+One dimensional spectra, whether from multispec spatial spectra, have
+several associated quantities which may appear in the image header as part
+of the coordinate system description.  The primary identification of a
+spectrum is an integer aperture number.  This number must be unique within
+a single image.  There is also an integer beam number used for various
+purposes such as discriminating object, sky, and arc spectra in
+multi-fiber/multi-aperture data or to identifying the order number in
+echelle data.  For spectra summed from spatial spectra the aperture number
+is the central line, column, or band.  In 3D images the aperture index
+wraps around the lowest non-dispersion axis.  Since most one dimensional
+spectra are derived from an integration over one or more spatial axes, two
+additional aperture parameters record the aperture limits.  These limits
+refer to the original pixel limits along the spatial axis.  This
+information is primarily for record keeping but in some cases it is used
+for spatial interpolation during dispersion calibration.  These values are
+set either by the \fBapextract\fR tasks or when summing neighboring vectors
+in spatial spectra.
+.LP
+An important task to be aware of for manipulating spectra between image
+formats is \fBscopy\fR.  This task allows selecting spectra from multispec
+images and grouping them in various ways and also "extracts" apertures from
+long slit and 3D spectra simply and without resort to the more general
+\fBapextract\fR package.
+.NH
+World Coordinate Systems
+.LP
+IRAF images have three types of coordinate systems.  The pixel array
+coordinates of an image or image section, i.e. the lines and
+columns, are called the \fIlogical\fR coordinates.  The logical coordinates of
+individual pixels change as sections of the image are used or extracted.
+Pixel coordinates are tied to the data, i.e. are fixed to features
+in the image, are called \fIphysical\fR coordinates.  Initially the logical
+and physical coordinates are the equivalent but differ when image sections
+or other tasks which modify the sampling of the pixels are applied.
+.LP
+The last type of coordinate system is called the \fIworld\fR coordinate
+system.  Like the physical coordinates, the world coordinates are tied to
+the features in the image and remain unchanged when sections of the image
+are used or extracted.  If a world coordinate system is not defined for an
+image, the physical coordinate system is considered to be the world
+coordinate system.  In spectral images the world coordinate system includes
+dispersion coordinates such as wavelengths.  In many tasks outside the
+spectroscopy packages, for example the \fBplot\fR, \fBtv\fR and
+\fBimages\fR packages, one may select the type of coordinate system to be
+used.  To make plots and get coordinates in dispersion units for spectra
+with these tasks one selects the "world" system.  The spectral tasks always
+use world coordinates.
+.LP
+The coordinate systems are defined in the image headers using a set of
+reserved keywords which are set, changed, and updated by various tasks.
+Some of the keywords consist of simple single values following the FITS
+convention.  Others, the WAT keywords, encode long strings of information,
+one for each coordinate axis and one applying to all axes, into a set of
+sequential keywords.  The values of these keywords must then be pasted
+together to recover the string.  The long strings contain multiple pieces
+called WCS \fIattributes\fR.  In general the WCS keywords should be left to
+IRAF tasks to modify.  However, if one wants modify them directly some
+tasks which may be used are \fBhedit\fR, \fBhfix\fR, \fBwcsedit\fR,
+\fBwcsreset\fR, \fBspecshift\fR, \fBdopcor\fR, and \fBsapertures\fR.  The
+first two are useful for the simple keywords, the two  "wcs" tasks are
+useful for the linear ndspec and equispec formats, the next two are for the
+common cases of shifting the coordinate zero point or applying a doppler
+correction, and the last one is the one to use for the more complex
+multispec format attributes.
+.NH
+Physical Coordinate System
+.LP
+The physical coordinate system is used by the spectral tasks when there is
+no dispersion coordinate information (such as before dispersion
+calibration), to map the physical dispersion axis to the logical dispersion
+axis, and in the multispec world coordinate system dispersion functions
+which are defined in terms of physical coordinates.
+.LP
+The transformation between logical and physical coordinates is defined by
+the header keywords LTVi, LTMi_j (where i and j are axis numbers) through
+the vector equation
+
+.EQ I
+    l vec~=~|m| cdot p vec + v vec
+.EN
+
+where $l vec$ is a logical coordinate vector, $p vec$ is a physical
+coordinate vector, $v vec$ is the origin translation vector specified by
+the LTV keywords and $|m|$ is the scale/rotation matrix
+specified by the LTM keywords.  For spectra rotation terms (nondiagonal
+matrix elements) generally do not make sense (in fact many tasks will not
+work if there is a rotation) so the transformations along each axis are
+given by the linear equation
+
+.EQ I
+    l sub i~=~LTMi_i cdot p sub i + LTVi.
+.EN
+
+If all the LTM/LTV keywords are missing they are assumed to have zero
+values except that the diagonal matrix terms, LTMi_i, are assumed to be 1.
+Note that if some of the keywords are present then a missing LTMi_i will
+take the value zero which generally causes an arithmetic or matrix
+inversion error in the IRAF tasks.
+.LP
+The dimensional mapping between logical and physical axes is given by the
+keywords WCSDIM and WAXMAP01.  The WCSDIM keyword gives the dimensionality
+of the physical and world coordinate system.  There must be coordinate
+information for that many axes in the header (though some may be missing
+and take their default values).  If the WCSDIM keyword is missing it is
+assumed to be the same as the logical image dimensionality.
+.LP
+The syntax of the WAXMAP keyword are pairs of integer values,
+one for each physical axis.  The first number of each pair indicates which
+current \fIlogical\fR axis corresponds to the original \fIphysical\fR axis
+(in order) or zero if that axis is missing.   When the first number is zero
+the second number gives the offset to the element of the original axis
+which is missing.  As an example consider a three dimensional image in
+which the second plane is extracted (an IRAF image section of [*,2,*]).
