Initial commit

32 files changed, 9176 insertions, 0 deletions

diff --git a/noao/imred/quadred/src/quad/doc/Geometry.fig b/noao/imred/quadred/src/quad/doc/Geometry.fig
new file mode 100644
index 00000000..429d987f
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/Geometry.fig
@@ -0,0 +1,91 @@
+# The following diagrams show the CCD geometry for the different readout modes.
+#
+# Single readout:
+#				G
+#		<-------------------------------->
+#			    A		    F	 
+#		<----------------------><-------->
+#		 B 	     	     C   D      E
+#		<->                 <--><>      <>
+#	^   ^	+-----------------------+--------+  ^	^
+#	|   |	|   		     	| 	 |  | e	|
+#	| c |	|   		     	|--------|  v  	|
+#	|   v	|  +----------------+   ||      ||      |
+#	|    	|  |		    |	||  o	||    	|
+#	|    	|  |		    |	||  v	||    	|
+#	|    	|  |		    |	||  e	||    	|
+#     a	|    	|  |		    |	||  r	||      | f
+#	|    	|  |		    |	||  s	||    	|
+#	|    	|  |		    |	||  c	||    	|
+#	|    	|  |		    |	||  a	||    	|
+#	|    	|  +----------------+   ||  n   ||    	|
+#	|   ^	|   		     	|--------|   	|
+#	| b |   |                       |        |  ^	|
+#	|   |	|   		     	| 	 |  | d	|
+#	v   V	*-----------------------+--------+  v	v
+#
+# Quad readout (single frame):
+#				G'
+#		<--------------------------------->
+#		     A/2    F/2  F/2      A/2
+#		<---------><---><---><----------->
+#		 B 	   D   2*E   D         C
+#		<->        <>  < >  <> 	     <-->
+#	^   ^	*----------+----.----+------------* ^	^
+#	|   |	|   	   |    .    |            | | e	|
+#	| c |	|   	   |----.----|            | v	|
+#	|   v	|  +-------+|  |.|  |+--------+   |   	|
+#  a/2	|    	|  |	   ||o |.|o ||        |   |  	| f/2
+#	|    	|  |   3   ||v |.|v ||   4    |   |   	|
+#	|    	|  |	   ||  |.|  ||        |   |  	|
+#	|    	|  |	   ||3 |.|4 ||        |   |  	|
+#       V    	...................................   	v
+#	^    	|  |	   ||o |.|o ||        |   |  	^
+#	|    	|  |   1   ||v |.|v ||   2    |   |  	|
+#	|    	|  |	   ||  |.|  ||        |   |   	|
+#   a/2	|    	|  +-------+|1 |.|2 |+--------+   |  	| f/2
+#	|   ^	|          ||  |.|  ||            |  	|
+#	| b |	|   	   |----.----|            | ^	|
+#	|   |	|   	   |    .    |            | | d	|
+#	v   v	*----------+----.----+------------* v	V
+#
+#
+# Quad readout (four frames):
+#
+#		       G"			G"
+#		<-------------->        <---------------->
+#		     A/2     F/2         F/2      A/2
+#		<---------><---->       <----><---------->
+#		 B 	   D   E        E   D          C
+#		<->        <>  <>	<>  <>	      <-->
+#	^   ^	*----------+----+	+----+------------* ^	^
+#	|   |	|   	   |    |	|    |            | | e	|
+#	| c |	|   	   |----|	|----|            | v	|
+#   a/2	|   v	|  +-------+|  ||	||  |+--------+   | ^ 	|
+#	|    	|  |	   ||o ||	||o ||        |   | |	| f/2
+#	|    	|  |   3   ||v ||	||v ||   4    |   | |	|
+#	|    	|  |	   ||  ||	||  ||        |   | |	|
+#	V    	|  |	   ||3 ||	||4 ||        |   | |	|
+#		+---------------+       +-----------------+ v	v
+#
+#
+#            	+---------------+	+-----------------+ ^	^
+#	^    	|  |	   ||o ||	||o ||        |   | |	|
+#	|    	|  |   1   ||v ||	||v ||   2    |   | |	|
+#	|    	|  |	   ||  ||	||  ||        |   | |	|
+#	|    	|  +-------+|1 ||	||2 |+--------+   | |	| f/2
+#   a/2	|   ^	|          ||  ||	||  ||            | v	|
+#	| b |	|   	   |----|	|----|            | ^	|
+#	|   |	|   	   |    |	|    |            | | d	|
+#	v   v	*----------+----+	+----+------------* v	v
+#
+# Where
+#		A  = xdata			a = ydata
+#		B  = txskip1			b = tyskip1
+#		C  = txskip2			c = tyskip2
+#		D  = bxskip1			d = byskip1
+#		E  = bxskip2			e = byskip2
+#		F  = xover			f = yover = a
+#		G  =  A + F
+#		G' =  A + F
+#		G" = (A + F) / 2
diff --git a/noao/imred/quadred/src/quad/doc/badpiximage.hlp b/noao/imred/quadred/src/quad/doc/badpiximage.hlp
new file mode 100644
index 00000000..46e13160
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/badpiximage.hlp
@@ -0,0 +1,51 @@
+.help badpiximage Jun87 noao.imred.ccdred
+.ih
+NAME
+badpiximage -- Create a bad pixel mask image from a bad pixel file
+.ih
+USAGE
+badpiximage fixfile template image
+.ih
+PARAMETERS
+.ls fixfile
+Bad pixel file.
+.le
+.ls template
+Template image used to define the size of the bad pixel mask image.
+.le
+.ls image
+Bad pixel mask image to be created.
+.le
+.ls goodvalue = 1
+Integer value assigned to the good pixels.
+.le
+.ls badvalue = 0
+Integer value assigned to the bad pixels.
+.le
+.ih
+DESCRIPTION
+A bad pixel mask image is created from the specified bad pixel file.
+The format of the bad pixel file is that used by \fBccdproc\fR to
+correct CCD defects (see instruments).  The bad pixel image is of pixel type short and
+has the value given by the parameter \fBgoodvalue\fR for the good
+pixels and the value given by the parameter \fBbadvalue\fR for the bad pixels.
+The image size and header parameters are taken from the specified
+template image.  The bad pixel mask image may be used to view the
+location of the bad pixels and blink against an data image using an
+image display, to mask or flag bad pixels later by image arithmetic,
+and to propagate the positions of the bad pixels through the
+reductions.
+.ih
+EXAMPLES
+1. To make a bad pixel mask image from the bad pixel file "cryocambp.dat"
+using the image "ccd005" as the template:
+
+	cl> badpiximage cryocambp.dat ccd005 cryocambp
+
+2. To make the bad pixel mask image with good values of 0 and bad values of 1:
+
+	cl> badpixim cryomapbp.dat ccd005 cryocambp good=0 bad=1
+.ih
+SEE ALSO
+ccdproc, instruments
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/ccdgeometry.hlp b/noao/imred/quadred/src/quad/doc/ccdgeometry.hlp
new file mode 100644
index 00000000..c01a09c8
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/ccdgeometry.hlp
@@ -0,0 +1,70 @@
+.help ccdgeometry Sep87 noao.imred.ccdred
+.ih
+NAME
+ccdgeometry - Discussion of CCD geometry and header parameters
+.ih
+DESCRIPTION
+The \fBccdred\fR package maintains and updates certain geometry
+information about the images.  This geometry is described by four image
+header parameters which may be present.  These are defined below by the
+parameter names used in the package.  Note that these names may be
+different in the image header using the image header translation
+feature of the package.
+
+.ls DATASEC
+The section of the image containing the CCD data.  If absent the
+entire image is assumed to be data.  Only the pixels within the
+data section are modified during processing.  Therefore, there may be
+additional calibration or observation information in the image.
+If after processing, the data section is the entire image it is
+not recorded in the image header.
+.le
+.ls CCDSEC
+The section of the CCD to corresponding to the data section.  This
+refers to the physical format, columns and lines, of the detector.  This is
+the coordinate system used during processing to relate calibration
+data to the image data; i.e. image data pixels are calibrated by
+calibration pixels at the same CCD coordinates regardless of image pixel
+coordinates.  This allows recording only parts of the CCD during data
+taking and calibrating with calibration frames covering some or all of
+the CCD.  The CCD section is maintained during trimming operations.
+Note that changing the format of the images by image operators outside
+of the \fBccdred\fR package will invalidate this coordinate system.
+The size of the CCD section must agree with that of the data section.
+If a CCD section is absent then it defaults to the data section such
+that the first pixel of the data section has CCD coordinate (1,1).
+.le
+.ls BIASSEC
+The section of the image containing prescan or overscan bias information.
+It consists of a strip perpendicular to the readout axis.  There may be
+both a prescan and overscan but the package currently only uses one.
+This parameter may be overridden during processing by the parameter
+\fIccdproc.biassec\fR.
+.le
+.ls TRIMSEC
+The section of the image extracted during processing when the trim
+operation is selected (\fIccdproc.trim\fR).  If absent when the trim
+operation is selected it defaults to the data section; i.e. the processed
+image consists only of the data section.  This parameter may be overridden
+during processing by the parameter \fIccdproc.trimsec\fR.  After trimming
+this parameter, if present, is removed from the image header.  The
+CCD section, data section, and bias section parameters are also modified
+by trimming.
+.le
+
+The geometry is as follows.  When a CCD image is recorded it consists
+of a data section corresponding to part or all of the CCD detector.
+Regions outside of the data section may contain additional information
+which are not affected except by trimming.  Most commonly this consists
+of prescan and overscan bias data.  When recording only part of the
+full CCD detector the package maintains information about that part and
+correctly applies calibrations for that part of the detector.  Also any
+trimming operation updates the CCD coordinate information.  If the
+images include the data section, bias section, trim section, and ccd
+section the processing may be performed entirely automatically.
+
+The sections are specified using the notation [c1:c2,l1:l2] where c1
+and c2 are the first and last columns and l1 and l2 are the first and
+last lines.  Currently c1 and l1 must be less than c2 and l2
+respectively and no subsampling is allowed.  This may be added later.
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/ccdgroups.hlp b/noao/imred/quadred/src/quad/doc/ccdgroups.hlp
new file mode 100644
index 00000000..48c29b99
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/ccdgroups.hlp
@@ -0,0 +1,163 @@
+.help ccdgroups Jun87 noao.imred.ccdred
+.ih
+NAME
+ccdgroups -- Group CCD images into image lists
+.ih
+USAGE
+ccdgroups images output
+.ih
+PARAMETERS
+.ls images
+List of CCD images to be grouped.
+.le
+.ls output
+Output root group filename.  The image group lists will be put in files
+with this root name followed by a number.
+.le
+.ls group = "ccdtype"
+Group type.  There are currently four grouping types:
+.ls ccdtype
+Group by CCD image type.
+.le
+.ls subset
+Group by subset parameter.
+.le
+.ls position
+Group by position in right ascension (in hours) and declination (in degrees).
+The groups are defined by a radius parameter (in arc seconds).
+.le
+.ls title
+Group by identical titles.
+.le
+.ls date
+Group by identical dates.
+.le
+.le
+.ls radius = 60.
+Grouping radius when grouping by positions.  This is given in arc seconds.
+.le
+.ls ccdtype = ""
+CCD image types to select from the input image list.  If null ("") then
+all image types are used.
+.le
+.ih
+DESCRIPTION
+The input images, possible restricted to a particular CCD image type,
+are grouped into image lists.  The "ccdtype" or "subset" groups
+produce output image lists with the given root name and the CCD type
+or subset as an extension (without a period).  For the other group
+types the
+image lists have file names given by
+the root output name and a numeric extension (without a period).
+If the package parameter \fIccdred.verbose\fR is yes then the
+image name and output group list is printed for each image.  The image lists can
+be used with the @ list feature for processing separate groups of observations.
+Note that grouping by CCD image type and subset is often not necessary since
+the \fBccdred\fR tasks automatically use this information (see
+\fBccdtypes\fR and \fBsubsets\fR).
+
+Besides CCD image type and subsets there are currently three ways to
+group images.  These are by position in the sky, by title, and by
+date.  Further groups may be added as suggested.  The title grouping is
+useful if consistent titles are used when taking data.  The date
+grouping is useful if multiple nights of observations are not organized
+by directories (it is recommended that data from separate nights be
+kept in separate directories).  The position grouping finds
+observations within a given radius on the sky of the first member of
+the group (this is not a clustering algorithm).  The right ascension
+and declination coordinates must be in standard units, hours and
+degrees respectively.  The grouping radius is in arc seconds.  This
+grouping type is useful for making sets of data in which separate
+calibration images are taken at each position.
+
+The date, title, and coordinates are accessed through the instrument
+translation file.  The standard names used are "date-obs", "title", "ra",
+and "dec".
+.ih
+EXAMPLES
+1. For each object 5 exposures were taken to be combined in order to remove
+cosmic rays.  If the titles are the same then (with ccdred.verbose=yes):
+
+.nf
+    cl> ccdgroups *.imh group group=title ccdtype=object
+    ccd005.imh  --> group1
+    ccd006.imh  --> group1
+    ccd007.imh  --> group1
+    ccd008.imh  --> group1
+    ccd009.imh  --> group1
+    ccd012.imh  --> group2
+    ccd013.imh  --> group2
+    ccd014.imh  --> group2
+    ccd015.imh  --> group2
+    ccd016.imh  --> group2
+    [... etc ...]
+    cl> combine @group1 obj1 proc+
+    cl> combine @group2 obj2 proc+
+    [... etc ...]
+.fi
+
+Note the numeric suffixes to the output root name "group".
+ 
+2. CCD observations were made in groups with a flat field, the object, and
+a comparison spectrum at each position.  To group and process this data:
+
+.nf
+    cl> ccdgroups *.imh obs group=position >> logfile
+    cl> ccdproc @obs1
+    cl> ccdproc @obs2
+    cl> ccdproc @obs3
+.fi
+
+Since no flat field is specified for the parameter \fIccdproc.flat\fR
+the flat field is taken from the input image list.
+
+3. If for some reason you want to group by date and position it is possible
+to use two steps.
+
+.nf
+    cl> ccdgroups *.imh date group=date
+    cl> ccdgroups @data1 pos1
+    cl> ccdgroups @data2 pos2
+.fi
+ 
+4. To get groups by CCD image type:
+ 
+.nf
+    cl> ccdgroups *.imh "" group=ccdtype
+    ccd005.imh  --> zero
+    ccd006.imh  --> zero
+    ccd007.imh  --> zero
+    ccd008.imh  --> dark
+    ccd009.imh  --> flat
+    ccd012.imh  --> flat
+    ccd013.imh  --> object
+    ccd014.imh  --> object
+    ccd015.imh  --> object
+    ccd016.imh  --> object
+    [... etc ...]
+.fi
+ 
+Note the use of a null root name and the extension is the standard
+CCDRED types (not necessarily those used in the image header).
+ 
+5. To get groups by subset:
+ 
+.nf
+    cl> ccdgroups *.imh filt group=subset
+    ccd005.imh  --> filt
+    ccd006.imh  --> filtB
+    ccd007.imh  --> filtB
+    ccd008.imh  --> filtB
+    ccd009.imh  --> filtV
+    ccd012.imh  --> filtV
+    ccd013.imh  --> filtV
+    ccd014.imh  --> filtB
+    ccd015.imh  --> filtB
+    ccd016.imh  --> filtB
+    [... etc ...]
+.fi
+ 
+.ih
+SEE ALSO
+ccdlist, ccdtypes, instruments, subsets
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/ccdhedit.hlp b/noao/imred/quadred/src/quad/doc/ccdhedit.hlp
new file mode 100644
index 00000000..1bc27d29
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/ccdhedit.hlp
@@ -0,0 +1,108 @@
+.help ccdhedit Jun87 noao.imred.ccdred
+.ih
+NAME
+ccdhedit -- CCD image header editor
+.ih
+USAGE
+ccdhedit images parameter value
+.ih
+PARAMETERS
+.ls images
+List of CCD images to be edited.
+.le
+.ls parameter
+Image header parameter.  The image header parameter will be translated by
+the header translation file for the images.
+.le
+.ls value
+The parameter value.  If the null string ("") is specified then the
+parameter is deleted from the image header, otherwise it is added or
+modified.  If the parameter is "imagetyp" then the value string giving
+the CCD image type is translated from the package CCD type to the
+instrument specific string.
+.le
+.ls type = "string"
+The parameter type.  The parameter types are "string", "real", or "integer".
+.le
+.ih
+DESCRIPTION
+The image headers of the specified CCD images are edited to add, modify,
+or delete a parameter.  The parameters may be those used by the \fBccdred\fR
+package.  The parameter name is translated to an image header parameter by the
+instrument translation file (see \fBinstruments\fR) if a translation is
+given.  Otherwise the parameter is that in the image header.  If the parameter
+is "imagetyp" the parameter value for the CCD image type may be that
+used by the package; i.e. dark, object, flat, etc.  The value string will be
+translated to the instrument image string in this case.  The translation
+facility allows use of this task in an instrument independent way.
+
+The value string is used to determine whether to delete or modify the
+image parameter.  If the null string, "", is given the specified parameter
+is deleted.  If parameters are added the header type must be specified
+as a string, real, or integer parameter.  The numeric types convert the
+value string to a number.
+.ih
+EXAMPLES
+The \fBccdred\fR package is usable even with little image header information.
+However, if desired the header information can be added to images which
+lack it.  In all the examples the parameters used are those of the package
+and apply equally well to any image header format provided there is an
+instrument translation file.
+
+.nf
+1.   cl> ccdhedit obj* imagetyp object
+2.   cl> ccdhedit flat* imagetyp flat
+3.   cl> ccdhedit zero* imagetyp zero
+4.   cl> ccdhedit obj0![1-3]* subset "V filter"
+5.   cl> ccdhedit obj0![45]* subset "R filter"
+6.   cl> ccdhedit flat001 subset "R filter"
+7.   cl> ccdhedit obj* exptime 500 type=integer
+.fi
+
+8. The following is an example of a CL script which sets the CCD image type,
+the subset, and the exposure time simultaneously.  The user may expand
+on this example to include other parameters or other initialization
+operations.
+
+.nf
+    cl> edit ccdheader.cl
+
+    ----------------------------------------------------------------
+    # Program to set CCD header parameters.
+
+    procedure ccdheader (images)
+
+    string	images			{prompt="CCD images"}
+    string	imagetyp		{prompt="CCD image type"}
+    string	subset			{prompt="CCD subset"}
+    string	exptime			{prompt="CCD exposure time"}
+
+    begin
+	    string	ims
+
+	    ims = images
+	    ccdhedit (ims, "imagetyp", imagetyp, type="string")
+	    ccdhedit (ims, "subset", subset, type="string")
+	    ccdhedit (ims, "exptime", exptime, type="real")
+    end
+    ----------------------------------------------------------------
+
+    cl> task ccdheader=ccdheader.cl
+    cl> ccdheader obj* imagetyp=object subset="V" exptime=500
+.fi
+
+9. The image header may be changed to force processing a calibration image
+as an object.  For example to flatten a flat field:
+
+.nf
+    cl> ccdhedit testflat imagetyp other
+    cl> ccdproc testflat
+.fi
+
+10. To delete processing flags:
+
+    cl> ccdhedit obj042 flatcor ""
+.ih
+SEE ALSO
+hedit, instruments, ccdtypes, subsets
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/ccdinst.hlp b/noao/imred/quadred/src/quad/doc/ccdinst.hlp
new file mode 100644
index 00000000..23ebea60
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/ccdinst.hlp
@@ -0,0 +1,389 @@
+.help ccdinstrument Nov90 noao.imred.ccdred
+.ih
+NAME
+ccdinstrument -- Setup and verify CCD instrument translation files
+.ih
+USAGE	
+ccdinstrument images
+.ih
+PARAMETERS
+.ls images
+List of images to be verified or used to setup a CCD instrument translation
+file.
+.le
+.ls instrument = ")_.instrument"
+CCD instrument translation file.  The default is to use the translation
+file defined in the \fBccdred\fR package parameters.  Note that one would
+need write permission to update this file though the task has a write
+command to save any changes to a different file.
+.le
+.ls ssfile = ")_.ssfile"
+Subset translation file.  The default is to use the file defined in
+the \fBccdred\fR package parameters.
+.le
+.ls edit = yes
+Edit the instrument translation file?  If "yes" an interactive
+mode is entered allowing translation parameters to be modified while if
+"no" the task is simply used to verify the translations noninteractively.
+.le
+.ls parameters = "basic"
+Parameters to be displayed.  The choices are "basic" to display only the
+most basic parameters (those needed for the simplest automation of
+\fBccdred\fR tasks),  "common" to display the common parameters used
+by the package (most of these are keywords to be written to the image
+rather than translated), and "all" to display all the parameters
+referenced by the package including the most obscure.  For most uses
+the "basic" set is all that is important and the other options are
+included for completeness.
+.le
+.ih
+DESCRIPTION
+The purpose of this task is to provide an interface to simplify setting
+up CCD instrument translation files and to verify the translations
+for a set of images.  Before this task was written users who needed to
+set up translation files for new instruments and observatories had
+to directly create the files with an editor.  Many people encountered
+difficulties and were prone to errors.  Also there was no task that
+directly verified the translations though \fBccdlist\fR provided some
+clues.
+
+The \fBccdred\fR package was designed to make intelligent use of
+information in image headers for determining things such as image
+calibration or object type and exposure times.  While the package may
+be used without this capability it is much more convenient to be
+able to use information from the image.  The package was also intended
+to be used with many different instruments, detectors, and observatories.
+The key to providing image header access across different observatories
+is the ability to translate the needs of the package to the appropriate
+keywords in the image header.  This is done through a file called
+an "instrument translation file".  For a complete description of
+this file and other instrument setup features of the package see
+\fBccdred.instruments\fR.
+
+The instrument translation file translates the parameter names used by
+the \fBccdred\fR package into image specific parameters and also
+supplies default values for parameters.  The translation proceeds as
+follows.  When a package task needs a parameter for an image, for
+example "imagetyp", it looks in the instrument translation file.  If
+the file is not found or none is specified then the image header
+keyword that is requested is assumed to have the same name.  If an
+instrument translation file is defined then the requested parameter is
+translated to an image header keyword, provided a translation entry is
+given.  If no translation is given the package name is used.  For
+example the package parameter "imagetyp" might be translated to
+"data-typ" (the old NOAO CCD keyword).  If the parameter is not found
+then the default value specified in the translation file, if present,
+is returned.
+
+For recording parameter information in the header, such
+as processing flags, translation is also used.  For example, if the
+flag specifying that the image has been corrected by a flat field is to
+be set then the package parameter name "flatcor" might be translated to
+"ff-flag".  If no translation is given then the new image header
+parameter is entered as "flatcor".
+
+The CCD image type requires a second level of translation also defined
+in the translation file.  Once the image keyword which identifies the
+type of CCD image, for example a flat field or object, is translated
+to an imahe keyword the specific
+string value must be translated to one of the CCD image types used
+by the package.  The translation works in the same way, the specific
+string found is translated to the \fBccdred\fR type and returned to
+the task.  This translation is tricky in that the exact string
+including all spaces and capitalizations must be correctly defined
+in the translation file.  The \fBccdinstrument\fR allows doing
+this automatically thus minimizing typing errors.
+
+The basic display format of the task is a table of five columns
+giving the parameter name used by the package, the image keyword
+to which it is translated, the default value (if any), the value
+the task will receive for the current image after translation,
+and the actual keyword value in the image.  A "?" is printed if
+a value cannot be determined.  The idea of the task is to make sure
+that the value a \fBccdred\fR task sees is the correct one and if not
+to modify the translation appropriately.  In verify mode when the
+\fBedit\fR parameter is not set the translation table is simply
+printed for each input image.
+
+In edit mode the user interactively gives commands at the ccdinstrument
+prompt to display or modify keywords.  The modifications can then be
+written to the instrument file or saved in a private copy.  The
+list of commands is shown below and may be printed using ? or help.
+
+.in 4
+.nf
+			CCDINSTRUMENT COMMANDS
+
+?	    Print command summary
+help	    Print command summary
+imheader    Page image header
+instrument  Print current instrument translation file
+next	    Next image
+newimage    Select a new image
+quit	    Quit
+read	    Read instrument translation file
+show	    Show current translations
+write	    Write instrument translation file
+
+translate   Translate image string selected by the imagetyp
+	    parameter to one of the CCDRED types given as an
+	    argument or queried:
+	    object, zero, dark, flat, comp, illum, fringe, other
+
+.fi
+The following are CCDRED parameters which may be translated.  You are
+queried for the image keyword to use or it may be typed after the command.
+An optional default value (returned if the image does not contain the
+keyword) may be typed as the second argument of the command.
+.nf
+
+	BASIC PARAMETERS
+imagetyp	Image type parameter (see also translate)
+subset		Subset or filter parameter
+exptime		Exposure time
+darktime	Dark time (may be same as the exposure time)
+.fi
+.in -4
+
+The commands may be followed by values such as file names for some of
+the general commands or the keyword and default value for the parameters
+to be translated.  Note this is the only way to specify a default value.
+If no arguments are given the user is prompted with the current value
+which may then be changed.
+
+The set of parameters shown above are only those considered "basic".
+In order to avoid confusion the task can limit the set of parameters
+displayed.  Without going into great detail, it is only the basic
+parameters which are generally required to have valid translations to
+allow the package to work well.  However, for completeness, and if someone
+wants to go wild with translations, further parameters may be displayed
+and changed.  The parameters displayed is controlled by the \fIparameters\fR
+keyword.  The additional parameters not shown above are:
+
+.in 4
+.nf
+	USEFUL DEFAULT GEOMETRY PARAMETERS
+biassec		Bias section (often has a default value)
+trimsec		Trim section (often has a default value)
+
+	COMMON PROCESSING FLAGS
+fixpix		Bad pixel replacement flag
+overscan	Overscan correction flag
+trim		Trim flag
+zerocor		Zero level correction flag
+darkcor		Dark count correction flag
+flatcor		Flat field correction flag
+
+	RARELY TRANSLATED PARAMETERS
+ccdsec		CCD section
+datasec		Data section
+fixfile		Bad pixel file
+
+fringcor	Fringe correction flag
+illumcor	Ilumination correction flag
+readcor		One dimensional zero level read out correction
+scancor		Scan mode correction flag
+
+illumflt	Ilumination flat image
+mkfringe	Fringe image
+mkillum		Iillumination image
+skyflat		Sky flat image
+
+ccdmean		Mean value
+fringscl	Fringe scale factor
+ncombine	Number of images combined
+date-obs	Date of observations
+dec		Declination
+ra		Right Ascension
+title		Image title
+.fi
+.in -4
+.ih
+EXAMPLES
+1. To verify the translations for a set of images using the default
+translation file:
+
+.nf
+	cl> setinst "" review-
+	cl> ccdinst dev$pix edit-
+	Image: dev$pix
+	Instrument file: 
+	Subset file: subsets
+
+	CCDRED    IMAGE     DEFAULT   CCDRED    IMAGE   
+	PARAM     KEYWORD   VALUE     VALUE     VALUE   
+	--------------------------------
+	imagetyp  imagetyp            none      ?
+	subset    subset                        ?
+	exptime   exptime             ?         ?
+	darktime  darktime            ?         ?
+
+	cl> setinst "" site=kpno dir=ccddb$ review-
+	cl> ccdinst dev$pix edit-
+	Image: dev$pix
+
+	Instrument file: ccddb$kpno/camera.dat
+	Subset file: subsets
+
+	CCDRED    IMAGE     DEFAULT   CCDRED    IMAGE   
+	PARAM     KEYWORD   VALUE     VALUE     VALUE   
+	--------------------------------
+	imagetyp  data-typ            object    OBJECT (0)
+	subset    f1pos               2         2
+	exptime   otime               600       600
+	darktime  ttime               600       600
+.fi
+
+2.  Set up an  instrument translation file from scratch.
+
+.nf
+	ccdinst ech???.imh instr=myccd edit+
+	Warning: OPEN: File does not exist (myccd)
+	Image: ech001.imh
+	Instrument file: myccd
+	Subset file: subsets
+	
+	CCDRED    IMAGE     DEFAULT   CCDRED    IMAGE   
+	PARAM     KEYWORD   VALUE     VALUE     VALUE   
+	------------------------------------------------------
+	imagetyp  imagetyp            none      ?
+	subset    subset                        ?
+	exptime   exptime             ?         ?
+	darktime  darktime            ?         ?
+	
+	ccdinstrument> imagetyp
+	Image keyword for image type (imagetyp): ccdtype
+	imagetyp  ccdtype             unknown   BIAS
+	ccdinstrument> translate
+	CCDRED image type for 'BIAS' (unknown): zero
+	imagetyp  ccdtype             zero      BIAS
+	ccdinstrument> subset
+	Image keyword for subset parameter (subset): filters
+	subset    filters             1         1 0
+	ccdinstrument> exptime integ
+	exptime   integ               0.        0.
+	ccdinstrument> darktime integ
+	darktime  integ               0.        0.
+	ccdinstrument> show
+	Image: ech001.imh
+	Instrument file: myccd
+	Subset file: subsets
+	
+	CCDRED    IMAGE     DEFAULT   CCDRED    IMAGE   
+	PARAM     KEYWORD   VALUE     VALUE     VALUE   
+	------------------------------------------------------
+	imagetyp  ccdtype             zero      BIAS
+	subset    filters             1         1 0
+	exptime   integ               0.        0.
+	darktime  integ               0.        0.
+	
+	ccdinstrument> next
+	Image: ech002.imh
+	Instrument file: myccd
+	Subset file: subsets
+	
+	CCDRED    IMAGE     DEFAULT   CCDRED    IMAGE   
+	PARAM     KEYWORD   VALUE     VALUE     VALUE   
+	------------------------------------------------------
+	imagetyp  ccdtype             unknown   PROJECTOR FLAT
+	subset    filters             1         1 0
+	exptime   integ               20.       20.
+	darktime  integ               20.       20.
+	
+	ccdinstrument> trans
+	CCDRED image type for 'PROJECTOR FLAT' (unknown): flat
+	imagetyp  ccdtype             flat      PROJECTOR FLAT
+	ccdinstrument> next
+	Image: ech003.imh
+	Instrument file: myccd
+	Subset file: subsets
+	
+	CCDRED    IMAGE     DEFAULT   CCDRED    IMAGE   
+	PARAM     KEYWORD   VALUE     VALUE     VALUE   
+	------------------------------------------------------
+	imagetyp  ccdtype             unknown   COMPARISON
+	subset    filters             1         1 0
+	exptime   integ               300       300
+	darktime  integ               300       300
+	
+	ccdinstrument> translate comp
+	imagetyp  ccdtype             comp      COMPARISON
+	ccdinstrument> next
+	Image: ech004.imh
+	Instrument file: myccd
+	Subset file: subsets
+	
+	CCDRED    IMAGE     DEFAULT   CCDRED    IMAGE   
+	PARAM     KEYWORD   VALUE     VALUE     VALUE   
+	------------------------------------------------------
+	imagetyp  ccdtype             unknown   OBJECT
+	subset    filters             1         1 0
+	exptime   integ               3600      3600
+	darktime  integ               3600      3600
+	
+	ccdinstrument> translate object
+	imagetyp  ccdtype             object    OBJECT
+	ccdinstrument> inst
+	imagetyp                      ccdtype 
+	BIAS                          zero    
+	subset                        filters 
+	exptime                       integ   
+	darktime                      integ   
+	'PROJECTOR FLAT'              flat    
+	COMPARISON                    comp    
+	OBJECT                        object  
+
+	ccdinstrument> next
+	Update instrument file myccd (yes)? 
+.fi
+
+3.  Set default geometry parameters.  Note that to set a default the
+arguments must be on the command line.
+
+.nf
+	cc> ccdinst ech001 instr=myccd param=common edit+
+	Image: ech001
+	Instrument file: myccd
+	Subset file: subsets
+	
+	CCDRED    IMAGE     DEFAULT   CCDRED    IMAGE   
+	PARAM     KEYWORD   VALUE     VALUE     VALUE   
+	------------------------------------------------------
+	imagetyp  ccdtype             zero      BIAS
+	subset    filters             1         1 0
+	exptime   integ               0.        0.
+	darktime  integ               0.        0.
+	
+	biassec   biassec             ?         ?
+	trimsec   trimsec             ?         ?
+	
+	fixpix    fixpix              no        ?
+	overscan  overscan            no        ?
+	trim      trim                no        ?
+	zerocor   zerocor             no        ?
+	darkcor   darkcor             no        ?
+	flatcor   flatcor             no        ?
+	
+	ccdinstrument> biassec biassec [803:830,*]
+	biassec   biassec   [803:830,*]  [803:830,*]  ?
+	ccdinstrument> trimsec trimsec [2:798,2:798]
+	trimsec   trimsec   [2:798,2:798]  [2:798,2:798]  ?
+	ccdinstrument> instr
+	trimsec                       trimsec  [2:798,2:798]
+	biassec                       biassec  [803:830,*]
+	imagetyp                      ccdtype 
+	BIAS                          zero    
+	subset                        filters 
+	exptime                       integ   
+	darktime                      integ   
+	'PROJECTOR FLAT'              flat    
+	COMPARISON                    comp    
+	OBJECT                        object  
+	
+	ccdinstrument> q
+	Update instrument file myccd (yes)? 
+.fi
+.ih
+SEE ALSO
+instruments, setinstrument
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/ccdlist.hlp b/noao/imred/quadred/src/quad/doc/ccdlist.hlp
new file mode 100644
index 00000000..9ce7dfdd
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/ccdlist.hlp
@@ -0,0 +1,133 @@
+.help ccdlist Jun87 noao.imred.ccdred
+.ih
+NAME
+ccdlist -- List CCD processing information
+.ih
+USAGE
+ccdlist images
+.ih
+PARAMETERS
+.ls images
+CCD images to be listed.  A subset of the these may be selected using the
+CCD image type parameter.
+.le
+.ls ccdtype = ""
+CCD image type to be listed.  If no type is specified then all the images
+are listed.  If an image type is specified then only images
+of that type are listed.  See \fBccdtypes\fR for a list of the package
+image types.
+.le
+.ls names = no
+List the image names only?  Used with the CCD image type parameter to make
+a list of the images of the specified type.
+.le
+.ls long = no
+Long format listing?  The images are listed in a long format containing some
+image parameters and the processing history.
+.le
+.ls ccdproc (pset)
+CCD processing parameter set.
+.le
+.ih
+DESCRIPTION
+Information from the specified input images is listed on the standard
+output.  A specific CCD image type may be selected from the input
+images by the parameter \fIccdtype\fR.  There are three list formats;
+the default one line per image format, an image name only format, and a
+multi-line long format.  The default one line format consists of the
+image name, image size, image pixel type, CCD image type, subset ID (if
+defined), processing flags, and title.  This format contains the same
+information as that produced by \fBimheader\fR as well as CCD specific
+information.  The processing flags identifying the processing operations
+performed on the image are given by the following single letter codes.
+
+.nf
+	B - Bad pixel replacement
+	O - Overscan bias subtraction
+	T - Trimming
+	Z - Zero level subtraction
+	D - Dark count subtraction
+	F - Flat field calibration
+	I - Iillumination correction
+	Q - Fringe correction
+.fi
+
+The long format has the same first line as the default format plus additional
+instrument information such as the exposure time and the full processing
+history.  In addition to listing the completed processing, the operations
+not yet done (as specified by the \fBccdproc\fR parameters) are also
+listed.
+
+The image name only format is intended to be used to generate lists of
+images of the same CCD image type.  These lists may be used as "@" file
+lists in IRAF tasks.
+.ih
+EXAMPLES
+1. To list the default format for all images:
+
+.nf
+    cl> ccdlist *.imh
+    ccd001.imh[544,512][short][unknown][V]:FOCUS L98-193
+    ccd007.imh[544,512][short][object][V]:N2968 V 600s
+    ccd015.imh[544,512][short][object][B]:N3098 B 500s
+    ccd024.imh[544,512][short][object][R]:N4036 R 600s
+    ccd045.imh[544,512][short][flat][V]:dflat 6v+blue 5s
+    ccd066.imh[544,512][short][flat][B]:dflat 6v+blue 5s
+    ccd103.imh[544,512][short][flat][R]:dflat 6v+blue 5s
+    ccd104.imh[544,512][short][zero][]:bias
+    ccd105.imh[544,512][short][dark][]:dark 3600s
+.fi
+
+These images have not been processed.
+
+2. To restrict the listing to just the object images:
+
+.nf
+    cl> ccdlist *.imh ccdtype=object
+    ccd007.imh[544,512][short][object][V]:N2968 V 600s
+    ccd015.imh[544,512][short][object][B]:N3098 B 500s
+    ccd024.imh[544,512][short][object][R]:N4036 R 600s
+.fi
+
+3. The long list for image "ccd007" is obtained by:
+
+.nf
+    cl> ccdlist ccd007 l+
+    ccd007[544,512][short][object][V]:N2968 R 600s
+	exptime = 200. darktime = 200.
+        [TO BE DONE] Overscan strip is [520:540,*]
+        [TO BE DONE] Trim image section is [3:510,3:510]
+        [TO BE DONE] Flat field correction
+.fi
+
+4. After processing the images have the short listing:
+
+.nf
+    cl> ccdlist *.imh ccdtype=object
+    ccd007.imh[508,508][real][object][V][OTF]:N2968 V 600s
+    ccd015.imh[508,508][real][object][B][OTF]:N3098 B 500s
+    ccd024.imh[544,512][short][object][R][OTF]:N4036 R 600s
+.fi
+
+The processing indicated is overscan subtraction, trimming, and flat fielding.
+
+5. The long listing for "ccd007" after processing is:
+
+.nf
+    cl> ccdlist ccd007 l+
+    ccd007[508,508][real][object][V][OTF]:N2968 R 600s
+	exptime = 200. darktime = 200.
+        Jun  2 18:18 Overscan section is [520:540,*] with mean=481.8784
+        Jun  2 18:18 Trim data section is [3:510,3:510]
+        Jun  2 18:19 Flat field image is FlatV.imh with scale=138.2713
+.fi
+
+6. To make a list file containing all the flat field images:
+
+    cl> ccdlist *.imh ccdtype=flat name+ > flats
+
+This file can be used as an @ file for processing.
+.ih
+SEE ALSO
+ccdtypes ccdgroups
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/ccdproc.hlp b/noao/imred/quadred/src/quad/doc/ccdproc.hlp
new file mode 100644
index 00000000..4be65f73
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/ccdproc.hlp
@@ -0,0 +1,720 @@
+.help ccdproc Oct90 noao.imred.ccdred
+.ih
+NAME
+ccdproc -- Process CCD images
+.ih
+USAGE	
+ccdproc images
+.ih
+PARAMETERS
+.ls images
+List of input CCD images to process.  The list may include processed
+images and calibration images.
+.le
+.ls ccdtype = ""
+CCD image type to select from the input image list.  If no type is given
+then all input images will be selected.  The recognized types are described
+in \fBccdtypes\fR.
+.le
+.ls max_cache = 0
+Maximum image caching memory (in Mbytes).  If there is sufficient memory
+the calibration images, such as zero level, dark count, and flat fields,
+will be cached in memory when processing many input images.  This
+reduces the disk I/O and makes the task run a little faster.  If the
+value is zero image caching is not used.
+.le
+.ls noproc = no
+List processing steps only?
+.le
+
+.ce
+PROCESSING SWITCHES
+.ls fixpix = yes
+Fix bad CCD lines and columns by linear interpolation from neighboring
+lines and columns?  If yes then a bad pixel file must be specified.
+.le
+.ls overscan = yes
+Apply overscan or prescan bias correction?  If yes then the overscan
+image section and the readout axis must be specified.
+.le
+.ls trim = yes
+Trim the image of the overscan region and bad edge lines and columns?
+If yes then the data section must be specified.
+.le
+.ls zerocor = yes
+Apply zero level correction?  If yes a zero level image must be specified.
+.le
+.ls darkcor = yes
+Apply dark count correction?  If yes a dark count image must be specified.
+.le
+.ls flatcor = yes
+Apply flat field correction?  If yes flat field images must be specified.
+.le
+.ls illumcor = no
+Apply iillumination correction?  If yes iillumination images must be specified.
+.le
+.ls fringecor = no
+Apply fringe correction?  If yes fringe images must be specified.
+.le
+.ls readcor = no
+Convert zero level images to readout correction images?  If yes then
+zero level images are averaged across the readout axis to form one
+dimensional zero level readout correction images.
+.le
+.ls scancor = no
+Convert flat field images to scan mode flat field images?  If yes then the
+form of scan mode correction is specified by the parameter \fIscantype\fR.
+.le
+
+.ce
+PROCESSING PARAMETERS
+.ls readaxis = "line"
+Read out axis specified as "line" or "column".
+.le
+.ls fixfile
+File describing the bad lines and columns.  If "image" is specified then
+the file is specified in the image header or instrument translation file.
+.le
+.ls biassec
+Overscan bias strip image section.  If "image" is specified then the overscan
+bias section is specified in the image header or instrument translation file.
+.le
+.ls trimsec
+image section for trimming.  If "image" is specified then the trim
+image section is specified in the image header or instrument translation file.
+.le
+.ls zero = ""
+Zero level calibration image.  The zero level image may be one or two
+dimensional.  The CCD image type and subset are not checked for these
+images and they take precedence over any zero level calibration images
+given in the input list.
+.le
+.ls dark = ""
+Dark count calibration image.  The CCD image type and subset are not checked
+for these images and they take precedence over any dark count calibration
+images given in the input list.
+.le
+.ls flat = ""
+Flat field calibration images.  The flat field images may be one or
+two dimensional.  The CCD image type is not checked for these
+images and they take precedence over any flat field calibration images given
+in the input list.  The flat field image with the same subset as the
+input image being processed is selected.
+.le
+.ls illum = ""
+Iillumination correction images.  The CCD image type is not checked for these
+images and they take precedence over any iillumination correction images given
+in the input list.  The iillumination image with the same subset as the
+input image being processed is selected.
+.le
+.ls fringe = ""
+Fringe correction images.  The CCD image type is not checked for these
+images and they take precedence over any fringe correction images given
+in the input list.  The fringe image with the same subset as the
+input image being processed is selected.
+.le
+.ls minreplace = 1.
+When processing flat fields, pixel values below this value (after
+all other processing such as overscan, zero, and dark corrections) are
+replaced by this value.  This allows flat fields processed by \fBccdproc\fR
+to be certain to avoid divide by zero problems when applied to object
+images.
+.le
+.ls scantype = "shortscan"
+Type of scan format used in creating the CCD images.  The modes are:
+.ls "shortscan"
+The CCD is scanned over a number of lines and then read out as a regular
+two dimensional image.  In this mode unscanned flat fields are numerically
+scanned to form scanned flat fields comparable to the observations.  If
+the flat field calibration images are taken in scanned mode then
+\fIscancor\fR should be no and the processing performed in the same manner
+as in unscanned mode.
+.le
+.ls "longscan"
+In this mode the CCD is clocked and read out continuously to form a long
+strip.  Flat fields are averaged across the readout axis to
+form a one dimensional flat field readout correction image.  This assumes
+that all recorded image lines are clocked over the entire active area of the
+CCD.
+.le
+.le
+.ls nscan
+Number of scan readout lines used in short scan mode.  This parameter is used
+when the scan type is "shortscan".
+.le
+
+
+.ce
+OVERSCAN FITTING PARAMETERS
+.ls interactive = no
+Fit the overscan vector interactively?  If yes the overscan vector is fit
+interactively using the \fBicfit\fR package.  If no then the fitting parameters
+given below are used.
+.le
+.ls function = "legendre"
+Overscan fitting function.  The function types are "legendre" polynomial,
+"chebyshev" polynomial, "spline1" linear spline, and "spline3" cubic
+spline.
+.le
+.ls order = 1
+Number of polynomial terms or spline pieces in the overscan fit.
+.le
+.ls sample = "*"
+Sample points to use in the overscan fit.  The string "*" specified all
+points otherwise an \fBicfit\fR range string is used.
+.le
+.ls naverage = 1
+Number of points to average or median to form fitting points.  Positive
+numbers specify averages and negative numbers specify medians.
+.le
+.ls niterate = 1
+Number of rejection iterations to remove deviant points from the overscan fit.
+If 0 then no points are rejected.
+.le
+.ls low_reject = 3., high_reject = 3.
+Low and high sigma rejection factors for rejecting deviant points from the
+overscan fit.
+.le
+.ls grow = 0.
+One dimensional growing radius for rejection of neighbors to deviant points.
+.le
+.ih
+DESCRIPTION
+\fBCcdproc\fR processes CCD images to correct and calibrate for
+detector defects, readout bias, zero level bias, dark counts,
+response, iillumination, and fringing.  It also trims unwanted
+lines and columns and changes the pixel datatype.  It is efficient
+and easy to use; all one has to do is set the parameters and then
+begin processing the images.  The task takes care of most of the
+record keeping and automatically does the prerequisite processing
+of calibration images.  Beneath this simplicity there is much that
+is going on.  In this section a simple description of the usage is
+given.  The following sections present more detailed discussions
+on the different operations performed and the order and logic
+of the processing steps.  For a user's guide to the \fBccdred\fR
+package see \fBguide\fR.  Much of the ease of use derives from using
+information in the image header.  If this information is missing
+see section 13.
+
+One begins by setting the task parameters.  There are many parameters
+but they may be easily reviewed and modified using the task \fBeparam\fR.
+The input CCD images to be processed are given as an image list.
+Previously processed images are ignored and calibration images are
+recognized, provided the CCD image types are in the image header (see
+\fBinstruments\fR and \fBccdtypes\fR).  Therefore it is permissible to
+use simple image templates such as "*.imh".  The \fIccdtype\fR parameter
+may be used to select only certain types of CCD images to process
+(see \fBccdtypes\fR).
+
+The processing operations are selected by boolean (yes/no) parameters.
+Because calibration images are recognized and processed appropriately,
+the processing operations for object images should be set.
+Any combination of operations may be specified and the operations are
+performed simultaneously.  While it is possible to do operations in
+separate steps this is much less efficient.  Two of the operation
+parameters apply only to zero level and flat field images.  These
+are used for certain types of CCDs and modes of operation.
+
+The processing steps selected have related parameters which must be
+set.  These are things like image sections defining the overscan and
+trim regions and calibration images.  There are a number of parameters
+used for fitting the overscan or prescan bias section.  These are
+parameters used by the standard IRAF curve fitting package \fBicfit\fR.
+The parameters are described in more detail in the following sections.
+
+In addition to the task parameters there are package parameters
+which affect \fBccdproc\fR.  These include the instrument and subset
+files, the text and plot log files, the output pixel datatype,
+the amount of memory available for calibration image caching,
+the verbose parameter for logging to the terminal, and the backup
+prefix.  These are described in \fBccdred\fR.
+
+Calibration images are specified by task parameters and/or in the
+input image list.  If more than one calibration image is specified
+then the first one encountered is used and a warning is issued for the
+extra images.  Calibration images specified by
+task parameters take precedence over calibration images in the input list.
+These images also need not have a CCD image type parameter since the task
+parameter identifies the type of calibration image.  This method is
+best if there is only one calibration image for all images
+to be processed.  This is almost always true for zero level and dark
+count images.  If no calibration image is specified by task parameter
+then calibration images in the input image list are identified and
+used.  This requires that the images have CCD image types recognized
+by the package.  This method is useful if one may simply say "*.imh"
+as the image list to process all images or if the images are broken
+up into groups, in "@" files for example, each with their own calibration
+frames.
+
+When an input image is processed the task first determines the processing
+parameters and calibration images.  If a requested operation has been
+done it is skipped and if all requested operations have been completed then
+no processing takes place.  When it determines that a calibration image
+is required it checks for the image from the task parameter and then
+for a calibration image of the proper type in the input list.
