;+ ; NAME: ; xdspec ; PURPOSE: ; End-to-end reduction tool for OSIRIS XD spectral data. ; DESCRIPTION: ; ; This program handles all steps of processing raw OSIRIS XD spectral data ; to create final averaged output spectra. This will work quite well for ; data on single point sources. If the objects are extended or if there ; are more than one object, you need to do the reductions by hand. ; ; CATEGORY: ; Spectroscopy ; ; CALLING SEQUENCE: ; xdspec ; ; INPUTS: ; ; OPTIONAL INPUT PARAMETERS: ; ; KEYWORD INPUT PARAMETERS: ; Unless otherwise indicated, these options are all flags. ; ; ABSPOSCAL - Run through the absolute position calibration step. ; ; ADDPATH - String of directory name to prepend to the DIRLIST for a ; location to look for the raw data. The same restriction ; applies to this as to DIRLIST. ; ; ALLCAL - Run through all the calibration steps. ; ; ALLSPEC - (Re)compute all spectral extractions. ; ; AVGSPEC - Force (re)computation of final average spectra. ; ; DIRLIST - String array list of directories for where to search for ; raw data. Do NOT include the final directory that is ; the same as the current directory and the root of the ; raw data files. ; ; FINAL - Enable final spectral extraction, this step combines any ; bad pixel masks and creates final mask (if not already ; present) and then extracts all spectra. ; ; FLUSH_INFO - Flush all remembered information. ; ; GAUSSCOR- Correction factor from the directly computed image FWHM (per order) ; See OPTSPEC for a more detailed explanation. ; ; GROUPCHECK - Flag, generate a summary plot of all spectra against their ; group leader. ; ; MASKTHRESH - When using a final mask image, you can adjust the mask ; threshold with this keyword. The mask image records the ; fraction of the time that a given pixel is recorded as ; being "bad". This fraction varies between 0.0 and 1.0. ; The default is to mark pixels bad that are seen to be bad ; more than 4% of the time. In other words, MASKTHRESH=0.04 ; is the default. ; ; NOSPEC - Inhibit any spectral extraction processing. ; ; PLOTRANGE - Two element vector, [start,stop], frame numbers to generate ; postscript plots for. ; ; PLOTS - How many and how much to plot. (only for optspec plots) ; 0 - All plots generated. ; 1 - No plots at all. ; 2 - Show strip image, average profile, order profiles (default) ; ; QUEUE - (String) Print queue to send postscript plots to. If this ; is not provided, then the idl.ps file is not spooled to ; a printer and is left behind when xdspec finishes. If you ; give a queue name, the idl.ps file is deleted after the ; file is spooled for printing. ; ; RELPOSCAL - Run through the relative position calibration step. ; ; SLOPECAL - Run through centerline slope calibration step. ; ; WAVECAL - Run the wavelength calibration steps on each order. ; ; OUTPUTS: ; ; All output is either to the various plot screens or to files. ; ; KEYWORD OUTPUT PARAMETERS: ; ; COMMON BLOCKS: ; COM_XDSPEC - Used to store information from one invocation of xdspec to ; the next. ; ; SIDE EFFECTS: ; ; RESTRICTIONS: ; ; If you use an 's' flag to eliminate an image and its spectrum from the ; output products, you will not necessarily get this image as a mate in ; cases where you might like it. You will almost always need to tweak ; the mate in the .tbl file by hand in these cases. ; ; PROCEDURE: ; ; This program assumes (and requires) that the current directory is NOT where ; the raw frames are to be found. The raw frames are in some other location ; and have no other files with them. This allows you to have the raw data ; in a location where you do not