+The keyword would then appear as WAXMAP01 = '1 0 0 1 2 0'.  If this keyword
+is missing the mapping is 1:1; i.e. the dimensionality and order of the
+axes are the same.
+.LP
+The dimensional mapping is important because the dispersion axis for
+the nspec spatial spectra as specified by the DISPAXIS keyword or task
+parameter, or the axis definitions for the equispec and or multispec
+formats are always in terms of the original physical axes.
+.NH
+Linear Spectral World Coordinate Systems
+.LP
+When there is a linear or logarithmic relation between pixels and
+dispersion coordinates which is the same for all spectra the WCS header
+format is simple and uses the FITS convention (with the CD matrix keywords
+proposed by Hanisch and Wells 1992) for the logical pixel to world
+coordinate transformation.  This format applies to one, two, and three
+dimensional data.  The higher dimensional data may have either linear
+spatial axes or the equispec format where each one dimensional spectrum
+stored along the lines of the image has the same dispersion.
+.LP
+The FITS image header keywords describing the spectral world coordinates
+are CTYPEi, CRPIXi, CRVALi, and CDi_j where i and j are axis numbers.  As
+with the physical coordinate transformation the nondiagonal or rotation
+terms are not expected in the spectral WCS and may cause problems if they
+are not zero.  The CTYPEi keywords will have the value LINEAR to identify
+the type of of coordinate system.  The transformation between dispersion
+coordinate, $w sub i$, and logical pixel coordinate, $l sub i$, along axis i is given by
+
+.EQ I
+    w sub i~=~CRVALi + CDi_i cdot (l sub i - CRPIXi)
+.EN
+
+If the keywords are missing then the values are assumed to be zero except
+for the diagonal elements of the scale/rotation matrix, the CDi_i, which
+are assumed to be 1.  If only some of the keywords are present then any
+missing CDi_i keywords will take the value 0 which will cause IRAF tasks to
+fail with arithmetic or matrix inversion errors.  If the CTYPEi keyword is
+missing it is assumed to be "LINEAR".
+.LP
+If the pixel sampling is logarithmic in the dispersion coordinate, as
+required for radial velocity cross-correlations, the WCS coordinate values
+are logarithmic and $w sub i$ (above) is the logarithm of the dispersion
+coordinate.  The spectral tasks (though not other tasks) will recognize
+this case and automatically apply the anti-log.  The two types of pixel
+sampling are identified by the value of the keyword DC-FLAG.  A value of 0
+defines a linear sampling of the dispersion and a value of 1 defines a
+logarithmic sampling of the dispersion.  Thus, in all cases the spectral
+tasks will display and analyze the spectra in the same dispersion units
+regardless of the pixel sampling.
+.LP
+Other keywords which may be present are DISPAXIS for 2 and 3 dimensional
+spatial spectra, and the WCS attributes "system", "wtype", "label", and
+"units".  The system attribute will usually have the value "world" for
+spatial spectra and "equispec" for equispec spectra.  The wtype attribute
+will have the value "linear".  Currently the label will be either "Pixel"
+or "Wavelength" and the units will be "Angstroms" for dispersion corrected
+spectra.  In the future there will be more generality in the units
+for dispersion calibrated spectra.
+.LP
+Figure 1 shows the WCS keywords for a two dimensional long slit spectrum.
+The coordinate system is defined to be a generic "world" system and the
+wtype attributes and CTYPE keywords define the axes to be linear.  The
+other attributes define a label and unit for the second axis, which is the
+dispersion axis as indicated by the DISPAXIS keyword.  The LTM/LTV keywords
+in this example show that a subsection of the original image has been
+extracted with a factor of 2 block averaging along the dispersion axis.
+The dispersion coordinates are given in terms of the \fIlogical\fR pixel
+coordinates by the FITS keywords as defined previously.
+
+.DS
+.ce
+Figure 1: Long Slit Spectrum
+
+.V1
+WAT0_001= 'system=world'
+WAT1_001= 'wtype=linear'
+WAT2_001= 'wtype=linear label=Wavelength units=Angstroms'
+WCSDIM  =                    2
+DISPAXIS=                    2
+DC-FLAG =                    0
+
+CTYPE1  = 'LINEAR  '
+LTV1    =                 -10.
+LTM1_1  =                   1.
+CRPIX1  =                  -9.
+CRVAL1  =     19.5743865966797
+CD1_1   =     1.01503419876099
+
+CTYPE2  = 'LINEAR  '
+LTV2    =                -49.5
+LTM2_2  =                  0.5
+CRPIX2  =                 -49.
+CRVAL2  =       4204.462890625
+CD2_2   =     12.3337936401367
+.V2
+.DE
+
+Figure 2 shows the WCS keywords for a three dimensional image where each
+line is an independent spectrum or associated data but where all spectra
+have the same linear dispersion.  This type of coordinate system has the
+system name "equispec".  The ancillary information about each aperture is
+found in the APNUM keywords.  These give the aperture number, beam number,
+and extraction limits.  In this example the LTM/LTV keywords have their
+default values; i.e. the logical and physical coordinates are the same.
+
+.DS
+.ce
+Figure 2: Equispec Spectrum
+
+.V1
+WAT0_001= 'system=equispec'
+WAT1_001= 'wtype=linear label=Wavelength units=Angstroms'
+WAT2_001= 'wtype=linear'
+WAT3_001= 'wtype=linear'
+WCSDIM  =                    3
+DC-FLAG =                    0
+APNUM1  = '41 3 7.37 13.48'
+APNUM2  = '15 1 28.04 34.15'
+APNUM3  = '33 2 43.20 49.32'
+
+CTYPE1  = 'LINEAR  '
+LTM1_1  =                   1.