+
+Having
+selected a calibration image it checks if it has been processed by
+looking for the image header flag CCDPROC.  If it is not present then
+the calibration image is processed.  When any image has been processed
+the CCDPROC flag is added.  For images processed directly by \fBccdproc\fR
+the individual processing flags are checked even if the CCDPROC flag is
+present.  However, the automatic processing of the calibration images is
+only done if the CCDPROC flag is absent!  This is to make the task more
+efficient by not having to check every flag for every calibration image
+for every input image.  Thus, if additional processing
+steps are added after images have been partially reduced then input images
+will be processed for the new steps but calibration images will not be
+processed automatically.
+
+After the calibration images have been identified, and processed if
+necessary, the images may be cached in memory.  This is done when there
+are more than two input images (it is actually less efficient to
+cache the calibration images for one or two input images) and the parameter
+\fImax_cache\fR is greater than zero.  When caching, as many calibration
+images as allowed by the specified memory are read into memory and
+kept there for all the input images.  Cached images are, therefore,
+only read once from disk which reduces the amount of disk I/O.  This
+makes a modest decrease in the execution time.  It is not dramatic
+because the actual processing is fairly CPU intensive.
+
+Once the processing parameters and calibration images have been determined
+the input image is processed for all the desired operations in one
+step; i.e. there are no intermediate results or images.  This makes
+the task efficient.  The corrected image is output as a temporary image
+until the entire image has been processed.  When the image has been
+completely processed then the original image is deleted (or renamed
+using the specified backup prefix) and the corrected image replaces
+the original image.  Using a temporary image protects the data in the
+event of an abort or computer failure.  Keeping the original image name
+eliminates much of the record keeping and the need to generate new
+image names.
+.sh
+1. Fixpix
+Regions of bad lines and columns may be replaced by linear
+interpolation from neighboring lines and columns when the parameter
+\fIfixpix\fR is set.  The bad regions are specified in a bad pixel
+file.  The file consists of lines with four fields, the starting and
+ending columns and the starting and ending lines.  Any number of
+regions may be specified.  Comment lines beginning with the character
+'#' may be included.  If a comment line preceding the bad regions
+contains the word "untrimmed" then the coordinate system refers to the
+original format of the images; i.e.  before trimming.  If an image has
+been trimmed previously then the trim region specified in the image
+header is used to convert the coordinates in the bad pixel file to
+those of the trimmed image.  If the file does not contain the word
+"untrimmed" then the coordinate system must match that of the image
+being corrected; i.e. untrimmed coordinates if the image has not been
+trimmed and trimmed coordinates if the image has been trimmed.
+Standard bad pixel files should always be specified in terms of the
+original format.
+
+The bad pixel file may be specified explicitly with the parameter \fIfixfile\fR
+or indirectly if the parameter has the value "image".  In the latter case
+the instrument file must contain the name of the file.
+.sh
+2. Overscan
+If an overscan or prescan correction is specified (\fIoverscan\fR
+parameter) then the image section (\fIbiassec\fR parameter) is averaged
+along the readout axis (\fIreadaxis\fR parameter) to form a
+correction vector.  A function is fit to this vector and for each readout
+line (image line or column) the function value for that line is
+subtracted from the image line.  The fitting function is generally
+either a constant (polynomial of 1 term) or a high order function
+which fits the large scale shape of the overscan vector.  Bad pixel
+rejection is also used to eliminate cosmic ray events.  The function
+fitting may be done interactively using the standard \fBicfit\fR
+iteractive graphical curve fitting tool.  Regardless of whether the fit
+is done interactively, the overscan vector and the fit may be recorded
+for later review in a metacode plot file named by the parameter
+\fIccdred.plotfile\fR.  The mean value of the bias function is also recorded in
+the image header and log file.
+.sh
+3. Trim
+When the parameter \fItrim\fR is set the input image will be trimmed to
+the image section given by the parameter \fItrimsec\fR.  This trim
+should, of course, be the same as that used for the calibration images.
+.sh
+4. Zerocor
+After the readout bias is subtracted, as defined by the overscan or prescan
+region, there may still be a zero level bias.  This level may be two
+dimensional or one dimensional (the same for every readout line).  A
+zero level calibration is obtained by taking zero length exposures;
+generally many are taken and combined.  To apply this zero
+level calibration the parameter \fIzerocor\fR is set.  In addition if
+the zero level bias is only readout dependent then the parameter \fIreadcor\fR
+is set to reduce two dimensional zero level images to one dimensional
+images.  The zero level images may be specified by the parameter \fIzero\fR
+or given in the input image list (provided the CCD image type is defined).
+
+When the zero level image is needed to correct an input image it is checked
+to see if it has been processed and, if not, it is processed automatically.
+Processing of zero level images consists of bad pixel replacement,
+overscan correction, trimming, and averaging to one dimension if the
+readout correction is specified.
+.sh
+5. Darkcor
+Dark counts are subtracted by scaling a dark count calibration image to
+the same exposure time as the input image and subtracting.  The
+exposure time used is the dark time which may be different than the
+actual integration or exposure time.  A dark count calibration image is
+obtained by taking a very long exposure with the shutter closed; i.e.
+an exposure with no light reaching the detector.  The dark count
+correction is selected with the parameter \fIdarkcor\fR and the dark
+count calibration image is specified either with the parameter
+\fIdark\fR or as one of the input images.  The dark count image is
+automatically processed as needed.  Processing of dark count images
+consists of bad pixel replacement, overscan and zero level correction,
+and trimming.
+.sh
+6. Flatcor
+The relative detector pixel response is calibrated by dividing by a
+scaled flat field calibration image.  A flat field image is obtained by
+exposure to a spatially uniform source of light such as an lamp or
+twilight sky.  Flat field images may be corrected for the spectral
+signature in spectroscopic images (see \fBresponse\fR and
+\fBapnormalize\fR), or for iillumination effects (see \fBmkillumflat\fR
+or \fBmkskyflat\fR).  For more on flat fields and iillumination corrections
+see \fBflatfields\fR.  The flat field response is dependent on the
+wavelength of light so if different filters or spectroscopic wavelength
+coverage are used a flat field calibration for each one is required.
+The different flat fields are  automatically selected by a subset
+parameter (see \fBsubsets\fR).
+
+Flat field calibration is selected with the parameter \fBflatcor\fR
+and the flat field images are specified with the parameter \fBflat\fR
+or as part of the input image list.  The appropriate subset is automatically
+selected for each input image processed.  The flat field image is
+automatically processed as needed.  Processing consists of bad pixel
+replacement, overscan subtraction, zero level subtraction, dark count
+subtraction, and trimming.  Also if a scan mode is used and the
+parameter \fIscancor\fR is specified then a scan mode correction is
+applied (see below).  The processing also computes the mean of the
+flat field image which is used later to scale the flat field before
+division into the input image.  For scan mode flat fields the ramp
+part is included in computing the mean which will affect the level
+of images processed with this flat field.  Note that there is no check for
+division by zero in the interest of efficiency.  If division by zero
+does occur a fatal error will occur.  The flat field can be fixed by
+replacing small values using a task such as \fBimreplace\fR or
+during processing using the \fIminreplace\fR parameter.  Note that the
+\fIminreplace\fR parameter only applies to flat fields processed by
+\fBccdproc\fR.
+.sh
+7. Illumcor
+CCD images processed through the flat field calibration may not be
+completely flat (in the absence of objects).  In particular, a blank
+sky image may still show gradients.  This residual nonflatness is called
+the iillumination pattern.  It may be introduced even if the detector is
+uniformly illuminated by the sky because the flat field lamp
+iillumination may be nonuniform.  The iillumination pattern is found from a
+blank sky, or even object image, by heavily smoothing and rejecting
+objects using sigma clipping.  The iillumination calibration image is
+divided into the data being processed to remove the iillumination
+pattern.  The iillumination pattern is a function of the subset so there
+must be an iillumination correction image for each subset to be
+processed.  The tasks \fBmkillumcor\fR and \fBmkskycor\fR are used to
+create the iillumination correction images.  For more on iillumination
+corrections see \fBflatfields\fR.
+
+An alternative to treating the iillumination correction as a separate
+operation is to combine the flat field and iillumination correction
+into a corrected flat field image before processing the object
+images.  This will save some processing time but does require creating
+the flat field first rather than correcting the images at the same
+time or later.  There are two methods, removing the large scale
+shape of the flat field and combining a blank sky image iillumination
+with the flat field.  These methods are discussed further in the
+tasks which create them; \fBmkillumcor\fR and \fBmkskycor\fR.
+.sh
+8. Fringecor
+There may be a fringe pattern in the images due to the night sky lines.
+To remove this fringe pattern a blank sky image is heavily smoothed
+to produce an iillumination image which is then subtracted from the
+original sky image.  The residual fringe pattern is scaled to the
+exposure time of the image to be fringe corrected and then subtracted.
+Because the intensity of the night sky lines varies with time an
+additional scaling factor may be given in the image header.
+The fringe pattern is a function of the subset so there must be
+a fringe correction image for each subset to be processed.
+The task \fBmkfringecor\fR is used to create the fringe correction images.
+.sh
+9. Readcor
+If a zero level correction is desired (\fIzerocor\fR parameter)
+and the parameter \fIreadcor\fR is yes then a single zero level
+correction vector is applied to each readout line or column.  Use of a
+readout correction rather than a two dimensional zero level image
+depends on the nature of the detector or if the CCD is operated in
+longscan mode (see below).  The readout correction is specified by a
+one dimensional image (\fIzero\fR parameter) and the readout axis
+(\fIreadaxis\fR parameter).  If the zero level image is two dimensional
+then it is automatically processed to a one dimensional image by
+averaging across the readout axis.  Note that this modifies the zero
+level calibration image.
+.sh
+10. Scancor
+CCD detectors may be operated in several modes in astronomical
+applications.  The most common is as a direct imager where each pixel
+integrates one point in the sky or spectrum.  However, the design of most CCD's
+allows the sky to be scanned across the CCD while shifting the
+accumulating signal at the same rate.  \fBCcdproc\fR provides for two
+scanning modes called "shortscan" and "longscan".  The type of scan
+mode is set with the parameter \fIscanmode\fR.
+
+In "shortscan" mode the detector is scanned over a specified number of
+lines (not necessarily at sideral rates).  The lines that scroll off
+the detector during the integration are thrown away.  At the end of the
+integration the detector is read out in the same way as an unscanned
+observation.  The advantage of this mode is that the small scale flat
+field response is averaged in one dimension over the number of lines
+scanned.  A flat field may be observed in the same way in which case
+there is no difference in the processing from unscanned imaging and the
+parameter \fIscancor\fR should be no.  However, one obtains an increase
+in the statistical accuracy of the flat fields if they are not scanned
+during the observation but digitally scanned during the processing.  In
+shortscan mode with \fIscancor\fR set to yes, flat field images are
+digitally scanned, if needed, by the specified number of scan lines
+(\fInscan\fR parameter).
+
+In "longscan" mode the detector is continuously read out to produce
+an arbitrarily long strip.  Provided data which has not passed over
+the entire detector is thrown away, the flat field corrections will
+be one dimensional.  If \fIscancor\fR is specified and the
+scan mode is "longscan" then a one dimensional flat field correction
+will be applied.  If the specified flat field (\fIflat\fR parameter)
+is a two dimensional image then when the flat field image is processed
+it will be averaged across the readout axis to form a one dimensional
+correction image.
+.sh
+11. Processing Steps
+The following describes the steps taken by the task.  This detailed
+outline provides the most detailed specification of the task.
+
+.ls 5 (1)
+An image to be processed is first checked that it is of the specified
+CCD image type.  If it is not the desired type then go on to the next image.
+.le
+.ls (2)
+A temporary output image is created of the specified pixel data type
+(\fBccdred.pixeltype\fR).  The header parameters are copied from the
+input image.
+.le
+.ls (3)
+If trimming is specified and the image has not been trimmed previously,
+the trim section is determined.
+.le
+.ls (4)
+If bad pixel replacement is specified and this has not been done
+previously, the bad pixel file is determined either from the task
+parameter or the instrument translation file.  The bad pixel regions
+are read.  If the image has been trimmed previously and the bad pixel
+file contains the word "untrimmed" then the bad pixel coordinates are
+translated to those of the trimmed image.
+.le
+.ls (5)
+If an overscan correction is specified and this correction has not been
+applied, the overscan section is averaged along the readout axis.  If
+trimming is to be done the overscan section is trimmed to the same
+limits.  A function is fit either interactively or noninteractively to
+the overscan vector.  The function is used to produce the overscan
+vector to be subtracted from the image.  This is done in real
+arithmetic.
+.le
+.ls (6)
+If the image is a zero level image go to processing step 12.
+If a zero level correction is desired and this correction has not been
+performed, find the zero level calibration image.  If the zero level
+calibration image has not been processed it is processed at this point.
+This is done by going to processing step 1 for this image.  After the
+calibration image has been processed, processing of the input image
+continues from this point.
+The processed calibration image may be
+cached in memory if it has not been previously and if there is enough memory.
+.le
+.ls (7)
+If the image is a dark count image go to processing step 12.
+If a dark count correction is desired and this correction has not been
+performed, find the dark count calibration image.  If the dark count
+calibration image has not been processed it is processed at this point.
+This is done by going to processing step 1 for this image.  After the
+calibration image has been processed, processing of the input image
+continues from this point.  The ratio of the input image dark time
+to the dark count image dark time is determined to be multiplied with
+each pixel of the dark count image before subtracting from the input
+image.
+The processed calibration image may be
+cached in memory if it has not been previously and if there is enough memory.
+.le
+.ls (8)
+If the image is a flat field image go to processing step 12.  If a flat
+field correction is desired and this correction has not been performed,
+find the flat field calibration image of the appropriate subset.  If
+the flat field calibration image has not been processed it is processed
+at this point.  This is done by going to processing step 1 for this
+image.  After the calibration image has been processed, processing of
+the input image continues from this point.  The mean of the image
+is determined from the image header to be used for scaling.  If no
+mean is found then a unit scaling is used.
+The processed calibration image may be
+cached in memory if it has not been previously and if there is enough memory.
+.le
+.ls (9)
+If the image is an iillumination image go to processing step 12.  If an
+iillumination correction is desired and this correction has not been performed,
+find the iillumination calibration image of the appropriate subset.
+The iillumination image must have the "mkillum" processing flag or the
+\fBccdproc\fR will abort with an error.  The mean of the image
+is determined from the image header to be used for scaling.  If no
+mean is found then a unit scaling is used.  The processed calibration
+image may be
+cached in memory if it has not been previously and there is enough memory.
+.le
+.ls (10)
+If the image is a fringe image go to processing step 12.  If a fringe
+correction is desired and this correction has not been performed,
+find the fringe calibration image of the appropriate subset.
+The iillumination image must have the "mkfringe" processing flag or the
+\fBccdproc\fR will abort with an error.  The ratio of the input
+image exposure time to the fringe image exposure time is determined.
+If there is a fringe scaling in the image header then this factor
+is multiplied by the exposure time ratio.  This factor is used
+for scaling.  The processed calibration image may be
+cached in memory if it has not been previously and there is enough memory.
+.le
+.ls (11)
+If there are no processing operations flagged, delete the temporary output
+image, which has been opened but not used, and go to 14.
+.le
+.ls (12)
+The input image is processed line by line with trimmed lines ignored.
+A line of the input image is read.  Bad pixel replacement and trimming
+is applied to the image.  Image lines from the calibration images
+are read from disk or the image cache.  If the calibration is one
+dimensional (such as a readout zero
+level correction or a longscan flat field correction) then the image
+vector is read only once.  Note that IRAF image I/O is buffered for
+efficiency and accessing a line at a time does not mean that image
+lines are read from disk a line at a time.  Given the input line, the
+calibration images, the overscan vector, and the various scale factors
+a special data path for each combination of corrections is used to
+perform all the processing in the most efficient manner.  If the
+image is a flat field any pixels less than the \fIminreplace\fR
+parameter are replaced by that minimum value.  Also a mean is
+computed for the flat field and stored as the CCDMEAN keyword.
+.le
+.ls (13)
+The input image is deleted or renamed to a backup image.  The temporary
+output image is renamed to the input image name.
+.le
+.ls (14)
+If the image is a zero level image and the readout correction is specified
+then it is averaged to a one dimensional readout correction.
+.le
+.ls (15)
+If the image is a flat field image and the scan mode correction is specified
+then the correction is applied.  For shortscan mode a
+modified two dimensional image is produced while for longscan mode a
+one dimensional average image is produced.
+.le
+.ls (16)
+The processing is completed and either the next input image is processed
+beginning at step 1 or, if it is a calibration image which is being
+processed for an input image, control returns to the step which initiated
+the calibration image processing.
+.le
+.sh
+12. Processing Arithmetic
+The \fBccdproc\fR task has two data paths, one for real image pixel datatypes
+and one for short integer pixel datatype.  In addition internal arithmetic
+is based on the rules of FORTRAN.  For efficiency there is
+no checking for division by zero in the flat field calibration.
+The following rules describe the processing arithmetic and data paths.
+
+.ls (1)
+If the input, output, or any calibration image is of type real the
+real data path is used.  This means all image data is converted to
+real on input.  If all the images are of type short all input data
+is kept as short integers.  Thus, if all the images are of the same type
+there is no datatype conversion on input resulting in greater
+image I/O efficiency.
+.le
+.ls (2)
+In the real data path the processing arithmetic is always real and,
+if the output image is of short pixel datatype, the result
+is truncated.
+.le
+.ls (3)
+The overscan vector and the scale factors for dark count, flat field,
+iillumination, and fringe calibrations are always of type real.  Therefore,
+in the short data path any processing which includes these operations
+will be coerced to real arithmetic and the result truncated at the end
+of the computation.
+.le
+.sh
+13. In the Absence of Image Header Information
+The tasks in the \fBccdred\fR package are most convenient to use when
+the CCD image type, subset, and exposure time are contained in the
+image header.  The ability to redefine which header parameters contain
+this information makes it possible to use the package at many different
+observatories (see \fBinstruments\fR).  However, in the absence of any
+image header information the tasks may still be used effectively.
+There are two ways to proceed.  One way is to use \fBccdhedit\fR
+to place the information in the image header.
+
+The second way is to specify the processing operations more explicitly
+than is needed when the header information is present.  The parameter
+\fIccdtype\fR is set to "" or to "none".  The calibration images are
+specified explicitly by task parameter since they cannot be recognized
+in the input list.  Only one subset at a time may be processed.
+
+If dark count and fringe corrections are to be applied the exposure
+times must be added to all the images.  Alternatively, the dark count
+and fringe images may be scaled explicitly for each input image.  This
+works because the exposure times default to 1 if they are not given in
+the image header.
+.ih
+EXAMPLES
+The user's \fBguide\fR presents a tutorial in the use of this task.
+
+1. In general all that needs to be done is to set the task parameters
+and enter
+
+	cl> ccdproc *.imh &
+
+This will run in the background and process all images which have not
+been processed previously.
+.ih
+TIME REQUIREMENTS
+.nf
+o SUN-3, 15 MHz 68020 with 68881 floating point hardware (no FPA)
+o 8 Mb RAM, 2 Fuji Eagle disks.
+o Input images = 544 x 512 short
+o Output image = 500 x 500 real
+o Operations are overscan subtraction (O), trimming to 500x500 (T),
+  zero level subtraction (Z), dark count scaling and subtraction (D),
+  and flat field scaling and subtraction (F).
+o UNIX statistics
+  (user, system, and clock time, and misc. memory and i/o statistics):
+
+[OTF] One calibration image and 9 object images:
+No caching:  110.6u 25.5s 3:18 68% 28+ 40K 3093+1645io   9pf+0w
+Caching:     111.2u 23.0s 2:59 74% 28+105K 2043+1618io   9pf+0w
+
+[OTZF] Two calibration images and 9 object images:
+No caching:  119.2u 29.0s 3:45 65% 28+ 50K 4310+1660io   9pf+0w
+Caching:     119.3u 23.0s 3:07 75% 28+124K 2179+1601io   9pf+0w
+
+[OTZDF] Three calibration images and 9 object images:
+No caching:  149.4u 31.6s 4:41 64% 28+ 59K 5501+1680io  19pf+0w
+Caching:     151.5u 29.0s 4:14 70% 27+227K 2346+1637io 148pf+0w
+
+[OTZF] 2 calibration images and 20 images processed:
+No caching:  272.7u 63.8u 8:47 63% 28+ 50K 9598+3713io  12pf+0w
+Caching:     271.2u 50.9s 7:00 76% 28+173K 4487+3613io  51pf+0w
+.fi
+.ih
+SEE ALSO
+.nf
+instruments, ccdtypes, flatfields, icfit, ccdred, guide, mkillumcor,
+mkskycor, mkfringecor
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/ccdred.hlp b/noao/imred/quadred/src/quad/doc/ccdred.hlp
new file mode 100644
index 00000000..0300bd38
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/ccdred.hlp
@@ -0,0 +1,98 @@
+.help package Jun87 noao.imred
+.ih
+NAME
+ccdred -- CCD image reduction package
+.ih
+USAGE
+ccdred
+.ih
+PARAMETERS
+.ls pixeltype = "real real"
+Output pixel datatype and calculation datatype.  When images are processed
+or created the output pixel datatype is determined by this parameter.
+The allowed types are "short" for short integer, and "real" for real
+floating point.  Note that if short input images are processed into
+real images the disk space required will generally increase.
+The calculation datatypes are also short and real with a default of
+real if none is specified.
+.le
+.ls verbose = no
+Print log information to the standard output?
+.le
+.ls logfile = "logfile"
+Text log file.  If no filename is specified then no log file is kept.
+.le
+.ls plotfile = ""
+Log metacode plot file for the overscan bias vector fits.  If
+no filename is specified then no metacode plot file is kept.
+.le
+.ls backup = ""
+Backup prefix for backup images.  If no prefix is specified then no backup
+images are kept when processing.  If specified then the backup image
+has the specified prefix.
+.le
+.ls instrument = ""
+CCD instrument translation file.  This is usually set with \fBsetinstrument\fR.
+.le
+.ls ssfile = "subsets"
+Subset translation file used to define the subset identifier.  See
+\fBsubsets\fR for more.
+.le
+.ls graphics = "stdgraph"
+Interactive graphics output device when fitting the overscan bias vector.
+.le
+.ls cursor = ""
+Graphics cursor input.  The default is the standard graphics cursor.
+.le
+.ls version = "June 1987"
+Package version.
+.le
+.ih
+DESCRIPTION
+The CCD reduction package is loaded when this command is entered.  The
+package contains parameters which affect the operation of the tasks
+it defines.  When images are processed or new image are created the
+output pixel datatype is that specified by the parameter \fBpixeltype\fR.
+Note that CCD processing replaces the original image by the processed
+image so the pixel type of the CCD images may change during processing.
+It is unlikely that real images will be processed to short images but
+the reverse is quite likely.  Processing images from short to real
+pixel datatypes will generally increase the amount of disk space
+required (a factor of 2 on most computers).
+
+The tasks produce log output which may be printed on the standard
+output (the terminal unless redirected) and appended to a file.  The
+parameter \fIverbose\fR determines whether processing information
+is printed.  This may be desirable initially, but when using background
+jobs the verbose output should be turned off.  The user may look at
+the end of the log file (for example with \fBtail\fR) to determine
+the status of the processing.
+
+The package was designed to work with data from many different observatories
+and instruments.  In order to accomplish this an instrument translation
+file is used to define a mapping between the package parameters and
+the particular image header format.  The instrument translation file
+is specified to the package by the parameter \fIinstrument\fR.  This
+parameter is generally set by the task \fBsetinstrument\fR.  The other
+file used is a subset file.  This is generally created and maintained
+by the package and the user need not do anything.  For more sophisticated
+users see \fBinstruments\fR and \fBsubsets\fR.
+
+The package has very little graphics
+output.  The exception is the overscan bias subtraction.  The bias
+vector is logged in the metacode plot file if given.  The plot file
+may be examined with the tasks in the \fBplot\fR package such as
+\fBgkimosaic\fR.  When interactively fitting the overscan vector
+the graphics input and output devices must be specified.  The defaults
+should apply in most cases.
+
+Because processing replaces the input image by the processed image it
+may be desired to save the original image.  This may be done by
+specifying a backup prefix with the parameter \fIbackup\fR.  For
+example, if the prefix is "orig" and the image is "ccd001", the backup
+image will be "origccd001".  The prefix may be a directory but it must
+end with '/' or '$' (for logical directories).
+.ih
+SEE ALSO
+instruments, setinstrument, subsets
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/ccdred.ms b/noao/imred/quadred/src/quad/doc/ccdred.ms
new file mode 100644
index 00000000..645514ec
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/ccdred.ms
@@ -0,0 +1,787 @@
+.RP
+.TL
+The IRAF CCD Reduction Package -- CCDRED
+.AU
+Francisco Valdes
+.AI
+IRAF Group - Central Computer Services
+.K2
+P.O. Box 26732, Tucson, Arizona 85726
+September 1987
+.AB
+The IRAF\(dg CCD reduction package, \fBccdred\fR, provides tools
+for the easy and efficient reduction of CCD images.  The standard
+reduction operations are replacement of bad pixels, subtraction of an
+overscan or prescan bias, subtraction of a zero level image,
+subtraction of a dark count image, division by a flat field calibration
+image, division by an illumination correction, subtraction of a fringe
+image, and trimming unwanted lines or columns.  Another common
+operation provided by the package is scaling and combining images with
+a number of algorithms for rejecting cosmic rays.  Data in the image
+header is used to make the reductions largely automated and
+self-documenting though the package may still be used in the absence of
+this data.  Also a translation mechanism is used to relate image header
+parameters to those used by the package to allow data from a variety of
+observatories and instruments to be processed.  This paper describes
+the design goals for the package and the main tasks and algorithms
+which satisfy these goals.
+.PP
+This paper is to be published as part of the proceedings of the
+Santa Cruz Summer Workshop in Astronomy and Astrophysics,
+\fIInstrumentation for Ground-Based Optical Astronomy:  Present and
+Future\fR, edited by Lloyd B. Robinson and published by
+Springer-Verlag.
+.LP
+\(dgImage Reduction and Analysis Facility (IRAF), a software system
+distributed by the National Optical Astronomy Observatories (NOAO).
+.AE
+.NH
+Introduction
+.PP
+The IRAF CCD reduction package, \fBccdred\fR, provides tools
+for performing the standard instrumental corrections and calibrations
+to CCD images.  The major design goals were:
+.IP
+.nf
+\(bu To be easy to use
+\(bu To be largely automated
+\(bu To be image header driven if the data allows
+\(bu To be usable for a variety of instruments and observatories
+\(bu To be efficient and capable of processing large volumes of data
+.fi
+.LP
+This paper describes the important tasks and algorithms and shows how
+these design goals were met.  It is not intended to describe every
+task, parameter, and usage in detail; the package has full
+documentation on each task plus a user's guide.
+.PP
+The standard CCD correction and calibration operations performed are
+replacement of bad columns and lines by interpolation from neighboring
+columns and lines, subtraction of a bias level determined from overscan
+or prescan columns or lines, subtraction of a zero level using a zero
+length exposure calibration image, subtraction of a dark count
+calibration image appropriately scaled to the dark time exposure of the
+image, division by a scaled flat field calibration image, division by
+an illumination image (derived from a blank sky image), subtraction of
+a scaled fringe image (also derived from a blank sky image), and
+trimming the image of unwanted lines or columns such as the overscan
+strip.  The processing may change the pixel datatype on disk (IRAF allows
+seven image datatypes); usually from 16 bit integer to real format.
+Two special operations are also supported for scan mode and one
+dimensional zero level and flat field calibrations; i.e. the same
+calibration is applied to each CCD readout line.  Any set of operations
+may be done simultaneously over a list of images in a highly efficient
+manner.  The reduction operations are recorded in the image header and
+may also be logged on the terminal and in a log file.
+.PP
+The package also provides tools for combining multiple exposures
+of object and calibration images to improve the statistical accuracy of
+the observations and to remove transient bad pixels.  The combining
+operation scales images of different exposure times, adjusts for
+variable sky background, statistically weights the images by their
+signal-to-noise, and provides a number of useful algorithms for
+detecting and rejecting transient bad pixels.
+.PP
+Other tasks are provided for listing reduction information about
+the images, deriving secondary calibration images (such as sky
+corrected flat fields or illumination correction images), and easily
+setting the package parameters for different instruments.
+.PP
+This paper is organized as follows.  There is a section giving an
+overview of how the package is used to reduce CCD data.  This gives the
+user's perspective and illustrates the general ease of use.  The next
+section describes many of the features of the package contributing to
+its ease of use, automation, and generality.  The next two sections
+describe the major tools and algorithms in some detail.  This includes
+discussions about achieving high efficiency.  Finally the status of the
+package and its use at NOAO is given.  References to additional
+documentation about IRAF and the CCD reduction package and an appendix
+listing the individual tasks in the package are found at the end of
+this paper.
+.NH
+A User's Overview
+.PP
+This section provides an overview of reducing data with the IRAF CCD
+reduction package.  There are many variations in usage depending on the
+type of data, whether the image headers contain information about the
+data which may be used by the tasks, and the scientific goal.  Only a
+brief example is given.  A more complete discussion of usage and
+examples is given in \fIA User's Guide to the IRAF CCDRED Package\fR.
+The package was developed within the IRAF system and so makes use of
+all the sophisticated features provided.  These features are also
+summarized here for those not familiar with IRAF since they are an
+important part of using the package.
+.PP
+Since the IRAF system is widely distributed and runs on a wide variety
+of computers, the site of the CCD reductions might be at the telescope,
+a system at the observatory provided for this purpose, or at the
+user's home computer.  The CCD images to be processed are either
+available immediately as the data is taken, transferred from the data taking
+computer via a network link (the method adopted at NOAO), or transferred
+to the reduction computer via a medium such as magnetic tape in FITS
+format.  The flexibility in reduction sites and hardware is one of the
+virtues of the IRAF-based CCD reduction package.
+.PP
+IRAF tasks typically have a number of parameters which give the user
+control over most aspects of the program.  This is possible since the
+parameters are kept in parameter files so that the user need not enter
+a large number of parameters every time the task is run.  The user may
+change any of these parameters as desired in several ways, such as by
+explicit assignment and using an easy to learn and use,
+fill-in-the-value type of screen editor.  The parameter values are
+\fIlearned\fR so that once a user sets the values they are maintained
+until the user changes them again; even between login sessions.
+.PP
+The first step in using the CCD reduction package is to set the default
+processing parameters for the data to be reduced.  These parameters include
+a database file describing the image header keyword translations and
+default values, the processing operations desired (operations
+required vary with instrument and observer), the calibration image names,
+and certain special parameters for special types of observations such
+as scan mode.  A special script task (a command procedure) is available
+to automatically set the default values, given the instrument name, to standard
+values defined by the support staff.  Identifying the instrument in this
+way may be all the novice user need do though most people quickly learn
+to adjust parameters at will.
+.PP
+As an example suppose there is an instrument identified as \fLrca4m\fR
+for an RCA CCD at the NOAO 4 meter telescope.  The user gives the command
+
+.ft L
+    cl> setinstrument rca4m
+.ft R
+
+which sets the default parameters to values suggested by the support staff
+for this instrument.  The user may then change these suggested values if
+desired.  In this example the processing switches are set to perform
+overscan bias subtraction, zero level image subtraction, flat fielding,
+and trimming.
+.PP
+The NOAO image headers contain information identifying the type of
+image, such as object, zero level, and flat field, the filter used to
+match flat fields with object images, the location of the overscan bias
+data, the trim size for the data, and whether the image has been
+processed.  With this information the user need not worry about
+selecting images, pairing object images with calibration images, or
+inadvertently reprocessing an image.
+.PP
+The first step is to combine multiple zero level and flat field observations
+to reduce the effects of statistical noise.  This is done by the
+commands
+
+.nf
+.ft L
+	cl> zerocombine *.imh
+	cl> flatcombine *.imh
+.ft R
+.fi
+
+The "cl> " is the IRAF command language prompt.  The first command says
+look through all the images and combine the zero level images.  The
+second command says look through all the images and combine the flat
+field images by filter.  What could be simpler?  Some \fIhidden\fR (default)
+parameters the user may modify are the combined image name, whether to
+process the images first, and the type of combining algorithm to use.
+.PP
+The next step is to process the images using the combined calibration
+images.  The command is
+
+.ft L
+	cl> ccdproc *.imh
+.ft R
+
+This command says look through all the images, find the object images,
+find the overscan data based on the image header and subtract the
+bias, subtract the zero level calibration image, divide by the flat field
+calibration image, and trim the bias data and edge lines and columns.
+During this operation the task recognizes that the
+zero level and flat field calibration images have not been processed
+and automatically processes them when they are needed.  The log output
+of this task, which may be to the terminal, to a file, or both, shows
+how this works.
+
+.nf
+.ft L
+  ccd003: Jun  1 15:12 Trim data section is [3:510,3:510]
+  ccd003: Jun  1 15:12 Overscan section is [520:540,*], mean=485.0
+  Dark:   Jun  1 15:12 Trim data section is [3:510,3:510]
+  Dark:   Jun  1 15:13 Overscan section is [520:540,*], mean=484.6
+  ccd003: Jun  1 15:13 Dark count image is Dark.imh
+  FlatV:  Jun  1 15:13 Trim data section is [3:510,3:510]
+  FlatV:  Jun  1 15:14 Overscan section is [520:540,*], mean=486.4
+  ccd003: Jun  1 15:15 Flat field image is FlatV.imh, scale=138.2
+  ccd004: Jun  1 15:16 Trim data section is [3:510,3:510]
+  ccd004: Jun  1 15:16 Overscan section is [520:540,*], mean=485.2
+  ccd004: Jun  1 15:16 Dark count image is Dark.imh
+  ccd004: Jun  1 15:16 Flat field image is FlatV.imh, scale=138.2
+                \fI<... more ...>\fL
+  ccd013: Jun  1 15:22 Trim data section is [3:510,3:510]
+  ccd013: Jun  1 15:23 Overscan section is [520:540,*], mean=482.4
+  ccd013: Jun  1 15:23 Dark count image is Dark.imh
+  FlatB:  Jun  1 15:23 Trim data section is [3:510,3:510]
+  FlatB:  Jun  1 15:23 Overscan section is [520:540,*], mean=486.4
+  ccd013: Jun  1 15:24 Flat field image is FlatB.imh, scale=132.3
+                \fI<... more ...>\fL
+.ft R
+.fi
+
+.PP
+The log gives the name of the image and a time stamp for each entry.
+The first image is ccd003.  It is to be trimmed to the specified
+size given as an \fIimage section\fR, an array notation used commonly
+in IRAF to specify subsections of images.  The location of the
+overscan data is also given by an image section which, in this case,
+was found in the image header.  The mean bias level of the overscan
+is also logged though the overscan is actually a function of the
+readout line with the order of the function selected by the user.
+.PP
+When the task comes to subtracting the zero level image it first
+notes that the calibration image has not been processed and switches
+to processing the zero level image.  Since it knows it is a zero level
+image the task does not attempt to zero level or flat field correct
+this image.  After the zero level image has been processed the task
+returns to the object image only to find that the flat field image
+also has not been processed.  It determines that the object image was
+obtained with a V filter and selects the flat field image having the same
+filter.  The flat field image is processed through the zero level correction
+and then the task again returns to the object image, ccd003, which it
+finishes processing.
+.PP
+The next image, ccd004, is also a V filter
+observation.  Since the zero level and V filter flat field have been
+processed the object image is processed directly.  This continues
+for all the object images except for a detour to process the B filter flat
+field when the task first encounters a B filter object image.
+.PP
+In summary, the basic usage of the CCD reduction package is quite simple.
+First, the instrument is identified and some parameters for the data
+are set.  Calibration images are then combined if needed.  Finally,
+the processing is done with the simple command
+
+.ft L
+    cl> ccdproc *.imh&
+.ft R
+
+where the processing is performed as a \fIbackground job\fR in this example.
+This simplicity was a major goal of the package.
+.NH
+Features of the Package
+.PP
+This section describes some of the special features of the package
+which contribute to its ease of use, generality, and efficiency.
+The major criteria for ease of use are to minimize the user's record keeping
+involving input and output image names, the types of images, subset
+parameters such as filters which must be kept separate, and the state
+of processing of each image.  The goal is to allow input images to
+be specified using simple wildcards, such as "*.imh" to specify all
+images, with the knowledge that the task will only operate on images
+for which it makes sense.  To accomplish this the tasks must be able to
+determine the type of image, subset, and the state of processing from
+the image itself.  This is done by making use of image header parameters.
+.PP
+For generality the package does not require any image header information
+except the exposure time.  It is really not very much more difficult to
+reduce such data.  Mainly, the user must be more explicit about specifying
+images and setting task parameters or add the information to the image
+headers.  Some default header information may also be set in the image
+header translation file (discussed below).
+.PP
+One important image header parameter is the image type.  This
+discriminates between object images and various types of calibration
+images such as flat field, zero level, dark count, comparison arcs,
+illumination, and fringe images.  This information is used in two
+ways.  For most of the tasks the user may select that only one type of
+image be considered.  Thus, all the flat field images may be selected
+for combining or only the processing status of the object images be
+listed.  The second usage is to allow the processing tasks to identify
+the standard calibration images and apply only those operations which
+make sense.  For example, flat field images are not divided by a
+flat field.  This allows the user to set the processing operations
+desired for the object images without fear of misprocessing the
+calibration images.  The image type is also used to automatically
+select calibration images from a list of images to be processed instead
+of explicitly identifying them.
+.PP
+A related parameter specifies the subset.  For certain operations the
+images must have a common value for this parameter.  This parameter is
+often the filter but it may also apply to a grating or aperture, for example.
+The subset parameter is used to identify the appropriate flat field
+image to apply to an image or to select common flat fields to be combined
+into a higher quality flat field.  This is automatic and the user need not
+keep track of which image was taken with which filter or grating.
+.PP
+The other important image header parameters are the processing flags.
+These identify when an image has been processed and also act as a history
+of the operation including calibration images used and other parameter
+information.  The usage of these parameters is obvious; it allows the
+user to include processed images in a wildcard list knowing that the
+processing will not be repeated and to quickly determine the processing
+status of the image.
+.PP
+Use of image header parameters often ties the software to the a
+particular observatory.  To maintain generality and usefulness for data
+other than that at NOAO, the CCD reduction package was designed to
+provide a translation between parameters requested by the package and
+those actually found in the image header.  This translation is defined
+in a simple text file which maps one keyword to another and also gives
+a default value to be used if the image header does not include a
+value.  In addition the translation file maps the arbitrary strings
+which may identify image types to the standard types which the package
+recognizes.  This is a relatively simple scheme and does not allow for
+forming combinations or for interpreting values which are not simple
+such as embedding an exposure time as part of a string.  A more complex
+translation scheme may prove desirable as experience is gained with
+other types of image header formats, but by then a general header translation
+ability and/or new image database structure may be a standard IRAF
+feature.
+.PP
+This feature has proven useful at NOAO.  During the course of
+developing the package the data taking system was modernized by
+updating keywords and adding new information in the image headers,
+generally following the lines laid out by the \fBccdred\fR package.
+However, there is a period of transition and it is also desirable to
+reduce preexisting data.  There are several different formats for this
+data.  The header translation files make coping with these different
+formats relatively easy.
+.PP
+A fundamental aspect of the package is that the processing
+modifies the images.  In other words, the reduction operations are
+performed directly on the image.  This "feature" further simplifies
+record keeping, frees the user from having to form unique output image
+names, and minimizes the amount of disk space required.  There
+are two safety features in this process.  First, the modifications do
+not take effect until the operation is completed on the image.  This
+allows the user to abort the task without leaving the image data in a
+partially processed state and protects data if the computer
+crashes.  The second feature is that there is a parameter which may be
+set to make a backup of the input data with a particular prefix; for
+example "b", "orig", or "imdir$" (a logical directory prefix).  This
+backup feature may be used when there is sufficient disk space, when
+learning to use the package, or just to be cautious.
+.PP
+In a similar effort to efficiently manage disk space, when combining
+images into a master object or calibration image, there is an option to
+delete the input images upon completion of the combining operation.
+Generally this is desirable when there are many calibration exposures,
+such as zero level or flat field images, which are not used after they
+are combined into a final calibration image.
+.PP
+The goal of generality for many instruments at
+different observatories inherently conflicts with the goal of ease of
+use.  Generality requires many parameters and options.  This is
+feasible in the CCD reduction package, as well as the other IRAF packages,
+because of the IRAF parameter handling mechanism.  In \fBccdred\fR
+there still remains the problem of setting the parameters appropriately
+for a particular instrument, image header format, and observatory.
+.PP
+To make this convenient there is a task, \fBsetinstrument\fR, that,
+based on an instrument name, runs a setup script for the instrument.
+An example of this task was given in the previous section.
+The script may do any type of operation but mainly it sets default
+parameters.  The setup scripts are generally created by the support staff
+for the instrument.  The combination of the setup script and the
+instrument translation file make the package, in a sense, programmable
+and achieves the desired instrument/observatory generality with ease of use.
+.NH
+CCD Processing
+.PP
+This section describes in some detail how the CCD processing is performed.
+The task which does the basic CCD processing is call \fBccdproc\fR.
+From the point of view of usage the task is very simple but a great deal
+is required to achieve this simplicity.  The approach we take in describing
+the task is to follow the flow of control as the task runs with digressions
+as appropriate.
+.PP
+The highest level of control is a loop over the input images; all the
+operations are performed successively on each image.  It is common for
+IRAF tasks which operate on individual images to allow the operation to
+be repeated automatically over a list of input images.  This is important
+in the \fBccdred\fR package because data sets are often large and the
+processing is generally the same for each image.  It would be tedious
+to have to give the processing command for each image to be processed.
+If an error occurs while processing an image the error is
+printed as a warning and processing continues with the next image.
+This provides protection primarily against mistyped or nonexistent images.
+.PP
+Before the first image is processed the calibration images are
+identified.  There are two ways to specify calibration images;
+explicitly via task parameters or implicitly as part of the list of
+images to be processed.  Explicitly identifying calibration images
+takes precedence over calibration images in the input list.  Specifying
+calibration images as part of the input image list requires that the
+image types can be determined from the image header.  Using the input
+list provides a mechanism for breaking processing up into sets of
+images (possibly using files containing the image names for each set)
+each having their own calibration images.  One can, of course,
+selectively specify input and calibration images, but whenever possible
+one would like to avoid having to specify explicit images to process
+since this requires record keeping by the user.
+.PP
+The first step in processing an image is to check that it is of the
+appropriate image type.  The user may select to process images of only
+one type.  Generally this is object images since calibration images are
+automatically processed as needed.  Images which are not of the desired
+type are skipped and the next image is considered.
+.PP
+A temporary output image is created next.  The output pixel datatype on
+disk may be changed at this point as selected by the user.
+For example it is common for the raw CCD images to be digitized as 16
+bit integers but after calibration it is sometimes desirable to have
+real format pixels.  If no output pixel datatype is specified the
+output image takes the same pixel datatype as the input image.  The
+processing is done by operating on the input image and writing the
+results to a temporary output image.  When the processing is complete
+the output image replaces the input image.  This gives the effect of
+processing the images in place but with certain safeguards.  If the
+computer crashes or the processing is interrupted the integrity of the
+input image is maintained.  The reasons for chosing to process the
+images in this way are to avoid having to generate new image names (a
+tiresome record keeping process for the user), to minimize disk
+usage, and generally the unprocessed images are not used once they have
+been processed.  When dealing with large volumes of data these reasons
+become fairly important.  However, the user may specify a backup prefix
+for the images in which case, once the processing is completed, the
+original input image is renamed by appending it to the prefix (or with
+an added digit if a previous backup image of the same name exits)
+before the processed output image takes the original input name.
+.PP
+The next step is to determine the image geometry.  Only a subsection of
+the raw image may contain the CCD data.  If this region is specified by
+a header parameter then the processing will affect only this region.
+This allows calibration and other data to be part of the image.
+Normally, the only other data in a image is overscan or prescan data.
+The location of this bias data is determined from the image header or
+from a task parameter (which overrides the image header value).  To
+relate calibration images of different sizes and to allow for readout
+of only a portion of the CCD detector, a header parameter may relate
+the image data coordinates to the full CCD coordinates.  Application of
+calibration image data and identifying bad pixel regions via a bad
+pixel file is done in this CCD coordinate system.  The final
+geometrical information is the region of the input image to be output
+after processing; an operation called trimming.  This is defined by an
+image header parameter or a task parameter.  Trimming of the image is
+selected by the user.  Any or all of this geometry information may be
+absent from the image and appropriate defaults are used.
+.PP
+Each selected operation which is appropriate for the image type is then
+considered.  If the operation has been performed previously it will not
+be repeated.  If all selected operations have been performed then the
+temporary output image is deleted and the input image is left
+unchanged.  The next image is then processed.
+.PP
+For each selected operation to be performed the pertinent data is
+determined.  This consists of such things as the name of the
+calibration image, scaling factors, the overscan bias function, etc.
+Note that at this point only the parameters are determined, the
+operation is not yet performed.  This is because operations are not
+performed sequentially but simultaneously as described below.  Consider
+flat fielding as an example.  First the input image is checked to see
+if it has been flat fielded.  Then the flat field calibration image is
+determined.  The flat field image is checked to see if it has been
+processed.  If it has not been processed then it is processed by
+calling a procedure which is essentially a copy of the main processing
+program.  After the flat field image has been processed, parameters
+affecting the processing, such as the flat field scale factor
+(essentially the mean of the flat field image), are determined.  A log
+of the operation is then printed if desired.
+.PP
+Once all the processing operations and parameters have been defined the
+actual processing begins.  One of the key design goals was that the
+processing be efficient.  There are two primary methods used to achieve
+this goal; separate processing paths for 16 bit integer data and
+floating point data and simultaneous operations.  If the image, the
+calibration images, and the output image (as selected by the user) are
+16 bit integer pixel datatypes then the image data is read and written
+as integer data.  This eliminates internal datatype conversions both
+during I/O and during computations.  However, many operations include
+use of real factors such as the overscan bias, dark count exposure
+scaling, and flat field scaling which causes the computation to be done
+in real arithmetic before the result is stored again as an integer
+value.  In any case there is never any loss of precision except when
+converting the output pixel to short integer.  If any of the images are
+not integer then a real internal data path is used in which input and
+output image data are converted to real as necessary.
+.PP
+For each data path the processing proceeds line-by-line.  For each line
+in the output image data region (ignoring pixels outside the data area
+and pixels which are trimmed) the appropriate input data and
+calibration data are obtained.  The calibration data is determined from
+the CCD coordinates of the output image and are not necessarily from
+the same image line or columns.  The input data is copied to the output
+array while applying bad pixel corrections and trimming.  The line is
+then processed using a specially optimized procedure.  This procedure
+applies all operations simultaneously for all combinations of
+operations.  As an example, consider subtracting an overscan bias,
+subtracting a zero level, and dividing by a flat field.  The basic
+kernel of the task, where the bulk of the CPU time is used, is
+
+.nf
+.ft L
+  do i = 1, n
+      out[i] = (out[i] - overscan - zero[i]) * flatscale / flat[i]
+.ft R
+.fi
+
+Here, \fIn\fR is the number of pixels in the line, \fIoverscan\fR is
+the overscan bias value for the line, \fIzero\fR is the zero level data
+from the zero level image, \fIflatscale\fR is the mean of the flat
+field image, and \fIflat\fR is the flat field data from the flat
+field image.  Note the operations are not applied sequentially but
+in a single statement.  This is the most efficient method and there is
+no need for intermediate images.
