IRAF help page for package noao.digiphot.daophot, program phot

• image
• coords
• output
• skyfile =
• plotfile =
• datapars =
• centerpars =
• fitskypars =
• photpars =
• interactive = no
• radplots = no
• verify = )_.verify
• verbose = )_.verbose
• update = )_.update
• graphics = stdgraph
• display = stdimage
• icommands =
• gcommands =

phot image coords output

image

coords

output

skyfile =

plotfile =

datapars =

centerpars =

fitskypars =

photpars =

interactive = no

radplots = no

verify = )_.verify

verbose = )_.verbose

update = )_.update

graphics = stdgraph

display = stdimage

icommands =

gcommands =

PHOT computes accurate centers, sky values, and magnitudes for a list of objects in the IRAF image image whose coordinates are listed in the text file coords or are marked on the image display interactively with the image cursor, and writes the computed x and y coordinates, sky values and magnitudes to the text file output. In interactive mode the user may either define the list of objects interactively or create an object list prior to entering PHOT. In either case the user may adjust the centering, sky fitting and photometry parameters until a satisfactory parameter set is achieved and optionally update the current parameter set. In non-interactive 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 coordinates and/or cursor commands.

PHOT computes accurate centers for each object using the centering parameters defined in the CENTERPARS task, computes an accurate sky value for each object using the sky fitting parameters defined in the FITSKYPARS task and computes magnitudes using the photometry parameters defined in the PHOTPARS task. The noise characteristics of the data are defined in the DATAPARS task.

By default PHOT executed from within DAOPHOT does NOT center the stars. This is because, in most cases, the coordinate list is generated by the DAOFIND task which has already computed accurate centers for the stars, Recentering would consume additional execution time, for no significant gain in accuracy. However in those cases in which the stars are selected interactively with the image cursor it MAY be desirable to center the stars before computing magnitudes by setting the CENTERPARS task parameter calgorithm = "centroid". Although this is not strictly necessary as the PSF fitting tasks PEAK, NSTAR and ALLSTAR all compute new centers, it does mean that the initial magnitudes fed to these tasks will be more accurate.

PHOT from within DAOPHOT uses the default sky fitting algorithm "mode". This algorithm which uses the mean, and median to estimate the value that the sky would have if the star of interest wasn't there, is in most cases the one which will give reasonable results in crowded fields in an automated way. Users interested in reducing small stellar groups should realizes that they can fix the sky by setting the FITSKYPARS parameter salgorithm to "constant" and supplying a value, or they can set the sky interactively using the "radplot" or "histplot" options. Users with rapidly varying sky backgrounds may wish to explore the "median" sky fitting algorithm which can be more stable than the "mode" algorithm against bimodal sky histograms. Users with very few counts in their data or with quantized data where the standard deviation is small with respect to the quantization level may wish to explore the "mean", and "centroid" sky fitting algorithms.

The magnitudes themselves are computed using fractional pixel integration of the counts within the photometry apertures, a magnitude scale set by the value of the magnitude zero point stored in the PHOTPARS task parameter zmag, and the exposure time stored in the image header keyword specified by the DATAPARS tasks exptime or the exposure time specified by the DATAPARS keyword itime.

The following list of cursor commands are currently available.

	Interactive Keystroke Commands
?	Print help
:	Colon commands
v	Verify critical parameters
w	Save current parameters
d	Plot radial profile of current star
i	Set parameters interactively using current star
c	Fit center for current star
t	Fit sky around cursor
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]	Measure 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
The following commands are available from inside the interactive setup menu.
 
                    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

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 parameters. A full description of the algorithms can be found in the document Specifications for the Apphot Package.

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  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 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 sky value, 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 a string identifying the filter, and otime is a string identifying the time of observation.

Rapert, sum, and area are the radius of the aperture in scale units, the total number of counts including sky in the aperture and the area of the aperture in square pixels. 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 * err / flux
         err = sqrt (flux / epadu + area * stdev**2 +
               area**2 * stdev**2 / nsky)

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

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 occurs 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
	 304      # There is bad data in the aperture

1. Run PHOT on the image n7790 using the default setup.

	da> phot n7790 default default
	... answer the verify prompts
	... the results will appear in n7790.mag.1

2. Setup the PHOT task parameters interactively in preparation for a subsequent batch run with a DAOFIND output file. Use the image display, the interactive setup menu defined by the i key command and a radial profile plot. Save the computed parameters.

	da> set stdimcur = stdimage
	... define the image cursor
	da> display n2264 1 fi+
	... display the image
	da> phot n2264 "" "default" calgorithm="centroid"
	... type ? to get help text on the screen
	... move the image cursor to a star
	... type i to enter the interactive setup menu
	... enter maximum radius in pixels of the radial profile
	... set the fwhmpsf, centering radius, inner and outer sky annuli,
	    apertures, and sigma using the graphics cursor and the
            stellar radial profile plot
	... typing  leaves everything at the default value
	... type the w key to save the parameters in the parameter files
	... type the v key to verify the parameters
	... type q to quit the program
	da> phot n2264 n2264.coo.1 "default" 
	... run phot on the output of DAOFIND
	... verify the parameters by answering the questions
	... the output will appear in n2264.mag.1