have write permission (ie., CDROM). All ; of the resulting files from running xdspec are written to the current ; directory and directories beneath there. ; ; Also, for simplicity of bookkeeping, I have assumed that the root of the ; raw data file names is the same as the directory where you are running ; xdspec and where the data live. For example: ; Data files of the form: 980115.001 ; Current directory: /usr/results/980115/ ; Data directory: /usr/data/980115/ ; In this case '/usr/data' should be in the DIRLIST or added with ADDPATH ; (if it isn't already present). ; ; If there are no flat field calibration frames on this night, you must use ; calibration specifications and flat fields from another night in that ; run. In this case, as you start XDSPEC you get a flat field selection ; popup window. Use this tool to browse through other nights until you ; find an appropriate calibration file. In selecting the flat you are ; actually selecting that flat and its associated files.cal specification ; file. In this case you probably shouldn't fiddle with _anything_ in ; the files.cal and if the original ever changes, you should probably start ; all over from scratch on any other nights that use the same stuff. ; You _can_ re-run the wavelength calibration steps in this case but it's ; probably not a good idea. Once you select the flat field, processing ; continues and there's very little that needs to be done on the calibration ; steps (actually nothing at all). ; ; During the wavelength calibration steps, here are the mouse operation ; options: (1st:sky spectrum) (2nd:synthetic) ; left measure nearest line grab nearest strong line ; middle delete nearest point nothing ; right done abort this line ; ; Here's the typical "flow" of running this program: ; xdspec <-- Initial call, sets up calibration information, and ; extracts initial spectra. Run this as many times ; as needed to get a complete set of initial spectra. ; ; xdspec,plotrange=[1,NNN],queue='printer name' ; this will generate the summary plots for all the ; spectra. Do only when all are done. You then review ; the plots with an eye toward spectra that should be ; removed from the averages. You mark one to be skipped ; by replacing the second column flag character ; by an 'x' (to exclude). After all have ; been marked, proceed to the next step ... ; ; xdspec,/final <-- Final processing, combines bad pixel maps, reextracts ; the spectra and generates final averages. You are done ; with this program at this point. ; ; Note, you can ignore any spectrum in the tbl file by marking it with an ; 'x' in the second column in the table. It will do no good to delete the ; line from the table as the line will come back. 'x' marks it to be ; ignored. If any extraction/reduction products exist for such a spectrum ; they will be deleted. ; ; MODIFICATION HISTORY: ; 97/12/11, Written by Marc W. Buie, Lowell Observatory ; 98/03/09, MWB, cleaned up logic needed when data are added to raw directory. ; 98/04/01, MWB, added some generalization items, and ADDPATH, DIRLIST ; 98/06, MWB, numerous changes to incorporate a numerical image profile for ; the optimal extraction on the FINAL pass. Also added support ; for those cases where more than one data directory can be found. ; 98/06/30, MWB, added user selection if data could be found in more than one ; directory. Also, some logic was cleaned up that dealt with ; spectra marked to be ignored. ; 98/08/25, MWB, changed the default plotting option, PLOTS=2 so that only ; three windows are automatically created and used. ; 98/09/17, MWB, fixed a minor bookkeeping problem