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/daophot/doc/substar.hlp | 323 ++++++++++++++++++++++++++++++++++
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+.help substar May00 noao.digiphot.daophot
+.ih
+NAME
+substar -- subtract photometry results from an image 
+.ih
+USAGE
+substar image photfile exfile psfimage subimage
+.ih
+PARAMETERS
+.ls image
+The list of images from which to subtract the scaled and shifted PSF.
+.le
+.ls photfile
+The list of PSF fitted photometry files. There must be one photometry file
+for every input image. If photfile is "default", "dir$default", or a directory
+specification, SUBSTAR will look for a file called image.nst.? where the
+question mark stands for the highest existing version number. Photfile is
+usually the output of the NSTAR task but may also be the output of the PEAK
+and ALLSTAR tasks or even the PHOT task. Photfile may be an APPHOT/DAOPHOT text
+database or an STSDAS table.
+.le
+.ls exfile
+The list of photometry files containing the ids of stars to be excluded
+from the subtraction. Exfile must be undefined or contain one exclude file
+for every input image. If exfile is "default", "dir$default", or a directory
+specification, SUBSTAR will look for a file called image.pst.? where the ?
+mark stands for the highest existing version number. Exfile is usually the
+output of the PSTSELECT task but may also be the output of the PEAK, NSTAR and
+ALLSTAR tasks or even the PHOT task. Exfile may be an APPHOT/DAOPHOT text
+database or an STSDAS table.
+.le
+.ls psfimage
+The list of images containing the PSF models computed by the DAOPHOT PSF task.
+The number of PSF images must be equal to the number of input images.  If
+psfimage is "default", "dir$default", or a directory specification,
+then PEAK will look for an image with the name image.psf.?, where
+? is the highest existing version number.
+.le
+.ls subimage
+The list of output subtracted images. There must be one output subtracted
+image for every input image.  If subimage is "default", "dir$default", or a
+directory specification, then SUBSTAR will write an image called image.sub.?
+where question mark stands for the next available version number. 
+.le
+.ls datapars = ""
+The name of the file containing the data dependent parameters. The parameters
+\fIscale\fR, \fIdatamin\fR, and \fIdatamax\fR are located here. If datapars
+is undefined then the default parameter set in uparm directory
+.le
+.ls daopars = ""
+The name of the file containing the daophot fitting parameters. The parameters
+\fIpsfrad\fR and \fIfitrad\fR are located here. If \fIdaopars\fR is undefined
+then the default parameter set in uparm directory is used.
+.le
+.ls wcsin = ")_.wcsin", wcsout = ")_.wcsout", wcspsf = ")_.wcspsf"
+The coordinate system of the input coordinates read from \fIphotfile\fR, of the
+psf model \fIpsfimage\fR, and of the output coordinates written to
+the standard output if \fIverbose\fR = "yes". The image header coordinate
+system is used to transform from the input coordinate system to the "logical"
+pixel coordinate system used internally, from the internal logical system to
+the PSF model system, 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 PSF model and 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, wcspsf, and wcsout parameters default to the values of the package
+parameters of the same name. The default values of the package parameters
+wcsin, wcspsf,  and wcsout are "logical", "physical" 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 caching is
+disabled.
+.le
+.ls verify = ")_.verify"
+Verify the critical SUBSTAR task parameters? Verify can be set to the DAOPHOT
+package parameter value (the default), "yes", or "no".
+.le
+.ls update = ")_update"
+Update the SUBSTAR task parameters if \fIverify\fR is "yes"? Update can be
+set to the default daophot package parameter value, "yes", or "no".
+.le
+.ls verbose = ")_.verbose"
+Print messages about the progress of the task ? Verbose can be set to the
+DAOPHOT package parameter value (the default), "yes", or "no".
+.le
+
+.ih
+DESCRIPTION
+SUBSTAR task takes an input photometry list \fIphotfile\fR containing
+the fitted coordinates and magnitudes, and an input PSF \fIpsfimage\fR, and
+for each star in the photometry list scales and shifts the PSF and subtracts
+it from the input image \fIimage\fR. The final subtracted image is saved in the
+output image \fIsubimage\fR.
+
+The input photometry list can be the output from of the PEAK, NSTAR or ALLSTAR
+tasks or even the PHOT task although most people would not want to use the PHOT
+output for this purpose.
+
+Selected stars may be omitted from the subtraction by supplying their ids in
+the file \fIexfile\fR. \fIExfile\fR is normally the output the PSTSELECT task
+and is used to tell SUBSTAR to subtract the PSF star neighbors, but not the
+PSF stars themselves.
+
+The coordinates read from \fIphotfile\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.
