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+.help revisions Jun88 noao.twodspec.apextract
+.nf
+
+approfile.x
+     When an aperture goes off the edge of an image there was an error
+     which allowed the imio data buffer from the image to go out of bounds.
+     (3/12/13, MJF)
+
+aptrace.x
+     The line1/line2 variables weren't being initialized to zero in the
+     ap_ctrace() procedure.  This woule lead to old values from a previous
+     run of the task being reused.  (2/6/13, MJF)
+
+=======
+V2.16.1
+=======
+
+approfile.x
+     Fixed a bug in the Marsh algorithm causing segfaults on 64-bit
+     platforms (Buglog 583)  (3/5/12, Valdes)
+
+apall.par
+     Changed the default for maxsep from 1000 to 100000.  This is because
+     the default is when the user doesn't want to skip apertures and it is
+     strange when the id jumps in the (rare) case that two apertures are
+     marked with a separation of more than 1000.  (2/17/09, Valdes)
+
+apedit.x
+    The 's' key now works on the current aperture rather than the nearest.
+    (10/7/08, Valdes)
+
+apcolon.x
+    The "all" mode was missing with :center.  (10/7/08, Valdes)
+
+apall1.par
+apfit1.par
+apnoise1.par
+apnorm1.par
+apscat1.par
+apparams.dat
+    When the apertures parameter was added in 1996 the :apertures and
+    :parameters commands were broken because of missing references in
+    the associated hidden psets.  (10/7/08, Valdes)
+
+=======
+V2.14.1
+=======
+
+========
+V2.12.2a
+========
+
+apextract.x
+    When using APFIT to output the difference the IMIO buffer which was
+    assumed to be static was invalidated because of I/O needed to create
+    the difference.  A special case was added to handle this case.
+    (7/7/04, Valdes)
+
+apcveval.x	+
+apedit.x
+apextract.x
+apfind.x
+apfindnew.x
+apfit.x
+apgmark.x
+apgscur.x
+apmask.x
+apnoise.x
+apprint.x
+approfile.x
+aprecenter.x
+apresize.x
+apskyeval.x
+apupdate.x
+apvalues.x
+apvariance.x
+apnearest.x
+apscatter.x
+aptrace.x
+mkpkg
+    Added an interface routine to CVEVAL to avoid calling it with
+    independent variables outside the range of the fit.  The fit range
+    may be short because of tracing problems.  So the profile shift
+    is now extended from the end points of the fitted range.
+    (5/21/04, Valdes)
+
+apupdate.x
+apdefault.x
+apfind.x
+aptrace.x
+apedit.x
+apcolon.x
+    Modified to check for inappropriate INDEF values in the "lower"
+    and "upper" aperture settings.  (3/26/04, Valdes)
+
+=======
+V2.12.2
+=======
+
+apextract.x
+    The edge weighting interpolation buffer space, interpbuf,  was
+    increased by one pixel.  This makes the data buffer wider so that
+    interpolation avoids using boundary extension except in cases where the
+    aperture actually approaches the image edge.  Note that this change
+    results in an improvement in the extracted spectra over the previous
+    release where wraparound boundary extension was used.  This also means
+    extractions will not be identical between the versions.
+    (1/23/04, Valdes)
+
+apextract.x
+    The new routine ap_asifit was not correct.  (1/22/04, Valdes)
+
+apextract.x
+approfile.x
+apvariance.x
+    A problem related to the change of 10/21/03 is when the trace goes
+    far outside the data buffer.  This could result in the number of points
+    specified for asifit being too small for the interpolation function.
+    An interface routine, ap_asifit, was added to do all the checks related
+    to using asifit for evaluating the edge pixels.  (12/10/03, Valdes)
+
+===========
+V2.12.2BETA
+===========
+
+apextract.x
+    The output name based on the input name for multiextension images
+    produces a multiextension output with the same extension description.
+    (12/3/03, Valdes)
+
+apgetim.x
+    1.	Restored ability to use image sections which was lost in the change
+	on 7/13/98 for V2.11.2.
+    2.	Support for multiextension data was added.  This consists of using
+	a standard name based on EXTNAME and EXTVER and without the
+	file type extension.  Note that this means that image names specified
+	by index will be converted to extension name and extension version.
+    (12/3/03, Valdes)
+
+apextract.x
+approfile.x
+apvariance.x
+    The call to asifit was specifying too many points to fit, a whole line
+    in the data buffer, because the data vector may be offset from the first
+    column of the data buffer.  This could cause a segmentation violation.
+    (10/21/03, Valdes)
+
+
+apwidth.cl
+    Script to compute aperture widths from database.  This was written
+    for a user and is saved here though it is not currently defined by
+    default.  (12/2/02, Valdes)
+
+apflat1.par
+    The indirect reference needs to be spelled out without abbreviation to
+    be "apflatten" instead of "apflat".  (11/18/02, Valdes)
+
+=======
+V2.12.1
+=======
+
+apextract.x
+approfile.x
+apvariance.x
+    Modified to handle edge pixels by interpolation.  (6/19/02, Valdes)
+
+=====
+V2.12
+=====
+
+apgraph.x
+apgmark.x
+    When there is just one aperture the background regions are marked
+    in apedit and in plotfile output.  (9/21/01, Valdes)
+
+doc/apall.hlp
+    The help page was indicating the extra information output was the
+    variance rather than the sigma.  (8/19/00, Valdes)
+
+apextract.x
+    The checking for the maximum number of apertures that fit in the allocated
+    memory (the "do j = i, napsex" loop) was incorrect because i was used
+    instead of the loop index j.  (3/20/00, Valdes)
+
+=========
+V2.11.3p1
+=========
+=======
+V2.11.3
+=======
+
+approfile.x
+    In the previous change to the weights in the Horne algorithm
+    the behavior when all data is rejected (say because the background
+    is set wrong and all data is below the background) the weights
+    would be set to MAX_REAL/10 which would cause CVFIT to fail.
+    (3/13/00, Valdes)
+
+apall1.par
+apdebug.par
+apfit1.par
+apnoise1.par
+apnorm1.par
+apparams.par
+    Reduced the polysep parameter.  (1/26/00, Valdes)
+
+apextractbak.x	-
+mkpkg
+    Removed this second old copy which was accidentally introduced into
+    mkpkg as well resulting in multiple copies of the same procedures
+    in the library in V2.11.3beta.  (12/9/99, Valdes)
+
+doc/apflatten.hlp
+    Removed extraneous parameters not actually in task parameter set.
+    (10/21/99, Valdes)
+
+mkpkg
+    Added missing dependencies.  (10/11/99, Valdes)
+
+=======
+V2.11.2
+=======
+
+apextract.x
+    Added a keyword SUBAP when using echelle output with subapertures.
+    (3/26/99, Valdes)
+
+apflatten.par
+apflat1.par
+    Removed background subtraction as an option.  (12/11/98, Valdes)
+
+apskyeval.x
+    If the background sample region does not have explicit regions then
+    the xmin/xmax region is used for the background.  (12/11/98, Valdes)
+
+apfit.x
+    Added errchk for ic_fit and ic_gfit.  (12/8/98, Valdes)
+
+apflat1.par
+    Reduced the polysep because it can go wrong.  (12/8/98, Valdes)
+
+apextract.x
+    Added check to fix cases with the lower and upper aperture limits
+    are reversed.
+    (7/13/98, Valdes)
+
+apgetim.x
+    Changed to call xtools routine that strips extensions.
+    (7/13/98, Valdes)
+
+approfile.x
+    In the Horne algorithm the weights for rejected points were set to zero
+    to eliminate them from the fit.  But if large regions are rejected
+    this leaves the fit unconstrained and can lead to bad results.  A
+    change was made to set the weights for the rejected points to 1/10
+    of the minimum weight for the good data.
+    (2/6/98, Valdes)
+
+apextract.x
+    For "echelle" format with "extras" the header was not setup properly
+    resulting in WCSDIM=2 instead of 3.  (2/6/98, Valdes)
+
+apids.x
+    1.  Fix bug in IDS structure which pointed outside of allocated memory.
+    2.  Variables ra/dec in ap_gids were being used both as pointers and
+	double.  The ra/dec pointer usage was removed.
+    3.	The realloc step at the end of ap_gids had the wrong check so it
+	would never be done.
+    (1/13/98, Valdes)
+
+=======
+V2.11.1
+=======
+=====
+V2.11
+=====
+
+doc/apsum.hlp
+doc/apsum.hlp
+    Added missing task name in revisions section.  (4/22/97, Valdes)
+
+apextract.x
+    Removed calls to impl from inside amove in order to error check them.
+    (1/24/97, Valdes)
+
+t_apall.x
+    1.  Added errchk for ap_dbwrite.
+    2.  Made writing the aplast file optional.
+    3.  It is a warning if the plot file can't be written.
+    (1/24/97, Valdes)
+
+apextract.x
+    The step where the data is multplied by the gain was multiplying
+    outside the data if dispaxis=1.  If the there are enough apertures
+    and the aperture widths decrease then it is possible to get
+    mulitplications of gain**naps which can cause a floating overflow.
+    This was fixed.  (11/12/96, Valdes)
+
+apertures.h
+t_apall.x
+aptrace.x
+apresize.x
+apalloc.x
+apextract.x
+apselect.x
+aprecenter.x
+apall.par
+apall1.par
+apfit1.par
+apflat1.par
+apnorm1.par
+apparams.par
+apnoise1.par
+apdebug.par
+apfit.par
+apflatten.par
+apmask.par
+apnoise.par
+apnormalize.par
+apresize.par
+apscatter.par
+apsum.par
+aptrace.par
+apedit.par
+apfind.par
+aprecenter.par
+mkpkg
+doc/apextract.hlp
+doc/apextras.hlp
+doc/apedit.hlp
+doc/apall.hlp
+doc/apfind.hlp
+doc/apresize.hlp
+doc/apsum.hlp
+doc/aptrace.hlp
+doc/apfit.hlp
+doc/apflatten.hlp
+doc/apmask.hlp
+doc/apnoise.hlp
+doc/apnormalize.hlp
+doc/aprecenter.hlp
+doc/apscatter.hlp
+    Added a new parameter "apertures" to select a subset of the apertures
+    to resize, recenter, trace, extract, etc.  The parameter "apertures"
+    which applied to the recentering was changed to "aprecenter".
+    (9/5/96, Valdes)
+
+apedit.key
+    Alphabetized the summary command lists.  (9/3/96, Valdes)
+
+apextract.x
+    1. Onedspec output format is now allowed when nsubaps is greater than 1.
+    2. Echelle format outputs all orders for a each subapertures in
+       separate files.
+    (4/3/96, Valdes)
+
+apmw.x
+apextract.x
+    The WCS for strip extraction was wrong.  (1/31/96, Valdes)
+
+apmw.x
+    An error in computing the WCS transformation now prints a more informative
+    message indicating the final extracted spectrum will be in pixel units.
+    (1/4/96, Valdes)
+
+apids.x
+apedit.x
+    Changed the behavior of the 'i' and 'o' keys with regard to the beam
+    numbers.  These keys will now assign a beam number from the apid table
+    for the selected aperture as well as all other apertures.  Previously
+    the beam number was not changed which resulted in a new aperture
+    number with a beam number that did not agree with the apid table.
+    (10/27/95, Valdes)
+
+doc/apextras.hlp +
+apextract.men
+apextract.hd
+    Added a help topic on the "extras" information.  (9/5/95, Valdes)
+
+apimmap.x
+    If the image header dispersion axis is unreasonable a warning is
+    printed and the "dispaxis" parameter is used instead.  (8/2/95, Valdes)
+
+apids.x
+apmw.x
+doc/apall.hlp
+doc/apdefault.hlp
+doc/apedit.hlp
+doc/apfind.hlp
+    Modified to allow aperture ID table to be from an image header
+    under the keywords SLFIBnnn.  The extracted image will have
+    these keywords deleted.  (7/25/95, Valdes)
+
+=======
+V2.10.4
+=======
+
+apscatter.x
+    When not smoothing along the dispersion there was a bug that when
+    the number of points being fit across the disperision changed
+    ICFIT was not reset causing an error "Range descriptor undefined".
+    The routine now reset the "new" flag when the number of points
+    changes.  (5/3/95, Valdes)
+
+t_apall.x
+    Using the same input and output image name in APSCATTER was still
+    not right.  (2/24/95, Valdes)
+
+apscatter.x
+    Made the output image datatype be at least real.  (2/23/95, Valdes)
+
+apextract.x
+    For normalization the weights were not forced causing the gain to
+    default to 0.  The change of 12/31/94 also fixed this by setting the
+    gain to 1.  The file was touched but not changed.  (1/27/95, Valdes)
+
+apextract.x
+apskyeval.x
+    Made the query for the readnoise only occur if needed.  Previously
+    the query was made in the sky step even if the sky error estimate
+    was not needed.  (12/31/94, Valdes)
+
+apedit.x
+    Needed to set clobber and review options so they are queried during
+    interactive extraction.  (10/28/94, Valdes)
+
+apimmap.x
+apgetim.x
+apgetdata.x
+apextract.x
+apmw.x
+    1.	If a 3D image is given then a warning is printed and the first plane
+	is used and the other planes are ignored.
+    2.  Various fixes to allow image sections to be used.
+    (10/12/94, Valdes)
+
+aptrace.x
+    An uninitialized memory problem was fixed.  (9/19/94, Valdes/Zarate)
+
+apicset.x
+    Fixed type mismatch in min/max function calls.  (6/13/94, Valdes/Zarate)
+
+apextract.x
+    Changed BANDID name for raw spectrum to "raw".  (5/3/94, Valdes)
+
+apvariance.x
+doc/apvariance.hlp
+doc/apall.hlp
+doc/apsum.hlp
+    The correction to bring the weighted and unweighted total fluxes to the
+    same value (called the bias factor) can produce odd values in special
+    cases; such as slitlets where only part of the image contains real
+    spectrum.  This could result in variance spectra with flux scaling
+    errors to the extreme of a negative (inverted) spectrum.  The bias
+    factor is now logged.  If the two total fluxes differ by more than a
+    factor of 2 a warning (which always appears on the standard output) is
+    given with the fluxes and the bias factor.  If the bias factor is
+    negative a warning is given and the bias factor is ignored.
+    (5/1/94, Valdes)
+
+doc/aptrace.hlp
+    Fixed typo in description of Legendre basis functions.  (4/1/94, Valdes)
+
+apextract.x
+doc/apextract.hlp
+    Added output BANDID keywords to document the various output data.
+    (2/4/94, Valdes)
+
+apnoise.x	+
+apnoise1.par	+
+apnoise.par	+
+apnoise.key	+
+doc/apnoise.hlp	+
+apextract.x
+t_apall.x
+x_apextract.x
+apextract.hd
+apextract.men
+apextract.cl
+mkpkg
+    A new task for computing the noise sigma as a function of data value
+    was added.  This allows checking the noise model parameter and
+    can be used as a diagnostic of the profile modeling.  (8/28/93, Valdes)
+
+apfit.x
+apextract.x
+    There were some additional problems with gain parameter dependencies
+    in the difference, fit, and normalization output functions.
+    (8/27/93, Valdes)
+
+apgetdata.x
+aptrace.x
+apedit.par
+apfind.par
+apfit.par
+apflatten.par
+apmask.par
+apnormalize.par
+aprecenter.par
+apresize.par
+apscatter.par
+apsum.par
+aptrace.par
+apall.par
+apall.hlp
+apedit.hlp
+apfind.hlp
+apflatten.hlp
+apmask.hlp
+apfit.hlp
+apnormalize.hlp
+aprecenter.hlp
+apresize.hlp
+apscatter.hlp
+apsum.hlp
+aptrace.hlp
+    The nsum parameter may be negative to select a median rather than
+    a sum of lines/columns.  The parameter files had to be modified to
+    remove the minimum range limit and the help files modified to
+    document the new option.  (8/10/93, Valdes)
+
+===========
+V2.10.3beta
+===========
+
+doc/apall.hlp
+doc/apsum.hlp
+    The format parameter description was added.  (6/24/93, Valdes)
+
+apfind.x
+apfindnew.x
+    Removed the threshold in peak finding requiring peaks to be above zero.
+    This works with the change to center1d to allow finding of apertures
+    when the data is negative.  (5/5/93, Valdes)
+
+apfit.x
+    Added CCDMEAN=1. to output image in the normalization, flattening routines.
+    (4/16/93, Valdes)
+
+apextract.par
+*.par
+apgetim.x
+    Moved the "dispaxis" parameter to a package paraemter.
+    (3/8/93, Valdes)
+
+approfile.x
+    The profile was not cleared when saturated pixels are found.  This
+    could cause NaNs to get into the data with the result that
+    cvfit could produce garbage.
+    (3/4/93, Valdes)
+
+debug.par
+apparams.par
+apnorm1.par
+apflat1.par
+apfit1.par
+apall1.par
+    1.  Changed the default "fit2d" polynomial parameters to polyorder=10,
+	polysep=0.95.
+    2.  Changed the default "niterate" from 2 to 5.
+    (3/3/93, Valdes)
+
+approfile.x
+doc/approfiles.hlp
+    For the "fit1d" algorithm I doubled the order it uses to fit
+    parallel to the disperison.  The order is still computed based
+    on the tilt of the spectrum and the order used for the tracing
+    but now that number is doubled.  (2/26/93, Valdes)
+
+apscatter.x
+    Revised the algorithm to keep the cross-dispersion fits in memory
+    rather than writing them to disk as an image.  This speeds things
+    up in the case of slow I/O.  (2/23/93, Valdes)
+
+t_apall.x
+apscatter.x
+    1.  The temporary file name was not being passed to apscatter by
+	t_apall resulting in use of the name ".imh" which is hidden.
+    2.  Increased the column buffering size from 512*100 to 500000.
+    (2/5/93, Valdes)
+
+apextract.x
+    imaccf was being used as a boolean when it should be an int.
+    (12/13/92, Valdes)
+
+debug.par
+    A DPAR parameter file for use with debugging.  (1/12/92, Valdes)
+
+apmw.x
+apextract.x
+    Rewrote this to allow extractions of an arbitrary number of apertures.
+    Previously this was limited by MWCS.  The output format is now
+    EQUISPEC. (1/12/92, Valdes)
+
+aprecenter.x
+    This routine was incorrectly selecting the apertures to be used.
+    is_in_range (Memi[ranges], i) --> is_in_range (Memi[ranges], AP_ID(aps[i]))
+    (1/8/93, Valdes and Hill)
+
+doc/apbackground.hlp
+    In responding to a concern about the 'b' key showing a fit even though
+    the background type was "median" I added a paragraph explaining this.
+    (1/8/93, Valdes)
+
+t_apall.x
+    The dispersion smoothing was turned off in noninteractive mode regardless
+    of the task parameter.  This has been fixed.
+    (12/8/92, Valdes)
+
+t_apall.x
+    Added error check for ap_plot.
+    (10/14/92, Valdes)
+
+apextract.x
+    1. When the dispersion axis is 1 the data buffer may contain garbage
+       because of using a malloc and because not all of this buffer is
+       necessarily used.  Later the multiplication by the gain can cause
+       an arithmetic exception.  The mallocs were replaced by callocs.
+    2. Added errchks for the impl[123]r routines.
+    (9/10/92, Valdes)
+
+mkpkg
+apextract.x
+apmw.x		+
+    1. Separated out the MWCS routines into another file.
+    2. Added an apmw_saveim procedure to produce simple 1D format as is done
+       in the ONEDSPEC package.
+    (8/24/92, Valdes)
+
+apskyeval.x
+    When doing the fitted background variable roundoff among machines led
+    to using different background points and, hence, gave noticibly different
+    results.  The background points are now rounded to the nearest 1000th of
+    a pixel which will produce the same background points on all machines.
+    (8/19/92, Valdes)
+
+apnorm1.x
+    Added missing t_nlost parameter.  (8/10/92, Valdes)
+
+aptrace.x
+    There was an incorrect order in checking for failed traces which ends
+    up referencing uninitialized memory.  This bug has been there for a
+    long time (V2.8-V2.10) but only showed up during testing on the
+    SGI port.  (7/31/92, Valdes)
+
+The following set of changes concern the treatment of the background sample
+regions and min/max fitting limits.  There was also a change in ICFIT
+to check the min/max fitting limits and increase them if the sample region
+is extended beyond the initial fitting limits.
+
+--------
+
+apdefault.x
+	Now calls AP_ICSET with the image limits rather than the aperture
+	limits as required by the change to that routine.  (7/30/92, Valdes)
+
+apedit.x
+    1.  The default aperture is reset after a colon command just in case
+        one of the default aperture parameters has changed.  This is
+        slightly inefficient but the alternative is a more complex
+        AP_COLON to determine if a parameter relates to the default
+        aperture.
+    2.  Now calls AP_ICSET after fitting to apply the constraint that the
+        fitting limits pass under the aperture.  (7/30/92, Valdes)
+
+apicset.x
+    1.  The input background limits for a new aperture (called
+	by AP_DEFAULT) are now the maximum limits defined by the image size
+	rather than the minimum limits defined by the aperture.
+    2.  If a null default sample is given it is mapped to "*".
+    3.  A sample with "*" will map to the maximum limits.
+    4.  Allow the input and output pointers to be the same in order
+	for the constraint that the fitting region pass under the
+	aperture can be applied.  (7/30/92, Valdes)
+
+--------
+
+doc/apall.hlp doc/apsum.hlp doc/apbackground.hlp
+    The documentation of the "median" and "minimum" options for the
+    background parameter needed to be added.  (7/14/92, Valdes)
+
+apextract.x
+    The profile array needed to be corrected for the gain.  This makes a
+    difference for the output formats that use the fitted profile
+    (tasks APFLATTEN, APFIT: formats fit, ratio, diff, flat).
+    (7/9/92, Valdes)
+
+apfit1.par
+    Was missing t_nlost.  (7/9/92, Valdes)
+
+apparams.par
+apnorm1.par
+apflat1.par
+apfit1.par
+apall1.par
+    Replace prompt pfiT with pfit as it should be.  (7/9/92, Valdes)
+
+=======
+V2.10.2
+=======
+
+apextract.x
+    The WCS for the 3D images was changed to produce a WCSDIM of 3.
+    (6/30/92, Valdes)
+
+=======
+V2.10.1
+=======
+
+=======
+V2.10.0
+=======
+
+apextract.x
+    1. The axis array which was set by a data statement was actually
+       modified in the routine causing an improper WCS type to be
+       set.
+    2. If no coordinate label and/or units are found they are now set based
+       on DC-FLAG.  Before calibrated long slit spectra ended up with the
+       right wavelength coordinates but a label of Pixel and no units.
+       (5/20/92, Valdes)
+
+apall1.par
+apparams.par
+apfit1.par
+apflat1.par
+apnorm1.par
+    The e_profile prompt contained a new line.  This was removed.
+    (5/18/92, Valdes)
+
+doc/apexv210.ms +
+doc/revisions.v3.ms -
+    Revisions summary document.  (5/11/92, Valdes)
+
+apcolon.x
+apedit.key
+doc/apedit.hlp
+    Added t_nlost to the list of colon commands.  (5/11/92, Valdes)
+
+apgetim.x
+    Added the qp and pl extensions to those stripped.  (5/8/92, Valdes)
+
+apextract.x
+    Added error checking such that if there is a problem with reading the
+    input image WCS and warning is printed and pixel coordinates are set
+    in the output image.  (5/8/92, Valdes)
+
+=====
+V2.10
+=====
+
+apextract.x
+    For a single aperture using MULTISPEC WCS a dummy axis mapping was added
+    to make the image appear to be the first line of a parent 2D image.
+    (4/27/92, Valdes)
+
+approfile.x
+    Added a maximum order for the aphorne fitting function.  (4/24/92, Valdes)
+
+apextract.x
+    Added a error check trap to clean up and free memory in case of an
+    error.  (4/24/92, Valdes)
+
+t_apall.x
+apdb.x
+apedit.x
+apcolon.x
+apfind.x
+apfindnew.x
+apertures.h
+    Made the number of apertures dynamic.  There is no longer a maximum
+    number of apertures allowed.  (3/18/92, Valdes)
+
+t_apall.x
+    Length of format string declared as SZ_FNAME but used as SZ_LINE.
+    Change declaration to SZ_LINE.  (3/12/92, MJF)
+
+apextract.x
+    Now the output extension is added only if the output name is the
+    same as the input name.  Thus, if someone used <image>.ms as an
+    output name they won't get <image>.ms.ms.  (2/12/92, Valdes)
+
+apvariance.x
+apskyeval.x
+approfile.x
+apextract.x
+appars.x
+    Trapped errors from getting the read noise and gain from the image header
+    to produce a meaningful warning message.  (2/10/92, Valdes)
+
+apedit.x
+apfind.x
+t_apall.x
+apids.x
+    1. Added code to ignore negative beam numbers during extraction.
+    2. Negative beam numbers are only generated if an explicit assignment
+       is made in the aperture id table or with 'j'; i.e. beam numbers
+       generated by adding or subtracting will not have a negative beam.
+    (2/10/92, Valdes)
+
+apids.x
+apedit.x
+    Modified to not allow apertures numbers < 1.  (1/22/92, Valdes)
+
+t_apall.x
+x_apextract.x
+    Added new entry point, apslitproc, for the slit processing tasks.
+    (1/15/92, Valdes)
+
+apfind.x
+apall.par
+apfind.par
+    If nfind < 0 then the specified number of evenly spaced apertures are
+    defined.  (1/14/92, Valdes)
+
+apextract.x
+apsum.par
+apnormalize.par
+apflatten.par
+apfit.par
+apall.par
+apparams.par
+apnorm1.par
+apflat1.par
+apfit1.par
+apall1.par
+doc/apsum.hlp
+doc/approfiles.hlp
+doc/apnormalize.hlp
+doc/apflatten.hlp
+doc/apfit.hlp
+doc/apall.hlp
+    1.  Replaced the "maxtilt" criteria for choosing the profile fitting
+    algorithm with an explicit "pfit" parameter.
+    2.  The parameter files were modified to remove "maxtilt", add
+    "pfit", and change the default "polyorder" parameter for the
+    fit2d algorithm from 4 to 6.
+    3.  The "pfit" parameter is redirected from the hidden parameter files
+    to the user parameter files allowing the users to select the profile
+    fitting algorithm.
+    (1/8/92, Valdes)
+
+t_apall.x
+apdb.x
+    1.  Added special strings for the reference parameter.  If the reference
+    parameter is "OLD" then only input images with existing database
+    entries are processed.  If the reference is "NEW" then only input
+    images without existing databse entries are processed.
+    2.  Added a new procedure, ap_dbaccess, to simply check for the presence
+    of a database file.  This is used for the above change.
+    (1/2/92, Valdes)
+
+aptrace.x
+apall.par
+aptrace.par
+apparams.par
+apall1.par
+doc/apall.hlp
+doc/aptrace.hlp
+    A new parameter has been added to set the number of steps which may
+    be lost during tracing.  (9/5/91, Valdes)
+
+apextract.x
+    Changed ap_setdisp to ap_wcs.  This routine uses MWCS and sets the
+    WCS to multispec.  (8/29/91, Valdes)
+
+apextract.x
+    Modified so that profile image is used in place of input image for
+    determining the profile and eliminated the use of a disk profile file.
+    This is inefficient if the same profile image is used for many input
+    images but it is much easier for the user to understand.
+    (8/27/91, Valdes)
+
+apvariance.x
+    The subaperture extraction did not work because of a typo.
+    (8/27/91, Valdes)
+
+apextract.x
+    The profile image capability had several bugs which were fixed.
+    (8/27/91, Valdes)
+
+approfile.x
+    Fixed another division by zero problem in ap_horne.  (8/27/91, Valdes)
+
+approfile.x
+    Failed to clear profile in the case the spectrum was negative.
+    (5/30/91, Valdes)
+
+apertures.h
+    Increased the maximum number of aperture from 100 to 1000.
+    (4/29/91, Valdes)
+
+apdefault.x
+apicset.x
+    The default aperture was setting the background fitting range to
+    the full image range rather than range covered by the sample region.
+    This could cause singular solution errors in some cases.
+    (3/27/91, Valdes)
+
+apfind.x
+    Allowed still finding the specified number if some apertures (up to
+    2) fail for some reason such as too near the edge.  This is done by
+    setting the number of candidates to nfind+2. (3/26/91, Valdes)
+
+aprecenter.x
+doc/aprecenter.hlp
+    When using the shift option the shift is now the median (including
+    averaging of central 2 shifts for even number of peaks) instead of
+    the average.  (3/26/91, Valdes)
+
+appars.x
+apall1.par
+apfit1.par
+apflat1.par
+apnorm1.par
+apparams.par
+    In order to allow writing to redirected parameters rather than overwrite
+    the redirection string a kluge was added using the prompt string.
+    The apput procedures check the prompt string for the first character
+    ">" and if present write to the parameter given in the rest of the
+    string.  All the hidden parameter files with redirected parameters
+    had to be changes.  (3/26/91, Valdes)
+
+apextract.par
+apall.par apall1.par
+apsum.par apdefault.par apparams.par
+apfit.par apfit1.par
+apflatten.par apflatten1.par
+apnormalize.par apnorm1.par
+    1.  Moved format parameter from package parameters to
+	APALL and APSUM.
+    2.  Moved dispaxis parameter from package parameters to APDEFAULT.
+    3.  Added new background types.
+    (3/21/91, Valdes)
+
+t_apall.x
+    Allow scattered light correction to be run by APSCRIPT.
+    (3/21/91, Valdes)
+
+apscatter.x
+    Moved CLIO call for anssmooth out of loop to a single call using a
+    procedure variable.
+    (3/21/91, Valdes)
+
+apextract.x
+apskyeval.x
+    Aded new background functions median and minimum.
+    (3/21/91, Valdes)
+
+=================================
+V3 of APEXTRACT Installed 8/23/90
+=================================
+
+apextract$exsum.x
+    Added a test for the existence of output images before extractions and
+    a query to select whether to clobber spectra or not.  (8/9/89, Valdes)
+
+apextract$exmvsum.x
+apextract$exfit.x
+    1.  The moving average for profile images did not work correctly.  It
+	subtracted the line moving out of the moving average but failed to
+	add in the line moving into the average.  This caused the profile
+	to depart more and more from the data as the extraction procedes
+	through the image.
+    2.  The moving average for profile images actually used naverage + 1
+	instead of naverage becuase in this case the line being extract is
+	also included in the average.
+    3.  The fitting of the model to the data had a funny behavior when the
+	model had negative values and variance weight was used.  The
+	negative values are now excluded from the fitting calculation in
+	this case.  Note that the model is supposed to not contain negative
+	values.  Also note that if variance weighting is not used then the
+	negative values are used in straight least-squares fitting.
+	(8/8/89, Valdes)
+
+apextract$apicset.x
+apextract$apedit.x
+apextract$apupdate.x
+    The region over which the background fitting is defined has been extended
+    to require overlapping the aperture. (7/31/89, Valdes)
+
+apextract$apcolon.x
+    Added gdeactivate/greactivate calls when using EPARAM.  (6/14/89, Valdes)
+
+apextract$apextract.x
+    If reference apertures are used without change (no recenter, edit, or
+    retrace) then the apertures were not written to the database.  This has
+    been changed to write (or query if interactive) the apertures if
+    dbwrite=yes.  (5/19/89, Valdes)
+
+apextract$exio.h
+apextract$exio.x
+apextract$exsum.x
+    1.  The maximum number of simultaneous extractions was increased from
+	20 to 50.
+    2.  The amount of buffering used for column access (dispaxis=1) was
+	increased from 100K pixels to 1M chars.  (5/12/89, Valdes)
+
+apextract$doc/apsum.hlp
+    Added a sentence about the proper alignment of echelle spectra.
+    (5/8/89, Valdes)
+
+apextract$t_apscatter.x +
+apextract$apscatter.par +
+apextract$apscat1.par +
+apextract$apscat2.par +
+apextract$doc/apscatter.hlp +
+apextract$mkpkg
+apextract$x_apextract.x
+apextract$apextract.cl
+apextract$apextract.men
+apextract$apextract.hd
+imred$echelle/apscatter.par +
+imred$echelle/apscat1.par +
+imred$echelle/apscat2.par +
+imred$echelle/echelle.cl
+imred$echelle/echelle.men
+    Added a new task, APSCATTER, to fit and subtract scattered light.
+    It includes two hidden psets, APSCAT1 and APSCAT2.  (3/3/89, Valdes)
+
+apextract$apnormalize.par
+imred$echelle/apnormalize.par
+    Input image parameter name needed to be changed from "images" to "input".
+    (2/28/89, Valdes)
+
+apextract$exio.x
+    Added errchk for imgeti related to getting DISPAXIS keyword which
+    might be missing.  (2/28/89, Valdes)
+
+apextract$exsum.x
+    Changed usage of CRPIX keyword to real from integer.  (1/25/89, Valdes)
+
+apextract$apgmark.x
+    The size of the aperture labels now decreases with increasing number
+    of apertures.  (1/24/89, Valdes)
+
+apextract$t_apnorm.x
+apextract$apnormalize.par
+imred$echelle/apnormalize.par
+apextract$doc/apnormalize.hlp
+    Changed parameter names "lowreject" to "low_reject" and "highreject"
+    to "high_reject" to be consistent with other ICFIT tasks.
+    (1/24/89, Valdes)
+
+apextract$aprecenter.x
+    The progress information was not using the verbose parameter.
+    (1/23/89, Valdes)
+
+apextract$apedit.x
+    Fixed bug causing 'i' info to only be visibly momentarily.
+    (12/16/88 Valdes)
+
+apextract$t_apnorm.x
+    When fitting the normalization spectrum interactively any deleted
+    points would be remembered in the following apertures.  Deleted points
+    are now cleared after interactive fitting.  (12/15/88 Valdes)
+
+apextract$apedit.x
+    Fixed a minor bug in the 's' option (center + wx --> wx) (12/15/88 Valdes)
+
+apextract$*.x
+apextract$apio.par
+apextract$doc/apio.hlp
+    Removed the beep option. (12/8/88 Valdes)
+
+apextract$exgmodaps.x
+    The temporary apertures array and number of apertures were not being
+    initialized correctly causing a segmentation violation every time
+    the program was run. Added an n = 0 statement and initialized all the
+    pointers to NULL. (10/13/88 Davis)
+
+apextract$exmvsum.x
+    When cleaning and using a moving average the replacement of the bad pixel
+    in a data profile back in the moving average was in error leading to 
+    bad results and possible memory corruption.  (10/9/88 Valdes)
+
+apextract$exfit.x
+apextract$exmvsum.x
+    1.  The sigma clipping test now uses the variance relation for testing the
+	residuals.
+    2.  A bug was causing the length of the profile image to be incorrectly
+	referenced leading to an out of bounds error.
+
+apextract$apedit.x
+apextract$exapsum.x
+    1.  After doing a ":line" new apertures were defined with the old line
+	as the aperture center.  This made tracing fail.
+	Now after changing the line the default aperture is updated and
+	the apeture center is explicitly set every time.
+    2.  In a rare circumstance a divide by zero error occured for the fitted
+	background.  This is now checked.  (7/19/88 Valdes)
+
+noao$lib/scr/apedit.key
+apextract$apedit.x
+    1.  Deleted a reference to :nfind in the cursor help.
+    2.  After deleting a background defintion it was no longer possible
+	to define a new one.  Now an attempt to define backgrounds
+        after they have been deleted is initialized to the default again.
+        (7/1/88 Valdes)
+
+apextract$exsum.x
+    Fixed a bug in blocking overwriting of existing echelle format spectra.
+    Fixed a minor bug in writing the aperture info to the header of a 1D
+    format sky spectrum.  (6/16/88 Valdes)
+
+apextract$apgmark.x
+    Labels are not written outside of graph range.  (5/20/88 Valdes)
+
+apextract$apedit.x
+apextract$exgraph.x
+noao$lib/scr/apedit.key
+    Added 'I' interrupt.  (4/20/88 Valdes)
+
+apextract$exio.x
+    EX_UNMAP when using column access was free a buffer supplied by
+    IMIO causing a memory corruption error on VMS.  (3/30/88)
+
+apextract$exgmodaps.x
+    Model apertures where not being match up correctly resulting in a
+    warning message.  (3/22/88 Valdes)
+
+apextract$exsum.x
+apextract$exstrip.x
+apextract$exrecen.x
+    Added iferr statements for asifit.  Without this the task crashed
+    when an aperture went off the edge.  (3/10/88 Valdes)
+
+apextract$* Major changes:
+	o Use profile template image
+	o Don't interpolate data profile before cleaning
+	o New background option
+	o Integrate apertures
+	o Restructure code
+	o And much more
+    (3/1/88 Valdes)
+
+==============
+APEXTRACT V2.0
+==============
+
+apextract$excextract.x -
+apextract$exlextract.x -
+    Removed these unused procedures. (1/5/88 Valdes)
+
+apextract$excstrip.x
+apextract$exlstrip.x
+    Free curfit pointer if ic_fit returns an error. (1/5/88 Valdes)
+
+apextract$excsum.x
+apextract$exlsum.x
+    Set background to zero if ic_fit returns an error. (1/5/88 Valdes)
+
+    Original:
+	iferr (call ic_fit (AP_IC(aps[i]), cv, Memr[x],
+	    Memr[bufin], Memr[w], ncols, YES, YES, YES, YES))
+	    ;
+
+    New:
+	iferr {
+	    call ic_fit (AP_IC(aps[i]), cv, Memr[x],
+	        Memr[bufin], Memr[w], ncols, YES, YES, YES, YES)
+	    call ex_apbkg (cv, ncols, center, low, high,
+	        skyout[line,i])
+	} then
+	    skyout[line,i] = 0.
+
+apextract$exapsum.x
+    Added check for no data in sum. (1/5/88 Valdes)
+
+    In procedure ex_apsum:
+	a = max (0.5, center + lower)
+	b = min (npts + 0.5, center + upper)
+
+	if (a >= b) {			<-- ADD
+	    sum = 0.			<-- ADD
+	    return			<-- ADD
+	}
+
+    In procedure ex_apbkg:
+	a = max (0.5, center + lower)
+	b = min (npts + 0.5, center + upper)
+
+	if (a >= b) {			<-- ADD
+	    bkg = 0.			<-- ADD
+	    return			<-- ADD
+	}
+
+apextract$apnormalize.x
+    There was no error checking on ap_dbread which caused misleading errors
+    (apio package not found).  This was fixed by updating the logic to be the
+    same as in apextract.x.  A quick fix for outside sites is to add an
+    errchk for ap_dbread.  (12/18/87 Valdes)
+
+apextract$apedit.x
+apextract$apgscur.x
+    When first entering APEDIT with apertures defined the first attempt to
+    point the cursur at the first aperture uses an indefinite y value since
+    no cursor read has yet taken place.  The choices are to set it to some
+    arbitrary value, some percentage level on screen, or do nothing.  I
+    chose to do nothing.  Thus, the cursor will not point at the current
+    aperture in this case but it will leave the cursor position unchanged.
+    (12/17/87 Valdes)
+
+apextract$apio.par
+apextract$exsum.x
+apextract$exoutsum.x
+apextract$apedit.x
+    Added new parameter "format" to APIO pset.  Added new output formats for
+    echelle and multispectra data consisting of a single 2D image.  Added new
+    information in header.  Old format is called "onedspec".
+
+    Removed debugging print statement.  When it was put in I don't know.
+    (12/17/87 Valdes)
+
+apextract$apextract.x
+    An error was introduced with the change of 11/9/87 such that the error
+    when a database file does not exists was no longer being trapped.  This
+    was intended for reference images but was not intended for creating new
+    database files.  An iferr was added.
+
+apextract$t_apnormalize.x
+apextract$trtrace.x
+apextract$exstrip.x
+apextract$exsum.x
+    ERRCHK declarations for IMGETI were added to detect a missing DISPAXIS.
+    Failing to catch this error caused misleading error messages and
+    other fatal errors. (11/9/87 Valdes)
+
+apextract$apextract.x
+apextract$apdb.x
+    An error reading apertures for a specified reference image is now
+    printed instead of assuming there are no reference apertures.
+    (11/9/87 Valdes)
+
+apextract$exfit.x
+    Changed the variance formula from
+	V = v0 + v1 * abs (S + B)
+    to
+	V = v0 + v1 * max (0, S + B)		if v0 > 0
+	V = v1 * max (1, S + B)			if v0 = 0
+    (11/9/87 Valdes; see also 8/6/87)
+
+apextract$t_apnormalize.x
+    When normalizing more than 20 apertures some of the apertures
+    were being lost in the output image.  This was fixed to only
+    fill between the apertures on the first set of apertures.
+
+    Normalizing when DISPAXIS=1 did not work.  There were a number of
+    errors.  This task was never tested with data in this orientation.
+    (9/22/87 Valdes)
+
+apextract$exfit.x
+apextract$apsum.par
+apextract$apstrip.par
+apextract$doc/apsum.hlp
+apextract$doc/apstrip.hlp
+    When computing the variance for doing variance weighting the
+    intensity could be negative.  An absolute value was added to
+    correct this.
+
+    Make defaults for naverage=100 and nclean=2 because people have
+    been using inadequate number of lines for low signal-to-noise
+    data and because of interpolation even an 1 pixel cosmic ray
+    expands to two pixels.  (8/6/87 Valdes)
+
+====
+V2.5
+====
+
+apextract$apio.par
+apextract$apio.x
+apextract$t_apnormalize.x
+apextract$exsum.x
+apextract$exstrip.x
+apextract$apfindnew.x
+apextract$apfind.x
+apextract$apextract.x
+apextract$apedit.x
+apextract$trtrace.x
+apextract$trltrace.x
+apextract$trctrace.x
+apextract$exgraph.x
+apextract$doc/apio.hlp
+    Valdes, May 19, 1987
+    1.  Added the parameter "verbose" to the APIO pset to allow turning off
+	log information to the terminal.
+    2.  Made changes to minimize switching between text and graphics mode.
+	With verbose=no there should be essentially no mode switching.  This
+	was done for terminals in which such switches is either annoying
+	or slow.
+
+apextract$mkpkg
+apextract$apcvset.x
+apextract$t_apnormalize.x
+apextract$trtrace.x
+apextract$exsum.x
+apextract$exstrip.x
+apextract$apgetdata.x
+apextract$apimmap.x +
+    Valdes, April 24, 1987
+    1.  Protection against using an image which is not 2 dimensional was added.
+
+apextract$apedit.x
+apextract$apextract.x
+apextract$apsum.par
+apextract$exapsum.x
+apextract$excsum.x
+apextract$exgprofs.x
+apextract$exlsum.x
+apextract$exoutsum.x
+apextract$exsum.x
+apextract$doc/apsum.hlp
+    Valdes, April 11, 1987
+    1.  Added additional option to APSUM to output the subtracted sky
+	background spectra when doing background subtraction.
+
+apextract$apextract.hd
+apextract$apextract.men
+apextract$apextract.par
+apextract$apgetim.x
+apextract$apnormalize.par
+apextract$mkpkg
+apextract$t_apnormalize.x +
+apextract$x_apextract.x
+apextract$doc/apnormalize.hlp +
+    Valdes, April 3, 1987
+    1.  New task APNORMALIZE installed.
+
+apextract$*x
+    Valdes, February 17, 1987
+    1.  Required GIO changes.
+
+apextract$apio.h
+apextract$exgraph.x
+apextract$apio.x
+apextract$excextract.x
+apextract$apextract.tar
+apextract$trltrace.x
+apextract$trctrace.x
+apextract$exlextract.x
+apextract$applot.x
+apextract$apedit.x
+    Valdes, February 13, 1987
+    1.	I've made a number of modifications to the APEXTRACT package to
+	correct problems in the way graphics and text are mixed.  The
+	main change was to make the graphics open very local to the
+	procedure doing the graphics.  Previously the graphics device
+	was opened at the beginning of the logical task and remained
+	open until the end.  This was done since the integrated nature
+	of the package has many procedures which may do graphics.  This
+	has the bad side effects that for the first graphics open of
+	the process the terminal enters graphics mode (graphics screen
+	on SUN and clear screen on VT640) well before any graphics is
+	performed and text I/O is a problem.  Putting GOPEN and GCLOSE
+	immediately around the code that does graphics fixed almost all
+	the problems.  The only time that text output is now done when
+	the graphics terminal is open is for '?' and ':show' type of
+	commands.  The only remaining problem is the page wait problem
+	associated with '?' occuring before a cursor read rather than
+	immediately after the text output causing the last written
+	status line to become confused with the page wait prompt.
+
+apextract$apfind.par
+    Valdes, February 12, 1987
+    1.  The parameter apfind.nfind was changed back to hidden in order
+	for apsum to work in the background.  Note the PSET mechanism
+	would fix this by allowing nfind to be specified on the command
+	line.
+
+apextract$apio.par
+    Valdes, February 9, 1987
+    1.  New users rarely look at or know about the log files produced by
+	the package tasks.  These files (particularly graphics) take up
+	a lot of space.  Therefore the default is now not to log
+	text or graphics output.
+
+apextract$apedit.x
+apextract$apsort.x
+apextract$exapsum.x
+apextract$trltrace.x
+apextract$trctrace.x
+apextract$doc/apedit.hlp
+noao$lib/scr/apedit.key
+    Valdes, February 2, 1987
+    1.  Added a new edit option, 'o', to reorder the aperture id and beam
+	numbers sequentially.  This is useful after apertures have been
+	deleted and added interactively.
+    2.  If the aperture went completely off the image (ie there is no
+	overlap of even part of the aperture with the image) a random value
+	was given the aperture sum because the value was not intialize to
+	zero.  It is now initialize to zero.
+    3.  There is now a requirement that more than three points be traced
+	before a trace will be fit.
+
+apextract$trltrace.x
+apextract$trctrace.x
+apextract$apgetdata.x
+    Valdes, January 30, 1987
+    1.  The middle line (default) was not calculated correctly.  
+    2.  The tracing would sometimes run beyond the end of the image.  The
+	value of this traced point is suspect.  It was found because there
+	would be a point off the end of the ICFIT graph which was set to
+	be the size of the image.
+    3.  Just in case a traced point is right at the edge I made the default
+	window for fitting the trace extend half a step beyond the edges
+	of the image.
+
+apextract$exsum.x
+apextract$exstrip.x
+    Valdes, January 30, 1987
+    1.  Skip Schaller (Steward) reported a problem with running out of memory
+	with an input list of 20 images.  Also when the user deleted input
+	images after they were processed but before the list was finished
+	(to reduce memory) the memory was not actually freed until the process
+	actually finished.  I found that the input images
+	where not being closed! (Sorry about this really stupid error.)
+	This may not be all the problem but it is probable since IMIO
+	maintains large buffers.
+
+apextract$apcolon.x
+    Valdes, January 15, 1987
+    1.  Replaced dictionary string and numeric case by macros for readability.
+
+apextract$apfind.par
+    Valdes, December 19, 1986
+    1.  Change the default NFIND parameter in APFIND to auto mode.
+
+apextract$apnearest.x
+    Valdes, December 12, 1986
+    1.  It is possible for more than one aperture to be equidistant from
+	the cursor, particularly when more than one aperture is defined for
+	the same feature.  This is ambiguous for those commands which operate on
+	the nearest aperture.  The modification will query the user if it
+	is found that there is more than one aperture at the same distance
+	from the cursor.
+
+apextract$peaks.x
+    Valdes, October 10, 1986
+    1.  VMS adjustable array dimension error found.  Replaced declaration
+	dimension by ARB since the passed dimension value may be zero.
+
+apextract$*
+    Valdes, September 16, 1986
+    1.  A new version of the package has been installed.  It is very
+	different from the old version.  The user parameter files must
+	be unlearned.
+
+====================
+New Package Released
+====================
+
+apextract$: Valdes, July 19, 1986
+    1.  APEDIT and TRACE modified to include a detection threshold parameter
+	for profile centering.
+    2.  The help pages were updated.
+
+apextract$apedit.x, apvalue.x: Valdes, July 17, 1986
+    1.  A bug was found that appears if you edit the apertures of a
+	previously traced image.  The center moves with use of 'l' or
+	'u'.  This is due to an inconsistency between whether the aperture
+	center is before or after the traced shift is added.  Changes
+	to APVALUE.X and the calls to it in APEDIT.X fix this.
+
+apextract$: Valdes, July 15, 1986
+    1.  TRACE had a bug when trying to specify an explicit starting
+	line to edit and trace from.  This was fixed.
+    2.  EXCEXTRACT.X, EXLEXTRACT.X, and EXGPROFS.X were modified to
+	check for errors from background fitting.  This arose when
+	trying to get the background for a spectrum which has gone
+	off the edge of the image.
+
+apextract$apedit.x, apsort.x : Valdes, July 9, 1986
+    1.  When changing the aperture number the apertures are sorted and
+	then the wrong aperture could become the current aperture if
+	another aperture exists with the same aperture number.  This was
+	fixed so that the sorting returns the correct current aperture
+	after sorting.  Also apindex.x is no longer needed.
+
+apextract$apedit.x: Valdes, July 7, 1986
+    1.  The 'd' delete key now does nothing if no apertures are defined.
+	Previously it would cause a failure of the task.
+
+apextract$apedit.x:  Valdes, July 7, 1986
+    1.  Added redraw and window commands.
+    2.  Help page and '?' menu updated.
+
+apextract$apedit.x:  Valdes, July 3, 1986
+    1.  APEDIT modified to use new ICFIT package.
+
+apextract$apgetim.x:  Valdes, July 1, 1986
+    1.  New procedure to strip the image extension.  This is necessary
+	to create proper database files and to avoid having two legal
+	names for images in the database.
+
+apextract$exapstrip.x:  Valdes, July 1, 1986
+    1.  Simple strip extraction without profile modeling interpolated
+	the data so that the lower edge of the aperture was centered
+	on the first pixel.  This is inconsistent with the other extractions
+	which put the center of the aperture at the center of a pixel.
+	This has been fixed.
+
+apextract:  Valdes, June 30, 1986:
+    1.  TRACE was not correctly initializing the new ICFIT package.
+	In particular the task parameters "function" and "order" had no
+	effect and when multiple files were used the last set parameters
+	were not retained.  Changes to t_trace.x, trctrace.x, trltrace.x.
+
+=====================================
+STScI Pre-release and SUN 2.3 Release
+=====================================
+
+apextract:  Valdes, June 20, 1986:
+    1.  New APEXTRACT installed.  This version includes background
+	subtraction and new ICFIT.
+
+apextract:  Valdes, June 2, 1986
+    1.  Another round of name changes.  EDITAPS -> APEDIT,
+	EXTRACT1 -> SUMEXTRACT, EXTRACT2 -> STRIPEXTRACT.
+
+apextract:  Valdes, May 16, 1986
+    1.  Renamed APDEFINE to EDITAPS.
+    2.  Moved parameters used in editing the apertures from EXTRACT1 and
+	EXTRACT2.  These are now obtained from EDITAPS regardless of which
+	task calls apedit.
+    3.  Added parameters "cradius", "cwidth", "ctype", "lower", and "upper"
+	to EDITAPS.  The first parameters control profile centering and the
+	last parameters set the default aperture limits.
+    1.  Added new keys.  'c' center current aperture of profile near the cursor.
+	'm' mark and center aperture on profile near the cursor.  's' shift
+	the center of the current aperture to the cursor position.  The change
+	allows centering of profiles using CENTER1D.
+
+apextract$extract.x:  Valdes, May 13, 1986
+    1.  EXTRACT has been broken up into two tasks; EXTRACT1 and EXTRACT2.
+	EXTRACT1 extracts weighted summed 1D spectra.  EXTRACT2 extracts
+	2D apertures corrected for shifts across the dispersion.
+
+apextract:  Valdes, April 23, 1986
+    1.  Modified EXTRACT to only warn about an existing output image.
+	This allows adding a new aperture without needing to delete
+	old apertures or reextract previous extractions.
+
+apextract:  Valdes, April 21, 1986
+    1.  All procedures which pass the number of current apertures as an
+	argument and then dimension the array with this number
+	were modified by dimensioning the array as dimension
+	APS_MAXAPS or ARB.  This was done because the number of apertures
+	might be zero.  This is a fatal error on VMS/VAX though not on UNIX/VAX.
+
+apextract:  Valdes, March 27, 1986
+    1.  Modified EXTRACT (exsum.x and exwt.x) to update the dispersion image
+	header parameters.  In particular if the input dispersion axis is 2
+	then the header parameters must be reset to dispersion axis 1.
+
+===========
+Release 2.2
+===========
+.endhelp
diff --git a/noao/twodspec/apextract/apall.par b/noao/twodspec/apextract/apall.par
new file mode 100644
index 00000000..7c97a920
--- /dev/null
+++ b/noao/twodspec/apextract/apall.par
@@ -0,0 +1,96 @@
+# APALL
+
+input,s,a,,,,List of input images
+output,s,h,"",,,List of output spectra
+apertures,s,h,"",,,Apertures
+format,s,h,"multispec","onedspec|multispec|echelle|strip",,Extracted spectra format
+references,s,h,"",,,List of aperture reference images
+profiles,s,h,"",,,"List of aperture profile images
+"
+interactive,b,h,yes,,,Run task interactively?
+find,b,h,yes,,,Find apertures?
+recenter,b,h,yes,,,Recenter apertures?
+resize,b,h,yes,,,Resize apertures?
+edit,b,h,yes,,,Edit apertures?
+trace,b,h,yes,,,Trace apertures?
+fittrace,b,h,yes,,,Fit the traced points interactively?
+extract,b,h,yes,,,Extract spectra?
+extras,b,h,yes,,,"Extract sky, sigma, etc.?"
+review,b,h,yes,,,"Review extractions?
+"
+line,i,h,INDEF,1,,Dispersion line
+nsum,i,h,10,,,"Number of dispersion lines to sum or median
+
+# DEFAULT APERTURE PARAMETERS
+"
+lower,r,h,-5,,,Lower aperture limit relative to center
+upper,r,h,5,,,Upper aperture limit relative to center
+apidtable,s,h,"",,,"Aperture ID table (optional)
+
+# DEFAULT BACKGROUND PARAMETERS
+"
+b_function,s,h,"chebyshev","chebyshev|legendre|spline1|spline3",,Background function
+b_order,i,h,1,1,,Background function order
+b_sample,s,h,"-10:-6,6:10",,,Background sample regions
+b_naverage,i,h,-3,,,Background average or median
+b_niterate,i,h,0,0,,Background rejection iterations
+b_low_reject,r,h,3.,0.,,Background lower rejection sigma
+b_high_reject,r,h,3.,0.,,Background upper rejection sigma
+b_grow,r,h,0.,0.,,"Background rejection growing radius
+
+# APERTURE CENTERING PARAMETERS
+"
+width,r,h,5.,0.,,Profile centering width
+radius,r,h,10.,,,Profile centering radius
+threshold,r,h,0.,0.,,"Detection threshold for profile centering
+
+# AUTOMATIC FINDING AND ORDERING PARAMETERS
+"
+nfind,i,q,,,,Number of apertures to be found automatically
+minsep,r,h,5.,1.,,Minimum separation between spectra
+maxsep,r,h,100000.,1.,,Maximum separation between spectra
+order,s,h,"increasing","increasing|decreasing",,"Order of apertures
+
+# RECENTERING PARAMETERS
+"
+aprecenter,s,h,"",,,Apertures for recentering calculation
+npeaks,r,h,INDEF,0.,,Select brightest peaks
+shift,b,h,yes,,,"Use average shift instead of recentering?
+
+# RESIZING PARAMETERS
+"
+llimit,r,h,INDEF,,,Lower aperture limit relative to center
+ulimit,r,h,INDEF,,,Upper aperture limit relative to center
+ylevel,r,h,0.1,,,Fraction of peak or intensity for automatic width
+peak,b,h,yes,,,Is ylevel a fraction of the peak?
+bkg,b,h,yes,,,"Subtract background in automatic width?"
+r_grow,r,h,0.,,,"Grow limits by this factor"
+avglimits,b,h,no,,,"Average limits over all apertures?
+
+# TRACING PARAMETERS
+"
+t_nsum,i,h,10,1,,Number of dispersion lines to sum
+t_step,i,h,10,1,,Tracing step
+t_nlost,i,h,3,1,,Number of consecutive times profile is lost before quitting
+t_function,s,h,"legendre","chebyshev|legendre|spline1|spline3",,Trace fitting function
+t_order,i,h,2,1,,Trace fitting function order
+t_sample,s,h,"*",,,Trace sample regions
+t_naverage,i,h,1,,,Trace average or median
+t_niterate,i,h,0,0,,Trace rejection iterations
+t_low_reject,r,h,3.,0.,,Trace lower rejection sigma
+t_high_reject,r,h,3.,0.,,Trace upper rejection sigma
+t_grow,r,h,0.,0.,,"Trace rejection growing radius
+
+# EXTRACTION PARAMETERS
+"
+background,s,h,"none","none|average|median|minimum|fit",,Background to subtract
+skybox,i,h,1,1,,Box car smoothing length for sky
+weights,s,h,"none","none|variance",,Extraction weights (none|variance)
+pfit,s,h,"fit1d","fit1d|fit2d",,Profile fitting type (fit1d|fit2d)
+clean,b,h,no,,,Detect and replace bad pixels?
+saturation,r,h,INDEF,1.,,Saturation level
+readnoise,s,h,"0.",,,Read out noise sigma (photons)
+gain,s,h,"1.",,,Photon gain (photons/data number)
+lsigma,r,h,4,0,,Lower rejection threshold
+usigma,r,h,4,0,,Upper rejection threshold
+nsubaps,i,h,1,1,,Number of subapertures per aperture
diff --git a/noao/twodspec/apextract/apall1.par b/noao/twodspec/apextract/apall1.par
new file mode 100644
index 00000000..12a28b32
--- /dev/null
+++ b/noao/twodspec/apextract/apall1.par
@@ -0,0 +1,117 @@
+# OUTPUT PARAMETERS
+
+apertures,s,h,)apall.apertures,,,>apall.apertures
+format,s,h,)apall.format,,,>apall.format
+extras,b,h,)apall.extras,,,>apall.extras
+dbwrite,s,h,yes,,,Write to database?
+initialize,b,h,yes,,,Initialize answers?
+verbose,b,h,)_.verbose,,,"Verbose output?
+
+# DEFAULT APERTURE PARAMETERS
+"
+lower,r,h,)apall.lower,,,>apall.lower
+upper,r,h,)apall.upper,,,>apall.upper
+apidtable,s,h,)apall.apidtable,,,">apall.apidtable
+
+# DEFAULT BACKGROUND PARAMETERS
+"
+b_function,s,h,)apall.b_function,,,>apall.b_function
+b_order,i,h,)apall.b_order,,,>apall.b_order
+b_sample,s,h,)apall.b_sample,,,>apall.b_sample
+b_naverage,i,h,)apall.b_naverage,,,>apall.b_naverage
+b_niterate,i,h,)apall.b_niterate,,,>apall.b_niterate
+b_low_reject,r,h,)apall.b_low_reject,,,>apall.b_low_reject
+b_high_reject,r,h,)apall.b_high_reject,,,>apall.b_high_reject
+b_grow,r,h,)apall.b_grow,,,">apall.b_grow
+
+# APERTURE CENTERING PARAMETERS
+"
+width,r,h,)apall.width,,,>apall.width
+radius,r,h,)apall.radius,,,>apall.radius
+threshold,r,h,)apall.threshold,,,">apall.threshold
+
+# AUTOMATIC FINDING AND ORDERING PARAMETERS
+"
+nfind,i,h,)apall.nfind,,,>apall.nfind
+minsep,r,h,)apall.minsep,,,>apall.minsep
+maxsep,r,h,)apall.maxsep,,,>apall.maxsep
+order,s,h,)apall.order,,,">apall.order
+
+# RECENTERING PARAMETERS
+"
+aprecenter,s,h,)apall.aprecenter,,,>apall.aprecenter
+npeaks,r,h,)apall.npeaks,,,>apall.npeaks
+shift,b,h,)apall.shift,,,">apall.shift
+
+# RESIZING PARAMETERS
+"
+llimit,r,h,)apall.llimit,,,>apall.llimit
+ulimit,r,h,)apall.ulimit,,,>apall.ulimit
+ylevel,r,h,)apall.ylevel,,,>apall.ylevel
+peak,b,h,)apall.peak,,,>apall.peak
+bkg,b,h,)apall.bkg,,,>apall.bkg
+r_grow,r,h,)apall.r_grow,,,>apall.r_grow
+avglimits,b,h,)apall.avglimits,,,">apall.avglimits
+
+# EDITING PARAMETERS
+"
+e_output,s,q,,,,Output spectra rootname
+e_profiles,s,q,,,,Profile reference image
+
+# TRACING PARAMETERS
+t_nsum,i,h,)apall.t_nsum,,,>apall.t_nsum
+t_step,i,h,)apall.t_step,,,>apall.t_step
+t_nlost,i,h,)apall.t_nlost,,,>apall.t_nlost
+t_width,r,h,)apall.width,,,>apall.width
+t_function,s,h,)apall.t_function,,,>apall.t_function
+t_order,i,h,)apall.t_order,,,>apall.t_order
+t_sample,s,h,)apall.t_sample,,,>apall.t_sample
+t_naverage,i,h,)apall.t_naverage,,,>apall.t_naverage
+t_niterate,i,h,)apall.t_niterate,,,>apall.t_niterate
+t_low_reject,r,h,)apall.t_low_reject,,,>apall.t_low_reject
+t_high_reject,r,h,)apall.t_high_reject,,,>apall.t_high_reject
+t_grow,r,h,)apall.t_grow,,,">apall.t_grow
+
+# EXTRACTION PARAMETERS
+"
+background,s,h,)apall.background,,,>apall.background
+skybox,i,h,)apall.skybox,,,>apall.skybox
+weights,s,h,)apall.weights,,,>apall.weights
+pfit,s,h,)apall.pfit,,,>apall.pfit
+clean,b,h,)apall.clean,,,>apall.clean
+nclean,r,h,0.5,,,Maximum number of pixels to clean
+niterate,i,h,5,0,,Number of profile fitting iterations
+saturation,r,h,)apall.saturation,,,>apall.saturation
+readnoise,s,h,)apall.readnoise,,,>apall.readnoise
+gain,s,h,)apall.gain,,,>apall.gain
+lsigma,r,h,)apall.lsigma,,,>apall.lsigma
+usigma,r,h,)apall.usigma,,,>apall.usigma
+polysep,r,h,0.90,0.1,0.95,Marsh algorithm polynomial spacing
+polyorder,i,h,10,1,,Marsh algorithm polynomial order
+nsubaps,i,h,)apall.nsubaps,,,">apall.nsubaps
+
+# ANSWER PARAMETERS
+"
+ansclobber,s,h,"no",,," "
+ansclobber1,s,h,"no",,," "
+ansdbwrite,s,h,"yes",,," "
+ansdbwrite1,s,h,"yes",,," "
+ansedit,s,h,"yes",,," "
+ansextract,s,h,"yes",,," "
+ansfind,s,h,"yes",,," "
+ansfit,s,h,"yes",,," "
+ansfitscatter,s,h,"yes",,," "
+ansfitsmooth,s,h,"yes",,," "
+ansfitspec,s,h,"yes",,," "
+ansfitspec1,s,h,"yes",,," "
+ansfittrace,s,h,"yes",,," "
+ansfittrace1,s,h,"yes",,," "
+ansflat,s,h,"yes",,," "
+ansnorm,s,h,"yes",,," "
+ansrecenter,s,h,"yes",,," "
+ansresize,s,h,"yes",,," "
+ansreview,s,h,"yes",,," "
+ansreview1,s,h,"yes",,," "
+ansscat,s,h,"yes",,," "
+anssmooth,s,h,"yes",,," "
+anstrace,s,h,"yes",,," "
diff --git a/noao/twodspec/apextract/apalloc.x b/noao/twodspec/apextract/apalloc.x
new file mode 100644
index 00000000..086db650
--- /dev/null
+++ b/noao/twodspec/apextract/apalloc.x
@@ -0,0 +1,34 @@
+include	"apertures.h"
+
+# AP_ALLOC -- Allocate and initialize an aperture structure.
+
+procedure ap_alloc (ap)
+
+pointer	ap		# Aperture
+
+begin
+	call calloc (ap, AP_LEN, TY_STRUCT)
+	AP_TITLE(ap) = NULL
+	AP_CV(ap) = NULL
+	AP_IC(ap) = NULL
+	AP_SELECT(ap) = YES
+end
+
+
+# AP_FREE -- Free an aperture structure and related CURFIT structures.
+
+procedure ap_free (ap)
+
+pointer	ap		# Aperture
+
+begin
+	if (ap != NULL) {
+	    if (AP_TITLE(ap) != NULL)
+		call mfree (AP_TITLE(ap), TY_CHAR)
+	    if (AP_CV(ap) != NULL)
+	        call cvfree (AP_CV(ap))
+	    if (AP_IC(ap) != NULL)
+	        call ic_closer (AP_IC(ap))
+	    call mfree (ap, TY_STRUCT)
+	}
+end
diff --git a/noao/twodspec/apextract/apanswer.x b/noao/twodspec/apextract/apanswer.x
new file mode 100644
index 00000000..0077af4a
--- /dev/null
+++ b/noao/twodspec/apextract/apanswer.x
@@ -0,0 +1,121 @@
+define	ANSWERS	"|no|yes|NO|YES|"
+
+
+# AP_ANSWER -- Prompt the user (if needed) and return bool based
+# on 4-valued response
+
+bool procedure ap_answer (param, prompt)
+
+char	param[ARB]		# Parameter name
+char	prompt[ARB]		# Prompt to be issued
+
+char	word[3]
+int	i, apgwrd()
+pointer	pmode
+
+begin
+	i = apgwrd (param, word, 3, ANSWERS)
+	switch (i) {
+	case 3:
+	    return (false)
+	case 4:
+	    return (true)
+	default:
+	    call malloc (pmode, SZ_LINE, TY_CHAR)
+	    call sprintf (Memc[pmode], SZ_LINE, "%s.p_mode")
+		call pargstr (param)
+	    call appstr (Memc[pmode], "q")
+	    repeat {
+	        call eprintf (prompt)
+	        call flush (STDERR)
+		ifnoerr (i = apgwrd (param, word, 3, ANSWERS))
+		    break
+	    }
+	    call appstr (param, word)
+	    call appstr (Memc[pmode], "h")
+	    call mfree (pmode, TY_CHAR)
+	}
+
+	switch (i) {
+	case 1, 3:
+	    return (false)
+	case 2, 4:
+	    return (true)
+	}
+end
+
+
+# APGANSB -- Convert 4-valued parameter to bool
+
+bool procedure apgansb (param)
+
+char	param[ARB]		# Parameter name
+
+char	word[3]
+int	apgwrd()
+
+begin
+	switch (apgwrd (param, word, 3, ANSWERS)) {
+	case 1, 3:
+	    return (false)
+	default:
+	    return (true)
+	}
+end
+
+
+# APGANS -- Convert 4-value parameter to bool except "no" is true.
+
+bool procedure apgans (param)
+
+char	param[ARB]		# Parameter name
+
+char	word[3]
+pointer	pmode
+bool	streq()
+
+begin
+	call malloc (pmode, SZ_LINE, TY_CHAR)
+	call sprintf (Memc[pmode], SZ_LINE, "%s.p_mode")
+	    call pargstr (param)
+	call apgstr (Memc[pmode], word, 3)
+	if (word[1] != 'h')
+	    call appstr (Memc[pmode], "h")
+	call mfree (pmode, TY_CHAR)
+	call apgstr (param, word, 3)
+	return (!streq (word, "NO"))
+end
+
+
+# APPANS -- Put 4-valued parameter based on interactive parameter.
+
+procedure appans (param, ival, nival)
+
+char	param[ARB]		# Parameter
+bool	ival			# Interactive value
+bool	nival			# Noninteractive value
+
+char	word[3]
+pointer	pmode
+bool	clgetb()
+
+begin
+	call malloc (pmode, SZ_LINE, TY_CHAR)
+	call sprintf (Memc[pmode], SZ_LINE, "%s.p_mode")
+	    call pargstr (param)
+	call apgstr (Memc[pmode], word, 3)
+	if (word[1] != 'h')
+	    call appstr (Memc[pmode], "h")
+	call mfree (pmode, TY_CHAR)
+	if (clgetb ("interactive")) {
+	    if (ival)
+		call appstr (param, "yes")
+	    else
+		call appstr (param, "NO")
+	} else {
+	    if (nival)
+		call appstr (param, "YES")
+	    else
+		call appstr (param, "NO")
+	}
+end
diff --git a/noao/twodspec/apextract/apcenter.x b/noao/twodspec/apextract/apcenter.x
new file mode 100644
index 00000000..88f089d1
--- /dev/null
+++ b/noao/twodspec/apextract/apcenter.x
@@ -0,0 +1,26 @@
+include	<pkg/center1d.h>
+
+# AP_CENTER -- Locate the center of an emission profile.  This is done
+# using the CENTER1D algorithm.  The procedure gets the centering
+# parameters using CL queries.  If the center is not found because of the
+# RADIUS or THRESHOLD centering criteria then INDEF is returned.
+
+real procedure ap_center (x, data, npts)
+
+real	x		# Initial guess
+real	data[npts]	# Data
+int	npts		# Number of data points
+
+real	width		# Centering width
+real	radius		# Centering radius
+real	threshold	# Detection threshold
+
+real	apgetr(), center1d()
+
+begin
+	width = apgetr ("width")
+	radius = apgetr ("radius")
+	threshold = apgetr ("threshold")
+
+	return (center1d (x, data, npts, width, EMISSION, radius, threshold))
+end
diff --git a/noao/twodspec/apextract/apcolon.x b/noao/twodspec/apextract/apcolon.x
new file mode 100644
index 00000000..9e910a95
--- /dev/null
+++ b/noao/twodspec/apextract/apcolon.x
@@ -0,0 +1,384 @@
+include	<gset.h>
+include <imhdr.h>
+include	<error.h>
+include	"apertures.h"
+
+# List of colon commands.
+define	CMDS "|show|parameters|database|logfile|plotfile|read|write|image\
+	|line|nsum|center|lower|upper|title\
+	|extras,b|apidtable,s|b_function,s|b_order,i|b_sample,s\
+	|b_naverage,i|b_niterate,i|b_low_reject,r|b_high_reject,r|b_grow,r\
+	|minsep,r|maxsep,r|order,s|apertures,s|npeaks,r|shift,b|llimit,r\
+	|ulimit,r|ylevel,r|peak,b|bkg,b|r_grow,r|avglimits,b|width,r|radius,r\
+	|threshold,r|t_nsum,i|t_step,i|t_width,r|t_function,s|t_order,i\
+	|t_sample,s|t_naverage,i|t_niterate,i|t_low_reject,r|t_high_reject,r\
+	|t_grow,r|nsubaps,i|background,s|skybox,i|clean,b|saturation,r\
+	|weights,s|readnoise,s|gain,s|lsigma,r|usigma,r|t_nlost,i|"
+
+define	SHOW		1	# Show apertures
+define	PARAMS		2	# Show parameters
+define	DATABASE	3	# Database
+define	LOGFILE		4	# Logfile
+define	PLOTFILE	5	# Plotfile
+define	READ		6	# Read aperture database entry
+define	WRITE		7	# Write aperture database entry
+define	IMAGE		8	# Image being edited
+define	LINE		9	# Set image line to display
+define	NSUM		10	# Set number of image lines to sum for display
+define	CENTER		11	# Set aperture center
+define	LOWER		12	# Set aperture lower limit
+define	UPPER		13	# Set aperture upper limit
+define	APTITLE		14	# Set aperture title
+
+
+# AP_COLON -- Process colon commands.  The colon commands may be abbreviated.
+# Optional arguments determine either the output or the value of a parameter.
+# Changes are signaled to the calling task with the flags NEWGRAPH, NEWIM,
+# and NEWDATA.  This task does CLIO including CLCMDW commands.
+
+procedure ap_colon (cmd, im, gp, apdef, aps, naps, current, image, line,
+    nsum, all, newgraph, newim, newdata, statline)
+
+char	cmd[ARB]		# Colon command
+pointer	im			# IMIO pointer
+pointer	gp			# GIO pointer
+pointer	apdef			# Default aperture
+pointer	aps			# Aperture pointers
+int	naps			# Number of apertures
+int	current			# Current aperture
+char	image[SZ_FNAME]		# Image name
+int	line			# Dispersion line
+int	nsum			# Number of lines to sum
+int	all			# All switch
+int	newgraph		# New graph flag
+int	newim			# New image flag
+int	newdata			# New data flag
+int	statline		# Status line used?
+
+bool	bval
+int	i, j, ival, apid, apbeam
+real	center, low, high, rval
+pointer	sp, wrd, str
+
+bool	strne(), apgetb()
+real	apgetr()
+int	nscan(), strdic(), imaccess(), apgeti(), stridxs()
+errchk	ap_apertures, ap_show, ap_params, ap_dbread, ap_dbwrite, ap_openio
+
+define	done_	99
+
+begin
+	call smark (sp)
+	call salloc (wrd, SZ_LINE, TY_CHAR)
+	call salloc (str, SZ_LINE, TY_CHAR)
+
+	# Scan the command string for the first word which may be abbreviated.
+	call sscan (cmd)
+	call gargwrd (Memc[wrd], SZ_LINE)
+	i = strdic (Memc[wrd], Memc[wrd], SZ_LINE, CMDS)
+	if (i == 0) {
+	    call printf ("Unrecognized or ambiguous command\007")
+	    statline = YES
+	    call sfree (sp)
+	    return
+	}
+	j = stridxs (",", Memc[wrd])
+
+	if (j == 0) {
+	    switch (i) {
+	    case SHOW:	# :show - Show aperture list
+	        call gargwrd (cmd, SZ_LINE)
+	        if (nscan() == 1) {
+		    call gdeactivate (gp, AW_CLEAR)
+	            call ap_show ("STDOUT", Memi[aps], naps)
+		    call greactivate (gp, AW_PAUSE)
+	        } else {
+		    iferr (call ap_show (cmd, Memi[aps], naps)) {
+		        call erract (EA_WARN)
+			statline = YES
+		    }
+	        }
+	    case PARAMS: # :parameters - Show parameters
+	        call gargwrd (cmd, SZ_LINE)
+	        if (nscan() == 1) {
+		    call mktemp ("junk", cmd, SZ_LINE) 
+	            iferr (call ap_params (cmd, image, line, nsum)) {
+		        call gdeactivate (gp, AW_CLEAR)
+	                call ap_params ("STDOUT", image, line, nsum)
+		        call greactivate (gp, AW_PAUSE)
+		    } else {
+		        call gpagefile (gp, cmd, ":parameters")
+		        call delete (cmd)
+		    }
+	        } else {
+		    iferr (call ap_params (cmd, image, line, nsum)) {
+		        call erract (EA_WARN)
+			statline = YES
+		    }
+	        }
+	    case DATABASE: # :database - Database name
+	        call gargwrd (cmd, SZ_LINE)
+	        if (nscan() == 1) {
+		    call clgstr ("database", cmd, SZ_LINE)
+		    call printf ("database %s")
+		        call pargstr (cmd)
+		    statline = YES
+	        } else
+		    call clpstr ("database", cmd)
+	    case LOGFILE: # :logfile - Logfile name
+	        call gargwrd (cmd, SZ_LINE)
+	        if (nscan() == 1) {
+		    call clgstr ("logfile", cmd, SZ_LINE)
+		    call printf ("logfile %s")
+		        call pargstr (cmd)
+		    statline = YES
+	        } else
+		    call clpstr ("logfile", cmd)
+	    case PLOTFILE: # :plotfile - Plotfile name
+	        call gargwrd (cmd, SZ_LINE)
+	        if (nscan() == 1) {
+		    call clgstr ("plotfile", cmd, SZ_LINE)
+		    call printf ("plotfile %s")
+		        call pargstr (cmd)
+		    statline = YES
+	        } else
+		    call clpstr ("plotfile", cmd)
+	    case READ: # :read - Read database entry
+	        iferr {
+	            call gargwrd (cmd, SZ_LINE)
+	            if (nscan() == 1)
+		        call ap_dbread (image, aps, naps)
+	            else {
+		        call xt_stripwhite (cmd)
+		        if (cmd[1] == EOS)
+		            call ap_dbread (image, aps, naps)
+		        else {
+		            call ap_dbread (cmd, aps, naps)
+			    call appstr ("ansdbwrite1", "yes")
+		        }
+		    }
+	        } then {
+		    call erract (EA_WARN)
+		    statline = YES
+		}
+		current = min (1, naps)
+	        newgraph = YES
+	    case WRITE: # :write - Write database entry
+	        iferr {
+	            call gargwrd (cmd, SZ_LINE)
+	            if (nscan() == 1)
+		        call ap_dbwrite (image, aps, naps)
+	            else {
+		        call xt_stripwhite (cmd)
+		        if (cmd[1] == EOS)
+		            call ap_dbwrite (image, aps, naps)
+		        else {
+		            call ap_dbwrite (cmd, aps, naps)
+			    call appstr ("ansdbwrite1", "yes")
+		        }
+		    }
+	        } then {
+		    call erract (EA_WARN)
+		    statline = YES
+		}
+	    case IMAGE: # :image - Define a new image
+	        call gargwrd (cmd, SZ_LINE)
+	        if (nscan() == 1) {
+		    call printf ("image %s")
+		        call pargstr (image)
+		    statline = YES
+	        } else {
+		    call xt_stripwhite (cmd)
+		    if ((cmd[1] != EOS) && (strne (cmd, image))) {
+		        if (imaccess (cmd, READ_ONLY) == YES)
+		            newim = YES
+		        else {
+			    call eprintf (
+			        "WARNING: Can't read image %s")
+			        call pargstr (cmd)
+			    statline = YES
+		        }
+		    }
+	        }
+	    case LINE: # :line - Image line or column
+	        call gargi (ival)
+	        if (nscan() < 2) {
+		    call printf ("line %d")
+		        call pargi (line)
+		    statline = YES
+	        } else if (ival != line) {
+		    call strcpy (image, cmd, SZ_LINE)
+		    line = ival
+		    newdata = YES
+	        }
+	    case NSUM: # :nsum - Number of image lines or columns to sum
+	        call gargi (ival)
+	        if (nscan() < 2) {
+		    call printf ("nsum %d")
+		        call pargi (nsum)
+		    statline = YES
+	        } else if (ival != nsum) {
+		    call strcpy (image, cmd, SZ_LINE)
+		    nsum = ival
+		    newdata = YES
+	        }
+	    case CENTER: # :center - Set aperture center
+	        if (current == 0)
+		    goto done_
+	        call gargr (rval)
+	        if (nscan() == 1) {
+	            call ap_values (current, Memi[aps], line, apid,
+			apbeam, center, low, high)
+		    call printf ("center %g")
+		        call pargr (center)
+		    statline = YES
+	        } else if (all == NO) {
+	            call ap_values (current, Memi[aps], line, apid,
+			apbeam, center, low, high)
+		    iferr (call ap_update (gp, Memi[aps+current-1], line, apid,
+			apbeam, rval, low, high)) {
+			call erract (EA_WARN)
+			statline = YES
+		    }
+	        } else {
+	            call ap_values (current, Memi[aps], line, apid,
+			apbeam, center, low, high)
+		    rval = rval - center
+		    do i = 1, naps {
+			call ap_values (i, Memi[aps], line, apid,
+			    apbeam, center, low, high)
+			center = center + rval
+			iferr (call ap_update (gp, Memi[aps+i-1], line, apid,
+			    apbeam, center, low, high)) {
+			    call erract (EA_WARN)
+			    statline = YES
+			}
+		    }
+	        }
+	    case LOWER: # :lower - Set lower aperture limit
+	        if (current == 0)
+		    goto done_
+	        call gargr (rval)
+	        if (nscan() == 1) {
+	            call ap_values (current, Memi[aps], line, apid,
+			apbeam, center, low, high)
+		    call printf ("low %g")
+		        call pargr (low)
+		    statline = YES
+	        } else if (all == NO) {
+		    call ap_values (current, Memi[aps], line, apid,
+			apbeam, center, low, high)
+		    iferr (call ap_update (gp, Memi[aps+current-1], line, apid,
+			apbeam, center, rval, high)) {
+			call erract (EA_WARN)
+			statline = YES
+		    }
+	        } else {
+		    do i = 1, naps {
+		        call ap_values (i, Memi[aps], line, apid,
+			    apbeam, center, low, high)
+		        iferr (call ap_update (gp, Memi[aps+i-1], line, apid,
+			    apbeam, center, rval, high))
+			    call erract (EA_WARN) {
+			    statline = YES
+			}
+		    }
+	        }
+	    case UPPER: # :upper - Set upper aperture limit
+	        if (current == 0)
+		    goto done_
+	        call gargr (rval)
+	        if (nscan() == 1) {
+	            call ap_values (current, Memi[aps], line, apid,
+			apbeam, center, low, high)
+		    call printf ("high %g")
+		        call pargr (high)
+		    statline = YES
+	        } else if (all == NO) {
+		    call ap_values (current, Memi[aps], line, apid,
+			apbeam, center, low, high)
+		    iferr (call ap_update (gp, Memi[aps+current-1], line, apid,
+			apbeam, center, low, rval)) {
+			call erract (EA_WARN)
+			statline = YES
+		    }
+	        } else {
+		    do i = 1, naps {
+		        call ap_values (i, Memi[aps], line, apid,
+			    apbeam, center, low, high)
+		        iferr (call ap_update (gp, Memi[aps+i-1], line, apid,
+			    apbeam, center, low, rval)) {
+			    call erract (EA_WARN)
+			    statline = YES
+			}
+		    }
+	        }
+	    case APTITLE:
+	        if (current == 0)
+		    goto done_
+	        call gargwrd (Memc[wrd], SZ_LINE)
+	        if (nscan() == 1) {
+		    call printf ("title %s")
+		        if (AP_TITLE(Memi[aps+current-1]) != NULL)
+			    call pargstr (Memc[AP_TITLE(Memi[aps+current-1])])
+		        else
+			    call pargstr ("[NONE]")
+		    statline = YES
+	        } else {
+		    call reset_scan ()
+		    call gargwrd (Memc[str], SZ_LINE)
+		    call gargstr (Memc[str], SZ_LINE)
+		    if (AP_TITLE(Memi[aps+current-1]) == NULL)
+		        call malloc (AP_TITLE(Memi[aps+current-1]), SZ_APTITLE,
+			    TY_CHAR)
+		    call strcpy (Memc[str+1],
+			Memc[AP_TITLE(Memi[aps+current-1])], SZ_APTITLE)
+	        }
+	    }
+
+	} else {
+	    Memc[wrd+j-1] = EOS
+	    switch (Memc[wrd+j]) {
+	    case 'b':
+	        call gargb (bval)
+	        if (nscan() < 2) {
+		    call printf ("%s %b")
+			call pargstr (Memc[wrd])
+		        call pargb (apgetb (Memc[wrd]))
+		    statline = YES
+	        } else
+	            call apputb (Memc[wrd], bval)
+	    case 'i':
+	        call gargi (ival)
+	        if (nscan() < 2) {
+		    call printf ("%s %d")
+			call pargstr (Memc[wrd])
+		        call pargi (apgeti (Memc[wrd]))
+		    statline = YES
+	        } else
+	            call apputi (Memc[wrd], ival)
+	    case 'r':
+	        call gargr (rval)
+	        if (nscan() < 2) {
+		    call printf ("%s %g")
+			call pargstr (Memc[wrd])
+		        call pargr (apgetr (Memc[wrd]))
+		    statline = YES
+	        } else
+	            call apputr (Memc[wrd], rval)
+	    case 's':
+	        call gargwrd (Memc[str], SZ_LINE)
+	        if (nscan() < 2) {
+		    call apgstr (Memc[wrd], Memc[str], SZ_LINE)
+		    call printf ("%s %s")
+			call pargstr (Memc[wrd])
+		        call pargstr (Memc[str])
+		    statline = YES
+	        } else
+	            call appstr (Memc[wrd], Memc[str])
+	    }
+	}
+
+done_	call sfree (sp)
+
+end
diff --git a/noao/twodspec/apextract/apcopy.x b/noao/twodspec/apextract/apcopy.x
new file mode 100644
index 00000000..e697bf88
--- /dev/null
+++ b/noao/twodspec/apextract/apcopy.x
@@ -0,0 +1,28 @@
+include	"apertures.h"
+
+# AP_COPY -- Make a copy of an aperture.
+# The title is not copied.
+
+procedure ap_copy (apin, apout)
+
+pointer	apin		# Aperture to copy
+pointer	apout		# New copy
+
+int	i
+
+begin
+	# Allocate memory, transfer the aperture parameters, and call procedures
+	# which copy the offset curve and background parameters.
+	call ap_alloc (apout)
+	AP_ID(apout) = AP_ID(apin)
+	AP_BEAM(apout) = AP_BEAM(apin)
+	AP_AXIS(apout) = AP_AXIS(apin)
+	do i = 1, 2 {
+	    AP_CEN(apout, i) = AP_CEN(apin, i)
+	    AP_LOW(apout, i) = AP_LOW(apin, i)
+	    AP_HIGH(apout, i) = AP_HIGH(apin, i)
+	}
+	call ap_cvset (apin, apout)
+	call ic_open (AP_IC(apout))
+	call ic_copy (AP_IC(apin), AP_IC(apout))
+end
diff --git a/noao/twodspec/apextract/apcveval.x b/noao/twodspec/apextract/apcveval.x
new file mode 100644
index 00000000..09e5beb5
--- /dev/null
+++ b/noao/twodspec/apextract/apcveval.x
@@ -0,0 +1,19 @@
+include	<math/curfit.h>
+
+# AP_CVEVAL -- Interface to CVEVAL that avoids extrapolation.
+# This is necessary because if the tracing was truncated due to loss
+# of the profile the trace limits will be smaller than the image axis.
+# In the longer term the aperture limits along the dispersion should be
+# used to limit the extent of the spectrum.
+
+real procedure ap_cveval (cv, x)
+
+pointer	cv		#I CURFIT pointer
+real	x		#I Point to be evaluated.
+
+real	x1, cvstatr(), cveval()
+
+begin
+	x1 = min (max (x, cvstatr(cv,CVXMIN)), cvstatr(cv,CVXMAX))
+	return (cveval (cv, x1))
+end
diff --git a/noao/twodspec/apextract/apcvset.x b/noao/twodspec/apextract/apcvset.x
new file mode 100644
index 00000000..656187d5
--- /dev/null
+++ b/noao/twodspec/apextract/apcvset.x
@@ -0,0 +1,47 @@
+include	<math/curfit.h>
+include	"apertures.h"
+
+# AP_CVSET -- Set the trace curve.
+# If the input template aperture is NULL then the output trace curve
+# is set to a constant zero otherwise a copy from the input template
+# aperture is made.
+
+procedure ap_cvset (apin, apout)
+
+pointer	apin		# Input template aperture
+pointer	apout		# Output aperture
+
+int	apaxis, dispaxis, ncoeffs
+real	a, b, c[1]
+pointer	sp, coeffs
+
+int	cvstati()
+
+begin
+	if (AP_CV(apout) != NULL)
+	    call cvfree (AP_CV(apout))
+
+	if (apin == NULL) {
+	    # Determine the aperture and alternate axes.
+	    apaxis = AP_AXIS(apout)
+	    dispaxis = mod (apaxis, 2) + 1
+
+	    # Determine the limits over which the curve is defined.
+	    a = AP_CEN(apout, dispaxis) + AP_LOW(apout, dispaxis)
+	    b = AP_CEN(apout, dispaxis) + AP_HIGH(apout, dispaxis)
+	    if (a == b)
+		b = b + 1
+
+	    # Set the curve to a legendre polynomial of order 1 and value 0.
+	    c[1] = 0.
+	    call cvset (AP_CV(apout), LEGENDRE, a, b, c, 1)
+	} else {
+	    # Use a SAVE and RESTORE to copy the CURFIT data.
+	    call smark (sp)
+	    ncoeffs = cvstati (AP_CV(apin), CVNSAVE)
+	    call salloc (coeffs, ncoeffs, TY_REAL)
+	    call cvsave (AP_CV(apin), Memr[coeffs])
+	    call cvrestore (AP_CV(apout), Memr[coeffs])
+	    call sfree (sp)
+	}
+end
diff --git a/noao/twodspec/apextract/apdb.x b/noao/twodspec/apextract/apdb.x
new file mode 100644
index 00000000..8bfb5244
--- /dev/null
+++ b/noao/twodspec/apextract/apdb.x
@@ -0,0 +1,314 @@
+include	<math/curfit.h>
+include	<pkg/dttext.h>
+include	"apertures.h"
+
+# AP_DBWRITE -- Write aperture data to the database.  The database is obtained
+# with a CL query.
+
+procedure ap_dbwrite (image, aps, naps)
+
+char	image[ARB]		# Image
+pointer	aps			# Apertures
+int	naps
+
+int	i, j, ncoeffs
+pointer	sp, database, str, dt, coeffs, ap
+
+int	cvstati(), ic_geti()
+real	ic_getr()
+bool	strne()
+pointer	dtmap1()
+
+errchk	dtmap1
+
+begin
+	# Set the aperture database file name and map as a NEW_FILE.
+	# The file name is "ap" appended with the image name with the
+	# special image section characters replaced by '_'.
+	# The reason for making image sections separate database
+	# files rather than combining all database entries for an image
+	# in one file is that then previous entries can be deleted
+	# by using NEW_FILE mode which deletes any existing database
+	# file before writing out the new apertures.
+
+	call smark (sp)
+	call salloc (database, SZ_FNAME, TY_CHAR)
+	call salloc (str, SZ_LINE, TY_CHAR)
+
+	call clgstr ("database", Memc[database], SZ_FNAME)
+	if ((Memc[database] == EOS) || (image[1] == EOS)) {
+	    call sfree (sp)
+	    return
+	}
+
+	# Map the database file name replacing special characters with '_'.
+	call sprintf (Memc[str], SZ_LINE, "ap%s")
+	    call pargstr (image)
+	for (i=str; Memc[i] != EOS; i = i + 1)
+	    switch (Memc[i]) {
+	    case '[', ':', ',',']','*',' ', '/':
+		Memc[i] = '_'
+	    }
+	dt = dtmap1 (Memc[database], Memc[str], NEW_FILE)
+
+	# Write aperture entries for all apertures.
+	for (j = 0; j < naps; j = j + 1) {
+	    ap = Memi[aps+j]
+
+	    call dtptime (dt)
+	    call dtput (dt, "begin\taperture %s %d %g %g\n")
+	        call pargstr (image)
+		call pargi (AP_ID(ap))
+	        call pargr (AP_CEN(ap, 1))
+	        call pargr (AP_CEN(ap, 2))
+	    if (AP_TITLE(ap) != NULL) {
+	        call dtput (dt, "\ttitle\t%s\n")
+		    call pargstr (Memc[AP_TITLE(ap)])
+	    }
+	    call dtput (dt, "\timage\t%s\n")
+	        call pargstr (image)
+	    call dtput (dt, "\taperture\t%d\n")
+	        call pargi (AP_ID(ap))
+	    call dtput (dt, "\tbeam\t%d\n")
+	        call pargi (AP_BEAM(ap))
+	    call dtput (dt, "\tcenter\t%g %g\n")
+	        call pargr (AP_CEN(ap, 1))
+	        call pargr (AP_CEN(ap, 2))
+	    call dtput (dt, "\tlow\t%g %g\n")
+	        call pargr (AP_LOW(ap, 1))
+	        call pargr (AP_LOW(ap, 2))
+	    call dtput (dt, "\thigh\t%g %g\n")
+	        call pargr (AP_HIGH(ap, 1))
+	        call pargr (AP_HIGH(ap, 2))
+	    if (AP_IC(ap) != NULL) {
+		call dtput (dt, "\tbackground\n")
+		call dtput (dt, "\t\txmin %g\n")
+		    call pargr (ic_getr (AP_IC(ap), "xmin"))
+		call dtput (dt, "\t\txmax %g\n")
+		    call pargr (ic_getr (AP_IC(ap), "xmax"))
+		call dtput (dt, "\t\tfunction %s\n")
+		    call ic_gstr (AP_IC(ap), "function", Memc[str], SZ_LINE)
+		    call pargstr (Memc[str])
+		call dtput (dt, "\t\torder %d\n")
+		    call pargi (ic_geti (AP_IC(ap), "order"))
+		call dtput (dt, "\t\tsample %s\n")
+		    call ic_gstr (AP_IC(ap), "sample", Memc[str], SZ_LINE)
+		    call pargstr (Memc[str])
+		call dtput (dt, "\t\tnaverage %d\n")
+		    call  pargi (ic_geti (AP_IC(ap), "naverage"))
+		call dtput (dt, "\t\tniterate %d\n")
+		    call  pargi (ic_geti (AP_IC(ap), "niterate"))
+		call dtput (dt, "\t\tlow_reject %g\n")
+		    call  pargr (ic_getr (AP_IC(ap), "low"))
+		call dtput (dt, "\t\thigh_reject %g\n")
+		    call  pargr (ic_getr (AP_IC(ap), "high"))
+		call dtput (dt, "\t\tgrow %g\n")
+		    call  pargr (ic_getr (AP_IC(ap), "grow"))
+	    }
+
+	    # Write out the curve.
+	    call dtput (dt, "\taxis\t%d\n")
+	        call pargi (AP_AXIS(ap))
+	    ncoeffs = cvstati (AP_CV(ap), CVNSAVE)
+	    call malloc (coeffs, ncoeffs, TY_REAL)
+	    call cvsave (AP_CV(ap), Memr[coeffs])
+	    call dtput (dt, "\tcurve\t%d\n")
+	        call pargi (ncoeffs)
+	    do i = 1, ncoeffs {
+	        call dtput (dt, "\t\t%g\n")
+		    call pargr (Memr[coeffs+i-1])
+	    }
+	    call mfree (coeffs, TY_REAL)
+
+	    call dtput (dt, "\n")
+	}
+	call dtunmap (dt)
+
+	# Log the write operation unless the output file is "last".
+	if (strne (image, "last")) {
+	    call sprintf (Memc[str], SZ_LINE,
+		"DATABASE - %d apertures for %s written to %s")
+	        call pargi (naps)
+	        call pargstr (image)
+	        call pargstr (Memc[database])
+	    call ap_log (Memc[str], YES, YES, NO)
+	    call appstr ("ansdbwrite1", "no")
+	}
+
+	call sfree (sp)
+end
+
+
+# AP_DBREAD - Get aperture information from the database.
+# If no apertures are found then the input apertures are unchanged.
+# The database is obtained with a CL query.
+
+procedure ap_dbread (image, aps, naps)
+
+char	image[ARB]		# Image
+pointer	aps			# Apertures
+int	naps			# Number of apertures
+
+int	i, j, n, ncoeffs
+pointer	sp, database, str, ap, dt, coeffs
+
+bool	strne()
+int	dtgeti()
+real	dtgetr()
+pointer	dtmap1()
+
+errchk	dtmap1
+
+begin
+	# Return if the database or image are undefined.
+	call smark (sp)
+	call salloc (database, SZ_FNAME, TY_CHAR)
+	call clgstr ("database", Memc[database], SZ_FNAME)
+
+	if ((Memc[database] == EOS) || (image[1] == EOS)) {
+	    call sfree (sp)
+	    return
+	}
+
+	# Set the aperture database file name and map it.
+	# The file name is "ap" appended with the image name with the
+	# special image section characters replaced by '_'.
+	call salloc (str, SZ_LINE, TY_CHAR)
+	call sprintf (Memc[str], SZ_LINE, "ap%s")
+	    call pargstr (image)
+	for (i=str; Memc[i] != EOS; i = i + 1)
+	    switch (Memc[i]) {
+	    case '[', ':', ',',']','*',' ', '/':
+		Memc[i] = '_'
+	    }
+
+	# If an error occurs return the error.
+	dt = dtmap1 (Memc[database], Memc[str], READ_ONLY)
+
+	# Read through the database finding records matching the input image.
+	n = naps
+	naps = 0
+	do i = 1, DT_NRECS(dt) {
+
+	    call dtgstr (dt, i, "image", Memc[str], SZ_LINE)
+	    if (strne (Memc[str], image))
+		next
+
+	    # If an aperture is found delete any input apertures.
+	    if (naps == 0)
+		for (j = 0; j < n; j = j + 1)
+		    call ap_free (Memi[aps+j])
+
+	    if (mod (naps, 100) == 0)
+		call realloc (aps, naps+100, TY_POINTER)
+
+	    call ap_alloc (ap)
+	    ifnoerr (call dtgstr (dt, i, "title", Memc[str], SZ_LINE)) {
+		call malloc (AP_TITLE(ap), SZ_APTITLE, TY_CHAR)
+		call strcpy (Memc[str], Memc[AP_TITLE(ap)], SZ_APTITLE)
+	    }
+	    AP_ID(ap) = dtgeti (dt, i, "aperture")
+	    iferr (AP_BEAM(ap) = dtgeti (dt, i, "beam"))
+		AP_BEAM(ap) = AP_ID(ap)
+	    call dtgstr (dt, i, "center", Memc[str], SZ_LINE)
+	    call sscan (Memc[str])
+	    call gargr (AP_CEN(ap, 1))
+	    call gargr (AP_CEN(ap, 2))
+	    call dtgstr (dt, i, "low", Memc[str], SZ_LINE)
+	    call sscan (Memc[str])
+	    call gargr (AP_LOW(ap, 1))
+	    call gargr (AP_LOW(ap, 2))
+	    call dtgstr (dt, i, "high", Memc[str], SZ_LINE)
+	    call sscan (Memc[str])
+	    call gargr (AP_HIGH(ap, 1))
+	    call gargr (AP_HIGH(ap, 2))
+	    ifnoerr (call dtgstr (dt, i, "background", Memc[str], SZ_LINE)) {
+		call ic_open (AP_IC(ap))
+		call ic_putr (AP_IC(ap), "xmin", dtgetr (dt, i, "xmin"))
+		call ic_putr (AP_IC(ap), "xmax", dtgetr (dt, i, "xmax"))
+		call dtgstr (dt, i, "function", Memc[str], SZ_LINE)
+		call ic_pstr (AP_IC(ap), "function", Memc[str])
+		call ic_puti (AP_IC(ap), "order", dtgeti (dt, i, "order"))
+		call dtgstr (dt, i, "sample", Memc[str], SZ_LINE)
+		call ic_pstr (AP_IC(ap), "sample", Memc[str])
+		call ic_puti (AP_IC(ap), "naverage", dtgeti (dt, i, "naverage"))
+		call ic_puti (AP_IC(ap), "niterate", dtgeti (dt, i, "niterate"))
+		call ic_putr (AP_IC(ap), "low", dtgetr (dt, i, "low_reject"))
+		call ic_putr (AP_IC(ap), "high", dtgetr (dt, i, "high_reject"))
+		call ic_putr (AP_IC(ap), "grow", dtgetr (dt, i, "grow"))
+	    }
+
+	    AP_AXIS(ap) = dtgeti (dt, i, "axis")
+	    ncoeffs = dtgeti (dt, i, "curve")
+	    call malloc (coeffs, ncoeffs, TY_REAL)
+	    call dtgar (dt, i, "curve", Memr[coeffs], ncoeffs, ncoeffs)
+	    call cvrestore (AP_CV(ap), Memr[coeffs])
+	    call mfree (coeffs, TY_REAL)
+
+	    Memi[aps+naps] = ap
+	    naps = naps + 1
+	}
+	call dtunmap (dt)
+
+	# Log the read operation.
+	call sprintf (Memc[str], SZ_LINE,
+	    "DATABASE  - %d apertures read for %s from %s")
+	    call pargi (naps)
+	    call pargstr (image)
+	    call pargstr (Memc[database])
+	call ap_log (Memc[str], YES, YES, NO)
+
+	# If no apertures were found then reset the number to the input value.
+	if (naps == 0)
+	    naps = n
+	else
+	    call appstr ("ansdbwrite1", "no")
+
+	call sfree (sp)
+end
+
+
+# AP_DBACCESS - Check if a database file can be accessed.
+# This does not check the contents of the file.
+# The database is obtained with a CL query.
+
+int procedure ap_dbaccess (image)
+
+char	image[ARB]		# Image
+int	access			# Database file access?
+
+int	i
+pointer	sp, database, str, dt
+pointer	dtmap1()
+errchk	dtmap1
+
+begin
+	call smark (sp)
+	call salloc (database, SZ_FNAME, TY_CHAR)
+	call clgstr ("database", Memc[database], SZ_FNAME)
+
+	if ((Memc[database] != EOS) && (image[1] != EOS)) {
+	    # Set the aperture database file name and map it.
+	    # The file name is "ap" appended with the image name with the
+	    # special image section characters replaced by '_'.
+	    call salloc (str, SZ_LINE, TY_CHAR)
+	    call sprintf (Memc[str], SZ_LINE, "ap%s")
+		call pargstr (image)
+	    for (i=str; Memc[i] != EOS; i = i + 1)
+		switch (Memc[i]) {
+		case '[', ':', ',',']','*',' ', '/':
+		    Memc[i] = '_'
+		}
+
+	    iferr {
+		dt = dtmap1 (Memc[database], Memc[str], READ_ONLY)
+		call dtunmap (dt)
+		access = YES
+	    } then
+		access = NO
+	} else
+	    access = NO
+
+	call sfree (sp)
+	return (access)
+end
diff --git a/noao/twodspec/apextract/apdebug.par b/noao/twodspec/apextract/apdebug.par
new file mode 100644
index 00000000..6b9fc8f9
--- /dev/null
+++ b/noao/twodspec/apextract/apdebug.par
@@ -0,0 +1,156 @@
+dispaxis = 2
+database = "database"
+verbose = yes
+logfile = "logfile"
+plotfile = " "
+
+apall1.input = 
+apall1.nfind = 
+apall1.output = ""
+apall1.apertures = ""
+apall1.format = "multispec"
+apall1.references = ""
+apall1.profiles = ""
+apall1.interactive = yes
+apall1.find = yes
+apall1.recenter = no
+apall1.resize = no
+apall1.edit = yes
+apall1.trace = yes
+apall1.fittrace = no
+apall1.extract = yes
+apall1.extras = yes
+apall1.review = no
+apall1.line = INDEF
+apall1.nsum = 10
+apall1.lower = -5.
+apall1.upper = 5.
+apall1.apidtable = ""
+apall1.b_function = "chebyshev"
+apall1.b_order = 1
+apall1.b_sample = "-10:-6,6:10"
+apall1.b_naverage = -3
+apall1.b_niterate = 0
+apall1.b_low_reject = 3.
+apall1.b_high_reject = 3.
+apall1.b_grow = 0.
+apall1.width = 5.
+apall1.radius = 10.
+apall1.threshold = 0.
+apall1.minsep = 5.
+apall1.maxsep = 1000.
+apall1.order = "increasing"
+apall1.aprecenter = ""
+apall1.npeaks = INDEF
+apall1.shift = yes
+apall1.llimit = INDEF
+apall1.ulimit = INDEF
+apall1.ylevel = 0.1
+apall1.peak = yes
+apall1.bkg = yes
+apall1.r_grow = 0.
+apall1.avglimits = no
+apall1.t_nsum = 10
+apall1.t_step = 10
+apall1.t_width = 5.
+apall1.t_nlost = 3
+apall1.t_function = "legendre"
+apall1.t_order = 2
+apall1.t_sample = "*"
+apall1.t_naverage = 1
+apall1.t_niterate = 0
+apall1.t_low_reject = 3.
+apall1.t_high_reject = 3.
+apall1.t_grow = 0.
+apall1.background = "none"
+apall1.skybox = 1
+apall1.weights = "none"
+apall1.pfit = "fit1d"
+apall1.clean = no
+apall1.saturation = INDEF
+apall1.readnoise = "0."
+apall1.gain = "1."
+apall1.lsigma = 4.
+apall1.usigma = 4.
+apall1.nsubaps = 1
+
+apall1.e_output = 
+apall1.e_profiles = 
+apall1.dbwrite = "yes"
+apall1.initialize = yes
+apall1.nclean = 0.5
+apall1.niterate = 5
+apall1.polysep = 0.90
+apall1.polyorder = 10
+
+apall1.ansclobber = "no"
+apall1.ansclobber1 = "no"
+apall1.ansdbwrite = "yes"
+apall1.ansdbwrite1 = "yes"
+apall1.ansedit = "yes"
+apall1.ansextract = "yes"
+apall1.ansfind = "yes"
+apall1.ansfit = "yes"
+apall1.ansfitscatter = "yes"
+apall1.ansfitsmooth = "yes"
+apall1.ansfitspec = "yes"
+apall1.ansfitspec1 = "yes"
+apall1.ansfittrace = "yes"
+apall1.ansfittrace1 = "yes"
+apall1.ansflat = "yes"
+apall1.ansnorm = "yes"
+apall1.ansrecenter = "yes"
+apall1.ansresize = "yes"
+apall1.ansreview = "yes"
+apall1.ansreview1 = "yes"
+apall1.ansscat = "yes"
+apall1.anssmooth = "yes"
+apall1.anstrace = "yes"
+
+apall1.ansclobber.p_mode = "h"
+apall1.ansclobber1.p_mode = "h"
+apall1.ansdbwrite.p_mode = "h"
+apall1.ansdbwrite1.p_mode = "h"
+apall1.ansedit.p_mode = "h"
+apall1.ansextract.p_mode = "h"
+apall1.ansfind.p_mode = "h"
+apall1.ansfit.p_mode = "h"
+apall1.ansfitscatter.p_mode = "h"
+apall1.ansfitsmooth.p_mode = "h"
+apall1.ansfitspec.p_mode = "h"
+apall1.ansfitspec1.p_mode = "h"
+apall1.ansfittrace.p_mode = "h"
+apall1.ansfittrace1.p_mode = "h"
+apall1.ansflat.p_mode = "h"
+apall1.ansnorm.p_mode = "h"
+apall1.ansrecenter.p_mode = "h"
+apall1.ansresize.p_mode = "h"
+apall1.ansreview.p_mode = "h"
+apall1.ansreview1.p_mode = "h"
+apall1.ansscat.p_mode = "h"
+apall1.anssmooth.p_mode = "h"
+apall1.anstrace.p_mode = "h"
+
+apall1.ansclobber.p_prompt = "h"
+apall1.ansclobber1.p_prompt = "h"
+apall1.ansdbwrite.p_prompt = "h"
+apall1.ansdbwrite1.p_prompt = "h"
+apall1.ansedit.p_prompt = "h"
+apall1.ansextract.p_prompt = "h"
+apall1.ansfind.p_prompt = "h"
+apall1.ansfit.p_prompt = "h"
+apall1.ansfitscatter.p_prompt = "h"
+apall1.ansfitsmooth.p_prompt = "h"
+apall1.ansfitspec.p_prompt = "h"
+apall1.ansfitspec1.p_prompt = "h"
+apall1.ansfittrace.p_prompt = "h"
+apall1.ansfittrace1.p_prompt = "h"
+apall1.ansflat.p_prompt = "h"
+apall1.ansnorm.p_prompt = "h"
+apall1.ansrecenter.p_prompt = "h"
+apall1.ansresize.p_prompt = "h"
+apall1.ansreview.p_prompt = "h"
+apall1.ansreview1.p_prompt = "h"
+apall1.ansscat.p_prompt = "h"
+apall1.anssmooth.p_prompt = "h"
+apall1.anstrace.p_prompt = "h"
diff --git a/noao/twodspec/apextract/apdefault.par b/noao/twodspec/apextract/apdefault.par
new file mode 100644
index 00000000..7868197c
--- /dev/null
+++ b/noao/twodspec/apextract/apdefault.par
@@ -0,0 +1,14 @@
+# APDEFAULT
+
+lower,r,h,-5.,,,Lower aperture limit relative to center
+upper,r,h,5.,,,Upper aperture limit relative to center
+apidtable,s,h,"",,,"Aperture ID table
+"
+b_function,s,h,"chebyshev","chebyshev|legendre|spline1|spline3",,Background function
+b_order,i,h,1,1,,Background function order
+b_sample,s,h,"-10:-6,6:10",,,Background sample regions
+b_naverage,i,h,-3,,,Background average or median
+b_niterate,i,h,0,0,,Background rejection iterations
+b_low_reject,r,h,3.,0.,,Background lower rejection sigma
+b_high_reject,r,h,3.,0.,,Background upper rejection sigma
+b_grow,r,h,0.,0.,,Background rejection growing radius
diff --git a/noao/twodspec/apextract/apdefault.x b/noao/twodspec/apextract/apdefault.x
new file mode 100644
index 00000000..bea10f7c
--- /dev/null
+++ b/noao/twodspec/apextract/apdefault.x
@@ -0,0 +1,42 @@
+include	<imhdr.h>
+include	"apertures.h"
+
+# AP_DEFAULT -- Create a default aperture.
+# The aperture ID, beam, axis, and the aperture center in both dimensions
+# are specified.  The aperture limits along the dispersion axis are set to
+# the full size of the image while along the dispersion axis they are queried.
+# The default offset curve is a constant zero curve.
+
+procedure ap_default (im, apid, apbeam, apaxis, apcenter, dispcenter, ap)
+
+pointer	im		# IMIO pointer
+int	apid		# Aperture ID
+int	apbeam		# Aperture beam number
+int	apaxis		# Aperture axis
+real	apcenter	# Center along the aperture axis
+real	dispcenter	# Center along the dispersion axis	
+pointer	ap		# Aperture pointer
+
+int	dispaxis
+real	apgetr()
+
+begin
+	dispaxis = mod (apaxis, 2) + 1
+
+	call ap_alloc (ap)
+	AP_ID(ap) = apid
+	AP_BEAM(ap) = apbeam
+	AP_AXIS(ap) = apaxis
+	AP_CEN(ap, apaxis) = apcenter
+	AP_LOW(ap, apaxis) = apgetr ("lower") 
+	if (IS_INDEFR(AP_LOW(ap,apaxis)))
+	    call error (1, "INDEF not allowed (lower)")
+	AP_HIGH(ap, apaxis) = apgetr ("upper") 
+	if (IS_INDEFR(AP_HIGH(ap,apaxis)))
+	    call error (1, "INDEF not allowed (upper)")
+	AP_CEN(ap, dispaxis) = dispcenter
+	AP_LOW(ap, dispaxis) = 1 - AP_CEN(ap, dispaxis)
+	AP_HIGH(ap, dispaxis) = IM_LEN(im, dispaxis) - AP_CEN(ap, dispaxis)
+	call ap_cvset (NULL, ap)
+	call ap_icset (NULL, ap, IM_LEN(im, apaxis))
+end
diff --git a/noao/twodspec/apextract/apdelete.x b/noao/twodspec/apextract/apdelete.x
new file mode 100644
index 00000000..1956a331
--- /dev/null
+++ b/noao/twodspec/apextract/apdelete.x
@@ -0,0 +1,23 @@
+# AP_DELETE -- Delete the specified aperture and return a new current aperture.