with 's' flagged frames. ; The output files from these frames were still hanging around and ; this has been changed so the output products are deleted. ; 99/11/24, MWB, changed lclxtrem call to accomodate new version. ; ;- pro xdspec,FLUSH_INFO=flush_info,WAVECAL=wavecal, $ ALLCAL=allcal,SLOPECAL=slopecal,RELPOSCAL=relposcal, $ ABSPOSCAL=absposcal,NOSPEC=nospec,ALLSPEC=allspec,FINAL=final, $ AVGSPEC=avgspec,PLOTRANGE=plotrange,QUEUE=queue,DIRLIST=in_dirlist, $ ADDPATH=addpath,GROUPCHECK=groupcheck,GAUSSCOR=gausscor,PLOTS=plots, $ MASKTHRESH=maskthresh common com_xdspec, info, calib, tbl if badpar(flush_info,[0,1,2,3],0,caller='XDSPEC: (FLUSH_INFO) ', $ default=0) then return if badpar(wavecal, [0,1,2,3],0,caller='XDSPEC: (WAVECAL) ', $ default=0) then return if badpar(allcal, [0,1,2,3],0,caller='XDSPEC: (ALLCAL) ', $ default=0) then return if badpar(slopecal, [0,1,2,3],0,caller='XDSPEC: (SLOPECAL) ', $ default=0) then return if badpar(relposcal, [0,1,2,3],0,caller='XDSPEC: (RELPOSCAL) ', $ default=0) then return if badpar(absposcal, [0,1,2,3],0,caller='XDSPEC: (ABSPOSCAL) ', $ default=0) then return if badpar(nospec, [0,1,2,3],0,caller='XDSPEC: (NOSPEC) ', $ default=0) then return if badpar(allspec, [0,1,2,3],0,caller='XDSPEC: (ALLSPEC) ', $ default=0) then return if badpar(final, [0,1,2,3],0,caller='XDSPEC: (FINAL) ', $ default=0) then return if badpar(avgspec, [0,1,2,3],0,caller='XDSPEC: (AVGSPEC) ', $ default=0) then return if badpar(plotrange, [0,2,3], 1,caller='XDSPEC: (PLOTSPEC) ', $ default=[-1,-1]) then return if badpar(queue, [0,7], 0,caller='XDSPEC: (QUEUE) ', $ default='[none]') then return if badpar(in_dirlist, [0,7],[0,1],caller='XDSPEC: (DIRLIST) ', $ default='[none]') then return if badpar(addpath, [0,7], 0,caller='XDSPEC: (ADDPATH) ', $ default='[none]') then return if badpar(groupcheck,[0,2,3], 1,caller='XDSPEC: (GROUPCHECK) ', $ default=[-1,-1]) then return if badpar(plots, [0,1,2,3],0,caller='XDSPEC: (PLOTS) ', $ default=2) then return if badpar(maskthresh,[0,4,5], 0,caller='XDSPEC: (MASKTHRESH) ', $ default=0.04) then return blanks=' ' setusym,1 ; force user symbol to filled circle. lscmd = '"ls" ' rmcmd = '"rm" ' loadct,5,/silent ; If common is empty, fill in the structure with empty stuff. if flush_info then info=0 sz_info=size(info) if sz_info[n_elements(sz_info)-2] ne 8 then begin info = { $ cwd: '', $ ddir: '', $ root: '', $ dirroot: '', $ bsrefn: -1, $ flaton: -1, $ flatoff: -1, $ caldate: '', $ tbldate: '' $ } endif ; Is the directory the same as the last time? If so, reset some of the info. cd,'.',current=cwd if cwd ne info.cwd then begin info.caldate='' info.tbldate='' info.ddir = '' info.bsrefn = -1 info.flaton = -1 info.flatoff= -1 ; root, derived from current directory. pos = rstrpos(cwd,'/') info.root = strmid(cwd,pos+1,99) info.cwd = cwd endif ; Locate the raw data. if in_dirlist[0] eq '[none]' then begin dirlist=['/gryll/data2/buie/rawfits/', $ '/gryll/data3/buie/rawfits/', $ '/gryll/data4/buie/rawfits/', $ '/gryll/data5/buie/rawfits/', $ '/gryll/data6/buie/rawfits/', $ '/cdrom/cdrom0/', $ '/usr1/data1/', $ '/usr1/data2/', $ '/usr1/data3/', $ '/usr1/data4/'] endif else begin dirlist=[in_dirlist] endelse ; Pre-pend a special location if addpath ne '[none]' then begin dirlist= [addslash(addpath),dirlist] endif ; Find where the data frames are located. First, look for dirlist/root, ; If nothing found look for just dirlist. dpath='not found' for i=0,n_elements(dirlist)-1 do begin if exists(dirlist[i]+info.root) then dpath=[dpath,dirlist[i]+info.root+'/'] endfor ; if n_elements(dpath) eq 1 then begin for i=0,n_elements(dirlist)-1 