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diff --git a/noao/digiphot/daophot/doc/nstar.hlp b/noao/digiphot/daophot/doc/nstar.hlp new file mode 100644 index 00000000..cf7c9936 --- /dev/null +++ b/noao/digiphot/daophot/doc/nstar.hlp @@ -0,0 +1,501 @@ +.help nstar May00 noao.digiphot.daophot +.ih +NAME +nstar -- fit the PSF to groups of stars simultaneously +.ih +USAGE +nstar image groupfile psfimage nstarfile rejfile +.ih +PARAMETERS +.ls image +The list of images containing the stellar groups to be fit. +.le +.ls groupfile +The list of input group photometry files containing the group membership +information and initial estimates for the positions and magnitudes of the stars +to be measured. There must be one group file for every input image. If +groupfile is "default", "dir$default", or a directory specification then NSTAR +will look for a file with the name image.grp.? where ? is the highest existing +version number. Groupfile is usually the output of the DAOPHOT GROUP task, but +may also be the output of the NSTAR and PSF tasks. Groupfile may be an +APPHOT/DAOPHOT text database or an STSDAS binary table. +.le +.ls psfimage +The list of images containing the PSF models computed by the DAOPHOT PSF task. +The number of PSF images must be equal to the number of input images. If +psfimage is "default", "dir$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 nstarfile +The list of output photometry files. There must be one output photometry +file for every input image. If nstarfile is "default", "dir$default", or a +directory specification, then NSTAR will write an output file with the name +image.nst.? where ? is the next available version number. Nstarfile is a text +database if the DAOPHOT package parameter text is "yes", an STSDAS table +database if it is "no". +.le +.ls rejfile +The list of output rejected photometry files containing the positions and sky +values of stars that could not be fit. If rejfile is undefined, results for all +the stars in photfile are written to \fInstarfile\fR, otherwise only the stars +which were successfully fit are written to \fInstarfile\fR and the remainder are +written to rejfile. If rejfile is "default", "dir$default", or a directory +specification NSTAR writes an output file with the name image.nst.? where ? is +the next available version number. Otherwise rejfile must specify one output +photometry file for every input image. Rejfile is a text database if the +DAOPHOT package parameter \fItext\fR is "yes", an STSDAS binary table database +if it is "no". +.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 is used. +.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 \fIgroupfile\fR, of the +psf model \fIpsfimage\fR, and of the output coordinates written to +\fInstarfile\fR and \fIrejfile\fR respectively. 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 NSTAR task parameters? Verify can be set to the DAOPHOT +package parameter value (the default), "yes", or "no". +.le +.ls update = ")_.update" +Update the NSTAR 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 +NSTAR computes x and y centers and magnitudes for all the stellar groups in +\fIgroupfile\fR by fitting the PSF \fIpsfimage\fR to the data in \fIimage\fR. +NSTAR reads the group membership information along with initial estimates of +the centers and magnitudes, and the sky values from the photometry file +\fIgroupfile\fR. \fIGroupfile\fR is usually the output of the DAOPHOT GROUP +task but may also be the output of the PSF and NSTAR tasks. The computed +centers and magnitudes are written to \fInstarfile\fR along with the sky +values, the number of iterations it took to fit the star, the goodness of fit +statistic chi and the image sharpness statistic sharp. If \fIrejfile\fR is +undefined, only stars that are successfully fit are written to \fInstarfile\fR, +and the remainder are written to \fIrejfile\fR. Otherwise all the stars are +written to \fInstarfile\fR. \fINstarfile\fR and \fIrejfile\fR are text +databases if the DAOPHOT package parameter \fItext\fR is "yes", an STSDAS table +database if it is "no". + +The coordinates read from \fIgroupfile\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 \fInstarfile\fR and \fIrejfile\fR are in the +coordinate system defined by \fIwcsout\fR with the exception of the psf model +center coordinates PSFX and PSFY which are always in the logical system of +the input image. 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 caching +is enabled and NSTAR 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 NSTAR +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 close to row order +and 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. + +By default NSTAR computes new centers for all the stars in \fIgroupfile\fR. +However if the DAOPARS parameter \fIrecenter\fR is "no", NSTAR assumes that the +x and y centers in \fIgroupfile\fR are the true centers and does not refit +them. This option can be quite useful in cases where accurate center values +have been derived from an image that has been through some non-linear image +restoration algorithm, but the photometry must be derived from the original +unrestored image. + +By default NSTAR computes the sky value for each group by