+CRPIX1  =                   1.
+CRVAL1  =             4204.463
+CD1_1   =     6.16689700000001
+
+CTYPE2  = 'LINEAR  '
+LTM2_2  =                   1.
+CD2_2   =                   1.
+
+CTYPE3  = 'LINEAR  '
+LTM3_3  =                   1.
+CD3_3   =                   1.
+.V2
+.DE
+.NH
+Multispec Spectral World Coordinate System
+.LP
+The \fImultispec\fR spectral world coordinate system applies only to one
+dimensional spectra; i.e. there is no analog for the spatial type spectra.
+It is used either when there are multiple 1D spectra with differing
+dispersion functions in a single image or when the dispersion functions are
+nonlinear.
+.LP
+The multispec coordinate system is always two dimensional though there may
+be an independent third axis.  The two axes are coupled and they both have
+axis type "multispec".  When the image is one dimensional the physical line
+is given by the dimensional reduction keyword WAXMAP.  The second, line
+axis, has world coordinates of aperture number.  The aperture numbers are
+integer values and need not be in any particular order but do need to be
+unique.  This aspect of the WCS is not of particular user interest but
+applications use the inverse world to physical transformation to select a
+spectrum line given a specified aperture.
+.LP
+The dispersion functions are specified by attribute strings with the
+identifier \fIspecN\fR where N is the \fIphysical\fR image line.  The
+attribute strings contain a series of numeric fields.  The fields are
+indicated symbolically as follows.
+
+.EQ I
+         specN~=~ap~beam~dtype~w1~dw~nw~z~aplow~aphigh~[functions sub i ]
+.EN
+
+where there are zero or more functions having the following fields,
+
+.EQ I
+    function sub i~=~ wt sub i~w0 sub i~ftype sub i~[parameters]~[coefficients]
+.EN
+
+The first nine fields in the attribute are common to all the dispersion
+functions.  The first field of the WCS attribute is the aperture number,
+the second field is the beam number, and the third field is the dispersion
+type with the same function as DC-FLAG in the \fInspec\fR and
+\fIequispec\fR formats.  A value of -1 indicates the coordinates are not
+dispersion coordinates (the spectrum is not dispersion calibrated), a value
+of 0 indicates linear dispersion sampling, a value of 1 indicates
+log-linear dispersion sampling, and a value of 2 indicates a nonlinear
+dispersion.
+.LP
+The next two fields are the dispersion coordinate of the first
+\fIphysical\fR pixel and the average dispersion interval per \fIphysical\fR
+pixel.  For linear and log-linear dispersion types the dispersion
+parameters are exact while for the nonlinear dispersion functions they are
+approximate.  The next field is the number of valid pixels, hence it is
+possible to have spectra with varying lengths in the same image.  In that
+case the image is as big as the biggest spectrum and the number of pixels
+selects the actual data in each image line.  The next (seventh) field is a
+doppler factor.  This doppler factor is applied to all dispersion
+coordinates by multiplying by $1/(1+z)$ (assuming wavelength dispersion
+units).  Thus a value of 0 is no doppler correction.  The last two fields
+are extraction aperture limits as discussed previously.
+.LP
+Following these fields are zero or more function descriptions.  For linear
+or log-linear dispersion coordinate systems there are no function fields.
+For the nonlinear dispersion systems the function fields specify a weight,
+a zero point offset, the type of dispersion function, and the parameters
+and coefficients describing it.  The function type codes, $ftype sub i$,
+are 1 for a chebyshev polynomial, 2 for a legendre polynomial, 3 for a
+cubic spline, 4 for a linear spline, 5 for a pixel coordinate array, and 6
+for a sampled coordinate array.  The number of fields before the next
+function and the number of functions are determined from the parameters of
+the preceding function until the end of the attribute is reached.
+.LP
+The equation below shows how the final wavelength is computed based on
+the $nfunc$ individual dispersion functions $W sub i (p)$.  Note that this
+is completely general in that different function types may be combined.
+However, in practice when multiple functions are used they are generally of
+the same type and represent a calibration before and after the actual
+object observation with the weights based on the relative time difference
+between the calibration dispersion functions and the object observation.
+
+.EQ I
+w~=~sum from i=1 to nfunc {wt sub i cdot (w0 sub i + W sub i (p)) / (1 + z)}
+.EN
+
+The multispec coordinate systems define a transformation between physical
+pixel, $p$, and world coordinates, $w$.  Generally there is an intermediate
+coordinate system used.  The following equations define these coordinates.
+The first one shows the transformation between logical, $l$, and physical,
+$p$, coordinates based on the LTM/LTV keywords.  The polynomial functions
+are defined in terms of a normalized coordinate, $n$, as shown in the
+second equation.  The normalized coordinates run between -1 and 1 over the
+range of physical coordinates, $p sub min$ and $p sub max$ which are
+parameters of the function, upon which the coefficients were defined.  The
+spline functions map the physical range into an index over the number of
+evenly divided spline pieces, $npieces$, which is a parameter of the
+function.  This mapping is shown in the third and fourth equations where
+$s$ is the continuous spline coordinate and $j$ is the nearest integer less
+than or equal to $s$.