+.PP
+Though the processing is logically performed line-by-line in the program,
+the image I/O from the disk is not done this way.  The IRAF virtual
+operating system image interface automatically provides multi-line
+buffering for maximal I/O efficiency.
+.PP
+In many image processing systems it has been standard to apply operations
+sequentially over an image.  This requires producing intermediate images.
+Since this is clearly inefficient in terms of I/O it has been the practice
+to copy the images into main memory and operate upon them there until
+the final image is ready to be saved.  This has led to the perception
+that in order to be efficient an image processing system \fImust\fR
+store images in memory.  This is not true and the IRAF CCD reduction
+package illustrates this.  The CCD processing does not use intermediate
+images and does not need to keep the entire image in main memory.
+Furthermore, though of lesser importance than I/O, the single statement method
+illustrated above is more efficient than multiple passes through the
+images even when the images are kept in main memory.  Finally, as CCD
+detectors increase in size and small, fast, and cheap processors become
+common it is a distinct advantage to not require the large amounts of
+memory needed to keep entire images in memory.
+.PP
+There is one area in which use of main memory can improve performance
+and \fBccdproc\fR does take advantage of it if desired.  The calibration
+images usually are the same for many input images.  By specifying the
+maximum amount of memory available for storing images in memory
+the calibration images may be stored in memory up to that amount.
+By parameterizing the memory requirement there is no builtin dependence
+on large memory!
+.PP
+After processing the input image the last steps are to log the operations
+in the image header using processing keywords and replace the input
+image by the output image as described earlier.  The CCD coordinates
+of the data are recorded in the header, even if not there previously, to
+allow further processing on the image after the image has been trimmed.
+.NH
+Combining Images
+.PP
+The second important tool in the CCD reduction package is a task to combine
+many images into a single, higher quality image.  While this may also be
+done with more general image processing tools (the IRAF task \fBimsum\fR
+for example) the \fBccdred\fR tasks include special CCD dependent features such
+as recognizing the image types and using the image header translation
+file.  Combining images is often done
+with calibration images, which are easy to obtain in number, where it
+is important to minimize the statistical noise so as to not affect the
+object images.  Sometimes object images also are combined.
+The task is called \fBcombine\fR and there are special versions of
+this task called \fBzerocombine, darkcombine\fR, and \fBflatcombine\fR
+for the standard calibration images.
+.PP
+The task takes a list of input images to be combined.  As output there
+is the combined image, an optional sigma image, and optional log output either
+to the terminal, to a log file, or both.  A subset or subsets
+of the input images may be selected based on the image type and a
+subset parameter such as the filter.  As with the processing task,
+this allows selecting images without having to explicitly list each
+image from a large data set.  When combining based on a subset parameter
+there is an output image, and possibly a sigma image, for each separate subset.
+The output image pixel datatype may also be changed during combining;
+usually from 16 bit integer input to real output.
+The sigma image is the standard deviation of the input images about the
+output image.
+.PP
+Except for summing the images together,
+combining images may require correcting for variations between the images
+due to differing exposure times, sky background, extinctions, and
+positions.  Currently, extinction corrections and registration are
+not included but scaling and shifting corrections are included.
+The scaling corrections may be done by exposure times or by computing
+the mode in each image.  Additive shifting is also done by computing
+the mode in the images.  The region of the image in which the mode
+is computed can be specified but by default the whole image is used.
+A scaling correction is used when the flux level or sensitivity is varying.
+The offset correction is used when the sky brightness is varying independently
+of the object brightness.  If the images are not scaled then special
+data paths combine the images more efficiently.
+.PP
+Except for medianing and summing, the images are combined by averaging.
+The average may be weighted by
+
+.nf
+.ft L
+	weight = (N * scale / mode) ** 2
+.ft R
+.fi
+
+where \fIN\fR is the number of images previously combined (the task
+records the number of images combined in the image header), \fIscale\fR
+is the relative scale (applied by dividing) from the exposure time or
+mode, and \fImode\fR is the background mode estimate used when adding a
+variable offset.
+.PP
+The combining operation is the heart of the task.  There are a number
+algorithms which may be used as well as applying statistical weights.
+The algorithms are used to detect and reject deviant pixels, such as
+cosmic rays.
+The choice of algorithm depends on the data, the number of images,
+and the importance of rejecting cosmic rays.  The more complex the
+algorithm the more time consuming the operation.
+The list below summarizes the algorithms.
+Further algorithms may be added in time.
+
+.IP "Sum - sum the input images"
+.br
+The input images are combined by summing.  Care must be taken
+not to exceed the range of the 16 bit integer datatype when summing if the
+output datatype is of this type.  Summing is the only algorithm in which
+scaling and weighting are not used.  Also no sigma image is produced.
+.IP "Average - average the input images"
+.br
+The input images are combined by averaging.  The images may be scaled
+and weighted.  There is no pixel rejection.  A sigma image is produced
+if more than one image is combined.
+.IP "Median - median the input images"
+.br
+The input images are combined by medianing each pixel.  Unless the images
+are at the same exposure level they should be scaled.  The sigma image
+is based on all the input images and is only an approximation to the
+uncertainty in the median estimates.
+.IP "Minreject, maxreject, minmaxreject - reject extreme pixels"
+.br
+At each pixel the minimum, maximum, or both are excluded from the
+average.  The images should be scaled and the average may be
+weighted.  The sigma image requires at least two pixels after rejection
+of the extreme values.  These are relatively fast algorithms and are
+a good choice if there are many images (>15).
+.IP "Threshold - reject pixels above and below specified thresholds"
+.br
+The input images are combined with pixels above and below specified
+threshold values (before scaling) excluded.  The images may be scaled
+and the average weighted.  The sigma image also has the rejected
+pixels excluded.
+.IP "Sigclip - apply a sigma clipping algorithm to each pixel"
+.br
+The input images are combined by applying a sigma clipping algorithm
+at each pixel.  The images should be scaled.  This only rejects highly
+deviant points and so
+includes more of the data than the median or minimum and maximum 
+algorithms.  It requires many images (>10-15) to work effectively.
+Otherwise the bad pixels bias the sigma significantly.  The mean
+used to determine the sigmas is based on the "minmaxrej" algorithm
+to eliminate the effects of bad pixels on the mean.  Only one
+iteration is performed and at most one pixel is rejected at each
+point in the output image.  After the deviant pixels are rejected the final
+mean is computed from all the data.  The sigma image excludes the
+rejected pixels.
+.IP "Avsigclip - apply a sigma clipping algorithm to each pixel"
+.br
+The input images are combined with a variant of the sigma clipping
+algorithm which works well with only a few images.  The images should
+be scaled.  For each line the mean is first estimated using the
+"minmaxrej" algorithm.  The sigmas at each point in the line are scaled
+by the square root of the mean, that is a Poisson scaling of the noise
+is assumed.  These sigmas are averaged to get a line estimate of the
+sigma.  Then the sigma at each point in the line is estimated by
+multiplying the line sigma by the square root of the mean at that point.  As
+with the sigma clipping algorithm only one iteration is performed and
+at most one pixel is rejected at each point.  After the deviant pixels
+are rejected the file mean is computed from all the data.  The sigma
+image excludes the rejected pixels.
+.RE
+.PP
+The "avsigclip" algorithm is the best algorithm for rejecting cosmic
+rays, especially with a small number of images, but it is also the most
+time consuming.  With many images (>10-15) it might be advisable to use
+one of the other algorithms ("maxreject", "median", "minmaxrej") because
+of their greater speed.
+.PP
+This task also has several design features to make it efficient and
+versatile.  There are separate data paths for integer data and real
+data; as with processing, if all input images and the output image are
+of the same datatype then the I/O is done with no internal conversions.
+With mixed datatypes the operations are done as real.  Even in the
+integer path the operations requiring real arithmetic to preserve the
+accuracy of the calculation are performed in that mode.  There is
+effectively no limit to the number of images which may be combined.
+Also, the task determines the amount of memory available and buffers
+the I/O as much as possible.  This is a case where operating on images
+from disk rather than in memory is essential.
+.NH
+Status and Conclusion
+.PP
+The initial implementation of the IRAF \fBccdred\fR package was
+completed in June 1987.  It has been in use at the National Optical
+Astronomy Observatories since April 1987.  The package was not
+distributed with Version 2.5 of IRAF (released in August 1987) but is
+available as a separate installation upon request.  It will be part of
+future releases of IRAF.
+.PP
+At NOAO the CCD reduction package is available at the telescopes as the
+data is obtained.  This is accomplished by transferring the images from
+the data taking computer to a Sun workstation (Sun Microsystems, Inc.)
+initially via tape and later by a direct link.  There are several
+reasons for adopting this architecture.  First, the data acquisition
+system is well established and is dedicated to its real-time function.
+The second computer was phased in without disrupting the essential
+operation of the telescopes and if it fails data taking may continue
+with data being stored on tape.  The role of the second computer is to
+provide faster and more powerful reduction and analysis capability not
+required in a data acquisition system.  In the future it can be more
+easily updated to  follow the state of the art in small computers.  As
+CCD detectors get larger the higher processing speeds will be essential
+to keep up with the data flow.
+.PP
+By writing the reduction software in the high level, portable, IRAF
+system the users have the capability to process their data from the
+basic CCD reductions to a full analysis at the telescope.  Furthermore,
+the same software is widely available on a variety of computers if
+later processing or reprocessing is desired; staff and visitors at NOAO
+may also reduce their data at the headquarters facilities.  The use of
+a high level system was also essential in achieving the design goals;
+it would be difficult to duplicate this complex package without
+the rich programming environment provided by the IRAF system.
+.NH
+References
+.PP
+The following documentation is distributed by the National Optical
+Astronomy Observatories, Central Computer Services, P.O. Box 26732,
+Tucson, Arizona, 85726.  A comprehensive description of the IRAF system
+is given in \fIThe IRAF Data Reduction and Analysis System\fR by Doug
+Tody (also appearing in \fIProceedings of the SPIE - Instrumentation in
+Astronomy VI\fR, Vol. 627, 1986).  A general guide to using IRAF is \fIA
+User's Introduction to the IRAF Command Language\fR by Peter Shames
+and Doug Tody.  Both these documents are also part of the IRAF
+documentation distributed with the system.
+.PP
+A somewhat more tutorial description of the \fBccdred\fR package is
+\fIA User's Guide to the IRAF CCDRED Package\fR by the author.
+Detailed task descriptions and supplementary documentation are
+given in the on-line help library and are part of the user's guide.
+.NH
+Appendix
+.PP
+The current set of tasks making up the IRAF CCD Reduction Package,
+\fBccdred\fR, are summarized below.
+
+.nf
+.ft L
+  badpiximage - Create a bad pixel mask image from a bad pixel file
+    ccdgroups - Group CCD images into image lists
+     ccdhedit - CCD image header editor
+      ccdlist - List CCD processing information
+      ccdproc - Process CCD images
+      combine - Combine CCD images
+  darkcombine - Combine and process dark count images
+  flatcombine - Combine and process flat field images
+  mkfringecor - Make fringe correction images from sky images
+   mkillumcor - Make flat field illumination correction images
+  mkillumflat - Make illumination corrected flat fields
+     mkskycor - Make sky illumination correction images
+    mkskyflat - Make sky corrected flat field images
+setinstrument - Set instrument parameters
+  zerocombine - Combine and process zero level images
+.fi
+.ft R
diff --git a/noao/imred/quadred/src/quad/doc/ccdtypes.hlp b/noao/imred/quadred/src/quad/doc/ccdtypes.hlp
new file mode 100644
index 00000000..2cec33ea
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/ccdtypes.hlp
@@ -0,0 +1,124 @@
+.help ccdtypes Jun87 noao.imred.ccdred
+.ih
+NAME
+ccdtypes -- Description of the CCD image types
+.ih
+CCDTYPES
+The following CCD image types may be specified as the value of the parameter
+\fIccdtype\fR:
+
+.nf
+	""	- (the null string) all image types
+	object	- object images
+	zero	- zero level images such as a bias or preflash
+	dark	- dark count images
+	flat	- flat field images
+	illum	- iillumination images
+	fringe	- fringe correction images
+	other   - other image types defined in the translation file
+	none	- images without an image type parameter
+	unknown - image types not defined in the translation file
+.fi
+.ih
+DESCRIPTION
+The \fBccdred\fR package recognizes certain standard CCD image types
+identified in the image header.  The tasks may select images of a
+particular CCD image type from image lists with the parameter
+\fIccdtype\fR and also recognize and take special actions for
+calibration images.
+
+In order to make use of CCD image type information the header keyword
+identifying the image type must be specified in the instrument
+translation file.  This entry has the form
+
+	imagetyp keyword
+
+where keyword is the image header keyword.  This allows the package to
+access the image type string.  There must also be a translation between
+the image type strings and the CCD types as recognized by the package.
+This information consists of lines in the instrument translation file
+of the form
+
+	header	package
+
+where header is the exact string given in the image header and package
+is one of the types recognized by the package.  The image header string
+can be virtually anything and if it contains blanks it must be
+quoted.  The package image types are those given above except for
+the null string, "none", and "unknown".  That is, these types may
+be specified as a CCD image type in selecting images but not as a translations
+of image type strings.
+
+There may be more than one image type that maps to the same package
+type.  In particular other standard CCD image types, such as comparison
+spectra, multiple exposure, standard star, etc., should be mapped to
+object or other.  There may also be more than one type of flat field, i.e. dome
+flat, sky flat, and lamp flat.  For more on the instrument translation
+file see the help for \fBinstruments\fR.
+.ih
+EXAMPLES
+1. The example entries in the instrument translation file are from the 1986
+NOAO CCD image header format produced by the CAMERA format tape writer.
+
+.nf
+    imagetyp			data-typ
+
+    'OBJECT (0)'		object
+    'DARK (1)'			dark
+    'PROJECTOR FLAT (2)'	flat
+    'SKY FLAT (3)'		other
+    'COMPARISON LAMP (4)'	other
+    'BIAS (5)'			zero
+    'DOME FLAT (6)'		flat
+.fi
+
+The image header keyword describing the image type is "data-typ".
+The values of the image type strings in the header contain blanks so they
+are quoted.  Also the case of the strings is important.  Note that there
+are two types of flat field images and two types of other images.
+
+2. One way to check the image types is with the task \fBccdlist\fR.
+
+.nf
+    cl> ccdlist *.imh
+    Zero.imh[504,1][real][zero][1][OT]:FOCUS L98-193
+    Flat1.imh[504,1][real][flat][1][OTZ]:dflat 6v+blue 5s
+    ccd002.imh[504,504][real][unknown][1][OTZF]:FOCUS L98-193
+    ccd003.imh[544,512][short][object][1]:L98-193
+    ccd004.imh[544,512][short][object][1]:L98-193
+    ccd005.imh[544,512][short][object][1]:L98-193
+    oldformat.imh[544,512][short][none][1]:M31 V
+.fi
+
+The unknown type has a header image type of "MUL (8)".  The old format
+image does not have any header type.
+
+3. To select only images of a particular type:
+
+.nf
+    cl> ccdlist *.imh ccdtype=object
+    ccd003.imh[544,512][short][object][1]:L98-193
+    ccd004.imh[544,512][short][object][1]:L98-193
+    ccd005.imh[544,512][short][object][1]:L98-193
+    cl> ccdlist *.imh ccdtype=unknown
+    ccd002.imh[504,504][real][unknown][1][OTZF]:FOCUS L98-193
+    cl> ccdlist *.imh ccdtype=none
+    oldformat.imh[544,512][short][none][1]:M31 V
+.fi
+
+4. To process images with \fBccdproc\fR:
+
+.nf
+    cl> ccdproc *.imh
+    cl> ccdproc *.imh ccdtype=object
+.fi
+
+In the first case all the images will be processed (the default value of
+\fIccdtype\fR is "").  However, the task recognizes the calibration
+images, such as zero level and flat fields, and processes them appropriately.
+In the second case only object images are processed and all other images
+are ignored (except if needed as a calibration image).
+.ih
+SEE ALSO
+instruments
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/combine.hlp b/noao/imred/quadred/src/quad/doc/combine.hlp
new file mode 100644
index 00000000..b3c0848e
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/combine.hlp
@@ -0,0 +1,1030 @@
+.help combine Sep92 noao.imred.ccdred
+.ih
+NAME
+combine -- Combine CCD images using various algorithms
+.ih
+USAGE	
+combine input output
+.ih
+PARAMETERS
+.ls input
+List of CCD images to combine.  Images of a particular CCD image type may be
+selected with the parameter \fIccdtype\fR with the remaining images ignored.
+.le
+.ls output
+Output combined image or list of images.  If the \fIproject\fR parameter is
+no (the typical case for CCD acquisition) then there will be one output image
+or, if the \fIsubsets\fR parameter is selected, one output image per subset.
+If the images consist of stacks then the \fIproject\fR option allows combining
+each input stack into separate output images as given by the image list.
+.le
+.ls plfile = "" (optional)
+Output pixel list file or list of files.  If no name is given or the
+list ends prematurely then no file is produced.  The pixel list file
+is a map of the number of pixels rejected or, equivalently,
+the total number of input images minus the number of pixels actually used.
+The file name is also added to the output image header under the
+keyword BPM.
+.le
+.ls sigma = "" (optional)
+Output sigma image or list of images.  If no name is given or the list ends
+prematurely then no image is produced.  The sigma is standard deviation,
+corrected for a finite population, of the input pixel values (excluding
+rejected pixels) about the output combined pixel values.
+.le
+
+.ls ccdtype = ""
+CCD image type to combine.  If specified only input images of the specified
+type are combined.  See \fBccdtypes\fR for the possible image types.
+.le
+.ls subsets = no
+Combine images by subset parameter?  If yes then the input images are
+grouped by subset parameter and each group combined into a separate output
+image.  The subset identifier is appended to the output image
+name(s).  See \fBsubsets\fR for more on the subset parameter.
+.le
+.ls delete = no
+Delete input images after combining?  Only those images combined are deleted.
+.le
+.ls clobber = no
+Clobber existing output images?
+.le
+
+.ls combine = "average" (average|median)
+Type of combining operation performed on the final set of pixels (after
+offsetting, masking, thresholding, and rejection).  The choices are
+"average" or "median".  The median uses the average of the two central
+values when the number of pixels is even.
+.le
+.ls reject = "none" (none|minmax|ccdclip|crreject|sigclip|avsigclip|pclip)
+Type of rejection operation performed on the pixels remaining after offsetting,
+masking and thresholding.  The algorithms are discussed in the
+DESCRIPTION section.  The rejection choices are:
+
+.nf
+      none - No rejection
+    minmax - Reject the nlow and nhigh pixels
+   ccdclip - Reject pixels using CCD noise parameters
+  crreject - Reject only positive pixels using CCD noise parameters
+   sigclip - Reject pixels using a sigma clipping algorithm
+ avsigclip - Reject pixels using an averaged sigma clipping algorithm
+     pclip - Reject pixels using sigma based on percentiles
+.fi
+
+.le
+.ls project = no
+Project (combine) across the highest dimension of the input images?  If
+no then all  the input images are combined to a single output image.  If
+yes then the highest dimension elements of each input image are combined to
+an output image and optional pixel list and sigma images.  Each element of
+the highest dimension may have a separate offset but there can only be one
+mask image.
+.le
+.ls outtype = "real" (short|integer|long|real|double)
+Output image pixel datatype.  The pixel datatypes are "double",
+"real", "long", "integer", and "short" with highest precedence first.
+If none is specified then the highest precedence datatype of the input
+images is used.  The datatypes may be abbreviated to a single character.
+.le
+.ls offsets = "none" (none|grid|<filename>)
+Input image offsets.  The offsets may be specified in a file consisting
+of one line per image with the offsets in each dimension forming the
+columns.  The special case of a grid may be specified by the string:
+
+.nf
+	grid [n1] [s1] [n2] [s2] ...
+.fi
+
+where ni is the number of images in dimension i and si is the step
+in dimension i.  For example "grid 5 100 5 100" specifies a 5x5
+grid with origins offset by 100 pixels.
+.le
+.ls masktype = "none" (none|goodvalue|badvalue|goodbits|badbits)
+Type of pixel masking to use.  If "none" then no pixel masking is done
+even if an image has an associated  pixel mask.  The other choices
+are to select the value in the pixel mask to be treated as good
+(goodvalue) or bad (badvalue) or the bits (specified as a value)
+to be treated as good (goodbits) or bad (badbits).  The pixel mask
+file name comes from the image header keyword BPM.
+.le
+.ls maskvalue = 0
+Mask value used with the \fImasktype\fR parameter.  If the mask type
+selects good or bad bits the value may be specified using IRAF notation
+for decimal, octal, or hexadecimal; i.e 12, 14b, 0cx to select bits 3
+and 4.
+.le
+.ls blank = 0.
+Output value to be used when there are no pixels.
+.le
+
+.ls scale = "none" (none|mode|median|mean|exposure|@<file>|!<keyword>)
+Multiplicative image scaling to be applied.  The choices are none, scale
+by the mode, median, or mean of the specified statistics section, scale
+by the exposure time in the image header, scale by the values in a specified
+file, or scale by a specified image header keyword.  When specified in
+a file the scales must be one per line in the order of the input
+images.
+.le
+.ls zero = "none" (none|mode|median|mean|@<file>|!<keyword>)
+Additive zero level image shifts to be applied.  The choices are none or
+shift by the mode, median, or mean of the specified statistics section,
+shift by values given in a file, or shift by values given by an image
+header keyword.  When specified in a file the zero values must be one
+per line in the order of the input images.
+.le
+.ls weight = "none" (none|mode|median|mean|exposure|@<file>|!<keyword>)
+Weights to be applied during the final averaging.  The choices are none,
+the mode, median, or mean of the specified statistics section, the exposure
+time, values given in a file, or values given by an image header keyword.
+When specified in a file the weights must be one per line in the order of
+the input images.
+.le
+.ls statsec = ""
+Section of images to use in computing image statistics for scaling and
+weighting.  If no section is given then the entire region of the input is
+sampled (for efficiency the images are sampled if they are big enough).
+When the images are offset relative to each other one can precede the image
+section with one of the modifiers "input", "output", "overlap".  The first
+interprets the section relative to the input image (which is equivalent to
+not specifying a modifier), the second interprets the section relative to
+the output image, and the last selects the common overlap and any following
+section is ignored.
+.le
+
+.ce
+Algorithm Parameters
+.ls lthreshold = INDEF, hthreshold = INDEF
+Low and high thresholds to be applied to the input pixels.  This is done
+before any scaling, rejection, and combining.  If INDEF the thresholds
+are not used.
+.le
+.ls nlow = 1,  nhigh = 1 (minmax)
+The number of low and high pixels to be rejected by the "minmax" algorithm.
+These numbers are converted to fractions of the total number of input images
+so that if no rejections have taken place the specified number of pixels
+are rejected while if pixels have been rejected by masking, thresholding,
+or nonoverlap, then the fraction of the remaining pixels, truncated
+to an integer, is used.
+.le
+.ls nkeep = 1
+The minimum number of pixels to retain or the maximum number to reject
+when using the clipping algorithms (ccdclip, crreject, sigclip,
+avsigclip, or pclip).  When given as a positive value this is the minimum
+number to keep.  When given as a negative value the absolute value is
+the maximum number to reject.  This is actually converted to a number
+to keep by adding it to the number of images.
+.le
+.ls mclip = yes (ccdclip, crreject, sigclip, avsigcliip)
+Use the median as the estimate for the true intensity rather than the
+average with high and low values excluded in the "ccdclip", "crreject",
+"sigclip", and "avsigclip" algorithms?  The median is a better estimator
+in the presence of data which one wants to reject than the average.
+However, computing the median is slower than the average.
+.le
+.ls lsigma = 3., hsigma = 3. (ccdclip, crreject, sigclip, avsigclip, pclip)
+Low and high sigma clipping factors for the "ccdclip", "crreject", "sigclip",
+"avsigclip", and "pclip" algorithms.  They multiply a "sigma" factor
+produced by the algorithm to select a point below and above the average or
+median value for rejecting pixels.  The lower sigma is ignored for the
+"crreject" algorithm.
+.le
+.ls rdnoise = "0.", gain = "1.", snoise = "0." (ccdclip, crreject)
+CCD readout noise in electrons, gain in electrons/DN, and sensitivity noise
+as a fraction.  These parameters are used with the "ccdclip" and "crreject"
+algorithms.  The values may be either numeric or an image header keyword
+which contains the value.
+.le
+.ls sigscale = 0.1 (ccdclip, crreject, sigclip, avsigclip)
+This parameter determines when poisson corrections are made to the
+computation of a sigma for images with different scale factors.  If all
+relative scales are within this value of unity and all relative zero level
+offsets are within this fraction of the mean then no correction is made.
+The idea is that if the images are all similarly though not identically
+scaled, the extra computations involved in making poisson corrections for
+variations in the sigmas can be skipped.  A value of zero will apply the
+corrections except in the case of equal images and a large value can be
+used if the sigmas of pixels in the images are independent of scale and
+zero level.
+.le
+.ls pclip = -0.5 (pclip)
+Percentile clipping algorithm parameter.  If greater than
+one in absolute value then it specifies a number of pixels above or
+below the median to use for computing the clipping sigma.  If less
+than one in absolute value then it specifies the fraction of the pixels
+above or below the median to use.  A positive value selects a point
+above the median and a negative value selects a point below the median.
+The default of -0.5 selects approximately the quartile point.
+See the DESCRIPTION section for further details.
+.le
+.ls grow = 0
+Number of pixels to either side of a rejected pixel along image lines
+to also be rejected.  This applies only to pixels rejected by one of
+the rejection algorithms and not the masked or threshold rejected pixels.
+.le
+
+PACKAGE PARAMETERS
+
+The package parameters are used to specify verbose and log output and the
+instrument and header definitions.
+.ih
+DESCRIPTION
+A set of CCD images are combined by weighted averaging or medianing.  Pixels
+may be rejected from the combining by using pixel masks, threshold levels,
+and rejection algorithms.  The images may be scaled multiplicatively or
+additively based on image statistics, image header keywords, or text files
+before rejection.  The images may be combined with integer pixel coordinate
+offsets to produce an image bigger than any of the input images.
+This task is a variant of the \fBimages.imcombine\fR task specialized
+for CCD images.
+
+The input images to be combined are specified by a list.  A subset or
+subsets of the input list may be selected using the parameters
+\fIccdtype\fR and  \fIsubsets\fR.  The \fIccdtype\fR parameter selects only
+images of a specified standard CCD image type.  The \fIsubsets\fR parameter
+breaks up the input list into sublists of common subset parameter (filter,
+grating, etc.).  For more information see \fBccdtypes\fR and
+\fBsubsets\fR.  This selection process is useful with wildcard templates to
+combine, for example, the flat field images for each filter in one step
+(see \fBflatcombine\fR).  When subsets of the input list are used the
+output image and optional pixel file and sigma image are given by root names
+with a subset identifier appended by the task.
+
+If the \fBproject\fR parameter is yes then the highest dimension elements
+of each input image are combined to make an output image of one lower
+dimension.  There is no limit to the number of elements combined in this
+case.  This case is If the \fBproject\fR is no then the entire input list
+is combined to form a single output image per subset.   In this case the
+images must all have the same dimensionality but they may have different
+sizes.  There is a software limit of approximately 100 images in this
+case.
+
+The output image header is a copy of the first image in the combined set.
+In addition, the number of  images combined is recorded under the keyword
+NCOMBINE, the exposure time is updated as the weighted average of the input
+exposure times, and any pixel list file created is recorded under the
+keyword BPM.  The output pixel type is set by the parameter \fIouttype\fR.
+If left blank then the input datatype of highest precision is used.
+
+In addition to one or more output combined images there may also be a pixel
+list image containing the number of pixels rejected at each point in the
+output image, an image containing the sigmas of the pixels combined about
+the final output combined pixels, and a log file.  The pixel list image is
+in the compact pixel list format which can be used as an image in other
+programs.  The sigma computation is the standard deviation corrected for a
+finite population (the n/(n-1) factor) including weights if a weighted
+average is used.
+
+Other input/output parameters are \fIdelete\fR and \fIclobber\fR.  The
+\fIdelete\fR parameter may be set to "yes" to delete the input images
+used in producing an output image after it has been created.  This is
+useful for minimizing disk space, particularly with large
+sets of calibration images needed to achieve high statistical accuracy
+in the final calibration image.  The \fBclobber\fR parameter allows
+the output image names to be existing images which are overwritten (at
+the end of the operation).
+
+An outline of the steps taken by the program is given below and the
+following sections elaborate on the steps.
+
+.nf
+o   Set the input image offsets and the final output image size.
+o   Set the input image scales and weights
+o   Write the log file output
+.fi
+
+For each output image line:
+
+.nf
+o   Get input image lines that overlap the output image line
+o   Reject masked pixels
+o   Reject pixels outside the threshold limits
+o   Reject pixels using the specified algorithm
+o   Reject neighboring pixels along each line
+o   Combine remaining pixels using the weighted average or median
+o   Compute sigmas of remaining pixels about the combined values
+o   Write the output image line, rejected pixel list, and sigmas
+.fi
+
+
+OFFSETS
+
+The images to be combined need not be of the same size or overlap.  They
+do have to have the same dimensionality which will also be the dimensionality
+of the output image.  Any dimensional images supported by IRAF may be
+used.  Note that if the \fIproject\fR flag is yes then the input images
+are the elements of the highest dimension; for example the planes of a
+three dimensional image.
+
+The overlap of the images is determined by a set of integer pixel offsets
+with an offset for each dimension of each input image.  For example
+offsets of 0, 10, and 20 in the first dimension of three images will
+result in combining the three images with only the first image in the
+first 10 colums, the first two images in the next 10 columns and
+all three images starting in the 31st column.  At the 31st output column
+the 31st column of the first image will be combined with the 21st column
+of the second image and the 1st column of the third image.
+
+The output image size is set by the maximum extent in each dimension
+of any input image after applying the offsets.  In the above example if
+all the images have 100 columns then the output image will have 130
+columns corresponding to the 30 column offset in the third image.
+
+The input image offsets are set using the \fIoffset\fR parameter.  There
+are three ways to specify the offsets.  If the word "none" or the empty
+string "" are used then all offsets will be zero and all pixels with the
+same coordinates will be combined.  The output image size will be equal to
+the biggest dimensions of the input images.
+
+If the input images have offsets in a regular grid or one wants to make
+an output image in which the input images are "mosaiced" together in
+a grid then the special offset string  beginning with the word "grid"
+is used.  The format is
+
+.nf
+	grid [n1] [s1] [n2] [s2] ...
+.fi
+
+where ni is the number of images in dimension i and si is the step in
+dimension i.  For example "grid 5 100 5 100" specifies a 5x5 grid with
+origins offset by 100 pixels.  Note that one must insure that the input
+images are specified in the correct order.  This may best be accomplished
+using a "@" list.  One useful application of the grid is to make a
+nonoverlapping mosaic of a number of images for display purposes.  Suppose
+there are 16 images which are 100x100.  The offset string "grid 4 101 4
+101" will produce a mosaic with a one pixel border having the value set
+by \fIblank\fR parameter between the images.
+
+The offsets may be defined in a file by specifying the file name
+in the \fIoffset\fR parameter.  (Note that the special file name STDIN
+may be used to type in the values terminated by the end-of-file
+character).  The file consists of a line for each input image.  The lines
+must be in the same order as the input images and so an "@" list may
+be useful.  The lines consist of whitespace separated offsets one for
+each dimension of the images.  In the first example cited above the
+offset file might contain:
+
+.nf
+	0 0
+	10 0
+	20 0
+.fi
+
+where we assume the second dimension has zero offsets.
+
+The offsets need not have zero for one of the images.  The offsets may
+include negative values or refer to some arbitrary common point.
+When the offsets are read by the program it will find the minimum
+value in each dimension and subtract it from all the other offsets
+in that dimension.  The above example could also be specified as:
+
+.nf
+	225 15
+	235 15
+	245 15
+.fi
+
+There may be cases where one doesn't want the minimum offsets reset
+to zero.  If all the offsets are positive and the comment "# Absolute"
+appears in the offset file then the images will be combined with
+blank values between the first output pixel and the first overlapping
+input pixel.  Continuing with the above example, the file
+
+.nf
+	# Absolute
+	10 10
+	20 10
+	30 10
+.fi
+
+will have the first pixel of the first image in the 11th pixel of the
+output image.  Note that there is no way to "pad" the other side of
+the output image.
+
+
+SCALES AND WEIGHTS
+
+In order to combine images with rejection of pixels based on deviations
+from some average or median they must be scaled to a common level.  There
+are two types of scaling available, a multiplicative intensity scale and an
+additive zero point shift.  The intensity scaling is defined by the
+\fIscale\fR parameter and the zero point shift by the \fIzero\fR
+parameter.  These parameters may take the values "none" for no scaling,
+"mode", "median", or "mean" to scale by statistics of the image pixels,
+"exposure" (for intensity scaling only) to scale by the exposure time
+keyword in the image header, any other image header keyword specified by
+the keyword name prefixed by the character '!', and the name of a file
+containing the scale factors for the input image prefixed by the
+character '@'.
+
+Examples of the possible parameter values are shown below where
+"myval" is the name of an image header keyword and "scales.dat" is
+a text file containing a list of scale factors.
+
+.nf
+	scale = none		No scaling
+	zero = mean		Intensity offset by the mean
+	scale = exposure	Scale by the exposure time
+	zero = !myval		Intensity offset by an image keyword
+	scale = @scales.dat	Scales specified in a file
+.fi
+
+The image statistics factors are computed by sampling a uniform grid
+of points with the smallest grid step that yields less than 10000
+pixels; sampling is used to reduce the time need to compute the statistics.
+If one wants to restrict the sampling to a region of the image the
+\fIstatsec\fR parameter is used.  This parameter has the following
+syntax:
+
+.nf
+	[input|output|overlap] [image section]
+.fi
+
+The initial modifier defaults to "input" if absent.  The modifiers are useful
+if the input images have offsets.  In that case "input" specifies
+that the image section refers to each input image, "output" specifies
+that the image section refers to the output image coordinates, and
+"overlap" specifies the mutually overlapping region of the input images.
+In the latter case an image section is ignored.
+
+The statistics are as indicated by their names.  In particular, the
+mode is a true mode using a bin size which is a fraction of the
+range of the pixels and is not based on a relationship between the
+mode, median, and mean.  Also masked pixels are excluded from the
+computations as well as during the rejection and combining operations.
+
+The "exposure" option in the intensity scaling uses the exposure time
+from the image header.  If one wants to use a nonexposure time image
+header keyword the !<keyword> syntax is available.
+
+If both an intensity scaling and zero point shift are selected the
+multiplicative scaling is done first.  Use of both makes sense
+if the intensity scaling is the exposure time to correct for
+different exposure times and then the zero point shift allows for
+sky brightness changes.
+
+The image statistics and scale factors are recorded in the log file
+unless they are all equal, which is equivalent to no scaling.  The
+intensity scale factors are normalized to a unit mean and the zero
+point shifts are adjust to a zero mean.
+
+Scaling affects not only the mean values between images but also the
+relative pixel uncertainties.  For example scaling an image by a
+factor of 0.5 will reduce the effective noise sigma of the image
+at each pixel by the square root of 0.5.  Changes in the zero
+point also changes the noise sigma if the image noise characteristics
+are Poissonian.  In the various rejection algorithms based on
+identifying a noise sigma and clipping large deviations relative to
+the scaled median or mean, one may need to account for the scaling induced
+changes in the image noise characteristics.
+
+In those algorithms it is possible to eliminate the "sigma correction"
+while still using scaling.  The reasons this might be desirable are 1) if
+the scalings are similar the corrections in computing the mean or median
+are important but the sigma corrections may not be important and 2) the
+image statistics may not be Poissonian, either inherently or because the
+images have been processed in some way that changes the statistics.  In the
+first case because computing square roots and making corrections to every
+pixel during the iterative rejection operation may be a significant
+computational speed limit the parameter \fIsigscale\fR selects how
+dissimilar the scalings must be to require the sigma corrections.  This
+parameter is a fractional deviation which, since the scale factors are
+normalized to unity, is the actual minimum deviation in the scale factors.
+For the zero point shifts the shifts are normalized by the mean shift
+before adjusting the shifts to a zero mean.  To always use sigma scaling
+corrections the parameter is set to zero and to eliminate the correction in
+all cases it is set to a very large number.
+
+If the final combining operation is "average" then the images may be
+weighted during the averaging.  The weights are specified in the
+same way as the scale factors.  In addition
+the NCOMBINE keyword, if present, will be used in the weights.
+The weights, scaled to a unit sum, are printed in the log output.
+
+The weights are only used for the final weighted average and sigma image
+output.  They are not used to form averages in the various rejection
+algorithms.
+
+
+PIXEL MASKS
+
+A pixel mask is a type of IRAF file having the extension ".pl" which
+identifies an integer value with each pixel of the images to which it is
+applied.  The integer values may denote regions, a weight, a good or bad
+flag, or some other type of integer or integer bit flag.  In the common
+case where many values are the same this file is compacted to be small and
+efficient to use.  It is also most compact and efficient if the majority of
+the pixels have a zero mask value so frequently zero is the value for good
+pixels.  Note that these files, while not stored as a strict pixel array,
+may be treated as images in programs.  This means they may be created by
+programs such as \fBmkpattern\fR, edited by \fBimedit\fR, examined by
+\fBimexamine\fR, operated upon by \fBimarith\fR, graphed by \fBimplot\fR,
+and displayed by \fBdisplay\fR.
+
+At the time of introducing this task, generic tools for creating
+pixel masks have yet to be written.  There are two ways to create a
+mask in V2.10.  First if a regular integer image can be created
+then it can be converted to pixel list format with \fBimcopy\fR:
+
+.nf
+	cl> imcopy template plfile.pl
+.fi
+
+by specifically using the .pl extension on output.  Other programs that
+can create integer images (such \fBmkpattern\fR or \fBccdred.badpiximage\fR)
+can create the pixel list file directly by simply using the ".pl"
+extension in the output image name.
+
+To use pixel masks with \fBcombine\fR one must associate a pixel
+mask file with an image by entering the pixel list file name in the
+image header under the keyword BPM (bad pixel mask).  This can be
+done with \fBhedit\fR.  Note that the same pixel mask may be associated
+with more than one image as might be the case if the mask represents
+defects in the detector used to obtain the images.
+
+If a pixel mask is associated with an image the mask is used when the
+\fImasktype\fR parameter is set to a value other than "none".  Note that
+when it is set to "none" mask information is not used even if it exists for
+the image.  The values of \fImasktype\fR which apply masks are "goodvalue",
+"badvalue", "goodbits", and "badbits".  They are used in conjunction with
+the \fImaskvalue\fR parameter.  When the mask type is "goodvalue" the
+pixels with mask values matching the specified value are included in
+combining and all others are rejected.  Similarly, for a mask type of
+"badvalue" the pixels with mask values matching the specified value are
+rejected and all others are accepted.  The bit types are useful for
+selecting a combination of attributes in a mask consisting of bit flags.
+The mask value is still an integer but is interpreted by bitwise comparison
+with the values in the mask file.
+
+If a mask operation is specified and an image has no mask image associated
+with it then the mask values are taken as all zeros.  In those cases be
+careful that zero is an accepted value otherwise the entire image will be
+rejected.
+
+
+THRESHOLD REJECTION
+
+In addition to rejecting masked pixels, pixels in the unscaled input
+images which are below or above the thresholds given by the parameters
+\fIlthreshold\fR and \fIhthreshold\fR are rejected.  Values of INDEF
+mean that no threshold value is applied.  Threshold rejection may be used
+to exclude very bad pixel values or as an alternative way of masking
+images.  In the latter case one can use a task like \fBimedit\fR
+or \fBimreplace\fR to set parts of the images to be excluded to some
+very low or high magic value.
+
+
+REJECTION ALGORITHMS
+
+The \fIreject\fR parameter selects a type of rejection operation to
+be applied to pixels not masked or thresholded.  If no rejection
+operation is desired the value "none" is specified.
+
+MINMAX
+.in 4
+A specified fraction of the highest and lowest pixels are rejected.
+The fraction is specified as the number of high and low pixels, the
+\fInhigh\fR and \fInlow\fR parameters, when data from all the input images
+are used.  If pixels have been rejected by offseting, masking, or
+thresholding then a matching fraction of the remaining pixels, truncated
+to an integer, are used.  Thus,
+
+.nf
+	nl = n * nlow/nimages + 0.001 
+	nh = n * nhigh/nimages + 0.001 
+.fi
+
+where n is the number of pixels surviving offseting, masking, and
+thresholding, nimages is the number of input images, nlow and nhigh
+are task parameters and nl and nh are the final number of low and
+high pixels rejected by the algorithm.  The factor of 0.001 is to
+adjust for rounding of the ratio.
+
+As an example with 10 input images and specifying one low and two high
+pixels to be rejected the fractions to be rejected are 0.1 and 0.2
+and the number rejected as a function of n is:
+
+.nf
+	 n   0  1  2  3  4  5  6  7  8  9 10
+	 nl  0  0  0  0  0  1  1  1  1  1  2
+	 nh  0  0  0  0  0  0  0  0  0  0  1
+.fi
+
+.in -4
+CCDCLIP
+.in 4
+If the images are obtained using a CCD with known read out noise, gain, and
+sensitivity noise parameters and they have been processed to preserve the
+relation between data values and photons or electrons then the noise
+characteristics of the images are well defined.  In this model the sigma in
+data values at a pixel with true value <I>, as approximated by the median
+or average with the lowest and highest value excluded, is given by:
+
+.nf
+	sigma = ((rn / g) ** 2 + <I> / g + (s * <I>) ** 2) ** 1/2
+.fi
+
+where rn is the read out noise in electrons, g is the gain in
+electrons per data value, s is a sensitivity noise given as a fraction,
+and ** is the exponentiation operator.  Often the sensitivity noise,
+due to uncertainties in the pixel sensitivities (for example from the
+flat field), is not known in which case a value of zero can be used.
+See the task \fBstsdas.wfpc.noisemodel\fR for a way to determine
+these vaues (though that task expresses the read out noise in data
+numbers and the sensitivity noise parameter as a percentage).
+
+The read out noise is specified by the \fIrdnoise\fR parameter.  The value
+may be a numeric value to be applied to all the input images or a image
+header keyword containing the value for each image.  Similarly, the
+parameter \fIgain\fR specifies the gain as either a value or image header
+keyword and the parameter \fIsnoise\fR specifies the sensitivity
+noise parameter as either a value or image header keyword.
+
+The algorithm operates on each output pixel independently.  It starts by
+taking the median or unweighted average (excluding the minimum and maximum)
+of the unrejected pixels provided there are at least two input pixels.  The
+expected sigma is computed from the CCD noise parameters and pixels more
+that \fIlsigma\fR times this sigma below or \fIhsigma\fR times this sigma
+above the median or average are rejected.  The process is then iterated
+until no further pixels are rejected.  If the average is used as the
+estimator of the true value then after the first round of rejections the
+highest and lowest values are no longer excluded.  Note that it is possible
+to reject all pixels if the average is used and is sufficiently skewed by
+bad pixels such as cosmic rays.
+
+If there are different CCD noise parameters for the input images
+(as might occur using the image header keyword specification) then
+the sigmas are computed for each pixel from each image using the
+same estimated true value.
+
+If the images are scaled and shifted and the \fIsigscale\fR threshold
+is exceedd then a sigma is computed for each pixel based on the
+image scale parameters; i.e. the median or average is scaled to that of the
+original image before computing the sigma and residuals.
+
+After rejection the number of retained pixels is checked against the
+\fInkeep\fR parameter.  If there are fewer pixels retained than specified
+by this parameter the pixels with the smallest residuals in absolute
+value are added back.  If there is more than one pixel with the same
+absolute residual (for example the two pixels about an average
+or median of two will have the same residuals) they are all added
+back even if this means more than \fInkeep\fR pixels are retained.
+Note that the \fInkeep\fR parameter only applies to the pixels used
+by the clipping rejection algorithm and does not apply to threshold
+or bad pixel mask rejection.
+
+This is the best clipping algorithm to use if the CCD noise parameters are
+adequately known.  The parameters affecting this algorithm are \fIreject\fR
+to select this algorithm, \fImclip\fR to select the median or average for
+the center of the clipping, \fInkeep\fR to limit the number of pixels
+rejected, the CCD noise parameters \fIrdnoise, gain\fR and \fIsnoise\fR,
+\fIlsigma\fR and \fIhsigma\fR to select the clipping thresholds,
+and \fIsigscale\fR to set the threshold for making corrections to the sigma
+calculation for different image scale factors.
+
+.in -4
+CRREJECT
+.in 4
+This algorithm is identical to "ccdclip" except that only pixels above
+the average are rejected based on the \fIhsigma\fR parameter.  This
+is appropriate for rejecting cosmic ray events and works even with
+two images.
+
+.in -4
+SIGCLIP
+.in 4
+The sigma clipping algorithm computes at each output pixel the median or
+average excluding the high and low values and the sigma about this
+estimate.  There must be at least three input pixels, though for this method
+to work well there should be at least 10 pixels.  Values deviating by more
+than the specified sigma threshold factors are rejected.  These steps are
+repeated, except that after the first time the average includes all values,
+until no further pixels are rejected or there are fewer than three pixels.
+
+After rejection the number of retained pixels is checked against the
+\fInkeep\fR parameter.  If there are fewer pixels retained than specified
+by this parameter the pixels with the smallest residuals in absolute
+value are added back.  If there is more than one pixel with the same
+absolute residual (for example the two pixels about an average
+or median of two will have the same residuals) they are all added
+back even if this means more than \fInkeep\fR pixels are retained.
+Note that the \fInkeep\fR parameter only applies to the pixels used
+by the clipping rejection algorithm and does not apply to threshold
+or bad pixel mask rejection.
+
+The  parameters affecting this algorithm are \fIreject\fR to select
+this algorithm, \fImclip\fR to select the median or average for the
+center of the clipping, \fInkeep\fR to limit the number of pixels
+rejected, \fIlsigma\fR and \fIhsigma\fR to select the
+clipping thresholds, and \fIsigscale\fR to set the threshold for
+making corrections to the sigma calculation for different image scale
+factors.
+
+.in -4
+AVSIGCLIP
+.in 4
+The averaged sigma clipping algorithm assumes that the sigma about the
+median or mean (average excluding the low and high values) is proportional
+to the square root of the median or mean at each point.  This is
+described by the equation:
+
+.nf
+	sigma(column,line) = sqrt (gain(line) * signal(column,line))
+.fi
+
+where the \fIestimated\fR signal is the mean or median (hopefully excluding
+any bad pixels) and the gain is the \fIestimated\fR proportionality
+constant having units of photons/data number.
+
+This noise model is valid for images whose values are proportional to the
+number of photons recorded.  In effect this algorithm estimates a
+detector gain for each line with no read out noise component when
+information about the detector noise parameters are not known or
+available.  The gain proportionality factor is computed
+independently for each output line by averaging the square of the residuals
+(at points having three or more input values) scaled by the median or
+mean.  In theory the proportionality should be the same for all rows but
+because of the estimating process will vary somewhat.
+
+Once the proportionality factor is determined, deviant pixels exceeding the
+specified thresholds are rejected at each point by estimating the sigma
+from the median or mean.  If any values are rejected the median or mean
+(this time not excluding the extreme values) is recomputed and further
+values rejected.  This is repeated until there are no further pixels
+rejected or the number of remaining input values falls below three.  Note
+that the proportionality factor is not recomputed after rejections.