+
+The coordinate system of the PSF model is the coordinate system defined by the
+\fIwcspsf\fR parameter. Normally the PSF model was derived from the input image
+and this parameter default to "logical". However if the PSF model was derived
+from a larger image which is a "parent" of the input image, then wcspsf should
+be set to "tv" or "physical" depending on the circumstances.
+
+The coordinates written to the standard output if \fIverbose\fR = yes 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 and output image pixels are cached in memory. If
+caching is enabled and SUBSTAR is run interactively the first subtraction
+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 SUBSTAR is accessing memory not disk. The point of caching 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 which SUBSTAR does internally  and are sparse caching may
+actually worsen not improve the execution time. Also at present there is no
+point in enabling caching 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
+caching in interactive is can be quite noticeable if measurements
+of objects in the top and bottom halves of the image are alternated.
+
+
+The SUBSTAR task is most commonly used to check on the quality of the PSF
+fitting produced by PEAK and NSTAR, to search for non-stellar objects and close
+binary stars, to generate an improved PSF in crowded fields, and to remove
+neighbors from bright stars which are to be used to determine aperture
+corrections.
+
+.ih
+EXAMPLES
+
+1. Subtract the NSTAR photometry results for the test image dev$ypix from the
+image dev$ypix.
+
+.nf
+   da> datapars.epadu = 14.0
+   da> datapars.readnoise = 75.0
+
+       ... set the gain and readout noise for the detector
+
+   da> daofind dev$ypix default fwhmpsf=2.5 sigma=5.0 threshold=20.0
+
+        ... answer verify prompts
+
+        ... find stars in the image
+
+        ... answer will appear in ypix.coo.1
+
+    da> phot dev$ypix default default annulus=10. dannulus=5.       \
+        apertures = 3.0
+
+        ... answer verify prompts
+
+        ... do aperture photometry on the detected stars
+
+        ... answer will appear in ypix.mag.1
+
+    da> display dev$ypix 1
+
+    da> psf dev$ypix default "" default default default psfrad=11.0 \
+        fitrad=3.0 mkstars=yes display=imdr
+
+        ... verify the critical parameters
+
+        ... move the image cursor to a candidate star and hit the a key,
+            a plot of the stellar data appears
+
+        ... type ? for a listing of the graphics cursor menu
+
+        ... type a to accept the star, d to reject it
+
+        ... move to the next candidate stars and repeat the previous
+            steps
+
+        ... type l to list all the psf stars
+
+        ... type f to fit the psf
+
+        ... move cursor to first psf star and type s to see residuals,
+            repeat for all the psf stars
+
+        ... type w to save the PSF model
+
+        ... type q to quit, and q again to confirm
+
+        ... the output will appear in ypix.psf.1.imh, ypix.pst.1 and
+            ypix.psg.1
+
+    da> group dev$ypix default default default
+
+        ... verify the prompts
+
+        ... the output will appear in ypix.grp.1
+
+    da> nstar dev$ypix default default default default
+
+        ... verify the prompts
+
+        ... the results will appear in ypix.nst.1 and ypix.nrj.1
+
+    da> pdump ypix.nst.1 sharpness,chi yes | graph
+
+        ... plot chi versus sharpness, the stars should cluster around
+            sharpness = 0.0 and chi = 1.0, note that the frame does
+            not have a lot of stars
+
+    da> substar dev$ypix default  "" default default
+
+        ... subtract the fitted stars
+
+    da> display ypix.sub.1 2
+
+        ... note that the psf stars subtract reasonably well but other
+            objects which are not stars don't
+.fi
+
+
+2. Rerun the previous example on a section of the test image  using the group
+file and PSF model derived in example 1 for the parent image and writing the
+results in the coordinate system of the parent image.
+
+.nf
+    da> nstar dev$ypix[150:450,150:450] default default default default \
+        wcsin=tv wcspsf=tv wcsout=tv
+
+        ... answer the verify prompts
+
+        ... fit the stars
+
+        ... the results will appear in ypix.nst.2 and ypix.nst.2
+
+    da> display dev$ypix[150:450,150:450] 1
+
+        ... display the image
+
+    da> pdump ypix.nst.2 xc,yc yes | tvmark 1 STDIN col=204
+
+        ... mark the stars
+
+    da> substar dev$ypix ypix.nst.2 "" default default
+
+        ... subtract stars from parent image
+
+        ... the output images is ypix.sub.2
+
+
+    da> substar dev$ypix[150:450,150:450] ypix.nst.2 "" default default  \
+        wcsin=tv wcspsf=tv wcsout=tv
+
+        ... subtract stars from the nstarinput image
+
+        ... the output images is ypix.sub.3
+
+.fi
+
+.ih
+TIME REQUIREMENTS
+.ih
+BUGS
+.ih
+SEE ALSO
+datapars,daopars,nstar,peak
+.endhelp
-- 
cgit 

