guide: Guide to using xdimsum with the xmosaic task
Package: xdimsum
XDIMSUM is a package for creating accurate sky subtracted images from sets of dithered observations. While the observations need not be in the infrared, the dominance of the variable sky background in infrared data requires the dithering and recombination of many short carefully sky subtracted exposures to produce deep images. Hence the package is called "Experimental Deep Infrared Mosaicing Software" or XDIMSUM.
There's no published reference. Generally people footnote it in the text and say something like:
DIMSUM is the Deep Infrared Mosaicing Software package developed by
Peter Eisenhardt, Mark Dickinson, Adam Stanford, and John Ward, and is
available via ftp from ftp://iraf.noao.edu/iraf/extern/xdimsum/.
XDIMSUM is a variant of the DIMSUM package developed by P. Eisenhardt, M. Dickensen, S.A. Stanford, and J. Ward. F. Valdes (IRAF group) added FITS image format support, wrote the tutorial task demos, wrote the original version of this document, and repackaged DIMSUM for distribution as an IRAF external package. More recently L. Davis (IRAF group) rewrote the major DIMSUM scripts to improve their clarity, robustness, and efficiency, added several new tasks for computing relative offsets, and wrote help pages for all the DIMSUM tasks. This new version of DIMSUM uses the same default algorithms as the original DIMSUM but has diverged sufficiently from the original that it has been renamed XDIMSUM.
XDIMSUM is being made available to the community as an external package in the hope that some of the enhancements may prove useful to others. Users should direct XDIMSUM installation questions, bug reports, questions about technical details, and comments and suggestions to the the IRAF group (iraf@noao.edu) not the original authors.
The main body of this document is a guide to the XDIMSUM xmosaic task which executes all the major XDIMSUM processing steps in turn. These processing steps are outlined in Section 2. Each major processing step is executed by one or more XDIMSUM tasks. By setting the xmosaic processing switches appropriately users can use xmosaic to perform any combination of these steps. The input data required by XDIMSUM and and the output data produced by it are described in Section 3. A detailed example is provided in Section 4.
The xmosaic task and most of the XDIMSUM subtasks are CL scripts. Users are encouraged to examine the scripts in orer to gain an understanding of the xmosaic algorithms and default parameter settings. The script source is located in the logical directory xdimsum$src and its subdirectories. Older versions of the current scripts and obsolete scripts are located in the logical directory xdimsum$src/obsolete.
This section describes the processing steps performed by the main XDIMSUM processing task xmosaic. These processing steps divide logically into two groups the first pass step and the mask pass step. Both steps perform similar operations and produce a sky subtracted, bad pixel corrected, cosmic ray corrected, registered, and combined image and exposure map.
The first pass step produces a good first estimate of the true combined image and exposure map by sky subtracting, bad pixel correcting, and cosmic ray correcting the input individual images, and creating a combined image fro the corrected input images. The combined image goes deeper than the individual images and is used to create an object mask which defines the location, size, and shape of all the objects in the combined image. The object mask is split or deregistered into a set of individual input image object masks. The mask pass step repeats all the first pass step but uses the object masks to improve the sky subtraction, cosmic ray correction, and image combining steps to produce a more accurate and if desired higher resolution version of the combined image.
If first and mask pass processing steps can be executed separately by running the xfirstpass and xmaskpass tasks in sequence, which is exactly what the xmosaic task itself does.
The first pass processing steps are: sky subtraction, bad pixel correction, cosmic ray correction, bad pixel mask updating, and image registration. The required input data are a list of dithered input images, a bad pixel, mask, and optionally a list of image offsets and scaling factors. If no offset list is provided the offsets the user must determine the offsets interactively.
If the fp_xslm switch is yes the xslm task produces a sky subtracted image for each images by computing its sky image from a set of neighboring images and subtracting this sky image from the input image.
The scaling factor for each input image is computed using an nsigrej sigma iterated rejection about the mean of the pixels in the image section defined by statsec. The number of iterations must be less than or equal to maxiter. The scaling factor is the reciprocal of the median of the unrejected pixels and is stored in the input and sky subtracted image header KEYWORD "SKYMED".
For each image in the input image list nmean neighboring images in the list are selected, scaled, and combined to form the sky image. Except at the ends of the list there is usually an equal number of images before and after the image to be sky subtracted. There must be at least nskymin images for sky subtraction to be performed. At each pixel nreject low and high pixels in the scaled images are rejected and the average of the remainder becomes the sky value for that pixel. The sky values are subtracted from the input image to create a sky subtracted image.
If the fp_maskfix switch is yes the maskfix task removes known bad pixels from the sky subtracted images. The bad pixel mask bpmask is used to identify and replace the bad pixels by interpolation. The bad pixel mask is an image containing 0's in bad pixel regions and 1's elsewhere.
If the fp_xzap switch is yes cosmic rays are removed from the sky subtracted images using the xzap task if newxzap is no, or the xnzap task if it is yes.
Xzap creates an internal object mask from the sky subtracted image data which is used to locate the strongest objects. The cosmic rays are detected with a threshold algorithm applied to the ratio of the original input image to the median filtered input image. Only pixels outside the internal object mask are considered to be cosmic ray candidates. The detected cosmic rays are replaced by the local median and a cosmic ray mask is prodiced which records the location of the cosmic rays.
Xnzap is a script task which calls the compiled task xcraverage task. Xcraverage detects and removes cosmic rays using a moving average combined with a central and deviant pixel rejection filter, a local sky estimate equal to the running median of the pixels around the averaging filter box, and a local sky sigma estimated by dividing the image into blocks and determining the percentile points of the pixels in the box. The cosmic rays are replaced by the local average and a cosmic ray mask is produced to record the location of the cosmic rays.
Cosmic ray masks contain 1's at the locations of detected cosmic rays and 0's elsewhere.
If the fp_badpixupdate switch is yes the badpixupdate task and the cosmic ray masks are used to update the bad pixel mask. Bad pixel mask pixels are updated, i.e. flagged as bad, if they are detected as cosmic rays in more than two images.
The shift list shiftlist defines the relative offsets between the individual input images. If the fp_mkshifts switch is yes the xdshifts task and the image display are used to create it interactively. For this method to work there must be at least one object common to all the images. Rough offsets are estimated by displaying each image and prompting the user to mark and measure the position of a reference object common to all the images. True offsets are computed by prompting the user to measure and mark a set of registration objects in the reference image reference, applying the initial offsets, centroiding on the registration objects in each sky subtracted image, and computing final shifts relative to the reference image.
The final shift list is a file containing four columns. These columns contain the image name, the pixel shifts in x and y, and a weight value which by default is 1.0. If the weight for an image is < 0, that image is excluded from the final mosaic.
If the fp_xnregistar switch is yes the xnregistar task is used to combine the images. The input sky subtracted, bad pixel corrected, and cosmic ray corrected images are shifted, scaled, combined, and reoriented to produce the first guess combined image and exposure map. The corrected input images are shifted by integer pixel amounts if fractional is no, otherwise they are shifted by the full fractional pixel offset.
If the mp_mkmask switch is yes the mkmask task is used to create two object masks from the first pass combined image and exposure map. The first mask sets the detection threshold to mp_nsigcrmsk and identifies only the brighter parts of the objects. This mask is used to check that the cores of those objects in the individual images are not identified as cosmic rays. The second mask sets the threshold to mp_nsigobjmsk and identifies extended object regions. This mask is used to improve the sky subtraction step.
The combined image masks are made from the first pass combined image as follows. First the combined image is divided by the square root of the exposure map to normalize for variations in the sky noise due to varying exposure times in each pixel. The sky RMS is computed using iterative sigma rejection and a recommended threshold value in terms of this RMS is determined. If mp_chkmasks is yes the uniform RMS image is displayed, the user examines it with the imexamine task, and determine a suitable threshold interactively. An algorithm which tracks and threshold detects above the sky is used to create an object mask containing 1's in object regions and 0's elsewhere.
If the mp_maskdereg switch is yes the maskdereg task and the sections file sections created by xnregistar during the first pass, are used to create object masks for the individual input images.
If the mp_xslm switch is yes the sky subtraction step is repeated using the xslm task and the individual object masks. The object masks are used to, reject object pixels from the scaling factor computation if use_omask is yes, and to reject object pixels from the sky image computation.
If the mp_maskfix switch the bad pixel mask fixing step is repeated using the maskfix task and the bad pixel mask. However in the mask step it is probable that the bad pixel mask is different from the one used in the first pass having been updated in the first pass step.
