From fa080de7afc95aa1c19a6e6fc0e0708ced2eadc4 Mon Sep 17 00:00:00 2001
From: Joseph Hunkeler <jhunkeler@gmail.com>
Date: Wed, 8 Jul 2015 20:46:52 -0400
Subject: Initial commit

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 noao/digiphot/apphot/doc/fitsky.hlp | 632 ++++++++++++++++++++++++++++++++++++
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+.help fitsky Dec92 noao.digiphot.apphot
+.ih
+NAME
+fitsky - determine the mode, sigma and skew of the sky pixels
+.ih
+USAGE
+fitsky image
+.ih
+PARAMETERS
+.ls image
+The list of images containing the sky regions to be fit.
+.le
+.ls coords = ""
+The list of text files containing initial coordinates for the objects to
+be centered. Objects are listed in coords one object per line with the
+initial coordinate values in columns one and two. The number of coordinate
+files must be zero, one, or equal to the number of images.
+If coords is "default", "dir$default", or a directory specification then an
+coords file name of the form dir$root.extension.version is constructed and
+searched for, where dir is the directory, root is the root image name,
+extension is "coo" and version is the next available version number for the
+file.
+.le
+.ls output = "default"
+The name of the results file or results directory. If output is
+"default", "dir$default", or a directory specification then an output file name
+of the form dir$root.extension.version is constructed, where dir is the
+directory, root is the root image name, extension is "sky" and version is
+the next available version number for the file. The number of output files
+must be zero, one, or equal to the number of image files.  In both interactive
+and batch mode full output is written to output. In interactive mode
+an output summary is also written to the standard output.
+.le
+.ls plotfile = ""
+The name of the file containing radial profile plots of the stars written
+to the output file. If plotfile is defined then a radial profile plot
+is written to plotfile every time a record is written to \fIoutput\fR.
+The user should be aware that this can be a time consuming operation.
+.le
+.ls datapars = ""
+The name of the file containing the data dependent parameters.
+The critical parameters \fIfwhmpsf\fR and \fIsigma\fR are located in
+datapars.  If datapars is undefined then the default parameter set in
+uparm directory is used.
+.le
+.ls fitskypars = ""
+The name of the text file containing the sky fitting parameters. The critical
+parameters \fIsalgorithm\fR, \fIannulus\fR, and \fIdannulus\fR are located here.
+If \fIfitskypars\fR is undefined then the default parameter set in uparm
+directory is used.
+.le
+.ls interactive = yes
+Run the task interactively ?
+.le
+.ls radplots = no
+If \fIradplots\fR is "yes" and PHOT is run in interactive mode, a radial
+profile of each star is plotted on the screen after the star is measured.
+.le
+.ls icommands = ""
+The image display cursor or image cursor command file.
+.le
+.ls gcommands = ""
+The graphics cursor or graphics cursor command file.
+.le
+.ls wcsin = ")_.wcsin", wcsout = ")_.wcsout"
+The coordinate system of the input coordinates read from \fIcoords\fR and
+of the output coordinates written to \fIoutput\fR respectively. The image
+header coordinate system is used to transform from the input coordinate
+system to the "logical" pixel coordinate system used internally,
+and from the internal "logical" pixel coordinate system to the output
+coordinate system. The input coordinate system options are "logical", tv",
+"physical", and "world". The output coordinate system options are "logical",
+"tv", and "physical". The image cursor coordinate system is assumed to
+be the "tv" system.
+.ls logical
+Logical coordinates are pixel coordinates relative to the current image.
+The  logical coordinate system is the coordinate system used by the image
+input/output routines to access the image data on disk. In the logical
+coordinate system the coordinates of the first pixel of a  2D image, e.g.
+dev$ypix  and a 2D image section, e.g. dev$ypix[200:300,200:300] are
+always (1,1).