+
+procedure ap_delete (current, aps, naps)
+
+int	current			# Return current aperture index
+pointer	aps[ARB]		# Aperture data
+int	naps			# Number of apertures
+
+int	i
+
+begin
+	if (current < 1)
+	    return
+
+	call ap_free (aps[current])
+	for (i = current; i < naps; i = i + 1)
+	    aps[i] = aps[i+1]
+
+	aps[naps] = NULL
+
+	naps = naps - 1
+	current = min (naps, current)
+end
diff --git a/noao/twodspec/apextract/apdemos/apdemo1.cl b/noao/twodspec/apextract/apdemos/apdemo1.cl
new file mode 100644
index 00000000..04704034
--- /dev/null
+++ b/noao/twodspec/apextract/apdemos/apdemo1.cl
@@ -0,0 +1,14 @@
+# Create demo data if needed.
+artdata
+mkexample ("multifiber", "apdemo", errors=no, verbose=yes, list=no)
+bye
+imdelete ("apdemo.ms.??h", verify=no)
+
+# Set parameters.
+verbose = yes
+logfile = ""
+plotfile = ""
+unlearn apall
+
+# Execute playback.
+stty (playback="apdemos$apdemo1.dat", verify=no, delay=500)
diff --git a/noao/twodspec/apextract/apdemos/apdemo1.dat b/noao/twodspec/apextract/apdemos/apdemo1.dat
new file mode 100644
index 00000000..c718b423
--- /dev/null
+++ b/noao/twodspec/apextract/apdemos/apdemo1.dat
@@ -0,0 +1,14 @@
+\O=NOAO/IRAF V2.10DEVELOP valdes@puppis Tue 13:26:44 31-Jul-90
+\T=gterm
+\G=gterm
+apall\n
+apdemo\n
+\n
+4\n
+\n
+no\n
+\n
+no\n
+no\n
+\n
+no\n
diff --git a/noao/twodspec/apextract/apdemos/apdemos.cl b/noao/twodspec/apextract/apdemos/apdemos.cl
new file mode 100644
index 00000000..3b040ef7
--- /dev/null
+++ b/noao/twodspec/apextract/apdemos/apdemos.cl
@@ -0,0 +1,17 @@
+procedure apdemos (demo)
+
+int	demo		{prompt="Demo number"}
+
+begin
+	int	demonum
+	file	demofile
+
+	if ($nargs == 0)
+	    type ("apdemos$apdemos.men")
+	demonum = demo
+	demofile = "apdemos$apdemo" // demonum // ".cl"
+	if (access (demofile))
+	    cl (< demofile)
+	else
+	    error (1, "Invalid demo number " // demonum)
+end
diff --git a/noao/twodspec/apextract/apdemos/apdemos.men b/noao/twodspec/apextract/apdemos/apdemos.men
new file mode 100644
index 00000000..4e0ca6e1
--- /dev/null
+++ b/noao/twodspec/apextract/apdemos/apdemos.men
@@ -0,0 +1,3 @@
+	MENU of APEXTRACT Demonstrations
+
+	1 - Simple demo of APALL
diff --git a/noao/twodspec/apextract/apdemos/apdemosdb/aplast b/noao/twodspec/apextract/apdemos/apdemosdb/aplast
new file mode 100644
index 00000000..93f85ea9
--- /dev/null
+++ b/noao/twodspec/apextract/apdemos/apdemosdb/aplast
@@ -0,0 +1,111 @@
+# Wed 11:02:05 22-Aug-90
+begin	aperture last 1 60.57419 256.
+	image	last
+	aperture	1
+	beam	1
+	center	60.57419 256.
+	low	-3.111816 -255.
+	high	2.949428 256.
+	background
+		xmin -100.
+		xmax 100.
+		function chebyshev
+		order 1
+		sample -10:-6,6:10
+		naverage -3
+		niterate 0
+		low_reject 3.
+		high_reject 3.
+		grow 0.
+	axis	1
+	curve	6
+		2.
+		2.
+		1.
+		512.
+		0.02659256
+		0.5026957
+
+# Wed 11:02:05 22-Aug-90
+begin	aperture last 2 70.70531 256.
+	image	last
+	aperture	2
+	beam	2
+	center	70.70531 256.
+	low	-2.926423 -255.
+	high	2.899426 256.
+	background
+		xmin -100.
+		xmax 100.
+		function chebyshev
+		order 1
+		sample -10:-6,6:10
+		naverage -3
+		niterate 0
+		low_reject 3.
+		high_reject 3.
+		grow 0.
+	axis	1
+	curve	6
+		2.
+		2.
+		1.
+		512.
+		-0.002646168
+		0.5073752
+
+# Wed 11:02:05 22-Aug-90
+begin	aperture last 3 80.78613 256.
+	image	last
+	aperture	3
+	beam	3
+	center	80.78613 256.
+	low	-2.953142 -255.
+	high	2.970872 256.
+	background
+		xmin -100.
+		xmax 100.
+		function chebyshev
+		order 1
+		sample -10:-6,6:10
+		naverage -3
+		niterate 0
+		low_reject 3.
+		high_reject 3.
+		grow 0.
+	axis	1
+	curve	6
+		2.
+		2.
+		1.
+		512.
+		0.01349655
+		0.5075101
+
+# Wed 11:02:05 22-Aug-90
+begin	aperture last 4 90.8806 256.
+	image	last
+	aperture	4
+	beam	4
+	center	90.8806 256.
+	low	-2.823333 -255.
+	high	2.915152 256.
+	background
+		xmin -100.
+		xmax 100.
+		function chebyshev
+		order 1
+		sample -10:-6,6:10
+		naverage -3
+		niterate 0
+		low_reject 3.
+		high_reject 3.
+		grow 0.
+	axis	1
+	curve	6
+		2.
+		2.
+		1.
+		512.
+		0.022075
+		0.5081324
diff --git a/noao/twodspec/apextract/apedit.key b/noao/twodspec/apextract/apedit.key
new file mode 100644
index 00000000..d28a8856
--- /dev/null
+++ b/noao/twodspec/apextract/apedit.key
@@ -0,0 +1,74 @@
+       		 APEXTRACT CURSOR KEY SUMMARY
+
+?  Print help             j  Set beam number        u  Set upper limit(s)
+a  Toggle all flag        l  Set lower limit(s)     w  Window graph
+b  Set background(s)      m  Mark aperture          y  Y level limit(s)
+c  Center aperture(s)     n  New uncentered ap.     z  Resize aperture(s)
+d  Delete aperture(s)     o  Order ap. numbers      I  Interrupt
+e  Extract spectra        q  Quit                   +  Next aperture
+f  Find apertures         r  Redraw graph           -  Previous aperture
+g  Recenter aperture(s)   s  Shift aperture(s)      .  Nearest aperture
+i  Set aperture ID        t  Trace aperture(s)      
+
+       		 APEXTRACT COLON COMMAND SUMMARY
+
+:apertures      :center         :npeaks         :show           :t_width
+:apidtable      :clean          :nsubaps        :skybox         :threshold
+:avglimits      :database       :nsum           :t_function     :title
+:b_function     :extras         :order          :t_grow         :ulimit
+:b_grow         :gain           :parameters     :t_high_reject  :upper
+:b_high_reject  :image          :peak           :t_low_reject   :usigma
+:b_low_reject   :line           :plotfile       :t_naverage     :weights
+:b_naverage     :llimit         :r_grow         :t_niterate     :width
+:b_niterate     :logfile        :radius         :t_nlost        :write
+:b_order        :lower          :read           :t_nsum         :ylevel
+:b_sample       :lsigma         :readnoise      :t_order        
+:background     :maxsep         :saturation     :t_sample       
+:bkg            :minsep         :shift          :t_step         
+
+		APEXTRACT CURSOR KEYS
+
+?    Print help
+a    Toggle the ALL flag
+b an Set background fitting parameters
+c an Center aperture(s)
+d an Delete aperture(s)
+e an Extract spectra (see APSUM)
+f    Find apertures up to the requested number (see APFIND)
+g an Recenter aperture(s) (see APRECENTER)
+i  n Set aperture ID
+j  n Set aperture beam number
+l ac Set lower limit of current aperture at cursor position
+m    Define and center a new aperture on the profile near the cursor
+n    Define a new aperture centered at the cursor
+o  n Enter desired aperture number for cursor selected aperture and remaining
+     apertures are reordered using apidtable and maxsep parameters
+     (see APFIND for ordering algorithm)
+q    Quit
+r    Redraw the graph
+s an Shift the center(s) of the current aperture to the cursor position
+t ac Trace aperture positions (see APTRACE)
+u ac Set upper limit of current aperture at cursor position
+w    Window the graph using the window cursor keys
+y an Set aperture limits to intercept the data at the cursor y position
+z an Resize aperture(s) (see APRESIZE)
+.  n Select the aperture nearest the cursor to be the current aperture
++  c Select the next aperture (in ID) to be the current aperture
+-  c Select the previous aperture (in ID) to be the current aperture
+I    Interrupt task immediately.  Database information is not saved.
+
+The letter a following the key indicates if all apertures are affected when
+the ALL flag is set.  The letter c indicates that the key affects the
+current aperture while the letter n indicates that the key affects the
+aperture whose center is nearest the cursor.
+
+			APEXTRACT COLON COMMANDS
+
+:show [file]	   Print a list of the apertures (default file is STDOUT)
+:parameters [file] Print current parameter values (default file is STDOUT)
+:read [name]       Read apertures from database (default to the current image)
+:write [name]      Write apertures to database (default to the current image)
+
+The remaining colon commands are task parameters and print the current
+value if no value is given or reset the current value to that specified.
+Use :parameters to see current parameter values.
diff --git a/noao/twodspec/apextract/apedit.par b/noao/twodspec/apextract/apedit.par
new file mode 100644
index 00000000..8e6c15f5
--- /dev/null
+++ b/noao/twodspec/apextract/apedit.par
@@ -0,0 +1,17 @@
+# APEDIT
+
+input,s,a,,,,List of input images to edit
+apertures,s,h,"",,,Apertures
+references,s,h,"",,,"Reference images
+"
+interactive,b,h,yes,,,Run task interactively?
+find,b,h,no,,,Find apertures?
+recenter,b,h,no,,,Recenter apertures?
+resize,b,h,no,,,Resize apertures?
+edit,b,h,yes,,,"Edit apertures?
+"
+line,i,h,INDEF,1,,Dispersion line
+nsum,i,h,10,,,Number of dispersion lines to sum or median
+width,r,h,5.,0.,,Profile centering width
+radius,r,h,10.,,,Profile centering radius
+threshold,r,h,0.,0.,,Detection threshold for profile centering
diff --git a/noao/twodspec/apextract/apedit.x b/noao/twodspec/apextract/apedit.x
new file mode 100644
index 00000000..e7170e92
--- /dev/null
+++ b/noao/twodspec/apextract/apedit.x
@@ -0,0 +1,604 @@
+include	<error.h>
+include	<gset.h>
+include	<imhdr.h>
+include	<mach.h>
+include	<pkg/gtools.h>
+include	"apertures.h"
+
+define	HELP	"noao$twodspec/apextract/apedit.key"
+define	PROMPT	"apextract options"
+
+# Sort flags
+define	ORDER	"|increasing|decreasing|"
+
+# AP_EDIT -- Define and edit apertures.  This is the main interactive
+# procedure for manipulating apertures.  The selected dispersion line
+# is graphed with possible summing of neighboring lines and then
+# cursor keys are used to define new apertures or edit existing apertures.
+# Note that the value of line may be changed.
+
+procedure ap_edit (image, line, nsum, aps, naps)
+
+char	image[SZ_FNAME]		# Image to be edited
+int	line			# Dispersion line
+int	nsum			# Number of dispersion lines to sum
+
+pointer	aps			# Aperture pointers
+int	naps			# Number of apertures
+
+char	cmd[SZ_LINE]
+int	i, npts, apaxis, dispaxis, statline
+int	current, newgraph, newim, newdata, all, wcs, key, apid, apbeam
+real	center, low, high, wx, wy
+bool	peak
+pointer	im, imdata, title
+pointer	sp, x, wts, apdef, gp, gt, ic_gt, cv, str, output, profiles, ids
+
+int	gt_gcur(), apgwrd(), scan(), nscan()
+real	ap_cveval(), ap_center()
+bool	ap_answer()
+pointer	gt_init()
+errchk	ap_getdata, ap_gopen, ap_default
+
+define	new_	10
+define	beep_	99
+
+begin
+	# Query user.
+	call smark (sp)
+	call salloc (str, SZ_LINE, TY_CHAR)
+	call sprintf (Memc[str], SZ_LINE, "Edit apertures for %s?")
+    	    call pargstr (image)
+	if (!ap_answer ("ansedit", Memc[str])) {
+	    call sfree (sp)
+	    return
+	}
+
+	# Set flags.
+	all = NO
+
+	# Get user aperture ID's
+	call ap_gids (ids)
+
+	# Map the image and get the image data.
+new_	call ap_getdata (image, line, nsum, im, imdata, npts, apaxis, title)
+	newdata = NO
+	newim = NO
+
+	# Allocate additional memory.
+	call salloc (x, npts, TY_REAL)
+	call salloc (wts, npts, TY_REAL)
+	call salloc (output, SZ_FNAME, TY_CHAR)
+	call salloc (profiles, SZ_FNAME, TY_CHAR)
+
+	# Set the default aperture and delete apertures which do not have
+	# the correct aperture axis.
+	call ap_default (im, INDEFI, 1, apaxis, INDEFR, real (line), apdef)
+	dispaxis = mod (apaxis, 2) + 1
+	for (i = naps; i > 0; i = i - 1)
+	    if (AP_AXIS(Memi[aps+i-1]) != apaxis)
+	        call ap_delete (i, Memi[aps], naps)
+
+	# Set up the graphics.
+	call ap_gopen (gp)
+	gt = gt_init()
+	call gt_sets (gt, GTTITLE, "Define and Edit Apertures")
+	call gt_sets (gt, GTPARAMS, Memc[title])
+
+	# Enter cursor loop.
+	current = min (1, naps)
+	key = 'r'
+	wy = INDEF
+	repeat {
+	    statline = NO
+
+	    # For those keys affecting the nearest aperture set the current
+	    # aperture to be the aperture nearest the cursor.
+	    switch (key) {
+	    case '.','b','c','d','e','g','i','j','o','t','y','z':
+		# The current aperture is the one nearest the cursor.
+	        call ap_nearest (current, line, Memi[aps], naps, wx)
+	    }
+
+	    # Set the current aperture values.
+	    call ap_values (current, Memi[aps], line, apid,
+		apbeam, center, low, high)
+
+	    # Select the operation to be performed.
+	    switch (key) {
+	    case '?': # Print help text.
+		call gpagefile (gp, HELP, PROMPT)
+
+	    case ':': # Colon commands.
+		if (cmd[1] == '/')
+		    call gt_colon (cmd, gp, gt, newgraph)
+		else {
+		    call ap_colon (cmd, im, gp, apdef, aps, naps, current,
+			image, line, nsum, all, newgraph, newim, newdata,
+			statline)
+		    if (newim == YES)
+			break
+		    if (newdata == YES) {
+			call mfree (imdata, TY_REAL)
+			call mfree (title, TY_CHAR)
+			call imunmap (im)
+			call ap_getdata (image, line, nsum, im, imdata, npts,
+			    apaxis, title)
+			call gt_sets (gt, GTPARAMS, Memc[title])
+			newdata = NO
+			newgraph = YES
+		    }
+		    call ap_free (apdef)
+		    iferr (call ap_default (im, INDEFI, 1, apaxis, INDEFR,
+			real (line), apdef))
+			call erract (EA_WARN)
+		}
+
+	    case '.': # Select current aperture.  This has been done already.
+		;
+
+	    case '+': # Go to next aperture.
+		current = min (naps, current + 1)
+
+	    case '-': # Go to last aperture.
+		current = min (naps, max (1, current - 1))
+
+	    case 'a': # Toggle all flag
+		if (all == NO)
+		    all = YES
+		else
+		    all = NO
+
+	    case 'b': # Set background fitting parameters.
+		if (current == 0)
+		   goto beep_
+
+		do i = 1, npts {
+		    Memr[x+i-1] = i - center
+		    Memr[wts+i-1] = 1
+		}
+
+		if (ic_gt == NULL) {
+		    ic_gt = gt_init()
+		    call gt_sets (ic_gt, GTTYPE, "line")
+	    	    wx = max (10., high - low)
+	    	    call gt_setr (ic_gt, GTXMIN, low - 2 * wx)
+	    	    call gt_setr (ic_gt, GTXMAX, high + 2 * wx)
+		}
+
+		call sprintf (Memc[str], SZ_LINE,
+		    "Set Background Subtraction for Aperture %d")
+		    call pargi (apid)
+		call gt_sets (ic_gt, GTTITLE, Memc[str])
+
+		if (AP_IC(Memi[aps+current-1]) == NULL)
+		    call ap_icset (apdef, Memi[aps+current-1], npts)
+
+		call icg_fit (AP_IC(Memi[aps+current-1]), gp, "gcur",
+		    ic_gt, cv, Memr[x], Memr[imdata], Memr[wts], npts)
+		call cvfree (cv)
+
+		# Set background limits
+		call ap_icset (Memi[aps+current-1], Memi[aps+current-1], npts)
+
+		if ((naps > 1) && (all == YES))
+		   do i = 1, naps
+		       if (i != current)
+			   call ap_icset (Memi[aps+current-1],
+			       Memi[aps+i-1], npts)
+		newgraph = YES
+
+	    case 'c': # Center current aperture or all apertures.
+		if (current == 0)
+		    goto beep_
+
+		if ((naps == 1) || (all == NO)) {
+		    center = ap_center (center, Memr[imdata], npts)
+		    if (!IS_INDEF(center))
+			call ap_update (gp, Memi[aps+current-1], line, apid,
+			    apbeam, center, low, high)
+		} else {
+		    do i = 1, naps {
+		        call ap_values (i, Memi[aps], line, apid,
+			    apbeam, center, low, high)
+			center = ap_center (center, Memr[imdata], npts)
+			if (!IS_INDEF(center))
+			    call ap_update (gp, Memi[aps+i-1], line, apid,
+				apbeam, center, low, high)
+		    }
+		}
+
+	    case 'd': # Delete apertures
+		if (current == 0)
+		    goto beep_
+
+		call gseti (gp, G_PLTYPE, 0)
+		if ((naps == 1) || (all == NO)) {
+		    call ap_gmark (gp, line, Memi[aps+current-1], 1)
+		    call ap_delete (current, Memi[aps], naps)
+		    call ap_gscur (current, gp, line, Memi[aps], wy)
+	            call ap_values (current, Memi[aps], line, apid,
+			apbeam, center, low, high)
+		} else {
+		    do i = 1, naps {
+			call ap_gmark (gp, line, Memi[aps+i-1], 1)
+			call ap_free (Memi[aps+i-1])
+		    }
+		    naps = 0
+		    current = 0
+		}
+		call gseti (gp, G_PLTYPE, 1)
+
+	    case 'e': # Sum extraction
+		if (current == 0)
+		    goto beep_
+
+		call imunmap (im)
+		call apgstr ("e_output", Memc[output], SZ_FNAME)
+		call apgstr ("e_profiles", Memc[profiles], SZ_FNAME)
+	        call apgstr ("format", Memc[str], SZ_LINE)
+		call appstr ("ansreview", "yes")
+		call appstr ("ansreview1", "yes")
+		call appstr ("ansclobber", "yes")
+		call appstr ("ansclobber1", "yes")
+		if (all == NO)
+	            call ap_extract (image, Memc[output],
+			Memc[str], Memc[profiles], Memi[aps+current-1], 1)
+		else
+	            call ap_extract (image, Memc[output],
+			Memc[str], Memc[profiles], Memi[aps], naps)
+		call ap_getdata (image, line, nsum, im, imdata, npts, apaxis,
+		    title)
+		newgraph = YES
+
+	    case 'f': # Find apertures
+		if (current == 0)
+		    call ap_findnew (line, Memr[imdata], npts,
+			apdef, aps, naps)
+		else
+		    call ap_findnew (line, Memr[imdata], npts,
+			Memi[aps+current-1], aps, naps)
+		call ap_gmark (gp, line, Memi[aps], naps)
+		current = naps
+
+	    case 'g': # Apply recenter algorithm.
+		if (current == 0)
+		    goto beep_
+
+		call imunmap (im)
+		if (all == NO) {
+		    call gseti (gp, G_PLTYPE, 0)
+		    call ap_gmark (gp, line, Memi[aps+current-1], 1)
+		    call ap_recenter (image, line, nsum,
+			Memi[aps+current-1], 1, YES)
+		    call gseti (gp, G_PLTYPE, 1)
+		    call ap_gmark (gp, line, Memi[aps+current-1], 1)
+		    call ap_values (current, Memi[aps], line, apid,
+			apbeam, center, low, high)
+		} else {
+		    call gseti (gp, G_PLTYPE, 0)
+		    do i = 1, naps
+		        call ap_gmark (gp, line, Memi[aps+i-1], 1)
+		    call ap_recenter (image, line, nsum, Memi[aps], naps, YES)
+		    call gseti (gp, G_PLTYPE, 1)
+		    do i = 1, naps
+		        call ap_gmark (gp, line, Memi[aps+i-1], 1)
+		}
+		call ap_getdata (image, line, nsum, im, imdata, npts, apaxis,
+		    title)
+
+	    case 'i': # Set aperture ID
+		if (current == 0)
+		    goto beep_
+
+		repeat {
+		    call printf ("Aperture (%d) = ")
+		        call pargi (AP_ID(Memi[aps+current-1]))
+		    call flush (STDOUT)
+		    if (scan () != EOF) {
+		        call gargi (apid)
+		        if (nscan() == 1) {
+			    if (apid < 1) {
+				call printf (
+				"Aperture numbers < 1 are not allowed: ")
+			    } else {
+				for (i=1; i<=naps; i=i+1)
+				    if (i != current &&
+					apid == AP_ID(Memi[aps+i-1]))
+					break
+				if (i <= naps) {
+				    call printf ("Aperture %d already used: ")
+					call pargi (apid)
+				} else {
+				    AP_ID(Memi[aps+current-1]) = apid
+				    call ap_ids (Memi[aps+current-1], 1, ids)
+				    break
+				}
+			    }
+			} else
+			    break
+		    }
+		}
+
+	    case 'j': # Set beam number
+		if (current == 0)
+		    goto beep_
+
+		repeat {
+		    call printf ("Beam (%d) = ")
+			call pargi (AP_BEAM(Memi[aps+current-1]))
+		    call flush (STDOUT)
+		    if (scan () != EOF) {
+			call gargi (apbeam)
+			if (nscan() == 1) {
+#			    if (apbeam < 0) {
+#				call printf (
+#				    "Beam numbers < 0 are not allowed: ")
+#			    } else {
+				if (all == NO)
+				    AP_BEAM(Memi[aps+current-1]) = apbeam
+				else
+				    do i = 1, naps
+					AP_BEAM(Memi[aps+i-1]) = apbeam
+				break
+#			    }
+			} else
+			    break
+		    }
+		}
+
+	    case 'l': # Set the low limit.
+		if (current == 0)
+		    goto beep_
+
+		wx = wx - center
+		if ((naps == 1) || (all == NO))
+		    call ap_update (gp, Memi[aps+current-1], line, apid,
+			apbeam, center, wx, high)
+		else {
+		    do i = 1, naps {
+			call ap_values (i, Memi[aps], line, apid,
+			    apbeam, center, low, high)
+			call ap_update (gp, Memi[aps+i-1], line, apid,
+			    apbeam, center, wx, high)
+		    }
+		}
+
+	    case 'm', 'n': # Define a new aperture.
+		if (mod (naps, 100) == 0)
+		    call realloc (aps, naps+100, TY_POINTER)
+
+		if (key == 'm')
+		    wx = ap_center (wx, Memr[imdata], npts)
+
+		if (!IS_INDEF(wx)) {
+		    naps = naps + 1
+		    if (naps > 1)
+			call ap_copy (Memi[aps+current-1], Memi[aps+naps-1])
+		    else
+			call ap_copy (apdef, Memi[aps+naps-1])
+
+		    AP_ID(Memi[aps+naps-1]) = INDEFI
+		    AP_CEN(Memi[aps+naps-1], apaxis) = wx -
+		    	ap_cveval (AP_CV(Memi[aps+naps-1]), real (line))
+		    AP_CEN(Memi[aps+naps-1], dispaxis) = line
+		    AP_LOW(Memi[aps+naps-1], dispaxis) =
+			1 - AP_CEN(Memi[aps+naps-1], dispaxis)
+		    AP_HIGH(Memi[aps+naps-1], dispaxis) = IM_LEN(im, dispaxis) -
+			AP_CEN(Memi[aps+naps-1], dispaxis)
+
+		    call ap_icset (Memi[aps+naps-1], Memi[aps+naps-1], npts)
+
+		    current = naps
+		    i = apgwrd ("order", cmd, SZ_LINE, ORDER)
+		    call ap_sort (current, Memi[aps], naps, i)
+		    call ap_ids (Memi[aps], naps, ids)
+		    call ap_titles (Memi[aps+current-1], 1, ids)
+
+		    call ap_values (current, Memi[aps], line, apid,
+			apbeam, center, low, high)
+		    call ap_gmark (gp, line, Memi[aps+current-1], 1)
+		}
+
+	    case 'o': # Order the aperture and beam numbers
+		if (naps == 0)
+		    goto beep_
+
+		do i = 1, naps
+		    if (i != current)
+		        AP_ID(Memi[aps+i-1]) = INDEFI
+
+		call printf ("Aperture (%d) = ")
+		    call pargi (AP_ID(Memi[aps+current-1]))
+		call flush (STDOUT)
+		if (scan () != EOF) {
+		    call gargi (apid)
+		    if (nscan() == 1) {
+			AP_ID(Memi[aps+current-1]) = apid
+			AP_BEAM(Memi[aps+current-1]) = apid
+		    }
+		}
+
+		i = apgwrd ("order", cmd, SZ_LINE, ORDER)
+		call ap_sort (current, Memi[aps], naps, i)
+		call ap_ids (Memi[aps], naps, ids)
+
+		# Reset the titles
+		do i = 1, naps
+		    if (AP_TITLE(Memi[aps+i-1]) != NULL)
+			call mfree (AP_TITLE(Memi[aps+i-1]), TY_CHAR)
+		call ap_titles (Memi[aps], naps, ids)
+			
+		newgraph = YES
+
+	    case 'r': # Redraw the graph.
+		newgraph = YES
+
+	    case 's': # Shift apertures
+		if (current == 0)
+		    goto beep_
+
+		call printf ("Center aperture %d (no)? ")
+		    call pargi (AP_ID(Memi[aps+current-1]))
+		call flush (STDOUT)
+		if (scan () != EOF) {
+		    call gargb (peak)
+		    if (nscan() == 1 && peak) {
+		        wy = ap_center (wx, Memr[imdata], npts)
+		        if (!IS_INDEF(wy))
+			    wx = wy
+		    }
+		}
+
+		if ((naps == 1) || (all == NO))
+		    call ap_update (gp, Memi[aps+current-1], line, apid,
+			apbeam, wx, low, high)
+		else {
+		    wx = wx - center
+		    do i = 1, naps {
+		        call ap_values (i, Memi[aps], line, apid,
+			    apbeam, center, low, high)
+			call ap_update (gp, Memi[aps+i-1], line, apid,
+			    apbeam, center + wx, low, high)
+		    }
+		}
+
+	    case 't': # Trace.
+		if (current == 0)
+		    goto beep_
+
+		call imunmap (im)
+		call appstr ("ansfittrace1", "yes")
+		if (all == NO)
+		    call ap_trace (image, line, Memi[aps+current-1], 1, YES)
+		else
+		    call ap_trace (image, line, Memi[aps], naps, YES)
+		call ap_getdata (image, line, nsum, im, imdata, npts, apaxis,
+		    title)
+		newgraph = YES
+
+	    case 'u': # Set the upper limit.
+		if (current == 0)
+		    goto beep_
+
+		wx = wx - center
+		if ((naps == 1) || (all == NO))
+		    call ap_update (gp, Memi[aps+current-1], line, apid,
+			apbeam, center, low, wx)
+		else {
+		    do i = 1, naps {
+			call ap_values (i, Memi[aps], line, apid,
+			    apbeam, center, low, high)
+			call ap_update (gp, Memi[aps+i-1], line, apid,
+			    apbeam, center, low, wx)
+		    }
+		}
+
+	    case 'w': # Window the graph.
+		call gt_window (gt, gp, "gcur", newgraph)
+
+	    case 'y': # Set aperture limits at the y level.
+		if (current == 0)
+		    goto beep_
+
+		if ((naps == 1) || (all == NO)) {
+		    low = -npts
+		    high = npts
+		    call ap_ylevel (Memr[imdata], npts, wy, false, false, 0.,
+			center, low, high)
+		    call ap_update (gp, Memi[aps+current-1], line, apid,
+			apbeam, center, low, high)
+		} else {
+		    do i = 1, naps {
+		        call ap_values (i, Memi[aps], line, apid,
+			    apbeam, center, low, high)
+		        low = -npts
+		        high = npts
+			call ap_ylevel (Memr[imdata], npts, wy, false, false,
+			    0., center, low, high)
+			call ap_update (gp, Memi[aps+i-1], line, apid,
+			    apbeam, center, low, high)
+		    }
+		}
+
+	    case 'z': # Apply resize algorithm.
+		if (current == 0)
+		    goto beep_
+
+		call imunmap (im)
+		if (all == NO) {
+		    call gseti (gp, G_PLTYPE, 0)
+		    call ap_gmark (gp, line, Memi[aps+current-1], 1)
+		    call ap_resize (image, line, nsum,
+			Memi[aps+current-1], 1, YES)
+		    call gseti (gp, G_PLTYPE, 1)
+		    call ap_gmark (gp, line, Memi[aps+current-1], 1)
+		    call ap_values (current, Memi[aps], line, apid,
+			apbeam, center, low, high)
+		} else {
+		    call gseti (gp, G_PLTYPE, 0)
+		    do i = 1, naps
+		        call ap_gmark (gp, line, Memi[aps+i-1], 1)
+		    call ap_resize (image, line, nsum, Memi[aps], naps, YES)
+		    call gseti (gp, G_PLTYPE, 1)
+		    do i = 1, naps
+		        call ap_gmark (gp, line, Memi[aps+i-1], 1)
+		}
+		call ap_getdata (image, line, nsum, im, imdata, npts, apaxis,
+		    title)
+
+	    case 'I': # Interrupt
+		call fatal (0, "Interrupt")
+
+	    default: # Ring bell for unrecognized commands.
+beep_		call printf ("Invalid or unrecognized command\007")
+		statline = YES
+	    }
+
+	    # Update the graph if needed.
+	    if (newgraph == YES) {
+		call ap_graph (gp, gt, Memr[imdata], npts, line,
+		    Memi[aps], naps)
+	        newgraph = NO
+	    }
+
+	    # Set the cursor to the current aperture and print the current
+	    # aperture on the status line.
+	    call ap_gscur (current, gp, line, Memi[aps], wy)
+	    if (statline == NO)
+	        call ap_print (current, line, all, Memi[aps])
+
+	} until (gt_gcur ("gcur", wx, wy, wcs, key, cmd, SZ_LINE) == EOF)
+
+	# Log the editing operation.
+	call sprintf (Memc[str], SZ_LINE, "EDIT - %d apertures edited for %s")
+       	    call pargi (naps)
+       	    call pargstr (image)
+	call ap_log (Memc[str], YES, NO, NO)
+
+	# Free memory.
+	call ap_fids (ids)
+	call mfree (imdata, TY_REAL)
+	call mfree (title, TY_CHAR)
+	call imunmap (im)
+	call gt_free (gt)
+	call gt_free (ic_gt)
+	call ap_free (apdef)
+
+	# If a new image is desired loop back.
+	if (newim == YES) {
+	    call clgstr ("database", Memc[output], SZ_LINE)
+	    call sprintf (Memc[str], SZ_LINE,
+	        "Write apertures for %s to %s")
+	        call pargstr (image)
+	        call pargstr (Memc[output])
+	    if (ap_answer ("ansdbwrite", Memc[str]))
+	        call ap_dbwrite (image, aps, naps)
+	    call strcpy (cmd, image, SZ_FNAME)
+	    call ap_dbread (image, aps, naps)
+	    goto new_
+	}
+
+	call appstr ("ansdbwrite1", "yes")
+	call sfree (sp)
+end
diff --git a/noao/twodspec/apextract/apertures.h b/noao/twodspec/apextract/apertures.h
new file mode 100644
index 00000000..aeb4bd94
--- /dev/null
+++ b/noao/twodspec/apextract/apertures.h
@@ -0,0 +1,32 @@
+# Aperture Definition
+
+# Aperture structure --  The aperture structure consists of an integer
+# identification number, a title,  the center of the aperture, the lower
+# and upper limits of the aperture measured relative to the center, the
+# axis for a curve giving an offset relative to the center, the CURFIT
+# pointer describing the curve and an ICFIT pointer for background
+# subtraction.  The center and lower and upper limits are pairs of real
+# numbers in the order column value and line value.  The edges of the
+# aperture are given by:
+# 
+#	low column = center column + low column offset + curve (line)
+#	high column = center column + high column offset + curve (line)
+#	low line = center line + low line offset + curve (column)
+#	high line = center line + high line offset + curve (column)
+#
+# The curve is aplied to the column positions if the curve axis is 1 and
+# to the line positions if the curve axis is 2.
+
+define	AP_LEN		13			# Length of aperture structure
+define	SZ_APTITLE	60			# Length of aperture title
+
+define	AP_ID		Memi[$1]		# Aperture ID
+define	AP_TITLE	Memi[$1+1]		# Pointer to title
+define	AP_BEAM		Memi[$1+2]		# Aperture beam number
+define	AP_CEN		Memr[P2R($1+3+$2-1)]	# Aperture center
+define	AP_LOW		Memr[P2R($1+5+$2-1)]	# Aperture limit
+define	AP_HIGH		Memr[P2R($1+7+$2-1)]	# Aperture limit
+define	AP_AXIS		Memi[$1+9]		# Axis for curve
+define	AP_CV		Memi[$1+10]		# Aperture curve
+define	AP_IC		Memi[$1+11]		# ICFIT pointer
+define	AP_SELECT	Memi[$1+12]		# Aperture selected?
diff --git a/noao/twodspec/apextract/apextract.cl b/noao/twodspec/apextract/apextract.cl
new file mode 100644
index 00000000..035ce189
--- /dev/null
+++ b/noao/twodspec/apextract/apextract.cl
@@ -0,0 +1,33 @@
+#{ APEXTRACT -- Aperture extraction package
+
+package apextract
+
+task	apall,
+	apedit,
+	apfind,
+	apfit,
+	apflatten,
+	apmask,
+	apnormalize,
+	aprecenter,
+	apresize,
+	apscatter,
+	apnoise,
+	apsum,
+	aptrace		= "apextract$x_apextract.e"
+task	apparams	= "apextract$apparams.par"
+task	apall1		= "apextract$apall1.par"
+task	apfit1		= "apextract$apfit1.par"
+task	apflat1		= "apextract$apflat1.par"
+task	apnorm1		= "apextract$apnorm1.par"
+task	apnoise1	= "apextract$apnoise1.par"
+task	apdefault	= "apextract$apdefault.par"
+task	apscat1		= "apextract$apscat1.par"
+task	apscat2		= "apextract$apscat2.par"
+
+set	apdemos		= "apextract$apdemos/"
+task	apdemos.pkg	= "apdemos$apdemos.cl"
+ 
+hidetask apparams, apall1, apfit1, apflat1, apnorm1, apscat1, apscat2, apnoise1
+
+clbye
diff --git a/noao/twodspec/apextract/apextract.hd b/noao/twodspec/apextract/apextract.hd
new file mode 100644
index 00000000..ad17623d
--- /dev/null
+++ b/noao/twodspec/apextract/apextract.hd
@@ -0,0 +1,27 @@
+# Help directory for the APEXTRACT package.
+
+$doc		 = "./doc/"
+
+apall		hlp=doc$apall.hlp
+apdefault	hlp=doc$apdefault.hlp
+apdemos		hlp=doc$apdemos.hlp
+apedit		hlp=doc$apedit.hlp
+apfind		hlp=doc$apfind.hlp
+apfit		hlp=doc$apfit.hlp
+apflatten	hlp=doc$apflatten.hlp
+apmask		hlp=doc$apmask.hlp
+apnoise		hlp=doc$apnoise.hlp
+apnormalize	hlp=doc$apnormalize.hlp
+aprecenter	hlp=doc$aprecenter.hlp
+apresize	hlp=doc$apresize.hlp
+apscatter	hlp=doc$apscatter.hlp
+apsum		hlp=doc$apsum.hlp
+aptrace		hlp=doc$aptrace.hlp
+
+package		hlp=doc$apextract.hlp,		 sys=doc$apextractsys.hlp
+apbackground	hlp=doc$apbackground.hlp
+approfiles	hlp=doc$approfiles.hlp
+apvariance	hlp=doc$apvariance.hlp
+extras		hlp=doc$apextras.hlp
+
+revisions	sys=Revisions
diff --git a/noao/twodspec/apextract/apextract.men b/noao/twodspec/apextract/apextract.men
new file mode 100644
index 00000000..c0db0005
--- /dev/null
+++ b/noao/twodspec/apextract/apextract.men
@@ -0,0 +1,23 @@
+          apall - Extract 1D spectra (all parameters in one task)
+      apdefault - Set the default aperture parameters and apidtable
+        apdemos - Various tutorial demonstrations
+         apedit - Edit apertures interactively
+	 apfind - Automatically find spectra and define apertures
+	  apfit - Fit 2D spectra and output the fit, difference, or ratio
+      apflatten - Remove overall spectral and profile shapes from flat fields
+        apnoise - Compute and examine noise characteristics of spectra
+         apmask - Create and IRAF pixel list mask of the apertures
+    apnormalize - Normalize 2D apertures by 1D functions
+     aprecenter - Recenter apertures
+       apresize - Resize apertures
+      apscatter - Fit and subtract scattered light
+          apsum - Extract 1D spectra
+	aptrace - Trace positions of spectra
+
+		ADDITIONAL HELP TOPICS
+
+   apbackground - Background subtraction algorithms
+     approfiles - Profile determination algorithms
+     apvariance - Extractions, variance weighting, cleaning, and noise model
+	 extras - Information about the extra information in 3D images
+        package - Package parameters and general description of package
diff --git a/noao/twodspec/apextract/apextract.par b/noao/twodspec/apextract/apextract.par
new file mode 100644
index 00000000..8b153ec8
--- /dev/null
+++ b/noao/twodspec/apextract/apextract.par
@@ -0,0 +1,8 @@
+# APEXTRACT Package
+
+dispaxis,i,h,2,1,2,"Dispersion axis (1=along lines, 2=along columns)"
+database,f,h,"database",,,Database
+verbose,b,h,no,,,Verbose output?
+logfile,s,h,"",,,Text log file
+plotfile,s,h,"",,,Plot file
+version,s,h,"APEXTRACT V3.0: August 1990"
diff --git a/noao/twodspec/apextract/apextract.x b/noao/twodspec/apextract/apextract.x
new file mode 100644
index 00000000..176ab251
--- /dev/null
+++ b/noao/twodspec/apextract/apextract.x
@@ -0,0 +1,1834 @@
+include	<error.h>
+include	<imhdr.h>
+include	<mach.h>
+include	<math/iminterp.h>
+include	<pkg/gtools.h>
+include	"apertures.h"
+
+# Background fitting types
+define	BACKGROUND	"|none|average|median|minimum|fit|"
+define	B_NONE		1
+define	B_AVERAGE	2
+define	B_MEDIAN	3
+define	B_MINIMUM	4
+define	B_FIT		5
+
+# Weight types
+define	WEIGHTS		"|none|variance|"
+define	W_NONE		1
+define	W_VARIANCE	2
+
+# Profile fitting algorithms
+define	P_FIT		"|fit1d|fit2d|"
+define	P_FIT1D		1
+define	P_FIT2D		2
+
+# Output formats
+define	FORMATS		"|onedspec|multispec|echelle|strip|normalize|flatten\
+			|ratio|difference|fit|noise|"
+define	ONEDSPEC	1	# Individual 1D spectra
+define	MULTISPEC	2	# Multiple spectra
+define	ECHELLE		3	# Echelle spectra
+define	STRIP		4	# Strip spectra
+define	NORM		5	# Normalized spectra
+define	FLAT		6	# Flat spectra
+define	RATIO		7	# Ratio of data to model
+define	DIFF		8	# Difference of data and model
+define	FIT		9	# Model
+define	NOISE		10	# Noise calculation
+
+
+# AP_EXTRACT -- Extract spectra by a weighted sum across the apertures.
+# 
+# This routine does clobber checks on the output images, manages the I/O
+# from the input image in as big of pieces as possible, and loops through
+# each aperture calling routines to determine the sky, do any fitting and
+# extraction, and output the spectra.
+# The extraction may be either a simple, unweighted extraction
+# which is very fast or a weighted extraction using CCD noise
+# parameters.  The weights require dividing out the basic spectrum and
+# smoothing the 2D spectral profile.  The general approach of variance
+# weighting is described by K. Horne (PASP V98, P609, 1986).  The
+# smoothing has two algorithms, fitting columns or lines parallel to the
+# dispersion axis for nearly aligned spectra or fitting a 2D function
+# using a method given by T. Marsh (PASP V101, P1032, 1989).  The profile
+# may also be used to reject cosmic rays by iteration.
+#
+# The extractions require enough memory to get at least one aperture plus
+# background (if needed) into memory.  If possible the region containing
+# all the apertures is read into memory.  The target maximum amount of
+# memory is set by the maxmimum size returned by BEGMEM and the
+# appropriate working set size is requested.  The optimal size can be
+# tuned through BEGMEM, which references a machine dependent include
+# file, if needed.  The algorithm should work well (minimize I/O as well
+# as paging) in all cases but very large image formats with highly tilted
+# spectra (where aperture extraction along the image axes is not really
+# appropriate).  These memory requirements were chosen to minimize image
+# I/O and because the variance weighted algorithms need to make multiple
+# passes through the image.  In principle simple, unweighted extractions
+# with no sky smoothing can be done sequentially but this was not done in
+# order to use nearly the same code for both weighted and unweighted
+# cases.
+#
+# If using variance weighting and a profile image is given then it is used
+# to determine the profile which is then applied to the target image
+# during the final extraction.  If the same profile image is used multiple
+# times it would be more efficient to store the profile but then issues
+# of consistency arise.  For now this possible feature is not implemented.
+
+procedure ap_extract (input, output, format, profiles, aps, naps)
+
+char	input[SZ_FNAME]		# Input image
+char	output[SZ_FNAME]	# Output image (optional root name)
+char	format[SZ_LINE]		# Output format
+char	profiles[SZ_FNAME]	# Profile filename (optional)
+pointer	aps[ARB]		# Apertures
+int	naps			# Number of apertures
+
+# CL parameters
+int	fmt			# Output format
+int	bkg			# Background type
+int	weights			# Extraction weights
+int	pfit			# Profile fitting algorithm
+bool	clean			# Reject cosmic rays?
+real	gain			# Photon/DN gain
+real	rdnoise			# Read out noise
+int	nsubaps			# Number of subapertures
+int	interptype		# Edge interpolation type
+
+int	i, j, k, napsex, aaxis, baxis, namax, na, nb, na1, interpbuf
+int	amin, amax, bmin, bmax
+int	new_size, old_size, max_size, best_size
+real	cmin, cmax, xmin, xmax, shift
+pointer	sp, str, bkgstr, wtstr, cleanstr, apsex
+pointer	a, b, c, astart, spec, specsky, specsig, raw, profile
+pointer	a1, a2, b1, b2, c1, c2, im, pim, ap, cv, ic, dbuf, pbuf, sbuf, svar, ptr
+pointer	asi
+
+bool	clgetb(), apgetb(), strne()
+int	apgeti(), apgwrd(), begmem(), ap_check()
+real	apgimr(), ap_cveval(), ic_getr()
+pointer	ap_immap(), imgs2r(), imgl2r()
+errchk	salloc, malloc, ap_immap, imgs2r, imgl2r, asiinit
+errchk	ap_check, ap_skyeval, ap_profile, ap_variance, ap_output, apgimr
+
+begin
+	call smark (sp)
+	call salloc (str, SZ_LINE, TY_CHAR)
+
+	napsex = 0
+	do i = 1, naps
+	    if (AP_SELECT(aps[i]) == YES)
+		napsex = napsex + 1
+	if (napsex == 0) {
+	    call sprintf (Memc[str], SZ_LINE,
+	        "EXTRACT - No apertures defined for %s")
+		call pargstr (input)
+	    call ap_log (Memc[str], YES, NO, YES)
+	    call sfree (sp)
+	    return
+	}
+
+	call salloc (bkgstr, SZ_FNAME, TY_CHAR)
+	call salloc (wtstr, SZ_FNAME, TY_CHAR)
+	call salloc (cleanstr, SZ_FNAME, TY_CHAR)
+	call salloc (apsex, napsex, TY_POINTER)
+
+	# Select apertures to extract and fix possible limit error.
+	napsex = 0
+	do i = 1, naps {
+	    if (AP_LOW(aps[i],1) > AP_HIGH(aps[i],1)) {
+		xmax = AP_LOW(aps[i],1)
+		AP_LOW(aps[i],1) = AP_HIGH(aps[i],1)
+		AP_HIGH(aps[i],1) = xmax
+	    }
+	    if (AP_LOW(aps[i],2) > AP_HIGH(aps[i],2)) {
+		xmax = AP_LOW(aps[i],2)
+		AP_LOW(aps[i],2) = AP_HIGH(aps[i],2)
+		AP_HIGH(aps[i],2) = xmax
+	    }
+	    if (AP_SELECT(aps[i]) == NO)
+		next
+	    Memi[apsex+napsex] = aps[i]
+	    napsex = napsex + 1
+	}
+
+	# Get CL parameters
+	bkg = apgwrd ("background", Memc[bkgstr], SZ_FNAME, BACKGROUND)
+	pfit = apgwrd ("pfit", Memc[str], SZ_LINE, P_FIT)
+	clean = apgetb ("clean")
+	if (clean)
+	    call strcpy ("yes", Memc[cleanstr], SZ_FNAME)
+	else
+	    call strcpy ("no", Memc[cleanstr], SZ_FNAME)
+	nsubaps = apgeti ("nsubaps")
+	interptype = II_LINEAR
+
+	# Do clobber checking.  Return if output exists and not clobbering.
+	call apgstr ("ansclobber", Memc[str], SZ_LINE)
+	call appstr ("ansclobber1", Memc[str])
+	fmt = ap_check (input, output, format, Memi[apsex], napsex, nsubaps)
+	if (fmt == 0) {
+	    call sfree (sp)
+	    return
+	}
+
+	# Force weights depending on format or cleaning.
+	switch (fmt) {
+	case FLAT, RATIO, DIFF, FIT, NOISE:
+	    weights = W_VARIANCE
+	default:
+	    if (clean) {
+		call strcpy ("variance", Memc[wtstr], SZ_FNAME)
+		weights = W_VARIANCE
+	    } else
+	        weights = apgwrd ("weights", Memc[wtstr], SZ_FNAME, WEIGHTS)
+	}
+
+	if (clgetb ("verbose")) {
+	    call printf ("Extracting apertures ...\n")
+	    call flush (STDOUT)
+	}
+	    
+	# Open input image and profile image if given.  Set axis parameters
+	# where 'a' is the aperture axis across the dispersion and 'b' is
+	# along the dispersion.
+
+	im = ap_immap (input, aaxis, baxis)
+	namax = IM_LEN(im, aaxis)
+	nb = IM_LEN(im, baxis)
+
+	pim = NULL
+	if (strne(profiles,input) && weights==W_VARIANCE && profiles[1]!=EOS) {
+	    pim = ap_immap (profiles, i, j)
+	    if (i!=aaxis||j!=baxis||IM_LEN(pim,i)!=namax||IM_LEN(pim,j)!=nb) {
+		call imunmap (pim)
+		call imunmap (im)
+		call sfree (sp)
+		call error (1,
+		    "Input image and profile image are not compatible")
+	    }
+	    call sprintf (Memc[str], SZ_LINE,
+	        "EXTRACT - Using profile image %s for %s")
+		call pargstr (profiles)
+		call pargstr (input)
+	    call ap_log (Memc[str], YES, YES, NO)
+	}
+
+	# Determine limits of apertures for use in defining memory requirements
+	# and I/O.
+
+	call salloc (a, 2 * napsex, TY_INT)
+	call salloc (b, 2 * napsex, TY_INT)
+	call salloc (c, 2 * napsex, TY_REAL)
+	a1 = a - 1
+	a2 = a1 + napsex
+	b1 = b - 1
+	b2 = b1 + napsex
+	c1 = c - 1
+	c2 = c1 + napsex
+
+	# Initialize image interpolator for edge pixel weighting.
+	switch (interptype) {
+	case II_LINEAR:
+	    interpbuf = 2
+	case II_POLY3:
+	    interpbuf = 3
+	case II_SINC:
+	    interpbuf = 16
+	default:
+	    interpbuf = 0
+	}
+	if (interptype > 0)
+	    call asiinit (asi, interptype)
+	else
+	    asi = NULL
+
+	na1 = 0
+	do i = 1, napsex {
+	    ap = Memi[apsex+i-1]
+	    cv = AP_CV(ap)
+	    ic = AP_IC(ap)
+
+	    # Dispersion axis limits
+	    bmin = min (nb, max (1, nint (AP_CEN(ap,baxis)+AP_LOW(ap,baxis))))
+	    bmax = max (1, min (nb, nint (AP_CEN(ap,baxis)+AP_HIGH(ap,baxis))))
+
+	    # Aperture axis shifts
+	    if (cv != NULL) {
+		cmin = MAX_REAL
+	        cmax = -MAX_REAL
+	        do j = bmin, bmax {
+	           shift = ap_cveval (cv, real (j))
+	           cmin = min (cmin, shift)
+	           cmax = max (cmax, shift)
+	        }
+	    } else {
+		cmin = 0.
+		cmax = 0.
+	    }
+
+	    # Background region limits.
+	    xmin = AP_LOW(ap,aaxis)
+	    xmax = AP_HIGH(ap,aaxis)
+	    if (weights == W_VARIANCE) {
+		xmin = xmin - 2
+		xmax = xmax + 2
+	    }
+	    xmin = xmin - interpbuf
+	    xmax = xmax + interpbuf
+	    if (bkg != B_NONE && AP_IC(ap) != NULL) {
+		xmin = min (xmin, ic_getr (ic, "xmin"))
+		xmax = max (xmax, ic_getr (ic, "xmax"))
+	    }
+
+	    Memi[a1+i] = min (namax, max (1, nint (AP_CEN(ap,aaxis)+xmin+cmin)))
+	    Memi[a2+i] = max (1, min (namax, nint (AP_CEN(ap,aaxis)+xmax+cmax)))
+	    Memi[b1+i] = bmin
+	    Memi[b2+i] = bmax
+	    Memr[c1+i] = cmin
+	    Memr[c2+i] = cmax
+	}
+	call alimi (Memi[a], 2*napsex, amin, amax)
+	call alimi (Memi[b], 2*napsex, bmin, bmax)
+
+	# The maximum size of the image in memory is 80% of the maximum
+	# working set size returned by begmem or 40% if a profile image
+	# is used.  Later I/O may exceed this since at least one
+	# aperture + background is needed in memory.
+
+	new_size = begmem (0, old_size, max_size)
+	namax = (amax - amin + 1)
+	nb = (bmax - bmin + 1)
+	if (pim == NULL)
+	    namax = min (namax, int (0.8 * max_size / SZ_REAL / nb))
+	else
+	    namax = min (namax, int (0.8 * max_size / SZ_REAL / nb / 2))
+	best_size = 1.2 * namax * nb * SZ_REAL
+	new_size = begmem (best_size, old_size, max_size)
+
+	# Allocate auxilary memory.  Some memory is only dependent on the
+	# number of dispersion points and subapertures and is the same for
+	# all apertures.  Other memory, such as the sky and profile depend on
+	# the aperture widths and tilts which may vary.  The input data is
+	# expected to have the aperture axis along the first dimension.  If
+	# the image is in this orientation then the IMIO buffer is used.
+	# Otherwise sequential I/O is used and transposed into the allocated
+	# memory.
+
+	iferr {
+	    call salloc (astart, nb, TY_INT)
+	    call salloc (spec, nsubaps * nb, TY_REAL)
+	    if (weights == W_VARIANCE) {
+		call salloc (raw, nsubaps * nb, TY_REAL)
+		call salloc (specsig, nsubaps * nb, TY_REAL)
+	    } else {
+		raw = NULL
+		specsig = NULL
+	    }
+	    profile = NULL
+	    if (aaxis == 2) {
+		call calloc (dbuf, namax * nb, TY_REAL)
+		if (pim != NULL)
+		    call calloc (pbuf, namax * nb, TY_REAL)
+	    }
+
+	    # For variance weighting the computations are done in photon units.
+	    if (weights == W_VARIANCE) {
+		gain = apgimr ("gain", im)
+		rdnoise = apgimr ("readnoise", im)
+	    } else {
+		gain = 1
+		rdnoise = 0
+	    }
+
+	    # Loop through each aperture doing the extractions.
+	    amax = 0
+	    do i = 1, napsex {
+		ap = Memi[apsex+i-1]
+
+		# Check if a new input data buffer is needed.  As many apertures
+		# as possible are read at once within the given memory limits
+		# though at least one aperture must be read.  Do a transpose if
+		# needed.
+
+		if (Memi[a1+i] < amin || Memi[a2+i] > amax) {
+		    amin = Memi[a1+i]
+		    amax = Memi[a2+i]
+		    do j = i,  napsex {
+			amin = min (amin, Memi[a1+j]) 
+			amax = max (amax, Memi[a2+j]) 
+			na = amax - amin + 1
+			if (na > namax)
+			    break
+		    }
+
+		    if (aaxis == 1) {
+			if (fmt == DIFF) {
+			    call mfree (dbuf, TY_REAL)
+			    call malloc (dbuf, na*nb, TY_REAL)
+			    call amovr (Memr[imgs2r(im,amin,amax,bmin,bmax)],
+				Memr[dbuf], na*nb)
+			} else
+			    dbuf = imgs2r (im, amin, amax, bmin, bmax)
+		    } else {
+			if (na > namax) {
+			    call mfree (dbuf, TY_REAL)
+			    namax = na
+			    call calloc (dbuf, namax * nb, TY_REAL)
+			}
+			do j = amin, amax {
+			    sbuf = imgl2r (im, j)
+			    sbuf = sbuf + bmin - 1
+			    ptr = dbuf + j - amin
+			    do k = bmin, bmax {
+				Memr[ptr] = Memr[sbuf]
+				sbuf = sbuf + 1
+				ptr = ptr + na
+			    }
+			}
+		    }
+		    if (pim != NULL) {
+			if (aaxis == 1)
+			    pbuf = imgs2r (pim, amin, amax, bmin, bmax)
+			else {
+			    if (na > namax) {
+				call mfree (pbuf, TY_REAL)
+				namax = na
+				call calloc (pbuf, namax * nb, TY_REAL)
+			    }
+			    do j = amin, amax {
+				sbuf = imgl2r (pim, j)
+				sbuf = sbuf + bmin - 1
+				ptr = pbuf + j - amin
+				do k = bmin, bmax {
+				    Memr[ptr] = Memr[sbuf]
+				    sbuf = sbuf + 1
+				    ptr = ptr + na
+				}
+			    }
+			}
+		    }
+		    if (weights == W_VARIANCE && gain != 1.) {
+			j = na * nb
+			call amulkr (Memr[dbuf], gain, Memr[dbuf], j)
+			if (pim != NULL)
+			    call amulkr (Memr[pbuf], gain, Memr[pbuf], j)
+		    }
+		}
+
+		# To minimize memory a variable integer offset is used to
+		# accomodate the aperture tilts.  The offsets are stored in
+		# the astart array and the width of any one line determined.
+		# If a stored profile is used it is read and it is ASSUMED to
+		# be valid for the input aperture with the same ID.  If no
+		# stored profile is found the profile fitting algorithm
+		# parameter determines whether to fit 1D function along the
+		# image axes (in which case all the profile offsets are the
+		# same) or if the Marsh algorithm for tilted spectra is
+		# used.  In the latter the offsets can be adjusted to mimize
+		# memory and a buffer of two pixels around the aperture is
+		# required by the algorithm.
+
+		if (weights == W_NONE) {
+		    xmin = AP_CEN(ap,aaxis) + AP_LOW(ap,aaxis)
+		    xmax = AP_CEN(ap,aaxis) + AP_HIGH(ap,aaxis)
+		    xmin = xmin - interpbuf
+		    xmax = xmax + interpbuf
+		    na1 = nint (xmax) - nint (xmin) + 1
+		    cv = AP_CV(ap)
+		    do j = bmin, bmax {
+			shift = ap_cveval (cv, real (j))
+			Memi[astart+j-bmin] = nint (xmin + shift)
+		    }
+		} else {
+		    if (pfit == P_FIT1D) {
+			xmin = AP_CEN(ap,aaxis) + AP_LOW(ap,aaxis) + Memr[c1+i]
+			xmax = AP_CEN(ap,aaxis) + AP_HIGH(ap,aaxis) + Memr[c2+i]
+			xmin = xmin - interpbuf
+			xmax = xmax + interpbuf
+			na1 = nint (xmax) - nint (xmin) + 1
+			call amovki (nint (xmin), Memi[astart], nb)
+		    } else if (pfit == P_FIT2D) {
+			xmin = AP_CEN(ap,aaxis) + AP_LOW(ap,aaxis) - 2
+			xmax = AP_CEN(ap,aaxis) + AP_HIGH(ap,aaxis) + 2
+			xmin = xmin - interpbuf
+			xmax = xmax + interpbuf
+			na1 = nint (xmax) - nint (xmin) + 1
+			cv = AP_CV(ap)
+			do j = bmin, bmax {
+			    shift = ap_cveval (cv, real (j))
+			    Memi[astart+j-bmin] = nint (xmin + shift)
+			}
+		    }
+		}
+
+		# Do the sky or background determination if needed.  An array
+		# of the same size as the 2D aperture is returned as well as
+		# a single estimate of the variance in the sky value at each
+		# line based on the fit.  If a profile image is used then the
+		# sky is for the profile image and the object sky is
+		# determined later in order to reuse the sky buffers.
+
+		if (bkg != B_NONE && AP_IC(ap) != NULL) {
+		    call malloc (sbuf, na1 * nb, TY_REAL)
+		    call malloc (svar, nb, TY_REAL)
+		    call malloc (specsky, nsubaps * nb, TY_REAL)
+		    if (pim == NULL)
+			call ap_skyeval (im, ap, dbuf, na, nb, amin, 1,
+			    Memr[sbuf], Memr[svar], Memr[specsky], na1, nb,
+			    Memi[astart], 1, nsubaps, rdnoise)
+		    else
+			call ap_skyeval (pim, ap, pbuf, na, nb, amin, 1,
+			    Memr[sbuf], Memr[svar], Memr[specsky], na1, nb,
+			    Memi[astart], 1, nsubaps, rdnoise)
+		} else {
+		    sbuf = NULL
+		    svar = NULL
+		    specsky = NULL 
+		}
+
+		# Use a quick sum for unweighted extraction.  For weighed
+		# extractions we use either a previously determined profile
+		# or call the profile routine.  If desired the profile is
+		# stored for later use.  Then the variance weighted
+		# extraction routine is called.
+
+		if (weights == W_NONE)
+		    call ap_sum (ap, dbuf, na, nb, amin, 1, sbuf, na1, nb,
+			Memi[astart], 1, Memr[spec], nsubaps, asi)
+		else {
+		    call malloc (profile, na1 * nb, TY_REAL)
+		    if (pim == NULL)
+			call ap_profile (im, ap, dbuf, na, nb, amin, 1, sbuf,
+			    svar, Memr[profile], na1, nb, Memi[astart], 1,
+			    asi)
+		    else {
+			call ap_profile (pim, ap, pbuf, na, nb, amin, 1, sbuf,
+			    svar, Memr[profile], na1, nb, Memi[astart], 1,
+			    asi)
+			if (sbuf != NULL)
+			    call ap_skyeval (im, ap, dbuf, na, nb, amin, 1,
+				Memr[sbuf], Memr[svar], Memr[specsky], na1, nb,
+				Memi[astart], 1, nsubaps, rdnoise)
+		    }
+
+		    call ap_variance (im, ap, dbuf, na, nb, amin, 1, sbuf, svar,
+			Memr[profile], na1, nb, Memi[astart], 1, Memr[spec],
+			Memr[raw], Memr[specsig], nsubaps, asi)
+		}
+
+		# Output the extracted spectrum.  The extras of sky, sigma,
+		# and unweighted spectrum may also be stored.  If the extra
+		# information is not available the pointers will be NULL.
+
+		if (weights == W_VARIANCE && gain != 1.) {
+		    call adivkr (Memr[spec], gain, Memr[spec], nb)
+		    if (raw != NULL)
+			call adivkr (Memr[raw], gain, Memr[raw], nb)
+		    if (specsky != NULL)
+			call adivkr (Memr[specsky], gain, Memr[specsky], nb)
+		    if (specsig != NULL)
+			call adivkr (Memr[specsig], gain, Memr[specsig], nb)
+		    call amulkr (Memr[profile], gain, Memr[profile], nb*na1)
+		}
+
+		call ap_output (input, output, format, Memc[bkgstr],
+		    Memc[wtstr], Memc[cleanstr], gain, im, Memi[apsex], napsex,
+		    i, nsubaps, spec, raw, specsky, specsig, dbuf, na, nb, amin,
+		    1, sbuf, profile, na1, nb, Memi[astart], 1)
+
+		call mfree (profile, TY_REAL)
+		call mfree (sbuf, TY_REAL)
+		call mfree (svar, TY_REAL)
+		call mfree (specsky, TY_REAL)
+	    }
+
+	    # Finish up and restore the working set size.
+	    if (asi != NULL)
+		call asifree (asi)
+	    if (pim != NULL) {
+		if (aaxis == 2)
+		    call mfree (pbuf, TY_REAL)
+		call imunmap (pim)
+	    }
+	    if (aaxis == 2)
+		call mfree (dbuf, TY_REAL)
+	    call imunmap (im)
+	    call fixmem (old_size)
+	    call sfree (sp)
+
+	} then {
+	    call mfree (profile, TY_REAL)
+	    call mfree (sbuf, TY_REAL)
+	    call mfree (svar, TY_REAL)
+	    call mfree (specsky, TY_REAL)
+
+	    if (asi != NULL)
+		call asifree (asi)
+	    if (pim != NULL) {
+		if (aaxis == 2)
+		    call mfree (pbuf, TY_REAL)
+		call imunmap (pim)
+	    }
+	    if (aaxis == 2)
+		call mfree (dbuf, TY_REAL)
+	    call imunmap (im)
+	    call fixmem (old_size)
+	    call sfree (sp)
+
+	    call erract (EA_ERROR)
+	}
+end
+
+
+# AP_CHECK -- Check if output spectra exist.  If the user allows clobbering,
+# delete the spectra.  Return the format.
+
+int procedure ap_check (input, output, format, aps, naps, nsubaps)
+
+char	input[ARB]			# Input image name
+char	output[ARB]			# Output root name
+char	format[ARB]			# Output format
+pointer	aps[naps]			# Apertures
+int	naps				# Number of apertures
+int	nsubaps				# Number of subapertures
+
+int	i, j, fmt
+pointer	sp, name, name1, input1, ksection, ans
+
+int	strdic(), imaccess(), stridxs()
+bool	streq(), ap_answer()
+
+begin
+	call smark (sp)
+	call salloc (name, SZ_LINE, TY_CHAR)
+	call salloc (name1, SZ_LINE, TY_CHAR)
+	call salloc (input1, SZ_LINE, TY_CHAR)
+	call salloc (ksection, SZ_LINE, TY_CHAR)
+	call salloc (ans, SZ_LINE, TY_CHAR)
+
+	fmt = strdic (format, format, SZ_LINE, FORMATS)
+	call imgimage (input, Memc[input1], SZ_LINE)
+
+	switch (fmt) {
+	case MULTISPEC, NORM, FLAT, RATIO, DIFF, FIT:
+	    i = stridxs ("[", Memc[input1])
+	    if (i > 0) {
+		call strcpy (Memc[input1+i-1], Memc[ksection], SZ_LINE)
+		Memc[input1+i-1] = EOS
+	    } else
+		Memc[ksection] = EOS
+	    if (output[1] == EOS)
+	        call strcpy (Memc[input1], Memc[name], SZ_LINE)
+	    else
+	        call strcpy (output, Memc[name], SZ_LINE)
+
+	    switch (fmt) {
+	    case MULTISPEC:
+		if (streq (Memc[input1], Memc[name])) {
+	            call strcat (".ms", Memc[name], SZ_LINE)
+		    call strcat (Memc[ksection], Memc[name], SZ_LINE)
+		}
+	    case NORM:
+		if (streq (Memc[input1], Memc[name])) {
+	            call strcat (".norm", Memc[name], SZ_LINE)
+		    call strcat (Memc[ksection], Memc[name], SZ_LINE)
+		}
+	    case FLAT:
+		if (streq (Memc[input1], Memc[name])) {
+	            call strcat (".flat", Memc[name], SZ_LINE)
+		    call strcat (Memc[ksection], Memc[name], SZ_LINE)
+		}
+	    case RATIO:
+		if (streq (Memc[input1], Memc[name])) {
+	            call strcat (".ratio", Memc[name], SZ_LINE)
+		    call strcat (Memc[ksection], Memc[name], SZ_LINE)
+		}
+	    case DIFF:
+		if (streq (Memc[input1], Memc[name])) {
+	            call strcat (".diff", Memc[name], SZ_LINE)
+		    call strcat (Memc[ksection], Memc[name], SZ_LINE)
+		}
+	    case FIT:
+		if (streq (Memc[input1], Memc[name])) {
+	            call strcat (".fit", Memc[name], SZ_LINE)
+		    call strcat (Memc[ksection], Memc[name], SZ_LINE)
+		}
+	    }
+	    if (imaccess (Memc[name], 0) == YES) {
+		call sprintf (Memc[ans], SZ_LINE,
+		    "Clobber existing output image %s?")
+		    call pargstr (Memc[name])
+		if (ap_answer ("ansclobber1", Memc[ans]))
+		    call imdelete (Memc[name])
+		else {
+		    call sprintf (Memc[ans], SZ_LINE,
+			"EXTRACT - Output spectrum %s already exists")
+			call pargstr (Memc[name])
+		    call ap_log (Memc[ans], YES, NO, YES)
+		    fmt = 0
+		}
+	    }
+	case ECHELLE:
+	    if (output[1] == EOS)
+	        call strcpy (Memc[input1], Memc[name], SZ_LINE)
+	    else
+	        call strcpy (output, Memc[name], SZ_LINE)
+
+	    do i = 1, nsubaps {
+		if (nsubaps == 1)
+		    call strcpy (Memc[name], Memc[name1], SZ_LINE)
+		else {
+		    call sprintf (Memc[name1], SZ_LINE, "%s%0*d")
+			call pargstr (Memc[name])
+			call pargi (int(log10(real(nsubaps)))+1)
+			call pargi (i)
+		}
+		if (streq (Memc[input1], Memc[name])) {
+		    call strcat (".ec", Memc[name1], SZ_LINE)
+		    call strcat (Memc[ksection], Memc[name1], SZ_LINE)
+		}
+
+		if (imaccess (Memc[name1], 0) == YES) {
+		    call sprintf (Memc[ans], SZ_LINE,
+			"Clobber existing output image %s?")
+			call pargstr (Memc[name1])
+		    if (ap_answer ("ansclobber1", Memc[ans]))
+			call imdelete (Memc[name1])
+		    else {
+			call sprintf (Memc[ans], SZ_LINE,
+			    "EXTRACT - Output spectrum %s already exists")
+			    call pargstr (Memc[name1])
+			call ap_log (Memc[ans], YES, NO, YES)
+			fmt = 0
+		    }
+		}
+	    }
+	case ONEDSPEC, STRIP:
+	    do i = 1, naps {
+		do j = 1, nsubaps {
+		    call sprintf (Memc[name], SZ_LINE, "%s.%0*d")
+			if (output[1] == EOS)
+			    call pargstr (Memc[input1])
+			else
+			    call pargstr (output)
+			call pargi (int(log10(real(nsubaps)))+4)
+			call pargi (AP_ID(aps[i])+(j-1)*1000)
+		    if (imaccess (Memc[name], 0) == YES) {
+			call sprintf (Memc[ans], SZ_LINE,
+			    "Clobber existing output image %s?")
+			    call pargstr (Memc[name])
+			if (ap_answer ("ansclobber1", Memc[ans]))
+			    call imdelete (Memc[name])
+			else {
+			    call sprintf (Memc[ans], SZ_LINE,
+				"EXTRACT - Output spectrum %s already exists")
+				call pargstr (Memc[name])
+			    call ap_log (Memc[ans], YES, NO, YES)
+			    fmt = 0
+			}
+		    }
+		}
+	    }
+	case NOISE:
+	    ;
+	default:
+	    call sfree (sp)
+	    call error (1, "EXTRACT - Unknown output format")
+	}
+
+	call sfree (sp)
+	return (fmt)
+end
+
+
+# AP_OUTPUT -- Review the extracted spectra and write them to an image.
+# This routine determines the output format and whether to also output sky
+# unweighted, and sigma spectra.  The appropriate header keywords have
+# to be added.
+
+procedure ap_output (image, output, format, bkg, wt, clean, gain, in, aps,
+	naps, iap, nsubaps, spec, raw sky, sig, dbuf, nc, nl, c1, l1, sbuf,
+	profile, nx, ny, xs, ys)
+
+char	image[ARB]		# Input image name
+char	output[ARB]		# Output root name
+char	format[ARB]		# Output format
+char	bkg[ARB]		# Background type
+char	wt[ARB]			# Weight type
+char	clean[ARB]		# Clean?
+real	gain			# Gain
+pointer	in			# Input IMIO pointer
+pointer	aps[naps]		# Apertures
+int	naps			# Number of apertures
+int	iap			# Aperture
+int	nsubaps			# Number of subapertures
+pointer	spec			# Output spectrum
+pointer	raw			# Output raw spectrum
+pointer	sky			# Output sky
+pointer	sig			# Output sigma
+pointer	dbuf			# Data buffer
+int	nc, nl			# Size of data buffer
+int	c1, l1			# Origin of data buffer
+pointer	sbuf			# Sky values (NULL if none)
+pointer	profile			# Profile (NULL if none)
+int	nx, ny			# Size of sky and profile array
+int	xs[ny], ys		# Origin of sky and profile array
+
+int	fmt			# Output format
+bool	extras			# Include raw spectrum, sky, and sigma
+
+real	low, high, step
+int	i, k, l, m, apid, apaxis, dispaxis
+pointer	sp, str, str1, name, name1, input, ksection
+pointer	ap, out, outsave, gt, apmw, buf
+pointer	sum2, sum4, nsum
+
+real	clgetr()
+int	scan(), strdic(), imaccf(), stridxs()
+bool	streq(), ap_answer(), apgetb()
+pointer	immap(), imgl2r(), impl2r(), impl3r()
+pointer	gt_init(), apmw_open()
+errchk	immap, impl2r, impl3r, imps2r, ap_strip, ap_pstrip, apmw_open
+errchk	ap_fitspec, ap_lnorm, ap_cnorm, ap_lflat, ap_cflat
+
+begin
+	# Allocate string and file name arrays.
+	call smark (sp)
+	call salloc (str, SZ_LINE, TY_CHAR)
+	call salloc (str1, SZ_LINE, TY_CHAR)
+	call salloc (name, SZ_LINE, TY_CHAR)
+	call salloc (name1, SZ_LINE, TY_CHAR)
+	call salloc (input, SZ_LINE, TY_CHAR)
+	call salloc (ksection, SZ_LINE, TY_CHAR)
+
+	fmt = strdic (format, format, SZ_LINE, FORMATS)
+	extras = apgetb ("extras")
+
+	ap = aps[iap]
+	apaxis = AP_AXIS(ap)
+	dispaxis = mod (apaxis, 2) + 1
+
+	# Set output name.
+	call imgimage (image, Memc[input], SZ_LINE)
+	i = stridxs ("[", Memc[input])
+	if (i > 0) {
+	    call strcpy (Memc[input+i-1], Memc[ksection], SZ_LINE)
+	    Memc[input+i-1] = EOS
+	    i = stridxs ("]", Memc[ksection])
+	    call strcpy (",append]", Memc[ksection+i-1], SZ_LINE)
+	} else
+	    Memc[ksection] = EOS
+	if (output[1] == EOS)
+	    call strcpy (Memc[input], Memc[name], SZ_LINE)
+	else
+	    call strcpy (output, Memc[name], SZ_LINE)
+
+	switch (fmt) {
+	case ECHELLE:
+	    ;
+	case MULTISPEC:
+	    if (streq (Memc[input], Memc[name])) {
+		call strcat (".ms", Memc[name], SZ_LINE)
+		call strcat (Memc[ksection], Memc[name], SZ_LINE)
+	    }
+	case NORM:
+	    if (streq (Memc[input], Memc[name])) {
+	        call strcat (".norm", Memc[name], SZ_LINE)
+		call strcat (Memc[ksection], Memc[name], SZ_LINE)
+	    }
+	case FLAT:
+	    if (streq (Memc[input], Memc[name])) {
+	        call strcat (".flat", Memc[name], SZ_LINE)
+		call strcat (Memc[ksection], Memc[name], SZ_LINE)
+	    }
+	case RATIO:
+	    if (streq (Memc[input], Memc[name])) {
+	        call strcat (".ratio", Memc[name], SZ_LINE)
+		call strcat (Memc[ksection], Memc[name], SZ_LINE)
+	    }
+	case DIFF:
+	    if (streq (Memc[input], Memc[name])) {
+	        call strcat (".diff", Memc[name], SZ_LINE)
+		call strcat (Memc[ksection], Memc[name], SZ_LINE)
+	    }
+	case FIT:
+	    if (streq (Memc[input], Memc[name])) {
+	        call strcat (".fit", Memc[name], SZ_LINE)
+		call strcat (Memc[ksection], Memc[name], SZ_LINE)
+	    }
+	case NOISE:
+	    Memc[name] = EOS
+	}
+
+
+	# Set the review graph title.
+	call sprintf (Memc[str], SZ_LINE, "%s: %s - Aperture %s")
+	    call pargstr (image)
+	    call pargstr (IM_TITLE(in))
+	    call pargi (AP_ID(ap))
+
+	gt = gt_init ()
+	call gt_sets (gt, GTTITLE, Memc[str])
+
+	# Query the user whether to review the extraction.
+	call sprintf (Memc[str], SZ_LINE,
+	    "Review extracted spectrum for aperture %d from %s?")
+	    call pargi (AP_ID(ap))
+	    call pargstr (image)
+
+	# If reviewing graph the spectrum, do a cursor loop, and allow
+	# the user to skip the output or define a new output image.
+	if (ap_answer ("ansreview1", Memc[str])) {
+	    call ap_graph1 (gt, Memr[spec], ny, nsubaps)
+	    
+	    if (fmt == ONEDSPEC && nsubaps == 1) {
+	        call printf (
+		    "Output image name [use # to skip output] (%s): ")
+		    call pargstr (Memc[name])
+		call flush (STDOUT)
+	        if (scan() != EOF) {
+	            call gargwrd (Memc[str], SZ_LINE)
+	            if (Memc[str] == '#') {
+			call gt_free (gt)
+			call sfree (sp)
+		        return
+		    }
+	            if (Memc[str] != EOS)
+		        call strcpy (Memc[str], Memc[name], SZ_LINE)
+		}
+	    }
+	}
+
+	# Output the image.
+	switch (fmt) {
+	case MULTISPEC:
+	    if (iap == 1) {
+		out = immap (Memc[name], NEW_COPY, in)
+
+		IM_PIXTYPE(out) = TY_REAL
+		IM_NDIM(out) = 1
+		IM_LEN(out, 1) = ny
+		IM_LEN(out, 2) = nsubaps * naps
+		IM_LEN(out, 3) = 1
+		if (extras) {
+		    if (sky != NULL)
+		        IM_LEN(out, 3) = IM_LEN(out, 3) + 1
+		    if (raw != NULL)
+		        IM_LEN(out, 3) = IM_LEN(out, 3) + 1
+		    if (sig != NULL)
+		        IM_LEN(out, 3) = IM_LEN(out, 3) + 1
+		}
+		if (IM_LEN(out, 2) > 1)
+		    IM_NDIM(out) = 2
+		if (IM_LEN(out, 3) > 1)
+		    IM_NDIM(out) = 3
+
+		apmw = apmw_open (in, out, dispaxis, nsubaps*naps, ny)
+
+		# Write BAND IDs.
+		k = 1
+		call sprintf (Memc[str1], SZ_LINE, "BANDID%d")
+		    call pargi (k)
+		call sprintf (Memc[str], SZ_LINE,
+		    "spectrum - background %s, weights %s, clean %s")
+		    call pargstr (bkg)
+		    call pargstr (wt)
+		    call pargstr (clean)
+		call imastr (out, Memc[str1], Memc[str])
+		k = k + 1
+		if (extras) {
+		    if (raw != NULL) {
+			call sprintf (Memc[str1], SZ_LINE, "BANDID%d")
+			    call pargi (k)
+			call sprintf (Memc[str], SZ_LINE,
+			    "raw - background %s, weights none, clean no")
+			    call pargstr (bkg)
+			call imastr (out, Memc[str1], Memc[str])
+			k = k + 1
+		    }
+		    if (sky != NULL) {
+			call sprintf (Memc[str1], SZ_LINE, "BANDID%d")
+			    call pargi (k)
+			call sprintf (Memc[str], SZ_LINE,
+			    "background - background %s")
+			    call pargstr (bkg)
+			call imastr (out, Memc[str1], Memc[str])
+			k = k + 1
+		    }
+		    if (sig != NULL) {
+			call sprintf (Memc[str1], SZ_LINE, "BANDID%d")
+			    call pargi (k)
+			call sprintf (Memc[str], SZ_LINE,
+			    "sigma - background %s, weights %s, clean %s")
+			    call pargstr (bkg)
+			    call pargstr (wt)
+			    call pargstr (clean)
+			call imastr (out, Memc[str1], Memc[str])
+		    }
+		}
+
+		do k = 1, naps {
+		    low = AP_CEN(aps[k],apaxis) + AP_LOW(aps[k],apaxis)
+		    high = AP_CEN(aps[k],apaxis) + AP_HIGH(aps[k],apaxis)
+		    step = (high - low) / nsubaps
+		    low = low - step
+		    do l = 1, nsubaps {
+			apid = AP_ID(aps[k]) + (l - 1) * 1000
+			low = low + step
+			high = low + step
+			call apmw_setap (apmw, (k-1)*nsubaps+l,
+			    apid, AP_BEAM(aps[k]), low, high)
+		    }
+		}
+		do k = 1, naps {
+		    if (AP_TITLE(aps[k]) != NULL) {
+			do l = 1, nsubaps {
+			    call sprintf (Memc[str], SZ_LINE, "APID%d")
+				call pargi ((k-1)*nsubaps+l)
+		    	    call imastr (out, Memc[str],
+				Memc[AP_TITLE(aps[k])])
+			}
+		    }
+		}
+	    }
+	
+	    do l = 1, nsubaps {
+		k = (iap - 1) * nsubaps + l
+		buf = impl2r (out, k)
+	        call amovr (Memr[spec+(l-1)*ny], Memr[buf], ny)
+		if (extras) {
+		    m = 2
+		    if (raw != NULL) {
+			buf = impl3r (out, k, m)
+	                call amovr (Memr[raw+(l-1)*ny], Memr[buf], ny)
+			m = m + 1
+		    }
+		    if (sky != NULL) {
+			buf = impl3r (out, k, m)
+	                call amovr (Memr[sky+(l-1)*ny], Memr[buf], ny)
+			m = m + 1
+		    }
+		    if (sig != NULL) {
+			buf = impl3r (out, k, m)
+	                call amovr (Memr[sig+(l-1)*ny], Memr[buf], ny)
+			m = m + 1
+		    }
+		}
+	    }
+	    if (iap == naps) {
+		call apmw_saveim (apmw, out, fmt)
+		call apmw_close (apmw)
+	        call imunmap (out)
+	    }
+
+	    if (Memc[name] != EOS) {
+		call sprintf (Memc[str], SZ_LINE,
+		    "EXTRACT - Aperture %d from %s --> %s")
+		    call pargi (AP_ID(ap))
+		    call pargstr (image)
+		    call pargstr (Memc[name])
+		call ap_log (Memc[str], YES, YES, NO)
+		call ap_plot1 (gt, Memr[spec], ny, nsubaps)
+	    }
+
+	case ECHELLE:
+	    do l = 1, nsubaps {
+		if (nsubaps == 1)
+		    call strcpy (Memc[name], Memc[name1], SZ_LINE)
+		else {
+		    call sprintf (Memc[name1], SZ_LINE, "%s%0*d")
+			call pargstr (Memc[name])
+			call pargi (int(log10(real(nsubaps)))+1)
+			call pargi (l)
+		}
+		if (streq (Memc[input], Memc[name])) {
+		    call strcat (".ec", Memc[name1], SZ_LINE)
+		    call strcat (Memc[ksection], Memc[name1], SZ_LINE)
+		}
+
+		if (iap == 1) {
+		    out = immap (Memc[name1], NEW_COPY, in)
+
+		    IM_PIXTYPE(out) = TY_REAL
+		    IM_NDIM(out) = 1
+		    IM_LEN(out, 1) = ny
+		    IM_LEN(out, 2) = naps
+		    IM_LEN(out, 3) = 1
+		    if (extras) {
+			if (sky != NULL)
+			    IM_LEN(out, 3) = IM_LEN(out, 3) + 1
+			if (raw != NULL)
+			    IM_LEN(out, 3) = IM_LEN(out, 3) + 1
+			if (sig != NULL)
+			    IM_LEN(out, 3) = IM_LEN(out, 3) + 1
+		    }
+		    if (IM_LEN(out, 2) > 1)
+			IM_NDIM(out) = 2
+		    if (IM_LEN(out, 3) > 1)
+			IM_NDIM(out) = 3
+
+		    apmw = apmw_open (in, out, dispaxis, naps, ny)
+
+		    # Write BAND IDs.
+		    k = 1
+		    call sprintf (Memc[str1], SZ_LINE, "BANDID%d")
+			call pargi (k)
+		    call sprintf (Memc[str], SZ_LINE,
+			"spectrum - background %s, weights %s, clean %s")
+			call pargstr (bkg)
+			call pargstr (wt)
+			call pargstr (clean)
+		    call imastr (out, Memc[str1], Memc[str])
+		    k = k + 1
+		    if (extras) {
+			if (raw != NULL) {
+			    call sprintf (Memc[str1], SZ_LINE, "BANDID%d")
+				call pargi (k)
+			    call sprintf (Memc[str], SZ_LINE,
+				"raw - background %s, weights none, clean no")
+				call pargstr (bkg)
+			    call imastr (out, Memc[str1], Memc[str])
+			    k = k + 1
+			}
+			if (sky != NULL) {
+			    call sprintf (Memc[str1], SZ_LINE, "BANDID%d")
+				call pargi (k)
+			    call sprintf (Memc[str], SZ_LINE,
+				"background - background %s")
+				call pargstr (bkg)
+			    call imastr (out, Memc[str1], Memc[str])
+			    k = k + 1
+			}
+			if (sig != NULL) {
+			    call sprintf (Memc[str1], SZ_LINE, "BANDID%d")
+				call pargi (k)
+			    call sprintf (Memc[str], SZ_LINE,
+				"sigma - background %s, weights %s, clean %s")
+				call pargstr (bkg)
+				call pargstr (wt)
+				call pargstr (clean)
+			    call imastr (out, Memc[str1], Memc[str])
+			}
+		    }
+
+		    # Write keyword to allow matching by subaperture.
+		    if (nsubaps > 1)
+			call imaddi (out, "SUBAP", l)
+
+		    do k = 1, naps {
+			low = AP_CEN(aps[k],apaxis) + AP_LOW(aps[k],apaxis)
+			high = AP_CEN(aps[k],apaxis) + AP_HIGH(aps[k],apaxis)
+			step = (high - low) / nsubaps
+			call apmw_setap (apmw, k, AP_ID(aps[k]),
+			    AP_BEAM(aps[k]), low+(l-1)*step, low+l*step)
+		    }
+		    do k = 1, naps {
+			if (AP_TITLE(aps[k]) != NULL) {
+			    call sprintf (Memc[str], SZ_LINE, "APID%d")
+				call pargi (k)
+			    call imastr (out, Memc[str],
+				Memc[AP_TITLE(aps[k])])
+			}
+		    }
+		} else {
+		    if (l == 1)
+			out = outsave
+		    else
+			out = immap (Memc[name1], READ_WRITE, 0)
+		}
+	    
+		k = iap
+		buf = impl2r (out, k)
+		call amovr (Memr[spec+(l-1)*ny], Memr[buf], ny)
+		if (extras) {
+		    m = 2
+		    if (raw != NULL) {
+			buf = impl3r (out, k, m)
+			call amovr (Memr[raw+(l-1)*ny], Memr[buf], ny)
+			m = m + 1
+		    }
+		    if (sky != NULL) {
+			buf = impl3r (out, k, m)
+			call amovr (Memr[sky+(l-1)*ny], Memr[buf], ny)
+			m = m + 1
+		    }
+		    if (sig != NULL) {
+			buf = impl3r (out, k, m)
+			call amovr (Memr[sig+(l-1)*ny], Memr[buf], ny)
+			m = m + 1
+		    }
+		}
+
+		if (iap == 1) {
+		    call apmw_saveim (apmw, out, fmt)
+		    call apmw_close (apmw)
+		}
+		if (l != 1 || iap == naps)
+		    call imunmap (out)
+		if (l == 1)
+		    outsave = out
+
+		if (nsubaps == 1) {
+		    call sprintf (Memc[str], SZ_LINE,
+			"EXTRACT - Aperture %d from %s --> %s")
+			call pargi (AP_ID(ap))
+			call pargstr (image)
+			call pargstr (Memc[name1])
+		} else {
+		    call sprintf (Memc[str], SZ_LINE,
+			"EXTRACT - Aperture %d-%d from %s --> %s")
+			call pargi (AP_ID(ap))
+			call pargi (l)
+			call pargstr (image)
+			call pargstr (Memc[name1])
+		}
+		call ap_log (Memc[str], YES, YES, NO)
+	    }
+
+	    call ap_plot1 (gt, Memr[spec], ny, nsubaps)
+			
+	case ONEDSPEC:
+	    do l = 1, nsubaps {
+		apid = AP_ID(ap) + (l - 1) * 1000
+		low = AP_CEN(ap,apaxis) + AP_LOW(ap,apaxis)
+		high = AP_CEN(ap,apaxis) + AP_HIGH(ap,apaxis)
+		step = (high - low) / nsubaps
+		low = low + (l - 1) * step
+		high = low + step
+
+		call sprintf (Memc[str], SZ_LINE, "%s.%0*d")
+		    call pargstr (Memc[name])
+		    call pargi (int(log10(real(nsubaps)))+4)
+		    call pargi (apid)
+		out = immap (Memc[str], NEW_COPY, in)
+		call sprintf (Memc[str], SZ_LINE,
+		    "EXTRACT - Aperture %d from %s --> %s.%0*d")
+		    call pargi (apid)
+		    call pargstr (image)
+		    call pargstr (Memc[name])
+		    call pargi (int(log10(real(nsubaps)))+4)
+		    call pargi (apid)
+		call ap_log (Memc[str], YES, YES, NO)
+
+		apmw = apmw_open (in, out, dispaxis, 1, ny)
+		call apmw_setap (apmw, 1, apid, AP_BEAM(ap), low, high)
+		if (AP_TITLE(ap) != NULL)
+		    call imastr (out, "APID1", Memc[AP_TITLE(ap)])
+
+		IM_PIXTYPE(out) = TY_REAL
+		IM_NDIM(out) = 1
+		IM_LEN(out, 1) = ny
+		IM_LEN(out, 2) = 1
+		IM_LEN(out, 3) = 1
+		if (extras) {
+		    if (sky != NULL)
+			IM_LEN(out, 3) = IM_LEN(out, 3) + 1
+		    if (raw != NULL)
+			IM_LEN(out, 3) = IM_LEN(out, 3) + 1
+		    if (sig != NULL)
+			IM_LEN(out, 3) = IM_LEN(out, 3) + 1
+		}
+		if (IM_LEN(out, 2) > 1)
+		    IM_NDIM(out) = 2
+		if (IM_LEN(out, 3) > 1)
+		    IM_NDIM(out) = 3
+
+		# Write BAND IDs.
+		k = 1
+		call sprintf (Memc[str1], SZ_LINE, "BANDID%d")
+		    call pargi (k)
+		call sprintf (Memc[str], SZ_LINE,
+		    "spectrum: background %s, weights %s, clean %s")
+		    call pargstr (bkg)
+		    call pargstr (wt)
+		    call pargstr (clean)
+		call imastr (out, Memc[str1], Memc[str])
+		k = k + 1
+		if (extras) {
+		    if (raw != NULL) {
+			call sprintf (Memc[str1], SZ_LINE, "BANDID%d")
+			    call pargi (k)
+			call sprintf (Memc[str], SZ_LINE,
+			    "spectrum: background %s, weights none, clean no")
+			    call pargstr (bkg)
+			call imastr (out, Memc[str1], Memc[str])
+			k = k + 1
+		    }
+		    if (sky != NULL) {
+			call sprintf (Memc[str1], SZ_LINE, "BANDID%d")
+			    call pargi (k)
+			call sprintf (Memc[str], SZ_LINE,
+			    "background: background %s")
+			    call pargstr (bkg)
+			call imastr (out, Memc[str1], Memc[str])
+			k = k + 1
+		    }
+		    if (sig != NULL) {
+			call sprintf (Memc[str1], SZ_LINE, "BANDID%d")
+			    call pargi (k)
+			call sprintf (Memc[str], SZ_LINE,
+			    "sigma - background %s, weights %s, clean %s")
+			    call pargstr (bkg)
+			    call pargstr (wt)
+			    call pargstr (clean)
+			call imastr (out, Memc[str1], Memc[str])
+		    }
+		}
+
+		buf = impl2r (out, 1)
+	        call amovr (Memr[spec+(l-1)*ny], Memr[buf], ny)
+		if (extras) {
+		    m = 2
+		    if (raw != NULL) {
+			buf = impl3r (out, 1, m)
+	                call amovr (Memr[raw+(l-1)*ny], Memr[buf], ny)
+			m = m + 1
+		    }
+		    if (sky != NULL) {
+			buf = impl3r (out, 1, m)
+	                call amovr (Memr[sky+(l-1)*ny], Memr[buf], ny)
+			m = m + 1
+		    }
+		    if (sig != NULL) {
+			buf = impl3r (out, 1, m)
+	                call amovr (Memr[sig+(l-1)*ny], Memr[buf], ny)
+			m = m + 1
+		    }
+		}
+
+		call apmw_saveim (apmw, out, fmt)
+		call apmw_close (apmw)
+		call imunmap (out)
+
+	    }
+
+	    call ap_plot1 (gt, Memr[spec], ny, nsubaps)
+
+	case STRIP:
+	    do l = 1, nsubaps {
+		apid = AP_ID(ap) + (l - 1) * 1000
+		low = AP_CEN(ap,apaxis) + AP_LOW(ap,apaxis)
+		high = AP_CEN(ap,apaxis) + AP_HIGH(ap,apaxis)
+		step = (high - low) / nsubaps
+		low = low + (l - 1) * step
+		high = low + step
+
+		call sprintf (Memc[str], SZ_LINE, "%s.%0*d")
+		    call pargstr (Memc[name])
+		    call pargi (int(log10(real(nsubaps)))+4)
+		    call pargi (apid)
+		out = immap (Memc[str], NEW_COPY, in)
+		call sprintf (Memc[str], SZ_LINE,
+		    "EXTRACT - Aperture %d from %s --> %s.%0*d")
+		    call pargi (apid)
+		    call pargstr (image)
+		    call pargstr (Memc[name])
+		    call pargi (int(log10(real(nsubaps)))+4)
+		    call pargi (apid)
+		call ap_log (Memc[str], YES, YES, NO)
+
+		apmw = apmw_open (in, out, dispaxis, 1, ny)
+		call apmw_setap (apmw, 1, apid, AP_BEAM(ap), low, high)
+		call sprintf (Memc[str], SZ_LINE, "%s - Aperture %d")
+		    call pargstr (IM_TITLE(out))
+		    call pargi (AP_ID(ap))
+		call strcpy (Memc[str], IM_TITLE(out), SZ_IMTITLE)
+		if (AP_TITLE(ap) != NULL)
+		    call imastr (out, "APID1", Memc[AP_TITLE(ap)])
+
+		IM_PIXTYPE(out) = TY_REAL
+		IM_NDIM(out) = 2
+		IM_LEN(out, 1) = ny
+		IM_LEN(out, 2) = high - low + 1
+
+		if (profile == NULL)
+		    call ap_strip (ap, low, high, out, dbuf, nc, nl, c1, l1,
+			sbuf, nx, ny, xs, ys)
+		else
+		    call ap_pstrip (ap, low, high, out, gain, Memr[spec],
+			Memr[profile], nx, ny, xs, ys)
+
+		call apmw_saveim (apmw, out, fmt)
+		call apmw_close (apmw)
+		call imunmap (out)
+	    }
+
+	    call ap_plot1 (gt, Memr[spec], ny, nsubaps)
+
+	case NORM, FLAT:
+	    if (iap == 1) {
+	        out = immap (Memc[name], NEW_COPY, in)
+	        IM_PIXTYPE(out) = TY_REAL
+		if (imaccf (out, "CCDMEAN") == YES)
+		    call imdelf (out, "CCDMEAN")
+	        call ap_fitspec (ap, in, Memr[spec], ny)
+		k = YES
+	    } else {
+	        call ap_fitspec (ap, in, Memr[spec], ny)
+		k = NO
+	    }
+	    if (apaxis == 1) {
+		if (fmt == NORM)
+		    call ap_lnorm (ap, out, gain, dbuf, nc, nl, c1, l1,
+			Memr[spec], ny, ys, k)
+		else
+		    call ap_lflat (ap, out, dbuf, nc, nl, c1, l1, Memr[spec],
+		        sbuf, Memr[profile], nx, ny, xs, ys, k)
+	    } else {
+		if (fmt == NORM)
+		    call ap_cnorm (ap, out, gain, dbuf, nc, nl, c1, l1,
+			Memr[spec], ny, ys, k)
+		else
+		    call ap_cflat (ap, out, dbuf, nc, nl, c1, l1, Memr[spec],
+		        sbuf, Memr[profile], nx, ny, xs, ys, k)
+	    }
+	    if (iap == naps)
+	        call imunmap (out)
+
+	    if (Memc[name] != EOS) {
+		call sprintf (Memc[str], SZ_LINE,
+		    "EXTRACT - Aperture %d from %s --> %s")
+		    call pargi (AP_ID(ap))
+		    call pargstr (image)
+		    call pargstr (Memc[name])
+		call ap_log (Memc[str], YES, YES, NO)
+		call ap_plot1 (gt, Memr[spec], ny, nsubaps)
+	    }
+
+	case RATIO, FIT:
+	    if (iap == 1) {
+		out = immap (Memc[name], NEW_COPY, in)
+	        IM_PIXTYPE(out) = TY_REAL
+		k = YES
+	    } else
+		k = NO
+	    if (apaxis == 1) {
+		switch (fmt) {
+		case RATIO:
+		    call ap_lflat (ap, out, dbuf, nc, nl, c1, l1, Memr[spec],
+		        sbuf, Memr[profile], nx, ny, xs, ys, k)
+		case FIT:
+		    call ap_lfit (ap, out, gain, Memr[spec], Memr[profile],
+			nx, ny, xs, ys, k)
+		}
+	    } else {
+		switch (fmt) {
+		case RATIO:
+		    call ap_cflat (ap, out, dbuf, nc, nl, c1, l1, Memr[spec],
+		        sbuf, Memr[profile], nx, ny, xs, ys, k)
+		case FIT:
+		    call ap_cfit (ap, out, gain, Memr[spec], Memr[profile],
+			nx, ny, xs, ys, k)
+		}
+	    }
+	    if (iap == naps)
+	        call imunmap (out)
+
+	    if (Memc[name] != EOS) {
+		call sprintf (Memc[str], SZ_LINE,
+		    "EXTRACT - Aperture %d from %s --> %s")
+		    call pargi (AP_ID(ap))
+		    call pargstr (image)
+		    call pargstr (Memc[name])
+		call ap_log (Memc[str], YES, YES, NO)
+		call ap_plot1 (gt, Memr[spec], ny, nsubaps)
+	    }
+
+	case DIFF:
+	    if (iap == 1) {
+	        out = immap (Memc[name], NEW_COPY, in)
+	        IM_PIXTYPE(out) = TY_REAL
+		do k = 1, IM_LEN(in,2) {
+		    buf = impl2r (out, k)
+		    call amovr (Memr[imgl2r(in,k)], Memr[buf], IM_LEN(out,1))
+		}
+		k = NO
+	    } else
+		k = NO
+	    if (apaxis == 1)
+		call ap_ldiff (ap, out, gain, dbuf, nc, nl, c1, l1, Memr[spec],
+		    Memr[profile], nx, ny, xs, ys, k)
+	    else
+		call ap_cdiff (ap, out, gain, dbuf, nc, nl, c1, l1, Memr[spec],
+		    Memr[profile], nx, ny, xs, ys, k)
+	    if (iap == naps)
+	        call imunmap (out)
+
+	    if (Memc[name] != EOS) {
+		call sprintf (Memc[str], SZ_LINE,
+		    "EXTRACT - Aperture %d from %s --> %s")
+		    call pargi (AP_ID(ap))
+		    call pargstr (image)
+		    call pargstr (Memc[name])
+		call ap_log (Memc[str], YES, YES, NO)
+		call ap_plot1 (gt, Memr[spec], ny, nsubaps)
+	    }
+
+	case NOISE:
+	    if (iap == 1) {
+		low = clgetr ("dmin")
+		high = clgetr ("dmax")
+		l = clgetr ("nbins")
+		if (high < low) {
+		    step = low; low = high; high = step
+		}
+		step = (high - low) / l
+		call malloc (sum2, l, TY_REAL)
+		call malloc (sum4, l, TY_REAL)
+		call malloc (nsum, l, TY_INT)
+		call aclrr (Memr[sum2], l)
+		call aclrr (Memr[sum4], l)
+		call aclri (Memi[nsum], l)
+	    }
+	    call ap_noise (ap, gain, dbuf, nc, nl, c1, l1, sbuf, Memr[spec],
+		Memr[profile], nx, ny, xs, ys, Memr[sum2], Memr[sum4],
+		Memi[nsum], l, low, high)
+	    if (iap == naps) {
+		do k = 0, l-1 {
+		    m = Memi[nsum+k]
+		    if (m > 10) {
+			Memr[sum2+k] = sqrt (Memr[sum2+k] / (m - 1))
+			step = max (0., Memr[sum4+k] / m - Memr[sum2+k]**2)
+			Memr[sum4+k] = sqrt (sqrt (step / m))
+		    } else {
+			Memr[sum2+k] = 0.
+			Memr[sum4+k] = 0.
+		    }
+		}
+		call ap_nplot (image, in, Memr[sum2], Memr[sum4], l,
+		    low, high)
+		call mfree (sum2, TY_REAL)
+		call mfree (sum4, TY_REAL)
+		call mfree (nsum, TY_INT)
+	    }
+
+	    if (Memc[name] != EOS) {
+		call sprintf (Memc[str], SZ_LINE,
+		    "EXTRACT - Aperture %d from %s --> %s")
+		    call pargi (AP_ID(ap))
+		    call pargstr (image)
+		    call pargstr (Memc[name])
+		call ap_log (Memc[str], YES, YES, NO)
+		call ap_plot1 (gt, Memr[spec], ny, nsubaps)
+	    }
+	}
+
+	call gt_free (gt)
+	call sfree (sp)
+end
+
+
+# AP_SUM -- Simple, unweighted aperture sum.
+
+procedure ap_sum (ap, dbuf, nc, nl, c1, l1, sbuf, nx, ny, xs, ys, spec,
+	nsubaps, asi)
+
+pointer	ap			# Aperture structure
+pointer	dbuf			# Data buffer
+int	nc, nl			# Size of data buffer
+int	c1, l1			# Origin of data buffer
+pointer	sbuf			# Sky values (NULL if none)
+int	nx, ny			# Size of profile array
+int	xs[ny], ys		# Origin of sky array
+real	spec[ny, nsubaps]	# Spectrum
+int	nsubaps			# Number of subapertures
+pointer	asi			# Interpolator for edge pixel weighting
+
+int	i, ix, iy, ix1, ix2
+real	low, high, step, x1, x2, wt1, wt2, s, sval, skyval
+real	ap_cveval()
+pointer	cv, data, sky
+errchk	asifit
+
+begin
+	i = AP_AXIS(ap)
+	low = AP_CEN(ap,i) + AP_LOW(ap,i)
+	high = AP_CEN(ap,i) + AP_HIGH(ap,i)
+	step = (high - low) / nsubaps
+	cv = AP_CV(ap)
+	do iy = 1, ny {
+	    s = ap_cveval (cv, real (iy + ys - 1)) - c1 + 1
+	    call ap_asifit (dbuf+(iy+ys-1-l1)*nc, nc, xs[iy]-c1+1,
+		low+s, high+s, data, asi)
+#	    data = dbuf + (iy + ys - 1 - l1) * nc + xs[iy] - c1 - 1
+#	    if (asi != NULL)
+#		call asifit (asi, Memr[data], nc-xs[iy]+c1)
+	    do i = 1, nsubaps {
+	        x1 = max (0.5, low + (i - 1) * step + s) + c1 - xs[iy]
+	        x2 = min (nc + 0.49, low + i * step + s) + c1 - xs[iy]
+	        if (x2 <= x1) {
+		    spec[iy,i] = 0.
+		    next
+	        }
+	        ix1 = nint (x1)
+	        ix2 = nint (x2)
+
+		# Compute end pixel weights.  Remember asi is offset by 1.
+		call ap_edge (asi, x1+1, x2+1, wt1, wt2)
+
+		# Sum pixels.
+		sval = wt1 * Memr[data+ix1] + wt2 * Memr[data+ix2]
+		do ix = ix1+1, ix2-1
+		    sval = sval + Memr[data+ix]
+
+		# Subtract sky if desired.
+	        if (sbuf != NULL) {
+		    sky = sbuf + (iy - 1) * nx - 1
+		    skyval = wt1 * Memr[sky+ix1] + wt2 * Memr[sky+ix2]
+	            do ix = ix1+1, ix2-1
+		        skyval = skyval + Memr[sky+ix]
+		    sval = sval - skyval
+	        }
+
+		# Save extracted pixel value.
+		spec[iy,i] = sval
+	    }
+	}
+end
+
+
+# AP_EDGE -- Compute edge weights.
+
+procedure ap_edge (asi, x1, x2, wt1, wt2)
+
+pointer	asi			#I Image interpolator pointer
+real	x1, x2			#I Aperture edges
+real	wt1, wt2		#I Weights
+
+int	ix1, ix2
+real	a, b
+real	asieval(), asigrl()
+
+begin
+	    # Edge pixel centers.
+	    ix1 = nint (x1)
+	    ix2 = nint (x2)
+
+	    # Default weights are fractions of pixel.
+	    if (ix1 == ix2) {
+		wt1 = (x2 - x1)
+		wt2 = 0
+	    } else {
+		wt1 = (ix1 - x1 + 0.5)
+		wt2 = (x2 - ix2 + 0.5)
+	    }
+
+	    # If there is an interpolator compute fraction of integral.
+	    # We require that data and integrals be positive.
+	    if (asi != NULL) {
+		if (asieval (asi, real(ix1)) > 0) {
+		    b = asigrl (asi, ix1-0.5, ix1+0.5)
+		    if (b > 0) {
+			if (ix1 == ix2)
+			    a = asigrl (asi, x1, x2)
+			else
+			    a = asigrl (asi, x1, ix1+0.5)
+			if (a > 0 && a < b)
+			    wt1 = a / b
+		    }
+		}
+		if (ix1 != ix2 && asieval (asi, real(ix2)) > 0) {
+		    b = asigrl (asi, ix2-0.5, ix2+0.5)
+		    if (b > 0) {
+			a = asigrl (asi, ix2-0.5, x2)
+			if (a > 0 && a < b)
+			    wt2 = a / b
+		    }
+		}
+	    }
+end
+
+
+# AP_STRIP -- Simple, unweighted aperture strip.
+# Interpolate so that the lower edge of the aperture is the first pixel.
+
+procedure ap_strip (ap, aplow, aphigh, out, dbuf, nc, nl, c1, l1, sbuf, nx, ny,
+	xs, ys)
+
+pointer	ap			# Aperture structure
+real	aplow, aphigh		# Aperture limits
+pointer	out			# Output IMIO pointer
+pointer	dbuf			# Data buffer
+int	nc, nl			# Size of data buffer
+int	c1, l1			# Origin of data buffer
+pointer	sbuf			# Sky values (NULL if none)
+int	nx, ny			# Size of profile array
+int	xs[ny], ys		# Origin of sky array
+
+int	i, na, iy, ix1, ix2, nasi
+real	low, high, s, x, ap_cveval(), asieval()
+pointer	obuf, cv, asi, data, sky, ptr, imps2r()
+
+begin
+	i = AP_AXIS(ap)
+	low = aplow - c1 + 1
+	high = aphigh - c1 + 1
+	cv = AP_CV(ap)
+	call asiinit (asi, II_LINEAR)
+
+	na = IM_LEN(out,2)
+	obuf = imps2r (out, 1, ny, 1, na)
+	call aclrr (Memr[obuf], na * ny)
+
+	do iy = 1, ny {
+	    i = iy + ys - 1
+	    s = ap_cveval (cv, real (i))
+	    ix1 = max (1, nint (low + s) - 1)
+	    ix2 = min (nc, nint (high + s) + 1)
+	    nasi = ix2 - ix1 + 1
+	    if (nasi < 3)
+		next
+	    data = dbuf + (i - l1) * nc + ix1 - 1
+	    iferr (call asifit (asi, Memr[data], nasi))
+		next
+	    
+	    x = low + s - ix1 + 1
+	    ptr = obuf + iy - 1
+	    if (sbuf == NULL) {
+	        do i = 1, na {
+		    if (x >= 1 && x <= nasi)
+		        Memr[ptr] = asieval (asi, x)
+		    x = x + 1.
+		    ptr = ptr + ny
+	        }
+	    } else {
+		sky = sbuf + (iy - 1) * nx + nint (low + s) - xs[iy] + c1 - 2
+	        do i = 1, na {
+		    if (x >= 1 && x <= nasi)
+		        Memr[ptr] = asieval (asi, x) - Memr[sky+i]
+		    x = x + 1.
+		    ptr = ptr + ny
+	        }
+	    }
+	}
+
+	call asifree (asi)
+end
+
+
+# AP_PSTRIP -- Profile based strip.
+# Interpolate the profile spectrum so that the lower aperture edge is the
+# first pixel.
+
+procedure ap_pstrip (ap, aplow, aphigh, out, gain, spec, profile, nx, ny,
+	xs, ys)
+
+pointer	ap			# Aperture structure
+real	aplow, aphigh		# Aperture limits
+pointer	out			# Output IMIO pointer
+real	gain			# Gain
+real	spec[ny]		# Spectrum
+real	profile[ny,nx]		# Profile
+int	nx, ny			# Size of profile array
+int	xs[ny], ys		# Origin of profile array
+
+int	na, ix, iy
+real	low, high, s, x, ap_cveval(), asieval()
+pointer	sp, cv, asi, data, impl2r()
+
+begin
+	call smark (sp)
+	call salloc (data, nx, TY_REAL)
+
+	ix = AP_AXIS(ap)
+	low = aplow
+	high = aphigh
+	cv = AP_CV(ap)
+	na = IM_LEN(out,2)
+	call asiinit (asi, II_LINEAR)
+
+	do iy = 1, ny {
+	    s = spec[iy] / gain
+	    do ix = 1, nx
+		Memr[data+ix-1] = s * profile[iy,ix]
+	    call asifit (asi, Memr[data], nx)
+	    s = ap_cveval (cv, real (iy+ys-1)) - xs[iy] + 1
+	    x = low + s
+	    do ix = 1, na {
+		profile[iy,ix] = asieval (asi, x)
+		x = x + 1
+	    }
+	}
+
+	do ix = 1, na
+	    call amovr (profile[1,ix], Memr[impl2r(out,ix)], ny)
+
+	call asifree (asi)
+end
+
+
+# AP_ASIFIT -- Return interpolation pointer and data pointer.
+#
+# The main reason for this routine is to shift the origin of the data by
+# one pixel so that the interpolator may be called to evaluate across
+# the extent of the first and last pixels.  This means the calling program
+# will reference asi fit between 1.5 and N+1.5.  It also means the returned
+# data pointer may start before the first point but will never be
+# dereferenced outside of the data range.