If the mp_xzap switch is the cosmic ray removal step is repeated using either the xzap or xnzap tasks. However in the mask step the object core mask created from the first pass combined image is used to prevent cosmic rays from being detected in the object core regions.
If the mp_badpixupdate switch is set the bad pixel mask updating step is removed using the badpixupdate task, the bad pixel mask, and the cosmic ray masks.
If the mp_xnregistar switch is yes then the images combining step is repeated using the xnregistar task. The final sky subtracted, bad pixel corrected, and cosmic ray corrected images are shifted, scaled, combined, and reoriented to create the final mosaic. In this second, more careful, pass subpixel shifts are used by default. The default algorithm block replicates each image by a factor of mag and shifts the images to a resolution of 1/mag of a pixel. The final mosaic image from the mask pass is, therefore, approximately mag times larger in each dimension with mag * mag times more pixels than the first pass image. As before an exposure map with the same resolution is also created.
The individual images may be of any type supported by IRAF, e.g. ".fits" or ".imh" but are assumed to be of the same size. They should have been dark and flat field corrected prior to entering xdimsum.
The input bad pixel file is an IRAF mask or ".pl" image consisting of 1's and 0's where the 0's define the bad pixels. It is assumed to be the same size as the input images and to be the same for all the input images. The bad pixel mask may be updated during the course of the reductions by the badpixupdate task.
The output corrected images have been sky subtracted by the xslm task, bad pixel corrected by the maskfix task, and cosmic ray corrected by the xzap or xnzap tasks. These images should be free of defects with mean background values around 0.0.
The output cosmic ray masks are IRAF pixel mask, i.e. ".pl" images produced by the xzap or xnzap tasks. Cosmic ray masks consist of 1's in cosmic ray regions and 0's elsewhere.
The output shifts file contains the image name, x and y shifts relative to the reference image, and weight required to combine the individual corrected images into a single output image and exposure map. The shifts file can be produced with the xdshifts task.
The output objects masks are IRAF pixel masks, i.e. ".pl" images produced by the mkmask and maskdereg tasks from the first pass combined image and exposure map. They are of two kinds: the inverse object core masks used by the xzap or xnzap tasks to unzap cosmic rays in object cores, and the object masks used by the xslm task to improve the sky subtraction. The object masks consist of 1's in object regions and 0's elsewhere. The inverse object masks are the reverse.
The output holes masks are IRAF pixel masks, i.e. ".pl" images produced by the sky subtraction task xslm during the mask pass. They define regions in the individual images where the sky subtraction is undefined. Holes masks consist of 0's in undefined regions and 1's elsewhere.
The first and maskpass steps each produced a combined image and an associated exposure map.
The following example uses artificial data created by the demos task to illustrate the main features of the xmosaic task.
To load the package type xdimsum.
cl> xdimsum
badpixupdate maskfix xdshifts xmosaic xslm
demos maskstat xfirstpass xmshifts xzap
iterstat mkmask xfshifts xnregistar
makemask orient xlist xnzap
maskdereg sigmanorm xmaskpass xrshifts
The main tasks are demos and xmosaic. The remaining tasks are called directly by xmosaic.
The artificial demonstration data is created by the demos task. By default the image format is ".imh". The the IRAF environment variable imdir which defines where the ".pix" pixel files are stored must be set before running xmosaic, as shown below.
cl> set imdir = "HDR$pixels/
In this the pixel file directory is the subdirectory of the current directory called pixels.
To use FITS images set the IRAF environment variable as follows
cl> set imtype = fits
cl> flpr
Now run the demos script and examine the data directory.
xd> demos mkxdimsum
Creating master field (please be patient) ...
Creating truth image demo_truth ...
Creating XDIMSUM bad pixel mask demo.pl ...
Creating image list demo.list ...
Creating XDIMSUM shift list demo.slist ...
Creating imcombine offset file demo.imc ...
Creating demo01 ...
Creating demo02 ...
Creating demo03 ...
Creating demo04 ...
Creating demo05 ...
Creating demo06 ...
Creating demo07 ...
Creating demo08 ...
Creating demo09 ...
Creating demo10 ...
Creating demo11 ...
Creating demo12 ...
Creating demo13 ...
Creating demo14 ...
Creating demo15 ...
Creating demo16 ...
Creating demo17 ...
Creating demo18 ...
Creating demo19 ...
Creating demo20 ...
Creating demo21 ...
Creating demo22 ...
Creating demo23 ...
Creating demo24 ...
Creating demo25 ...
xd> dir
demo.imc demo04.imh demo11.imh demo18.imh demo25.imh
demo.list demo05.imh demo12.imh demo19.imh demo_truth.imh
demo.pl demo06.imh demo13.imh demo20.imh pixels
demo.slist demo07.imh demo14.imh demo21.imh
demo01.imh demo08.imh demo15.imh demo22.imh
demo02.imh demo09.imh demo16.imh demo23.imh
demo03.imh demo10.imh demo17.imh demo24.imh
The files demo??.imh are 25 dithered 100x100 images with low S/N "taken" in an approximately 5x5 pattern. The dither is small so there are large overlaps between adjacent images. Each image has a bad column and a few bad pixels. The bad pixel mask is in the file demo.pl. Each image also contains a few cosmic rays. The input image list is in the file demo.list. The file demo.slist contains the relative offsets and weight for each sky subtracted input image. The image demo_truth.imh is the image from which the dithered images were extracted. The goal of xdimsum is to come as close to reproducing this image as possible.
Set up the xmosaic task parameters as shown below using the eparam task. Note that all the processing options are set to "yes" and all the interactive switches are enabled. Because all the interactive processing options are enabled the image display window must be open before xmosaic is started.
xd> unlearn xmosaic
xd> epar xmosaic
I R A F
Image Reduction and Analysis Facility
PACKAGE = xdimsum
TASK = xmosaic
inlist = @demo.list The list of input images
referenc= demo13 The reference image in input image list
output = mosaic Root name for output combined images
expmap = .exp Root name for output exposure map image or suffix
(statsec= ) The image section for computing sky stats
(nsigrej= 5.) The nsigma rejection for computing sky stats
(maxiter= 10) The maximum number of iterations fo computing sk
(fp_xslm= yes) Do the first pass sky subtraction step ?
(mp_xslm= yes) Do the mask pass sky subtraction step ?
(mp_useo= yes) Use object mask to compute sky statistics ?
(sslist = .sub) The output sky-subtracted images or suffix
(hmasks = .hom) The output holes masks or suffix
(forcesc= yes) Force recalculation of image medians ?
(nmean = 6) Number of images to use in sky image
(nreject= 1) Number of pixels for sky image minmax reject
(nskymin= 3) Minimum number of image to use for sky image
(fp_mask= yes) Do first pass bad pixel correction step ?
(mp_mask= yes) Do mask pass bad pixel correction step ?
(bpmask = demo.pl) The input pixel mask image
(forcefi= yes) Force bad pixel fixing ?
(fp_xzap= yes) Do first pass cosmic ray correction step ?
(mp_xzap= yes) Do mask pass cosmic ray correction step ?
(crmasks= .crm) The output cosmic ray masks or suffix
(newxzap= no) Use new version of xzap ?
(fp_badp= yes) Do first pass bad pixel mask update ?
(mp_badp= yes) Do mask pass bad pixel mask update ?
(fp_mksh= yes) Determine shifts interactively ?
(fp_chks= yes) Check and confirm new shifts ?
(fp_crad= 5.) Centroiding radius in pixels for mkshifts
(fp_maxs= 5.) Maximum centroiding shift in pixels for mkshifts
(fp_xnre= yes) Do first pass image combining step ?
(mp_xnre= yes) Do mask pass image combining step ?
(mp_mag = 4) Magnification factor for mask pass output image
(mp_blk = yes) Use block replication to magnify the image ?
(shiftli= myshiftlist) Input or output shifts file
(section= .corners) The output sections file or suffix
(fractio= no) Use fractional pixel shifts if mag = 1 ?
(pixin = yes) Are input coords in ref object pixels ?
(ab_sens= yes) Is A through B counterclockwise ?
(xscale = 1.) X pixels per A coordinate unit
(yscale = 1.) Y pixels per B coordinate unit
(a2x_ang= 0.) Angle in degrees from A CCW to X
(ncoavg = 1) Number of internal coaverages per frame
(secpexp= 60.) Seconds per unit exposure time
(y2n_ang= 0.) Angle in degrees from Y to N N through E
(rotatio= yes) Is N through E counterclockwise?
