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

---
 noao/digiphot/apphot/doc/center.hlp | 638 ++++++++++++++++++++++++++++++++++++
 1 file changed, 638 insertions(+)
 create mode 100644 noao/digiphot/apphot/doc/center.hlp

(limited to 'noao/digiphot/apphot/doc/center.hlp')

diff --git a/noao/digiphot/apphot/doc/center.hlp b/noao/digiphot/apphot/doc/center.hlp
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+.help center May00 noao.digiphot.apphot
+.ih
+NAME
+center -- compute accurate centers for a list of objects
+.ih
+USAGE
+center image
+.ih
+PARAMETERS
+.ls image
+The list of images containing the objects to be centered.
+.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 "ctr" 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 centerpars = ""
+The name of the file containing the centering algorithm parameters.
+The critical parameters \fIcalgorithm\fR and \fIcbox\fR are located in
+centerpars. If centerpars is undefined then the default parameter
+set in uparm is used.
+.le
+.ls interactive = yes
+Interactive or non-interactive mode?
+.le
+.ls radplots = no
+If \fIradplots\fR is "yes" and CENTER is run in interactive mode, a radial
+profile of each star is plotted on the screen after the center is fit.
+.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
+.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 \fIverify\fR is
+set to 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 CENTER to work interactively from a contour plot.
+.le
+
+.ih
+DESCRIPTION
+CENTER computes accurate centers for a set of objects in the IRAF image
+\fIimage\fR, whose initial coordinates are read from the image display cursor, 
+from the text file \fIcoords\fR, or from a cursor command file.
+The computed x and y coordinates, the errors,  and the fitting parameters
+are written 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 CENTER 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 CENTER
+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 halves of the image are alternated.
+
+CENTER can be run either interactively or in batch mode by setting the
+parameter \fIinteractive\fR. In interactive mode starting x and y positions
+can either be read directly from the image cursor or read from the text
+file \fIcoords\fR. In interactive mode the user can examine, adjust, and
+save the algorithm parameters, change ojects interactively, query for
+the next or nth object in the list, or fit the entire coordinate list with
+the chosen parameter set.  In batch mode the positions can be read from the
+text file \fIcoords\fR or the image cursor can be redirected to a text file
+containing a list of cursor commands as specified by the parameter
+\fIicommands\fR. 
+
+.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 center of current star
+spbar	Fit center of current star, output results
+m	Move to next star in coordinate list
+n	Center next star in coordinate list, output results
+l	Center remaining stars in coordinate list, output results
+e	Print error messages
+r	Rewind the coordinate list
+q	Exit task
+
+
+	Colon Commands
+
+:show	[data/center]	List the parameters
+:m      [n]	        Move to next [nth] star in coordinate list
+:n      [n]	        Center 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 of PSF (scale units)
+:emission	[y/n]		Emission feature (y), absorption (n)
+:sigma		[value]		Standard deviation of sky (counts)
+:datamin	[value]		Minimum good data value (counts)
+:datamax	[value]		Maximum good data 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)
+
+# Centering parameters 
+
+:calgorithm	[string]	Centering algorithm
+:cbox		[value]		Width of centering box (scale units)
+:cthreshold	[value]		Centering intensity threshold (sigma)
+:cmaxiter	[value]		Maximum number of iterations
+:maxshift	[value]		Maximum center shift (scale units)
+:minsnratio	[value]		Minimum signal to noise for centering
+:clean		[y/n]		Clean subraster before centering
+:rclean		[value]		Cleaning radius (scale units)
+:rclip		[value]		Clipping radius (scale units)
+:kclean		[value]		Clean K-sigma rejection limit (sigma)
+
+# Plotting and marking parameters
+
+:mkcenter	[y/n]		Mark computed centers on the display
+:radplot	[y/n]		Plot radial profile of object
+
+
+The following keystroke commands are available from the interactive setup
+menu.
+
+                    Interactive Center Setup Menu
+
+	v	Mark and verify the critical center parameters (f,s,c)
+
+	f	Mark and verify the full-width half-maximum of the psf
+	s	Mark and verify the standard deviation of the background
+	l	Mark and verify the minimum good data value
+	u	Mark and verify the maximum good data value
+
+	c	Mark and verify the centering box half-width
+	n	Mark and verify the cleaning radius
+	p	Mark and verify the clipping radius
+.fi
+
+.ih
+ALGORITHMS
+
+Descriptions of the data dependent parameters and the centering
+algorithm parameters can be found in the online manual pages for
+\fIdatapars\fR and \fIcenterpars\fR.
+
+.ih
+OUTPUT
+
+In interactive mode the following quantities are written to the terminal
+as each object is measured. Error is a simple string which indicates
+whether an error condition has been flagged.  The centers and their errors are
+in pixel units.
+
+.nf
+	image  xinit  yinit  xcenter  ycenter  xerr  yerr  error
+.fi
+
+In both interactive and batch mode the 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
+	   xcenter  ycenter  xshift  yshift  xerr  yerr  cier 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. Cier and error are the centering error code and accompanying
+error message respectively.  Xinit, yinit, xcenter, ycenter, xshift, yshift,
+and xerr, yerr are self explanatory and output in pixel units. The sense of