+.le
+.ls tv
+Tv coordinates are the pixel coordinates used by the display servers. Tv
+coordinates  include  the effects of any input image section, but do not
+include the effects of previous linear transformations. If the input
+image name does not include an image section, then tv coordinates are
+identical to logical coordinates.  If the input image name does include a
+section, and the input image has not been linearly transformed or copied from
+a parent image, tv coordinates are identical to physical coordinates.
+In the tv coordinate system the coordinates of the first pixel of a
+2D image, e.g. dev$ypix and a 2D image section, e.g. dev$ypix[200:300,200:300]
+are (1,1) and (200,200) respectively.
+.le
+.ls physical
+Physical coordinates are pixel coordinates invariant  with respect to linear
+transformations of the physical image data.  For example, if the current image
+was created by extracting a section of another image,  the  physical
+coordinates of an object in the current image will be equal to the physical
+coordinates of the same object in the parent image,  although the logical
+coordinates will be different.  In the physical coordinate system the
+coordinates of the first pixel of a 2D image, e.g. dev$ypix and a 2D
+image section, e.g. dev$ypix[200:300,200:300] are (1,1) and (200,200)
+respectively.
+.le
+.ls world
+World coordinates are image coordinates in any units which are invariant
+with respect to linear transformations of the physical image data. For
+example, the ra and dec of an object will always be the same no matter
+how the image is linearly transformed. The units of input world coordinates
+must be the same as those expected by the image header wcs, e. g.
+degrees and degrees for celestial coordinate systems.
+.le
+The wcsin and wcsout parameters default to the values of the package
+parameters of the same name. The default values of the package parameters
+wcsin and wcsout are "logical" and "logical" respectively.
+.le
+.le
+.ls cache = ")_.cache"
+Cache the image pixels in memory. Cache may be set to the value of the apphot
+package parameter (the default), "yes", or "no". By default cacheing is 
+disabled.
+.le
+.ls verify = ")._verify"
+Verify the critical parameters in non-interactive mode ? Verify may be set to
+ the apphot package parameter value (the default), "yes", or "no.
+.le
+.ls update = ")_.update"
+Update the critical parameters in non-interactive mode if verify is yes ?
+Update may be set to the apphot package parameter value (the default), "yes",
+or "no.
+
+.le
+.ls verbose = ")_.verbose"
+Print messages on the terminal in non-interactive mode ? Verbose may be set to
+the apphot package parameter value (the default), "yes", or "no.
+
+.le
+.ls graphics = ")_.graphics"
+The default graphics device.  Graphics may be set to the apphot package
+parameter value (the default), "yes", or "no.
+.le
+.ls display = ")_.display"
+The default display device. Display may be set to the apphot package parameter
+value (the default), "yes", or "no. By default graphics overlay is disabled.
+Setting display to one of "imdr", "imdg", "imdb", or "imdy" enables graphics
+overlay with the IMD graphics kernel.  Setting display to "stdgraph" enables
+FITSKY to work interactively from a contour plot.
+.le
+
+.ih
+DESCRIPTION
+FITSKY computes accurate sky values for a set of objects in the IRAF image
+\fIimage\fR, whose coordinates are read from the text file \fIcoords\fR or
+the image display cursor, and writes the computed sky values to the text
+file \fIoutput\fR.
+
+The coordinates read from \fIcoords\fR are assumed to be in coordinate
+system defined by \fIwcsin\fR. The options are "logical", "tv", "physical",
+and "world" and the transformation from the input coordinate system to
+the internal "logical" system is defined by the image coordinate system.
+The simplest default is the "logical" pixel system. Users working on with
+image sections but importing pixel coordinate lists generated from the parent
+image must use the "tv" or "physical" input coordinate systems.
+Users importing coordinate lists in world coordinates, e.g. ra and dec,
+must use the "world" coordinate system and may need to convert their
+equatorial coordinate units from hours and degrees to degrees and degrees first.