(mp_mkma= yes) Create the combined image object mask ?
(omask = .msk) The output combined image mask or suffix
(mp_chkm= yes) Check the object masks ?
(mp_kpch= yes) Keep checking the object masks ?
(mp_stat= ) The combined image section for computing mask st
(mp_nsig= 1.5) The nsigma factor for cosmic ray masking
(mp_nsig= 1.1) The nsigma factor for object masking
(mp_mask= yes) Deregister masks ?
(ocrmask= .ocm) The output cosmic ray unzapping masks or suffix
(objmask= .obm) The output object masks or suffix
(mp_npre= 0) Number of previous object masks to combine
(del_big= no) Delete combined image masks at task termination
(del_sma= no) Delete the individual object masks at task termi
(mode = ql)
The xmosaic parameters have been set to produce the same results as the original DIMSUM package reduce task.
Before starting xmosaic|fR make sure that the hidden fInsigrej, maxiter, bpmask, shiftlist, secpexp, and ncoavg parameters are set correctly.
If either of the fp_mkshifts or mp_chkmasks parameters are set to yes then make sure the image display server is running before starting xmosaic.
To view the xmosaic help page use the phelp task as shown below.
cl> phelp xmosaic
xd> xmosaic
Xmosaic starts by querying for the input image list, the reference image name,
and the root output image and exposure map names as shown below.
The list of input images (@demo.list):
The reference image in input image list (demo13):
Root name for output combined images (mosaic):
Root name for output exposure map image or suffix (.exp):
First some time and data information is printed.
start xmosaic
Wed 16:24:50 29-Nov-2000
start xfirstpass
Wed 16:24:54 29-Nov-2000
Now the xslm task computes the scaling factor for each input image and stores it in the input image header keyword SKYMED.
Begin first pass sky subtraction
Wed 16:24:55 29-Nov-2000
-------Sky subtracting images with xslm--------------
Calculating scaling for demo01
Setting scaling factor to 1 / 4542.815
Calculating scaling for demo02
Setting scaling factor to 1 / 4581.675
Calculating scaling for demo03
Setting scaling factor to 1 / 4622.226
Calculating scaling for demo04
Setting scaling factor to 1 / 4662.35
Calculating scaling for demo05
Setting scaling factor to 1 / 4701.921
Calculating scaling for demo06
Setting scaling factor to 1 / 4742.414
Calculating scaling for demo07
Setting scaling factor to 1 / 4781.861
Calculating scaling for demo08
Setting scaling factor to 1 / 4821.828
Calculating scaling for demo09
Setting scaling factor to 1 / 4862.715
Calculating scaling for demo10
Setting scaling factor to 1 / 4900.551
Calculating scaling for demo11
Setting scaling factor to 1 / 4942.805
Calculating scaling for demo12
Setting scaling factor to 1 / 4983.287
Calculating scaling for demo13
Setting scaling factor to 1 / 5021.519
Calculating scaling for demo14
Setting scaling factor to 1 / 5061.425
Calculating scaling for demo15
Setting scaling factor to 1 / 5101.519
Calculating scaling for demo16
Setting scaling factor to 1 / 5141.901
Calculating scaling for demo17
Setting scaling factor to 1 / 5183.9
Calculating scaling for demo18
Setting scaling factor to 1 / 5221.122
Calculating scaling for demo19
Setting scaling factor to 1 / 5262.929
Calculating scaling for demo20
Setting scaling factor to 1 / 5303.046
Calculating scaling for demo21
Setting scaling factor to 1 / 5342.895
Calculating scaling for demo22
Setting scaling factor to 1 / 5382.554
Calculating scaling for demo23
Setting scaling factor to 1 / 5421.473
Calculating scaling for demo24
Setting scaling factor to 1 / 5460.839
Calculating scaling for demo25
Setting scaling factor to 1 / 5500.626
Once the scaling factors are determined a set of neighboring images and are scaled and combined to produce the sky image for each input image. The sky image is subtracted from the input image to produce the sky subtracted image.
Creating sky subtracted image demo01.sub
Frame 1 Sky frames: start = 1 finish = 4 nreject = 1
Creating sky subtracted image demo02.sub
Frame 2 Sky frames: start = 1 finish = 4 nreject = 1
Creating sky subtracted image demo03.sub
Frame 3 Sky frames: start = 1 finish = 5 nreject = 1
Creating sky subtracted image demo04.sub
Frame 4 Sky frames: start = 1 finish = 7 nreject = 1
Creating sky subtracted image demo05.sub
Frame 5 Sky frames: start = 2 finish = 8 nreject = 1
Creating sky subtracted image demo06.sub
Frame 6 Sky frames: start = 3 finish = 9 nreject = 1
Creating sky subtracted image demo07.sub
Frame 7 Sky frames: start = 4 finish = 10 nreject = 1
Creating sky subtracted image demo08.sub
Frame 8 Sky frames: start = 5 finish = 11 nreject = 1
Creating sky subtracted image demo09.sub
Frame 9 Sky frames: start = 6 finish = 12 nreject = 1
Creating sky subtracted image demo10.sub
Frame 10 Sky frames: start = 7 finish = 13 nreject = 1
Creating sky subtracted image demo11.sub
Frame 11 Sky frames: start = 8 finish = 14 nreject = 1
Creating sky subtracted image demo12.sub
Frame 12 Sky frames: start = 9 finish = 15 nreject = 1
Creating sky subtracted image demo13.sub
Frame 13 Sky frames: start = 10 finish = 16 nreject = 1
Creating sky subtracted image demo14.sub
Frame 14 Sky frames: start = 11 finish = 17 nreject = 1
Creating sky subtracted image demo15.sub
Frame 15 Sky frames: start = 12 finish = 18 nreject = 1
Creating sky subtracted image demo16.sub
Frame 16 Sky frames: start = 13 finish = 19 nreject = 1
Creating sky subtracted image demo17.sub
Frame 17 Sky frames: start = 14 finish = 20 nreject = 1
Creating sky subtracted image demo18.sub
Frame 18 Sky frames: start = 15 finish = 21 nreject = 1
Creating sky subtracted image demo19.sub
Frame 19 Sky frames: start = 16 finish = 22 nreject = 1
Creating sky subtracted image demo20.sub
Frame 20 Sky frames: start = 17 finish = 23 nreject = 1
Creating sky subtracted image demo21.sub
Frame 21 Sky frames: start = 18 finish = 24 nreject = 1
Creating sky subtracted image demo22.sub
Frame 22 Sky frames: start = 19 finish = 25 nreject = 1
Creating sky subtracted image demo23.sub
Frame 23 Sky frames: start = 21 finish = 25 nreject = 1
Creating sky subtracted image demo24.sub
Frame 24 Sky frames: start = 22 finish = 25 nreject = 1
Creating sky subtracted image demo25.sub
Frame 25 Sky frames: start = 22 finish = 25 nreject = 1
The subtracted images are stored in the "*.sub.imh" images.
Next the maskfix task uses the bad pixel mask file demo.pl to interpolate over the bad pixel regions in the sky subtracted images.
Begin first pass bad pixel correction
Wed 16:28:45 29-Nov-2000
-------Correcting bad pixels with maskfix------------
Fixing bad pixels in file demo01.sub using mask demo.pl
Fixing bad pixels in file demo02.sub using mask demo.pl
Fixing bad pixels in file demo03.sub using mask demo.pl
Fixing bad pixels in file demo04.sub using mask demo.pl
Fixing bad pixels in file demo05.sub using mask demo.pl
Fixing bad pixels in file demo06.sub using mask demo.pl
Fixing bad pixels in file demo07.sub using mask demo.pl
Fixing bad pixels in file demo08.sub using mask demo.pl
Fixing bad pixels in file demo09.sub using mask demo.pl
Fixing bad pixels in file demo10.sub using mask demo.pl
Fixing bad pixels in file demo11.sub using mask demo.pl
Fixing bad pixels in file demo12.sub using mask demo.pl
Fixing bad pixels in file demo13.sub using mask demo.pl
Fixing bad pixels in file demo14.sub using mask demo.pl
Fixing bad pixels in file demo15.sub using mask demo.pl
Fixing bad pixels in file demo16.sub using mask demo.pl
Fixing bad pixels in file demo17.sub using mask demo.pl
Fixing bad pixels in file demo18.sub using mask demo.pl
Fixing bad pixels in file demo19.sub using mask demo.pl
Fixing bad pixels in file demo20.sub using mask demo.pl
Fixing bad pixels in file demo21.sub using mask demo.pl
Fixing bad pixels in file demo22.sub using mask demo.pl
Fixing bad pixels in file demo23.sub using mask demo.pl
Fixing bad pixels in file demo24.sub using mask demo.pl
Fixing bad pixels in file demo25.sub using mask demo.pl
Next the xzap task is used to detect and remove cosmic rays from the sky subtracted images.