do begin if exists(dirlist[i]+info.root+'.001') then $ dpath=[dpath,dirlist[i]] endfor ; endif if n_elements(dpath) eq 1 then begin print,'Raw data for ',info.root,' could not be found. Aborting.' return endif else if n_elements(dpath) eq 2 then begin info.ddir = dpath[1] endif else begin dpath=dpath[1:n_elements(dpath)-1] print,'There appear to be multiple data directories for this date.' dpath=picker(dpath) info.ddir = dpath[0] endelse rootloc = strpos(info.ddir,info.root) info.dirroot=info.ddir if rootloc ne -1 then $ info.ddir = strmid(info.ddir,0,rootloc) ; Take a census of the raw data cd,info.dirroot,current=currentdir spawn,lscmd+info.root+'.???',rawlist cd,currentdir if rawlist[0] eq '' then begin print,'Raw data could not be found. Aborting.' return endif ; Look for the information table for this dataset. If not found, build it. tablname=info.root+'.tbl' if not exists(tablname) then begin print,' ---> generating information table file.' tcal={height:2,nor:1,por:1,slope:0.,x1:0,x2:255,y0:128, $ cof:[1,0.001],npts:256,o:[0,255],w:findgen(256), $ flatname:'[none]',flat:1} openw,lun,tablname,/get_lun for i=0,n_elements(rawlist)-1 do begin getstrip,tcal,info.dirroot+'/'+info.root, $ fix(strmid(rawlist[i],strlen(info.root)+1,3)),strip,hdr ; hdr=headfits(info.dirroot+rawlist[i]) objname=nobname(strtrim(strcompress(sxpar(hdr,"OBJECT")),2)) objname=repstr(objname,'/','_') repeat begin if objname eq '' then begin ans='' read,prompt='File '+rawlist[i]+' has no object name. ' + $ 'Enter name> ',ans objname=nobname(strtrim(strcompress(ans),2)) endif endrep until objname ne '' exptime=sxpar(hdr,"EXPTIME") avego =sxpar(hdr,"AVEGO") dateobs=strtrim(sxpar(hdr,"DATE-OBS"),2) ut =strtrim(sxpar(hdr,"UT"),2) airmass=sxpar(hdr,"AIRMASS") imtype =strmid(sxpar(hdr,"IMAGETYP"),0,1) reads,dateobs,day,mon,yr,format='(i2,1x,i2,1x,i4)' reads,ut,hr,mn,sc,format='(i2,1x,i2,1x,i4)' hr = float(hr)+float(mn)/60.0+float(sc)/3600.0 jdcnv,yr,mon,day,hr,jd jd = jd + (avego*exptime/2.0)/3600.0d0/24.0d0 printf,lun,imtype,rawlist[i],objname+blanks,jd,airmass,exptime,avego,-1,-1, $ format='(a1," - ",a,1x,a16,1x,f13.5,1x,f5.3,1x,f8.3,1x,i3,2(1x,i3))' endfor free_lun,lun endif ; Check to see if table is newer than what is in memory, if it is, reload. spawn,lscmd+'-l '+tablname,result if result[0] ne info.tbldate then begin rdtbl,tablname,tbl info.tbldate = result[0] endif ; Check all the spectra flagged as bad. Make sure the mate and relsig are ; blanked out. Also make sure no products exist for anything marked 'x'. z=where(tbl.imflag eq 'x',countz) if countz ne 0 then begin for i=0,countz-1 do begin if tbl.mate[z[i]] ne -1 then begin tbl.mate[z[i]] = -1 tbl.relsig[z[i]] = -1.0 tbl.dirty=1 endif outmask='mask.'+string(tbl.imnum[z[i]],format='(i3.3)') outbadp='Spec/'+info.root+'b.'+string(tbl.imnum[z[i]],format='(i3.3)') outspec='Spec/'+info.root+'s.'+string(tbl.imnum[z[i]],format='(i3.3)') outprof='Spec/'+info.root+'p.'+string(tbl.imnum[z[i]],format='(i3.3)') outscor='Spec/'+info.root+'c.'+string(tbl.imnum[z[i]],format='(i3.3)') cmd=rmcmd if exists(outmask) then cmd=cmd+' '+outmask if exists(outbadp) then cmd=cmd+' '+outbadp if exists(outspec) then cmd=cmd+' '+outspec if exists(outprof) then cmd=cmd+' '+outprof if exists(outscor) then cmd=cmd+' '+outscor if cmd ne rmcmd then begin print,'x-spec cleanup: ',cmd spawn,cmd endif endfor endif ; Extra check, don't keep any files for stuff marked 's'. z=where(tbl.imflag eq 's',countz) if countz ne 0 then begin for i=0,countz-1 do begin outmask='mask.'+string(tbl.imnum[z[i]],format='(i3.3)') outbadp='Spec/'+info.root+'b.'