+
+.EQ I
+    p mark~=~(l - LTV1) / LTM1_1
+.EN
+.EQ I
+    n lineup~=~(p - p sub middle ) / (2 cdot p sub range )
+.EN
+.EQ I
+      lineup~=~(p - (p sub max + p sub min )/2) / (2 cdot (p sub max - p sub min ))
+.EN
+.EQ I
+    s lineup~=~(p - p sub min ) / (p sub max - p sub min ) cdot npieces
+.EN
+.EQ I
+    j lineup~=~roman "int" (s)
+.EN
+.NH 2
+Linear and Log Linear Dispersion Function
+.LP
+The linear and log-linear dispersion functions are described by a
+wavelength at the first \fIphysical\fR pixel and a wavelength increment per
+\fIphysical\fR pixel.  A doppler correction may also be applied.  The
+equations below show the two forms.  Note that the coordinates returned are
+always wavelength even though the pixel sampling and the dispersion
+parameters may be log-linear.
+
+.EQ I
+    w mark~=~(w1 + dw cdot (p - 1)) / (1 + z)
+.EN
+.EQ I
+    w lineup~=~10 sup {(w1 + dw cdot (p - 1)) / (1 + z)}
+.EN
+
+Figure 3 shows an example from a multispec image with
+independent linear dispersion coordinates.  This is a linearized echelle
+spectrum where each order (identified by the beam number) is stored as a
+separate image line.
+
+.DS
+.ce
+Figure 3: Echelle Spectrum with Linear Dispersion Function
+
+.V1
+WAT0_001= 'system=multispec'
+WAT1_001= 'wtype=multispec label=Wavelength units=Angstroms'
+WAT2_001= 'wtype=multispec spec1 = "1 113 0 4955.44287109375 0.05...
+WAT2_002= '5 256 0. 23.22 31.27" spec2 = "2 112 0 4999.0810546875...
+WAT2_003= '58854293 256 0. 46.09 58.44" spec3 = "3 111 0 5043.505...
+WAT2_004= '928358078002 256 0. 69.28 77.89"
+WCSDIM  =                    2
+
+CTYPE1  = 'MULTISPE'
+LTM1_1  =                   1.
+CD1_1   =                   1.
+
+CTYPE2  = 'MULTISPE'
+LTM2_2  =                   1.
+CD2_2   =                   1.
+.V2
+.DE
+.NH 2
+Chebyshev Polynomial Dispersion Function
+.LP
+The parameters for the chebyshev polynomial dispersion function are the
+$order$ (number of coefficients) and the normalizing range of physical
+coordinates, $p sub min$ and $p sub max$, over which the function is
+defined and which are used to compute $n$.  Following the parameters are
+the $order$ coefficients, $c sub i$.  The equation below shows how to
+evaluate the function using an iterative definition where $x sub 1 = 1$,
+$x sub 2 = n$, and $x sub i = 2 cdot n cdot x sub {i-1} - x sub {i-2}$.
+
+.EQ I
+    W~=~sum from i=1 to order {c sub i cdot x sub i}
+.EN
+.NH 2
+Legendre Polynomial Dispersion Function
+.LP
+The parameters for the legendre polynomial dispersion function are the
+order (number of coefficients) and the normalizing range of physical
+coordinates, pmin and pmax, over which the function is defined
+and which are used to compute n.  Following the parameters are the
+order coefficients, c sub i.  The equation below shows how to evaluate the
+function using an iterative definition where $x sub 1 = 1$, $x sub 2 = n$, and
+$x sub i = ((2i-3) cdot n cdot x sub {i-1} - (i-2) cdot x sub {i-2}) / (i-1)$.
+
+.EQ I
+    W~=~sum from i=1 to order {c sub i cdot x sub i}
+.EN
+.LP
+Figure 4 shows an example from a multispec image with independent nonlinear
+dispersion coordinates.  This is again from an echelle spectrum.  Note that
+the IRAF \fBechelle\fR package determines a two dimensional dispersion
+function, in this case a bidimensional legendre polynomial, with the
+independent variables being the order number and the extracted pixel
+coordinate.  To assign and store this function in the image is simply a
+matter of collapsing the two dimensional dispersion function by fixing the
+order number and combining all the terms with the same order.
+
+.DS
+.ce
+Figure 4: Echelle Spectrum with Legendre Polynomial Function
+
+.V1
+WAT0_001= 'system=multispec'
+WAT1_001= 'wtype=multispec label=Wavelength units=Angstroms'
+WAT2_001= 'wtype=multispec spec1 = "1 113 2 4955.442888635351 0.05...
+WAT2_002= '83 256 0. 23.22 31.27 1. 0. 2 4 1. 256. 4963.0163112090...
+WAT2_003= '976664 -0.3191636898579552 -0.8169352858733255" spec2 =...
+WAT2_004= '9.081188912082 0.06387049476832223 256 0. 46.09 58.44 1...
+WAT2_005= '56. 5007.401409453303 8.555959076467951 -0.176732458267...
+WAT2_006= '09935064388" spec3 = "3 111 2 5043.505764869474 0.07097...
+WAT2_007= '256 0. 69.28 77.89 1. 0. 2 4 1. 256. 5052.586239197408 ...
+WAT2_008= '271 -0.03173489817897474 -7.190562320405975E-4"
+WCSDIM  =                    2
+
+CTYPE1  = 'MULTISPE'
+LTM1_1  =                   1.
+CD1_1   =                   1.
+
+CTYPE2  = 'MULTISPE'
+LTM2_2  =                   1.
+CD2_2   =                   1.
+.V2
+.DE
+.NH 2
+Linear Spline Dispersion Function
+.LP
+The parameters for the linear spline dispersion function are the number of
+spline pieces, $npieces$, and the range of physical coordinates, $p sub min$
+and $p sub max$, over which the function is defined and which are used to
+compute the spline coordinate $s$.  Following the parameters are the
+$npieces+1$ coefficients, $c sub i$.  The two coefficients used in a linear
+combination are selected based on the spline coordinate, where $a$ and $b$
+are the fractions of the interval in the spline piece between the spline
+knots, $a=(j+1)-s$, $b=s-j$, and $x sub 0 =a$, and $x sub 1 =b$.