Begin first pass cosmic ray removal
Wed 16:29:03 29-Nov-2000
-------Zapping cosmic rays using xzap -------------
Creating cosmic ray corrected image demo01.sub
Creating cosmic ray corrected image demo02.sub
Creating cosmic ray corrected image demo03.sub
Creating cosmic ray corrected image demo04.sub
Creating cosmic ray corrected image demo05.sub
Creating cosmic ray corrected image demo06.sub
Creating cosmic ray corrected image demo07.sub
Creating cosmic ray corrected image demo08.sub
Creating cosmic ray corrected image demo09.sub
Creating cosmic ray corrected image demo10.sub
Creating cosmic ray corrected image demo11.sub
Creating cosmic ray corrected image demo12.sub
Creating cosmic ray corrected image demo13.sub
Creating cosmic ray corrected image demo14.sub
Creating cosmic ray corrected image demo15.sub
Creating cosmic ray corrected image demo16.sub
Creating cosmic ray corrected image demo17.sub
Creating cosmic ray corrected image demo18.sub
Creating cosmic ray corrected image demo19.sub
Creating cosmic ray corrected image demo20.sub
Creating cosmic ray corrected image demo21.sub
Creating cosmic ray corrected image demo22.sub
Creating cosmic ray corrected image demo23.sub
Creating cosmic ray corrected image demo24.sub
Creating cosmic ray corrected image demo25.sub
The cosmic ray masks are stored in the files "*.sub.crm.pl".
Next the badpixupdate task and the cosmic ray masks are used to update the
bad pixel mask. Pixels that are bad in 3 or more cosmic ray masks are
assumed to be bad in the bad pixel mask.
Begin first pass bad pixel mask update
Wed 16:29:43 29-Nov-2000
-------Updating bad pixel file with badpixupdate ----
By default the image registration step is non-interactive, i.e. fp_mkshifts = no. In this case the user must supply a shifts file shiftlist which contains the image name, xshift, yshift, and weight or exposure time of the images to be combined. See the file demo.slist for a sample shifts file. In general it is usually easier to determine the shifts outside of the main xmosaic script with the xdshifts task than it is to determine it inside the xmosaic task where a mistake is more costly. Users with time series data, i.e. data where each image is shifted by a comparable amount from the previous one, the xmshifts, xfshifts, or xrshifts tasks can be used to compute the required shifts file.
The following example shows show to make the shift list interactively from the mosaic task.
The first sky subtracted image is loaded into the image display by the
imexamine task and the n and p keys are used to examine each image in
order to select an object common to all.
Examine images ...
Select reference star which is present in all images
Type n key to display next image
Type p key to display previous image
Type q key to quit
Examine all the images and select the star above and slightly to the right of the galaxy as the reference star. Type 'q' to quit the image examining menu.
Now the first image in the sky subtracted image list is displayed, the temporary file myshiftlist.exam is opened. Mark the reference object with the 'a' keystroke, move to the next image with 'n' keystroke, mark the reference object with the 'a' key, ... Repeat until all the images have been displayed and the reference object marked. The reference object selected must be common to all images. The first image is display automatically and then subsequent images are displayed by typing 'n'. DO NOT TYPE 'q' UNTIL ALL IMAGES HAVE BEEN MARKED.
Determine relative shifts using above reference star ...
Move cursor to the selected star
Type a key to measure the selected star
Type n key to move to the next image
Type q key to quit
Log file myshiftlist.exam open
# COL LINE COORDINATES
# R MAG FLUX SKY PEAK E PA ENCLOSED GAUSSIAN DIRECT
63.90 47.13 63.90 47.13
13.18 15.80 4778. -1.094 325.2 INDEF -6 3.96 4.20 4.16
57.42 47.25 57.42 47.25
7.79 16.38 2810. 3.951 424.7 INDEF -55 3.99 3.38 3.61
50.86 46.68 50.86 46.68
9.29 15.93 4244. 5.545 396.2 INDEF 8 3.46 3.21 3.10
44.51 46.73 44.51 46.73
7.30 15.58 5837. -1.388 463.3 0.61 68 3.65 2.93 2.44
37.93 46.40 37.93 46.40
8.47 15.70 5257. -1.161 463.6 INDEF 29 3.36 2.82 2.55
62.60 40.00 62.60 40.00
10.79 15.34 7332. 1.875 352.8 0.69 -52 3.94 4.24 3.15
56.06 39.90 56.06 39.90
9.33 15.68 5326. 6.569 358. 1.02 5 3.66 3.73 3.88
51.00 40.90 51.00 40.90
9.88 15.80 4782. 7.608 408.1 INDEF -64 3.89 3.26 3.19
44.88 40.71 44.88 40.71
6.64 15.79 4829. 6.467 517.4 1.62 28 2.86 2.42 2.16
38.05 40.83 38.05 40.83
8.44 15.77 4916. -0.1289 439.2 7.41 76 3.98 2.90 3.17
63.07 34.29 63.07 34.29
14.95 15.75 5014. 1.413 378.6 0.08 -22 17.97 3.74 13.72
56.74 33.84 56.74 33.84
10.58 15.59 5797. 1.553 384.7 1.19 83 3.83 3.39 3.78
50.11 33.58 50.11 33.58
13.60 15.60 5768. 4.054 352.1 49.8 -66 5.24 4.14 6.12
43.37 33.46 43.37 33.46
8.73 15.72 5159. -0.7891 381.1 INDEF 5 3.99 3.58 3.25
39.14 34.82 39.14 34.82
9.22 15.64 5549. -1.216 381.9 INDEF 51 4.14 3.38 3.08
63.10 28.36 63.10 28.36
9.78 15.24 8045. -2.753 353. 0.43 -82 6.23 3.74 3.19
57.05 28.32 57.05 28.32
7.34 15.48 6430. 1.968 400.7 0.44 -60 4.41 3.28 3.08
50.47 28.01 50.47 28.01
17.98 INDEF -5523. 9.998 INDEF INDEF INDEF 37.04 INDEF 33.41
43.59 27.71 43.59 27.71
13.87 16.20 3311. 3.808 353.9 INDEF -50 7.69 3.61 4.73
37.66 27.21 37.66 27.21
7.27 15.39 6972. 0.3169 464.5 0.16 -56 4.07 2.59 2.23
62.16 21.07 62.16 21.07
9.41 15.13 8856. -0.9043 415.9 0.14 -30 6.50 3.27 3.22
57.73 22.19 57.73 22.19
11.48 16.06 3754. 1.908 346.4 INDEF 80 4.52 3.87 4.43
51.10 22.17 51.10 22.17
8.89 15.76 4978. 4.53 420.9 INDEF 86 3.68 3.20 2.92
44.61 21.66 44.61 21.66
7.61 15.59 5794. 4.416 376.1 0.88 -81 4.25 3.56 3.28
38.24 21.86 38.24 21.86
12.19 16.08 3703. 8.723 319.3 INDEF -21 8.00 3.85 5.54
Because mp_chkshifts = yes the output of imexamine is displayed with the editor. This allows deleting multiple measurements or other incorrect data. In the above example there are no mistakes and the file does not need to be modified. The final file looks like this
# [1] demo01.sub.imh - Example artificial galaxy cluster
# COL LINE COORDINATES R MAG FLUX SKY PEAK E PA
ENCLOSED GAUSSIAN DIRECT
63.90 47.13 63.90 47.13 13.18 15.80 4778. -1.094 325.2 INDEF -6
3.96 4.20 4.16
# [2] demo02.sub.imh - Example artificial galaxy cluster
57.42 47.25 57.42 47.25 7.79 16.38 2810. 3.951 424.7 INDEF -55
3.99 3.38 3.61
# [3] demo03.sub.imh - Example artificial galaxy cluster
50.86 46.68 50.86 46.68 9.29 15.93 4244. 5.545 396.2 INDEF 8
3.46 3.21 3.10
# [4] demo04.sub.imh - Example artificial galaxy cluster
44.51 46.73 44.51 46.73 7.30 15.58 5837. -1.388 463.3 0.61 68
