A Modicum of Help in Using Reduce --------------------------------- updated 2 October 1995 prme, updates flagged by *** ***One of the main goals of the modifications has been to make the different reduce switches more independent, so that one can do the interactive parts in one session, and fire off a bunch of batch noninteractive reductions when you leave for the day. The main changes involve xzap, badpixupdate, and interactive mask checking. *** in the comments to a parameter is just my attempt to make the comments more accurate. The three inputs to reduce are a list of images, a reference image within this list, and the base name for the output image. The input images should have been linearized and flattened, and a good choice for the ref image is the 2nd or 3rd image in the list. The parameters are listed in the order in which the reductions are usually performed. You can set it up to do partial reductions, like through the firstpass stage (just turn off everything after fp_registar), and then start up reduce again later to finish it off by turning off everything that has been done and turning on what needs to be done). Here is the parameter list with some comments - img_lst - a text file giving the list of input images out_img - base name for output firstpass and maskpass images *** kpchking - See the "chk" parameter below. If chk is yes, you will be given the chance to continue modifying the mask files until you set kpchking to no. ref_img - name of the reference alignment image in this list prefix - a prefix for sky-subtracted images which will default to "ss_"; the firstpass sky-sub images will be deleted but the maskpass versions will remain at the end of reduce *** chk - Do you want chances to check shifts and masks? answering yes allows you to edit intermediate files in the process of making the shiftlist (you always get to edit the actual shiftlist since you might want to zero out some bad frames [by setting the last number 1 on that image line to 0]) and to prompt you to look at the masks. *** Mask checking now puts you in a loop until you answer no the "Keep checking mask?" question. fp_xslm - set to yes to make sky-sub images the first time (no masks) fp_fixpix- set to yes to interpolate over bad pixels, as defined in the bpimage; acts on the sky-sub images only in the first pass *** fp_xzap - set to yes to remove cosmic rays in the sky-sub images in the first pass; uses a set of default parameters which work well for 256x256 IR array data with fwhm=2 pixels. Creates set of crmask* files, one per frame, which get used in later steps so that turning on xzap in the mask pass stage is not necessary. *** xzap now writes the crmask file name in the image header, and acts different in the mask pass, so you may want to leave it on there. *** fp_badpixupd- set to yes to add frequently zapped pixels from xzap to the bpimage. *** Modified to work with an unlimited number of input images to avoid the crash that occurs when too many files are open. mk_shifts- set to yes to create shiftlist by first centering the same star in all sky-sub images, then centering several stars in the ref image, and finally editing the shiftlist to zero any bad frames fp_register- set to yes to make a registered image in the first pass through with no masking masking - set to yes to make an object mask from the firstpass image. A little trick is employed here to prevent objects from getting cosmic ray zapped by mistake. maskdereg- almost always set this to yes if you are doing the maskpass, it creates object masks for each frame from the master mask mp_xslm - set to yes to do sky-subtraction the second time through with masking mp_fixpix- set to yes to fixpix the new sky-sub images using the bpimage *** mp_xzap - set to no to avoid repeating *running* xzap; cosmic rays will still be taken care of by use of the crmask files created the first time xzap was run (assuming you did this in the firstpass through the data) *** However here xzap can use the object masks to avoid zapping objects. *** mp_badpixupd- set to yes to add frequently zapped pixels from xzap to the bpimage *** Modified to fix crash when more than 100 input images created too many open files. mp_registar - finally register the masked sky-sub images - this creates the final image nmed - number of neighboring frames used to create a sky image; 6 or 8 works well bpimage - the bad pixel mask image (with 0 for the good pixels and 1 for the bad pix) mfac - the pixels are replicated by this number in the maskpass stage when the sky-sub frames are registered so that no interpolation is necessary when doing the shifting. 2 or 4 are a good numbers. secpexp - the exposure time of the frame ncoavg - Number of internal coaverages per frame, so the total integration time is secpexp * ncoavg for a given input image rjct - Number of pixels for minmax reject when making the sky frame, usually use 1 or 2 nskymin - Minimum number of frames to use for sky at beginning or end of list; usually set at 2 or 4 forcescale - Force recalculation of image medians in sky scaling after masking, usually set to yes premask - Mask working sky images in maskpass, usually set to yes pixin - set to yes if input coords are measured pixels of a ref object *** This is the case if you set mk_shifts to yes. *** the "historical" parameters allow for registration in the case where you can't (or don't want to) use a reference object. We have used commanded arcsecond offsets and guide probe readouts in such cases. The parameters allow for two coordinate systems: the xy pixel coordinate system of the array, and the ab coordinate system of the offsets or guide probes. scale_x - historical, automatically set to 1 if pixin=yes. (i.e. if you are using measured reference objects for shifts) *** if you were using arcsecond offsets and the pixel size was 0.25 arcsec in the x direction, you would enter 4 here scale_y - ditto ang_a2x - *** Automatically set to 0 if pixin = yes. It is the angle in degrees from a CCW to x where a,b can be a different coord system than the x,y coordinate system of your frame senseab - *** Is a through b counterclockwise? Automatically set to yes if pixin is yes ang_y2N - *** dimsum will output your registered image within 45 degrees of N up and E left if you set ang_y2N and rotation correctly. ang_y2N is the angle in degrees from pixel y to celestial north, in the direction N through E for a displayed input frame. rotation - For a displayed input frame, is N through E counterclockwise (yes or no)? nsig_obj_msk - factor times suggested threshold for object masking, try 1.0; during the masking stage the task will automatically find a masking level. *** If chk=yes you probably need to type in the suggested threshold value again, however. If you usually like the result of this procedure then set to 1.0; if you want fewer pixels masked set the level higher (e.g. 2) and vice versa. nsig_cr_msk - factor times suggested threshold for cr masking, try 1.5; the first part of the masking stage makes an object mask which is used to correct cosmic ray masks for any real objects which were zapped. *** generally this might the core of a star, hence the higher threshold.