+
+.EQ I
+    W~=~sum from i=0 to 1 {c sub (i+j) cdot x sub i}
+.EN
+.NH 2
+Cubic Spline Dispersion Function
+.LP
+The parameters for the cubic spline dispersion function are the number of
+spline pieces, $npieces$, and the range of physical coordinates, $p sub min$
+and $p sub max$, over which the function is defined and which are used
+to compute the spline coordinate $s$.  Following the parameters are the
+$npieces+3$ coefficients, $c sub i$.  The four coefficients used are
+selected based on the spline coordinate.  The fractions of the interval
+between the integer spline knots are given by $a$ and $b$, $a=(j+1)-s$,
+b=$s-j$, and $x sub 0 =a sup 3$, $x sub 1 =(1+3 cdot a cdot (1+a cdot b))$,
+$x sub 2 =(1+3 cdot b cdot (1+a cdot b))$, and $x sub 3 =b sup 3$.
+
+.EQ I
+    W~=~sum from i=0 to 3 {c sub (i+j) cdot x sub i}
+.EN
+.NH 2
+Pixel Array Dispersion Function
+.LP
+The parameters for the pixel array dispersion function consists of just the
+number of coordinates $ncoords$.  Following this are the wavelengths at
+integer physical pixel coordinates starting with 1.  To evaluate a
+wavelength at some physical coordinate, not necessarily an integer, a
+linear interpolation is used between the nearest integer physical coordinates
+and the desired physical coordinate where $a$ and $b$ are the usual
+fractional intervals $k= roman "int" (p)$, $a=(k+1)-p$, $b=p-k$,
+and $x sub 0 =a$, and $x sub 1 =b$.
+
+.EQ I
+    W~=~sum from i=0 to 1 {c sub (i+j) cdot x sub i}
+.EN
+.NH 2
+Sampled Array Dispersion Function
+.LP
+The parameters for the sampled array dispersion function consists of
+the number of coordinate pairs, $ncoords$, and a dummy field.
+Following these are the physical coordinate and wavelength pairs
+which are in increasing order.  The nearest physical coordinates to the
+desired physical coordinate are located and a linear interpolation
+is computed between the two sample points.
diff --git a/noao/onedspec/doc/telluric.hlp b/noao/onedspec/doc/telluric.hlp
new file mode 100644
index 00000000..f0bfe597
--- /dev/null
+++ b/noao/onedspec/doc/telluric.hlp
@@ -0,0 +1,350 @@
+.help telluric Mar97 noao.onedspec
+.ih
+NAME
+telluric -- remove telluric features from 1D spectra
+.ih
+SUMMARY
+Telluric calibration spectra are shifted and scaled to best divide out
+telluric features from data spectra.  This may be done non-interactively to
+minimize the RMS in some region or regions of the data spectra and
+interactively with a graphically search.
+.ih
+USAGE
+telluric input output cal
+.ih
+PARAMETERS
+.ls input
+List of input data images containing one dimensional spectra to be
+corrected.  All spectra in each image are corrected. The spectra need not
+be wavelength calibrated.
+.le
+.ls output
+List of output corrected images.  The list must either match the input list
+or be an empty list.  If an empty list is specified the input spectra will
+be replaced by the corrected spectra.  The input spectra will also be
+replaced if the input and output image names are the same.  Any other image
+name must be for a new image otherwise a warning message will be given and
+the task will proceed to the next input image.
+.le
+.ls cal  
+List of telluric calibration images.  If a single image is specified it
+will apply to all the input images.  Otherwise the list of calibration
+images must match the list of input images.
+.le
+.ls ignoreaps = no
+Ignore aperture numbers between the input spectra and the calibration
+spectra?  If "no" then the calibration image must contain a spectrum
+with the same aperture number as each spectrum in the input image.
+Otherwise the first spectrum in the calibration image will be used
+for all spectra in the input image.
+.le
+.ls xcorr = yes
+Cross-correlate each input spectrum with the calibration spectrum to
+determine an shift for the calibration spectrum?  Only regions specified by
+the sample regions parameter will be used in the cross-correlation.
+.le
+.ls tweakrms = yes
+Search for the minimum RMS in the corrected spectrum by adjusting the
+shifts and scales between the input spectrum and the calibration spectrum?
+The RMS is minimized in the specified sample regions.
+.le
+.ls interactive = yes
+Enter an interactive graphical mode to search for the best shift
+and scale between the input spectra and calibration spectra?  This
+is done after the optional automatic cross-correlation and RMS minimization
+step.  A query is made for each input spectrum so that the interactive
+step may be skipped during the execution of the task.
+.le
+.ls sample = "*"
+Sample regions to use for cross-correlation, automatic RMS minimization,
+and RMS values.  The sample regions are specified by a list of comma
+separated ranges.  The ranges are colon separate coordinate values.
+For dispersion calibrated spectra the coordinate values are in the
+dispersion units otherwise they are in pixel coordinates.  The string "*"
+selects the entire spectrum.  The sample regions may be changed
+interactively either with the cursor or with a colon command.
+.le
+.ls threshold = 0.
+Since the calibration consists of division by the scaled calibration data
+it is possible for totally saturated lines to have zero or negative values.
+The task will quit if detects negative or zero calibration values.  The
+\fIthreshold\fR allows applying a minimum threshold to the calibration
+values so the task may continue.
+.le
+.ls lag = 10
+The cross-correlation lag to use when \fIxcorr\fR = yes.  The lag
+is given in pixels.   This is the distance to either side of the
+initial shift over which the cross-correlation profile is computed.
+If a value of zero is given then the cross-correlation step is not done.
+.le
+.ls shift = 0., dshift = 1.