+string(tbl.imnum[z[i]],format='(i3.3)') outspec='Spec/'+info.root+'s.'+string(tbl.imnum[z[i]],format='(i3.3)') outprof='Spec/'+info.root+'p.'+string(tbl.imnum[z[i]],format='(i3.3)') outscor='Spec/'+info.root+'c.'+string(tbl.imnum[z[i]],format='(i3.3)') cmd=rmcmd if exists(outmask) then cmd=cmd+' '+outmask if exists(outbadp) then cmd=cmd+' '+outbadp if exists(outspec) then cmd=cmd+' '+outspec if exists(outprof) then cmd=cmd+' '+outprof if exists(outscor) then cmd=cmd+' '+outscor if cmd ne rmcmd then begin print,'s-spec cleanup: ',cmd spawn,cmd endif endfor endif ; Force all frames flagged with 't' to '-' z=where(tbl.imflag eq 't',countz) if countz ne 0 then tbl.imflag[z]='-' ; Scan the list of files and make sure there is information for all the ; frames, if any are missing, collect the information and add to the ; information structure. for i=0,n_elements(rawlist)-1 do begin z=where(rawlist[i] eq tbl.fn) if z[0] eq -1 then begin print,' ---> adding ',rawlist[i],' to information table.' tcal={height:2,nor:1,por:1,slope:0.,x1:0,x2:255,y0:128, $ cof:[1,0.001],npts:256,o:[0,255],w:findgen(256), $ flatname:'[none]',flat:1} getstrip,tcal,info.dirroot+'/'+info.root, $ fix(strmid(rawlist[i],strlen(info.root)+1,3)),strip,hdr ; hdr=headfits(info.dirroot+rawlist[i]) imnum=intarr(n_elements(rawlist)) parts = str_sep(rawlist[i],'.') imnum = fix(parts[1]) objname=nobname(strtrim(strcompress(sxpar(hdr,"OBJECT")),2)) exptime=sxpar(hdr,"EXPTIME") avego =sxpar(hdr,"AVEGO") dateobs=strtrim(sxpar(hdr,"DATE-OBS"),2) ut =strtrim(sxpar(hdr,"UT"),2) airmass=sxpar(hdr,"AIRMASS") imtype =strmid(sxpar(hdr,"IMAGETYP"),0,1) imflag ='-' reads,dateobs,day,mon,yr,format='(i2,1x,i2,1x,i4)' reads,ut,hr,mn,sc,format='(i2,1x,i2,1x,i4)' hr = float(hr)+float(mn)/60.0+float(sc)/3600.0 jdcnv,yr,mon,day,hr,jd jd = jd + (avego*exptime/2.0)/3600.0d0/24.0d0 imtype = [tbl.imtype,imtype] imflag = [tbl.imflag,imflag] fn = [tbl.fn,rawlist[i]] ;print,'tbl.imnum',tbl.imnum ;print,'pre imnum',imnum imnum = [tbl.imnum,imnum] ;print,'pst imnum',imnum objnam = [tbl.objnam,objname] jd = [tbl.jd,jd] airmas = [tbl.airmas,airmass] exptim = [tbl.exptim,exptime] avego = [tbl.avego,avego] mate = [tbl.mate, -1] relsig = [tbl.relsig, -1.0] z=uniq(fn,sort(fn)) tbl = { $ nobs: n_elements(z), $ imtype: imtype[z], $ imflag: imflag[z], $ fn: fn[z], $ imnum: imnum[z], $ objnam: objnam[z], $ jd: jd[z], $ airmas: airmas[z], $ exptim: exptim[z], $ avego: avego[z], $ mate: mate[z], $ relsig: relsig[z], $ dirty: 1 $ } endif endfor ; Look for calibration/extraction info. If not found, must generate it. if not exists('files.cal') then begin info.caldate='' ; If there are no flat frames we must get the calibration information ; from another night. z=where(tbl.imtype eq 'f',count) if count eq 0 then begin print,'' print,"This night's data does not contain any flat fielding data. This means that" print,"you must use a flat field and calibration information from another night." print,"Using the pop-up dialog that just appeared, you must locate a flat field" print,"image that will work for the data on this night. If you think there is" print,"relevant calibration data on this night, the click cancel and review the" print,"information table that can be found in ",info.root,".tbl before running this" print,"program again." print,'' flatname=dialog_pickfile(filter='*.flat',title='Select Flat Field', $ /noconfirm,/must_exist,get_path=fpath) if flatname eq '' then return spawn,'cp -p '+flatname+' .' spawn,'cp -p '+fpath+'files.cal .' ; Flats are present, create new calibration information. endif else begin print,' ---> Creating new calibration