+
+If the images are scaled differently and the sigma scaling correction
+threshold is exceedd then a correction is made in the sigma
+calculations for these differences, again under the assumption that
+the noise in an image scales as the square root of the mean intensity.
+
+After rejection the number of retained pixels is checked against the
+\fInkeep\fR parameter.  If there are fewer pixels retained than specified
+by this parameter the pixels with the smallest residuals in absolute
+value are added back.  If there is more than one pixel with the same
+absolute residual (for example the two pixels about an average
+or median of two will have the same residuals) they are all added
+back even if this means more than \fInkeep\fR pixels are retained.
+Note that the \fInkeep\fR parameter only applies to the pixels used
+by the clipping rejection algorithm and does not apply to threshold
+or bad pixel mask rejection.
+
+This algorithm works well for even a few input images.  It works better if
+the median is used though this is slower than using the average.  Note that
+if the images have a known read out noise and gain (the proportionality
+factor above) then the "ccdclip" algorithm is superior.  The two algorithms
+are related in that the average sigma proportionality factor is an estimate
+of the gain.
+
+The  parameters affecting this algorithm are \fIreject\fR to select
+this algorithm, \fImclip\fR to select the median or average for the
+center of the clipping, \fInkeep\fR to limit the number of pixels
+rejected, \fIlsigma\fR and \fIhsigma\fR to select the
+clipping thresholds, and \fIsigscale\fR to set the threshold for
+making corrections to the sigma calculation for different image scale
+factors.
+
+.in -4
+PCLIP
+.in 4
+The percentile clipping algorithm is similar to sigma clipping using the
+median as the center of the distribution except that, instead of computing
+the sigma of the pixels from the CCD noise parameters or from the data
+values, the width of the distribution is characterized by the difference
+between the median value and a specified "percentile" pixel value.  This
+width is then multipled by the scale factors \fIlsigma\fR and \fIhsigma\fR
+to define the clipping thresholds above and below the median.  The clipping
+is not iterated.
+
+The pixel values at each output point are ordered in magnitude and the
+median is determined.  In the case of an even number of pixels the average
+of the two middle values is used as the median value and the lower or upper
+of the two is the median pixel when counting from the median pixel to
+selecting the percentile pixel.  The parameter \fIpclip\fR selects the
+percentile pixel as the number (if the absolute value is greater
+than unity) or fraction of the pixels from the median in the ordered set.
+The direction of the percentile pixel from the median is set by the sign of
+the \fIpclip\fR parameter with a negative value signifying pixels with
+values less than the median.  Fractional values are internally converted to
+the appropriate number of pixels for the number of input images.  A minimum
+of one pixel and a maximum corresponding to the extreme pixels from the
+median are enforced.  The value used is reported in the log output.  Note
+that the same percentile pixel is used even if pixels have been rejected by
+offseting, masking, or thresholding; for example, if the 3nd pixel below
+the median is specified then the 3rd pixel will be used whether there are
+10 pixels or 5 pixels remaining after the preliminary steps.
+
+Some examples help clarify the definition of the percentile pixel.  In the
+examples assume 10 pixels.  The median is then the average of the
+5th and 6th pixels.  A \fIpclip\fR value of 2 selects the 2nd pixel
+above the median (6th) pixel which is the 8th pixel.  A \fIpclip\fR
+value of -0.5 selects the point halfway between the median and the
+lowest pixel.  In this case there are 4 pixels below the median,
+half of that is 2 pixels which makes the percentile pixel the 3rd pixel.
+
+The percentile clipping algorithm is most useful for clipping small
+excursions, such as the wings of bright objects when combining
+disregistered observations for a sky flat field, that are missed when using
+the pixel values to compute a sigma.  It is not as powerful, however, as
+using the CCD noise parameters (provided they are accurately known) to clip
+about the median.
+
+The  parameters affecting this algorithm are \fIreject\fR to select this
+algorithm, \fIpclip\fR to select the percentile pixel, \fInkeep\fR to limit
+the number of pixels rejected, and \fIlsigma\fR and \fIhsigma\fR to select
+the clipping thresholds.
+
+.in -4
+GROW REJECTION
+
+Neighbors of pixels rejected by the rejection algorithms along image lines
+may also be rejected.  The number of neighbors to be rejected on either
+side is specified by the \fIgrow\fR parameter.  The rejection only
+applies to neighbors along each image line.  This is because the
+task operates independently on each image line and does not have the
+ability to go back to previous lines or maintain a list of rejected
+pixels to later lines.
+
+This rejection step is also checked against the \fInkeep\fR parameter
+and only as many pixels as would not violate this parameter are
+rejected.  Unlike it's application in the rejection algorithms at
+this stage there is no checking on the magnitude of the residuals
+and the pixels retained which would otherwise be rejected are randomly
+selected.
+
+
+COMBINING
+
+After all the steps of offsetting the input images, masking pixels,
+threshold rejection, scaling, and applying a rejection algorithms the
+remaining pixels are combined and output.  The pixels may be combined
+by computing the median or by computing a weighted average.
+
+
+SIGMA OUTPUT
+
+In addition to the combined image and optional sigma image may be
+produced.  The sigma computed is the standard deviation, corrected for a
+finite population by a factor of n/(n-1), of the unrejected input pixel
+values about the output combined pixel values.
+.ih
+EXAMPLES
+1.  To average and median images without any other features:
+
+.nf
+	cl> combine obj* avg combine=average reject=none
+	cl> combine obj* med combine=median reject=none
+.fi
+
+2.  To reject cosmic rays:
+
+.nf
+	cl> combine obs1,obs2 Obs reject=crreject rdnoise=5.1, gain=4.3
+.fi
+
+3.  To make a grid for display purposes with 21 64x64 images:
+
+.nf
+	cl> combine @list grid offset="grid 5 65 5 65"
+.fi
+
+4.  To apply a mask image with good pixels marked with a zero value and
+    bad pixels marked with a value of one:
+
+.nf
+	cl> hedit ims* bpm badpix.pl add+ ver-
+	cl> combine ims* final combine=median masktype=goodval
+.fi
+
+5.  To scale image by the exposure time and then adjust for varying
+    sky brightness and make a weighted average:
+
+.nf
+	cl> combine obj* avsig combine=average reject=avsig \
+	>>> scale=exp zero=mode weight=exp  expname=exptime
+.fi
+.ih
+TIME REQUIREMENTS
+The following times were obtain with a Sun 4/470.  The tests combine
+1000x200 images consisting of Poisson noise and cosmic rays generated
+with the \fBartdata\fR package.  The times, especially the total time,
+are approximate and depend on user loads.
+
+.nf
+IMAGES:   Number of images (1000x200) and datatype (R=real, S=short)
+COMBINE:  Combine option
+REJECT:   Rejection option with grow = 0
+	      minmax:    nlow = 1, nhigh = 1
+	      ccdclip:   lsigma = 3., hsigma = 3, sigscale = 0.
+	      sigclip:   lsigma = 3., hsigma = 3, sigscale = 0.
+	      avsigclip: lsigma = 3., hsigma = 3, sigscale = 0.
+	      pclip:     lsigma = 3., hsigma = 3, pclip = -0.5
+	      /a:        mclip = no  (clip about the average)
+	      /m:        mclip = yes (clip about the median)
+O M T S:  Features used (Y=yes, N=no)
+O:        offset = "grid 5 10 2 10"
+M:        masktype = goodval, maskval = 0
+	      Pixel mask has 2 bad lines and 20 bad columns 
+T:        lthreshold = INDEF, hthreshold = 1100.
+S:        scale = mode, zero = none, weight = mode
+TIME:     cpu time in seconds, total time in minutes and seconds
+
+
+IMAGES  COMBINE  REJECT        O M T S     TIME
+
+  10R   average  none          N N N N    1.3 0:08
+  10R   average  minmax        N N N N    4.3 0:10
+  10R   average  pclip         N N N N   17.9 0:32
+  10R   average  ccdclip/a     N N N N   11.6 0:21
+  10R   average  crreject/a    N N N N   11.4 0:21
+  10R   average  sigclip/a     N N N N   13.6 0:29
+  10R   average  avsigclip/a   N N N N   15.9 0:35
+  10R   average  ccdclip/m     N N N N   16.9 0:32
+  10R   average  crreject/m    N N N N   17.0 0:28
+  10R   average  sigclip/m     N N N N   19.6 0:42
+  10R   average  avsigclip/m   N N N N   20.6 0:43
+
+  10R   median   none          N N N N    6.8 0:17
+  10R   median   minmax        N N N N    7.8 0:15
+  10R   median   pclip         N N N N   16.9 1:00
+  10R   median   ccdclip/a     N N N N   18.0 0:34
+  10R   median   crreject/a    N N N N   17.7 0:30
+  10R   median   sigclip/a     N N N N   21.1 1:13
+  10R   median   avsigclip/a   N N N N   23.1 0:41
+  10R   median   ccdclip/m     N N N N   16.1 0:27
+  10R   median   crreject/m    N N N N   16.0 0:27
+  10R   median   sigclip/m     N N N N   18.1 0:29
+  10R   median   avsigclip/m   N N N N   19.6 0:32
+
+  10R   average  none          N N N Y    6.1 0:36
+  10R   median   none          N N N Y   10.4 0:49
+  10R   median   pclip         N N N Y   20.4 1:10
+  10R   median   ccdclip/m     N N N Y   19.5 0:36
+  10R   median   avsigclip/m   N N N Y   23.0 1:06
+
+  10R   average  none          N Y N N    3.5 0:12
+  10R   median   none          N Y N N    8.9 0:21
+  10R   median   pclip         N Y N N   19.9 0:45
+  10R   median   ccdclip/m     N Y N N   18.0 0:44
+  10R   median   avsigclip/m   N Y N N   20.9 0:28
+
+  10R   average  none          Y N N N    4.3 0:13
+  10R   median   none          Y N N N    9.6 0:21
+  10R   median   pclip         Y N N N   21.8 0:54
+  10R   median   ccdclip/m     Y N N N   19.3 0:44
+  10R   median   avsigclip/m   Y N N N   22.8 0:51
+
+  10R   average  none          Y Y Y Y   10.8 0:22
+  10R   median   none          Y Y Y Y   16.1 0:28
+  10R   median   pclip         Y Y Y Y   27.4 0:42
+  10R   median   ccdclip/m     Y Y Y Y   25.5 0:39
+  10R   median   avsigclip/m   Y Y Y Y   28.9 0:44
+
+  10S   average  none          N N N N    2.2 0:06
+  10S   average  minmax        N N N N    4.6 0:12
+  10S   average  pclip         N N N N   18.1 0:33
+.fi
+.ih
+REVISIONS
+.ls COMBINE V2.10.2
+The weighting was changed from using the square root of the exposure time
+or image statistics to using the values directly.  This corresponds
+to variance weighting.  Other options for specifying the scaling and
+weighting factors were added; namely from a file or from a different
+image header keyword.  The \fInkeep\fR parameter was added to allow
+controlling the maximum number of pixels to be rejected by the clipping
+algorithms.  The \fIsnoise\fR parameter was added to include a sensitivity
+or scale noise component to the noise model.  Errors will now delete
+the output images.
+.le
+.ls COMBINE V2.10
+This task was greatly revised to provide many new features.  These features
+are:
+
+.nf
+    o Bad pixel masks
+    o Combining offset and different size images
+    o Blank value for missing data
+    o Combining across the highest dimension (the project option)
+    o Separating threshold rejection, the rejection algorithms,
+      and the final combining statistic
+    o New CCDCLIP, CRREJECT, and PCLIP algorithms
+    o Rejection now may reject more than one pixel per output pixel
+    o Choice of a central median or average for clipping
+    o Choice of final combining operation
+    o Simultaneous multiplicative and zero point scaling
+.fi
+.le
+.ih
+LIMITATIONS
+Though this task is essentially not limited by the physical
+limits of the host (number of open files, amount of memory) there is a
+software limit in the IRAF virtual operating system of about 120 separate
+images which may be combined.  To combine more images one may combine smaller
+groups and then combine those or one may stack the images into a higher
+dimensional image using \fBimstack\fR and use the \fIproject\fR option.
+.ih
+SEE ALSO
+image.imcombine, instruments, ccdtypes, icfit, ccdred, guide, darkcombine,
+flatcombine, zerocombine, onedspec.scombine wfpc.noisemodel
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/contents.ms b/noao/imred/quadred/src/quad/doc/contents.ms
new file mode 100644
index 00000000..8ba2624a
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/contents.ms
@@ -0,0 +1,34 @@
+.sp 1i
+.ps +2
+.ft B
+.ce
+Contents
+.sp 3
+.ps -2
+.ft R
+.sp
+1.\h'|0.4i'\fBIntroduction\fP\l'|5.6i.'\0\01
+.sp
+2.\h'|0.4i'\fBGetting Started\fP\l'|5.6i.'\0\02
+.sp
+3.\h'|0.4i'\fBProcessing Your Data\fP\l'|5.6i.'\0\05
+.br
+\h'|0.4i'3.1.\h'|0.9i'Combining Calibration Images\l'|5.6i.'\0\06
+.br
+\h'|0.4i'3.2.\h'|0.9i'Calibrations and Corrections\l'|5.6i.'\0\07
+.sp
+4.\h'|0.4i'\fBSpecial Processing Operations\fP\l'|5.6i.'\0\08
+.br
+\h'|0.4i'4.1.\h'|0.9i'Spectroscopic Flat Fields\l'|5.6i.'\0\08
+.br
+\h'|0.4i'4.2.\h'|0.9i'Illumination Corrections\l'|5.6i.'\0\09
+.br
+\h'|0.4i'4.3.\h'|0.9i'Sky Flat Fields\l'|5.6i.'\010
+.br
+\h'|0.4i'4.4.\h'|0.9i'Illumination Corrected Flat Fields\l'|5.6i.'\010
+.br
+\h'|0.4i'4.5.\h'|0.9i'Fringe Corrections\l'|5.6i.'\010
+.sp
+5.\h'|0.4i'\fBSummary\fP\l'|5.6i.'\011
+.sp
+\h'|0.4i'\fBReferences\fP\l'|5.6i.'\011
diff --git a/noao/imred/quadred/src/quad/doc/cosmicrays.hlp b/noao/imred/quadred/src/quad/doc/cosmicrays.hlp
new file mode 100644
index 00000000..c50a129f
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/cosmicrays.hlp
@@ -0,0 +1,220 @@
+.help cosmicrays Dec87 noao.imred.ccdred
+.ih
+NAME
+cosmicrays -- Detect and replace cosmic rays
+.ih
+USAGE
+cosmicrays input output
+.ih
+PARAMETERS
+.ls input
+List of input images in which to detect cosmic rays.
+.le
+.ls output
+List of output images in which the detected cosmic rays will be replaced
+by an average of neighboring pixels.  If the output image name differs
+from the input image name then a copy of the input image is made with
+the detected cosmic rays replaced.  If no output images are specified
+then the input images are modified in place.  In place modification of
+an input image also occurs when the output image name is the same as
+the input image name.
+.le
+.ls badpix = ""
+List of bad pixel files to be created, one for each input image.  If no
+file names are given then no bad pixel file is created.  The bad pixel 
+file is a simple list of pixel coordinates for each replaced cosmic ray.
+This file may be used in conjunction with \fBbadpixelimage\fR to create
+a mask image.
+.le
+.ls ccdtype = ""
+If specified only the input images of the desired CCD image type will be
+selected.
+.le
+.ls threshold = 25.
+Detection threshold above the mean of the surrounding pixels for cosmic
+rays.  The threshold will depend on the noise characteristics of the
+image and how weak the cosmic rays may be for detection.  A typical value
+is 5 or more times the sigma of the background.
+.le
+.ls fluxratio = 2.
+The ratio (as a percent) of the mean neighboring pixel flux to the candidate
+cosmic ray pixel for rejection.  The value depends on the seeing and the
+characteristics of the cosmic rays.  Typical values are in the range
+2 to 10 percent.
+.le
+.ls npasses = 5
+Number of cosmic ray detection passes.  Since only the locally strongest
+pixel is considered a cosmic ray, multiple detection passes are needed to
+detect and replace multiple pixel cosmic ray events.
+.le
+.ls window = 5
+Size of cosmic ray detection window.  A square window of either 5 by 5 or
+7 by 7 is used to detect cosmic rays.  The smaller window allows detection
+in the presence of greater background gradients but is less sensitive at
+discriminating multiple event cosmic rays from stars.  It is also marginally
+faster.
+.le
+.ls interactive = yes
+Examine parameters interactively?  A plot of the mean flux within the
+detection window (x100) vs the flux ratio (x100) is plotted and the user may
+set the flux ratio threshold, delete and undelete specific events, and
+examine specific events.  This is useful for new data in which one is
+uncertain of an appropriate flux ratio threshold.  Once determined the
+task need not be used interactively.
+.le
+.ls answer
+This parameter is used for interactive queries when processing a list of
+images.  The responses may be "no", "yes", "NO", or "YES".  The upper case
+responses permanently enable or disable the interactive review while
+the lower case reponses allow selective examination of certain input
+images.
+.le
+.ih
+OTHER PARAMETERS
+There are other parameters which may be defined by the package, as is the
+case with \fBccdred\fR, or as part of the task, as is the case with
+standalone version in the \fBgeneric\fR package.
+
+.ls verbose
+If yes then a time stamped log of the operation is printed on the standard
+output.
+.le
+.ls logfile
+If a log file is specified then a time stamped log of the operation is
+recorded.
+.le
+.ls plotfile
+If a plot file is specified then the graph of the flux ratio (x100) vs
+the mean flux (x100) is recorded as metacode.  This may be spooled or examined
+later.
+.le
+.ls graphics = "stdgraph"
+Interactive graphic output device for interactive examination of the
+detection parameters.
+.le
+.ls cursor = ""
+Interactive graphics cursor input.  If null the graphics display cursor
+is used, otherwise a file containing cursor input may be specified.
+.le
+.ls instrument
+The \fBccdred\fR instrument file is used for mapping header keywords and
+CCD image types.
+.le
+.ih
+CURSOR COMMANDS
+
+.nf
+d	Mark candidate for replacement (applys to '+' points)
+q	Quit and replace the selected pixels
+r	Redraw the graph
+s	Make a surface plot for the candidate nearest the cursor
+t	Set the flux ratio threshold at the y cursor position
+u	Mark candidate to not be replaced (applys to 'x' points)
+w	Adjust the graph window (see \fBgtools\fR)
+.fi
+
+There are no colon commands except those for the windowing options (type
+:\help or see \fBgtools\fR).
+.ih
+DESCRIPTION
+Cosmic ray events in each input image are detected and replaced by the
+average of the four neighbors.  The replacement may be performed
+directly on the input image if no output image is specified or if the
+output image name is the same as the input image name.  If a new image
+is created it is a copy of the input image except for the replaced
+pixels.  The processing keyword CRCOR is added to the output image
+header.  Optional output includes a log file to which a processing log
+is appended, a verbose log output to the standard output (the same as
+that in the log file), a plot file showing the parameters of the
+detected cosmic ray candidates and the flux ratio threshold used, and a
+bad pixel file containing the coordinates of the replaced pixels.  The
+bad pixel file may be used for plotting purposes or to create a mask
+image for display and analysis using the task \fBbadpiximage\fR.  This
+bad pixel file will be replaced by the IRAF bad pixel facility when it
+becomes available.  If one wants more than a simple mask image then by
+creating a different output image a difference image between the
+original and the modified image may be made using \fBimarith\fR.
+
+This task may be applied to an image previously processed to detect
+additional cosmic rays.  A warning will be given (because of the
+CRCOR header parameter) and the previous processing header keyword will
+be overwritten.
+
+The cosmic ray detection algorithm consists of the following steps.
+First a pixel must be the brightest pixel within the specified
+detection window (either 5x5 or 7x7).  The mean flux in the surrounding
+pixels with the second brightest pixel excluded (which may also be a
+cosmic ray event) is computed and the candidate pixel must exceed this
+mean by the amount specified by the parameter \fIthreshold\fR.  A plane
+is fit to the border pixels of the window and the fitted background is
+subtracted.  The mean flux (now background subtracted) and the ratio of
+this mean to the cosmic ray candidate (the brightest pixel) are
+computed.  The mean flux (x100) and the ratio (x100) are recorded for
+interactive examination if desired.
+
+Once the list of cosmic ray candidates has been created and a threshold
+for the flux ratio established (either by the parameter \fIfluxratio\fR
+or modified interactively) the pixels with ratios below the threshold
+are replaced in the output by the average of the four neighboring pixels
+(with the second strongest pixel in the detection window excluded if it is
+one of these pixels).  Additonal pixels may then be detected and replaced
+in further passes as specified by the parameter \fInpasses\fR.  Note that
+only pixels in the vicinity of replaced pixels need be considered in
+further passes.
+
+The division between the peaks of real objects and cosmic rays is made
+based on the flux ratio between the mean flux (excluding the center
+pixel and the second strongest pixel) and the candidate pixel.  This
+threshold depends on the point spread function and the distribution of
+multiple cosmic ray events and any additional neighboring light caused
+by the events.  This threshold is not strongly coupled to small changes
+in the data so that once it is set for a new type of image data it may
+be used for similar images.  To set it initially one may examine the
+scatter plot of the flux ratio as a function of the mean flux.  This
+may be done interactively or from the optional plot file produced.
+
+When the interactive flag is set the user is queried for each image.
+Responses may be made for specific images or for all images by using
+lower or upper case answers respectively.  When the parameters are
+examined interactively the user may change the flux ratio threshold
+('t' key).  Changes made are stored in the parameter file and, thus,
+learned for further images.  Pixels to be deleted are marked by crosses
+and pixels which are peaks of objects are marked by pluses.  The user
+may explicitly delete or undelete any point if desired but this is only
+for special cases near the threshold.  In the future keys for
+interactive display of the specific detections will be added.
+Currently a surface plot of any candidate may be displayed graphically
+in four 90 degree rotated views using the 's' key.  Note that the
+initial graph does not show all the points some of which are clearly
+cosmic rays because they have negative mean flux or flux ratio.  To
+view all data one must rewindow the graph with the 'w' key or ":/"
+commands (see \fBgtools\fR).
+.ih
+EXAMPLES
+1. To replace cosmic rays in a set of images ccd*:
+
+.nf
+	cl> cosmicrays ccd* new//ccd*
+	ccd001: Examine parameters interactively? (yes):
+	[A scatter plot graph is made.  One can adjust the threshold.]
+	[Looking at a few points using the 's' key can be instructive.]
+	[When done type 'q'.]
+	ccd002: Examine parameters interactively? (yes): NO
+	[No further interactive examination is done.]
+.fi
+
+After cleaning one typically displays the images and  possibly blinks them.
+A difference image or mask image may also be created.
+
+2.  To create a mask image a bad pixel file must be specified.  In the
+following we replace the cosmic rays in place and create a bad pixel
+file and mask image:
+
+.nf
+	cl> cosmicrays ccd001 ccd001 badpix=ccd001.bp
+	cl> badpiximage ccd001.bp ccd001 ccd001bp
+.fi
+.ih
+SEE ALSO
+badpixelimage gtools
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/darkcombine.hlp b/noao/imred/quadred/src/quad/doc/darkcombine.hlp
new file mode 100644
index 00000000..ef9eb81c
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/darkcombine.hlp
@@ -0,0 +1,125 @@
+.help darkcombine Sept93 arcon.quad
+.ih
+NAME
+darkcombine -- Combine and process dark count images
+.ih
+USAGE
+darkcombine input
+.ih
+PARAMETERS
+.ls input
+List of dark count images to combine.  The \fIccdtype\fR parameter
+may be used to select the zero level images from a list containing all
+types of data.
+.le
+.ls output = "Dark"
+Output dark count root image name.
+.le
+.ls combine = "average" (average|median)
+Type of combining operation performed on the final set of pixels (after
+rejection).  The choices are
+"average" or "median".  The median uses the average of the two central
+values when the number of pixels is even.
+.le
+.ls reject = "avsigclip" (none|minmax|ccdclip|crreject|sigclip|avsigclip|pclip)
+Type of rejection operation.  See \fBcombine\fR for details.
+.le
+.ls ccdtype = "zero"
+CCD image type to combine.  If no image type is given then all input images
+are combined.
+.le
+.ls process = no
+Process the input images before combining?
+.le
+.ls delete = no
+Delete input images after combining?  Only those images combined are deleted.
+.le
+.ls clobber = no
+Clobber existing output images?
+.le
+.ls scale = "none" (none|mode|median|mean|exposure)
+Multiplicative image scaling to be applied.  The choices are none, scale
+by the mode, median, or mean of the specified statistics section, or scale
+by the exposure time given in the image header.
+.le
+.ls statsec = ""
+Section of images to use in computing image statistics for scaling.
+If no section is given then the entire region of the image is
+sampled (for efficiency the images are sampled if they are big enough).
+.le
+
+.ce
+Algorithm Parameters
+.ls nlow = 1,  nhigh = 1 (minmax)
+The number of low and high pixels to be rejected by the "minmax" algorithm.
+.le
+.ls nkeep = 1
+The minimum number of pixels to retain or the maximum number to reject
+when using the clipping algorithms (ccdclip, crreject, sigclip,
+avsigclip, or pclip).  When given as a positive value this is the minimum
+number to keep.  When given as a negative value the absolute value is
+the maximum number to reject.  This is actually converted to a number
+to keep by adding it to the number of images.
+.le
+.ls mclip = yes (ccdclip, crreject, sigclip, avsigcliip)
+Use the median as the estimate for the true intensity rather than the
+average with high and low values excluded in the "ccdclip", "crreject",
+"sigclip", and "avsigclip" algorithms?  The median is a better estimator
+in the presence of data which one wants to reject than the average.
+However, computing the median is slower than the average.
+.le
+.ls lsigma = 3., hsigma = 3. (ccdclip, crreject, sigclip, avsigclip, pclip)
+Low and high sigma clipping factors for the "ccdclip", "crreject", "sigclip",
+"avsigclip", and "pclip" algorithms.  They multiply a "sigma" factor
+produced by the algorithm to select a point below and above the average or
+median value for rejecting pixels.  The lower sigma is ignored for the
+"crreject" algorithm.
+.le
+.ls rdnoise = "0.", gain = "1.", snoise = "0." (ccdclip, crreject)
+CCD readout noise in electrons, gain in electrons/DN, and sensitivity noise
+as a fraction.  These parameters are used with the "ccdclip" and "crreject"
+algorithms.  The values may be either numeric or an image header keyword
+which contains the value.
+.le
+.ls pclip = -0.5 (pclip)
+Percentile clipping algorithm parameter.  If greater than
+one in absolute value then it specifies a number of pixels above or
+below the median to use for computing the clipping sigma.  If less
+than one in absolute value then it specifies the fraction of the pixels
+above or below the median to use.  A positive value selects a point
+above the median and a negative value selects a point below the median.
+The default of -0.5 selects approximately the quartile point.
+See \fBcombine\fR for further details.
+.le
+.ls blank = 0.
+Output value to be used when there are no pixels.
+.le
+.ih
+DESCRIPTION
+The dark count images in the input image list are combined.
+The input images may be processed first if desired.
+The original images may be deleted automatically if desired.
+
+This task is a script which applies \fBquadproc\fR and \fBcombine\fR.  The
+parameters and combining algorithms are described in detail in the help for
+\fBcombine\fR.  This script has default parameters specifically set for
+dark count images and simplifies the combining parameters.  There are other
+combining options not included in this task.  For these additional
+features, such as thresholding, offseting, masking, and projecting, use
+\fBcombine\fR.
+
+The version of \fBdarkcombine\fR in the \fBquad\fR package differs from that
+in \fBccdred\fR in that \fBquadproc\fR rather than \fBccdproc\fR is used to
+process the images if this is requested. The \fBquad\fR version MUST be
+used if process=yes and the input list contains any multi-readout images which
+have not been overscan corrected and trimmed.
+.ih
+EXAMPLES
+1. The image data contains four dark count images.  To automatically select
+them and combine them as a background job using the default combining algorithm:
+
+    cl> darkcombine ccd*.imh&
+.ih
+SEE ALSO
+quadproc, combine
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/flatcombine.hlp b/noao/imred/quadred/src/quad/doc/flatcombine.hlp
new file mode 100644
index 00000000..c463655d
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/flatcombine.hlp
@@ -0,0 +1,139 @@
+.help flatcombine Sept93 arcon.quad
+.ih
+NAME
+flatcombine -- Combine and process flat field images
+.ih
+USAGE
+flatcombine input
+.ih
+PARAMETERS
+.ls input
+List of flat field images to combine.  The \fIccdtype\fR parameter
+may be used to select the flat field images from a list containing all
+types of data.
+.le
+.ls output = "Flat"
+Output flat field root image name.  The subset ID is appended.
+.le
+.ls combine = "average" (average|median)
+Type of combining operation performed on the final set of pixels (after
+rejection).  The choices are
+"average" or "median".  The median uses the average of the two central
+values when the number of pixels is even.
+.le
+.ls reject = "avsigclip" (none|minmax|ccdclip|crreject|sigclip|avsigclip|pclip)
+Type of rejection operation.  See \fBcombine\fR for details.
+.le
+.ls ccdtype = "flat"
+CCD image type to combine.  If no image type is given then all input images
+are combined.
+.le
+.ls process = no
+Process the input images before combining?
+.le
+.ls subsets = yes
+Combine images by subset parameter?  If yes then the input images are
+grouped by subset parameter and each group combined into a separate output
+image.  The subset identifier is appended to the output and sigma image
+names.  See \fBsubsets\fR for more on the subset parameter.  This is generally
+used with flat field images.
+.le
+.ls delete = no
+Delete input images after combining?  Only those images combined are deleted.
+.le
+.ls clobber = no
+Clobber existing output images?
+.le
+.ls scale = "none" (none|mode|median|mean|exposure)
+Multiplicative image scaling to be applied.  The choices are none, scale
+by the mode, median, or mean of the specified statistics section, or scale
+by the exposure time given in the image header.
+.le
+.ls statsec = ""
+Section of images to use in computing image statistics for scaling.
+If no section is given then the entire region of the image is
+sampled (for efficiency the images are sampled if they are big enough).
+.le
+
+.ce
+Algorithm Parameters
+.ls nlow = 1,  nhigh = 1 (minmax)
+The number of low and high pixels to be rejected by the "minmax" algorithm.
+.le
+.ls nkeep = 1
+The minimum number of pixels to retain or the maximum number to reject
+when using the clipping algorithms (ccdclip, crreject, sigclip,
+avsigclip, or pclip).  When given as a positive value this is the minimum
+number to keep.  When given as a negative value the absolute value is
+the maximum number to reject.  This is actually converted to a number
+to keep by adding it to the number of images.
+.le
+.ls mclip = yes (ccdclip, crreject, sigclip, avsigcliip)
+Use the median as the estimate for the true intensity rather than the
+average with high and low values excluded in the "ccdclip", "crreject",
+"sigclip", and "avsigclip" algorithms?  The median is a better estimator
+in the presence of data which one wants to reject than the average.
+However, computing the median is slower than the average.
+.le
+.ls lsigma = 3., hsigma = 3. (ccdclip, crreject, sigclip, avsigclip, pclip)
+Low and high sigma clipping factors for the "ccdclip", "crreject", "sigclip",
+"avsigclip", and "pclip" algorithms.  They multiply a "sigma" factor
+produced by the algorithm to select a point below and above the average or
+median value for rejecting pixels.  The lower sigma is ignored for the
+"crreject" algorithm.
+.le
+.ls rdnoise = "0.", gain = "1.", snoise = "0." (ccdclip, crreject)
+CCD readout noise in electrons, gain in electrons/DN, and sensitivity noise
+as a fraction.  These parameters are used with the "ccdclip" and "crreject"
+algorithms.  The values may be either numeric or an image header keyword
+which contains the value.
+.le
+.ls pclip = -0.5 (pclip)
+Percentile clipping algorithm parameter.  If greater than
+one in absolute value then it specifies a number of pixels above or
+below the median to use for computing the clipping sigma.  If less
+than one in absolute value then it specifies the fraction of the pixels
+above or below the median to use.  A positive value selects a point
+above the median and a negative value selects a point below the median.
+The default of -0.5 selects approximately the quartile point.
+See \fBcombine\fR for further details.
+.le
+.ls blank = 1.
+Output value to be used when there are no pixels.
+.le
+.ih
+DESCRIPTION
+The flat field images in the input image list are combined.  If there
+is more than one subset (such as a filter or grating) then the input
+flat field images are grouped by subset and an combined separately.
+The input images may be processed first if desired.  However if all
+zero level bias effects are linear then this is not necessary and some
+processing time may be saved.  The original images may be deleted
+automatically if desired.
+
+This task is a script which applies \fBquadproc\fR and \fBcombine\fR.  The
+parameters and combining algorithms are described in detail in the help for
+\fBcombine\fR.  This script has default parameters specifically set for
+flat field images and simplifies the combining parameters.  There are other
+combining options not included in this task.  For these additional
+features, such as thresholding, offseting, masking, and projecting, use
+\fBcombine\fR.
+
+The version of \fBzerocombine\fR in the \fBquad\fR package differs from that
+in \fBccdred\fR in that \fBquadproc\fR rather than \fBccdproc\fR is used to
+process the images if this is requested. The \fBquad\fR version MUST be
+used if process=yes and the input list contains any multi-readout images which
+have not been overscan corrected and trimmed.
+.ih
+EXAMPLES
+1. The image data contains four flat field images for three filters.
+To automatically select them and combine them as a background job
+using the default combining algorithm:
+
+    cl> flatcombine ccd*.imh&
+
+The final images are "FlatV", "FlatB", and "FlatR".
+.ih
+SEE ALSO
+quadproc, combine, subsets
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/flatfields.hlp b/noao/imred/quadred/src/quad/doc/flatfields.hlp
new file mode 100644
index 00000000..94766960
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/flatfields.hlp
@@ -0,0 +1,177 @@
+.help flatfields Jun87 noao.imred.ccdred
+
+.ih
+NAME
+flatfields -- Discussion of CCD flat field calibrations
+.ih
+DESCRIPTION
+This topic describes the different types of CCD flat fields and
+the tasks available in the \fBccdred\fR and spectroscopy packages for
+creating them.  Flat field calibration is the most important operation
+performed on CCD data.  This operation calibrates the relative response
+of the detector at each pixel.  In some cases this is as simple as
+taking a special type of observation called a flat field.  However, in
+many cases this calibration observation must be corrected for
+iillumination, scanning, wavelength, and aperture effects.
+
+The discussion is in three sections; direct imaging, scan mode,
+and spectroscopy.  Though there are many similarities between these
+modes of operation there are important differences in how corrections
+are applied to the basic flat field observations.  The application of
+the flat field calibrations to the observations using \fBccdproc\fR is
+the same in all cases, however.
+.sh
+1. Direct Imaging
+The starting point for determining the flat field calibration is an
+observation of something which should have uniform response at all
+points on the detector.  In addition the color of the light falling at
+each pixel should be the same as that in an observation so the same
+filter must be used when determining the flat field (the issue of the
+matching the color of the objects observed at the appropriate pixels is
+ignored here).  The best calibration observation is of a blank sky.  If
+an accurate blank sky observation can be obtained then this is all that
+is needed for a flat field calibration.  This type of flat field might
+be called a \fIsky flat\fR, though this term is more often used for a
+type of flat field described below.  There are two difficulties with
+this type of calibration; finding a really blank sky and getting a
+sufficiently accurate measurement without using all the observing
+time.
+
+It is usually not possible to get a blank sky observation accurate
+enough to calibrate the individual pixels without introducing
+undesirable noise.  What is generally done is to use a lamp to either
+uniformly illuminate a part of the dome or directly illuminate the
+field of view.  The first type of observation is called a \fIdome
+flat\fR and the second is called a \fIprojection flat\fR.  We shall call
+both of these types of observations \fBlamp flat fields\fR.  If the
+iillumination is truely uniform then these types of observations are
+sufficient for flat field calibration.  To get a very accurate flat
+field many observations are made and then combined (see
+\fBflatcombine\fR).
+
+Unfortunately, it is sometimes the case that the lamp flat fields
+do not illuminate the telescope/detector in the same way as the actual
+observations.  Calibrating with these flat fields will introduce a
+residual large scale iillumination pattern, though it will correctly
+calibrate the relative pixel responses locally.  There are two ways to
+correct for this effect.  The first is to correct the flat field
+observation.  The second is to apply the uncorrected flat field to the
+observations and then apply an \fIiillumination\fR correction as a
+separate operation.  The first is more efficient since it consists of a
+single correction applied to each observation but in some cases the
+approximate correction is desired immediately, the observation needed
+to make the correction has not been taken yet, or the residual
+iillumination error is not discovered until later.
+
+For the two methods there are two types of correction.  One is to
+use a blank sky observation to correct for the residual iillumination
+pattern.  This is different than using the sky observation directly as
+a flat field calibration in that only the large scale pattern is
+needed.  Determining the large scale iillumination does not require high
+signal-to-noise at each pixel and faint objects in the image can be
+either eliminated or ignored.  The second method is to remove the large
+scale shape from the lamp flat field.  This is not as good as using a
+blank sky observation but, if there is no such observation and the
+iillumination pattern is essentially only in the lamp flat field, this
+may be sufficient.
+
+From the above two paragraphs one sees there are four options.
+There is a task in the \fBccdred\fR package for each of these options.
+To correct a lamp flat field observation by a blank sky observation,
+called a \fIsky flat\fR, the task is \fBmkskyflat\fR.  To correct the
+flat field for its own large scale gradients, called an \fIiillumination
+flat\fR, the task is \fBmkillumflat\fR.  To create a secondary
+correction to be applied to data processed with the lamp flat field
+image the tasks are \fBmkskycor\fR and \fBmkillumcor\fR which are,
+respectively, based on a blank sky observation and the lamp flat field
+iillumination pattern.
+
+With this introduction turn to the individual documentation for these
+four tasks for further details.
+.sh
+2. Scan Mode
+There are two types of scan modes supported by the \fBccdred\fR
+package; \fIshortscan\fR and \fIlongscan\fR (see \fBccdproc\fR for
+further details).  They both affect the manner in which flat field
+calibrations are handled.  The shortscan mode produces images which are
+the same as direct images except that the light recorded at each pixel
+was collected by a number of different pixels.  This improves the flat
+field calibration.  If the flat field images, of the same types
+described in the direct imaging section, are observed in the same way
+as all other observations, i.e. in scan mode, then there is no
+difference from direct imaging (except in the quality of the flat
+fields).  There is a statistical advantage to observing the lamp or sky
+flat field without scanning and then numerically averaging to simulate
+the result of the scanning.  This improves the accuracy of
+the flat fields and might possibly allow direct blank sky observations
+to be used for flat fields.  The numerical scanning is done in
+\fBccdproc\fR by setting the appropriate scanning parameters.
+
+In longscan mode the CCD detector is read out in such a way that
+each output image pixel is the sum of the light falling on all pixels
+along the direction of the scan.  This reduces the flat field calibration
+to one dimension, one response value for each point across the scan.
+The one dimensional calibration is obtained from a longscan observation
+by averaging all the readout lines.
+This is done automatically in \fBccdproc\fR by setting the appropriate
+parameters.  In this case very good flat fields can be obtained from
+one or more blank sky observations or an unscanned lamp observation.  Other
+corrections are not generally used.
+.sh
+3. Spectroscopy
+Spectroscopic flat fields differ from direct imaging in that the
+spectrum of the sky or lamp and transmission variations with wavelength
+are part of the observation.  Application of such images will introduce
+the inverse of the spectrum and transmission into the observation.  It
+also distorts the observed counts making signal-to-noise estimates
+invalid.  This, and the low signal in the dispersed light, makes it
+difficult to use blank sky observations directly as flat fields.  As
+with direct imaging, sky observation may be used to correct for
+iillumination errors if necessary.  At sufficiently high dispersion the
+continuous lamp spectrum may be flat enough that the spectral signature
+of the lamp is not a problem.  Alternatively, flux calibrating the
+spectra will also remove the flat field spectral signature.  The
+spectroscopic flat fields also have to be corrected for regions outside
+of the slit or apertures to avoid bad response effects when applying
+the flat field calibration to the observations.
+
+The basic scheme for removing the spectral signature is to average
+all the lines or columns across the dispersion and within the aperture
+to form an estimate of the spectrum.  In addition to the averaging, a
+smooth curve is fit to the lamp spectrum to remove noise.  This smooth
+shape is then divided back into each line or column to eliminate the
+shape of the spectrum without changing the shape of the spectrum
+in the spatial direction or the small scale response variations.
+Regions outside of the apertures are replaced by unity.
+This method requires that the dispersion be aligned fairly close to
+either the CCD lines or columns.
+
+This scheme is used in both longslit and multiaperture spectra.
+The latter includes echelle, slitlets, aperture masks, and fiber feeds.
+For narrow apertures which do not have wider slits for the lamp
+exposures there may be problems with flexure and defining a good
+composite spectrum.  The algorithm for longslit spectra is simpler and
+is available in the task \fBresponse\fR in the \fBlongslit\fR package.
+For multiaperture data there are problems of defining where the spectra
+lie and avoiding regions off of the aperture where there is no signal.
+The task which does this is \fBapnormalize\fR in the \fBapextract\fR
+package.   Note that the lamp observations must first be processed
+explicitly for bias and dark count corrections.
+
+Longslit spectra may also suffer the same types of iillumination
+problems found in direct imaging.  However, in this case the iillumination
+pattern is determined from sky observations (or the flat field itself)
+by finding the large scale pattern across the dispersion and at a number
+of wavelengths while avoiding the effects of night sky spectrum.  The
+task which makes this type of correction in the \fBlongslit\fR package
+is \fBiillumination\fR.  This produces an iillumination correction.
+To make sky flats or the other types of corrections image arithmetic
+is used.  Note also that the sky observations must be explicitly
+processed through the flat field stage before computing the iillumination.
+.ih
+SEE ALSO
+.nf
+ccdproc, guide, mkillumcor, mkillumflat, mkskycor, mkskyflat
+apextract.apnormalize, longslit.response, longslit.iillumination
+.fi
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/guide.hlp b/noao/imred/quadred/src/quad/doc/guide.hlp
new file mode 100644
index 00000000..d7639a6f
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/guide.hlp
@@ -0,0 +1,715 @@
+.help guide Sept93 arcon.quad
+.ce
+User's Guide to the QUAD Package
+.sh
+1. Introduction
+
+     This guide provides a brief description of the \fBquad\fR package including
+examples of its use for reducing simple CCD data. The \fBquad\fR package 
+contains all the basic tasks necessary for the reduction of CCD data obtained
+using the CTIO array controller Arcon. It is based on the IRAF CCD reduction
+package \fBccdred\fR written by Frank Valdes. It incorporates a few special
+tasks needed to deal with the peculiarities of Arcon data but most of the
+routines are taken directly from the standard package. The way in which one
+uses the routines and the basic reduction recipe is unchanged.
+
+This guide is generic in that it is not tied to any particular type of data.
+There may be more specific guides (or "cookbooks") for your data. Detailed
+descriptions of the tasks and features of the package are provided in the help
+documentation for the package.
+
+With Arcon the CCD is often readout using four ("quad") or two ("dual")
+amplifiers in order to reduce readout time. A feature of such images is that
+each readout typically has a slightly different, DC bias level, gain, and
+readout noise. As a result both zero frames and uniformly illuminated
+exposures show a characteristic chequer board pattern, the sections of the
+image read through each amplifier having different levels. In addition, there
+will be a separate overscan strip, used to monitor the zero level, for each
+readout. The location of these overscan strips in the raw frame depends on
+which amplifiers are used (for more on this see \fBquadreadout\fR). Because
+of these peculiarities the \fBquad\fR package must be used for the first
+reduction steps, overscan correction and trimming, of multi-readout images; 
+subsequent steps can be performed using \fBquad\fR or \fBccdred\fR. Either
+package can be used for the complete reduction of conventional single readout
+CCD images.
+
+     The purpose of \fBquad\fR package is to provide tools for the removal of 
+all the "instrumental signatures" from CCD data taken with Arcon. The standard
+reduction operations are: replacement of bad columns and lines by interpolation
+from neighboring columns and lines; subtraction of a bias level
+determined from overscan or prescan columns or lines; subtraction of a
+zero level using a zero exposure time calibration image; subtraction
+of a dark count calibration image appropriately scaled to the dark time
+exposure; division by a scaled flat field calibration image; division
+by an iillumination image (derived from a blank sky image); subtraction
+of a scaled fringe image (also derived from a blank sky image); and
+trimming the image of unwanted lines or columns such as the overscan
+strip.  Any set of these operations may be done simultaneously over a list of
+images in a highly efficient manner.  The reduction operations are
+recorded in the image header and may also be logged on the terminal and
+in a log file.
+
+     The package also provides tools for combining multiple exposures
+of object and calibration images to improve the statistical accuracy of
+the observations and to remove transient bad pixels.  The combining
+operation scales images of different exposure times, adjusts for
+variable sky background, statistically weights the images by their
+signal-to-noise, and provides a number of useful algorithms for
+detecting and rejecting transient bad pixels.
+
+     Other tasks are provided for listing reduction information about
+the images, deriving secondary calibration images (such as sky
+corrected flat fields or iillumination correction images), and easily
+setting the package parameters for different instruments.
+
+The \fBquad\fR package also includes some tasks which can be used for the
+examination of multi-readout images, prior to reducing them, by for instance
+calculating simple image statistics, generating histograms, etc. 
+
+     There are several important features provided by the \fBccdred\fR package 
+underpining \fBquad\fR,  which makes the reduction of CCD images convenient;
+particularly to minimize record keeping.  One of these is the ability to 
+recognize the different types of CCD images.  This ability allows the user to 
+select a certain class of images to be processed or listed and allows the
+processing tasks to identify calibration images and process them differently 
+from object images.  The standard CCD image types are \fIobject\fR,
+\fIzero\fR level, \fIdark\fR count, and \fIflat\fR field.  For more on
+the image types see \fBccdtypes\fR.
+
+     The tasks can also identify the different filters (or other subset
+parameter) which require different flat field images.  This means you don't
+have to separate the images by filter and process each set separately.
+This feature is discussed further in \fBsubsets\fR.
+
+     The tasks keep track of the reduction steps completed on each
+image and ignore images which have been processed.  This feature,
+along with recognizing the image types and subsets, makes it possible to
+specify all the images to a task with a wildcard template, such as
+"*.imh", rather than indicating each image by name.  You will find this
+extremely important with large sets of observations.
+
+     A fundamental aspect of the package is that the processing
+modifies the images.  In other words, the reduction operations are
+performed directly on the image.  This "feature" further simplifies
+record keeping, frees the user from having to form unique output image
+names, and minimizes the amount of disk space required.  There
+are two safety features in this process.  First, the modifications do
+not take effect until the operation is completed on the image.  This
+allows you to abort the task without messing up the image data and
+protects data if the computer crashes.  The second feature is that
+there is a package parameter which may be set to make a backup of the
+input data with a particular prefix such as "orig" or "imdir$".  This
+backup feature may be used when there is sufficient disk space, when learning
+to use the package, or just to be cautious.
+
+     In a similar effort to efficiently manage disk space, when combining
+images into a master object or calibration image there is an option to
+delete the input images upon completion of the combining operation.
+Generally this is desirable when there are many calibration exposures,
+such as zero level or flat field images, which are not used after they
+are combined into a final calibration image.
+
+     The following sections guide you through the basic use of the
+\fBquad\fR package.  Only the important parameters which you might
+want to change are described.  It is assumed that the support personnel
+have created the necessary instrument files (see \fBinstruments\fR)
+which will set the default parameters for the data you will be
+reducing.  If this is not the case you may need to delve more deeply
+into the details of the tasks.  Information about all the parameters
+and how the various tasks operate are given in the help documentation
+for the tasks and in additional special help topics.  Some useful help
+documentation is indicated in the discussion and also in the
+\fBReferences\fR section.