3.65 2.93 2.44
# [5] demo05.sub.imh - Example artificial galaxy cluster
37.93 46.40 37.93 46.40 8.47 15.70 5257. -1.161 463.6 INDEF 29
3.36 2.82 2.55
# [6] demo06.sub.imh - Example artificial galaxy cluster
62.60 40.00 62.60 40.00 10.79 15.34 7332. 1.875 352.8 0.69 -52
3.94 4.24 3.15
# [7] demo07.sub.imh - Example artificial galaxy cluster
56.06 39.90 56.06 39.90 9.33 15.68 5326. 6.569 358. 1.02 5
3.66 3.73 3.88
# [8] demo08.sub.imh - Example artificial galaxy cluster
51.00 40.90 51.00 40.90 9.88 15.80 4782. 7.608 408.1 INDEF -64
3.89 3.26 3.19
# [9] demo09.sub.imh - Example artificial galaxy cluster
44.88 40.71 44.88 40.71 6.64 15.79 4829. 6.467 517.4 1.62 28
2.86 2.42 2.16
# [10] demo10.sub.imh - Example artificial galaxy cluster
38.05 40.83 38.05 40.83 8.44 15.77 4916. -0.1289 439.2 7.41 76
3.98 2.90 3.17
# [11] demo11.sub.imh - Example artificial galaxy cluster
63.07 34.29 63.07 34.29 14.95 15.75 5014. 1.413 378.6 0.08 -22
17.97 3.74 13.72
# [12] demo12.sub.imh - Example artificial galaxy cluster
56.74 33.84 56.74 33.84 10.58 15.59 5797. 1.553 384.7 1.19 83
3.83 3.39 3.78
# [13] demo13.sub.imh - Example artificial galaxy cluster
50.11 33.58 50.11 33.58 13.60 15.60 5768. 4.054 352.1 49.8 -66
5.24 4.14 6.12
# [14] demo14.sub.imh - Example artificial galaxy cluster
43.37 33.46 43.37 33.46 8.73 15.72 5159. -0.7891 381.1 INDEF 5
3.99 3.58 3.25
# [15] demo15.sub.imh - Example artificial galaxy cluster
39.14 34.82 39.14 34.82 9.22 15.64 5549. -1.216 381.9 INDEF 51
4.14 3.38 3.08
# [16] demo16.sub.imh - Example artificial galaxy cluster
63.10 28.36 63.10 28.36 9.78 15.24 8045. -2.753 353. 0.43 -82
6.23 3.74 3.19
# [17] demo17.sub.imh - Example artificial galaxy cluster
57.05 28.32 57.05 28.32 7.34 15.48 6430. 1.968 400.7 0.44 -60
4.41 3.28 3.08
# [18] demo18.sub.imh - Example artificial galaxy cluster
50.47 28.01 50.47 28.01 17.98 INDEF -5523. 9.998 INDEF INDEF INDEF
37.04 INDEF 33.41
# [19] demo19.sub.imh - Example artificial galaxy cluster
43.59 27.71 43.59 27.71 13.87 16.20 3311. 3.808 353.9 INDEF -50
7.69 3.61 4.73
# [20] demo20.sub.imh - Example artificial galaxy cluster
37.66 27.21 37.66 27.21 7.27 15.39 6972. 0.3169 464.5 0.16 -56
4.07 2.59 2.23
# [21] demo21.sub.imh - Example artificial galaxy cluster
62.16 21.07 62.16 21.07 9.41 15.13 8856. -0.9043 415.9 0.14 -30
6.50 3.27 3.22
# [22] demo22.sub.imh - Example artificial galaxy cluster
57.73 22.19 57.73 22.19 11.48 16.06 3754. 1.908 346.4 INDEF 80
4.52 3.87 4.43
# [23] demo23.sub.imh - Example artificial galaxy cluster
51.10 22.17 51.10 22.17 8.89 15.76 4978. 4.53 420.9 INDEF 86
3.68 3.20 2.92
# [24] demo24.sub.imh - Example artificial galaxy cluster
44.61 21.66 44.61 21.66 7.61 15.59 5794. 4.416 376.1 0.88 -81
4.25 3.56 3.28
# [25] demo25.sub.imh - Example artificial galaxy cluster
38.24 21.86 38.24 21.86 12.19 16.08 3703. 8.723 319.3 INDEF -21
8.00 3.85 5.54
Next mark as many stars (or compact objects) as can be reliably measured in the reference image as instructed below. In this example only the star we selected as the reference stars is suitable.
Select reference image registration stars ...
Move to reference star measured previously
Type a to measure reference star
Move to other promising looking stars
Type a to measure other registration stars
Type q key to quit
Log file myshiftlist.stars open
# COL LINE COORDINATES
# R MAG FLUX SKY PEAK E PA ENCLOSED GAUSSIAN DIRECT
50.17 33.61 50.17 33.61
13.56 15.90 4378. 5027. 376.8 INDEF -51 4.79 3.84 4.75
As before the marked objects are displayed with the editor and again the file does not have to be edited. The final file appears as shown below.
[1] demo13 - Example artificial galaxy cluster
# COL LINE COORDINATES R MAG FLUX SKY PEAK E PA
ENCLOSED GAUSSIAN DIRECT
50.20 33.54 50.20 33.54 13.56 15.88 4439. 5027. 359.3 INDEF -53
4.79 4.02 4.75
The position of the reference objects in each of the input images is measured with the xdimsum.ximcentroid task using the initial shifts determined from the object common to all the images and final offsets relative to the reference image are computed. The measurements are recorded in the file shiftlist which can be reviewed using the editor. The final shifts file is shown below.
demo01.sub.imh 13.966 13.554 1.0
demo02.sub.imh 7.718 13.360 1.0
demo03.sub.imh 0.751 12.866 1.0
demo04.sub.imh -5.438 12.733 1.0
demo05.sub.imh -11.825 12.675 1.0
demo06.sub.imh 12.663 6.243 1.0
demo07.sub.imh 6.204 5.880 1.0
demo08.sub.imh 1.320 7.394 1.0
demo09.sub.imh -5.090 7.054 1.0
demo10.sub.imh -11.789 7.198 1.0
demo11.sub.imh 13.352 0.354 1.0
demo12.sub.imh 6.719 0.039 1.0
demo13.sub.imh -0.064 -0.073 1.0
demo14.sub.imh -6.832 -0.273 1.0
demo15.sub.imh -11.140 0.899 1.0
demo16.sub.imh 13.723 -5.582 1.0
demo17.sub.imh 6.996 -5.604 1.0
demo18.sub.imh 0.500 -5.827 1.0
demo19.sub.imh -6.102 -6.268 1.0
demo20.sub.imh -12.949 -6.568 1.0
demo21.sub.imh 12.097 -12.923 1.0
demo22.sub.imh 8.005 -11.602 1.0
demo23.sub.imh 1.074 -11.789 1.0
demo24.sub.imh -5.114 -12.033 1.0
demo25.sub.imh -12.087 -11.925 1.0
The shifts file is used to register the images and combine them with exposure time weighting. An exposure map is also created. These images are the first pass mosaic and exposure map. The images are stored in the file mosaic_fp.imh and mosaic_fp.exp.imh. The xnregistar task is used to do the image combining step.
------- Checking the shiftlist---------------------------
Begin first pass image combining
Wed 16:29:46 29-Nov-2000
-------Coadding images using xnregistar --------------
Creating individual composite masks ...
Using bad pixel mask file: demo.pl
Creating mask for image: demo01.sub
Creating mask for image: demo02.sub
Creating mask for image: demo03.sub
Creating mask for image: demo04.sub
Creating mask for image: demo05.sub
Creating mask for image: demo06.sub
Creating mask for image: demo07.sub
Creating mask for image: demo08.sub
Creating mask for image: demo09.sub
Creating mask for image: demo10.sub
Creating mask for image: demo11.sub
Creating mask for image: demo12.sub
Creating mask for image: demo13.sub
Creating mask for image: demo14.sub
Creating mask for image: demo15.sub
Creating mask for image: demo16.sub
Creating mask for image: demo17.sub
Creating mask for image: demo18.sub
Creating mask for image: demo19.sub
Creating mask for image: demo20.sub
Creating mask for image: demo21.sub
Creating mask for image: demo22.sub
Creating mask for image: demo23.sub
Creating mask for image: demo24.sub
Creating mask for image: demo25.sub
Combining the input images ...