+
+The coordinates written to \fIoutput\fR are in the coordinate
+system defined by \fIwcsout\fR. The options are "logical", "tv",
+and "physical". The simplest default is the "logical" system. Users
+wishing to correlate the output coordinates of objects measured in
+image sections or mosaic pieces with coordinates in the parent
+image must use the "tv" or "physical" coordinate systems.
+
+If \fIcache\fR is yes and the host machine physical memory and working set size
+are large enough, the input image pixels are cached in memory. If cacheing
+is enabled and FITSKY is run interactively the first measurement will appear
+to take a long time as the entire image must be read in before the measurement
+is actually made. All subsequent measurements will be very fast because FITSKY
+is accessing memory not disk. The point of cacheing is to speed up random
+image access by making the internal image i/o buffers the same size as the
+image itself. However if the input object lists are sorted in row order and
+sparse cacheing may actually worsen not improve the execution time. Also at
+present there is no point in enabling cacheing for images that are less than
+or equal to 524288 bytes, i.e. the size of the test image dev$ypix, as the
+default image i/o buffer is exactly that size. However if the size of dev$ypix
+is doubled by converting it to a real image with the chpixtype task then the
+effect of cacheing in interactive is can be quite noticeable if measurements
+of objects in the top and bottom halfs of the image are alternated.
+
+FITSKY can be run either interactively or in batch mode by setting the parameter
+\fIinteractive\fR. In interactive mode the user may either define the
+list of objects to be measured interactively with the image cursor or
+create an object list prior to running  FITSKY. In either case the user may
+adjust the sky fitting parameters until a satisfactory measurement is achieved.
+coordinate list with that set of parameters. In batch mode 
+positions are read from the text file \fIcoords\fR or the image cursor
+parameter \fIicommands\fR can be redirected to a cursor command file.
+
+.ih
+CURSOR COMMANDS
+
+The following cursor commands are currently available.
+
+.nf
+	Interactive Keystroke Commands
+
+?	Print help
+:	Colon commands
+v	Verify the critical parameters
+w	Save the current parameters
+d	Plot radial profile of current star 
+i	Interactively set parameters using current star
+f	Fit sky for current star
+spbar	Fit sky for current star, output results
+m	Move to next star in coordinate list
+m	Fit sky for next star in coordinate list, output results
+l	Fit sky for remaining stars in coordinate list, output results
+e	Print error messages
+r	Rewind the coordinate list
+q	Exit task
+
+
+        Colon commands
+
+:show	[data/sky]	List the parameters
+:m [n]	Move to the next [nth] star in coordinate list
+:n [n]	Fit sky to next [nth] star in coordinate list, output results
+
+	Colon Parameter Editing Commands
+
+# Image and file name parameters
+
+:image		[string]	Image name
+:coords		[string]	Coordinate file name
+:output 	[string]	Output file name
+
+# Data dependent parameters
+
+:scale		[value]		Image scale (units per pixel)
+:fwhmpsf	[value]		Full width half maximum PSF (scale units)
+:emission	[y/n]		Emission feature (y), absorption (n)
+:sigma		[value]		Standard deviation of sky (counts)
+:datamin	[value]		Minimum good pixel value (counts)
+:datamax	[value]		Maximum good pixel value (counts)
+
+# Noise parameters
+
+:noise		[string]	Noise model (constant|poisson)
+:gain		[string]	Gain image header keyword
+:ccdread	[string]	Readout noise image header keyword
+:epadu		[value]		Gain (electrons per adu)
+:readnoise	[value]		Readout noise (electrons)
+
+# Observations parameters
+
+:exposure	[string]	Exposure time image header keyword
+:airmass	[string]	Airmass image header keyword
+:filter		[string]	Filter image header keyword
+:obstime	[string]	Time of observation image header keyword
+:itime		[value]		Exposure time (time units)
+:xairmass	[value]		Airmass value (number)
+:ifilter	[string]	Filter id string
+:otime		[string]	Time of observation (time units)
+
+# Sky fitting algorithm parameters
+
+:salgorithm	[string]	Sky fitting algorithm 
+:skyvalue	[value]		User supplied sky value (counts)
+:annulus 	[value]		Inner radius of sky annulus (scale units)
+:dannulus	[value]		Width of sky annulus (scale units)
+:khist		[value]		Sky histogram extent (+/- sky sigma)
+:smooth		[y/n]		Lucy smooth the sky histogram 
+:binsize	[value]		Resolution of sky histogram (sky sigma)
+:smaxiter	[value]		Maximum number of iterations
+:sloclip	[value]		Low side clipping factor (percent)
+:shiclip	[value]		High side clipping factor (percent)
+:snreject	[value]		Maximum number of rejection cycles
+:sloreject	[value]		Low side pixel rejection limits (sky sigma)
+:shireject	[value]		High side pixel rejection limits (sky sigma)
+:rgrow		[value]		Region growing radius (scale units)
+
+# Marking and plotting parameters
+
+:mksky		[y/n]		Mark sky annuli on the display
+:radplot	[y/n]		Plot radial profile of sky pixels
+
+
+The following commands are available from within the interactive setup menu.
