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phot noao.digiphot.apphot


NAME · USAGE · PARAMETERS · DESCRIPTION · CURSOR_COMMANDS · ALGORITHMS
OUTPUT · ERRORS · EXAMPLES · BUGS · SEE_ALSO

NAME

phot -- do aperture photometry on a list of stars

USAGE

phot image

PARAMETERS

image
The list of images containing the objects to be measured.
skyfile = ""
The list of text files containing the sky values, of the measured objects, one object per line with x, y, the sky value, sky sigma, sky skew, number of sky pixels and number of rejected sky pixels in columns one to seven respectively. The number of sky files must be zero, one, or equal to the number of input images. A skyfile value is only requested if fitskypars.salgorithm = "file" and if PHOT is run non-interactively.
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$default", or a directory specification then a coords file name of the form dir$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.
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 "mag" 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.
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 output . The user should be aware that this can be a time consuming operation.
datapars = ""
The name of the file containing the data dependent parameters. The critical parameters fwhmpsf and sigma are located here. If datapars is undefined then the default parameter set in uparm directory is used.
centerpars = ""
The name of the file containing the centering parameters. The critical parameters calgorithm and cbox are located here. If centerpars is undefined then the default parameter set in uparm directory is used.
fitskypars = ""
The name of the text file containing the sky fitting parameters. The critical parameters salgorithm , annulus , and dannulus are located here. If fitskypars is undefined then the default parameter set in uparm directory is used.
photpars = ""
The name of the file containing the photometry parameters. The critical parameter apertures is located here. If photpars is undefined then the default parameter set in uparm directory is used.
interactive = yes
Run the task interactively ?
radplots = no
If radplots 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.
icommands = ""
The image display cursor or image cursor command file.
gcommands = ""
The graphics cursor or graphics cursor command file.
wcsin = ")_.wcsin", wcsout = ")_.wcsout"
The coordinate system of the input coordinates read from coords and of the output coordinates written to output 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.
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).
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.
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.
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.
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.
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.
verify = ")_.verify"
Verify the critical parameters in non-interactive mode. Verify may be set to the value of the apphot package parameter (the default), "yes", or "no".
update = ")_.update"
Automatically update the algorithm parameters in non-interactive mode if verify is "yes". Update may be set to the value of the apphot package parameter (the default), "yes", or "no".
verbose = ")_.verbose"
Print results on the screen in non-interactive mode? Verbose may be set to the value of the apphot package parameter (the default), "yes", or "no".
graphics = ")_.graphics"
The default graphics device. Graphics may be set to the value of the apphot package parameter (the default), "yes", or "no".
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 PHOT to work interactively from a contour plot.

DESCRIPTION

PHOT computes accurate centers, sky values, and magnitudes for a list of objects in the IRAF image image whose coordinates are read from the text file coords or the image display cursor, and writes the computed x and y coordinates, sky values, and magnitudes to the text file output .

The coordinates read from coords are assumed to be in coordinate system defined by wcsin . 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 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 output are in the coordinate system defined by wcsout . 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 mosaic pieces with coordinates in the parent image must use the "tv" or "physical" coordinate systems.

In interactive mode the user may either define the list of objects to be measured interactively with the image curspr or create an object list prior to running PHOT. In either case the user may adjust the centering, sky fitting, and photometry algorithm parameters until a satisfactory fit is achieved and optionally store the final results in output . In batch mode the initial positions are read from the text file coords or the image cursor parameter icommands can be redirected to a text file containing a list of cursor commands. In batch mode the current set of algorithm parameters is used.

If cache 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 PHOT 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 PHOT 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.

PHOT computes accurate centers for each object using the centering parameters defined in centerpars , computes an accurate sky value for each object using the sky fitting parameters defined in fitskypars , and computes magnitudes using the photometry parameters defined in photpars . The image data characteristics of the data are specified in datapars .

CURSOR COMMANDS

The following list of cursor commands are currently available.