Combining the exposure time images ...
After registration the final mosaic and exposure map are reoriented so
that north is up and east is to the left. In this example the images are left
in their observed orientation. The effective exposure time and other header
parameters in the final mosaic are updated.
finish xfirstpass
Wed 16:30:19 29-Nov-2000
This marks the end of the first pass.
The mask pass begins by calling the mkmask task to create a mask of the object cores. Mkmask uses the first pass combined image, first pass exposure map, and first pass offsets file, to create the mask object cores mask. The maskdereg task "deregisters" this mask to create object core masks for the individual images. The object cores masks are used to unzap cosmic rays detected in the cores of images during the first pass.
Wed 16:30:19 29-Nov-2000
start xmaskpass
Wed 16:30:19 29-Nov-2000
Begin mask pass inverse object mask creation
Wed 16:30:20 29-Nov-2000
-------Making mask for unzapping object cores ------------
Recommended thresholding level for mask is 0.32639925
z1=-0.6386976 z2=1.241897
By default the main object cores mask is created automatically. However if chkmasks is yes the process is interactive. In this case the first pass combined image normalized by the exposure map is displayed with imexamine and the recommended threshold value is printed on the terminal, and the user is prompted for a new cutoff value which is interpreted as a value above the median background. The user can use the imexamine commands like 'm', 'l', and 'c' to determine this cutoff.
Cutoff point for replacement: .32
Now the first pass mosaic image and the computed mask are displayed and the user can decide whether or not to make a new mask with a different threshold. In the example type "no". The mask is then deregistered.
z1=-1.261593 z2=1.342784
z1=0. z2=1.
Keep checking mask? (yes): no
-------Inverting mask for unzapping ----------------------
Begin mask pass individual inverse object mask creation
Wed 16:30:37 29-Nov-2000
-------Deregistering unzap mask subsections ---------------
Making object masks for image: demo01
Making object masks for image: demo02
Making object masks for image: demo03
Making object masks for image: demo04
Making object masks for image: demo05
Making object masks for image: demo06
Making object masks for image: demo07
Making object masks for image: demo08
Making object masks for image: demo09
Making object masks for image: demo10
Making object masks for image: demo11
Making object masks for image: demo12
Making object masks for image: demo13
Making object masks for image: demo14
Making object masks for image: demo15
Making object masks for image: demo16
Making object masks for image: demo17
Making object masks for image: demo18
Making object masks for image: demo19
Making object masks for image: demo20
Making object masks for image: demo21
Making object masks for image: demo22
Making object masks for image: demo23
Making object masks for image: demo24
Making object masks for image: demo25
The individual object core masks are stored in the file "*.sub.ocm.pl. The master object core mask is stored in the file "mosaic_fp.mski.pl".
Next a lower threshold mask of the full objects is now made. The same steps of image display and threshold adjustment are performed as in the previous step and the new object mask is also deregistered. The object masks are used in a second pass of sky subtraction to avoid using pixels covered by faint objects as part of the sky.
Begin mask pass object mask creation
Wed 16:30:39 29-Nov-2000
-------Making mask for sky subtraction -------------------
Recommended thresholding level for mask is 0.32639925
z1=-0.6386976 z2=1.241897
Cutoff point for replacement: .32
z1=-1.261593 z2=1.342784
z1=0. z2=1.
Keep checking mask? (yes): no
Begin mask pass individual object mask creation
Wed 16:30:59 29-Nov-2000
-------Deregistering sky subtraction mask subsections -----
Making object masks for image: demo01
Making object masks for image: demo02
Making object masks for image: demo03
Making object masks for image: demo04
Making object masks for image: demo05
Making object masks for image: demo06
Making object masks for image: demo07
Making object masks for image: demo08
Making object masks for image: demo09
Making object masks for image: demo10
Making object masks for image: demo11
Making object masks for image: demo12
Making object masks for image: demo13
Making object masks for image: demo14
Making object masks for image: demo15
Making object masks for image: demo16
Making object masks for image: demo17
Making object masks for image: demo18
Making object masks for image: demo19
Making object masks for image: demo20
Making object masks for image: demo21
Making object masks for image: demo22
Making object masks for image: demo23
Making object masks for image: demo24
Making object masks for image: demo25
The individual object masks are stored in the file "*.sub.obm.pl" and the mask object mask is stored in the file "mosaic_fp.msk.pl".
Next the sky subtracted images are recomputed using the object masks created above to eliminate objects from both the sky statistics computation and the image combining step. For some images a holes mask may also be created. Holes mask define regions of the sky subtracted data which are undefined, i.e. contain no data. The holes mask are used in the image combining step to compute the combined image and the exposure map.
Begin mask pass sky subtraction
Wed 16:31:01 29-Nov-2000
Calculating scaling for demo01
Using object mask : demo01.sub.obm.pl
Setting scaling factor to 1 / 4540.263
Calculating scaling for demo02
Using object mask : demo02.sub.obm.pl
Setting scaling factor to 1 / 4580.704
Calculating scaling for demo03
Using object mask : demo03.sub.obm.pl
Setting scaling factor to 1 / 4621.996
Calculating scaling for demo04
Using object mask : demo04.sub.obm.pl
Setting scaling factor to 1 / 4660.359
Calculating scaling for demo05
Using object mask : demo05.sub.obm.pl
Setting scaling factor to 1 / 4701.139
Calculating scaling for demo06
Using object mask : demo06.sub.obm.pl
Setting scaling factor to 1 / 4739.956
Calculating scaling for demo07
Using object mask : demo07.sub.obm.pl
Setting scaling factor to 1 / 4780.889
Calculating scaling for demo08
Using object mask : demo08.sub.obm.pl
Setting scaling factor to 1 / 4820.484
Calculating scaling for demo09
Using object mask : demo09.sub.obm.pl
Setting scaling factor to 1 / 4860.14
Calculating scaling for demo10
Using object mask : demo10.sub.obm.pl
Setting scaling factor to 1 / 4899.388
Calculating scaling for demo11
Using object mask : demo11.sub.obm.pl
Setting scaling factor to 1 / 4941.429
Calculating scaling for demo12
Using object mask : demo12.sub.obm.pl
Setting scaling factor to 1 / 4981.195
Calculating scaling for demo13
Using object mask : demo13.sub.obm.pl
Setting scaling factor to 1 / 5019.37
Calculating scaling for demo14
Using object mask : demo14.sub.obm.pl
Setting scaling factor to 1 / 5061.904
Calculating scaling for demo15
Using object mask : demo15.sub.obm.pl
Setting scaling factor to 1 / 5100.764
Calculating scaling for demo16
Using object mask : demo16.sub.obm.pl
Setting scaling factor to 1 / 5140.057
Calculating scaling for demo17
Using object mask : demo17.sub.obm.pl
Setting scaling factor to 1 / 5181.636
Calculating scaling for demo18
Using object mask : demo18.sub.obm.pl
Setting scaling factor to 1 / 5220.013
Calculating scaling for demo19
Using object mask : demo19.sub.obm.pl
Setting scaling factor to 1 / 5261.546
Calculating scaling for demo20
Using object mask : demo20.sub.obm.pl
Setting scaling factor to 1 / 5300.255
Calculating scaling for demo21
Using object mask : demo21.sub.obm.pl
Setting scaling factor to 1 / 5340.667
Calculating scaling for demo22
Using object mask : demo22.sub.obm.pl
Setting scaling factor to 1 / 5379.909
Calculating scaling for demo23
Using object mask : demo23.sub.obm.pl
Setting scaling factor to 1 / 5420.455
Calculating scaling for demo24
Using object mask : demo24.sub.obm.pl
Setting scaling factor to 1 / 5460.285
Calculating scaling for demo25
Using object mask : demo25.sub.obm.pl
Setting scaling factor to 1 / 5498.279