+
+procedure ap_asifit (dbuf, nc, xs, low, high, data, asi)
+
+pointer	dbuf			#I Data buffer pointer
+int	nc			#I Size of data buffer
+int	xs			#I Start of aperture array (in dbuf coords)
+real	low			#I Low aperture edge (in dbuf coords)
+real	high			#I High aperture edge (in dbuf coords)
+pointer	data			#O Data pointer
+pointer	asi			#I ASI pointer
+
+int	i, ix1, ix2, n
+real	x1, x2
+pointer	fit
+
+begin
+	# Check for in bounds data.
+	x1 = max (0.5, low)
+	x2 = min (nc + 0.49, high)
+	if (x1 >= x2)
+	    return
+
+	# Set data pointer relative to the aperture start with an offset for
+	# one indexing; i.e. pixel i is referenced as Memr[data+i].  The
+	# aperture start may put this outside the data buffer but we expect
+	# routines using the pointer to never index outside of the buffer.
+
+	data = (dbuf + xs - 1) - 1
+
+	# If not using an interpolator we are done.
+
+	if (asi == NULL)
+	    return
+
+	# If the aperture, with one extra pixel on each end for integration
+	# across the end pixel, is within the data buffer then fit an
+	# interpolator directly.  Otherwise we need to use a temporary
+	# padded buffer.  The origin of the fitted buffer is relative
+	# to the data pointer.  Note that this means that evaluating the
+	# fit requires the aperture start coordinates to be incremented
+	# by 1.
+
+	ix1 = 0
+	ix2 = nint (x2) + 1 - (xs - 1)
+	n = ix2 + ix1 + 1
+	if (data + ix1 >= dbuf && data + ix2 <= dbuf + nc - 1) {
+	    call asifit (asi, Memr[data+ix1], n)
+	    return
+	}
+
+	# One or the other end point is out of bounds so to avoid potential
+	# NAN and segmentation errors use an internal array to pad.
+
+	call malloc (fit, n, TY_REAL)
+	do i = 0, n-1 {
+	    if (data + i < dbuf)
+		Memr[fit+i] = Memr[dbuf]
+	    else if (data + i > dbuf + nc - 1)
+		Memr[fit+i] = Memr[dbuf+nc-1]
+	    else
+		Memr[fit+i] = Memr[data+i]
+	}
+	call asifit (asi, Memr[fit], n)
+	call mfree (fit, TY_REAL)
+end
diff --git a/noao/twodspec/apextract/apfind.par b/noao/twodspec/apextract/apfind.par
new file mode 100644
index 00000000..f879a4a7
--- /dev/null
+++ b/noao/twodspec/apextract/apfind.par
@@ -0,0 +1,18 @@
+# APFIND
+
+input,s,a,,,,List of input images
+apertures,s,h,"",,,Apertures
+references,s,h,"",,,"Reference images
+"
+interactive,b,h,no,,,Run task interactively?
+find,b,h,yes,,,Find apertures?
+recenter,b,h,no,,,Recenter apertures?
+resize,b,h,no,,,Resize apertures?
+edit,b,h,yes,,,"Edit apertures?
+"
+line,i,h,INDEF,1,,Dispersion line
+nsum,i,h,1,,,Number of dispersion lines to sum or median
+nfind,i,q,,,,Number of apertures to be found automatically
+minsep,r,h,5.,1.,,Minimum separation between spectra
+maxsep,r,h,1000.,1.,,Maximum separation between spectra
+order,s,h,"increasing","increasing|decreasing",,Order of apertures
diff --git a/noao/twodspec/apextract/apfind.x b/noao/twodspec/apextract/apfind.x
new file mode 100644
index 00000000..f58dd4f4
--- /dev/null
+++ b/noao/twodspec/apextract/apfind.x
@@ -0,0 +1,132 @@
+include	<imhdr.h>
+include	<mach.h>
+include	"apertures.h"
+
+# Sort flags
+define	ORDER	"|increasing|decreasing|"
+
+# AP_FIND -- Find and set apertures automatically.
+
+procedure ap_find (image, line, nsum, aps, naps)
+
+char	image[SZ_FNAME]		# Image name
+int	line			# Image dispersion line
+int	nsum			# Number of dispersion lines to sum
+pointer	aps			# Aperture pointers
+int	naps			# Number of apertures
+
+real	minsep, center
+int	i, j, npts, apaxis, nfind, nx
+pointer	im, imdata, title, sp, str, x, ids
+
+bool	clgetb(), ap_answer()
+int	apgeti(), apgwrd()
+real	apgetr(), ap_center(), ap_cveval()
+
+errchk	ap_getdata, ap_default
+
+begin
+	# Find apertures only if there are no other apertures defined.
+	if (naps != 0)
+	     return
+
+	# Query user.
+	call smark (sp)
+	call salloc (str, SZ_LINE, TY_CHAR)
+	call sprintf (Memc[str], SZ_LINE, "Find apertures for %s?")
+            call pargstr (image)
+	if (!ap_answer ("ansfind", Memc[str])) {
+	    call sfree (sp)
+	    return
+	}
+
+	if (clgetb ("verbose"))
+	    call printf ("Finding apertures ...\n")
+
+	# Get CL parameters.
+	nfind = apgeti ("nfind")
+	if (nfind == 0)
+	    return
+	minsep = apgetr ("minsep")
+
+	# Map the image and get the image data.
+	call ap_getdata (image, line, nsum, im, imdata, npts, apaxis, title)
+
+	# If nfind > 0 find the peaks.  Otherwise divide the image evenly
+	# into apertures.
+
+	if (nfind > 0) {
+	    # Allocate working memory.
+	    call salloc (x, nfind+2, TY_REAL)
+
+	    # Find the peaks.
+	    nx = 0
+	    call find_peaks (Memr[imdata], npts, 0., 1, nfind+2, minsep,
+		-MAX_REAL, Memr[x], nx)
+	    #call find_peaks (Memr[imdata], npts, 0., 1, nfind+2, minsep,
+	    #	0, Memr[x], nx)
+	    #call asrtr (Memr[x], Memr[x], nx)
+
+	    # Center on the peaks.
+	    naps = 0
+	    for (i = 1; i <= nx && naps < nfind; i = i + 1) {
+		center = Memr[x+i-1]
+		center = ap_center (center, Memr[imdata], npts)
+
+		if (!IS_INDEF(center)) {
+		    if (mod (naps, 100) == 0)
+			call realloc (aps, naps+100, TY_POINTER)
+		    if (naps == 0)
+			call ap_default (im, INDEFI, 1, apaxis, INDEFR,
+			    real (line), Memi[aps+naps])
+		    else
+			call ap_copy (Memi[aps], Memi[aps+naps])
+
+		    AP_CEN(Memi[aps+naps], AP_AXIS(Memi[aps+naps])) = center -
+			ap_cveval (AP_CV(Memi[aps+naps]), real (line))
+		    naps = naps + 1
+		}
+	    }
+
+	} else {
+	    nfind = abs (nfind)
+	    minsep = real (npts) / nfind
+	    naps = 0
+	    do i = 1, nfind {
+		if (mod (naps, 100) == 0)
+		    call realloc (aps, naps+100, TY_POINTER)
+		center = (i - 0.5) * minsep
+		IF (naps == 0)
+		    call ap_default (im, INDEFI, 1, apaxis, INDEFR,
+			real (line), Memi[aps+naps])
+		else
+		    call ap_copy (Memi[aps], Memi[aps+naps])
+
+		AP_CEN(Memi[aps+naps], AP_AXIS(Memi[aps+naps])) = center -
+		    ap_cveval (AP_CV(Memi[aps+naps]), real (line))
+		naps = naps + 1
+	    }
+	}
+	    
+	# Set the aperture ID's
+	i = apgwrd ("order", Memc[str], SZ_LINE, ORDER)
+	call ap_sort (j, Memi[aps], naps, i)
+	call ap_gids (ids)
+	call ap_ids (Memi[aps], naps, ids)
+	call ap_titles (Memi[aps], naps, ids)
+	call ap_fids (ids)
+
+	# Log the apertures found and write them to the database.
+	call sprintf (Memc[str], SZ_LINE, "FIND - %d apertures found for %s")
+	    call pargi (naps)
+	    call pargstr (image)
+	call ap_log (Memc[str], YES, YES, NO)
+
+	call appstr ("ansdbwrite1", "yes")
+
+	# Free memory and unmap the image.
+	call mfree (imdata, TY_REAL)
+	call mfree (title, TY_CHAR)
+	call imunmap (im)
+	call sfree (sp)
+end
diff --git a/noao/twodspec/apextract/apfindnew.x b/noao/twodspec/apextract/apfindnew.x
new file mode 100644
index 00000000..66762f78
--- /dev/null
+++ b/noao/twodspec/apextract/apfindnew.x
@@ -0,0 +1,83 @@
+include	<mach.h>
+include	"apertures.h"
+
+# Sort flags
+define	ORDER	"|increasing|decreasing|"
+
+# AP_FINDNEW -- Find and set new apertures automatically.  This task is
+# called from the aperture editor so we don't want to read the image vector
+# again.  It also differs from AP_FIND in that existing apertures are
+# maintained and new apertures are added.
+
+procedure ap_findnew (line, data, npts, apdef, aps, naps)
+
+int	line			# Dispersion line of data
+real	data[npts]		# Image data in which to find features
+int	npts			# Number of pixels
+pointer	apdef			# Default aperture pointer
+pointer	aps			# Aperture pointers
+int	naps			# Number of apertures returned
+
+int	i, j, nx, nfind
+real	center, minsep
+pointer	sp, str, x, ids
+
+bool	clgetb()
+int	apgeti(), apgwrd()
+real	apgetr(), ap_center(), ap_cveval()
+
+begin
+	# Determine the maximum number of apertures to be found and return
+	# if that limit has been reached.
+	nfind = apgeti ("nfind")
+	if (nfind <= naps)
+	    return
+
+	if (clgetb ("verbose"))
+	    call printf ("Finding apertures ...\n")
+
+	# Set the positions of the currently defined apertures.
+	call smark (sp)
+	call salloc (str, SZ_FNAME, TY_CHAR)
+	call salloc (x, max (nfind, naps), TY_REAL)
+	nx = naps
+	for (i = 0; i < nx; i = i + 1)
+	    Memr[x+i] = AP_CEN (Memi[aps+i], AP_AXIS(Memi[aps+i])) +
+		ap_cveval (AP_CV(Memi[aps+i]), real (line))
+
+	# Find peaks not already identified.
+	minsep = apgetr ("minsep")
+	#call find_peaks (data, npts, 0., 1, nfind, minsep, 0., Memr[x], nx)
+	call find_peaks (data, npts, 0., 1, nfind, minsep, -MAX_REAL,
+	    Memr[x], nx)
+	call asrtr (Memr[x+naps], Memr[x+naps], nx - naps)
+
+	# Center on the new peaks and define new apertures.
+	for (i = naps + 1; i <= nx; i = i + 1) {
+	    center = Memr[x+i-1]
+	    center = ap_center (center, data, npts)
+
+	    if (!IS_INDEF(center)) {
+		if (mod (naps, 100) == 0)
+		    call realloc (aps, naps+100, TY_POINTER)
+
+		call ap_copy (apdef, Memi[aps+naps])
+
+		AP_ID(Memi[aps+naps]) = INDEFI
+		if (AP_TITLE(Memi[aps+naps]) != NULL)
+		    call mfree (AP_TITLE(Memi[aps+naps]), TY_CHAR)
+		AP_CEN(Memi[aps+naps], AP_AXIS(Memi[aps+naps])) = center -
+		    ap_cveval (AP_CV(Memi[aps+naps]), real (line))
+		naps = naps + 1
+	    }
+	}
+
+	# Set the aperture ID's
+	i = apgwrd ("order", Memc[str], SZ_LINE, ORDER)
+	call ap_sort (j, Memi[aps], naps, i)
+	call ap_gids (ids)
+	call ap_ids (Memi[aps], naps, ids)
+	call ap_titles (Memi[aps], naps, ids)
+	call ap_fids (ids)
+	call sfree (sp)
+end
diff --git a/noao/twodspec/apextract/apfit.par b/noao/twodspec/apextract/apfit.par
new file mode 100644
index 00000000..1d6da386
--- /dev/null
+++ b/noao/twodspec/apextract/apfit.par
@@ -0,0 +1,30 @@
+# APFIT
+
+input,s,a,,,,List of images to fit
+output,s,a,,,,List of output images
+apertures,s,h,"",,,Apertures
+fittype,s,a,"difference","fit|difference|ratio",,Type of output fit
+references,s,h,"",,,"List of reference images
+"
+interactive,b,h,yes,,,Run task interactively?
+find,b,h,yes,,,Find apertures?
+recenter,b,h,yes,,,Recenter apertures?
+resize,b,h,yes,,,Resize apertures?
+edit,b,h,yes,,,Edit apertures?
+trace,b,h,yes,,,Trace apertures?
+fittrace,b,h,yes,,,Fit traced points interactively?
+fit,b,h,yes,,,"Fit apertures?
+"
+line,i,h,INDEF,1,,Dispersion line
+nsum,i,h,10,,,Number of dispersion lines to sum or median
+threshold,r,h,10.,,,"Division threshold for ratio fit
+"
+background,s,h,"none","none|average|median|minimum|fit",,Background to subtract
+pfit,s,h,"fit1d","fit1d|fit2d",,Profile fitting type (fit1d|fit2d)
+clean,b,h,no,,,Detect and replace bad pixels?
+skybox,i,h,1,1,,Box car smoothing length for sky
+saturation,r,h,INDEF,,,Saturation level
+readnoise,s,h,"0.",,,Read out noise sigma (photons)
+gain,s,h,"1.",,,Photon gain (photons/data number)
+lsigma,r,h,4.,0.,,Lower rejection threshold
+usigma,r,h,4.,0.,,Upper rejection threshold
diff --git a/noao/twodspec/apextract/apfit.x b/noao/twodspec/apextract/apfit.x
new file mode 100644
index 00000000..67bf149d
--- /dev/null
+++ b/noao/twodspec/apextract/apfit.x
@@ -0,0 +1,737 @@
+include	<imhdr.h>
+include	<imset.h>
+include	<pkg/gtools.h>
+include	"apertures.h"
+
+
+# AP_FITSPEC -- Fit a spectrum by a smoothing function.
+
+procedure ap_fitspec (ap, in, spec, ny)
+
+pointer	ap			# Aperture (used for labels)
+pointer	in			# Input image (used for labels)
+real	spec[ny]		# spectrum
+int	ny			# Number of points in spectra
+
+int	i, fd, apaxis, clgeti()
+real	clgetr()
+pointer	sp, str, x, wts, cv, gp, gt, ic, ic1, gt_init()
+bool	ap_answer()
+data	ic1 /NULL/
+errchk	icg_fit, ic_fit
+
+common	/apn_com/ ic, gt
+
+begin
+	call smark (sp)
+	call salloc (str, SZ_LINE, TY_CHAR)
+	call salloc (x, ny, TY_REAL)
+	call salloc (wts, ny, TY_REAL)
+
+	do i = 1, ny {
+	    Memr[x+i-1] = i
+	    Memr[wts+i-1] = 1
+	}
+
+	if (ic == NULL || ic1 == NULL) {
+	    call ic_open (ic)
+	    ic1 = ic
+	    call clgstr ("function", Memc[str], SZ_LINE)
+	    call ic_pstr (ic, "function", Memc[str])
+	    call ic_puti (ic, "order", clgeti ("order"))
+	    call clgstr ("sample", Memc[str], SZ_LINE)
+	    call ic_pstr (ic, "sample", Memc[str])
+	    call ic_puti (ic, "naverage", clgeti ("naverage"))
+	    call ic_puti (ic, "niterate", clgeti ("niterate"))
+	    call ic_putr (ic, "low", clgetr ("low_reject"))
+	    call ic_putr (ic, "high", clgetr ("high_reject"))
+	    call ic_putr (ic, "grow", clgetr ("grow"))
+	    call ic_pstr (ic, "ylabel", "")
+
+	    gt = gt_init()
+	}
+
+	call ic_putr (ic, "xmin", 1.)
+	call ic_putr (ic, "xmax", real (ny))
+	apaxis = AP_AXIS(ap)
+	switch (apaxis) {
+	case 1:
+	    call ic_pstr (ic, "xlabel", "Line")
+	case 2:
+	    call ic_pstr (ic, "xlabel", "Column")
+	}
+	call gt_sets (gt, GTTYPE, "line")
+
+	# Fit spectrum by a smoothing function.
+	call sprintf (Memc[str], SZ_LINE,
+	    "%s: %s - Aperture %s")
+	    call pargstr (IM_HDRFILE(in))
+	    call pargstr (IM_TITLE(in))
+	    call pargi (AP_ID(ap))
+	call gt_sets (gt, GTTITLE, Memc[str])
+
+	# Query the user to fit the spectrum interactively.
+	call sprintf (Memc[str], SZ_LINE,
+	    "Fit spectrum for aperture %d for %s interactively?")
+	    call pargi (AP_ID(ap))
+	    call pargstr (IM_HDRFILE(in))
+	if (ap_answer ("ansfitspec1", Memc[str])) {
+	    call ap_gopen (gp)
+	    call icg_fit (ic, gp, "gcur", gt, cv, Memr[x], spec,
+		Memr[wts], ny)
+	    call amovkr (1., Memr[wts], ny)
+	} else
+	    call ic_fit (ic, cv, Memr[x], spec, Memr[wts], ny,
+		YES, YES, YES, YES)
+
+	# Make a graph to the plot log.
+	call ap_popen (gp, fd, "fitspec")
+	if (gp != NULL) {
+	    call icg_graphr (ic, gp, gt, cv, Memr[x], spec, Memr[wts], ny)
+	    call ap_pclose (gp, fd)
+	}
+
+	call cvvector (cv, Memr[x], spec, ny)
+	call cvfree (cv)
+end
+
+
+procedure ap_fitfree ()
+
+pointer	ic, gt
+common	/apn_com/ ic, gt
+
+begin
+	call ic_closer (ic)
+	call gt_free (gt)
+end
+
+
+# AP_LNORM -- Normalize the input line apertures by the norm spectra.
+
+procedure ap_lnorm (ap, out, gain, dbuf, nc, nl, c1, l1, spec, ny, ys, init)
+
+pointer	ap			# Aperture structure
+pointer	out			# Output IMIO pointer
+real	gain			# Gain
+pointer	dbuf			# Data buffer
+int	nc, nl			# Size of data buffer
+int	c1, l1			# Origin of data buffer
+real	spec[ny]		# Normalization spectrum
+int	ny			# Size of profile array
+int	ys			# Start of spectrum in image
+int	init			# Fill between apertures with 1?
+
+bool	clgetb()		# Center normalize?
+real	threshold, clgetr()	# Division threshold
+
+int	i, ncols, nlines, ix1, ix2, iy, nsum
+real	cen, low, high, s, x1, x2, sum, ap_cveval(), asumr()
+pointer	cv, datain, dataout, imps2r(), impl2r()
+
+begin
+	threshold = clgetr ("threshold")
+
+	cen = AP_CEN(ap,1)
+	low = AP_CEN(ap,1) + AP_LOW(ap,1)
+	high = AP_CEN(ap,1) + AP_HIGH(ap,1)
+	cv = AP_CV(ap)
+	ncols = IM_LEN(out, 1)
+	nlines = IM_LEN(out, 2)
+
+	# Normalize by the aperture width and apply threshold.
+	call adivkr (spec, high - low, spec, ny)
+	if (clgetb ("cennorm")) {
+	    sum = 0.
+	    nsum = 0
+	    do i = 1, nlines {
+		iy = i - ys + 1
+		if (iy < 1 || iy > ny)
+		    next
+		s = cen + ap_cveval (cv, real (i))
+		ix1 = max (1, int (s))
+		ix2 = min (ncols, int (s + 1))
+		if (ix1 > ix2)
+		    next
+		datain = dbuf + (i - l1) * nc + ix1 - c1
+		if (ix1 == ix2)
+		    sum = sum + Memr[datain]
+		else
+		    sum = sum + (ix2-s)*Memr[datain] + (s-ix1)*Memr[datain+1]
+		nsum = nsum + 1
+	    }
+	    if (nsum > 0) {
+	        sum = (asumr (spec, ny) / ny) / (sum / nsum / gain)
+		call adivkr (spec, sum, spec, ny)
+	    }
+	}
+	if (!IS_INDEF (threshold))
+	    call arltr (spec, ny, threshold, threshold)
+
+	do i = 1, nlines {
+	    if (init == YES) {
+	        dataout = impl2r (out, i)
+	        call amovkr (1., Memr[dataout], ncols)
+	    }
+
+	    iy = i - ys + 1
+	    if (iy < 1 || iy > ny)
+		next
+	    s = ap_cveval (cv, real (i))
+	    x1 = max (0.5, low + s) 
+	    x2 = min (ncols + 0.49, high + s) 
+	    if (x1 > x2)
+		next
+
+	    ix1 = nint (x1)
+	    ix2 = nint (x2)
+
+	    datain = dbuf + (i - l1) * nc + ix1 - c1
+	    if (init == YES)
+		dataout = dataout + ix1 - 1
+	    else
+	        dataout = imps2r (out, ix1, ix2, i, i)
+	    call adivkr (Memr[datain], spec[iy] * gain, Memr[dataout],
+		ix2-ix1+1)
+	}
+
+	call imaddr (out, "CCDMEAN", 1.)
+end
+
+
+# AP_CNORM -- Normalize the input column apertures by the norm spectra.
+
+procedure ap_cnorm (ap, out, gain, dbuf, nc, nl, c1, l1, spec, ny, ys, init)
+
+pointer	ap			# Aperture structure
+pointer	out			# Output IMIO pointer
+real	gain			# Gain
+pointer	dbuf			# Data buffer
+int	nc, nl			# Size of data buffer
+int	c1, l1			# Origin of data buffer
+real	spec[ny]		# Normalization spectrum
+int	ny			# Size of profile array
+int	ys			# Start of spectrum in image
+int	init			# Fill between apertures with 1?
+
+bool	clgetb()		# Center normalize?
+real	threshold, clgetr()	# Division threshold
+
+int	ncols, nlines, ix, iy, ix1, ix2, iy1, iy2, nsum
+real	cen, low, high, s, sum, ap_cveval(), asumr()
+pointer	sp, y1, y2, cv, datain, dataout, buf, imps2r(), impl2r()
+
+begin
+	threshold = clgetr ("threshold")
+
+	call smark (sp)
+	call salloc (y1, 2 * ny, TY_INT)
+	y1 = y1 - ys
+	y2 = y1 + ny
+
+	cen = AP_CEN(ap,2)
+	low = AP_CEN(ap,2) + AP_LOW(ap,2)
+	high = AP_CEN(ap,2) + AP_HIGH(ap,2)
+	cv = AP_CV(ap)
+	ncols = IM_LEN(out, 1)
+	nlines = IM_LEN(out, 2)
+
+	# Normalize by the aperture width and apply threshold.
+	call adivkr (spec, high - low, spec, ny)
+	if (clgetb ("cennorm")) {
+	    sum = 0.
+	    nsum = 0
+	    do ix = ys, ys+ny-1 {
+		s = cen + ap_cveval (cv, real (ix))
+		iy1 = max (1, int (s))
+		iy2 = min (nlines, int (s + 1))
+		if (iy1 > iy2)
+		    next
+		datain = dbuf + (ix - l1) * nc + iy1 - c1
+		if (iy1 == iy2)
+		    sum = sum + Memr[datain]
+		else
+		    sum = sum + (iy2-s)*Memr[datain] + (s-iy1)*Memr[datain+1]
+		nsum = nsum + 1
+	    }
+	    if (nsum > 0) {
+	        sum = (asumr (spec, ny) / ny) / (sum / nsum / gain)
+		call adivkr (spec, sum, spec, ny)
+	    }
+	}
+	if (!IS_INDEF (threshold))
+	    call arltr (spec, ny, threshold, threshold)
+
+	do ix = ys, ys+ny-1 {
+	    s = ap_cveval (cv, real (ix))
+	    Memi[y1+ix] = nint (low + s) 
+	    Memi[y2+ix] = nint (high + s) 
+	}
+	call alimi (Memi[y1+ys], 2 * ny, iy1, iy2)
+
+	do iy = 1, nlines {
+	    if (init == YES) {
+	        buf = impl2r (out, iy)
+	        call amovkr (1., Memr[buf], ncols)
+	    }
+
+	    if (iy < iy1 || iy > iy2)
+		next
+
+	    for (ix1=ys; ix1<=ys+ny-1; ix1=ix1+1) {
+		if (iy < Memi[y1+ix1] || iy > Memi[y2+ix1])
+		    next
+		for (ix2=ix1+1; ix2<=ys+ny-1; ix2=ix2+1)
+		    if (iy < Memi[y1+ix2] || iy > Memi[y2+ix2])
+			break
+		ix2 = ix2 - 1
+
+	        datain = dbuf + (ix1 - l1) * nc + iy - c1
+	        if (init == YES)
+		    dataout = buf + ix1 - 1
+	        else
+	            dataout = imps2r (out, ix1, ix2, iy, iy)
+		do ix = ix1, ix2 {
+		    Memr[dataout] = Memr[datain] / spec[ix-ys+1] / gain
+		    datain = datain +  nc
+		    dataout = dataout + 1
+		}
+		ix1 = ix2
+	    }
+	}
+
+	call imaddr (out, "CCDMEAN", 1.)
+
+	call sfree (sp)
+end
+
+
+# AP_LFLAT -- Flatten the input line apertures by the norm spectra.
+
+procedure ap_lflat (ap, out, dbuf, nc, nl, c1, l1, spec, sbuf, profile, nx, ny,
+	xs, ys, init)
+
+pointer	ap			# Aperture structure
+pointer	out			# Output IMIO pointer
+pointer	dbuf			# Data buffer
+int	nc, nl			# Size of data buffer
+int	c1, l1			# Origin of data buffer
+real	spec[ny]		# Normalization spectrum
+pointer	sbuf			# Sky buffer
+real	profile[ny,nx]		# Profile
+int	nx, ny			# Size of profile array
+int	xs[ny], ys		# Start of spectrum in image
+int	init			# Fill between apertures with 1?
+
+real	threshold, clgetr()	# Division threshold
+
+int	i, ncols, nlines, ix, iy, ix1, ix2
+real	low, high, s, x1, x2, ap_cveval()
+pointer	cv, datain, dataout, sky, imps2r(), impl2r()
+
+begin
+	threshold = clgetr ("threshold")
+	if (IS_INDEF(threshold))
+	    threshold = 0.
+	threshold = max (0., threshold)
+
+	low = AP_CEN(ap,1) + AP_LOW(ap,1)
+	high = AP_CEN(ap,1) + AP_HIGH(ap,1)
+	cv = AP_CV(ap)
+	ncols = IM_LEN(out, 1)
+	nlines = IM_LEN(out, 2)
+
+	do i = 1, nlines {
+	    if (init == YES) {
+	        dataout = impl2r (out, i)
+	        call amovkr (1., Memr[dataout], ncols)
+	    }
+
+	    iy = i - ys + 1
+	    if (iy < 1 || iy > ny)
+		next
+	    s = ap_cveval (cv, real (i))
+	    x1 = max (0.5, low + s) 
+	    x2 = min (ncols + 0.49, high + s) 
+	    if (x1 > x2)
+		next
+
+	    ix1 = nint (x1)
+	    ix2 = nint (x2)
+
+	    datain = dbuf + (i - l1) * nc + ix1 - c1
+	    if (init == YES)
+		dataout = dataout + ix1 - 1
+	    else
+	        dataout = imps2r (out, ix1, ix2, i, i)
+	    if (sbuf != NULL)
+		sky = sbuf + (iy - 1) * nx - xs[iy]
+	    do ix = ix1, ix2 {
+		s = spec[iy] * profile[iy, ix-xs[iy]+1]
+		if (sbuf != NULL)
+		    s = s + Memr[sky+ix]
+		if (s > threshold)
+		    Memr[dataout] = Memr[datain] / s
+		else
+		    Memr[dataout] = 1.
+		datain = datain + 1
+		dataout = dataout + 1
+	    }
+	}
+
+	call imaddr (out, "CCDMEAN", 1.)
+end
+
+
+# AP_CFLAT -- Flatten the input column apertures by the norm spectra.
+
+procedure ap_cflat (ap, out, dbuf, nc, nl, c1, l1, spec, sbuf, profile, nx, ny,
+    xs, ys, init)
+
+pointer	ap			# Aperture structure
+pointer	out			# Output IMIO pointer
+pointer	dbuf			# Data buffer
+int	nc, nl			# Size of data buffer
+int	c1, l1			# Origin of data buffer
+real	spec[ny]		# Normalization spectrum
+pointer	sbuf			# Sky buffer
+real	profile[ny,nx]		# Profile
+int	nx, ny			# Size of profile array
+int	xs[ny], ys		# Start of spectrum in image
+int	init			# Fill between apertures with 1?
+
+real	threshold, clgetr()	# Division threshold
+
+int	ncols, nlines, ix, iy, ix1, ix2, iy1, iy2
+real	low, high, s, ap_cveval()
+pointer	sp, y1, y2, cv, datain, dataout, sky, buf, imps2r(), impl2r()
+
+begin
+	threshold = clgetr ("threshold")
+	if (IS_INDEF(threshold))
+	    threshold = 0.
+	threshold = max (0., threshold)
+
+	call smark (sp)
+	call salloc (y1, 2 * ny, TY_INT)
+	y1 = y1 - ys
+	y2 = y1 + ny
+
+	low = AP_CEN(ap,2) + AP_LOW(ap,2)
+	high = AP_CEN(ap,2) + AP_HIGH(ap,2)
+	cv = AP_CV(ap)
+	ncols = IM_LEN(out, 1)
+	nlines = IM_LEN(out, 2)
+
+	do ix = ys, ys+ny-1 {
+	    s = ap_cveval (cv, real (ix))
+	    Memi[y1+ix] = nint (low + s) 
+	    Memi[y2+ix] = nint (high + s) 
+	}
+	call alimi (Memi[y1+ys], 2 * ny, iy1, iy2)
+
+	do iy = 1, nlines {
+	    if (init == YES) {
+	        buf = impl2r (out, iy)
+	        call amovkr (1., Memr[buf], ncols)
+	    }
+
+	    if (iy < iy1 || iy > iy2)
+		next
+
+	    for (ix1=ys; ix1<=ys+ny-1; ix1=ix1+1) {
+		if (iy < Memi[y1+ix1] || iy > Memi[y2+ix1])
+		    next
+		for (ix2=ix1+1; ix2<=ys+ny-1; ix2=ix2+1)
+		    if (iy < Memi[y1+ix2] || iy > Memi[y2+ix2])
+			break
+		ix2 = ix2 - 1
+
+	        datain = dbuf + (ix1 - l1) * nc + iy - c1
+	        if (init == YES)
+		    dataout = buf + ix1 - 1
+	        else
+	            dataout = imps2r (out, ix1, ix2, iy, iy)
+	        if (sbuf != NULL)
+		    sky = sbuf - ys * nx + iy - xs[iy]
+	        do ix = ix1, ix2 {
+		    s = spec[ix-ys+1] * profile[ix-ys+1, iy-xs[ix-ys+1]+1]
+		    if (sbuf != NULL)
+			s = s + Memr[sky+ix*nx]
+		    if (s > threshold)
+		        Memr[dataout] = Memr[datain] / s
+		    else
+		        Memr[dataout] = 1.
+		    datain = datain + nc
+		    dataout = dataout + 1
+	        }
+		ix1 = ix2
+	    }
+	}
+
+	call imaddr (out, "CCDMEAN", 1.)
+
+	call sfree (sp)
+end
+
+
+# AP_LDIFF -- Model residuals.
+
+procedure ap_ldiff (ap, out, gain, dbuf, nc, nl, c1, l1, spec, profile, nx, ny,
+	xs, ys, init)
+
+pointer	ap			# Aperture structure
+pointer	out			# Output IMIO pointer
+real	gain			# Gain
+pointer	dbuf			# Data buffer
+int	nc, nl			# Size of data buffer
+int	c1, l1			# Origin of data buffer
+real	spec[ny]		# Normalization spectrum
+real	profile[ny,nx]		# Profile
+int	nx, ny			# Size of profile array
+int	xs[ny], ys		# Start of spectrum in image
+int	init			# Fill between apertures with 1?
+
+int	i, ncols, nlines, ix, iy, ix1, ix2
+real	low, high, s, x1, x2, ap_cveval()
+pointer	cv, datain, dataout, imps2r(), impl2r()
+
+begin
+	low = AP_CEN(ap,1) + AP_LOW(ap,1)
+	high = AP_CEN(ap,1) + AP_HIGH(ap,1)
+	cv = AP_CV(ap)
+	ncols = IM_LEN(out, 1)
+	nlines = IM_LEN(out, 2)
+
+	do i = 1, nlines {
+	    if (init == YES) {
+	        dataout = impl2r (out, i)
+	        call aclrr (Memr[dataout], ncols)
+	    }
+
+	    iy = i - ys + 1
+	    if (iy < 1 || iy > ny)
+		next
+	    s = ap_cveval (cv, real (i))
+	    x1 = max (0.5, low + s) 
+	    x2 = min (ncols + 0.49, high + s) 
+	    if (x1 > x2)
+		next
+
+	    ix1 = nint (x1)
+	    ix2 = nint (x2)
+
+	    datain = dbuf + (i - l1) * nc + ix1 - c1
+	    if (init == YES)
+		dataout = dataout + ix1 - 1
+	    else
+	        dataout = imps2r (out, ix1, ix2, i, i)
+	    do ix = ix1, ix2 {
+		s = spec[iy] * profile[iy, ix-xs[iy]+1]
+		Memr[dataout] = (Memr[datain] - s) / gain
+		datain = datain + 1
+		dataout = dataout + 1
+	    }
+	}
+end
+
+
+# AP_CDIFF -- Model residuals
+
+procedure ap_cdiff (ap, out, gain, dbuf, nc, nl, c1, l1, spec, profile, nx, ny,
+    xs, ys, init)
+
+pointer	ap			# Aperture structure
+pointer	out			# Output IMIO pointer
+real	gain			# Gain
+pointer	dbuf			# Data buffer
+int	nc, nl			# Size of data buffer
+int	c1, l1			# Origin of data buffer
+real	spec[ny]		# Normalization spectrum
+real	profile[ny,nx]		# Profile
+int	nx, ny			# Size of profile array
+int	xs[ny], ys		# Start of spectrum in image
+int	init			# Fill between apertures with 1?
+
+int	ncols, nlines, ix, iy, ix1, ix2, iy1, iy2
+real	low, high, s, ap_cveval()
+pointer	sp, y1, y2, cv, datain, dataout, buf, imps2r(), impl2r()
+
+begin
+	call smark (sp)
+	call salloc (y1, 2 * ny, TY_INT)
+	y1 = y1 - ys
+	y2 = y1 + ny
+
+	low = AP_CEN(ap,2) + AP_LOW(ap,2)
+	high = AP_CEN(ap,2) + AP_HIGH(ap,2)
+	cv = AP_CV(ap)
+	ncols = IM_LEN(out, 1)
+	nlines = IM_LEN(out, 2)
+
+	do ix = ys, ys+ny-1 {
+	    s = ap_cveval (cv, real (ix))
+	    Memi[y1+ix] = nint (low + s) 
+	    Memi[y2+ix] = nint (high + s) 
+	}
+	call alimi (Memi[y1+ys], 2 * ny, iy1, iy2)
+
+	do iy = 1, nlines {
+	    if (init == YES) {
+	        buf = impl2r (out, iy)
+	        call aclrr (Memr[buf], ncols)
+	    }
+
+	    if (iy < iy1 || iy > iy2)
+		next
+
+	    for (ix1=ys; ix1<=ys+ny-1; ix1=ix1+1) {
+		if (iy < Memi[y1+ix1] || iy > Memi[y2+ix1])
+		    next
+		for (ix2=ix1+1; ix2<=ys+ny-1; ix2=ix2+1)
+		    if (iy < Memi[y1+ix2] || iy > Memi[y2+ix2])
+			break
+		ix2 = ix2 - 1
+
+	        datain = dbuf + (ix1 - l1) * nc + iy - c1
+	        if (init == YES)
+		    dataout = buf + ix1 - 1
+	        else
+	            dataout = imps2r (out, ix1, ix2, iy, iy)
+	        do ix = ix1, ix2 {
+		    s = spec[ix-ys+1] * profile[ix-ys+1, iy-xs[ix-ys+1]+1]
+		    Memr[dataout] = (Memr[datain] - s) / gain
+		    datain = datain + nc
+		    dataout = dataout + 1
+	        }
+		ix1 = ix2
+	    }
+	}
+
+	call sfree (sp)
+end
+
+
+# AP_LFIT -- Model fit
+
+procedure ap_lfit (ap, out, gain, spec, profile, nx, ny, xs, ys, init)
+
+pointer	ap			# Aperture structure
+pointer	out			# Output IMIO pointer
+real	gain			# Gain
+real	spec[ny]		# Normalization spectrum
+real	profile[ny,nx]		# Profile
+int	nx, ny			# Size of profile array
+int	xs[ny], ys		# Start of spectrum in image
+int	init			# Fill between apertures with 1?
+
+int	i, ncols, nlines, ix, iy, ix1, ix2
+real	low, high, s, x1, x2, ap_cveval()
+pointer	cv, dataout, imps2r(), impl2r()
+
+begin
+	low = AP_CEN(ap,1) + AP_LOW(ap,1)
+	high = AP_CEN(ap,1) + AP_HIGH(ap,1)
+	cv = AP_CV(ap)
+	ncols = IM_LEN(out, 1)
+	nlines = IM_LEN(out, 2)
+
+	do i = 1, nlines {
+	    if (init == YES) {
+	        dataout = impl2r (out, i)
+	        call aclrr (Memr[dataout], ncols)
+	    }
+
+	    iy = i - ys + 1
+	    if (iy < 1 || iy > ny)
+		next
+	    s = ap_cveval (cv, real (i))
+	    x1 = max (0.5, low + s) 
+	    x2 = min (ncols + 0.49, high + s) 
+	    if (x1 > x2)
+		next
+
+	    ix1 = nint (x1)
+	    ix2 = nint (x2)
+
+	    if (init == YES)
+		dataout = dataout + ix1 - 1
+	    else
+	        dataout = imps2r (out, ix1, ix2, i, i)
+	    do ix = ix1, ix2 {
+		s = spec[iy] * profile[iy, ix-xs[iy]+1]
+		Memr[dataout] = s / gain
+		dataout = dataout + 1
+	    }
+	}
+end
+
+
+# AP_CFIT -- Model fit
+
+procedure ap_cfit (ap, out, gain, spec, profile, nx, ny, xs, ys, init)
+
+pointer	ap			# Aperture structure
+pointer	out			# Output IMIO pointer
+real	gain			# Gain
+real	spec[ny]		# Normalization spectrum
+real	profile[ny,nx]		# Profile
+int	nx, ny			# Size of profile array
+int	xs[ny], ys		# Start of spectrum in image
+int	init			# Fill between apertures with 1?
+
+int	ncols, nlines, ix, iy, ix1, ix2, iy1, iy2
+real	low, high, s, ap_cveval()
+pointer	sp, y1, y2, cv, dataout, buf, imps2r(), impl2r()
+
+begin
+	call smark (sp)
+	call salloc (y1, 2 * ny, TY_INT)
+	y1 = y1 - ys
+	y2 = y1 + ny
+
+	low = AP_CEN(ap,2) + AP_LOW(ap,2)
+	high = AP_CEN(ap,2) + AP_HIGH(ap,2)
+	cv = AP_CV(ap)
+	ncols = IM_LEN(out, 1)
+	nlines = IM_LEN(out, 2)
+
+	do ix = ys, ys+ny-1 {
+	    s = ap_cveval (cv, real (ix))
+	    Memi[y1+ix] = nint (low + s) 
+	    Memi[y2+ix] = nint (high + s) 
+	}
+	call alimi (Memi[y1+ys], 2 * ny, iy1, iy2)
+
+	do iy = 1, nlines {
+	    if (init == YES) {
+	        buf = impl2r (out, iy)
+	        call aclrr (Memr[buf], ncols)
+	    }
+
+	    if (iy < iy1 || iy > iy2)
+		next
+
+	    for (ix1=ys; ix1<=ys+ny-1; ix1=ix1+1) {
+		if (iy < Memi[y1+ix1] || iy > Memi[y2+ix1])
+		    next
+		for (ix2=ix1+1; ix2<=ys+ny-1; ix2=ix2+1)
+		    if (iy < Memi[y1+ix2] || iy > Memi[y2+ix2])
+			break
+		ix2 = ix2 - 1
+
+	        if (init == YES)
+		    dataout = buf + ix1 - 1
+	        else
+	            dataout = imps2r (out, ix1, ix2, iy, iy)
+	        do ix = ix1, ix2 {
+		    s = spec[ix-ys+1] * profile[ix-ys+1, iy-xs[ix-ys+1]+1]
+		    Memr[dataout] = s / gain
+		    dataout = dataout + 1
+	        }
+		ix1 = ix2
+	    }
+	}
+
+	call sfree (sp)
+end
diff --git a/noao/twodspec/apextract/apfit1.par b/noao/twodspec/apextract/apfit1.par
new file mode 100644
index 00000000..5420917d
--- /dev/null
+++ b/noao/twodspec/apextract/apfit1.par
@@ -0,0 +1,118 @@
+# OUTPUT PARAMETERS
+
+apertures,s,h,)apall.apertures,,,>apfit.apertures
+format,s,h,)apsum.format,,,>apsum.format
+extras,b,h,)apsum.extras,,,>apsum.extras
+dbwrite,s,h,yes,,,Write to database?
+initialize,b,h,yes,,,Initialize answers?
+verbose,b,h,)_.verbose,,,"Verbose output?
+
+# DEFAULT APERTURE PARAMETERS
+"
+lower,r,h,)apdefault.lower,,,>apdefault.lower
+upper,r,h,)apdefault.upper,,,>apdefault.upper
+apidtable,s,h,)apdefault.apidtable,,,">apdefault.apidtable
+
+# DEFAULT BACKGROUND PARAMETERS
+"
+b_function,s,h,)apdefault.b_function,,,>apdefault.b_function
+b_order,i,h,)apdefault.b_order,,,>apdefault.b_order
+b_sample,s,h,)apdefault.b_sample,,,>apdefault.b_sample
+b_naverage,i,h,)apdefault.b_naverage,,,>apdefault.b_naverage
+b_niterate,i,h,)apdefault.b_niterate,,,>apdefault.b_niterate
+b_low_reject,r,h,)apdefault.b_low_reject,,,>apdefault.b_low_reject
+b_high_reject,r,h,)apdefault.b_high_reject,,,>apdefault.b_high_reject
+b_grow,r,h,)apdefault.b_grow,,,">apdefault.b_grow
+
+# APERTURE CENTERING PARAMETERS
+"
+width,r,h,)apedit.width,,,>apedit.width
+radius,r,h,)apedit.radius,,,>apedit.radius
+threshold,r,h,)apedit.threshold,,,">apedit.threshold
+
+# AUTOMATIC FINDING AND ORDERING PARAMETERS
+"
+nfind,i,h,)apfind.nfind,,,>apfind.nfind
+minsep,r,h,)apfind.minsep,,,>apfind.minsep
+maxsep,r,h,)apfind.maxsep,,,>apfind.maxsep
+order,s,h,)apfind.order,,,">apfind.order
+
+# RECENTERING PARAMETERS
+"
+aprecenter,s,h,)aprecenter.aprecenter,,,>aprecenter.aprecenter
+npeaks,r,h,)aprecenter.npeaks,,,>aprecenter.npeaks
+shift,b,h,)aprecenter.shift,,,">aprecenter.shift
+
+# RESIZING PARAMETERS
+"
+llimit,r,h,)apresize.llimit,,,>apresize.llimit
+ulimit,r,h,)apresize.ulimit,,,>apresize.ulimit
+ylevel,r,h,)apresize.ylevel,,,>apresize.ylevel
+peak,b,h,)apresize.peak,,,>apresize.peak
+bkg,b,h,)apresize.bkg,,,>apresize.bkg
+r_grow,r,h,)apresize.r_grow,,,>apresize.r_grow
+avglimits,b,h,)apresize.avglimits,,,">apresize.avglimits
+
+# EDITING PARAMETERS
+"
+e_output,s,q,,,,Output spectra rootname
+e_profiles,s,q,,,,Profile reference image
+
+# TRACING PARAMETERS
+t_nsum,i,h,)aptrace.nsum,,,>aptrace.nsum
+t_step,i,h,)aptrace.step,,,>aptrace.step
+t_nlost,i,h,)aptrace.nlost,,,>aptrace.nlost
+t_width,r,h,)apedit.width,,,>apedit.width
+t_function,s,h,)aptrace.function,,,>aptrace.function
+t_order,i,h,)aptrace.order,,,>aptrace.order
+t_sample,s,h,)aptrace.sample,,,>aptrace.sample
+t_naverage,i,h,)aptrace.naverage,,,>aptrace.naverage
+t_niterate,i,h,)aptrace.niterate,,,>aptrace.niterate
+t_low_reject,r,h,)aptrace.low_reject,,,>aptrace.low_reject
+t_high_reject,r,h,)aptrace.high_reject,,,>aptrace.high_reject
+t_grow,r,h,)aptrace.grow,,,">aptrace.grow
+
+# EXTRACTION PARAMETERS
+"
+background,s,h,)apfit.background,,,>apfit.background
+skybox,i,h,)apfit.skybox,,,>apfit.skybox
+weights,s,h,"none",,,Extraction weights (none|variance)
+pfit,s,h,)apfit.pfit,,,>apfit.pfit
+clean,b,h,)apfit.clean,,,>apfit.clean
+nclean,r,h,0.5,,,Maximum number of pixels to clean
+niterate,i,h,5,0,,Number of profile fitting iterations
+saturation,r,h,)apfit.saturation,,,>apfit.saturation
+readnoise,s,h,)apfit.readnoise,,,>apfit.readnoise
+gain,s,h,)apfit.gain,,,>apfit.gain
+lsigma,r,h,)apfit.lsigma,,,>apfit.lsigma
+usigma,r,h,)apfit.usigma,,,>apfit.usigma
+polysep,r,h,0.90,0.1,0.95,Marsh algorithm polynomial spacing
+polyorder,i,h,10,1,,Marsh algorithm polynomial order
+nsubaps,i,h,1,,,"Number of subapertures per aperture
+
+# ANSWER PARAMETERS
+"
+ansclobber,s,h,"no",,," "
+ansclobber1,s,h,"no",,," "
+ansdbwrite,s,h,"yes",,," "
+ansdbwrite1,s,h,"yes",,," "
+ansedit,s,h,"yes",,," "
+ansextract,s,h,"yes",,," "
+ansfind,s,h,"yes",,," "
+ansfit,s,h,"yes",,," "
+ansfitscatter,s,h,"yes",,," "
+ansfitsmooth,s,h,"yes",,," "
+ansfitspec,s,h,"yes",,," "
+ansfitspec1,s,h,"yes",,," "
+ansfittrace,s,h,"yes",,," "
+ansfittrace1,s,h,"yes",,," "
+ansflat,s,h,"yes",,," "
+ansmask,s,h,"yes",,," "
+ansnorm,s,h,"yes",,," "
+ansrecenter,s,h,"yes",,," "
+ansresize,s,h,"yes",,," "
+ansreview,s,h,"yes",,," "
+ansreview1,s,h,"yes",,," "
+ansscat,s,h,"yes",,," "
+anssmooth,s,h,"yes",,," "
+anstrace,s,h,"yes",,," "
diff --git a/noao/twodspec/apextract/apflat1.par b/noao/twodspec/apextract/apflat1.par
new file mode 100644
index 00000000..0fac8391
--- /dev/null
+++ b/noao/twodspec/apextract/apflat1.par
@@ -0,0 +1,117 @@
+# OUTPUT PARAMETERS
+
+format,s,h,)apsum.format,,,>apsum.format
+extras,b,h,)apsum.extras,,,>apsum.extras
+dbwrite,s,h,yes,,,Write to database?
+initialize,b,h,yes,,,Initialize answers?
+verbose,b,h,)_.verbose,,,"Verbose output?
+
+# DEFAULT APERTURE PARAMETERS
+"
+lower,r,h,)apdefault.lower,,,>apdefault.lower
+upper,r,h,)apdefault.upper,,,>apdefault.upper
+apidtable,s,h,)apdefault.apidtable,,,">apdefault.apidtable
+
+# DEFAULT BACKGROUND PARAMETERS
+"
+b_function,s,h,)apdefault.b_function,,,>apdefault.b_function
+b_order,i,h,)apdefault.b_order,,,>apdefault.b_order
+b_sample,s,h,)apdefault.b_sample,,,>apdefault.b_sample
+b_naverage,i,h,)apdefault.b_naverage,,,>apdefault.b_naverage
+b_niterate,i,h,)apdefault.b_niterate,,,>apdefault.b_niterate
+b_low_reject,r,h,)apdefault.b_low_reject,,,>apdefault.b_low_reject
+b_high_reject,r,h,)apdefault.b_high_reject,,,>apdefault.b_high_reject
+b_grow,r,h,)apdefault.b_grow,,,">apdefault.b_grow
+
+# APERTURE CENTERING PARAMETERS
+"
+width,r,h,)apedit.width,,,>apedit.width
+radius,r,h,)apedit.radius,,,>apedit.radius
+threshold,r,h,)apedit.threshold,,,">apedit.threshold
+
+# AUTOMATIC FINDING AND ORDERING PARAMETERS
+"
+nfind,i,h,)apfind.nfind,,,>apfind.nfind
+minsep,r,h,)apfind.minsep,,,>apfind.minsep
+maxsep,r,h,)apfind.maxsep,,,>apfind.maxsep
+order,s,h,)apfind.order,,,">apfind.order
+
+# RECENTERING PARAMETERS
+"
+aprecenter,s,h,)aprecenter.aprecenter,,,>aprecenter.aprecenter
+npeaks,r,h,)aprecenter.npeaks,,,>aprecenter.npeaks
+shift,b,h,)aprecenter.shift,,,">aprecenter.shift
+
+# RESIZING PARAMETERS
+"
+llimit,r,h,)apresize.llimit,,,>apresize.llimit
+ulimit,r,h,)apresize.ulimit,,,>apresize.ulimit
+ylevel,r,h,)apresize.ylevel,,,>apresize.ylevel
+peak,b,h,)apresize.peak,,,>apresize.peak
+bkg,b,h,)apresize.bkg,,,>apresize.bkg
+r_grow,r,h,)apresize.r_grow,,,>apresize.r_grow
+avglimits,b,h,)apresize.avglimits,,,">apresize.avglimits
+
+# EDITING PARAMETERS
+"
+e_output,s,q,,,,Output spectra rootname
+e_profiles,s,q,,,,Profile reference image
+
+# TRACING PARAMETERS
+t_nsum,i,h,)aptrace.nsum,,,>aptrace.nsum
+t_step,i,h,)aptrace.step,,,>aptrace.step
+t_nlost,i,h,)aptrace.nlost,,,>aptrace.nlost
+t_width,r,h,)apedit.width,,,>apedit.width
+t_function,s,h,)aptrace.function,,,>aptrace.function
+t_order,i,h,)aptrace.order,,,>aptrace.order
+t_sample,s,h,)aptrace.sample,,,>aptrace.sample
+t_naverage,i,h,)aptrace.naverage,,,>aptrace.naverage
+t_niterate,i,h,)aptrace.niterate,,,>aptrace.niterate
+t_low_reject,r,h,)aptrace.low_reject,,,>aptrace.low_reject
+t_high_reject,r,h,)aptrace.high_reject,,,>aptrace.high_reject
+t_grow,r,h,)aptrace.grow,,,">aptrace.grow
+
+# EXTRACTION PARAMETERS
+"
+background,s,h,"none",,,>apflatten.background
+skybox,i,h,1,,,>apflatten.skybox
+weights,s,h,"none",,,Extraction weights (none|variance)
+pfit,s,h,)apflatten.pfit,,,>apflatten.pfit
+clean,b,h,)apflatten.clean,,,>apflatten.clean
+nclean,r,h,0.5,,,Maximum number of pixels to clean
+niterate,i,h,5,0,,Number of profile fitting iterations
+saturation,r,h,)apflatten.saturation,,,>apflatten.saturation
+readnoise,s,h,)apflatten.readnoise,,,>apflatten.readnoise
+gain,s,h,)apflatten.gain,,,>apflatten.gain
+lsigma,r,h,)apflatten.lsigma,,,>apflatten.lsigma
+usigma,r,h,)apflatten.usigma,,,>apflatten.usigma
+polysep,r,h,0.90,0.1,0.90,Marsh algorithm polynomial spacing
+polyorder,i,h,10,1,,Marsh algorithm polynomial order
+nsubaps,i,h,1,,,"Number of subapertures per aperture
+
+# ANSWER PARAMETERS
+"
+ansclobber,s,h,"no",,," "
+ansclobber1,s,h,"no",,," "
+ansdbwrite,s,h,"yes",,," "
+ansdbwrite1,s,h,"yes",,," "
+ansedit,s,h,"yes",,," "
+ansextract,s,h,"yes",,," "
+ansfind,s,h,"yes",,," "
+ansfit,s,h,"yes",,," "
+ansfitscatter,s,h,"yes",,," "
+ansfitsmooth,s,h,"yes",,," "
+ansfitspec,s,h,"yes",,," "
+ansfitspec1,s,h,"yes",,," "
+ansfittrace,s,h,"yes",,," "
+ansfittrace1,s,h,"yes",,," "
+ansflat,s,h,"yes",,," "
+ansmask,s,h,"yes",,," "
+ansnorm,s,h,"yes",,," "
+ansrecenter,s,h,"yes",,," "
+ansresize,s,h,"yes",,," "
+ansreview,s,h,"yes",,," "
+ansreview1,s,h,"yes",,," "
+ansscat,s,h,"yes",,," "
+anssmooth,s,h,"yes",,," "
+anstrace,s,h,"yes",,," "
diff --git a/noao/twodspec/apextract/apflatten.par b/noao/twodspec/apextract/apflatten.par
new file mode 100644
index 00000000..84e5906c
--- /dev/null
+++ b/noao/twodspec/apextract/apflatten.par
@@ -0,0 +1,37 @@
+# APFLATTEN
+
+input,s,a,,,,List of images to flatten
+output,s,a,,,,List of output flatten images
+apertures,s,h,"",,,Apertures
+references,s,h,"",,,"List of reference images
+"
+interactive,b,h,yes,,,Run task interactively?
+find,b,h,yes,,,Find apertures?
+recenter,b,h,yes,,,Recenter apertures?
+resize,b,h,yes,,,Resize apertures?
+edit,b,h,yes,,,Edit apertures?
+trace,b,h,yes,,,Trace apertures?
+fittrace,b,h,yes,,,Fit traced points interactively?
+flatten,b,h,yes,,,Flatten spectra?
+fitspec,b,h,yes,,,"Fit normalization spectra interactively?
+"
+line,i,h,INDEF,1,,Dispersion line
+nsum,i,h,10,,,Number of dispersion lines to sum or median
+threshold,r,h,10.,,,"Threshold for flattening spectra
+"
+pfit,s,h,"fit1d","fit1d|fit2d",,Profile fitting type (fit1d|fit2d)
+clean,b,h,no,,,Detect and replace bad pixels?
+saturation,r,h,INDEF,,,Saturation level
+readnoise,s,h,"0.",,,Read out noise sigma (photons)
+gain,s,h,"1.",,,Photon gain (photons/data number)
+lsigma,r,h,4.,0.,,Lower rejection threshold
+usigma,r,h,4.,0.,,"Upper rejection threshold
+"
+function,s,h,"legendre","chebyshev|legendre|spline1|spline3",,Fitting function for normalization spectra
+order,i,h,1,1,,Fitting function order
+sample,s,h,"*",,,Sample regions
+naverage,i,h,1,,,Average or median
+niterate,i,h,0,0,,Number of rejection iterations
+low_reject,r,h,3.,0.,,Lower rejection sigma
+high_reject,r,h,3.,0.,,High upper rejection sigma
+grow,r,h,0.,0.,,Rejection growing radius
diff --git a/noao/twodspec/apextract/apgetdata.x b/noao/twodspec/apextract/apgetdata.x
new file mode 100644
index 00000000..6645a6c3
--- /dev/null
+++ b/noao/twodspec/apextract/apgetdata.x
@@ -0,0 +1,99 @@
+include	<imhdr.h>
+
+# AP_GETDATA -- Get the summed dispersion line.
+# Return the IMIO pointer, pointer to image data, the aperture axis and title.
+# The pointers must be freed by the calling program.  Note that the value of
+# line may be changed.
+
+procedure ap_getdata (image, line, nsum, im, imdata, npts, apaxis, title)
+
+char	image[SZ_FNAME]		# Image name
+int	line			# Dispersion line to graph
+int	nsum			# Number of dispersion lines to sum
+pointer	im			# IMIO pointer
+pointer	imdata			# Pointer to image data
+int	npts			# Number of pixels 
+int	apaxis			# Aperture axis
+pointer	title			# Title for image data
+
+int	i, j, k, l, n, dispaxis
+pointer	buf, medbuf
+
+real	asumr(), amedr()
+pointer	ap_immap(), imgs2r()
+
+errchk	ap_immap, imgs2r
+
+begin
+	# Map the image
+	im = ap_immap (image, apaxis, dispaxis)
+
+	# Determine the dispersion and aperture axes.
+	if (IS_INDEFI (line))
+	    line = IM_LEN(im, dispaxis) / 2
+	else
+	    line = max (1, min (IM_LEN(im, dispaxis), line))
+
+	# Allocate memory for the image line and title.
+	npts = IM_LEN(im, apaxis)
+	call calloc (imdata, npts, TY_REAL)
+	call malloc (title, SZ_LINE, TY_CHAR)
+
+	# Sum the specified number of dispersion lines.
+	n = max (1, abs (nsum))
+	switch (apaxis) {
+	case 1:
+	    i = max (1, line - n / 2)
+	    j = min (IM_LEN(im, dispaxis), i + n - 1)
+	    i = max (1, j - n + 1)
+	    buf = imgs2r (im, 1, npts, i, j)
+	    j = j - i + 1
+	    if (j < 3 || nsum > 0) {
+		do k = 1, j
+		    call aaddr (Memr[buf+(k-1)*npts], Memr[imdata],
+			Memr[imdata], npts)
+		call sprintf (Memc[title], SZ_LINE,
+		    "Image=%s, Sum of lines %d-%d")
+		    call pargstr (image)
+		    call pargi (i)
+		    call pargi (i+j-1)
+	    } else {
+		call malloc (medbuf, j, TY_REAL)
+		do k = 0, npts-1 {
+		    do l = 0, j-1
+			Memr[medbuf+l] = Memr[buf+l*npts+k]
+		    Memr[imdata+k] = amedr (Memr[medbuf], j)
+		}
+		call mfree (medbuf, TY_REAL)
+		call sprintf (Memc[title], SZ_LINE,
+		    "Image=%s, Median of lines %d-%d")
+		    call pargstr (image)
+		    call pargi (i)
+		    call pargi (i+j-1)
+	    }
+
+	case 2:
+	    i = max (1, line - n / 2)
+	    j = min (IM_LEN(im, dispaxis), i + n - 1)
+	    i = max (1, j - n + 1)
+	    buf = imgs2r (im, i, j, 1, npts)
+	    j = j - i + 1
+	    if (j < 3 || nsum > 0) {
+		do k = 1, npts
+		    Memr[imdata+k-1] = asumr (Memr[buf+(k-1)*j], j)
+		call sprintf (Memc[title], SZ_LINE,
+		    "Image=%s, Sum of columns %d-%d")
+		    call pargstr (image)
+		    call pargi (i)
+		    call pargi (i+j-1)
+	    } else {
+		do k = 1, npts
+		    Memr[imdata+k-1] = amedr (Memr[buf+(k-1)*j], j)
+		call sprintf (Memc[title], SZ_LINE,
+		    "Image=%s, Median of columns %d-%d")
+		    call pargstr (image)
+		    call pargi (i)
+		    call pargi (i+j-1)
+	    }
+	}
+end
diff --git a/noao/twodspec/apextract/apgetim.x b/noao/twodspec/apextract/apgetim.x
new file mode 100644
index 00000000..c5bc96f8
--- /dev/null
+++ b/noao/twodspec/apextract/apgetim.x
@@ -0,0 +1,73 @@
+# AP_GETIM -- Standardize image name so that different ways of specifying
+# the images map to the same database and output rootnames.
+
+int procedure ap_getim (list, image, maxchar)
+
+int	list			#I Image list
+char	image[maxchar]		#O Image name
+int	maxchar			#I Maximum number of chars in image name
+
+char	ksection[SZ_FNAME]	#O Image name
+
+int	i, j, stat, cl_index, cl_size
+pointer	im
+pointer	sp, cluster, section
+
+int	imtgetim(), strlen(), stridxs(), ctoi()
+pointer	immap()
+
+begin
+	# Get next image name.
+	stat = imtgetim (list, image, maxchar)
+	if (stat == EOF)
+	    return (stat)
+
+	call smark (sp)
+	call salloc (cluster, SZ_FNAME, TY_CHAR)
+	call salloc (section, SZ_FNAME, TY_CHAR)
+
+	call imparse (image, Memc[cluster], SZ_FNAME, ksection, SZ_FNAME,
+	    Memc[section], SZ_FNAME, cl_index, cl_size)
+
+	# Strip the extension.
+	call xt_imroot (Memc[cluster], Memc[cluster], SZ_FNAME)
+
+	# Generate standard ksection.  Only map image if index used.
+	# Don't worry about cases with both an index and ksection.
+
+	if (cl_index < 0 && ksection[1] == EOS)
+	    ;
+	else if (cl_index == 0)
+	    ksection[1] = EOS
+	else {
+	    if (cl_index > 0) {
+		im = immap (image, READ_ONLY, 0)
+		ksection[1] = '['
+		call imgstr (im, "extname", ksection[2], SZ_FNAME-1)
+		i = strlen (ksection)
+		ifnoerr (call imgstr (im, "extver" ,
+		    ksection[i+2], SZ_FNAME-i-1)) {
+		    ksection[i+1] = ','
+		    i = strlen (ksection)
+		}
+		ksection[i+1] = ']'
+		ksection[i+2] = EOS
+		call imunmap (im)
+	    } else {
+		i = stridxs (",", ksection[2]) + 2
+		if (i > 2) {
+		    j = ctoi (ksection, i, j)
+		    ksection[i] = ']'
+		    ksection[i+1] = EOS
+		}
+	    }
+	}
+
+	call sprintf (image, maxchar, "%s%s%s")
+	    call pargstr (Memc[cluster])
+	    call pargstr (ksection)
+	    call pargstr (Memc[section])
+
+	call sfree (sp)
+	return (stat)
+end
diff --git a/noao/twodspec/apextract/apgmark.x b/noao/twodspec/apextract/apgmark.x
new file mode 100644
index 00000000..72ad6a68
--- /dev/null
+++ b/noao/twodspec/apextract/apgmark.x
@@ -0,0 +1,126 @@
+include	<pkg/rg.h>
+include	"apertures.h"
+
+# AP_GMARK -- Mark an aperture.
+
+define	SZ_TEXT	10	# Maximum size of aperture number string
+
+procedure ap_gmark (gp, imvec, aps, naps)
+
+pointer	gp			# GIO pointer
+int	imvec			# Image vector
+pointer	aps[ARB]		# Aperture data
+int	naps			# Number of apertures
+
+int	i, apaxis
+real	x1, x2, y1, y2, dy, xc, xl, xu
+pointer	sp, text, format, ap
+
+int	itoc()
+real	ap_cveval()
+
+begin
+	# The aperture is marked at the top of the graph.
+	call smark (sp)
+	call salloc (text, SZ_TEXT, TY_CHAR)
+
+	call ggwind (gp, xl, xu, y1, y2)
+	x1 = min (xl, xu)
+	x2 = max (xl, xu)
+	dy = 0.025 * (y2 - y1)
+	y1 = y2 - 4 * dy
+
+	if (naps > 20) {
+	    call salloc (format, SZ_LINE, TY_CHAR)
+	    call sprintf (Memc[format], SZ_LINE, "h=c,v=b,s=%4.2f")
+		call pargr (20. / naps)
+	}
+ 
+	for (i = 1; i <= naps; i = i + 1) {
+	    ap = aps[i]
+	    apaxis = AP_AXIS(ap)
+
+	    xc = AP_CEN(ap, apaxis) + ap_cveval (AP_CV(ap), real (imvec))
+	    xl = xc + AP_LOW(ap, apaxis)
+	    xu = xc + AP_HIGH(ap, apaxis)
+	    call gline (gp, xc, y1 - 2 * dy, xc, y1 + 2 * dy)
+	    call gline (gp, xl, y1 - dy, xl, y1 + dy)
+	    call gline (gp, xu, y1 - dy, xu, y1 + dy)
+	    call gline (gp, xl, y1, xu, y1)
+	    if ((xc > x1) && (xc < x2)) {
+	        if (itoc (AP_ID(ap), Memc[text], SZ_TEXT) > 0) {
+		    if (naps > 20)
+		        call gtext (gp, xc, y1 + 2.5 * dy, Memc[text],
+			    Memc[format])
+		    else
+		        call gtext (gp, xc, y1 + 2.5 * dy, Memc[text],
+			    "h=c,v=b")
+		}
+	    }
+	}
+
+	call sfree (sp)
+end
+
+
+# AP_GMARKB -- Mark backgrounds.
+
+procedure ap_gmarkb (gp, imvec, aps, naps)
+
+pointer	gp			# GIO pointer
+int	imvec			# Image vector
+pointer	aps[ARB]		# Aperture data
+int	naps			# Number of apertures
+
+int	i, j, nx, apaxis
+real	x1, x2, y1, y2, dy, xc, xl, xu
+pointer	sp, sample, x, ap, rg
+
+real	ap_cveval()
+pointer	rg_xrangesr()
+
+begin
+	call smark (sp)
+	call salloc (sample, SZ_LINE, TY_CHAR)
+
+	# The background is marked at the bottom of the graph.
+	call ggwind (gp, xl, xu, y1, y2)
+	x1 = min (xl, xu)
+	x2 = max (xl, xu)
+	dy = 0.005 * (y2 - y1)
+	y1 = y1 + 4 * dy
+
+	# Allocate x array.
+	nx = x2 - x1 + 2
+	call salloc (x, nx, TY_REAL)
+
+	for (i = 1; i <= naps; i = i + 1) {
+	    ap = aps[i]
+	    apaxis = AP_AXIS(ap)
+
+	    xc = AP_CEN(ap, apaxis) + ap_cveval (AP_CV(ap), real (imvec))
+
+	    if (AP_IC(ap) == NULL)
+		next
+	    call ic_gstr (AP_IC(ap), "sample", Memc[sample], SZ_LINE)
+
+	    do j = 0, nx-1
+		Memr[x+j] = x1 + j - xc
+	    rg = rg_xrangesr (Memc[sample], Memr[x], nx)
+
+	    do j = 1, RG_NRGS(rg) {
+		xl = Memr[x+RG_X1(rg,j)-1] + xc
+		xu = Memr[x+RG_X2(rg,j)-1] + xc
+		if (xl > x1 && xl < x2)
+		    call gline (gp, xl, y1-dy, xl, y1+dy)
+		if (xu > x1 && xu < x2)
+		    call gline (gp, xu, y1-dy, xu, y1+dy)
+		call gline (gp, xl, y1, xu, y1)
+
+	    }
+
+	    call rg_free (rg)
+	}
+
+	call sfree (sp)
+end
diff --git a/noao/twodspec/apextract/apgraph.x b/noao/twodspec/apextract/apgraph.x
new file mode 100644
index 00000000..47d71646
--- /dev/null
+++ b/noao/twodspec/apextract/apgraph.x
@@ -0,0 +1,145 @@
+include	<pkg/gtools.h>
+include	"apertures.h"
+
+
+# AP_GRAPH -- Graph the image data and call ap_gmark to mark the apertures.
+
+procedure ap_graph (gp, gt, imdata, npts, imvec, aps, naps)
+
+pointer	gp			# GIO pointer
+pointer	gt			# GTOOLS pointer
+real	imdata[npts]		# Image data
+int	npts			# Number points in image data
+int	imvec			# Image vector
+pointer	aps[ARB]		# Aperture pointers
+int	naps			# Number of apertures
+
+real	x1, x2
+
+begin
+	call gclear (gp)
+
+	x1 = 1.
+	x2 = npts
+	call gswind (gp, x1, x2, INDEF, INDEF)
+	call gascale (gp, imdata, npts, 2)
+	call gt_swind (gp, gt)
+	call gt_labax (gp, gt)
+	call gvline (gp, imdata, npts, x1, x2)
+
+	call ap_gmark (gp, imvec, aps, naps)
+	if (naps == 1)
+	    call ap_gmarkb (gp, imvec, aps, naps)
+end
+
+
+# AP_PLOT -- Make a plot of the apertures if plot output is defined.
+
+procedure ap_plot (image, line, nsum, aps, naps)
+
+char	image[SZ_FNAME]		# Image to be edited
+int	line			# Dispersion line
+int	nsum			# Number of dispersion lines to sum
+
+pointer	aps[ARB]		# Aperture pointers
+int	naps			# Number of apertures
+
+int	npts, apaxis, fd
+pointer	im, imdata, title, gp, gt, gt_init()
+errchk	ap_getdata, ap_popen
+
+begin
+	call ap_popen (gp, fd, "aps")
+	if (gp == NULL)
+	    return
+
+	# Map the image and get the image data.
+	call ap_getdata (image, line, nsum, im, imdata, npts, apaxis, title)
+
+	gt = gt_init()
+	call gt_sets (gt, GTTITLE, Memc[title])
+	call gt_sets (gt, GTPARAMS, "")
+	call gt_setr (gt, GTXMIN, INDEF)
+	call gt_setr (gt, GTXMAX, INDEF)
+	call gt_setr (gt, GTYMIN, INDEF)
+	call gt_setr (gt, GTYMAX, INDEF)
+
+	call ap_graph (gp, gt, Memr[imdata], npts, line, aps, naps)
+
+	call mfree (imdata, TY_REAL)
+	call mfree (title, TY_CHAR)
+	call ap_pclose (gp, fd)
+	call gt_free (gt)
+	call imunmap (im)
+end
+
+
+# AP_GRAPH1 -- Make a graph of the extracted 1D spectrum.
+
+procedure ap_graph1 (gt, bufout, npts, nspec)
+
+pointer	gt			# GTOOLS pointer
+real	bufout[npts, nspec]	# Data
+int	npts			# Number of data points
+int	nspec			# Number of spectra
+
+real	wx, wy
+int	i, wcs, key, gt_gcur()
+pointer	sp, str, gp
+errchk	ap_gopen
+
+begin
+	call smark (sp)
+	call salloc (str, SZ_LINE, TY_CHAR)
+
+	call ap_gopen (gp)
+	call gclear (gp)
+	call gswind (gp, 1., real (npts), INDEF, INDEF)
+	call gascale (gp, bufout, npts * nspec, 2)
+	call gt_swind (gp, gt)
+	call gt_labax (gp, gt)
+	do i = 1, nspec
+	    call gvline (gp, bufout[1,i], npts, 1., real (npts))
+	call gflush (gp)
+
+	while (gt_gcur ("gcur", wx, wy, wcs, key, Memc[str],
+	    SZ_LINE) != EOF) {
+	    switch (key) {
+	    case 'I':
+		call fatal (0, "Interrupt")
+	    }
+	}
+
+	call sfree (sp)
+end
+
+
+# AP_PLOT1 -- Make a plot of the extracted 1D spectrum.
+
+procedure ap_plot1 (gt, bufout, npts, nspec)
+
+pointer	gt			# GTOOLS pointer
+real	bufout[npts,nspec]	# Data
+int	npts			# Number of data points
+int	nspec			# Number of spectra
+
+int	i, fd
+pointer	gp
+errchk	ap_popen
+
+begin
+	call ap_popen (gp, fd, "spec")
+	if (gp == NULL)
+	    return
+
+	call gclear (gp)
+	call gswind (gp, 1., real (npts), INDEF, INDEF)
+	call gascale (gp, bufout, npts * nspec, 2)
+	call gt_swind (gp, gt)
+	call gt_labax (gp, gt)
+	do i = 1, nspec
+	    call gvline (gp, bufout[1,i], npts, 1., real (npts))
+	call gflush (gp)
+
+	call ap_pclose (gp, fd)
+end
diff --git a/noao/twodspec/apextract/apgscur.x b/noao/twodspec/apextract/apgscur.x
new file mode 100644
index 00000000..5306ff9a
--- /dev/null
+++ b/noao/twodspec/apextract/apgscur.x
@@ -0,0 +1,28 @@
+include	"apertures.h"
+
+# AP_GSCUR -- Set the graphics cursor to the aperture given by the index.
+# It computes the position of the cursor for the specified dispersion line.
+
+procedure ap_gscur (index, gp, line, aps, y)
+
+int	index			# Index of aperture
+pointer	gp			# GIO pointer
+int	line			# Dispersion line
+pointer	aps[ARB]		# Apertures
+real	y			# Y cursor coordinate
+
+int	apaxis
+real	x
+pointer	ap
+
+real	ap_cveval()
+
+begin
+	if (index < 1 || IS_INDEF (y))
+	    return
+
+	ap = aps[index]
+	apaxis = AP_AXIS(ap)
+	x = AP_CEN(ap, apaxis) + ap_cveval (AP_CV(ap), real (line))
+	call gscur (gp, x, y)
+end
diff --git a/noao/twodspec/apextract/apicset.x b/noao/twodspec/apextract/apicset.x
new file mode 100644
index 00000000..b837a991
--- /dev/null
+++ b/noao/twodspec/apextract/apicset.x
@@ -0,0 +1,84 @@
+include	<imhdr.h>
+include	"apertures.h"
+
+# AP_ICSET -- Set the background fitting ICFIT structure for an aperture.
+# If the input template aperture is NULL then the output background fitting
+# ICFIT pointer is initialized otherwise a copy from the input template
+# aperture is made.
+
+procedure ap_icset (apin, apout, imlen)
+
+pointer	apin		# Input template aperture pointer
+pointer	apout		# Output aperture pointer
+int	imlen		# Image length along aperture axis
+
+int	i
+real	x, x1, x2
+pointer	ic, sp, str
+
+int	apgeti(), ctor()
+real	apgetr()
+
+begin
+	call smark (sp)
+	call salloc (str, SZ_LINE, TY_CHAR)
+
+	if (AP_IC(apout) == NULL)
+	    call ic_open (AP_IC(apout))
+	ic = AP_IC(apout)
+
+	if (apin == NULL) {
+	    call apgstr ("b_function", Memc[str], SZ_LINE)
+	    call ic_pstr (ic, "function", Memc[str])
+	    call ic_puti (ic, "order", apgeti ("b_order"))
+	    call apgstr ("b_sample", Memc[str], SZ_LINE)
+	    for (i=str; Memc[i]==' '; i=i+1)
+		;
+	    if (Memc[i] == EOS)
+		call strcpy ("*", Memc[str], SZ_LINE)
+	    call ic_pstr (ic, "sample", Memc[str])
+	    call ic_puti (ic, "naverage", apgeti ("b_naverage"))
+	    call ic_puti (ic, "niterate", apgeti ("b_niterate"))
+	    call ic_putr (ic, "low", apgetr ("b_low_reject"))
+	    call ic_putr (ic, "high", apgetr ("b_high_reject"))
+	    call ic_putr (ic, "grow", apgetr ("b_grow"))
+	    if (AP_AXIS(apout) == 1)
+		    call ic_pstr (ic, "xlabel", "Column")
+		else
+		    call ic_pstr (ic, "xlabel", "Line")
+	} else {
+	    if (AP_IC(apin) == NULL) {
+		call ic_closer (AP_IC(apout))
+		AP_IC(apout) = NULL
+		ic = NULL
+	    } else if (AP_IC(apin) != ic)
+	        call ic_copy (AP_IC(apin), ic)
+	}
+
+	# Set the background limits
+	if (ic != NULL) {
+	    i = AP_AXIS(apout)
+	    x1 = AP_LOW(apout, i)
+	    x2 = AP_HIGH(apout, i)
+
+	    call ic_gstr (ic, "sample", Memc[str], SZ_LINE)
+	    for (i=str; Memc[i]!=EOS; i=i+1)
+		if (Memc[i] == ':')
+		    Memc[i] = ','
+	    for (i=1; Memc[str+i-1]!=EOS; i=i+1) {
+		if (Memc[str+i-1] == '*') {
+		    x1 = min (x1, real(-imlen))
+		    x2 = max (x2, real(imlen))
+		} else if (ctor (Memc[str], i, x) > 0) {
+		    x1 = min (x1, x)
+		    x2 = max (x2, x)
+		    i = i - 1
+	        }
+	    }
+
+	    call ic_putr (ic, "xmin", x1)
+	    call ic_putr (ic, "xmax", x2)
+	}
+
+	call sfree (sp)
+end
diff --git a/noao/twodspec/apextract/apids.x b/noao/twodspec/apextract/apids.x
new file mode 100644
index 00000000..572890a5
--- /dev/null
+++ b/noao/twodspec/apextract/apids.x
@@ -0,0 +1,401 @@
+include	<error.h>
+include	<mach.h>
+include	"apertures.h"
+
+# Data structure for user aperture id table.
+define	IDS_LEN		4		# Length of ID structure
+define	IDS_NIDS	Memi[$1]	# Number of aperture IDs
+define	IDS_APS		Memi[$1+1]	# Aperture numbers (pointer)
+define	IDS_BEAMS	Memi[$1+2]	# Beam numbers (pointer)
+define	IDS_TITLES	Memi[$1+3]	# Titles (pointer)
+
+# AP_GIDS -- Get user aperture ID's.
+
+procedure ap_gids (ids)
+
+pointer	ids		# ID structure
+
+int	nids, ap, beam, fd, nalloc
+double	ra, dec
+pointer	sp, key, str, aps, beams, titles, im, list
+
+int	nowhite(), open(), fscan(), nscan()
+pointer	immap(), imofnlu(), imgnfn()
+errchk	open
+
+begin
+	call smark (sp)
+	call salloc (key, SZ_FNAME, TY_CHAR)
+	call salloc (str, SZ_LINE, TY_CHAR)
+
+	nids = 0
+	nalloc = 0
+
+	call apgstr ("apidtable", Memc[key], SZ_FNAME)
+	if (nowhite (Memc[key], Memc[key], SZ_FNAME) > 0) {
+	    iferr {
+		# Read aperture information from an image.
+		ifnoerr (im = immap (Memc[key], READ_ONLY, 0)) {
+		    list = imofnlu (im, "SLFIB[0-9]*")
+		    while (imgnfn (list, Memc[key], SZ_FNAME) != EOF) {
+			call imgstr (im, Memc[key], Memc[str], SZ_LINE)
+			call sscan (Memc[str])
+			call gargi (ap)
+			if (nscan() == 0)
+			    next
+			if (ap < 1) {
+			    call imcfnl (list)
+			    call imunmap (im)
+			    call error (1,
+				"Aperture numbers in apidtable must be > 0")
+			}
+			if (nalloc == 0) {
+			    nalloc = 50
+			    call malloc (aps, nalloc, TY_INT)
+			    call malloc (beams, nalloc, TY_INT)
+			    call malloc (titles, nalloc, TY_POINTER)
+			} else if (nids == nalloc) {
+			    nalloc = nalloc + 50
+			    call realloc (aps, nalloc, TY_INT)
+			    call realloc (beams, nalloc, TY_INT)
+			    call realloc (titles, nalloc, TY_POINTER)
+			}
+			Memi[aps+nids] = ap
+			call gargi (Memi[beams+nids])
+			call gargd (ra)
+			call gargd (dec)
+			if (nscan() != 4) {
+			    call reset_scan ()
+			    call gargi (ap)
+			    call gargi (beam)
+			    Memc[str] = EOS
+			    call gargstr (Memc[str], SZ_LINE)	
+			    call xt_stripwhite (Memc[str])
+			    if (Memc[str] == EOS)
+				Memi[titles+nids] = NULL
+			    else {
+				call malloc (Memi[titles+nids], SZ_APTITLE,
+				    TY_CHAR)
+				call strcpy (Memc[str], Memc[Memi[titles+nids]],
+				    SZ_APTITLE)
+			    }
+			} else {
+			    Memc[str] = EOS
+			    call gargstr (Memc[str], SZ_LINE)	
+			    call xt_stripwhite (Memc[str])
+			    call malloc (Memi[titles+nids], SZ_APTITLE, TY_CHAR)
+			    if (Memc[str] == EOS) {
+				call sprintf (Memc[Memi[titles+nids]],
+				    SZ_APTITLE, "(%.2h %.2h)")
+				    call pargd (ra)
+				    call pargd (dec)
+			    } else {
+				call sprintf (Memc[Memi[titles+nids]],
+				    SZ_APTITLE, "%s (%.2h %.2h)")
+				    call pargstr (Memc[str])
+				    call pargd (ra)
+				    call pargd (dec)
+			    }
+			}
+			nids = nids + 1
+		    }	
+		    call imcfnl (list)
+		    call imunmap (im)
+
+		# Read aperture information from a file.
+		} else {
+		    fd = open (Memc[key], READ_ONLY, TEXT_FILE)
+		    while (fscan (fd) != EOF) {
+			call gargi (ap)
+			if (nscan() == 0)
+			    next
+			if (ap < 1) {
+			    call close (fd)
+			    call error (1,
+				"Aperture numbers in apidtable must be > 0")
+			}
+			if (nalloc == 0) {
+			    nalloc = 50
+			    call malloc (aps, nalloc, TY_INT)
+			    call malloc (beams, nalloc, TY_INT)
+			    call malloc (titles, nalloc, TY_POINTER)
+			} else if (nids == nalloc) {
+			    nalloc = nalloc + 50
+			    call realloc (aps, nalloc, TY_INT)
+			    call realloc (beams, nalloc, TY_INT)
+			    call realloc (titles, nalloc, TY_POINTER)
+			}
+			Memi[aps+nids] = ap
+			Memi[beams+nids] = ap
+			Memc[str] = EOS
+			call gargi (beam)
+			if (nscan() == 2)
+			    Memi[beams+nids] = beam
+			call gargstr (Memc[str], SZ_LINE)	
+			call xt_stripwhite (Memc[str])
+			if (Memc[str] == EOS)
+			    Memi[titles+nids] = NULL
+			else {
+			    call malloc (Memi[titles+nids], SZ_APTITLE, TY_CHAR)
+			    call strcpy (Memc[str], Memc[Memi[titles+nids]],
+				SZ_APTITLE)
+			}
+			nids = nids + 1
+		    }	
+		    call close (fd)
+		}
+	    } then
+		call erract (EA_WARN)
+	}
+
+	if (nalloc > nids) {
+	    call realloc (aps, nids, TY_INT)
+	    call realloc (beams, nids, TY_INT)
+	    call realloc (titles, nids, TY_INT)
+	}
+
+	if (nids > 0) {
+	    call malloc (ids, IDS_LEN, TY_STRUCT)
+	    IDS_NIDS(ids) = nids
+	    IDS_APS(ids) = aps
+	    IDS_BEAMS(ids) = beams
+	    IDS_TITLES(ids) = titles
+	}
+
+	call sfree (sp)
+end
+
+
+procedure ap_fids (ids)
+
+pointer	ids		# ID structure
+int	i
+
+begin
+	if (ids != NULL) {
+	    do i = 1, IDS_NIDS(ids)
+		call mfree (Memi[IDS_TITLES(ids)+i-1], TY_CHAR)
+	    call mfree (IDS_APS(ids), TY_INT)
+	    call mfree (IDS_BEAMS(ids), TY_INT)
+	    call mfree (IDS_TITLES(ids), TY_POINTER)
+	    call mfree (ids, TY_STRUCT)
+	}
+end
+
+
+
+# AP_IDS -- Set aperture IDs
+# Do not allow negative or zero aperture numbers.
+
+procedure ap_ids (aps, naps, ids)
+
+pointer	aps[ARB]	# Aperture pointers
+int	naps		# Number of apertures
+int	ids		# ID structure
+
+int	i, j, k, l, m,  axis, nids, ap, beam, skip, nused
+real	maxsep, apgetr()
+pointer	sp, used, a, b
+
+begin
+	if (naps < 1)
+	    return
+
+	axis = AP_AXIS(aps[1])
+	maxsep = apgetr ("maxsep")
+
+	# Dereference ID structure pointers.
+	if (ids != NULL) {
+	    nids = IDS_NIDS(ids)
+	    a = IDS_APS(ids)
+	    b = IDS_BEAMS(ids)
+	} else
+	    nids = 0
+
+	# Make a list of used aperture numbers
+	call smark (sp)
+	call salloc (used, naps, TY_INT)
+	nused = 0
+	do i = 1, naps
+	    if (!IS_INDEFI(AP_ID(aps[i]))) {
+		Memi[used+nused] = AP_ID(aps[i])
+		nused = nused + 1
+	    }
+
+	# Find first aperture with a defined aperture number.
+	for (i=1; i<=naps && IS_INDEFI(AP_ID(aps[i])); i=i+1)
+	    ;
+
+	# If there are no defined aperture numbers start with 1 or first
+	# aperture in the ID table.
+
+	if (i > naps) {
+	    i = 1
+	    if (nids > 0) {
+		ap = Memi[a]
+		beam = Memi[b]
+	    } else {
+		ap = i
+		beam = ap
+	    }
+	    AP_ID(aps[i]) = ap
+	    AP_BEAM(aps[i]) = beam
+	    Memi[used+nused] = ap
+	    nused = nused + 1
+	} else {
+	    ap = AP_ID(aps[i])
+	    for (l = 1; l <= nids && ap != Memi[a+l-1]; l = l + 1)
+		;
+	    if (l <= nids)
+		AP_BEAM(aps[i]) = Memi[b+l-1]
+	    else
+		AP_BEAM(aps[i]) = ap
+	}
+
+	# Work backwards through the undefined apertures.
+	for (j = i - 1; j > 0; j = j - 1) {
+	    skip = abs (AP_CEN(aps[j],axis)-AP_CEN(aps[j+1],axis)) / maxsep
+	    if (ids != NULL) {
+	        ap = AP_ID(aps[j+1])
+		for (l = 1; l <= nids && ap != Memi[a+l-1]; l = l + 1)
+		    ;
+		if (nids <= naps)
+		    skip = 0
+		m = l - skip
+		if (l > nids) {
+		    l = 1
+		    for (k = 2; k <= nids; k = k + 1)
+		        if (abs (ap - Memi[a+k-1]) < abs (ap - Memi[a+l-1]))
+			    l = k
+		    m = l - skip + 1
+		}
+		repeat {
+		    m = m - 1
+		    if (m > 0) {
+			ap = Memi[a+m-1]
+			beam = Memi[b+m-1]
+		    } else {
+			ap = Memi[a+l-1] + m
+			beam = max (0, Memi[b+l-1] + m)
+		    }
+		    if (ap == 0)
+			next
+		    for (k = 0; k < nused && abs(ap) != Memi[used+k]; k = k + 1)
+			;
+		    if (k == nused)
+			break
+		 }
+	    } else {
+	        ap = AP_ID(aps[j+1]) - skip
+	        repeat {
+		    ap = ap - 1
+		    beam = abs (ap)
+		    if (ap == 0)
+			next
+		    for (k = 0; k < nused && abs(ap) != Memi[used+k]; k = k + 1)
+		        ;
+		    if (k == nused)
+		        break
+	        }
+	    }
+	    ap = abs (ap)
+	    AP_ID(aps[j]) = ap
+	    AP_BEAM(aps[j]) = beam
+	    Memi[used+nused] = ap
+	    nused = nused + 1
+	}
+
+	# Work forwards through the undefined apertures.
+	for (i = i + 1; i <= naps; i = i + 1) {
+	    if (IS_INDEFI(AP_ID(aps[i]))) {
+	        skip = abs (AP_CEN(aps[i],axis)-AP_CEN(aps[i-1],axis)) / maxsep
+	        if (nids > 0) {
+	            ap = AP_ID(aps[i-1])
+		    for (l = 1; l <= nids && ap != Memi[a+l-1]; l = l + 1)
+		        ;
+		    if (nids <= naps)
+		        skip = 0
+		    m = l + skip
+		    if (l > nids) {
+		        l = 1
+		        for (k = 2; k <= nids; k = k + 1)
+		            if (abs (ap-Memi[a+k-1]) < abs (ap-Memi[a+l-1]))
+			        l = k
+		        m = l + skip - 1
+		    }
+		    m = nids - m + 1
+		    repeat {
+		        m = m - 1
+		        if (m > 0) {
+			    ap = Memi[a+nids-m]
+			    beam = Memi[b+nids-m]
+			} else {
+			    ap = Memi[a+l-1] - m
+			    beam = max (0, Memi[b+l-1] - m)
+			}
+			if (ap == 0)
+			    next
+		        for (k=0; k<nused && abs(ap)!=Memi[used+k]; k=k+1)
+			    ;
+		        if (k == nused)
+			    break
+		     }
+	        } else {
+	            ap = AP_ID(aps[i-1]) + skip
+	            repeat {
+		        ap = ap + 1
+		        beam = abs (ap)
+			if (ap == 0)
+			    next
+		        for (k=0; k<nused && abs(ap)!=Memi[used+k]; k=k+1)
+		            ;
+		        if (k == nused)
+		            break
+	            }
+	        }
+		ap = abs(ap)
+	        AP_ID(aps[i]) = ap
+	        AP_BEAM(aps[i]) = beam
+	        Memi[used+nused] = ap
+	        nused = nused + 1
+	    }
+	}
+
+	call sfree (sp)
+end
+
+
+procedure ap_titles (aps, naps, ids)
+
+pointer	aps[ARB]	# Aperture pointers
+int	naps		# Number of apertures
+pointer	ids		# ID structure
+
+int	i, j, nids
+pointer	a, titles, title
+
+begin
+	if (ids == NULL)
+	    return
+
+	nids = IDS_NIDS(ids)
+	a = IDS_APS(ids)
+	titles = IDS_TITLES(ids)
+
+	do i = 1, naps {
+	    if (AP_TITLE(aps[i]) != NULL)
+		next
+	    do j = 1, nids {
+		if (AP_ID(aps[i]) == Memi[a+j-1]) {
+		    title = Memi[titles+j-1]
+	            if (title != NULL) {
+	                if (AP_TITLE(aps[i]) == NULL)
+		            call malloc (AP_TITLE(aps[i]), SZ_APTITLE, TY_CHAR)
+	                call strcpy (Memc[title], Memc[AP_TITLE(aps[i])],
+			    SZ_APTITLE)
+	            } else if (AP_TITLE(aps[i]) != NULL)
+	                call mfree (AP_TITLE(aps[i]), TY_CHAR)
+		}
+	    }
+	}
+end
diff --git a/noao/twodspec/apextract/apimmap.x b/noao/twodspec/apextract/apimmap.x
new file mode 100644
index 00000000..f001dc39
--- /dev/null
+++ b/noao/twodspec/apextract/apimmap.x
@@ -0,0 +1,48 @@
+include	<imhdr.h>
+
+# AP_IMMAP -- Map an input image for the APEXTRACT package.
+
+pointer procedure ap_immap (image, apaxis, dispaxis)
+
+char	image[ARB]	# Image to map
+int	apaxis		# Aperture axis
+int	dispaxis	# Dispersion axis
+
+pointer	im, immap()
+int	i, j, imgeti(), clgeti()
+errchk	immap
+
+data	i/0/, j/0/
+
+begin
+	im = immap (image, READ_ONLY, 0)
+	if (IM_NDIM(im) == 1) {
+	    call imunmap (im)
+	    call error (0, "Image must be two dimensional")
+	} else if (IM_NDIM(im) > 2) {
+	    if (i == 0)
+	    call eprintf (
+    "Warning: Image(s) are not two dimensional (ignoring higher dimensions)\n")
+	    i = i + 1
+	} else
+	    i = 0
+
+	iferr (dispaxis = imgeti (im, "dispaxis"))
+	    dispaxis = clgeti ("dispaxis")
+	if (dispaxis < 1 || dispaxis > 2) {
+	    apaxis = dispaxis
+	    dispaxis = max (1, min (2, clgeti ("dispaxis")))
+	    if (j == 0) {
+		call eprintf (
+		    "WARNING: Dispersion axis %d invalid; using axis %d\n")
+		    call pargi (apaxis)
+		    call pargi (dispaxis)
+	    }
+	    j = j + 1
+	} else
+	    j = 0
+
+	apaxis = mod (dispaxis, 2) + 1
+
+	return (im)
+end
diff --git a/noao/twodspec/apextract/apinfo.x b/noao/twodspec/apextract/apinfo.x
new file mode 100644
index 00000000..372860ae
--- /dev/null
+++ b/noao/twodspec/apextract/apinfo.x
@@ -0,0 +1,96 @@
+include	"apertures.h"
+
+# AP_INFO -- Print information about an aperture.
+
+procedure ap_info (ap)
+
+pointer	ap		# Aperture pointer
+
+int	n, ic_geti(), strlen()
+real	ic_getr()
+pointer	sp, str1, str2
+
+begin
+	call smark (sp)
+
+	if (AP_IC(ap) != NULL) {
+	    call salloc (str1, SZ_LINE, TY_CHAR)
+	    call salloc (str2, SZ_LINE, TY_CHAR)
+
+	    n = 0
+	    call ic_gstr (AP_IC(ap), "function", Memc[str1], SZ_LINE)
+	    call sprintf (Memc[str2], SZ_LINE, "background: func=%s ord=%d")
+		call pargstr (Memc[str1])
+		call pargi (ic_geti (AP_IC(ap), "order"))
+	    n = strlen (Memc[str2])
+	    call printf ("%s")
+		call pargstr (Memc[str2])
+
+	    call ic_gstr (AP_IC(ap), "sample", Memc[str1], SZ_LINE)
+	    if (Memc[str1] != '*') {
+	        call sprintf (Memc[str2], SZ_LINE, " sample=\"%s\"")
+		    call pargstr (Memc[str1])
+	        n = n + strlen (Memc[str2])
+		if (n > 80) {
+		    call printf ("\n\t")
+		    n = 8 + strlen (Memc[str2])
+		}
+		call printf ("%s")
+		    call pargstr (Memc[str2])
+	    }
+	    if (ic_geti (AP_IC(ap), "naverage") != 1) {
+		call sprintf (Memc[str2], SZ_LINE, " nav=%d")
+		    call pargi (ic_geti (AP_IC(ap), "naverage"))
+	        n = n + strlen (Memc[str2])
+		if (n > 80) {
+		    call printf ("\n\t")
+		    n = 8 + strlen (Memc[str2])
+		}
+		call printf ("%s")
+		    call pargstr (Memc[str2])
+	    }
+	    if (ic_geti (AP_IC(ap), "niterate") > 0) {
+		call sprintf (Memc[str2], SZ_LINE, " nit=%d")
+		    call pargi (ic_geti (AP_IC(ap), "niterate"))
+	        n = n + strlen (Memc[str2])
+		if (n > 80) {
+		    call printf ("\n\t")
+		    n = 8 + strlen (Memc[str2])
+		}
+		call printf ("%s")
+		    call pargstr (Memc[str2])
+		call sprintf (Memc[str2], SZ_LINE, " low=%3.1f")
+		    call pargr (ic_getr (AP_IC(ap), "low"))
+	        n = n + strlen (Memc[str2])
+		if (n > 80) {
+		    call printf ("\n\t")
+		    n = 8 + strlen (Memc[str2])
+		}
+		call printf ("%s")
+		    call pargstr (Memc[str2])
+		call sprintf (Memc[str2], SZ_LINE, " high=%3.1f")
+		    call pargr (ic_getr (AP_IC(ap), "high"))
+	        n = n + strlen (Memc[str2])
+		if (n > 80) {
+		    call printf ("\n\t")
+		    n = 8 + strlen (Memc[str2])
+		}
+		call printf ("%s")
+		    call pargstr (Memc[str2])
+	        if (ic_getr (AP_IC(ap), "grow") > 0) {
+		    call sprintf (Memc[str2], SZ_LINE, " grow=%d")
+		        call pargr (ic_getr (AP_IC(ap), "grow"))
+	            n = n + strlen (Memc[str2])
+		    if (n > 80) {
+		        call printf ("\n\t")
+		        n = 8 + strlen (Memc[str2])
+		    }
+		    call printf ("%s")
+		        call pargstr (Memc[str2])
+	        }
+	    }
+	    call printf ("\n")
+	}
+
+	call sfree (sp)
+end
diff --git a/noao/twodspec/apextract/apio.x b/noao/twodspec/apextract/apio.x
new file mode 100644
index 00000000..bfd2c6e6
--- /dev/null
+++ b/noao/twodspec/apextract/apio.x
@@ -0,0 +1,144 @@
+include	<time.h>
+
+# AP_LOG -- Verbose, log, and error output.
+
+procedure ap_log (str, log, verbose, err)
+
+char	str[ARB]	# String
+int	log		# Write to log if logfile defined?
+int	verbose		# Write to stdout if verbose?
+int	err		# Write to stdout?
+
+int	fd, open()
+long	clktime()
+bool	clgetb()
+pointer	sp, logfile, date
+errchk	open
+
+begin
+	call smark (sp)
+	call salloc (logfile, SZ_LINE, TY_CHAR)
+	call salloc (date, SZ_DATE, TY_CHAR)
+	call cnvdate (clktime(0), Memc[date], SZ_DATE)
+
+	if (err == YES || (verbose == YES && clgetb ("verbose"))) {
+	    call printf ("%s: %s\n")
+	        call pargstr (Memc[date])
+	        call pargstr (str)
+	    call flush (STDOUT)
+	}
+
+	if (log == YES) {
+	    call clgstr ("logfile", Memc[logfile], SZ_FNAME)
+	    if (Memc[logfile] != EOS) {
+	        fd = open (Memc[logfile], APPEND, TEXT_FILE)
+	        call fprintf (fd, "%s: %s\n")
+	            call pargstr (Memc[date])
+	            call pargstr (str)
+	        call flush (fd)
+	        call close (fd)
+	    }
+	}
+
+	call sfree (sp)
+end
+
+
+# AP_GOPEN/AP_GCLOSE -- Open and close the graphics device.
+# The device "stdgraph" is used.
+
+procedure ap_gopen (gp)
+
+pointer	gp		# GIO pointer
+pointer	gplast		# Last GIO pointer
+
+int	flag
+pointer	gopen()
+errchk	gopen
+
+data	flag/NO/
+common	/apgio/ gplast
+
+begin
+	if (flag == NO) {
+	    flag = YES
+	    call ap_gclose ()
+	}
+
+	if (gplast == NULL)
+	    gplast = gopen ("stdgraph", NEW_FILE, STDGRAPH)
+
+	gp = gplast
+end
+
+procedure ap_gclose ()
+
+int	flag
+pointer	gplast
+
+data	flag/NO/
+common	/apgio/ gplast
+
+begin
+	if (flag == NO) {
+	    flag = YES
+	    gplast = NULL
+	}
+
+	if (gplast != NULL) {
+	    call gclose (gplast)
+	    gplast = NULL
+	}
+end
+
+
+# AP_POPEN -- Open the plot device or metacode file.  This includes CLIO
+# to get the plot device.
+
+procedure ap_popen (gp, fd, type)
+
+pointer	gp		# GIO pointer
+int	fd		# FIO channel for metacode file
+char	type[ARB]	# Plot type
+
+bool	streq(), strne()
+int	open(), nowhite(), strncmp()
+pointer	sp, str, gopen()
+errchk	gopen, open
+
+begin
+	call smark (sp)
+	call salloc (str, SZ_FNAME, TY_CHAR)
+	call clgstr ("plotfile", Memc[str], SZ_LINE)
+
+	gp = NULL
+	fd = NULL
+	if (nowhite (Memc[str], Memc[str], SZ_FNAME) > 0) {
+	    if (strncmp ("debug", Memc[str], 5) == 0) {
+		if (streq (type, Memc[str+5]) || streq ("all", Memc[str+5])) {
+		    fd = open (Memc[str], APPEND, BINARY_FILE)
+		    gp = gopen ("stdvdm", APPEND, fd)
+		}
+	    } else if (strne ("fits", type)) {
+		fd = open (Memc[str], APPEND, BINARY_FILE)
+		gp = gopen ("stdvdm", APPEND, fd)
+	    }
+	}
+
+	call sfree (sp)
+end
+
+
+# AP_PCLOSE -- Close plot file.
+
+procedure ap_pclose (gp, fd)
+
+pointer	gp		# GIO pointer
+int	fd		# FIO channel for metacode file
+
+begin
+	if (gp != NULL)
+	    call gclose (gp)
+	if (fd != NULL)
+	    call close (fd)
+end
diff --git a/noao/twodspec/apextract/apmask.par b/noao/twodspec/apextract/apmask.par
new file mode 100644
index 00000000..7f8e114b
--- /dev/null
+++ b/noao/twodspec/apextract/apmask.par
@@ -0,0 +1,19 @@
+# APMASK
+
+input,s,a,,,,List of input images
+output,s,a,,,,List of output masks
+apertures,s,h,"",,,Apertures
+references,s,h,"",,,List of reference images
+
+interactive,b,h,yes,,,Run task interactively?
+find,b,h,yes,,,Find apertures?
+recenter,b,h,no,,,Recenter apertures?
+resize,b,h,no,,,Resize apertures?
+edit,b,h,yes,,,Edit apertures?
+trace,b,h,yes,,,Trace apertures?
+fittrace,b,h,yes,,,Fit the traced points interactively?
+mask,b,h,yes,,,"Create mask images?
+"
+line,i,h,INDEF,1,,Starting dispersion line
+nsum,i,h,10,,,Number of dispersion lines to sum or median
+buffer,r,h,0.,,,Buffer distance from apertures
diff --git a/noao/twodspec/apextract/apmask.x b/noao/twodspec/apextract/apmask.x
new file mode 100644
index 00000000..4dc4da19
--- /dev/null
+++ b/noao/twodspec/apextract/apmask.x
@@ -0,0 +1,155 @@
+include	<imhdr.h>
+include	<pmset.h>
+include	"apertures.h"
+
+# AP_MASK -- Create an aperture mask.
+# The mask is boolean with pixels within the apertures having value 1 and
+# pixels outside the mask having values 0.  An additional  buffer distance 
+# may be specified.
+
+procedure ap_mask (image, output,  aps, naps)
+
+char	image[SZ_FNAME]		# Image name
+char	output[SZ_FNAME]	# Output mask name
+pointer	aps[ARB]		# Apertures
+int	naps			# Number of apertures
+
+real	buffer			# Buffer distance
+
+int	i, j, aaxis, baxis, nc, nl, na, nb, apmin, apmax, low, high
+real	aplow, aphigh, shift
+long	v[2]
+short	val
+pointer	im, pm, ap, cv, a1, b1
+pointer	sp, name, str, buf, a, b, amin, bmax
+
+real	clgetr(), ap_cveval()
+bool	ap_answer()
+pointer	ap_immap(), pm_newmask()
+errchk	ap_immap, pm_savef
+
+begin
+	# Query user.
+	call smark (sp)
+	call salloc (name, SZ_LINE, TY_CHAR)
+	call salloc (str, SZ_LINE, TY_CHAR)
+	call sprintf (Memc[str], SZ_LINE, "Create aperture mask for %s?")
+	    call pargstr (image)
+	if (!ap_answer ("ansmask", Memc[str])) {
+	    call sfree (sp)
+	    return
+	}
+
+	# Get buffer distance.
+	buffer = clgetr ("buffer")
+
+	# Make the image and initialize the mask.
+	im = ap_immap (image, aaxis, baxis)
+	pm = pm_newmask (im, 1)
+	nc = IM_LEN(im,1)
+	nl = IM_LEN(im,2)
+	na = IM_LEN(im,aaxis)
+	nb = IM_LEN(im,baxis)
+
+	# Allocate memory.
+	call salloc (buf, nc, TY_SHORT)
+	call salloc (a, naps*nb, TY_SHORT)
+	call salloc (b, naps*nb, TY_SHORT)
+	call salloc (amin, naps, TY_SHORT)
+	call salloc (bmax, naps, TY_SHORT)
+	val = 1
+
+	# Go through and compute all the limits as well as the maximum
+	# range of each aperture.  This information must be computed for
+	# an aperture axis of 2 and it is also done for aperture axis
+	# of 1 just to keep the code the same.
+
+	do i = 1, naps {
+	    ap = aps[i]
+	    cv = AP_CV(ap)
+	    aplow = AP_CEN(ap,aaxis) + AP_LOW(ap,aaxis) - buffer
+	    aphigh = AP_CEN(ap,aaxis) + AP_HIGH(ap,aaxis) + buffer
+	    apmin = aplow
+	    apmax = aphigh
+	    a1 = a + (i - 1) * nb
+	    b1 = b + (i - 1) * nb
+	    do j = 1, nb {
+		shift = ap_cveval (cv, real (j))
+		low = nint (aplow + shift)
+		high = nint (aphigh + shift)
+		Mems[a1+j-1] = low
+		Mems[b1+j-1] = high
+		apmin = min (low, apmin)
+		apmax = max (high, apmax)
+	    }
+	    Mems[amin+i-1] = apmin
+	    Mems[bmax+i-1] = apmax
+	}
+
+	# For each line create a pixel array mask.  For aperture axis 1 this
+	# is simple while for aperture axis 2 we have to look through each
+	# line to see if any apertures intersect the line.
+
+	switch (aaxis) {
+	case 1:
+	    do j = 1, nl {
+	        v[2] = j
+		call aclrs (Mems[buf], nc)
+		a1 = a + j - 1
+		b1 = b + j - 1
+	        do i = 1, naps {
+		    low = Mems[a1]
+		    high = Mems[b1]
+		    low = max (1, low)
+		    high = min (na, high)
+		    if (low <= high)
+			call amovks (val, Mems[buf+low-1], high-low+1)
+		    a1 = a1 + nb
+		    b1 = b1 + nb
+	        }
+	        call pmplps (pm, v, Mems[buf], 1, nc, PIX_SRC)
+	    }
+	case 2:
+	    do j = 1, nl {
+		v[2] = j
+		call aclrs (Mems[buf], nc)
+		do i = 1, naps {
+		    if (j < Mems[amin+i-1] || j > Mems[bmax+i-1])
+			next
+
+		    a1 = a + (i - 1) * nb
+		    b1 = b + (i - 1) * nb
+		    for (low=0; low<nb; low=low+1) {
+			if (j < Mems[a1+low] || j > Mems[b1+low])
+			    next
+			for (high=low+1; high<nb; high=high+1)
+			    if (j < Mems[a1+high] || j > Mems[b1+high])
+				break
+			call amovks (val, Mems[buf+low], high-low)
+			low = high - 1
+		    }
+		}
+	        call pmplps (pm, v, Mems[buf], 1, nc, PIX_SRC)
+	    }
+	}
+	    
+	# Log the output and finish up.
+	if (output[1] == EOS) {
+	    call sprintf (Memc[name], SZ_LINE, "%s.pl")
+	        call pargstr (image)
+	} else
+	    call strcpy (output, Memc[name], SZ_LINE)
+	call sprintf (Memc[str], SZ_LINE, "Aperture mask for %s")
+	    call pargstr (image)
+
+	call pm_savef (pm, Memc[name], Memc[str], 0)
+	call pm_close (pm)
+	call imunmap (im)
+
+	call sprintf (Memc[str], SZ_LINE, "MASK - Aperture mask for %s --> %s")
+       	    call pargstr (image)
+	    call pargstr (Memc[name])
+	call ap_log (Memc[str], YES, YES, NO)
+
+	call sfree (sp)
+end
diff --git a/noao/twodspec/apextract/apmw.x b/noao/twodspec/apextract/apmw.x
new file mode 100644
index 00000000..9fcd35d7
--- /dev/null
+++ b/noao/twodspec/apextract/apmw.x
@@ -0,0 +1,280 @@
+include	<error.h>
+include	<imhdr.h>
+include	<imio.h>
+include	<mwset.h>
+
+
+# APMW_OPEN   -- Open APMW structure.
+# APMW_CLOSE  -- Close APMW structure.
+# APMW_SETAP  -- Set aperture values in APMW structure.
+# APMW_SAVEIM -- Set WCS in image header.
+# APMW_WCSFIX -- Fix up WCS
+
+# Output formats
+define	ONEDSPEC	1	# Individual 1D spectra
+define	MULTISPEC	2	# Multiple spectra
+define	ECHELLE		3	# Echelle spectra
+define	STRIP		4	# Strip spectra
+define	NORM		5	# Normalized spectra
+define	FLAT		6	# Flat spectra
+define	RATIO		7	# Ratio of data to model
+define	DIFF		8	# Difference of data and model
+define	FIT		9	# Model
+define	NOISE		10	# Noise calculation
+
+
+# Data structure for the apertures.  This version assumes the coordinates
+# are the same for all the apertures.
+
+define	APMW_LEN	(8 + $1 * 6)		# Structure length
+
+define	APMW_LABEL	Memi[$1]			# WCS label
+define	APMW_UNITS	Memi[$1+1]			# WCS units
+define	APMW_DTYPE	Memi[$1+2]			# Dispersion type
+define	APMW_NW		Memi[$1+3]			# Number of pixels
+define	APMW_W1		Memd[P2D($1+4)]			# Starting coordinate
+define	APMW_DW		Memd[P2D($1+6)]			# Coordinate per pixel
+define	APMW_AP		Memi[$1+6*($2-1)+8]		# Aperture
+define	APMW_BEAM	Memi[$1+6*($2-1)+9]		# Beam
+define	APMW_APLOW	Memd[P2D($1+6*($2-1)+10)]	# Aperture low
+define	APMW_APHIGH	Memd[P2D($1+6*($2-1)+12)]	# Aperture high
+
+
+# APMW_OPEN -- Open APMW structure.