+the xshift and yshift definitions is the following.
+
+.nf
+	xshift = xcenter - xinit
+	yshift = ycenter - yinit
+.fi
+
+In interactive mode a radial profile of each measured object is plotted
+in the graphics window if \fIradplots\fR is "yes".
+
+In interactive and batchmode 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 the object centering was error free then the field cier will be zero.
+Non-zero values in the cier column flag the following error conditions.
+
+.nf
+	0        # No error
+	101      # The centering box is off the image
+	102      # The centering box is partially off the image
+	103      # The S/N ratio is low in the centering box
+	104      # There are two few points for a good fit
+	105      # The x or y center fit is singular
+	106      # The x or y center fit did not converge
+	107      # The x or y center shift is greater than maxshift
+	108      # There is bad data in the centering box
+.fi
+
+.ih
+EXAMPLES
+
+1. Compute the centers for a few  stars in dev$ypix using the image display
+and the image cursor. Setup the task parameters using the interactive
+setup menu defined by the i keystroke command and a radial profile plot.
+
+.nf
+	ap> display dev$ypix 1 fi+
+
+	... display the image
+
+	ap> center dev$ypix
+
+	... type ? to see help screen
+
+	... move image cursor to a star
+	... type i to enter the interactive setup menu
+	... enter the maximum radius in pixels for the radial profile or
+	    accept the default with a CR
+	... type  v to get the default menu
+	... set the fwhmpsf, sigma, and centering box half-width using the
+	    graphics cursor and the stellar radial profile plot
+	... typing <CR> after a prompt leaves the parameter at its default
+	    value
+	... type q to exit setup menu
+
+	... type the v key to verify the critical parameters
+
+	... type the w key to save the parameters in the parameter files
+
+	... move the image cursor to the stars of interest and tap
+	    the space bar
+
+	... type q to quit followed by q to confirm the quit
+
+	... the output will appear in ypix.ctr.1
+
+.fi
+
+2. Compute the centers for a few stars in dev$ypix using the 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$ypix >G ypix.plot1
+
+	... store the contour plot of ypix in the file ypix.plot
+
+	ap> center dev$ypix display=stdgraph
+
+	... type ? to see the help screen
+
+	... move graphics cursor to a star
+	... 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 key to get the default setup menu
+	... enter maximum radius in pixels of the radial profile
+	... set the fwhmpsf, sigma, and centering box half-width
+	    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 the v key to verify 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 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.ctr.2 
+
+	ap> set stdimcur = <default>
+
+	... reset stdimcur to its previous value
+.fi
+
+
+3. Setup and run CENTER interactively on a list of objects temporarily
+overriding the fwhmpsf, sigma, and cbox parameters determined in examples
+1 or 2.
+
+.nf
+	ap> daofind dev$ypix fwhmpsf=2.6 sigma=25.0 verify-
+
+	... make a coordinate list 
+
+	... the output will appear in the text file ypix.coo.1
+
+	ap> center dev$ypix cbox=7.0 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
+
+	... the output will appear in ypix.ctr.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$ypix[150:450,150:450] 1
+
+	... display the image section
+
+	ap> center dev$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.ctr.4
+
+	ap> pdump ypix.ctr.4 xc,yc yes | tvmark 1 STDIN col=204 
+.fi
+
+
+5. Run CENTER in batch mode using the coordinate file and the previously
+saved parameters. Verify the critical parameters.
+
+.nf
+	ap> center dev$ypix coords=ypix.coo.1 verify+ inter-
+
+	... output will appear in ypix.ctr.5 ...
+.fi
+
+
+6. Repeat example 5 but assume that the input coordinate are ra and dec
+in degrees and degrees, turn off verification, and submit the task to to
+the background.
+
+.nf
+	ap> display dev$ypix
+
+	ap> rimcursor wcs=world > radec.coo
+
+	... move to selected stars and type any key
+
+	... type ^Z to quit
+
+	ap> center dev$ypix coords=radec.coo wcsin=world verify- inter- &
+
+	... output will appear in ypix.ctr.6
+
+	ap> pdump ypix.ctr.6 xc,yc yes | tvmark 1 STDIN col=204
+
+	... mark the stars on the display
+
+
+7. Run CENTER interactively without using the image display.
+
+.nf
+	ap> show stdimcur
+
+	... record the default value of stdimcur
+
+	ap> set stdimcur = text
+
+	... set the image cursor to the standard input
+
+	ap> center dev$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 fwhmpsf, sigma, and centering box half-width
+	    using the graphics cursor and the stellar radial profile plot
+	... typing <CR> after the prompt leaves the parameter at its default
+	    value
+
+	... 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.ctr.7 
+
+	ap> set stdimcur = <default>
+
+	... reset the value of stdimcur
+.fi
+
+8. Use a image cursor command file to drive the CENTER task. The cursor command
+file shown below sets the fwhmpsf, calgorithm, and cbox parameters, computes
+the centers for 3 stars, updates the parameter files, and quits the task.
+
+.nf
+	ap> type cmdfile
+	: calgorithm gauss
+	: fwhmpsf 2.5
+	: cbox 9.0
+	442 410 101 \040 
+	349 188 101 \040 
+	225 131 101 \040 
+	w
+	q
+
+	ap> center dev$ypix icommands=cmdfile  verify-
+
+	... full output will appear in ypix.ctr.8
+.fi
+
+.ih
+BUGS
+
+It is the responsibility of the user to make sure that the image displayed
+in the image display is the same as the image 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 centerpars mkcenter 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, centerpars
+.endhelp
-- 
cgit 