+.sh
+2. Getting Started
+
+     The first step is to load \fBquad\fR.  This is done by loading
+the \fBarcon\fR package, and then the \fBquad\fR package.  Loading a
+package consists of typing its name. 
+
+     When you load the \fBquad\fR package the menu of tasks or commands
+is listed.  This appears as follows:
+
+.nf
+  cl> quad
+      badpiximage       combine           mkillumcor        qstatistics
+      ccdgroups         cosmicrays        mkillumflat       quadproc
+      ccdhedit          darkcombine       mkskycor          quadscale
+      ccdinstrument     flatcombine       mkskyflat         setinstrument
+      ccdlist           mkfringecor       qhistogram        zerocombine
+.fi
+
+A summary of the tasks and additional help topics is obtained by typing:
+
+    cl> help
+
+This list and how to get additional help on specific topics is described
+in the \fBReferences\fR section at the end of this guide.
+
+     The first command to use is \fBsetinstrument\fR, which sets the package
+appropriately for the CCD images to be reduced.  The support personnel
+should tell you the instrument identification, but if not a list
+of known instruments may be listed by using '?' for the instrument name.
+
+.nf
+    cl> setinstrument
+    Instrument ID (type ? for a list) \fI<enter instrument id or ?>\fR
+        <Set quad package parameters using eparam>
+        <Set quadproc task parameters using eparam>
+.fi
+
+This task sets the default parameters and then allows you to modify the
+package parameters and the processing parameters using the parameter
+editor \fBeparam\fR.  If you are not familiar with \fBeparam\fR see the
+help or CL introduction documentation.  For most terminals you move up
+and down through the parameters with the terminal arrow keys, you
+change the parameters by simply typing the desired value, and you exit
+with control Z or control D.  Note that you can change parameters for
+any task at any time with \fBeparam\fR and you do not have to run
+\fBsetinstrument\fR again, even if you logout, until you need to reduce
+data from a different instrument.
+
+     The \fBquad\fR package parameters control general I/O functions of
+the tasks in the package.  The parameters you might wish to change are
+the output pixel type and the verbose option.  Except when the input
+images are short integers, the noise is significantly greater than one
+digital unit, and disk space is critical, it is probably better to
+allow the processing to convert the images to real pixel datatype.  The
+verbose parameter simply prints the information written to the log file
+on the terminal.  This can be useful when little else is being done and
+you are just beginning.  However, when doing background processing and
+other IRAF reduction tasks it is enough to simply look at the end of
+the logfile with the task \fBtail\fR to see the current state of the
+processing.
+
+     The \fBquadproc\fR parameters control the CCD processing.  There are
+many parameters but they all may be conveniently set at this point.
+Many of the parameters have default values set appropriately for the
+instrument you specified.  The images to be processed can be specified
+later.  What needs to be set are the processing operations that you
+want done and the parameters required for each operation.  The
+processing operations are selected by entering yes or no for each one.
+The following items briefly describe each of the possible processing
+operations and the additional parameters required.
+
+.ls \fIfixpix\fR - Fix bad CCD lines and columns?
+The bad pixels (cosmetic defects) in the detector are given in a file
+specified by the parameter \fIfixfile\fR.  This information is used
+to replace the pixels by interpolating from the neighboring pixels.
+A standard file for your instrument may be set by \fBsetinstrument\fR
+or if the word "image" is given then the file is defined in the instrument
+data file.  For more on the bad pixel file see \fBinstruments\fR.
+.le
+.ls \fIoverscan\fR - Apply overscan strip correction?
+The overscan or prescan region is specified by the parameter
+\fIbiassec\fR.  This is given as an IRAF image section. For guidance on 
+seting this parameter see the help page for \fBquadproc\fR. The overscan
+region is averaged along the readout axis, specified by the parameter
+\fIreadaxis\fR, to create a one dimensional bias vector.  This bias is
+fit by a function to remove cosmic rays and noise.  There are a number
+of parameters at the end of the parameter list which control the
+fitting.
+.le
+.ls \fItrim\fR - Trim the image?
+The image is trimmed to the image section given by the parameter
+\fItrimsec\fR. For guidance on setting this parameter see the help page
+for \fBquadproc\fR.
+.le
+.ls \fIzerocor\fR - Apply zero level correction?
+The zero level image to be subtracted is specified by the parameter
+\fIzero\fR.  If none is given then the calibration image will be sought
+in the list of images to be processed.
+.le
+.ls \fIdarkcor\fR - Apply dark count correction?
+The dark count image to be subtracted is specified by the parameter
+\fIdark\fR.  If none is given then the calibration image will be sought
+in the list of images to be processed.
+.le
+.ls \fIflatcor\fR - Apply flat field correction?
+The flat field images to be used are specified by the parameter
+\fIflat\fR.  There must be one flat field image for each filter
+or subset (see \fBsubsets\fR) to be processed.  If a flat field
+image is not given then the calibration image will be sought
+in the list of images to be processed.
+.le
+.ls \fIreadcor\fR - Convert zero level image to readout correction?
+If a one dimensional zero level readout correction vector is to be subtracted
+instead of a two dimensional zero level image then, when this parameter is set,
+the zero level images will be averaged to one dimension.  The readout axis
+must be specified by the parameter \fIreadaxis\fR.  The default for your
+instrument is set by \fBsetinstrument\fR.
+.le
+.ls \fIscancor\fR - Convert flat field image to scan correction?
+If the instrument is operated in a scan mode then a correction to the
+flat field may be required.  There are two types of scan modes, "shortscan"
+and "longscan".  In longscan mode flat field images will be averaged
+to one dimension and the readout axis must be specified.  Shortscan mode
+is a little more complicated.  The scan correction is used if the flat
+field images are not observed in scan mode.  The number of scan lines
+must be specified by the parameter \fInscan\fR.  If they are observed in
+scan mode, like the object observations, then the scan correction
+operations should \fInot\fR be specified.  For details of scan mode operations
+see \fBquadproc\fR.  The scan parameters
+should be set by \fBsetinstrument\fR.  If in doubt consult someone
+familiar with the instrument and mode of operation.
+.le
+
+     This description of the parameters is longer than the actual operation of
+setting the parameters.  The only parameters likely to change during processing
+are the calibration image parameters.
+
+     When processing many images using the same calibration files a modest
+performance improvement can be achieved by keeping (caching) the
+calibration images in memory to avoid disk accesses.  This option
+is available by specifying the amount of memory available for image
+caching with the parameter \fImax_cache\fR.  If the value is zero then
+the images are accessed from disk as needed while if there is
+sufficient memory the calibration images may be kept in memory during
+the task execution.
+.sh
+3. Processing Your Data
+
+     The processing path depends on the type of data, the type of
+instrument, types of calibration images, and the observing
+sequence.  In this section we describe two types of operations common
+in reducing most data; combining calibration images and performing the
+standard calibration and correction operations.  Some additional special
+operations are described in the following section.
+
+     However, the first thing you might want to try before any
+processing is to get a listing of the CCD images showing the CCD image
+types, subsets, and processing flags.  The task for this is
+\fBccdlist\fR.  It has three types of output; a short one line per
+image format, a longer format which shows the state of the processing,
+and a format which prints the image names only (used to create files
+containing lists of images of a particular CCD image type).  To get a
+quick listing type:
+
+.nf
+    cl> ccdlist *.imh
+    ccd001.imh[544,512][short][unknown][V]:FOCUS L98-193
+    ccd007.imh[544,512][short][object][V]:N2968 V 600s
+    ccd015.imh[544,512][short][object][B]:N3098 B 500s
+    ccd024.imh[544,512][short][object][R]:N4036 R 600s
+    ccd045.imh[544,512][short][flat][V]:dflat 5s
+    ccd066.imh[544,512][short][flat][B]:dflat 5s
+    ccd103.imh[544,512][short][flat][R]:dflat 5s
+    ccd104.imh[544,512][short][zero][]:bias
+    ccd105.imh[544,512][short][dark][]:dark 3600s
+.fi
+
+     The example shows only a sample of the images.  The short format
+listing tells you the name of the image, its size and pixel type, the
+CCD image type as seen by the package, the subset identifier (in this
+case the filter), and the title.  If the data had been processed then
+there would also be processing flags.  If the CCD image types do not
+seem right then there may be a problem with the instrument
+specification.
+
+     Many of the tasks in the \fBquad\fR package have the parameter
+\fIccdtype\fR which selects a particular type of image.  To list
+only the object images from the previous example:
+
+.nf
+    cl> ccdlist *.imh ccdtype=object
+    ccd007.imh[544,512][short][object][V]:N2968 V 600s
+    ccd015.imh[544,512][short][object][B]:N3098 B 500s
+    ccd024.imh[544,512][short][object][R]:N4036 R 600s
+.fi
+
+If no CCD image type is specified (by using the null string "")
+then all image types are selected.  This may be
+necessary if your instrument data does not contain image type identifications.
+.sh
+3.1 Combining Calibration Images
+
+     If you do not need to combine calibration images because you only
+have one image of each type, you can skip this section.  Calibration
+images, particularly zero level and flat field images, are combined in
+order to minimize the effects of noise and reject cosmic ray hits in the
+calibrations.  The basic tool for combining images is the task
+\fBcombine\fR.  There are simple variants of this task whose default
+parameters are set appropriately for each type of calibration image.
+These are the ones you will use for calibration images leaving
+\fBcombine\fR for combining object images.  Zero level images are
+combined with \fBzerocombine\fR, dark count images with
+\fBdarkcombine\fR, and flat field images with \fBflatcombine\fR.
+
+     For example, to combine flat field images the command is:
+
+.nf
+    cl> flatcombine *.imh
+    Jun  1 14:26 combine: maxreject
+            Images      N    Exp   Mode  Scale Offset Weight
+        ccd045.imh      1    5.0  INDEF  1.000     0.  0.048
+        ccd046.imh      1    5.0  INDEF  1.000     0.  0.048
+        	<... list of files ...>
+        ccd065.imh      1    5.0  INDEF  1.000     0.  0.048
+        ----------- ------ ------
+         FlatV.imh     21    5.0
+.fi
+
+This output is printed when verbose mode is set.  The same information
+is recorded in the log file.  In this case the flat fields are combined
+by rejecting the maximum value at each point in the image (the
+"maxreject" algorithm).  The images are scaled by the exposure times,
+which are all the same in this example.  The mode is not evaluated for
+exposure scaling and the relative weights are the same because the
+exposure times are the same.  The example only shows part of the
+output; \fBflatcombine\fR automatically groups the flat field images by
+filter to produce the calibration images "FlatV", "FlatB", and
+"FlatR".
+.sh
+3.2 Calibrations and Corrections
+
+     Processing the CCD data is easy and largely automated.
+First, set the task parameters with the following command:
+
+    cl> eparam quadproc
+
+You may have already set the parameters when you ran
+\fBsetinstrument\fR, though the calibration image parameters
+\fIzero\fR, \fIdark\fR, and \fIflat\fR may still need to be set or
+changed.  Once this is done simply give the command
+
+.nf
+    cl> quadproc *.imh
+    ccd003: Jun  1 15:13 Overscan section is [520:540,*] with mean=485.0
+    ccd003: Jun  1 15:14 Trim data section is [3:510,3:510]
+    ccd003: Jun  1 15:14 Overscan section is [520:540,*] with mean=485.0
+    FlatV:  Jun  1 15:14 Trim data section is [3:510,3:510]
+    FlatV:  Jun  1 15:15 Overscan section is [520:540,*] with mean=486.4
+    ccd003: Jun  1 15:15 Flat field image is FlatV.imh with scale=138.2
+    ccd004: Jun  1 15:16 Trim data section is [3:510,3:510]
+    ccd004: Jun  1 15:16 Overscan section is [520:540,*] with mean=485.2
+    ccd004: Jun  1 15:16 Flat field image is FlatV.imh with scale=138.2
+                <... more ...>
+    ccd013: Jun  1 15:22 Trim data section is [3:510,3:510]
+    ccd013: Jun  1 15:23 Overscan section is [520:540,*] with mean=482.4
+    FlatB:  Jun  1 15:23 Trim data section is [3:510,3:510]
+    FlatB:  Jun  1 15:23 Overscan section is [520:540,*] with mean=486.4
+    ccd013: Jun  1 15:24 Flat field image is FlatB.imh with scale=132.3
+                <... more ...>
+.fi
+
+     The output shown is with verbose mode set.  It is the same as
+recorded in the log file.  It illustrates the principle of automatic
+calibration image processing.  The first object image, "ccd003", was
+being processed when the flat field image was required.  Since the
+image was taken with the V filter the appropriate flat field was
+determined to be "FlatV".  Since it had not been processed, the
+processing of "ccd003" was interrupted to process "FlatV".  The
+processed calibration image may have been cached if there was enough
+memory.  Once "FlatV" was processed (note that the flat field was not
+flattened because the task knows this image is a flat field) the
+processing of "ccd003" was completed.  The next image, "ccd004", is
+also a V filter image so the already processed, and possibly cached,
+flat field "FlatV" is used again.  The first B band image is "ccd013"
+and, as before, the B filter flat field calibration image is processed
+automatically.  The same automatic calibration processing and image
+caching occurs when using zero level and dark count calibration
+images.
+
+     Commonly the processing is done with the verbose mode turned off
+and the task run as a background job.  This is done with the commands
+
+.nf
+    cl> quad.verbose=no
+    cl> quadproc *.imh &
+.fi
+
+The already processed images in the input list are recognized as having been
+processed and are not affected.  To check the status of the processing we
+can look at the end of the log file with:
+
+    cl> tail logfile
+
+After processing we can repeat the \fBccdlist\fR command to find:
+
+.nf
+    cl> ccdlist *.imh ccdtype=object
+    ccd007.imh[508,508][real][object][V][OTF]:N2968 V 600s
+    ccd015.imh[508,508][real][object][B][OTF]:N3098 B 500s
+    ccd024.imh[544,512][short][object][R][OTF]:N4036 R 600s
+.fi
+
+The processing flags indicate the images have been overscan corrected,
+trimmed, and flat fielded.
+
+     As you can see, processing images is very easy.  There is one source
+of minor confusion for beginning users and that is dealing with calibration
+images.  First, there is no reason that calibration images
+may not be processed explicitly with \fBquadproc\fR, just remember to set
+the \fIccdtype\fR to the calibration image type or to "".  When processing
+object images the calibration images to be used may be specified either
+with the task parameter for the particular calibration image or by
+including the calibration image in the list of input images.  Calibration
+images specified by parameter value take precedence and the task
+does not check its CCD image type.  Calibration images given in the
+input list must have a valid CCD image type.  In case too many
+calibration images are specified, say because the calibration images
+combined to make the master calibration images were not deleted and
+so are part of the image list "*.imh", only the first one will be used.
+Another point to know is that flat field, iillumination, and fringe images
+are subset (filter) dependent and so a calibration image for each filter
+must be specified.
+.sh
+4. Special Processing Operations
+
+     The special processing operations are mostly concerned with the
+flat field response correction.  There are also special processing
+operations available in \fBquadproc\fR for one dimensional readout
+corrections in the zero level and flat field calibrations.  These
+were described briefly above and in more detail in \fBquadproc\fR
+and are not discussed further in this guide.  The processing
+operations described in this section are for preparing flat fields
+for two dimensional spectroscopic data, for correcting flat fields
+for iilluminations effects, for making a separate iillumination correction,
+and for applying corrections for fringe effects.  For additional
+discussion about flat fields and iillumination corrections see the
+help topic \fBflatfields\fR.
+.sh
+4.1 Spectroscopic Flat Fields
+
+     For spectroscopic data the flat fields may have to be processed to
+remove the general shape of the lamp spectrum and to replace regions outside
+of the aperture where there is no flat field information with values that
+will not cause bad response effects when the flat field is applied to the
+data.  If the shape of the lamp spectrum is not important and if the
+longslit spectra have the regions outside of the slit either off the
+detector or trimmed then you may use the flat field without special
+processing.
+
+   First you must process the flat field images explicitly with
+
+    cl> quadproc *.imh ccdtype=flat
+
+where "*.imh" may be replaced with any list containing the flat fields.
+If zero level and dark count corrections are required these calibration
+images must be available at this time.
+
+     Load the \fBtwodspec\fR package and then either the \fBlongslit\fR
+package, for longslit data, or the \fBapextract\fR package, for
+multiaperture data such as echelles, multifiber, or aperture mask
+spectra.  The task for removing the longslit quartz spectrum is
+\fBresponse\fR.  There is also a task for removing iillumination
+effects, including the slit profile, from longslit spectra called
+\fBiillumination\fR.  For more about processing longslit spectra see the
+help for these tasks and the paper \fIReduction of Longslit Spectra
+with IRAF\fR.  The cookbook \fIReduction of Longslit Spectroscopic
+Data Using IRAF (KPNO ICCD and Cryogenic Camera Data)\fR also provides
+a very good discussion even if your data is from a different instrument.
+
+     For multiaperture data the task for removing the relative shapes of
+the spectra is called \fBapnormalize\fR.  Again, consult the help documentation
+for this task for further details.  Since you will probably also be
+using the package for extracting the spectra you may be interested
+in the document \fIThe IRAF APEXTRACT Package\fR.
+.sh
+4.2 Iillumination Corrections
+
+     The flat field calibration images may not have the same iillumination
+pattern as the observations of the sky due to the way the lamp illuminates the
+optical system.  In this case when the flat field correction is applied
+to the data there will be gradients in the sky background.  To remove
+these gradients a blank sky calibration image is heavily smoothed
+to produce an iillumination image.  The iillumination image
+is then divided into the images during processing to correct for the
+iillumination difference between the flat field and the objects.
+Like the flat fields, the iillumination corrections images may be subset
+dependent so there should be an iillumination image for each subset.
+
+The task which makes iillumination correction images is \fBmkskycor\fR.
+Some examples are
+
+.nf
+    cl> mkskycor sky004 Illum004
+    cl> mkskycor sky*.imh ""
+.fi
+
+In the first example the sky image "sky004" is used to make the iillumination
+correction image "Illum004".  In the second example the sky images are
+converted to iillumination correction images by specifying no output image
+names.  Like \fBquadproc\fR if the input images have not been processed they
+are first processed automatically.
+
+To apply the iillumination correction
+
+.nf
+    cl> quadproc *.imh ccdtype=object illumcor+ illum=Illum004
+    cl> quadproc *.imh ccdtype=object illumcor+ illum=sky*.imh
+.fi
+
+The iillumination images could also be set using \fBeparam\fR or given
+on the command line.
+.sh
+4.3 Sky Flat Fields
+
+    You will notice that when you process images with an iillumination
+correction you are dividing each image by a flat field calibration and
+an iillumination correction.  If the iillumination corrections are not
+done as a later step but at the same time as the rest of the processing
+one will get the same calibration by multiplying the flat field by
+the iillumination correction and using this product alone as the
+flat field.  Such an image is called a \fIsky flat\fR since it is
+a flat field which has been corrected to yield a flat sky when applied
+to the observations.  This approach has the advantage of one less
+calibration image and two less computations (scaling and dividing the
+iillumination correction).  As an added short cut, rather than compute
+the iillumination image with \fBmkskycor\fR and then multiplying, the
+task \fBmkskyflat\fR does all this in one step.  Thus, \fBmkskyflat\fR
+takes an input blank sky image, processes it if needed, determines the
+appropriate flat field (sky flats are also subset dependent) from the
+\fBquadproc\fR parameters or the input image list, and produces an
+output sky flat.  Further if no output image is specified the task
+converts the input blank sky calibration image into a sky flat.
+
+     Two examples in which a new image is created and in which the
+input images are converted to sky flats are
+
+.nf
+    cl> mkskyflat sky004 Skyflat
+    cl> mkskyflat sky*.imh ""
+.fi
+.sh
+4.4 Iillumination Corrected Flat Fields
+
+     A third method to account for iillumination problems in the flat fields
+is to remove the large scale pattern from the flat field itself.  This is
+useful if there are no reasonable blank sky calibration images and the
+astronomical exposures are evenly illuminated but the flat fields are not.
+This is done by smoothing the flat field images instead of blank sky
+images.  As with using the sky images there are two methods, creating
+an iillumination correction to be applied as a separate step or fixing
+the original flat field.  The smoothing algorithm is
+the same as that used in the other tasks.  The tasks to make these types
+of corrections are \fBmkillumcor\fR and \fBmkillumflat\fR.  The usage
+is pretty much the same as the other iillumination correction tasks
+except that it is more reasonable to replace the original flat fields
+by the corrected flat fields when fixing the flat field.  Examples
+of an iillumination correction and removing the iillumination pattern
+from the flat field are
+
+.nf
+    cl> mkillumcor flat025 Illum025
+    cl> mkillumflat flat*.imh ""
+.fi
+
+As with the other tasks, the input images are processed if necessary.
+.sh
+4.5 Fringe Corrections
+
+    Some CCD detectors suffer from fringing effects due to the night
+sky emission lines which are not removed by the other calibration
+and correction operations.  To correct for the fringing you need a
+really blank sky image.  There is not yet a task to remove objects from
+sky images because this is often done with an interactive image display
+tool (which will soon be added).  The blank sky image is heavily smoothed
+to determine the mean sky background and then this is subtracted from the
+original image.  The image should then be essentially zero except for the
+fringe pattern.  This fringe correction image is scaled to the same
+exposure time as the image to be corrected and then subtracted to remove
+the fringing.  Note that since the night sky lines are variable there
+may need to be an additional scaling applied.  Determining this scaling
+requires either an interactive display tool or a very clever task.
+Such tasks will also be added in the future.
+
+     The task to make a fringe correction image is \fBmkfringecor\fR.
+the sky background is determined in exactly the same way as the iillumination
+pattern, in fact the same sky image may be used for both the sky
+iillumination and for the fringe correction.  The task works consistently
+with the "mk" tasks in that the input images are processed first if needed
+and then the output correction image is produced with the specified name
+or replaces the input image if no output image is specified.
+As examples,
+
+.nf
+    cl> mkfringecor sky004 Fringe
+    cl> mkfringecor sky*.imh ""
+.fi
+.sh
+6. Summary
+
+     The \fBquad\fR package is very easy to use.  First load the package;
+it is in the \fBarcon\fR package.  If this is your first time reducing data
+from a particular instrument or if you have changed instruments then run
+\fBsetinstrument\fR. Set the processing parameters for the operations you want
+performed.  If you need to combine calibration images to form a master 
+calibration image use one of the combine tasks.  Spectroscopic flat fields may
+need to be processed first in order to remove the lamp spectrum.
+Finally, just type
+
+    cl> quadproc *.imh&
+.sh
+7. References
+
+     A general guide to using IRAF is \fIA User's Introduction to the IRAF
+Command Language\fR.  This document may be found in the IRAF documentation
+sets and is available from the National Optical Astronomy Observatories,
+Central Computer Services (NOAO-CCS).
+
+     A more detailed description of the \fBccdred\fR package, on which
+\fBquad\fR is based,  including a discussion of the design and some of the
+algorithms see \fIThe IRAF CCD Reduction Package -- CCDRED\fR by F. Valdes.
+This paper is available from NOAO-CCS and appears in the proceedings of the 
+Santa Cruz Summer Workshop in Astronomy and Astrophysics, \fIInstrumentation
+for Ground-Based Optical Astronomy: Present and Future\fR, edited by 
+Lloyd B. Robinson and published by Springer-Verlag.
+
+     The task descriptions and supplementary documentation are available
+on-line through the help task by typing
+
+    cl> help \fItopic\fR
+
+where \fItopic\fR is one of the following.
+
+.nf
+             SPECIAL TASKS FOR MULTI-READOUT CCD IMAGES
+ 
+       quadproc - Process multi-readout CCD images
+      quadscale - Apply correction for amplifier dependent gain differences
+    qstatistics - Calculate image statistics for multi-readout CCD images
+     qhistogram - Make histogram of multi-readout CCD image
+    darkcombine - Combine and process dark count images
+    flatcombine - Combine and process flat field images
+    zerocombine - Combine and process zero level images
+ 
+ 
+            STANDARD CCDRED TASKS
+ 
+    badpiximage - Create a bad pixel mask image from a bad pixel file
+      ccdgroups - Group CCD images into image lists
+       ccdhedit - CCD image header editor
+  ccdinstrument - Review and edit instrument translation files
+        ccdlist - List CCD processing information
+        combine - Combine CCD images
+     cosmicrays - Detect and replace cosmic rays
+    mkfringecor - Make fringe correction images from sky images
+     mkillumcor - Make flat field iillumination correction images
+    mkillumflat - Make iillumination corrected flat fields
+       mkskycor - Make sky iillumination correction images
+      mkskyflat - Make sky corrected flat field images
+  setinstrument - Set instrument parameters
+ 
+              ADDITIONAL HELP TOPICS
+ 
+    ccdgeometry - Discussion of CCD coordinate/geometry keywords
+       ccdtypes - Description of the CCD image types
+     flatfields - Discussion of CCD flat field calibrations
+          guide - Introductory guide to using the CCDRED package
+    instruments - Instrument specific data files
+        package - CCD image reduction package
+    quadreadout - Description of multi-readout CCD data
+        subsets - Description of CCD subsets
+.fi
+
+Printed copies of the on-line help documentation may be made with the
+command
+
+    cl> help topic | lprint
+
+     In addition to the package documentation for \fBquad\fR,
+\fBlongslit\fR, and \fBapextract\fR there may be specific guides for
+certain instruments.  These specific guides, called "cookbooks", give
+specific examples and parameter values for the CCD data.
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/guide.ms b/noao/imred/quadred/src/quad/doc/guide.ms
new file mode 100644
index 00000000..62d87bb9
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/guide.ms
@@ -0,0 +1,794 @@
+.RP
+.TL
+User's Guide to the CCDRED Package
+.AU
+Francisco Valdes
+.AI
+IRAF Group - Central Computer Services
+.K2
+P.O. Box 26732, Tucson, Arizona 85726
+June 1987
+Revised February 1988
+.AB
+The IRAF CCD reduction package, \fBccdred\fR, provides tools
+for the easy and efficient reduction of CCD images.  The standard
+reduction operations are replacement of bad pixels, subtraction of an
+overscan or prescan bias, subtraction of a zero level image,
+subtraction of a dark count image, division by a flat field calibration
+image, division by an illumination correction, subtraction of a fringe
+image, and trimming unwanted lines or columns.  Another common
+operation provided by the package is scaling and combining images with
+a number of algorithms for rejecting cosmic rays.  Data in the image
+header is used to make the reductions largely automated and
+self-documenting though the package may still be used in the absence of
+this data.  Also a translation mechanism is used to relate image header
+parameters to those used by the package to allow data from a variety of
+observatories and instruments to be processed.  This guide provides a brief
+description of the IRAF CCD reduction package and examples of reducing
+simple CCD data.
+.AE
+.NH
+Introduction
+.LP
+     This guide provides a brief description of the IRAF CCD reduction
+package \fBccdred\fR and examples of reducing simple CCD data.  It is a
+generic guide in that it is not tied to any particular type of data.
+There may be more specific guides (or "cookbooks") for your data.
+Detailed descriptions of the tasks and features of the package are
+provided in the help documentation for the package.
+
+     The purpose of the CCDRED package is to provide tools for the easy
+and efficient reduction of CCD images.  The standard reduction
+operations are replacement of bad columns and lines by interpolation
+from neighboring columns and lines, subtraction of a bias level
+determined from overscan or prescan columns or lines, subtraction of a
+zero level using a zero length exposure calibration image, subtraction
+of a dark count calibration image appropriately scaled to the dark time
+exposure, division by a scaled flat field calibration image, division
+by an illumination image (derived from a blank sky image), subtraction
+of a scaled fringe image (also derived from a blank sky image), and
+trimming the image of unwanted lines or columns such as the overscan
+strip.  Any set of operations may be done simultaneously over a list of
+images in a highly efficient manner.  The reduction operations are
+recorded in the image header and may also be logged on the terminal and
+in a log file.
+
+     The package also provides tools for combining multiple exposures
+of object and calibration images to improve the statistical accuracy of
+the observations and to remove transient bad pixels.  The combining
+operation scales images of different exposure times, adjusts for
+variable sky background, statistically weights the images by their
+signal-to-noise, and provides a number of useful algorithms for
+detecting and rejecting transient bad pixels.
+
+     Other tasks are provided for listing reduction information about
+the images, deriving secondary calibration images (such as sky
+corrected flat fields or illumination correction images), and easily
+setting the package parameters for different instruments.
+
+     There are several important features provided by the package to
+make the reduction of CCD images convenient; particularly to minimize
+record keeping.  One of these is the ability to recognize the different
+types of CCD images.  This ability allows the user to select a certain
+class of images to be processed or listed and allows the processing
+tasks to identify calibration images and process them differently from
+object images.  The standard CCD image types are \fIobject\fR,
+\fIzero\fR level, \fIdark\fR count, and \fIflat\fR field.  For more on
+the image types see \fBccdtypes\fR.
+
+     The tasks can also identify the different filters (or other subset
+parameter) which require different flat field images.  This means you don't
+have to separate the images by filter and process each set separately.
+This feature is discussed further in \fBsubsets\fR.
+
+     The tasks keep track of the reduction steps completed on each
+image and ignore images which have been processed.  This feature,
+along with recognizing the image types and subsets, makes it possible to
+specify all the images to a task with a wildcard template, such as
+"*.imh", rather than indicating each image by name.  You will find this
+extremely important with large sets of observations.
+
+     A fundamental aspect of the package is that the processing
+modifies the images.  In other words, the reduction operations are
+performed directly on the image.  This "feature" further simplifies
+record keeping, frees the user from having to form unique output image
+names, and minimizes the amount of disk space required.  There
+are two safety features in this process.  First, the modifications do
+not take effect until the operation is completed on the image.  This
+allows you to abort the task without messing up the image data and
+protects data if the computer crashes.  The second feature is that
+there is a package parameter which may be set to make a backup of the
+input data with a particular prefix such as "orig" or "imdir$".  This
+backup feature may be used when there is sufficient disk space, when learning
+to use the package, or just to be cautious.
+
+     In a similar effort to efficiently manage disk space, when combining
+images into a master object or calibration image there is an option to
+delete the input images upon completion of the combining operation.
+Generally this is desirable when there are many calibration exposures,
+such as zero level or flat field images, which are not used after they
+are combined into a final calibration image.
+
+     The following sections guide you through the basic use of the
+\fBccdred\fR package.  Only the important parameters which you might
+want to change are described.  It is assumed that the support personnel
+have created the necessary instrument files (see \fBinstruments\fR)
+which will set the default parameters for the data you will be
+reducing.  If this is not the case you may need to delve more deeply
+into the details of the tasks.  Information about all the parameters
+and how the various tasks operate are given in the help documentation
+for the tasks and in additional special help topics.  Some useful help
+documentation is indicated in the discussion and also in the
+\fBReferences\fR section.
+.NH
+Getting Started
+.LP
+     The first step is to load \fBccdred\fR.  This is done by loading
+the \fBnoao\fR package, followed by the image reduction package
+\fBimred\fR, and finally the \fBccdred\fR package.  Loading a
+package consists of typing its name.  Note that some of these packages may be
+loaded automatically when you logon to IRAF.
+
+     When you load the \fBccdred\fR package the menu of tasks or commands
+is listed.  This appears as follows:
+
+.nf
+.KS
+.ft L
+    cl> ccdred
+      badpiximage       ccdtest           mkfringecor       setinstrument
+      ccdgroups         combine           mkillumcor        zerocombine
+      ccdhedit          cosmicrays        mkillumflat       
+      ccdlist           darkcombine       mkskycor          
+      ccdproc           flatcombine       mkskyflat         
+.ft R
+.KE
+.fi
+
+A summary of the tasks and additional help topics is obtained by typing:
+
+.ft L
+    cl> help
+.ft R
+
+This list and how to get additional help on specific topics is described
+in the \fBReferences\fR section at the end of this guide.
+
+     The first command to use is \fBsetinstrument\fR, which sets the package
+appropriately for the CCD images to be reduced.  The support personnel
+should tell you the instrument identification, but if not a list
+of known instruments may be listed by using '?' for the instrument name.
+
+.nf
+.ft L
+    cl> setinstrument
+    Instrument ID (type ? for a list) \fI<enter instrument id or ?>
+        <Set ccdred package parameters using eparam>
+        <Set ccdproc task parameters using eparam>
+.ft R
+.fi
+
+This task sets the default parameters and then allows you to modify the
+package parameters and the processing parameters using the parameter
+editor \fBeparam\fR.  If you are not familiar with \fBeparam\fR see the
+help or CL introduction documentation.  For most terminals you move up
+and down through the parameters with the terminal arrow keys, you
+change the parameters by simply typing the desired value, and you exit
+with control Z or control D.  Note that you can change parameters for
+any task at any time with \fBeparam\fR and you do not have to run
+\fBsetinstrument\fR again, even if you logout, until you need to reduce
+data from a different instrument.
+
+     The \fBccdred\fR package parameters control general I/O functions of
+the tasks in the package.  The parameters you might wish to change are
+the output pixel type and the verbose option.  Except when the input
+images are short integers, the noise is significantly greater than one
+digital unit, and disk space is critical, it is probably better to
+allow the processing to convert the images to real pixel datatype.  The
+verbose parameter simply prints the information written to the log file
+on the terminal.  This can be useful when little else is being done and
+you are just beginning.  However, when doing background processing and
+other IRAF reduction tasks it is enough to simply look at the end of
+the logfile with the task \fBtail\fR to see the current state of the
+processing.
+
+     The \fBccdproc\fR parameters control the CCD processing.  There are
+many parameters but they all may be conveniently set at this point.
+Many of the parameters have default values set appropriately for the
+instrument you specified.  The images to be processed can be specified
+later.  What needs to be set are the processing operations that you
+want done and the parameters required for each operation.  The
+processing operations are selected by entering yes or no for each one.
+The following items briefly describe each of the possible processing
+operations and the additional parameters required.
+
+.LP
+\fIfixpix\fR - Fix bad CCD lines and columns?
+.IP
+The bad pixels (cosmetic defects) in the detector are given in a file
+specified by the parameter \fIfixfile\fR.  This information is used
+to replace the pixels by interpolating from the neighboring pixels.
+A standard file for your instrument may be set by \fBsetinstrument\fR
+or if the word "image" is given then the file is defined in the instrument
+data file.  For more on the bad pixel file see \fBinstruments\fR.
+.LP
+\fIoverscan\fR - Apply overscan strip correction?
+.IP
+The overscan or prescan region is specified by the parameter
+\fIbiassec\fR.  This is given as an IRAF image section.  The overscan
+region is averaged along the readout axis, specified by the parameter
+\fIreadaxis\fR, to create a one dimensional bias vector.  This bias is
+fit by a function to remove cosmic rays and noise.  There are a number
+of parameters at the end of the parameter list which control the
+fitting.  The default overscan bias section and fitting parameters for
+your instrument should be set by \fBsetinstrument\fR.  If the word
+"image" is given the overscan bias section is defined in the image
+header or the instrument translation file.  If an overscan section is
+not set you can use \fBimplot\fR to determine the columns or rows for
+the bias region and define an overscan image section.  If you are
+unsure about image sections consult with someone or read the
+introductory IRAF documentation.
+.LP
+\fItrim\fR - Trim the image?
+.IP
+The image is trimmed to the image section given by the parameter
+\fItrimsec\fR.  A default trim section for your instrument should be
+set by \fBsetinstrument\fR, however, you may override this default if
+desired.  If the word "image" is given the data
+image section is given in the image header or the instrument
+translation file.  As with the overscan image section it is
+straightforward to specify, but if you are unsure consult someone.
+.LP
+\fIzerocor\fR - Apply zero level correction?
+.IP
+The zero level image to be subtracted is specified by the parameter
+\fIzero\fR.  If none is given then the calibration image will be sought
+in the list of images to be processed.
+.LP
+\fIdarkcor\fR - Apply dark count correction?
+.IP
+The dark count image to be subtracted is specified by the parameter
+\fIdark\fR.  If none is given then the calibration image will be sought
+in the list of images to be processed.
+.LP
+\fIflatcor\fR - Apply flat field correction?
+.IP
+The flat field images to be used are specified by the parameter
+\fIflat\fR.  There must be one flat field image for each filter
+or subset (see \fBsubsets\fR) to be processed.  If a flat field
+image is not given then the calibration image will be sought
+in the list of images to be processed.
+.LP
+\fIreadcor\fR - Convert zero level image to readout correction?
+.IP
+If a one dimensional zero level readout correction vector is to be subtracted
+instead of a two dimensional zero level image then, when this parameter is set,
+the zero level images will be averaged to one dimension.  The readout axis
+must be specified by the parameter \fIreadaxis\fR.  The default for your
+instrument is set by \fBsetinstrument\fR.
+.LP
+\fIscancor\fR - Convert flat field image to scan correction?
+.IP
+If the instrument is operated in a scan mode then a correction to the
+flat field may be required.  There are two types of scan modes, "shortscan"
+and "longscan".  In longscan mode flat field images will be averaged
+to one dimension and the readout axis must be specified.  Shortscan mode
+is a little more complicated.  The scan correction is used if the flat
+field images are not observed in scan mode.  The number of scan lines
+must be specified by the parameter \fInscan\fR.  If they are observed in
+scan mode, like the object observations, then the scan correction
+operations should \fInot\fR be specified.  For details of scan mode operations
+see \fBccdproc\fR.  The scan parameters
+should be set by \fBsetinstrument\fR.  If in doubt consult someone
+familiar with the instrument and mode of operation.
+.LP
+
+     This description of the parameters is longer than the actual operation of
+setting the parameters.  The only parameters likely to change during processing
+are the calibration image parameters.
+
+     When processing many images using the same calibration files a modest
+performance improvement can be achieved by keeping (caching) the
+calibration images in memory to avoid disk accesses.  This option
+is available by specifying the amount of memory available for image
+caching with the parameter \fImax_cache\fR.  If the value is zero then
+the images are accessed from disk as needed while if there is
+sufficient memory the calibration images may be kept in memory during
+the task execution.
+.NH
+Processing Your Data
+.LP
+     The processing path depends on the type of data, the type of
+instrument, types of calibration images, and the observing
+sequence.  In this section we describe two types of operations common
+in reducing most data; combining calibration images and performing the
+standard calibration and correction operations.  Some additional special
+operations are described in the following section.
+
+     However, the first thing you might want to try before any
+processing is to get a listing of the CCD images showing the CCD image
+types, subsets, and processing flags.  The task for this is
+\fBccdlist\fR.  It has three types of of output; a short one line per
+image format, a longer format which shows the state of the processing,
+and a format which prints the image names only (used to create files
+containing lists of images of a particular CCD image type).  To get a
+quick listing type:
+
+.nf
+.ft L
+    cl> ccdlist *.imh
+    ccd001.imh[544,512][short][unknown][V]:FOCUS L98-193
+    ccd007.imh[544,512][short][object][V]:N2968 V 600s
+    ccd015.imh[544,512][short][object][B]:N3098 B 500s
+    ccd024.imh[544,512][short][object][R]:N4036 R 600s
+    ccd045.imh[544,512][short][flat][V]:dflat 5s
+    ccd066.imh[544,512][short][flat][B]:dflat 5s
+    ccd103.imh[544,512][short][flat][R]:dflat 5s
+    ccd104.imh[544,512][short][zero][]:bias
+    ccd105.imh[544,512][short][dark][]:dark 3600s
+.ft R
+.fi
+
+     The example shows only a sample of the images.  The short format
+listing tells you the name of the image, its size and pixel type, the
+CCD image type as seen by the package, the subset identifier (in this
+case the filter), and the title.  If the data had been processed then
+there would also be processing flags.  If the CCD image types do not
+seem right then there may be a problem with the instrument
+specification.
+
+     Many of the tasks in the \fBccdred\fR package have the parameter
+\fIccdtype\fR which selects a particular type of image.  To list
+only the object images from the previous example:
+
+.nf
+.ft L
+    cl> ccdlist *.imh ccdtype=object
+    ccd007.imh[544,512][short][object][V]:N2968 V 600s
+    ccd015.imh[544,512][short][object][B]:N3098 B 500s
+    ccd024.imh[544,512][short][object][R]:N4036 R 600s
+.ft R
+.fi
+
+If no CCD image type is specified (by using the null string "")
+then all image types are selected.  This may be
+necessary if your instrument data does not contain image type identifications.
+.NH 2
+Combining Calibration Images
+.LP
+     If you do not need to combine calibration images because you only
+have one image of each type, you can skip this section.  Calibration
+images, particularly zero level and flat field images, are combined in
+order to minimize the effects of noise and reject bad pixels in the
+calibrations.  The basic tool for combining images is the task
+\fBcombine\fR.  There are simple variants of this task whose default
+parameters are set appropriately for each type of calibration image.
+These are the ones you will use for calibration images leaving
+\fBcombine\fR for combining object images.  Zero level images are
+combined with \fBzerocombine\fR, dark count images with
+\fBdarkcombine\fR, and flat field images with \fBflatcombine\fR.
+
+     For example, to combine flat field images the command is:
+
+.nf
+.ft L
+    cl> flatcombine *.imh
+    Jun  1 14:26 combine: maxreject
+            Images      N    Exp   Mode  Scale Offset Weight
+        ccd045.imh      1    5.0  INDEF  1.000     0.  0.048
+        ccd046.imh      1    5.0  INDEF  1.000     0.  0.048
+        	\fI<... list of files ...>\fL
+        ccd065.imh      1    5.0  INDEF  1.000     0.  0.048
+        ----------- ------ ------
+         FlatV.imh     21    5.0
+.ft R
+.fi
+
+This output is printed when verbose mode is set.  The same information
+is recorded in the log file.  In this case the flat fields are combined
+by rejecting the maximum value at each point in the image (the
+"maxreject" algorithm).  The images are scaled by the exposure times,
+which are all the same in this example.  The mode is not evaluated for
+exposure scaling and the relative weights are the same because the
+exposure times are the same.  The example only shows part of the
+output; \fBflatcombine\fR automatically groups the flat field images by
+filter to produce the calibration images "FlatV", "FlatB", and
+"FlatR".
+.NH 2
+Calibrations and Corrections
+.LP
+     Processing the CCD data is easy and largely automated.
+First, set the task parameters with the following command:
+
+.ft L
+    cl> eparam ccdproc
+.ft R
+
+You may have already set the parameters when you ran
+\fBsetinstrument\fR, though the calibration image parameters
+\fIzero\fR, \fIdark\fR, and \fIflat\fR may still need to be set or
+changed.  Once this is done simply give the command
+
+.nf
+.ft L
+    cl> ccdproc *.imh
+    ccd003: Jun  1 15:13 Overscan section is [520:540,*] with mean=485.0
+    ccd003: Jun  1 15:14 Trim data section is [3:510,3:510]
+    ccd003: Jun  1 15:14 Overscan section is [520:540,*] with mean=485.0
+    FlatV:  Jun  1 15:14 Trim data section is [3:510,3:510]
+    FlatV:  Jun  1 15:15 Overscan section is [520:540,*] with mean=486.4
+    ccd003: Jun  1 15:15 Flat field image is FlatV.imh with scale=138.2
+    ccd004: Jun  1 15:16 Trim data section is [3:510,3:510]
+    ccd004: Jun  1 15:16 Overscan section is [520:540,*] with mean=485.2
+    ccd004: Jun  1 15:16 Flat field image is FlatV.imh with scale=138.2
+                \fI<... more ...>\fL
+    ccd013: Jun  1 15:22 Trim data section is [3:510,3:510]
+    ccd013: Jun  1 15:23 Overscan section is [520:540,*] with mean=482.4
+    FlatB:  Jun  1 15:23 Trim data section is [3:510,3:510]
+    FlatB:  Jun  1 15:23 Overscan section is [520:540,*] with mean=486.4
+    ccd013: Jun  1 15:24 Flat field image is FlatB.imh with scale=132.3
+                \fI<... more ...>\fL
+.ft R
+.fi
+
+     The output shown is with verbose mode set.  It is the same as
+recorded in the log file.  It illustrates the principle of automatic
+calibration image processing.  The first object image, "ccd003", was
+being processed when the flat field image was required.  Since the
+image was taken with the V filter the appropriate flat field was
+determined to be "FlatV".  Since it had not been processed, the
+processing of "ccd003" was interrupted to process "FlatV".  The
+processed calibration image may have been cached if there was enough
+memory.  Once "FlatV" was processed (note that the flat field was not
+flattened because the task knows this image is a flat field) the
+processing of "ccd003" was completed.  The next image, "ccd004", is
+also a V filter image so the already processed, and possibly cached,
+flat field "FlatV" is used again.  The first B band image is "ccd013"
+and, as before, the B filter flat field calibration image is processed
+automatically.  The same automatic calibration processing and image
+caching occurs when using zero level and dark count calibration
+images.
+
+     Commonly the processing is done with the verbose mode turned off
+and the task run as a background job.  This is done with the commands
+
+.nf
+.ft L
+    cl> ccdred.verbose=no
+    cl> ccdproc *.imh &
+.ft R
+.fi
+
+The already processed images in the input list are recognized as having been
+processed and are not affected.  To check the status of the processing we
+can look at the end of the log file with:
+
+.ft L
+    cl> tail logfile
+.ft R
+
+After processing we can repeat the \fBccdlist\fR command to find:
+
+.nf
+.ft L
+    cl> ccdlist *.imh ccdtype=object
+    ccd007.imh[508,508][real][object][V][OTF]:N2968 V 600s
+    ccd015.imh[508,508][real][object][B][OTF]:N3098 B 500s
+    ccd024.imh[544,512][short][object][R][OTF]:N4036 R 600s
+.ft R
+.fi
+
+The processing flags indicate the images have been overscan corrected,
+trimmed, and flat fielded.
+
+     As you can see, processing images is very easy.  There is one source
+of minor confusion for beginning users and that is dealing with calibration
+images.  First, there is no reason that calibration images
+may not be processed explicitly with \fBccdproc\fR, just remember to set
+the \fIccdtype\fR to the calibration image type or to "".  When processing
+object images the calibration images to be used may be specified either
+with the task parameter for the particular calibration image or by
+including the calibration image in the list of input images.  Calibration
+images specified by parameter value take precedence and the task
+does not check its CCD image type.  Calibration images given in the
+input list must have a valid CCD image type.  In case too many
+calibration images are specified, say because the calibration images
+combined to make the master calibration images were not deleted and
+so are part of the image list "*.imh", only the first one will be used.
+Another point to know is that flat field, illumination, and fringe images
+are subset (filter) dependent and so a calibration image for each filter
+must be specified.
+.NH
+Special Processing Operations
+.LP
+     The special processing operations are mostly concerned with the
+flat field response correction.  There are also special processing
+operations available in \fBccdproc\fR for one dimensional readout
+corrections in the zero level and flat field calibrations.  These
+were described briefly above and in more detail in \fBccdproc\fR
+and are not discussed further in this guide.  The processing
+operations described in this section are for preparing flat fields
+for two dimensional spectroscopic data, for correcting flat fields
+for illuminations effects, for making a separate illumination correction,
+and for applying corrections for fringe effects.  For additional
+discussion about flat fields and illumination corrections see the
+help topic \fBflatfields\fR.
+.NH 2
+Spectroscopic Flat Fields
+.LP
+     For spectroscopic data the flat fields may have to be processed to
+remove the general shape of the lamp spectrum and to replace regions outside
+of the aperture where there is no flat field information with values that
+will not cause bad response effects when the flat field is applied to the
+data.  If the shape of the lamp spectrum is not important and if the
+longslit spectra have the regions outside of the slit either off the
+detector or trimmed then you may use the flat field without special
+processing.