+
+pointer procedure apmw_open (in, out, dispaxis, naps, nw)
+
+pointer	in		#I Input IMIO pointer
+pointer	out		#I Output IMIO pointer
+int	dispaxis	#I Input dispersion axis
+int	naps		#I Number of apertures
+int	nw		#I Number of dispersion pixels
+pointer	apmw		#O Returned APMW pointer
+
+int	imgeti()
+double	mw_c1trand()
+pointer	mw, ct, mw_openim(), mw_sctran()
+errchk	mw_openim, mw_sctran, mw_c1trand, apmw_wcsfix
+
+begin
+	# Allocate data structure.
+	call malloc (apmw, APMW_LEN(naps), TY_STRUCT)
+	call malloc (APMW_LABEL(apmw), SZ_LINE, TY_CHAR)
+	call malloc (APMW_UNITS(apmw), SZ_LINE, TY_CHAR)
+
+	# Set defaults.
+	call strcpy ("Pixel", Memc[APMW_LABEL(apmw)], SZ_LINE)
+	Memc[APMW_UNITS(apmw)] = EOS
+	APMW_DTYPE(apmw,i) = -1
+	APMW_NW(apmw,i) = nw
+	APMW_W1(apmw,i) = 1.
+	APMW_DW(apmw,i) = 1.
+
+	# Get WCS info from input image.
+	iferr {
+	    mw = mw_openim (in)
+	    iferr (APMW_DTYPE(apmw) = imgeti (in, "DC-FLAG"))
+		APMW_DTYPE(apmw) = -1
+	    iferr (call mw_gwattrs (mw, dispaxis, "label",
+		Memc[APMW_LABEL(apmw)], SZ_LINE)) {
+		if (APMW_DTYPE(apmw) == -1)
+		    call strcpy ("Pixel", Memc[APMW_LABEL(apmw)], SZ_LINE)
+		else
+		    call strcpy ("Wavelength", Memc[APMW_LABEL(apmw)], SZ_LINE)
+	    }
+	    iferr (call mw_gwattrs (mw, dispaxis, "units",
+		Memc[APMW_UNITS(apmw)], SZ_LINE)) {
+		if (APMW_DTYPE(apmw) == -1)
+		    Memc[APMW_UNITS(apmw)] = EOS
+		else
+		    call strcpy ("Angstroms", Memc[APMW_UNITS(apmw)], SZ_LINE)
+	    }
+
+	    call apmw_wcsfix (in, mw)
+	    iferr (ct = mw_sctran (mw, "logical", "world", dispaxis))
+		call error (1,
+	    "Coordinate system ignored (rotated?). Using pixel coordinates.")
+	    APMW_W1(apmw) = mw_c1trand (ct, 1D0)
+	    APMW_DW(apmw) = mw_c1trand (ct, double (nw))
+	    APMW_DW(apmw) = (APMW_DW(apmw)-APMW_W1(apmw))/(nw-1)
+	} then
+	    call erract (EA_WARN)
+
+	call mw_close (mw)
+
+	return (apmw)
+end
+
+
+# APMW_CLOSE -- Close APMW structure.
+
+procedure apmw_close (apmw)
+
+pointer	apmw		# APMW pointer
+
+begin
+	call mfree (APMW_LABEL(apmw), TY_CHAR)
+	call mfree (APMW_UNITS(apmw), TY_CHAR)
+	call mfree (apmw, TY_STRUCT)
+end
+
+
+# APMW_SETAP -- Set aperture values in APMW structure.
+
+procedure apmw_setap (apmw, line, ap, beam, aplow, aphigh)
+
+pointer	apmw		# APMW pointer
+int	line		# Image line
+int	ap		# Aperture
+int	beam		# Beam
+real	aplow		# Aperture lower limit
+real	aphigh		# Aperture upper limit
+
+begin
+	APMW_AP(apmw,line) = ap
+	APMW_BEAM(apmw,line) = beam
+	APMW_APLOW(apmw,line) = aplow
+	APMW_APHIGH(apmw,line) = aphigh
+end
+
+
+# APMW_SAVEIM -- Save WCS in image header.
+
+procedure apmw_saveim (apmw, im, fmt)
+
+pointer	apmw			#I APMW pointer
+pointer	im			#I IMIO pointer
+int	fmt			#I Output format
+
+int	i, naps, wcsdim, axes[3], imaccf()
+double	r[3], w[3], cd[9]
+bool	strne()
+pointer	sp, key, str, mw, list, mw_open(), imofnlu(), imgnfn()
+errchk	imdelf
+data	axes/1,2,3/
+
+begin
+	call smark (sp)
+	call salloc (key, SZ_FNAME, TY_CHAR)
+	call salloc (str, SZ_LINE, TY_CHAR)
+
+	if (fmt == STRIP)
+	    naps = 1
+	else
+	    naps = IM_LEN(im, 2)
+
+	# Workaround for truncation of header during image header copy.
+	IM_HDRLEN(im) = IM_LENHDRMEM(im)
+
+	# Delete keywords.
+	list = imofnlu (im, "SLFIB[0-9]*")
+	while (imgnfn (list, Memc[key], SZ_FNAME) != EOF)
+	    call imdelf (im, Memc[key])
+	call imcfnl (list)
+
+	# Add aperture parameters to image header.
+	do i = 1, naps {
+	    call sprintf (Memc[key], SZ_FNAME, "APNUM%d")
+		call pargi (i)
+	    call sprintf (Memc[str], SZ_LINE, "%d %d %.2f %.2f")
+		call pargi (APMW_AP(apmw,i))
+		call pargi (APMW_BEAM(apmw,i))
+		call pargd (APMW_APLOW(apmw,i))
+		call pargd (APMW_APHIGH(apmw,i))
+	    call imastr (im, Memc[key], Memc[str])
+	    if (naps == 1) {
+		call sprintf (Memc[key], SZ_FNAME, "APID%d")
+		    call pargi (i)
+		ifnoerr (call imgstr (im, Memc[key], Memc[str], SZ_LINE)) {
+		    if (strne (Memc[str], IM_TITLE(im))) {
+			call imastr (im, "MSTITLE", IM_TITLE(im))
+			call strcpy (Memc[str], IM_TITLE(im), SZ_IMTITLE)
+		    }
+		    call imdelf (im, Memc[key])
+		}
+	    }
+	}
+
+	# Add dispersion parameters to image header.
+	if (APMW_DTYPE(apmw) != -1)
+	    call imaddi (im, "DC-FLAG", APMW_DTYPE(apmw))
+	else if (imaccf (im, "DC-FLAG") == YES)
+	    call imdelf (im, "DC-FLAG")
+	if (APMW_NW(apmw) < IM_LEN(im,1))
+	    call imaddi (im, "NP2", APMW_NW(apmw))
+	else if (imaccf (im, "NP2") == YES)
+	    call imdelf (im, "NP2")
+	iferr (call imdelf (im, "dispaxis"))
+	    ;
+	if (fmt == STRIP)
+	    call imaddi (im, "dispaxis", 1)
+
+	# Set WCS in image header.
+	wcsdim = IM_NPHYSDIM(im)
+	mw = mw_open (NULL, wcsdim)
+	if (fmt == STRIP)
+	    call mw_newsystem (mw, "linear", wcsdim)
+	else
+	    call mw_newsystem (mw, "equispec", wcsdim)
+	call mw_swtype (mw, axes, wcsdim, "linear", "")
+	if (Memc[APMW_LABEL(apmw)] != EOS)
+	    call mw_swattrs (mw, 1, "label", Memc[APMW_LABEL(apmw)])
+	if (Memc[APMW_UNITS(apmw)] != EOS)
+	    call mw_swattrs (mw, 1, "units", Memc[APMW_UNITS(apmw)])
+
+	call aclrd (r, 3)
+	call aclrd (w, 3)
+	call aclrd (cd, 9)
+	r[1] = 1.
+	w[1] = APMW_W1(apmw)
+	cd[1] = APMW_DW(apmw)
+	if (wcsdim == 2)
+	    cd[4] = 1.
+	if (wcsdim == 3) {
+	    cd[5] = 1.
+	    cd[9] = 1.
+	}
+	call mw_swtermd (mw, r, w, cd, wcsdim)
+
+	call mw_saveim (mw, im)
+	call mw_close (mw)
+
+	call sfree (sp)
+end
+
+
+# APMW_WCSFIX -- Fix up WCS to avoid CDELT=0 which occurs if there are WCS
+# keywords in the header but no CDELT.
+
+procedure apmw_wcsfix (im, mw)
+
+pointer	im			# IMIO pointer
+pointer	mw			# MWCS pointer
+
+int	i, ndim, mw_stati()
+double	val
+pointer	sp, r, w, cd
+errchk	mw_gwtermd, mw_swtermd
+
+begin
+	call mw_seti (mw, MW_USEAXMAP, NO)
+	ndim = mw_stati (mw, MW_NDIM)
+
+	call smark (sp)
+	call salloc (r, ndim, TY_DOUBLE)
+	call salloc (w, ndim, TY_DOUBLE)
+	call salloc (cd, ndim*ndim, TY_DOUBLE)
+
+	# Check cd terms.  Assume no rotation.
+	call mw_gwtermd (mw, Memd[r], Memd[w], Memd[cd], ndim)
+	do i = 0, ndim-1 {
+	    val = Memd[cd+i*(ndim+1)]
+	    if (val == 0D0) {
+		Memd[w+i] = 1D0
+	        Memd[cd+i*(ndim+1)] = 1D0
+	    }
+	}
+	call mw_swtermd (mw, Memd[r], Memd[w], Memd[cd], ndim)
+
+	call sfree (sp)
+end
diff --git a/noao/twodspec/apextract/apnearest.x b/noao/twodspec/apextract/apnearest.x
new file mode 100644
index 00000000..f3e027c5
--- /dev/null
+++ b/noao/twodspec/apextract/apnearest.x
@@ -0,0 +1,75 @@
+include	<mach.h>
+include	"apertures.h"
+
+# AP_NEAREST -- Find the index of the aperture nearest cursor position x.
+
+define	DELTA	0.01		# Tolerance for equidistant apertures
+
+procedure ap_nearest (index, line, aps, naps, x)
+
+int	index			# Index of aperture nearest x
+int	line			# Dispersion line
+pointer	aps[ARB]		# Aperture pointers
+int	naps			# Number of apertures
+real	x			# Point nearest aperture
+
+int	i, j, apaxis
+char	ch
+real	d, delta
+pointer	ap
+
+int	fscan(), nscan()
+real	ap_cveval()
+
+begin
+	if (naps == 0)
+	    return
+
+	index = 0
+	delta = MAX_REAL
+
+	for (i = 1; i <= naps; i = i + 1) {
+	    ap = aps[i]
+	    apaxis = AP_AXIS(ap)
+	    d = abs (AP_CEN(ap, apaxis)+ap_cveval(AP_CV(ap),real(line))-x)
+	    if (d < delta - DELTA) {
+		j = 1
+		index = i
+		delta = d
+	    } else if (d < delta + DELTA)
+		j = j + 1
+	}
+
+	# If there is more than one aperture equally near ask the user.
+	if (j > 1) {
+	    call printf ("Apertures")
+	    for (i = 1; i <= naps; i = i + 1) {
+	        ap = aps[i]
+	        apaxis = AP_AXIS(ap)
+	        d = abs (AP_CEN(ap, apaxis)+ap_cveval(AP_CV(ap),real(line))-x)
+	        if (d < delta + DELTA) {
+		    call printf (" %d")
+			call pargi (AP_ID (ap))
+		}
+	    }
+	    call printf (" are equally near the cursor.\n")
+10	    call printf ("Choose an aperture (%d): ")
+		call pargi (AP_ID (aps[index]))
+	    call flush (STDOUT)
+	    if (fscan (STDIN) != EOF) {
+		call scanc (ch)
+		if (ch == '\n')
+		    return
+
+		call reset_scan()
+		call gargi (j)
+		if (nscan() == 0)
+		    goto 10
+		for (i=1; (i<=naps)&&(AP_ID(aps[i])!=j); i=i+1)
+		    ;
+		if (i > naps)
+		    goto 10
+		index = i
+	    }
+	}
+end
diff --git a/noao/twodspec/apextract/apnoise.key b/noao/twodspec/apextract/apnoise.key
new file mode 100644
index 00000000..4920453a
--- /dev/null
+++ b/noao/twodspec/apextract/apnoise.key
@@ -0,0 +1,14 @@
+	APNOISE CURSOR COMMANDS
+
+
+?  Print command help
+q  Quit
+r  Redraw	
+w  Window the graph (see :/help)
+I  Interupt immediately
+
+:gain <value>		Check or set the gain model parameter
+:readnoise <value>	Check or set the read noise model parameter
+
+Also see the CURSOR MODE commads (:.help) and the windowing commands
+(:/help).
diff --git a/noao/twodspec/apextract/apnoise.par b/noao/twodspec/apextract/apnoise.par
new file mode 100644
index 00000000..365bc1c3
--- /dev/null
+++ b/noao/twodspec/apextract/apnoise.par
@@ -0,0 +1,30 @@
+# APSIGMA
+
+input,s,a,,,,List of images to evaluate
+apertures,s,h,"",,,Apertures
+references,s,h,"",,,"List of reference images
+"
+dmin,r,a,,,,Data minimum for sigma bins
+dmax,r,a,,,,Data maximum for sigma bins
+nbins,i,a,,1,,Number of sigma bins
+interactive,b,h,yes,,,Run task interactively?
+find,b,h,yes,,,Find apertures?
+recenter,b,h,yes,,,Recenter apertures?
+resize,b,h,yes,,,Resize apertures?
+edit,b,h,yes,,,Edit apertures?
+trace,b,h,yes,,,Trace apertures?
+fittrace,b,h,yes,,,"Fit traced points interactively?
+"
+line,i,h,INDEF,1,,Dispersion line
+nsum,i,h,10,,,Number of dispersion lines to sum or median
+threshold,r,h,10.,,,"Division threshold for ratio fit
+"
+background,s,h,"none","none|average|median|minimum|fit",,Background to subtract
+pfit,s,h,"fit1d","fit1d|fit2d",,Profile fitting type (fit1d|fit2d)
+clean,b,h,no,,,Detect and replace bad pixels?
+skybox,i,h,1,1,,Box car smoothing length for sky
+saturation,r,h,INDEF,,,Saturation level
+readnoise,s,h,"0.",,,Read out noise sigma (photons)
+gain,s,h,"1.",,,Photon gain (photons/data number)
+lsigma,r,h,4.,0.,,Lower rejection threshold
+usigma,r,h,4.,0.,,Upper rejection threshold
diff --git a/noao/twodspec/apextract/apnoise.x b/noao/twodspec/apextract/apnoise.x
new file mode 100644
index 00000000..d22c09ae
--- /dev/null
+++ b/noao/twodspec/apextract/apnoise.x
@@ -0,0 +1,256 @@
+include	<gset.h>
+include	<pkg/gtools.h>
+include	"apertures.h"
+
+
+# AP_NOISE -- Model residuals.
+
+procedure ap_noise (ap, gain, dbuf, nc, nl, c1, l1, sbuf, spec, profile, nx, ny,
+	xs, ys, sum2, sum4, nsum, nbin, dmin, dmax)
+
+pointer	ap			# Aperture structure
+real	gain			# Gain
+pointer	dbuf			# Data buffer
+int	nc, nl			# Size of data buffer
+int	c1, l1			# Origin of data buffer
+pointer	sbuf			# Sky buffer (NULL if no sky)
+real	spec[ny]		# Normalization spectrum
+real	profile[ny,nx]		# Profile
+int	nx, ny			# Size of profile array
+int	xs[ny], ys		# Start of spectrum in image
+real	sum2[nbin]		# Sum of residuals squared in bin
+real	sum4[nbin]		# Sum of residuals squared in bin
+int	nsum[nbin]		# Number of values in bin
+int	nbin			# Number of bins
+real	dmin, dmax		# Data limits of bins
+
+int	i, ix, iy, ix1, ix2
+real	dstep, low, high, s, x1, x2, model, data, ap_cveval()
+pointer	cv, sptr, dptr
+
+begin
+	dstep = (dmax - dmin) / nbin
+
+	i = AP_AXIS(ap)
+	low = AP_CEN(ap,i) + AP_LOW(ap,i)
+	high = AP_CEN(ap,i) + AP_HIGH(ap,i)
+	cv = AP_CV(ap)
+
+	do iy = 1, ny {
+	    i = iy + ys - 1
+	    s = ap_cveval (cv, real (i))
+	    x1 = max (0.5, low + s) 
+	    x2 = min (c1 + nc - 0.49, high + s) 
+	    if (x1 > x2)
+		next
+
+	    ix1 = nint (x1) - xs[iy] + 1
+	    ix2 = nint (x2) - xs[iy] + 1
+
+	    s = spec[iy]
+	    if (sbuf != NULL)
+		sptr = sbuf + (iy - 1) * nx - 1
+	    dptr = dbuf + (i - l1) * nc + nint(x1) - c1
+	    do ix = ix1, ix2 {
+		if (sbuf != NULL) {
+		    model = (s * profile[iy,ix] + Memr[sptr]) / gain
+		    sptr = sptr + 1
+		} else
+		    model = (s * profile[iy,ix]) / gain
+		data = Memr[dptr] / gain
+		dptr = dptr + 1
+
+		if (model < dmin || model >= dmax)
+		    next
+		i = (model - dmin) / dstep + 1
+		sum2[i] = sum2[i] + (data - model) ** 2
+		sum4[i] = sum4[i] + (data - model) ** 4
+		nsum[i] = nsum[i] + 1
+	    }
+	}
+end
+
+
+define	HELP	"noao$twodspec/apextract/apnoise.key"
+define	PROMPT	"apextract options"
+
+# AP_NPLOT -- Plot and examine noise characteristics.
+
+procedure ap_nplot (image, im, sigma, sigerr, npts, dmin, dmax)
+
+char	image[SZ_FNAME]		# Image
+pointer	im			# Image pointer
+real	sigma[npts]		# Sigma values
+real	sigerr[npts]		# Sigma errors
+int	npts			# Number of sigma values
+real	dmin, dmax		# Data min and max
+
+real	rdnoise			# Read noise
+real	gain			# Gain
+
+int	i, newgraph, wcs, key
+real	wx, wy, x, x1, x2, dx, y, ymin, ymax
+pointer	sp, cmd, gp, gt
+
+int	gt_gcur()
+real	apgimr()
+#int	apgwrd()
+#bool	ap_answer()
+pointer	gt_init()
+errchk	ap_gopen
+
+begin
+	# Query user.
+	call smark (sp)
+	call salloc (cmd, SZ_LINE, TY_CHAR)
+	#call sprintf (Memc[cmd], SZ_LINE, "Edit apertures for %s?")
+    	#    call pargstr (image)
+	#if (!ap_answer ("ansedit", Memc[cmd])) {
+	#    call sfree (sp)
+	#    return
+	#}
+
+	gain = apgimr ("gain", im)
+	rdnoise = apgimr ("readnoise", im)
+
+	dx = (dmax - dmin) / npts
+	x1 = dmin + dx / 2
+	x2 = dmax - dx / 2
+	ymin = sigma[1] - sigerr[1]
+	ymax = sigma[1] + sigerr[1]
+	do i = 2, npts {
+	    ymin = min (ymin, sigma[i] - sigerr[i])
+	    ymax = max (ymax, sigma[i] + sigerr[i])
+	}
+
+	# Set up the graphics.
+	call sprintf (Memc[cmd], SZ_LINE, "Noise characteristics of image %s")
+	    call pargstr (image)
+	call ap_gopen (gp)
+	gt = gt_init()
+	call gt_sets (gt, GTTITLE, Memc[cmd])
+	call gt_sets (gt, GTXLABEL, "Data value")
+	call gt_sets (gt, GTYLABEL, "Sigma")
+	call gt_sets (gt, GTTYPE, "mark")
+	call gt_sets (gt, GTMARK, "plus")
+
+	# Enter cursor loop.
+	key = 'r'
+	repeat {
+	    switch (key) {
+	    case '?': # Print help text.
+		call gpagefile (gp, HELP, PROMPT)
+
+	    case ':': # Colon commands.
+		if (Memc[cmd] == '/')
+		    call gt_colon (Memc[cmd], gp, gt, newgraph)
+		else
+		    call ap_ncolon (Memc[cmd], rdnoise, gain, newgraph)
+
+	    case 'q':
+		break
+
+	    case 'r': # Redraw the graph.
+		newgraph = YES
+
+	    case 'w': # Window graph
+		call gt_window (gt, gp, "gcur", newgraph)
+
+	    case 'I': # Interrupt
+		call fatal (0, "Interrupt")
+
+	    default: # Ring bell for unrecognized commands.
+		call printf ("\007")
+	    }
+
+	    # Update the graph if needed.
+	    if (newgraph == YES) {
+		call sprintf (Memc[cmd], SZ_LINE,
+		    "Read noise = %g e-, Gain = %g e-/DN")
+		    call pargr (rdnoise)
+		    call pargr (gain)
+		call gt_sets (gt, GTPARAMS, Memc[cmd])
+
+		call gclear (gp)
+		y = sqrt ((rdnoise/gain)**2 + dmax/gain)
+		call gswind (gp, dmin, dmax, ymin, max (ymax, y))
+		call gt_swind (gp, gt)
+		call gt_labax (gp, gt)
+		do i = 1, npts {
+		    if (sigma[i] > 0) {
+			x = x1 + (i-1) * dx
+			call gmark (gp, x, sigma[i], GM_VEBAR+GM_HLINE, -dx/2,
+			    -sigerr[i])
+		    }
+		}
+		do i = 1, npts {
+		    x = x1 + (i-1) * dx
+		    y = sqrt ((rdnoise/gain)**2 + x/gain)
+		    if (i == 1)
+			call gamove (gp, x, y)
+		    else
+			call gadraw (gp, x, y)
+		}
+	        newgraph = NO
+	    }
+
+	} until (gt_gcur ("gcur", wx, wy, wcs, key, Memc[cmd], SZ_LINE) == EOF)
+
+	# Free memory.
+	call gt_free (gt)
+	call sfree (sp)
+end
+
+
+# List of colon commands.
+define	CMDS		 "|readnoise|gain|"
+define	RDNOISE		1	# Read noise
+define	GAIN		2	# Gain
+
+# AP_NCOLON -- Respond to colon command from ap_nplot.
+
+procedure ap_ncolon (command, rdnoise, gain, newgraph)
+
+char	command[ARB]		# Colon command
+real	rdnoise			# Readout noise
+real	gain			# Gain
+int	newgraph		# New graph?
+
+real	rval
+int	ncmd, nscan(), strdic()
+pointer	sp, cmd
+
+begin
+	# Scan the command string and get the first word.
+	call smark (sp)
+	call salloc (cmd, SZ_LINE, TY_CHAR)
+
+	call sscan (command)
+	call gargwrd (cmd, SZ_LINE)
+	ncmd = strdic (cmd, cmd, SZ_LINE, CMDS)
+
+	switch (ncmd) {
+	case RDNOISE:
+	    call gargr (rval)
+	    if (nscan() == 2) {
+		rdnoise = rval
+		newgraph = YES
+	    } else {
+		call printf ("rdnoise %g\n")
+		    call pargr (rdnoise)
+	    }
+	case GAIN:
+	    call gargr (rval)
+	    if (nscan() == 2) {
+		gain = rval
+		newgraph = YES
+	    } else {
+		call printf ("gain %g\n")
+		    call pargr (gain)
+	    }
+	default:
+	    call printf ("Unrecognized or ambiguous command\007")
+	}
+
+	call sfree (sp)
+end
diff --git a/noao/twodspec/apextract/apnoise1.par b/noao/twodspec/apextract/apnoise1.par
new file mode 100644
index 00000000..3b5532a7
--- /dev/null
+++ b/noao/twodspec/apextract/apnoise1.par
@@ -0,0 +1,118 @@
+# OUTPUT PARAMETERS
+
+apertures,s,h,)apall.apertures,,,>apnoise.apertures
+format,s,h,)apsum.format,,,>apsum.format
+extras,b,h,)apsum.extras,,,>apsum.extras
+dbwrite,s,h,yes,,,Write to database?
+initialize,b,h,yes,,,Initialize answers?
+verbose,b,h,)_.verbose,,,"Verbose output?
+
+# DEFAULT APERTURE PARAMETERS
+"
+lower,r,h,)apdefault.lower,,,>apdefault.lower
+upper,r,h,)apdefault.upper,,,>apdefault.upper
+apidtable,s,h,)apdefault.apidtable,,,">apdefault.apidtable
+
+# DEFAULT BACKGROUND PARAMETERS
+"
+b_function,s,h,)apdefault.b_function,,,>apdefault.b_function
+b_order,i,h,)apdefault.b_order,,,>apdefault.b_order
+b_sample,s,h,)apdefault.b_sample,,,>apdefault.b_sample
+b_naverage,i,h,)apdefault.b_naverage,,,>apdefault.b_naverage
+b_niterate,i,h,)apdefault.b_niterate,,,>apdefault.b_niterate
+b_low_reject,r,h,)apdefault.b_low_reject,,,>apdefault.b_low_reject
+b_high_reject,r,h,)apdefault.b_high_reject,,,>apdefault.b_high_reject
+b_grow,r,h,)apdefault.b_grow,,,">apdefault.b_grow
+
+# APERTURE CENTERING PARAMETERS
+"
+width,r,h,)apedit.width,,,>apedit.width
+radius,r,h,)apedit.radius,,,>apedit.radius
+threshold,r,h,)apedit.threshold,,,">apedit.threshold
+
+# AUTOMATIC FINDING AND ORDERING PARAMETERS
+"
+nfind,i,h,)apfind.nfind,,,>apfind.nfind
+minsep,r,h,)apfind.minsep,,,>apfind.minsep
+maxsep,r,h,)apfind.maxsep,,,>apfind.maxsep
+order,s,h,)apfind.order,,,">apfind.order
+
+# RECENTERING PARAMETERS
+"
+aprecenter,s,h,)aprecenter.aprecenter,,,>aprecenter.aprecenter
+npeaks,r,h,)aprecenter.npeaks,,,>aprecenter.npeaks
+shift,b,h,)aprecenter.shift,,,">aprecenter.shift
+
+# RESIZING PARAMETERS
+"
+llimit,r,h,)apresize.llimit,,,>apresize.llimit
+ulimit,r,h,)apresize.ulimit,,,>apresize.ulimit
+ylevel,r,h,)apresize.ylevel,,,>apresize.ylevel
+peak,b,h,)apresize.peak,,,>apresize.peak
+bkg,b,h,)apresize.bkg,,,>apresize.bkg
+r_grow,r,h,)apresize.r_grow,,,>apresize.r_grow
+avglimits,b,h,)apresize.avglimits,,,">apresize.avglimits
+
+# EDITING PARAMETERS
+"
+e_output,s,q,,,,Output spectra rootname
+e_profiles,s,q,,,,Profile reference image
+
+# TRACING PARAMETERS
+t_nsum,i,h,)aptrace.nsum,,,>aptrace.nsum
+t_step,i,h,)aptrace.step,,,>aptrace.step
+t_nlost,i,h,)aptrace.nlost,,,>aptrace.nlost
+t_width,r,h,)apedit.width,,,>apedit.width
+t_function,s,h,)aptrace.function,,,>aptrace.function
+t_order,i,h,)aptrace.order,,,>aptrace.order
+t_sample,s,h,)aptrace.sample,,,>aptrace.sample
+t_naverage,i,h,)aptrace.naverage,,,>aptrace.naverage
+t_niterate,i,h,)aptrace.niterate,,,>aptrace.niterate
+t_low_reject,r,h,)aptrace.low_reject,,,>aptrace.low_reject
+t_high_reject,r,h,)aptrace.high_reject,,,>aptrace.high_reject
+t_grow,r,h,)aptrace.grow,,,">aptrace.grow
+
+# EXTRACTION PARAMETERS
+"
+background,s,h,)apnoise.background,,,>apnoise.background
+skybox,i,h,)apnoise.skybox,,,>apnoise.skybox
+weights,s,h,"none",,,Extraction weights (none|variance)
+pfit,s,h,)apnoise.pfit,,,>apnoise.pfit
+clean,b,h,)apnoise.clean,,,>apnoise.clean
+nclean,r,h,0.5,,,Maximum number of pixels to clean
+niterate,i,h,5,0,,Number of profile fitting iterations
+saturation,r,h,)apnoise.saturation,,,>apnoise.saturation
+readnoise,s,h,)apnoise.readnoise,,,>apnoise.readnoise
+gain,s,h,)apnoise.gain,,,>apnoise.gain
+lsigma,r,h,)apnoise.lsigma,,,>apnoise.lsigma
+usigma,r,h,)apnoise.usigma,,,>apnoise.usigma
+polysep,r,h,0.90,0.1,0.95,Marsh algorithm polynomial spacing
+polyorder,i,h,10,1,,Marsh algorithm polynomial order
+nsubaps,i,h,1,,,"Number of subapertures per aperture
+
+# ANSWER PARAMETERS
+"
+ansclobber,s,h,"no",,," "
+ansclobber1,s,h,"no",,," "
+ansdbwrite,s,h,"yes",,," "
+ansdbwrite1,s,h,"yes",,," "
+ansedit,s,h,"yes",,," "
+ansextract,s,h,"yes",,," "
+ansfind,s,h,"yes",,," "
+ansfit,s,h,"yes",,," "
+ansfitscatter,s,h,"yes",,," "
+ansfitsmooth,s,h,"yes",,," "
+ansfitspec,s,h,"yes",,," "
+ansfitspec1,s,h,"yes",,," "
+ansfittrace,s,h,"yes",,," "
+ansfittrace1,s,h,"yes",,," "
+ansflat,s,h,"yes",,," "
+ansmask,s,h,"yes",,," "
+ansnorm,s,h,"yes",,," "
+ansrecenter,s,h,"yes",,," "
+ansresize,s,h,"yes",,," "
+ansreview,s,h,"yes",,," "
+ansreview1,s,h,"yes",,," "
+ansscat,s,h,"yes",,," "
+anssmooth,s,h,"yes",,," "
+anstrace,s,h,"yes",,," "
diff --git a/noao/twodspec/apextract/apnorm1.par b/noao/twodspec/apextract/apnorm1.par
new file mode 100644
index 00000000..1a182dce
--- /dev/null
+++ b/noao/twodspec/apextract/apnorm1.par
@@ -0,0 +1,118 @@
+# OUTPUT PARAMETERS
+
+apertures,s,h,)apall.apertures,,,>apnorm.apertures
+format,s,h,)apsum.format,,,>apsum.format
+extras,b,h,)apsum.extras,,,>apsum.extras
+dbwrite,s,h,yes,,,Write to database?
+initialize,b,h,yes,,,Initialize answers?
+verbose,b,h,)_.verbose,,,"Verbose output?
+
+# DEFAULT APERTURE PARAMETERS
+"
+lower,r,h,)apdefault.lower,,,>apdefault.lower
+upper,r,h,)apdefault.upper,,,>apdefault.upper
+apidtable,s,h,)apdefault.apidtable,,,">apdefault.apidtable
+
+# DEFAULT BACKGROUND PARAMETERS
+"
+b_function,s,h,)apdefault.b_function,,,>apdefault.b_function
+b_order,i,h,)apdefault.b_order,,,>apdefault.b_order
+b_sample,s,h,)apdefault.b_sample,,,>apdefault.b_sample
+b_naverage,i,h,)apdefault.b_naverage,,,>apdefault.b_naverage
+b_niterate,i,h,)apdefault.b_niterate,,,>apdefault.b_niterate
+b_low_reject,r,h,)apdefault.b_low_reject,,,>apdefault.b_low_reject
+b_high_reject,r,h,)apdefault.b_high_reject,,,>apdefault.b_high_reject
+b_grow,r,h,)apdefault.b_grow,,,">apdefault.b_grow
+
+# APERTURE CENTERING PARAMETERS
+"
+width,r,h,)apedit.width,,,>apedit.width
+radius,r,h,)apedit.radius,,,>apedit.radius
+threshold,r,h,)apedit.threshold,,,">apedit.threshold
+
+# AUTOMATIC FINDING AND ORDERING PARAMETERS
+"
+nfind,i,h,)apfind.nfind,,,>apfind.nfind
+minsep,r,h,)apfind.minsep,,,>apfind.minsep
+maxsep,r,h,)apfind.maxsep,,,>apfind.maxsep
+order,s,h,)apfind.order,,,">apfind.order
+
+# RECENTERING PARAMETERS
+"
+aprecenter,s,h,)aprecenter.aprecenter,,,>aprecenter.aprecenter
+npeaks,r,h,)aprecenter.npeaks,,,>aprecenter.npeaks
+shift,b,h,)aprecenter.shift,,,">aprecenter.shift
+
+# RESIZING PARAMETERS
+"
+llimit,r,h,)apresize.llimit,,,>apresize.llimit
+ulimit,r,h,)apresize.ulimit,,,>apresize.ulimit
+ylevel,r,h,)apresize.ylevel,,,>apresize.ylevel
+peak,b,h,)apresize.peak,,,>apresize.peak
+bkg,b,h,)apresize.bkg,,,>apresize.bkg
+r_grow,r,h,)apresize.r_grow,,,>apresize.r_grow
+avglimits,b,h,)apresize.avglimits,,,">apresize.avglimits
+
+# EDITING PARAMETERS
+"
+e_output,s,q,,,,Output spectra rootname
+e_profiles,s,q,,,,Profile reference image
+
+# TRACING PARAMETERS
+t_nsum,i,h,)aptrace.nsum,,,>aptrace.nsum
+t_step,i,h,)aptrace.step,,,>aptrace.step
+t_nlost,i,h,)aptrace.nlost,,,>aptrace.nlost
+t_width,r,h,)apedit.width,,,>apedit.width
+t_function,s,h,)aptrace.function,,,>aptrace.function
+t_order,i,h,)aptrace.order,,,>aptrace.order
+t_sample,s,h,)aptrace.sample,,,>aptrace.sample
+t_naverage,i,h,)aptrace.naverage,,,>aptrace.naverage
+t_niterate,i,h,)aptrace.niterate,,,>aptrace.niterate
+t_low_reject,r,h,)aptrace.low_reject,,,>aptrace.low_reject
+t_high_reject,r,h,)aptrace.high_reject,,,>aptrace.high_reject
+t_grow,r,h,)aptrace.grow,,,">aptrace.grow
+
+# EXTRACTION PARAMETERS
+"
+background,s,h,)apnorm.background,,,>apnorm.background
+skybox,i,h,)apnorm.skybox,,,>apnorm.skybox
+weights,s,h,)apnorm.weights,,,>apnorm.weights
+pfit,s,h,)apnorm.pfit,,,>apnorm.pfit
+clean,b,h,)apnorm.clean,,,>apnorm.clean
+nclean,r,h,0.5,,,Maximum number of pixels to clean
+niterate,i,h,5,0,,Number of profile fitting iterations
+saturation,r,h,)apnorm.saturation,,,>apnorm.saturation
+readnoise,s,h,)apnorm.readnoise,,,>apnorm.readnoise
+gain,s,h,)apnorm.gain,,,>apnorm.gain
+lsigma,r,h,)apnorm.lsigma,,,>apnorm.lsigma
+usigma,r,h,)apnorm.usigma,,,>apnorm.usigma
+polysep,r,h,0.90,0.1,0.95,Marsh algorithm polynomial spacing
+polyorder,i,h,10,1,,Marsh algorithm polynomial order
+nsubaps,i,h,1,,,"Number of subapertures per aperture
+
+# ANSWER PARAMETERS
+"
+ansclobber,s,h,"no",,," "
+ansclobber1,s,h,"no",,," "
+ansdbwrite,s,h,"yes",,," "
+ansdbwrite1,s,h,"yes",,," "
+ansedit,s,h,"yes",,," "
+ansextract,s,h,"yes",,," "
+ansfind,s,h,"yes",,," "
+ansfit,s,h,"yes",,," "
+ansfitscatter,s,h,"yes",,," "
+ansfitsmooth,s,h,"yes",,," "
+ansfitspec,s,h,"yes",,," "
+ansfitspec1,s,h,"yes",,," "
+ansfittrace,s,h,"yes",,," "
+ansfittrace1,s,h,"yes",,," "
+ansflat,s,h,"yes",,," "
+ansmask,s,h,"yes",,," "
+ansnorm,s,h,"yes",,," "
+ansrecenter,s,h,"yes",,," "
+ansresize,s,h,"yes",,," "
+ansreview,s,h,"yes",,," "
+ansreview1,s,h,"yes",,," "
+ansscat,s,h,"yes",,," "
+anssmooth,s,h,"yes",,," "
+anstrace,s,h,"yes",,," "
diff --git a/noao/twodspec/apextract/apnormalize.par b/noao/twodspec/apextract/apnormalize.par
new file mode 100644
index 00000000..2fc64432
--- /dev/null
+++ b/noao/twodspec/apextract/apnormalize.par
@@ -0,0 +1,41 @@
+# APNORMALIZE
+
+input,s,a,,,,List of images to normalize
+output,s,a,,,,List of output normalized images
+apertures,s,h,"",,,Apertures
+references,s,h,"",,,"List of reference images
+"
+interactive,b,h,yes,,,Run task interactively?
+find,b,h,yes,,,Find apertures?
+recenter,b,h,yes,,,Recenter apertures?
+resize,b,h,yes,,,Resize apertures?
+edit,b,h,yes,,,Edit apertures?
+trace,b,h,yes,,,Trace apertures?
+fittrace,b,h,yes,,,Fit traced points interactively?
+normalize,b,h,yes,,,Normalize spectra?
+fitspec,b,h,yes,,,"Fit normalization spectra interactively?
+"
+line,i,h,INDEF,1,,Dispersion line
+nsum,i,h,10,,,Number of dispersion lines to sum or median
+cennorm,b,h,no,,,Normalize to the aperture center?
+threshold,r,h,10.,,,"Threshold for normalization spectra
+"
+background,s,h,"none","none|average|median|minimum|fit",,Background to subtract
+weights,s,h,"none","none|variance",,Extraction weights (none|variance)
+pfit,s,h,"fit1d","fit1d|fit2d",,Profile fitting type (fit1d|fit2d)
+clean,b,h,no,,,Detect and replace bad pixels?
+skybox,i,h,1,1,,Box car smoothing length for sky
+saturation,r,h,INDEF,,,Saturation level
+readnoise,s,h,"0.",,,Read out noise sigma (photons)
+gain,s,h,"1.",,,Photon gain (photons/data number)
+lsigma,r,h,4.,0.,,Lower rejection threshold
+usigma,r,h,4.,0.,,"Upper rejection threshold
+"
+function,s,h,"legendre","chebyshev|legendre|spline1|spline3",,Fitting function for normalization spectra
+order,i,h,1,1,,Fitting function order
+sample,s,h,"*",,,Sample regions
+naverage,i,h,1,,,Average or median
+niterate,i,h,0,0,,Number of rejection iterations
+low_reject,r,h,3.,0.,,Lower rejection sigma
+high_reject,r,h,3.,0.,,High upper rejection sigma
+grow,r,h,0.,0.,,Rejection growing radius
diff --git a/noao/twodspec/apextract/apparams.dat b/noao/twodspec/apextract/apparams.dat
new file mode 100644
index 00000000..897e4f2e
--- /dev/null
+++ b/noao/twodspec/apextract/apparams.dat
@@ -0,0 +1,68 @@
+"OUTPUT PARAMETERS"
+format		s	%s	26
+extras		b	%b	26
+dbwrite		s	%s	26
+
+"DEFAULT APERTURE PARAMETERS"
+lower		r	%g	26
+upper		r	%g	26
+apidtable	s	%s	26
+
+"DEFAULT BACKGROUND PARAMETERS"
+b_function	s	%s	26
+b_order		i	%d	26
+b_sample	s	%s	26
+b_naverage	i	%d	26
+b_niterate	i	%d	26
+b_low_reject	r	%g	26
+b_high_reject	r	%g	26
+b_grow		r	%g	26
+
+"APERTURE CENTERING PARAMETERS: FINDING, RECENTERING, MARKING"
+width		r	%g	26
+radius		r	%g	26
+threshold	r	%g	26
+
+"AUTOMATIC APERTURE FINDING AND ORDERING PARAMETERS"
+minsep		r	%g	26
+maxsep		r	%g	26
+order		s	%s	26
+
+"RECENTERING PARAMETERS"
+apertures	s	%s	26
+npeaks		r	%g	26
+shift		b	%b	26
+
+"RESIZING PARAMETERS"
+llimit		r	%g	26
+ulimit		r	%g	26
+ylevel		r	%g	26
+peak		b	%b	26
+bkg		b	%b	26
+r_grow		r	%g	26
+avglimits	b	%b	26
+
+"TRACING PARAMETERS"
+t_nsum		i	%d	26
+t_step		i	%d	26
+t_width		r	%g	26
+t_function	s	%s	26
+t_order		i	%d	26
+t_sample	s	%s	26
+t_naverage	i	%d	26
+t_niterate	i	%d	26
+t_low_reject	r	%g	26
+t_high_reject	r	%g	26
+t_grow		r	%g	26
+
+"EXTRACTION PARAMETERS"
+weights		s	%s	26
+background	s	%s	26
+clean		b	%b	26
+saturation	r	%g	26
+readnoise	r	%g	26
+gain		r	%g	26
+lsigma		r	%g	26
+usigma		r	%g	26
+skybox		i	%d	26
+nsubaps		i	%d	26
diff --git a/noao/twodspec/apextract/apparams.h b/noao/twodspec/apextract/apparams.h
new file mode 100644
index 00000000..ac3e37cb
--- /dev/null
+++ b/noao/twodspec/apextract/apparams.h
@@ -0,0 +1,92 @@
+# PP_TABLE -- This table assigns pset pointers for each parameter.
+
+define	PP_PP_LENTABLE	61
+
+# APDEFAULT
+
+define	PP_APIDTABLE		Memi[$1]
+define	PP_LOWER		Memi[$1+1]
+define	PP_UPPER		Memi[$1+2]
+define	PP_B_FUNCTION		Memi[$1+3]
+define	PP_B_ORDER		Memi[$1+4]
+define	PP_B_SAMPLE		Memi[$1+5]
+define	PP_B_NAVERAGE		Memi[$1+6]
+define	PP_B_NITERATE		Memi[$1+7]
+define	PP_B_LOW_REJECT		Memi[$1+8]
+define	PP_B_HIGH_REJECT	Memi[$1+9]
+define	PP_B_GROW		Memi[$1+10]
+
+#APFIND
+
+define	PP_NFIND		Memi[$1+11]
+define	PP_MINSEP		Memi[$1+12]
+define	PP_MAXSEP		Memi[$1+13]
+define	PP_ORDER		Memi[$1+14]
+
+# APRECENTER
+
+define	PP_APERTURES		Memi[$1+15]
+define	PP_NPEAKS		Memi[$1+16]
+define	PP_SHIFT		Memi[$1+17]
+
+# APRESIZE
+
+define	PP_LLIMIT		Memi[$1+18]
+define	PP_ULIMIT		Memi[$1+19]
+define	PP_YLEVEL		Memi[$1+20]
+define	PP_PEAK			Memi[$1+21]
+define	PP_BKG			Memi[$1+22]
+
+# APEDIT
+
+define	PP_WIDTH		Memi[$1+23]
+define	PP_RADIUS		Memi[$1+24]
+define	PP_THRESHOLD		Memi[$1+25]
+define	PP_E_OUTPUT		Memi[$1+26]
+define	PP_E_SKY		Memi[$1+27]
+define	PP_E_PROFILES		Memi[$1+28]
+
+# APTRACE
+
+define	PP_FITTRACE		Memi[$1+29]
+define	PP_T_NSUM		Memi[$1+30]
+define	PP_STEP			Memi[$1+31]
+define	PP_T_FUNCTION		Memi[$1+32]
+define	PP_T_ORDER		Memi[$1+33]
+define	PP_T_SAMPLE		Memi[$1+34]
+define	PP_T_NAVERAGE		Memi[$1+35]
+define	PP_T_NITERATE		Memi[$1+36]
+define	PP_T_LOW_REJECT		Memi[$1+37]
+define	PP_T_HIGH_REJECT	Memi[$1+38]
+define	PP_T_GROW		Memi[$1+39]
+
+# APSUM or APSTRIP
+
+define	PP_SKYEXTRACT		Memi[$1+40]
+define	PP_BACKGROUND		Memi[$1+41]
+define	PP_CLEAN		Memi[$1+42]
+define	PP_WEIGHTS		Memi[$1+43]
+define	PP_FIT(pp)		Memi[$1+61]
+define	PP_NAVERAGE		Memi[$1+44]
+define	PP_INTERPOLATOR		Memi[$1+45]
+define	PP_NCLEAN		Memi[$1+46]
+define	PP_LSIGMA		Memi[$1+47]
+define	PP_USIGMA		Memi[$1+48]
+define	PP_V0			Memi[$1+49]
+define	PP_V1			Memi[$1+50]
+
+# APNORMALIZE
+
+define	PP_N_THRESHOLD		Memi[$1+51]
+define	PP_N_FUNCTION		Memi[$1+52]
+define	PP_N_ORDER		Memi[$1+53]
+define	PP_N_SAMPLE		Memi[$1+54]
+define	PP_N_NAVERAGE		Memi[$1+55]
+define	PP_N_NITERATE		Memi[$1+56]
+define	PP_N_LOW_REJECT		Memi[$1+57]
+define	PP_N_HIGH_REJECT	Memi[$1+58]
+define	PP_N_GROW		Memi[$1+59]
+
+# APSCATTER
+
+define	PP_BUFFER		Memi[$1+60]
diff --git a/noao/twodspec/apextract/apparams.par b/noao/twodspec/apextract/apparams.par
new file mode 100644
index 00000000..61b2b2ce
--- /dev/null
+++ b/noao/twodspec/apextract/apparams.par
@@ -0,0 +1,117 @@
+# OUTPUT PARAMETERS
+
+format,s,h,)apsum.format,,,>apsum.format
+extras,b,h,)apsum.extras,,,>apsum.extras
+dbwrite,s,h,yes,,,Write to database?
+initialize,b,h,yes,,,Initialize answers?
+verbose,b,h,)_.verbose,,,"Verbose output?
+
+# DEFAULT APERTURE PARAMETERS
+"
+lower,r,h,)apdefault.lower,,,>apdefault.lower
+upper,r,h,)apdefault.upper,,,>apdefault.upper
+apidtable,s,h,)apdefault.apidtable,,,">apdefault.apidtable
+
+# DEFAULT BACKGROUND PARAMETERS
+"
+b_function,s,h,)apdefault.b_function,,,>apdefault.b_function
+b_order,i,h,)apdefault.b_order,,,>apdefault.b_order
+b_sample,s,h,)apdefault.b_sample,,,>apdefault.b_sample
+b_naverage,i,h,)apdefault.b_naverage,,,>apdefault.b_naverage
+b_niterate,i,h,)apdefault.b_niterate,,,>apdefault.b_niterate
+b_low_reject,r,h,)apdefault.b_low_reject,,,>apdefault.b_low_reject
+b_high_reject,r,h,)apdefault.b_high_reject,,,>apdefault.b_high_reject
+b_grow,r,h,)apdefault.b_grow,,,">apdefault.b_grow
+
+# APERTURE CENTERING PARAMETERS
+"
+width,r,h,)apedit.width,,,>apedit.width
+radius,r,h,)apedit.radius,,,>apedit.radius
+threshold,r,h,)apedit.threshold,,,">apedit.threshold
+
+# AUTOMATIC FINDING AND ORDERING PARAMETERS
+"
+nfind,i,h,)apfind.nfind,,,>apfind.nfind
+minsep,r,h,)apfind.minsep,,,>apfind.minsep
+maxsep,r,h,)apfind.maxsep,,,>apfind.maxsep
+order,s,h,)apfind.order,,,">apfind.order
+
+# RECENTERING PARAMETERS
+"
+aprecenter,s,h,)aprecenter.aprecenter,,,>aprecenter.aprecenter
+npeaks,r,h,)aprecenter.npeaks,,,>aprecenter.npeaks
+shift,b,h,)aprecenter.shift,,,">aprecenter.shift
+
+# RESIZING PARAMETERS
+"
+llimit,r,h,)apresize.llimit,,,>apresize.llimit
+ulimit,r,h,)apresize.ulimit,,,>apresize.ulimit
+ylevel,r,h,)apresize.ylevel,,,>apresize.ylevel
+peak,b,h,)apresize.peak,,,>apresize.peak
+bkg,b,h,)apresize.bkg,,,>apresize.bkg
+r_grow,r,h,)apresize.r_grow,,,>apresize.r_grow
+avglimits,b,h,)apresize.avglimits,,,">apresize.avglimits
+
+# EDITING PARAMETERS
+"
+e_output,s,q,,,,Output spectra rootname
+e_profiles,s,q,,,,Profile reference image
+
+# TRACING PARAMETERS
+t_nsum,i,h,)aptrace.nsum,,,>aptrace.nsum
+t_step,i,h,)aptrace.step,,,>aptrace.step
+t_nlost,i,h,)aptrace.nlost,,,>aptrace.nlost
+t_width,r,h,)apedit.width,,,>apedit.width
+t_function,s,h,)aptrace.function,,,>aptrace.function
+t_order,i,h,)aptrace.order,,,>aptrace.order
+t_sample,s,h,)aptrace.sample,,,>aptrace.sample
+t_naverage,i,h,)aptrace.naverage,,,>aptrace.naverage
+t_niterate,i,h,)aptrace.niterate,,,>aptrace.niterate
+t_low_reject,r,h,)aptrace.low_reject,,,>aptrace.low_reject
+t_high_reject,r,h,)aptrace.high_reject,,,>aptrace.high_reject
+t_grow,r,h,)aptrace.grow,,,">aptrace.grow
+
+# EXTRACTION PARAMETERS
+"
+background,s,h,)apsum.background,,,>apsum.background
+skybox,i,h,)apsum.skybox,,,>apsum.skybox
+weights,s,h,)apsum.weights,,,>apsum.weights
+pfit,s,h,)apsum.pfit,,,>apsum.pfit
+clean,b,h,)apsum.clean,,,>apsum.clean
+nclean,r,h,0.5,,,Maximum number of pixels to clean
+niterate,i,h,5,0,,Number of profile fitting iterations
+saturation,r,h,)apsum.saturation,,,>apsum.saturation
+readnoise,s,h,)apsum.readnoise,,,>apsum.readnoise
+gain,s,h,)apsum.gain,,,>apsum.gain
+lsigma,r,h,)apsum.lsigma,,,>apsum.lsigma
+usigma,r,h,)apsum.usigma,,,>apsum.usigma
+polysep,r,h,0.90,0.1,0.95,Marsh algorithm polynomial spacing
+polyorder,i,h,10,1,,Marsh algorithm polynomial order
+nsubaps,i,h,)apsum.nsubaps,,,">apsum.nsubaps
+
+# ANSWER PARAMETERS
+"
+ansclobber,s,h,"no",,," "
+ansclobber1,s,h,"no",,," "
+ansdbwrite,s,h,"yes",,," "
+ansdbwrite1,s,h,"yes",,," "
+ansedit,s,h,"yes",,," "
+ansextract,s,h,"yes",,," "
+ansfind,s,h,"yes",,," "
+ansfit,s,h,"yes",,," "
+ansfitscatter,s,h,"yes",,," "
+ansfitsmooth,s,h,"yes",,," "
+ansfitspec,s,h,"yes",,," "
+ansfitspec1,s,h,"yes",,," "
+ansfittrace,s,h,"yes",,," "
+ansfittrace1,s,h,"yes",,," "
+ansflat,s,h,"yes",,," "
+ansmask,s,h,"yes",,," "
+ansnorm,s,h,"yes",,," "
+ansrecenter,s,h,"yes",,," "
+ansresize,s,h,"yes",,," "
+ansreview,s,h,"yes",,," "
+ansreview1,s,h,"yes",,," "
+ansscat,s,h,"yes",,," "
+anssmooth,s,h,"yes",,," "
+anstrace,s,h,"yes",,," "
diff --git a/noao/twodspec/apextract/apparams.x b/noao/twodspec/apextract/apparams.x
new file mode 100644
index 00000000..526b4bcd
--- /dev/null
+++ b/noao/twodspec/apextract/apparams.x
@@ -0,0 +1,95 @@
+define	PARAMS		"apextract$apparams.dat"
+define	LEN_LINE	80
+
+# AP_PARAMS -- Show the parameters.
+
+procedure ap_params (file, image, line, nsum)
+
+char	file[ARB]		# Aperture file
+char	image[ARB]		# Image name
+int	line			# Image line
+int	nsum			# Number of lines to sum
+
+int	in, out, len, nchar
+pointer	sp, param, type, format, instr, outstr, str
+bool	apgetb()
+int	apgeti(), open(), fscan(), nscan(), strlen()
+real	apgetr()
+errchk	open
+
+begin
+	# Open input parameter file and output stream.
+	in = open (PARAMS, READ_ONLY, TEXT_FILE)
+	out = open (file, APPEND, TEXT_FILE)
+
+	call smark (sp)
+	call salloc (param, SZ_LINE, TY_CHAR)
+	call salloc (type, 10, TY_CHAR)
+	call salloc (format, 10, TY_CHAR)
+	call salloc (instr, SZ_LINE, TY_CHAR)
+	call salloc (outstr, SZ_LINE, TY_CHAR)
+	call salloc (str, SZ_LINE, TY_CHAR)
+	Memc[outstr] = EOS
+
+	call fprintf (out, "%32tAPEXTRACT PARAMETERS\n")
+	call fprintf (out, "image=%s%27tline=%d%53tnsum=%d\n")
+	    call pargstr (image)
+	    call pargi (line)
+	    call pargi (nsum)
+	call fprintf (out, "database=%s%27tlogfile=%s%53tplotfile=%s\n\n")
+	    call clgstr ("database", Memc[str], SZ_LINE)
+	    call pargstr (Memc[str])
+	    call clgstr ("logfile", Memc[str], SZ_LINE)
+	    call pargstr (Memc[str])
+	    call clgstr ("plotfile", Memc[str], SZ_LINE)
+	    call pargstr (Memc[str])
+
+	len = 0
+	while (fscan (in) != EOF) {
+	    call gargwrd (Memc[param], SZ_LINE)
+	    call gargwrd (Memc[type], 10)
+	    call gargwrd (Memc[format], 10)
+	    call gargi (nchar)
+	    if (nscan() < 4)
+		nchar = LEN_LINE
+
+	    if (len + nchar > LEN_LINE) {
+		call strcat ("\n", Memc[outstr], SZ_LINE)
+		call fprintf (out, Memc[outstr])
+		Memc[outstr] = EOS
+		len = 0
+	    }
+
+	    if (nscan() == 1) {
+		call sprintf (Memc[outstr], SZ_LINE, "%%%dt%s")
+		    call pargi ((LEN_LINE - strlen (Memc[param])) / 2)
+		    call pargstr (Memc[param])
+	    } else if (nscan() == 4) {
+	        call sprintf (Memc[str], SZ_LINE, "%%%dt%s=")
+		    call pargi (len+1)
+		    call pargstr (Memc[param])
+	        call strcat (Memc[str], Memc[outstr], SZ_LINE)
+
+	        call sprintf (Memc[str], SZ_LINE, Memc[format])
+	        switch (Memc[type]) {
+	        case 'b':
+		    call pargb (apgetb (Memc[param]))
+	        case 'i':
+		    call pargi (apgeti (Memc[param]))
+	        case 'r':
+		    call pargr (apgetr (Memc[param]))
+	        case 's':
+		    call apgstr (Memc[param], Memc[instr], SZ_LINE)
+		    call pargstr (Memc[instr])
+	        }
+	        call strcat (Memc[str], Memc[outstr], SZ_LINE)
+	    }
+	    len = len + nchar
+	}
+	call strcat ("\n", Memc[outstr], SZ_LINE)
+	call fprintf (out, Memc[outstr])
+
+	call close (in)
+	call close (out)
+	call sfree (sp)
+end
diff --git a/noao/twodspec/apextract/appars.x b/noao/twodspec/apextract/appars.x
new file mode 100644
index 00000000..8f68c0c9
--- /dev/null
+++ b/noao/twodspec/apextract/appars.x
@@ -0,0 +1,261 @@
+include <math/iminterp.h>
+
+procedure apopset (pset)
+
+char	pset[ARB]		# Pset name
+pointer	pp, clopset ()
+common	/apparam/ pp
+
+begin
+	pp = clopset (pset)
+end
+
+
+procedure apcpset ()
+
+pointer	pp
+common	/apparam/ pp
+
+begin
+	call clcpset (pp)
+end
+
+
+procedure apgstr (param, str, maxchar)
+
+char	param[ARB]		# Parameter name
+char	str[ARB]		# String to return
+int	maxchar			# Maximum length of string
+
+pointer	pp
+common	/apparam/ pp
+
+begin
+	call clgpset (pp, param, str, maxchar)
+end
+
+
+bool procedure apgetb (param)
+
+char	param[ARB]		# Parameter name
+bool	clgpsetb()
+pointer	pp
+common	/apparam/ pp
+
+begin
+	return (clgpsetb (pp, param))
+end
+
+
+int procedure apgeti (param)
+
+char	param[ARB]		# Parameter name
+int	clgpseti()
+pointer	pp
+common	/apparam/ pp
+
+begin
+	return (clgpseti (pp, param))
+end
+
+
+real procedure apgetr (param)
+
+char	param[ARB]		# Parameter name
+real	clgpsetr()
+pointer	pp
+common	/apparam/ pp
+
+begin
+	return (clgpsetr (pp, param))
+end
+
+
+real procedure apgimr (param, im)
+
+char	param[ARB]		# Parameter name
+pointer	im			# IMIO pointer
+int	i, ctor()
+pointer	pp, sp, str
+real	rval, imgetr()
+common	/apparam/ pp
+errchk	imgetr
+
+begin
+	call smark (sp)
+	call salloc (str, SZ_FNAME, TY_CHAR)
+	call clgpset (pp, param, Memc[str], SZ_FNAME)
+	i = 1
+	if (ctor (Mems[str], i, rval) == 0)
+	    rval = imgetr (im, Memc[str])
+	call sfree (sp)
+	return (rval)
+end
+
+
+int procedure apgwrd (param, keyword, maxchar, dictionary)
+
+char	param[ARB]		# CL parameter string
+char	keyword[ARB]		# String matched in dictionary
+int	maxchar			# Maximum size of str
+char	dictionary[ARB]		# Dictionary string
+
+int	i, strdic()
+pointer	pp
+common	/apparam/ pp
+
+begin
+	call clgpset (pp, param, keyword, maxchar)
+	i = strdic (keyword, keyword, maxchar, dictionary)
+	if (i <= 0)
+	    call error (1, "Ambiguous or unknown parameter value")
+	return (i)
+end
+
+
+# APGINTERP -- Select an interpolator from a CL input string.  The procedure
+# is coded to be protected from changes in the values of the interpolator
+# types in interpdef.h.
+
+int procedure apginterp (param)
+
+char	param[ARB]		# CL parameter prompt string
+int	index, iicodes[5]
+pointer	sp, word
+int	apgwrd()
+errchk	apgwrd
+data	iicodes /II_NEAREST, II_LINEAR, II_POLY3, II_POLY5, II_SPLINE3/
+
+pointer	pp
+common	/apparam/ pp
+
+begin
+	call smark (sp)
+	call salloc (word, SZ_FNAME, TY_CHAR)
+
+	index = max (1, min (5, apgwrd (param, Memc[word], SZ_FNAME,
+	    "|nearest|linear|poly3|poly5|spline3|")))
+
+	call sfree (sp)
+	return (iicodes[index])
+end
+
+
+procedure appstr (param, str)
+
+char	param[ARB]		# Parameter name
+char	str[ARB]		# String to be put
+pointer	pp, sp, str1, str2
+common	/apparam/ pp
+
+int	i, strmatch(), stridxs()
+
+begin
+	if (strmatch (param, "p_") == 0) {
+	    call smark (sp)
+	    call salloc (str1, SZ_FNAME, TY_CHAR)
+	    call salloc (str2, SZ_LINE, TY_CHAR)
+	    call sprintf (Memc[str1], SZ_FNAME, "%s.p_prompt")
+		call pargstr (param)
+	    call clgpset (pp, Memc[str1], Memc[str2], SZ_LINE)
+	    if (Memc[str2] == '>') {
+		i = stridxs (" \\\t\n", Memc[str2])
+		if (i > 0)
+		    Memc[str2+i-1] = EOS
+		call clpstr (Memc[str2+1], str)
+	    } else
+		call clppset (pp, param, str)
+	    call sfree (sp)
+	} else
+	    call clppset (pp, param, str)
+end
+
+
+procedure apputb (param, bval)
+
+char	param[ARB]		# Parameter name
+bool	bval			# Value to be put
+pointer	pp, sp, str1, str2
+common	/apparam/ pp
+
+int	i, strmatch(), stridxs()
+
+begin
+	if (strmatch (param, "p_") == 0) {
+	    call smark (sp)
+	    call salloc (str1, SZ_FNAME, TY_CHAR)
+	    call salloc (str2, SZ_LINE, TY_CHAR)
+	    call sprintf (Memc[str1], SZ_FNAME, "%s.p_prompt")
+		call pargstr (param)
+	    call clgpset (pp, Memc[str1], Memc[str2], SZ_LINE)
+	    if (Memc[str2] == '>') {
+		i = stridxs (" \\\t\n", Memc[str2])
+		if (i > 0)
+		    Memc[str2+i-1] = EOS
+		call clputb (Memc[str2+1], bval)
+	    } else
+		call clppsetb (pp, param, bval)
+	    call sfree (sp)
+	} else
+	    call clppsetb (pp, param, bval)
+end
+
+
+procedure apputi (param, ival)
+
+char	param[ARB]		# Parameter name
+int	ival			# Value to be put
+pointer	pp, sp, str1, str2
+common	/apparam/ pp
+
+int	i, strmatch(), stridxs()
+
+begin
+	if (strmatch (param, "p_") == 0) {
+	    call smark (sp)
+	    call salloc (str1, SZ_FNAME, TY_CHAR)
+	    call salloc (str2, SZ_LINE, TY_CHAR)
+	    call sprintf (Memc[str1], SZ_FNAME, "%s.p_prompt")
+		call pargstr (param)
+	    call clgpset (pp, Memc[str1], Memc[str2], SZ_LINE)
+	    if (Memc[str2] == '>') {
+		i = stridxs (" \\\t\n", Memc[str2])
+		if (i > 0)
+		    Memc[str2+i-1] = EOS
+		call clputi (Memc[str2+1], ival)
+	    } else
+		call clppseti (pp, param, ival)
+	    call sfree (sp)
+	} else
+	    call clppseti (pp, param, ival)
+end
+
+
+procedure apputr (param, rval)
+
+char	param[ARB]		# Parameter name
+real	rval			# Value to be put
+pointer	pp, sp, str1, str2
+common	/apparam/ pp
+
+int	i, strmatch(), stridxs()
+
+begin
+	if (strmatch (param, "p_") == 0) {
+	    call smark (sp)
+	    call salloc (str1, SZ_FNAME, TY_CHAR)
+	    call salloc (str2, SZ_LINE, TY_CHAR)
+	    call sprintf (Memc[str1], SZ_FNAME, "%s.p_prompt")
+		call pargstr (param)
+	    call clgpset (pp, Memc[str1], Memc[str2], SZ_LINE)
+	    if (Memc[str2] == '>') {
+		i = stridxs (" \\\t\n", Memc[str2])
+		if (i > 0)
+		    Memc[str2+i-1] = EOS
+		call clputr (Memc[str2+1], rval)
+	    } else
+		call clppsetr (pp, param, rval)
+	    call sfree (sp)
+	} else
+	    call clppsetr (pp, param, rval)
+end
diff --git a/noao/twodspec/apextract/apprint.x b/noao/twodspec/apextract/apprint.x
new file mode 100644
index 00000000..b2bf17f0
--- /dev/null
+++ b/noao/twodspec/apextract/apprint.x
@@ -0,0 +1,34 @@
+include	"apertures.h"
+
+# AP_PRINT -- Print the parameters of the indexed aperture.
+
+procedure ap_print (index, line, all, aps)
+
+int	index			# Index of aperture
+int	line			# Dispersion line
+int	all			# All flag
+pointer	aps[ARB]		# Apertures
+
+int	apaxis
+pointer	ap
+real	ap_cveval()
+
+begin
+	if (index < 1)
+	    return
+
+	if (all == YES)
+	    call printf ("ALL: ")
+	else
+	    call printf ("     ")
+
+	ap = aps[index]
+	apaxis = AP_AXIS(ap)
+	call printf (
+"aperture = %d  beam = %d  center = %.2f  low = %.2f  upper = %.2f\n")
+	    call pargi (AP_ID(ap))
+	    call pargi (AP_BEAM(ap))
+	    call pargr (AP_CEN(ap, apaxis)+ap_cveval (AP_CV(ap), real (line)))
+	    call pargr (AP_LOW(ap, apaxis))
+	    call pargr (AP_HIGH(ap, apaxis))
+end
diff --git a/noao/twodspec/apextract/approfile.x b/noao/twodspec/apextract/approfile.x
new file mode 100644
index 00000000..eeb31a6d
--- /dev/null
+++ b/noao/twodspec/apextract/approfile.x
@@ -0,0 +1,765 @@
+include	<mach.h>
+include	<gset.h>
+include	<math/curfit.h>
+include	"apertures.h"
+
+
+# AP_PROFILE -- Determine spectrum profile with pixel rejection.
+#
+# The profile is determined by dividing each dispersion point by an estimate
+# of the spectrum and then smoothing and normalizing to unit integral.
+# This routine has two algorithms (procedures) for smoothing, one for nearly
+# aligned spectra and one for tilted spectra.  The selection is determined
+# by the calling program and signaled by whether there is a variation in
+# the profile offsets.  For both smoothing algorithms the same iterative
+# rejection algorithm may be used to eliminate deviant points from affecting
+# the profile.  This rejection is selected by the "clean" parameter.
+# A plot of the final profile along the dispersion may be made for the
+# special plotfile "debugfits" or "debugall".
+#
+# Dispersion points with saturated pixels are ignored as well a when the
+# total sky subtracted flux is negative.
+
+procedure ap_profile (im, ap, dbuf, nc, nl, c1, l1, sbuf, svar, profile, nx, ny,
+	xs, ys, asi)
+
+pointer	im		# IMIO pointer
+pointer	ap		# Aperture structure
+pointer	dbuf		# Data buffer
+int	nc, nl		# Size of data buffer
+int	c1, l1		# Origin of data buffer
+pointer	sbuf		# Sky values (NULL if none)
+pointer	svar		# Sky variances
+real	profile[ny,nx]	# Profile (returned)
+int	nx, ny		# Size of profile array
+int	xs[ny], ys	# Origin of profile array
+pointer	asi		# Image interpolator for edge pixel weighting
+
+real	gain		# Gain
+real	rdnoise		# Readout noise
+real	saturation	# Maximum value for an unsaturated pixel
+bool	clean		# Clean cosmic rays?
+real	lsigma, usigma	# Rejection sigmas.
+
+int	fd, ix, iy, ix1, ix2, xs1, xs2, nsum
+int	i, niterate, ixrej, iyrej, nrej, nreject
+real	p, s, chisq, tfac, rrej, predict, var0, var, vmin, resid, wt1, wt2, dat
+pointer	sp, str, spec, x1, x2, y, reject, xreject, data, sky, cv, gp
+
+int	apgeti()
+real	apgetr(), ap_cveval(), apgimr()
+bool	apgetb()
+errchk	salloc, ap_horne, ap_marsh, apgimr, ap_asifit
+
+begin
+	# Allocate memory. Adjust pointers to be one indexed.
+	call smark (sp)
+	call salloc (str, SZ_LINE, TY_CHAR)
+	call salloc (spec, ny, TY_REAL)
+	call salloc (x1, ny, TY_REAL)
+	call salloc (x2, ny, TY_REAL)
+	call salloc (y, ny, TY_REAL)
+	call salloc (reject, nx*ny, TY_BOOL)
+	if (sbuf == NULL) {
+	    call salloc (sky, nx, TY_REAL)
+	    sky = sky - 1
+	}
+	spec=spec-1; x1=x1-1; x2=x2-1; y=y-1
+
+	# Get task parameters.
+	gain = apgimr ("gain", im)
+	rdnoise = apgimr ("readnoise", im) ** 2
+	saturation = apgetr ("saturation")
+	if (!IS_INDEF(saturation))
+	    saturation = saturation * gain
+	lsigma = apgetr ("lsigma")
+	usigma = apgetr ("usigma")
+	clean = apgetb ("clean")
+	if (clean)
+	    niterate = apgeti ("niterate")
+	else
+	    niterate = 0
+
+	# Initialize.
+	if (rdnoise == 0.)
+	    vmin = 1.
+	else
+	    vmin = rdnoise
+	if (sbuf == NULL) {
+	    call aclrr (Memr[sky+1], nx)
+	    var0 = rdnoise
+	}
+	cv = AP_CV(ap)
+
+	# Set aperture limits and initialize rejection flags.
+	call alimi (xs, ny, xs1, xs2)
+	i = AP_AXIS(ap)
+	p = AP_CEN(ap,i) + AP_LOW(ap,i)
+	s = AP_CEN(ap,i) + AP_HIGH(ap,i)
+	xreject = reject
+	do iy = 1, ny {
+	    dat = ap_cveval (cv, real (iy + ys - 1)) - c1 + 1
+	    Memr[x1+iy] = p + dat
+	    Memr[x2+iy] = s + dat
+	    Memr[x1+iy] = max (0.5, Memr[x1+iy]) + c1 - xs[iy]
+	    Memr[x2+iy] = min (nc + 0.49, Memr[x2+iy]) + c1 - xs[iy]
+	    ix1 = nint (Memr[x1+iy])
+	    ix2 = nint (Memr[x2+iy])
+	    Memr[y+iy] = iy
+	    do ix = 1, nx {
+		if (ix < ix1 || ix > ix2)
+		    Memb[xreject] = false
+		else
+		    Memb[xreject] = true
+		xreject = xreject + 1
+	    }
+	}
+
+	# Estimate spectrum by summing across the aperture with partial
+	# pixel estimates at the aperture edges.  The initial profile
+	# estimates are obtained by normalizing by the spectrum estimate.
+	# Profiles where the spectrum is below sky are set to zero.
+
+	call aclrr (profile, nx * ny)
+	nrej = 0
+	do iy = 1, ny {
+	    if (Memr[x1+iy] >= Memr[x2+iy]) {
+		Memr[spec+iy] = 0.
+	        do ix = 1, nx
+		    profile[iy,ix] = 0.
+		next
+	    }
+
+	    call ap_asifit (dbuf+(iy+ys-1-l1)*nc, nc, xs[iy]-c1+1,
+		Memr[x1+iy]-c1+xs[iy], Memr[x2+iy]-c1+xs[iy], data, asi)
+	    if (sbuf != NULL)
+		sky = sbuf + (iy - 1) * nx - 1
+	    call ap_edge (asi, Memr[x1+iy]+1, Memr[x2+iy]+1, wt1, wt2)
+	    ix1 = nint (Memr[x1+iy])
+	    ix2 = nint (Memr[x2+iy])
+	    s = 0.
+	    do ix = ix1, ix2 {
+		if (!IS_INDEF(saturation))
+		    if (Memr[data+ix] > saturation) {
+			s = 0.
+			nrej = nrej + 1
+			break;
+		    }
+		dat = Memr[data+ix] - Memr[sky+ix]
+		if (ix1 == ix2)
+		    dat = wt1 * dat
+		else if (ix == ix1)
+		    dat = wt1 * dat
+		else if (ix == ix2)
+		    dat = wt2 * dat
+		s = s + dat
+	    }
+
+	    if (s > 0.) {
+	        do ix = ix1, ix2
+		    profile[iy,ix] = max (0., (Memr[data+ix]-Memr[sky+ix])/s)
+	    } else {
+	        do ix = ix1, ix2
+		    profile[iy,ix] = 0.
+	    }
+	    Memr[spec+iy] = s
+	}
+
+	if (nrej == ny)
+	    call error (1, "All profiles contain saturated pixels")
+	else if (nrej > 0) {
+	    call sprintf (Memc[str], SZ_LINE,
+		"EXTRACT: %d profiles with saturated pixels in aperture %d")
+		call pargi (nrej)
+		call pargi (AP_ID(ap))
+	    if (nrej < ny / 3)
+	        call ap_log (Memc[str], YES, NO, NO)
+	    else
+	        call ap_log (Memc[str], YES, NO, YES)
+	}
+
+	# Smooth the profile and possibly reject deviant pixels.
+	nreject = 0
+	tfac = 2.
+	do i = 0, niterate {
+
+	    # Estimate profile.
+	    if (xs1 == xs2)
+	        call ap_horne (im, cv, dbuf, nc, nl, c1, l1, Memr[spec+1], sbuf,
+		    svar, Memb[reject], profile, nx, ny, xs, ys,
+		    Memr[x1+1], Memr[x2+1])
+	    else
+	        call ap_marsh (im, dbuf, nc, nl, c1, l1, Memr[spec+1], sbuf,
+		    svar, Memb[reject], profile, nx, ny, xs, ys,
+		    Memr[x1+1], Memr[x2+1])
+
+	    if (i == niterate)
+		break
+
+	    # Reject pixels.  The rejection threshold is based on the overall
+	    # chi square.  Pixels are rejected on the basis of the current
+	    # chi square and the largest residual not rejected is compared
+	    # against the final chi square to possibly trigger another round
+	    # of rejections.
+
+	    chisq = 0.; nsum = 0; ixrej = 0; iyrej = 0; rrej = 0.; nrej = 0
+	    do iy = 1, ny {
+	        s = Memr[spec+iy]
+		if (s <= 0.)
+		    next
+		call ap_asifit (dbuf+(iy+ys-1-l1)*nc, nc, xs[iy]-c1+1,
+		    Memr[x1+iy]-c1+xs[iy], Memr[x2+iy]-c1+xs[iy], data, asi)
+		if (sbuf != NULL) {
+		    sky = sbuf + (iy - 1) * nx - 1
+		    var0 = rdnoise + Memr[svar+iy-1]
+		}
+		call ap_edge (asi, Memr[x1+iy]+1, Memr[x2+iy]+1, wt1, wt2)
+		xreject = reject + (iy - 1) * nx - 1
+	        ix1 = nint (Memr[x1+iy])
+	        ix2 = nint (Memr[x2+iy])
+	        do ix = ix1, ix2 {
+	            if (Memb[xreject+ix]) {
+	                nsum = nsum + 1
+	                predict = max (0., s * profile[iy,ix] + Memr[sky+ix])
+	                var = max (vmin, var0 + predict)
+	                resid = (Memr[data+ix] - predict) / sqrt (var)
+	                chisq = chisq + resid**2
+		        if (resid < -tfac*lsigma || resid > tfac*usigma) {
+		            if (ix < ix1 || ix > ix2)
+			        p = 0.
+			    else if (ix1 == ix2)
+		                p = wt1
+		            else if (ix == ix1)
+		                p = wt1
+		            else if (ix == ix2)
+		                p = wt2
+		            else 
+			        p = 1
+		            Memr[spec+iy] = Memr[spec+iy] -
+				p * (Memr[data+ix] - predict)
+	                    nrej = nrej + 1
+			    Memb[xreject+ix] = false
+		        } else if (abs (resid) > abs (rrej)) {
+		            rrej = resid
+		            if (ix < ix1 || ix > ix2)
+			        p = 0.
+			    else if (ix1 == ix2)
+		                p = wt1
+		            else if (ix == ix1)
+			        p = wt1
+		            else if (ix == ix2)
+			        p = wt2
+		            else 
+			        p = 1
+		            dat = p * (Memr[data+ix] - predict)
+		            ixrej = ix
+		            iyrej = iy
+			}
+	            }
+	        }
+	    }
+
+	    if (nsum == 0)
+		call error (1, "All pixels rejected")
+	    tfac = sqrt (chisq / nsum)
+	    if (rrej < -tfac * lsigma || rrej > tfac * usigma) {
+	        Memr[spec+iyrej] = Memr[spec+iyrej] - dat
+		xreject = reject + (iyrej - 1) * nx - 1
+	        Memb[xreject+ixrej] = false
+	        nrej = nrej + 1
+	    }
+
+	    nreject = nreject + nrej
+	    if (nrej == 0)
+		break
+	}
+
+	# These plots are too big for production work but can be turned on
+	# for debugging.
+
+	call ap_popen (gp, fd, "fits")
+	if (gp != NULL) {
+	    ix1 = xs1
+	    ix2 = xs2 + nx - 1
+	    if (xs1 != xs2) {
+		ix1 = ix1 + 1
+		ix2 = ix2 - 1
+	    }
+	    do ix = ix1, ix2 {
+		nrej = 0
+		do iy = 1, ny {
+		    i = ix - xs[iy] + 1
+		    if (i < 1 || i > nx)
+			next
+		    if (Memr[spec+iy] <= 0.)
+			next
+		    data = dbuf + (iy + ys - 1 - l1) * nc + ix - c1 - 1
+		    if (sbuf != NULL)
+		        s = Memr[sbuf+(iy-1)*nx+i-1]
+		    else
+			s = Memr[sky+i]
+		    nrej = nrej + 1
+		    Memr[y+nrej] = iy + ys - 1
+		    Memr[x1+nrej] = max (-.1, min (1.1,
+			(Memr[data+1] - s) / Memr[spec+iy]))
+		    Memr[x2+nrej] = profile[iy,i]
+		}
+		call gclear (gp)
+		call gascale (gp, Memr[x1+1], nrej, 2)
+		call grscale (gp, Memr[x2+1], nrej, 2)
+		call gswind (gp, Memr[y+1], Memr[y+nrej], INDEF, INDEF)
+		if (AP_AXIS(ap) == 1) {
+		    call sprintf (Memc[str], SZ_LINE, "Column %d")
+			call pargi (ix)
+		    call glabax (gp, Memc[str], "Line", "Profile")
+		} else {
+		    call sprintf (Memc[str], SZ_LINE, "Line %d")
+			call pargi (ix)
+		    call glabax (gp, Memc[str], "Column", "Profile")
+		}
+		call gpmark (gp, Memr[y+1], Memr[x1+1], nrej, GM_POINT, 1., 1.)
+		call gpline (gp, Memr[y+1], Memr[x2+1], nrej)
+	    }
+	}
+	call ap_pclose (gp, fd)
+
+	# Log the number of rejected pixels.
+	if (clean) {
+	    call sprintf (Memc[str], SZ_LINE,
+		"EXTRACT: %d pixels rejected for profile from aperture %d")
+		call pargi (nreject)
+		call pargi (AP_ID(ap))
+	    call ap_log (Memc[str], YES, NO, NO)
+	}
+
+	call sfree (sp)
+end
+
+
+# AP_HORNE -- Determine profile by fitting a low order function parallel to
+# dispersion along image lines or columns after dividing by a spectrum
+# estimate.  An initial profile estimate and a rejection array are
+# required for setting the weights.  This is a straightforward algorithm
+# similar to images.fit1d except that it is noninteractive.  The fitting
+# function is fixed at a cubic spline and the number of pieces is set by
+# the amount of tilt such that there is one cubic spline piece per
+# passage across the tilted spectrum plus an amount based on the order
+# of the tracing function.  It is named after Keith Horne
+# since this is what is outlined in his paper.  The profile array is used
+# cleverly to minimize memory requirements.  The storage order of the
+# profile array, which is transposed relative to the data, is determined
+# by this procedure.
+
+procedure ap_horne (im, cvtrace, dbuf, nc, nl, c1, l1, spec, sbuf, svar, reject,
+	profile, nx, ny, xs, ys, x1, x2)
+
+pointer	im			# IMIO pointer
+pointer	cvtrace			# Trace pointer
+pointer	dbuf			# Data buffer
+int	nc, nl			# Size of data buffer
+int	c1, l1			# Origin of data buffer
+real	spec[ny]		# Spectrum estimate
+pointer	sbuf			# Sky values (NULL if none)
+pointer	svar			# Sky variances
+bool	reject[nx,ny]		# Rejection flags
+real	profile[ny,nx]		# Initial profile in, improved profile out
+int	nx, ny			# Size of profile array
+int	xs[ny], ys		# Origin of profile array
+real	x1[ny], x2[ny]		# Aperture limits in profile array
+
+int	cvtype			# Curfit type
+int	order			# Order of curfit function.
+real	rdnoise			# Readout noise in RMS data numbers.
+
+int	ix, iy, ierr
+real	p, s, sk, var, vmin, var0, wmin
+pointer	sp, y, w, cv, dbuf1, data, sky
+
+#int	apgeti()
+int	cvstati()
+real	apgimr()
+errchk	salloc, apgimr
+
+begin
+	call smark (sp)
+	call salloc (y, ny, TY_REAL)
+	call salloc (w, ny, TY_REAL)
+
+	# Get CL parameters
+	#cvtype = apgeti ("e_function")
+	#order = apgeti ("e_order")
+	rdnoise = apgimr ("readnoise", im) ** 2
+
+	# Initialize.
+	call alimr (x1, ny, p, s)
+	cvtype = SPLINE3
+	order = int (s - p + 1) + max (0, cvstati (cvtrace, CVNCOEFF) - 2)
+	#order = min (20, order)
+	order = 2 * order
+	call cvinit (cv, cvtype, order, 1., real (ny))
+	do iy = 1, ny
+	    Memr[y+iy-1] = iy
+	if (rdnoise == 0.)
+	    vmin = 1.
+	else
+	    vmin = rdnoise
+	dbuf1 = dbuf + (ys - l1 - 1) * nc - c1 - 1
+	if (sbuf == NULL) {
+	    sk = 0.
+	    var0 = rdnoise
+	}
+
+	# For each line parallel to the dispersion divide by a spectrum
+	# estimate and then fit the smoothing function.  Use the input
+	# profile and rejection array to set the weights.
+
+	do ix = 1, nx { 
+	    data = dbuf1 + ix
+	    if (sbuf != NULL)
+		sky = sbuf - nx - 1 + ix
+	    wmin = MAX_REAL
+	    do iy = 1, ny {
+	        s = spec[iy]
+	        if (s > 0. && reject[ix,iy]) {
+		    if (sbuf != NULL) {
+			sk = Memr[sky+iy*nx]
+			var0 = rdnoise + Memr[svar+iy-1]
+		    }
+		    p = profile[iy,ix]
+		    var = max (vmin, var0 + max (0., s * p + sk))
+		    var = (s ** 2) / var
+		    wmin = min (wmin, var)
+		    Memr[w+iy-1] = var
+		    profile[iy,ix] = (Memr[data+iy*nc+xs[iy]] - sk) / s
+		} else
+		    Memr[w+iy-1] = 0.
+	    }
+	    if (wmin == MAX_REAL)
+		call amovkr (1., Memr[w], ny)
+	    else
+		call amaxkr (Memr[w], wmin / 10., Memr[w], ny)
+	    call cvfit (cv, Memr[y], profile[1,ix], Memr[w], ny, WTS_USER, ierr)
+	    call cvvector (cv, Memr[y], profile[1,ix], ny)
+	    call amaxkr (profile[1,ix], 0., profile[1,ix], ny)
+	}
+
+	call cvfree (cv)
+	call sfree (sp)
+end
+
+
+# AP_MARSH -- Determine profile by Marsh algorithm (PASP V101, P1032, 1989).
+# This algorithm fits low order polynomials to weighted points sampled
+# at uniform intervals parallel to the aperture trace.  The polynomials
+# are coupled through the weights and so requires a 2D matrix inversion.
+# This is a relatively slow algorithm but does provide low order smoothing
+# for arbitrary profile shapes in highly tilted spectra.  An estimate
+# of the profile, a rejection array, sky and sky variance, and aperture
+# limit arrays are required.
+
+procedure ap_marsh (im, dbuf, nc, nl, c1, l1, spec, sbuf, svar, reject,
+	profile, nx, ny, xs, ys, x1, x2)
+
+pointer	im			# IMIO pointer
+pointer	dbuf			# Data buffer
+int	nc, nl			# Size of data buffer
+int	c1, l1			# Origin of data buffer
+real	spec[ny]		# Spectrum estimate
+pointer	sbuf			# Sky values (NULL if none)
+pointer	svar			# Sky variances
+bool	reject[nx,ny]		# Rejection flags
+real	profile[ny,nx]		# Initial profile in, improved profile out
+int	nx, ny			# Size of profile array
+int	xs[ny], ys		# Origin of profile array
+real	x1[ny], x2[ny]		# Aperture limits in profile array
+
+real	spix			# Polynomial pixel separation
+int	npols			# Number of polynomials
+int	order			# Order of function.
+real	rdnoise			# Readout noise in RMS data numbers.
+
+int	il, jl, kl, ll, ix, iy, ix1, ix2, nside, nadd
+int	ip, ip1, ip2, index1, index2, index3
+real	p, s, s2, dat, sk, var, vmin, var0
+real	dx0, dx1, dx2, dx3, dx4, xj, xk, xt, xz, qj, qk, xadd
+double	sum1, sum2
+pointer	sp, work, work1, work2, work3, work4, ysum, data, sky
+
+int	apgeti()
+real	apgetr(), apgimr()
+errchk	salloc, apgimr
+
+begin
+	# Get CL parameters
+	#npols = apgeti ("npols")
+	spix = apgetr ("polysep")
+	order = apgeti ("polyorder")
+	rdnoise = apgimr ("readnoise", im) ** 2
+
+	# Set dimensions.
+	npols = (x2[1] - x1[1] + 2) / spix
+	spix = (x2[1] - x1[1] + 2) / real (npols)
+	nside = npols * order
+	nadd = nside * nside
+	if (spix > 1.)
+	    call error (4, "Polynomial separation too large")
+
+	# Allocate memory.  One index pointers.
+	call smark (sp)
+	call salloc (work, nadd+3*nside, TY_REAL)
+	call salloc (work4, nside, TY_INT)
+	call salloc (ysum, ny, TY_REAL)
+	work = work - 1
+	work1 = work + nadd
+	work2 = work1 + nside
+	work3 = work2 + nside
+	work4 = work4 - 1
+	ysum=ysum-1
+	if (sbuf == NULL) {
+	    call salloc (sky, nx, TY_REAL)
+	    sky = sky - 1
+	}
+
+	# Initialize.
+	call aclrr (Memr[work+1], nadd+3*nside)
+	call aclri (Memi[work4+1], nside)
+	if (rdnoise == 0.)
+	    vmin = 1.
+	else
+	    vmin = rdnoise
+	if (sbuf == NULL) {
+	    call aclrr (Memr[sky+1], nx)
+	    var0 = rdnoise
+	}
+
+	# Factors for weights.
+	dx0 = 0.5 - spix
+	dx1 = abs (dx0)
+	dx2 = 1. - (dx0 / spix) ** 2
+	dx3 = 0.5 + spix
+	dx4 = sqrt (2.) * spix
+
+	# Accumulate least terms for least squares matrix equation AX = B.
+
+	# First accumulate B.
+	do jl = 0, npols-1 {
+ 	    do iy = 1, ny {
+	        if (spec[iy] <= 0.)
+		    next
+
+		xj = x1[iy] - 1 + spix * (real (jl) + 0.5)
+		ix1 = nint (xj - spix)
+		ix2 = nint (xj + spix)
+		if (ix1 < 1 || ix2 > nx) {
+		    Memr[ysum+iy] = 0.
+		    next
+		}
+
+		data = dbuf + (iy + ys - 1 - l1) * nc + xs[iy] - c1 - 1
+		if (sbuf != NULL) {
+		    sky = sbuf + (iy - 1) * nx - 1
+		    var0 = rdnoise + Memr[svar+iy-1]
+		}
+
+		# Evaluate qj, the contribution of polynomial number jl+1
+		# for the pixel ix1,jj.  Four cases are considered.  The
+		# first two account for the triangular interpolation
+		# function partially overlapping a pixel, on one side
+		# only.  The third is for the function wholly inside a
+		# pixel, and finally for the pixel wholly covered by the
+		# interpolation function.
+
+	        s = spec[iy]
+	        sum1 = 0.
+	        do ix = ix1, ix2 {
+		    if (!reject[ix,iy])
+			next
+	            p = profile[iy,ix]
+		    sk = Memr[sky+ix]
+                    dat = Memr[data+ix] - sk
+		    var = max (vmin, var0 + max (0., s * p + sk))
+
+                    xz = xj - real (ix)
+                    xt = abs (xz)
+                    if (xt >= dx1) {
+                        if (xt >= 0.5)
+                            qj = ((xt - dx3) / dx4) ** 2
+                        else
+                            qj = 1.- ((xt - dx0) / dx4) ** 2
+                        
+                    } else if (xt <= dx0)
+                        qj = 1.
+                    else
+                        qj = dx2 - (xz / spix) ** 2
+                    sum1 = sum1 + qj * s * dat / var
+                }
+	        Memr[ysum+iy] = sum1
+	    }
+
+	    index1 = order * jl
+	    do il = 1, order {
+	        sum1 = 0.
+	        ip = il - 1
+	        do iy = 1, ny
+	            if (spec[iy] > 0.)
+			sum1 = sum1 + Memr[ysum+iy] * ((real (iy) / ny) ** ip)
+	        Memr[work1+index1+il] = sum1
+	    }
+	}
+
+	# Now accumulate matrix A.  Since it is symmetric we only need to
+	# evaluate half of it.  Since it is banded we only need to evaluate
+	# contribution if two polynomial terms can be affected by the same
+	# pixel.
+
+	ip1 = nside - 1
+	ip2 = order * ip1
+	do jl = 0, npols-1 {
+	    do kl = 0, jl {
+		if (spix * (jl - kl - 2) > 0.)
+		    next
+		do iy = 1, ny {
+		    if (spec[iy] <= 0.)
+			next
+		    if (sbuf != NULL) {
+			sky = sbuf + (iy - 1) * nx - 1
+			var0 = rdnoise + Memr[svar+iy-1]
+		    }
+
+		    # Compute left and right limits of polynomials jl+1
+		    # and kl+1 for this value of y Evaluate sum over row
+		    # of qj[jl+1] times qj[kl+1] where qj[i] is fraction
+		    # of polynomial i which contributes to to pixel ix,jj.
+
+		    xj = x1[iy] - 1 + spix * (real (jl) + 0.5)
+		    xk = x1[iy] - 1 + spix * (real (kl) + 0.5)
+		    ix1 = nint (xj - spix)
+		    ix2 = nint (xk + spix)
+
+                    if (ix2 < ix1 || ix1 < 1 || ix2 > nx) {
+			Memr[ysum+iy] = 0.
+			next
+		    }
+
+                    s  = spec[iy]
+                    s2 = s * s
+                    sum1 = 0.
+                    do ix = ix1, ix2 {
+                        if (reject[ix,iy]) {
+                            p = profile[iy,ix]
+			    sk = Memr[sky+ix]
+			    var = max (vmin, var0 + max (0., s * p + sk))
+
+                            xz = xj - real (ix)
+                            xt = abs (xz)
+                            if (xt >= dx1) {
+                                if (xt >= 0.5)
+                                    qj = ((xt-dx3)/dx4)**2
+                                else
+                                    qj = 1.- ((xt-dx0)/dx4)**2
+                            } else if (xt <= dx0)
+                                qj = 1.
+                            else
+                                qj = dx2 - (xz / spix) ** 2
+                            if (kl != jl) {
+                                xz = xk - real (ix)
+                                xt = abs (xz)
+                                if (xt >= dx1) {
+                                    if (xt >= 0.5)
+                                        qk = ((xt-dx3)/dx4)**2
+                                    else
+                                        qk = 1.-((xt-dx0)/dx4)**2
+                                } else if (xt <= dx0)
+                                    qk = 1.
+                                else
+                                    qk = dx2 - (xz / spix) ** 2
+                            } else
+                                qk = qj
+                            sum1 = sum1 + qj * qk * s2 / var
+                        }
+                    }
+                    Memr[ysum+iy] = sum1
+		}
+
+	        do il = 1, order {
+	            do ll = 1, il {
+	                sum1 = 0.
+	                ip = il + ll - 2
+	                do iy = 1, ny
+	                    if (spec[iy] > 0.)
+	                        sum1 = sum1 +
+				    Memr[ysum+iy] * ((real (iy) / ny)**ip)
+	                index1 = nside * (order*jl+il-1) + order * kl + ll
+	                Memr[work+index1] = sum1
+	                if (ll != il) {
+	                    ip = ip1 * (ll - il)
+	                    index2 = index1 + ip
+	                    Memr[work+index2] = sum1
+	                } else
+	                    index2 = index1 
+	                if (kl != jl) {
+	                    index3 = index2 + ip2 * (kl - jl)
+	                    Memr[work+index3] = sum1
+	                    if (ll != il)
+	                        Memr[work+index3-ip] = sum1
+	                }
+	            }
+	        }
+	    }
+	}
+
+	# Solve matrix equation AX = B for X.  A is a real symmetric,
+	# positive definite matrix, dimension (order*npols)**2.  X is 
+	# the vector representing the coefficients fitted to the 
+	# normalized profile.  Coefficients are reordered for later speed.
+
+	call hfti (Memr[work+1], nside, nside, nside, Memr[work1+1], 1, 1,
+	    0.01, ip, p, Memr[work2+1], Memr[work3+1], Memi[work4+1])
+
+	do jl = 1, order {
+	    do il = 1, npols {
+	        index1 = order * (il - 1) + jl
+	        index2 = npols * (jl - 1) + il
+	        Memr[work+index2] = Memr[work1+index1]
+	    }
+	}
+
+	# Evaluate fit and make profile positive only.
+	do iy = 1, ny {
+	    ix1 = nint (x1[iy])
+	    ix2 = nint (x2[iy])
+	    xadd = x1[iy] - 1
+	    s = 0.
+	    do ix = 1, nx {
+	        xj = real (ix) - xadd - 0.5
+	        xk = real (ix) - xadd + 0.5
+	        ip1 = int (xj / spix + 0.5)
+	        ip2 = int (xk / spix + 1.5)
+	        ip1 = max (1, min (ip1, npols))
+	        ip2 = max (1, min (ip2, npols))
+	        sum1 = 0.
+	        do jl = 0, order-1 {
+	            index1 = npols * jl
+	            sum2 = 0.
+	            do il = ip1, ip2 {
+	                xz = xadd + spix * (real (il-1) + 0.5) - real (ix)
+	                xt = abs (xz)
+	                if (xt >= dx1) {
+	                    if (xt >= 0.5)
+	                        qj = ((xt - dx3) / dx4) ** 2
+	                    else
+	                        qj = 1. - ((xt - dx0) / dx4) ** 2
+	                } else if (xt <= dx0)
+	                    qj = 1.
+	                else
+	                    qj = dx2 - (xz / spix) ** 2
+	                sum2 = sum2 + qj * Memr[work+index1+il]
+	            }
+	            sum1 = sum1 + sum2 * ((real (iy)/ ny) ** jl)
+	        }
+	        profile[iy,ix] = max (0.d0, sum1)
+	    }
+	}
+
+	call sfree (sp)
+end
diff --git a/noao/twodspec/apextract/aprecenter.par b/noao/twodspec/apextract/aprecenter.par
new file mode 100644
index 00000000..a76b4c76
--- /dev/null
+++ b/noao/twodspec/apextract/aprecenter.par
@@ -0,0 +1,17 @@
+# APRECENTER
+
+input,s,a,,,,List of input images
+apertures,s,h,"",,,Apertures
+references,s,h,"",,,"Reference images
+"
+interactive,b,h,no,,,Run task interactively?
+find,b,h,yes,,,Find apertures?
+recenter,b,h,yes,,,Recenter apertures?
+resize,b,h,no,,,Resize apertures?
+edit,b,h,yes,,,"Edit apertures?
+"
+line,i,h,INDEF,1,,Dispersion line
+nsum,i,h,1,,,Number of dispersion lines to sum or median
+aprecenter,s,h,"",,,Apertures for recentering calculation
+npeaks,r,h,INDEF,0.,,Select brightest peaks
+shift,b,h,yes,,,Use average shift instead of recentering?
diff --git a/noao/twodspec/apextract/aprecenter.x b/noao/twodspec/apextract/aprecenter.x
new file mode 100644
index 00000000..fb3b9a86
--- /dev/null
+++ b/noao/twodspec/apextract/aprecenter.x
@@ -0,0 +1,166 @@
+include	"apertures.h"
+
+define	NRANGES	50
+
+# AP_RECENTER -- Recenter apertures.
+
+procedure ap_recenter (image, line, nsum, aps, naps, apedit)
+
+char	image[SZ_FNAME]		# Image name
+int	line			# Image dispersion line
+int	nsum			# Number of dispersion lines to sum
+pointer	aps[ARB]		# Aperture pointers
+int	naps			# Number of apertures
+int	apedit			# Called by apedit?
+
+pointer	ranges			# Apertures to select
+int	npeaks			# Number of bright peaks to select 
+bool	shift			# Shift instead of center?
+
+real	center, delta
+int	i, j, k, na, npts, apaxis
+pointer	sp, str, im, imdata, title, index, peaks, deltas
+
+int	decode_ranges()
+real	apgetr(), ap_center(), ap_cveval(), asokr()
+bool	clgetb(), ap_answer(), apgetb(), is_in_range()
+errchk	ap_getdata
+
+begin
+	# Check if apertures are defined.
+	na = 0
+	do i = 1, naps
+	    if (AP_SELECT(aps[i]) == YES)
+		na = na + 1
+	if (na < 1)
+	    return
+
+	# Query user.
+	call smark (sp)
+	call salloc (str, SZ_LINE, TY_CHAR)
+	if (apedit == NO) {
+	    call sprintf (Memc[str], SZ_LINE, "Recenter apertures for %s?")
+	        call pargstr (image)
+	    if (!ap_answer ("ansrecenter", Memc[str])) {
+	        call sfree (sp)
+	        return
+	    }
+
+	    if (clgetb ("verbose"))
+	        call printf ("Recentering apertures ...\n")
+	}
+
+	# Get parameters
+	delta = apgetr ("npeaks")
+	shift = apgetb ("shift")
+	if (IS_INDEFR (delta))
+	    npeaks = naps
+	else if (delta < 1.)
+	    npeaks = max (1., delta * naps)
+	else
+	    npeaks = delta
+
+	# Map the image and get the image data.
+	call ap_getdata (image, line, nsum, im, imdata, npts, apaxis, title)
+
+	if (npeaks == naps && !shift) {
+	    na = 0
+	    do i = 1, naps {
+		if (AP_SELECT(aps[i]) == NO)
+		    next
+	        center = AP_CEN(aps[i], apaxis) +
+		    ap_cveval (AP_CV(aps[i]), real (line))
+	        center = ap_center (center, Memr[imdata], npts)
+	        if (!IS_INDEF(center)) {
+		    AP_CEN(aps[i], apaxis) = center -
+		        ap_cveval (AP_CV(aps[i]), real (line))
+		    na = na + 1
+		}
+	    }
+	} else {
+	    call salloc (ranges, 3*NRANGES, TY_INT)
+	    call salloc (index, naps, TY_REAL)
+	    call salloc (peaks, naps, TY_REAL)
+	    call salloc (deltas, naps, TY_REAL)
+
+	    call apgstr ("aprecenter", Memc[str], SZ_LINE)
+	    if (decode_ranges (Memc[str], Memi[ranges], NRANGES, i) == ERR)
+		call error (0, "Bad aperture list")
+
+	    j = 0
+	    do i = 1, naps {
+	        if (!is_in_range (Memi[ranges], AP_ID(aps[i])))
+		    next
+	        center = AP_CEN(aps[i], apaxis) +
+		    ap_cveval (AP_CV(aps[i]), real (line))
+	        delta = ap_center (center, Memr[imdata], npts)
+	        if (!IS_INDEF(delta)) {
+		    k = max (1, min (npts, int (delta+0.5)))
+		    Memr[index+j] = i
+		    Memr[peaks+j] = -Memr[imdata+k-1]
+		    Memr[deltas+j] = delta - center
+		    j = j + 1
+	        }
+	    }
+
+	    if (j > 0 && npeaks > 0) {
+	        if (npeaks < j) {
+	            call xt_sort3 (Memr[peaks], Memr[deltas], Memr[index], j)
+		    j = npeaks
+	        }
+
+	        if (shift) {
+		    if (mod (j, 2) == 0)
+			delta = (asokr (Memr[deltas], j, j/2) +
+				asokr (Memr[deltas], j, 1+j/2)) / 2
+		    else
+			delta = asokr (Memr[deltas], j, 1+j/2)
+		    na = 0
+		    do i = 1, naps {
+			if (AP_SELECT(aps[i]) == NO)
+			    next
+		        center = AP_CEN(aps[i], apaxis) + delta
+		        AP_CEN(aps[i], apaxis) = center
+			na = na + 1
+		    }
+	        } else {
+		    na = 0
+		    do k = 1, j {
+		        delta = Memr[deltas+k-1]
+		        i = Memr[index+k-1]
+			if (AP_SELECT(aps[i]) == NO)
+			    next
+			center = AP_CEN(aps[i], apaxis) + delta
+			AP_CEN(aps[i], apaxis) = center
+			na = na + 1
+		    }
+		}
+	    }
+	}
+		    
+	# Log the operation, write the apertures to the database,
+	# unmap the image and free memory.
+	if (shift) {
+	    call sprintf (Memc[str], SZ_LINE,
+	        "RECENTER  - %d apertures shifted by %.2f for %s.")
+	        call pargi (na)
+		call pargr (delta)
+	        call pargstr (image)
+	} else {
+	    call sprintf (Memc[str], SZ_LINE,
+	        "RECENTER - %d apertures recentered for %s")
+	        call pargi (na)
+	        call pargstr (image)
+	}
+	if (apedit == NO)
+	    call ap_log (Memc[str], YES, YES, NO)
+	else
+	    call ap_log (Memc[str], YES, NO, NO)
+
+	call appstr ("ansdbwrite1", "yes")
+
+	call mfree (imdata, TY_REAL)
+	call mfree (title, TY_CHAR)
+	call imunmap (im)
+	call sfree (sp)
+end
diff --git a/noao/twodspec/apextract/apresize.par b/noao/twodspec/apextract/apresize.par
new file mode 100644
index 00000000..4cbcf4b7
--- /dev/null
+++ b/noao/twodspec/apextract/apresize.par
@@ -0,0 +1,21 @@
+# APRESIZE
+
+input,s,a,,,,List of input images
+apertures,s,h,"",,,Apertures
+references,s,h,"",,,"Reference images
+"
+interactive,b,h,no,,,Run task interactively?
+find,b,h,yes,,,Find apertures?
+recenter,b,h,no,,,Recenter apertures?
+resize,b,h,yes,,,Resize apertures?
+edit,b,h,yes,,,"Edit apertures?
+"
+line,i,h,INDEF,1,,Dispersion line
+nsum,i,h,1,,,Number of dispersion lines to sum or median
+llimit,r,h,INDEF,,,Lower aperture limit relative to center
+ulimit,r,h,INDEF,,,Upper aperture limit relative to center
+ylevel,r,h,0.1,,,Fraction of peak or intensity for automatic width
+peak,b,h,yes,,,Is ylevel a fraction of the peak?
+bkg,b,h,yes,,,Subtract background in automatic width?
+r_grow,r,h,0.,,,"Grow limits by this factor"
+avglimits,b,h,no,,,Average limits over all apertures?
diff --git a/noao/twodspec/apextract/apresize.x b/noao/twodspec/apextract/apresize.x
new file mode 100644
index 00000000..8443223a
--- /dev/null
+++ b/noao/twodspec/apextract/apresize.x
@@ -0,0 +1,142 @@
+include	"apertures.h"
+
+# AP_RESIZE -- Resize apertures.
+
+procedure ap_resize (image, line, nsum, aps, naps, apedit)
+
+char	image[SZ_FNAME]		# Image name
+int	line			# Image dispersion line
+int	nsum			# Number of dispersion lines to sum
+int	apedit			# Called from apedit?
+
+pointer	aps[ARB]		# Aperture pointers
+int	naps			# Number of apertures
+
+real	llimit, ulimit		# Maximum aperture limits
+real	ylevel			# Fraction of intensity for resize
+bool	peak			# Is ylevel a fraction of the peak?
+bool	bkg			# Subtract background?
+real	grow			# Expand limits by this factor
+bool	avglimits		# Average limits?
+
+real	center, low, high
+int	i, na, npts, apaxis
+pointer	sp, str, im, imdata, title
+
+bool	clgetb(), ap_answer(), apgetb()
+real	apgetr(), ap_cveval()
+errchk	ap_getdata
+
+begin
+	# Check if apertures are defined.
+	na = 0
+	do i = 1, naps
+	    if (AP_SELECT(aps[i]) == YES)
+		na = na + 1
+	if (na == 0)
+	    return
+
+	call smark (sp)
+	call salloc (str, SZ_LINE, TY_CHAR)
+	if (apedit == NO) {
+	    call sprintf (Memc[str], SZ_LINE, "Resize apertures for %s?")
+	        call pargstr (image)
+	    if (!ap_answer ("ansresize", Memc[str])) {
+	        call sfree (sp)
+	        return
+	    }
+
+	    if (clgetb ("verbose"))
+	        call printf ("Resizing apertures ...\n")
+	}
+
+	# Map the image and get the image data.
+	call ap_getdata (image, line, nsum, im, imdata, npts, apaxis, title)
+
+	# Resize the apertures.
+	llimit = apgetr ("llimit")
+	ulimit = apgetr ("ulimit")
+	ylevel = apgetr ("ylevel")
+	bkg = apgetb ("bkg")
+	peak = apgetb ("peak")
+	grow = apgetr ("r_grow")
+	avglimits = apgetb ("avglimits")
+
+	if (IS_INDEF(llimit))
+	    llimit = -npts
+	if (IS_INDEF(ulimit))
+	    ulimit = npts
+	
+	high = max (llimit, ulimit)
+	llimit = min (llimit, ulimit)
+	ulimit = high
+
+	if (IS_INDEF (ylevel)) {
+	    do i = 1, naps {
+		if (AP_SELECT(aps[i]) == YES) {
+		    AP_LOW(aps[i], apaxis) = llimit
+		    AP_HIGH(aps[i], apaxis) = ulimit
+		}
+	    }
+	    avglimits = true
+	} else {
+	    do i = 1, naps {
+		if (AP_SELECT(aps[i]) == YES) {
+		    low = llimit
+		    high = ulimit
+		    center = AP_CEN(aps[i], apaxis) +
+			ap_cveval (AP_CV(aps[i]), real (line))
+		    call ap_ylevel (Memr[imdata], npts, ylevel, peak, bkg, grow,
+			center, low, high)
+		    AP_LOW(aps[i], apaxis) = min (low, high)
+		    AP_HIGH(aps[i], apaxis) = max (low, high)
+		}
+	    }
+
+	    if (avglimits) {
+		low = 0.
+		high = 0.
+		do i = 1, naps {
+		    if (AP_SELECT(aps[i]) == YES) {
+			low = low + AP_LOW(aps[i], apaxis)
+			high = high + AP_HIGH(aps[i], apaxis)
+		    }
+		}
+		low = low / na
+		high = high / na
+		do i = 1, naps {
+		    if (AP_SELECT(aps[i]) == YES) {
+			AP_LOW(aps[i], apaxis) = low
+			AP_HIGH(aps[i], apaxis) = high
+		    }
+		}
+	    }
+	}
+
+	# Log the operation, write the apertures to the database,
+	# unmap the image and free memory.
+	if (na == 1 || avglimits) {
+	    call sprintf (Memc[str], SZ_LINE,
+        	"APRESIZE  - %d apertures resized for %s (%.2f, %.2f)")
+	        call pargi (na)
+	        call pargstr (image)
+		call pargr (AP_LOW(aps[1], apaxis))
+		call pargr (AP_HIGH(aps[1], apaxis))
+	} else {
+	    call sprintf (Memc[str], SZ_LINE,
+	        "RESIZE - %d apertures resized for %s")
+	        call pargi (na)
+	        call pargstr (image)
+	}
+	if (apedit == NO)
+	    call ap_log (Memc[str], YES, YES, NO)
+	else
+	    call ap_log (Memc[str], YES, NO, NO)
+
+	call appstr ("ansdbwrite1", "yes")
+
+	call mfree (imdata, TY_REAL)
+	call mfree (title, TY_CHAR)
+	call imunmap (im)
+	call sfree (sp)
+end
diff --git a/noao/twodspec/apextract/apscat1.par b/noao/twodspec/apextract/apscat1.par
new file mode 100644
index 00000000..8cb5cf7b
--- /dev/null
+++ b/noao/twodspec/apextract/apscat1.par
@@ -0,0 +1,11 @@
+# APSCAT1
+
+apertures,s,h,)apscatter.apertures,,,>apall.apertures
+function,s,h,"spline3","spline3|legendre|chebyshev|spline1",,Fitting function
+order,i,h,1,1,,Order of fitting function
+sample,s,h,"*",,,Sample points to use in fit
+naverage,i,h,1,,,Number of points in sample averaging
+low_reject,r,h,5.,0.,,Low rejection in sigma of fit
+high_reject,r,h,2.,0.,,High rejection in sigma of fit
+niterate,i,h,5,0,,Number of rejection iterations
+grow,r,h,0.,0.,,Rejection growing radius in pixels
diff --git a/noao/twodspec/apextract/apscat2.par b/noao/twodspec/apextract/apscat2.par
new file mode 100644
index 00000000..2463f110
--- /dev/null
+++ b/noao/twodspec/apextract/apscat2.par
@@ -0,0 +1,10 @@
+# APSCAT2
+
+function,s,h,"spline3","spline3|legendre|chebyshev|spline1",,Fitting function
+order,i,h,1,1,,Order of fitting function
+sample,s,h,"*",,,Sample points to use in fit
+naverage,i,h,1,,,Number of points in sample averaging
+low_reject,r,h,3.,0.,,Low rejection in sigma of fit
+high_reject,r,h,3.,0.,,High rejection in sigma of fit
+niterate,i,h,0,0,,Number of rejection iterations
+grow,r,h,0.,0.,,Rejection growing radius in pixels
diff --git a/noao/twodspec/apextract/apscatter.par b/noao/twodspec/apextract/apscatter.par
new file mode 100644
index 00000000..b7f45991
--- /dev/null
+++ b/noao/twodspec/apextract/apscatter.par
@@ -0,0 +1,25 @@
+# APSCATTER
+
+input,s,a,,,,List of input images to subtract scattered light
+output,s,a,,,,List of output corrected images
+apertures,s,h,"",,,Apertures
+scatter,s,h,"",,,List of scattered light images (optional)
+references,s,h,"",,,"List of aperture reference images
+"
+interactive,b,h,yes,,,Run task interactively?