+The initial shift and shift step in pixels.  This initializes the shift
+search parameters for the first spectrum.  If \fIdshift\fR is zero then
+there will be no search for a new shift and the 'x' interactive function is
+disabled.  These parameters may be changed interactively.  After the
+first spectrum subsequent spectra begin with the values from the last
+spectrum.
+.le
+.ls scale = 1., dscale = 0.2
+The initial scale and scale step.  This initializes the scale
+search parameters for the first spectrum.  If \fIdscale\fR is zero then
+there will be no search for a new scale and the 'y' interactive function is
+disabled.  These parameters may be changed interactively.  After the
+first spectrum subsequent spectra begin with the values from the last
+spectrum.
+.le
+.ls offset = 1.
+The interactive search displays three candidate corrected spectra which
+have been normalized to a mean of one.  The offset is added and subtracted
+to separate the three candidates.  The value may be changed interactively.
+.le
+.ls smooth = 1
+The displayed candidate corrected spectra are smoothed by a moving
+boxcar average with a box size specified by this parameter.  The smoothing
+only applies to the displayed spectra and does not affect the measured
+RMS or the output corrected spectra.  The value may be changed interactively.
+.le
+.ls cursor = ""
+Input cursor for the interactive graphics.  A null value selects the
+graphics cursor otherwise a file of cursor values may be specified.
+.le
+.ls airmass
+Query parameter for the airmass.  If the airmass is not in the image
+header under the keyword AIRMASS the user is queried for the airmass.
+This parameter should not be specified on the command line.
+.le
+.ls answer
+Query parameter for responding to the interactive question.  This parameter
+should not be specified on the command line.
+.le
+.ls interp = poly5
+The \fBpackage\fR parameter specifying the interpolation function for shifting
+the calibration spectra to match the input spectra.
+.le
+.ih
+DESCRIPTION
+Input one dimensional spectra are corrected to remove telluric features by
+dividing by shifted and scaled calibration spectra.  The calibration
+spectra are generally of hot, nearly featureless stars; hence this procedure
+is sometimes referred to as a B-star correction.  The shifting
+allows for possible small shifts or errors in the dispersion zeropoints.
+The intensity scaling allows for differences in the airmass and variations
+in the abundance of the telluric species.  The intensity scaling
+uses Beer's law which is the approximation that the change in absorption
+with abundance is an exponential relation.  
+
+The following describes the correction.  Let J(x_i) be the calibration
+spectrum at a set of pixels x_i.  An interpolation function is fit to this
+spectrum to give J(x).  The shifted and scaled calibration function
+is then
+
+.nf
+    (1)  J'(x) = max (threshold, J(x+dx)) ** (A / A_cal * scale)
+.fi
+
+where dx is the pixel shift parameter, A is the airmass of the input
+spectrum, A_cal is the airmass of the calibration spectrum, and
+scale is the scale parameter.  The operator "**" is exponentiation.
+The max operation limits the calibration spectrum to be greater
+than or equal to the specified threshold value.  If the calibration
+value is ever less than or equal to zero then the task will quit
+with a warning error.
+
+The output corrected spectrum is then computed as
+
+.nf
+    (2)  I'(x_i) = I(x_i) / (J'(x_i) / <J'>)
+.fi
+
+where I' is the corrected spectrum, I is the input spectrum, and <J'> is
+the mean of the shifted and scaled calibration spectrum to keep the output
+intensities comparable to the input spectrum.  The value of <J'> is
+printed in the output as the "normalization".  If the spectra are
+dispersion calibrated, possibly with different dispersion parameters, then
+the x values in (2) from the input spectrum are converted to matching
+pixels in the calibration spectrum using the dispersion functions of the
+two spectra.
+
+The purpose of this task is to determine the best values of the
+shift and scale parameters dx and scale.  There
+are automatic and interactive methods provided.  The automatic
+methods are cross-correlation of the calibration and input spectra
+to find a shift and an iterative search for the in both
+shift and scale that minimizes the RMS of I' in some region.
+The automatic methods are performed first, if selected, followed
+by the interactive, graphical step.  The following describes
+the steps in the order in which they occur.
+
+The initial values of the shift and scale are set by the parameters
+\fIshift\fR and \fIscale\fR for the first spectrum.  After that the values
+determined for the previous spectrum, those actually applied to correcting
+that spectrum, are used as the initial values for the next spectrum.  The
+search steps and sample regions are also initialized by task parameters but
+may be modified during the interactive step and the modified values apply
+to subsequent spectra.
+
+If the \fIxcorr\fR parameter is yes and the \fIlag\fR parameter is
+not zero the calibration spectrum is cross-correlated against the input
+spectrum.  Each spectrum is prepared as follows.  A large scale continuum
+is fit by a quadratic chebyshev using 5 iterations of sigma clipping with a
+clipping factor of 3 sigma below the fit and 1 sigma above the fit and
+rejecting the deviant points along with one pixel on either side.  This
+attempts to eliminate the effects of absorption lines.  The continuum fit
+is subtracted from the spectrum and the spectrum is extended and tapered by
+a cosine function of length given by the \fIlag\fR parameter.
+
+The prepared spectra are then cross-correlated by shifting the calibration
+spectrum plus and minus the specified \fIlag\fR amount about the current
+shift value.  Only the regions in the input spectrum specified by the
+sample regions parameter are used in the correlation.  This produces a
+correlation profile whose peak defines the relative shift between the two
+spectra.  The current shift value is updated.  This method assumes the
+common telluric features dominate within the specified sample regions.  The
+lag size should be roughly the profile widths of the telluric features.