+
+
+                      Interactive Fitsky Setup Menu
+
+	v	Mark and verify the critical parameters (a,d,s)
+
+	s	Mark and verify the standard deviation of the sky
+	l	Mark and verify the minimum good data value
+	u	Mark and verify the maximum good data value
+
+	a	Mark and verify the inner radius of the sky annulus
+	d	Mark and verify the width of the sky annulus
+	g	Mark and verify the region growing radius
+.fi
+
+.ih
+ALGORITHMS
+A brief description of the data dependent parameters and the sky fitting
+parameters can be found in the online manual pages for the DATAPARS
+and FITSKYPARS tasks.
+
+.ih
+OUTPUT
+In interactive mode the following quantities are printed on the standard
+output as each object is measured.
+
+.nf
+    image  xinit  yinit  msky  stdev  sskew  nsky  nsrej  error
+.fi
+
+In both interactive and batch mode full output is written to the 
+text file \fIoutput\fR. At the beginning of each file is a header listing
+the current values of the parameters when the first stellar record was
+written. These parameters can be subsequently altered. For each star
+measured the following record is written.
+
+.nf
+    image  xinit  yinit  id  coords  lid
+	msky  stdev  sskew  nsky  nsrej  sier  error
+.fi
+
+Image and coords are the name of the image and coordinate file respectively.
+Id and lid are the sequence numbers of stars in the output and coordinate
+files respectively. Sier and error are the error code and accompanying
+error message respectively. Xinit and yinit are the center coordinates
+of the sky annulus in pixels. Msky, stdev and sskew are the sky value,
+standard deviation and skew respectively. Nsky and nsrej are the number of
+sky pixels used and the number of sky pixels rejected respectively.
+
+In interactive mode a radial profile of each measured object is plotted
+in the graphics window if \fIradplots\fR is "yes".
+
+In interactive and batch mode a radial profile plot is written to
+\fIplotfile\fR  if it is defined each time the result of an object
+measurement is written to \fIoutput\fR .
+
+.ih
+ERRORS
+If all goes well during the sky fitting process then the error code sier
+will be 0. Non-zero values of sier flag the following error conditions.
+
+.nf
+	0         # No error
+	201       # There are no sky pixels in the sky annulus
+	202       # Sky annulus is partially off the image
+	203       # The histogram of sky pixels has no width
+	204       # The histogram of sky pixels is flat or concave
+	205       # There are too few points for a good sky fit
+	206       # The sky fit is singular
+	207       # The sky fit did not converge
+	208       # The graphics stream is undefined
+	209       # The file of sky values does not exist
+	210       # The sky file is at EOF
+	211       # Cannot read the sky value correctly
+	212       # The best fit parameters are non-physical
+.fi
+
+.ih
+EXAMPLES
+
+1. Compute the sky values for a few  stars in dev$ypix using the display
+and the image cursor. Setup the task parameters using the interactive
+setup menu defined by the i key command and a radial profile plot.