+find,b,h,yes,,,Find apertures?
+recenter,b,h,yes,,,Recenter apertures?
+resize,b,h,yes,,,Resize apertures?
+edit,b,h,yes,,,Edit apertures?
+trace,b,h,yes,,,Trace apertures?
+fittrace,b,h,yes,,,Fit the traced points interactively?
+subtract,b,h,yes,,,Subtract scattered light?
+smooth,b,h,yes,,,Smooth scattered light along the dispersion?
+fitscatter,b,h,yes,,,Fit scattered light interactively?
+fitsmooth,b,h,yes,,,"Smooth the scattered light interactively?
+"
+line,i,h,INDEF,1,,Dispersion line
+nsum,i,h,10,,,Number of dispersion lines to sum or median
+buffer,r,h,1.,0.,,Buffer distance from apertures
+apscat1,pset,h,"",,,Fitting parameters across the dispersion
+apscat2,pset,h,"",,,Fitting parameters along the dispersion
diff --git a/noao/twodspec/apextract/apscatter.x b/noao/twodspec/apextract/apscatter.x
new file mode 100644
index 00000000..44f56a72
--- /dev/null
+++ b/noao/twodspec/apextract/apscatter.x
@@ -0,0 +1,662 @@
+include	<error.h>
+include	<imhdr.h>
+include	<imset.h>
+include	<pkg/gtools.h>
+include	"apertures.h"
+ 
+define	MAXBUF	500000		# Buffer size (number of reals) for col access
+ 
+ 
+# AP_SCATTER -- Fit and subtract the scattered light from between the apertures.
+#
+# Each line of the input image across the dispersion is read.  The points to
+# be fit are selected from between the apertures (which includes a buffer
+# distance).  The fitting is done using the ICFIT package.  If not smoothing
+# along the dispersion write the scattered light subtracted output directly
+# thus minimizing I/O.  If smoothing save the fits in memory.  During the
+# smoothing process the fits are evaluated at each point along the dispersion
+# and then fit to the create the scattered light subtracted output image.  A
+# scattered light image is only created after the output image by subtracting
+# the input from the output.
+
+procedure ap_scatter (input, output, scatter, aps, naps, line)
+ 
+char	input[SZ_FNAME]		# Input image
+char	output[SZ_FNAME]	# Output image
+char	scatter[SZ_FNAME]	# Scattered light image
+pointer	aps[ARB]		# Apertures
+int	naps			# Number of apertures
+int	line			# Line to be edited
+ 
+bool	smooth
+int	i, aaxis, daxis, npts, nlines, nscatter, nscatter1, new
+pointer	sp, str, in, out, scat, cv, cvs, gp, indata, outdata, col, x, y, w 
+pointer	ic1, ic2, ic3, gt1, gt2
+data	ic3/NULL/
+
+real	clgetr()
+int	clgeti(), ap_gline(), ap_gdata()
+bool	clgetb(), ap_answer(), apgansb()
+pointer	gt_init(), immap(), ap_immap(), imgl2r(), impl2r()
+
+common	/aps_com/ ic1, ic2, gt1, gt2
+ 
+begin
+	if (naps < 1)
+	    return
+ 
+	# Query the user.
+	call smark (sp)
+	call salloc (str, SZ_LINE, TY_CHAR)
+	call sprintf (Memc[str], SZ_LINE, "Subtract scattered light in %s?")
+	        call pargstr (input)
+	if (!ap_answer ("ansscat", Memc[str])) {
+	    call sfree (sp)
+	    return
+	}
+
+	call sprintf (Memc[str], SZ_LINE,
+	    "Fit scattered light for %s interactively?")
+	    call pargstr (input)
+	if (ap_answer ("ansfitscatter", Memc[str]))
+	    ;
+
+	call sprintf (Memc[str], SZ_LINE, "Smooth the scattered light in %s?")
+	    call pargstr (input)
+	if (ap_answer ("anssmooth", Memc[str])) {
+	    call sprintf (Memc[str], SZ_LINE,
+	        "Smooth the scattered light for %s interactively?")
+	        call pargstr (input)
+	    if (ap_answer ("ansfitsmooth", Memc[str]))
+		;
+	}
+	smooth = apgansb ("anssmooth")
+
+	# Initialize the ICFIT pointers.
+	if (ic1 == NULL || ic3 == NULL) {
+	    call ic_open (ic1)
+	    call clgstr ("apscat1.function", Memc[str], SZ_LINE)
+	    call ic_pstr (ic1, "function", Memc[str])
+	    call ic_puti (ic1, "order", clgeti ("apscat1.order"))
+	    call clgstr ("apscat1.sample", Memc[str], SZ_LINE)
+	    call ic_pstr (ic1, "sample", Memc[str])
+	    call ic_puti (ic1, "naverage", clgeti ("apscat1.naverage"))
+	    call ic_puti (ic1, "niterate", clgeti ("apscat1.niterate"))
+	    call ic_putr (ic1, "low", clgetr ("apscat1.low_reject"))
+	    call ic_putr (ic1, "high", clgetr ("apscat1.high_reject"))
+	    call ic_putr (ic1, "grow", clgetr ("apscat1.grow"))
+	    call ic_pstr (ic1, "ylabel", "")
+	    gt1 = gt_init()
+	    call gt_sets (gt1, GTTYPE, "line")
+ 
+	    call ic_open (ic2)
+	    call clgstr ("apscat2.function", Memc[str], SZ_LINE)
+	    call ic_pstr (ic2, "function", Memc[str])
+	    call ic_puti (ic2, "order", clgeti ("apscat2.order"))
+	    call clgstr ("apscat2.sample", Memc[str], SZ_LINE)
+	    call ic_pstr (ic2, "sample", Memc[str])
+	    call ic_puti (ic2, "naverage", clgeti ("apscat2.naverage"))
+	    call ic_puti (ic2, "niterate", clgeti ("apscat2.niterate"))
+	    call ic_putr (ic2, "low", clgetr ("apscat2.low_reject"))
+	    call ic_putr (ic2, "high", clgetr ("apscat2.high_reject"))
+	    call ic_putr (ic2, "grow", clgetr ("apscat2.grow"))
+	    call ic_pstr (ic2, "ylabel", "")
+	    gt2 = gt_init()
+	    call gt_sets (gt2, GTTYPE, "line")
+
+	    ic3 = ic1
+	}
+ 
+	# Map the input and output images.  Warn and return on an error.
+	iferr (in = ap_immap (input, aaxis, daxis)) {
+	    call sfree (sp)
+	    call erract (EA_WARN)
+	    return
+	}
+	iferr (out = immap (output, NEW_COPY, in)) {
+	    call imunmap (in)
+	    call sfree (sp)
+	    call erract (EA_WARN)
+	    return
+	}
+	if (IM_PIXTYPE(out) != TY_DOUBLE)
+	    IM_PIXTYPE(out) = TY_REAL
+ 
+	# Allocate memory for curve fitting.
+	call ap_sort (i, aps, naps, 1)
+	npts = IM_LEN (in, aaxis)
+	nlines = IM_LEN (in, daxis)
+	call salloc (col, npts, TY_REAL)
+	call salloc (x, npts, TY_REAL)
+	call salloc (y, npts, TY_REAL)
+	call salloc (w, npts, TY_REAL)
+ 
+	do i = 1, npts
+	    Memr[col+i-1] = i
+	call ic_putr (ic1, "xmin", Memr[col])
+	call ic_putr (ic1, "xmax", Memr[col+npts-1])
+ 
+	# If the interactive flag is set then use icg_fit to set the
+	# fitting parameters.  AP_GLINE returns EOF when the user
+	# is done.
+ 
+	if (apgansb ("ansfitscatter")) {
+	    call ap_gopen (gp)
+ 
+	    if (IS_INDEFI (line))
+		i = nlines / 2
+	    else
+		i = line
+	    indata = NULL
+	    while (ap_gline (ic1, gt1, NULL, in, aaxis, aaxis, i, indata) !=
+		EOF) {
+	        call ap_gscatter1 (aps, naps, i, Memr[indata], npts,
+		    Memr[x], Memr[y], Memr[w], nscatter)
+	        call icg_fit (ic1, gp, "gcur", gt1, cv, Memr[x], Memr[y],
+		    Memr[w], nscatter)
+	    }
+	    call cvfree (cv)
+	}
+ 
+	# Loop through the input image and create an output image.
+	# To minimize I/O if not smoothing write the final image
+	# directly otherwise save the fit.  AP_SMOOTH will then
+	# smooth along the dispersion and compute the scattered
+	# light subtracted image.
+ 
+	if (clgetb ("verbose")) {
+	    call printf (
+		"Fitting the scattered light across the dispersion ...\n")
+	    call flush (STDOUT)
+	}
+ 
+	if (!smooth) {
+	    nscatter = 0
+	    i = 0
+	    while (ap_gdata (in, out, NULL, aaxis, MAXBUF, i,
+		indata, outdata) != EOF) {
+		call ap_gscatter1 (aps, naps, i, Memr[indata], npts, Memr[x],
+		    Memr[y], Memr[w], nscatter1)
+		if (nscatter != nscatter1)
+		    new = YES
+		else
+		    new = NO
+		nscatter = nscatter1
+		call ic_fit (ic1, cv, Memr[x], Memr[y], Memr[w], nscatter,
+		    new, YES, new, new)
+		call cvvector (cv, Memr[col], Memr[outdata], npts)
+		call asubr (Memr[indata], Memr[outdata], Memr[outdata], npts)
+	    }
+	    call cvfree (cv)
+	} else {
+	    call salloc (cvs, nlines, TY_POINTER)
+	    call amovki (NULL, Memi[cvs], nlines)
+
+	    new = YES
+	    i = 0
+	    while (ap_gdata (in, NULL, NULL, aaxis, MAXBUF, i,
+		indata, outdata) != EOF) {
+		call ap_gscatter1 (aps, naps, i, Memr[indata], npts, Memr[x],
+		    Memr[y], Memr[w], nscatter)
+		call ic_fit (ic1, Memi[cvs+i-1], Memr[x], Memr[y], Memr[w],
+		    nscatter, new, YES, new, new)
+	    }
+     
+	    # Smooth and subtract along the dispersion.
+	    call ap_smooth (in, out, aaxis, daxis, aps, naps, ic2, gt2, cvs)
+	    do i = 1, nlines
+		call cvfree (Memi[cvs+i-1])
+	}
+
+	call imastr (out, "apscatter", "Scattered light subtracted")
+	call imunmap (out)
+	call imunmap (in)
+ 
+	# If a scattered light image is desired compute it from the difference
+	# of the input and output images.
+ 
+	if (scatter[1] != EOS) {
+	    in = immap (input, READ_ONLY, 0)
+	    out = immap (output, READ_ONLY, 0)
+	    ifnoerr (scat = immap (scatter, NEW_COPY, in)) {
+		if (IM_PIXTYPE(scat) != TY_DOUBLE)
+		    IM_PIXTYPE(scat) = TY_REAL
+		npts = IM_LEN(in,1)
+		nlines = IM_LEN(in,2)
+		do i = 1, nlines
+		    call asubr (Memr[imgl2r(in,i)], Memr[imgl2r(out,i)],
+			Memr[impl2r(scat,i)], npts)
+		call imunmap (scat)
+	    } else
+		call erract (EA_WARN)
+	    call imunmap (in)
+	    call imunmap (out)
+	}
+ 
+	# Make a log.
+	call sprintf (Memc[str], SZ_LINE,
+	    "SCATTER - Scattered light subtracted from %s")
+	    call pargstr (input)
+	call ap_log (Memc[str], YES, YES, NO)
+ 
+	call sfree (sp)
+end
+
+
+# SCAT_FREE -- Free scattered light memory.
+
+procedure scat_free ()
+
+pointer	ic1, ic2, gt1, gt2
+pointer	sp, str
+
+int	ic_geti()
+real	ic_getr()
+
+common	/aps_com/ ic1, ic2, gt1, gt2
+
+begin
+	if (ic1 != NULL) {
+	    call smark (sp)
+	    call salloc (str, SZ_LINE, TY_CHAR)
+ 
+	    call ic_gstr (ic1, "function", Memc[str], SZ_LINE)
+	    call clpstr ("apscat1.function", Memc[str])
+	    call ic_gstr (ic1, "sample", Memc[str], SZ_LINE)
+	    call clpstr ("apscat1.sample", Memc[str])
+	    call clputi ("apscat1.order", ic_geti (ic1, "order"))
+	    call clputi ("apscat1.naverage", ic_geti (ic1, "naverage"))
+	    call clputi ("apscat1.niterate", ic_geti (ic1, "niterate"))
+	    call clputr ("apscat1.low", ic_getr (ic1, "low"))
+	    call clputr ("apscat1.high", ic_getr (ic1, "high"))
+	    call clputr ("apscat1.grow", ic_getr (ic1, "grow"))
+ 
+	    call ic_gstr (ic2, "function", Memc[str], SZ_LINE)
+	    call clpstr ("apscat2.function", Memc[str])
+	    call ic_gstr (ic2, "sample", Memc[str], SZ_LINE)
+	    call clpstr ("apscat2.sample", Memc[str])
+	    call clputi ("apscat2.order", ic_geti (ic2, "order"))
+	    call clputi ("apscat2.naverage", ic_geti (ic2, "naverage"))
+	    call clputi ("apscat2.niterate", ic_geti (ic2, "niterate"))
+	    call clputr ("apscat2.low", ic_getr (ic2, "low"))
+	    call clputr ("apscat2.high", ic_getr (ic2, "high"))
+	    call clputr ("apscat2.grow", ic_getr (ic2, "grow"))
+ 
+	    call ic_closer (ic1)
+	    call gt_free (gt1)
+	    call ic_closer (ic2)
+	    call gt_free (gt2)
+	    call sfree (sp)
+	}
+end
+ 
+ 
+# AP_SMOOTH -- Smooth the scattered light by fitting one dimensional functions.
+#
+# The output image consists of smooth one dimensional fits across the
+# dispersion.  This routine reads each line along the dispersion and fits
+# a function to smooth the fits made across the dispersion.  The output
+# image is used both as input of the cross dispersion fits and as output
+# of the scattered light subtracted image.
+ 
+procedure ap_smooth (in, out, aaxis, daxis, aps, naps, ic, gt, cvs)
+ 
+pointer	in			# Input IMIO pointer
+pointer	out			# Output IMIO pointer
+int	aaxis, daxis		# Aperture and dispersion axes
+pointer	aps[ARB]		# Apertures
+int	naps			# Number of apertures
+pointer	ic			# ICFIT pointer
+pointer	gt			# GTOOLS pointer
+pointer	cvs			# CURFIT pointers
+ 
+int	i, npts, nlines, new
+pointer	cv, gp, indata, outdata, x, w 
+
+int	ap_gline(), ap_gdata()
+bool	clgetb(), apgansb()
+ 
+begin
+	if (!apgansb ("anssmooth"))
+	    return
+ 
+	# Allocate memory for curve fitting.
+	npts = IM_LEN (in, daxis)
+	nlines = IM_LEN (in, aaxis)
+	call salloc (x, npts, TY_REAL)
+	call salloc (w, npts, TY_REAL)
+ 
+	do i = 1, npts
+	    Memr[x+i-1] = i
+	call amovkr (1., Memr[w], npts)
+	call ic_putr (ic, "xmin", Memr[x])
+	call ic_putr (ic, "xmax", Memr[x+npts-1])
+ 
+	# If the interactive flag is set then use icg_fit to set the
+	# fitting parameters.  AP_GLINE returns EOF when the user
+	# is done.
+ 
+	if (apgansb ("ansfitsmooth")) {
+	    call ap_gopen (gp)
+ 
+	    i = nlines / 2
+	    outdata = NULL
+	    while (ap_gline (ic, gt, cvs, out, daxis, aaxis, i, outdata) !=
+		EOF) {
+	        call icg_fit (ic, gp, "gcur", gt, cv, Memr[x],
+		    Memr[outdata], Memr[w], npts)
+		call amovkr (1., Memr[w], npts)
+	    }
+	    call mfree (outdata, TY_REAL)
+	}
+ 
+	# Loop through the input image and create an output image.
+	if (clgetb ("verbose")) {
+	    call printf ("Smoothing scattered light along the dispersion ...\n")
+	    call flush (STDOUT)
+	}
+ 
+	# Use the new flag to optimize the fitting.
+	new = YES
+	i = 0
+	while (ap_gdata (in, out, cvs, daxis, MAXBUF, i,
+	    indata, outdata) != EOF) {
+	    call ic_fit (ic, cv, Memr[x], Memr[outdata], Memr[w], npts,
+		new, YES, new, new)
+	    call cvvector (cv, Memr[x], Memr[outdata], npts)
+	    call asubr (Memr[indata], Memr[outdata], Memr[outdata], npts)
+	    new = NO
+	}
+	call cvfree (cv)
+end
+ 
+ 
+# AP_GSCATTER -- Get scattered light pixels.
+#
+# The pixels outside the apertures extended by the specified buffer
+# distance are selected.  The x and weight arrays are also set.
+# The apertures must be sorted by position.
+ 
+procedure ap_gscatter1 (aps, naps, line, data, npts, x, y, w, nscatter)
+ 
+pointer	aps[naps]		# Apertures
+int	naps			# Number of apertures
+int	line			# Line
+real	data[npts]		# Image data
+int	npts			# Number of points
+real	x[npts]			# Scattered light positions
+real	y[npts]			# Image data
+real	w[npts]			# Weights
+int	nscatter		# Number of scattered light pixels
+ 
+real	buf			# Aperture buffer
+ 
+int	i, j, axis
+int	low, high
+real	center, ap_cveval(), clgetr()
+ 
+begin
+	buf = clgetr ("buffer") + 0.5
+	call aclrr (x, npts)
+ 
+	axis = AP_AXIS(aps[1])
+	do i = 1, naps {
+	    center = AP_CEN(aps[i],axis) + ap_cveval (AP_CV(aps[i]), real(line))
+	    low = max (1, int (center + AP_LOW(aps[i],axis) - buf))
+	    high = min (npts, int (center + AP_HIGH(aps[i],axis) + buf))
+	    do j = low, high
+		x[j] = 1
+	}
+
+	nscatter = 0
+	do i = 1, npts {
+	    if (x[i] == 0.) {
+		nscatter = nscatter + 1
+		x[nscatter] = i
+		y[nscatter] = data[i]
+		w[nscatter] = 1.
+	    }
+	}
+end
+ 
+ 
+# AP_GDATA -- Get the next line of image data.  Return EOF at end.
+# This task optimizes column access if needed.  It assumes sequential access.
+ 
+int procedure ap_gdata (in, out, cvs, axis, maxbuf, index, indata, outdata)
+ 
+pointer	in			# Input IMIO pointer
+pointer	out			# Output IMIO pointer (NULL if no output)
+pointer	cvs			# CURFIT pointers
+int	axis			# Image axis
+int	maxbuf			# Maximum buffer size chars for column axis
+int	index			# Last line (input), current line (returned)
+pointer	indata			# Input data pointer
+pointer	outdata			# Output data pointer
+ 
+real	val, ap_cveval()
+int	i, last_index, col1, col2, nc, nd, ncols, nlines, ncols_block
+pointer	inbuf, outbuf, ptr, imgl2r(), impl2r(), imgs2r(), imps2r()
+ 
+begin
+	# Increment to the next image vector.
+	index = index + 1
+ 
+	# Initialize for the first vector.
+	if (index == 1) {
+	    ncols = IM_LEN (in, 1)
+	    if (IM_NDIM (in) == 1)
+		nlines = 1
+	    else
+		nlines = IM_LEN (in, 2)
+ 
+	    switch (axis) {
+	    case 1:
+		nd = ncols
+		last_index = nlines
+	    case 2:
+		nd = nlines
+		last_index = ncols
+	        ncols_block =
+		    max (1, min (ncols, maxbuf / nlines))
+		col2 = 0
+ 
+	        call malloc (indata, nlines, TY_REAL)
+		if (out != NULL)
+		    call malloc (outdata, nlines, TY_REAL)
+	    }
+	}
+ 
+	# Finish up if the last vector has been done.
+	if (index > last_index) {
+	    if (axis == 2) {
+	        call mfree (indata, TY_REAL)
+		if (out != NULL) {
+		    ptr = outbuf + index - 1 - col1
+		    do i = 1, nlines {
+			Memr[ptr] = Memr[outdata+i-1]
+			ptr = ptr + nc
+		    }
+		    call mfree (outdata, TY_REAL)
+		}
+	    }
+	    index = 0
+	    return (EOF)
+	}
+ 
+	# Get the next image vector.
+	switch (axis) {
+	case 1:
+	    indata = imgl2r (in, index)
+	    if (out != NULL)
+		outdata = impl2r (out, index)
+	case 2:
+	    if (out != NULL)
+		if (index > 1) {
+		    ptr = outbuf + index - 1 - col1
+		    do i = 1, nlines {
+			Memr[ptr] = Memr[outdata+i-1]
+			ptr = ptr + nc
+		    }
+		}
+ 
+	    if (index > col2) {
+		col1 = col2 + 1
+		col2 = min (ncols, col1 + ncols_block - 1)
+		nc = col2 - col1 + 1
+		inbuf = imgs2r (in, col1, col2, 1, nlines)
+		if (out != NULL)
+		    outbuf = imps2r (out, col1, col2, 1, nlines)
+	    }
+ 
+	    ptr = inbuf + index - col1
+	    do i = 1, nlines {
+		Memr[indata+i-1] = Memr[ptr]
+		ptr = ptr + nc
+	    }
+	}
+	if (cvs != NULL) {
+	    val = index
+	    do i = 1, nd
+		Memr[outdata+i-1] = ap_cveval (Memi[cvs+i-1], val)
+	}
+ 
+	return (index)
+end
+ 
+ 
+define	CMDS	"|quit|line|column|buffer|"
+define	QUIT	1		# Quit
+define	LINE	2		# Line to examine
+define	COLUMN	3		# Column to examine
+define	BUFFER	4		# Buffer distance
+ 
+# AP_GLINE -- Get image data to be fit interactively.  Return EOF
+# when the user enters EOF or CR.  The out of bounds
+# requests are silently limited to the nearest edge.
+ 
+int procedure ap_gline (ic, gt, cvs, im, axis, aaxis, line, data)
+ 
+pointer	ic			# ICFIT pointer
+pointer	gt			# GTOOLS pointer
+pointer	cvs			# CURFIT pointers
+pointer	im			# IMIO pointer
+int	axis			# Image axis
+int	aaxis			# Aperture axis
+int	line			# Line to get
+pointer	data			# Image data
+ 
+real	rval, clgetr(), ap_cveval()
+int	i, stat, cmd, ival, strdic(), scan(), nscan()
+pointer	sp, name, str, imgl2r(), imgs2r()
+ 
+begin
+	call smark (sp)
+	call salloc (name, SZ_FNAME, TY_CHAR)
+	call salloc (str, SZ_LINE, TY_CHAR)
+
+	stat = OK
+	if (data != NULL) {
+	    cmd = 0
+	    repeat {
+	        switch (cmd) {
+	        case QUIT:
+		    stat = EOF
+		    break
+	        case LINE:
+		    call gargi (ival)
+		    if (axis == 2 || nscan() == 1) {
+		        call printf ("line %d - ")
+		        call pargi (line)
+		    } else {
+		        line = max (1, min (IM_LEN(im,2), ival))
+		        break
+		    }
+	        case COLUMN:
+		    call gargi (ival)
+		    if (axis == 1 || nscan() == 1) {
+		        call printf ("column %d - ")
+		        call pargi (line)
+		    } else {
+		        line = max (1, min (IM_LEN(im,1), ival))
+		        break
+		    }
+	        case BUFFER:
+		    if (axis == aaxis) {
+			call gargr (rval)
+			if (nscan() == 1) {
+			    call printf ("buffer %g - ")
+				call pargr (clgetr ("buffer"))
+			} else {
+			    call clputr ("buffer", rval)
+			    break
+			}
+		    }
+	        }
+ 
+		if (axis == aaxis) {
+		    if (axis == 1)
+			call printf (
+			    "Command (quit, buffer <value>, line <value>): ")
+		    else
+			call printf (
+			    "Command (quit, buffer <value>, column <value>): ")
+		} else {
+		    if (axis == 1)
+			call printf (
+			    "Command (quit, line <value>): ")
+		    else
+			call printf (
+			    "Command (quit, column <value>): ")
+		}
+		call flush (STDOUT)
+		stat = scan ()
+		if (stat == EOF)
+		    break
+		call gargwrd (Memc[str], SZ_LINE)
+		cmd = strdic (Memc[str], Memc[str], SZ_LINE, CMDS)
+	    }
+
+	}
+
+	if (stat != EOF) {
+	    call imstats (im, IM_IMAGENAME, Memc[name], SZ_FNAME)
+	    switch (axis) {
+	    case 1:
+		call sprintf (Memc[str], SZ_LINE, "%s: Fit line %d\n%s")
+		    call pargstr (Memc[name])
+		    call pargi (line)
+		    call pargstr (IM_TITLE(im))
+		call gt_sets (gt, GTTITLE, Memc[str])
+		call ic_pstr (ic, "xlabel", "Column")
+		if (axis == aaxis)
+		    data = imgl2r (im, line)
+		else {
+		    if (data == NULL)
+			call malloc (data, IM_LEN(im,1), TY_REAL)
+		    rval = line
+		    do i = 1, IM_LEN(im,1)
+			Memr[data+i-1] = ap_cveval (Memi[cvs+i-1], rval)
+		}
+	    case 2:
+		call sprintf (Memc[str], SZ_LINE, "%s: Fit column %d\n%s")
+		    call pargstr (Memc[name])
+		    call pargi (line)
+		    call pargstr (IM_TITLE(im))
+		call gt_sets (gt, GTTITLE, Memc[str])
+		call ic_pstr (ic, "xlabel", "Line")
+		if (axis == aaxis)
+		    data = imgs2r (im, line, line, 1, IM_LEN(im,2))
+		else {
+		    if (data == NULL)
+			call malloc (data, IM_LEN(im,2), TY_REAL)
+		    rval = line
+		    do i = 1, IM_LEN(im,2)
+			Memr[data+i-1] = ap_cveval (Memi[cvs+i-1], rval)
+		}
+	    }
+	}
+ 
+	call sfree (sp)
+	return (stat)
+end
diff --git a/noao/twodspec/apextract/apselect.x b/noao/twodspec/apextract/apselect.x
new file mode 100644
index 00000000..47730f47
--- /dev/null
+++ b/noao/twodspec/apextract/apselect.x
@@ -0,0 +1,40 @@
+include	"apertures.h"
+
+define	NRANGES	100
+
+
+# AP_SELECT -- Select apertures.
+# The AP_SELECT field of the aperture structure is set.
+
+procedure ap_select (apertures, aps, naps)
+
+char	apertures[ARB]		#I Aperture selection string
+pointer	aps[ARB]		#U Aperture pointers
+int	naps			#I Number of apertures
+
+pointer	sp, ranges
+int	i, decode_ranges()
+bool	is_in_range()
+
+begin
+	# Check if apertures are defined.
+	if (naps < 1)
+	    return
+
+	call smark (sp)
+	call salloc (ranges, 3*NRANGES, TY_INT)
+
+	# Decode aperture string.
+	if (decode_ranges (apertures, Memi[ranges], NRANGES, i) == ERR)
+	    call error (0, "Bad aperture list")
+
+	# Select apertures.
+	do i = 1, naps {
+	    if (is_in_range (Memi[ranges], AP_ID(aps[i])))
+		AP_SELECT(aps[i]) = YES
+	    else
+		AP_SELECT(aps[i]) = NO
+	}
+
+	call sfree (sp)
+end
diff --git a/noao/twodspec/apextract/apshow.x b/noao/twodspec/apextract/apshow.x
new file mode 100644
index 00000000..16f4d504
--- /dev/null
+++ b/noao/twodspec/apextract/apshow.x
@@ -0,0 +1,46 @@
+include	"apertures.h"
+
+# AP_SHOW -- List the apertures to a text file.
+
+procedure ap_show (file, aps, naps)
+
+char	file[ARB]		# Aperture file
+pointer	aps[ARB]		# Aperture pointers
+int	naps			# Number of apertures
+
+pointer	ap
+int	i, apaxis, fd, open()
+errchk	open
+
+begin
+	if (naps == 0)
+	    return
+
+	# Open the output file.  Return if an error occurs.
+	fd = open (file, APPEND, TEXT_FILE)
+
+	call fprintf (fd, "# APERTURES\n\n%4s %4s %7s %7s %7s %s\n")
+	    call pargstr ("##ID")
+	    call pargstr ("BEAM")
+	    call pargstr ("CENTER")
+	    call pargstr ("LOW")
+	    call pargstr ("HIGH")
+	    call pargstr ("TITLE")
+	for (i = 1; i <= naps; i = i + 1) {
+	    ap = aps[i]
+	    apaxis = AP_AXIS(ap)
+	    call fprintf (fd, "%4d %4d %7.2f %7.2f %7.2f")
+		call pargi (AP_ID(ap))
+		call pargi (AP_BEAM(ap))
+		call pargr (AP_CEN(ap, apaxis))
+		call pargr (AP_LOW(ap, apaxis))
+		call pargr (AP_HIGH(ap, apaxis))
+	    if (AP_TITLE(ap) != NULL) {
+		call fprintf (fd, " %s")
+		    call pargstr (Memc[AP_TITLE(ap)])
+	    }
+	    call fprintf (fd, "\n")
+	}
+
+	call close (fd)
+end
diff --git a/noao/twodspec/apextract/apskyeval.x b/noao/twodspec/apextract/apskyeval.x
new file mode 100644
index 00000000..05f47f14
--- /dev/null
+++ b/noao/twodspec/apextract/apskyeval.x
@@ -0,0 +1,368 @@
+include	<math/iminterp.h>
+include <mach.h>
+include	"apertures.h"
+
+# Background fitting types
+define	BACKGROUND	"|none|average|median|minimum|fit|"
+define	B_NONE		1
+define	B_AVERAGE	2
+define	B_MEDIAN	3
+define	B_MINIMUM	4
+define	B_FIT		5
+
+define	NSAMPLE		20	# Maximum number of background sample regions
+
+
+# AP_SKYEVAL -- Evaluate sky within aperture.
+#
+# The sky pixels specified by the background sample string are used to
+# determine a sky function at each line which is then evaluated for each
+# pixel in the aperture as given by the SBUF array with starting offsets
+# given by XS.  The fitting consists of either a straight average or a
+# function fit using ICFIT.  The sky regions are specified relative to the
+# aperture center.  To avoid systematics due to shifting of the aperture
+# relative to the integer pixel positions the sky regions are linearly
+# interpolated.  The average uses the integral of the interpolation
+# function within the sample region endpoints.  The fit samples the
+# interpolation on a pixel grid with the aperture exactly centered on
+# a pixel.  A crude sky variance is computed for each line based solely
+# on the variance model and the square root of the number of "pixels"
+# used for the fit.  This variance is used to boost the variance of
+# the sky subtracted spectrum during variance weighting.  Because sky
+# noise may be significant in short slits a box car smoothing may be
+# used giving a lower variance per pixel but bad errors near sky lines.
+# An unweighted aperture sum of the sky is returned in case the user
+# wants to save the subtracted 1D sky spectrum.
+
+procedure ap_skyeval (im, ap, dbuf, nc, nl, c1, l1, sbuf, svar, sky, nx, ny,
+	xs, ys, nsubaps, rdnoise)
+
+pointer	im		# IMIO pointer
+pointer	ap		# Aperture structure
+pointer	dbuf		# Data buffer
+int	nc, nl		# Size of data buffer
+int	c1, l1		# Origin of data buffer
+real	sbuf[nx,ny]	# Sky values
+real	svar[ny]	# Sky variances
+real	sky[ny,nsubaps]	# Extracted sky (out)
+int	nx, ny		# Size of profile array
+int	xs[ny], ys	# Origin of profile array
+int	nsubaps		# Number of subapertures
+real	rdnoise		# Readout noise in RMS data numbers.
+
+int	bkg		# Background type
+int	skybox		# Sky box car smoothing
+
+int	i, j, ix1, ix2, nsample, nsky, nfit, ix, iy
+real	center, xmin, xmax, a, b, c, s, avg
+pointer	ic, cv, cv1, asi, sp, str, data, as, bs, x, y, w
+
+int	apgwrd(), apgeti(), ctor()
+real	ic_getr(), ap_cveval(), asieval(), asigrl(), amedr()
+errchk	salloc, ic_fit
+
+begin
+	call smark (sp)
+	call salloc (str, SZ_LINE, TY_CHAR)
+
+	# Get CL parameters and set shift and fitting function pointers.
+	bkg = apgwrd ("background", Memc[str], SZ_LINE, BACKGROUND)
+	skybox = apgeti ("skybox")
+
+	cv = AP_CV(ap)
+	ic = AP_IC(ap)
+
+	# Set center and maximum limits relative to data buffer.
+	# The limits are required to overlap the aperture and include
+	# an extra point at each end for interpolation.  Shifts
+	# and boundary limits will be enforced later.
+
+	i = AP_AXIS(ap)
+	center = AP_CEN(ap,i)
+	xmin = center + min (AP_LOW(ap,i), ic_getr (ic, "xmin"))
+	xmax = center + max (AP_HIGH(ap,i), ic_getr (ic, "xmax"))
+	ix1 = nint (xmin) - 1
+	ix2 = nint (xmax) + 1
+	nfit = ix2 - ix1 + 1
+
+	# Allocate memory and parse sample string.
+	# The colons in the sample string must be changed to avoid
+	# sexigesimal interpretation.
+
+	call salloc (as, NSAMPLE, TY_REAL)
+	call salloc (bs, NSAMPLE, TY_REAL)
+
+	call ic_gstr (ic, "sample", Memc[str], SZ_LINE)
+	for (i=str; Memc[i]!=EOS; i=i+1)
+	    if (Memc[i] == ':')
+		Memc[i] = '$'
+
+	nsample = 0
+	for (i=1; Memc[str+i-1]!=EOS; i=i+1) {
+	    if (ctor (Memc[str], i, a) > 0) {
+		i = i - 1
+		if (Memc[str+i] == '$') {
+		    i = i + 2
+		    if (ctor (Memc[str], i, b) > 0) {
+			i = i - 1
+			Memr[as+nsample] = center + min (a, b)
+			Memr[bs+nsample] = center + max (a, b)
+			nsample = nsample + 1
+			if (nsample == NSAMPLE)
+			    break
+		    }
+	        }
+	    }
+	}
+
+	if (nsample == 0) {
+	    Memr[as] = xmin
+	    Memr[bs] = xmax
+	    nsample = 1
+	}
+
+	if (bkg == B_MEDIAN)
+	    call salloc (y, nfit, TY_REAL)
+	else if (bkg == B_FIT) {
+	    call salloc (x, nfit, TY_REAL)
+	    call salloc (y, nfit, TY_REAL)
+	    call salloc (w, nfit, TY_REAL)
+	}
+
+	# Initialize the image interpolator.
+	call asiinit (asi, II_LINEAR)
+
+	# Determine sky at each dispersion point.
+	call aclrr (svar, ny)
+	do iy = 1, ny {
+
+	    # Fit image interpolation function including extra points
+	    # and apply image boundary limits.
+
+	    i = iy + ys - 1
+	    s = ap_cveval (cv, real (i))
+	    ix1 = max (c1, nint (xmin + s) - 1)
+	    ix2 = min (c1+nc-1, nint (xmax + s) + 1)
+	    nfit = ix2 - ix1 + 1
+	    if (nfit < 3) {
+		call aclrr (sbuf[1,iy], nx)
+		svar[iy] = 0.
+		next
+	    }
+	    data = dbuf + (i - l1) * nc + ix1 - c1
+	    if (bkg == B_AVERAGE || bkg == B_FIT) {
+		iferr (call asifit (asi, Memr[data], nfit)) {
+		    call aclrr (sbuf[1,iy], nx)
+		    svar[iy] = 0.
+		    next
+		}
+	    }
+
+	    # Determine background
+	    switch (bkg) {
+	    case B_AVERAGE:
+		# The background is computed by integrating the interpolator 
+	        avg = 0.
+		nsky = 0
+	        c = 0.
+		for (i=0; i < nsample; i=i+1) {
+		    a = max (real (ix1), Memr[as+i] + s) - ix1 + 1
+		    b = min (real (ix2), Memr[bs+i] + s) - ix1 + 1
+		    if (b - a > 0.) {
+			avg = avg + asigrl (asi, a, b)
+			c = c + b - a
+			nsky = nsky + nint (b) - nint(a) + 1
+		    }
+	        }
+	        if (c > 0.)
+	            avg = avg / c
+		call amovkr (avg, sbuf[1,iy], nx) 
+		if (nsky > 1)
+		    svar[iy] = max (0., (rdnoise + avg) / (nsky - 1))
+	    case B_MEDIAN:
+		# The background is computed by the median pixel
+	        avg = 0.
+		nsky = 0
+		for (i=0; i < nsample; i=i+1) {
+		    a = max (real (ix1), Memr[as+i] + s) - ix1 + 1
+		    b = min (real (ix2), Memr[bs+i] + s) - ix1 + 1
+		    do j = nint (a), nint (b) {
+			Memr[y+nsky] = Memr[data+j-1]
+			nsky = nsky + 1
+		    }
+	        }
+		if (nsky > 0)
+		    avg = amedr (Memr[y], nsky)
+		call amovkr (avg, sbuf[1,iy], nx) 
+		if (nsky > 1)
+		    svar[iy] = max (0., (rdnoise + avg) / (nsky - 1))
+	    case B_MINIMUM:
+		# The background is computed by the minimum pixel
+	        avg = MAX_REAL
+		nsky = 0
+		for (i=0; i < nsample; i=i+1) {
+		    a = max (real (ix1), Memr[as+i] + s) - ix1 + 1
+		    b = min (real (ix2), Memr[bs+i] + s) - ix1 + 1
+		    do j = nint (a), nint (b) {
+			avg = min (avg, Memr[data+j-1])
+			nsky = nsky + 1
+		    }
+	        }
+		if (nsky == 0)
+		    avg = 0
+		call amovkr (avg, sbuf[1,iy], nx) 
+		if (nsky > 1)
+		    svar[iy] = max (0., (rdnoise + avg) / (nsky - 1))
+	    case B_FIT:
+		# The fitting is done in a coordinate system relative to
+		# aperture center.
+
+		c = center + s
+	        a = ix1 + c - int (c)
+	        do i = 1, nfit-1 {
+	            Memr[x+i-1] = nint (1000. * (a - c)) / 1000.
+		    Memr[y+i-1] = asieval (asi, a-ix1+1)
+		    Memr[w+i-1] = 1.
+		    a = a + 1.
+	        }
+
+	        iferr {
+	            call ic_fit (ic, cv1, Memr[x], Memr[y], Memr[w], nfit-1,
+	                YES, YES, YES, YES)
+
+		    avg = 0.
+	            do i = 1, nx {
+		        a = xs[iy] + i - 1
+			b = ap_cveval (cv1, a - c)
+			avg = avg + b
+			sbuf[i,iy] = b
+	            }
+		    avg = avg / nx
+	        } then {
+		    avg = 0.
+		    call aclrr (sbuf[1,iy], nx)
+		}
+
+		nsky = 0.
+		for (i=0; i < nsample; i=i+1) {
+		    a = max (real (ix1), Memr[as+i] + s) - ix1 + 1
+		    b = min (real (ix2), Memr[bs+i] + s) - ix1 + 1
+		    nsky = nsky + nint (b) - nint (a) + 1
+		}
+		if (nsky > 1)
+		    svar[iy] = max (0., (rdnoise + avg) / (nsky - 1))
+	    }
+	}
+
+	# Do box car smoothing if desired.
+	if (skybox > 1) {
+	    ix2 = skybox ** 2
+	    avg = 0.
+	    a = 0.
+	    iy = 1
+	    for (i=1; i<=skybox; i=i+1) {
+		avg = avg + sbuf[1,i]
+		a = a + svar[i]
+	    }
+	    for (; i<=ny; i=i+1) {
+		b = sbuf[1,iy]
+		c = svar[iy]
+		sbuf[1,iy] = avg / skybox
+		svar[iy] = a / ix2
+		avg = avg + sbuf[1,i] - b
+		a = a + svar[i] - c
+		iy = iy + 1
+	    }
+	    sbuf[1,iy] = avg / skybox
+	    svar[iy] = a / ix2
+	    i = ny - skybox + 1
+	    for (iy=ny; iy > ny-skybox/2; iy=iy-1)
+		svar[iy] = svar[i]
+	    for (; i > 1; i=i-1) {
+		svar[iy] = svar[i]
+		iy = iy - 1
+	    }
+	    for (; iy > 1; iy=iy-1)
+		svar[iy] = svar[1]
+
+	    switch (bkg) {
+	    case B_AVERAGE, B_MEDIAN, B_MINIMUM:
+		i = ny - skybox + 1
+	        for (iy=ny; iy > ny-skybox/2; iy=iy-1)
+		    call amovkr (sbuf[1,i], sbuf[1,iy], nx)
+	        for (; i > 1; i=i-1) {
+		    call amovkr (sbuf[1,i], sbuf[1,iy], nx)
+		    iy = iy - 1
+	        }
+	        for (; iy > 1; iy=iy-1)
+		    call amovkr (sbuf[1,1], sbuf[1,iy], nx)
+	    case B_FIT:
+	        i = ny - skybox + 1
+	        for (iy=ny; iy > ny-skybox/2; iy=iy-1)
+		    sbuf[1,iy] = sbuf[1,i]
+	        for (; i > 1; i=i-1) {
+		    sbuf[1,iy] = sbuf[1,i]
+		    iy = iy - 1
+	        }
+	        for (; iy > 1; iy=iy-1)
+		    sbuf[1,iy] = sbuf[1,1]
+		do ix1 = 2, nx {
+		    avg = 0.
+		    iy = 1
+		    for (i=1; i<=skybox; i=i+1)
+			avg = avg + sbuf[ix1,i]
+		    for (; i<=ny; i=i+1) {
+			b = sbuf[ix1,iy]
+			sbuf[ix1,iy] = avg / skybox
+			avg = avg + sbuf[ix1,i] - b
+			iy = iy + 1
+		    }
+		    sbuf[ix1,iy] = avg / skybox
+		    i = ny - skybox + 1
+		    for (iy=ny; iy > ny-skybox/2; iy=iy-1)
+			sbuf[ix1,iy] = sbuf[ix1,i]
+		    for (; i > 1; i=i-1) {
+			sbuf[ix1,iy] = sbuf[ix1,i]
+			iy = iy - 1
+		    }
+		    for (; iy > 1; iy=iy-1)
+			sbuf[ix1,iy] = sbuf[ix1,1]
+		}
+	    }
+	}
+
+	# Compute the unweighted aperture sky spectrum.
+	i = AP_AXIS(ap)
+	a = AP_CEN(ap,i) + AP_LOW(ap,i)
+	b = AP_CEN(ap,i) + AP_HIGH(ap,i)
+	c = (b - a) / nsubaps
+
+	do iy = 1, ny {
+	    data = dbuf + (iy + ys - 1 - l1) * nc + xs[iy] - c1 - 1
+	    s = ap_cveval (cv, real (iy + ys - 1)) - c1 + 1
+	    do i = 1, nsubaps {
+		xmin = max (0.5, a + (i - 1) * c + s) + c1 - xs[iy]
+		xmax = min (nc + 0.49, a + i * c + s) + c1 - xs[iy]
+		if (xmin >= xmax) {
+		    sky[iy,i] = 0.
+		    next
+		}
+		ix1 = nint (xmin)
+		ix2 = nint (xmax)
+
+		if (ix1 == ix2)
+		    sky[iy,i] = (xmax - xmin) * sbuf[ix1,iy]
+		else {
+		    sky[iy,i] = (ix1 - xmin + 0.5) * sbuf[ix1,iy]
+		    sky[iy,i] = sky[iy,i] + (xmax - ix2 + 0.5) * sbuf[ix2,iy]
+		}
+		do ix = ix1+1, ix2-1
+		    sky[iy,i] = sky[iy,i] + sbuf[ix,iy]
+	    }
+	}
+
+	if (bkg == B_FIT)
+	    call cvfree (cv1)
+	call asifree (asi)
+	call sfree (sp)
+end
diff --git a/noao/twodspec/apextract/apsort.x b/noao/twodspec/apextract/apsort.x
new file mode 100644
index 00000000..85b21cc5
--- /dev/null
+++ b/noao/twodspec/apextract/apsort.x
@@ -0,0 +1,55 @@
+include	"apertures.h"
+
+# Sort flags:
+define	INC	1	# Sort by aperture position in increasing order
+define	DEC	2	# Sort by position in decreasing order
+
+# AP_SORT -- Sort the apertures.
+
+procedure ap_sort (current, aps, naps, flag)
+
+int	current			# Current aperture
+pointer	aps[ARB]		# Aperture data
+int	naps			# Number of apertures
+int	flag			# Sort flag
+
+int	i, j, apaxis
+pointer	ap
+
+begin
+	if (naps < 1)
+	    return
+
+	switch (flag) {
+	case INC:
+	    apaxis = AP_AXIS (aps[1])
+	    for (i = 1; i <= naps - 1; i = i + 1) {
+	        for (j = i + 1; j <= naps; j = j + 1) {
+		    if (AP_CEN(aps[i], apaxis) > AP_CEN(aps[j], apaxis)) {
+		        ap = aps[i]
+		        aps[i] = aps[j]
+		        aps[j] = ap
+		        if (current == i)
+			    current = j
+		        else if (current == j)
+			    current = i
+		    }
+	        }
+	    }
+	case DEC:
+	    apaxis = AP_AXIS (aps[1])
+	    for (i = 1; i <= naps - 1; i = i + 1) {
+	        for (j = i + 1; j <= naps; j = j + 1) {
+		    if (AP_CEN(aps[i], apaxis) < AP_CEN(aps[j], apaxis)) {
+		        ap = aps[i]
+		        aps[i] = aps[j]
+		        aps[j] = ap
+		        if (current == i)
+			    current = j
+		        else if (current == j)
+			    current = i
+		    }
+	        }
+	    }
+	}
+end
diff --git a/noao/twodspec/apextract/apsum.par b/noao/twodspec/apextract/apsum.par
new file mode 100644
index 00000000..b5b58013
--- /dev/null
+++ b/noao/twodspec/apextract/apsum.par
@@ -0,0 +1,34 @@
+# APSUM
+
+input,s,a,,,,List of input images
+output,s,h,"",,,List of output spectra
+apertures,s,h,"",,,Apertures
+format,s,h,"multispec","onedspec|multispec|echelle|strip",,Extracted spectra format
+references,s,h,"",,,List of aperture reference images
+profiles,s,h,"",,,"List of aperture profile images
+"
+interactive,b,h,yes,,,Run task interactively?
+find,b,h,yes,,,Find apertures?
+recenter,b,h,no,,,Recenter apertures?
+resize,b,h,no,,,Resize apertures?
+edit,b,h,yes,,,Edit apertures?
+trace,b,h,yes,,,Trace apertures?
+fittrace,b,h,yes,,,Fit the traced points interactively?
+extract,b,h,yes,,,Extract apertures?
+extras,b,h,no,,,"Extract sky, sigma, etc.?"
+review,b,h,yes,,,"Review extractions?
+"
+line,i,h,INDEF,1,,Dispersion line
+nsum,i,h,10,,,"Number of dispersion lines to sum or median
+"
+background,s,h,"none",,,Background to subtract (none|average|fit)
+weights,s,h,"none","none|variance",,Extraction weights (none|variance)
+pfit,s,h,"fit1d","fit1d|fit2d",,Profile fitting type (fit1d|fit2d)
+clean,b,h,no,,,Detect and replace bad pixels?
+skybox,i,h,1,1,,Box car smoothing length for sky
+saturation,r,h,INDEF,,,Saturation level
+readnoise,s,h,"0.",,,Read out noise sigma (photons)
+gain,s,h,"1.",,,Photon gain (photons/data number)
+lsigma,r,h,4.,0.,,Lower rejection threshold
+usigma,r,h,4.,0.,,Upper rejection threshold
+nsubaps,i,h,1,1,,Number of subapertures per aperture
diff --git a/noao/twodspec/apextract/aptrace.par b/noao/twodspec/apextract/aptrace.par
new file mode 100644
index 00000000..9134a012
--- /dev/null
+++ b/noao/twodspec/apextract/aptrace.par
@@ -0,0 +1,27 @@
+# APTRACE
+
+input,s,a,,,,List of input images to trace
+apertures,s,h,"",,,Apertures
+references,s,h,"",,,List of reference images
+
+interactive,b,h,yes,,,Run task interactively?
+find,b,h,yes,,,Find apertures?
+recenter,b,h,no,,,Recenter apertures?
+resize,b,h,no,,,Resize apertures?
+edit,b,h,no,,,Edit apertures?
+trace,b,h,yes,,,Trace apertures?
+fittrace,b,h,yes,,,"Fit the traced points interactively?
+"
+line,i,h,INDEF,1,,Starting dispersion line
+nsum,i,h,10,,,Number of dispersion lines to sum
+step,i,h,10,1,,Tracing step
+nlost,i,h,3,1,,"Number of consecutive times profile is lost before quitting
+"
+function,s,h,"legendre","chebyshev|legendre|spline1|spline3",,Trace fitting function
+order,i,h,2,1,,Trace fitting function order
+sample,s,h,"*",,,Trace sample regions
+naverage,i,h,1,,,Trace average or median
+niterate,i,h,0,0,,Trace rejection iterations
+low_reject,r,h,3.,0.,,Trace lower rejection sigma
+high_reject,r,h,3.,0.,,Trace upper rejection sigma
+grow,r,h,0.,0.,,Trace rejection growing radius
diff --git a/noao/twodspec/apextract/aptrace.x b/noao/twodspec/apextract/aptrace.x
new file mode 100644
index 00000000..c38af01c
--- /dev/null
+++ b/noao/twodspec/apextract/aptrace.x
@@ -0,0 +1,669 @@
+include	<imhdr.h>
+include	<math/curfit.h>
+include	<pkg/center1d.h>
+include	<pkg/gtools.h>
+include	"apertures.h"
+
+define	MAXBUF	100000		# Column buffer size
+
+
+# AP_TRACE -- Trace features in a two dimensional image.
+#
+# Given an image pointer, the starting dispersion position, and a set
+# of apertures defining the centers of features, trace the feature
+# centers to other dispersion positions and fit a curve to the positions.
+# The user specifies the dispersion step size, the number of dispersion
+# lines to sum, and parameters for the feature centering function
+# fitting.
+
+procedure ap_trace (image, line, aps, naps, apedit)
+
+char	image[SZ_FNAME]		# Image name
+int	line			# Starting dispersion position
+pointer	aps[ARB]		# Apertures
+int	naps			# Number of apertures
+int	apedit			# Called from APEDIT?
+
+int	step			# Tracing step
+int	nsum			# Number of dispersion lines to sum
+int	nlost			# Number of steps lost before quitting
+real	cradius			# Centering radius
+real	cwidth			# Centering width
+real	cthreshold		# Detection threshold for centering
+
+int	i, na, dispaxis, apaxis
+real	center
+pointer	im, ic, ic1, sp, str
+data	ic1 /NULL/
+
+int	apgeti()
+real	apgetr()
+bool	clgetb(), ap_answer()
+pointer	ap_immap()
+
+errchk	ap_immap, ic_open, ap_ltrace, ap_ctrace, ap_default
+
+common	/apt_com/ ic
+
+begin
+	na = 0
+	do i = 1, naps
+	    if (AP_SELECT(aps[i]) == YES)
+		na = na + 1
+	if (naps > 0 && na == 0)
+	    return
+
+	# Query user.
+	call smark (sp)
+	call salloc (str, SZ_LINE, TY_CHAR)
+	if (apedit == NO) {
+	    call sprintf (Memc[str], SZ_LINE, "Trace apertures for %s?")
+	        call pargstr (image)
+	    if (!ap_answer ("anstrace", Memc[str])) {
+	        call sfree (sp)
+	        return
+	    }
+
+	    call sprintf (Memc[str], SZ_LINE,
+	        "Fit traced positions for %s interactively?")
+	        call pargstr (image)
+	    if (ap_answer ("ansfittrace", Memc[str])) {
+	        call apgstr ("ansfittrace", Memc[str], SZ_LINE)
+	        call appstr ("ansfittrace1", Memc[str])
+	    } else
+	        call appstr ("ansfittrace1", "NO")
+
+	    if (clgetb ("verbose"))
+	        call printf ("Tracing apertures ...\n")
+	}
+
+	# Tracing parameters
+	step = apgeti ("t_step")
+	nsum = max (1, abs (apgeti ("t_nsum")))
+	nlost = apgeti ("t_nlost")
+	if (ic == NULL || ic1 == NULL) {
+	    call ic_open (ic)
+	    ic1 = ic
+	    call apgstr ("t_function", Memc[str], SZ_LINE)
+	    call ic_pstr (ic, "function", Memc[str])
+	    call ic_puti (ic, "order", apgeti ("t_order"))
+	    call apgstr ("t_sample", Memc[str], SZ_LINE)
+	    call ic_pstr (ic, "sample", Memc[str])
+	    call ic_puti (ic, "naverage", apgeti ("t_naverage"))
+	    call ic_puti (ic, "niterate", apgeti ("t_niterate"))
+	    call ic_putr (ic, "low", apgetr ("t_low_reject"))
+	    call ic_putr (ic, "high", apgetr ("t_high_reject"))
+	    call ic_putr (ic, "grow", apgetr ("t_grow"))
+	}
+
+	im = ap_immap (image, apaxis, dispaxis)
+
+	# If no apertures are defined default to the center of the image.
+	if (naps == 0) {
+	    naps = 1
+	    center = IM_LEN (im, apaxis) / 2.
+	    call ap_default (im, 1, 1, apaxis, center, real (line),
+		aps[naps])
+	    call sprintf (Memc[str], SZ_LINE,
+	       "TRACE - Default aperture defined centered on %s")
+	       call pargstr (image)
+	    call ap_log (Memc[str], YES, NO, YES)
+	}
+
+	# Centering parameters
+	cwidth = apgetr ("t_width")
+	cradius = apgetr ("radius")
+	cthreshold = apgetr ("threshold")
+
+	switch (dispaxis) {
+	case 1:
+	    call ap_ctrace (image, im, ic, line, step, nsum, nlost, cradius,
+		cwidth, cthreshold, aps, naps)
+	case 2:
+	    call ap_ltrace (image, im, ic, line, step, nsum, nlost, cradius,
+		cwidth, cthreshold, aps, naps)
+	}
+
+	# Log the tracing and write the traced apertures to the database.
+
+	call sprintf (Memc[str], SZ_LINE,
+	    "TRACE - %d apertures traced in %s.")
+       	    call pargi (na)
+       	    call pargstr (image)
+	if (apedit == NO)
+	    call ap_log (Memc[str], YES, YES, NO)
+	else
+	    call ap_log (Memc[str], YES, NO, NO)
+
+	call appstr ("ansdbwrite1", "yes")
+
+	call imunmap (im)
+	call sfree (sp)
+end
+
+
+procedure ap_trfree ()
+
+pointer	ic
+common	/apt_com/ ic
+
+begin
+	call ic_closer (ic)
+end
+
+
+# AP_CTRACE -- Trace feature positions for aperture axis 2.
+
+procedure ap_ctrace (image, im, ic, start, step, nsum, nlost, cradius, cwidth,
+    threshold, aps, naps)
+
+char	image[ARB]		# Image to be traced.
+pointer	im			# IMIO pointer
+pointer	ic			# ICFIT pointer
+int	start			# Starting column
+int	step			# Tracing step size
+int	nsum			# Number of lines or columns to sum
+int	nlost			# Number of steps lost before quiting
+real	cradius			# Centering radius
+real	cwidth			# Centering width
+real	threshold		# Detection threshold for centering
+pointer	aps[ARB]		# Apertures
+int	naps			# Number of apertures
+
+int	nlines, col, col1, col2, line1, line2
+int	i, j, n, nx, ny, ntrace, istart, lost, fd
+real	yc, yc1
+pointer	co, data, sp, str, x, y, wts, gp, gt
+
+real	center1d(), ap_cveval()
+bool	ap_answer()
+pointer comap(), gt_init()
+
+errchk	ap_cveval, xt_csum, xt_csumb, center1d, icg_fit, ic_fit
+errchk	ap_gopen, ap_popen
+
+begin
+	# Set up column access buffering.
+
+	co = comap (im, MAXBUF)
+
+	# Determine the number of lines to be traced and allocate memory.
+
+	nx = IM_LEN(im, 1)
+	ny = IM_LEN(im, 2)
+	if (IS_INDEFI (start))
+	    start = nx / 2
+	nlines = 5 * cwidth
+	istart = (start - 1) / step + 1
+	ntrace = istart + (nx - start) / step
+
+	# Allocate memory for the traced positions and the weights for fitting.
+
+	call smark (sp)
+	call salloc (str, SZ_LINE, TY_CHAR)
+	call salloc (x, ntrace, TY_REAL)
+	call salloc (y, ntrace, TY_REAL)
+	call salloc (wts, ntrace, TY_REAL)
+	call aclrr (Memr[y], ntrace)
+	data = NULL
+
+	# Initialize the ICFIT limits and the GTOOLS parameters.
+	# Set initial interactive flag.
+
+	call ic_putr (ic, "xmin", 1.)
+	call ic_putr (ic, "xmax", real (nx))
+	call ic_pstr (ic, "xlabel", "Column")
+	call ic_pstr (ic, "ylabel", "Line")
+
+	gt = gt_init()
+	call gt_setr (gt, GTXMIN, 1. - step / 2)
+	call gt_setr (gt, GTXMAX, real (nx + step / 2))
+
+	# Trace each feature.
+
+	line1 = 0
+	line2 = 0
+	do j = 1, naps {
+	    if (AP_SELECT(aps[j]) == NO)
+		next
+
+	    # Trace from the starting column to the last column while the
+	    # position is not INDEF.
+
+	    lost = 0
+	    yc = AP_CEN(aps[j], 2) + ap_cveval (AP_CV(aps[j]), real (start))
+	    do i = istart, ntrace {
+		Memr[y+i-1] = INDEF
+		if (lost < nlost) {
+		    # Update the scrolling buffer if the feature center is less
+		    # than cwidth from the edge of the buffer.
+		    if (((yc-line1) < cwidth) || ((line2-yc) < cwidth)) {
+		        line1 = max (1, int (yc + .5 - nlines / 2))
+		        line2 = min (ny, line1 + nlines - 1)
+		        line1 = max (1, line2 - nlines + 1)
+		    }
+
+		    # Sum columns to form the 1D vector for centering.
+
+	            col = start + (i - istart) * step
+		    col1 = max (1, col - nsum / 2)
+		    col2 = min (nx, col1 + nsum - 1)
+		    col1 = max (1, col2 - nsum + 1)
+
+		    # If columns in the sum overlap then use buffering.
+
+		    if (step < nsum)
+		        call xt_csumb (co, col1, col2, line1, line2, data)
+		    else
+		        call xt_csum (co, col1, col2, line1, line2, data)
+
+		    # Center the feature for the new column using the previous
+		    # center as the starting point.  Convert to position
+		    # relative to the start of the data buffer for centering
+		    # and then convert back to position relative to the
+		    # edge of the image.
+
+		    yc1 = center1d (yc-line1+1, Memr[data], line2-line1+1,
+			cwidth, EMISSION, cradius, threshold)
+
+		    if (!IS_INDEF (yc1)) {
+			lost = 0
+		        yc = yc1 + line1 - 1
+			Memr[y+i-1] = yc
+			if (IS_INDEF (Memr[y+i-2])) {
+	    		    call sprintf (Memc[str], SZ_LINE,
+		   "TRACE - Trace of aperture %d in %s recovered at column %d.")
+			        call pargi (AP_ID(aps[j]))
+			        call pargstr (image)
+			        call pargi (col)
+			    call ap_log (Memc[str], YES, NO, YES)
+			}
+		    } else {
+			lost = lost + 1
+	    		call sprintf (Memc[str], SZ_LINE,
+		    "TRACE - Trace of aperture %d in %s lost at column %d.")
+			    call pargi (AP_ID(aps[j]))
+			    call pargstr (image)
+			    call pargi (col)
+			call ap_log (Memc[str], YES, NO, YES)
+		    }
+		}
+	    }
+
+	    # Trace from the starting column to the first column while the
+	    # position is not INDEF.
+
+	    lost = 0
+	    yc = AP_CEN(aps[j], 2) + ap_cveval (AP_CV(aps[j]), real (start))
+	    do i = istart - 1, 1, -1 {
+		Memr[y+i-1] = INDEF
+		if (lost < nlost) {
+		    # Update the scrolling buffer if the feature center is less
+		    # than cwidth from the edge of the buffer.
+
+		    if (((yc-line1) < cwidth) || ((line2-yc) < cwidth)) {
+		        line1 = max (1, int (yc + .5 - nlines / 2))
+		        line2 = min (ny, line1 + nlines - 1)
+		        line1 = max (1, line2 - nlines + 1)
+		    }
+
+		    # Sum columns to form the 1D vector for centering.
+
+	            col = start + (i - istart) * step
+		    col1 = max (1, col - nsum / 2)
+		    col2 = min (nx, col1 + nsum - 1)
+		    col1 = max (1, col2 - nsum + 1)
+
+		    # If columns in the sum overlap then use buffering.
+
+		    if (step < nsum)
+		        call xt_csumb (co, col1, col2, line1, line2, data)
+		    else
+		        call xt_csum (co, col1, col2, line1, line2, data)
+
+		    # Center the feature for the new column using the previous
+		    # center as the starting point.  Convert to position
+		    # relative to the start of the data buffer for centering
+		    # and then convert back to position relative to the
+		    # edge of the image.
+
+		    yc1 = center1d (yc-line1+1, Memr[data], line2-line1+1,
+			cwidth, EMISSION, cradius, threshold)
+
+		    if (!IS_INDEF (yc1)) {
+			lost = 0
+		        yc = yc1 + line1 - 1
+			Memr[y+i-1] = yc
+			if (IS_INDEF (Memr[y+i])) {
+	    		    call sprintf (Memc[str], SZ_LINE,
+		   "TRACE - Trace of aperture %d in %s recovered at column %d.")
+			        call pargi (AP_ID(aps[j]))
+			        call pargstr (image)
+			        call pargi ((i - 1) * step + 1)
+			    call ap_log (Memc[str], YES, NO, YES)
+			}
+		    } else {
+			lost = lost + 1
+	    		call sprintf (Memc[str], SZ_LINE,
+		    "TRACE - Trace of aperture %d in %s lost at column %d.")
+			    call pargi (AP_ID(aps[j]))
+			    call pargstr (image)
+			    call pargi ((i - 1) * step + 1)
+			call ap_log (Memc[str], YES, NO, YES)
+		    }
+		}
+	    }
+
+	    # Order the traced points and exclude INDEF positions.
+
+	    n = 0
+	    do i = 1, ntrace {
+		if (IS_INDEF (Memr[y+i-1]))
+		    next
+		n = n + 1
+		Memr[x+n-1] = start + (i - istart) * step
+		Memr[y+n-1] = Memr[y+i-1]
+		Memr[wts+n-1] = 1.
+	    }
+
+	    # If all positions are INDEF print a message and go on to the next
+	    # aperture.
+
+	    if (n < 2) {
+		call eprintf (
+		    "Not enough points traced for aperture %d of %s\n")
+		    call pargi (AP_ID(aps[j]))
+		    call pargstr (image)
+		next
+	    }
+		    
+	    # Fit a curve to the traced positions and graph the result.
+
+	    call sprintf (Memc[str], SZ_LINE, "Aperture %d of %s")
+	        call pargi (AP_ID(aps[j]))
+		call pargstr (image)
+	    call gt_sets (gt, GTTITLE, Memc[str])
+
+	    call sprintf (Memc[str], SZ_LINE,
+		"Fit curve to aperture %d of %s interactively")
+		call pargi (AP_ID(aps[j]))
+		call pargstr (image)
+	    if (ap_answer ("ansfittrace1", Memc[str])) {
+		call ap_gopen (gp)
+	        call icg_fit (ic, gp, "gcur", gt,
+		    AP_CV(aps[j]), Memr[x], Memr[y], Memr[wts], n)
+	    } else
+	        call ic_fit (ic, AP_CV(aps[j]), Memr[x], Memr[y], Memr[wts], n,
+		    YES, YES, YES, YES)
+
+	    call ap_popen (gp, fd, "trace")
+	    if (gp != NULL) {
+		call icg_graphr (ic, gp, gt, AP_CV(aps[j]),
+		    Memr[x], Memr[y], Memr[wts], n)
+		call ap_pclose (gp, fd)
+	    }
+
+	    call asubkr (Memr[y], AP_CEN(aps[j], 2), Memr[y], n)
+	    call ic_fit (ic, AP_CV(aps[j]), Memr[x], Memr[y], Memr[wts], n,
+		YES, YES, YES, YES)
+	}
+
+	# Free allocated memory.
+
+	call gt_free (gt)
+	call mfree (data, TY_REAL)
+	call counmap (co)
+	call sfree (sp)
+end
+
+
+# AP_LTRACE -- Trace feature positions for aperture axis 1.
+
+procedure ap_ltrace (image, im, ic, start, step, nsum, nlost, cradius, cwidth,
+    threshold, aps, naps)
+
+char	image[ARB]		# Image to be traced
+pointer	im			# IMIO pointer
+pointer	ic			# ICFIT pointer
+int	start			# Starting line
+int	step			# Tracing step size
+int	nsum			# Number of lines or columns to sum
+int	nlost			# Number of steps lost before quiting
+real	cradius			# Centering radius
+real	cwidth			# Centering width
+real	threshold		# Detection threshold for centering
+pointer	aps[ARB]		# Apertures
+int	naps			# Number of apertures
+
+real	xc1
+int	i, j, n, nx, ny, ntrace, istart, line, line1, line2, fd
+pointer	data, sp, str, x, y, wts, xc, lost, x1, x2, gp, gt
+
+real	center1d(), ap_cveval()
+bool	ap_answer()
+pointer	gt_init()
+
+errchk	ap_cveval, xt_lsum, xt_lsumb, center1d, icg_fit, ic_fit
+errchk	ap_gopen, ap_popen
+
+begin
+	# Determine the number of lines to be traced and allocate memory.
+
+	nx = IM_LEN(im, 1)
+	ny = IM_LEN(im, 2)
+	if (IS_INDEFI (start))
+	    start = ny / 2
+
+	istart = (start - 1) / step + 1
+	ntrace = istart + (ny - start) / step
+
+	# Allocate memory for the traced positions and the weights for fitting.
+
+	call smark (sp)
+	call salloc (str, SZ_LINE, TY_CHAR)
+	call salloc (x, ntrace * naps, TY_REAL)
+	call salloc (y, ntrace, TY_REAL)
+	call salloc (wts, ntrace, TY_REAL)
+	call salloc (xc, naps, TY_REAL)
+	call salloc (lost, naps, TY_INT)
+	call aclrr ( Memr[x], ntrace * naps)
+	data = NULL
+
+	# Set the dispersion lines to be traced.
+
+	do i = 1, ntrace
+	    Memr[y+i-1] = start + (i - istart) * step
+
+	# Trace from the starting line to the last line.
+
+	x1 = x + istart - 1
+	do i = 1, naps {
+	    if (AP_SELECT(aps[i]) == NO)
+		next
+	    Memr[xc+i-1] = AP_CEN(aps[i], 1) +
+		ap_cveval (AP_CV(aps[i]), real (start))
+	    Memi[lost+i-1] =  0
+	}
+
+	do i = istart, ntrace {
+	    line = Memr[y+i-1]
+	    line1 = max (1, line - nsum / 2)
+	    line2 = min (ny, line1 + nsum - 1)
+	    line1 = max (1, line2 - nsum + 1)
+
+	    # If the sums overlap use buffering.
+
+	    if (step < nsum)
+	        call xt_lsumb (im, 1, nx, line1, line2, data)
+	    else
+	        call xt_lsum (im, 1, nx, line1, line2, data)
+
+	    do j = 1, naps {
+		if (AP_SELECT(aps[j]) == NO)
+		    next
+		x2 = x1 + (j - 1) * ntrace
+		Memr[x2] = INDEF
+		if (Memi[lost+j-1] < nlost) {
+		    xc1 = center1d (Memr[xc+j-1], Memr[data], nx,
+			cwidth, EMISSION, cradius, threshold)
+		    if (IS_INDEF(xc1)) {
+			Memi[lost+j-1] = Memi[lost+j-1] + 1
+			call sprintf (Memc[str], SZ_LINE,
+			"TRACE - Trace of aperture %d in %s lost at line %d.")
+			    call pargi (AP_ID(aps[j]))
+			    call pargstr (image)
+			    call pargi (line)
+			call ap_log (Memc[str], YES, NO, YES)
+		    } else {
+			Memi[lost+j-1] = 0
+			Memr[xc+j-1] = xc1
+			Memr[x2] = xc1
+			if (IS_INDEF (Memr[x2-1])) {
+			    call sprintf (Memc[str], SZ_LINE,
+		    "TRACE - Trace of aperture %d in %s recovered at line %d.")
+				call pargi (AP_ID(aps[j]))
+				call pargstr (image)
+				call pargi (line)
+			    call ap_log (Memc[str], YES, NO, YES)
+			}
+		    }
+		}
+	    }
+	    x1 = x1 + 1
+	}
+
+	# Trace from the starting line to the first line.
+
+	x1 = x + istart - 2
+	do i = 1, naps {
+	    if (AP_SELECT(aps[i]) == NO)
+		next
+	    Memr[xc+i-1] = AP_CEN(aps[i], 1) +
+		ap_cveval (AP_CV(aps[i]), real (start))
+	    Memi[lost+i-1] = 0
+	}
+
+	do i = istart - 1, 1, -1 {
+	    line = Memr[y+i-1]
+	    line1 = max (1, line - nsum / 2)
+	    line2 = min (ny, line1 + nsum - 1)
+	    line1 = max (1, line2 - nsum + 1)
+
+	    # If the sums overlap use buffering.
+
+	    if (step < nsum)
+	        call xt_lsumb (im, 1, nx, line1, line2, data)
+	    else
+	        call xt_lsum (im, 1, nx, line1, line2, data)
+
+	    do j = 1, naps {
+		if (AP_SELECT(aps[j]) == NO)
+		    next
+		x2 = x1 + (j - 1) * ntrace
+		Memr[x2] = INDEF
+		if (Memi[lost+j-1] < nlost) {
+		    xc1 = center1d (Memr[xc+j-1], Memr[data], nx,
+			cwidth, EMISSION, cradius, threshold)
+		    if (IS_INDEF(xc1)) {
+			Memi[lost+j-1] = Memi[lost+j-1] + 1
+			call sprintf (Memc[str], SZ_LINE,
+			    "TRACE - Trace of aperture %d in %s lost at line %d.")
+			    call pargi (AP_ID(aps[j]))
+			    call pargstr (image)
+			    call pargi (line)
+			call ap_log (Memc[str], YES, NO, YES)
+		    } else {
+			Memi[lost+j-1] = 0
+			Memr[xc+j-1] = xc1
+			Memr[x2] = xc1
+			if (IS_INDEF (Memr[x2+1])) {
+			    call sprintf (Memc[str], SZ_LINE,
+		    "TRACE - Trace of aperture %d in %s recovered at line %d.")
+				call pargi (AP_ID(aps[j]))
+				call pargstr (image)
+				call pargi (line)
+			    call ap_log (Memc[str], YES, NO, YES)
+			}
+		    }
+		}
+	    }
+	    x1 = x1 - 1
+	}
+
+	# Initialize the the GTOOLS parameters.
+	call ic_putr (ic, "xmin", 1.)
+	call ic_putr (ic, "xmax", real (ny))
+	call ic_pstr (ic, "xlabel", "Line")
+	call ic_pstr (ic, "ylabel", "Column")
+
+	gt = gt_init()
+	call gt_setr (gt, GTXMIN, 1. - step / 2)
+	call gt_setr (gt, GTXMAX, real (ny + step / 2))
+
+	do j = 1, naps {
+	    if (AP_SELECT(aps[j]) == NO)
+		next
+
+	    # Order the traced points and exclude INDEF positions.
+
+	    x1 = x + (j - 1) * ntrace
+	    n = 0
+
+	    do i = 1, ntrace {
+		if (IS_INDEF (Memr[x1+i-1]))
+		    next
+		n = n + 1
+		Memr[x1+n-1] = Memr[x1+i-1]
+		Memr[y+n-1] = start + (i - istart) * step
+		Memr[wts+n-1] = 1.
+	    }
+
+	    # If all positions are INDEF print a message and go on to the next
+	    # aperture.
+
+	    if (n < 2) {
+		call eprintf (
+		    "Not enough points traced for aperture %d of %s\n")
+		    call pargi (AP_ID(aps[j]))
+		    call pargstr (image)
+		next
+	    }
+
+	    # Fit a curve to the traced positions and graph the result.
+
+	    call sprintf (Memc[str], SZ_LINE, "Aperture %d of %s")
+	        call pargi (AP_ID(aps[j]))
+		call pargstr (image)
+	    call gt_sets (gt, GTTITLE, Memc[str])
+
+	    call sprintf (Memc[str], SZ_LINE,
+		"Fit curve to aperture %d of %s interactively")
+		call pargi (AP_ID(aps[j]))
+		call pargstr (image)
+	    if (ap_answer ("ansfittrace1", Memc[str])) {
+		call ap_gopen (gp)
+	        call icg_fit (ic, gp, "gcur", gt,
+		    AP_CV(aps[j]), Memr[y], Memr[x1], Memr[wts], n)
+	    } else
+	        call ic_fit (ic, AP_CV(aps[j]), Memr[y], Memr[x1], Memr[wts], n,
+		    YES, YES, YES, YES)
+
+	    call ap_popen (gp, fd, "trace")
+	    if (gp != NULL) {
+		call icg_graphr (ic, gp, gt, AP_CV(aps[j]),
+		    Memr[y], Memr[x1], Memr[wts], n)
+		call ap_pclose (gp, fd)
+	    }
+
+	    # Subtract the aperture center and refit offset curve.
+	    call asubkr (Memr[x1], AP_CEN(aps[j], 1), Memr[x1], n)
+	    call ic_fit (ic, AP_CV(aps[j]), Memr[y], Memr[x1], Memr[wts], n,
+		YES, YES, YES, YES)
+	}
+
+	# Free allocated memory.
+
+	call gt_free (gt)
+	call mfree (data, TY_REAL)
+	call sfree (sp)
+end
diff --git a/noao/twodspec/apextract/apupdate.x b/noao/twodspec/apextract/apupdate.x
new file mode 100644
index 00000000..d3344b5f
--- /dev/null
+++ b/noao/twodspec/apextract/apupdate.x
@@ -0,0 +1,44 @@
+include <gset.h>
+include	"apertures.h"
+
+# AP_UPDATE -- Update an aperture.
+
+procedure ap_update (gp, ap, line, apid, apbeam, center, low, high)
+
+pointer	gp		# GIO pointer
+pointer	ap		# Aperture pointer
+int	line		# Dispersion line
+int	apid		# New aperture ID
+int	apbeam		# New aperture beam
+real	center		# New center at dispersion line
+real	low		# New lower limit
+real	high		# New upper limit
+
+real	ap_cveval(), ic_getr()
+
+begin
+	# Check for bad values.
+	if (IS_INDEFR(center) || IS_INDEFR(low) || IS_INDEFR(high))
+	    call error (1, "INDEF not allowed")
+
+	# Erase the current aperture.
+	call gseti (gp, G_PLTYPE, 0)
+	call ap_gmark (gp, line, ap, 1)
+
+	# Update the aperture.
+	AP_ID(ap) = apid
+	AP_BEAM(ap) = apbeam
+	AP_CEN(ap, AP_AXIS(ap)) = center - ap_cveval (AP_CV(ap), real (line))
+        AP_LOW(ap, AP_AXIS(ap)) = min (low, high)
+        AP_HIGH(ap, AP_AXIS(ap)) = max (low, high)
+	if (AP_IC(ap) != NULL) {
+	    call ic_putr (AP_IC(ap), "xmin",
+		min (low, high, ic_getr (AP_IC(ap), "xmin")))
+	    call ic_putr (AP_IC(ap), "xmax",
+		max (low, high, ic_getr (AP_IC(ap), "xmax")))
+	}
+
+	# Mark the new aperture.
+	call gseti (gp, G_PLTYPE, 1)
+	call ap_gmark (gp, line, ap, 1)
+end
diff --git a/noao/twodspec/apextract/apvalues.x b/noao/twodspec/apextract/apvalues.x
new file mode 100644
index 00000000..2072907e
--- /dev/null
+++ b/noao/twodspec/apextract/apvalues.x
@@ -0,0 +1,32 @@
+include	"apertures.h"
+
+# AP_VALUES -- Return the values for an aperture
+
+procedure ap_values (current, aps, line, apid, apbeam, center, low, high)
+
+int	current			# Index to current aperture
+pointer	aps[ARB]		# Apertures
+int	line			# Line
+int	apid			# Aperture ID
+int	apbeam			# Aperture beam
+real	center			# Aperture center
+real	low			# Lower limit of aperture
+real	high			# Upper limit of aperture
+
+int	apaxis
+pointer	ap
+
+real	ap_cveval()
+
+begin
+	if (current > 0) {
+	    ap = aps[current]
+	    apaxis = AP_AXIS(ap)
+
+	    apid = AP_ID(ap)
+	    apbeam = AP_BEAM(ap)
+	    center = AP_CEN(ap, apaxis) + ap_cveval (AP_CV(ap), real (line))
+	    low = AP_LOW(ap, apaxis)
+	    high = AP_HIGH(ap, apaxis)
+	}
+end
diff --git a/noao/twodspec/apextract/apvariance.x b/noao/twodspec/apextract/apvariance.x
new file mode 100644
index 00000000..015eed74
--- /dev/null
+++ b/noao/twodspec/apextract/apvariance.x
@@ -0,0 +1,420 @@
+include	<gset.h>
+include	"apertures.h"
+
+
+# AP_VARIANCE -- Variance weighted extraction based on profile and CCD noise.
+# If desired reject deviant pixels.  In addition to the variance weighted
+# spectrum, the unweighted and uncleaned "raw" spectrum is extracted and
+# a sigma spectrum is returned.  Wavelengths with saturated pixels are
+# flagged with 0 value and negative sigma if cleaning.
+
+procedure ap_variance (im, ap, dbuf, nc, nl, c1, l1, sbuf, svar, profile,
+	nx, ny, xs, ys, spec, raw, specsig, nsubaps, asi)
+
+pointer	im			# IMIO pointer
+pointer	ap			# Aperture structure
+pointer	dbuf			# Data buffer
+int	nc, nl			# Size of data buffer
+int	c1, l1			# Origin of data buffer
+pointer	sbuf			# Sky values (NULL if none)
+pointer	svar			# Sky variance
+real	profile[ny,nx]		# Profile (returned)
+int	nx, ny			# Size of profile array
+int	xs[ny], ys		# Origin of profile array
+real	spec[ny,nsubaps]	# Spectrum
+real	raw[ny,nsubaps]		# Raw spectrum
+real	specsig[ny,nsubaps]	# Sky variance in, spectrum sigma out
+int	nsubaps			# Number of subapertures
+pointer	asi			# Image interpolator for edge pixel weighting
+
+real	rdnoise			# Readout noise in RMS data numbers.
+real	gain			# Gain in photons per data number.
+real	saturation		# Maximum value for an unsaturated pixel.
+bool	clean			# Clean cosmic rays?
+real	nclean			# Number of pixels to clean
+real	lsigma, usigma		# Rejection sigmas.
+
+bool	sat
+int	fd, iterate, niterate, nrej, irej, nreject
+int	i, ix, iy, ix1, ix2
+real	low, high, step, shift, x1, x2, wt1, wt2, s, w, dat, sk, var, var0
+real	sum, wsum, wvsum, sum1, sum2, total1, total2
+real	vmin, resid, rrej
+pointer	cv, gp
+pointer	sp, str, work, wt, xplot, yplot, eplot, fplot, data, sky, data1
+
+real	apgetr(), apgimr(), ap_cveval()
+bool	apgetb()
+errchk	apgimr, ap_asifit
+
+begin
+	# Get task parameters.
+	gain = apgimr ("gain", im)
+	rdnoise = apgimr ("readnoise", im) ** 2
+	saturation = apgetr ("saturation")
+	if (!IS_INDEF(saturation))
+	    saturation = saturation * gain
+	clean = apgetb ("clean")
+	lsigma = apgetr ("lsigma")
+	usigma = apgetr ("usigma")
+	call ap_popen (gp, fd, "clean")
+
+	# Allocate memory and one index.
+	call smark (sp)
+	call salloc (str, SZ_LINE, TY_CHAR)
+	call salloc (work, 6*nx, TY_REAL)
+	wt = work - 1
+	xplot = wt + nx
+	yplot = xplot + nx
+	eplot = yplot + nx
+	fplot = eplot + nx
+	data1 = fplot + nx
+	if (sbuf == NULL) {
+	    call salloc (sky, nx, TY_REAL)
+	    call aclrr (Memr[sky], nx)
+	    sky = sky - 1
+	    var0 = rdnoise
+	}
+
+	# Initialize
+	if (rdnoise == 0.)
+	    vmin = 1.
+	else
+	    vmin = rdnoise
+	if (clean) {
+	    nclean = apgetr ("nclean")
+	    if (nclean < 1.)
+	        niterate = max (1., nclean * nx)
+	    else
+		niterate = max (1., min (real (nx), nclean))
+	} else
+	    niterate = 0
+
+	call aclrr (spec, ny * nsubaps)
+	call aclrr (raw, ny * nsubaps)
+	call amovkr (-1., specsig, ny * nsubaps)
+
+	i = AP_AXIS(ap)
+	low = AP_CEN(ap,i) + AP_LOW(ap,i)
+	high = AP_CEN(ap,i) + AP_HIGH(ap,i)
+	step = (high - low) / nsubaps
+	cv = AP_CV(ap)
+
+	# For each line compute the weighted spectrum and then iterate
+	# to reject deviant pixels.  Rejected pixels are flagged by negative
+	# variance.
+
+	nreject = 0
+	total1 = 0.
+	total2 = 0.
+	do iy = 1, ny {
+	    shift = ap_cveval (cv, real (iy + ys - 1)) - c1 + 1
+	    x1 = max (0.5, low + shift) + c1 - xs[iy]
+	    x2 = min (nc + 0.49, high + shift) + c1 - xs[iy]
+	    if (x1 >= x2)
+		next
+	    ix1 = nint (x1)
+	    ix2 = nint (x2)
+
+	    call ap_asifit (dbuf+(iy+ys-1-l1)*nc, nc, xs[iy]-c1+1,
+		low+shift, high+shift, data, asi)
+#	    data = dbuf + (iy + ys - 1 - l1) * nc + xs[iy] - c1 - 1
+	    if (sbuf != NULL) {
+		sky = sbuf + (iy - 1) * nx - 1
+		var0 = rdnoise + Memr[svar+iy-1]
+	    }
+
+	    # Set pixel weights for summing.
+#	    if (asi != NULL)
+#		call asifit (asi, Memr[data], nc-xs[iy]+c1)
+	    call ap_edge (asi, x1+1, x2+1, wt1, wt2)
+
+	    # First estimate spectrum by summing across the aperture.
+	    # Accumulate the raw spectrum and set up various arrays for
+	    # plotting and later access.
+
+	    sat = false
+	    sum = 0.
+	    wsum = 0.
+	    wvsum = 0.
+	    do ix = ix1, ix2 {
+		if (ix1 == ix2)
+		    w = wt1
+		else if (ix == ix1)
+		    w = wt1
+		else if (ix == ix2)
+		    w = wt2
+		else
+		    w = 1.
+		dat = Memr[data+ix]
+		if (!IS_INDEF(saturation))
+		    if (dat > saturation)
+			sat = true
+		sk = Memr[sky+ix]
+		raw[iy,1] = raw[iy,1] + w * (dat - sk)
+
+	        Memr[xplot+ix] = ix + xs[iy] - 1
+	        Memr[yplot+ix] = dat - sk
+		Memr[data1+ix] = dat - sk
+		Memr[wt+ix] = w
+		var = max (vmin, var0 + max (0., dat))
+		w = profile[iy,ix] / var
+		var = sqrt (var)
+		Memr[eplot+ix] = var
+		sum = sum + w * (dat - sk)
+		wsum = wsum + w * profile[iy,ix]
+		wvsum = wvsum + (w * var) ** 2
+	    }
+	    if (wsum > 0.) {
+	        spec[iy,1] = sum / wsum
+	        specsig[iy,1] = sqrt (wvsum) / abs (wsum)
+	    } else {
+	        spec[iy,1] = 0.
+	        specsig[iy,1] = -1.
+	    }
+
+	    sum = 0.
+	    wsum = 0.
+	    wvsum = 0.
+	    sum1 = 0.
+	    sum2 = 0.
+	    do ix = ix1, ix2 {
+		sum1 = sum1 + Memr[wt+ix] * Memr[data1+ix]
+		if (Memr[eplot+ix] <= 0.)
+		    next
+		sk = Memr[sky+ix]
+	        s = max (0., spec[iy,1]) * profile[iy,ix]
+	        var = max (vmin, var0 + (s + sk))
+	        w = profile[iy,ix] / var
+		var = sqrt (var)
+	        Memr[eplot+ix] = var
+	        Memr[fplot+ix] = s
+	        sum = sum + w * Memr[data1+ix]
+	        wsum = wsum + w * profile[iy,ix]
+	        wvsum = wvsum + (w * var) ** 2
+	    }
+	    if (wsum > 0.) {
+	        spec[iy,1] = sum / wsum
+	        specsig[iy,1] = sqrt (wvsum) / abs (wsum)
+		sum2 = sum2 + spec[iy,1]
+	    } else {
+	         spec[iy,1] = 0.
+	         specsig[iy,1] = -1.
+		 sum1 = 0.
+		 sum2 = 0.
+	    }
+
+	    # Reject cosmic rays one at a time.
+	    nrej = 0
+	    do iterate = 1, niterate {
+	        irej = 0
+	        rrej = 0.
+
+		# Compute revised variance estimate using profile model 
+		# skip rejected pixels, find worst pixel.
+
+	        do ix = ix1, ix2 {
+	            if (Memr[eplot+ix] <= 0.)
+			next
+	            s = max (0., spec[iy,1]) * profile[iy,ix]
+		    sk = Memr[sky+ix]
+	            var = sqrt (max (vmin, var0 + max (0., s + sk)))
+	            Memr[fplot+ix] = s
+	            Memr[eplot+ix] = var
+
+		    resid = (Memr[data1+ix] - Memr[fplot+ix]) / var
+		    if (abs (resid) > abs (rrej)) {
+			rrej = resid
+			irej = ix
+	            }
+	        }
+
+		# Reject worst outlier.
+
+	        if (rrej <= -lsigma || rrej >= usigma) {
+	            Memr[eplot+irej] = -Memr[eplot+irej]
+		    Memr[data1+irej] = Memr[fplot+irej]
+	            nrej = nrej + 1
+	        } else
+		    break
+
+		# Update spectrum estimate excluding rejected pixels.
+	        sum = 0.
+	        wsum = 0.
+	        wvsum = 0.
+		sum1 = 0.
+		sum2 = 0.
+	        do ix = ix1, ix2 {
+		    sum1 = sum1 + Memr[wt+ix] * Memr[data1+ix]
+	            if (Memr[eplot+ix] <= 0.)
+			next
+	            w = profile[iy,ix] / Memr[eplot+ix]**2
+	            sum = sum + w * Memr[data1+ix]
+	            wsum = wsum + w * profile[iy,ix]
+	            wvsum = wvsum + (w * Memr[eplot+ix]) ** 2
+	        }
+
+	        if (wsum > 0.) {
+	            spec[iy,1] = sum / wsum
+	            specsig[iy,1] = sqrt (wvsum) / abs (wsum)
+		    sum2 = sum2 + spec[iy,1]
+	        } else {
+	            spec[iy,1] = 0.
+	            specsig[iy,1] = -1.
+		    sum1 = 0.
+		    sum2 = 0.
+	        }
+	    }
+
+	    nreject = nreject + nrej
+	    total1 = total1 + sum1
+	    total2 = total2 + sum2
+
+	    # Calculate subapertures if desired.
+	    if (nsubaps > 1) {
+		do i = 1, nsubaps {
+		    x1 = max (0.5, low + (i - 1) * step + shift) + c1 - xs[iy]
+		    x2 = min (nc + 0.49, low + i * step + shift) + c1 - xs[iy]
+		    if (x1 >= x2) {
+			spec[iy,i] = 0.
+			raw[iy,i] = 0.
+			specsig[iy,i] = -1.
+			next
+		    }
+		    ix1 = nint (x1)
+		    ix2 = nint (x2)
+		    call ap_edge (asi, x1+1, x2+1, wt1, wt2)
+
+	            sum = 0.
+	            wvsum = 0.
+		    raw[iy,i] = 0.
+	            do ix = ix1, ix2 {
+			if (ix1 == ix2)
+			    w = wt1
+			else if (ix == ix1)
+			    w = wt1
+			else if (ix == ix2)
+			    w = wt2
+			else
+			    w = 1.
+			raw[iy,i] = raw[iy,i] + w * Memr[yplot+ix]
+	                if (Memr[eplot+ix] <= 0.)
+			    next
+	                w = profile[iy,ix] / Memr[eplot+ix]**2
+	                sum = sum + w * Memr[data1+ix]
+	                wvsum = wvsum + (w * Memr[eplot+ix]) ** 2
+	            }
+
+	            if (wsum > 0.) {
+	                spec[iy,i] = sum / wsum
+	                specsig[iy,i] = sqrt (wvsum) / abs (wsum)
+	            } else {
+	                spec[iy,i] = 0.
+	                specsig[iy,i] = -1.
+	            }
+		}
+	    }
+
+	    # Flag points with saturated pixels.
+	    if (sat)
+	        do i = 1, nsubaps
+		    specsig[iy,i] = -specsig[iy,i]
+
+	    # Plot profile with cosmic rays if desired.
+	    if (gp != NULL && nrej > 0 && spec[iy,1] > 0.) {
+		call sprintf (Memc[str], SZ_LINE, "Profile %4d")
+		    call pargi (iy)
+		s = Memr[yplot+ix1] - abs (Memr[eplot+ix1])
+		w = Memr[yplot+ix1] + abs (Memr[eplot+ix1])
+		do ix = ix1+1, ix2 {
+		    s = min (s, Memr[yplot+ix] - abs (Memr[eplot+ix]))
+		    w = max (w, Memr[yplot+ix] + abs (Memr[eplot+ix]))
+		}
+		sum = w - s
+		x1 = ix1 + xs[iy] - 2
+		x2 = ix2 + xs[iy]
+		s = s - 0.1 * sum
+		w = w + 0.1 * sum
+		call gclear (gp)
+		call gswind (gp, x1, x2, s, w)
+		call glabax (gp, Memc[str], "", "")
+
+	        do ix = ix1, ix2 {
+	            if (Memr[eplot+ix] > 0.) {
+			call gmark (gp, Memr[xplot+ix], Memr[yplot+ix],
+			    GM_PLUS, 2., 2.)
+			call gmark (gp, Memr[xplot+ix], Memr[yplot+ix],
+			    GM_VEBAR, 2., -6.*Memr[eplot+ix])
+	            } else {
+			call gmark (gp, Memr[xplot+ix], Memr[yplot+ix],
+			    GM_CROSS, 2., 2.)
+			call gmark (gp, Memr[xplot+ix], Memr[yplot+ix],
+			    GM_VEBAR, 1., 6.*Memr[eplot+ix])
+	            }
+	        }
+		call gpline (gp, Memr[xplot+ix1], Memr[fplot+ix1], ix2-ix1+1)
+	    }
+	}
+
+	# To avoid any bias, scale weighted extraction to same total flux
+	# as raw spectrum (with rejected pixels replaced by fit).
+
+	if (total1 * total2 <= 0.) {
+	    call sprintf (Memc[str], SZ_LINE,
+		"EXTRACT: WARNING - Aperture %d:")
+		call pargi (AP_ID(ap))
+	    call ap_log (Memc[str], YES, NO, YES)
+	    call sprintf (Memc[str], SZ_LINE,
+		"   Total variance weighted spectrum flux is %g")
+		call pargr (total2)
+	    call ap_log (Memc[str], YES, NO, YES)
+	    call sprintf (Memc[str], SZ_LINE,
+		"   Total unweighted spectrum flux is %g")
+		call pargr (total1)
+	    call ap_log (Memc[str], YES, NO, YES)
+	    call sprintf (Memc[str], SZ_LINE,
+		"   Variance spectrum bias factor ignored")
+	    call ap_log (Memc[str], YES, NO, YES)
+	} else {
+	    sum = total1 / total2
+	    call amulkr (spec, sum, spec, ny * nsubaps)
+	    call amulkr (specsig, sum, specsig, ny * nsubaps)
+	    if (sum < .5 || sum > 2) {
+		call sprintf (Memc[str], SZ_LINE,
+		    "EXTRACT: WARNING - Aperture %d:")
+		    call pargi (AP_ID(ap))
+		call ap_log (Memc[str], YES, NO, YES)
+		call sprintf (Memc[str], SZ_LINE,
+		    "   Total variance weighted spectrum flux is %g")
+		    call pargr (total2)
+		call ap_log (Memc[str], YES, NO, YES)
+		call sprintf (Memc[str], SZ_LINE,
+		    "   Total unweighted spectrum flux is %g")
+		    call pargr (total1)
+		call ap_log (Memc[str], YES, NO, YES)
+		call sprintf (Memc[str], SZ_LINE,
+		    "EXTRACT: Aperture %d variance spectrum bias factor is %g")
+		    call pargi (AP_ID(ap))
+		    call pargr (total1 / total2)
+		call ap_log (Memc[str], YES, NO, YES)
+	    } else {
+		call sprintf (Memc[str], SZ_LINE,
+		    "EXTRACT: Aperture %d variance spectrum bias factor is %g")
+		    call pargi (AP_ID(ap))
+		    call pargr (total1 / total2)
+		call ap_log (Memc[str], YES, NO, NO)
+	    }
+	}
+
+	# Log the number of rejected pixels.
+	if (clean) {
+	    call sprintf (Memc[str], SZ_LINE,
+		"EXTRACT: %d pixels rejected from aperture %d")
+		call pargi (nreject)
+		call pargi (AP_ID(ap))
+	    call ap_log (Memc[str], YES, NO, NO)
+	}
+
+	call ap_pclose (gp, fd)
+	call sfree (sp)
+end
diff --git a/noao/twodspec/apextract/apwidth.cl b/noao/twodspec/apextract/apwidth.cl
new file mode 100644
index 00000000..94a247d7
--- /dev/null
+++ b/noao/twodspec/apextract/apwidth.cl
@@ -0,0 +1,59 @@
+# APWIDTH -- Script to report widths from APALL database files.
+# The input is the image name and database directory.
+# The output is image name, aperture number, x center, y center, and width.
+#
+# To install this script copy it to a directory, such as your IRAF login
+# directory "home$" in this example.  Define the task in your loginuser.cl
+# or login.cl with
+#
+#    task apwidth = home$apwidth.cl
+#
+# Note that you can substitute some other path to the script if desired.
+
+procedure apwidth (image)
+
+file	image			{prompt="Image name"}
+file	database = "database"	{prompt="Database"}
+
+begin
+	file	dbfile
+	string	im
+	int	ap, axis
+	real	xc, yc, aplow1, aphigh1, aplow2, aphigh2, width
+
+	# Form database name from the database and image names.
+	dbfile = database // "/ap" // image
+
+	# Check that the database file actually exists.
+	if (!access(dbfile))
+	    error (1, "Databse file not found (" // dbfile // ")")
+
+	# Loop through each line of the database file.  Extract information
+	# and print the output line when the axis keyword is found.  This
+	# assumes the aperture limits are read before the axis.
+
+	axis = INDEF
+	list = dbfile
+	while (fscan (list, line) != EOF) {
+	    if (fscan (line, s1) < 1)
+		next
+	    if (s1 == "begin")
+		i = fscan (line, s1, s1, im, ap, xc, yc)
+	    else if (s1 == "low")
+		i = fscan (line, s1, aplow1, aplow2)
+	    else if (s1 == "high")
+		i = fscan (line, s1, aphigh1, aphigh2)
+	    else if (s1 == "axis")
+		i = fscan (line, s1, axis)
+
+	    if (axis != INDEF) {
+		if (axis == 1)
+		    width = aphigh1 - aplow1
+		else
+		    width = aphigh2 - aplow2
+		printf ("%s %2d %8.4g %8.4g %8.4g\n", im, ap, xc, yc, width)
+		axis = INDEF
+	    }
+	}
+	list = ""
+end
diff --git a/noao/twodspec/apextract/apylevel.x b/noao/twodspec/apextract/apylevel.x
new file mode 100644
index 00000000..aa208453
--- /dev/null
+++ b/noao/twodspec/apextract/apylevel.x
@@ -0,0 +1,103 @@
+# AP_YLEVEL -- Set the aperture to intercept the specified y level.
+
+procedure ap_ylevel (imdata, npts, ylevel, peak, bkg, grow, center, low, high)
+
+real	imdata[npts]		# Image data
+int	npts			# Number of image points
+real	ylevel			# Y value
+bool	peak			# Is y a fraction of peak?
+bool	bkg			# Subtract a background?
+real	grow			# Grow factor
+real	center			# Center of aperture
+real	low, high		# Equal flux points
+
+int	i1, i2, j1, j2, k1, k2
+real	y, y1, y2, a, b, ycut, x
+
+begin
+	if ((center < 1.) || (center >= npts) || IS_INDEF (ylevel))
+	    return
+
+	if (bkg) {
+	    i1 = nint (center) 
+	    i2 = max (1, nint (center + low))
+	    for (k1=i1; k1 > i2 && imdata[k1] <= imdata[k1-1]; k1=k1-1)
+		;
+	    for (; k1 > i2 && imdata[k1] >= imdata[k1-1]; k1=k1-1)
+		;
+	   
+	    i2 = min (npts, nint (center + high))
+	    for (k2=i1; k2 < i2 && imdata[k2] <= imdata[k2+1]; k2=k2+1)
+		;
+	    for (; k2 < i2 && imdata[k2] >= imdata[k2+1]; k2=k2+1)
+		;
+	   
+	    a = imdata[k1]
+	    b = (imdata[k2] - imdata[k1]) / (k2 - k1)
+	} else {
+	    k1 = center
+	    a = 0.
+	    b = 0.
+	}
+	    
+	i1 = center
+	i2 = i1 + 1
+	y1 = imdata[i1] - a - b * (i1 - k1)
+	y2 = imdata[i2] - a - b * (i2 - k1)
+	y = y1 * (i2 - center) + y2 * (center - i1)
+
+	if (peak)
+	    ycut = ylevel * y
+	else
+	    ycut = ylevel
+
+	if (y > ycut) {
+	    for (j1 = i1; j1 >= 1; j1 = j1 - 1) {
+		y1 = imdata[j1] - a - b * (j1 - k1)
+		if (y1 <= ycut)
+		    break
+	    }
+	    if (j1 >= 1) {
+	        j2 = j1 + 1
+		y2 = imdata[j2] - a - b * (j2 - k1)
+	        x = (ycut + y2 * j1 - y1 * j2) / (y2 - y1) - center
+	        low = max (low, (1.+grow)*x)
+	    }
+
+	    for (j2 = i2; j2 <= npts; j2 = j2 + 1) {
+		y2 = imdata[j2] - a - b * (j2 - k1)
+		if (y2 <= ycut)
+		    break
+	    }
+	    if (j2 <= npts) {
+	        j1 = j2 - 1
+		y1 = imdata[j1] - a - b * (j1 - k1)
+	        x = (ycut + y2*j1 - y1*j2) / (y2 - y1) - center
+	        high = min (high, (1.+grow)*x)
+	    }
+	} else {
+	    for (j1 = i1; j1 >= 1; j1 = j1 - 1) {
+		y1 = imdata[j1] - a - b * (j1 - k1)
+		if (y1 >= ycut)
+		    break
+	    }
+	    if (j1 >= 1) {
+	        j2 = j1 + 1
+		y2 = imdata[j2] - a - b * (j2 - k1)
+	        x = (ycut + y2 * j1 - y1 * j2) / (y2 - y1) - center
+	        low = max (low, (1.+grow)*x)
+	    }
+
+	    for (j2 = i2; j2 <= npts; j2 = j2 + 1) {
+		y2 = imdata[j2] - a - b * (j2 - k1)
+		if (y2 >= ycut)
+		    break
+	    }
+	    if (j2 <= npts) {
+	        j1 = j2 - 1
+		y1 = imdata[j1] - a - b * (j1 - k1)
+	        x = (ycut + y2*j1 - y1*j2) / (y2 - y1) - center
+	        high = min (high, (1.+grow)*x)
+	    }
+	}
+end
diff --git a/noao/twodspec/apextract/doc/apall.hlp b/noao/twodspec/apextract/doc/apall.hlp
new file mode 100644
index 00000000..c4e50072
--- /dev/null
+++ b/noao/twodspec/apextract/doc/apall.hlp
@@ -0,0 +1,557 @@
+.help apall Sep96 noao.twodspec.apextract
+.ih
+NAME
+apall -- Extract one dimensional sums across the apertures
+.ih
+USAGE
+apall input
+.ih
+PARAMETERS
+.ls input
+List of input images.
+.le
+.ls output = ""
+List of output root names for extracted spectra.  If the null
+string is given or the end of the output list is reached before the end
+of the input list then the input image name is used as the output root name.
+This will not conflict with the input image since an aperture number
+extension is added for onedspec format, the extension ".ms" for multispec
+format, or the extension ".ec" for echelle format.
+.le
+.ls apertures = ""
+Apertures to recenter, resize, trace, and extract.  This only applies
+to apertures read from the input or reference database.  Any new
+apertures defined with the automatic finding algorithm or interactively
+are always selected.  The syntax is a list comma separated ranges
+where a range can be a single aperture number, a hyphen separated
+range of aperture numbers, or a range with a step specified by "x<step>";
+for example, "1,3-5,9-12x2".
+.le
+.ls format = "multispec" (onedspec|multispec|echelle|strip)
+Format for output extracted spectra.  "Onedspec" format extracts each
+aperture to a separate image while "multispec" and "echelle" extract
+multiple apertures for the same image to a single output image.
+The "multispec" and "echelle" format selections differ only in the
+extension added.  The "strip" format produces a separate 2D image in
+which each column or line along the dispersion axis is shifted to
+exactly align the aperture based on the trace information.
+.le
+.ls references = ""
+List of reference images to be used to define apertures for the input
+images.  When a reference image is given it supersedes apertures
+previously defined for the input image. The list may be null, "", or
+any number of images less than or equal to the list of input images.
+There are three special words which may be used in place of an image
+name.  The word "last" refers to the last set of apertures written to
+the database.  The word "OLD" requires that an entry exist
+and the word "NEW" requires that the entry not exist for each input image.
+Input images without/with a database entry are skipped silently.
+.le
+.ls profiles = ""
+List of profile images for variance weighting or cleanning.   If variance
+weighting or cleanning a profile of each aperture is computed from the
+input image unless a profile image is specified, in which case the
+profile is computed from the profile image.  The profile image must
+have the same dimensions and dispersion and it is assumed that the
+spectra have the same position and profile shape as in the object
+spectra.  Use of a profile image is generally not required even for
+faint input spectra but the option is available for those who wish
+to use it.
+.le
+
+.ce
+PROCESSING PARAMETERS
+.ls interactive = yes
+Run this task interactively?  If the task is not run interactively then
+all user queries are suppressed and interactive aperture editing, trace
+fitting, and extraction review are disabled.
+.le
+.ls find = yes
+Find the spectra and define apertures automatically?  In order for
+spectra to be found automatically there must be no apertures for the
+input image or reference image defined in the database.
+.le
+.ls recenter = yes
+Recenter the apertures?
+.le
+.ls resize = yes
+Resize the apertures?
+.le
+.ls edit = yes
+Edit the apertures?  The \fIinteractive\fR parameter must also be yes.
+.le
+.ls trace = yes
+Trace the apertures?
+.le
+.ls fittrace = yes
+Interactively fit the traced positions by a function?  The \fIinteractive\fR
+parameter must also be yes.
+.le
+.ls extract = yes
+Extract the one dimensional aperture sums?
+.le
+.ls extras = yes
+Extract the raw spectrum (if variance weighting is used), the sky spectrum
+(if background subtraction is used), and sigma spectrum (if variance
+weighting is used)?  This information is extracted to the third dimension
+of the output image.
+.le
+.ls review = yes
+Review the extracted spectra?  The \fIinteractive\fR parameter must also be
+yes.
+.le
+
+.ls line = INDEF, nsum = 10
+The dispersion line (line or column perpendicular to the dispersion
+axis) and number of adjacent lines (half before and half after unless
+at the end of the image) used in finding, recentering, resizing,
+and editing operations.  A line of INDEF selects the middle of the
+image along the dispersion axis.  A positive nsum selects a sum of
+lines and a negative selects a median of lines.
+.le
+
+.ce
+DEFAULT APERTURE PARAMETERS
+.ls lower = -5., upper = 5.
+Default lower and upper aperture limits relative to the aperture center.
+These limits are used for apertures found with \fBapfind\fR and when
+defining the first aperture in \fBapedit\fR.
+.le
+.ls apidtable = ""
+Aperture identification table.  This may be either a text file or an
+image.  A text file consisting of lines with an aperture number, beam
+number, 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.  This
+information is used to assign aperture information automatically in
+\fBapfind\fR and \fBapedit\fR.
+.le
+
+.ce
+DEFAULT BACKGROUND PARAMETERS
+.ls b_function = "chebyshev"
+Default background fitting function.  The fitting function types are
+"chebyshev" polynomial, "legendre" polynomial, "spline1" linear spline, and
+"spline3" cubic spline.
+.le
+.ls b_order = 1
+Default background function order.  The order refers to the number of
+terms in the polynomial functions or the number of spline pieces in the spline
+functions.
+.le
+.ls b_sample = "-10:-6,6:10"
+Default background sample.  The sample is given by a set of colon separated
+ranges each separated by either whitespace or commas.  The string "*" refers
+to all points.  Note that the background coordinates are relative to the
+aperture center and not image pixel coordinates so the endpoints need not
+be integer.
+.le
+.ls b_naverage = -3
+Default number of points to average or median.  Positive numbers
+average that number of sequential points to form a fitting point.
+Negative numbers median that number, in absolute value, of sequential
+points.  A value of 1 does no averaging and each data point is used in the
+fit.
+.le
+.ls b_niterate = 0
+Default number of rejection iterations.  If greater than zero the fit is
+used to detect deviant fitting points and reject them before repeating the
+fit.  The number of iterations of this process is given by this parameter.
+.le
+.ls b_low_reject = 3., b_high_reject = 3.
+Default background lower and upper rejection sigmas.  If greater than zero
+points deviating from the fit below and above the fit by more than this
+number of times the sigma of the residuals are rejected before refitting.
+.le
+.ls b_grow = 0.
+Default reject growing radius.  Points within a distance given by this
+parameter of any rejected point are also rejected.
+.le
+
+.ce
+APERTURE CENTERING PARAMETERS
+.ls width = 5.
+Width of spectrum profiles.  This parameter is used for the profile
+centering algorithm in this and other tasks.
+.le
+.ls radius = 10.
+The profile centering error radius for the centering algorithm.
+.le
+.ls threshold = 0.
+Centering threshold for the centering algorithm.  The range of pixel intensities
+near the initial centering position must exceed this threshold.
+.le
+
+.ce
+AUTOMATIC FINDING AND ORDERING PARAMETERS
+.ls nfind
+Maximum number of apertures to be defined.  This is a query parameter
+so the user is queried for a value except when given explicitly on
+the command line.
+.le
+.ls minsep = 5.
+Minimum separation between spectra.  Weaker spectra or noise within this
+distance of a stronger spectrum are rejected.
+.le
+.ls maxsep = 1000.
+Maximum separation between adjacent spectra.  This parameter
+is used to identify missing spectra in uniformly spaced spectra produced
+by fiber spectrographs.  If two adjacent spectra exceed this separation
+then it is assumed that a spectrum is missing and the aperture identification
+assignments will be adjusted accordingly.
+.le
+.ls order = "increasing"
+When assigning aperture identifications order the spectra "increasing"
+or "decreasing" with increasing pixel position (left-to-right or
+right-to-left in a cross-section plot of the image).
+.le
+
+.ce
+RECENTERING PARAMETERS
+.ls aprecenter = ""
+List of apertures to be used in shift calculation.
+.le
+.ls npeaks = INDEF
+Select the specified number of apertures with the highest peak values
+to be recentered.  If the number is INDEF all apertures will be selected.
+If the value is less than 1 then the value is interpreted as a fraction
+of total number of apertures.
+.le
+.ls shift = yes
+Use the average shift from recentering the apertures selected by the
+\fIaprecenter\fR parameter to apply to the apertures selected by the
+\fIapertures\fR parameter.  The recentering is then a constant shift for
+all apertures.
+.le
+
+.ce
+RESIZING PARAMETERS
+.ls llimit = INDEF, ulimit = INDEF
+Lower and upper aperture size limits.  If the parameter \fIylevel\fR is
+INDEF then these limits are assigned to all apertures.  Otherwise
+these parameters are used as limits to the resizing operation.