+
+If the \fItweakrms\fR parameter is yes and \fIdshift\fR is greater than
+zero trial corrections at the current shift value and plus and minus one
+shift step with the scale value fixed at its current value are made and the
+RMS in the sample regions computed.  If the RMS is smallest at the current
+shift value the shift step is divided in half otherwise the current shift
+value is set to the shift with the lowest RMS.  The process is then
+repeated with the new shift and shift step values.  This continues until
+either the shift step is less than 0.01 pixels or the shift is more than
+two pixels from the initial shift.  In the latter case the final shift is
+reset to the original shift.
+
+The scale factor is then varied if \fIdscale\fR is greater than zero by the
+scale step at a fixed shift in the same way as above to search for a
+smaller RMS in the sample regions.  This search terminates when the scale
+step is less than 0.01 or if the scale value has departed by 100% of the
+initial value.  In the latter case the scale value is left unchanged.
+
+The search over the shifts and scales is repeated a second time after which
+the tweak algorithm terminates.
+
+After the optional cross-correlation and tweak steps the interactive search
+mode may be entered.  This occurs if \fIinteractive\fR = yes.  A query is
+asking whether to search interactively.  The answers may be "no", "yes",
+"NO", or "YES".  The lower case answers apply to the current spectrum and
+the upper case answers apply to all subsequent spectra.  This means that if
+an answer of "NO" or "YES" is given then there will be no further queries
+for the remaining input spectra.
+
+If the interactive step is selected a graph of three candidate corrections
+for the input spectrum is displayed.  There also may be a graph of the
+calibration or input spectrum shown for reference.  Initially the
+calibration spectrum is displayed.  The additional graph may be toggled off
+and on and between the input and calibration spectra with the 'c' and 'd'
+keys.  The three candidate corrected spectra will be with the current shift
+and scale in the middle and plus or minus one step in either the shift or
+scale.  Initially the spectra will be at different scale values.
+Information about the current shift and scale and the step used is given in
+the graph title.
+
+One may toggle between shift steps and scale steps with the 'x' (for shift)
+or 'y' (for scale) keys.  The RMS in the title is the RMS within the
+currently defined sample regions.  If one of the step values is zero then a
+display of different values of that parameter will not be selected.  The
+step size will need to be set with a colon command to search in that
+parameter.
+
+If 'x' is typed when the three spectra are at different shifts then the
+nearest spectrum to the y cursor at the x cursor position will be
+selected.  If the central spectrum is selected the step size is divided in
+half otherwise the current shift is changed and the  selected spectrum
+becomes the middle spectrum.  Three new spectra are then shown.  The same
+applies if 'y' is typed when the three spectra are at different scales.
+This allows an interactive search similar to the iterative tweakrms method
+described previously except the user can use whatever criteria is desired
+to search for the best scale and shift.
+
+There are additional keystrokes and colon commands to set or change sample
+regions, reset the current shift, scale, and step sizes, expand the step
+size in the current mode, adjust the offsets between the spectra, and
+get help.  The 'w' key and GTOOLS colon commands are available to window
+the graphs.  Any changes in the x limits apply to both graphs while y limit
+adjustments apply to the graph pointed to by the cursor.
+
+Two other commands require a short explanation.  The 'a' key may
+be used to run the tweakrms algorithm starting from the current
+shift, scale, and steps and the current sample regions.  This allows
+one to graphically set or reset the sample regions before doing
+the RMS minimization.  The ":smooth" command and associated
+\fIsmooth\fR task parameter allow the corrected spectra to be
+displayed with a boxcar smoothing to better see faint features in
+noise.  It is important to realize that the smoothing is only
+done on the displayed spectra.  The telluric correction and computed RMS
+are done in the unsmoothed data.
+
+After the interactive step is quit with 'q' or if the interactive
+step is not done then the final output spectrum is computed and
+written to the output image.  A brief log output is printed for
+each spectrum.
+.ih
+CURSOR KEYS AND COLON COMMANDS
+.nf
+? - print help
+a - automatic RMS minimization within sample regions
+c - toggle calibration spectrum display
+d - toggle data spectrum display
+e - expand (double) the step for the current selection
+q - quit
+r - redraw the graphs
+s - add or reset sample regions
+w - window commands (see :/help for additional information)
+x - graph and select from corrected shifted candidates
+y - graph and select from corrected scaled candidates
+
+:help           - print help
+:shift  [value] - print or reset the current shift
+:scale  [value] - print or reset the current scale
+:dshift [value] - print or reset the current shift step
+:dscale [value] - print or reset the current scale step
+:offset [value] - print or reset the current offset between spectra
+:sample [value] - print or reset the sample regions
+:smooth [value] - print or reset the smoothing box size
+.fi
+.ih
+EXAMPLES
+1.  To interactively search for a best correction with the default
+cross-correlation and tweak steps:
+
+.nf
+    cl> telluric spec001.ms telspec001.ms spec005.ms
+.fi
+
+2.  To search only for a scale factor:
+
+.nf
+    cl> telluric spec001.ms telspec001.ms spec005.ms xcorr- dshift=0.
+.fi
+
+3.  To processes a set of spectra non-interactively with the same calibration
+spectrum and to replace the input spectra with the corrected spectra and
+log the processing:
+
+.nf
+    cl> telluric spec* "" calspec inter- > log
+.fi
+
+4.  To apply the simplest scaling by the ratio of the airmasses alone:
+
+.nf
+    cl> telluric spec* tel//spec* calspec inter- xcorr- tweak- inter- \
+    >>> scale=1. shift=0.
+.fi
+.ih
+REVISIONS
+.ls TELLURIC V2.12.3
+The normalization is printed.
+.le
+.ls TELLURIC V2.11.2
+Threshold parameter added.
+.le
+.ls TELLURIC V2.11
+This task is new in this version.