	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
c	Fit center for current star
t	Fit sky around the cursor
a	Average sky values fit around several cursor positions
s	Fit sky around current centered star
p	Do photometry for current star, using current sky
o	Do photometry for current star, using current sky, output results
f	Do photometry for current star
spbar	Do photometry for current star, output results
m	Move to next star in coordinate list
n	Do photometry for next star in coordinate list, output results
l	Do photometry for remaining stars in coordinate list, output results
e	Print error messages
r	Rewind coordinate list
q	Exit task


Photometry parameters are listed or set with the following commands.

	Colon commands

:show	[data/center/sky/phot]	List the parameters
:m [n]	Move to next [nth] star in coordinate list
:n [n]	Do photometry for 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]		Integration time (time units)
:xairmass	[value]		Airmass value (number)
:ifilter	[string]	Filter id string
:otime		[string]	Time of observation (time units)

# Centering algorithm parameters

:calgorithm	[string]	Centering algorithm
:cbox		[value]		Width of the 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 S/N ratio 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)

# 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)
:binsize	[value]		Resolution of sky histogram (sky sigma)
:smooth		[y/n]		Lucy smooth the sky histogram
:sloclip	[value]	        Low-side clipping factor in percent
:shiclip	[value]	        High-side clipping factor in percent
:smaxiter	[value]		Maximum number of iterations
: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)

# Photometry parameters

:apertures	[string]	List of aperture radii (scale units)
:zmag		[value]		Zero point of magnitude scale

# Plotting and marking parameters

:mkcenter	[y/n]		Mark computed centers on display
:mksky		[y/n]		Mark the sky annuli on the display
:mkapert	[y/n]		Mark apertures on the display
:radplot	[y/n]		Plot radial profile of object


                    Interactive Phot Setup Menu

	v	 Mark and verify the critical parameters (f,s,c,a,d,r)

	f	 Mark and verify the full-width half-maximum of 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 width
	n	 Mark and verify the cleaning radius
	p	 Mark and verify the clipping radius

	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

	r	 Mark and verify the aperture radii

ALGORITHMS

A brief description of the data dependent parameters, centering algorithms, sky fitting algorithms and photometry parameters can be found in the online help pages for the DATAPARS, CENTERPARS, FITSKYPARS, and PHOTPARS tasks.

OUTPUT

In interactive mode the following quantities are printed on the standard output as each object is measured. Err is a simple string indicating whether or not an error was detected in the centering algorithm, the sky fitting algorithm or the photometry algorithm. Mag are the magnitudes in apertures 1 through N respectively and xcenter, ycenter and msky are the x and y centers and the sky value respectively.

    image  xcenter  ycenter  msky  mag[1 ... N]  error

In both interactive and batch mode full output is written to the text file output . 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

	image  xinit  yinit  id  coords  lid
	   xcenter  ycenter  xshift  yshift  xerr  yerr  cier error
	   msky  stdev  sskew  nsky  nsrej  sier  serror
	   itime  xairmass  ifilter  otime
	   rapert  sum  area  flux mag  merr  pier  perr

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 cerror are the centering algorithm 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.

	xshift = xcenter - xinit
	yshift = ycenter - yinit

Sier and serror are the sky fitting error code and accompanying error message respectively. Msky, stdev and sskew are the best estimate of the sky value (per pixel), standard deviation and skew respectively. Nsky and nsrej are the number of sky pixels and the number of sky pixels rejected respectively.

Itime is the exposure time, xairmass is self-evident, ifilter is an id string identifying the filter used in the observations, and otime is a string containing the time of the observation in whatever units the user has set up.

Rapert, sum, area, and flux are the radius of the aperture in scale units, the total number of counts including sky in the aperture, the area of the aperture in square pixels, and the total number of counts excluding sky in the aperture. Mag and merr are the magnitude and error in the magnitude in the aperture (see below).

	flux = sum - area * msky
	 mag = zmag - 2.5 * log10 (flux) + 2.5 * log10 (itime)
	merr = 1.0857 * error / flux
       error = sqrt (flux / epadu + area * stdev**2 +
               area**2 * stdev**2 / nsky)

Pier and perror are photometry error code and accompanying error message.