+A value of INDEF places the aperture limits at the image edge (for the
+dispersion line used).
+.le
+.ls ylevel = 0.1
+Data level at which to set aperture limits.  If it is INDEF then the
+aperture limits are set at the values given by the parameters
+\fIllimit\fR and \fIulimit\fR.  If it is not INDEF then it is a
+fraction of the peak or an actual data level depending on the parameter
+\fIpeak\fR.  It may be relative to a local background or to zero
+depending on the parameter \fIbkg\fR.
+.le
+.ls peak = yes
+Is the data level specified by \fIylevel\fR a fraction of the peak?
+.le
+.ls bkg = yes
+Subtract a simple background when interpreting the \fBylevel\fR parameter.
+The background is a slope connecting the first inflection points
+away from the aperture center.
+.le
+.ls r_grow = 0.
+Change the lower and upper aperture limits by this fractional amount.
+The factor is multiplied by each limit and the result added to limit.
+.le
+.ls avglimits = no
+Apply the average lower and upper aperture limits to all apertures.
+.le
+
+.ce
+TRACING PARAMETERS
+.ls t_nsum = 10
+Number of dispersion lines to be summed at each step along the dispersion.
+.le
+.ls t_step = 10
+Step along the dispersion axis between determination of the spectrum
+positions.
+.le
+.ls t_nlost = 3
+Number of consecutive steps in which the profile is lost before quitting
+the tracing in one direction.  To force tracing to continue through
+regions of very low signal this parameter can be made large.  Note,
+however, that noise may drag the trace away before it recovers.
+.le
+.ls t_function = "legendre"
+Default trace fitting function.  The fitting function types are
+"chebyshev" polynomial, "legendre" polynomial, "spline1" linear spline, and
+"spline3" cubic spline.
+.le
+.ls t_order = 2
+Default trace function order.  The order refers to the number of
+terms in the polynomial functions or the number of spline pieces in the spline
+functions.
+.le
+.ls t_sample = "*"
+Default fitting sample.  The sample is given by a set of colon separated
+ranges each separated by either whitespace or commas.  The string "*" refers
+to all points.
+.le
+.ls t_naverage = 1
+Default number of points to average or median.  Positive numbers
+average that number of sequential points to form a fitting point.
+Negative numbers median that number, in absolute value, of sequential
+points.  A value of 1 does no averaging and each data point is used in the
+.le
+.ls t_niterate = 0
+Default number of rejection iterations.  If greater than zero the fit is
+used to detect deviant traced positions and reject them before repeating the
+fit.  The number of iterations of this process is given by this parameter.
+.le
+.ls t_low_reject = 3., t_high_reject = 3.
+Default lower and upper rejection sigma.  If greater than zero traced
+points deviating from the fit below and above the fit by more than this
+number of times the sigma of the residuals are rejected before refitting.
+.le
+.ls t_grow = 0.
+Default reject growing radius.  Traced points within a distance given by this
+parameter of any rejected point are also rejected.
+.le
+
+.ce
+EXTRACTION PARAMETERS
+.ls background = "none" (none|average|median|minimum|fit)
+Type of background subtraction.  The choices are "none" for no background
+subtraction, "average" to average the background within the background
+regions, "median" to use the median in the background regions, "minimum" to
+use the minimum in the background regions, or "fit" to fit across the
+dispersion using the background within the background regions.  Note that
+the "average" option does not do any medianing or bad pixel checking,
+something which is recommended.  The fitting option is slower than the
+other options and requires additional fitting parameter.
+.le
+.ls skybox = 1
+Box car smoothing length for sky background when using background
+subtraction.  Since the background noise is often the limiting factor
+for good extraction one may box car smooth the sky to improve the
+statistics in smooth background regions at the expense of distorting
+the subtraction near spectral features.  This is most appropriate when
+the sky regions are limited due to a small slit length.
+.le
+.ls weights = "none" (none|variance)
+Type of extraction weighting.  Note that if the \fIclean\fR parameter is
+set then the weights used are "variance" regardless of the weights
+specified by this parameter.  The choices are:
+.ls "none"
+The pixels are summed without weights except for partial pixels at the
+ends.
+.le
+.ls "variance"
+The extraction is weighted by the variance based on the data values
+and a poisson/ccd model using the \fIgain\fR and \fIreadnoise\fR
+parameters.
+.le
+.le
+.ls pfit = "fit1d" (fit1d|fit2d)
+Profile fitting algorithm to use with variance weighting or cleaning.
+When determining a profile the two dimensional spectrum is divided by
+an estimate of the one dimensional spectrum to form a normalized two
+dimensional spectrum profile.  This profile is then smoothed by fitting
+one dimensional functions, "fit1d", along the lines or columns most closely
+corresponding to the dispersion axis or a special two dimensional
+function, "fit2d", described by Marsh (see \fBapprofile\fR).
+.le
+.ls clean = no
+Detect and replace deviant pixels?
+.le
+.ls saturation = INDEF
+Saturation or nonlinearity level in data units.  During variance weighted
+extractions wavelength points having any pixels above this value are
+excluded from the profile determination and the sigma spectrum extraction
+output, if selected by the \fIextras\fR parameter, flags wavelengths with
+saturated pixels with a negative sigma.
+.le
+.ls readnoise = 0.
+Read out noise in photons.  This parameter defines the minimum noise
+sigma.  It is defined in terms of photons (or electrons) and scales
+to the data values through the gain parameter.  A image header keyword
+(case insensitive) may be specified to get the value from the image.
+.le
+.ls gain = 1
+Detector gain or conversion factor between photons/electrons and
+data values.  It is specified as the number of photons per data value.
+A image header keyword (case insensitive) may be specified to get the value
+from the image.
+.le
+.ls lsigma = 4., usigma = 4.
+Lower and upper rejection thresholds, given as a number of times the
+estimated sigma of a pixel, for cleaning.
+.le
+.ls nsubaps = 1
+During extraction it is possible to equally divide the apertures into
+this number of subapertures.  For multispec format all subapertures will
+be in the same file with aperture numbers of 1000*(subap-1)+ap where
+subap is the subaperture (1 to nsubaps) and ap is the main aperture
+number.  For echelle format there will be a separate echelle format
+image containing the same subaperture from each order.  The name
+will have the subaperture number appended.  For onedspec format
+each subaperture will be in a separate file with extensions and
+aperture numbers as in the multispec format.
+.le
+.ih
+ADDITIONAL PARAMETERS
+Dispersion axis and I/O parameters are taken from the package parameters.
+.ih
+DESCRIPTION
+This task provides functions for defining, modifying, tracing, and
+extracting apertures from two dimensional spectra.  The functions
+desired are selected using switch parameters.  When the task is
+run interactively queries are made at each step allowing additional
+control of the operations performed on each input image.
+
+The functions, in the order in which they are generally performed, are
+summarized below.
+.ls o
+Automatically find a specified number of spectra and assign default
+apertures.  Apertures may also be inherited from another image or
+defined using an interactive graphical interface called the \fIaperture
+editor\fR.
+.le
+.ls o
+Recenter selected reference apertures on the image spectrum profiles.
+.le
+.ls o
+Resize the selected reference apertures based on spectrum profile width.
+.le
+.ls o
+Interactively define or adjust aperture definitions using a graphical
+interface called the \fIaperture editor\fR.  All function may also
+be performed from this editor and, so, provides an alternative
+method of processing and extracting spectra.
+.le
+.ls o
+Trace the positions of the selected spectra profiles from a starting image line
+or column to other image lines or columns and fit a smooth function.
+The trace function is used to shift the center of the apertures
+at each dispersion point in the image.
+.le
+.ls o
+Extract the flux in the selected apertures into one dimensional spectra in
+various formats.  This includes possible background subtraction, variance
+weighting, and bad pixel rejection.
+.le
+
+Each of these functions has different options and parameters.  In
+addition to selecting any of these functions in this task, they may
+also be selected using the aperture editor and as individual
+commands (which themselves allow selection of other functions).  When
+broken down into individual tasks the parameters are also sorted by
+their function though there are then some mutual parameter
+interdependencies.  This functional decomposition is what was available
+prior to the addition of the \fBapall\fR task.  It is recommended that
+this task be used because it collects all the parameters in one
+place eliminating confusion over where a particular parameter
+is defined.  However, documenting the various functions
+is better organized in terms of the separate descriptions given for
+each of the functions; namely under the help topics
+\fBapdefault, apfind, aprecenter, apresize, apedit,
+aptrace\fR, and \fBapsum\fR.
+.ih
+EXAMPLES
+1.  This example may be executed if desired.  First we create an artificial
+spectrum with four spectra and a background.  After it is created you
+can display or plot it.  Next we define the dispersion axis and set the
+verbose flag to better illustrate what is happening.  The task APALL
+is run with the default parameters except for background fitting and
+subtracting added.  The text beginning with # are comments of things to
+try and do.
+
+.nf
+  ap> artdata
+  ar> unlearn artdata
+  ar> mk1dspec apdemo1d nl=50
+  ar> mk2dspec apdemo2d model=STDIN
+  apdemo1d 1. gauss 3 0 20 .01
+  apdemo1d .8 gauss 3 0 40 .01
+  apdemo1d .6 gauss 3 0 60 .01
+  apdemo1d .4 gauss 3 0 80 .01
+  [EOF=Control D or Control Z]
+  ar> mknoise apdemo2d background=100. rdnoise=3. poisson+
+  ar> bye
+  # Display or plot the spectrum
+  ap> dispaxis=2; verbose=yes
+  ap> unlearn apall
+  ap> apall apdemo2d back=fit
+  Searching aperture database ...
+  Find apertures for apdemo2d?  (yes): 
+  Finding apertures ...
+  Number of apertures to be found automatically (1): 4
+  Jul 31 16:55: FIND - 4 apertures found for apdemo2d.
+  Resize apertures for apdemo2d?  (yes): 
+  Resizing apertures ...
+  Jul 31 16:55: RESIZE - 4 apertures resized for apdemo2d.
+  Edit apertures for apdemo2d?  (yes):
+  # Get a list of commands with '?'
+  # See all the parameters settings with :par
+  # Try deleting and marking a spectrum with 'd' and 'm'
+  # Look at the background fitting parameters with 'b' (exit with 'q')
+  # Exit with 'q'
+  Trace apertures for apdemo2d?  (yes): 
+  Fit traced positions for apdemo2d interactively?  (yes):
+  Tracing apertures ...
+  Fit curve to aperture 1 of apdemo2d interactively  (yes):
+  # You can use ICFIT commands to adjust the fit.
+  Fit curve to aperture 2 of apdemo2d interactively  (yes): n 
+  Fit curve to aperture 3 of apdemo2d interactively  (no): 
+  Fit curve to aperture 4 of apdemo2d interactively  (no): y 
+  Jul 31 16:56: TRACE - 4 apertures traced in apdemo2d.
+  Write apertures for apdemo2d to apdemosdb  (yes): 
+  Jul 31 16:56: DATABASE - 4 apertures for apdemo2d written to database.
+  Extract aperture spectra for apdemo2d?  (yes): 
+  Review extracted spectra from apdemo2d?  (yes):
+  Extracting apertures ...
+  Review extracted spectrum for aperture 1 from apdemo2d?  (yes):
+  # Type 'q' to quit
+  Jul 31 16:56: EXTRACT - Aperture 1 from apdemo2d --> apdemo2d.ms
+  Review extracted spectrum for aperture 2 from apdemo2d?  (yes): N
+  Jul 31 16:56: EXTRACT - Aperture 2 from apdemo2d --> apdemo2d.ms
+  Jul 31 16:56: EXTRACT - Aperture 3 from apdemo2d --> apdemo2d.ms
+  Jul 31 16:57: EXTRACT - Aperture 4 from apdemo2d --> apdemo2d.ms
+.fi
+
+2. To extract a series of similar spectra noninteractively using a
+reference for the aperture definitions, then recentering and resizing
+but not retracing:
+
+.nf
+  ap> apall fib*.imh ref=flat inter- trace-
+.fi
+
+Note that the interactive flag automatically turns off the edit, fittrace,
+and review options and the reference image eliminates the find
+(find only occurs if there are no initial apertures).
+.ih
+REVISIONS
+.ls APALL V2.11
+The "apertures" parameter can be used to select apertures for resizing,
+recentering, tracing, and extraction.  This parameter name was previously
+used for selecting apertures in the recentering algorithm.  The new
+parameter name for this is now "aprecenter".
+
+The aperture ID table information may now be contained in the
+image header under the keywords SLFIBnnn.
+
+The "nsubaps" parameter now allows onedspec and echelle output formats.
+The echelle format is appropriate for treating each subaperture as
+a full echelle extraction.
+.le
+.ls APALL V2.10.3
+The dispersion axis parameter was moved to purely a package parameter.
+
+As a final step when computing a weighted/cleaned spectrum the total
+fluxes from the weighted spectrum and the simple unweighted spectrum
+(excluding any deviant and saturated pixels) are computed and a
+"bias" factor of the ratio of the two fluxes is multiplied into
+the weighted spectrum and the sigma estimate.  This makes the total
+fluxes the same.  In this version the bias factor is recorded in the logfile
+if one is kept.  Also a check is made for unusual bias factors.
+If the two fluxes disagree by more than a factor of two a warning
+is given on the standard output and the logfile with the individual
+total fluxes as well as the bias factor.  If the bias factor is
+negative a warning is also given and no bias factor is applied.
+In the previous version a negative (inverted) spectrum would result.
+.le
+.ih
+SEE ALSO
+apdefault, apfind, aprecenter, apresize, apedit, aptrace, apsum
+.endhelp
diff --git a/noao/twodspec/apextract/doc/apbackground.hlp b/noao/twodspec/apextract/doc/apbackground.hlp
new file mode 100644
index 00000000..93a49e42
--- /dev/null
+++ b/noao/twodspec/apextract/doc/apbackground.hlp
@@ -0,0 +1,79 @@
+.help apbackground Aug90 noao.twodspec.apextract
+
+.ce
+Background Determination
+
+
+Data from slit spectra allow the determination and subtraction
+of the background sky using information from regions near the object
+of interest.  Background subtraction may also apply to cases of
+scattered light though other techniques for scattered light removal
+may be more appropriate.  The APEXTRACT package provides for determining
+the background level at each wavelength (line or column along the dispersion
+axis) from a set of regions and extrapolating and subtracting the
+background at each pixel extracted from the object profile.  The
+type of background used during extraction is specified by the parameter
+\fIbackground\fR.  If the value "none" is used then no background is
+subtracted and any background parameters defined for an aperture are
+ignored.  If the value is "average", "median", "minimum" or "fit" then a
+background is determined, including a variance estimate when using variance
+weighted extraction (see \fIapvariance\fR), and the subtracted background
+spectrum may be output if the \fIextras\fR parameter is set.
+
+The basic aperture definition structure used in the APEXTRACT package
+includes associated background regions and fitting parameters.  The
+background regions are specified by a list of colon delimited ranges
+defined relative to the center of the aperture.  There are generally
+two ranges, one on each side of the object, though one sided or more
+complex sets may be used to avoid contaminated or missing parts
+of the slit.  The default ranges are defined by the parameter
+\fIb_sample\fR.  Often the ranges are better set graphically using a
+cursor by invoking the 'b' option of the aperture editor.
+
+If the background type is "average", "median", or "minimum" then pixels
+occupying these regions are averaged, medianed, or the minimum found to
+produce a single background level for all object pixels at each wavelength.  
+Note that the "average" choice does not exclude any pixels which may
+yield a background contaminated by cosmic rays.  The "median" or "minimum"
+is recommended instead.
+
+If the background type is "fit" then a function is fit to the pixels in the
+background regions using the ICFIT options (see \fBicfit\fR).  The
+parameter \fIb_naverage\fR may be used to compute averages or medians of
+groups or all of the points within each sample region.  The fit is defined
+by a function type \fIb_function\fR; one of legendre polynomial, chebyshev
+polynomial, linear spline, or cubic spline, and function order
+\fIb_order\fR (number of polynomial terms or spline pieces).  An
+interactive rejection of grossly deviant points from the fit may also be
+used.  The fitted function can define a constant, sloped, or higher order
+background for the object pixels.
+
+Note that the background setting function, the 'b' key in \fBapedit\fR,
+may be used to set the background regions for all the background options
+but it will always show the result of a fit regardless of the background
+type.
+
+After determining a background by averaging, medianing, minimizing, or
+fitting, a box car smoothing step may be applied.  The box car size is
+given by the parameter \fIskybox\fR.  When the number of available
+background pixels is small, due to a small slit for instance, the noise
+introduced to the extracted object spectrum may be unsatisfactorily large.
+By smoothing the background one can reduce the noise when the background
+consists of a smooth continuum.  The trade-off, however, is that near sharp
+features the smoothing will smear the features out and give a poorer
+subtraction of these features.  One could extract both the object and
+background separately and apply a background smoothing separately using
+other image processing tools.  However, this is not possible for variance
+weighted extraction because of the intimate connection between the
+background levels, the profile determination, and the variance estimates
+based on both.  Thus, this smoothing feature is included.
+
+The background determined by the methods outlined above is actually
+subtracted as a separate step during extraction.  The background
+is also used during profile fitting when cleaning or using variance
+weighted extraction.  See \fBapvariance\fR and \fBapprofile\fR for
+further discussion.
+.ih
+SEE ALSO
+approfile apvariance apdefault icfit apall apsum
+.endhelp
diff --git a/noao/twodspec/apextract/doc/apdefault.hlp b/noao/twodspec/apextract/doc/apdefault.hlp
new file mode 100644
index 00000000..e17fe50d
--- /dev/null
+++ b/noao/twodspec/apextract/doc/apdefault.hlp
@@ -0,0 +1,95 @@
+.help apdefault Jul95 noao.twodspec.apextract
+.ih
+NAME
+apdefault -- Set default aperture parameters for the package
+.ih
+USAGE
+apdefault
+.ih
+PARAMETERS
+.ls lower = -5., upper = 5.
+Default lower and upper aperture limits relative to the aperture center.
+These limits are used for apertures found with \fBapfind\fR and when
+defining the first aperture in \fBapedit\fR.
+.le
+.ls apidtable = ""
+Aperture identification table.  This may be either a text file or an
+image.  A text file consisting of lines with an aperture number, beam
+number, 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.  This
+information is used to assign aperture information automatically in
+\fBapfind\fR and \fBapedit\fR.
+.le
+
+.ce
+Default Background Subtraction Parameters
+.ls b_function = "chebyshev"
+Default background fitting function.  The fitting function types are
+"chebyshev" polynomial, "legendre" polynomial, "spline1" linear spline, and
+"spline3" cubic spline.
+.le
+.ls b_order = 1
+Default background function order.  The order refers to the number of
+terms in the polynomial functions or the number of spline pieces in the spline
+functions.
+.le
+.ls b_sample = "-10:-6,6:10"
+Default background sample.  The sample is given by a set of colon separated
+ranges each separated by either whitespace or commas.  The string "*" refers
+to all points.  Note that the background coordinates are relative to the
+aperture center and not image pixel coordinates so the endpoints need not
+be integer.
+.le
+.ls b_naverage = -3
+Default number of points to average or median.  Positive numbers
+average that number of sequential points to form a fitting point.
+Negative numbers median that number, in absolute value, of sequential
+points.  A value of 1 does no averaging and each data point is used in the
+fit.
+.le
+.ls b_niterate = 0
+Default number of rejection iterations.  If greater than zero the fit is
+used to detect deviant fitting points and reject them before repeating the
+fit.  The number of iterations of this process is given by this parameter.
+.le
+.ls b_low_reject = 3., b_high_reject = 3.
+Default background lower and upper rejection sigmas.  If greater than zero
+points deviating from the fit below and above the fit by more than this
+number of times the sigma of the residuals are rejected before refitting.
+.le
+.ls b_grow = 0.
+Default reject growing radius.  Points within a distance given by this
+parameter of any rejected point are also rejected.
+.le
+.ih
+DESCRIPTION
+This task sets the values of the default aperture parameters for the
+tasks \fBapedit\fR and \fBapfind\fR which define new apertures.  For a
+description of the components of an aperture see the paper \fBThe
+APEXTRACT Package\fR.  In \fBapedit\fR the default aperture limits and
+background parameters are only used if there are no other
+apertures defined.  The aperture identification table is used when
+reordering the apertures with the 'o' key.  When run the parameters are
+displayed and modified using the \fBeparam\fR task.
+
+The aperture limits and background fitting sample regions are defined
+relative to the center of the aperture.  The background fitting parameters
+are those used by the ICFIT package.  They may be modified interactively
+with the 'b' key in the task \fBapedit\fR.  For more on background fitting
+and subtracting see \fBapbackground\fR.
+.ih
+EXAMPLES
+To review and modify the default aperture parameters:
+
+	cl> apdefault
+.ih
+.ih
+REVISIONS
+.ls APDEFAULT V2.11
+The aperture ID table information may now be contained in the
+image header under the keywords SLFIBnnn.
+.le
+SEE ALSO
+apbackground, apedit, apfind, icfit
+.endhelp
diff --git a/noao/twodspec/apextract/doc/apedit.hlp b/noao/twodspec/apextract/doc/apedit.hlp
new file mode 100644
index 00000000..324f6e5d
--- /dev/null
+++ b/noao/twodspec/apextract/doc/apedit.hlp
@@ -0,0 +1,374 @@
+.help apedit Sep96 noao.twodspec.apextract
+.ih
+NAME
+apedit -- Edit apertures
+.ih
+USAGE
+apedit input
+.ih
+PARAMETERS
+.ls input
+List of input images for which apertures are to be edited.
+.le
+.ls apertures = ""
+Apertures to recenter, resize, trace, and extract.  This only applies
+to apertures read from the input or reference database.  Any new
+apertures defined with the automatic finding algorithm or interactively
+are always selected.  The syntax is a list comma separated ranges
+where a range can be a single aperture number, a hyphen separated
+range of aperture numbers, or a range with a step specified by "x<step>";
+for example, "1,3-5,9-12x2".
+.le
+.ls references = ""
+List of reference images to be used to define apertures for the input
+images.  When a reference image is given it supersedes apertures
+previously defined for the input image. The list may be null, "", or
+any number of images less than or equal to the list of input images.
+If the reference image list is shorter than the input image list the
+last reference image is used for the remaining input images.
+There are three special words which may be used in place of an image
+name.  The word "last" refers to the last set of apertures written to
+the database.  The word "OLD" requires that an entry exist
+and the word "NEW" requires that the entry not exist for each input image.
+.le
+
+.ls interactive = no
+Run this task interactively?  If the task is not run interactively then
+all user queries are suppressed and interactive aperture editing is
+disabled.
+.le
+.ls find = no
+Find the spectra and define apertures automatically?  In order for
+spectra to be found automatically there must be no apertures for the
+input image or reference image defined in the database.
+.le
+.ls recenter = no
+Recenter the apertures?
+.le
+.ls resize = no
+Resize the apertures?
+.le
+.ls edit = yes
+Edit the apertures?  The \fIinteractive\fR parameter must also be yes.
+.le
+
+.ls line = INDEF
+The dispersion line (line or column perpendicular to the dispersion axis) to
+be graphed.  A value of INDEF uses the middle of the image.
+.le
+.ls nsum = 10
+Number of dispersion lines to be summed or medianed.  The lines are taken
+around the specified dispersion line.  A positive nsum selects a sum of
+lines and a negative selects a median of lines.
+.le
+.ls width = 5.
+Width of spectrum profiles.  This parameter is used for the profile
+centering algorithm in this and other tasks.
+.le
+.ls radius = 5.
+The profile centering error radius for the centering algorithm.
+.le
+.ls threshold = 0.
+Centering threshold for the centering algorithm.  The range of pixel intensities
+near the initial centering position must exceed this threshold.
+.le
+.ih
+ADDITIONAL PARAMETERS
+I/O parameters and the default dispersion axis are taken from the
+package parameters, the default aperture parameters are taken from the
+task \fBapdefault\fR.  Parameters for the various functions of finding,
+recentering, and resizing are taken from the parameters for the
+appropriate task.
+
+When this operation is performed from the task \fBapall\fR all parameters
+except the package parameters are included in that task.
+.ih
+CURSOR KEYS
+When editing the apertures interactively the following cursor keys are
+available.
+
+.nf
+?    Print help
+a    Toggle the ALL flag
+b an Set background fitting parameters
+c an Center aperture(s)
+d an Delete aperture(s)
+e an Extract spectra (see APSUM)
+f    Find apertures up to the requested number (see APFIND)
+g an Recenter aperture(s) (see APRECENTER)
+i  n Set aperture ID
+j  n Set aperture beam number
+l ac Set lower limit of current aperture at cursor position
+m    Define and center a new aperture on the profile near the cursor
+n    Define a new aperture centered at the cursor
+o  n Enter desired aperture number for cursor selected aperture and
+     remaining apertures are reordered using apidtable and maxsep
+     parameters (see APFIND for ordering algorithm)
+q    Quit
+r    Redraw the graph
+s an Shift the center(s) of the current aperture to the cursor
+     position
+t ac Trace aperture positions (see APTRACE)
+u ac Set upper limit of current aperture at cursor position
+w    Window the graph using the window cursor keys
+y an Set aperture limits to intercept the data at the cursor y
+     position
+z an Resize aperture(s) (see APRESIZE)
+.  n Select the aperture nearest the cursor for current aperture
++  c Select the next aperture (in ID) to be the current aperture
+-  c Select the previous aperture (in ID) to be the current aperture
+I    Interrupt task immediately.  Database information is not saved.
+.fi
+
+The letter a following the key indicates if all apertures are affected when
+the ALL flag is set.  The letter c indicates that the key affects the
+current aperture while the letter n indicates that the key affects the
+aperture whose center is nearest the cursor.
+.ih
+COLON COMMANDS
+
+.nf
+:show [file]	   Print a list of the apertures (default STDOUT)
+:parameters [file] Print current parameter values (default STDOUT)
+:read [name]       Read from database (default current image)
+:write [name]      Write to database (default current image)
+.fi
+
+The remaining colon commands are task parameters and print the current
+value if no value is given or reset the current value to that specified.
+Use :parameters to see current parameter values.
+
+.nf
+:apertures      :apidtable      :avglimits      :b_function
+:b_grow         :b_high_reject  :b_low_reject   :b_naverage
+:b_niterate     :b_order        :b_sample       :background
+:bkg            :center         :clean          :database
+:extras         :gain           :image          :line
+:llimit         :logfile        :lower          :lsigma
+:maxsep         :minsep         :npeaks         :nsubaps
+:nsum           :order          :parameters     :peak
+:plotfile       :r_grow         :radius         :read
+:readnoise      :saturation     :shift          :show
+:skybox         :t_function     :t_grow         :t_high_reject
+:t_low_reject   :t_naverage     :t_niterate     :t_nsum
+:t_order        :t_sample       :t_step         :t_width
+:threshold      :title          :ulimit         :upper
+:usigma         :weights        :width          :write
+:ylevel		:t_nlost
+.fi
+.ih
+DESCRIPTION
+For each image in the input image list, apertures are defined and edited
+interactively.  The aperture editor is invoked when the parameters
+\fIinteractive\fR and \fIedit\fR are both yes.  When this is the case
+the task will query whether to edit each image.  The responses are
+"yes", "no", "YES", and "NO", where the upper case responses suppress
+queries for all following images.
+
+When the aperture editor is entered a graph of the image lines or
+columns specified by the parameters \fIline\fR and \fInsum\fR is
+drawn.  In the \fBapextract\fR package a dispersion line is either a
+line or column in the image at one point along the dispersion axis.
+The dispersion axis may be defined in the image header under the
+keyword DISPAXIS or by the package parameter \fIdispaxis\fR.  The
+parameter \fBnsum\fR determines how many dispersion lines surrounding
+the specified dispersion line are summed or medianed.  This improves the
+signal in the profiles of weaker spectra.  Once the graph is drawn an
+interactive cursor loop is entered.  The set of cursor keys and colon
+commands is given above and may be printed when the task is running using
+the '?' key.  The CURSOR MODE keys and graph formatting options are also
+available (see \fBcursor\fR and \fBgtools\fR).
+
+A status line, usually at the bottom of the graphics terminal,
+indicates the current aperture and shows the ALL flag, 'a' key, if set.  The
+concept of the current aperture is used by several of the aperture
+editing commands.  Other commands operate on the aperture whose center
+is nearest the cursor.  It is important to know which commands operate
+on the current aperture and which operate on the nearest aperture to
+the cursor.
+
+The cursor keys and colon commands are used to define new apertures,
+delete existing apertures, modify the aperture number, beam number,
+title, center, and limits, set background fitting parameters, trace the
+positions of the spectra in the apertures, and extract aperture
+spectra.  When creating new apertures default parameters are supplied
+in two ways; if no apertures are defined then the default parameters
+are taken from the task \fBapdefault\fR while if there is a current
+aperture then a copy of its parameters are made.
+
+The keys for creating a new aperture are 'm' and 'n' and 'f'.  The key
+'m' marks a new aperture and centers the aperture on the profile
+nearest the cursor.  The centering algorithm is described under the
+help topic \fBcenter1d\fR and the parameters controlling the centering are
+\fIwidth\fR, \fIradius\fR, and \fIthreshold\fR.  The key 'n' defines a
+new aperture at the position of the cursor without centering.  This is
+used if there is no spectrum profile such as when defining sky apertures
+or when defining apertures in extended profiles.  The 'f' key finds new
+apertures using the algorithm described in the task \fBapfind\fR.  The
+number of apertures found in this way is limited by the parameter
+\fBnfind\fR and the number includes any previously defined
+apertures.  The new aperture number, beam number, and title are assigned using
+the aperture assignment algorithm described in \fBapfind\fR.
+
+The aperture number for the aperture \fInearest\fR the cursor is changed
+with the 'j' key and the beam number is changed with the 'k' key.  The
+user is prompted for a new aperture number or beam number.  The
+aperture title may be set or changed with the :title colon command.
+
+The 'o' key may be used to reorder or correct the aperture
+identifications and beam numbers.  This is useful if the aperture
+numbers become disordered due to deletions and additions or if the
+first spectrum is missing when using the automatic identification
+algorithm.  An aperture number is requested for the aperture pointed to
+by the cursor.  The remaining apertures are reordered relative to this
+aperture number.  There is a aperture number, beam number, and title
+assignment algorithm which uses information about the maximum
+separation between consecutive apertures, the direction of increasing
+aperture numbers, and an optional aperture identification table.  See
+\fBapfind\fR for a description of the algorithm.
+
+After defining a new aperture it becomes the current aperture.  The
+current aperture is indicated on the status line and the '.', '+', and
+'-' keys are used to select a new current aperture.
+
+Apertures are deleted with 'd' key.  The aperture \fInearest\fR the
+cursor is deleted.
+
+The aperture center may be changed with the 'c', 's', and 'g' keys and the
+":center value" colon command.  The 'c' key applies the centering algorithm
+to the aperture \fInearest\fR the colon.  The 's' key shifts the center
+of the \fIcurrent\fR aperture to the position of the cursor.  The 'g'
+applies the \fBaprecenter\fR algorithm.  The :center command sets the
+center of the \fIcurrent\fR aperture to the value specified.  Except
+for the last option these commands may be applied to all apertures
+if the ALL flag is set.
+
+The aperture limits are defined relative to the aperture center.  The
+limits may be changed with the 'l', 'u', 'y', and 'z' keys and with the
+":lower value" and ":upper value" commands.  The 'l' and 'u' keys set
+the lower and upper limits of the \fIcurrent\fR aperture at the position
+of the cursor.  The colon commands allow setting the limits explicitly.
+The 'y' key defines both limits for the \fInearest\fR aperture as
+points at which the y cursor position intercepts the data profile.
+This requires that the aperture include a spectrum profile and that
+the y cursor value lie below the peak of the profile.  The 'z'
+key applies the \fBapresize\fR algorithm.  Except for the colon
+commands these commands may be applied to all apertures if the ALL
+flag is set.
+
+The key 'b' modifies the background fitting parameters for the aperture
+\fInearest\fR the cursor.  The default background parameters are
+specified by the task \fBapdefault\fR.  Note that even though
+background parameters are defined, background subtraction is not
+performed during extraction unless specified.
+When the 'b' key is used the \fBicfit\fR graphical interface is entered
+showing the background regions and function fit for the current image
+line.  Note that the background regions are specified relative to
+the aperture center and follows changes in the aperture position.
+
+The two types of
+extraction which may be specified are to average all points within
+a set of background regions or fit a function to the points in
+the background regions.  In the first case only the background sample
+parameter is used.  In the latter case the other parameters are
+also used in conjunction with the \fBicfit\fR function fitting commands.
+See \fBapbackground\fR for more on the background parameters.
+
+Each aperture may have different background
+fitting parameters but newly defined apertures inherit the background
+fitting parameters of the last current aperture.  This will usually be
+satisfactory since the background regions are defined relative to the
+aperture center rather than in absolute coordinates.  If the ALL flag
+is set then all apertures will be given the same background
+parameters.
+
+The algorithms used in the tasks \fBapfind, aprecenter, apresize, aptrace\fR,
+and \fBapsum\fR are available from the editor with the keys 'f', 'g', 'z',
+'t', and 'e'
+respectively.  Excluding finding, if the ALL flag is not set then the
+nearest aperture
+to the cursor is used.  This allows selective recentering, resizing,
+tracing and extracting.
+If the ALL flag is set then all apertures are traced or extracted.
+When extracting the output, rootname and profile name are queried.
+
+Some general purpose keys window the graph 'w' using the \fBgtools\fR
+commands, redraw the graph 'r', and quit 'q'.
+
+The final cursor key is the 'a' key.  The cursor keys which modify the
+apertures were defined as operating on either the aperture nearest the
+cursor or the current aperture.  The 'a' key allows these keys to
+affect all the apertures simultaneously.  The 'a' key sets a flag which
+is shown on the status line when it is set.  When set, the operation on
+one aperture is duplicated on the remaining apertures.  The operations
+which apply to all apertures are set background 'b', center 'c', delete
+'d', extract 'e', recenter 'g', set lower limit 'l', shift 's', trace
+'t', set upper limit 'u', set limits at the y cursor 'y', and resize
+'z'.  The 'b', 'l', 's', and 'u' keys first set the background,
+aperture limits, or shift for the appropriate aperture and then are
+applied to the other apertures relative to their centers.
+
+All the parameters used in any of the operations may be examined or
+changed through colon commands.  The :parameters command lists all
+parameter values and :show lists the apertures.  The :read and :write
+are used to force an update or save the current apertures and to read
+apertures for the current image or from some other image.  The commands
+all have optional arguments.  For the commands which show information
+the argument specifies a file to which the information is to be
+written.  The default is the standard output.  The database read and
+write and the change image commands take an image name.  If an image
+name is not given for the read and write commands the
+current image name is used.  The change image command default is to
+print the current image name.  The remaining commands take a value.  If
+a value is not given then the current value is printed.
+
+The aperture editor may be selected from nearly every task using the
+\fBedit\fR parameter.
+.ih
+EXAMPLES
+The aperture editor is a very flexible and interactive tool
+for which it is impossible illustrate all likely uses.  The following
+give some simple examples.
+
+1.  To define and edit apertures for image "n1.001":
+
+	cl> apedit n1.001
+
+2.  To define apertures for one image and then apply them to several other
+images:
+
+.nf
+	cl> apedit n1.* ref=n1.001
+	Edit apertures for n1.001? (yes)
+	Edit apertures for n1.002? (yes) NO
+.fi
+
+Answer "yes" to the first query for editing n1.001.  To
+the next query (for n1.002) respond with "NO".  The remaining
+images then will not be edited interactively.  Note that after
+defining the apertures for n1.001 they are recorded in the database
+and subsequent images will be able to use them as reference apertures.
+
+3.  Using the ":image name" and ":read image" colon commands and the
+'f', 'g', 'z', 't' and 'e' keys the user can perform all the functions
+available in the package without ever leaving the editor.  The 'a' key
+to set the ALL flag is very useful when dealing with many spectra in a
+single image.
+.ih
+.ih
+REVISIONS
+.ls APEDIT V2.11
+The "apertures" parameter can be used to select apertures for resizing,
+recentering, tracing, and extraction.  This parameter name was previously
+used for selecting apertures in the recentering algorithm.  The new
+parameter name for this is now "aprecenter".
+
+The aperture ID table information may now be contained in the
+image header under the keywords SLFIBnnn.
+.le
+SEE ALSO
+.nf
+apdefault, apfind, aprecenter, apresize, aptrace, apsum, apall
+center1d, cursor, gtools, icfit
+.fi
+.endhelp
diff --git a/noao/twodspec/apextract/doc/apextract.hlp b/noao/twodspec/apextract/doc/apextract.hlp
new file mode 100644
index 00000000..401d93e7
--- /dev/null
+++ b/noao/twodspec/apextract/doc/apextract.hlp
@@ -0,0 +1,365 @@
+.help package Feb94 noao.twodspec.apextract
+.ih
+NAME
+apextract -- Identify, manipulate, and extract spectra in 2D images
+.ih
+USAGE
+apextract
+.ih
+PARAMETERS
+.ls dispaxis = 2
+Image axis along which the spectra dispersion run.  The dispersion axis
+is 1 when the dispersion is along lines so that spectra are horizontal
+when displayed normally.  The dispersion axis is 2 when the dispersion
+is along columns so that spectra are vertical when displayed normally.
+This parameter is superseded when the dispersion axis is defined in
+the image header by the parameter DISPAXIS.
+.le
+.ls database = "database"
+Database for storing aperture definitions.  Currently the database is
+a subdirectory of text files with prefix "ap" followed by the entry name,
+usually the image name.
+.le
+.ls verbose = no
+Print detailed processing and log information?  The output is to the
+standard output stream which is the user's terminal unless redirected.
+.le
+.ls logfile = ""
+Text logfile of operations performed.  If a file name is specified
+log and history information produced by all the tasks in the package
+is appended to the file.
+.le
+.ls plotfile = ""
+Binary plot metacode file of aperture locations, traces, rejected points,
+etc.  If a file name is given metacode plots are appended.  The contents
+of the file may be manipulated with the tasks in the \fBplot\fR package.
+The most common is \fBgkimosaic\fR.  Special plotfile names may be used
+to select only particular plots or plots not normally output.  These are
+debugall, debugfitspec, debugaps, debugspec, debugfits, debugtrace,
+and debugclean which plot everything, the fitted spectrum, the apertures,
+the extracted spectrum, profile fit plots, the trace, and the rejected
+points during cleaned extraction.
+.le
+.ls version = "APEXTRACT V3.0: August 1990"
+Version of the package.  This is the third major version of the package.
+.le
+.ih
+DESCRIPTION
+The primary function of the \fBapextract\fR package is the extraction of
+spectra from two dimensional formats to one dimensional formats.  In
+other words, the pixels at each wavelength are summed, possibly
+subtracting a background or sky from other pixels at that wavelength,
+to produce a vector of spectral fluxes as a function of wavelength.
+It has become common to have many spectra in one two dimensional
+image produced by instruments using echelles, fibers, and aperture
+masks.  Thus, the package provides many features for the efficient
+extractions of multiple spectra as well as single spectra.  There are
+also some additional, special purpose tasks for modeling spectra
+and using the aperture definitions, described below,
+to create masks and modified flat field images.
+
+The package assumes that one of the image axes is the dispersion axis,
+specified by the \fIdispaxis\fR package parameter or image header
+parameter of the same name, and the other is the spatial axes.
+This means that all pixels at the same column or line (the
+orientation may be in either direction) are considered to be at the
+same wavelength.  Even if this is not exactly
+true the resolution loss is generally quite small and the simplicity and
+absence of interpolation problems justify this approach.  The
+alternatives are to rotate the image with \fBrotate\fR or use the more
+complex \fBlongslit\fR package.  Though extraction is strictly along
+lines and columns the position of the spectrum along the spatial axis
+is allowed to shift smoothly with wavelength.  This accounts for small
+misalignments and distortions.
+
+The two dimensional regions occupied by the spectra are defined by
+digital apertures having a fixed width but with spatial position smoothly
+varying with wavelength.  The apertures have a number of attributes.
+The aperture definitions are created and modified by the tasks in this
+package and stored in a database specified by the parameter \fIdatabase\fR.
+The database is currently a directory containing simple text files
+in a human readable format.  The elements of an aperture definition
+are as follows.
+
+
+.ce
+Elements of an Aperture Definition
+.ls aperture
+An integer aperture identification number.  The aperture number
+must be unique within a set of apertures.  The aperture number is
+the primary means of referencing an aperture and the resulting
+extracted spectra.  The aperture numbers are part of the extracted
+spectra image headers.  The numbers may be any integer and in any order
+but the most typical case is to have sequential numbers beginning
+with 1.
+.le
+.ls beam
+An integer beam number.  The beam number need not be unique; i.e.
+several apertures may have the same beam number.  The beam numbers are
+recorded in the image headers of the extracted spectra.  The beam
+number is often used to identify types of spectra such as object,
+sky, arc, etc.
+.le
+.ls center
+A pair of numbers specifying the center of the aperture along the spatial
+and dispersion axes in the two dimensional image.  The center along
+the dispersion is usually defined as the middle of the image.  The
+rest of the aperture parameters are defined relative to the aperture
+center making it easy to move apertures.
+.le
+.ls low, high
+Pairs of numbers specifying the lower and upper limits of the
+aperture relative to the center along the spatial and dispersion axes.
+The lower limits are usually negative and the upper limits positive
+but there is no actual restriction; i.e. the aperture can actually
+be offset from the center position.  Currently the dispersion
+aperture limits are such that the entire length of the image along the
+dispersion axis is used.  In the future this definition can be
+easily used for objective prism spectra.
+.le
+.ls curve, axis
+An IRAF "curfit" function specifying a shift to be added to the center
+position along the spatial axis, given by the axis parameter which is
+the complement of the dispersion axis parameter \fIdispaxis\fR, as a
+function of the dispersion coordinate.  This trace function is one of
+the standard IRAF \fBicfit\fR types; a legendre polynomial, a chebyshev
+polynomial, a linear spline, or a cubic spline.
+.le
+.ls background
+Background definition parameters.  For the "average" background subtraction
+option only the set of background sample regions (defined relative to
+the aperture center) are used.  For the "fit" option the parameters
+are those used by the \fBicfit\fR package for fitting a function to
+the points in the background sample regions.
+.le
+
+This information as well as the image (or database entry) name are stored
+in a text file, with name given by the prefix "ap" followed by the entry
+name, in the database directory.  An example with the special entry  name
+"last", stored in the file "database$aplast", is given below. The "begin"
+line marks the beginning of an aperture definition.
+
+
+.ce
+Sample Aperture Database Entry
+
+.nf
+# Fri 17:43:41 03-Aug-90
+begin	aperture last 1 70.74564 256.
+	image	last
+	aperture	1
+	beam	1
+	center	70.74564 256.
+	low	-5. -255.
+	high	5. 256.
+	background
+		xmin -100.
+		xmax 100.
+		function chebyshev
+		order 1
+		sample -10:-6,6:10
+		naverage -3
+		niterate 0
+		low_reject 3.
+		high_reject 3.
+		grow 0.
+	axis	1
+	curve	5
+		2.
+		1.
+		1.
+		512.
+		0.
+.fi
+
+There are a number of logical functions which may be performed to
+create, modify, and use the aperture definitions.  These functions
+are:
+.ls o
+Automatically find a specified number of spectra and assign default
+apertures.  Apertures may also be inherited from another image or
+defined using an interactive graphical interface called the \fIaperture
+editor\fR.
+.le
+.ls o
+Recenter apertures on the image spectrum profiles.
+.le
+.ls o
+Resize apertures based on spectrum profile width.
+.le
+.ls o
+Interactively define or adjust aperture definitions using a graphical
+interface called the \fIaperture editor\fR.  All function may also
+be performed from this editor and, so, provides an alternative
+method of processing and extracting spectra.
+.le
+.ls o
+Trace the positions of spectra profiles from a starting image line
+or column to other image lines or columns and fit a smooth function.
+The trace function is used to shift the center of the apertures
+at each dispersion point in the image.
+.le
+.ls o
+Extract the flux in the apertures into one dimensional spectra in various
+formats.  This includes possible background subtraction, variance
+weighting, and bad pixel rejection.
+.le
+
+The package is logically organized around these functions.  Each
+function has a task devoted to it.  The description of the parameters
+and algorithms for each function are organized according to these
+tasks; namely under the help topics \fBapdefault, apfind, aprecenter,
+apresize, apedit, aptrace\fR, and \fBapsum\fR.  However, each task has
+parameters to allow selecting some or all of the other functions, hence
+it is not necessary to use the individual tasks and often it is more
+convenient to use just the extraction task for all operations.  It is
+also possible to perform all the functions from within a graphical
+interface called the aperture editor.  This is usually only used to
+define and modify aperture definitions but it also has the capability
+to trace spectra and extract them.
+
+Each of the functions has many different options and parameters.  When
+broken down into individual tasks the parameters are also sorted by
+their function though there are then some mutual interdependencies.
+This parameter decomposition was what was available prior to the
+addition of the task \fBapall\fR.  This is the central task of the
+package which performs any and all of the functions required for the
+extraction of spectra and also collects all the parameters into one
+parameter set.  It is recommended that \fBapall\fR be used because it
+collects all the parameters in one place eliminating confusion over
+where a particular parameter is defined.
+
+In summary, the package consists of a number of logical functions which
+are documented by the individual tasks named for that function, but the
+functions are also integrated into each task and the aperture editor to
+providing many different ways for the user to choose to perform the
+functions.
+
+The package menu and help summary is shown below.
+
+
+.ce
+The APEXTRACT Package Tasks
+
+.nf
+     apall        apedit       apflatten    aprecenter   apsum
+     apdefault    apfind       apmask       apresize     aptrace
+     apdemos      apfit        apnormalize  apscatter
+
+          apall - Extract 1D spectra (all parameters in one task)
+      apdefault - Set the default aperture parameters and apidtable
+        apdemos - Various tutorial demonstrations
+         apedit - Edit apertures interactively
+	 apfind - Automatically find spectra and define apertures
+	  apfit - Fit 2D spectra and output the fit, difference,
+		  or ratio
+      apflatten - Remove overall spectral and profile shapes from
+		  flat fields
+         apmask - Create and IRAF pixel list mask of the apertures
+    apnormalize - Normalize 2D apertures by 1D functions
+     aprecenter - Recenter apertures
+       apresize - Resize apertures
+      apscatter - Fit and subtract scattered light
+          apsum - Extract 1D spectra
+	aptrace - Trace positions of spectra
+
+		Additional topics
+
+   apbackground - Background subtraction algorithms
+      apextract - Package parameters and general description of
+		  package
+     approfiles - Profile determination algorithms
+     apvariance - Extractions, variance weighting, cleaning, and
+		  noise model
+.fi
+
+The extracted spectra are recorded in one, two, or three dimensional
+images depending on the \fIformat\fR and \fIextras\fR parameters.  If
+the \fIextras\fR parameter is set to yes the formats are three
+dimensional with each plane in the third dimension containing
+associated information for the spectra in the first plane.  See
+\fBapsum\fR for further details.  When \fIextras\fR=no only the
+extracted spectra are output.
+
+If the format parameter is "onedspec" the output extractions are one
+dimensional images with names formed from an output rootname and an
+aperture number extension; i.e. root.0001 for aperture 1.  There will
+be as many output images as there are apertures for each input image,
+all with the same output rootname but with different aperture
+extensions.  This format is provided to be compatible with the original
+format used by the \fBonedspec\fR package.
+
+If the format parameter is "echelle" or "multispec" the output aperture
+extractions are put into a two dimensional image with a name formed from
+the output rootname and the extension ".ec" or ".ms".  Each line in
+the output image corresponds to one aperture.  Thus in this format
+there is one output image for each input image.  These are the preferred
+output formats for reasons of compactness, ease of handling, and efficiency.
+These formats are compatible with the \fBonedspec\fR, \fBechelle\fR, and
+\fBmsred\fR packages.  The format is a standard IRAF image with
+specialized image header keywords.  Below is an example of the keywords.
+
+
+.ce
+MULTISPEC/ECHELLE Format Image Header Keywords
+
+.nf
+    ap> imhead test.ms
+    test.ms[512,2,4][real]: Title
+	BANDID1 = 'spectrum - background fit, weights variance, clean yes'
+	BANDID2 = 'spectrum - background fit, weights none, clean no'
+	BANDID3 = 'background - background fit'
+	BANDID4 = 'sigma - background fit, weights variance, clean yes'
+	APNUM1  = '1 1 87.11 94.79'
+	APNUM2  = '2 1 107.11 114.79'
+	APID1   = 'Galaxy center'
+	APID2   = 'Galaxy edge'
+	WCSDIM  =                    3
+	CTYPE1  = 'PIXEL   '
+	CTYPE2  = 'LINEAR  '
+	CTYPE3  = 'LINEAR  '
+	CRVAL1  =                   1.
+	CRPIX1  =                   1.
+	CD1_1   =                   1.
+	CD2_2   =                   1.
+	CD3_3   =                   1.
+	LTM1_1  =                   1.
+	LTM2_2  =                   1.
+	LTM3_3  =                   1.
+	WAT0_001= 'system=equispec
+	WAT1_001= 'wtype=linear label=Pixel
+	WAT2_001= 'wtype=linear
+	WAT3_001= 'wtype=linear
+.fi
+
+The BANDIDn keywords describe the various elements of the 3rd dimension.
+Except for the first one the other bands only occur when \fIextras\fR is
+yes and when sky subtraction and/or variance and cleaning are done.  The
+relation between the line and the aperture numbers is given by the header
+parameters APNUMn where n is the line and the value gives extraction and
+coordinate information about the spectrum.  The first field is the aperture
+number and the second is the beam number.  After dispersion calibration of
+echelle format spectra the beam number becomes the order number.  The other
+two numbers are the aperture limits at the line or column at which the
+aperture was defined.
+The APID keywords provide an optional title for each extracted spectrum
+in addition to the overall image title.
+
+The rest of the keywords are part of the IRAF World Coordinate System
+(WCS).  If the image being extracted has been previously calibrated
+(say with \fBlongslit.transform\fR) then the dispersion coordinates
+will be carried in CRVAL1 and CD1_1.
+
+There is one other value for the format parameter, "strip".  This produces
+two dimensional extractions rather than one dimensional extractions.
+Each aperture is output to a two dimensional image with a width set by the
+nearest integer which includes the aperture.  The output names are
+generated in the same way as for "onedspec" format.  The aperture is
+shifted by interpolation so that it is exactly aligned with the image
+columns.  If not variance weighting the actual image data is output
+with appropriate shifting while for variance weighting and/or cleaning
+the profile model is output (similar to \fBapfit\fR except for being
+aligned).  This format is that provided in the previous version of
+the package by the \fBapstrip\fR task.  It is now relegated to a
+special case.
+.endhelp
diff --git a/noao/twodspec/apextract/doc/apextractsys.hlp b/noao/twodspec/apextract/doc/apextractsys.hlp
new file mode 100644
index 00000000..a93d9f56
--- /dev/null
+++ b/noao/twodspec/apextract/doc/apextractsys.hlp
@@ -0,0 +1,415 @@
+.help apextract Aug90 noao.twodspec.apextract
+
+.ce
+APEXTRACT System Notes
+
+
+\fBIntroduction\fR
+
+The \fBapextract\fR package is a complex package with a simple
+purpose, the extraction of one dimensional spectra from two dimensional
+images.  The complexity arises from the many algorithms and parameters
+involved.  To manage the complexity of the algorithms, features, parameters,
+functionality, and documentation the package has been organized in terms
+of logical functions which may be invoked in a number of ways.  The
+logical functions are:
+.ls o
+Automatically find a specified number of spectra and assign default
+apertures.  Apertures may also be inherited from another image or
+defined using an interactive graphical interface called the \fIaperture
+editor\fR.
+.le
+.ls o
+Recenter apertures on the image spectrum profiles.
+.le
+.ls o
+Resize apertures based on spectrum profile width.
+.le
+.ls o
+Interactively define or adjust aperture definitions using a graphical
+interface called the \fIaperture editor\fR.  All function may also
+be performed from this editor and, so, provides an alternative
+method of processing and extracting spectra.
+.le
+.ls o
+Trace the positions of spectra profiles from a starting image line
+or column to other image lines or columns and fit a smooth function.
+The trace function is used to shift the center of the apertures
+at each dispersion point in the image.
+.le
+.ls o
+Extract the flux in the apertures into one dimensional spectra in various
+formats.  This includes possible background subtraction, variance
+weighting, and bad pixel rejection.
+.le
+
+The package is logically organized around these functions.  Each
+function has a task devoted to it.  The description of the parameters
+and algorithms for each function are organized according to these
+tasks; namely under the help topics \fBapdefault, apfind, aprecenter,
+apresize, apedit, aptrace\fR, and \fBapsum\fR.  However, each task has
+parameters to allow selecting some or all of the other functions, hence
+it is not necessary to use the individual tasks and often it is more
+convenient to use just the extraction task for all operations.  It is
+also possible to perform all the functions from within a graphical
+interface called the aperture editor.  This is usually only used to
+define and modify aperture definitions but it also has the capability
+to trace spectra and extract them.
+
+Each of the functions has many different options and parameters.  When
+broken down into individual tasks the parameters are also sorted by
+their function though there are then some mutual interdependencies.
+This parameter decomposition was what was available prior to the
+addition of the task \fBapall\fR.  This is the central task of the
+package which performs any and all of the functions required for the
+extraction of spectra and also collects all the parameters into one
+parameter set.  It is recommended that \fBapall\fR be used because it
+collects all the parameters in one place eliminating confusion over
+where a particular parameter is defined.
+
+In summary, the package consists of a number of logical functions which
+are documented by the individual tasks named for that function, but the
+functions are also integrated into each task and the aperture editor to
+providing many different ways for the user to choose to perform the
+functions.
+
+This document describes some of the implementation details and features
+which are hidden from the normal user.
+
+
+\fBParameters\fR
+
+The tasks actually use hidden parameter sets for almost all parameters.
+To see all the parameter sets type
+
+.nf
+	ap> ?_ apextract
+.fi
+
+The relation between the tasks and the hidden parameter sets is given below.
+
+.nf
+	PSET	   TASK
+	apparams - apdefault, apfind, aprecenter, apresize,
+		   apedit, aptrace, apsum, apmask, apscatter
+	apall1   - apall
+	apfit1   - apfit
+	apflat1  - apflatten
+	apnorm1  - apnormalize
+.fi
+
+The hidden parameter sets may be viewed in any of the normal ways
+\fBeparam\fR, \fBlparam\fR, or just by typing their name, except
+their names may not be abbreviated.  Their purpose is to redirect
+parameters to visible parameter sets, to hide some parameters which
+are not meant to be changed by the user, and to include parameters
+used for queries.
+
+Most of the redirected parameters go to a single visible parameter set
+or to package parameters.
+The interesting exception is \fBapparams\fR which provides the
+parameter linkage between the various functional tasks like
+\fBapfind\fR, \fBaptrace\fR, \fBapsum\fR, etc.  Below is a reproduction
+of this parameter set.
+
+.ce
+APPARAMS Hidden Parameter Set
+
+.nf
+				   I R A F  
+                    Image Reduction and Analysis Facility
+PACKAGE = apextract
+   TASK = apparams
+    
+(format =            )_.format) Extracted spectra format
+(extras =        )apsum.extras) Extract sky, sigma, etc.?
+(dbwrite=                  yes) Write to database?
+(initial=                  yes) Initialize answers?
+(verbose=           )_.verbose) Verbose output?
+                                
+                                # DEFAULT APERTURE PARAMETERS
+
+(upper  =     )apdefault.upper) Upper aperture limit relative to center
+(apidtab= )apdefault.apidtable) Aperture ID table (optional)
+                                
+                                # DEFAULT BACKGROUND PARAMETERS
+
+(b_funct= )apdefault.b_function) Background function
+(b_order=   )apdefault.b_order) Background function order
+(b_sampl=  )apdefault.b_sample) Background sample regions
+(b_naver= )apdefault.b_naverage) Background average or median
+(b_niter= )apdefault.b_niterate) Background rejection iterations
+(b_low_r= )apdefault.b_low_reject) Background lower rejection sigma
+(b_high_= )apdefault.b_high_reject) Background upper rejection sigma
+(b_grow =    )apdefault.b_grow) Background rejection growing radius
+                                
+                                # APERTURE CENTERING PARAMETERS
+
+(width  =        )apedit.width) Profile centering width
+(radius =       )apedit.radius) Profile centering radius
+(thresho=    )apedit.threshold) Detection threshold for profile centering
+                                
+                                # AUTOMATIC FINDING AND ORDERING PARAMETERS
+
+(nfind  =        )apfind.nfind) Number of apertures to be found automatically
+(minsep =       )apfind.minsep) Minimum separation between spectra
+(maxsep =       )apfind.maxsep) Maximum separation between spectra
+(order  =        )apfind.order) Order of apertures
+                                
+                                # RECENTERING PARAMETERS
+
+(apertur= )aprecenter.apertures) Select apertures
+(npeaks =   )aprecenter.npeaks) Select brightest peaks
+(shift  =    )aprecenter.shift) Use average shift instead of recentering?
+                                
+                                # RESIZING PARAMETERS
+
+(llimit =     )apresize.llimit) Lower aperture limit relative to center
+(ulimit =     )apresize.ulimit) Upper aperture limit relative to center
+(ylevel =     )apresize.ylevel) Fraction of peak or intensity for automatic widt(peak   =       )apresize.peak) Is ylevel a fraction of the peak?
+(bkg    =        )apresize.bkg) Subtract background in automatic width?
+(r_grow =     )apresize.r_grow) Grow limits by this factor
+(avglimi=  )apresize.avglimits) Average limits over all apertures?
+                                
+                                # EDITING PARAMETERS
+
+e_output=                       Output spectra rootname
+e_profil=                       Profile reference image
+(t_nsum =        )aptrace.nsum) Number of dispersion lines to sum
+(t_step =        )aptrace.step) Tracing step
+(t_width=        )apedit.width) Centering width for tracing
+(t_funct=    )aptrace.function) Trace fitting function
+(t_order=       )aptrace.order) Trace fitting function order
+(t_sampl=      )aptrace.sample) Trace sample regions
+(t_naver=    )aptrace.naverage) Trace average or median
+(t_niter=    )aptrace.niterate) Trace rejection iterations
+(t_low_r=  )aptrace.low_reject) Trace lower rejection sigma
+(t_high_= )aptrace.high_reject) Trace upper rejection sigma
+(t_grow =        )aptrace.grow) Trace rejection growing radius
+                                
+                                # EXTRACTION PARAMETERS
+
+(backgro=    )apsum.background) Background to subtract (none|average|fit)
+(skybox =        )apsum.skybox) Box car smoothing length for sky
+(weights=       )apsum.weights) Extraction weights (none|variance)
+(clean  =         )apsum.clean) Detect and replace bad pixels?
+(niterat=                    2) Number of profile fitting iterations
+(saturat=    )apsum.saturation) Saturation level
+(readnoi=     )apsum.readnoise) Read out noise sigma (photons)
+(gain   =          )apsum.gain) Photon gain (photons/data number)
+(lsigma =        )apsum.lsigma) Lower rejection threshold
+(usigma =        )apsum.usigma) Upper rejection threshold
+(maxtilt=                    3) Maximum excursion for line/column fitting
+(polysep=                 0.95) Marsh algorithm polynomial spacing
+(polyord=                   10) Marsh algorithm polynomial order
+(nsubaps=       )apsum.nsubaps) Number of subapertures per aperture
+                                
+                                # ANSWER PARAMETERS
+
+(ansclob=                   no)  
+(ansclob=                   no)  
+(ansdbwr=                  yes)  
+(ansdbwr=                  yes)  
+(ansedit=                  yes)  
+(ansextr=                  yes)
+(ansfind=                  yes)  
+(ansfit =                  yes)  
+(ansfits=                  yes)  
+(ansfits=                  yes)  
+(ansfits=                  yes)  
+(ansfits=                  yes)  
+(ansfitt=                  yes)  
+(ansfitt=                  yes)  
+(ansflat=                  yes)  
+(ansmask=                  yes)  
+(ansnorm=                  yes)  
+(ansrece=                  yes)  
+(ansresi=                  yes)  
+(ansrevi=                  yes)  
+(ansrevi=                  yes)  
+(ansscat=                  yes)  
+(anssmoo=                  yes)  
+(anstrac=                   no)  
+(mode   =                    q)
+.fi
+
+Note how the parameters are redirected to a variety of tasks.
+
+
+\fBInvisible Parameters\fR
+
+The following algorithm parameters are not visible to the normal user
+and are described only here.
+.ls dbwrite = yes
+Write to database?  Writing to the database is a function just like
+find, edit, extract, etc.  When the task is interactive a query is
+made whether to write to the database which may be answered with the
+usual four values.  When noninteractive the database writing is automatic.
+This parameter provides the possibility of turning off database writing.
+.le
+.ls initialize = yes
+Initialize default queries?  Normally each invocation of a task results
+in new queries independent of the last responses in a prior invocation
+and based only on the functions selected; NO for those not selected and
+yes for those selected.  By setting this to no either the prior values
+may be used or the response values may be set independently of the
+function flags.  This is used in scripts to tie together different
+invocations of the task and to finely control the queries.
+.le
+.ls e_output, e_profile
+These are query parameters used when extraction is invoked from the
+aperture editor.
+.le
+ 
+The following parameters are part of the variance weighted and cleaning
+extractions.  They are described further in \fBapprofiles\fR.
+.ls niterate = 2
+Number of rejection iterations in the profile determination when cleaning.
+Iteration of the profile is slow and the low order fitting function
+is not very sensitive to deviant points.
+.le
+.ls maxtilt = 3
+Maximum excursion separating the two profile fitting algorithms.
+.le
+.ls polysep = 0.95
+Marsh algorithm polynomial spacing.
+.le
+.ls polyorder = 10
+Marsh algorithm polynomial order.
+.le
+
+
+\fBQuery Mechanism and Invisible Query Parameters\fR
+
+The querying mechanism of the \fBapextract\fR package is a nice feature
+but has some complexities in implementation.  At the bottom of the
+mechanism are CL checks of the parameters described below.  The parameter
+is accessed first as a hidden parameter.  If the value is YES or NO
+then the appropriate function is performed or not.  If the value is
+lower case then the task supplies a prompt string, which varies by
+including the image and/or aperture involved, the mode of the
+parameter is changed to query, and the parameter is requested again
+leading to a CL query of the user with the current default value.
+Finally, the parameter is returned to hidden mode.
+
+If the \fIinitialize\fR parameter is no then the initial default
+query values are those set before the task is invoked.  This provides
+very fine control of the query mechanism and linking different
+invocations of the tasks to previous user responses.   It is intended
+only for complex scripts such as those in the spectroscopic \fBimred\fR
+packages.  Normally the initial values of the parameters are set
+during task startup  based on the function flags.  If a flag is no
+then the related query parameter is NO.  If the function flag is yes
+then when the task is interactive the initial value is yes otherwise
+it is YES.  The solely interactive functions, such as editing, are
+set to NO when the task is noninteractive regardless of the function
+selection.
+.ls ansclobber, ansclobber1
+Used to define the action to be taken if an output image would be clobbered.
+Normally the action is to query if interactive and not clobber if
+noninteractive.  The first parameter acts as the function switch and
+the second as the actual query.
+.le
+.ls ansdbwrite, ansdbwrite1
+The second parameter is used by the task to mark whether any changes have
+been made that might require a database update.  The first parameter is
+the actual query parameter for the \fIdbwrite\fR function flag.
+.le
+.ls ansedit
+Query parameter for the interactive editing function.
+.le
+.ls ansextract
+Query parameter for the extraction function.
+.le
+.ls ansfind
+Query parameter for the find function.
+.le
+.ls ansfit
+Query parameter for the fit function of \fBapfit\fR.
+.le
+.ls ansfitscatter
+Query parameter for the interactive fitscatter function of \fBapscatter\fR.
+.le
+.ls ansfitsmooth
+Query parameter for the interactive fitsmooth function of \fBapscatter\fR.
+.le
+.ls ansfitspec
+Query parameter for the interactive fitspec function of \fBapflatten\fR
+and \fBapnormalize\fR.  This applies to each image.
+.le
+.ls ansfitspec1
+Query parameter for the interactive fitspec function of \fBapflatten\fR
+and \fBapnormalize\fR.  This applies to each aperture in an image.
+.le
+.ls ansfittrace
+Query parameter for the interactive fittrace function.
+This applies to each image.
+.le
+.ls ansfittrace1
+Query parameter for the interactive fittrace function.
+This applies to each aperture in an image.
+.le
+.ls ansflat
+Query parameter for the flatten function of \fBapflatten\fR.
+.le
+.ls ansmask
+Query parameter for the mask function of \fBapmask\fR.
+.le
+.ls ansnorm
+Query parameter for the normalize function of \fBapnormalize\fR.
+.le
+.ls ansrecenter
+Query parameter for the recenter function.
+.le
+.ls ansresize
+Query parameter for the resize function.
+.le
+.ls ansreview
+Query parameter for the interactive extraction review function.
+This applies to each image.
+.le
+.ls ansreview1
+Query parameter for the interactive extraction review function.
+This applies to each aperture in an image.
+.le
+.ls ansscat
+Query parameter for the subtract function of \fBapscatter\fR.
+.le
+.ls anssmooth
+Query parameter for the smooth function of \fBapscatter\fR.
+.le
+.ls anstrace
+Query parameter for the trace function.
+.le
+
+
+\fBTask Entry Points\fR
+
+Logical tasks in IRAF are organized as multiple procedures in one physical
+task selected by the IRAF main.  The \fBapextract\fR package extends
+this concept to a lower level.  All of the package tasks go through
+one procedure, \fBapall\fR.  This procedure handles all of the
+startup details and breaks the logical task down into selected
+functions which are implemented as other procedures.  There are
+a couple of interesting and unusual features of this organization.
+
+IRAF physical tasks may map multiple logical task names to the same
+procedure.  However, the procedure will not know under what name it
+was called.  In this package we want to know the logical task name
+in order to select the appropriate hidden parameter set and to
+make minor adjustments in what the tasks do while maintaining the
+same basic logical flow and source code.  To do this dummy entry
+points are used whose only function is to call \fBapall\fR and
+pass an indication of the task name.
+
+Based on the task name a named parameter set is opened with \fBclopset\fR
+and then all CLIO calls use the returned pointer and can be blind to the
+actual parameter set used.
+
+In addition to the tasks defined in the package and their associated
+parameter sets there is one more task entry point called \fBapscript\fR
+with parameter set \fBapscript\fR.  It is intended for use in scripts
+as it's name implies.  For this reason it does not need an intermediate
+hidden parameter set.  For examples of it's use see the \fBimred\fR
+packages such as \fBnessie\fR.
+.endhelp
diff --git a/noao/twodspec/apextract/doc/apextras.hlp b/noao/twodspec/apextract/doc/apextras.hlp
new file mode 100644
index 00000000..36a51b26
--- /dev/null
+++ b/noao/twodspec/apextract/doc/apextras.hlp
@@ -0,0 +1,61 @@
+.help extras Sep95 noao.twodspec.apextract
+.ih
+NAME
+extras -- Information about the extra bands in 3D output
+.ih
+DESCRIPTION
+When one dimensional spectra are extracted by the tasks in the
+\fBapextract\fR package the user may specify that additional
+extra associated information be extracted at the same time.  This
+information is produced when the \fIextras\fR parameter is "yes".
+
+The associated information is recorded as additional "bands" (the IRAF term
+for the third dimension of a three dimensional image) of the output
+extracted spectral image.  Extracted spectra are currently stored as IRAF
+images with dispersion information given in the image header.  The
+image axes for such images are:
+
+.nf
+    1 (columns) - dispersion axis
+    2 (lines)   - spectrum axis (each line is a separate spectrum)
+    3 (bands)   - extras axis (each band is associated data)
+.fi
+
+The lengths of the second and third axes, that is the number of
+lines and bands, may be one or more.  If there is only one band
+the image will be two dimensional and if there is only one line
+and one band the image will be one dimensional.  Note that the
+\fIformat\fR parameter controls whether multiple apertures are
+written to separate images or to a single image.  Thus, if
+the format is "onedspec" this means that the second dimension
+will always be of length one and, if the \fIextras\fR parameter
+is no, the output images will be one dimensional.
+
+The associated data in the image bands depends on which extraction
+options are performed.  The various types of data are:
+
+.nf
+    The primary spectrum flux values.
+    Simple aperture sum if variance weighting or cleaning was done.
+    Background spectrum if background subtraction was done.
+    Sigma spectrum if variance weighting or cleaning was done.
+.fi
+
+The primary spectrum is always the first band and will be the cleaned
+and/or variance weighted and/or background subtracted spectrum.  The
+simple aperture sum spectrum allows comparing against the results of the
+variance weighting or pixel rejection options.  When background
+subtraction is performed the subtracted background is recorded in
+one of the bands.  When variance weighting or pixel rejection is
+performed the software generates an estimate of the uncertainty
+in the extracted flux as a sigma.
+
+The identity of the various bands is given by the image header
+keywords BANDIDn (where n is the band number).  This also serves
+to document which extraction options were used.
+
+For more information get help under the topic "apextract.package".
+.ih
+SEE ALSO
+apextract.package
+.endhelp
diff --git a/noao/twodspec/apextract/doc/apfind.hlp b/noao/twodspec/apextract/doc/apfind.hlp
new file mode 100644
index 00000000..65260394
--- /dev/null
+++ b/noao/twodspec/apextract/doc/apfind.hlp
@@ -0,0 +1,180 @@
+.help apfind Sep96 noao.twodspec.apextract
+.ih
+NAME
+apfind -- Find spectra and define apertures automatically
+.ih
+USAGE
+apfind input
+.ih
+PARAMETERS
+.ls input
+List of input images in which spectra are to be identified and
+apertures defined automatically.
+.le
+.ls apertures = ""
+Apertures to recenter, resize, trace, and extract.  This only applies
+to apertures read from the input or reference database.  Any new
+apertures defined with the automatic finding algorithm or interactively
+are always selected.  The syntax is a list comma separated ranges
+where a range can be a single aperture number, a hyphen separated
+range of aperture numbers, or a range with a step specified by "x<step>";
+for example, "1,3-5,9-12x2".
+.le
+.ls references = ""
+List of reference images to be used to define apertures for the input
+images.  When a reference image is given it supersedes apertures
+previously defined for the input image. The list may be null, "", or
+any number of images less than or equal to the list of input images.
+There are three special words which may be used in place of an image
+name.  The word "last" refers to the last set of apertures written to
+the database.  The word "OLD" requires that an entry exist
+and the word "NEW" requires that the entry not exist for each input image.
+.le
+
+.ls interactive = no
+Run this task interactively?  If the task is not run interactively then
+all user queries are suppressed and interactive aperture editing is
+disabled.
+.le
+.ls find = yes
+Find the spectra and define apertures automatically?  In order for
+spectra to be found automatically there must be no apertures for the
+input image or reference image defined in the database and the
+parameter \fInfind\fR must be greater than zero.
+.le
+.ls recenter = no
+Recenter the apertures?
+.le
+.ls resize = no
+Resize the apertures?
+.le
+.ls edit = yes
+Edit the apertures?  The \fIinteractive\fR parameter must also be yes.
+.le
+
+.ls line = INDEF
+The dispersion line (line or column perpendicular to the dispersion axis) to
+be used in finding the spectra.  A value of INDEF selects the middle of the
+image.
+.le
+.ls nsum = 1
+Number of dispersion lines to be summed or medianed.  The lines are taken
+around the specified dispersion line.  A positive value sums lines and
+a negative value medians lines.
+.le
+.ls nfind = 1
+Maximum number of apertures to be defined.  This is a query parameter
+so the user is queried for a value except when given explicitly on
+the command line.
+.le
+.ls minsep = 5.
+Minimum separation between spectra.  Weaker spectra or noise within this
+distance of a stronger spectrum are rejected.
+.le
+.ls maxsep = 1000.
+Maximum separation between adjacent spectra.  This parameter
+is used to identify missing spectra in uniformly spaced spectra produced
+by fiber spectrographs.  If two adjacent spectra exceed this separation
+then it is assumed that a spectrum is missing and the aperture identification
+assignments will be adjusted accordingly.
+.le
+.ls order = "increasing"
+When assigning aperture identifications order the spectra "increasing"
+or "decreasing" with increasing pixel position (left-to-right or
+right-to-left in a cross-section plot of the image).
+.le
+.ih
+ADDITIONAL PARAMETERS
+I/O parameters and the default dispersion axis are taken from the
+package parameters, the default aperture parameters are taken from the
+task \fBapdefault\fR, and parameters used for centering and editing the
+apertures are taken from \fBapedit\fR.
+
+When this operation is performed from the task \fBapall\fR all parameters
+except the package parameters are included in that task.
+.ih
+DESCRIPTION
+For each image in the input image list spectra are identified and
+default apertures defined.  The automatic aperture finding is performed
+only if 1) there are no apertures defined for the reference image, 2)
+there are no apertures defined for the input image, 3) the parameter
+\fIfind\fR is yes, and 4) the parameter \fInfind\fR is greater than
+zero.
+
+The automatic finding algorithm uses the following steps.  First, all local
+maxima are found.  The maxima are sorted by peak value and the weaker
+of the peaks separated by less than the value given by the parameter
+\fIminsep\fR are rejected.  Finally, at most the \fInfind\fR strongests
+peaks are kept.  \fBNfind\fR is a query parameter, so if it is not
+specified explicitly on the command line, the desired number of spectra
+to be found is requested.  After the peaks have been found the
+\fBcenter1d\fR algorithm is used to refine the centers of the
+profiles.  Apertures having the default parameters set with the task
+\fBapdefault\fR are defined at each center.  This algorithm is also
+available with the 'f' key in the task \fBapedit\fR with the change that
+existing apertures are kept and count toward the maximum number
+specified by \fBnfind\fR.
+
+The automatic assignment of aperture numbers, beam numbers, and titles
+has several options.  The simplest is when no aperture identification
+table, parameter \fIapidtable\fR, is specified and the maximum separation
+parameter, \fImaxsep\fR, is very large.  In this case the aperture and
+beam numbers are sequential starting from one and numbered either from
+left-to-right or right-to-left depending on the \fIorder\fR parameter.
+There are no aperture titles in this case.  If two adjacent spectra are
+separated by more than the specified maximum then the aperture numbers
+jump by the integer part of the ratio of the separation to the
+specified maximum separation.  This is used when the image is expected
+to have evenly spaced spectra, such as in multifiber spectrographs, in
+which some may be missing due to broken fibers.  Finally, the
+aperture identification table (either a text file or an image
+having a set of SLFIBnnn keyowrds) may contain lines with aperture number,
+beam number, and (optional) title.  The sequential numbers are then
+indices into this table.  Note that the skipping of missing spectra and
+the ordering applies to entries in this table as well.
+
+The ways in which the automatic method can fail for evenly spaced
+spectra with missing members are when the first spectrum is missing on
+the side from which the ordering begins and when the expected rather
+the actual number of spectra is used.  In the first case one can use
+the interactive 'o' key of the aperture editing facility to specify the
+identity of any aperture and then all other apertures will be
+appropriately reidentified.  If more spectra are sought than actually
+exist then noise spikes may be mistakenly found.  This problem can be
+eliminated by specifying the actual number of spectra or minimized by
+using the threshold centering parameter.
+
+The \fIrecenter\fR parameter allows recentering apertures if defined by
+a reference image.  Since the purpose of this task is to find new
+apertures it is usually the case that there are no reference images and
+recentering is not done.  The default apertures are of fixed width.
+The \fIresize\fR parameter may be used to adjust the widths in a
+variety of ways.  The aperture positions and any other parameters may
+also be edited with the aperture editing function if selected by the
+\fIapedit\fR parameter and the task is run interactively.
+
+If the task is interactive the user is queried whether to perform
+various steps on each image.  The queries may be answered with one of
+the four values "yes", "no", "YES" and "NO", where an upper case
+response suppresses all further queries to this question.
+
+The aperture finding algorithm may be selected from nearly every task
+in the package.
+.ih
+EXAMPLES
+	cl> apfind image nfind=10
+.ih
+.ih
+REVISIONS
+.ls APFIND V2.11
+The "apertures" parameter can be used to select apertures for resizing,
+recentering, tracing, and extraction.  This parameter name was previously
+used for selecting apertures in the recentering algorithm.  The new
+parameter name for this is now "aprecenter".
+
+The aperture ID table information may now be contained in the
+image header under the keywords SLFIBnnn.
+.le
+SEE ALSO
+center1d, apdefault, aprecenter, apresize, apedit, apall
+.endhelp
diff --git a/noao/twodspec/apextract/doc/apfit.hlp b/noao/twodspec/apextract/doc/apfit.hlp
new file mode 100644
index 00000000..60dd9b4c
--- /dev/null
+++ b/noao/twodspec/apextract/doc/apfit.hlp
@@ -0,0 +1,263 @@
+.help apfit Sep96 noao.twodspec.apextract
+.ih
+NAME
+apfit -- Fit 2D spectra using APEXTRACT profile algorithms
+.ih
+USAGE
+apfit input output fittype
+.ih
+PARAMETERS
+.ls input
+List of input images to be fit.
+.le
+.ls output = ""
+List of output images to be created with the  fitting results.  If the null
+string is given or the end of the output list is reached before the end
+of the input list then the input image name is used and an extension
+of ".fit", ".diff", or ".ratio" is added based on the type of fit.
+.le
+.ls apertures = ""
+Apertures to recenter, resize, trace, and fit.  This only applies
+to apertures read from the input or reference database.  Any new
+apertures defined with the automatic finding algorithm or interactively
+are always selected.  The syntax is a list comma separated ranges
+where a range can be a single aperture number, a hyphen separated
+range of aperture numbers, or a range with a step specified by "x<step>";
+for example, "1,3-5,9-12x2".
+.le
+.ls fittype = "difference"
+Type of fitted output.  The choices are:
+.ls "fit"
+The fitted spectra are output.
+.le
+.ls "difference"
+The difference (or residuals) of the data and the fit (data - fit).
+.le
+.ls "ratio"
+The ratio of the data to the fit.  If a fitted pixel goes below a specified
+threshold the ratio is set to 1.
+.le
+.le
+.ls references = ""
+List of reference images to be used to define apertures for the input
+images.  When a reference image is given it supersedes apertures
+previously defined for the input image. The list may be null, "", or
+any number of images less than or equal to the list of input images.
+There are three special words which may be used in place of an image
+name.  The word "last" refers to the last set of apertures written to
+the database.  The word "OLD" requires that an entry exist
+and the word "NEW" requires that the entry not exist for each input image.
+.le
+
+.ls interactive = yes
+Run this task interactively?  If the task is not run interactively then
+all user queries are suppressed and interactive aperture editing and trace
+fitting are disabled.
+.le
+.ls find = yes
+Find the spectra and define apertures automatically?  In order for
+spectra to be found automatically there must be no apertures for the
+input image or reference image defined in the database.
+.le
+.ls recenter = yes
+Recenter the apertures?
+.le
+.ls resize = yes
+Resize the apertures?
+.le
+.ls edit = yes
+Edit the apertures?  The \fIinteractive\fR parameter must also be yes.
+.le
+.ls trace = yes
+Trace the apertures?
+.le
+.ls fittrace = yes
+Interactively fit the traced positions by a function?  The \fIinteractive\fR
+parameter must also be yes.
+.le
+.ls fit = yes
+Fit the spectra and produce a fitted output image?
+.le
+
+The following two parameters are used in the finding, recentering, resizing,
+editing, and tracing operations.
+.ls line = INDEF
+The starting dispersion line (line or column perpendicular to the dispersion
+axis) for the tracing.  A value of INDEF starts at the middle of the image.
+.le
+.ls nsum = 1
+Number of dispersion lines to be summed or medianed at each step along
+the dispersion.  For tracing only summing is done and the sign is
+ignored.
+.le
+
+.ls threshold = 10.
+Division threshold for ratio fit type.  If a pixel in the fitted spectrum
+is less than this value then a ratio of 1 is output.
+.le
+
+The following parameters control the profile and spectrum fitting.
+.ls background = "none"
+Type of background subtraction.  The choices are "none" for no
+background subtraction, "average" to average the background within the
+background regions, or "fit" to fit across the dispersion using the
+background within the background regions.  Note that the "average"
+option does not do any medianing or bad pixel checking; it is faster
+than fitting however.  Background subtraction also requires that the
+background fitting parameters are properly defined.  For the "average"
+option only the background sample regions parameter is used.
+.le
+.ls pfit = "fit1d" (fit1d|fit2d)
+Profile fitting algorithm to use with variance weighting or cleaning.
+When determining a profile the two dimensional spectrum is divided by
+an estimate of the one dimensional spectrum to form a normalized two
+dimensional spectrum profile.  This profile is then smoothed by fitting
+one dimensional functions, "fit1d", along the lines or columns most closely
+corresponding to the dispersion axis or a special two dimensional
+function, "fit2d", described by Marsh (see \fBapprofile\fR).
+.le
+.ls clean = no
+Detect and replace deviant pixels?
+.le
+.ls skybox = 1
+Box car smoothing length for sky background when using background
+subtraction.  Since the background noise is often the limiting factor
+for good extraction one may box car smooth the sky to improve the
+statistics in smooth background regions at the expense of distorting
+the subtraction near spectral features.  This is most appropriate when
+the sky regions are limited due to a small slit length.
+.le
+.ls saturation = INDEF
+Saturation or nonlinearity level.  During variance weighted extractions
+wavelength points having any pixels above this value are excluded from the
+profile determination.
+.le
+.ls readnoise = 0.
+Read out noise in photons.  This parameter defines the minimum noise
+sigma.  It is defined in terms of photons (or electrons) and scales
+to the data values through the gain parameter.  A image header keyword
+(case insensitive) may be specified to get the value from the image.
+.le
+.ls gain = 1
+Detector gain or conversion factor between photons/electrons and
+data values.  It is specified as the number of photons per data value.
+A image header keyword (case insensitive) may be specified to get the value
+from the image.
+.le
+.ls lsigma = 3., usigma = 3.
+Lower and upper rejection thresholds, given as a number of times the
+estimated sigma of a pixel, for cleaning.
+.le
+.ih
+ADDITIONAL PARAMETERS
+I/O parameters and the default dispersion axis are taken from the
+package parameters, the default aperture parameters from
+\fBapdefault\fR, automatic aperture finding parameters from
+\fBapfind\fR, recentering parameters from \fBaprecenter\fR, resizing
+parameters from \fBapresize\fR, parameters used for centering and
+editing the apertures from \fBapedit\fR, and tracing parameters from
+\fBaptrace\fR.
+.ih
+DESCRIPTION
+The two dimensional spectra within the defined apertures of the input
+images are fit by a model and new output images are created with either
+the model spectra, the difference between the input and model spectra,
+or the ratio of input and model spectra.  The type of output is
+selected by the parameter \fIfittype\fR which may have one of the
+values "fit", "difference", or "ratio".
+
+Aperture definitions may be inherited from those of other images by
+specifying a reference image with the \fBreferences\fR parameter.
+Images in the reference list are matched with those in the
+input list in order.  If the reference image list is shorter than the
+number of input images, the last reference image is used for all
+remaining input images.  Thus, a single reference image may be given
+for all the input images or different reference images may be given for
+each input image.  The special reference name "last" may be used to
+select the last set apertures used in any of the \fBapextract\fR tasks.
+
+If an aperture reference image is not specified or no apertures are
+found for the specified reference image, previously defined apertures
+for the input image are sought in the aperture database.  Note that
+reference apertures supersede apertures for the input image.  If no
+apertures are defined they may be created automatically, the \fIfind\fR
+option, or interactively in the aperture editor, if the
+\fIinteractive\fR and \fIedit\fR options are set.
+
+The functions performed by the task are selected by a set of flag
+parameters.  The functions are an automatic spectrum finding and
+aperture defining algorithm (see \fBapfind\fR) which is ignored if
+apertures are already defined, automatic recentering and resizing
+algorithms (see \fBaprecenter\fR and \fBapresize\fR), an interactive
+aperture editing function (see \fBapedit\fR), a spectrum position tracing
+and trace function fit (see \fBaptrace\fR), and the main function of
+this task, two dimensional model fitting.
+
+Each function selection will produce a query for each input spectrum if
+the \fIinteractive\fR parameter is set.  The queries are answered by
+"yes", "no", "YES", or "NO", where the upper case responses suppress
+the query for following images.  There are other queries associated
+with tracing which first ask whether the operation is to be done
+interactively and, if yes, lead to queries for each aperture.  If the
+\fIinteractive\fR parameter is not set then aperture editing and
+interactive trace fitting are ignored.
+
+The two dimensional spectrum model consists of a smooth two dimensional
+normalized profile multiplied by the variance weighted one dimensional
+spectrum.  The profile is computed by dividing the data within the aperture
+by the one dimensional spectrum, smoothing with either low order function
+fits parallel to the dispersion axis or a special two dimensional function
+as selected by the \fIpfit\fR parameter.  The smooth profile is then used
+to improve the spectrum estimate using variance weighting and to eliminate
+deviant or cosmic ray pixels by sigma tests.  The profile algorithm is
+described in detail in \fBapprofiles\fR and the variance weighted spectrum
+is described in \fBapvariance\fR.
+
+The process of determining the profile and variance weighted spectrum,
+and hence the two dimensional spectrum model, is identical to that used
+for variance weighted extraction of the one dimensional spectra in the
+tasks \fBapall\fR or \fBapsum\fR.  Most of the parameters of in this
+task are the same as those in the extraction tasks and so further
+information about them may be found in the descriptions of those tasks.
+
+Because of the connection with variance weighted extraction and cleaning
+of one dimensional spectra, this task is useful as a diagnostic tool for
+understanding and evaluating the variance weighting algorithm.
+For example the "difference" image provides the residuals in a
+two dimensional visual form.
+
+The "fit" output image does not include any background determination;
+i.e the fit is background subtracted.  Pixels outside the modeled
+spectra are set to zero.
+
+The "difference" output image is simply the difference between the
+background subtracted "fit" and the data.  Thus the difference within
+the apertures should approximate the background and outside the
+apertures the difference will be identical with the input image.
+
+The "ratio" output image does include any background in the model
+before taking the ratio of the data and model.  If a model pixel
+is less than the given \fIthreshold\fR parameter the output ratio
+is set to one.  This is used to avoid division by zero and set a
+limit to noise in ratio image.  Outside of the apertures the ratio
+output pixels are set to one.
+.ih
+EXAMPLES
+1.  To compute the residuals of a model fit where the image already has
+aperture defined:
+
+	cl> apfit ls1 inter- rec- res- trace- read=3 gain=1 back=fit
+
+.ih
+REVISIONS
+.ls APFIND V2.11
+The "apertures" parameter can be used to select apertures for resizing,
+recentering, tracing, and extraction.  This parameter name was previously
+used for selecting apertures in the recentering algorithm.  The new
+parameter name for this is now "aprecenter".
+.le
+.ih
+SEE ALSO
+apbackground, approfile, apvariance,
+apdefault, apfind, aprecenter, apresize, apedit, aptrace, apsum, apall
+.endhelp
diff --git a/noao/twodspec/apextract/doc/apflatten.hlp b/noao/twodspec/apextract/doc/apflatten.hlp
new file mode 100644
index 00000000..f7e1b8c0
--- /dev/null
+++ b/noao/twodspec/apextract/doc/apflatten.hlp
@@ -0,0 +1,304 @@
+.help apflatten Sep96 noao.twodspec.apextract
+.ih
+NAME
+apflatten -- Create flat fields for fiber or narrow aperture spectra
+.ih
+USAGE
+apflatten input output
+.ih
+PARAMETERS
+.ls input
+List of input flat field observations.
+.le
+.ls output = ""
+List of output flat field images.  If no output name is given then the
+input name is used as a root with the extension ".flat".
+.le
+.ls apertures = ""
+Apertures to recenter, resize, trace, and flatten.  This only applies
+to apertures read from the input or reference database.  Any new
+apertures defined with the automatic finding algorithm or interactively
+are always selected.  The syntax is a list comma separated ranges
+where a range can be a single aperture number, a hyphen separated
+range of aperture numbers, or a range with a step specified by "x<step>";
+for example, "1,3-5,9-12x2".
+.le
+.ls references = ""
+List of reference images to be used to define apertures for the input
+images.  When a reference image is given it supersedes apertures
+previously defined for the input image. The list may be null, "", or
+any number of images less than or equal to the list of input images.
+There are three special words which may be used in place of an image
+name.  The word "last" refers to the last set of apertures written to
+the database.  The word "OLD" requires that an entry exist
+and the word "NEW" requires that the entry not exist for each input image.
+.le
+
+.ls interactive = yes
+Run this task interactively?  If the task is not run interactively then
+all user queries are suppressed and interactive aperture editing and trace
+fitting are disabled.
+.le
+.ls find = yes
+Find the spectra and define apertures automatically?  In order for
+spectra to be found automatically there must be no apertures for the
+input image or reference image defined in the database.
+.le
+.ls recenter = yes
+Recenter the apertures?
+.le
+.ls resize = yes
+Resize the apertures?
+.le
+.ls edit = yes
+Edit the apertures?  The \fIinteractive\fR parameter must also be yes.
+.le
+.ls trace = yes
+Trace the apertures?
+.le
+.ls fittrace = yes
+Interactively fit the traced positions by a function?  The \fIinteractive\fR
+parameter must also be yes.
+.le
+.ls flatten = yes
+Remove the profile shape and flat field spectrum leaving only
+sensitivity variations?
+.le
+.ls fitspec = yes
+Fit normalization spectrum interactively?  The \fIinteractive\fR
+parameter must also be yes.
+.le
+
+.ls line = INDEF, nsum = 1
+The dispersion line (line or column perpendicular to the dispersion
+axis) and number of adjacent lines (half before and half after unless
+at the end of the image) used in finding, recentering, resizing,
+and editing operations.  For tracing this is the starting line and
+the same number of lines are summed at each tracing point.  A line of
+INDEF selects the middle of the image along the dispersion axis.
+A positive nsum sums the lines and a negative value takes the median.
+However, for tracing only sums are allowed and the absolute value
+is used.
+.le
+.ls threshold = 10.
+Division threshold.  If a pixel in the two dimensional normalization spectrum
+is less than this value then a flat field value of 1 is output.
+.le
+
+The following parameters control the profile and spectrum fitting.
+.ls pfit = "fit1d" (fit1d|fit2d)
+Profile fitting algorithm to use with variance weighting or cleaning.
+When determining a profile the two dimensional spectrum is divided by
+an estimate of the one dimensional spectrum to form a normalized two
+dimensional spectrum profile.  This profile is then smoothed by fitting
+one dimensional functions, "fit1d", along the lines or columns most closely
+corresponding to the dispersion axis or a special two dimensional
+function, "fit2d", described by Marsh (see \fBapprofile\fR).
+.le
+.ls clean = no
+Detect and replace deviant pixels?
+.le
+.ls saturation = INDEF
+Saturation or nonlinearity level.  During variance weighted extractions
+wavelength points having any pixels above this value are excluded from the
+profile determination.
+.le
+.ls readnoise = 0.
+Read out noise in photons.  This parameter defines the minimum noise
+sigma.  It is defined in terms of photons (or electrons) and scales
+to the data values through the gain parameter.  A image header keyword
+(case insensitive) may be specified to get the value from the image.
+.le
+.ls gain = 1
+Detector gain or conversion factor between photons/electrons and
+data values.  It is specified as the number of photons per data value.
+A image header keyword (case insensitive) may be specified to get the value
+from the image.
+.le
+.ls lsigma = 3., usigma = 3.
+Lower and upper rejection thresholds, given as a number of times the
+estimated sigma of a pixel, for cleaning.
+.le
+
+The following parameters are used to fit the normalization spectrum using
+the ICFIT routine.
+.ls function = "legendre"
+Fitting function for the normalization spectra.  The choices are "legendre"
+polynomial, "chebyshev" polynomial, linear spline ("spline1"), and
+cubic spline ("spline3").
+.le
+.ls order = 1
+Number of polynomial terms or number of spline pieces for the fitting function.
+.le
+.ls sample = "*"
+Sample regions for fitting points.  Intervals are separated by "," and an
+interval may be one point or a range separated by ":".
+.le
+.ls naverage = 1
+Number of points within a sample interval to be subaveraged or submedianed to
+form fitting points.  Positive values are for averages and negative points
+for medians.
+.le
+.ls niterate = 0
+Number of sigma clipping rejection iterations.
+.le
+.ls low_reject = 3. , high_reject = 3.
+Lower and upper sigma clipping rejection threshold in units of sigma determined
+from the RMS sigma of the data to the fit.
+.le
+.ls grow = 0.
+Growing radius for rejected points (in pixels).  That is, any rejected point
+also rejects other points within this distance of the rejected point.
+.le
+.ih
+ADDITIONAL PARAMETERS
+I/O parameters and the default dispersion axis are taken from the
+package parameters, the default aperture parameters from
+\fBapdefault\fR, automatic aperture finding parameters from
+\fBapfind\fR, recentering parameters from \fBaprecenter\fR, resizing
+parameters from \fBapresize\fR, parameters used for centering and
+editing the apertures from \fBapedit\fR, and tracing parameters from
+\fBaptrace\fR.
+.ih
+DESCRIPTION
+It is sometimes the case that it is undesirable to simply divide
+two dimensional format spectra taken through fibers, aperture masks
+with small apertures such as holes and slitlets, or small slits in
+echelle formats by a flat field observation of a lamp.  This is due
+to the sharp dropoff of the flat field and object profiles and
+absence of signal outside of the profile.  Slight shifts or changes
+in profile shape introduce bad edge effects, unsightly "grass" is
+produced where there is no signal (which may also confuse extraction
+programs), and the division will also remove the characteristic
+profile of the object which might be needed for tracking the
+statistical significance, variance weighted extraction, and more.
+A straight flat field division also has the problem of changing the
+shape of the spectrum in wavelength, again compromising the
+poisson statistics and artificially boosting low signal regions.
+
+There are three approaches to consider.  First, the
+flat field correction can be done after extraction to one dimension.
+This is valid provided the flat field and object profiles don't shift
+much.  However, for extractions that depend on a smooth profile,
+such as the variance weighting algorithms of this package, the sensitivity
+corrections must remain small; i.e. no large fringes or other
+small scale variations that greatly perturb the true photon profile.
+The second approach is to divide out the overall spectral shape of
+the flat field spectrum, fill regions outside of the signal with
+one and leave the profile shape intact.  This will still cause profile
+division problems described earlier but is mentioned here since it
+implemented in a related task called \fBapnormalize\fR.  The last
+approach is to model both the profile and overall spectrum shape and
+remove it from the flat field leaving only the sensitivity variations.
+This is what the task \fBapflatten\fR does.
+
+The two dimensional flat field spectra within the defined apertures of
+the input images are fit by a model having the profile of the data and
+a smooth spectral shape.  This model is then divided into the flat
+field image within the aperture, replacing points of low signal, set
+with the \fIthreshold\fR parameter, within the aperture and all points
+outside the aperture by one to produce an output sensitivity variation
+only flat field image.
+
+A two dimensional normalized profile is computed by dividing the data
+within the aperture by the one dimensional spectrum and smoothing with
+low order function fits parallel to the dispersion axis if the aperture
+is well aligned with the axis or parallel to the traced aperture center
+if the trace is tilted relative to the dispersion axis.  The smooth
+profile is then used to improve the spectrum estimate using variance
+weighting and to eliminate deviant or cosmic ray pixels by sigma
+tests.  The profile algorithm is described in detail in
+\fBapprofiles\fR and the variance weighted spectrum is described in
+\fBapvariance\fR.
+
+The process of determining the profile and variance weighted spectrum,
+and hence the two dimensional spectrum model, is identical to that used
+for variance weighted extraction of the one dimensional spectra in the
+tasks \fBapall\fR or \fBapsum\fR and in making a two dimensional
+spectrum model in the task \fBapfit\fR.  Most of the parameters in
+this task are the same in those tasks and so further information about
+them may be found in their descriptions.  In fact, up to this point the
+task is the same as \fBapfit\fR and, if the flat field were normalized
+by this model it would produce the "ratio" output of that task.
+
+This task deviates from \fBapfit\fR in that the final variance weighted
+one dimensional spectrum of the flat field is subjected to a smoothing
+operation.  This is done by fitting a function to the spectrum using
+the \fBicfit\fR routine.  This may be done interactively or
+noninteractively depending on the \fBinteractive\fR parameter.  The
+default fitting parameters are part of this task.  The goal of the
+fitting is to follow the general spectral shape of the flat field light
+(usually a lamp) but not the small bumps and wiggles which are the one
+dimensional projection of sensitivity variations.  When the fitted
+function is multiplied into the normalize profile and then the two
+dimensional model divided into the data the sensitivity variations not
+part of the fitted spectrum are what is left in the final output flat
+field.
+
+The remainder of this description covers the basic steps defining the
+apertures to be used.  These steps and parameter are much the same as
+in any of the other \fBapextract\fR tasks.
+
+Aperture definitions may be inherited from those of other images by
+specifying a reference image with the \fBreferences\fR parameter.
+Images in the reference list are matched with those in the input list
+in order.  If the reference image list is shorter than the number of
+input images, the last reference image is used for all remaining input
+images.  Thus, a single reference image may be given for all the input
+images or different reference images may be given for each input
+image.  The special reference name "last" may be used to select the
+last set apertures used in any of the \fBapextract\fR tasks.
+
+If an aperture reference image is not specified or no apertures are
+found for the specified reference image, previously defined apertures
+for the input image are sought in the aperture database.  Note that
+reference apertures supersede apertures for the input image.  If no
+apertures are defined they may be created automatically, the \fIfind\fR
+option, or interactively in the aperture editor, if the
+\fIinteractive\fR and \fIedit\fR options are set.
+
+The functions performed by the task are selected by a set of flag
+parameters.  The functions are an automatic spectrum finding and
+aperture defining algorithm (see \fBapfind\fR) which is ignored if
+apertures are already defined, automatic recentering and resizing
+algorithms (see \fBaprecenter\fR and \fBapresize\fR), an interactive
+aperture editing function (see \fBapedit\fR), a spectrum position tracing
+and trace function fit (see \fBaptrace\fR), and the main function of
+this task, the flat field profile and spectral shape modeling and removal.
+
+Each function selection will produce a query for each input spectrum if
+the \fIinteractive\fR parameter is set.  The queries are answered by
+"yes", "no", "YES", or "NO", where the upper case responses suppress
+the query for following images.  There are other queries associated
+with tracing which first ask whether the operation is to be done
+interactively and, if yes, lead to queries for each aperture.  If the
+\fIinteractive\fR parameter is not set then aperture editing
+interactive trace fitting, and interactive spectrum shape fitting are ignored.
+.ih
+REVISIONS
+.ls APFLATTEN V2.11
+The "apertures" parameter can be used to select apertures for resizing,
+recentering, tracing, and extraction.  This parameter name was previously
+used for selecting apertures in the recentering algorithm.  The new
+parameter name for this is now "aprecenter".
+.le
+.ih
+EXAMPLES
+1.  To make a two dimensional flat field from a lamp observation:
+
+.nf
+	cl> apflatten fiber1 flat read=3 gain=1 back=fit
+	Yes find
+	No resize
+	No edit
+	Yes trace
+	Yes trace interactively
+	NO
+	Yes flatten
+	Yes fit interactively
+.fi
+.ih
+SEE ALSO
+apbackground, approfile, apvariance, apfit, icfit,
+apdefault, apfind, aprecenter, apresize, apedit, aptrace, apsum
+.endhelp
diff --git a/noao/twodspec/apextract/doc/apmask.hlp b/noao/twodspec/apextract/doc/apmask.hlp
new file mode 100644
index 00000000..78d775f9
--- /dev/null
+++ b/noao/twodspec/apextract/doc/apmask.hlp
@@ -0,0 +1,123 @@
+.help apmask Sep96 noao.twodspec.apextract
+.ih
+NAME
+apmask -- Make pixel mask from apertures definitions
+.ih
+USAGE
+apfind input
+.ih
+PARAMETERS
+.ls input
+List of input images with aperture definitions.
+.le
+.ls output
+List of output mask names.  As a convention the extension ".pl" (pixel
+list) should be used.
+.le
+.ls apertures = ""
+Apertures to recenter, resize, trace, and create a mask.  This only applies
+to apertures read from the input or reference database.  Any new
+apertures defined with the automatic finding algorithm or interactively
+are always selected.  The syntax is a list comma separated ranges
+where a range can be a single aperture number, a hyphen separated
+range of aperture numbers, or a range with a step specified by "x<step>";
+for example, "1,3-5,9-12x2".
+.le
+.ls references = ""
+List of reference images to be used to define apertures for the input
+images.  When a reference image is given it supersedes apertures
+previously defined for the input image. The list may be null, "", or
+any number of images less than or equal to the list of input images.
+There are three special words which may be used in place of an image
+name.  The word "last" refers to the last set of apertures written to
+the database.  The word "OLD" requires that an entry exist
+and the word "NEW" requires that the entry not exist for each input image.
+.le
+
+.ls interactive = no
+Run this task interactively?  If the task is not run interactively then
+all user queries are suppressed and interactive aperture editing is
+disabled.
+.le
+.ls find = yes
+Find the spectra and define apertures automatically?  In order for
+spectra to be found automatically there must be no apertures for the
+input image or reference image defined in the database and the
+parameter \fInfind\fR must be greater than zero.
+.le
+.ls recenter = no
+Recenter the apertures?
+.le
+.ls resize = no
+Resize the apertures?
+.le
+.ls edit = yes
+Edit the apertures?  The \fIinteractive\fR parameter must also be yes.
+.le
+.ls trace = yes
+Trace apertures?
+.le
+.ls fittrace = yes
+Fit the traced points interactively?  The \fIinteractive\fR parameter
+must also be yes.
+.le
+.ls mask = yes
+Create mask images?
+.le
+
+.ls line = INDEF
+The dispersion line (line or column perpendicular to the dispersion axis) to
+be used in finding, recentering, resizing, editing, and starting to
+trace spectra.  A value of INDEF selects the middle of the image.
+.le
+.ls nsum = 1
+Number of dispersion lines to be summed or medianed.  The lines are taken
+around the specified dispersion line.  A positive value takes the
+sum and a negative value selects a median.
+.le
+.ls buffer = 0.
+Buffer to add to aperture limits.  One use for this is to increase
+the width of the apertures when a mask is used to fit data between
+the apertures.
+.le
+.ih
+ADDITIONAL PARAMETERS
+I/O parameters and the default dispersion axis are taken from the
+package parameters, the default aperture parameters from
+\fBapdefault\fR, automatic aperture finding parameters from
+\fBapfind\fR, recentering parameters from \fBaprecenter\fR, resizing
+parameters from \fBapresize\fR, parameters used for centering and
+editing the apertures from \fBapedit\fR, and tracing parameters from
+\fBaptrace\fR.
+.ih
+DESCRIPTION
+Pixel list masks are created from the aperture definitions in the input
+images.  Pixel list masks are a compact way to define arbitrary
+regions of an image.  The masks may be used directly as an image with values
+of 1 (in an aperture) and 0 (outside an aperture).  Alternatively,
+some tasks may use a mask to define regions to be operated upon.
+When this task was written there were no such tasks though eventually
+some tasks will be converted to use this general format.  The intent
+of making an aperture mask is to someday allow using it with the task
+\fBimsurfit\fR to fit a background or scattered light surface.
+(See \fBapscatter\fR for an alternative method).
+.ih
+EXAMPLES
+1. To replace all data outside the apertures by zero:
+
+.nf
+	cl> apmask image image.pl nfind=10
+	cl> imarith image * image.pl image1
+.fi
+.ih
+REVISIONS
+.ls APMASK V2.11
+The "apertures" parameter can be used to select apertures for resizing,
+recentering, tracing, and extraction.  This parameter name was previously
+used for selecting apertures in the recentering algorithm.  The new
+parameter name for this is now "aprecenter".
+.le
+.ih
+SEE ALSO
+apdefault, aprecenter, apresize, apedit, aptrace, apall
+.endhelp
diff --git a/noao/twodspec/apextract/doc/apnoise.hlp b/noao/twodspec/apextract/doc/apnoise.hlp
new file mode 100644
index 00000000..a4f69f83
--- /dev/null
+++ b/noao/twodspec/apextract/doc/apnoise.hlp
@@ -0,0 +1,231 @@
+.help apnoise Sep96 noao.twodspec.apextract
+.ih
+NAME
+apnoise -- Compute and examine noise characteristics of spectra
+.ih
+USAGE
+apnoise input dmin dmax nbins
+.ih
+PARAMETERS
+.ls input
+List of input spectra to examine.
+.le
+.ls apertures = ""
+Apertures to recenter, resize, trace, and extract.  This only applies
+to apertures read from the input or reference database.  Any new
+apertures defined with the automatic finding algorithm or interactively
+are always selected.  The syntax is a list comma separated ranges
+where a range can be a single aperture number, a hyphen separated
+range of aperture numbers, or a range with a step specified by "x<step>";
+for example, "1,3-5,9-12x2".
+.le
+.ls references = ""
+List of reference images to be used to define apertures for the input
+images.  When a reference image is given it supersedes apertures
+previously defined for the input image. The list may be null, "", or
+any number of images less than or equal to the list of input images.
+There are three special words which may be used in place of an image
+name.  The word "last" refers to the last set of apertures written to
+the database.  The word "OLD" requires that an entry exist
+and the word "NEW" requires that the entry not exist for each input image.
+.le
+
+.ls dmin, dmax, nbins
+The noise sigma is computed in a set of bins over the specified
+range of image data numbers.
+.le
+
+.ls interactive = yes
+Run this task interactively?  If the task is not run interactively then
+all user queries are suppressed and interactive aperture editing and trace
+fitting are disabled.
+.le
+.ls find = yes
+Find the spectra and define apertures automatically?  In order for
+spectra to be found automatically there must be no apertures for the
+input image or reference image defined in the database.
+.le
+.ls recenter = yes
+Recenter the apertures?
+.le
+.ls resize = yes
+Resize the apertures?
+.le
+.ls edit = yes
+Edit the apertures?  The \fIinteractive\fR parameter must also be yes.
+.le
+.ls trace = yes
+Trace the apertures?
+.le
+.ls fittrace = yes
+Interactively fit the traced positions by a function?  The \fIinteractive\fR
+parameter must also be yes.
+.le
+
+.ls line = INDEF, nsum = 1
+The dispersion line (line or column perpendicular to the dispersion
+axis) and number of adjacent lines (half before and half after unless
+at the end of the image) used in finding, recentering, resizing,
+and editing operations.  For tracing this is the starting line and
+the same number of lines are summed at each tracing point.  A line of
+INDEF selects the middle of the image along the dispersion axis.
+A positive nsum sums the lines and a negative value takes the median.
+However, for tracing only sums are allowed and the absolute value
+is used.
+.le
+.ls threshold = 10.
+Division threshold.  If a pixel in the two dimensional normalization spectrum
+is less than this value then a flat field value of 1 is output.
+.le
+
+The following parameters control the profile and spectrum fitting.
+.ls background = "none"
+Type of background subtraction.  The choices are "none" for no
+background subtraction, "average" to average the background within the
+background regions, or "fit" to fit across the dispersion using the
+background within the background regions.  Note that the "average"
+option does not do any medianing or bad pixel checking; it is faster
+than fitting however.  Background subtraction also requires that the
+background fitting parameters are properly defined.  For the "average"
+option only the background sample regions parameter is used.
+.le
+.ls pfit = "fit1d" (fit1d|fit2d)
+Profile fitting algorithm to use with variance weighting or cleaning.
+When determining a profile the two dimensional spectrum is divided by
+an estimate of the one dimensional spectrum to form a normalized two
+dimensional spectrum profile.  This profile is then smoothed by fitting
+one dimensional functions, "fit1d", along the lines or columns most closely
+corresponding to the dispersion axis or a special two dimensional
+function, "fit2d", described by Marsh (see \fBapprofile\fR).
+.le
+.ls clean = no
+Detect and replace deviant pixels?
+.le
+.ls skybox = 1
+Box car smoothing length for sky background when using background
+subtraction.  Since the background noise is often the limiting factor
+for good extraction one may box car smooth the sky to improve the
+statistics in smooth background regions at the expense of distorting
+the subtraction near spectral features.  This is most appropriate when
+the sky regions are limited due to a small slit length.
+.le
+.ls saturation = INDEF
+Saturation or nonlinearity level.  During variance weighted extractions
+wavelength points having any pixels above this value are excluded from the
+profile determination.
+.le
+.ls readnoise = "0."
+Read out noise in photons.  This parameter defines the minimum noise
+sigma.  It is defined in terms of photons (or electrons) and scales
+to the data values through the gain parameter.  A image header keyword
+(case insensitive) may be specified to get the value from the image.
+.le
+.ls gain = "1."
+Detector gain or conversion factor between photons/electrons and
+data values.  It is specified as the number of photons per data value.
+A image header keyword (case insensitive) may be specified to get the value
+from the image.
+.le
+.ls lsigma = 3., usigma = 3.
+Lower and upper rejection thresholds, given as a number of times the
+estimated sigma of a pixel, for cleaning.
+.le
+.ih
+ADDITIONAL PARAMETERS
+I/O parameters and the default dispersion axis are taken from the
+package parameters, the default aperture parameters from
+\fBapdefault\fR, automatic aperture finding parameters from
+\fBapfind\fR, recentering parameters from \fBaprecenter\fR, resizing
+parameters from \fBapresize\fR, parameters used for centering and
+editing the apertures from \fBapedit\fR, and tracing parameters from
+\fBaptrace\fR.
+.ih
+CURSOR COMMANDS
+The following cursor keys and colon commands are available during the
+display of the noise sigmas and noise model.  See \fBapedit\fR for
+the commands for that mode.
+
+.nf
+?  Print command help
+q  Quit
+r  Redraw	
+w  Window the graph (see :/help)
+I  Interupt immediately
+
+:gain <value>		Check or set the gain model parameter
+:readnoise <value>	Check or set the read noise model parameter
+
+Also see the CURSOR MODE commands (:.help) and the windowing commands
+(:/help).