+.le
+.ih
+SEE ALSO
+skytweak
+.endhelp
diff --git a/noao/onedspec/doc/telluric.key b/noao/onedspec/doc/telluric.key
new file mode 100644
index 00000000..11a42cc3
--- /dev/null
+++ b/noao/onedspec/doc/telluric.key
@@ -0,0 +1,35 @@
+		TELLURIC COMMAND SUMMARY
+
+? - print help
+a - automatic RMS minimization within sample regions
+c - toggle calibration spectrum display
+d - toggle data spectrum display
+e - expand (double) the step for the current selection
+q - quit
+r - redraw the graphs
+s - add or reset sample regions
+w - window commands (see :/help for additional information)
+x - graph and select from corrected shifted candidates
+y - graph and select from corrected scaled candidates
+
+:help           - print help
+:shift  [value] - print or reset the current shift
+:scale  [value] - print or reset the current scale
+:dshift [value] - print or reset the current shift step
+:dscale [value] - print or reset the current scale step
+:offset [value] - print or reset the current offset between spectra
+:sample [value] - print or reset the sample regions
+:smooth [value] - print or reset the smoothing box size
+
+
+The stacked display shows three corrected candidate spectra.  The center
+one is for the current shift and scale and the other two are one step
+higher or lower in the shift or scale.  The current values and the
+step is shown in the title.  Toggle between the shift and scale candidates
+with 'x' or 'y'.  Select the best spectrum with the cursor and typing
+'x' or 'y'.  Selecting the middle spectrum with 'x' in the shift display
+divides the shift step in half.  Selecting one of the other spectra
+changes the current shift.  Selecting the middle spectrum with 'y'
+in the scale display divides the scale step in half.  Selecting one of
+the other spectra changes the current scale.  When 'q' is typed the
+final shift and scale will be that of the middle spectrum.
diff --git a/noao/onedspec/doc/wspectext.hlp b/noao/onedspec/doc/wspectext.hlp
new file mode 100644
index 00000000..9840b7b4
--- /dev/null
+++ b/noao/onedspec/doc/wspectext.hlp
@@ -0,0 +1,96 @@
+.help wspectext Oct93 onedspec
+.ih
+NAME
+wspectext -- convert 1D image spectra to an ascii text spectra
+.ih
+USAGE
+wspectext input output
+.ih
+PARAMETERS
+.ls input
+Input list of 1D image spectra to be converted.  If the image is
+not one dimensional an warning will be given and the image will be skipped.
+.le
+.ls output
+Output list of ascii text spectra filenames.  The list must match the
+input list.
+.le
+.ls header = yes
+This parameter determines whether or not a descriptive header precedes the
+wavelength and flux values written to the text file.  When \fIheader =
+no\fR, only a two column list of wavelengths and fluxes is output.
+.le
+.ls wformat = ""
+The wavelength coordinate output format.  If it is undefined the formatting
+option stored with the WCS in the image header is used.  If the WCS
+formatting option is not defined then a free format is used.  See
+\fBlistpixels\fR for a description of the format syntax.
+.le
+.ih
+DESCRIPTION
+IRAF one dimensional spectra are converted to ascii text files.  The
+text files consist of an optional FITS type header followed by a two
+column list of wavelengths and flux values.  The format of the wavelengths
+can be set but the flux values are given in free format.  This task
+is a combination of \fBwtextimage\fR and \fBlistpixels\fR.  The output
+of this task may be converted back to an image spectrum with the
+task \fBrspectext\fR.
+
+Spectra which are not in 1D images such as multispec format or long slit
+may first be converted to 1D images using \fBscopy\fR with format="onedspec".
+.ih
+EXAMPLES
+1.  Write a text file with a header.
+
+.nf
+    cl> wspectext spec001 text001 header+ wformat="%0.2f"
+    cl> type text001
+    BITPIX  =                    8  /  8-bit ASCII characters
+    NAXIS   =                    1  /  Number of Image Dimensions
+    NAXIS1  =                  100  /  Length of axis
+    ORIGIN  = 'NOAO-IRAF: WTEXTIMAGE'  /
+    IRAF-MAX=                   0.  /  Max image pixel (out of date)
+    IRAF-MIN=                   0.  /  Min image pixel (out of date)
+    IRAF-B/P=                   32  /  Image bits per pixel
+    IRAFTYPE= 'REAL FLOATING     '  /  Image datatype
+    OBJECT  = 'TITLE             '  /
+    FILENAME= 'TEST              '  /  IRAF filename
+    FORMAT  = '5G14.7            '  /  Text line format
+    APNUM1  = '1 1     '
+    DC-FLAG =                    0
+    WCSDIM  =                    1
+    CTYPE1  = 'LINEAR  '
+    CRVAL1  =                4000.
+    CRPIX1  =                   1.
+    CDELT1  =     10.1010101010101
+    CD1_1   =     10.1010101010101
+    LTM1_1  =                   1.
+    WAT0_001= 'system=equispec                                 '
+    WAT1_001= 'wtype=linear label=Wavelength units=Angstroms   '
+    END
+										    
+    4000.00  1000.
+    4010.10  1005.54
+    4020.20  1011.05
+    ...
+.fi
+
+2.  Write a simple text file with two columns of wavelength and flux.
+
+.nf
+    cl> wspectext spec001 text002 header- wformat="%0.2f"
+    cl> type text002
+    4000.00  1000.
+    4010.10  1005.54
+    4020.20  1011.05
+    ...
+.fi
+.ih
+REVISIONS
+.ls WSPECTEXT V2.10.3
+This is a new task with this version.
+.le
+.ih
+SEE ALSO
+rspectext, wtextimage, listpixels, scopy, imspec
+.endhelp