Creating sky subtracted image demo01.sub
Frame 1 Sky frames: start = 1 finish = 4 nreject = 1
Using object mask : demo01.sub.obm.pl
Creating sky subtracted image demo02.sub
Frame 2 Sky frames: start = 1 finish = 4 nreject = 1
Using object mask : demo02.sub.obm.pl
Creating sky subtracted image demo03.sub
Frame 3 Sky frames: start = 1 finish = 5 nreject = 1
Using object mask : demo03.sub.obm.pl
Creating sky subtracted image demo04.sub
Frame 4 Sky frames: start = 1 finish = 7 nreject = 1
Using object mask : demo04.sub.obm.pl
Creating sky subtracted image demo05.sub
Frame 5 Sky frames: start = 2 finish = 8 nreject = 1
Using object mask : demo05.sub.obm.pl
Creating sky subtracted image demo06.sub
Frame 6 Sky frames: start = 3 finish = 9 nreject = 1
Using object mask : demo06.sub.obm.pl
Creating sky subtracted image demo07.sub
Frame 7 Sky frames: start = 4 finish = 10 nreject = 1
Using object mask : demo07.sub.obm.pl
Creating sky subtracted image demo08.sub
Frame 8 Sky frames: start = 5 finish = 11 nreject = 1
Using object mask : demo08.sub.obm.pl
Creating sky subtracted image demo09.sub
Frame 9 Sky frames: start = 6 finish = 12 nreject = 1
Using object mask : demo09.sub.obm.pl
Creating sky subtracted image demo10.sub
Frame 10 Sky frames: start = 7 finish = 13 nreject = 1
Using object mask : demo10.sub.obm.pl
Creating sky subtracted image demo11.sub
Frame 11 Sky frames: start = 8 finish = 14 nreject = 1
Using object mask : demo11.sub.obm.pl
Creating sky subtracted image demo12.sub
Frame 12 Sky frames: start = 9 finish = 15 nreject = 1
Using object mask : demo12.sub.obm.pl
Creating sky subtracted image demo13.sub
Frame 13 Sky frames: start = 10 finish = 16 nreject = 1
Using object mask : demo13.sub.obm.pl
Creating sky subtracted image demo14.sub
Frame 14 Sky frames: start = 11 finish = 17 nreject = 1
Using object mask : demo14.sub.obm.pl
Creating sky subtracted image demo15.sub
Frame 15 Sky frames: start = 12 finish = 18 nreject = 1
Using object mask : demo15.sub.obm.pl
Creating sky subtracted image demo16.sub
Frame 16 Sky frames: start = 13 finish = 19 nreject = 1
Using object mask : demo16.sub.obm.pl
Creating sky subtracted image demo17.sub
Frame 17 Sky frames: start = 14 finish = 20 nreject = 1
Using object mask : demo17.sub.obm.pl
Creating sky subtracted image demo18.sub
Frame 18 Sky frames: start = 15 finish = 21 nreject = 1
Using object mask : demo18.sub.obm.pl
Creating sky subtracted image demo19.sub
Frame 19 Sky frames: start = 16 finish = 22 nreject = 1
Using object mask : demo19.sub.obm.pl
Creating sky subtracted image demo20.sub
Frame 20 Sky frames: start = 17 finish = 23 nreject = 1
Using object mask : demo20.sub.obm.pl
Creating sky subtracted image demo21.sub
Frame 21 Sky frames: start = 18 finish = 24 nreject = 1
Using object mask : demo21.sub.obm.pl
Creating sky subtracted image demo22.sub
Frame 22 Sky frames: start = 19 finish = 25 nreject = 1
Using object mask : demo22.sub.obm.pl
Creating sky subtracted image demo23.sub
Frame 23 Sky frames: start = 21 finish = 25 nreject = 1
Using object mask : demo23.sub.obm.pl
Creating sky subtracted image demo24.sub
Frame 24 Sky frames: start = 22 finish = 25 nreject = 1
Using object mask : demo24.sub.obm.pl
Creating sky subtracted image demo25.sub
Frame 25 Sky frames: start = 22 finish = 25 nreject = 1
Using object mask : demo25.sub.obm.pl
Creating holes mask: demo25.sub.hom.pl
The new sky subtracted images are stored in the files "*.sub.imh". The holes masks are stored in the file "*.sub.hom.pl".
As before the bad pixels are interpolated away in the new sky subtracted images. One possible difference is that the bad pixel mask may have additional bad pixels due to earlier detection as apparent cosmic ray events occurring repeatedly in the same pixel.
Begin mask pass bad pixel correction
Wed 16:36:21 29-Nov-2000
-------Correcting bad pixels with maskfix------------------
Fixing bad pixels in file demo01.sub using mask demo.pl
Fixing bad pixels in file demo02.sub using mask demo.pl
Fixing bad pixels in file demo03.sub using mask demo.pl
Fixing bad pixels in file demo04.sub using mask demo.pl
Fixing bad pixels in file demo05.sub using mask demo.pl
Fixing bad pixels in file demo06.sub using mask demo.pl
Fixing bad pixels in file demo07.sub using mask demo.pl
Fixing bad pixels in file demo08.sub using mask demo.pl
Fixing bad pixels in file demo09.sub using mask demo.pl
Fixing bad pixels in file demo10.sub using mask demo.pl
Fixing bad pixels in file demo11.sub using mask demo.pl
Fixing bad pixels in file demo12.sub using mask demo.pl
Fixing bad pixels in file demo13.sub using mask demo.pl
Fixing bad pixels in file demo14.sub using mask demo.pl
Fixing bad pixels in file demo15.sub using mask demo.pl
Fixing bad pixels in file demo16.sub using mask demo.pl
Fixing bad pixels in file demo17.sub using mask demo.pl
Fixing bad pixels in file demo18.sub using mask demo.pl
Fixing bad pixels in file demo19.sub using mask demo.pl
Fixing bad pixels in file demo20.sub using mask demo.pl
Fixing bad pixels in file demo21.sub using mask demo.pl
Fixing bad pixels in file demo22.sub using mask demo.pl
Fixing bad pixels in file demo23.sub using mask demo.pl
Fixing bad pixels in file demo24.sub using mask demo.pl
Fixing bad pixels in file demo25.sub using mask demo.pl
Another round of cosmic ray detection is done using the more sensitive object masks based on the first pass mosaic rather than generating a mask for each individual observation. As before any repeated cosmic ray detections are flagged as likely bad pixels in the bad pixel file.
Begin mask pass cosmic ray correction
Wed 16:36:39 29-Nov-2000
-------Zapping cosmic rays using xzap --------------------
Creating cosmic ray corrected image demo01.sub
Using object mask : demo01.sub.ocm.pl
Creating cosmic ray corrected image demo02.sub
Using object mask : demo02.sub.ocm.pl
Creating cosmic ray corrected image demo03.sub
Using object mask : demo03.sub.ocm.pl
Creating cosmic ray corrected image demo04.sub
Using object mask : demo04.sub.ocm.pl
Creating cosmic ray corrected image demo05.sub
Using object mask : demo05.sub.ocm.pl
Creating cosmic ray corrected image demo06.sub
Using object mask : demo06.sub.ocm.pl
Creating cosmic ray corrected image demo07.sub
Using object mask : demo07.sub.ocm.pl
Creating cosmic ray corrected image demo08.sub
Using object mask : demo08.sub.ocm.pl
Creating cosmic ray corrected image demo09.sub
Using object mask : demo09.sub.ocm.pl
Creating cosmic ray corrected image demo10.sub
Using object mask : demo10.sub.ocm.pl
Creating cosmic ray corrected image demo11.sub
Using object mask : demo11.sub.ocm.pl
Creating cosmic ray corrected image demo12.sub
Using object mask : demo12.sub.ocm.pl
Creating cosmic ray corrected image demo13.sub
Using object mask : demo13.sub.ocm.pl
Creating cosmic ray corrected image demo14.sub
Using object mask : demo14.sub.ocm.pl
Creating cosmic ray corrected image demo15.sub
Using object mask : demo15.sub.ocm.pl
Creating cosmic ray corrected image demo16.sub
Using object mask : demo16.sub.ocm.pl
Creating cosmic ray corrected image demo17.sub
Using object mask : demo17.sub.ocm.pl
Creating cosmic ray corrected image demo18.sub
Using object mask : demo18.sub.ocm.pl
Creating cosmic ray corrected image demo19.sub
Using object mask : demo19.sub.ocm.pl
Creating cosmic ray corrected image demo20.sub
Using object mask : demo20.sub.ocm.pl
Creating cosmic ray corrected image demo21.sub
Using object mask : demo21.sub.ocm.pl
Creating cosmic ray corrected image demo22.sub
Using object mask : demo22.sub.ocm.pl
Creating cosmic ray corrected image demo23.sub
Using object mask : demo23.sub.ocm.pl
Creating cosmic ray corrected image demo24.sub
Using object mask : demo24.sub.ocm.pl
Creating cosmic ray corrected image demo25.sub
Using object mask : demo25.sub.ocm.pl
begin badpixupdate
Wed 16:37:34 29-Nov-2000
-------Updating bad pixel file with badpixupdate ----------
The final step is to block replicate each image by the factor mag and shift and combine with quarter pixel accuracy. This produces the final mosaic image with extension "_mp" and a final exposure map. The bad pixel mask, the final cosmic ray masks, and the holes masks are used to computed the final image and exposure map.