+.fi
+.ih
+DESCRIPTION
+\fBApnoise\fR computes the noise sigma as a function of data value
+using the same profile model used for weighted extraction and
+cosmic ray cleanning.  In particular, the residuals used in computing the
+noise sigma are the same as those during cleanning.  By looking
+at the noise sigma as a function of data value as compared to that
+predicted by the noise model based on the read out noise and gain
+parameters one can then better refine these values for proper
+rejection of cosmic rays without rejection of valid data.
+So this task can be used to check or deduce these values and also
+to adjust them to include additional sources of error such as
+flat field noise and, especially, an additional source of noise due
+to the accuracy of the profile modeling.
+
+The first part of this task follows the standard model of allowing
+one to define apertures by finding, recentering, editing, and
+tracing.  If one has previously defined apertures then these
+steps can be skipped.  Once the apertures are defined the apertures
+are internally extracted using the profile modeling (see \fBapprofile\fR)
+with the optional background subtraction, cleanning, and choices of
+profile fitting algorithm, "fit1d" or "fit2d".  But rather than
+outputing the extracted spectrum as in \fBapsum\fR or \fBapall\fR
+or various functions of the data and profile model as in \fBapfit\fR,
+\fBapnormalize\fR, or \fBapflatten\fR, the task computes the
+residuals for all points in all apertures (essentially the same
+as the difference output of \fBapfit\fR) and determines the
+sigma (population corrected RMS) as a function of model data value
+in the specified bins.  The bins are defined by a minimum and
+maximum data value (found using \fBminmax\fR, \fBimplot\fR, or
+\fBimexamine\fR) and the number of bins.
+
+The noise sigma values, with their estimated uncertainties, are then
+plotted as a function of data numer.  A curve representing the specified
+read out noise and gain is also plotted.  The user then has the
+option of varying these two parameters with colon commands.  The
+aim of this is to find a noise model which either represents the
+measure noise sigmas or at least exceeds them so that only valid
+outliers such as cosmic rays will be rejected during cleanning.
+The interactive graphical mode only has this function.  The other
+keys and colon commands are the standard ones for redrawing, windowing,
+and quitting.
+.ih
+EXAMPLES
+1.  To check that the read noise and gain parameters are reasonable for
+cleaning \fBapnoise\fR is run.  In this case it is assumed that the
+apertures have already been defined and traced.
+
+.nf
+	cl> minmax lsobj
+	    lsobj  -2.058870315551758  490.3247375488282
+	cl> apnoise lsobj 0 500 50 rece- resi- edit- trace-
+	    A graph of the noise sigma for data between 0 and 500
+	    data numbers is given with a line showing the
+	    expected value for the current read noise and gain.
+	    The read noise and gain may be varied if desired.
+	    Exit with 'q'
+.fi
+.ih
+REVISIONS
+.ls APNOISE V2.11
+The "apertures" parameter can be used to select apertures for resizing,
+recentering, tracing, and extraction.  This parameter name was previously
+used for selecting apertures in the recentering algorithm.  The new
+parameter name for this is now "aprecenter".
+.le
+.ih
+SEE ALSO
+apbackground, approfile, apvariance, apfit, icfit, minmax,
+apdefault, apfind, aprecenter, apresize, apedit, aptrace, apsum
+.endhelp
diff --git a/noao/twodspec/apextract/doc/apnormalize.hlp b/noao/twodspec/apextract/doc/apnormalize.hlp
new file mode 100644
index 00000000..fda3fd31
--- /dev/null
+++ b/noao/twodspec/apextract/doc/apnormalize.hlp
@@ -0,0 +1,324 @@
+.help apnormalize Sep96 noao.twodspec.apextract
+.ih
+NAME
+apnormalize -- Normalize 2D apertures by 1D functions
+.ih
+USAGE
+apnormalize input output
+.ih
+PARAMETERS
+.ls input
+List of input images to be normalized.
+.le
+.ls output
+List of output image names for the normalized input images.  If no output
+name is given then the input name is used as a root with the extension
+".norm" added.
+.le
+.ls apertures = ""
+Apertures to recenter, resize, trace, and normalize.  This only applies
+to apertures read from the input or reference database.  Any new
+apertures defined with the automatic finding algorithm or interactively
+are always selected.  The syntax is a list comma separated ranges
+where a range can be a single aperture number, a hyphen separated
+range of aperture numbers, or a range with a step specified by "x<step>";
+for example, "1,3-5,9-12x2".
+.le
+.ls references = ""
+List of reference images to be used to define apertures for the input
+images.  When a reference image is given it supersedes apertures
+previously defined for the input image. The list may be null, "", or
+any number of images less than or equal to the list of input images.
+There are three special words which may be used in place of an image
+name.  The word "last" refers to the last set of apertures written to
+the database.  The word "OLD" requires that an entry exist
+and the word "NEW" requires that the entry not exist for each input image.
+.le
+
+.ls interactive = yes
+Run this task interactively?  If the task is not run interactively then
+all user queries are suppressed and interactive aperture editing and trace
+fitting are disabled.
+.le
+.ls find = yes
+Find the spectra and define apertures automatically?  In order for
+spectra to be found automatically there must be no apertures for the
+input image or reference image defined in the database.
+.le
+.ls recenter = yes
+Recenter the apertures?
+.le
+.ls resize = yes
+Resize the apertures?
+.le
+.ls edit = yes
+Edit the apertures?  The \fIinteractive\fR parameter must also be yes.
+.le
+.ls trace = yes
+Trace the apertures?
+.le
+.ls fittrace = yes
+Interactively fit the traced positions by a function?  The \fIinteractive\fR
+parameter must also be yes.
+.le
+.ls normalize = yes
+Normalize the aperture spectra by a one dimensional function?
+.le
+.ls fitspec = yes
+Fit normalization spectrum interactively?  The \fIinteractive\fR
+parameter must also be yes.
+.le
+
+.ls line = INDEF, nsum = 1
+The dispersion line (line or column perpendicular to the dispersion
+axis) and number of adjacent lines (half before and half after unless
+at the end of the image) used in finding, recentering, resizing,
+and editing operations.  For tracing this is the starting line and
+the same number of lines are summed at each tracing point.  A line of
+INDEF selects the middle of the image along the dispersion axis.
+A negative nsum selects a median rather than a sum except that
+tracing always uses a sum.
+.le
+.ls cennorm = no
+Normalize to the aperture center rather than the mean?
+.le
+.ls threshold = 10.
+All pixels in the normalization spectrum less than this value are replaced
+by this value.
+.le
+
+The following parameters control the normalization spectrum extraction.
+.ls background = "none"
+Type of background subtraction.  The choices are "none" for no
+background subtraction, "average" to average the background within the
+background regions, or "fit" to fit across the dispersion using the
+background within the background regions.  Note that the "average"
+option does not do any medianing or bad pixel checking; it is faster
+than fitting however.  Background subtraction also requires that the
+background fitting parameters are properly defined.  For the "average"
+option only the background sample regions parameter is used.
+.le
+.ls weights = "none"
+Type of extraction weighting.  Note that if the \fIclean\fR parameter is
+set then the weights used are "variance" regardless of the weights
+specified by this parameter.  The choices are:
+.ls "none"
+The pixels are summed without weights except for partial pixels at the
+ends.
+.le
+.ls "variance"
+The extraction is weighted by estimated variances of the pixels using
+a poisson noise model.
+.le
+.le
+.ls pfit = "fit1d" (fit1d|fit2d)
+Profile fitting algorithm to use with variance weighting or cleaning.
+When determining a profile the two dimensional spectrum is divided by
+an estimate of the one dimensional spectrum to form a normalized two
+dimensional spectrum profile.  This profile is then smoothed by fitting
+one dimensional functions, "fit1d", along the lines or columns most closely
+corresponding to the dispersion axis or a special two dimensional
+function, "fit2d", described by Marsh (see \fBapprofile\fR).
+.le
+.ls clean = no
+Detect and replace deviant pixels?
+.le
+.ls skybox = 1
+Box car smoothing length for sky background when using background
+subtraction.  Since the background noise is often the limiting factor
+for good extraction one may box car smooth the sky to improve the
+statistics in smooth background regions at the expense of distorting
+the subtraction near spectral features.  This is most appropriate when
+the sky regions are limited due to a small slit length.
+.le
+.ls saturation = INDEF
+Saturation or nonlinearity level.  During variance weighted extractions
+wavelength points having any pixels above this value are excluded from the
+profile determination.
+.le
+.ls readnoise = 0.
+Read out noise in photons.  This parameter defines the minimum noise
+sigma.  It is defined in terms of photons (or electrons) and scales
+to the data values through the gain parameter.  A image header keyword
+(case insensitive) may be specified to get the value from the image.
+.le
+.ls gain = 1
+Detector gain or conversion factor between photons/electrons and
+data values.  It is specified as the number of photons per data value.
+A image header keyword (case insensitive) may be specified to get the value
+from the image.
+.le
+.ls lsigma = 3., usigma = 3.
+Lower and upper rejection thresholds, given as a number of times the
+estimated sigma of a pixel, for cleaning.
+.le
+
+The following parameters are used to fit the normalization spectrum using
+the ICFIT routine.
+.ls function = "legendre"
+Fitting function for the normalization spectra.  The choices are "legendre"
+polynomial, "chebyshev" polynomial, linear spline ("spline1"), and
+cubic spline ("spline3").
+.le
+.ls order = 1
+Number of polynomial terms or number of spline pieces for the fitting function.
+.le
+.ls sample = "*"
+Sample regions for fitting points.  Intervals are separated by "," and an
+interval may be one point or a range separated by ":".
+.le
+.ls naverage = 1
+Number of points within a sample interval to be subaveraged or submedianed to
+form fitting points.  Positive values are for averages and negative points
+for medians.
+.le
+.ls niterate = 0
+Number of sigma clipping rejection iterations.
+.le
+.ls low_reject = 3. , high_reject = 3.
+Lower and upper sigma clipping rejection threshold in units of sigma determined
+from the RMS sigma of the data to the fit.
+.le
+.ls grow = 0.
+Growing radius for rejected points (in pixels).  That is, any rejected point
+also rejects other points within this distance of the rejected point.
+.le
+.ih
+ADDITIONAL PARAMETERS
+I/O parameters and the default dispersion axis are taken from the
+package parameters, the default aperture parameters from
+\fBapdefault\fR, automatic aperture finding parameters from
+\fBapfind\fR, recentering parameters from \fBaprecenter\fR, resizing
+parameters from \fBapresize\fR, parameters used for centering and
+editing the apertures from \fBapedit\fR, and tracing parameters from
+\fBaptrace\fR.
+.ih
+DESCRIPTION
+For each image in the input image list the two dimensional spectra
+defined by a set of apertures are normalized by a one dimensional
+normalization function derived by extracting and smoothing the spectrum
+by fitting a function with the \fBicfit\fR procedure.  The value of the
+fitting function at each point along the dispersion, divided by the
+aperture width to form a mean or scaled to the same mean as the center
+pixel of the aperture depending on the \fIcennorm\fR parameter, is
+divided into the two dimensional input aperture.  All points outside
+the apertures are set to unity.
+
+The purpose of this task is to remove a general shape from the aperture
+spectra.  If low order (order = 1 for instance) functions are used then
+only the amplitudes of the spectra are affected, shifting each aperture
+to approximately unit intensity per pixel.  If high order functions are
+used only the small spatial scale variations are preserved.  This
+is useful for making flat field images with the spectral signature of the
+continuum source removed or for producing two dimensional normalized
+spectra similar to the task \fBonedspec.continuum\fR.  For flat fields
+this algorithm retains the profile shape which may be useful for
+removing the profile response in short slit data.  However, often
+one does not want the profile of the flat fielded observation to be
+modified in which case the task \fBapflatten\fR should be used.
+
+The normalization spectrum is first extracted in the same way as is
+the one dimensional extraction in \fBapsum\fR or \fBapall\fR.  In
+particular the same parameters for selecting weighting and cleaning
+are available.  After extraction the spectrum is fit using the
+\fBicfit\fR routine.  This may be done interactively or noninteractively
+depending on the \fIinteractive\fR parameter.  The default fitting
+parameters are part of this task.  The goal of the fitting depends
+on the application.  One may be trying to simply continuum normalize,
+in which case one wants to iteratively reject and grow the rejected
+points to exclude the lines and fit the continuum with a
+moderate order function (see \fBcontinuum\fR for more discussion).  
+If one wants to simply normalize all spectra to a common flux, say to
+remove a blaze function in echelle data, then an order of 1 will
+normalize by a constant.  For flat field and profile correction of
+small slits one wants to fit the large scale shape of the
+spectrum but not fit the small bumps and wiggles due to sensitivity
+variations and fringing.
+
+The smoothed extracted spectrum represents the total flux within the
+aperture.  There are two choices for scaling to a normalization per
+pixel.  One is to divide by the aperture width, thus computing an average
+flux normalization.  In this case the peak of the spectrum will be
+greater than unity.  This is done when \fIcennorm\fR = no.  When this
+parameter has the value yes then the mean of the normalization spectrum
+is scaled to the mean of the aperture center, computed by linearly
+interpolating the two pixels about the traced center.  This will give
+values near one for the pixels at the center of the aperture in the
+final output image.
+
+Before division of each pixel by the appropriate dispersion point in
+the normalization spectrum, all pixels below the value specified by the
+\fIthreshold\fR parameter in the normalization spectrum are replaced by
+the threshold value.  This suppresses division by very small numbers.
+Finally, the pixels within the aperture are divided by the normalization
+function and the pixels outside the apertures are set to 1.
+
+The remainder of this description covers the basic steps defining the
+apertures to be used.  These steps and parameter are much the same as
+in any of the other \fBapextract\fR tasks.
+
+Aperture definitions may be inherited from those of other images by
+specifying a reference image with the \fBreferences\fR parameter.
+Images in the reference list are matched with those in the input list
+in order.  If the reference image list is shorter than the number of
+input images, the last reference image is used for all remaining input
+images.  Thus, a single reference image may be given for all the input
+images or different reference images may be given for each input
+image.  The special reference name "last" may be used to select the
+last set apertures used in any of the \fBapextract\fR tasks.
+
+If an aperture reference image is not specified or no apertures are
+found for the specified reference image, previously defined apertures
+for the input image are sought in the aperture database.  Note that
+reference apertures supersede apertures for the input image.  If no
+apertures are defined they may be created automatically, the \fIfind\fR
+option, or interactively in the aperture editor, if the
+\fIinteractive\fR and \fIedit\fR options are set.
+
+The functions performed by the task are selected by a set of flag
+parameters.  The functions are an automatic spectrum finding and
+aperture defining algorithm (see \fBapfind\fR) which is ignored if
+apertures are already defined, automatic recentering and resizing
+algorithms (see \fBaprecenter\fR and \fBapresize\fR), an interactive
+aperture editing function (see \fBapedit\fR), a spectrum position tracing
+and trace function fit (see \fBaptrace\fR), and the main function of
+this task, the one dimensional normalization of the aperture
+profiles.
+
+Each function selection will produce a query for each input spectrum if
+the \fIinteractive\fR parameter is set.  The queries are answered by
+"yes", "no", "YES", or "NO", where the upper case responses suppress
+the query for following images.  There are other queries associated
+with tracing which first ask whether the operation is to be done
+interactively and, if yes, lead to queries for each aperture.  If the
+\fIinteractive\fR parameter is not set then aperture editing,
+interactive trace fitting, and interactive spectrum shape fitting are ignored.
+.ih
+EXAMPLES
+To make a flat field image which leaves the total counts of the object
+images approximately unchanged from a quartz echelle or slitlet image:
+
+.nf
+	cl> apnormalize qtz001,qtz002 flat001,flat002
+	Yes find
+	No resize
+	No edit
+	Yes trace
+	Yes trace interactively
+	NO
+	Yes flatten
+	Yes fit interactively
+.fi
+.ih
+REVISIONS
+.ls APNORMALIZE V2.11
+The "apertures" parameter can be used to select apertures for resizing,
+recentering, tracing, and extraction.  This parameter name was previously
+used for selecting apertures in the recentering algorithm.  The new
+parameter name for this is now "aprecenter".
+.le
+.ih
+SEE ALSO
+apbackground, approfile, apvariance, apfit, icfit,
+apdefault, apfind, aprecenter, apresize, apedit, aptrace, apsum
+.endhelp
diff --git a/noao/twodspec/apextract/doc/approfiles.hlp b/noao/twodspec/apextract/doc/approfiles.hlp
new file mode 100644
index 00000000..43ae774a
--- /dev/null
+++ b/noao/twodspec/apextract/doc/approfiles.hlp
@@ -0,0 +1,131 @@
+.help approfiles Feb93 noao.twodspec.apextract
+
+.ce
+Spectrum Profile Determinations
+
+
+The foundation of variance weighted or optimal extraction, cosmic ray
+detection and removal, two dimensional flat field normalization, and
+spectrum fitting and modeling is the accurate determination of the
+spectrum profile across the dispersion as a function of wavelength.
+The previous version of the APEXTRACT package accomplished this by
+averaging a specified number of profiles in the vicinity of each
+wavelength after correcting for shifts in the center of the profile.
+This technique was sensitive to perturbations from cosmic rays
+and the exact choice of averaging parameters.  The current version of
+the package uses two different algorithm which are much more stable.
+
+The basic idea is to normalize each profile along the dispersion to
+unit flux and then fit a low order function to sets of unsaturated
+points at nearly the same point in the profile parallel to the
+dispersion.  The important point here is that points at the same
+distance from the profile center should have the nearly the same values
+once the continuum shape and spectral features have been divided out.
+Any variations are due to slow changes in the shape of the profile with
+wavelength, differences in the exact point on the profile, pixel
+binning or sampling, and noise.  Except for the noise, the variations
+should be slow and a low order function smoothing over many points will
+minimize the noise and be relatively insensitive to bad pixels such as
+cosmic rays.  Effects from bad pixels may be further eliminated by
+chi-squared iteration and clipping.  Since there will be many points
+per degree of freedom in the fitting function the clipping may even be
+quite aggressive without significantly affecting the profile
+estimates.  Effects from saturated pixels are minimized by excluding
+from the profile determination any profiles containing one or more
+saturated pixels as defined by the \fIsaturation\fR parameter.
+
+The normalization is, in fact, the one dimensional spectrum.  Initially
+this is the simple sum across the aperture which is then updated by the
+variance weighted sum with deviant pixels possibly removed.  This updated
+one dimensional spectrum is what is meant by the profile normalization
+factor in the discussion below.  The two dimensional spectrum model or
+estimate is the product of the normalization factor and the profile.  This
+model is used for estimating the pixel intensities and, thence, the
+variances.
+
+There are two important requirements that must be met by the profile fitting
+algorithm.  First it is essential that the image data not be
+interpolated.  Any interpolation introduces correlated errors and
+broadens cosmic rays to an extent that they may be confused with the
+spectrum profile, particularly when the profile is narrow.  This was
+one of the problems limiting the shift and average method used
+previously.  The second requirement is that data fit by the smoothing
+function vary slowly with wavelength.  This is what precludes, for
+instance, fitting profile functions across the dispersion since narrow,
+marginally sampled profiles require a high order function using only a
+very few points.  One exception to this, which is sometimes useful but
+of less generality, is methods which assume a model for the profile
+shape such as a gaussian.  In the methods used here there is no
+assumption made about the underlying profile other than it vary
+smoothly with wavelength.
+
+These requirements lead to two fitting algorithms which the user
+selects with the \fIpfit\fR parameter.  The primary method, "fit1d",
+fits low order, one dimensional functions to the lines or columns
+most nearly parallel to the dispersion.  While this is intended for
+spectra which are well aligned with the image axes, even fairly large
+excursions or tilts can be adequately fit in this
+way.  When the spectra become strongly tilted then single lines or
+columns may cross the actual profile relatively quickly causing the
+requirement of a slow variation to be violated.  One thought is to use
+interpolation to fit points always at the same distance from the
+profile.  This is ruled out by the problems introduced by
+image interpolation.  However, there is a clever method which, in
+effect, fits low order polynomials parallel to the direction defined by
+tracing the spectrum but which does not interpolate the image data.
+Instead it weights and couples polynomial coefficients.  This
+method was developed by Tom Marsh and is described in detail in the
+paper, "The Extraction of Highly Distorted Spectra", PASP 101, 1032,
+Nov. 1989.  Here we refer to this method as the Marsh or "fit2d"
+algorithm and do not attempt to explain it further.
+
+The choice of when to use the one dimensional or the two dimensional
+fitting is left to the user.  The "fit1d" algorithm is preferable since it
+is faster, easier to understand, and has proved to be very robust.  The
+"fit2d" algorithm usually works just as well but is slower and has been
+seen to fail on some data.  The user may simply try both to achieve the
+best results.
+
+What follows are some implementation details of the preceding ideas in the
+APEXTRACT package.  For column/line fitting, the fitting function is a
+cubic spline.  A base number of spline pieces is set by rounding up the
+maximum trace excursion; an excursion of 1.2 pixels would use a spline of 2
+pieces.  To this base number is added the number of coefficients in the
+trace function in excess of two; i.e. the number of terms in excess of a
+linear function.  This is done because if the trace wiggles a large amount
+then a higher order function will be needed to fit a line or column as the
+profile shifts under it.  Finally the number of pieces is doubled
+because experience shows that for low tilts it doesn't matter but for
+large tilts this improves the results dramatically.
+
+For the Marsh algorithm there are two parameters to be set, the
+polynomial order parallel to the dispersion and the spacing between
+parallel, coupled polynomials.  The algorithm requires that the spacing
+be less than a pixel to provide sufficient sampling.  The spacing is
+arbitrarily set at 0.95 pixels.  Because the method always fits
+polynomials to points at the same position of the profile the order
+should be 1 except for variations in the profile shape with
+wavelength.  To allow for this the profile order is set at 10; i.e. a
+9th order function.  A final parameter in the algorithm is the number
+of polynomials across the profile but this is obviously  determined
+from the polynomial spacing and the width of the aperture including an
+extra pixel on either side.
+
+Both fitting algorithms weight the pixels by their variance as computed
+from the background and background variance if background subtraction
+is specified, the spectrum estimate from the profile and the spectrum
+normalization, and the detector noise parameters.  A poisson
+plus constant gaussian readout noise model is used.  The noise model is
+described further in \fBapvariance\fR.
+
+As mentioned earlier, the profile fitting can be iterated to remove
+deviant pixels.  This is done by rejecting pixels greater than a
+specified number of sigmas above or below the expected value based
+on the profile, the normalization factor, the background, the
+detector noise parameters, and the overall chi square of the residuals.
+Rejected points are removed from the profile normalization and
+from the fits.
+.ih
+SEE ALSO
+apbackground apvariance apall apsum apfit apflatten
+.endhelp
diff --git a/noao/twodspec/apextract/doc/aprecenter.hlp b/noao/twodspec/apextract/doc/aprecenter.hlp
new file mode 100644
index 00000000..5a05cb36
--- /dev/null
+++ b/noao/twodspec/apextract/doc/aprecenter.hlp
@@ -0,0 +1,148 @@
+.help aprecenter Sep96 noao.twodspec.apextract
+.ih
+NAME
+aprecenter -- Recenter apertures automatically
+.ih
+USAGE
+aprecenter input
+.ih
+PARAMETERS
+.ls input
+List of input images in which apertures are to be recentered.
+.le
+.ls apertures = ""
+Apertures to recenter, resize, trace, and extract.  This only applies
+to apertures read from the input or reference database.  Any new
+apertures defined with the automatic finding algorithm or interactively
+are always selected.  The syntax is a list comma separated ranges
+where a range can be a single aperture number, a hyphen separated
+range of aperture numbers, or a range with a step specified by "x<step>";
+for example, "1,3-5,9-12x2".
+.le
+.ls references = ""
+List of reference images to be used to define apertures for the input
+images.  When a reference image is given it supersedes apertures
+previously defined for the input image. The list may be null, "", or
+any number of images less than or equal to the list of input images.
+There are three special words which may be used in place of an image
+name.  The word "last" refers to the last set of apertures written to
+the database.  The word "OLD" requires that an entry exist
+and the word "NEW" requires that the entry not exist for each input image.
+.le
+.ls interactive = no
+Run this task interactively?  If the task is not run interactively then
+all user queries are suppressed and interactive aperture editing is
+disabled.
+.le
+.ls find = yes
+Find the spectra and define apertures automatically?  In order for
+spectra to be found automatically there must be no apertures for the
+input image or reference image defined in the database.
+.le
+.ls recenter = yes
+Recenter the apertures?
+.le
+.ls resize = no
+Resize the apertures?
+.le
+.ls edit = yes
+Edit the apertures?  The \fIinteractive\fR parameter must also be yes.
+.le
+
+.ls line = INDEF
+The dispersion line (line or column perpendicular to the dispersion axis) to
+be used in recentering the spectra.  A value of INDEF selects the middle of the
+image.
+.le
+.ls nsum = 1
+Number of dispersion lines to be summed or medianed.  The lines are taken
+around the specified dispersion line.  A positive value takes a sum
+and a negative values selects a median.
+.le
+.ls aprecenter = ""
+List of apertures to be used in shift calculation.
+.le
+.ls npeaks = INDEF
+Select the specified number of apertures with the highest peak values
+to be recentered.  If the number is INDEF all apertures will be selected.
+If the value is less than 1 then the value is interpreted as a fraction
+of total number of apertures.
+.le
+.ls shift = yes
+Use the median shift from recentering the selected apertures to apply to
+all apertures.  The recentering is then a constant shift for all apertures.
+The median is the average of the two central values for an even number
+of apertures.
+.le
+.ih
+ADDITIONAL PARAMETERS
+I/O parameters and the default dispersion axis are taken from the
+package parameters, the default aperture parameters are taken from the
+task \fBapdefault\fR, automatic aperture finding parameters are taken
+from \fBapfind\fR, and parameters used for centering and editing the
+apertures are taken from \fBapedit\fR.
+
+When this operation is performed from the task \fBapall\fR all parameters
+except the package parameters are included in that task.
+.ih
+DESCRIPTION
+For each image in the input image list, the aperture center positions
+are redefined by centering at the specified dispersion line using the
+\fBcenter1d\fR algorithm with centering parameters from \fBapedit\fR.
+Normally this is done when inheriting apertures from an aperture
+reference image.  The recentering does not change the "trace" of the
+aperture but simple adds a shift across the dispersion axis.
+
+There are a several recentering options.  Each selected aperture may be
+recentered independently.  However, if some or all of the spectra are
+relatively weak this may actually be worse than using the reference
+apertures defined by strong spectra or flat fields in the case of
+fibers or aperture masks.  One may select a subset of apertures to be
+used in calculating shift.  This is done with a the \fIaprecenter\fR
+list of aperture numbers (see
+\fBranges\fR for the syntax) and/or by selecting a specific number or
+fraction of the apertures with the strongest peak values.  The list
+selection is done first and the strongest remaining apertures are used
+to satisfy the \fBnpeaks\fR value.  Though some or all of the apertures
+may be recentered independently the most common case of recentering
+reference apertures is to account for detector shifts.  In this case
+one expects that any shift should be common to all apertures.  The
+\fIshift\fR parameter allows using the new centers for all selected
+apertures to compute a median shift to be added to ALL apertures.  Using
+a median shift for all apertures is the default.
+
+The \fIfind\fR parameter allows automatically finding apertures if none
+are defined for the image or by a reference image.  Since the purpose
+of this task is to recenter reference apertures it is usually the case
+that reference images are used and apertures are not defined by this
+task.  One case in which the apertures from the image itself might be
+recentered is if one wants to use a different dispersion line.  The
+\fIresize\fR parameter may be used to adjust the widths in a variety
+of ways based on the spectra profiles specific to each image.  The
+aperture positions and any other parameters may also be edited with the
+aperture editing function if selected by the \fIapedit\fR parameter and
+the task is run interactively.  The recentering algorithm may be run
+from the aperture editor using the 'g' keystroke.
+
+If the task is interactive the user is queried whether to perform
+various steps on each image.  The queries may be answered with one of
+the four values "yes", "no", "YES" and "NO", where an upper case
+response suppresses all further queries to this question.
+
+The aperture recentering algorithm may be selected from nearly every task
+in the package.
+.ih
+EXAMPLES
+	cl> aprecenter newimage reference=flat
+.ih
+REVISIONS
+.ls APRECENTER V2.11
+The "apertures" parameter can be used to select apertures for resizing,
+recentering, tracing, and extraction.  This parameter name was previously
+used for selecting apertures in the recentering algorithm.  The new
+parameter name for this is now "aprecenter".
+.le
+.ih
+SEE ALSO
+center1d, ranges, apfind, apresize, apedit, apall
+.endhelp
diff --git a/noao/twodspec/apextract/doc/apresize.hlp b/noao/twodspec/apextract/doc/apresize.hlp
new file mode 100644
index 00000000..d8ab4774
--- /dev/null
+++ b/noao/twodspec/apextract/doc/apresize.hlp
@@ -0,0 +1,201 @@
+.help apresize Sep96 noao.twodspec.apextract
+.ih
+NAME
+apresize -- Resize apertures automatically
+.ih
+USAGE
+apresize input
+.ih
+PARAMETERS
+.ls input
+List of input images in which apertures are to be resized.
+.le
+.ls apertures = ""
+Apertures to recenter, resize, trace, and extract.  This only applies
+to apertures read from the input or reference database.  Any new
+apertures defined with the automatic finding algorithm or interactively
+are always selected.  The syntax is a list comma separated ranges
+where a range can be a single aperture number, a hyphen separated
+range of aperture numbers, or a range with a step specified by "x<step>";
+for example, "1,3-5,9-12x2".
+.le
+.ls references = ""
+List of reference images to be used to define apertures for the input
+images.  When a reference image is given it supersedes apertures
+previously defined for the input image. The list may be null, "", or
+any number of images less than or equal to the list of input images.
+There are three special words which may be used in place of an image
+name.  The word "last" refers to the last set of apertures written to
+the database.  The word "OLD" requires that an entry exist
+and the word "NEW" requires that the entry not exist for each input image.
+.le
+
+.ls interactive = no
+Run this task interactively?  If the task is not run interactively then
+all user queries are suppressed and interactive aperture editing is
+disabled.
+.le
+.ls find = yes
+Find the spectra and define apertures automatically?  In order for
+spectra to be found automatically there must be no apertures for the
+input image or reference image defined in the database.
+.le
+.ls recenter = no
+Recenter the apertures?
+.le
+.ls resize = yes
+Resize the apertures?
+.le
+.ls edit = yes
+Edit the apertures?  The \fIinteractive\fR parameter must also be yes.
+.le
+
+.ls line = INDEF
+The dispersion line (line or column perpendicular to the dispersion axis) to
+be used in resizing the spectra.  A value of INDEF selects the middle of the
+image.
+.le
+.ls nsum = 1
+Number of dispersion lines to be summed or medianed.  The lines are taken
+around the specified dispersion line.  A positive value takes a
+sum and a negative value selects a median.
+.le
+.ls llimit = INDEF, ulimit = INDEF
+Lower and upper aperture size limits.  If the parameter \fIylevel\fR is
+INDEF then these limits are assigned to all apertures.  Otherwise
+these parameters are used as limits to the resizing operation.
+A value of INDEF places the aperture limits at the image edge (for the
+dispersion line used).
+.le
+.ls ylevel = 0.1
+Data level at which to set aperture limits.  If it is INDEF then the
+aperture limits are set at the values given by the parameters
+\fIllimit\fR and \fIulimit\fR.  If it is not INDEF then it is a
+fraction of the peak or an actual data level depending on the parameter
+\fIpeak\fR.  It may be relative to a local background or to zero
+depending on the parameter \fIbkg\fR.
+.le
+.ls peak = yes
+Is the data level specified by \fIylevel\fR a fraction of the peak?
+.le
+.ls bkg = yes
+Subtract a simple background when interpreting the \fBylevel\fR parameter.
+The background is a slope connecting the first minima
+away from the aperture center.
+.le
+.ls r_grow = 0.
+Change the lower and upper aperture limits by this fractional amount.
+The factor is multiplied by each limit and the result added to limit.
+.le
+.ls avglimits = no
+Apply the average lower and upper aperture limits to all apertures.
+.le
+.ih
+ADDITIONAL PARAMETERS
+I/O parameters and the default dispersion axis are taken from the
+package parameters, the default aperture parameters are taken from the
+task \fBapdefault\fR, automatic aperture finding parameters are taken
+from \fBapfind\fR, and parameters used for centering and editing the
+apertures are taken from \fBapedit\fR.
+
+When this operation is performed from the task \fBapall\fR all parameters
+except the package parameters are included in that task.
+.ih
+DESCRIPTION
+For each image in the input image list, the aperture limits are
+redefined to be either specified values or by finding the points at
+which the spectrum profile, linearly interpolated, first crosses a
+specified value moving away from the aperture center at the specified
+dispersion line.  In the latter case the limits may then be increased
+or decreased by a specified percentage, a maximum lower and upper limit,
+may be imposed, and the independent limits may be averaged and the
+single values applied to all the apertures.
+
+The simplest resizing choice is to reset all the aperture limits to
+the values specified by \fIllimit\fR and \fIulimit\fR.  This option
+is selected if the parameter \fIylevel\fR is INDEF.
+
+There are several options for specifying a data level at which an
+aperture is sized.  The most common method (the default) is to specify
+a fraction of the peak value since this is data independent and physically
+reasonable.  This is done by setting the fraction with the parameter
+\fIylevel\fR and the parameter \fIpeak\fR to yes.  If the peak parameter
+is no then the level is a data value.
+
+The levels may be relative to zero, as might be used with fibers or
+high dispersion / high signal-to-noise data, or relative to a local
+linear background, as would be appropriate for slit data having a
+significant background.  A background is found and used if the
+parameter \fIbkg\fR is set.  The background determination is very
+simple.  Starting at the peak two background points are found, one in
+each direction, which are inflection points; i.e. the first pixels
+which are less than their two neighbors.  A linear slope is fit and
+subtracted for the purposes of measuring the peak and setting the
+aperture limits.  Note that if the slope is significant the actual
+limits may not correspond to the intercepts of a line at constant data
+value.
+
+Once aperture limits, a distance relative to the center, are determined
+they are increased or decreased by a percentage, expressed as a fraction,
+given by the parameter \fIr_grow\fR.  To illustrate the operation,
+if xlow is the initial lower limit then the final lower limit will be:
+
+	xlow final = xlow * (1 + r_grow)
+
+A value of zero leaves the aperture limits unchanged.
+
+After the aperture limits are found, based on the above steps, a fixed lower
+limit, given by the parameter \fIllimit\fR, is applied to the lower
+aperture points and, similarly, a fixed upper limit is applied to the
+upper aperture points.  This feature protects against absurdly wide apertures.
+
+Finally, if the parameter \fIavglimits\fR is set the individual aperture
+limits are averaged to form an average aperture.  This average aperture
+is then assigned to all apertures.  This option allows keeping common
+aperture sizes but allowing variation due to seeing changes.
+
+The resizing algorithm is available in the interactive aperture editor.
+Here one may select individual apertures or all apertures using the
+'a' switch.  The resizing algorithm described above is selected using
+the 'z' key.  An simple alternative is the 'y' key which resizes
+apertures to the y level marked by the cursor.
+
+If the task is interactive the user is queried whether to perform
+various steps on each image.  The queries may be answered with one of
+the four values "yes", "no", "YES" and "NO", where an upper case
+response suppresses all further queries to this question.
+
+The aperture resizing algorithm may be selected from nearly every task
+in the package with the \fIresize\fR parameter.
+.ih
+EXAMPLES
+1.  To resize all apertures to the range -4 to 4:
+
+	cl> apresize image llimit=-4 ulimit=4 ylevel=INDEF
+
+2.  To resize all aperture to a point which is 5% of the peak relative
+to a local background:
+
+	cl> apresize image ylevel=.05 peak+ bkg+
+
+3.  To resize all apertures to the point where the data exceeds 100
+data units:
+
+	cl> apresize image ylevel=100 peak- bkg-
+
+4.  To resize all apertures to default values of the task except
+averaging all the results at the end:
+
+	cl> apresize image avg+
+.ih
+REVISIONS
+.ls APRESIZE V2.11
+The "apertures" parameter can be used to select apertures for resizing,
+recentering, tracing, and extraction.  This parameter name was previously
+used for selecting apertures in the recentering algorithm.  The new
+parameter name for this is now "aprecenter".
+.le
+.ih
+SEE ALSO
+center1d, ranges, apfind, aprecenter, apedit, apall
+.endhelp
diff --git a/noao/twodspec/apextract/doc/apscatter.hlp b/noao/twodspec/apextract/doc/apscatter.hlp
new file mode 100644
index 00000000..902c57a8
--- /dev/null
+++ b/noao/twodspec/apextract/doc/apscatter.hlp
@@ -0,0 +1,253 @@
+.help apscatter Sep96 noao.twodspec.apextract
+.ih
+NAME
+apscatter -- Fit and subtract scattered light
+.ih
+USAGE
+apscatter input output
+.ih
+PARAMETERS
+.ls input
+List of input images in which to determine and subtract scattered light.
+.le
+.ls output
+List of output scattered light subtracted images.  If no output images
+are specified or the end of the output list is reached before the end 
+of the input list then the output image will overwrite the input image.
+.le
+.ls apertures = ""
+Apertures to recenter, resize, trace, and extract.  All apertures are
+used to define the scattered light region.  This only applies
+to apertures read from the input or reference database.  Any new
+apertures defined with the automatic finding algorithm or interactively
+are always selected.  The syntax is a list comma separated ranges
+where a range can be a single aperture number, a hyphen separated
+range of aperture numbers, or a range with a step specified by "x<step>";
+for example, "1,3-5,9-12x2".
+.le
+.ls scatter = ""
+List of scattered light images.  This is the scattered light subtracted
+from the input image.  If no list is given or the end of the list is
+reached before the end of the input list then no scattered light image
+is created.
+.le
+.ls references = ""
+List of reference images to be used to define apertures for the input
+images.  When a reference image is given it supersedes apertures
+previously defined for the input image. The list may be null, "", or
+any number of images less than or equal to the list of input images.
+There are three special words which may be used in place of an image
+name.  The word "last" refers to the last set of apertures written to
+the database.  The word "OLD" requires that an entry exist
+and the word "NEW" requires that the entry not exist for each input image.
+.le
+
+.ls interactive = yes
+Run this task interactively?  If the task is not run interactively then
+all user queries are suppressed and interactive aperture editing, trace
+fitting, and interactive scattered light fitting are disabled.
+.le
+.ls find = yes
+Find the spectra and define apertures automatically?  In order for
+spectra to be found automatically there must be no apertures for the
+input image or reference image defined in the database.
+.le
+.ls recenter = yes
+Recenter the apertures?
+.le
+.ls resize = yes
+Resize the apertures?
+.le
+.ls edit = yes
+Edit the apertures?  The \fIinteractive\fR parameter must also be yes.
+.le
+.ls trace = yes
+Trace the apertures?
+.le
+.ls fittrace = yes
+Interactively fit the traced positions by a function?  The \fIinteractive\fR
+parameter must also be yes.
+.le
+.ls subtract = yes
+Subtract the scattered light from the input images?
+.le
+.ls smooth = yes
+Smooth the cross-dispersion fits along the dispersion?
+.le
+.ls fitscatter = yes
+Fit the scattered light across the dispersion interactively?
+The \fIinteractive\fR parameter must also be yes.
+.le
+.ls fitsmooth = yes
+Smooth the cross-dispersion fits along the dispersion?
+The \fIinteractive\fR parameter must also be yes.
+.le
+
+.ls line = INDEF, nsum = 1
+The dispersion line (line or column perpendicular to the dispersion
+axis) and number of adjacent lines (half before and half after unless
+at the end of the image) used in finding, recentering, resizing,
+and editing operations.  For tracing this is the starting line and
+the same number of lines are summed at each tracing point.  This is
+also the initial line for interactive fitting of the scattered light.
+A line of INDEF selects the middle of the image along the dispersion
+axis.  A positive nsum takes a sum and a negative value selects a
+median except that tracing always uses a sum.
+.le
+
+.ls buffer = 1.
+Buffer distance from the aperture edges to be excluded in selecting the
+scattered light pixels to be used.
+.le
+.ls apscat1 = ""
+Fitting parameters across the dispersion.  This references an additional
+set of parameters for the ICFIT package.  The default is the "apscat1"
+parameter set.  See below for additional information.
+.le
+.ls apscat2 = ""
+Fitting parameters along the dispersion.  This references an additional
+set of parameters for the ICFIT package.  The default is the "apscat2"
+parameter set.  See below for additional information.
+.le
+.ih
+ICFIT PARAMETERS FOR FITTING THE SCATTERED LIGHT
+There are two additional parameter sets which define the parameters used
+for fitting the scattered light across the dispersion and along the
+dispersion.  The default parameter sets are \fBapscat1\fR and \fBapscat2\fR.
+The parameters may be examined and edited by either typing their names
+or by typing ":e" when editing the main parameter set with \fBeparam\fR
+and with the cursor pointing at the appropriate parameter set name.
+These parameters are used by the ICFIT package and a further
+description may be found there.
+
+.ls function = "spline3" (apscat1 and apscat2)
+Fitting function for the scattered light across and along the dispersion.
+The choices are "legendre" polynomial, "chebyshev" polynomial,
+linear spline ("spline1"), and cubic spline ("spline3").
+.le
+.ls order = 1 (apscat1 and apscat2)
+Number of polynomial terms or number of spline pieces for the fitting function.
+.le
+.ls sample = "*" (apscat1 and apscat2)
+Sample regions for fitting points.  Intervals are separated by "," and an
+interval may be one point or a range separated by ":".
+.le
+.ls naverage = 1 (apscat1 and apscat2)
+Number of points within a sample interval to be subaveraged or submedianed to
+form fitting points.  Positive values are for averages and negative points
+for medians.
+.le
+.ls niterate = 5 (apscat1), niterate = 0 (apscat2)
+Number of sigma clipping rejection iterations.
+.le
+.ls low_reject = 5. (apscat1) , low_reject = 3. (apscat2)
+Lower sigma clipping rejection threshold in units of sigma determined
+from the RMS sigma of the data to the fit.
+.le
+.ls high_reject = 2. (apscat1) , high_reject = 3. (apscat2)
+High sigma clipping rejection threshold in units of sigma determined
+from the RMS sigma of the data to the fit.
+.le
+.ls grow = 0. (apscat1 and apscat2)
+Growing radius for rejected points (in pixels).  That is, any rejected point
+also rejects other points within this distance of the rejected point.
+.le
+.ih
+ADDITIONAL PARAMETERS
+I/O parameters and the default dispersion axis are taken from the
+package parameters, the default aperture parameters from
+\fBapdefault\fR, automatic aperture finding parameters from
+\fBapfind\fR, recentering parameters from \fBaprecenter\fR, resizing
+parameters from \fBapresize\fR, parameters used for centering and
+editing the apertures from \fBapedit\fR, and tracing parameters from
+\fBaptrace\fR.
+.ih
+DESCRIPTION
+The scattered light outside the apertures defining the two dimensional
+spectra is extracted, smoothed, and subtracted from each input image.  The
+approach is to first select the pixels outside the defined apertures
+and outside a buffer distance from the edge of any aperture at each
+point along the dispersion independently.  A one dimensional function
+is fit using the \fBicfit\fR package.  This fitting uses an iterative
+algorithm to further reject high values and thus fit the minima between
+the spectra.  (This even works reasonably well if no apertures are
+defined).  Because each fit is done independently the scattered light
+thus determined will not be smooth along the dispersion.  If desired
+each line along the dispersion in the scattered light surface may then
+be smoothed by again fitting a one dimensional function using the
+\fBicfit\fR package.  The final scattered light surface is then
+subtracted from the input image to form the output image.  The
+scattered light surface may be output if desired.
+
+The reason for using two one dimensional fits as opposed to a surface fit
+is that the actual shape of the scattered light is often not easily modeled
+by a simple two dimensional function.  Also the one dimensional function
+fitting offers more flexibility in defining functions and options as
+provided by the \fBicfit\fR package.
+
+The organization of the task is like the other tasks in the package
+which has options for defining apertures using a reference image,
+defining apertures through an automatic finding algorithm (see
+\fBapfind\fR), automatically recentering or resizing the apertures (see
+\fBaprecenter\fR and \fBapresize\fR), interactively editing the
+apertures (see \fBapedit\fR), and tracing the positions of the spectra
+as a function of dispersion position (see \fBaptrace\fR).  Though
+unlikely, the actual scattered light subtraction operation may be
+suppressed when the parameter \fIsubtract\fR is no.  If the scattered
+light determination and fitting is done interactively (the
+\fIinteractive\fR parameter set to yes) then the user is queried
+whether or not to do the fitting and subtraction for each image.  The
+responses are "yes", "no", "YES", or "NO", where the upper case
+queries suppress this query for the following images.  When the task is
+interactive there are further queries for each step of the operation
+which may also be answered both individually or collectively for all
+other input images using the four responses.
+
+When the scattered light operation is done interactively the user may
+set the fitting parameters for the scattered light functions both
+across and along the dispersion interactively.  Initially the central
+line or column is used but after exiting (with 'q') a prompt is given
+for selecting additional lines or columns and for changing the buffer
+distance.  Note that the point of the interactive stage is to set the
+fitting parameters.  When the entire image is finally fit the last set
+of fitting parameters are used for all lines or columns.
+
+The default fitting parameters are organized as separate parameter sets
+called \fBapscat1\fR for the first fits across the dispersion and
+\fBapscat2\fR for the second smoothing fits along the dispersion.
+Changes to these parameters made interactively during execution of
+this task are updated in the parameter sets.  The general idea for
+these parameters is that when fitting the pixels from between the
+apertures the iteration and rejection thresholds are set to eliminate
+high values while for smoothing along the dispersion a simple smooth
+function is all that is required.
+.ih
+EXAMPLES
+1.  To subtract the scattered light from a set of images to form a
+new set of images:
+
+	cl> apscatter raw* %raw%new%*
+
+This example uses a substitution in the names from raw to new.
+By default this would be done interactively
+
+2.  To subtract the scattered light in place and save the scattered light
+images:
+
+	cl> apscatter im* "" scatter="s//im*" ref=im1 interact-
+
+The prefix s is added to the original names for the scattered light.
+This operation is done noninteractively using a reference spectrum
+to define the apertures.
+.ih
+REVISIONS
+.ls APSCATTER V2.11
+The "apertures" parameter can be used to select apertures for resizing,
+recentering, tracing, and extraction.  This parameter name was previously
+used for selecting apertures in the recentering algorithm.  The new
+parameter name for this is now "aprecenter".
+.le
+.ih
+SEE ALSO
+apfind, aprecenter, apresize,  apedit, aptrace, apsum, apmask, icfit
+.endhelp
diff --git a/noao/twodspec/apextract/doc/apsum.hlp b/noao/twodspec/apextract/doc/apsum.hlp
new file mode 100644
index 00000000..6fa7ad0e
--- /dev/null
+++ b/noao/twodspec/apextract/doc/apsum.hlp
@@ -0,0 +1,402 @@
+.help apsum Sep96 noao.twodspec.apextract
+.ih
+NAME
+apsum -- Extract one dimensional sums across the apertures
+.ih
+USAGE
+apsum input
+.ih
+PARAMETERS
+.ls input
+List of input images containing apertures to be extracted.
+.le
+.ls output = ""
+List of output rootnames for the extracted spectra.  If the null
+string is given or the end of the output list is reached before the end
+of the input list then the input image name is used as the output rootname.
+This will not conflict with the input image since an aperture number
+extension is added for onedspec format, the extension ".ms" for multispec
+format, or the extension ".ec" for echelle format.
+.le
+.ls apertures = ""
+Apertures to recenter, resize, trace, and extract.  This only applies
+to apertures read from the input or reference database.  Any new
+apertures defined with the automatic finding algorithm or interactively
+are always selected.  The syntax is a list comma separated ranges
+where a range can be a single aperture number, a hyphen separated
+range of aperture numbers, or a range with a step specified by "x<step>";
+for example, "1,3-5,9-12x2".
+.le
+.ls format = "multispec" (onedspec|multispec|echelle|strip)
+Format for output extracted spectra.  "Onedspec" format extracts each
+aperture to a separate image while "multispec" and "echelle" extract
+multiple apertures for the same image to a single output image.
+The "multispec" and "echelle" format selections differ only in the
+extension added.  The "strip" format produces a separate 2D image in
+which each column or line along the dispersion axis is shifted to
+exactly align the aperture based on the trace information.
+.le
+.ls references = ""
+List of reference images to be used to define apertures for the input
+images.  When a reference image is given it supersedes apertures
+previously defined for the input image. The list may be null, "", or
+any number of images less than or equal to the list of input images.
+There are three special words which may be used in place of an image
+name.  The word "last" refers to the last set of apertures written to
+the database.  The word "OLD" requires that an entry exist
+and the word "NEW" requires that the entry not exist for each input image.
+.le
+.ls profiles = ""
+List of profile images for variance weighting or cleanning.   If variance
+weighting or cleanning a profile of each aperture is computed from the
+input image unless a profile image is specified, in which case the
+profile is computed from the profile image.  The profile image must
+have the same dimensions and dispersion and it is assumed that the
+spectra have the same position and profile shape as in the object
+spectra.  Use of a profile image is generally not required even for
+faint input spectra but the option is available for those who wish
+to use it.
+.le
+
+.ls interactive = yes
+Run this task interactively?  If the task is not run interactively then
+all user queries are suppressed and interactive aperture editing, trace
+fitting, and extraction review are disabled.
+.le
+.ls find = yes
+Find the spectra and define apertures automatically?  In order for
+spectra to be found automatically there must be no apertures for the
+input image or reference image defined in the database.
+.le
+.ls recenter = no
+Recenter the apertures?
+.le
+.ls resize = no
+Resize the apertures?
+.le
+.ls edit = yes
+Edit the apertures?  The \fIinteractive\fR parameter must also be yes.
+.le
+.ls trace = yes
+Trace the apertures?
+.le
+.ls fittrace = yes
+Interactively fit the traced positions by a function?  The \fIinteractive\fR
+parameter must also be yes.
+.le
+.ls extract = yes
+Extract the one dimensional aperture sums?
+.le
+.ls extras = no
+Extract the raw spectrum (if variance weighting is used), the sky spectrum
+(if background subtraction is used), and variance spectrum (if variance
+weighting is used)?  This information is extracted to the third dimension
+of the output image.
+.le
+.ls review = yes
+Review the extracted spectra?  The \fIinteractive\fR parameter must also be
+yes.
+.le
+
+.ls line = INDEF, nsum = 10
+The dispersion line (line or column perpendicular to the dispersion
+axis) and number of adjacent lines (half before and half after unless
+at the end of the image) used in finding, recentering, resizing,
+and editing operations.  For tracing this is the starting line and
+the same number of lines are summed at each tracing point.  A line of
+INDEF selects the middle of the image along the dispersion axis.
+A positive nsum takes a sum while a negative value selects a median
+except that tracing always uses a sum.
+.le
+
+.ls background = "none" (none|average|median|minimum|fit)
+Type of background subtraction.  The choices are "none" for no background
+subtraction, "average" to average the background within the background
+regions, "median" to use the median in the background regions, "minimum" to
+use the minimum in the background regions, or "fit" to fit across the
+dispersion using the background within the background regions.  Note that
+the "average" option does not do any medianing or bad pixel checking,
+something which is recommended.  The fitting option is slower than the
+other options and requires additional fitting parameter.
+.le
+.ls weights = "none"
+Type of extraction weighting.  Note that if the \fIclean\fR parameter is
+set then the weights used are "variance" regardless of the weights
+specified by this parameter.  The choices are:
+.ls "none"
+The pixels are summed without weights except for partial pixels at the
+ends.
+.le
+.ls "variance"
+The extraction is weighted by the variance based on the data values
+and a poisson/ccd model using the \fIgain\fR and \fIreadnoise\fR
+parameters.
+.le
+.le
+.ls pfit = "fit1d" (fit1d|fit2d)
+Profile fitting algorithm to use with variance weighting or cleaning.
+When determining a profile the two dimensional spectrum is divided by
+an estimate of the one dimensional spectrum to form a normalized two
+dimensional spectrum profile.  This profile is then smoothed by fitting
+one dimensional functions, "fit1d", along the lines or columns most closely
+corresponding to the dispersion axis or a special two dimensional
+function, "fit2d", described by Marsh (see \fBapprofile\fR).
+.le
+.ls clean = no
+Detect and replace deviant pixels?
+.le
+.ls skybox = 1
+Box car smoothing length for sky background when using background
+subtraction.  Since the background noise is often the limiting factor
+for good extraction one may box car smooth the sky to improve the
+statistics in smooth background regions at the expense of distorting
+the subtraction near spectral features.  This is most appropriate when
+the sky regions are limited due to a small slit length.
+.le
+.ls saturation = INDEF
+Saturation or nonlinearity level in data units.  During variance weighted
+extractions wavelength points having any pixels above this value are
+excluded from the profile determination and the sigma spectrum extraction
+output, if selected by the \fIextras\fR parameter, flags wavelengths with
+saturated pixels with a negative sigma.
+.le
+.ls readnoise = 0.
+Read out noise in photons.  This parameter defines the minimum noise
+sigma.  It is defined in terms of photons (or electrons) and scales
+to the data values through the gain parameter.  A image header keyword
+(case insensitive) may be specified to get the value from the image.
+.le
+.ls gain = 1
+Detector gain or conversion factor between photons/electrons and
+data values.  It is specified as the number of photons per data value.
+A image header keyword (case insensitive) may be specified to get the value
+from the image.
+.le
+.ls lsigma = 4., usigma = 4.
+Lower and upper rejection thresholds, given as a number of times the
+estimated sigma of a pixel, for cleaning.
+.le
+.ls nsubaps = 1
+During extraction it is possible to equally divide the apertures into
+this number of subapertures.  For multispec format all subapertures will
+be in the same file with aperture numbers of 1000*(subap-1)+ap where
+subap is the subaperture (1 to nsubaps) and ap is the main aperture
+number.  For echelle format there will be a separate echelle format
+image containing the same subaperture from each order.  The name
+will have the subaperture number appended.  For onedspec format
+each subaperture will be in a separate file with extensions and
+aperture numbers as in the multispec format.
+.le
+.ih
+ADDITIONAL PARAMETERS
+I/O parameters and the default dispersion axis are taken from the
+package parameters, the default aperture parameters from
+\fBapdefault\fR, automatic aperture finding parameters from
+\fBapfind\fR, recentering parameters from \fBaprecenter\fR, resizing
+parameters from \fBapresize\fR, parameters used for centering and
+editing the apertures from \fBapedit\fR, and tracing parameters from
+\fBaptrace\fR.
+
+When this operation is performed from the task \fBapall\fR all
+parameters except the package parameters are included in that task.
+.ih
+DESCRIPTION
+For each image in the input image list, the two dimensional spectra are
+extracted to one dimensional spectra by summing the pixels across the
+dispersion axis at each wavelength along the dispersion axis within a
+set of defined apertures.  The extraction apertures consist of an
+aperture number, a beam number, a title, a center, limits relative to
+the center, a curve describing shifts of the aperture center across the
+dispersion axis as a function of the wavelength, and parameters for
+background fitting and subtraction.  See \fBapextract\fR for a more
+detailed discussion of the aperture structures.
+
+The extracted spectra are recorded in one, two, or three dimensional
+images depending on the \fIformat\fR and \fIextras\fR parameters.  The
+output image rootnames are specified by the \fIoutput\fR list. If the
+list is empty or shorter than the input list the missing names are
+taken to be the same as the input image names.  Because the rootnames
+have extensions added it is common to default to the input names in
+order to preserve a naming relation between the input two dimensional
+spectra and the extracted spectra.
+
+When the parameter \fIextras\fR=no only the extracted spectra are
+output.  If the format parameter \fIformat\fR="onedspec" the output
+aperture extractions are one dimensional images with names formed from
+the output rootname and a numeric extension given by the aperture
+number; i.e. root.0001 for aperture 1.  Note that there will be as many
+output images as there are apertures for each input image, all with the
+same output rootname but with different aperture extensions.  The
+aperture beam number associated with each aperture is recorded in the
+output image under the keyword BEAM-NUM.  The output image name format
+and the BEAM-NUM entry in the image are chosen to be compatible with
+the \fBonedspec\fR package.
+
+If the format parameter is "echelle" or "multispec" the output aperture
+extractions are put into a two dimensional image with a name formed from
+the output rootname and the extension ".ech" or ".ms".  Each line in
+the output image corresponds to one aperture.  Thus in this format
+there is one output image for each input image.  These are the preferred
+output formats for reasons of compactness and ease of handling.  These
+formats are compatible with the \fBonedspec\fR, \fBechelle\fR, and
+\fBmsred\fR packages.  The relation between the line and the aperture
+numbers is given by the header parameter APNUMn where n is the line and
+the value is the aperture number and other numeric information.
+
+If the \fIextras\fR parameter is set to yes then the above formats
+become three dimensional.  Each plane in the third dimension contains
+associated information for the spectra in the first plane.  If variance
+weighted extractions are done the unweighted spectra are recorded.  If
+background subtraction is done the background spectra are recorded.  If
+variance weighted extractions are done the sigma spectrum (the
+estimated sigma of each spectrum pixel based on the individual
+variances of the pixels summed) is recorded.  The order of the
+additional information is as given above.  For example, an unweighted
+extraction with background subtraction will have one additional plane
+containing the sky spectra while a variance weighted extraction with
+background subtractions will have the variance weighted spectra, the
+unweighted spectra, the background spectra, and the sigma spectra in
+consecutive planes.
+
+Aperture definitions may be inherited from those of other images by
+specifying a reference image with the \fBreferences\fR parameter.
+Images in the reference list are matched with those in the
+input list in order.  If the reference image list is shorter than the
+number of input images, the last reference image is used for all
+remaining input images.  Thus, a single reference image may be given
+for all the input images or different reference images may be given for
+each input image.  The special reference name "last" may be used to
+select the last set apertures used in any of the \fBapextract\fR tasks.
+
+If an aperture reference image is not specified or no apertures are
+found for the specified reference image, previously defined apertures
+for the input image are sought in the aperture database.  Note that
+reference apertures supersede apertures for the input image.  If no
+apertures are defined they may be created automatically, the \fIfind\fR
+option, or interactively in the aperture editor, if the
+\fIinteractive\fR and \fIedit\fR options are set.
+
+The functions performed by the task are selected by a set of flag
+parameters.  The functions are an automatic spectrum finding and
+aperture defining algorithm (see \fBapfind\fR) which is ignored if
+apertures are already defined, automatic recentering and resizing
+algorithms (see \fBaprecenter\fR and \fBapresize\fR), an interactive
+aperture editing function (see \fBapedit\fR), a spectrum position tracing
+and trace function fit (see \fBaptrace\fR), and the main function of
+this task, one dimensional spectrum extraction.
+
+Each function selection will produce a query for each input spectrum if
+the \fIinteractive\fR parameter is set.  The queries are answered by
+"yes", "no", "YES", or "NO", where the upper case responses suppress
+the query for following images.  There are other queries associated
+with tracing and extracted spectrum review which first ask whether the
+operation is to be done interactively and, if yes, lead to queries for
+each aperture.  The cursor keys available during spectrum review are
+minimal, only the CURSOR MODE keys for expanding and adjusting the
+graph are available and the quit key 'q'.  If the \fIinteractive\fR
+parameter is not set then aperture editing, interactive trace fitting,
+and spectrum review are ignored.
+
+Background sky subtraction is done during the extraction based on
+background regions and parameters defined by the default parameters or
+changed during the interactive setting of the apertures.  The background
+subtraction options are to do no background subtraction, subtract the
+average, median, or minimum of the pixels in the background regions, or to
+fit a function and subtract the function from under the extracted object
+pixels.  The background regions are specified in pixels from
+the aperture center and follow changes in center of the spectrum along the
+dispersion.  The syntax is colon separated ranges with multiple ranges
+separated by a comma or space.  The background fitting uses the \fBicfit\fR
+routines which include medians, iterative rejection of deviant points, and
+a choice of function types and orders.  Note that it is important to use a
+method which rejects cosmic rays such as using either medians over all the
+background regions (\fIbackground\fR = "median") or median samples during
+fitting (\fIb_naverage\fR < -1).  The background subtraction algorithm and
+options are described in greater detail in \fBapsum\fR and
+\fBapbackground\fR.
+
+Since the background noise is often the limiting factor for good
+extraction one may box car smooth the sky to improve the statistics in
+smooth background regions at the expense of distorting the subtraction
+near spectra features.  This is most appropriate when the sky region is
+limited due to small slit length.  The smoothing length is specified by
+the parameter \fIskybox\fR.
+
+For a more extended discussion about the background determination see
+\fBapbackground\fR.
+
+The aperture extractions consists of summing all the background
+subtracted pixel values at a given wavelength within the aperture
+limits.  The aperture limits form a fixed width aperture but the center
+varies smoothly to follow changes in the position of the spectrum
+across the dispersion axis.  At the ends of the aperture partial pixels
+are used.
+
+The pixels in the sum may be weighted as specified by the \fIweights\fR
+parameter.  If the weights parameter is "none" and the \fIclean\fR
+parameter is no then the simple sum of the pixels (with fractional
+endpoints) is extracted.  If the weights parameter is "variance" or if
+the \fBclean\fR parameter is yes the pixels are weighted by their
+estimated variance derived from a noise model based on the \fIgain\fR
+and \fIreadnoise\fR parameters and a smooth profile function.  Normally
+the profile function is determined from the data being extracted.
+However, one may substitute a "profile" image as specified by the
+\fIprofiles\fR parameter for computing the profile.  This requires that
+the profile image have spectra of identical position and profile as
+the image being extracted.  For example, this would likely be the case
+with fiber spectra and an off-telescope spectrograph and a strong flat
+field or object spectrum could be used for weak spectra.  Note that
+experience has shown that even for very weak spectra there is little
+improvement with using a separate profile image but the user is free
+to experiment.
+
+When the \fIclean\fR parameter is set pixels deviating by more than a
+specified number of sigma from the profile function are excluded from the
+variance weighted sum.  Note that the \fIclean\fR parameter always selects
+variance weights.  For a more complete discussion of the extraction sums,
+variance weighting, cleaning, the noise model, and profile function
+determination see \fBapvariance\fR and \fBapprofiles\fR.
+.ih
+EXAMPLES
+1.  To simply extract the spectra from a multislit observation:
+
+	cl> apsum multislit1
+
+The positions of the slits are defined using either automatic finding
+or with the aperture editor.  The positions of the slits are traced if
+necessary and then the apertures are extracted to the image
+"multslit1.ms".  The steps of defining the slit positions and tracing
+can be done as part of this command or previously using the other tasks
+in the \fBapextract\fR package.
+.ih
+REVISIONS
+.ls APSUM V2.11
+The "apertures" parameter can be used to select apertures for resizing,
+recentering, tracing, and extraction.  This parameter name was previously
+used for selecting apertures in the recentering algorithm.  The new
+parameter name for this is now "aprecenter".
+
+The "nsubaps" parameter now allows onedspec and echelle output formats.
+The echelle format is appropriate for treating each subaperture as
+a full echelle extraction.
+
+The dispersion axis parameter was moved to purely a package parameter.
+
+As a final step when computing a weighted/cleaned spectrum the total
+fluxes from the weighted spectrum and the simple unweighted spectrum
+(excluding any deviant and saturated pixels) are computed and a
+"bias" factor of the ratio of the two fluxes is multiplied into
+the weighted spectrum and the sigma estimate.  This makes the total
+fluxes the same.  In this version the bias factor is recorded in the logfile
+if one is kept.  Also a check is made for unusual bias factors.
+If the two fluxes disagree by more than a factor of two a warning
+is given on the standard output and the logfile with the individual
+total fluxes as well as the bias factor.  If the bias factor is
+negative a warning is also given and no bias factor is applied.
+In the previous version a negative (inverted) spectrum would result.
+.le
+.ih
+SEE ALSO
+apbackground, apvariance, approfile,
+apdefault, apfind, aprecenter, apresize, apedit, aptrace, apall
+.endhelp
diff --git a/noao/twodspec/apextract/doc/aptrace.hlp b/noao/twodspec/apextract/doc/aptrace.hlp
new file mode 100644
index 00000000..3b9ddd38
--- /dev/null
+++ b/noao/twodspec/apextract/doc/aptrace.hlp
@@ -0,0 +1,354 @@
+.help aptrace Sep96 noao.twodspec.apextract
+.ih
+NAME
+aptrace -- Trace spectra for aperture extraction
+.ih
+USAGE
+.nf
+aptrace images
+.fi
+.ih
+PARAMETERS
+.ls input
+List of input images to be traced.
+.le
+.ls apertures = ""
+Apertures to recenter, resize, trace, and extract.  This only applies
+to apertures read from the input or reference database.  Any new
+apertures defined with the automatic finding algorithm or interactively
+are always selected.  The syntax is a list comma separated ranges
+where a range can be a single aperture number, a hyphen separated
+range of aperture numbers, or a range with a step specified by "x<step>";
+for example, "1,3-5,9-12x2".
+.le
+.ls references = ""
+List of reference images to be used to define apertures for the input
+images.  When a reference image is given it supersedes apertures
+previously defined for the input image. The list may be null, "", or
+any number of images less than or equal to the list of input images.
+There are three special words which may be used in place of an image
+name.  The word "last" refers to the last set of apertures written to
+the database.  The word "OLD" requires that an entry exist
+and the word "NEW" requires that the entry not exist for each input image.
+.le
+
+.ls interactive = yes
+Run this task interactively?  If the task is not run interactively then
+all user queries are suppressed and interactive aperture editing and trace
+fitting are disabled.
+.le
+.ls find = yes
+Find the spectra and define apertures automatically?  In order for
+spectra to be found automatically there must be no apertures for the
+input image or reference image defined in the database.
+.le
+.ls recenter = no
+Recenter the apertures?
+.le
+.ls resize = yes
+Resize the apertures?
+.le
+.ls edit = yes
+Edit the apertures?  The \fIinteractive\fR parameter must also be yes.
+.le
+.ls trace = yes
+Trace the apertures?
+.le
+.ls fittrace = yes
+Interactively fit the traced positions by a function?  The \fIinteractive\fR
+parameter must also be yes.
+.le
+
+.ls line = INDEF, nsum = 1
+The dispersion line (line or column perpendicular to the dispersion
+axis) and number of adjacent lines (half before and half after unless
+at the end of the image) used in finding, recentering, resizing,
+and editing operations.  For tracing this is the starting line and
+the same number of lines are summed at each tracing point.  A line of
+INDEF selects the middle of the image along the dispersion axis.
+A positive nsum selects the number of lines to sum while a negative
+value selects a median.  Tracing always uses a sum.
+.le
+.ls step = 10
+Step along the dispersion axis between determination of the spectrum
+positions.
+.le
+.ls nlost = 3
+Number of consecutive steps in which the profile is lost before quitting
+the tracing in one direction.  To force tracing to continue through
+regions of very low signal this parameter can be made large.  Note,
+however, that noise may drag the trace away before it recovers.
+.le
+
+The following parameters are the defaults used to fit the traced positions
+by a function of the dispersion line.  These parameters are those used by
+the ICFIT package.
+.ls function = "legendre"
+Default trace fitting function.  The fitting function types are
+"chebyshev" polynomial, "legendre" polynomial, "spline1" linear spline, and
+"spline3" cubic spline.
+.le
+.ls order = 2
+Default trace function order.  The order refers to the number of
+terms in the polynomial functions or the number of spline pieces in the spline
+functions.
+.le
+.ls sample = "*"
+Default fitting sample.  The sample is given by a set of colon separated
+ranges each separated by either whitespace or commas.  The string "*" refers
+to all points.
+.le
+.ls naverage = 1
+Default number of points to average or median.  Positive numbers
+average that number of sequential points to form a fitting point.
+Negative numbers median that number, in absolute value, of sequential
+points.  A value of 1 does no averaging and each data point is used in the
+.le
+.ls niterate = 0
+Default number of rejection iterations.  If greater than zero the fit is
+used to detect deviant traced positions and reject them before repeating the
+fit.  The number of iterations of this process is given by this parameter.
+.le
+.ls low_reject = 3., high_reject = 3.
+Default lower and upper rejection sigma.  If greater than zero traced
+points deviating from the fit below and above the fit by more than this
+number of times the sigma of the residuals are rejected before refitting.
+.le
+.ls grow = 0.
+Default reject growing radius.  Traced points within a distance given by this
+parameter of any rejected point are also rejected.
+.le
+.ih
+ADDITIONAL PARAMETERS
+I/O parameters and the default dispersion axis are taken from the
+package parameters, the default aperture parameters from
+\fBapdefault\fR, automatic aperture finding parameters from
+\fBapfind\fR, recentering parameters from \fBaprecenter\fR, resizing
+parameters from \fBapresize\fR, and parameters used for centering and
+editing the apertures from \fBapedit\fR.
+
+When this operation is performed from the task \fBapall\fR all parameters
+except the package parameters are included in that task.
+.ih
+DESCRIPTION
+For each image in the input image list the position of the spectrum
+within each aperture are determined at a number of points along the
+dispersion axis and a smooth function is fit to these positions.  The
+fitted curve defines a shift to be added to the aperture center at each
+wavelength.  Other options allow defining apertures using a reference
+image, defining apertures through an automatic finding algorithm (see
+\fBapfind\fR), automatically recentering apertures (see
+\fBaprecenter\fR), automatically resizing apertures (see
+\fBapresize\fR), and interactively editing the apertures prior to
+tracing (see \fBapedit\fR).  Tracing is selected with the parameter
+\fItrace\fR.  If the tracing is done interactively (the
+\fIinteractive\fR parameter set to yes) then the user is queried
+whether or not to trace each image.  The responses are "yes", "no",
+"YES", or "NO", where the upper case queries suppress this query
+for the following images.
+
+The tracing begins with the specified dispersion line.  A dispersion
+line is a line or column of the image perpendicular to the dispersion
+axis.  The dispersion axis is defined in the image header or by the
+package parameter \fIdispaxis\fR.  If the starting dispersion line is
+INDEF then the middle dispersion line of the image is used.  The
+positions of the spectra are determined using the \fBcenter1d\fR
+algorithm and the centering parameters from the \fBapedit\fR task.
+(See help under \fBcenter1d\fR for a description of the one dimensional
+position measuring algorithm.) The positions are redetermined at other
+points along the dispersion axis by stepping from the starting line in
+steps specified by the user.  A number of dispersion lines around each
+dispersion line to be measured may be summed to improve the position
+determinations, particularly for weak profiles.  This number usually is
+set equal to the tracing step.
+
+It is important to understand how to set the step size and the
+relationship between the step size and the centering error radius.
+Larger steps reduce the computational time, which is an important
+consideration.  However, if the step is too large then the tracing may
+fail to follow the systematic changes in the positions of the
+spectrum.  The centering error radius, \fIradius\fR, is used to limit
+the maximum position change between two successive steps.  If the
+positions of a spectrum changes by more than the specified amount or
+the data contrast falls below the \fIthreshold\fR parameter then
+the position is marked as lost.
+
+The centering radius should be large enough to follow changes in the
+spectrum positions from point to point but small enough to detect an error
+in the tracing by a sudden abrupt change in position, such as caused by
+crowding with other spectra or by the disappearance of the spectrum.  The
+\fInlost\fR parameter determines how many consecutive steps the position
+may fail to be found before tracing in that direction is stopped.  If this
+parameter is small the trace will stop quickly upon loss of the profile
+while if it is very large it will continue to try and recover the profile.
+
+The parameter \fIthreshold\fR checks for the vanishing of a spectrum by
+requiring a minimum range in the data used for centering.  If the
+tracing fails when the spectra are strong and well defined the problem
+is usually that the step size is too large and/or the centering error
+radius is too small.
+
+The traced positions of a spectrum include some measurement variation
+from point to point.  Since the actual position of the spectrum in the
+image should be a smooth curve, a function of the dispersion line is fit
+to the measured points.  The fitted function is stored as part of the
+aperture description.  It is an offset to be added to the aperture's
+center as a function of the dispersion line.  Even if the fitting is not
+done interactively plots of the trace and the fit are recorded in the
+plot file or device specified by the parameter \fIplotfile\fR.
+
+Fitting the traced spectrum positions with a smooth function may be
+performed interactively when parameters \fIfittrace\fR and
+\fIinteractive\fR are yes.  This allows changing the default fitting
+parameters.  The function fitting is done with the interactive curve
+fitting tools described under the help topic \fBicfit\fR.  There are
+two levels of queries when fitting the spectrum positions
+interactively; prompts for each image and prompts for each aperture in
+an image.  These prompts may be answered individually with the lower
+case responses "yes" or "no" or answered for all further prompts with
+the responses "YES" or "NO".  Responding with "yes" or "YES" to the
+image prompt allows interactive fitting of the traced positions for the
+spectra.  Prompts are then given for each aperture in the image.  When
+an spectrum is not fit interactively the last set of fitting parameters
+are used (initially the default function and order given by the task
+parameters).  Note that answering "YES" or "NO" to a aperture prompt
+applies to all further aperture in the current image only.  Responding
+with "no" or "NO" to the image prompt fits the spectrum positions for
+all apertures in all images with the last set of fitting parameters.
+
+The tracing may also be done from the interactive aperture editor with
+the 't' key.  The aperture tracing algorithm may be selected from many
+of the tasks in the package with the \fItrace\fR parameter.
+.ih
+APTRACE DATABASE COEFFICIENTS
+The path of an aperture is described by a function that gives an additive
+offset relative to the aperture center as stored under the database keyword
+center.  The function is saved in the database as a series of
+coefficients.  The section containing the coefficients starts with the
+keyword "curve" 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
+.ih
+REVISIONS
+.ls APTRACE V2.11
+The "apertures" parameter can be used to select apertures for resizing,
+recentering, tracing, and extraction.  This parameter name was previously
+used for selecting apertures in the recentering algorithm.  The new
+parameter name for this is now "aprecenter".
+.le
+.ih
+SEE ALSO
+apdefault, apfind, aprecenter, apresize, apedit, apall,
+center1d, icfit, gtools
+.endhelp
diff --git a/noao/twodspec/apextract/doc/apvariance.hlp b/noao/twodspec/apextract/doc/apvariance.hlp
new file mode 100644
index 00000000..6ff1e073
--- /dev/null
+++ b/noao/twodspec/apextract/doc/apvariance.hlp
@@ -0,0 +1,159 @@
+.help apvariance Aug90 noao.twodspec.apextract
+
+.ce
+Variance Weighted and Cleaned Extractions
+
+
+There are two types of aperture extraction (estimating the background
+subtracted flux across a fixed width aperture at each image line or
+column) in the APEXTRACT package.  One is a simple sum of pixel values
+across an aperture.  It is selected by specifying "none" for the
+\fIweights\fR parameter.  The second type weights each pixel in the sum
+by it's estimated variance based on a spectrum model and detector noise
+parameters.  This type of extraction is selected by specifying
+"variance" for the weighting parameter.  These two extractions are
+defined by the following equations.
+
+.nf
+	none:	S = sum { I - B }
+    variance:	S = sum { (P**2 / V) (I - B) / P } / sum { P**2 / V }
+.fi
+
+S is the one dimensional spectrum flux at a particular wavelength (line
+or column along the dispersion axis).  The sum is over all pixels at
+that wavelength within the aperture limits.  If the aperture endpoints
+occupy only a fraction of a pixel then the pixel value above the
+background is multiplied by the fraction.  I is the pixel value and B
+is the estimated background at that pixel (see \fBapbackground\fR), P
+is estimated normalized profile value for that pixel (see
+\fBapprofile\fR), and V is the estimated variance of the pixel based on
+the noise model described below.  Note that the quantity (I-B)/P is an
+independent estimate of the total flux from one pixel since the
+integral of P is one and it is these estimates that are variance
+weighted.
+
+Variance weighting is often called "optimal" extraction since it
+produces the best unbiased signal-to-noise estimate of the flux in the
+two dimensional profile.  The theory and application of this type of
+weighting has been described in several papers.  The ones which were
+closely examined and used as a model for the algorithms in this
+software are "An Optimal Extraction Algorithm for CCD Spectroscopy",
+PASP 98, 609, 1986, by Keith Horne and "The Extraction of Highly
+Distorted Spectra", PASP 100, 1032, 1989, by Tom Marsh.
+
+The noise model for the image data used in the variance weighting,
+cleaning, and profile fitting consists of a constant gaussian noise and
+a photon count dependent poisson noise.  The signal is related to the
+number of photons detected in a pixel by a \fRgain\fR parameter given
+as the number of photons per data number.  The gaussian noise is given
+by a \fIreadnoise\fR parameter which is a defined as a sigma in
+photons.  The poisson noise is approximated as gaussian with sigma
+given by the number of photons.
+
+Some additional effects which should be considered in principle, and
+which are possibly important in practice, are that the variance
+estimate should be based on the actual number of photons detected before
+correction for pixel sensitivity; i.e. before flat field correction.
+Furthermore the uncertainty in the flat field should also be included
+in the weighting.  However, the profile must be determined free of
+sensitivity effects including rapid larger scale variations such as
+fringing.  Thus, ideally one should input the unflat-fielded
+observation and the flat field data and carry out the extractions with
+the above points in mind.  However, due to the complexity often
+involved in basic CCD reductions and special steps required for
+producing spectroscopic flat fields this level of sophistication is not
+provided by the current package.  The package does provide, however,
+for propagation of an approximate uncertainty in the background
+estimate when using background subtraction.
+
+The noise model is described by the following equations.
+
+.nf
+    (1) V = max (VMIN, (R**2 + I + VB) / G**2)
+	    max (VMIN, (R**2 + S * P + B + VB) / G**2)
+
+    (2) VB = 0.                 if (B = 0)
+	   = B / (N - 1)        if (B > 0)
+
+    (3) VMIN = 1 / G**2         if (R = 0)
+	       R**2 / G**2      if (R > 0)
+.fi
+
+V is the desired variance of a pixel to use for variance weighting.  R
+is the photon read out noise specified by the parameter \fIreadnoise\fR
+and G is the photon per data value gain specified by the parameter
+\fIgain\fR.  There are two forms to (1).  The first is used in the
+initial pass of estimating the spectrum flux S and the actual pixel
+value I (which includes any background) is used for the poisson term.
+The other form is used in a second pass (and further passes if
+cleaning) using the estimated data value based on the normalized
+profile P scaled to the estimated total flux plus the estimated
+background B; i.e. I estimated = S * P + B.
+
+The background variance VB is computed using the poisson noise model
+based on the estimated background counts.  If no background subtraction
+is done then both B and VB are set to zero.  If a background is
+determined the background is either an average or function fit to
+pixels in defined background regions.  If a fit is used B need not be a
+constant.   Because the background estimate is based on a finite number of
+pixels, the poisson variance estimate is divided by the number N (minus
+one) of pixels used in determining the background.  The number of
+pixels used includes any box car smoothing.  Thus, the larger the
+number of background pixels the smaller the background noise
+contribution to the variance weighting.  This method is only
+approximate since no correction is made for the number of degrees of
+freedom and correlations when using the fitting method of background
+estimation.
+
+VMIN is a minimum variance need to avoid generating zero or negative
+variances from the data.  The definition of VMIN is such that if a zero
+read out noise is specified (which is certainly possible such as with
+photon counting detectors) then a minimum of 1 photon is imposed.
+Otherwise the minimum is set by the read out noise even if the poisson
+count part is (unphysically) negative.
+
+One deviation from the linear photon response mode which is considered
+is saturation.   A data level specified by the parameter
+\fIsaturation\fR is used to exclude data from the profile fitting.
+During extraction the saturated pixels are not treated any differently
+than unsaturated pixels except that dispersion points with saturated
+pixels are flagged by reversing the sign of the final estimated sigma;
+the sigma output is enabled with the \fIextras\fR parameter.  Exclusion
+of saturated pixels from the extraction, as is done with deviant
+pixels, was tried but this resulted in higher noise in the spectrum.
+
+If removal of cosmic rays and other deviant pixels is desired, called
+cleaning and selected with a \fIclean\fR parameter, they are
+iteratively rejected based on the estimated variance and excluded from
+the weighted sum.  Note that a cleaned extraction is always variance
+weighted regardless of the value of the \fIweights\fR parameter.  This
+makes sense since the detector noise parameters must be specified and
+the spectrum profile computed, so all of the computational effort must
+be done anyway, and the variance weighting is as good or superior to a
+simple unweighted extraction.
+
+The detection and removal of deviant pixels is straightforward.  Based
+on the noise model described earlier, pixels deviating by more than a
+specified number of sigma (square root of the variance) above or below
+the model are removed from the weighted sum.  A new spectrum estimate
+is made and the rejection is repeated.  The rejections are made one at
+a time starting with the most deviant and up to half the pixels in the
+aperture may be rejected.  The total number of rejected pixels in the
+spectrum is recorded in the logfile and a profile plot of data and
+model profile is recorded in the plotfile.
+
+As a final step when computing a weighted/cleaned spectrum the total
+fluxes from the weighted spectrum and the simple unweighted spectrum
+(excluding any deviant and saturated pixels) are computed and a
+"bias" factor of the ratio of the two fluxes is multiplied into
+the weighted spectrum and the sigma estimate.  This makes the total
+fluxes the same.  The bias factor is recorded in the logfile
+if one is kept.  Also a check is made for unusual bias factors.
+If the two fluxes disagree by more than a factor of two a warning
+is given on the standard output and the logfile with the individual
+total fluxes as well as the bias factor.  If the bias factor is
+negative a warning is also given and no bias factor is applied.
+.ih
+SEE ALSO
+apbackground approfiles apall apsum
+.endhelp
diff --git a/noao/twodspec/apextract/doc/dictionary b/noao/twodspec/apextract/doc/dictionary
new file mode 100644
index 00000000..1046499c
--- /dev/null
+++ b/noao/twodspec/apextract/doc/dictionary
@@ -0,0 +1,282 @@
+ADU
+APALL
+APAXIS
+APEDIT
+APEXTRACT
+APFIND
+APFIT
+APFLATTEN
+APFORMAT
+APID
+APID2
+APIO
+APMASK
+APNORMALIZE
+APNUM2
+APNUMn
+APPARAMS
+APRECENTER
+APRESIZE
+APSCATTER
+APSTRIP
+APSUM
+APTRACE
+CCD
+CL
+DISPAXIS
+ECHELLE
+EOF
+EPARAM
+FIT1D
+FLAT1D
+Fri
+Horne
+Horne's
+ICFIT
+IMARITH
+IMREPLACE
+IMSURFIT
+INDEF
+IRAF
+Jul
+Jul90
+Nfind
+P.O
+PASP
+PSET
+RMS
+SETDISP
+SN
+STDIN
+STDOUT
+Slitlet
+VB
+VMIN
+Valdes
+ansclob
+ansclobber
+ansclobber1
+ansdbwr
+ansdbwrite
+ansdbwrite1
+ansedit
+ansextr
+ansextract
+ansfind
+ansfit
+ansfits
+ansfitscatter
+ansfitsmooth
+ansfitspec
+ansfitspec1
+ansfitt
+ansfittrace
+ansfittrace1
+ansflat
+ansmask
+ansnorm
+ansrece
+ansrecenter
+ansresi
+ansresize
+ansrevi
+ansreview
+ansreview1
+ansscat
+anssmoo
+anssmooth
+anstrac
+anstrace
+ap
+apall
+apall1
+apbackground
+apdefault
+apdefault.apidtable
+apdefault.b
+apdefault.lower
+apdefault.upper
+apdemo1d
+apdemo2d
+apdemo2d.ms
+apdemos
+apdemosdb
+apedit
+apedit.radius
+apedit.threshold
+apedit.width
+apertur
+apextract
+apextractsys
+apfind
+apfind.maxsep
+apfind.minsep
+apfind.nfind
+apfind.order
+apfit
+apfit1
+apflat1
+apflatten
+apidtab
+apidtable
+apio
+aplast
+apmask
+apnorm1
+apnormalize
+apparams
+approfile
+approfiles
+aprecenter
+aprecenter.apertures
+aprecenter.npeaks
+aprecenter.shift
+apresize
+apresize.avglimits
+apresize.bkg
+apresize.llimit
+apresize.peak
+apresize.r
+apresize.ulimit
+apresize.ylevel
+apscat1
+apscat2
+apscatter
+apscript
+apstrip
+apsum
+apsum.background
+apsum.clean
+apsum.extras
+apsum.gain
+apsum.lsigma
+apsum.nsubaps
+apsum.readnoise
+apsum.saturation
+apsum.skybox
+apsum.usigma
+apsum.weights
+aptrace
+aptrace.function
+aptrace.grow
+aptrace.high
+aptrace.low
+aptrace.naverage
+aptrace.niterate
+aptrace.nsum
+aptrace.order
+aptrace.sample
+aptrace.step
+apvariance
+artdata
+avg
+avglimi
+avglimits
+backgro
+bkg
+ccd
+cennorm
+center1d
+chebyshev
+cl
+clopset
+computerese
+curfit
+dbwrite
+dispaxi
+dispaxis
+dropoff
+ech
+ech001
+echelle
+echelles
+elp
+eparam
+fiber1
+fitscatter
+fitsmooth
+fitspec
+fittrace
+fittype
+flat001,flat002
+funct
+gaussian
+gkimosaic
+gtools
+icfit
+im
+im1
+image.pl
+image1
+imarith
+imh
+imred
+imred.generic.flat1d
+imsurfit
+keystroke
+legendre
+llimit
+logfile
+longslit
+lparam
+ls1
+lsigma
+maxsep
+maxtilt
+minsep
+mk1dspec
+mk2dspec
+mknoise
+msred
+multislit1
+multspec.ms
+naverage
+ndhelp
+nessie
+newimage
+nfind
+niter
+niterat
+niterate
+nl
+noao.twodspec.apextract
+npeaks
+nsubaps
+nsum
+onedspec
+onedspec.continuum
+pl
+plotfile
+poisson
+polyord
+polysep
+pset
+psets
+qtz001,qtz002
+rdnoise
+readnoi
+readnoise
+rec
+ref
+res
+root.0001
+rootname
+rootnames
+sampl
+saturat
+setdisp
+skybox
+slitlet
+slitlets
+spline1
+spline3
+thresho
+twodspec
+ulimit
+usigma
+whitespace
+widt
+xlow
+xmax
+xmin
+ylevel
diff --git a/noao/twodspec/apextract/doc/old/Tutorial.hlp b/noao/twodspec/apextract/doc/old/Tutorial.hlp
new file mode 100644
index 00000000..fd0ff8e8
--- /dev/null
+++ b/noao/twodspec/apextract/doc/old/Tutorial.hlp
@@ -0,0 +1,278 @@
+.help Tutorial Sep86 "Apextract Tutorial"
+.ih
+TOPICS
+The APEXTRACT tutorial consists of a number of topics.  The topics are brief
+and describe the simplest operations.  More sophisticated discussions are
+available for the tasks in the printed documentation and through the on-line
+\fBhelp\fR facility; i.e. "help taskname".  To obtain information
+on a particular topic type "tutor topic" where the topic is one of the
+following:
+
+.nf
+			TOPICS
+
+         topics - List of topics
+       overview - An overview of the \fBapextract\fR tasks
+   organization - How the package is organized
+      apertures - Definition of apertures
+       defining - How to define apertures
+     references - Using reference images to define apertures
+        queries - Description of interactive queries
+	 cosmic - Problems with cosmic ray removal
+	    all - Print all of this tutorial
+.fi
+.ih
+OVERVIEW
+The \fBapextract\fR tasks extract spectra from two dimensional images.
+One image axis is the dispersion axis and the other image axis is the
+aperture axis.  The user defines apertures whose position along the
+aperture axis is a function of position along the dispersion axis and
+whose width is fixed.  There are two types of aperture extractions.
+\fIStrip\fR extraction produces two dimensional images in which the
+center of the aperture is exactly centered along one of the lines or
+columns of the image and the edges of the image just include the
+edges of the aperture.  \fISum\fR extraction sums the pixels across
+the aperture at each point along the dispersion to produce a one
+dimensional spectrum.  The extraction algorithms include
+fitting and subtracting a background, modeling the profiles across the
+dispersion, detecting and removing deviant pixels which do not fit the
+model profiles, and weighting the pixels in the sum extraction according
+to the signal-to-noise.
+
+To extract spectra one must define the dispersion axis by placing the
+parameter DISPAXIS in the image headers using the task \fBsetdisp\fR.
+Then apertures are defined either automatically, interactively, or by
+reference to an image in which apertures have been previously defined.
+Initially the apertures are aligned parallel to the dispersion axis
+but if the spectra are not aligned with the dispersion axis and have
+profiles which can be traced then the position of the aperture along
+the aperture axis can be made a function of position along the dispersion
+axis.  Finally, the extraction operation is performed for each aperture.
+.ih
+ORGANIZATION
+The tasks in the \fBapextract\fR package are highly integrated.  This
+means that tasks call each other.  For example, the aperture
+editing task may be called from the finding, tracing, or extraction
+tasks.  Also from within the aperture editor the finding, tracing, and
+extraction tasks may be run on selected apertures.  This organization
+provides the flexibility to process images either step-by-step,
+image-by-image, or very interactively from the aperture editor.  For
+example, one may defined apertures for all the images, trace all the
+images, and then extract all the images or, alternatively, define,
+trace, and extract each image individually.
+
+This organization also implies that parameters from many tasks are used
+during the execution of a single task.  For example, the editing
+parameters are used in any of the tasks which may enter the interactive
+editing task.  Two tasks, \fBapio\fR and \fBapdefault\fR, only set
+parameters but these parameters are package parameters which affect all
+the other tasks.  There are two effects of this parameter
+organization.  First, only parameters from the task being executed may
+be specified on the command line or with menu mode.  However, the
+parameters are logically organized and the parameter list for any
+particular task is not excessively long or complex.  For example, the
+number of parameters potentially used by the task \fBapsum\fR is 57
+parameters instead of just the parameters logically related to the
+extraction itself.
+
+Another feature of the package organization is the ability to
+control the flow and interactivity of the tasks.  The parameter
+\fIinteractive\fR selects whether the user will be queried about various
+operations and if the aperture editor, trace fitting, and extraction
+review will be performed.  The parameters \fBdbwrite,
+find, recenter, edit, trace, fittrace, sum, review\fR, and
+\fBstrip\fR select which operations may be performed by a particular
+task.  When a task is run interactively the user is queried about
+whether to perform each operation on each image.  A query may be answered
+individually or as a group.  In the latter case the query will not be
+repeated for other images but will always take the specified action.
+This allows the user to begin interactively and then reduce
+the interactivity as the images are processed and parameters are refined.
+For additional discussion of these parameters see the topic QUERIES.
+
+Finally, the package has attempted to provide good logging facilities.
+There are log files for both time stamped text output and plots.
+The text log is still minimal but the plot logging is complete
+and allows later browsing and hardcopy review of batch processing.
+See \fBapio\fR for further discussion.
+
+This package organization is somewhat experimental.  Let us know what
+you think.
+.ih
+APERTURES
+An aperture consists of the following elements:
+
+.ls id    
+An integer aperture identification number.  The identification number
+must be unique.  The aperture number is used as the default extension
+of the extracted spectra.
+.le
+.ls beam    
+An integer beam number.  The beam number need not be unique; i.e.
+several apertures may have the same beam number.  The beam number will
+be recorded in the image header of the extracted spectrum.  Note that
+the \fBonedspec\fR package restricts the beam numbers to the range 0 to
+49.
+.le
+.ls cslit, cdisp
+The center of the aperture along the slit and dispersion axes in the two
+dimensional image.
+.le
+.ls lslit, ldisp
+The lower limits of the aperture, relative to the aperture center,
+along the slit and dispersion axes.  The lower limits need not be less
+than the center.
+.le
+.ls uslit, udisp
+The upper limits of the aperture, relative to the aperture center,
+along the slit and dispersion axes.  The upper limits need not be greater
+than the center.
+.le
+.ls curve
+An shift to be added to the center position for the slit axis which is
+a function of position along the dispersion axis.  The function is one
+of the standard IRAF \fBicfit\fR types; a legendre polynomial, a chebyshev
+polynomial, a linear spline, or a cubic spline.
+.le
+.ls background
+Background fitting parameters used by the \fBicfit\fR package for background
+subtraction.  Background parameters need not be used if background
+subtraction is not needed.  The background sample regions are specified
+relative to aperture center.
+.le
+
+The aperture center is the only absolute coordinate relative to the
+image or image section.  The size and shape of the aperture are
+specified relative to the aperture center.  The center and aperture
+limits in image coordinates along the slit axis are functions of the
+dispersion coordinate, lambda, given by
+
+.nf
+	center(lambda) = cslit + curve(lambda)
+	 lower(lambda) = center(lambda) + lslit
+	 upper(lambda) = center(lambda) + uslit
+.fi
+
+Note that both the lower and upper constants are added to the center
+defined by the aperture center and the curve offset.  The aperture limits
+along the dispersion axis are constant,
+
+.nf
+	        center(s) = cdisp
+	         lower(s) = center(s) + ldisp
+	         upper(s) = center(s) + udisp
+.fi
+
+Usually the aperture size along the dispersion is equal to the entire image.
+.ih
+DEFINING APERTURES
+If a reference image is specified the \fBapextract\fR tasks first search
+the database for it's apertures.  Note that this supercedes any apertures
+previously defined for the input image.  If no reference apertures are
+found then the apertures for the input image are sought.
+If no apertures are defined at this point then apertures
+may be defined automatically, interactively, or, by default, in the center
+of the image.  The automatic method, \fBapfind\fR, locates spectra as peaks
+across the dispersion and then defines default apertures given by the
+parameters from \fBapdefault\fR.  The algorithm is controlled
+by specifying the number of apertures and a minimum separation between
+spectra.  Only the strongest peaks are selected.
+
+The interactive method, \fBapedit\fR, allows the user to mark the positions
+of apertures and to adjust the aperture parameters such as the limits.
+The aperture editor may be used edit apertures defined by any of the
+other methods.
+
+If no apertures are defined when tracing or extraction is begun, that is
+following the optional editing, then a default aperture is defined
+centered along the aperture axis of the image.  This ultimate default
+may be useful for spectra defined by image sections; i.e. the image
+section is a type of aperture.  Image sections are sometimes used with
+multislit spectra.
+.ih
+REFERENCE IMAGES
+The \fBapextract\fR tasks define apertures for an input image by
+first searching the database for apertures recorded under the name
+of the reference image.  Use of a reference image implies
+superceding the input image apertures.  Reference images are specified
+by an image list which is paired with
+the input image list.  If the number of reference images
+is less than the number of input images then the last reference image
+is used for all following images.  Generally, the reference image list
+consists of the null string if reference images are not to be used,
+a single image which is applied to all input images, or a list
+which exactly matches the input list.  The special reference image
+name "last" may be used to refer to the last apertures written to
+the database; usually the previous input image.
+
+The task parameter \fIrecenter\fR specifies whether the
+reference apertures are to be recentered on the spectra in the input
+image.  If recentering is desired the \fBcenter1d\fR centering algorithm
+is used with centering parameters taken from the task \fBapedit\fR.
+The spectra in the image must all have well defined profiles for the
+centering.  It does not make sense to center an aperture defined for
+a region of sky or background or for an arc spectrum.
+
+Recentering is used when the only change between two spectra is
+a shift along the aperture axis.  This can reduce the number of
+images which must be traced if tracing is required by using a
+traced reference image and just recentering on the next spectra.
+Recentering of a traced reference image is also useful when
+the spectra are too weak to be traced reliably.  Recentering would be
+most commonly used with echelle or multiaperture spectra.
+
+Recentering is not used when extracting sky or arc calibration spectra
+from long slit or multislit images.  This is because it is desirable
+to extract from the same part of the detector as the object spectra and
+because recentering does not make sense when there is no profile across
+the aperture.  Centering or recentering is also not used when dealing
+with apertures covering parts of extended objects in long slit spectra.
+.ih
+QUERIES
+When the interactive parameter is specified as yes in a task then the user
+is queried at each step of the task.  The queries refer to either a
+particular image or a particular aperture in an image.  The acceptable
+responses to the queries are the strings "yes", "no", "YES", and "NO".
+The lower case answers refer only to the specific query.  The upper
+case answers apply to all repetitions of query for other images and
+apertures.  The upper case reponses then suppress the query and take
+the specified action every time.  This allows tasks to be highly interactive
+by querying at each step and for each image or to skip or perform
+each step for all images without queries.
+
+The two steps of fitting a function to traced positions and reviewing
+one dimensional extracted spectra, selected with the parameters
+\fIaptrace.fittrace\fR and \fIapsum.review\fR have two levels of queries.
+First a query is made for the image being traced or extracted.  If
+the answer is "yes" or "YES" then a query is made for each aperture.
+A response of "YES" or "NO" applies only to the remaining apertures
+and not to apertures of a later image.
+.ih
+COSMIC RAYS
+The cleaning and modeling features available during aperture extraction
+are fairly good.  They are described in the documentation for the
+tasks.  It can only go so far towards discriminating cosmic rays
+because of problems described below.  Further work on the algorithm may
+improve the performance but it is best, when feasible, to first
+eliminate at least the strongest cosmic rays from the data before
+extracting.  One recommended method is to use \fBlineclean\fR with a
+high rejection threshold and a high order.
+
+There are two difficult problems encountered in using the
+\fBapextract\fR tasks for cosmic ray detection.  First, the spectral
+profiles are first interpolated to a common center before comparison
+with the average profile model.  The interpolation often splits single
+strong spikes into two high points of half the intensity, as is
+intuitively obvious.  Furthermore, for very strong spikes there is
+ringing in the interpolator which makes the interpolated profile depart
+significantly from the original profile.  The fact that the
+interpolated profile now has two or more deviant points makes it much
+harder to decide which points are in the profile.  This leads to the
+second problem.  The average profile model is scaled to fit the
+spectrum profile.  When there are several high points it is very
+difficult to discriminate between a higher scale factor and bad
+points.  The algorithm has been enhanced to initially exclude the point which
+most pulls the scale factor to higher values.  If there are two high
+points due to the interpolator splitting a strong spike then this helps
+but does not eliminate errors in the extracted spectra.
+.endhelp
diff --git a/noao/twodspec/apextract/doc/old/apextract.ms b/noao/twodspec/apextract/doc/old/apextract.ms
new file mode 100644
index 00000000..3e71890b
--- /dev/null
+++ b/noao/twodspec/apextract/doc/old/apextract.ms
@@ -0,0 +1,725 @@
+.EQ
+delim $$
+define sl '{s lambda}'
+.EN
+.RP
+.TL
+The IRAF APEXTRACT Package
+.AU
+Francisco Valdes
+.AI
+IRAF Group - Central Computer Services
+.K2
+P.O. Box 26732, Tucson, Arizona 85726
+.AB
+The IRAF \fBapextract\fR package provides tools for the extraction of
+one and two dimensional spectra from two dimensional images
+such as echelle, long slit, multi-fiber, and multi-slit spectra.
+Apertures of fixed width along the spatial define the regions of
+the two dimensional images to be extracted at each point along the
+dispersion axis.  Apertures may follow changes in the positions of
+the spectra as a function of position along the dispersion axis.
+The spatial and dispersion axes may be oriented along either image axis.
+Extraction to one dimensional spectra consists of a weighted sum of the pixels
+within the apertures at each point along the dispersion axis.  The
+weighting options provide the simple sum of the pixel values and a
+weighting by the expected uncertainty of each pixel.  Two dimensional
+extractions interpolate the spectra in the spatial axis to produce
+image strips with the position of the  spectra exactly aligned with one
+of the image dimensions.  The extractions also include optional
+background subtraction, modeling, and bad pixel detection and replacement.
+The tasks are flexible in their ability to define and edit apertures,
+operate on lists of images, use apertures defined for reference
+images, and operate both very interactively or noninteractively.
+The extraction tasks are efficient and require only one pass through
+the data.  This paper describes the tasks, the algorithms, the data
+structures, as well as some examples and possible future developments.
+.AE
+.NH
+Introduction
+.PP
+The IRAF \fBapextract\fR package provides tools for the extraction of
+one and two dimensional aperture spectra from two dimensional format
+images such as those produced by echelle, long slit, multi-fiber, and
+multi-slit spectrographs.  This type of data is becoming increasingly
+popular because of the efficiency of data collection and recent
+technological improvements such as fibers and digital detectors.
+The trend is also to greater and greater numbers of spectra per
+image.  Extraction is one of the fundamental operations performed
+on these types of two dimensional spectral images, so a great deal of effort
+has gone into the design and development of this package.  
+.PP
+The tasks are flexible and have many options.  To make the best use of
+them it is important to understand how they work.  This paper provides
+a general description of the tasks, the algorithms, the data structures,
+as well as some examples of usage.  Specific descriptions of parameters
+and usage may be found in the IRAF help pages for the tasks included
+as appendices to this paper.  The image reduction "cookbooks" also
+provide complete examples of usage for specific instruments or types
+of instruments.
+.PP
+The tasks  in the \fBapextract\fR pacakge are summarized below.
+
+.ce
+The \fBApextract\fR Package
+.TS
+center;
+n.
+apdefault \&- Set the default aperture parameters
+apedit \&- Edit apertures interactively
+apfind \&- Automatically find spectra and define apertures
+apio \&- Set the I/O parameters for the APEXTRACT tasks
+apnormalize \&- Normalize 2D apertures by 1D functions
+apstrip \&- Extract two dimensional aperture strips
+apsum \&- Extract one dimensional aperture sums
+aptrace \&- Trace positions of spectra
+.TE
+
+The tasks are highly integrated so that one task may call another tasks
+or use its parameters.  Thus, these tasks reflect the logical organization
+of the package rather than a set of disparate tools.  One reason for
+this organization is group the parameters by function into easy to manage
+\fIparameter sets (psets)\fR.  The tasks \fBapdefault\fR and \fBapio\fR
+are just psets for specifying the default aperture parameters and the
+I/O parameters of the package; in other words, they do nothing but
+provide a grouping of parameters.  Executing these tasks is a shorthand
+for the command "eparam apdefault" or "eparam apio".  The other tasks
+provide both a logical grouping of parameters and function.  For
+example the task \fBaptrace\fR traces the positions of the spectra
+in the images and has the parameters related to tracing.  The task
+\fBapsum\fR, however, may trace the spectra as part of the overall
+extraction process and it uses the functionality and parameters of
+the \fBaptrace\fR task without requiring all the tracing parameters
+be included as part of its parameter set.  As we examine each task
+in detail it will become more apparent how this integration of function
+and parameters works.
+.PP
+The \fBapextract\fR package identifies the image axes with the spatial
+and dispersion axes.  Thus, during extraction pixels of constant
+wavelength are those along a line or column.  In this paper the terms
+\fIslit\fR or \fIspatial\fR axis and \fIdispersion\fR or \fIwavelength\fR
+axis are used to refer to the image axes corresponding to the spatial
+and dispersion axes.  Often a small degree of misalignment between the
+image axes and the true dispersion and spatial axes is not important.
+The main effect of misalignment is a broadening of the spectral
+features due to the difference in wavelength on opposite sides of the
+extraction aperture.  If the misalignment is significant, however, the
+image may be rotated with the task \fBrotate\fR in the \fBimages\fR
+package or remapped with the \fBlongslit\fR package tasks for
+coordinate rectification.
+.PP
+It does not matter which image axis is the dispersion axis since the
+tasks work equally well in either orientation.  However, the dispersion
+axis must be defined, with the \fBtwodspec\fR task \fBsetdisp\fR,
+before these tasks may be used.  This task is a simple script which
+adds the parameter DISPAXIS to the image headers.  The \fBapextract\fR
+tasks, like the \fBlongslit\fR tasks, look in the header to determine
+the dispersion axis.
+.NH
+Apertures
+.PP
+Apertures are the basic data structures used in the package; hence the
+package name.  An aperture defines a region of the two dimensional image
+to be extracted.  The aperture definitions are stored in a database.
+An aperture consists of the following components.
+
+.IP ID
+.br
+An integer identification number.  The identification number must be
+unique.  It is used as the default extension during extraction of
+the spectra.  Typically the IDs are consecutive positive integers
+ordered by increasing or decreasing slit position.
+.IP BEAM
+.br
+An integer beam number.  The beam number need not be
+unique; i.e. several apertures may have the same beam number.
+The beam number will be recorded in the image header of the
+the extracted spectrum.  By default the beam number is the same as
+the ID.
+.IP APAXIS
+.IP CENTER[2]
+.br
+The center of the aperture along the slit and dispersion axes in the two
+dimensional image.
+.IP LOWER[2]
+.br
+The lower limits of the aperture, relative to the aperture center,
+along the slit and dispersion axes.  The lower limits need not be less
+than the center.
+.IP UPPER[2]
+.br
+The upper limits of the aperture, relative to the aperture center,
+along the slit and dispersion axes.  The upper limits need not be greater
+than the center.
+.IP CURVE
+.br
+An offset to be added to the center position for the \fIslit\fR axis which is
+a function of the wavelength.  The function is one of the standard IRAF
+types; a legendre polynomial, a chebyshev polynomial, a linear spline,
+or a cubic spline.
+.IP background
+.br
+Parameters for background subtraction based on the interactive
+curve fitting (\fBicfit\fR) tools.
+
+.PP
+The aperture center is the only absolute coordinate (relative to the
+image or image section).  The other aperture parameters and the
+background fitting regions are defined relative to the center.  Thus,
+an aperture may be repositioned easily by changing the center
+coordinates.  Also a constant aperture size, shape (curve), and
+background regions may be maintained for many apertures.  The center
+and aperture limits, in image coordinates, along the slit axis are
+given by:
+
+.EQ I
+  ~roman center ( lambda )~mark = roman cslit + roman curve ( lambda )
+.EN
+.EQ I
+roman lower ( lambda )~lineup = roman center ( lambda ) + roman lslit
+.EN
+.EQ I
+roman upper ( lambda )~lineup = roman center ( lambda ) + roman uslit
+.EN
+
+where $lambda$ is the wavelength coordinate.  Note that both the lower and
+upper constants are added to the center defined by the aperture center and
+the offset curve.  The aperture limits along the dispersion axis are
+constant since there is no offset curve:
+
+.EQ I
+roman center (s)~lineup = roman cdisp
+.EN
+.EQ I
+roman lower (s)~lineup = roman center (s) + roman ldisp
+.EN
+.EQ I
+roman upper (s)~lineup = roman center (s) + roman udisp
+.EN
+
+.PP
+Apertures for a particular image may be defined in several ways.  
+These methods are arranged in a hierarchy.
+
+.IP (1)
+The database is first searched for previously defined apertures.
+.IP (2)
+If no apertures are found and a reference image is specified then the
+database is searched for apertures defined for the reference image.
+.IP (3)
+The user may then edit the apertures interactively with graphics
+commands if the \fIapedit\fR parameter is set.  This includes creating
+new apertures and deleting or modifying existing apertures.  This
+interactive editing procedure may be entered from any of the \fBapextract\fR
+tasks.
+.IP (4)
+For the tasks \fBtrace\fR, \fBsumextract\fR, and \fBstripextract\fR
+if no apertures are defined at this point a default aperture
+is created consisting of the entire image with center at the center of
+the image.  Note that if an image section is used then the aperture
+spans the image section only.
+.IP (5)
+Any apertures created, modified, or adopted from a reference image are recorded
+in the database for the image.
+
+.PP
+There are several important points to appreciate in the above logic.
+First, any of the tasks may be used without prior use of the others.
+For example one may use extract with the \fIapedit\fR switch set and
+define the apertures to be extracted (except for tracing).
+Alternatively the apertures may be defined with \fBapedit\fR
+interactively and then traced and extracted noninteractively.  Second,
+image sections may be used to define apertures (step 4).  For example
+a list of image sections (such as are used in multislit spectra) may be
+extracted directly and noninteractively.  Third, multiple images may
+use a reference image to define the same apertures.  There are several
+more options which are illustrated in the examples section.
+.PP
+Another subtlety is the way in which reference images may be
+specified.  The tasks in the package all accept list of images
+(including image sections).  Reference images may also be given as a
+list of images.  The lists, however, need not be of the same length.
+The reference images in the reference image list are paired in order
+with the input images.  If the reference list ends before the image
+list then the last reference image is used for the remaining images.
+The most common situations are when there is no reference image, when
+only one reference image is given for a set of input images, and when a
+matching list of reference images is given.  In the second case the
+reference image refers to all the input images while in the last case
+each input image has a reference image.
+.PP
+There is a trick which may be played with the reference images.  If a list
+of input images is given and the reference image is the same as the first
+input image then only the first image need be done interactively.
+This is because after the apertures for the first image have been defined
+they are recorded in the database.  Then when the database is searched
+for apertures for the second image, the apertures of the reference image
+will be available.
+.NH
+.PP
+\fBApedit\fR is a generally interactive task which graphs a line of
+an image along the slit axis and allows the user to define and edit
+apertures with the graphics cursor.  The defined apertures are recorded
+in a database.  The task \fBtrace\fR traces the positions of the
+spectrum profiles from one wavelength to other wavelengths in the image
+and fits a smooth curve to the positions.  This allows apertures
+to follow shifts in the spectrum along the slit axis.  The tasks
+\fBsumextract\fR and \fBstripextract\fR perform the actual aperture
+extraction to one and two dimensional spectra.  They have options for
+performing background subtraction, detecting and replacing bad pixels,
+modeling the spectrum profile, and weighting the pixels in the aperture
+when summing across the dispersion.
+.NH
+Tracing
+.PP
+The spectra to be extracted are not always aligned exactly with the
+image columns or lines (the extraction axes).
+For consistent extraction it is important that the same
+part of the spectrum profile be extracted at each wavelength point.
+Thus, the extraction apertures allow for shifts along the spatial axis
+at each dispersion point.  The shifts are defined by a curve which is a
+function of the wavelength.  The curve is determined by tracing the
+positions of the spectrum profile at a number of wavelengths and
+fitting a function to these positions.