+
+   First you must process the flat field images explicitly with
+
+.ft L
+    cl> ccdproc *.imh ccdtype=flat
+.ft R
+
+where "*.imh" may be replaced with any list containing the flat fields.
+If zero level and dark count corrections are required these calibration
+images must be available at this time.
+
+     Load the \fBtwodspec\fR package and then either the \fBlongslit\fR
+package, for longslit data, or the \fBapextract\fR package, for
+multiaperture data such as echelles, multifiber, or aperture mask
+spectra.  The task for removing the longslit quartz spectrum is
+\fBresponse\fR.  There is also a task for removing illumination
+effects, including the slit profile, from longslit spectra called
+\fBillumination\fR.  For more about processing longslit spectra see the
+help for these tasks and the paper \fIReduction of Longslit Spectra
+with IRAF\fR.  The cookbook \fIReduction of Longslit Spectroscopic
+Data Using IRAF (KPNO ICCD and Cryogenic Camera Data)\fR also provides
+a very good discussion even if your data is from a different instrument.
+
+     For multiaperture data the task for removing the relative shapes of
+the spectra is called \fBapnormalize\fR.  Again, consult the help documentation
+for this task for further details.  Since you will probably also be
+using the package for extracting the spectra you may be interested
+in the document \fIThe IRAF APEXTRACT Package\fR.
+.NH 2
+Illumination Corrections
+.LP
+     The flat field calibration images may not have the same illumination
+pattern as the observations of the sky due to the way the lamp illuminates the
+optical system.  In this case when the flat field correction is applied
+to the data there will be gradients in the sky background.  To remove
+these gradients a blank sky calibration image is heavily smoothed
+to produce an illumination image.  The illumination image
+is then divided into the images during processing to correct for the
+illumination difference between the flat field and the objects.
+Like the flat fields, the illumination corrections images may be subset
+dependent so there should be an illumination image for each subset.
+
+The task which makes illumination correction images is \fBmkskycor\fR.
+Some examples are
+
+.nf
+.ft L
+    cl> mkskycor sky004 Illum004
+    cl> mkskycor sky*.imh ""
+.ft R
+.fi
+
+In the first example the sky image "sky004" is used to make the illumination
+correction image "Illum004".  In the second example the sky images are
+converted to illumination correction images by specifying no output image
+names.  Like \fBccdproc\fR if the input images have not been processed they
+are first processed automatically.
+
+To apply the illumination correction
+
+.nf
+.ft L
+    cl> ccdproc *.imh ccdtype=object illumcor+ illum=Illum004
+    cl> ccdproc *.imh ccdtype=object illumcor+ illum=sky*.imh
+.ft R
+.fi
+
+The illumination images could also be set using \fBeparam\fR or given
+on the command line.
+.NH 2
+Sky Flat Fields
+.LP
+    You will notice that when you process images with an illumination
+correction you are dividing each image by a flat field calibration and
+an illumination correction.  If the illumination corrections are not
+done as a later step but at the same time as the rest of the processing
+one will get the same calibration by multiplying the flat field by
+the illumination correction and using this product alone as the
+flat field.  Such an image is called a \fIsky flat\fR since it is
+a flat field which has been corrected to yield a flat sky when applied
+to the observations.  This approach has the advantage of one less
+calibration image and two less computations (scaling and dividing the
+illumination correction).  As an added short cut, rather than compute
+the illumination image with \fBmkskycor\fR and then multiplying, the
+task \fBmkskyflat\fR does all this in one step.  Thus, \fBmkskyflat\fR
+takes an input blank sky image, processes it if needed, determines the
+appropriate flat field (sky flats are also subset dependent) from the
+\fBccdproc\fR parameters or the input image list, and produces an
+output sky flat.  Further if no output image is specified the task
+converts the input blank sky calibration image into a sky flat.
+
+     Two examples in which a new image is created and in which the
+input images are converted to sky flats are
+
+.nf
+.ft L
+    cl> mkskyflat sky004 Skyflat
+    cl> mkskyflat sky*.imh ""
+.ft R
+.fi
+.NH 2
+Illumination Corrected Flat Fields
+.LP
+     A third method to account for illumination problems in the flat fields
+is to remove the large scale pattern from the flat field itself.  This is
+useful if there are no reasonable blank sky calibration images and the
+astronomical exposures are evenly illuminated but the flat fields are not.
+This is done by smoothing the flat field images instead of blank sky
+images.  As with using the sky images there are two methods, creating
+an illumination correction to be applied as a separate step or fixing
+the original flat field.  The smoothing algorithm is
+the same as that used in the other tasks.  The tasks to make these types
+of corrections are \fBmkillumcor\fR and \fBmkillumflat\fR.  The usage
+is pretty much the same as the other illumination correction tasks
+except that it is more reasonable to replace the original flat fields
+by the corrected flat fields when fixing the flat field.  Examples
+of an illumination correction and removing the illumination pattern
+from the flat field are
+
+.nf
+.ft L
+    cl> mkillumcor flat025 Illum025
+    cl> mkillumflat flat*.imh ""
+.ft R
+.fi
+
+As with the other tasks, the input images are processed if necessary.
+.NH 2
+Fringe Corrections
+.LP
+    Some CCD detectors suffer from fringing effects due to the night
+sky emission lines which are not removed by the other calibration
+and correction operations.  To correct for the fringing you need a
+really blank sky image.  There is not yet a task to remove objects from
+sky images because this is often done with an interactive image display
+tool (which will soon be added).  The blank sky image is heavily smoothed
+to determine the mean sky background and then this is subtracted from the
+original image.  The image should then be essentially zero except for the
+fringe pattern.  This fringe correction image is scaled to the same
+exposure time as the image to be corrected and then subtracted to remove
+the fringing.  Note that since the night sky lines are variable there
+may need to be an additional scaling applied.  Determining this scaling
+requires either an interactive display tool or a very clever task.
+Such tasks will also be added in the future.
+
+     The task to make a fringe correction image is \fBmkfringecor\fR.
+the sky background is determined in exactly the same way as the illumination
+pattern, in fact the same sky image may be used for both the sky
+illumination and for the fringe correction.  The task works consistently
+with the "mk" tasks in that the input images are processed first if needed
+and then the output correction image is produced with the specified name
+or replaces the input image if no output image is specified.
+As examples,
+
+.nf
+.ft L
+    cl> mkfringecor sky004 Fringe
+    cl> mkfringecor sky*.imh ""
+.ft R
+.fi
+.NH
+Demonstration
+.LP
+     A simple demonstration task is available.  To run this demonstration
+load the \fBccdtest\fR package; this is a subpackage of the main
+\fBccdred\fR package.  Then simply type
+
+.ft L
+	cl> demo
+.ft R
+
+The demonstration will then create some artificial CCD data and reduce
+them giving descriptive comments as it goes along.  This demonstration uses
+the "playback" facility of the command language and is actually substituting
+it's own commands for terminal input.  Initially you must type carriage return
+or space after each comment ending with "...".  If you wish to have the
+demonstration run completely automatically at it's own speed then type 'g'
+a the "..." prompt.  Thereafter, it will simple pause long enough to give
+you a chance to read the comments.  When the demo is finished you will
+need to remove the files created.  However, feel free to examine the reduced
+images, the log file, etc.  \fINote that the demonstration changes the
+setup parameters so be sure to run \fBsetinstrument\fI again and check
+the setup parameters.\fR
+.NH
+Summary
+.LP
+     The \fBccdred\fR package is very easy to use.  First load the package;
+it is in the \fBimred\fR package which is in the \fBnoao\fR package.
+If this is your first time reducing data from a particular instrument
+or if you have changed instruments then run \fBsetinstrument\fR.
+Set the processing parameters for the operations you want performed.
+If you need to combine calibration images to form a master calibration
+image use one of the combine tasks.  Spectroscopic flat fields may
+need to be processed first in order to remove the lamp spectrum.
+Finally, just type
+
+.ft L
+    cl> ccdproc *.imh&
+.ft R
+.SH
+References
+.LP
+     A general guide to using IRAF is \fIA User's Introduction to the IRAF
+Command Language\fR.  This document may be found in the IRAF documentation
+sets and is available from the National Optical Astronomy Observatories,
+Central Computer Services (NOAO-CCS).
+
+     A more detailed description of the \fBccdred\fR package including
+a discussion of the design and some of the algorithms see \fIThe IRAF
+CCD Reduction Package -- CCDRED\fR" by F. Valdes.  This paper is available
+from NOAO-CCS and appears in the proceedings of the Santa Cruz Summer
+Workshop in Astronomy and Astrophysics, \fIInstrumentation for Ground-Based
+Optical Astronomy: Present and Future\fR, edited by Lloyd B. Robinson and
+published by Springer-Verlag.
+
+     The task descriptions and supplementary documentation are available
+in printed form in the IRAF documentation sets, a special set
+containing documentation for just the \fBccdred\fR package, and on-line
+through the help task by typing
+
+.ft L
+    cl> help \fItopic\fR
+.ft R
+
+where \fItopic\fR is one of the following.
+
+.nf
+.ft L
+  badpiximage - Create a bad pixel mask image from a bad pixel file
+    ccdgroups - Group CCD images into image lists
+     ccdhedit - CCD image header editor
+      ccdlist - List CCD processing information
+      ccdproc - Process CCD images
+      ccdtest - CCD test and demonstration package
+      combine - Combine CCD images
+   cosmicrays - Detect and replace cosmic rays
+  darkcombine - Combine and process dark count images
+  flatcombine - Combine and process flat field images
+  mkfringecor - Make fringe correction images from sky images
+   mkillumcor - Make flat field illumination correction images
+  mkillumflat - Make illumination corrected flat fields
+     mkskycor - Make sky illumination correction images
+    mkskyflat - Make sky corrected flat field images
+setinstrument - Set instrument parameters
+  zerocombine - Combine and process zero level images
+
+          ADDITIONAL HELP TOPICS
+
+       ccdred - CCD image reduction package
+     ccdtypes - Description of the CCD image types
+   flatfields - Discussion of CCD flat field calibrations
+        guide - Introductory guide to using the CCDRED package
+  instruments - Instrument specific data files
+      subsets - Description of CCD subsets
+.ft R
+.fi
+
+Printed copies of the on-line help documentation may be made with the
+command
+
+.ft L
+    cl> help \fItopic\fL | lprint
+.ft R
+
+     In addition to the package documentation for \fBccdred\fR,
+\fBlongslit\fR, and \fBapextract\fR there may be specific guides for
+certain instruments.  These specific guides, called "cookbooks", give
+specific examples and parameter values for the CCD data.
diff --git a/noao/imred/quadred/src/quad/doc/instruments.hlp b/noao/imred/quadred/src/quad/doc/instruments.hlp
new file mode 100644
index 00000000..2b2c92f7
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/instruments.hlp
@@ -0,0 +1,248 @@
+.help instruments Jun87 noao.imred.ccdred
+
+.ih
+NAME
+instruments -- Instrument specific data files
+.ih
+DESCRIPTION
+The \fBccdred\fR package has been designed to accommodate many different
+instruments, detectors, and observatories.  This is done by having
+instrument specific data files.  Note that by instrument we mean a
+combination of detector, instrument, application, and observatory, so
+there might be several "instruments" associated with a particular CCD
+detector.  Creating and maintaining the instrument files is generally
+the responsibility of the support staff, though the user may create or
+copy and modify his/her own instrument/application specific files.  The
+task \fBsetinstrument\fR makes this information available to the user
+and package easily.
+
+There are three instrument data files, all of which are optional.  The
+package may be used without the instrument files but much of the
+convenience of the package, particularly with respect to using the CCD
+image types, will be lost.  The three files are an instrument image
+header translation file, an initialization task which mainly sets
+default task parameters, and a bad pixel file identifying the cosmic
+bad pixels in the detector.  These files are generally stored in a
+system data directory which is a subdirectory of the logical
+directory "ccddb$".  Each file has a root name which identifies the
+instrument.
+.sh
+1. Instrument Translation File
+The instrument translation file translates the parameter names used by
+the \fBccdred\fR pacakge into instrument specific parameters and also
+supplies instrument specific default values.  The package parameter
+\fIccdred.instrument\fR specifies this file to the package.  The task
+\fBsetinstrument\fR sets this parameter, though it can be set
+explicitly like any other parameter.  For the standard instrument
+translation file the root name is the instrument identification and the
+extension is "dat" ("*.dat" files are protected from being removed in a
+"stripped" system, i.e. when all nonessential files are removed).
+Private instrument files may be given any name desired.
+
+The instrument translation proceeds as follows.  When a package task needs
+a parameter for an image, for example "imagetyp", it looks in the instrument
+translation file.  If the file is not found or none is specified then the
+image header keyword that is requested has the same name.  If an
+instrument translation file is defined then the requested
+parameter is translated to an image header keyword, provided a translation
+entry is given.  If no translation is given the package name is used.  For
+example the package parameter "imagetyp" might be translated to "data-typ"
+(the old NOAO CCD keyword).  If the parameter is not found then the default
+value specified in the translation file, if present, is returned.  For recording
+parameter information in the header, such as processing flags, the
+translation is also used.  The default value has no meaning in this case.
+For example, if the flag specifying that the image has been corrected
+by a flat field is to be set then the package parameter name "flatcor"
+might be translated to "ff-flag".  If no translation is given then the
+new image header parameter is entered as "flatcor".
+
+The format of the translation file are lines consisting of the package
+parameter name, followed by the image header keyword, followed by the
+default value.  The first two fields are parameter names.  The fields
+are separated by whitespace (blanks and tabs).  String  default values
+containing blanks must be quoted.  An example is given below.
+
+.nf
+    exptime     itime
+    darktime    itime
+    imagetyp    data-typ
+    subset      f1pos
+    biassec     biassec    [411:431,2:573]
+    datasec     datasec    [14:385,2:573]
+
+    fixpix      bp-flag    0
+    overscan    bt-flag    0
+    zerocor     bi-flag    0
+    darkcor     dk-flag    0
+    flatcor     ff-flag    0
+    fringcor    fr-flag    0 
+.fi
+
+The first two lines translate the CCD image type, and the subset parameter
+without default values (see \fBccdtypes\fR and \fBsubsets\fR for more
+information).  The next two lines give the overscan bias strip
+section and the data section with default values for the instrument.
+Note that these parameters may be overridden in the task \fBccdproc\fR.
+The blank line is ignored.
+
+The next set of translations requires further discussion.  For processing
+flags the package assumes that the absence of a keyword means that the
+processing has not been done.  If processing is always to be done with
+the \fBCCDRED\fR package and no processing keywords are recorded in the raw data
+then these parameters should be absent (unless you don't like the names
+used by the package).  However, for compatibility with the original NOAO
+CCD images, which may be processed outside of IRAF and which use 0 as the
+no processing value, the processing flags are translated and the false values
+are indicated by the default values.
+
+In addition to the parameter name translations the translation file
+contains translations between the value of the image type parameter
+and the image types used by the package.  These lines
+consist of the image header type string as the first field (with quotes
+if there are blanks) and the image type as recognized by the package.  The
+following example will make this clearer.
+
+.nf
+	'OBJECT (0)'		object
+	'DARK (1)'		dark
+	'PROJECTOR FLAT (2)'	flat
+	'SKY FLAT (3)'		other
+	'COMPARISON LAMP (4)'	other
+	'BIAS (5)'		zero
+	'DOME FLAT (6)'		flat
+.fi
+
+The values of the image type strings in the header contain blanks so they
+are quoted.  Also the case of the strings is important.  Note that there
+are two types of flat field images and three types of object images.
+
+The CCD image types recognized by the package are:
+
+.nf
+	zero   - zero level image such as a bias or preflash
+	dark   - dark count image
+	flat   - flat field image
+	illum  - iillumination image such as a sky image
+	fringe - fringe correction image
+	object - object image
+.fi
+
+There may be more than one image type that maps to the same package
+type.  In particular other standard CCD image types, such as comparison
+spectra, multiple exposure, standard star, etc., should be mapped to
+object or other.  There may also be more than one type of flat field,
+i.e. dome flat, sky flat, and lamp flat.  For more on the CCD image
+types see \fBccdtypes\fR.
+
+The complete set of package parameters are given below.
+The package parameter names are generally the same as the
+standard image header keywords being adopted by NOAO.
+
+.nf
+	General Image Header and Default Parameters
+    ccdmean		darktime	exptime		fixfile
+    imagetyp		ncombine	biassec		subset
+    title		datasec
+
+	       CCDRED Processing Flags
+    ccdproc		darkcor		fixpix		flatcor
+    fringcor		illumcor	overscan	trim
+    zerocor
+
+	       CCDRED CCD Image Types
+    dark		flat		fringe		illum
+    none		object		unknown		zero
+.fi
+
+The translation mechanism described here may become more
+sophisticated in the future and a general IRAF system facility may be
+implemented eventually.  For the present the translation mechanism is
+quite simple.
+.sh
+2. Instrument Setup Script
+The task \fBsetinstrument\fR translates an instrument ID into a
+CL script in the instrument directory.  This script is then executed.
+Generally this script simply sets the task parameters for an
+instrument/application.  However, it could do anything else the support
+staff desires.  Below are the first few lines of a typical instrument setup
+script.
+
+.nf
+	ccdred.instrument = "ccddb$kpno/example.dat"
+	ccdred.pixeltype = "real"
+	ccdproc.fixpix = yes
+	ccdproc.overscan = yes
+	ccdproc.trim = yes
+	ccdproc.zerocor = no
+	ccdproc.darkcor = no
+	ccdproc.flatcor = yes
+	ccdproc.biassec = "[411:431,2:573]"
+	ccdproc.datasec = "[14:385,2:573]"
+.fi
+
+The instrument parameter should always be set unless there is no
+translation file for the instrument.  The \fBccdproc\fR parameters
+illustrate setting the appropriate processing flags for the
+instrument.  The overscan bias and trim data sections show an alternate
+method of setting these instrument specific parameters.  They may be
+set in the setup script in which case they are given explicitly in the
+user parameter list for \fBccdproc\fR.  If the value is "image" then
+the parameters may be determined either through the default value in
+the instrument translation file, as illustrated in the previous
+section, or from the image header itself.
+
+The instrument setup script for setting default task parameters may be
+easily created by the support person as follows.  Set the package
+parameters using \fBeparam\fR or with CL statements.  Setting the
+parameters might involve testing.  When satisfied with the way the
+package is set then the parameters may be dumped to a setup script
+using the task \fBdparam\fR.  The final step is editing this script to
+delete unimportant and query parameters.  For example,
+
+.nf
+	cl> dparam ccdred >> file.cl
+	cl> dparam ccdproc >> file.cl
+	cl> dparam combine >> file.cl
+		...
+	cl> ed file.cl
+.fi
+.sh
+3. Instrument Bad Pixel File
+The bad pixel file describes the bad pixels, columns, and lines in the
+detector which are to be replaced by interpolation when processing the
+images.  This file is clearly detector specific.  The file consists of
+lines describing rectangular regions of the image.
+The regions are specified by four numbers giving the starting and ending
+columns followed by the starting and ending lines.  The starting and
+ending points may be the same to specify a single column or line.  The
+example below illustrates a bad pixel file.
+
+.nf
+	# RCA1 CCD untrimmed
+	25 25 1 512
+	108 108 1 512
+	302 302 403 512
+	1 512 70 70
+	245 246 312 315
+.fi
+
+If there is a comment line in the file containing the word "untrimmed"
+then the coordinates of the bad pixel regions apply to the original image.
+If the image has been trimmed and the bad pixels are replaced at a later
+stage then this word indicates that the trim region be determined from the
+image header and the necessary coordinate conversion made.  If the word
+"untrimmed" does not appear then the coordinates are assumed to apply to
+the image directly; i.e. the trimmed coordinates if the image has been
+trimmed or the original coordinates if the image has not been trimmed.
+The standard bad pixel files should always refer to the original, untrimmed
+coordinates.
+
+The first two bad pixel regions are complete bad columns (the image
+is 512 x 512), the next line is a partial bad column, the next line is
+a bad line, and the last line is a small bad region.  These files are
+easy to create, provided you have a good image to work from and a way
+to measure the positions with an image or graphics display.
+.ih
+SEE ALSO
+ccdtypes, subsets, setinstrument
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/mkfringecor.hlp b/noao/imred/quadred/src/quad/doc/mkfringecor.hlp
new file mode 100644
index 00000000..797f4d11
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/mkfringecor.hlp
@@ -0,0 +1,90 @@
+.help mkfringecor Feb88 noao.imred.ccdred
+.ih
+NAME
+mkfringecor -- Make fringe correction images from sky images
+.ih
+USAGE
+mkfringecor input output
+.ih
+PARAMETERS
+.ls input
+List of input images for making fringe correction images.
+.le
+.ls output
+List of output fringe correction images.  If none is
+specified or if the name is the same as the input image then the output
+image replaces the input image.
+.le
+.ls ccdtype = ""
+CCD image type to select from the input images.  If none is specified
+then all types are used.
+.le
+.ls xboxmin = 5, xboxmax = 0.25, yboxmin = 5, yboxmax = 0.25
+Minimum and maximum smoothing box size along the x and y axes.  The
+minimum box size is used at the edges and grows to the maximum size in
+the middle of the image.  This allows the smoothed image to better
+represent gradients at the edge of the image.  If a size is less then 1
+then it is interpreted as a fraction of the image size.  If a size is
+greater than or equal to 1 then it is the box size in pixels.  A size
+greater than the size of image selects a box equal to the size of the
+image.
+.le
+.ls clip = yes
+Clean the input images of objects?  If yes then a clipping algorithm is
+used to detect and exclude objects from the smoothing.
+.le
+.ls lowsigma = 2.5, highsigma = 2.5
+Sigma clipping thresholds above and below the smoothed background.
+.le
+.ls ccdproc (parameter set)
+CCD processing parameters.
+.le
+.ih
+DESCRIPTION
+The input blank sky images are automatically processed up through the
+iillumination correction before computing the fringe correction images.
+The fringe corrections are subset dependent.
+The slowly varying background is determined and subtracted leaving only
+the fringe pattern caused by the sky emission lines.  These fringe images
+are then scaled and subtracted from the observations by \fBccdproc\fR.
+The background is determined by heavily smoothing the image using a
+moving "boxcar" average.  The effects of the objects and fringes in the
+image is minimized by using a sigma clipping algorithm to detect and
+exclude them from the average.  Note, however, that objects left in the
+fringe image will affect the fringe corrected observations.  Any objects
+in the sky image should be removed using \fBskyreplace\fR (not yet
+available).
+
+The smoothing algorithm is a moving average over a two dimensional
+box.  The algorithm is unconvential in that the box size is not fixed.
+The box size is increased from the specified minimum at the edges to
+the maximum in the middle of the image.  This permits a better estimate
+of the background at the edges, while retaining the very large scale
+smoothing in the center of the image.  Note that the sophisticated
+tools of the \fBimages\fR package may be used for smoothing but this
+requires more of the user and, for the more sophisticated smoothing
+algorithms such as surface fitting, more processing time.
+
+To minimize the effects of the fringes and any objects in the blank sky
+calibration images a sigma clipping algorithm is used to detect and
+exclude features from the background.  This is done by computing the
+rms of the image lines relative to the smoothed background and
+excluding points exceeding the specified threshold factors times the
+rms.  This is done before each image line is added to the moving
+average, except for the first few lines where an iterative process is
+used.
+.ih
+EXAMPLES
+1. The two examples below make an fringe correction image from a blank
+sky image, "sky017".  In the first example a separate fringe
+image is created and in the second the fringe image replaces the
+sky image.
+
+.nf
+    cl> mkskycor sky017 Fringe
+    cl> mkskycor sky017 frg017
+.fi
+.ih
+SEE ALSO
+ccdproc
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/mkillumcor.hlp b/noao/imred/quadred/src/quad/doc/mkillumcor.hlp
new file mode 100644
index 00000000..0effd7a2
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/mkillumcor.hlp
@@ -0,0 +1,92 @@
+.help mkillumcor Oct88 noao.imred.ccdred
+.ih
+NAME
+mkillumcor -- Make flat field iillumination correction images
+.ih
+USAGE
+mkillumcor input output
+.ih
+PARAMETERS
+.ls input
+List of input images for making flat field iillumination correction images.
+.le
+.ls output
+List of output flat field iillumination correction images.  If none is
+specified or if the name is the same as the input image then the output
+image replaces the input image.
+.le
+.ls ccdtype = "flat"
+CCD image type to select from the input images.  If none is specified
+then all types are used.
+.le
+.ls xboxmin = 5, xboxmax = 0.25, yboxmin = 5, yboxmax = 0.25
+Minimum and maximum smoothing box size along the x and y axes.  The
+minimum box size is used at the edges and grows to the maximum size in
+the middle of the image.  This allows the smoothed image to better
+represent gradients at the edge of the image.  If a size is less then 1
+then it is interpreted as a fraction of the image size.  If a size is
+greater than or equal to 1 then it is the box size in pixels.  A size
+greater than the size of image selects a box equal to the size of the
+image.
+.le
+.ls clip = yes
+Clean the input images of objects?  If yes then a clipping algorithm is
+used to detect and exclude deviant points from the smoothing.
+.le
+.ls lowsigma = 2.5, highsigma = 2.5
+Sigma clipping thresholds above and below the smoothed iillumination.
+.le
+.ls divbyzero = 1.
+The iillumination correction is the inverse of the smoothed flat field.
+This may produce division by zero.  A warning is given if division
+by zero takes place and the result (the iillumination correction value)
+is replaced by the value of this parameter.
+.le
+.ls ccdproc (parameter set)
+CCD processing parameters.
+.le
+.ih
+DESCRIPTION
+First, the input flat field images are automatically processed if
+needed.  Then, the large scale iillumination pattern of the images is
+determined by heavily smoothing them using a moving "boxcar" average.
+The iillumination correction, the inverse of the iillumination pattern,
+is applied by \fBccdproc\fR to CCD images to remove the iillumination
+pattern introduced by the flat field.  The combination of the flat
+field calibration and the iillumination correction based on the flat
+field is equivalent to removing the iillumination from the flat field
+(see \fBmkillumflat\fR).  This two step calibration is generally used
+when the observations have been previously flat field calibrated.  This
+task is closely related to \fBmkskycor\fR which determines the
+iillumination correction from a blank sky image; this is preferable to
+using the iillumination from the flat field as it corrects for the
+residual iillumination error.  For a general discussion of the options
+for flat fields and iillumination corrections see \fBflatfields\fR.
+
+The smoothing algorithm is a moving average over a two dimensional
+box.  The algorithm is unconvential in that the box size is not fixed.
+The box size is increased from the specified minimum at the edges to
+the maximum in the middle of the image.  This permits a better estimate
+of the background at the edges, while retaining the very large scale
+smoothing in the center of the image.  Note that the sophisticated
+tools of the \fBimages\fR package may be used for smoothing but this
+requires more of the user and, for the more sophisticated smoothing
+algorithms such as surface fitting, more processing time.
+
+To minimize the effects of bad pixels a sigma clipping algorithm is
+used to detect and reject these pixels from the iillumination.  This is
+done by computing the rms of the image lines relative to the smoothed
+iillumination and excluding points exceeding the specified threshold
+factors times the rms.  This is done before each image line is added to
+the moving average, except for the first few lines where an iterative
+process is used.
+.ih
+EXAMPLES
+1. The example below makes an iillumination correction image from the
+flat field image, "flat017".
+
+    cl> mkillumcor flat017 Illum
+.ih
+SEE ALSO
+ccdproc, flatfields, mkillumflat, mkskycor, mkskyflat
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/mkillumflat.hlp b/noao/imred/quadred/src/quad/doc/mkillumflat.hlp
new file mode 100644
index 00000000..8288fb85
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/mkillumflat.hlp
@@ -0,0 +1,101 @@
+.help mkillumflat Oct88 noao.imred.ccdred
+.ih
+NAME
+mkillumflat -- Make illumination corrected flat fields
+.ih
+USAGE
+mkillumflat input output
+.ih
+PARAMETERS
+.ls input
+List of input flat field images to be illumination corrected.
+.le
+.ls output
+List of output illumination corrected flat field images.
+If none is specified or if the name is the same as the
+input image then the output image replaces the input image.
+.le
+.ls ccdtype = "flat"
+CCD image type to select from the input images.
+.le
+.ls xboxmin = 5, xboxmax = 0.25, yboxmin = 5, yboxmax = 0.25
+Minimum and maximum smoothing box size along the x and y axes.  The
+minimum box size is used at the edges and grows to the maximum size in
+the middle of the image.  This allows the smoothed image to better
+represent gradients at the edge of the image.  If a size is less then 1
+then it is interpreted as a fraction of the image size.  If a size is
+greater than or equal to 1 then it is the box size in pixels.  A size
+greater than the size of image selects a box equal to the size of the
+image.
+.le
+.ls clip = yes
+Clean the input images of objects?  If yes then a clipping algorithm is
+used to detect and exclude objects from the smoothing.
+.le
+.ls lowsigma = 2.5, highsigma = 2.5
+Sigma clipping thresholds above and below the smoothed illumination.
+.le
+.ls divbyzero = 1.
+The illumination flat field is the ratio of the flat field to a
+smoothed flat field.  This may produce division by zero.  A warning is
+given if division by zero takes place and the result (the illumination
+corrected flat field value) is replaced by the value of this
+parameter.
+.le
+.ls ccdproc (parameter set)
+CCD processing parameters.
+.le
+.ih
+DESCRIPTION
+First, the input flat field images are processed as needed.  Then the
+large scale illumination pattern of the images is removed.  The
+illumination pattern is determined by heavily smoothing the image using
+a moving "boxcar" average.  The output image is the ratio of the input
+image to the illumination pattern.  The illumination pattern is
+normalized by its mean to preserve the mean level of the input image.
+
+When this task is applied to flat field images only the small scale
+response effects are retained.  This is appropriate if the flat field
+images have illumination effects which differ from the astronomical
+images and blank sky images are not available for creating sky
+corrected flat fields.  When a high quality blank sky image is
+available the related task \fBmkskyflat\fR should be used.  Note that
+the illumination correction, whether from the flat field or a sky
+image, may be applied as a separate step by using the task
+\fBmkillumcor\fR or \fBmkskycor\fR and applying the illumination
+correction as a separate operation in \fBccdproc\fR.  However, creating
+an illumination corrected flat field image before processing is more
+efficient since one less operation per image processed is needed.  For
+more discussion about flat fields and illumination corrections see
+\fBflatfields\fR.
+
+The smoothing algorithm is a moving average over a two dimensional
+box.  The algorithm is unconvential in that the box size is not fixed.
+The box size is increased from the specified minimum at the edges to
+the maximum in the middle of the image.  This permits a better estimate
+of the background at the edges, while retaining the very large scale
+smoothing in the center of the image.  Note that the sophisticated
+tools of the \fBimages\fR package may be used for smoothing but this
+requires more of the user and, for the more sophisticated smoothing
+algorithms such as surface fitting, more processing time.
+
+To minimize the effects of bad pixels a sigma clipping algorithm is
+used to detect and reject these pixels from the illumination.  This is
+done by computing the rms of the image lines relative to the smoothed
+illumination and excluding points exceeding the specified threshold
+factors times the rms.  This is done before each image line is added to
+the moving average, except for the first few lines where an iterative
+process is used.
+.ih
+EXAMPLES
+1. Two examples in which a new image is created and in which the
+input flat fields are corrected in place are:
+
+.nf
+    cl> mkllumflat flat004 FlatV
+    cl> mkillumflat flat* ""
+.fi
+.ih
+SEE ALSO
+ccdproc, flatfields, mkfringecor, mkillumcor, mkskycor, mkskyflat
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/mkskycor.hlp b/noao/imred/quadred/src/quad/doc/mkskycor.hlp
new file mode 100644
index 00000000..15cfacf6
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/mkskycor.hlp
@@ -0,0 +1,103 @@
+.help mkskycor Feb88 noao.imred.ccdred
+.ih
+NAME
+mkskycor -- Make sky iillumination correction images
+.ih
+USAGE
+mkskycor input output
+.ih
+PARAMETERS
+.ls input
+List of input images for making sky iillumination correction images.
+.le
+.ls output
+List of output flat field iillumination correction images.  If none is
+specified or if the name is the same as the input image then the output
+image replaces the input image.
+.le
+.ls ccdtype = ""
+CCD image type to select from the input images.  If none is specified
+then all types are used.
+.le
+.ls xboxmin = 5, xboxmax = 0.25, yboxmin = 5, yboxmax = 0.25
+Minimum and maximum smoothing box size along the x and y axes.  The
+minimum box size is used at the edges and grows to the maximum size in
+the middle of the image.  This allows the smoothed image to better
+represent gradients at the edge of the image.  If a size is less then 1
+then it is interpreted as a fraction of the image size.  If a size is
+greater than or equal to 1 then it is the box size in pixels.  A size
+greater than the size of image selects a box equal to the size of the
+image.
+.le
+.ls clip = yes
+Clean the input images of objects?  If yes then a clipping algorithm is
+used to detect and exclude objects from the smoothing.
+.le
+.ls lowsigma = 2.5, highsigma = 2.5
+Sigma clipping thresholds above and below the smoothed iillumination.
+.le
+.ls ccdproc (parameter set)
+CCD processing parameters.
+.le
+.ih
+DESCRIPTION
+The large scale iillumination pattern of the input images, generally
+blank sky calibration images, is determined by heavily smoothing
+the image using a moving "boxcar" average.  The effects of objects in
+the image may be minimized by using a sigma clipping algorithm to
+detect and exclude the objects from the average.  This
+iillumination image is applied by \fBccdproc\fR to CCD images to remove
+the iillumination pattern.
+
+The input images are automatically processed up through flat field
+calibration before computing the iillumination.  The iillumination
+correction is that needed to make the processed images flat
+over large scales.  The input images are generally blank sky calibration
+images which have the same iillumination and instrumental effects
+as the object observations.  Object images may be used but removal
+of the objects may not be very good; particularly large, bright objects.
+For further discussion of flat fields and iillumination corrections
+see \fBflatfields\fR.
+
+You will notice that when you process images with an iillumination
+correction you are dividing each image by a flat field calibration and
+an iillumination correction.  If the iillumination corrections are not
+done as a later step but at the same time as the rest of the processing
+one will get the same calibration by multiplying the flat field by the
+iillumination correction and using this product alone as the flat
+field.  This approach has the advantage of one less calibration image
+and two less computations (scaling and dividing the iillumination
+correction).  Such an image, called a \fIsky flat\fR, may be created by
+\fBmkskyflat\fR as an alternative to this task.
+
+The smoothing algorithm is a moving average over a two dimensional
+box.  The algorithm is unconvential in that the box size is not fixed.
+The box size is increased from the specified minimum at the edges to
+the maximum in the middle of the image.  This permits a better estimate
+of the background at the edges, while retaining the very large scale
+smoothing in the center of the image.  Note that the sophisticated
+tools of the \fBimages\fR package may be used for smoothing but this
+requires more of the user and, for the more sophisticated smoothing
+algorithms such as surface fitting, more processing time.
+
+Blank sky images may not be completely blank so a sigma clipping
+algorithm may be used to detect and exclude objects from the
+iillumination pattern.  This is done by computing the rms of the image
+lines relative to the smoothed background and excluding points
+exceeding the specified threshold factors times the rms.  This is done
+before each image line is added to the moving average, except for the
+first few lines where an iterative process is used.
+.ih
+EXAMPLES
+1. The two examples below make an iillumination image from a blank sky image,
+"sky017".  In the first example a separate iillumination image is created
+and in the second the iillumination image replaces the sky image.
+
+.nf
+    cl> mkskycor sky017 Illum
+    cl> mkskycor sky017 sky017
+.fi
+.ih
+SEE ALSO
+ccdproc, flatfields, mkillumcor, mkillumflat, mkskyflat
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/mkskyflat.hlp b/noao/imred/quadred/src/quad/doc/mkskyflat.hlp
new file mode 100644
index 00000000..3d9ac1ca
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/mkskyflat.hlp
@@ -0,0 +1,111 @@
+.help mkskyflat Feb88 noao.imred.ccdred
+.ih
+NAME
+mkskyflat -- Make sky corrected flat field images
+.ih
+USAGE
+mkskyflat input output
+.ih
+PARAMETERS
+.ls input
+List of blank sky images to be used to create sky corrected flat field
+calibration images.
+.le
+.ls output
+List of output sky corrected flat field calibration images (called
+sky flats).  If none is specified or if the name is the same as the
+input image then the output image replaces the input image.
+.le
+.le
+.ls ccdtype = ""
+CCD image type to select from the input images.
+.le
+.ls xboxmin = 5, xboxmax = 0.25, yboxmin = 5, yboxmax = 0.25
+Minimum and maximum smoothing box size along the x and y axes.  The
+minimum box size is used at the edges and grows to the maximum size in
+the middle of the image.  This allows the smoothed image to better
+represent gradients at the edge of the image.  If a size is less then 1
+then it is interpreted as a fraction of the image size.  If a size is
+greater than or equal to 1 then it is the box size in pixels.  A size
+greater than the size of image selects a box equal to the size of the
+image.
+.le
+.ls clip = yes
+Clean the input images of objects?  If yes then a clipping algorithm is
+used to detect and exclude objects from the smoothing.
+.le
+.ls lowsigma = 2.5, highsigma = 2.5
+Sigma clipping thresholds above and below the smoothed iillumination.
+.le
+.ls ccdproc (pset)
+CCD processing parameter set.
+.le
+.ih
+DESCRIPTION
+A sky corrected flat field calibration image, called a sky flat, is a
+flat field that when applied to observations of the sky have no large
+scale gradients.  Flat field images are generally obtained by exposures
+to lamps either illuminating the telescope field or a surface in the dome
+at which the telescope is pointed.  Because the detector is not illuminated
+in the same way as an observation of the sky there may be large
+scale iillumination patterns introduced into the observations with such
+a flat field.  To correct this type of flat field a blank sky observation
+(which has been divided by the original flat field) is heavily smoothed
+to remove the noise leaving only the residual large scale iillumination
+pattern.  This iillumination pattern is divided into the original flat
+field to remove this residual.
+
+The advantage of creating a sky flat field is that when processing
+the observations no additional operations are required.  However,
+if the observations have already been processed with the original
+flat field then the residual iillumination pattern of blank sky
+calibration images may be created as an iillumination correction
+to be applied by \fBccdproc\fR.  Such a correction is created by the
+task \fBmkskycor\fR.  If a good blank sky image is not
+available then it may be desirable to remove the iillumination pattern
+of the flat field image using \fBmkillumflat\fR or \fBmkillumcor\fR
+provided the sky observations are truly uniformly illuminated.
+For more on flat fields and iillumination corrections see \fBflatfields\fR.
+
+The input, blank sky images are first processed, based on the
+\fBccdproc\fR parameters, if needed.  These parameters also determine
+the flat field image to be used in making the sky flat.  The residual
+iillumination pattern is determined by heavily smoothing the image using
+a moving "boxcar" average.  The effects of objects in the input image
+may be minimized by using a sigma clipping algorithm to detect and
+exclude the objects from the average.  The output image is ratio of the
+flat field image, for the same subset as the input image, to the
+residual iillumination pattern determined from the processed blank sky
+input image.  The iillumination pattern is normalized by its mean to
+preserve the mean level of the flat field image.
+
+The smoothing algorithm is a moving average over a two dimensional
+box.  The algorithm is unconvential in that the box size is not fixed.
+The box size is increased from the specified minimum at the edges to
+the maximum in the middle of the image.  This permits a better estimate
+of the background at the edges, while retaining the very large scale
+smoothing in the center of the image.  Note that the sophisticated
+tools of the \fBimages\fR package may be used for smoothing but this
+requires more of the user and, for the more sophisticated smoothing
+algorithms such as surface fitting, more processing time.
+
+Blank sky images may not be completely blank so a sigma clipping
+algorithm may be used to detect and exclude objects from the
+iillumination pattern.  This is done by computing the rms of the image
+lines relative to the smoothed background and excluding points
+exceeding the specified threshold factors times the rms.  This is done
+before each image line is added to the moving average, except for the
+first few lines where an iterative process is used.
+.ih
+EXAMPLES
+1. Two examples in which a new image is created and in which the
+input sky images are converted to sky flats are:
+
+.nf
+    cl> mkskyflat sky004 Skyflat
+    cl> mkskyflat sky* ""
+.fi
+.ih
+SEE ALSO
+ccdproc, flatfields, mkfringecor, mkillumcor, mkillumflat, mkskycor
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/quad.hlp b/noao/imred/quadred/src/quad/doc/quad.hlp
new file mode 100644
index 00000000..7f8754ee
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/quad.hlp
@@ -0,0 +1,121 @@
+.help package Sep93 arcon.quad
+.ih
+NAME
+quad -- reduction package for CCD images obtained with Arcon
+
+.ih
+USAGE
+quad
+
+This package \fBmust\fR be used in place of \fBccdred\fR for the first steps
+(overscan correction and trimming) of multi-readout (quad or dual) images.
+Either package can be used for the subsequent stages, and for the complete
+reduction of single readout images.
+
+.ih
+PARAMETERS
+.ls pixeltype = "real real"
+Output pixel datatype and calculation datatype.  When images are processed
+or created the output pixel datatype is determined by this parameter.
+The allowed types are "short" for short integer, and "real" for real
+floating point.  The calculation datatypes are also short and real with a
+default of real if none is specified. Note that Arcon generates images of type
+"ushort" (unsigned 16-bit integers). In general both the output and calculation
+types should, therefore, be set to "real" to avoid truncation and wrap
+around errors, although this means that the reduced images will occupy twice as
+much disk space.
+.le
+.ls verbose = no
+Print log information to the standard output?
+.le
+.ls logfile = "logfile"
+Text log file.  If no filename is specified then no log file is kept.
+.le
+.ls plotfile = ""
+Log metacode plot file for the overscan bias vector fits.  If
+no filename is specified then no metacode plot file is kept.
+.le
+.ls backup = ""
+Backup prefix for backup images.  If no prefix is specified then no backup
+images are kept when processing.  If specified then the backup image
+has the specified prefix.
+.le
+.ls instrument = ""
+CCD instrument translation file.  This is usually set with \fBsetinstrument\fR.
+.le
+.ls ssfile = "subsets"
+Subset translation file used to define the subset identifier.  See
+\fBsubsets\fR for more.
+.le
+.ls graphics = "stdgraph"
+Interactive graphics output device when fitting the overscan bias vector.
+.le
+.ls cursor = ""
+Graphics cursor input.  The default is the standard graphics cursor.
+.le
+.ls version = "Version 2.0 - Sept 93"
+Package version.
+.le
+.ih
+DESCRIPTION
+The \fBquad\fR package contains all the basic tasks necessary for the
+reduction of CCD data obtained with Arcon. With Arcon images are often readout
+using four ("quad") or two ("dual") amplifiers in order to reduce readout time.
+The \fBquad\fR package includes the few special tasks needed to deal with such
+multi-readout data, as well as many standard tasks taken directly from the 
+\fBccdred\fR package. The \fBquad\fR package must be used for the first
+reduction steps, overscan correction and trimming, of multi-readout images;
+subsequent steps can be performed using \fBquad\fR or \fBccdred\fR. Either
+package can be used for the complete reduction of conventional single readout
+CCD images.
+
+The \fBquad\fR package also contains the tasks \fBqstatistics\fR and 
+\fBqhistogram\fR which can be used for examining raw multi-readout images. 
+
+The \fBquad\fR package task itself has several parameters which are common to 
+many of the tasks in the package.  When images are processed or new image are
+created the output pixel datatype is that specified by the parameter
+\fBpixeltype\fR. Note that CCD processing replaces the original image by the
+processed image so the pixel type of the CCD images may change during
+processing.  It is unlikely that real images will be processed to short images
+but the reverse is quite likely.  Processing images from short to real
+pixel datatypes will generally increase the amount of disk space
+required (a factor of 2 on most computers).
+
+The tasks produce log output which may be printed on the standard
+output (the terminal unless redirected) and appended to a file.  The
+parameter \fIverbose\fR determines whether processing information
+is printed.  This may be desirable initially, but when using background
+jobs the verbose output should be turned off.  The user may look at
+the end of the log file (for example with \fBtail\fR) to determine
+the status of the processing.
+
+The package was designed to work with data from many different observatories
+and instruments.  In order to accomplish this an instrument translation
+file is used to define a mapping between the package parameters and
+the particular image header format.  The instrument translation file
+is specified to the package by the parameter \fIinstrument\fR.  This
+parameter is generally set by the task \fBsetinstrument\fR.  The other
+file used is a subset file.  This is generally created and maintained
+by the package and the user need not do anything.  For more sophisticated
+users see \fBinstruments\fR and \fBsubsets\fR.
+
+The package has very little graphics
+output.  The exception is the overscan bias subtraction.  The bias
+vector is logged in the metacode plot file if given.  The plot file
+may be examined with the tasks in the \fBplot\fR package such as
+\fBgkimosaic\fR.  When interactively fitting the overscan vector
+the graphics input and output devices must be specified.  The defaults
+should apply in most cases.
+
+Because processing replaces the input image by the processed image it
+may be desired to save the original image.  This may be done by
+specifying a backup prefix with the parameter \fIbackup\fR.  For
+example, if the prefix is "orig" and the image is "ccd001", the backup
+image will be "origccd001".  The prefix may be a directory but if so it must
+end with '/' or '$' (for logical directories) and the directory must already
+exist.
+.ih
+SEE ALSO
+instruments, setinstrument, subsets
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/quadman.hlp b/noao/imred/quadred/src/quad/doc/quadman.hlp
new file mode 100644
index 00000000..55bfe10d
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/quadman.hlp
@@ -0,0 +1,1330 @@
+.help quadman Sep93 Version-0.0
+.ce
+\fIV-ARCON. Reduction of CCD data obtained with Arcon\fR
+
+.nf
+     1. Introduction
+     2. Getting the Data
+     3. Reducing the Data
+          3.1   Introduction
+          3.2   Reading the Data from Tape
+          3.3   Setting Up the Translation File
+                3.3.1  Setinstrument for CCD Used
+                3.3.2  Setting the Subsets Parameter and Preparations 
+          3.4   Preparing Individual Calibration Frames
+	  3.5   Processing the calibration frames
+          3.6   Preparing a Final Flat Field
+          3.7   Processing the Images
+          3.8   Creating the Bad Pixel File
+          3.9   Writing the Data to Tape
+
+
+
+
+
+
+					A thinly disguised version of CCDMAN
+
+
+						     Lisa Wells
+
+                                                    Mario Hamuy
+
+						 September 30, 1993
+.fi
+.bp
+.ls \fI1. Introduction\fR
+
+CCDRED is a package in IRAF used for CCD data reduction. It is primarily used
+for CCD imaging although various aspects are also used for spectral reduction.
+This document is intended as a guideline to reducing direct CCD images using
+IRAF. If you are reducing spectra, see Section III or IV of
+this manual. If you do not have experience using IRAF we suggest that
+you start by
+reading "An Introduction to IRAF" which will give you a general idea of IRAF
+structure as well as a few fundamental tools. If you plan to use this package
+extensively, there is a demo on the computer as well which will run through
+the reduction process interactively. Once you login and enter IRAF
+type the following:
+
+.nf
+      cl> noao
+      no> imred
+      im> ccdred
+      cc> ccdtest
+      cc>
+.fi
+
+The cc> prompt indicates the package has been loaded. 'ccdtest' contains several
+tasks one of which is 'demo'. Now type 'demo' and follow the instructions. It
+will prompt you, from time to time, to continue to the next section.