+
+.nf
+        ap> display dev$ypix 1 fi+
+
+        ... display the image
+
+        ap> fitsky dev$ypix
+
+        ... type ? to print an optional help page
+
+        ... move the image cursor to a star
+        ... type i to enter the interactive setup menu
+        ... enter maximum radius in pixels of the radial profile or hit
+            CR to accept the default
+        ... set the inner and outer sky annuli, and sigma  using the
+            graphics cursor and the stellar radial profile plot
+        ... typing <CR> leaves everything at the default value
+        ... type q to quit the setup menu
+
+        ... type the v key to verify the parameters
+
+        ... type the w key to save the parameters in the parameter files
+
+        ... move the image cursor to the stars of interest and tap
+            the space bar
+
+        ... a one line summary of the fitted parameters will appear on the
+            standard output for each star measured
+
+        ... type q to quit and q again to confirm the quit
+
+        ... the output will appear in ypix.sky.1
+.fi
+
+2. Compute the sky values for a few stars in dev$ypix using a contour plot
+and the graphics cursor. This option is only useful for those (now very few)
+users who have access to a graphics terminal but not to an image display
+server. Setup the task parameters using the interactive setup menu defined by
+the i key command as in example 1.
+
+.nf
+        ap> show stdimcur
+
+        ... record the default value of stdimcur
+
+        ap> set stdimcur = stdgraph
+
+        ... define the image cursor to be the graphics cursor
+
+        ap> contour dev$ypix
+
+        ... make a contour plot of dev$ypix
+
+        ap> contour dev$ypix >G ypix.plot1
+
+        ... store the contour plot of dev$ypix in the file ypix.plot1
+
+        ap> fitsky dev$ypix display=stdgraph
+
+        ... type ? to get an optional help page
+
+        ... move graphics cursor to a star
+        ... type i to enter the interactive setup menu
+        ... enter maximum radius in pixels of the radial profile or CR
+            to accept the default value
+        ... set the inner and outer sky annuli, and sigma using the
+            graphics cursor and the stellar radial profile plot
+        ... typing <CR> leaves everything at the default value
+        ... type q to quit the setup menu
+
+        ... type the v key to verify the critical parameters
+
+        ... type the w key to save the parameters in the parameter files
+
+        ... retype :.read ypix.plot1 to reload the contour plot
+
+        ... move the graphics cursor to the stars of interest and tap
+            the space bar
+
+        ... a one line summary of the fitted parameters will appear on the
+            standard output for each star measured
+
+        ... type q to quit and q again to verify
+
+        ... full output will appear in the text file ypix.sky.2
+
+        ap> set stdimcur = <default>
+
+        ... reset stdimcur to its previous value
+.fi
+
+3. Setup and run FITSKY interactively on a list of objects temporarily
+overriding the fwhmpsf, sigma, annulus, and dannulus parameters determined
+in examples 1 or 2.
+
+.nf
+        ap> daofind dev$ypix fwhmpsf=2.6 sigma=25.0 verify-
+
+        ... make a coordinate list
+
+        ... the output will appear in the text file ypix.coo.1
+
+        ap> fitsky dev$ypix annulus=12.0 dannulus=5.0 coords=ypix.coo.1
+
+        ... type ? for optional help
+
+
+        ... move the graphics cursor to the stars and tap space bar
+
+                                or
+
+        ... select stars from the input coordinate list with m / :m #
+            and measure with spbar
+
+        ... measure stars selected from the input coordinate list
+            with n / n #
+
+        ... a one line summary of results will appear on the standard output
+            for each star measured
+
+        ... type q to quit and q again to confirm the quit
+
+        ... the output will appear in ypix.sky.3 ...
+.fi
+
+
+4. Display and measure some stars in an image section and write the output
+coordinates in the coordinate system of the parent image.