averaging the +individual sky values in \fIgroupfile\fR for all the stars in the group. If +\fIgroupsky\fR is "no" then the sky value for a particular pixel which +contributes to the group fit is set to the mean of the sky values of only those +stars for which the pixel is within one fitting radius. However if the DAOPARS +parameter \fIfitksy\fR is "yes", then NSTAR computes a new group sky value as +part of the non-linear least-squares fit. Recomputing the sky can significantly +reduce the scatter in the magnitudes in regions where the sky background is +varying rapidly, but users may need to increase \fIfitrad\fR to include more +sky pixels in the fit. Users should experiment cautiously with this option. + +Only pixels within the good data range delimited by the DATAPARS task +parameters \fIdatamin\fR and \fIdatamax\fR are included in the fit. Most users +set \fIdatamin\fR and \fIdatamax\fR so as to exclude pixels outside the +linearity regime of the detector. By default all the data is fit. Users are +advised to determine accurate values for these parameters and set the +appropriate parameters in DATAPARS before beginning any DAOPHOT reductions. + +Only pixels within the fitting radius \fIfitrad\fR / \fIscale\fR are included +in the fit for each star. \fIFitrad\fR is located in the DAOPARS task and +\fIscale\fR is located in the DATAPARS task. Since the non-linear least-squares +fitting algorithm determines three unknowns, the x and y position of the star's + centroid and its brightness, the value of \fIfitrad\fR must be sufficiently +large to include at least three pixels in the fit for each star. To accelerate +the convergence of the non-linear least-squares fitting algorithm pixels within +\fIfitrad\fR are assigned weights which are inversely proportional to the +radial distance of the pixel from the x and y centroid of the star, falling +from a maximum at the centroid to zero at the fitting radius. \fIFitrad\fR must + be sufficiently large to include at least three pixels with non-zero weights +in the fit for each star. Values of \fIfitrad\fR close to the full-width at +half-maxima of the PSF are recommended. In actual fact NSTAR imposes a minimum +number of pixel limit of four. + +NSTAR performs a weighted fit to the PSF. The weight of each pixel is computed +by combining, the radial weighting function described above, with weights +derived from the random errors NSTAR predicts based on the values of the +DATAPARS parameters \fIreadnoise\fR and \fIepadu\fR, and the flat-fielding and +profile interpolation errors specified by the DAOPARS \fIflaterr\fR and +\fIproferr\fR parameters. To obtain optimal fits, users are strongly advised +to determine those parameters accurately and to enter their values in DATAPARS +and DAOPARS before beginning any DAOPHOT reductions. + +For each group of stars to be fit, NSTAR extracts a subraster from \fIimage\fR +which extends approximately \fIpsfrad\fR / \fIscale\fR + 1 pixels wide past +the limiting values of the x and y coordinates of the stars in the group. +\fIPsfrad\fR is the PSF radius specified in the DAOPARS task, and \fIscale\fR +is the image scale specified by the DATAPARS task. \fIPsfrad\fR may be less +than or equal to but can never exceed the value of the image header parameter +"PSFRAD" in \fIpsfimage\fR. \fIPsfrad\fR should always be several pixels larger +than \fIfitrad\fR to permit the x and y centroids to wander during the fitting +process. + +As well as the computed x and y centers and magnitudes, NSTAR outputs the number + of times the PSF fit had to be iterated before reaching convergence. The +minimum number of iterations is four. The maximum number of iteration permitted +is specified by the \fImaxiter\fR parameter in the DAOPARS task. Obviously the +results for stars which have reached the maximum iteration count should be +viewed with suspicion. However since the convergence criteria are quite strict, +(the computed magnitude must change by less than .0005 magnitudes or 0.10 +sigma whichever is larger, and the x and y centroids must change by less than +0.002 pixels from one iteration to the next), even these stars may be +reasonably well measured. It must be emphasized that every star in the group +must individually satisfy the convergence criteria in order for the group to be + considered adequately reduced. + +NSTAR computes a goodness of fit statistic chi which is essentially the ratio +of the observed pixel-to-pixel scatter in the fitting residuals to the expected +scatter. Since the expected scatter is dependent on the DATAPARS task parameters +\fIreadnoise\fR and \fIepadu\fR, and the DAOPARS parameters \fIflaterr\fR and +\fIproferr\fR it is important for these values to be set correctly. A plot of +chi versus magnitude should scatter around unity with little or no trend in +chi with magnitude, except at the bright end where saturation effects may be +present. + +Finally NSTAR computes the statistic sharp which estimates the intrinsic angular +size of the measured object outside the atmosphere. Sharp is roughly defined as +the difference between the square of the width of the object and the square of +the width of PSF. Sharp has values close to zero for single stars, large +positive