+
+The examples shown here are just that, examples. The user must decide
+upon the reduction procedure, naming, convention, etc..., appropriate for
+his/her own data and use the cookbook and examples as guidelines only. The
+examples are shown with prompts, for the package containing the tasks (do not
+type the prompts, of course). It is strongly recommended that you perform an
+'lpar' on every task immediately before using it, unless you are familiar with
+all of its parameters. This is not always shown in the examples, but is normal
+practice even among seasoned IRAF users.
+
+IRAF uses two conventions that you should always keep in mind. 
+First, images consist of lines and columns (not rows and columns). Keep in mind
+that the mountain Forth systems for the CCDs are zero-indexed and use rows and
+lines. IRAF uses one-indexed coordinates for images (see figure 1). Second,
+the "order" of a function is the number of independent coefficients for a
+polynomial, or the number of intervals for a spline curve. For example, a cubic
+(third-degree) polynomial is described as "order=4" (four coefficients).
+
+If you require personal assistance in your reductions please contact
+either Mauricio Navarrete or Nelson Saavedra on Tololo (ex 422),
+or Mario Hamuy(ex 210) in La Serena.
+.le
+.bp
+.ls \fI2. Getting the Data\fR
+
+Many observers often get confused about the number and kind of calibration
+frames that must be taken to properly reduce their data. During a whole
+run you should get the following:
+
+1) Bias frames for each night are essential no matter what setup and chip
+you are using. 20-30 of these should be taken and combined.
+
+2) Dome flats should be taken for each filter you are using. Preferably
+this should be done every day, but you can get by with just one per run,
+as long as you take a sufficient number of them, say 20-30.
+
+3) Twilight sky flats are necessary if you want to do photometry to better
+than 2%-3%, if you are doing surface photometry of extended objects,
+or if sky subtraction is critical. We suggest that everyone take sky flats
+since it is a good check of your dome flat iillumination. For some CCDs it
+is better to use a sky flat to flatten your objects and this may depend
+upon the filters being used.
+It was found at the 0.9-m and 1.5-m telescopes that
+sky flats do better in flattening your
+images in the U and B filters. It is therefore
+suggested that you concentrate on getting many U and B sky flats (10 or more)
+since you will probably process your data using them.
+These will be combined in the first steps of the reduction.
+
+4) Darks are worth taking to check that things are working but dark correction
+is not necessary for any of the CCDs now used at CTIO. The dark current
+should be <10 e-/hour/pixel, if greater, then something is wrong and you
+should get it fixed.
+
+5) Photometric standard stars should be taken when needed and as many as
+necessary (>20) to properly calibrate your objects.
+
+You should refer to the instrument manual for more details. We
+suggest that you start taking your calibration frames early in the afternoon so
+that you have enough time left for supper. It is important to note on your
+calibration frames, the positions of bad pixels and then avoid observing
+your objects on these regions of the CCD, especially if you plan to do
+photometry. At the end of the reductions, you may wish to use a bad pixel map
+to correct the bad pixels. This will be discussed later (section 3.8)
+in more detail.
+.le
+.bp
+.ce
+\fI3. Reducing the Data\fR
+.ls \fI3.1 Introduction\fR
+
+A full reduction of CCD data requires the following operations (see the
+flow diagram on the next page):
+
+.nf
+      1) Combine the bias, flats and darks.
+      2) Fit and subtract a readout bias given by the overscan strip.
+      3) Trim the image of overscan strip and border rows and columns.
+      4) Subtract the dark, if appropriate.
+      5) Prepare a final flat.
+      6) Divide by the flat field.
+      7) Fix the bad pixels in all the images.
+      8) Fringing corrections may be done at the end.
+.fi
+
+The most general processing, described in this manual, consists of
+overscan subtracting, trimming, bias subtracting, dark subtracting,
+and flat fielding your data. Although dark subtraction is rarely used,
+it is included in this example for generality.
+
+Individual bias, darks, dome and sky flats must be properly combined to give
+good signal to noise calibration frames and to remove cosmic rays. The
+algorithm used to combine the images must have 10 or more frames to do a good
+job of cleaning the cosmic rays. IRAF offers several algorithms for combining
+the individual frames. You should always carefully inspect all the individual
+frames, and the final image to check
+for potential problems.
+
+Having obtained the combined calibration images you should flatten your sky flat
+using the dome flat and examine the result for any significant iillumination 
+variation. If these variations are significant they may be fit in order to
+correct your dome flat. 
+Fringing corrections may be
+applied. This should be done separately. This is only needed for the RCA
+chips at the 4 meter PF/CCD and the TI chips in the I band. We do not
+currently support this but direction can be given as to what might possibly
+work.
+
+At this level
+the images should be finished except for fixing any bad pixels that may not
+have been taken care of in the flat fielding. Once this is done you may
+do photometry. A photometry manual is available to do your analysis,
+see section VI of this manual, which describe the use of the
+aperture photometry routines in IRAF and the transformation from
+instrumental to standard magnitudes. There is also a manual which was
+written by the IRAF group in Tucson which is a good guide; "A User's
+Guide to Stellar CCD Photometry with IRAF".
+.bp
+.nf
+
+                   ==========================
+                   =      Set Instrument    =
+                   =  and Translation File  =
+                   ==========================
+                             *****
+                              ***
+                               *
+               ==================================
+               =  Combining Calibration Frames  =
+               =    and Removing Cosmic Rays    =
+               ==================================
+                             *****
+                              ***
+                               *
+		===============================
+		=          Processing         =
+		=      Calibration Frames     =
+		===============================
+			     *****
+			      ***
+			       *
+                ================================
+                =    Preparing a Flat Field    =
+                ================================
+                             *****
+                              ***
+                               *
+		   ==========================
+		   =  Processing the data   =
+		   ==========================
+			     *****
+			      ***
+			       *
+		   ==========================
+		   =   Fixing bad pixels    =
+		   ==========================
+			     *****
+			      ***
+			       *
+                   ==========================
+                   =   Fringe Corrections   =
+                   =       (optional)       =
+                   ==========================
+.fi
+.le
+.bp
+.ls \fI3.2 Reading the data from Tape\fR
+
+Load the 'dataio' package and allocate the appropriate tape drive:
+
+.nf
+      cl> dataio
+      da> alloc mta
+.fi
+
+If you wish to read fits files from an exabyte, use 'mtx' as the device
+designation. Now mount your tape on the tape drive and be sure you've
+removed the write ring. It is best to create a separate directory for
+each night. This is done using the command 'mkdir night1'. Now change
+to this directory by typing 'cd night1'. Read the data using the task
+'rfits'. You must specify the tape drive name, the list of files you wish
+to read and the "root" file name. If you transferred your data to the
+SUN using 'getpix' then you may wish to use the naming convention given
+to your files, in this case just set the parameter 'oldirafname' to yes.
+In choosing the root file name, it is usually a good idea to include a
+digit in the name to indicate the tape number (eg, "tape1" for the
+first tape; files would be called "tape10001, tape10002,.."); alternatively,
+an offset may be added (eg, offset=89 means the first files would be
+called "tape10090, tape10091,.." or 1+89, 2+89,..).
+
+.nf
+      da> epar rfits          (check the parameter list)
+      da> rfits mta 1-999 tape1
+.fi
+
+The file list "1-999" should more than cover the number of files on tape;
+the task will end gracefully at the end of the tape. When finished,
+rewind the tape and deallocate the drive,
+
+.nf
+      da> rew mta
+      da> dealloc mta
+.fi
+
+and remove your tape from the drive. We assume that you kept the old IRAF
+name given to your files throughout the rest of this manual.
+
+.nf
+                     \fIrfits\fR
+
+    fits_file = "mta"       FITS data source
+    file_list = "1-999"     File list
+    iraf_file = "tape1"     IRAF filename
+  (make_image = yes)        Create an IRAF image?
+ (long_header = no)         Print FITS header cards?
+(short_header = yes)        Print short header?
+    (datatype = "")         IRAF data type
+       (blank = 0.)         Blank value
+       (scale = yes)        Scale the data?
+ (oldirafname = no)         Use old IRAF name in place of iraf_file?
+      (offset = 0)          Tape file offset
+        (mode = "ql")           
+.fi
+.le
+.bp
+.ce
+\fI3.3 Setting Up the Translation File\fR
+.ls \fI3.3.1 Setinstrument for CCD Used\fR
+
+Start by loading the 'imred' and 'ccdred' packages.
+
+.nf
+      cl> noao
+      no> imred
+      im> ccdred
+      cc>
+.fi
+
+Because the 'ccdred' package was
+designed to work with data from many different observatories and instruments,
+an \fIinstrument translation file\fR is required to define a mapping
+between the package parameters and the particular image header format.
+An example of a translation file is shown on the next page.
+You must define a translation file using the task 'setinstrument'.
+Edit the parameters for the task 'setinstrument' according to the
+list given below and run it.
+The choices for instrument can be found in Appendix A. If the CCD you
+used is not listed, use the generic "ccd" or "cfccd" in the instrument
+parameter in the task.
+
+.nf
+      cc> epar setinstrument       (check the parameter list)
+      cc> setinstrument
+.fi
+
+The task will run and prompt you for the instrument ID (a "?" will list
+the possible choices). Answer 'cfccd' and the task will send you into 
+the parameter editing mode for
+the task 'ccdred'. It will automatically set the \fIinstrument\fR
+(translation) parameter
+so do not change it. It is a good idea while processing your calibration
+frames to save a copy of the unprocessed images. This will be done
+by the package 'ccdred' if you specify a prefix or subdirectory in the
+parameter 'backup'. In our example, the files will be saved with the prefix
+'B'. When you type 'ctrl-z' to exit you will then be sent to 'ccdproc'
+to edit its parameters. We will edit
+'ccdproc' later so don't worry about it for now.
+
+.nf
+               \fIsetinstrument parameters\fR
+
+   \fIinstrument\fR = "cfccd"     Instrument ID (type ? for a list)
+        (\fIsite\fR = "ctio")     Site ID
+   (\fIdirectory\fR = "ccddb$")   Instrument directory
+      (review = yes)        Review instrument parameters?
+        query = ""          Instrument ID (type q to quit)
+        (mode = "ql")           
+
+                 \fIccdred parameters\fR
+
+   (pixeltype = "real real") Output and calculation pixel datatypes
+     (verbose = no)         Print log information to the standard output?
+     (logfile = "ccdlog")   Text log file
+    (plotfile = "ccdplot")  Log metacode plot file
+      (\fIbackup\fR = "B")        Backup directory or prefix
+  (\fIinstrument\fR = "ccddb$ctio/cfccd.dat") CCD instrument file
+      (\fIssfile\fR = "subsets")  Subset translation file
+    (graphics = "stdgraph") Interactive graphics output device
+      (cursor = "")         Graphics cursor input
+     (version = "2: October 1987") 
+        (mode = "ql")           
+      ($nargs = 0)              
+
+.fi
+
+An example of the \fIinstrument translation file\fR follows.
+
+.nf
+
+          exptime exptime
+          darktime darktime
+          imagetyp imagetyp
+          subset filters
+          biassec biassec
+          datasec datasec
+	  trimsec trimsec
+          fixfile fixfile
+
+          fixpix                bp-flag 0
+          overscan              bt-flag 0
+          zerocor               bi-flag 0
+          darkcor               dk-flag 0
+          flatcor               ff-flag 0
+          fringcor              fr-flag 0
+
+          OBJECT		object
+          DARK			dark
+          "PROJECTOR FLAT"	flat
+          "SKY FLAT"		other
+          COMPARISON		other
+          BIAS			zero
+          "DOME FLAT"		flat
+          MASK			other
+.fi
+
+
+The instrument file consists of first, the IRAF parameter and its associated
+image header keyword from the objects. These header values may vary depending
+upon the instrument being used.
+The second section is the
+header flag section which is added to the object as it is being processed to
+mark that the operation has been done. Once an image is zero corrected, the
+keyword bi-flag parameter is added to the image header and set to '0' so that
+the process is not repeated later. The last section is the image-type 
+specification. This is used when the imagetyp parameter is read. The header
+value 'OBJECT' is translated to 'object', and a 'SKY FLAT' becomes 'other'.
+If you need to modify the translation file you may copy this file to your
+directory and change the appropriate parameters. If the name of the imagetype
+contains 2 words, then you must put quotes around the designation, for example,
+look at the 'SKY FLAT' line in the above file. Comparison arcs are not used
+in direct imaging and are not needed.
+
+Without the proper translation file, the task 'ccdlist' will give the following:
+
+.nf
+  cc> ccdlist *.imh
+
+  bias001.imh[400,420][short][unknown][]:median of 4 ave of 6 bias 
+  flat002.imh[400,420][short][unknown][]:median of 4 ave of 6 flat
+  flat003.imh[400,420][short][unknown][]:median of 4 ave of 6 flat
+  obj004.imh[400,420][short][unknown][]:IC 481  V-filter ........
+  obj005.imh[400,420][short][unknown][]:IC 481  B-filter.........
+         :	:	:	:	:	:	:	:
+  obj036.imh[400,420][short][unknown][]:Sky flat B-filter .......
+  obj037.imh[400,420][short][unknown][]:Sky flat V-filter .......
+         :	:	:	:	:	:	:	:
+.fi
+
+The [unknown] in the listing means that the frame type is unknown, ie, if
+it is a dark, flat, bias,... etc. The blank brackets should contain the
+filter type and will be taken care of in the next section.
+.le
+.bp
+.ls \fI3.3.2 Setting the Subsets Parameter and Preparing for Processing\fR
+
+The 'ccdred' package groups observations into subsets. The image header
+parameter used to identify the subsets is defined in the \fIinstrument
+translation file\fR. For example, to select subsets by the header parameter
+'filters' the instrument translation file would contain the line
+
+.nf
+     subset filters
+.fi
+
+Now do a 'ccdlist' and you should see the
+correct image type specified for each frame:
+
+.nf
+  cc> ccdlist *.imh
+
+  bias001.imh[400,420][short][zero][]:median of 4 ave of 6 bias
+  flat002.imh[400,420][short][flat][]:median of 4 ave of 6 flat
+  flat003.imh[400,420][short][flat][]:median of 4 ave of 6 flat
+  obj004.imh[400,420][short][object][]:IC 481  V-filter ......
+  obj005.imh[400,420][short][object][]:IC 481  B-filter.......
+	:          :        :        :        :    :       :
+	:          :        :        :        :    :       :
+  obj036.imh[400,420][short][object][]:Sky flat B-filter .....
+  obj037.imh[400,420][short][object][]:Sky flat V-filter .....
+	:          :        :        :        :    :       :
+.fi
+
+Doing this will create a file in your directory called 'subsets'. This is a
+file with a listing of the filter type read from the image header consisting
+of the combination of the upper and lower filter bolt positions. The flats
+were taken with a color balance filter so they have different values from the
+objects in the list. Therefore, you need to edit this file to set the filter
+types properly. The bias and dark were probably taken with a setting that
+corresponds to one of the filters, but it will be ignored. If however, the
+filter type set in the header corresponds to something other than a standard
+filter, set this to some arbitrary value, for example below it is assumed that
+the filter positions for the bias were '0 1', so this is set to '0'.
+
+.nf
+      cc> edit subsets
+.fi
+
+An example of the necessary changes is:
+
+.nf
+       \fISubsets Before     |        Subsets After\fR
+      '1 0'      1        |       '1 0'      U
+      '2 0'      2        |       '2 0'      B
+      '3 0'      3        |       '3 0'      V
+      '4 0'      4        |       '4 0'      R
+      '5 0'      5        |       '5 0'      I
+      '0 1'     01        |       '0 1'      0
+      '1 1'     11        |       '1 1'      U
+      '2 1'     21        |       '2 1'      B
+      '3 1'     31        |       '3 1'      V
+      '4 1'     41        |       '4 1'      R
+      '5 1'     51        |       '5 1'      I
+.fi
+
+If any of the parameters are not specified properly after doing 'ccdlist',
+then the translation file may be set up improperly. Consult
+Mauricio Navarrete, Nelson Saavedra, or Mario Hamuy.
+
+You must also specify the overscan and trim region.
+The overscan is the region to the far right of the image when plotting a line
+of the image (see figure 2a). The overscan region should be
+specified by the beginning and ending column followed by the beginning and
+ending line. This region should begin at least 5-10 pixels from the edge of
+the active region of the CCD. The correct position can be found by plotting
+several lines using ':l #1 #2' (#1 and #2 specify a range of lines to be
+averaged and plotted) in 'implot', and expanding the right side (see figure 2b).
+Notice the signal decays toward the right just the other side of the step with
+an e-folding distance of a few pixels. The overscan strip should begin in 3 to
+4 e-folding distances from the break. You want to fit this region all along
+the image so the range of lines should include everything. Be sure to write
+down these values so you don't forget them.
+
+The trim region is the section of the image to be kept after processing.
+Choose this area excluding the overscan region
+and any bad lines or columns at the edges of the image. Figures 2c and 2d show
+a plot of a line and column, respectively. They show the edges which should be
+trimmed from the image. Later (section 3.5)
+you will edit the parameters for 'ccdproc' and enter the overscan and trim
+section.
+
+The bad pixel file will be used after the images have been flattened. In many
+cases the flatfielding will correct the bad pixel regions also so it is best
+left until the end. If you specify the bad pixel file during the processing
+be aware that the corrections are done on the file first.
+.le
+.bp
+.ls \fI3.4 Preparing Individual Calibration Frames\fR
+
+If you have taken many calibration frames (bias, dome flats, darks
+and sky flats) that you wish to combine in order to remove cosmic
+rays, we suggest you to perform a combination of images separately for
+each night. In some cases, when the instrument response remains
+stable during your run, it is worth combining data from many nights,
+especially the darks and sky flats, to improve the signal-to-noise
+ratio. If you have already combined the data on the mountain skip
+over this section and go on to the next one.
+
+Most likely you used "getpix" to transfer your data from the LSI
+to the SUN so you have preserved the naming convention. This makes
+it very easy to combine your images.
+
+There are tasks which combine each type of object together. For the
+bias do an 'epar' on the 'zerocombine' task, and fill the parameters
+according to the list given below. We suggest selecting the 'avsigclip'
+rejection operation which applies a
+sigma clipping algorithm to each pixel to remove cosmic rays. This
+algorithm requires at least three input images (best with
+more than 10) to work effectively. According to your particular needs you may
+select other options to combine the data like minmax, ccdclip, etc.
+No scaling is performed on the biases.
+If your bias frames vary greatly, then there
+is something wrong with your setup. In this case, have someone check
+out the electronics.
+
+.nf
+      cc> epar zerocombine           (check the list given below)
+.fi
+
+Then combine the bias frames. Optionally you may add a '&' at the end
+of the command line to submit the task as a background job.
+
+.nf
+      cc> zerocombine bias*.imh output=zero1 &
+.fi
+
+Now, proceed with the combination of the darks.
+
+.nf
+      cc> epar darkcombine            (check the list given below)
+      cc> darkcombine dark*.imh output=dark1 &
+.fi
+
+Before combining the flat frames, you must
+find a region free of bad pixels to be used to scale the individual
+flat frames. The box should be chosen where there is signal.
+Once you have determined the position of the box, you
+should first run 'imstat' for all your images using this region.
+
+.nf
+      cc>  imstat flat*[200:250,300:330]
+
+      #          IMAGE             NPIX   MEAN   STDDEV  MIN   MAX
+      flat001.imh[200:250,300:330] 37901  5489.  1510.   678.  9020.
+      flat002.imh[200:250,300:330] 37901  5485.  1508.   694.  8484.
+      flat003.imh[200:250,300:330] 37901  5478.  1507.   691.  8472.
+      flat004.imh[200:250,300:330] 37901  5475.  1506.   671.  8397.
+      flat005.imh[200:250,300:330] 37901  5474.  1506.   659.  8540.
+      flat006.imh[200:250,300:330] 37901  5472.  1505.   663.  8422.
+      flat007.imh[200:250,300:330] 37901  5467.  1504.   655. 15513.
+      flat008.imh[200:250,300:330] 37901  5464.  1502.   673.  8471.
+      flat009.imh[200:250,300:330] 37901  5458.  1501.   684.  8503.
+.fi
+
+If the mean varies by a large amount, say greater than a few percent, then
+you should use the mode section for the scaling.
+In the example below the flats are combined with scaling.
+Enter this region in the 'statsec' parameter in the following format,
+
+.nf
+      [x1:x2,y1:y2]
+.fi
+      
+where the values x1 and x2 are the limits of the box in the x-axis, y1
+and y2 are the limits along the y-axis. This will only be
+used if 'median' is specified in the 'scale' parameter of the task
+'flatcombine'. In this example we have chosen to combine the individual
+flats using the 'ccdclip' option, which rejects pixels using the CCD noise
+parameters, namely the read-out-noise and the gain. You must enter these
+values in the parameters 'rdnoise' and 'gain' in 'flatcombine'. In this
+example we have entered a read-out-noise of 5 electrons, and a gain of
+2.5 electrons/ADU.
+
+.nf
+       cc> epar flatcombine          (check the list given below)
+.fi
+
+Proceed with the combination of the flats.
+
+.nf
+       cc> flatcombine flat.*imh output=flat1 &
+.fi
+
+If you have 3 or more sky flats, they may be combined in the same manner
+as the dome flats (change the 'ccdtype' parameter to 'other').
+
+.nf
+      cc> epar flatcombine        (check the list given below)
+      cc> flatcombine sky.*imh output=sky1 &
+.fi
+
+The output at this point is a set of images clean of cosmic rays called zero1,
+dark1, flat1, and sky1, where the 1 stands for the first night and the flats
+and skys end in their respective filter type ie, flat1U, flat1B,... Using the
+parameter subsets, the combination occurred for all the flats and skys of the
+same filter type (subset). We suggest that you examine these images, either by
+displaying, or imploting them. For example;
+
+.nf
+      cc> display zero1
+      cc> implot zero1
+.fi
+
+We suggest also to look at the logfile created by the package 'ccdred' in
+order to check that the images were properly combined by the same filter
+type.
+
+.nf
+      cc> page ccdlog
+.fi
+.bp
+
+.nf
+                         \fIzerocombine\fR
+
+        input = "bias*.imh"     List of zero level images to combine
+      (output = "zero1")        Output zero level name
+     (\fIcombine\fR = "average")      Type of combine operation
+      (\fIreject\fR = "avsigclip")    Type of rejection
+     (\fIccdtype\fR = "zero")         CCD image type to combine
+     (process = no)             Process images before combining?
+      (delete = no)             Delete input images after combining?
+     (clobber = no)             Clobber existing output image?
+       (\fIscale\fR = "none")         Image scaling
+     (statsec = "")             Image section for computing statistics
+        (nlow = 0)              minmax: Number of low pixels to reject
+       (nhigh = 1)              minmax: Number of high pixels to reject
+       (nkeep = 1)              Minimum to keep (pos) or maximum to reject
+       (mclip = yes)            Use median in sigma clipping algorithms?
+      (lsigma = 3.)             Lower sigma clipping factor
+      (hsigma = 3.)             Upper sigma clipping factor
+     (rdnoise = "0")            ccdclip: CCD readout noise (electrons)
+        (gain = "1")            ccdclip: CCD gain (electrons/DN)
+      (snoise = "0.")           ccdclip: Sensitivity noise (fraction)
+       (pclip = -0.5)           pclip: Percentile clipping parameter
+       (blank = 0.)             Value if there are no pixels
+        (mode = "ql")           
+
+                         \fIdarkcombine\fR
+
+        input = "dark.*imh"     List of dark images to combine
+      (output = "dark1")        Output flat field root name
+     (\fIcombine\fR = "average")      Type of combine operation
+      (\fIreject\fR = "avsigclip")    Type of rejection
+     (\fIccdtype\fR = "dark")         CCD image type to combine
+     (process = no)             Process images before combining?
+      (delete = no)             Delete input images after combining?
+     (clobber = no)             Clobber existing output image?
+       (\fIscale\fR = "exposure")     Image scaling
+     (statsec = "")             Image section for computing statistics
+        (nlow = 1)              minmax: Number of low pixels to reject
+       (nhigh = 1)              minmax: Number of high pixels to reject
+       (nkeep = 1)              Minimum to keep (pos) or maximum to reject
+       (mclip = yes)            Use median in sigma clipping algorithms?
+      (lsigma = 3.)             Lower sigma clipping factor
+      (hsigma = 3.)             Upper sigma clipping factor
+     (rdnoise = "0.")           ccdclip: CCD readout noise (electrons)
+        (gain = "1.")           ccdclip: CCD gain (electrons/DN)
+      (snoise = "0.")           ccdclip: Sensitivity noise (fraction)
+       (pclip = -0.5)           pclip: Percentile clipping parameter
+       (blank = 0.)             Value if there are no pixels
+        (mode = "ql")           
+
+                    \fIflatcombine for dome flats\fR
+
+        input = "flat.*imh"     List of flat field images to combine
+      (output = "flat1")        Output flat field root name
+     (combine = "median")       Type of combine operation
+      (reject = "ccdclip")      Type of rejection
+     (ccdtype = "flat")         CCD image type to combine
+     (process = no)             Process images before combining?
+     (subsets = yes)            Combine images by subset parameter?
+      (delete = no)             Delete input images after combining?
+     (clobber = no)             Clobber existing output image?
+       (scale = "median")       Image scaling
+     (statsec = "[m:n,p:q]")    Image section for computing statistics
+        (nlow = 1)              minmax: Number of low pixels to reject
+       (nhigh = 1)              minmax: Number of high pixels to reject
+       (nkeep = 1)              Minimum to keep (pos) or maximum to reject
+       (mclip = yes)            Use median in sigma clipping algorithms?
+      (lsigma = 3.)             Lower sigma clipping factor
+      (hsigma = 3.)             Upper sigma clipping factor
+     (rdnoise = "5")            ccdclip: CCD readout noise (electrons)
+        (gain = "2.5")          ccdclip: CCD gain (electrons/DN)
+      (snoise = "0.")           ccdclip: Sensitivity noise (fraction)
+       (pclip = -0.5)           pclip: Percentile clipping parameter
+       (blank = 1.)             Value if there are no pixels
+        (mode = "ql")           
+
+                   \fIflatcombine for sky flats\fR
+
+        input = "sky.*imh"      List of flat field images to combine
+      (output = "sky1")         Output flat field root name
+     (combine = "median")       Type of combine operation
+      (reject = "ccdclip")      Type of rejection
+     (ccdtype = "other")        CCD image type to combine
+     (process = no)             Process images before combining?
+     (subsets = yes)            Combine images by subset parameter?
+      (delete = no)             Delete input images after combining?
+     (clobber = no)             Clobber existing output image?
+       (scale = "median")       Image scaling
+     (statsec = "[m:n,p:q]")    Image section for computing statistics
+        (nlow = 1)              minmax: Number of low pixels to reject
+       (nhigh = 1)              minmax: Number of high pixels to reject
+       (nkeep = 1)              Minimum to keep (pos) or maximum to reject
+       (mclip = yes)            Use median in sigma clipping algorithms?
+      (lsigma = 3.)             Lower sigma clipping factor
+      (hsigma = 3.)             Upper sigma clipping factor
+     (rdnoise = "5")            ccdclip: CCD readout noise (electrons)
+        (gain = "2.5")          ccdclip: CCD gain (electrons/DN)
+      (snoise = "0.")           ccdclip: Sensitivity noise (fraction)
+       (pclip = -0.5)           pclip: Percentile clipping parameter
+       (blank = 1.)             Value if there are no pixels
+        (mode = "ql")           
+.fi
+.le
+.bp
+.ls \fI3.5 Processing the calibration frames\fR
+
+Although all the following steps may be done only in one step, our
+approach is to do them separately to allow you to start at any point in
+this section in case you have already started reducing the images on
+the mountain.
+
+You must start by overscan subtracting and trimming 'zero1'. Edit the
+parameters for the 'ccdproc' task according to the list given below.
+There is a series of parameters that are set to 'yes' and 'no'. You must set
+only 'overscan' and 'trim' to 'yes' and the rest to 'no'. Also
+'ccdtype' must be
+set to 'zero'. Be sure to properly specify the parameters 
+'biassec' and 'trimsec' which you determined while reading section 3.3.2.
+The range of columns comes first separated by a ':' and the range of lines
+is again separated by a ':', i.e., [29:425,21:402].
+
+\fIDo not change these parameters until having
+processed all your images\fR.
+
+.nf
+      cc> epar ccdproc        (check the list given below)
+      cc> ccdproc zero1
+.fi
+
+If the parameter 'interactive' was set to 'yes' you will be required to
+fit interactively the overscan region with a certain function. Once
+presented by the task with the plot of the overscan region (see figure 3)
+you may change the fitting function, for example, with ':function chebyshev'
+and its order with
+':order 4'. To try a new fit type 'f'.  We suggest a spline3 of order 2.
+You may also select the sample to be fit using the 's' command twice.
+If you are happy with
+the fit type 'q' to quit. The task will then process 'zero1' accordingly.
+
+Continue by overscan subtracting, trimming and bias subtracting 'dark1'.
+In this case you have to change in 'ccdproc' the 'ccdtype' parameter
+to 'dark' and the
+'zerocor' parameter to 'yes'.
+
+.nf
+      cc> epar ccdproc        (check the list given below)
+      cc> ccdproc dark1
+.fi
+
+The dark image must be examined before proceeding. \fIFor instance, if the
+dark level is low enough (<10 counts/hour/pixel)
+compared to the flats, you will
+probably disregard dark subtracting your images, to avoid
+introducing noise in your data.\fR
+However, if you notice some structure in the dark image, it would be
+worth trying to dark correct the data. In the following examples, for
+generality's sake, we consider dark subtraction as part of the overall
+processing.  If this is not your case, do not forget to set the 'darkcor'
+parameter in 'ccdproc' to 'no' and leave it alone.
+
+Then process the flats. Check that the 'ccdtype' parameter is set
+to 'flat', that 'overscan', 'trim', 'zerocor' and 'darkcor' are all set
+to 'yes' and execute the task.
+
+.nf
+      cc> epar ccdproc        (check the list given below)
+      cc> ccdproc flat1*imh
+.fi
+
+IRAF records all the reduction operations in the image headers.  You
+may check from the headers of 'zero1', 'dark1', 'sky1' and 'flat1' that
+BT-FLAG, BI-FLAG, DK-FLAG are properly set. For instance,
+
+.nf
+      cc> imheader flat1R l+
+.fi
+
+It is also possible to check this by using the 'ccdlist' task which will check
+the header automatically and list the operations which have been performed on
+the image.
+
+.nf
+      cc> ccdlist flat1R
+
+.fi
+You should get the following,
+
+.nf
+        flat1R[496,501][real][flat][R][OTZ]:dflat R
+
+.fi
+'ccdlist' should tell you the image name (flat1R), the image size [496,501]
+left after trimming, the pixel type [real] of the image (the processed
+images should normally have pixels in real format, as opposed to
+the raw images which generally have pixels in 'short' format),
+the image type [flat], the filter used in the observation
+[R], the level of processing of the image [OTZ], and the image title (dflat R).
+
+At this level you should have the flats processed up through [OTZ] which
+means that the image has been [O]verscan subtracted, [T]rimmed, and
+[Z]ero subtracted. Additional codes for other operations in 'ccdproc'
+are [F]lat correction, [B]ad pixel correction, [I]illumination correction.
+
+.nf
+			\fIccdproc for zero1\fR
+
+       images = "zero1"         List of CCD images to correct
+     (\fIccdtype\fR = "zero")         CCD image type to correct
+   (max_cache = 0)              Maximum image caching memory (in Mbytes)
+      (noproc = no)             List processing steps only?
+      (fixpix = no)             Fix bad CCD lines and columns?
+    (\fIoverscan\fR = yes)            Apply overscan strip correction?
+        (\fItrim\fR = yes)            Trim the image?
+     (\fIzerocor\fR = no)             Apply zero level correction?
+     (\fIdarkcor\fR = no)             Apply dark count correction?
+     (\fIflatcor\fR = no)             Apply flat field correction?
+    (illumcor = no)             Apply iillumination correction?
+   (fringecor = no)             Apply fringe correction?
+     (readcor = no)             Convert zero level image to readout cor?
+     (scancor = no)             Convert flat field image to scan correction?
+    (readaxis = "line")         Read out axis (column|line)
+     (fixfile = "")             File describing the bad lines and columns
+     (\fIbiassec\fR = "[m:n,*]")      Overscan strip image section
+     (\fItrimsec\fR = "[r:s,t:u]")    Trim data section
+        (\fIzero\fR = "zero1")        Zero level calibration image
+        (\fIdark\fR = "dark1")        Dark count calibration image
+        (\fIflat\fR = "")             Flat field images
+       (illum = "")             Iillumination correction images
+      (fringe = "")             Fringe correction images
+  (minreplace = 1.)             Minimum flat field value
+    (scantype = "shortscan")    Scan type (shortscan|longscan)
+       (nscan = 1)              Number of short scan lines\n
+ (interactive = yes)            Fit overscan interactively?
+    (function = "spline3")      Fitting function
+       (order = 2)              Number of polynomial terms or spline pieces
+      (sample = "*")            Sample points to fit
+    (naverage = 1)              Number of sample points to combine
+    (niterate = 1)              Number of rejection iterations
+  (low_reject = 3.)             Low sigma rejection factor
+ (high_reject = 3.)             High sigma rejection factor
+        (grow = 0.)             Rejection growing radius
+        (mode = "ql")           
+
+			\fIccdproc for dark1\fR
+
+       images = "dark1"         List of CCD images to correct
+     (\fIccdtype\fR = "dark")         CCD image type to correct
+   (max_cache = 0)              Maximum image caching memory (in Mbytes)
+      (noproc = no)             List processing steps only?
+      (fixpix = no)             Fix bad CCD lines and columns?
+    (\fIoverscan\fR = yes)            Apply overscan strip correction?
+        (\fItrim\fR = yes)            Trim the image?
+     (\fIzerocor\fR = yes)            Apply zero level correction?
+     (\fIdarkcor\fR = no)             Apply dark count correction?
+     (\fIflatcor\fR = no)             Apply flat field correction?
+    (illumcor = no)             Apply iillumination correction?
+   (fringecor = no)             Apply fringe correction?
+     (readcor = no)             Convert zero level image to readout corr?
+     (scancor = no)             Convert flat field image to scan correction?
+    (readaxis = "line")         Read out axis (column|line)
+     (fixfile = "")             File describing the bad lines and columns
+     (\fIbiassec\fR = "[m:n,*]")      Overscan strip image section
+     (\fItrimsec\fR = "[r:s,t:u]")    Trim data section
+        (\fIzero\fR = "zero1")        Zero level calibration image
+        (\fIdark\fR = "dark1")        Dark count calibration image
+        (\fIflat\fR = "")             Flat field images
+       (illum = "")             Iillumination correction images
+      (fringe = "")             Fringe correction images
+  (minreplace = 1.)             Minimum flat field value
+    (scantype = "shortscan")    Scan type (shortscan|longscan)
+       (nscan = 1)              Number of short scan lines\n
+ (interactive = yes)            Fit overscan interactively?
+    (function = "spline3")      Fitting function
+       (order = 2)              Number of polynomial terms or spline pieces
+      (sample = "*")            Sample points to fit
+    (naverage = 1)              Number of sample points to combine
+    (niterate = 1)              Number of rejection iterations
+  (low_reject = 3.)             Low sigma rejection factor
+ (high_reject = 3.)             High sigma rejection factor
+        (grow = 0.)             Rejection growing radius
+        (mode = "ql")           
+
+			\fIccdproc for flat1\fR
+
+       images = "flat1*imh"     List of CCD images to correct
+     (\fIccdtype\fR = "flat")         CCD image type to correct
+   (max_cache = 0)              Maximum image caching memory (in Mbytes)
+      (noproc = no)             List processing steps only?
+      (fixpix = no)             Fix bad CCD lines and columns?
+    (\fIoverscan\fR = yes)            Apply overscan strip correction?
+        (\fItrim\fR = yes)            Trim the image?
+     (\fIzerocor\fR = yes)            Apply zero level correction?
+     (\fIdarkcor\fR = yes)            Apply dark count correction?
+     (\fIflatcor\fR = no)             Apply flat field correction?
+    (illumcor = no)             Apply iillumination correction?
+   (fringecor = no)             Apply fringe correction?
+     (readcor = no)             Convert zero level image to readout corr?
+     (scancor = no)             Convert flat field image to scan correction?
+    (readaxis = "line")         Read out axis (column|line)
+     (fixfile = "")             File describing the bad lines and columns
+     (\fIbiassec\fR = "[m:n,*]")      Overscan strip image section
+     (\fItrimsec\fR = "[r:s,t:u]")    Trim data section
+        (\fIzero\fR = "zero1")        Zero level calibration image
+        (\fIdark\fR = "dark1")        Dark count calibration image
+        (\fIflat\fR = "")             Flat field images
+       (illum = "")             Iillumination correction images
+      (fringe = "")             Fringe correction images
+  (minreplace = 1.)             Minimum flat field value
+    (scantype = "shortscan")    Scan type (shortscan|longscan)
+       (nscan = 1)              Number of short scan lines\n
+ (interactive = yes)            Fit overscan interactively?
+    (function = "spline3")      Fitting function
+       (order = 2)              Number of polynomial terms or spline pieces
+      (sample = "*")            Sample points to fit
+    (naverage = 1)              Number of sample points to combine
+    (niterate = 1)              Number of rejection iterations
+  (low_reject = 3.)             Low sigma rejection factor
+ (high_reject = 3.)             High sigma rejection factor
+        (grow = 0.)             Rejection growing radius
+        (mode = "ql")           
+.fi
+.le
+.bp
+.ls \fI3.6 Preparing a Final Flat Field\fR
+
+Next we want to check the iillumination of the flat by applying it to the sky
+flat. Load the 'imred' and 'ccdred' packages if they are
+not already loaded.
+There is no tried and true method for testing the iillumination of
+the sky flats except for applying them on a long exposure taken in the same
+filter and implotting it or doing image statistics.
+
+We must use 'ccdproc' to overscan subtract, trim, bias subtract, dark subtract
+(if needed), and flat field the sky images. Again, we assume here
+that the dark is
+necessary for the reductions. Be sure that the images you are using for
+the flat field division have the proper filter identification.
+First edit the parameters for 'ccdproc', and then run
+this task to process your skys to see if the iillumination of the dome
+flat is uniform;
+
+.nf
+      cl> noao
+      im> imred
+      im> ccdred
+      cc> epar ccdproc        (check the parameter list)
+      cc> ccdproc sky1R
+.fi
+
+Now we must check the sky to see if it really is flat. This is done
+using 'implot' and plotting some lines or a group of lines,
+
+.nf
+      cc> implot sky1R
+            :l 150 200
+            :c 200 250
+	    q
+.fi
+
+Ideally if the iillumination was uniform, sky1R should not show any variation.
+In plotting several lines together, you may get a small slope (see figure 4).
+If you see any    
+variations, including a slope even near the edges of the image, then you must
+run the task 'mkskyflat'. Select a smoothing box size which preserves the large
+scale features while adequately suppressing the noise.  The scale of the
+largest features expected shouldn't be smaller than say 1/10 to 1/12 the
+image size.
+
+.nf
+      cc> epar mkskyflat      (check the parameter list)
+      cc> mkskyflat sky1R finalflat1R
+.fi
+
+The output image is the corrected flat image so call it "finalflat1R".
+We need to recopy the sky flat to process it again. Do an imcopy of the sky1R
+from the backup image after deleting the processed one.
+
+.nf
+      cc> imdel sky1R
+      cc> imcopy Bsky1R sky1R
+      cc> epar ccdproc        (change the parameter 'flat' from
+			       flat1R to finalflat1R)
+      cc> ccdproc sky1R
+.fi
+
+Again, check to see if the sky is really flat. If it is flat
+(see figure 5), then you are
+done and must process the flats for your other filters. If it is not flat,
+go back to the beginning and ask for help. It may be that you need to play
+with the smoothing parameters. Repeat these steps until you are satisfied.
+Now you can process your images.
+
+.nf
+
+			\fIccdproc for sky flats\fR
+
+       images = "sky1*imh"      List of CCD images to correct
+     (\fIccdtype\fR = "other")        CCD image type to correct
+   (max_cache = 0)              Maximum image caching memory (in Mbytes)
+      (noproc = no)             List processing steps only?
+      (fixpix = no)             Fix bad CCD lines and columns?
+    (\fIoverscan\fR = yes)            Apply overscan strip correction?
+        (\fItrim\fR = yes)            Trim the image?
+     (\fIzerocor\fR = yes)            Apply zero level correction?
+     (\fIdarkcor\fR = yes)            Apply dark count correction?
+     (\fIflatcor\fR = yes)            Apply flat field correction?
+    (illumcor = no)             Apply iillumination correction?
+   (fringecor = no)             Apply fringe correction?
+     (readcor = no)             Convert zero level image to readout corr?
+     (scancor = no)             Convert flat field image to scan correction?
+    (readaxis = "line")         Read out axis (column|line)
+     (fixfile = "")             File describing the bad lines and columns
+     (\fIbiassec\fR = "[m:n,*]")      Overscan strip image section
+     (\fItrimsec\fR = "[r:s,t:u]")    Trim data section
+        (\fIzero\fR = "zero1")        Zero level calibration image
+        (\fIdark\fR = "dark1")        Dark count calibration image
+        (\fIflat\fR = "flat1*imh")    Flat field images
+       (illum = "")             Iillumination correction images
+      (fringe = "")             Fringe correction images
+  (minreplace = 1.)             Minimum flat field value
+    (scantype = "shortscan")    Scan type (shortscan|longscan)
+       (nscan = 1)              Number of short scan lines\n
+ (interactive = yes)            Fit overscan interactively?
+    (function = "spline3")      Fitting function
+       (order = 2)              Number of polynomial terms or spline pieces
+      (sample = "*")            Sample points to fit
+    (naverage = 1)              Number of sample points to combine
+    (niterate = 1)              Number of rejection iterations
+  (low_reject = 3.)             Low sigma rejection factor
+ (high_reject = 3.)             High sigma rejection factor
+        (grow = 0.)             Rejection growing radius
+        (mode = "ql")           
+.fi
+.bp
+.nf
+                      \fImkskyflat\fR
+
+        input = "sky1R"     Input CCD images
+       output = "finalflat1R"     Output images (same as input if none)
+     (ccdtype = "")         CCD image type to select
+     (\fIxboxmin\fR = 0.1)        Minimum smoothing box size in x at edges
+     (\fIxboxmax\fR = 0.1)        Maximum smoothing box size in x
+     (\fIyboxmin\fR = 0.1)        Minimum smoothing box size in y at edges
+     (\fIyboxmax\fR = 0.1)        Maximum smoothing box size in y
+        (clip = yes)        Clip input pixels?
+    (lowsigma = 2.5)        Low clipping sigma
+   (highsigma = 2.5)        High clipping sigma
+     (ccdproc = "")         CCD processing parameters
+        (mode = "ql")
+.fi
+.le
+.bp
+.ls \fI3.7 Processing the Images\fR
+
+This can be setup to be done all at once. The final flat has been made so now
+we divide it into your objects.
+If the calibration frames themselves
+have not been processed it will do this as well. The program takes into
+account the differing filters. Be sure that you have deleted all the individual
+calibration frames that were combined. Edit the parameters for 'ccdproc' and run
+it. For tasks that take a long time, it is a good idea to set them going as a
+background job and send the output to a file which you can watch to keep track
+of the progress. You may wish to make a list of the objects to be processed
+to avoid reprocessing your sky flats.
+
+.nf
+      cc> epar ccdproc        (check the parameter list)
+      cc> ccdproc obj*.imh
+.fi
+
+To check the progress of the task, just type 
+
+.nf
+      cc> tail ccdlog
+.fi
+
+This will print out the last lines of the file named 'ccdlog'
+which is the latest 
+operation done by the task 'ccdproc'.
+Once this is done, check your images to see
+that they have been properly flat fielded. If you are satisfied, then you may
+now check your images for bad pixel regions, the structure of which may not have
+been processed out of your images.
+
+We suggest also to do a 'ccdlist' on the objects in order to
+check whether the frames have been duly processed, i.e.,
+
+.nf
+     cc> ccdlist obj*.imh
+.fi
+
+You should get a listing of your images in the format that follows,
+
+.nf
+
+      obj1010.imh[496,501][real][object][R][OTZF]:rubin 152 R
+      obj1011.imh[496,501][real][object][I][OTZF]:rubin 152 I
+      obj1012.imh[496,501][real][object][B][OTZF]:rubin 149 B
+      obj1013.imh[496,501][real][object][V][OTZF]:rubin 149 V
+      obj1014.imh[496,501][real][object][R][OTZF]:rubin 149 R
+      obj1015.imh[496,501][real][object][I][OTZF]:rubin 149 I
+      obj1016.imh[496,501][real][object][B][OTZF]:rubin 149 B
+      obj1017.imh[496,501][real][object][V][OTZF]:rubin 149 V
+      obj1018.imh[496,501][real][object][R][OTZF]:rubin 149 R
+      obj1019.imh[496,501][real][object][I][OTZF]:rubin 149 I
+.fi
+
+where the [OTZF] code reveals the degree of processing of the images.
+
+.nf
+                   \fIccdproc for objects\fR
+
+       images = "obj*imh)"      List of CCD images to correct
+     (\fIccdtype\fR = "object")       CCD image type to correct
+   (max_cache = 0)              Maximum image caching memory (in Mbytes)
+      (noproc = no)             List processing steps only?
+      (fixpix = no)             Fix bad CCD lines and columns?
+    (\fIoverscan\fR = yes)            Apply overscan strip correction?
+        (\fItrim\fR = yes)            Trim the image?
+     (\fIzerocor\fR = yes)            Apply zero level correction?
+     (\fIdarkcor\fR = yes)            Apply dark count correction?
+     (\fIflatcor\fR = yes)            Apply flat field correction?
+    (illumcor = no)             Apply iillumination correction?
+   (fringecor = no)             Apply fringe correction?
+     (readcor = no)             Convert zero level image to readout corr?
+     (scancor = no)             Convert flat field image to scan correction?
+    (readaxis = "line")         Read out axis (column|line)
+     (fixfile = "")             File describing the bad lines and columns
+     (\fIbiassec\fR = "[m:n,*]")      Overscan strip image section
+     (\fItrimsec\fR = "[r:s,t:u]")    Trim data section
+        (\fIzero\fR = "zero1")        Zero level calibration image
+        (\fIdark\fR = "dark1")        Dark count calibration image
+        (\fIflat\fR = "finalflat1*imh")    Flat field images
+       (illum = "")             Iillumination correction images
+      (fringe = "")             Fringe correction images
+  (minreplace = 1.)             Minimum flat field value
+    (scantype = "shortscan")    Scan type (shortscan|longscan)
+       (nscan = 1)              Number of short scan lines\n
+ (interactive = yes)            Fit overscan interactively?
+    (function = "spline3")      Fitting function
+       (order = 2)              Number of polynomial terms or spline pieces
+      (sample = "*")            Sample points to fit
+    (naverage = 1)              Number of sample points to combine
+    (niterate = 1)              Number of rejection iterations
+  (low_reject = 3.)             Low sigma rejection factor
+ (high_reject = 3.)             High sigma rejection factor
+        (grow = 0.)             Rejection growing radius
+        (mode = "ql")           
+
+.fi
+
+.le
+.bp
+.ls \fI3.8 Creating the Bad Pixel File\fR
+
+Now it is time to check your images to see if structure remains in the bad
+pixel regions. If you were careful to observe your objects far away from any
+obvious bad regions then you may only need to 'fix' pixels for cosmetic reasons.