+.PP
+The task \fBtrace\fR performs the tracing and curve fitting and records
+the curve in the database.  The starting point along the
+dispersion axis (a line or column) for the tracing is specified by the
+user.  The position of the profile is then determined using the
+\fBcenter1d\fR algorithm described elsewhere (see the help page for
+\fBcenter1d\fR or the paper \fIThe Long Slit Reduction Package\fR).
+The user specifies a step along the dispersion axis.  At each step the
+positions of the profiles are redetermined using the preceding
+position as the initial guess.  In order to enhance and trace weak
+spectra the user may specify a number of neighboring profiles to be
+summed before determining the profile positions.
+.PP
+Once the
+positions have been traced from the starting point to the ends of the
+aperture, or until the positions become indeterminate, a curve of a
+specified type and order is fit to the positions as a function of
+wavelength.  The function fitting is performed with the \fBicfit\fR
+tools (see the IRAF help page).  The curve fitting may be performed
+interactively or noninteractively.  Note that when the curve is fit
+interactively the actually positions measured are graphed.  However, the
+curve is stored in the aperture definition as an offset relative to the
+aperture center.
+.PP
+The tracing requires that the spectrum profile have a shape from which
+\fBcenter1d\fR can determine a position.  This pretty much means
+gaussian type profiles.  To extract a part of a long slit spectrum
+which does not have such a profile the user must trace a profile from
+another part of the image or a different image and then shift the
+center of the aperture without changing the shape.  For example the
+center of a extended galaxy spectrum can be traced and the aperture
+shifted to other parts of the galaxy.
+.NH
+Extraction
+.PP
+There are two types of extraction; strip extraction and sum
+extraction.  Strip extraction produces two dimensional images with
+pixels corresponding to the center of an aperture aligned along the
+lines or columns.  Sum extraction consists of the weighted sum of the
+pixels within an aperture along the image axis nearest the spatial axis
+at each point along the dispersion direction.  It is important to
+understand that the extraction is along image lines or columns while
+the actual dispersion/spatial coordinates may not be aligned exactly
+with the image axes.  If this misalignment is important then for simple
+rotations the task \fBrotate\fR in the \fBimages\fR package may be used
+while for more complex coordinate rectifications the tasks in the
+\fBlongslit\fR package may be used.
+.NH 2
+Sum Extraction
+.PP
+Denote the image axis nearest the spatial axis by the index $s$ and
+the other image axis corresponding to the dispersion axis by $lambda$.
+The extraction is defined by the equation
+
+.EQ I (1)
+f sub lambda~=~sum from s (W sub sl (I sub sl - B sub sl ) / P sub sl ) /
+sum from s W sub sl
+.EN
+
+where the sums are over all pixels along the spatial axis within some
+aperture.  The $W$ are weights, the $I$ are pixel intensities,
+the $B$ are background intensities, and the $P$ are a normalized
+profile model.
+.PP
+There are many possible choices for the extraction weights.  The extraction
+task currently provides two:
+
+.EQ I (2a)
+W sub sl~mark =~P sub sl
+.EN
+.EQ I (2b)
+W sub sl~lineup =~P sub sl sup 2 / V sub sl
+.EN
+
+where $V sub sl$ is the variance of the pixel intensities given by the
+model
+
+.EQ I
+	V sub sl~=~v sub 0 + v sub 1~max (0,~I sub sl )~~~~if v sub 0~>~0
+.EN
+.EQ I
+	V sub sl~=~v sub 1~max (1,~I sub sl )~~~~~~~~~if v sub 0~=~0
+.EN
+
+Substituting these weights in equation (1) yields the extraction equations
+
+.EQ I (3a)
+f sub lambda~mark =~sum from s (I sub sl - B sub sl )
+.EN
+.EQ I (3b)
+f sub lambda~lineup =~sum from s (P sub sl (I sub sl - B sub sl ) / V sub sl ) /
+sum from s (P sub sl sup 2 / V sub sl )
+.EN
+
+.PP
+The first type of weighting (2a), called \fIprofile\fR weighting, weights
+by the profile.  Since the weights cancel this gives the simple extraction (3a)
+consisting of the direct summation of the pixels within the aperture.
+It has the virtue of being simple and computationally fast (since the
+profile model does not have to be determined).
+.PP
+The second type of weighting (2b), called \fIvariance\fR weighting,
+uses a model for the variance of the pixel intensities.
+The model is based on Poisson statistics for a linear quantum detector.
+The first term is commanly call the \fIreadout\fR noise and the second term
+is the Poisson noise.  The actual value of $v sub 1$ is the reciprical of
+the number of photons per digital intensity unit (ADU).  A simple variant of
+this type of weighting is to let $v sub 1$ equal zero.  Since the actual
+scale of the variance cancels we can then set $v sub 0$ to unity to obtain
+
+.EQ I (4)
+f sub lambda~=~sum from s (P sub sl (I sub sl - B sub sl )) /
+sum from s P sub sl sup 2 .
+.EN
+
+The interpretation of this extraction is that the variance of the intensities
+is constant.  It gives greater weight to the stronger parts of the spectrum
+profile than does the profile weighting (3a) since the weights are
+$P sub sl sup 2$.  Equation (4) has the virtue that one need not know the
+readout noise or the ADU to photon number conversion.
+.NH 3
+Optimal Extraction
+.PP
+Variance weighted extraction is sometimes called optimal extraction because
+it is optimal in a statistical sense.  Specifically,
+the relative contribution of a pixel to the sum is related to the uncertainty
+of its intensity.  The uncertainty is measured by the expected variance of
+a pixel with that intensity.  The degree of optimality depends on how well
+the relative variances of the pixels are known.
+.PP
+A discussion of the concepts behind optimal extraction is given in the paper
+\fIAn Optimal Extraction Algorithm for CCD Spectroscopy\fR by Keith Horne
+(\fBPASP\fR, June 1986).  The weighting described in Horne's paper is the
+same as the variance weighting described in this paper.  The differences
+in the algorithms are primarily in how the model profiles $P sub sl$ are
+determined.
+.NH 3
+Profile Determination
+.PP
+The profiles of the spectra along the spatial axis are determined when
+either the detection and replacement of bad pixels or variance
+weighting are specified.  The requirements on the profiles are that
+they have the same shape as the image profiles at a each dispersion
+point and that they be as noise free and uncontaminated as possible.
+The algorithm used to create these profiles is to average a specified
+number of consecutive background subtracted image profiles immediately
+preceding the wavelength to which a profile refers.  When there are an
+insufficient number of image profiles preceding the wavelength being
+extracted then the following image profiles are also used to make up
+the desired number.  The image profiles are interpolated to a common
+center before averaging using the curve given in the aperture
+definition.  The averaging reduces the noise in the image data while
+the centering eliminates shifts in the spectrum as a function of
+wavelength which would broaden the profile relative to the profile of a
+single image line or column.  It is assumed that the spectrum profile
+changes slowly with wavelength so that by using profiles near a given
+wavelength the average profile shape will correctly reflect the profile
+of the spectrum at that wavelength.
+.PP
+The average profiles are determined in parallel with the extraction,
+which proceeds sequentially through the image.  Initially the first set
+of spectrum profiles is read from the image and interpolated to a common
+center.  The profiles are averaged excluding the first profile to be
+extracted; the image profiles in the average never include the image
+profile to be extracted.  Subsequently the average profile is updated
+by adding the last extracted image profile and subtracting the image
+profile which no longer belongs in the average.  This allows each image
+profile to be accessed and interpolated only once and makes the
+averaging computationally efficient.  This scheme also allows excluding
+bad pixels from the average profile.  The average profile is used to
+locate and replace bad pixels in the image profile being extracted as
+discussed in the following sections.  Then when this profile is added
+into the average for the next image profile the detected bad pixels are
+no longer in the profile.
+.PP
+In summary this algorithm for determining the spectrum profile
+has the following advantages:
+
+.IP (1)
+No model dependent smoothing is done.
+.IP (2)
+There is no assumption required about the shape of the profile.
+The only requirement is that the profile shape change slowly.
+.IP (3)
+Only one pass through the image is required and each image profile
+is accessed only once.
+.IP (4)
+The buffered moving average is very efficient computationally.
+.IP (5)
+Bad pixels are detected and removed from the profile average as the
+extraction proceeds.
+
+.NH 3
+Detection and Elimination of Bad Pixels
+.PP
+One of the important features of the aperture extraction package is the
+detection and elimination of bad pixels.  The average profile described
+in the previous section is used to find pixels which deviate from this
+profile.  The algorithm is straightforward.  A model spectrum of the
+image profile is obtained by scaling the normalized profile to the
+image profile.  The scale factor is determined using chi squared fitting:
+
+.EQ I (6)
+M sub sl~=~P sub sl~left { sum from s ((I sub sl - B sub sl ) P sub sl /
+V sub sl)~/~ sum from s (P sub sl sup 2 / V sub sl ) right } .
+.EN
+
+The RMS of this fit is determined and pixels deviating by more than a
+user specified factor times this RMS are rejected.  The fit is then
+repeated excluding the rejected points.  These steps are repeated until
+the user specified number of points have been rejected or no further deviant
+points are detected.  The rejected points in the image profile are then
+replaced by their model values.
+.PP
+This algorithm is based only on the assumption that the spatial profile
+of the spectrum (no matter what it is) changes slowly with wavelength.
+It is very sensitive at detecting departures from the expected profile.
+Its main defect is that in the first pass at the fit all of the image profile
+is used.  If there is a very badly deviant point and the rest of the profile
+is weak then the scale factor may favor the bad pixel more than the
+rest of the profile resulting in rejecting good profile points and not
+the bad pixel.
+.NH 3
+Relation of Optimal Extraction to Model Extraction
+.PP
+Equation (1) defines the extraction process in terms of a weighted sum
+of the pixel intensities.  However, the actual extraction operations
+performed by the task \fBsumextract\fR are 
+
+.EQ I (7a)
+f sub lambda~mark =~sum from s (I sub sl - B sub sl )
+.EN
+.EQ I (7b)
+f sub lambda~lineup =~sum from s M sub sl
+.EN
+
+where $M sub sl$ is the model spectrum fit to the background subtracted
+image spectrum $(I sub sl - B sub sl )$
+defined in the previous section (equation 6).  It is not obvious at first that
+(7b) is equivalent to (3b).  However, if one sums (6) and uses the fact
+that the sum of the normalized profile is unity one is left with equation (3b).
+.PP
+Equations (6) and (7b) provide an alternate way to think about the
+extracted one dimensional spectra.  Sum extraction of the model spectrum
+is used instead of the weighted sum for variance weighted extraction
+because the model spectrum is a product of the profile determination
+and the bad pixel cleaning process.  It is then more convenient
+and efficient to use the simple equations (7).
+.NH 2
+Strip Extraction
+.PP
+The task \fBstripextract\fR uses one dimensional image interpolation
+to shift the pixels along the spatial axes so that in the resultant
+output image the center of the aperture is exactly aligned with the
+image lines or columns.  The cleaning of bad pixels is an option
+in this extraction using the methods described above.  In addition
+the model spectrum described above may be extracted as a two
+dimensional image.  In fact, the only difference between strip extraction
+and sum extraction is whether the final step of summing the pixels
+in the aperture along the spatial axis is performed.
+.PP
+The primary use of \fBstripextract\fR is as a diagnostic tool.  It
+allows the user to see the background subtracted, cleaned and/or model
+spectrum as an image before it is summed to a one dimensional spectrum.
+In addition the two dimensional format allows use of other IRAF tools such as
+smoothing operators.  When appropriate
+it is a much simpler method of removing detector distortions and alignment
+errors than the full two dimensional mapping and image transformation
+available with the \fBlongslit\fR package.
+.NH
+Examples
+.de CS
+.nf
+.ft L
+..
+.de CE
+.fi
+.ft R
+..
+.PP
+This section is included because the flexibility and many options of
+the tasks allows a wide range of applications.  The examples illustrate
+the use of the task parameters for manipulating input images, output
+images, and reference images, and setting apertures interactively and
+noninteractively.  They do not illustrate the different possibilities
+in extraction or the interactive aperture definition and editing
+features.  These examples are meant to be relevant to actual data
+reduction and analysis problems.  For the purpose of these examples we
+will assume the dispersion axis is along the second image axis; i.e.
+DISPAXIS = 2.
+.PP
+The simplest problem is the extraction of an object spectrum which
+is centered on column 200.  To extract the spectrum with an aperture
+width of 20 pixels an image section can be used.
+
+.CS
+cl> sumextract image[190:209,*] obj1d
+cl> stripextract image[190:209,*] obj2d
+.CE
+
+To set the aperture center and limits interactively the edit option can be
+used with or without the image section.  This also allows fractional pixel
+centering and limits.
+.PP
+If the object slit position changes the spectrum profile can be traced first
+and then extracted.
+
+.CS
+cl> trace image[190:209,*]
+cl> sumextract image[190:209,*] obj1d
+cl> stripextract image[190:209,*] obj2d
+.CE
+
+By default the apertures are defined and/or edited interactively in
+\fBtrace\fR and editing is not the default in \fBsumextract\fR or
+\fBstripextract\fR.
+.PP
+A more typical example involves many images.  In this case a list of images
+is used though, of course, each image could be done separately as
+in the previous examples.  There are three common forms of lists, a
+pattern matching template, a comma separated list, and an "@" file.
+In addition the template editing metacharacter, "%", may be used
+to create new output image names based on input image names.
+If the object positions are different in each image then we can select
+apertures with image sections or using the editing option.  Some examples
+are
+
+.CS
+cl> sumextract image1[10:29,*],image2[32:51] obj1,obj2
+cl> sumextract image* e//image* edit+
+cl> sumextract image* image%%ex%* edit+
+cl> sumextract @images @images edit+
+.CE
+
+The "@" files can be created from the other two types of lists using the
+\fBsections\fR task in the \fBimages\fR package.  An important feature
+of the image templates is the use of the concatenation operator.  Note,
+however, this a feature of image templates and not file templates.
+Also the output root name may be the same as the input
+name because an extension is added provided there are no image
+sections in the input images.
+.PP
+If the object positions are the same then the apertures can be defined once
+and the remaining objects can be extracted using a reference image.
+
+.CS
+cl> apedit image1
+cl> sumextract image* image* ref=image1
+.CE
+
+Rather than using \fBapedit\fR one can use \fBsumextract\fR alone with
+the edit switch set.  The command is
+
+.CS
+cl> sumextract image* image* ref=image1 edit+
+.CE
+
+The task queries whether to edit the apertures for each image.
+For the first image respond with "yes" and set the apertures interactively.
+For the second task respond with "NO".  Since the aperture for "image1"
+was recorded when the first image was extracted it then acts as the reference
+for the remaining images.  The emphatic response "NO" turns off the edit switch
+for all the other images.  One difference between this example and the
+previous one is that the task cannot be run as a background batch task.
+.PP
+The extension to using traced apertures in the preceding examples is
+very similar.
+
+.CS
+cl> apedit image1
+cl> trace image* ref=image1 edit-
+cl> sumextract image* image*
+cl> stripextract image* image*
+.CE
+
+.PP
+Another common type of data has multiple spectra on each image.  Some examples
+are echelle and multislit spectra.  Echelle extractions usually are done
+interactively with tracing.  Thus, the commands are
+
+.CS
+cl> trace ech*
+cl> sumextract ech* ech*
+.CE
+
+For multislit spectra the slitlets are usually referenced by creating
+an "@" file containing the image sections.  The usage for extraction
+is then
+
+.CS
+cl> sumextract @slits @slitsout
+.CE
+
+.PP
+The aperture definitions can be transfered from a reference image to
+other images using \fBapedit\fR.  There is no particular reason to
+do this except that reference images would not be needed in 
+\fBtrace\fR, \fBsumextract\fR or \fBstripextract\fR.  The transfer
+is accomplished with the following command
+
+.CS
+cl> apedit image1
+cl> apedit image* ref=image1 edit-
+.CE
+
+The above can also be combined into one step by editing the first image
+and then responding with "NO" to the second image query.
+.NH
+Future Developments
+.PP
+The IRAF extraction package \fBapextract\fR is going to continue to
+evolve because 1) the extraction of one and two dimensional spectra
+from two dimensional images is an important part of reducing echelle,
+longslit, multislit, and multiaperture spectra, 2) the final strategy
+for handling multislit and multiaperture spectra produced by aperture
+masks or fiber optic mapping has not yet been determined, and 3) the
+extraction package and the algorithms have not received sufficient user
+testing and evaluation.  Changes may include some of the following.
+
+.IP (1)
+Determine the actual variance from the data rather than using the Poisson
+CCD model.
+.IP (2)
+Another task, possibly called \fBapfind\fR, is needed to automatically find
+profile positions in multiaperture, multislit, and echelle spectra.
+.IP (3)
+The bad pixel detection and removal algorithm does not handle well the case
+of a very strong cosmic ray event on top of a very weak spectrum profile.
+A heuristic method to make the first fitting pass of the average
+profile to the image data less prone to errors due to strong cosmic rays
+is needed.
+.IP (4)
+The aperture definition structure is general enough to allow the aperture
+limits along the dispersion dimension to be variable.  Eventually aperture
+definition and editing will be available using an image display.  Then
+both graphics and image display editing switches will be available.
+An image display interface will make extraction of objective prism
+spectra more convenient than it is now.
+.IP (5)
+Other types of extraction weighting may be added.
+.IP (6)
+Allow the extraction to be locally perpendicular to the traced curve.
diff --git a/noao/twodspec/apextract/doc/old/apextract1.ms b/noao/twodspec/apextract/doc/old/apextract1.ms
new file mode 100644
index 00000000..b586daad
--- /dev/null
+++ b/noao/twodspec/apextract/doc/old/apextract1.ms
@@ -0,0 +1,811 @@
+.EQ
+delim $$
+define sl '{s lambda}'
+.EN
+.RP
+.TL
+The IRAF APEXTRACT Package
+.AU
+Francisco Valdes
+.AI
+IRAF Group - Central Computer Services
+.K2
+P.O. Box 26732, Tucson, Arizona 85726
+.AB
+The IRAF \fBapextract\fR package provides tools for the extraction of
+one and two dimensional spectra from two dimensional images
+such as echelle, long slit, multifiber, and multislit spectra.
+Apertures of fixed spatial width define the regions of
+the two dimensional images to be extracted at each point along the
+dispersion axis.  Apertures may follow changes in the positions of
+the spectra as a function of position along the dispersion axis.
+The spatial and dispersion axes may be oriented along either image axis.
+Extraction to one dimensional spectra consists of a weighted sum of the pixels
+within the apertures at each point along the dispersion axis.  The
+weighting options provide the simple sum of the pixel values and a
+weighting by the expected uncertainty of each pixel.  Two dimensional
+extractions interpolate the spectra in the spatial axis to produce
+image strips with the position of the  spectra exactly aligned with one
+of the image dimensions.  The extractions also include optional
+background subtraction, modeling, and bad pixel detection and replacement.
+The tasks are flexible in their ability to define and edit apertures,
+operate on lists of images, use apertures defined for reference
+images, and operate both very interactively or noninteractively.
+The extraction tasks are efficient and require only one pass through
+the data.  This paper describes the package organization, the tasks,
+the algorithms, and the data structures.
+.AE
+.NH
+Introduction
+.PP
+The IRAF \fBapextract\fR package provides tools for the extraction of
+one and two dimensional aperture spectra from two dimensional format
+images such as those produced by echelle, long slit, multifiber, and
+multislit spectrographs.  This type of data is becoming increasingly
+common because of the efficiency of data collection and technological
+improvements in spectrographs and detectors.  The trend is to greater
+and greater numbers of spectra per image.  Extraction is one of the
+fundamental operations performed on these types of two dimensional
+spectral images, so a great deal of effort has gone into the design and
+development of this package and to making it easy to use.
+.PP
+The tasks are flexible and have many options.  To make the best use of
+them it is important to understand how they work.  This paper provides
+a general description of the package organization, the tasks, the algorithms,
+and the data structures.  Specific descriptions of parameters
+and usage may be found in the IRAF help pages for the tasks which
+are included as appendices to this paper.  The image reduction "cookbooks"
+also provide examples of usage for specific instruments or types
+of instruments.
+.PP
+Extraction of spectra consists of three logical steps.  First, locating
+the spectra in the two dimensional image.  This includes defining the
+dispersion direction, the positions of the spectra at some point
+along the dispersion direction, the spatial extent or aperture to be
+used for extraction, and possible information about where the background
+for each spectrum is to be determined.  This information is maintained
+in the package as structures called \fIapertures\fR.  The second step is
+to measure the positions of the spectra at other points along the dispersion.
+This process is called tracing.  Tracing is optional if the spectra
+are exactly aligned with the dispersion direction.  The final step is
+to extract the spectra into one or two dimensional images.
+.PP
+The \fBapextract\fR package identifies the image axes with the spatial
+and dispersion axes.  Thus, during extraction, pixels of constant
+wavelength are assumed to be along a line or column.  In this paper the
+terms \fIslit\fR or \fIspatial\fR axis and \fIdispersion\fR or
+\fIwavelength\fR axis are used to refer to the image axes corresponding
+to the spatial and dispersion axes.  To simplify the presentation a
+cut across the dispersion axis will be called a line even though it
+could also be a column.
+.PP
+Often a small degree of
+misalignment between the image axes and the true dispersion and spatial
+axes is not important.  The main effect of misalignment is a broadening
+of the spectral features due to the difference in wavelength on
+opposite sides of the extraction aperture.  If the misalignment is
+significant, however, the image may be rotated with the task
+\fBrotate\fR in the \fBimages\fR package or remapped with the
+\fBlongslit\fR package tasks for coordinate rectification.
+.PP
+It does not matter which image axis is the dispersion axis since the
+tasks work equally well in either orientation.  However, the dispersion
+axis must be defined, with the \fBtwodspec\fR task \fBsetdisp\fR,
+before these tasks may be used.  This task is a simple script which
+adds the parameter DISPAXIS to the image headers.  The \fBapextract\fR
+tasks, like the \fBlongslit\fR tasks, look in the header to determine
+the dispersion axis.
+.NH
+The APEXTRACT Package
+.PP
+In this section the organization of the \fBapextract\fR package and the
+functions and parameters of the tasks are briefly described.  More detailed
+descriptions are given in the help pages for the tasks.  The tasks in the
+package are:
+
+.ce
+.ft B
+The APEXTRACT Tasks
+
+.ft L
+.nf
+	  apdefault - Set the default aperture parameters
+	     apedit - Edit apertures interactively
+	     apfind - Automatically find spectra and define apertures
+	       apio - Set the I/O parameters for the APEXTRACT tasks
+	apnormalize - Normalize 2D apertures by 1D functions
+	    apstrip - Extract two dimensional aperture strips
+	      apsum - Extract one dimensional aperture sums
+	    aptrace - Trace positions of spectra
+.fi
+.ft R
+
+.PP
+The tasks are highly integrated so that each task includes some or all of
+the functions and parameters of the other tasks.  Thus, these tasks
+reflect the logical organization of the extraction process rather than
+a set of disparate tools.  One reason for this organization is to group
+the parameters by function into easy to manage \fIparameter sets
+(psets)\fR.  The tasks \fBapdefault\fR and \fBapio\fR are just psets
+for specifying the default aperture parameters and the I/O parameters
+of the package; in other words, they do nothing but provide a grouping
+of parameters.  Executing these tasks is a shorthand for the command
+"eparam apdefault" or "eparam apio".
+.PP
+The input/output parameters in \fBapio\fR specify the aperture database,
+an optional log file for brief, time stamped log information, an optional
+metacode plot file for saving plots of the apertures, the traces, and the
+quick look extracted spectra, and the graphics input and output devices
+(almost always the user's terminal).  One point about the plot file is
+that the plots are recorded even if the user chooses not to view these
+graphs as the task is run interactively or noninteractively.  This allows
+reviewing the traces and spectra with a tool like \fBgkimosaic\fR.
+.PP
+The default aperture parameters specify the aperture limits (basically
+the width of the aperture and position relative to the center of the
+spectrum) and the background fitting parameters.  The background
+parameters are the standard parameters used by the \fBicfit\fR package
+with which the user is assumed to be familiar.  For more on this see
+the help information for \fBicfit\fR.
+.PP
+The other tasks are both psets and executable tasks.  There are a
+number features which are common to all these tasks.  First, they
+follow the same steps in defining apertures for the input images.
+These steps are:
+.IP (1)
+If a reference image is specified then the database is searched for
+apertures previously defined for this image.
+.IP (2)
+If apertures are found for the reference image they may be recentered
+on the spectra in the input image at a specified line.  This does not
+change the shape of the apertures but only adds a shift in the center
+coordinate of the apertures along the spatial axis.
+.IP (3)
+If a reference image is not specified or if no reference apertures are found
+then the database is searched for previous apertures for the input image.
+.IP (4)
+If there are no apertures defined either from a reference image or previous
+apertures for the input image then an automatic algorithm may be used to find
+a specified number of spectra (based on peak values) and assign them default
+apertures.
+.IP (5)
+Finally, a sophisticated graphical aperture editor may be used to examine,
+define, and modify apertures.
+.IP (6)
+When tracing, extracting, or normalizing flat field spectra,
+if no apertures have been defined by the steps above then a single default
+aperture, centered in the image, is defined.
+
+Any apertures created, modified, or adopted from a reference image
+may be recorded in the database for the input image.
+.PP
+The operations listed above are selected by parameters common to each of the
+tasks.  For example the parameter \fIedit\fR selects whether to enter
+the aperture editor and is present in each of the executable tasks.
+On the other hand the parameters specific to the aperture editor,
+while accessed by any of the tasks, reside only in the parameter set of
+the task \fBapedit\fR.  In this way parameters are distributed
+by logical function rather than including them in each task.
+.PP
+In addition to the aperture editing and finding functions available in
+every task, some of the tasks include functions for tracing, extracting,
+or normalizing the spectra.  The tasks \fBapsum\fR and \fBapstrip\fR,
+which extract one and two dimensional spectra, are at the top of the
+hierarchy and include all the logical functions provided by the package.
+Thus, in most cases the user need only use the task \fBapsum\fR to define
+apertures, trace the spectra, and extract them.
+.PP
+Another feature common to the tasks is their interactive and noninteractive
+modes.  When the parameter \fIinteractive\fR is set to \fIno\fR then the
+aperture editing, interactive trace fitting, and review of the extracted
+one dimensional spectra functions of the package are bypassed.  Note that
+this means you do not have to explicitly set the parameter \fIedit\fR,
+or those for other purely interactive functions,
+to \fIno\fR when extracting spectra noninteractively.  In the noninteractive
+mode there are also no queries.
+.PP
+The interactive mode includes the interactive graphical functions of
+aperture editing, trace fitting, and extraction review.  In addition
+the user is queried at each step.  For example the user will be queried
+whether to edit the apertures for a particular image if the task
+parameter for editing is set.  The queries have four responses: \fIyes,
+no, YES,\fR and \fINO\fR.  The lower case responses apply only to the
+particular query.  The upper case responses apply to any further
+queries of the same type and suppress the query from appearing again.
+This is particularly useful when dealing with many images or many
+apertures.  For example, when fitting the traced points interactively
+the user may examine the first few and then say \fINO\fR to skip the
+remaining apertures using the last defined fitting parameters.  Note
+that if a plot file is specified the graphs showing the traced points
+and the fits are recorded even if they are not viewed interactively.
+.NH
+Algorithms
+.PP
+The \fBapextract\fR package consists of a number of logical functions or,
+in computerese, algorithms.  These algorithms manipulate the aperture
+structure data and create output data in the form of images.  In
+this section the various algorithms are described.  In addition to the
+algorithms specific to the package, there are some general algorithms
+and tools used which appear in other IRAF tasks.  Specifically there are the
+interactive curve fitting tools called \fBicfit\fR and the one
+dimensional centering algorithm called \fBcenter1d\fR.  These are
+mentioned below and described in detail elsewhere in the help documentation.
+.NH 2
+Finding Spectra
+.PP
+When dealing with images containing large numbers of spectra it may be
+desirable to locate the spectra and define apertures automatically.  The
+\fBapfind\fR algorithm provides this ability from any of the executable
+tasks and from the aperture editor using the 'f' key.  It takes a cut
+across the dispersion axis by summing one or more image lines.
+All the local maxima are identified and ranked by intensity.  Starting
+with the highest maxima any other peaks within a specified minimum
+separation are eliminated.  The weakest remaining peaks exceeding the
+specified number are eliminated next.  The positions of the
+spectra based on peak positions are refined by centering using the
+\fBcenter1d\fR algorithm.  Finally identical apertures are assigned
+for each spectrum found.
+.PP
+When the algorithm is invoked by a task, with the parameter \fIfind\fR,
+there must be no previous or reference apertures in the database.
+The apertures assigned to the spectra have the parameters
+specified in the \fBapdefault\fR pset.  When the algorithm is invoked
+from the aperture editor with the 'f' key then new apertures are
+added to any existing apertures up to the total number of apertures,
+existing plus new, given by the \fInfind\fR parameter.  If there
+is a current aperture then copies of it are used to define the
+apertures for the new spectra.  Thus, one method for defining many
+apertures is to use the editor to define one aperture, set its
+limits and background parameters, and then find the remaining apertures
+automatically.
+.NH 2
+Centering and Recentering
+.PP
+When new apertures are defined (except for a special key to mark apertures
+without centering) or when apertures are recentered, either with the
+centering key in the editor or with the task parameter \fIrecenter\fR,
+the center is determined using the \fBcenter1d\fR algorithm.
+This is described in the help documentation under the name \fBcenter1d\fR.
+Briefly, the data line is convolved with an asymmetric function of specified
+width.  The convolution integral is evaluated using image interpolation.
+The sign of the convolution acts as a gradient to move from the starting
+position to the final position where the convolution is zero.  This algorithm
+is good to about 5% of a pixel.  It has two important parameters; the
+width of the convolution and the error distance between the starting
+and final positions.  The width of the convolution determines the scale
+of features to which the centering is sensitive.  The error distance is
+the greatest change allowed in the initial positions.  If this error
+distance is exceeded then the centering fails and either a new aperture
+is not defined or the position of an existing aperture is not changed.
+.NH 2
+The Aperture Editor
+.PP
+The aperture editor is a sophisticated tool for defining and modifying
+apertures.  It may also be used to selectively trace and extract
+spectra.  Thus, the aperture editor may be used alone to perform all
+the functions for extracting spectra.  The aperture editor uses a
+graphical presentation.  A line or sum of lines is displayed.  The
+apertures are marked above the line and identified with the aperture
+number.  Information about the current aperture is shown on the status
+line.  The cursor is used to mark new apertures, shift the center or
+aperture limits, and perform a variety of functions.  Because there may
+be many apertures which the user wants to modify in the same way there
+is a mode switch to apply commands to all the apertures.  The switch is
+toggled with the 'a' key and the mode is indicated on the status line.
+.PP
+There are also a number of colon commands.  These allow resetting parameters
+explicitly rather than by cursor and interacting with the aperture
+database and the image data.  The background fitting parameters such as
+the background regions and function order are set by switching to the
+interactive curve fitting package \fBicfit\fR.  The line being edited is
+used to set the parameters.  No background is actually extracted at this
+stage.  The ALL mode applies to the background parameters as well.
+.PP
+The aperture editor has many commands.  For a description of the
+commands see the help information for the task \fBapedit\fR.  In
+summary the aperture editor is used to interactively define apertures,
+both centered on spectra and at arbitrary positions, adjust the limits
+and background parameters, and possibly select apertures to be traced
+and extracted.  These functions may be applied independently on each
+aperture for maximum flexibility or applied to all apertures for ease
+of use with many apertures.
+.NH 2
+Tracing
+.PP
+The spectra to be extracted are not always aligned exactly with the
+image columns or lines.  For consistent
+extraction it is important that the same part of the spectrum profile
+be extracted at each wavelength point.  Thus, the extraction apertures
+allow for shifts along the spatial axis at each wavelength.  The
+shifts are defined by a curve which is a function of the wavelength.
+The curve is determined by tracing the positions of the spectrum
+profile at a number of wavelengths and fitting a function to these
+positions.
+.PP
+The \fIaptrace\fR algorithm performs the tracing and curve fitting.
+The starting point along the dispersion axis (a line or column) for
+the tracing is specified by the user.  The positions of the spectrum
+profiles are determined using the \fBcenter1d\fR algorithm
+(see the previous section on centering and  the help page for \fBcenter1d\fR).
+The user specifies a step along the dispersion axis.  At each step the
+positions of the profiles are redetermined using the preceding
+positions as the initial guesses.  If the positions are lost at one step
+an attempt is made to recover the spectrum in the next step.  If this
+also fails then tracing of that spectrum in that direction is finished.
+In order to enhance and trace weak spectra the user may specify a number
+of neighboring profiles to be summed before determining the profile positions.
+In addition to the other centering parameters, there is also a
+\fIthreshold\fR parameter to define a minimum contrast between the spectrum
+and the background.
+.PP
+Once the positions have been traced from the starting point to the ends of the
+aperture, or until the positions become indeterminate, a curve of a
+specified type and order is fit to the positions as a function of
+wavelength.  The function fitting is performed with the \fBicfit\fR
+tools (see the help documentation for \fBicfit\fR).  The curve fitting
+may be performed interactively or noninteractively.  Note that when the
+curve is fit interactively the actual positions measured are graphed.
+However, the curve is stored in the aperture definition as an offset
+relative to the aperture center.
+.PP
+The tracing requires that the spectrum profile be continuous and have
+some kind of maxima.  This means that arc calibration spectra or
+arbitrary regions of an extended object in a long slit spectrum cannot
+be traced.  Flat topped spectra such as quartz lamp images taken through
+slits can be measured provided the width of the centering function is
+somewhat wider than the profile (to avoid centering on little peaks
+within the slit).  For images which cannot be traced, reference apertures
+from images that can be traced are used.  This is how apertures for
+arc spectra are defined and extracted.  For sky apertures or the
+wings of extended objects the reference apertures can be shifted
+by the aperture editor without altering the shape of the aperture.
+.NH 2
+Sum Extraction
+.PP
+Sum extraction consists of the weighted sum of the pixels along the spatial axis
+within the aperture limits at each point along the dispersion axis.
+A background at each point along the dispersion may be determined by fitting a
+function to data in the vicinity of the spectrum and subtracting the
+function values estimated at each point within the aperture.  The estimated
+background may be output as a one dimensional spectrum.  Other options
+include the detection and replacement of deviant points such as due to
+cosmic rays.
+.PP
+Denote the image axis nearest the spatial axis by the index $s$ and
+the other image axis corresponding to the dispersion axis by $lambda$.
+The weighted extraction is defined by the equation
+
+.EQ I (1)
+f sub lambda~=~sum from s (W sub sl (I sub sl - B sub sl ) / P sub sl ) /
+sum from s W sub sl
+.EN
+
+where the sums are over all pixels along the spatial axis within some
+aperture.  The $W$ are weights, the $I$ are pixel intensities,
+the $B$ are background intensities, and the $P$ are a normalized
+profile model.
+.PP
+There are many possible choices for the extraction weights.  The extraction
+task \fBapsum\fR currently provides two:
+
+.EQ I (2a)
+W sub sl~mark =~P sub sl
+.EN
+.EQ I (2b)
+W sub sl~lineup =~P sub sl sup 2 / V sub sl
+.EN
+
+where $V sub sl$ is the variance of the pixel intensities given by the
+model
+
+.EQ I
+	V sub sl~=~v sub 0 + v sub 1~max (0,~I sub sl )~~~~if v sub 0~>~0
+.EN
+.EQ I
+	V sub sl~=~v sub 1~max (1,~I sub sl )~~~~~~~~~if v sub 0~=~0
+.EN
+
+Substituting these weights in equation (1) yields the extraction equations
+
+.EQ I (3a)
+f sub lambda~mark =~sum from s (I sub sl - B sub sl )
+.EN
+.EQ I (3b)
+f sub lambda~lineup =~sum from s (P sub sl (I sub sl - B sub sl ) / V sub sl ) /
+sum from s (P sub sl sup 2 / V sub sl )
+.EN
+
+.PP
+The first type of weighting (2a), called \fIprofile\fR weighting, weights
+by the profile.  Since the weights cancel this gives the simple extraction (3a)
+consisting of the direct summation of the pixels within the aperture.
+It has the virtue of being simple and computationally fast (since the
+profile model does not have to be determined).
+.PP
+The second type of weighting (2b), called \fIvariance\fR weighting,
+uses a model for the variance of the pixel intensities.
+The model is based on Poisson statistics for a linear quantum detector.
+The first term is commonly call the \fIreadout\fR noise and the second term
+is the Poisson noise.  The actual value of $v sub 1$ is the reciprocal of
+the number of photons per digital intensity unit (ADU).  A simple variant of
+this type of weighting is to let $v sub 1$ equal zero.  Since the actual
+scale of the variance cancels we can then set $v sub 0$ to unity to obtain
+
+.EQ I (4)
+f sub lambda~=~sum from s (P sub sl (I sub sl - B sub sl )) /
+sum from s P sub sl sup 2 .
+.EN
+
+The interpretation of this extraction is that the variance of the intensities
+is constant.  It gives greater weight to the stronger parts of the spectrum
+profile than does the profile weighting (3a) since the weights are
+$P sub sl sup 2$.  Equation (4) has the virtue that one need not know the
+readout noise or the ADU to photon number conversion.
+.NH 3
+Optimal Extraction
+.PP
+Variance weighted extraction is sometimes called optimal extraction because
+it is optimal in a statistical sense.  Specifically,
+the relative contribution of a pixel to the sum is related to the uncertainty
+of its intensity.  The uncertainty is measured by the expected variance of
+a pixel with that intensity.  The degree of optimality depends on how well
+the relative variances of the pixels are known.
+.PP
+A discussion of the concepts behind optimal extraction is given in the paper
+\fIAn Optimal Extraction Algorithm for CCD Spectroscopy\fR by Keith Horne
+(\fBPASP\fR, June 1986).  The weighting described in Horne's paper is the
+same as the variance weighting described in this paper.  The differences
+in the algorithms are primarily in how the model profiles $P sub sl$ are
+determined.
+.NH 3
+Profile Determination
+.PP
+The profiles of the spectra along the spatial axis are determined when
+either the detection and replacement of bad pixels or variance
+weighting are specified.  The requirements on the profiles are that
+they have the same shape as the image profiles at a each dispersion
+point and that they be as noise free and uncontaminated as possible.
+The algorithm used to create these profiles is to average a specified
+number of consecutive background subtracted image profiles immediately
+preceding the wavelength to which a profile refers.  When there are an
+insufficient number of image profiles preceding the wavelength being
+extracted then the following image profiles are also used to make up
+the desired number.  The image profiles are interpolated to a common
+center before averaging using the curve given in the aperture
+definition.  The averaging reduces the noise in the image data while
+the centering eliminates shifts in the spectrum as a function of
+wavelength which would broaden the profile relative to the profile of a
+single image line or column.  It is assumed that the spectrum profile
+changes slowly with wavelength so that by using profiles near a given
+wavelength the average profile shape will correctly reflect the profile
+of the spectrum at that wavelength.
+.PP
+The average profiles are determined in parallel with the extraction,
+which proceeds sequentially through the image.  Initially the first set
+of spectrum profiles is read from the image and interpolated to a common
+center.  The profiles are averaged excluding the first profile to be
+extracted; the image profiles in the average never include the image
+profile to be extracted.  Subsequently the average profile is updated
+by adding the last extracted image profile and subtracting the image
+profile which no longer belongs in the average.  This allows each image
+profile to be accessed and interpolated only once and makes the
+averaging computationally efficient.  This scheme also allows excluding
+bad pixels from the average profile.  The average profile is used to
+locate and replace bad pixels in the image profile being extracted as
+discussed in the following sections.  Then when this profile is added
+into the average for the next image profile the detected bad pixels are
+no longer in the profile.
+.PP
+In summary this algorithm for determining the spectrum profile
+has the following advantages:
+
+.IP (1)
+No model dependent smoothing is done.
+.IP (2)
+There is no assumption required about the shape of the profile.
+The only requirement is that the profile shape change slowly.
+.IP (3)
+Only one pass through the image is required and each image profile
+is accessed only once.
+.IP (4)
+The buffered moving average is very efficient computationally.
+.IP (5)
+Bad pixels are detected and removed from the profile average as the
+extraction proceeds.
+
+.NH 3
+Detection and Elimination of Bad Pixels
+.PP
+One of the important features of the aperture extraction package is the
+detection and elimination of bad pixels.  The average profile described
+in the previous section is used to find pixels which deviate from this
+profile.  The algorithm is straightforward.  A model spectrum of the
+image profile is obtained by scaling the normalized profile to the
+image profile.  The scale factor is determined using chi-squared fitting:
+
+.EQ I (6)
+M sub sl~=~P sub sl~left { sum from s ((I sub sl - B sub sl ) P sub sl /
+V sub sl )~/~ sum from s (P sub sl sup 2 / V sub sl ) right } .
+.EN
+
+The RMS of this fit is determined and pixels deviating by more than a
+user specified factor times this RMS are rejected.  The fit is then
+repeated excluding the rejected points.  These steps are repeated until
+the user specified number of points have been rejected or no further deviant
+points are detected.  The rejected points in the image profile are then
+replaced by their model values.
+.PP
+This algorithm is based only on the assumption that the spatial profile
+of the spectrum (no matter what it is) changes slowly with wavelength.
+It is very sensitive at detecting departures from the expected
+profile.  It has two problems currently.  Because the input line is
+first interpolated to the same center as the profile, single bad pixels
+are generally broadened to two bad pixels, making it harder to find the
+bad data.  Also, in the first pass at the fit all of the image profile
+is used so if there is a very badly deviant point and the rest of the
+profile is weak then the scale factor may favor the bad pixel more than
+the rest of the profile.  This may result in rejecting good profile
+points and not the bad pixel.
+.NH 3
+Relation of Optimal Extraction to Model Extraction
+.PP
+Equation (1) defines the extraction process in terms of a weighted sum
+of the pixel intensities.  However, the actual extraction operations
+performed by the task \fBapsum\fR are 
+
+.EQ I (7a)
+f sub lambda~mark =~sum from s (I sub sl - B sub sl )
+.EN
+.EQ I (7b)
+f sub lambda~lineup =~sum from s M sub sl
+.EN
+
+where $M sub sl$ is the model spectrum fit to the background subtracted
+image spectrum $(I sub sl - B sub sl )$
+defined in the previous section (equation 6).  It is not obvious at first that
+(7b) is equivalent to (3b).  However, if one sums (6) and uses the fact
+that the sum of the normalized profile is unity one is left with equation (3b).
+.PP
+Equations (6) and (7b) provide an alternate way to think about the
+extracted one dimensional spectra.  Sum extraction of the model spectrum
+is used instead of the weighted sum for variance weighted extraction
+because the model spectrum is a product of the profile determination
+and the bad pixel cleaning process.  It is then more convenient
+and efficient to use the simple equations (7).
+.NH 2
+Strip Extraction
+.PP
+The task \fBapstrip\fR uses one dimensional image interpolation
+to shift the pixels along the spatial axis so that in the resultant
+output image the center of the aperture is exactly aligned with the
+image lines or columns.  The cleaning of bad pixels is an option
+in this extraction using the methods described above.  In addition
+the model spectrum, described above, may be extracted as a two
+dimensional image.  In fact, the only difference between strip extraction
+and sum extraction is whether the final step of summing the pixels
+in the aperture along the spatial axis is performed.
+.PP
+The primary use of \fBapstrip\fR is as a diagnostic tool.  It
+allows the user to see the background subtracted, cleaned, and/or model
+spectrum as an image before it is summed to a one dimensional spectrum.
+In addition the two dimensional format allows use of other IRAF tools such as
+smoothing operators.  When appropriate
+it is a much simpler method of removing detector distortions and alignment
+errors than the full two dimensional mapping and image transformation
+available with the \fBlongslit\fR package.
+.NH 2
+Aperture Normalization
+.PP
+The special algorithm/task \fBapnormalize\fR normalizes the two dimensional
+image data within an aperture by a smooth function of the dispersion
+coordinate.  Unlike the extraction tasks the output of this algorithm is
+a two dimensional image of the same format as the input image.  This function
+is used primarily for creating flat field images in which the large
+scale shape of the quartz spectra and the variations in level between the
+spectra are removed and the regions between the spectra, where there is no
+signal, are set to unity.  It may also be used to normalize two dimensional
+spectra to a unit continuum at some point in the spectrum, such as the center.
+.PP
+The algorithm is to extract a one dimensional spectrum for each aperture,
+fit a smooth function to the spectrum, and then divide this spectrum
+back into the two dimensional image.  Points outside the apertures are
+set to 1.  This is the same algorithm used in the \fBlongslit\fR package
+by the task \fBresponse\fR except that it applies to arbitrary apertures
+rather than to image sections.
+.PP
+Apertures are defined in the same way as for extraction.  The normalization
+spectrum may be obtained from a different aperture than the aperture to be
+normalized.  Generally the normalization apertures are either the same or
+narrower than the apertures to be normalized.  The continuum fitting also
+uses the \fBicfit\fR package.  Sample regions and iterative sigma clipping
+are used to remove spectral lines from the continuum fits.
+.PP
+There are two commonly used approaches to fitting the extracted spectra
+in flat field images.  First, a constant function is fit.  This has the
+effect of simply normalizing the apertures to near unity without affecting
+the shape of spectra in any way.  This removes response effects at all scales,
+from spectra flatten with this flat field.  However, it does not
+preserve total counts, it introduces the shape of the quartz spectrum,
+and it removes the blaze function.  The second approach is to fit the
+large scale shape of the quartz spectra.  This removes smaller scale
+response effects such a fringing and individual pixel responses while
+preserving the total counts by leaving the blaze function alone.  There are
+cases where each of these approaches is applicable.
+.NH
+Apertures
+.PP
+Apertures are the basic data structures used in the package; hence the
+package name.  An aperture defines a region of the two dimensional image
+to be extracted.  The aperture definitions are stored in a database.
+An aperture consists of the following components:
+
+.IP ID
+.br
+An integer identification number.  The identification number must be
+unique.  It is used as the default extension during extraction of
+the spectra.  Typically the IDs are consecutive positive integers
+ordered by increasing or decreasing slit position.
+.IP BEAM
+.br
+An integer beam number.  The beam number need not be
+unique; i.e. several apertures may have the same beam number.
+The beam number will be recorded in the image header of the
+the extracted spectrum.  By default the beam number is the same as
+the ID.
+.IP CENTER[2]
+.br
+The center of the aperture along the slit and dispersion axes in the two
+dimensional image.
+.IP LOWER[2]
+.br
+The lower limits of the aperture, relative to the aperture center,
+along the slit and dispersion axes.  The lower limits need not be less
+than the center.
+.IP UPPER[2]
+.br
+The upper limits of the aperture, relative to the aperture center,
+along the slit and dispersion axes.  The upper limits need not be greater
+than the center.
+.IP APAXIS
+.br
+The aperture or spatial axis.
+.IP CURVE
+.br
+An offset to be added to the center position for the aperture axis as
+a function of the wavelength.  The function is one of the standard IRAF
+types; a legendre polynomial, a chebyshev polynomial, a linear spline,
+or a cubic spline.
+.IP BACKGROUND
+.br
+Parameters for background subtraction along the aperture axis based on
+the interactive curve fitting (\fBicfit\fR) tools.
+
+.PP
+The aperture center is the only absolute coordinate (relative to the
+image or image section).  The other aperture parameters and the
+background fitting regions are defined relative to the center.  Thus,
+an aperture may be repositioned easily by changing the center
+coordinates.  Also constant aperture size, shape (curve), and
+background regions may be maintained for many apertures.
+.PP
+The edges of the aperture along the spatial axis at each point along the
+dispersion axis are given by evaluating the offset curve at that dispersion
+coordinate and adding the aperture center and the lower or upper limits
+for the aperture axis.  The edges of the aperture along the dispersion axis
+do not have an offset curve and are currently fixed to define the entire
+length of the image.  In the future this may not be the case such as
+in applications with objective prism spectra.
+.PP
+Apertures for a particular image may be defined in several ways.  They
+may be defined and modified graphically with an aperture editor.  Default
+apertures may be defined automatically with parameters from the
+\fBapdefault\fR pset using an aperture finding algorithm.  Another
+method is to specify that the apertures for one image use the aperture
+definitions from another "reference" image.  In the rare cases where
+apertures are not defined at the stage of tracing or extracting then
+a single default aperture centered in the image is created.
+.NH 2
+The Database
+.PP
+The aperture information is stored in a database.  The structure and type of
+database is expected to change in the future and as far as the package and
+user need be concerned it is just a black box with some name specified in
+the database name parameter.  However, accepting that the database structure may
+change it may be of use to the user to understand the nature of the current
+text file / directory format database.  The database is a directory containing
+text files.  It is automatically created if necessary.  The aperture data
+for all the apertures from a single image are stored in a text file
+with the name given by the image name (with special characters replaced
+with '_') prefixed with "ap".  Updates of the aperture data are performed
+by overwriting the database file.
+.PP
+The content of a file consists of a comment (beginning with a #) giving
+the date created/updated, a record identification (there is one record
+per aperture) with the image name, aperture number and aperture
+coordinate in the aperture and dispersion axes.  The following lines
+give information about the aperture.  The position and shape of an
+aperture is given by a center coordinate along the aperture axis (given
+by the axis keyword) and the dispersion axis.  There are lower and
+upper limits for the aperture relative to this center, again along both
+axis.  Currently the limits along the dispersion axis are the image
+boundaries.  The background keyword introduces the background
+subtraction parameters.  Finally there is an offset or trace function
+which is added to the center at each point along the dispersion axis.
+function.  The offset is generally zero at the dispersion point
+corresponding to the aperture center.
+.PP
+This offset or trace function is described by a \fBcurfit\fR array under
+the keyword curve.  The first value is the number of elements in this
+array.  The first element is a magic number specifying the function
+type.  The next number is the order or number of spline pieces.  The
+next two elements give the range over which the curve is defined.  In
+the \fBapextract\fR case it is the edges of the image along the dispersion.
+The remaining elements are the function coefficients.  The form of the
+the function is specific to the IRAF \fBcurfit\fR math routines.  Note that
+the coefficients apply to an independent variable which is -1 at the
+beginning of the defined range (element 3) and 1 at the end of the range
+(element 4).  For further details consult the IRAF group.
+.PP
+An example database file for one aperture from an image "ech001" is given
+below.
+
+.ft L
+.nf
+	# Fri 14:33:35 08-May-87
+	begin	aperture ech001 1 22.75604 100.
+		image	ech001
+		aperture	1
+		beam	1
+		center	22.75604 100.
+		low	-2.680193 -99.
+		high	3.910698 100.
+		background
+			xmin -262.
+			xmax 262.
+			function chebyshev
+			order 1
+			sample -10:-6,6:10
+			naverage -3
+			niterate 0
+			low_reject 3.
+			high_reject 3.
+			grow 0.
+		axis	1
+		curve	6
+			2.
+			2.
+			1.
+			200.
+			-0.009295368
+			-0.3061974
+.fi
+.ft R
+.NH
+Future Developments
+.PP
+The IRAF extraction package \fBapextract\fR is going to continue to
+evolve because the extraction of one and two dimensional spectra
+from two dimensional images is an important part of reducing echelle,
+longslit, multislit, and multiaperture spectra.  Changes may include
+some of the following:
+
+.IP (1)
+Determine the actual variance from the data rather than using the Poisson
+CCD model.  Also output the variance vector if desired.
+.IP (2)
+The bad pixel detection and removal algorithm does not handle well the case
+of a very strong cosmic ray event on top of a very weak spectrum profile.
+A heuristic method to make the first fitting pass of the average
+profile to the image data less prone to errors due to strong cosmic rays
+is needed.  Also the detection should be done by interpolating the profile
+to the original image data rather than the other way around, in order to
+avoid broadening cosmic rays by interpolation.
+.IP (3)
+The aperture definition structure is general enough to allow the aperture
+limits along the dispersion dimension to be variable.  Eventually aperture
+definition and editing will be available using an image display.  Then
+both graphics and image display editing switches will be available.
+An image display interface will make extraction of objective prism
+spectra more convenient than it is now.
+.IP (4)
+Other types of extraction weighting may be added.
diff --git a/noao/twodspec/apextract/doc/old/apextract2.ms b/noao/twodspec/apextract/doc/old/apextract2.ms
new file mode 100644
index 00000000..35b42390
--- /dev/null
+++ b/noao/twodspec/apextract/doc/old/apextract2.ms
@@ -0,0 +1,14 @@
+.RP
+.TL
+Cleaning and Optimal Extraction with the IRAF APEXTACT Package
+.AU
+Francisco Valdes
+.AI
+IRAF Group - Central Computer Services
+.K2
+P.O. Box 26732, Tucson, Arizona 85726
+.AB
+.AE
+.NH
+Introduction
+.PP
diff --git a/noao/twodspec/apextract/doc/revisions.v3.ms b/noao/twodspec/apextract/doc/revisions.v3.ms
new file mode 100644
index 00000000..f78362a5
--- /dev/null
+++ b/noao/twodspec/apextract/doc/revisions.v3.ms
@@ -0,0 +1,522 @@
+.nr PS 9
+.nr VS 11
+.RP
+.ND
+.TL
+APEXTRACT Package Revisions Summary: IRAF Version 2.10
+.AU
+Francisco Valdes
+.AI
+IRAF Group - Central Computer Services
+.K2
+P.O. Box 26732, Tucson, Arizona 85726
+September 1990
+.AB
+This paper summarizes the changes in Version 3 of the IRAF \fBapextract\fR
+package which is part of IRAF Version 2.10.  The major new features and
+changes are:
+
+.IP \(bu
+New techniques for cleaning and variance weighting extracted spectra
+.IP \(bu
+A new task, \fBapall\fR, which integrates all the parameters used for
+one dimensional extraction of spectra
+.IP \(bu
+A new extended output format for recording both weighted and unweighted
+extractions, subtracted background, and variance information.
+.IP \(bu
+Special featurers for automatically numbering and identifying large
+numbers of apertures.
+.IP \(bu
+New tasks and algorithms, \fBaprecenter\fR and \fBapresize\fR,
+for automatically recentering and resizing aperture definitions
+.IP \(bu
+A new task, \fBapflatten\fR, for creating flat fields from
+fiber and slitlet spectra
+.IP \(bu
+A new task, \fBapfit\fR, providing various types of fitting for
+two dimensional multiobject spectra. 
+.IP \(bu
+A new task, \fBapmask\fR, for creating mask images from aperture definitions.
+.AE
+.NH
+Introduction
+.PP
+A new version of the IRAF \fBapextract\fR package has been completed.
+It is Version 3 and is part of IRAF Version 2.10.  The package will
+be made available as an external package prior to the release of V2.10.
+This paper describes the changes and new features of the package.  It
+does not describe them in detail.  Full details of the algorithms,
+functions, and parameters are found in the task descriptions.
+Reference is made to the previous version so familiarity with that
+version is useful though not necessary.  There were three goals for the
+new package: new and improved cleaning and variance weighting (optimal
+extraction) algorithms, the addition of recommended or desirable new
+tasks and algorithms (particularly to support large numbers of spectra
+from fiber and aperture mask instruments), and special support for the
+new image reduction scripts.  Features relating to the last point are
+not discussed here.
+.PP
+Table 1 summarizes the major new features and changes in the package.
+
+.ce
+Table 1:  Summary of Major New Features and Changes
+
+.IP \(bu
+New techniques for cleaning and variance weighting extracted spectra
+.IP \(bu
+A new task, \fBapall\fR, which integrates all the parameters used for
+one dimensional extraction of spectra
+.IP \(bu
+A new extended output format for recording both weighted and unweighted
+extractions, subtracted background, and variance information.
+.IP \(bu
+Special featurers for automatically numbering and identifying large
+numbers of apertures.
+.IP \(bu
+New tasks and algorithms, \fBaprecenter\fR and \fBapresize\fR, for
+automatically recentering and resizing aperture definitions
+.IP \(bu
+A new task, \fBapflatten\fR, for creating flat fields from fiber and slitlet
+spectra
+.IP \(bu
+A new task, \fBapfit\fR, providing various types of fitting for two dimensional
+multiobject spectra.
+.IP \(bu
+A new task, \fBapmask\fR, for creating mask images from aperture definitions.
+.NH
+Cleaned and Variance Weighted Extractions: apsum and apall
+.PP
+There are two types of aperture extraction (estimating the background
+subtracted flux across a fixed width aperture at each image line or
+column) just as in the previous version.  One is a simple sum of pixel
+values across an aperture.  In the previous version this was called
+"profile" weighting while in this version it is simply called
+unweighted or "none".  The second type weights each pixel in the sum by
+its estimated variance based on a spectrum model and detector noise
+parameters.  As before this type of extraction is selected by
+specifying "variance" for the weighting parameter.
+.PP
+Variance weighting is often called "optimal" extraction since it
+produces the best unbiased signal-to-noise estimate of the flux in the
+two dimensional profile.  It also has the advantage that wider
+apertures may be used without penalty of added noise.  The theory and
+application of this type of weighting has been described in several
+papers.  The ones which were closely examined and used as a model for
+the algorithms in this software are \fIAn Optimal Extraction Algorithm
+for CCD Spectroscopy\fR, \fBPASP 98\fR, 609, 1986, by Keith Horne and
+\fIThe Extraction of Highly Distorted Spectra\fR, \fBPASP 100\fR, 1032,
+1989, by Tom Marsh.
+.PP
+The noise model for the image data used in the variance weighting,
+cleaning, and profile fitting consists of a constant gaussian noise and
+a photon count dependent poisson noise.  The signal is related to the
+number of photons detected in a pixel by a gain parameter given
+as the number of photons per data number.  The gaussian noise is given
+by a readout noise parameter which is a defined as a sigma in
+photons.  The poisson noise is approximated as gaussian with sigma
+given by the number of photons.  The method of specifying this noise
+model differs from the previous version in that the more common CCD
+detector parameters of readout noise and gain are used rather than the
+linear variance parameters "v0" and "v1".
+.PP
+Some additional effects which should be considered in principle, and
+which are possibly important in practice, are that the variance
+estimate should be based on the actual number of photons detected before
+correction for pixel sensitivity; i.e. before flat field correction.
+Furthermore the uncertainty in the flat field should also be included
+in the weighting.  However, the profile must be determined free of
+sensitivity effects including rapid larger scale variations such as
+fringing.  Thus, ideally one should input the unflat-fielded
+observation and the flat field data and carry out the extractions with
+the above points in mind.  However, due to the complexity often
+involved in basic CCD reductions and special steps required for
+producing spectroscopic flat fields this level of sophistication is not
+provided by the current package.
+.PP
+The package does provide, however, for propagation of an approximate
+uncertainty in the background estimate when using background subtraction.
+If background subtraction is done, a background variance is computed
+using the poisson noise model based on the estimated background counts.
+Because the background estimate is based on a finite number of
+pixels, the poisson variance estimate is divided by the number (minus
+one) of pixels used in determining the background.  The number of
+pixels used includes any box car smoothing.  Thus, the larger the
+number of background pixels the smaller the background noise
+contribution to the variance weighting.  This method is only
+approximate since no correction is made for the number of degrees of
+freedom and correlations when using the fitting method of background
+estimation.
+.PP
+If removal of cosmic rays and other deviant pixels is desired (called
+cleaning) they are iteratively rejected based on the estimated variance
+and excluded from the weighted sum.  Unlike the previous version, a
+cleaned extraction is always variance weighted.  This makes sense since
+the detector noise parameters must be specified and the spectrum
+profile computed, so all of the computational effort must be done
+anyway, and the variance weighting is as good or superior to a simple
+unweighted extraction.
+.PP
+The detection and removal of deviant pixels is straightforward.  Based
+on the noise model, pixels deviating by more than a
+specified number of sigma (square root of the variance) above or below
+the model are removed from the weighted sum.  A new spectrum estimate
+is made and the rejection is repeated.  The rejections are made one at
+a time starting with the most deviant and up to half the pixels in the
+aperture may be rejected.
+.NH
+Spectrum Profile Determination: apsum, apall, apflatten, apfit
+.PP
+The foundation of variance weighted or optimal extraction, cosmic ray
+detection and removal, two dimensional flat field normalization, and
+spectrum fitting and modeling is the accurate determination of the
+spectrum profile across the dispersion as a function of wavelength.
+The previous version of the \fBapextract\fR package accomplished this by
+averaging a specified number of profiles in the vicinity of each
+wavelength after correcting for shifts in the center of the profile.
+This technique was sensitive to perturbations from cosmic rays
+and the exact choice of averaging parameters.  The current version of
+the package uses a different algorithm, actually a combination of
+two algorithms, which is much more stable.
+.PP
+The basic idea is to normalize each profile along the dispersion to
+unit flux and then fit a low order function to sets of unsaturated
+points at nearly the same point in the profile parallel to the
+dispersion.  The important point here is that points at the same
+distance from the profile center should have the nearly the same values
+once the continuum shape and spectral features have been divided out.
+Any variations are due to slow changes in the shape of the profile with
+wavelength, differences in the exact point on the profile, pixel
+binning or sampling, and noise.  Except for the noise, the variations
+should be slow and a low order function smoothing over many points will
+minimize the noise and be relatively insensitive to bad pixels such as
+cosmic rays.  Effects from bad pixels may be further eliminated by
+chi-squared iteration and clipping.  Since there will be many points
+per degree of freedom in the fitting function the clipping may even be
+quite aggressive without significantly affecting the profile
+estimates.  Effects from saturated pixels are minimized by excluding
+from the profile determination any profiles containing one or more
+saturated pixels.
+.PP
+The normalization is, in fact, the one dimensional spectrum.  Initially
+this is the simple sum across the aperture which is then updated
+by the variance weighted sum with deviant pixels possibly removed.
+This updated one dimensional spectrum is what is meant by the
+profile normalization factor in the discussion below.  The two dimensional
+spectrum model or estimate is the product of the normalization factor
+and the profile.  This model is used for estimating
+the pixel intensities and, thence, the variances.
+.PP
+There are two important requirements that must be met by the profile fitting
+algorithm.  First it is essential that the image data not be
+interpolated.  Any interpolation introduces correlated errors and
+broadens cosmic rays to an extent that they may be confused with the
+spectrum profile, particularly when the profile is narrow.  This was
+one of the problems limiting the shift and average method used
+previously.  The second requirement is that data fit by the smoothing
+function vary slowly with wavelength.  This is what precludes, for
+instance, fitting profile functions across the dispersion since narrow,
+marginally sampled profiles require a high order function using only a
+very few points.  One exception to this, which is sometimes useful but
+of less generality, is methods which assume a model for the profile
+shape such as a gaussian.  In the methods used here there is no
+assumption made about the underlying profile other than it vary
+smoothly with wavelength.
+.PP
+These requirements lead to two fitting algorithms based on how well the
+dispersion axis is aligned with the image columns or lines.  When the
+spectra are well aligned with the image axes one dimensional functions
+are fit to the image columns or lines.  Small excursions of a few
+pixels over the length of the spectrum can be adequately fit in this
+way.  When the spectra become strongly tilted then single lines or
+columns may cross the actual profile relatively quickly causing the
+requirement of a slow variation to be violated.  One thought is to use
+interpolation to fit points always at the same distance from the
+profile.  This is ruled out by the problems introduced by image
+interpolation.  However, there is a clever method which, in effect,
+fits low order polynomials parallel to the direction defined by tracing
+the spectrum but which does not interpolate the image data.  Instead it
+weights and couples polynomial coefficients.  This method was developed
+by Tom Marsh and is described in detail in the paper, \fIThe Extraction
+of Highly Distorted Spectra\fR, \fBPASP 101\fR, 1032, Nov. 1989.  Here
+we refer to this method as the Marsh algorithm and do not attempt to
+explain it further.
+.PP
+Both fitting algorithms weight the pixels by their variance as computed
+from the background and background variance if background subtraction
+is specified, the spectrum estimate from the profile and the spectrum
+normalization, and the detector noise parameters.  The noise model is
+that described earlier.
+.PP
+The profile fitting can be iterated to remove deviant pixels.  This is
+done by rejecting pixels greater than a specified number of sigmas
+above or below the expected value based on the profile, the
+normalization factor, the background, the detector noise parameters,
+and the overall chi square of the residuals.  Rejected points are
+removed from the profile normalization and from the fits.
+.NH
+New Extraction Task: apall
+.PP
+All of the functions of the \fBapextract\fR package are actually part
+of one master program.  The organization of the package into tasks by
+function with parameters to allow selection of some of the other
+functions, for example the aperture editor may be entered from
+virtually every task, was done to highlight the logic and organize the
+parameters into small sets.  However, there was often confusion about
+which parameters were being used and the need to set parameters in one
+task, say \fBaptrace\fR, in order to use the trace option in another
+task, say \fBapsum\fR.  In practice, for the most common function of
+extraction of two dimensional spectra to one dimension most users end up
+using \fBapsum\fR for all the functions.
+.PP
+In the new version, the old organization is retained (with the addition
+of new functions and some changes in parameters) but a new task,
+\fBapall\fR, is also available.  This task contains all of the
+parameters needed for extraction with a parameter organization which is
+nicely formated for use with \fBeparam\fR.  The parameters in
+\fBapall\fR are independent of the those in the other tasks.  It is
+expected that many, if not most users will opt to use this task for
+spectrum extraction in preference to the individual functions.
+.PP
+The organization by function is still used in the documentation.  This
+is still the best way to organize the descriptions of the various
+algorithms and parameters.  As an example, the profile tracing algorithm
+is described in most detail under the topic \fBaptrace\fR.
+.NH
+Extraction Output Formats: apsum and apall
+.PP
+The extracted spectra are recorded in one, two, or three dimensional
+images depending on the \fIformat\fR and \fIextras\fR parameters.  If
+the \fIextras\fR parameter is selected the formats are three
+dimensional with each plane in the third dimension containing
+associated information for the spectra in the first plane.  This
+information includes the unweighted spectrum and a sigma spectrum
+(estimated from the variances and weights of the pixels extracted) when
+using variance weighting, and the background spectrum when background
+subtraction is used.  When \fIextras\fR is not selected only the
+extracted spectra are output.
+.PP
+The formats are basically the same as in the previous version;
+onedspec, multispec, and echelle.  In addition, the function of the
+task \fBapstrip\fR in the previous version has been transferred to the
+extraction tasks by simply specifying "strip" for the format.
+.PP
+There are some additions to the header parameters in multispec and
+echelle format.  Two additional fields have been added to the
+aperture number parameter giving the aperture limits (at the reference
+dispersion point).  Besides being informative it may be used for
+interpolating dispersion solutions spatially.  A second, optional keyword per
+spectrum has been added to contain a title.  This is useful for
+multiobject spectra.
+.NH
+Easier and Extended Aperture Identifications: apfind and apedit
+.PP
+When dealing with a large number of apertures, such as occur with
+multifiber and multiaperture data, the burden of making and maintaining
+useful aperture identifications becomes large.  Several very useful
+improvements were made in this area.  These improvements generally
+apply equally to aperture identifications made by the automated
+\fBapfind\fR algorithm and those made interactively using
+\fBapedit\fR.  In the simplest usage of defining apertures
+interactively or with the aperture finding algorithm, aperture numbers
+are assigned sequentially beginning with 1.  In the new version the
+parameter "order" allows the direction of increasing aperture numbers
+with respect to the direction of increasing pixel coordinate (either
+column or line) to be set.  An "increasing" order parameter value
+numbers the apertures from left to right (the direction naturally
+plotted) in the same sense as the pixel coordinates.  A "decreasing"
+order reverses this sense.
+.PP
+Some instruments, particularly multifiber instruments, produce nearly
+equally spaced spectra for which one wants to maintain a consistent
+numbering sequence.  However, at times some spectra may be missing
+due to broken or unassigned fibers and one would like to skip an
+aperture identification number to maintain the same fiber assignments.
+To do this automatically, a new parameter called \fImaxsep\fR has been
+added.  This parameter defines the maximum separation between two
+apertures beyond which a jump in the aperture sequence is made.  In
+other words the sequence increment is given by rounding down the
+separation divided by this parameter.  How accurately this value has
+to be specified depends on how large the gaps may be and the natural
+variability in the aperture positions.  In conjunction with the
+minimum separation parameter this algorithm works quite well in
+accounting for missing spectra.
+.PP
+One flaw in this scheme is when the first spectrum is missing causing
+the identifications will be off.  In this case the modified interactive
+aperture editing command 'o' asks for the aperture identification
+number of the aperture pointed at by the cursor and then automatically
+renumbers the other apertures relative to that aperture.  The other
+possible flaw is identification of noise as a spetrum but this is
+controlled by the \fIthreshold\fR parameter and, provided the actual
+number of spectra is known, say by counting off a graph, then the
+\fInfind\fR parameter generally limits this type of problem.
+.PP
+A new attribute of an aperture is a title.  If present this title
+is propagated through the extraction into the image headers.  The title
+may be set interactively but normally the titles are supplied in
+another new feature, an "aperture identification" file specified by
+the parameter \fIapidtable\fR.  This file provides
+the most flexibility in making aperture identification assignments.
+The file consists of lines with three fields, a unique aperture number,
+a beam or aperture type number which may be repeated, and the
+aperture title.  The aperture identification lines from the file are
+assigned sequentially in the same order as would be done if using
+the default indexing including skipping of missing spectra based on
+the maximum separation.
+.PP
+By default the beam number is the same as the aperture number.  When
+using an aperture identification file the beam number can be used
+to assign spectrum types which other software may use.  For example,
+some of the specialized fiber reduction packages use the beam number
+to identify sky fibers and embedded arc fibers.
+.NH
+New Aperture Recentering Task: aprecenter
+.PP
+An automated recentering algorithm has been added.  It may be called
+through the new \fBaprecenter\fR command, from any of the tasks containing
+the \fIrecenter\fR parameter, or from the aperture editor.  The purpose of
+this new feature is to allow automatically adjusting the aperture
+centers to follow small changes in the positions of spectra expected to be at
+essentially the same position, such as with fiber fed spectrographs.
+This does not change the shape of the trace but simply adds a shift
+across the dispersion axis.
+.PP
+Typically, one uses a strong image to define reference apertures and
+then for subsequent objects uses the reference positions with a
+recentering to correct for flexure effects.  However, it may be
+inappropriate to base a new center on weak spectra or to have multiple
+spectra recentered independently.  The recentering options provide for
+selecting specific apertures to be recentered, selecting only a
+fraction of the strongest (highest peak data level) spectra and
+averaging the shifts determined (possible from only a subset of the
+spectra) and applying the average shift to all the apertures.
+Note that one may still specify the dispersion line and number of 
+dispersion lines to sum in order to improve the signal for centering.
+.NH
+New Aperture Resizing Task: apresize
+.PP
+An automated resizing algorithm has been added.  It may be called
+through the new \fBapresize\fR command, from any of the tasks
+containing the \fIresize\fR parameter, or from the aperture editor with
+the new key 'z' (the y cursor level command is still available with the
+'y' key).  The purpose of this new feature is to allow automatically
+adjusting the aperture widths to follow changes in seeing and to
+provide a greater variety of global aperture sizing methods.
+.PP
+In all the methods the aperture limits are set at the pixel positions
+relative to the center which intersect the linearly interpolated data
+at some data value.  The methods differ in how the data level is
+determined.  The methods are:
+
+.IP \(bu
+Set size at a specified absolute data level
+.IP \(bu
+Set size at a specified data level above a background
+.IP \(bu
+Set size at a specified fraction of the peak pixel value
+.IP \(bu
+Set size at a specified fraction of the peak pixel value above a background
+.LP
+The automatic background is quite simple; a line connecting the first
+local minima from the aperture center.
+.PP
+The limits determined by one of the above methods may be further
+adjusted.  The limits may be increased or decreased by a specified
+fraction.  This allows setting wider limits based on more accurately
+determined limits from the stronger part of the profile; for example
+doubling the limits obtained from the half intensity point.  A maximum
+extent may be imposed.  Finally, if there is more than one aperture and one
+wants to maintain the same aperture size, the apertures sizes
+determined individually may be averaged and substituted for all the
+apertures.
+.NH
+New Aperture Mask Output: apmask
+.PP
+A new task, \fBapmask\fR, has been added to produce a mask file/image
+of 1's and 0's defined by the aperture definitions.  This is based on
+the new IRAF mask facilities.  The output is a compact binary file
+which may be used directly as an image in most applications.  In
+particular the mask file can be used with tasks such as \fBimarith\fR,
+\fBimreplace\fR, and \fBdisplay\fR.  Because the mask facility is new,
+there is little that can be done with masks other than using it as an
+image.  However, eventually many tasks will be able to use mask
+images.  The aperture mask will be particularly well suited to work
+with \fBimsurfit\fR for fitting a surface to the data outside the apertures.
+This would be an alternative for scattered light modeling to the
+\fBapscatter\fR tasks.
+.NH
+Aperture Flat Fields and Normalization: apflatten and apnormalize
+.PP
+Slitlet, echelle, and fiber spectra have the characteristic that the
+signal falls off to near zero values outside regions of the image
+containing spectra.  Also fiber profiles are usually undersampled
+causing problems with gradients across the pixels.  Directly dividing
+by a flat field produces high noise (if not division by zero) where the
+signal is low, introduces the spectrum of the flat field light, and
+changes the profile shape.
+.PP
+One method for modifying the flat field to avoid these problems is
+provided by the task \fBimred.generic.flat1d\fR.  However, this task
+does not use any knowledge of where the spectra are.  There are two
+tasks in the \fBapextract\fR package which can be used to modify flat
+field images.  \fBapnormalize\fR is not new.  It divides the spectra
+within specified apertures by a one dimensional spectrum, either a
+constant for simple throughput normalization or some smoothed version
+of the spectrum in the aperture to remove the spectral shape.  Pixels
+outside specified apertures are set to unity to avoid division
+effects.  This task has the effect of preserving the profile shape in
+the flat field which may be desired for attempts to remove slit
+profiles.
+.PP
+Retaining the profile shape of the flat field can give very bad edge
+effects, however, if there is image flexure.  A new task similar to
+\fBflat1d\fR but which uses aperture information is \fBapflatten\fR.
+It uses the spectrum profile model described earlier.  For nearly image
+axes aligned spectra this amounts very nearly to the line or column
+fitting of \fBflat1d\fR.  As with \fBapnormalize\fR there is an option
+to fit the one dimensional spectrum to remove the large scale shape of
+the spectrum while preserving small scale sensitivity variations.  The
+smoothed spectrum is multiplied by the normalized profile and divided
+into the data in each aperture.  Pixels outside the aperture are set to
+1.  Pixels with model values below a threshold are also set to 1.  This
+produces output images which have the small scale sensitivity
+variations, a normalized mean, and the spectrum profile removed.
+.NH
+Two Dimensional Spectrum Fitting: apfit
+.PP
+The profile and spectrum fitting used for cleaning and variance
+weighted extraction may be used and output in the new task
+\fBapfit\fR.  The task \fBapfit\fR is similar in structure to
+\fBfit1d\fR.  One may output the fit, difference, or ratio.  The fit
+may be used to examine the spectrum model used for the cleaning and
+variance weighted extraction.  The difference and ratio may used to
+display small variations and any deviant pixels.  While specific uses
+are not given this task will probably be used in interesting ways not
+anticipated by the author.
+.NH
+I/O and Dispersion Axis Parameters: apextract and apio
+.PP
+The general parameters, primarily concerning input and output devices
+and files, were previously in the parameter set \fBapio\fR.  This "pset"
+task has been removed and those parameters are now found as part of
+the package parameters, i.e. \fBapextract\fR.  There is one new parameter
+in the \fBapextract\fR package parameters, dispaxis.  In the previous
+version of the package one needed to run the task \fBsetdisp\fR to insert
+information in the image header identifying the dispersion direction
+of the spectra in the image.  Often people would forget this step
+and receive an error message to that effect.  The new parameter
+allows skipping this step.  If the DISPAXIS image header parameter
+is missing the package parameter value is inserted into the image
+header as part of the processing.  Note that if the parameter is
+present in the image header either because \fBsetdisp\fR was used or the
+image creation process inserted it (a future ideal case) then that
+value is used in preference to the package parameter.
+.NH
+Strip Extraction: apstrip
+.PP
+The task \fBapstrip\fR from the previous version has been removed.
+However, it is possible to obtain two dimensional strips aligned with
+the image axes by specifying a format of "strip" when using \fBapsum\fR
+or \fBapall\fR.  While the author doesn't anticipate a good scientific
+use for this feature others may find it useful.
diff --git a/noao/twodspec/apextract/mkpkg b/noao/twodspec/apextract/mkpkg
new file mode 100644
index 00000000..bcc342c4
--- /dev/null
+++ b/noao/twodspec/apextract/mkpkg
@@ -0,0 +1,76 @@
+# APEXTRACT
+
+$call	relink
+$exit
+
+update:
+	$call	relink
+	$call	install
+	;
+
+relink:
+	$update	libpkg.a
+	$call	apextract
+	;
+
+install:
+	$move	xx_apextract.e noaobin$x_apextract.e
+	;
+
+apextract:
+	$omake	x_apextract.x
+	$link	x_apextract.o libpkg.a -lxtools\
+		-lcurfit -liminterp -lllsq -o xx_apextract.e
+	;
+
+libpkg.a:
+	apalloc.x	apertures.h
+	apanswer.x	
+	apcenter.x	<pkg/center1d.h>
+	apcolon.x	apertures.h <error.h> <gset.h> <imhdr.h>
+	apcopy.x	apertures.h
+	apcveval.x	<math/curfit.h>
+	apcvset.x	apertures.h <math/curfit.h>
+	apdb.x		apertures.h <math/curfit.h> <pkg/dttext.h>
+	apdefault.x	apertures.h <imhdr.h>
+	apdelete.x	
+	apedit.x	apertures.h <gset.h> <imhdr.h> <mach.h> <pkg/gtools.h>
+	apextract.x	apertures.h <error.h> <imhdr.h> <mach.h>\
+			<math/iminterp.h> <pkg/gtools.h>
+	apfind.x	apertures.h <imhdr.h> <mach.h>
+	apfindnew.x	apertures.h <mach.h>
+	apfit.x		apertures.h <imhdr.h> <imset.h> <pkg/gtools.h>
+	apgetdata.x	<imhdr.h>
+	apgetim.x	
+	apgmark.x	apertures.h <pkg/rg.h>
+	apgraph.x	apertures.h <pkg/gtools.h>
+	apgscur.x	apertures.h
+	apicset.x	apertures.h <imhdr.h>
+	apids.x		apertures.h <error.h> <mach.h>
+	apimmap.x	<imhdr.h>
+	apinfo.x	apertures.h
+	apio.x		<time.h>
+	apmask.x	apertures.h <imhdr.h> <pmset.h>
+	apmw.x		<error.h> <imhdr.h> <imio.h> <mwset.h>
+	apnearest.x	apertures.h <mach.h>
+	apnoise.x	apertures.h <gset.h> <pkg/gtools.h>
+	apparams.x	
+	appars.x	<math/iminterp.h>
+	apprint.x	apertures.h
+	approfile.x	apertures.h <gset.h> <mach.h> <math/curfit.h>
+	aprecenter.x	apertures.h
+	apresize.x	apertures.h
+	apscatter.x	apertures.h <error.h> <imhdr.h> <imset.h> <pkg/gtools.h>
+	apselect.x	apertures.h
+	apshow.x	apertures.h
+	apskyeval.x	apertures.h <math/iminterp.h> <mach.h>
+	apsort.x	apertures.h
+	aptrace.x	apertures.h <imhdr.h> <math/curfit.h> <pkg/center1d.h>\
+			<pkg/gtools.h>
+	apupdate.x	apertures.h <gset.h>
+	apvalues.x	apertures.h
+	apvariance.x	apertures.h <gset.h>
+	apylevel.x	
+	peaks.x	
+	t_apall.x	apertures.h <error.h> <imhdr.h> <pkg/gtools.h>
+	;
diff --git a/noao/twodspec/apextract/peaks.x b/noao/twodspec/apextract/peaks.x
new file mode 100644
index 00000000..fe525f88
--- /dev/null
+++ b/noao/twodspec/apextract/peaks.x
@@ -0,0 +1,313 @@
+# PEAKS -- The following procedures are general numerical functions
+# dealing with finding peaks in a data array.
+#
+# FIND_PEAKS		Find additional peaks in the data array.
+# FIND_LOCAL_MAXIMA	Find the local maxima in the data array.
+# IS_LOCAL_MAX		Test a point to determine if it is a local maximum.
+# FIND_CONTRAST		Find the peaks satisfying the contrast constraint.
+# FIND_ISOLATED		Flag peaks which are within separation of a peak
+#			with a higher peak value.
+# FIND_NMAX		Select up to the nmax highest ranked peaks.
+# COMPARE		Compare procedure for sort used in FIND_PEAKS.
+
+# FIND_PEAKS -- Find the peaks in the data array.
+#
+# The peaks are found using the following algorithm:
+#
+# 1.  Find the local maxima which are not near the edge of existing peaks.
+# 2.  Reject those below the absolute threshold.
+# 3.  Reject those below the contrast threshold.
+# 4.  Determine the ranks of the remaining peaks.
+# 5.  Flag weaker peaks within separation of a stronger peak.
+# 6.  Add strongest peaks to the peaks array.
+#
+# Indefinite data points are ignored.
+
+procedure find_peaks (data, npts, contrast, edge, nmax, separation, threshold,
+    peaks, npeaks)
+
+real	data[npts]		# Input data array
+int	npts			# Number of data points
+
+real	contrast		# Maximum contrast between strongest and weakest
+int	edge			# Minimum distance from the edge
+int	nmax			# Maximum number of peaks to be returned
+real	separation		# Minimum separation between peaks
+real	threshold		# Minimum threshold level for peaks
+
+real	peaks[nmax]		# Positons of input peaks / output peaks
+int	npeaks			# Number of input peaks / number of output peaks
+
+int	i, nx
+pointer	sp, x, y, rank
+
+int	compare()
+extern	compare()
+
+common	/sort/ y
+
+begin
+	if (npeaks >= nmax)
+	    return
+
+	call smark (sp)
+	call salloc (x, npts, TY_INT)
+	call salloc (y, npts, TY_REAL)
+
+	# Find the positions of the local maxima.
+	call find_local_maxima (data, npts, peaks, npeaks, edge, separation,
+	    threshold, Memi[x], Memr[y], nx)
+
+	# Eliminate points not satisfying the contrast constraint.
+	call find_contrast (data, Memi[x], Memr[y], nx, contrast)
+
+	# Rank the peaks by peak value.
+	call salloc (rank, nx, TY_INT)
+	for (i = 1; i <= nx; i = i + 1)
+	    Memi[rank + i - 1] = i
+	call qsort (Memi[rank], nx, compare)
+
+	# Reject weaker peaks within a specified separation of a stronger peak.
+	call find_isolated (Memi[x], Memi[rank], nx, separation)
+
+	# Add the strongest peaks.
+	call find_nmax (Memi[x], Memi[rank], nx, nmax, peaks, npeaks)
+
+	call sfree (sp)
+end
+
+
+# FIND_LOCAL_MAXIMA -- Find the local maxima in the data array.
+
+procedure find_local_maxima (data, npts, peaks, npeaks, edge, separation,
+    threshold, x, y, nx)
+
+real	data[npts]		# Input data array
+int	npts			# Number of input points
+real	peaks[ARB]		# Positions of peaks
+int	npeaks			# Number of peaks
+int	edge			# Edge buffer distance
+real	separation		# Minimum separation from peaks
+real	threshold		# Data threshold
+int	x[npts]			# Output positions
+real	y[npts]			# Output data values
+int	nx			# Number of maxima
+
+int	i, j
+
+bool	is_local_max()
+
+begin
+	# Find the local maxima above the threshold and not near the edge.
+	nx = 0
+	for (i = edge + 1; i <= npts - edge; i = i + 1) {
+	    if ((data[i] >= threshold) && (is_local_max (i, data, npts))) {
+	        nx = nx + 1
+	        x[nx] = i
+	    }
+	}
+
+	# Flag maxima within separation of previous peaks.
+	for (j = 1; j <= npeaks; j = j + 1) {
+	    for (i = 1; i <= nx; i = i + 1) {
+		if (IS_INDEFI (x[i]))
+		    next
+		if (x[i] < peaks[j] - separation)
+		    next
+		if (x[i] > peaks[j] + separation)
+		    break
+		x[i] = INDEFI
+	    }
+	}
+
+	# Eliminate flagged maxima and set y values.
+	j = 0
+	for (i = 1; i <= nx; i = i + 1) {
+	    if (!IS_INDEFI (x[i])) {
+		j = j + 1
+		x[j] = x[i]
+		y[j] = data[x[j]]
+	    }
+	}
+
+	nx = j
+end
+
+
+# IS_LOCAL_MAX -- Test a point to determine if it is a local maximum.
+#
+# Indefinite points are ignored.
+
+bool procedure is_local_max (index, data, npts)
+
+# Procedure parameters:
+int	index			# Index to test for local maximum
+real	data[npts]		# Data values
+int	npts			# Number of points in the data vector
+
+int	i, j, nright, nleft
+
+begin
+	# INDEFR points cannot be local maxima.
+	if (IS_INDEFR (data[index]))
+	    return (false)
+
+	# Find the left and right indices where data values change and the
+	# number of points with the same value.  Ignore INDEFR points.
+	nleft = 0
+	for (i = index - 1; i >= 1; i = i - 1) {
+	    if (!IS_INDEFR (data[i])) {
+		if (data[i] != data[index])
+		    break
+		nleft = nleft + 1
+	    }
+	}
+	nright = 0
+	for (j = index + 1; i <= npts; j = j + 1) {
+	    if (!IS_INDEFR (data[j])) {
+		if (data[j] != data[index])
+		    break
+		nright = nright + 1
+	    }
+	}
+
+	# Test for failure to be a local maxima
+	if ((i == 0) && (j == npts)) {
+	    return (FALSE)		# Data is constant
+	} else if (i == 0) {
+	    if (data[j] > data[index])
+	        return (FALSE)		# Data increases to right
+	} else if (j == npts) {
+	    if (data[i] > data[index])	# Data increase to left
+		return (FALSE)
+	} else if ((data[i] > data[index]) || (data[j] > data[index])) {
+	    return (FALSE)		# Not a local maximum
+	} else if (!((nleft - nright == 0) || (nleft - nright == 1))) {
+	    return (FALSE)		# Not center of plateau
+	}
+
+	# Point is a local maxima
+	return (TRUE)
+end
+
+
+
+# FIND_CONTRAST -- Find the peaks with positions satisfying contrast constraint.
+
+procedure find_contrast (data, x, y, nx, contrast)
+
+real	data[ARB]		# Input data values
+int	x[ARB]			# Input/Output peak positions
+real	y[ARB]			# Output peak data values
+int	nx			# Number of peaks input
+real	contrast		# Contrast constraint
+
+int	i, j
+real	minval, maxval, threshold
+
+begin
+	if ((nx == 0.) || (contrast <= 0.))
+	    return
+
+	call alimr (y, nx, minval, maxval)
+	threshold = contrast * maxval
+
+	j = 0
+	do i = 1, nx {
+	    if (y[i] < threshold) {
+		j = j + 1
+		x[j] = x[i]
+		y[j] = y[i]
+	    }
+	}
+
+	nx = j
+end
+
+# FIND_ISOLATED -- Flag peaks which are within separation of a peak
+# with a higher peak value.
+#
+# The peak positions, x, and their ranks, rank, are input.
+# The rank array contains the indices of the peak positions in order from
+# the highest peak value to the lowest peak value.  Starting with
+# highest rank (rank[1]) all peaks of lower rank within separation
+# are marked by setting their positions to INDEFI.
+
+procedure find_isolated (x, rank, nx, separation)
+
+int	x[ARB]			# Positions of points
+int	rank[ARB]		# Rank of peaks
+int	nx			# Number of peaks
+real	separation		# Minimum allowed separation
+
+int	i, j
+
+begin
+	if ((nx == 0) || (separation <= 0.))
+	    return
+
+	# Eliminate close neighbors.  The eliminated
+	# peaks are marked by setting their positions to INDEFI.
+
+	for (i = 1; i < nx; i = i + 1) {
+	    if (IS_INDEFI (x[rank[i]]))
+		next
+	    for (j = i + 1; j <= nx; j = j + 1) {
+		if (IS_INDEFI (x[rank[j]]))
+		    next
+		if (abs (x[rank[i]] - x[rank[j]]) < separation)
+		    x[rank[j]] = INDEFI
+	    }
+	}
+end
+
+
+# FIND_NMAX -- Select up to the nmax highest ranked peaks.
+
+procedure find_nmax (x, rank, nx, nmax, peaks, npeaks)
+
+int	x[ARB]			# Peak positions
+int	rank[ARB]		# Ranks of peaks
+int	nx			# Number of input / output peaks
+int	nmax			# Max number of peaks to be selected
+real	peaks[nmax]		# Output peak position array
+int	npeaks			# Output number of peaks
+
+int	i
+
+begin
+	for (i = 1; (i <= nx) && (npeaks < nmax); i = i + 1) {
+	    if (IS_INDEFI (x[rank[i]]))
+		next
+	    npeaks = npeaks + 1
+	    peaks[npeaks] = x[rank[i]]
+	}
+end
+
+
+# COMPARE -- Compare procedure for sort used in FIND_PEAKS.
+# Larger values are indexed first.  INDEFR values are indexed last.
+
+int procedure compare (index1, index2)
+
+# Procedure parameters:
+int	index1				# Comparison index
+int	index2				# Comparison index
+
+pointer	y
+
+common	/sort/ y
+
+begin
+	# INDEFR points are considered to be smallest possible values.
+	if (IS_INDEFR (Memr[y - 1 + index1]))
+	    return (1)
+	else if (IS_INDEFR (Memr[y - 1 + index2]))
+	    return (-1)
+	else if (Memr[y - 1 + index1] < Memr[y - 1 + index2])
+	    return (1)
+	else if (Memr[y - 1 + index1] > Memr[y - 1 + index2])
+	    return (-1)
+	else
+	    return (0)
+end
diff --git a/noao/twodspec/apextract/t_apall.x b/noao/twodspec/apextract/t_apall.x
new file mode 100644
index 00000000..415066ba
--- /dev/null
+++ b/noao/twodspec/apextract/t_apall.x
@@ -0,0 +1,576 @@
+include	<imhdr.h>
+include	<error.h>
+include	<pkg/gtools.h>
+include	"apertures.h"
+
+define	APFIND		1
+define	APRECENTER	2
+define	APRESIZE	3
+define	APEDIT		4
+define	APTRACE		5
+define	APSUM		6
+define	APNORM		7
+define	APSCAT		8
+define	APALL		9
+define	APFIT		10
+define	APFLAT		11
+define	APMASK		12
+define	APSCRIPT	13
+define	APSLITPROC	14
+define	APNOISE		15
+
+
+# APEXTRACT TASK ENTRY POINTS
+#
+# The entry point for each task selects the operations to be performed
+# and initializes the pset to be used for the algorithm parameters.
+
+procedure t_apfind ()
+begin
+	call apall (APFIND)
+end
+
+procedure t_aprecenter ()
+begin
+	call apall (APRECENTER)
+end
+
+procedure t_apresize ()
+begin
+	call apall (APRESIZE)
+end
+
+procedure t_apedit ()
+begin
+	call apall (APEDIT)
+end
+
+procedure t_aptrace ()
+begin
+	call apall (APTRACE)
+end
+
+procedure t_apsum ()
+begin
+	call apall (APSUM)
+end
+
+procedure t_apnorm ()
+begin
+	call apall (APNORM)
+end
+
+procedure t_apscatter ()
+begin
+	call apall (APSCAT)
+end
+
+procedure t_apall ()
+begin
+	call apall (APALL)
+end
+
+procedure t_apflat ()
+begin
+	call apall (APFLAT)
+end
+
+procedure t_apfit ()
+begin
+	call apall (APFIT)
+end
+
+procedure t_apmask ()
+begin
+	call apall (APMASK)
+end
+
+procedure t_apscript ()
+begin
+	call apall (APSCRIPT)
+end
+
+procedure t_apslitproc ()
+begin
+	call apall (APSLITPROC)
+end
+
+procedure t_apnoise ()
+begin
+	call apall (APNOISE)
+end
+
+
+# APALL -- Master aperture definition and extraction procedure.
+
+procedure apall (ltask)
+
+int	ltask			# Logical task
+
+bool	find			# Find apertures?
+bool	recenter		# Recenter apertures?
+bool	resize			# Resize apertures?
+bool	edit			# Edit apertures?
+bool	trace			# Trace apertures?
+bool	extract			# Extract apertures?
+bool	fit			# Extract fit?
+bool	norm			# Normalize spectra?
+bool	flat			# Flatten spectra?
+bool	scat			# Subtract scattered light?
+bool	mask			# Aperture mask?
+bool	noise			# Noise calculation?
+
+int	input			# List of input spectra
+int	refs			# List of reference spectra
+int	out			# List of output spectra
+pointer	format			# Output format or fit type
+int	scatout			# List of scattered light images
+int	profs			# List of profile spectra
+int	line			# Dispersion line
+int	nsum			# Lines to sum
+
+pointer	aps			# Pointer to array of aperture pointers
+int	naps			# Number of apertures
+
+char	nullstr[1]
+int	i
+pointer	sp, image, output, reference, profiles, str, str1
+
+bool	clgetb(), apgetb(), streq(), ap_answer(), apgans(), apgansb()
+int	imtopenp(), clgeti(), ap_getim(), ap_dbaccess(), strncmp()
+
+errchk	ap_dbacess, ap_dbread, ap_find, ap_recenter, ap_resize, ap_edit
+errchk	ap_trace, ap_plot, ap_extract, ap_scatter, ap_mask, ap_dbwrite
+
+data	nullstr /0,0/
+
+begin
+	# Allocate memory for the apertures, filenames, and strings.
+	call smark (sp)
+	call salloc (image, SZ_FNAME, TY_CHAR)
+	call salloc (output, SZ_FNAME, TY_CHAR)
+	call salloc (reference, SZ_FNAME, TY_CHAR)
+	call salloc (format, SZ_LINE, TY_CHAR)
+	call salloc (profiles, SZ_FNAME, TY_CHAR)
+	call salloc (str, SZ_LINE, TY_CHAR)
+	call salloc (str1, SZ_LINE, TY_CHAR)
+
+	switch (ltask) {
+	case APALL:
+	    call apopset ("apall1")
+	case APFIT:
+	    call apopset ("apfit1")
+	case APFLAT:
+	    call apopset ("apflat1")
+	case APNORM:
+	    call apopset ("apnorm1")
+	case APSCRIPT:
+	    call apopset ("apscript")
+	case APSLITPROC:
+	    call apopset ("apslitproc")
+	case APNOISE:
+	    call apopset ("apnoise1")
+	default:
+	    call apopset ("apparams")
+	}
+
+	input = imtopenp ("input")
+	refs = imtopenp ("references")
+	line = clgeti ("line")
+	nsum = clgeti ("nsum")
+	out = NULL
+	profs = NULL
+	scatout = NULL
+
+	switch (ltask) {
+	case APSUM, APALL, APFIT, APNORM, APFLAT, APSCAT,
+	    APMASK, APSCRIPT, APSLITPROC:
+	    out = imtopenp ("output")
+	}
+
+	switch (ltask) {
+	case APSUM, APALL:
+	    profs = imtopenp ("profiles")
+	    call apgstr ("format", Memc[format], SZ_LINE)
+	case APFIT:
+	    call clgstr ("fittype", Memc[format], SZ_LINE)
+	case APNORM:
+	    call strcpy ("normalize", Memc[format], SZ_LINE)
+	case APFLAT:
+	    call strcpy ("flatten", Memc[format], SZ_LINE)
+	case APSCAT:
+	    scatout = imtopenp ("scatter")
+	case APSCRIPT, APSLITPROC:
+	    scatout = imtopenp ("scatter")
+	    profs = imtopenp ("profiles")
+	    call apgstr ("format", Memc[format], SZ_LINE)
+	case APNOISE:
+	    call strcpy ("noise", Memc[format], SZ_LINE)
+	}
+
+	trace = false
+	extract = false
+	fit = false
+	norm = false
+	flat = false
+	scat = false
+	mask = false
+	noise = false
+
+	if (apgetb ("initialize")) {
+	    find = clgetb ("find")
+	    recenter = clgetb ("recenter")
+	    resize = clgetb ("resize")
+	    edit = clgetb ("edit")
+
+	    switch (ltask) {
+	    case APTRACE, APSUM, APALL, APFIT, APNORM,
+		APFLAT, APSCAT, APMASK, APSCRIPT, APSLITPROC, APNOISE:
+	        trace = clgetb ("trace")
+	    }
+
+	    switch (ltask) {
+	    case APSUM, APALL:
+	        extract = clgetb ("extract")
+	    case APFIT:
+	        fit = clgetb ("fit")
+	    case APNORM:
+	        norm = clgetb ("normalize")
+	    case APFLAT:
+	        flat = clgetb ("flatten")
+	    case APSCAT:
+	        scat = clgetb ("subtract")
+	    case APMASK:
+	        mask = clgetb ("mask")
+	    case APSCRIPT, APSLITPROC:
+	        extract = clgetb ("extract")
+	        scat = clgetb ("subtract")
+		if (extract && scat)
+		    call error (1,
+		    "APSCRIPT: Can't combine scattered light and extraction")
+	    case APNOISE:
+		noise = true
+	    }
+
+	    call ap_init (find, recenter, resize, edit, trace, extract, fit,
+	        norm, flat, scat, mask, noise)
+	} else {
+	    find = apgans ("ansfind")
+	    recenter = apgans ("ansrecenter")
+	    resize = apgans ("ansresize")
+	    edit = apgans ("ansedit")
+
+	    switch (ltask) {
+	    case APTRACE, APSUM, APALL, APFIT, APNORM,
+		APFLAT, APSCAT, APMASK, APSCRIPT, APSLITPROC, APNOISE:
+	        trace = apgans ("anstrace")
+	    }
+
+	    switch (ltask) {
+	    case APSUM, APALL:
+	        extract = apgans ("ansextract")
+	    case APFIT:
+	        fit = apgans ("ansfit")
+	    case APNORM:
+	        norm = apgans ("ansnorm")
+	    case APFLAT:
+	        flat = apgans ("ansflat")
+	    case APSCAT:
+	        scat = apgans ("ansscat")
+	    case APMASK:
+	        mask = apgans ("ansmask")
+	    case APSCRIPT, APSLITPROC:
+	        extract = apgans ("ansextract")
+	        scat = apgans ("ansscat")
+		if (extract && scat)
+		    call error (1,
+		    "APSCRIPT: Can't combine scattered light and extraction")
+	    }
+	}
+
+	# Initialize the apertures.
+	naps = 0
+	Memc[reference] = EOS
+	Memc[profiles] = EOS
+	call malloc (aps, 100, TY_POINTER)
+
+	# Process the apertures from each input image.
+	while (ap_getim (input, Memc[image], SZ_FNAME) != EOF) {
+	    if (ap_getim (refs, Memc[str], SZ_LINE) != EOF)
+		call strcpy (Memc[str], Memc[reference], SZ_FNAME)
+	    if (extract || fit || flat || norm || scat || mask)
+		if (ap_getim (out, Memc[output], SZ_FNAME) == EOF)
+		    Memc[output] = EOS
+
+	    # Get apertures.
+	    call appstr ("ansdbwrite1", "no")
+	    if (streq (Memc[reference], nullstr) ||
+		streq (Memc[reference], Memc[image])) {
+		if (clgetb ("verbose"))
+		    call printf ("Searching aperture database ...\n")
+		iferr (call ap_dbread (Memc[image], aps, naps))
+		    ;
+	    } else if (streq (Memc[reference], "OLD")) {
+		iferr (call ap_dbread (Memc[image], aps, naps))
+		    next
+	    } else {
+		if (strncmp (Memc[reference], "NEW", 3) == 0) {
+		    if (ap_dbaccess (Memc[image]) == YES)
+			next
+		    call strcpy (Memc[reference+3], Memc[reference], SZ_FNAME)
+		}
+		if (clgetb ("verbose"))
+		    call printf ("Searching aperture database ...\n")
+		iferr (call ap_dbread (Memc[reference], aps, naps)) {
+		    call eprintf (
+			"WARNING: Reference image (%s) apertures not found\n")
+			call pargstr (Memc[reference])
+		    next
+		}
+		if (naps > 0)
+		    call appstr ("ansdbwrite1", "yes")
+	    }
+	    call clgstr ("apertures", Memc[str], SZ_LINE)
+	    call ap_select (Memc[str], Memi[aps], naps)
+
+	    iferr {
+		# Find apertures.
+		if (find && naps == 0)
+		    call ap_find (Memc[image], line, nsum, aps, naps)
+
+		# Recenter apertures.
+		else if (recenter)
+		    call ap_recenter (Memc[image], line, nsum, Memi[aps], naps,
+			NO)
+
+		# Resize apertures.
+		if (resize)
+		    call ap_resize (Memc[image], line, nsum, Memi[aps], naps,
+			NO)
+
+		# Edit apertures.
+		if (edit)
+		    call ap_edit (Memc[image], line, nsum, aps, naps)
+
+		# Trace apertures.
+		if (trace)
+		    call ap_trace (Memc[image], line, Memi[aps], naps, NO)
+
+		# Write database and make aperture plot.
+		if (apgansb ("ansdbwrite1")) {
+		    call clgstr ("database", Memc[str1], SZ_LINE)
+	            call sprintf (Memc[str], SZ_LINE,
+		        "Write apertures for %s to %s")
+	                call pargstr (Memc[image])
+	                call pargstr (Memc[str1])
+	            if (ap_answer ("ansdbwrite", Memc[str]))
+		        call ap_dbwrite (Memc[image], aps, naps)
+		}
+	        iferr (call ap_dbwrite ("last", aps, naps))
+		    ;
+		iferr (call ap_plot (Memc[image], line, nsum, Memi[aps], naps))
+		    call erract (EA_WARN)
+
+		# Extract 1D spectra but do not extract negative beams
+		if (extract) {
+		    do i = 1, naps {
+			if (AP_BEAM(Memi[aps+i-1]) < 0)
+			    AP_SELECT(Memi[aps+i-1]) = NO
+		    }
+
+	    	    if (ap_getim (profs, Memc[str1], SZ_LINE) != EOF)
+			call strcpy (Memc[str1], Memc[profiles], SZ_FNAME)
+		    call sprintf (Memc[str], SZ_LINE,
+		        "Extract aperture spectra for %s?")
+	                call pargstr (Memc[image])
+		    if (ap_answer ("ansextract", Memc[str])) {
+			call sprintf (Memc[str], SZ_LINE,
+			    "Review extracted spectra from %s?")
+			    call pargstr (Memc[image])
+			if (ap_answer ("ansreview", Memc[str])) {
+			    call apgstr ("ansreview", Memc[str], SZ_LINE)
+			    call appstr ("ansreview1", Memc[str])
+			} else
+			    call appstr ("ansreview1", "NO")
+	                call ap_extract (Memc[image], Memc[output],
+			    Memc[format], Memc[profiles], Memi[aps], naps)
+		    }
+		}
+
+		# Fit apertures.
+		if (fit) {
+		    call sprintf (Memc[str], SZ_LINE,
+			"Fit apertures in %s?")
+	                call pargstr (Memc[image])
+		    if (ap_answer ("ansfit", Memc[str])) {
+	                call ap_extract (Memc[image], Memc[output],
+			    Memc[format], nullstr, Memi[aps], naps)
+		    }
+		}
+
+		# Normalize apertures.
+		if (norm) {
+		    call sprintf (Memc[str], SZ_LINE,
+			"Normalize apertures in %s?")
+	                call pargstr (Memc[image])
+		    if (ap_answer ("ansnorm", Memc[str])) {
+			call sprintf (Memc[str], SZ_LINE,
+			    "Fit spectra from %s interactively?")
+			    call pargstr (Memc[image])
+			if (ap_answer ("ansfitspec", Memc[str])) {
+			    call apgstr ("ansfitspec", Memc[str], SZ_LINE)
+			    call appstr ("ansfitspec1", Memc[str])
+			} else
+			    call appstr ("ansfitspec1", "NO")
+	                call ap_extract (Memc[image], Memc[output],
+			    Memc[format], nullstr, Memi[aps], naps)
+		    }
+		}
+
+		# Flatten apertures.
+		if (flat) {
+		    call sprintf (Memc[str], SZ_LINE,
+			"Flatten apertures in %s?")
+	                call pargstr (Memc[image])
+		    if (ap_answer ("ansflat", Memc[str])) {
+			call sprintf (Memc[str], SZ_LINE,
+			    "Fit spectra from %s interactively?")
+			    call pargstr (Memc[image])
+			if (ap_answer ("ansfitspec", Memc[str])) {
+			    call apgstr ("ansfitspec", Memc[str], SZ_LINE)
+			    call appstr ("ansfitspec1", Memc[str])
+			} else
+			    call appstr ("ansfitspec1", "NO")
+	                call ap_extract (Memc[image], Memc[output],
+			    Memc[format], nullstr, Memi[aps], naps)
+		    }
+		}
+ 
+		# Substract scattered light.
+		if (scat) {
+		    if (ap_getim (scatout, Memc[str1], SZ_LINE) == EOF)
+		        Memc[str1] = EOS
+		    if (Memc[output] == EOS ||
+			streq (Memc[image], Memc[output])) {
+		        call mktemp ("tmp", Memc[str], SZ_LINE)
+	                call ap_scatter (Memc[image], Memc[str],
+			    Memc[str1], Memi[aps], naps, line)
+		        call imdelete (Memc[image])
+		        call imrename (Memc[str], Memc[image])
+		    } else
+	                call ap_scatter (Memc[image], Memc[output],
+			    Memc[str1], Memi[aps], naps, line)
+		}
+
+		# Make a aperture mask.
+		if (mask)
+		    call ap_mask (Memc[image], Memc[output], Memi[aps], naps)
+
+		# Fit noise.
+		if (noise)
+		    call ap_extract (Memc[image], nullstr,
+			Memc[format], nullstr, Memi[aps], naps)
+
+	    } then
+		call erract (EA_WARN)
+
+	    # Free memory.
+	    for (i = 1; i <= naps; i = i + 1)
+		call ap_free (Memi[aps+i-1])
+	    naps = 0
+	}
+
+	# Free memory and finish up.
+	call imtclose (input)
+	call imtclose (refs)
+	if (out != NULL)
+	    call imtclose (out)
+	if (profs != NULL)
+	    call imtclose (profs)
+	if (norm || flat)
+	    call ap_fitfree ()
+	if (scat) {
+	    if (scatout != NULL)
+	        call imtclose (scatout)
+	    call scat_free ()
+	}
+	call ap_gclose ()
+	call ap_trfree ()
+	call apcpset ()
+	call sfree (sp)
+end
+
+
+procedure ap_init (find, recenter, resize, edit, trace, extract, fit,
+	norm, flat, scat, mask, noise)
+
+bool	find, recenter, resize, edit, trace
+bool	extract, fit, norm, flat, scat, mask, noise
+
+pointer	sp, str
+bool	clgetb()
+
+begin
+	call smark (sp)
+	call salloc (str, SZ_LINE, TY_CHAR)
+
+	if (find)
+	    call appans ("ansfind", find, find)
+	if (recenter)
+	    call appans ("ansrecenter", recenter, recenter)
+	if (resize)
+	    call appans ("ansresize", resize, resize)
+	if (edit)
+	    call appans ("ansedit", edit, false)
+	if (trace) {
+	    call appans ("anstrace", trace, trace)
+	    call appans ("ansfittrace", clgetb ("fittrace"), false)
+	}
+	if (extract) {
+	    call appans ("ansextract", extract, extract)
+            call appans ("ansreview", clgetb ("review"), false)
+	}
+	if (fit) {
+	    call appans ("ansfit", fit, fit)
+            call appstr ("ansreview1", "NO")
+	}
+	if (norm) {
+	    call appans ("ansnorm", norm, norm)
+	    call appans ("ansfitspec", clgetb ("fitspec"), false)
+            call appstr ("ansreview1", "NO")
+	}
+	if (flat) {
+	    call appans ("ansflat", flat, flat)
+	    call appans ("ansfitspec", clgetb ("fitspec"), false)
+            call appstr ("ansreview1", "NO")
+	}
+	if (scat) {
+	    call appans ("ansscat", scat, scat)
+            call appans ("anssmooth", clgetb ("smooth"), clgetb ("smooth"))
+            call appans ("ansfitscatter", clgetb ("fitscatter"), false)
+            call appans ("ansfitsmooth", clgetb ("fitsmooth"), false)
+	}
+	if (mask)
+	    call appans ("ansmask", mask, mask)
+	if (noise)
+            call appstr ("ansreview1", "NO")
+
+	if (extract || fit || norm || flat) {
+	    if (clgetb ("interactive"))
+	        call appstr ("ansclobber", "no")
+            else
+	        call appstr ("ansclobber", "NO")
+	}
+
+	call apgstr ("dbwrite", Memc[str], SZ_LINE)
+	if (clgetb ("interactive"))
+	    call appstr ("ansdbwrite", Memc[str])
+	else {
+	    if (Memc[str] == 'y' || Memc[str] == 'Y')
+	        call appstr ("ansdbwrite", "YES")
+	    else
+	        call appstr ("ansdbwrite", "NO")
+	}
+
+	call sfree (sp)
+end
diff --git a/noao/twodspec/apextract/x_apextract.x b/noao/twodspec/apextract/x_apextract.x
new file mode 100644
index 00000000..47a5fc1a
--- /dev/null
+++ b/noao/twodspec/apextract/x_apextract.x
@@ -0,0 +1,15 @@
+task	apall		= t_apall,
+	apedit		= t_apedit,
+	apfind		= t_apfind,
+	apfit		= t_apfit,
+	apflatten	= t_apflat,
+	apmask		= t_apmask,
+	apnormalize	= t_apnorm,
+	aprecenter	= t_aprecenter,
+	apresize	= t_apresize,
+	apscatter	= t_apscatter,
+	apscript	= t_apscript,
+	apslitproc	= t_apslitproc,
+	apnoise		= t_apnoise,
+	apsum		= t_apsum,
+	aptrace		= t_aptrace