3. Compute the magnitudes for a few stars in N4147 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. Since there is no input coordinate file containing accurate centers from DAOFIND the centering algorithm must be turned back on.

	ap> set stdimcur = stdimage
	... define the image cursor
	ap> display n4147 1 fi+
	... display the image
	ap> phot n4147 "" "default" calgorithm="centroid"
	... type ? to get help text on the screen
	... move the image cursor to a star
	... type i to enter the interactive setup menu
	... enter maximum radius in pixels of the radial profile
	... set the fwhmpsf, centering radius, inner and outer sky annuli,
	    apertures, and sigma using the graphics cursor and the
            stellar radial profile plot
	... typing  leaves everything at the default value
	... type the w key to save the parameters in the parameter files
	... type the v key to verify the parameters
	... 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
	... the output will appear in n4147.mag.1

4. Compute the magnitudes for a few stars in M92 using the contour plot and the graphics cursor. Setup the task parameters using the interactive setup menu defined by the i key command. Since there is no input coordinate file containing accurate centers from DAOFIND the centering algorithm must be turned back on.

	ap> set stdimcur = stdgraph
	... define the image cursor to be the graphics cursor
	ap> contour m92 >G m92.plot1
	... store the contour plot of m92 in the file m92.plot
	ap> phot m92 "" "default" calgorithm="centroid"  display=stdgraph
	... type :.read m92.plot1 to load the contour plot on the screen
	... move graphics cursor to a star
	... type i to enter the interactive setup menu
	... enter maximum radius in pixels of the radial profile
	... set the fwhmpsf, centering radius, inner and outer sky annuli,
	    apertures, and sigma using the graphics cursor and the
            stellar radial profile plot
	... typing  leaves everything at the default value
	... type the w key to save the parameters in the parameter files
	... type the v key to verify the critical parameters
	... retype :.read m92.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
	... full output will appear in the text file m92.mag.1 

5. Setup and run PHOT interactively on a list of objects, using a contour plot as the image display and the parameters defined and saved in example 2.

	ap> set stdimcur = stdgraph
	... define the image cursor to be the graphics cursor
	ap> contour m92
	... adjust plot parameters until the contour plot is satisfactory
	ap> =gcur
	... enter cursor mode
	... type :.write m92.plot2 to save the plot in a metacode file
	... type any key to quit cursor mode
	ap> daofind m92 
	... verify the critical parameters by answering the prompts
	... the output will appear in the text file m92.coo.1
	ap> phot m92 m92.coo.1 "default" display=stdgraph
	... type :.read m92.plot2 to read in the contour plot
	... move the graphics cursor to the stars and tap space bar
				or
	... use n, :n, and/or commands to measure objects in the
	    coordinate list
	... a one line summary of results will appear on the standard output
	    for each star measured
	... the output will appear in m92.mag.2 ...

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

	ap> phot m92 m92.coo.1 "default" verify+
	... the user will be asked to verify each critical parameter
	    a simple return will preserve the existing value
	... output will appear in m92.mag.3

7. Run PHOT in batch mode using the coordinate file and the previously saved parameters. The task can be submitted to the background by appending an ampersand to the command line listed below. Be sure to turn off the verify switch in that case.

	ap> phot m92 m92.coo.1 "default" verify-
	... output will appear in m92.mag.4

8. Run PHOT interactively on the sun workstation using the imtool window, a coordinate list, and the current set of parameters. This example assumes Since the input coordinate file does not contain accurate centers from DAOFIND the centering algorithm must be turned back on.

	ap> set stdimcur = text
	... set the image cursor to the standard input
	ap> display m92 1
	... display the image in the imtool window and put the mouse
	    in the imtool window
	ap> phot m92 m92.coo.2 "default" calgorithm="centroid"
	... type :m 3 to set the coordinates to the third star
	    in the list
	... type i to enter the interactive setup menu
	... enter the maximum radius in pixels of the radial profile
	... set the fwhmpsf, centering radius, inner and outer sky annulus
	    radii, photometry apertures, and sigma using the graphics cursor
	    and the stellar radial profile plot
	... typing  leaves everything at the 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
	... full output will appear in the text file m92.mag.5 

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 currently disabled. The TVMARK task in the proto package can be used to draw simple marks on the display. All the DAOPHOT marking commands will however function if a contour plot is used in lieu of the image display.

Users should not be confused by the normally enabled markcur option in the SUN/IMTOOL setup window. This feature is under the control of the IMTOOL window and the DAOPHOT package has no control over it.

datapars, centerpars, fitskypars, photpars,