+We suggest you to examine these files using the display window,
+imtool (this can only be done at one of the SUN consoles), and then plotting
+them using 'implot'. Start by loading the 'noao', 'images', 'tv', 'imred',
+and 'ccdred' packages. Display
+a processed image and plot it using 'implot',
+
+.nf
+      cl> noao
+      no> images
+      im> tv
+      tv> imred
+      im> ccdred
+      cc> display obj002 1
+      cc> implot obj002
+.fi
+
+Do not exit from implot, but move the cursor to the imtool window and press
+'F6'. The cursor coordinates are now visible at the bottom of the screen.
+Find the position of a bad pixel using this, return to the graph and
+plot it using 'implot' with the ':l #'(line) and ':c #'(column) commands.
+You can define them more precisely using 'implot' by overplotting lines and
+columns around the center of the bad regions. Do this by typing 'o' followed
+by ':c #' and ':l #'. Once you have these regions written down, check some of
+your images to see if the bad pixels are a problem, ie >1% in signal. If it is
+a problem then create a file called 'badpix' with the listing of
+the pixels you wish to fix;
+
+.nf
+      cc> edit badpix           (according to the following format)
+.fi
+
+The following example is to illustrate the format of a bad pixel file.
+
+.nf
+      84 87 1 450
+      87 90 105 109
+      87 89 110 111
+      124 126 112 116
+      206 206 80 80
+.fi
+
+Each line stands for a rectangular region of the image to be fixed. The regions
+are specified by four numbers giving the starting and ending columns followed
+by the starting and ending lines. The starting and ending points may be the
+same to specify a single column, line or pixel. Note that each region is
+"fixed" by interpolating across its shortest dimension and that regions are
+processed in the order that they appear in the bad pixel list. For bad regions
+of complex shape, some care may be required in specifying the regions in order
+to achieve an optimal result. \fIIt is strongly recommended that you test your
+bad pixel file by using it to correct a copy of one of your images before going
+into production\fR. This bad pixel file will be specified in the task 'ccdproc'
+in the parameter 'fixfile'. So now edit and run the task:
+
+.nf
+       cc> epar ccdproc
+       cc> ccdproc obj*.imh
+.fi
+
+Remember that 'ccdproc' already knows that the images
+have been processed so those
+operations will not be performed again. Now you have final images that are ready
+to be used. If you plan to do photometry in IRAF see section VI of this manual.
+
+.nf
+                             \fIccdproc\fR
+
+       images = "obj*imh)"      List of CCD images to correct
+     (\fIccdtype\fR = "object")       CCD image type to correct
+   (max_cache = 0)              Maximum image caching memory (in Mbytes)
+      (noproc = no)             List processing steps only?
+      (\fIfixpix\fR = yes)            Fix bad CCD lines and columns?
+    (\fIoverscan\fR = yes)            Apply overscan strip correction?
+        (\fItrim\fR = yes)            Trim the image?
+     (\fIzerocor\fR = yes)            Apply zero level correction?
+     (\fIdarkcor\fR = yes)            Apply dark count correction?
+     (\fIflatcor\fR = yes)            Apply flat field correction?
+    (illumcor = no)             Apply iillumination correction?
+   (fringecor = no)             Apply fringe correction?
+     (readcor = no)             Convert zero level image to readout corr?
+     (scancor = no)             Convert flat field image to scan correction?
+    (readaxis = "line")         Read out axis (column|line)
+     (\fIfixfile\fR = "badpix")       File describing the bad lines and columns
+     (\fIbiassec\fR = "[m:n,*]")      Overscan strip image section
+     (\fItrimsec\fR = "[r:s,t:u]")    Trim data section
+        (\fIzero\fR = "zero1")        Zero level calibration image
+        (\fIdark\fR = "dark1")        Dark count calibration image
+        (\fIflat\fR = "finalflat1*imh")    Flat field images
+       (illum = "")             Iillumination correction images
+      (fringe = "")             Fringe correction images
+  (minreplace = 1.)             Minimum flat field value
+    (scantype = "shortscan")    Scan type (shortscan|longscan)
+       (nscan = 1)              Number of short scan lines\n
+ (interactive = yes)            Fit overscan interactively?
+    (function = "spline3")      Fitting function
+       (order = 2)              Number of polynomial terms or spline pieces
+      (sample = "*")            Sample points to fit
+    (naverage = 1)              Number of sample points to combine
+    (niterate = 1)              Number of rejection iterations
+  (low_reject = 3.)             Low sigma rejection factor
+ (high_reject = 3.)             High sigma rejection factor
+        (grow = 0.)             Rejection growing radius
+        (mode = "ql")           
+
+.fi
+.le
+.bp
+.ls \fI3.9 Writing the Data to Tape\fR
+
+Allocate the device, for the SUNs it is "mta". Then mount your tape, don't
+forget to put in a write ring. If you wish to use the exabyte drive, use "mtx"
+for the device name. Load the package 'dataio' and do an epar on 'wfits'.
+
+.nf
+      cl> dataio
+      da> epar wfits
+      da> wfits *.imh mta.6250 new+ 
+.fi
+
+The parameter newtape should be "yes"
+if you are starting on a new tape. Otherwise you will not want to overwrite
+data which has already been placed on a tape, so use "no". 
+
+After writing all the desired files to tape, deallocate the drive and retrieve
+your tape.
+
+.nf
+      da> dealloc mta
+.fi
+.le
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/quadproc.hlp b/noao/imred/quadred/src/quad/doc/quadproc.hlp
new file mode 100644
index 00000000..8d445097
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/quadproc.hlp
@@ -0,0 +1,672 @@
+.help quadproc Sept93 arcon.quad
+.ih
+NAME
+quadproc -- Process multi-readout CCD images
+.ih
+USAGE	
+quadproc images
+.ih
+PARAMETERS
+.ls images
+List of input CCD images to process.  The list may include processed
+images and calibration images.
+.le
+.ls ccdtype = ""
+CCD image type to select from the input image list.  If no type is given
+then all input images will be selected.  The recognized types are described
+in \fBccdtypes\fR.
+.le
+.ls max_cache = 0
+Maximum image caching memory (in Mbytes).  If there is sufficient memory
+the calibration images, such as zero level, dark count, and flat fields,
+will be cached in memory when processing many input images.  This
+reduces the disk I/O and makes the task run a little faster.  If the
+value is zero image caching is not used.
+.le
+.ls noproc = no
+List processing steps only?
+.le
+
+.ce
+PROCESSING SWITCHES
+.ls fixpix = yes
+Fix bad CCD lines and columns by linear interpolation from neighboring
+lines and columns?  If yes then a bad pixel file must be specified.
+.le
+.ls overscan = yes
+Apply overscan or prescan bias correction?  If yes then the overscan
+image section and the readout axis must be specified.
+.le
+.ls trim = yes
+Trim the image of the overscan region and bad edge lines and columns?
+If yes then the trim section must be specified.
+.le
+.ls zerocor = yes
+Apply zero level correction?  If yes a zero level image must be specified.
+.le
+.ls darkcor = yes
+Apply dark count correction?  If yes a dark count image must be specified.
+.le
+.ls flatcor = yes
+Apply flat field correction?  If yes flat field images must be specified.
+.le
+.ls illumcor = no
+Apply iillumination correction?  If yes iillumination images must be specified.
+.le
+.ls fringecor = no
+Apply fringe correction?  If yes fringe images must be specified.
+.le
+.ls readcor = no
+Convert zero level images to readout correction images?  If yes then
+zero level images are averaged across the readout axis to form one
+dimensional zero level readout correction images.
+.le
+.ls scancor = no
+Convert flat field images to scan mode flat field images?  If yes then the
+form of scan mode correction is specified by the parameter \fIscantype\fR.
+.le
+
+.ce
+PROCESSING PARAMETERS
+.ls readaxis = "line"
+Read out axis specified as "line" or "column".
+.le
+.ls fixfile
+File describing the bad lines and columns.  If "image" is specified then
+the file is specified in the image header or instrument translation file.
+See Section 2. of Description for further information on bad pixel files.
+.le
+.ls biassec
+Overscan bias strip image section.  If "image" is specified then the overscan
+bias section is specified in the image header or instrument translation file.
+See Section 3. of Description for further information on setting this parmeter.
+.le
+.ls trimsec
+image section for trimming.  If "image" is specified then the trim
+image section is specified in the image header or instrument translation file.
+See Section 4. of Description for further information on setting this parmeter.
+.le
+.ls zero = ""
+Zero level calibration image.  The zero level image may be one or two
+dimensional.  The CCD image type and subset are not checked for these
+images and they take precedence over any zero level calibration images
+given in the input list.
+.le
+.ls dark = ""
+Dark count calibration image.  The CCD image type and subset are not checked
+for these images and they take precedence over any dark count calibration
+images given in the input list.
+.le
+.ls flat = ""
+Flat field calibration images.  The flat field images may be one or
+two dimensional.  The CCD image type is not checked for these
+images and they take precedence over any flat field calibration images given
+in the input list.  The flat field image with the same subset as the
+input image being processed is selected.
+.le
+.ls illum = ""
+Iillumination correction images.  The CCD image type is not checked for these
+images and they take precedence over any iillumination correction images given
+in the input list.  The iillumination image with the same subset as the
+input image being processed is selected.
+.le
+.ls fringe = ""
+Fringe correction images.  The CCD image type is not checked for these
+images and they take precedence over any fringe correction images given
+in the input list.  The fringe image with the same subset as the
+input image being processed is selected.
+.le
+.ls minreplace = 1.
+When processing flat fields, pixel values below this value (after
+all other processing such as overscan, zero, and dark corrections) are
+replaced by this value.  This allows flat fields processed by \fBquadproc\fR
+to be certain to avoid divide by zero problems when applied to object
+images.
+.le
+.ls scantype = "shortscan"
+Type of scan format used in creating the CCD images.  The modes are:
+.ls "shortscan"
+The CCD is scanned over a number of lines and then read out as a regular
+two dimensional image.  In this mode unscanned flat fields are numerically
+scanned to form scanned flat fields comparable to the observations.  If
+the flat field calibration images are taken in scanned mode then
+\fIscancor\fR should be no and the processing performed in the same manner
+as in unscanned mode.
+.le
+.ls "longscan"
+In this mode the CCD is clocked and read out continuously to form a long
+strip.  Flat fields are averaged across the readout axis to
+form a one dimensional flat field readout correction image.  This assumes
+that all recorded image lines are clocked over the entire active area of the
+CCD.
+.le
+.le
+.ls nscan
+Number of scan readout lines used in short scan mode.  This parameter is used
+when the scan type is "shortscan".
+.le
+
+.ce
+OVERSCAN FITTING PARAMETERS
+.ls interactive = no
+Fit the overscan vector interactively?  If yes the overscan vector is fit
+interactively using the \fBicfit\fR package.  If no then the fitting parameters
+given below are used.
+.le
+.ls function = "legendre"
+Overscan fitting function.  The function types are "legendre" polynomial,
+"chebyshev" polynomial, "spline1" linear spline, and "spline3" cubic
+spline.
+.le
+.ls order = 1
+Number of polynomial terms or spline pieces in the overscan fit.
+.le
+.ls sample = "*"
+Sample points to use in the overscan fit.  The string "*" specified all
+points otherwise an \fBicfit\fR range string is used.
+.le
+.ls naverage = 1
+Number of points to average or median to form fitting points.  Positive
+numbers specify averages and negative numbers specify medians.
+.le
+.ls niterate = 1
+Number of rejection iterations to remove deviant points from the overscan fit.
+If 0 then no points are rejected.
+.le
+.ls low_reject = 3., high_reject = 3.
+Low and high sigma rejection factors for rejecting deviant points from the
+overscan fit.
+.le
+.ls grow = 0.
+One dimensional growing radius for rejection of neighbors to deviant points.
+.le
+.ih
+DESCRIPTION
+\fBQuadproc\fR processes CCD images to remove all "instrumental signatures" from
+the data. The operations performed are:
+.ls
+.nf
+o correct detector defects (bad lines and columns)
+o determine readout bias level using overscan and subtract it
+o trim off the overscan regions and unwanted border pixels
+o subtract zero level bias
+o subtract dark counts
+o correct for pixel-to-pixel sensitivity variations
+o correct for non-uniform iillumination
+o correct for fringing
+.fi
+.le
+.sp 1
+\fBQuadproc\fR is a cl script based on the task \fBccdproc\fR in the
+\fBccdred\fR package. It is specifically designed to deal with Arcon data
+obtained in multi-readout mode (see \fBquadformat\fR). A feature of such
+images is that each readout typically has a slightly different, DC bias
+level, gain, and readout noise. As a result both zero frames and uniformly 
+illuminated exposures show a characteristic chequer board pattern, the
+sections of the image read through each amplifier having different levels.
+In addition, there will be a separate overscan strip, used to monitor the zero
+level, for each readout. The location of these overscan strips in the raw
+frame depends on which amplifiers are used. \fBQuadproc\fR splits each 
+multi-readout image into subimages, one for each amplifier, and also calculates
+the biassec and trimsec appropriately for each. It then calls \fBccdproc\fR to
+perform the first three operations listed above. The sub-images are then glued
+back together. Finaly, \fBccdproc\fR is called a second time to perform all the
+remaining reduction steps. 
+
+\fBQuadproc\fR MUST be used for the reduction of multi-readout data up to and
+including the trimming step, and it is convenient to use it for the entire
+reduction process. However, once ALL images have been trimmed it is possible
+to finish the reductions using \fBccdproc\fR if the \fBquad\fR package is not
+available at your home institution. \fBQuadproc\fR recognizes mono-readout
+images and processes them directly using \fBccdproc\fR. If your images are a
+mixture of multi- and mono- readout use \fBquadproc\fR; if you only have
+mono-readout data use \fBccdproc\fR.
+
+\fBQuadproc\fR is identical to \fBccdproc\fR in the way it is used, and has
+exactly the same parameters; as far as possible it also behaves in the same way.
+To run it, all one has to do is set the parameters and then begin processing
+the images.  The task takes care of most of the record keeping and
+automatically does the prerequisite processing of calibration images. For
+ease of reference, the following sections provide a simple outline of how to
+use the task, together with a description of the operations performed. They 
+are taken almost verbatim from the help page for \fBccdproc\fR. If you are 
+already familiar with that task you should read sections 2., 3. and 4. below,
+which include information on the preparation of the badpixel file, and on how
+to specify \fBbiassec\fR and \fBtrimsec\fR parameters. See section 12. for a
+description of the differences between the two tasks. For a user's guide and 
+cookbook for the \fBquad\fR package see \fBguide\fR.
+.sh
+1. Parameters
+There are many parameters but they may be easily reviewed and modified using
+the task \fBeparam\fR.
+The input CCD images to be processed are given as an image list.
+Previously processed images are ignored and calibration images are
+recognized, provided the CCD image types are in the image header (see
+\fBinstruments\fR and \fBccdtypes\fR).  \fBQuadproc\fR separates multi- and
+mono-readout images in the input list and handles them accordingly.
+Therefore it is permissible to use simple image templates such as "*.imh".
+The \fIccdtype\fR parameter may be used to select only certain types of CCD
+images to process (see \fBccdtypes\fR).
+
+The processing operations are selected by boolean (yes/no) parameters.
+Because calibration images are recognized and processed appropriately,
+the processing operations for object images should be set. Any combination of
+operations may be specified. Two of the operations, \fBreadcor\fR and \fBscancor\fR, are only applicable to zero level and flat field images respectively. These
+are used for certain types of CCDs and modes of operation.
+
+The processing steps selected have related parameters which must be
+set.  These are things like image sections defining the overscan and
+trim regions and calibration images.  There are a number of parameters
+used for fitting the overscan or prescan bias section.  These are
+parameters used by the standard IRAF curve fitting package \fBicfit\fR.
+The parameters are described in more detail in the following sections.
+
+In addition to the task parameters there are package parameters
+which affect \fBquadproc\fR.  These include the instrument and subset
+files, the text and plot log files, the output pixel datatype,
+the verbose parameter for logging to the terminal, and the backup
+prefix.  These are described in \fBquad\fR.
+
+Calibration images are specified by task parameters and/or in the
+input image list.  If more than one calibration image is specified
+then the first one encountered is used. Calibration images specified by
+task parameters take precedence over calibration images in the input list.
+These images also need not have a CCD image type parameter since the task
+parameter identifies the type of calibration image.  This method is
+best if there is only one calibration image for all images
+to be processed, almost always true for zero level and dark
+count images.  If no calibration image is specified by task parameter
+then calibration images in the input image list are identified and
+used.  This requires that the images have CCD image types recognized
+by the package.  This method is useful if one may simply say "*.imh"
+as the image list to process all images or if the images are broken
+up into groups, in "@" files for example, each with their own calibration
+frames.
+.sh
+2. Fixpix
+Regions of bad lines and columns may be replaced by linear
+interpolation from neighboring lines and columns when the parameter
+\fIfixpix\fR is set.  The bad regions are specified in a bad pixel
+file.  The file consists of lines with four fields, the starting and
+ending columns and the starting and ending lines.  Any number of
+regions may be specified. Currently, the coordinates given for the bad regions
+must be those that would be applicable if the CCD was used in SINGLE READOUT
+MODE, even if multi-readout images are being reduced. A task is being written
+to aid in the preparation of an appropriate bad-pixel file given measurements
+made on a raw multi-readout image.
+
+Comment lines beginning with the character '#' may be included. If a comment
+line preceding the bad regions contains the word "untrimmed" then the
+coordinate system refers to the original format of the images; i.e.  before 
+trimming.  If an image has been trimmed previously then the trim region
+specified in the image header is used to convert the coordinates in the bad
+pixel file to those of the trimmed image.  If the file does not contain the
+word "untrimmed" then the coordinate system must match that of the image
+being corrected; i.e. untrimmed coordinates if the image has not been
+trimmed and trimmed coordinates if the image has been trimmed.
+Standard bad pixel files should always be specified in terms of the original
+format.
+
+The bad pixel file may be specified explicitly with the parameter \fIfixfile\fR
+or indirectly if the parameter has the value "image".  In the latter case
+the instrument file must contain the name of the file.
+.sh
+3. Overscan
+The portion of the image used to determine the readout bias level is specified
+with the parameter \fBbiassec\fR. This may be an explicit image section, or it
+may be set to the special value "image". In the latter case the value given in
+the image header is used.  The image header value uses the entire overscan 
+strip without allowing any margin between the data section and the bias
+section.  Because Arcon uses a DC-coupled preamplifier the transition
+between data and overscan is very sharp indeed. Nonetheless, we recommend that
+you do skip the first few pixels of the overscan strip. To decide this issue
+for yourself, use implot to plot the average of several lines from a high 
+exposure level image such as a flat field. Expand the transition region 
+between data and overscan and decide how many pixels of the overscan are
+contaminated.
+
+In the case of multi-readout images, the way in which an explicit value for
+\fBbiassec\fR must be set, is unfortunately somewhat non-intuitive.  Currently,
+the value recorded in the image header is that which would be appropriate had
+the detector been read out using a single amplifier; an explicit image section
+must be specified in the same way. \fBQuadproc\fR calculates the sections
+to use for the sub-images corresponding to each readout based on such "single
+readout" sections. To determine the section you must enter, use \fBimhead\fR
+or \fBhselect\fR to determine the value of \fBbiassec\fR stored in the image 
+header. If this is, for instance,  "[1025:1060,1:1028]" then setting 
+\fBbiassec\fR = "[1029:1060,1:1028]" would leave  a margin of 4 pixels
+(1029 - 1025).  Note that if two readouts are used in the horizontal direction 
+(quad or serial-split dual readout) the overscan strip for each amplifier is
+only half as wide as that in single readout mode. Thus in the example a 15
+pixel (36 / 2 - 3) wide strip is used for each readout.
+
+If an overscan or prescan correction is specified (\fIoverscan\fR
+parameter) then the specified image section is averaged
+along the readout axis (\fIreadaxis\fR parameter) to form a
+correction vector.  A function is fit to this vector and for each readout
+line (image line or column) the function value for that line is
+subtracted from the image line.  The fitting function is generally
+either a constant (polynomial of 1 term) or a high order function
+which fits the large scale shape of the overscan vector.  Bad pixel
+rejection is also used to eliminate cosmic ray events.  The function
+fitting may be done interactively using the standard \fBicfit\fR
+iteractive graphical curve fitting tool.  Regardless of whether the fit
+is done interactively, the overscan vector and the fit may be recorded
+for later review in a metacode plot file named by the parameter
+\fIquad.plotfile\fR.  The mean value of the bias function is also recorded in
+the image header and log file.
+
+The overscan subtraction performed by \fBquadproc\fR corrects the 
+amplifier-to-amplifier differences in the bias level, so that no
+readout structure should be visible in processed zero images. However, you
+will still see the chequer board structure in flatfield and object exposures
+(unless the sky level is zero) because of gain difference between the
+amplifiers.
+.sh
+4. Trim
+When the parameter \fItrim\fR is set the input image will be trimmed to
+the image section given by the parameter \fItrimsec\fR. This may be an explicit
+image section, or it may be set to the special value "image". In the latter
+case the value given in the image header is used.  The image header value keeps
+the entire imaging section of the CCD.
+
+In the case of multi-readout images, the way in which an explicit value for
+\fBtrimsec\fR must be set, is unfortunately somewhat non-intuitive.  Currently,
+the value recorded in the image header is that which would be appropriate had
+the detector been read out using a single amplifier; an explicit image section
+must be specified in the same way. \fBQuadproc\fR calculates the sections
+to use for the sub-images corresponding to each readout based on such "single
+readout" sections. In addition one is currently restricted to trimming exactly
+the same number of columns from each side of the CCD; there is no such 
+restriction on the number of lines which can be trimmed from the top and bottom
+edges of the image. To determine the section you must enter, use \fBimhead\fR
+or \fBhselect\fR to determine the value of \fBtrimsec\fR stored in the image
+header. If this is, for instance, "[1:1024,1:1028]" then setting
+\fBtrimsec\fR = "[10:1015,20:998]" would trim 9 columns from the left and right
+edges and 19 and 29 lines from the bottom and top edges respectively. If you
+need to perform an asymmetric trim in the horizontal direction this can be
+done, after processing, by using \fBimcopy\fR to copy the required portion of
+the image.
+
+The trim section used for science images should, of course, be the same as 
+that used for the calibration images.
+.sh
+5. Zerocor
+After the readout bias is subtracted, as defined by the overscan or prescan
+region, there may still be a zero level bias.  This level may be two
+dimensional or one dimensional (the same for every readout line).  A
+zero level calibration is obtained by taking zero length exposures;
+generally many are taken and combined.  To apply this zero
+level calibration the parameter \fIzerocor\fR is set.  In addition if
+the zero level bias is only readout dependent then the parameter \fIreadcor\fR
+is set to reduce two dimensional zero level images to one dimensional
+images.  The zero level images may be specified by the parameter \fIzero\fR
+or given in the input image list (provided the CCD image type is defined).
+
+When the zero level image is needed to correct an input image it is checked
+to see if it has been processed and, if not, it is processed automatically.
+Processing of zero level images consists of bad pixel replacement,
+overscan correction, trimming, and averaging to one dimension if the
+readout correction is specified.
+.sh
+6. Darkcor
+Dark counts are subtracted by scaling a dark count calibration image to
+the same exposure time as the input image and subtracting.  The
+exposure time used is the dark time which may be different than the
+actual integration or exposure time.  A dark count calibration image is
+obtained by taking a very long exposure with the shutter closed; i.e.
+an exposure with no light reaching the detector.  The dark count
+correction is selected with the parameter \fIdarkcor\fR and the dark
+count calibration image is specified either with the parameter
+\fIdark\fR or as one of the input images.  The dark count image is
+automatically processed as needed.  Processing of dark count images
+consists of bad pixel replacement, overscan and zero level correction,
+and trimming.
+.sh
+7. Flatcor
+The relative detector pixel response is calibrated by dividing by a
+scaled flat field calibration image.  A flat field image is obtained by
+exposure to a spatially uniform source of light such as an lamp or
+twilight sky.  Flat field images may be corrected for the spectral
+signature in spectroscopic images (see \fBresponse\fR and
+\fBapnormalize\fR), or for iillumination effects (see \fBmkillumflat\fR
+or \fBmkskyflat\fR).  For more on flat fields and iillumination corrections
+see \fBflatfields\fR.  The flat field response is dependent on the
+wavelength of light so if different filters or spectroscopic wavelength
+coverage are used a flat field calibration for each one is required.
+The different flat fields are  automatically selected by a subset
+parameter (see \fBsubsets\fR).
+
+Flat field calibration is selected with the parameter \fBflatcor\fR
+and the flat field images are specified with the parameter \fBflat\fR
+or as part of the input image list.  The appropriate subset is automatically
+selected for each input image processed.  The flat field image is
+automatically processed as needed.  Processing consists of bad pixel
+replacement, overscan subtraction, zero level subtraction, dark count
+subtraction, and trimming.  Also if a scan mode is used and the
+parameter \fIscancor\fR is specified then a scan mode correction is
+applied (see below).  The processing also computes the mean of the
+flat field image which is used later to scale the flat field before
+division into the input image.  For scan mode flat fields the ramp
+part is included in computing the mean which will affect the level
+of images processed with this flat field.  Note that there is no check for
+division by zero in the interest of efficiency.  If division by zero
+does occur a fatal error will occur.  The flat field can be fixed by
+replacing small values using a task such as \fBimreplace\fR or
+during processing using the \fIminreplace\fR parameter.  Note that the
+\fIminreplace\fR parameter only applies to flat fields processed by
+\fBquadproc\fR.
+.sh
+8. Illumcor
+CCD images processed through the flat field calibration may not be
+completely flat (in the absence of objects).  In particular, a blank
+sky image may still show gradients.  This residual nonflatness is called
+the iillumination pattern.  It may be introduced even if the detector is
+uniformly illuminated by the sky because the flat field lamp
+iillumination may be nonuniform.  The iillumination pattern is found from a
+blank sky, or even object image, by heavily smoothing and rejecting
+objects using sigma clipping.  The iillumination calibration image is
+divided into the data being processed to remove the iillumination
+pattern.  The iillumination pattern is a function of the subset so there
+must be an iillumination correction image for each subset to be
+processed.  The tasks \fBmkillumcor\fR and \fBmkskycor\fR are used to
+create the iillumination correction images.  For more on iillumination
+corrections see \fBflatfields\fR.
+
+An alternative to treating the iillumination correction as a separate
+operation is to combine the flat field and iillumination correction
+into a corrected flat field image before processing the object
+images.  This will save some processing time but does require creating
+the flat field first rather than correcting the images at the same
+time or later.  There are two methods, removing the large scale
+shape of the flat field and combining a blank sky image iillumination
+with the flat field.  These methods are discussed further in the
+tasks which create them; \fBmkillumcor\fR and \fBmkskycor\fR.
+.sh
+9. Fringecor
+There may be a fringe pattern in the images due to the night sky lines.
+To remove this fringe pattern a blank sky image is heavily smoothed
+to produce an iillumination image which is then subtracted from the
+original sky image.  The residual fringe pattern is scaled to the
+exposure time of the image to be fringe corrected and then subtracted.
+Because the intensity of the night sky lines varies with time an
+additional scaling factor may be given in the image header.
+The fringe pattern is a function of the subset so there must be
+a fringe correction image for each subset to be processed.
+The task \fBmkfringecor\fR is used to create the fringe correction images.
+.sh
+10. Readcor
+If a zero level correction is desired (\fIzerocor\fR parameter)
+and the parameter \fIreadcor\fR is yes then a single zero level
+correction vector is applied to each readout line or column.  Use of a
+readout correction rather than a two dimensional zero level image
+depends on the nature of the detector or if the CCD is operated in
+longscan mode (see below).  The readout correction is specified by a
+one dimensional image (\fIzero\fR parameter) and the readout axis
+(\fIreadaxis\fR parameter).  If the zero level image is two dimensional
+then it is automatically processed to a one dimensional image by
+averaging across the readout axis.  Note that this modifies the zero
+level calibration image.
+.sh
+11. Scancor
+CCD detectors may be operated in several modes in astronomical
+applications.  The most common is as a direct imager where each pixel
+integrates one point in the sky or spectrum.  However, the design of most CCD's
+allows the sky to be scanned across the CCD while shifting the
+accumulating signal at the same rate.  \fBQuadproc\fR provides for two
+scanning modes called "shortscan" and "longscan".  The type of scan
+mode is set with the parameter \fIscanmode\fR.
+
+In "shortscan" mode the detector is scanned over a specified number of
+lines (not necessarily at sideral rates).  The lines that scroll off
+the detector during the integration are thrown away.  At the end of the
+integration the detector is read out in the same way as an unscanned
+observation.  The advantage of this mode is that the small scale flat
+field response is averaged in one dimension over the number of lines
+scanned.  A flat field may be observed in the same way in which case
+there is no difference in the processing from unscanned imaging and the
+parameter \fIscancor\fR should be no.  However, one obtains an increase
+in the statistical accuracy of the flat fields if they are not scanned
+during the observation but digitally scanned during the processing.  In
+shortscan mode with \fIscancor\fR set to yes, flat field images are
+digitally scanned, if needed, by the specified number of scan lines
+(\fInscan\fR parameter).
+
+In "longscan" mode the detector is continuously read out to produce
+an arbitrarily long strip.  Provided data which has not passed over
+the entire detector is thrown away, the flat field corrections will
+be one dimensional.  If \fIscancor\fR is specified and the
+scan mode is "longscan" then a one dimensional flat field correction
+will be applied.  If the specified flat field (\fIflat\fR parameter)
+is a two dimensional image then when the flat field image is processed
+it will be averaged across the readout axis to form a one dimensional
+correction image.
+.sh
+12. Outline of Processing Steps
+
+Because of the special handling required for multi-readout data
+\fBquadproc\fR internally reduces the data in two stages.
+
+.ls Stage one
+The operations which may be performed in the first stage are badpixel
+correction, determination and subtraction of the readout bias level, and
+trimming. This stage is only performed if one or more of the \fBfixpix\fR,
+\fBoverscan\fR or \fBtrim\fR flags is set to yes.
+
+First, all the calibration images which will be needed are identified. Any
+which were obtained in multi-readout mode AND which have not already been
+trimmed are selected for processing during this stage. This is necessary to
+ensure that the calibration images will be reduced properly. Similarly, the
+input list is searched and all multi-readout images, which have not already
+been trimmed are selected for processing.
+
+The images selected in this way are then processed sequentially. Each is split
+into separate images one for each amplifier. The values of the trimsec and
+biassec header keywords for each of these sub-images are set as required. 
+\fBccdproc\fR is then run to correct bad pixels, determine and subtract the
+readout bias and trim each sub-image. Finaly, the pieces are glued back 
+together again to form the complete image and the header information is 
+tidied up. The resulting image is initialy created as a temporary image.
+When stage one processing is complete the original image is deleted (or
+renamed using the specified backup prefix) and the corrected image replaces
+the original image.  Using a temporary image protects the data in the
+event of an abort or computer failure.  Keeping the original image name
+eliminates much of the record keeping and the need to generate new
+image names.
+.le
+.ls Stage two
+\fBCcdproc\fR is now run a second time to process ALL input images. For those
+images which were NOT selected for processing during stage one all the selected
+processing steps are carried out during this second pass. For those which were
+selected in stage one only the remaining processing steps will be performed.
+Again the output processed image is initialy created as a temporary image.
+When stage two processing is complete the original image is deleted (or
+renamed using the specified backup prefix) and the corrected image replaces
+the original image.
+.le
+
+The following difference in the behaviour of \fBquadproc\fB and \fBccdproc\fR
+should be noted:
+.ls
+Because it is a script, and because it is reads and writes each image several
+times during processing \fBquadproc\fR is not very efficiant. This will be 
+rectified when the present prototype code is replaced by the final version.
+.le
+.ls
+If backups are enable then \fBquadproc\fR will produce two intermediate 
+images for every input image which is modified in both processing stages.
+These backup images may quickly fill up the available disk space.
+.le
+.ls
+Images may not be processed in the order they appear in the input list. Stage
+one processing is performed (if necessary) on all calibration images, then on
+all images in the input list. Any images which have already been trimmed, or
+which were taken in mono-readout mode will be skipped. Stage two processing is 
+then done sequentially on all images in the input list.
+.le
+.sh
+13. Processing Arithmetic
+The \fBquadproc\fR task has two data paths, one for real image pixel datatypes
+and one for short integer pixel datatype.  In addition internal arithmetic
+is based on the rules of FORTRAN.  For efficiency there is
+no checking for division by zero in the flat field calibration.
+The following rules describe the processing arithmetic and data paths.
+
+.ls (1)
+If the input, output, or any calibration image is of type real the
+real data path is used.  This means all image data is converted to
+real on input.  If all the images are of type short all input data
+is kept as short integers.  Thus, if all the images are of the same type
+there is no datatype conversion on input resulting in greater
+image I/O efficiency.
+.le
+.ls (2)
+In the real data path the processing arithmetic is always real and,
+if the output image is of short pixel datatype, the result
+is truncated.
+.le
+.ls (3)
+The overscan vector and the scale factors for dark count, flat field,
+iillumination, and fringe calibrations are always of type real.  Therefore,
+in the short data path any processing which includes these operations
+will be coerced to real arithmetic and the result truncated at the end
+of the computation.
+.le
+.sh
+14. In the Absence of Image Header Information
+The tasks in the \fBquad\fR package are most convenient to use when
+the CCD image type, subset, and exposure time are contained in the
+image header. This is true for all data obtained with Arcon.  The ability to
+redefine which header parameters contain this information makes it possible
+to use the package at many different observatories (see \fBinstruments\fR). 
+However, in the absence of any image header information the tasks may still
+be used effectively.  There are two ways to proceed.  One way is to use
+\fBccdhedit\fR to place the information in the image header.
+
+The second way is to specify the processing operations more explicitly
+than is needed when the header information is present.  The parameter
+\fIccdtype\fR is set to "" or to "none".  The calibration images are
+specified explicitly by task parameter since they cannot be recognized
+in the input list.  Only one subset at a time may be processed.
+
+If dark count and fringe corrections are to be applied the exposure
+times must be added to all the images.  Alternatively, the dark count
+and fringe images may be scaled explicitly for each input image.  This
+works because the exposure times default to 1 if they are not given in
+the image header.
+.ih
+EXAMPLES
+The user's \fBguide\fR presents a tutorial in the use of this task.
+
+1. In general all that needs to be done is to set the task parameters
+and enter
+
+	cl> quadproc *.imh &
+
+This will run in the background and process all images which have not
+been processed previously.
+.ih
+SEE ALSO
+quadformat, ccdproc, instruments, ccdtypes, flatfields, icfit, quad, guide,
+mkillumcor, mkskycor, mkfringecor
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/quadreadout.hlp b/noao/imred/quadred/src/quad/doc/quadreadout.hlp
new file mode 100644
index 00000000..355fdb61
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/quadreadout.hlp
@@ -0,0 +1,19 @@
+With Arcon it is possible to read out a CCD using more than one amplifier in
+parallel, leading to a substantial reduction in readout time.  Once properly
+reduced, such data is indistinguishable from that obtained when reading out
+through only a single amplifier.  However, the raw images are rather different
+and consequently must be processed somewhat differently. Firstly, each readout
+will typically have a slightly different, zero level, gain, and readout noise,
+and may differ slightly in its departures from perfect linearity. As a result
+both zero frames and uniformly illuminated exposures will show a characteristic
+chequer board pattern, the sections of the data read through each amplifier
+having different levels.  Secondly, there will be a separate overscan strip,
+used to monitor the zero level, for each readout. The location of these overscan
+strips in the raw frame depends on which amplifiers are used. When all four 
+amplifiers are used the four overscan regions form a vertical stripe down the
+centre of the raw image. A CCD read out through two amplifiers can have its
+two overscan strips, running side by side down the center of the picture; or 
+they may be one above the other, on the same side of the picture; or the strip
+for the upper and lower halves of the CCD can be at opposited sides of the
+image (in which case there will also be a horizontal displacement of the data
+in the two sections).
diff --git a/noao/imred/quadred/src/quad/doc/setinstrument.hlp b/noao/imred/quadred/src/quad/doc/setinstrument.hlp
new file mode 100644
index 00000000..410dd20f
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/setinstrument.hlp
@@ -0,0 +1,97 @@
+.help setinstrument Oct87 noao.imred.ccdred
+.ih
+NAME
+setinstrument -- Set instrument parameters
+.ih
+USAGE	
+setinstrument instrument
+.ih
+PARAMETERS
+.ls instrument
+Instrument identification for instrument parameters to be set.  If '?'
+then a list of the instrument identifiers is printed.
+.le
+.ls site = "kpno"
+Site ID.
+.le
+.ls directory = "ccddb$"
+Instrument directory containing instrument files.  The instrument files
+are found in the subdirectory given by the site ID. 
+.le
+.ls review = yes
+Review the instrument parameters?  If yes then \fBeparam\fR is run for
+the parameters of \fBccdred\fR and \fBccdproc\fR.
+.le
+.ls query
+Parameter query if initial instrument is not found.
+.le
+.ih
+DESCRIPTION
+The purpose of the task is to allow the user to easily set default
+parameters for a new instrument.  The default parameters are generally
+defined by support personal in an instrument directory for a particular
+site.  The instrument directory is the concatenation of the specified
+directory and the site.  For example if the directory is "ccddb$" and
+the site is "kpno" then the instrument directory is "ccddb$kpno/".
+The user may have his own set of instrument files in a local directory.
+The current directory is used by setting the directory and site to the
+null string ("").
+
+The user specifies an instrument identifier.  This instrument may
+be specific to a particular observatory, telescope, instrument, and
+detector.  If the character '?' is specified or the instrument file is
+not found then a list of instruments
+in the instrument directory is produced by paging the file "instruments.men".
+The task then performs the following operations:
+.ls (1)
+If an instrument translation file with the name given by the instrument
+ID and the extension ".dat" is found then the instrument translation
+file parameter, \fIccdred.instrument\fR, is set to this file.
+If it does not exist then the user is queried again.  Note that a
+null instrument, "", is allowed to set no translation file.
+.le
+.ls (2)
+If an instrument setup script with the name given by the instrument ID
+and the extension ".cl" is found then the commands in the file are
+executed (using the command \fIcl < script\fR.  This script generally
+sets default parameters.
+.le
+.ls (3)
+If the review flag is set the task \fBeparam\fR is run to allow the user
+to examine and modify the parameters for the package \fBccdred\fR and task
+\fBccdproc\fR.
+.le
+.ih
+EXAMPLES
+1. To get a list of the instruments;
+
+.nf
+	cl> setinstrument ?
+	[List of instruments]
+
+2. To set the instrument and edit the processing parameters:
+
+	cl> setinstrument ccdlink
+	[Edit CCDRED parameters]
+	[Edit CCDPROC parameters]
+
+3. To use your own instrument translation file and/or setup script in
+your working directory.
+
+	cl> setinst.site=""
+	cl> setinst.dir=""
+	cl> setinst myinstrument
+
+To make these files see help under \fBinstruments\fR.  Copying and modifying
+system files is also straightforward.
+
+	cl> copy ccddb$kpno/fits.dat .
+	cl> edit fits.dat
+	cl> setinst.site=""
+	cl> setinst.dir=""
+	cl> setinst fits
+.fi
+.ih
+SEE ALSO
+instruments, ccdred, ccdproc
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/subsets.hlp b/noao/imred/quadred/src/quad/doc/subsets.hlp
new file mode 100644
index 00000000..2823bd6d
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/subsets.hlp
@@ -0,0 +1,97 @@
+.help subsets Jun87 noao.imred.ccdred
+.ih
+NAME
+subsets -- Description of CCD subsets
+.ih
+DESCRIPTION
+The \fBccdred\fR package groups observation into subsets.
+The image header parameter used to identify the subsets is defined
+in the instrument translation file (see help for \fBinstruments\fR).
+For example to select subsets by the header parameter "filters" the
+instrument translation file would contain the line:
+
+	subset	filters
+
+Observations are generally grouped into subsets based on a common
+instrument configuration such as a filter, aperture mask,
+grating setting, etc.  This allows combining images from several
+different subsets automatically and applying the appropriate
+flat field image when processing the observations.  For example
+if the subsets are by filter then \fBflatcombine\fR will search
+through all the images, find the flat field images (based on the
+CCD type parameter), and combine the flat field images from
+each filter separately.  Then when processing the images the
+flat field with the same filter as the observation is used.
+
+Each subset is assigned a short identifier.  This is listed when
+using \fBccdlist\fR and is appended to a root name when combining
+images.  Because the subset parameter in the image header may be
+any string there must be a mapping applied to generate unique
+identifiers.  This mapping is defined in the file given by
+the package parameter \fIccdred.ssfile\fR.  The file consists of
+lines with two fields:
+
+	'subset string'	subset_id
+
+where the subset string is the image header string and the subset_id is
+the identifier.  A field must be quoted if it contains blanks.  The
+user may create this file but generally it is created by the tasks.  The
+tasks use the first word of the subset string as the default identifier
+and a number is appended if the first word is not unique.  The
+following steps define the subset identifier:
+
+.ls (1)
+Search the subset file, if present, for a matching subset string and
+use the defined subset identifier.
+.le
+.ls (2)
+If there is no matching subset string use the first word of the
+image header subset string and, if it is not unique,
+add successive integers until it is unique.
+.le
+.ls (3)
+If the identifier is not in the subset file create the file and add an
+entry if necessary.
+.le
+.ih
+EXAMPLES
+1. The subset file is "subsets" (the default).  The subset parameter is
+translated to "f1pos" in the image header (the old NOAO CCD parameter)
+which is an integer filter position.  After running a task, say
+"ccdlist *.imh" to cause all filters to be checked, the subset file contains:
+
+.nf
+	'2'	2
+	'5'	5
+	'3'	3
+.fi
+
+The order reflects the order in which the filters were encountered.
+Suppose the user wants to have more descriptive names then the subset
+file can be created or edited to the form:
+
+.nf
+	'2'	U
+	'3'	B
+	'4'	V
+.fi
+
+(This is only an example and does not mean these are standard filters.)
+
+2. As another example suppose the image header parameter is "filter" and
+contains more descriptive strings.  The subset file might become:
+
+.nf
+	'GG 385 Filter'	GG
+	'GG 495 Filter'	GG1
+	'RG 610 Filter'	RG
+	'H-ALPHA'	H_ALPHA
+.fi
+
+In this case use of the first word was not very good but it is unique.
+It is better if the filters are encoded with the thought that the first
+word will be used by \fBccdred\fR; it should be short and unique.
+.ih
+SEE ALSO
+instruments
+.endhelp
diff --git a/noao/imred/quadred/src/quad/doc/zerocombine.hlp b/noao/imred/quadred/src/quad/doc/zerocombine.hlp
new file mode 100644
index 00000000..ad1b021d
--- /dev/null
+++ b/noao/imred/quadred/src/quad/doc/zerocombine.hlp
@@ -0,0 +1,127 @@
+.help zerocombine Sep93 arcon.quad
+.ih
+NAME
+zerocombine -- Combine and process zero level images
+.ih
+USAGE
+zerocombine input
+.ih
+PARAMETERS
+.ls input
+List of zero level images to combine.  The \fIccdtype\fR parameter
+may be used to select the zero level images from a list containing all
+types of data.
+.le
+.ls output = "Zero"
+Output zero level root image name.
+.le
+.ls combine = "average" (average|median)
+Type of combining operation performed on the final set of pixels (after
+rejection).  The choices are
+"average" or "median".  The median uses the average of the two central
+values when the number of pixels is even.
+.le
+.ls reject = "minmax" (none|minmax|ccdclip|crreject|sigclip|avsigclip|pclip)
+Type of rejection operation.  See \fBcombine\fR for details.
+.le
+.ls ccdtype = "zero"
+CCD image type to combine.  If no image type is given then all input images
+are combined.
+.le
+.ls process = no
+Process the input images before combining?
+.le
+.ls delete = no
+Delete input images after combining?  Only those images combined are deleted.
+.le
+.ls clobber = no
+Clobber existing output images?
+.le
+.ls scale = "none" (none|mode|median|mean|exposure)
+Multiplicative image scaling to be applied.  The choices are none, scale
+by the mode, median, or mean of the specified statistics section, or scale
+by the exposure time given in the image header.
+.le
+.ls statsec = ""
+Section of images to use in computing image statistics for scaling.
+If no section is given then the entire region of the image is
+sampled (for efficiency the images are sampled if they are big enough).
+.le
+
+.ce
+Algorithm Parameters
+.ls nlow = 0,  nhigh = 1 (minmax)
+The number of low and high pixels to be rejected by the "minmax" algorithm.
+.le
+.ls nkeep = 1
+The minimum number of pixels to retain or the maximum number to reject
+when using the clipping algorithms (ccdclip, crreject, sigclip,
+avsigclip, or pclip).  When given as a positive value this is the minimum
+number to keep.  When given as a negative value the absolute value is
+the maximum number to reject.  This is actually converted to a number
+to keep by adding it to the number of images.
+.le
+.ls mclip = yes (ccdclip, crreject, sigclip, avsigcliip)
+Use the median as the estimate for the true intensity rather than the
+average with high and low values excluded in the "ccdclip", "crreject",
+"sigclip", and "avsigclip" algorithms?  The median is a better estimator
+in the presence of data which one wants to reject than the average.
+However, computing the median is slower than the average.
+.le
+.ls lsigma = 3., hsigma = 3. (ccdclip, crreject, sigclip, avsigclip, pclip)
+Low and high sigma clipping factors for the "ccdclip", "crreject", "sigclip",
+"avsigclip", and "pclip" algorithms.  They multiply a "sigma" factor
+produced by the algorithm to select a point below and above the average or
+median value for rejecting pixels.  The lower sigma is ignored for the
+"crreject" algorithm.
+.le
+.ls rdnoise = "0.", gain = "1.", snoise = "0." (ccdclip, crreject)
+CCD readout noise in electrons, gain in electrons/DN, and sensitivity noise
+as a fraction.  These parameters are used with the "ccdclip" and "crreject"
+algorithms.  The values may be either numeric or an image header keyword
+which contains the value.
+.le
+.ls pclip = -0.5 (pclip)
+Percentile clipping algorithm parameter.  If greater than
+one in absolute value then it specifies a number of pixels above or
+below the median to use for computing the clipping sigma.  If less
+than one in absolute value then it specifies the fraction of the pixels
+above or below the median to use.  A positive value selects a point
+above the median and a negative value selects a point below the median.
+The default of -0.5 selects approximately the quartile point.
+See \fBcombine\fR for further details.
+.le
+.ls blank = 0.
+Output value to be used when there are no pixels.
+.le
+.ih
+DESCRIPTION
+The zero level images in the input image list are combined.
+The input images may be processed first if desired.
+The original images may be deleted automatically if desired.
+
+This task is a script which applies \fBquadproc\fR and \fBcombine\fR.  The
+parameters and combining algorithms are described in detail in the help for
+\fBcombine\fR.  This script has default parameters specifically set for
+zero level images and simplifies the combining parameters.  There are other
+combining options not included in this task.  For these additional
+features, such as thresholding, offseting, masking, and projecting, use
+\fBcombine\fR.
+
+The version of \fBzerocombine\fR in the \fBquad\fR package differs from that
+in \fBccdred\fR in that \fBquadproc\fR rather than \fBccdproc\fR is used to
+process the images if this is requested. The \fBquad\fR version MUST be
+used if process=yes and the input list contains any multi-readout images which
+have not been overscan corrected and trimmed.
+
+.ih
+EXAMPLES
+1. The image data contains four zero level images.
+To automatically select them and combine them as a background job
+using the default combining algorithm:
+
+    cl> zerocombine ccd*.imh&
+.ih
+SEE ALSO
+quadproc, combine
+.endhelp