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diff --git a/noao/digiphot/apphot/doc/fitsky.hlp b/noao/digiphot/apphot/doc/fitsky.hlp new file mode 100644 index 00000000..5fc07de9 --- /dev/null +++ b/noao/digiphot/apphot/doc/fitsky.hlp @@ -0,0 +1,632 @@ +.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 |