Begin mask pass image combining
Wed 16:37:36 29-Nov-2000
-------Magnifying and coadding images with xnregistar -----
Creating individual composite masks ...
Using bad pixel mask file: demo.pl
Creating mask for image: demo01.sub
Cannot find holes mask file: demo01.sub.hom.pl
Using crmask file: demo01.sub.crm.pl
Creating mask for image: demo02.sub
Cannot find holes mask file: demo02.sub.hom.pl
Using crmask file: demo02.sub.crm.pl
Creating mask for image: demo03.sub
Cannot find holes mask file: demo03.sub.hom.pl
Using crmask file: demo03.sub.crm.pl
Creating mask for image: demo04.sub
Cannot find holes mask file: demo04.sub.hom.pl
Using crmask file: demo04.sub.crm.pl
Creating mask for image: demo05.sub
Cannot find holes mask file: demo05.sub.hom.pl
Using crmask file: demo05.sub.crm.pl
Creating mask for image: demo06.sub
Cannot find holes mask file: demo06.sub.hom.pl
Using crmask file: demo06.sub.crm.pl
Creating mask for image: demo07.sub
Cannot find holes mask file: demo07.sub.hom.pl
Using crmask file: demo07.sub.crm.pl
Creating mask for image: demo08.sub
Cannot find holes mask file: demo08.sub.hom.pl
Using crmask file: demo08.sub.crm.pl
Creating mask for image: demo09.sub
Cannot find holes mask file: demo09.sub.hom.pl
Using crmask file: demo09.sub.crm.pl
Creating mask for image: demo10.sub
Cannot find holes mask file: demo10.sub.hom.pl
Using crmask file: demo10.sub.crm.pl
Creating mask for image: demo11.sub
Cannot find holes mask file: demo11.sub.hom.pl
Using crmask file: demo11.sub.crm.pl
Creating mask for image: demo12.sub
Cannot find holes mask file: demo12.sub.hom.pl
Using crmask file: demo12.sub.crm.pl
Creating mask for image: demo13.sub
Cannot find holes mask file: demo13.sub.hom.pl
Using crmask file: demo13.sub.crm.pl
Creating mask for image: demo14.sub
Cannot find holes mask file: demo14.sub.hom.pl
Using crmask file: demo14.sub.crm.pl
Creating mask for image: demo15.sub
Cannot find holes mask file: demo15.sub.hom.pl
Using crmask file: demo15.sub.crm.pl
Creating mask for image: demo16.sub
Cannot find holes mask file: demo16.sub.hom.pl
Using crmask file: demo16.sub.crm.pl
Creating mask for image: demo17.sub
Cannot find holes mask file: demo17.sub.hom.pl
Using crmask file: demo17.sub.crm.pl
Creating mask for image: demo18.sub
Cannot find holes mask file: demo18.sub.hom.pl
Using crmask file: demo18.sub.crm.pl
Creating mask for image: demo19.sub
Cannot find holes mask file: demo19.sub.hom.pl
Using crmask file: demo19.sub.crm.pl
Creating mask for image: demo20.sub
Cannot find holes mask file: demo20.sub.hom.pl
Using crmask file: demo20.sub.crm.pl
Creating mask for image: demo21.sub
Cannot find holes mask file: demo21.sub.hom.pl
Using crmask file: demo21.sub.crm.pl
Creating mask for image: demo22.sub
Cannot find holes mask file: demo22.sub.hom.pl
Using crmask file: demo22.sub.crm.pl
Creating mask for image: demo23.sub
Cannot find holes mask file: demo23.sub.hom.pl
Using crmask file: demo23.sub.crm.pl
Creating mask for image: demo24.sub
Cannot find holes mask file: demo24.sub.hom.pl
Using crmask file: demo24.sub.crm.pl
Creating mask for image: demo25.sub
Using holes mask file: demo25.sub.hom.pl
Using crmask file: demo25.sub.crm.pl
Block replicating the input images ...
Block replicating the exposure time images ...
Combining the input images ...
Combining the exposure time images ...
finish xmaskpass
Wed 16:40:47 29-Nov-2000
finish xmosaic
Wed 16:40:47 29-Nov-2000
Now examine the results. Load the truth image, the first pass mosaic, and the mask pass mosaic into the image display. Note that the final sizes are different so things will not appear exactly registered.
di> display demo_truth 1 fill+
di> display mosaic_fp 2 fill+
di> display mosaic_mp 3 fill+
All input and output image and file names and input and output image and file lists are now task parameters rather than being silently passed as keyword names, silently assumed to have already been created by a previous step, or silently created by the current step. For example the input object mask list required by the xslm task is now a parameter. Similarly the output sky subtraction and holes mask lists produced the the xslm task are now parameters. These changes make tracing the data flow from one processing step to another simpler.
In most cases the output images and masks are assigned sensible default names if explicit output image and mask lists are not provided. For example in the case of the sky subtraction task xslm the suffix ".sub" is appended to the input images names to produce the output sky subtracted image names, and the suffixes ".ssm" and ".hom" are appended to sky subtracted image names to create the sky subtraction and holes mask names. In general if an output image or mask list parameter value begins with a '.' it is assumed to be a suffix rather than a complete name. The default image and mask name scheme means that users need not concern themselves with the names of the intermediate data products.
Suffixes instead of prefixes are used to create default names. Using suffixes means that the input and output image lists no longer need to be in the same directory.
A new cosmic ray removal task xnzap has been added to the XDIMSUM package. Xnzap is a script wrapper for the xcraverage task. Xnzap is an alternative to the default xzap task. It is significantly faster than xzap but not yet as well tested. Users are encouraged to experiment with xnzap and / or xcraverage on their own. User feedback on their effectiveness is welcome.
The code for interactively computing the relative shifts in a set of dithered images has been rewritten and moved into a separate task called xdshifts.
Three new script tasks for computing shifts for images taken in series with approximately constant shifts between adjacent images: xmshifts, xfshifts, and xrshifts, have been added to XDIMSUM. These scripts use modified versions of the existing starfind and imcentroid tasks called xstarfind and ximcentroid.
The main processing scripts xmosaic, xfirstpass, and xmaskpass can now be run repeatedly from scratch without requiring the user to delete any intermediate files. It has also been made simpler to restart these scripts at an intermediate point in the processing.
The mask deregistration task maskdereg now permits the user to create individual object masks which are a combination of the current mask and the N previous ones. This feature is useful in cases where the detector retains significant memory of previous exposures.
The image and mask statistics computation parameters used by the sky subtraction and cosmic ray removal tasks xslm and xzap, statsec, mstatsec, maxiter, and nreject can now be set by the user. Their default values are now "", "", 20, and 3.0 respectively, instead of being fixed at the values "", "", 10, and 5.0.
The maskstat task now outputs the computed mask statistics to the output parameters mean, msigma, median, and mmode in the same manner as the iterstat itask does.
The first pass image combining step performed by the xmosaic or xfirstpass tasks now includes an option for doing fractional pixel shifts.
The mask pass image combining step performed by the xmosaic or xmask pass tasks now includes an option for doing image magnification using bilinear interpolation rather than block replication. This means that non-integer magnification factors are supported.
Calls to existing IRAF tasks have been reviewed to make sure that all the task parameters are set in order to avoid unpleasant surprises if these parameters are not set at the expected defaults.
Complicated image operations requiring several steps have been replaced by a single call to the imexpr task where appropriate.
The image registration and combining step has been rewritten to use a new version of the imcombine task called xcombine which does not suffer from the number of open file limit and has better support for pixel masks. The registration should be much faster in most cases.
The sections, fileroot, imgets, minmax, iterstat, and maskstat tasks which return values to their parameters have been cached so that XDIMSUM tasks will work correctly in the background.
On normal task termination there are now no temporary files or images left either in the tmp$ directory or in the current working directory.