+
+.nf
+        ap> display dev$ypix[150:450,150:450] 1
+
+        ... display the image section
+
+        ap> fitsky dev$ypix[150:450,150:450] wcsout=tv
+
+        ... move cursor to stars and type spbar
+
+        ... type q to quit and q again to confirm quit
+
+        ... output will appear in ypix.sky.4
+
+        ap> pdump ypix.sky.4 xi,yi yes | tvmark 1 STDIN col=204
+.fi
+
+5. Run FITSKY in batch mode using the coordinate file and the previously
+saved parameters. Verify the critical parameters.
+
+.nf
+        ap> fitsky dev$ypix coords=ypix.coo.1 verify+ inter-
+
+        ... output will appear in ypix.sky.5 ...
+.fi
+
+6. Repeat example 5 but assume that the input coordinate are ra and dec
+in degrees and degrees, turn off verification, and submit the task to to
+the background.
+
+.nf
+        ap> display dev$ypix 1
+
+        ap> rimcursor wcs=world > radec.coo
+
+        ... move to selected stars and type any key
+
+        ... type ^Z to quit
+
+        ap> fitsky dev$ypix coords=radec.coo wcsin=world verify- inter- &
+
+        ... output will appear in ypix.sky.6
+
+        ap> pdump ypix.sky.6 xi,yi yes | tvmark 1 STDIN col=204
+
+        ... mark the stars on the display
+.fi
+
+7. Run FITSKY interactively without using the image display.
+
+.nf
+        ap> show stdimcur
+
+        ... record the default value of stdimcur
+
+        ap> set stdimcur = text
+
+        ... set the image cursor to the standard input
+
+        ap> fitsky dev$ypix coords=ypix.coo.1
+
+        ... type ? for optional help
+
+        ... type :m 3 to set the initial coordinates to those of the
+            third star in the list
+
+        ... type i to enter the interactive setup menu
+        ... enter the maximum radius in pixels for the radial profile or
+            accept the default with a CR
+        ... type v to enter the default menu
+        ... set the inner and outer sky annuli, and sigma using the
+            graphics cursor and the stellar radial profile plot
+        ... typing <CR> after the prompt leaves the parameter at its default
+            value
+        ... type q to quit the setup menu
+
+        ... type r to rewind the coordinate list
+
+        ... type l to measure all the stars in the coordinate list
+
+        ... a one line summary of the answers will appear on the standard
+            output for each star measured
+
+        ... type q to quit followed by q to confirm the quit
+
+        ... full output will appear in the text file ypix.sky.7
+
+        ap> set stdimcur = <default>
+
+        ... reset the value of stdimcur
+.fi
+
+8. Use an image cursor command file to drive the FITSKY task. The cursor command
+file shown below sets the annulus and dannulus parameters, computes the sky
+values for 3 stars, updates the parameter files, and quits the task.
+
+.nf
+        ap> type cmdfile
+        : annulus 12.0
+        : dannulus 5.0
+        442 410 101 \040
+        349 188 101 \040
+        225 131 101 \040
+        w
+        q
+
+        ap> fitsky dev$ypix icommands=cmdfile verify-
+
+        ... full output will appear in ypix.sky.8
+.fi
+
+.ih
+TIME REQUIREMENTS
+
+.ih
+BUGS
+It is currently the responsibility of the user to make sure that the
+image displayed in the frame is the same as that specified by the image
+parameter.
+
+Commands which draw to the image display are disabled by default.
+To enable graphics overlay on the image display, set the display
+parameter to "imdr", "imdg", "imdb", or "imdy" to get red, green,
+blue or yellow overlays and set the fitskypars mksky switch to"yes".
+It may be necessary to run gflush and to redisplay the image
+to get the overlays position correctly.
+
+.ih
+SEE ALSO
+datapars, fitskypars, phot, polyphot, radprof
+.endhelp
-- 
cgit 