values for blended doubles and partially resolved galaxies and large +negative values for cosmic rays and blemishes. + +NSTAR implements a highly sophisticated star rejection algorithm. First of all, + any group of stars which is more than a certain size is simply not fit. The +maximum group size is specified by the \fImaxgroup\fR parameter in the DAOPARS +task. Larger groups may run into numerical precision problems during the fits. +Users should exercise care in increasing the \fImaxgroup\fR parameter. If two +stars in a group have centroids separated by a critical distance, currently set +arbitrarily to 0.37 * the FWHM of the stellar core, their photocentric position +and combined magnitude is assigned to the brighter of the two stars, and the +fainter is eliminated. Any star which converges to 12.5 magnitudes greater than + the magnitude of the PSF is considered to be non-existent and eliminated from +the group. + +After iteration 5, if the faintest star in the group has a brightness less than + one sigma above zero, it is eliminated. After iterations 10, if the faintest +star in the group has a brightness less than 1.5 sigma above zero, it is +eliminated. After iterations 15 to 50 or whenever the solutions has converged +whichever comes first, if the faintest star in the group has a brightness less +than 2.0 sigma above zero, it is eliminated. After iterations 5, 10 and 15, +if two stars are separated by more than 0.37 * FWHM and less than 1.0 * FWHM +and if the fainter of the two is more uncertain than 1.0, 1.5 or 2.0 sigma +respectively the fainter one is eliminated. + +Whenever a star is eliminated the iteration counter is backed up by one and +reduction proceeds with a smaller set of stars. Backing up the counter gives +the second least certain star in the group two iterations to settle into a new +fit before its fate is decided. The star rejection algorithm depends upon the +DATAPARS \fIreadnoise\fR and \fIgain\fR parameters and the DAOPARS parameter +\fIflaterr\fR and \fIproferr\fR. Therefore these parameters should be set to +reasonable values before running NSTAR. + +NSTAR operates in a very similar manner to PEAK. However because it fits groups + of stars simultaneously it is much more accurate than PEAK in crowded regions. +The ALLSTAR task also fits groups of stars simultaneously, both grouping the +stars dynamically as well as producing a subtracted image. Essentially it +replaces GROUP, GRPSELECT, NSTAR and SUBSTAR. However the user has little +control over the grouping process and does not know at the end which stars were +actually fit together. NSTAR is the task of choice when a user wants to +maintain rigorous control over the composition of the stellar groups. + +.ih +OUTPUT + +If \fIverbose\fR = yes, a single line is output to the terminal for each star +fit or rejected. Full output is written to \fInstarfile\fR and \fIrejfile\fR. +At the beginning of these two files a header listing the current values of the +parameters is written. For each star fit/rejected the following quantities are +written to the output file. + +.nf + id group xcenter ycenter mag merr msky niter sharpness + chi pier perr +.fi + +Id is the id number of the star and group is its group number. Xcenter and +ycenter are the fitted coordinates in pixels. Mag and merr are the fitted +magnitude and magnitude error respectively. Msky is the individual sky value +for the star. Niter is the number of iterations it took to fit the star and +sharpness and chi are the sharpness and goodness of fit statistic respectively. +Pier and perror are the photometry error code and accompanying error message +respectively. + +.ih +ERRORS + +If no errors occur during the fitting process then pier is 0. Non-zero +values of pier flag the following error conditions. + +.nf + 0 # No error + 1 # The star is in a group too large to fit + 2 # The sky is undefined + 3 # There are too few good pixels to fit the star + 4 # The fit is singular + 5 # The star is too faint + 6 # The star has merged with a brighter star + 7 # The star is off the image +.fi + +.ih +EXAMPLES + +1. Fit the PSF to a list stars in the test image dev$ypix. Good stars for +making the PSF model can be found at (442,410), (348,189), and (379,67). + +.nf + da> datapars.epadu = 14.0 + da> datapars.readnoise = 75.0 + + ... set the gain and readout noise for the detector + + da> daofind dev$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. Run nstar on a section of the input 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$ypix[150:450,150:450] default default default default \ + wcsin=tv wcspsf=tv wcsout=tv + + ... answer the verify prompts + + ... fit the stars + + ... the results will appear in ypix.nst.2 and ypix.nrj.2 + + da> display dev$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 nstar input image + + ... the output images is ypix.sub.3 + +.fi + + + +3. Run nstar exactly as in example 1 but submit the task to the background. +Turn off verify and verbose. + +.nf + da> nstar dev$ypix default default default default verbose- \ + verify- & + + ... the results will appear in ypix.nst.3 and ypix.nrj.3 +.fi + + +.ih +TIME REQUIREMENTS +.ih +BUGS +.ih +SEE ALSO +datapars,daopars,peak,allstar +.endhelp |