In interactive mode a radial profile of each measured object is plotted in the graphics window if radplots is "yes".

In interactive and batchmode a radial profile plot is written to plotfile if it is defined each time the result of an object measurement is written to output .

ERRORS

If the object centering was error free then the field cier will be zero. Non-zero values of cier flag the following error conditions.

	0        # No error
	101      # The centering box is off 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

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.

	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 parameter are non-physical

If no error occursor during the measurement of the magnitudes then pier is 0. Non-zero values of pier flag the following error conditions.

	0         # No error
	301       # The aperture is off the image
	302       # The aperture is partially off the image
	303       # The sky value is undefined
	305       # There is bad data in the aperture

EXAMPLES

1. Compute the magnitudes 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.

	ap> display dev$ypix 1 fi+

	... display the image

	ap> phot 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 fwhmpsf, centering radius, inner and outer sky annuli,
	    photometry apertures, 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.mag.1

2. Compute the magnitudes 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.

        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> phot 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 fwhmpsf, centering radius, inner and outer sky annuli,
	    apertures, 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.mag.2 

        ap> set stdimcur = <default>

        ... reset stdimcur to its previous value

3. Setup and run PHOT interactively on a list of objects temporarily overriding the fwhmpsf, sigma, cbox, annulus, dannulus, and apertures parameters determined in examples 1 or 2.

        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> phot dev$ypix cbox=7.0 annulus=12.0 dannulus=5.0 \
           apertures="3.0,5.0" 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.mag.3 ...

4. Display and measure some stars in an image section and write the output coordinates in the coordinate system of the parent image.

        ap> display dev$ypix[150:450,150:450] 1

        ... display the image section

        ap> phot 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.mag.4

        ap> pdump ypix.mag.4 xc,yc yes | tvmark 1 STDIN col=204

5. Run PHOT in batch mode using the coordinate file and the previously saved parameters. Verify the critical parameters.

        ap> phot dev$ypix coords=ypix.coo.1 verify+ inter-

        ... output will appear in ypix.mag.5 ...

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.

        ap> display dev$ypix 1

        ap> rimcursor wcs=world > radec.coo

        ... move to selected stars and type any key

        ... type ^Z to quit

        ap> phot dev$ypix coords=radec.coo wcsin=world verify- inter- &

        ... output will appear in ypix.mag.6

        ap> pdump ypix.mag.6 xc,yc yes | tvmark 1 STDIN col=204

        ... mark the stars on the display

7. Run PHOT interactively without using the image display.

        ap> show stdimcur

        ... record the default value of stdimcur

        ap> set stdimcur = text

        ... set the image cursor to the standard input

        ap> phot 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, centering radius, inner and outer sky annuli,
	    apertures, 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.mag.7

        ap> set stdimcur = <default>

        ... reset the value of stdimcur

8. Use a image cursor command file to drive the PHOT task. The cursor command file shown below sets the cbox, annulus, dannulus, and apertures parameters computes the centers, sky values, and magnitudes for 3 stars, updates the parameter files, and quits the task.

        ap> type cmdfile
        : cbox 9.0
        : annulus 12.0
        : dannulus 5.0
        : apertures 5.0
        442 410 101 \040
        349 188 101 \040
        225 131 101 \040
        w
        q

        ap> phot dev$ypix icommands=cmdfile  verify-

        ... full output will appear in ypix.mag.8

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 centerpars mkcenter switch to "yes", the fitskypars mksky switch to"yes", or the photpars mkapert switch to "yes". It may be necessary to run gflush and to redisplay the image to get the overlays position correctly.

SEE ALSO

datapars, centerpars, fitskypars, photpars, qphot, wphot, polyphot


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