support information.' ans='' read,prompt='Create new calibraton (N) or copy from old (O)? ',ans if strlowcase(strmid(ans,0,1)) eq 'n' then begin openw,lun,'files.cal',/get_lun printf,lun,'OSIRIS XD v2.0' printf,lun,'36' nor=0 read,prompt='How many orders to extract? (3 or 4) ',nor,format='(i)' printf,lun,nor,format='(i1)' printf,lun,'2' if nor eq 4 then begin printf,lun,'96 255 251.85 -0.329 2.3042016 -0.0019167348 -1.6455014e-07' printf,lun,' 0 255 151.97 -0.252 1.8679308 -0.0014568482 0.' printf,lun,' 0 255 91.56 -0.205 1.4937664 -0.0011471715 -7.1757334e-8' printf,lun,' 0 80 50.45 -0.161 1.1742377 -0.0008556351 -1.4269414e-6' endif else begin printf,lun,' 45 255 245.13 -0.328 2.3617096e+00 -1.9464493e-03 1.9557774e-08' printf,lun,' 0 255 146.87 -0.249 1.8353825e+00 -1.4372170e-03 -6.9383532e-08' printf,lun,' 0 255 87.97 -0.205 1.4681654e+00 -1.1459589e-03 -8.2887709e-08' endelse printf,lun,'[none]' free_lun,lun endif else begin print,'' print,'Choose an existing files.cal file from a previous night as a' print,'starting point for the calibration information.' print,'' calname=dialog_pickfile(filter='files.cal',title='Select Old File', $ /noconfirm,/must_exist,get_path=fpath) if calname eq '' then return spawn,'cp -p '+calname+' .' ldcalir,'files.cal',calib,valid,/noflat,/silent wrcalir,calib,'files.cal' endelse allcal=1 endelse endif spawn,lscmd+'-l files.cal',result if result[0] ne info.caldate then begin ldcalir,'files.cal',calib,valid,/silent if not valid then begin print,'calibration support file, files.cal, is invalid.' return endif info.caldate=result[0] endif imx = 1000 ; top scaling for bright star ; Get object reference for slope stuff if allcal or slopecal or relposcal then begin print,'' print,'When determining the calibration information this program needs to have' print,'access to an image which contains a single bright star. The most' print,'important consideration is the need for a image with a single strong' print,'point source with little to no sky signal. The dialog box that has' print,'just appeared allows you an opportunity to select the needed image.' print,'' if info.bsrefn lt 0 then begin frlist=strarr(tbl.nobs) for i=0,tbl.nobs-1 do begin frlist[i] = tbl.fn[i] + ' ' + tbl.objnam[i] endfor bs=picker(frlist,title='Select bright object',index=bsref,ysize=40) if bs eq '[[[CANCEL]]]' then return bsimage=readfits(info.dirroot+tbl.fn[bsref],/silent) setwin,0,xsize=256,ysize=256 tv,bytscl(bsimage,min=0,max=imx,top=!d.n_colors-1) words=str_sep(tbl.fn[bsref],'.') info.bsrefn=fix(words[1]) endif endif ; Get flat field images if allcal or absposcal or calib.flatname eq '[none]' then begin print,'' print,'You must also identify the flat field image pair (one with lights on' print,'and one with lights off). The dialog box that has just appeared allows' print,'you an opportunity to select the needed image pair.' print,'' if info.flaton lt 0 or info.flatoff lt 0 then begin frlist=strarr(tbl.nobs) for i=0,tbl.nobs-1 do begin frlist[i] = tbl.fn[i] + ' ' + tbl.objnam[i] endfor ffs=picker(frlist,title='Flat with lights',ysize=40,index=ff1) if ffs eq '[[[CANCEL]]]' then return ffs=picker(frlist,title='Flat no lights',ysize=40,index=ff2) if ffs eq '[[[CANCEL]]]' then return words=str_sep(tbl.fn[ff1],'.') info.flaton=fix(words[1]) words=str_sep(tbl.fn[ff2],'.') info.flatoff=fix(words[1]) endif endif ; Set slope of each order (if requested) if allcal or slopecal then begin print,'' print,'The first determination of the calibration information is to find the slope' print,'of each spectral order. You will proceed through each order to set this' print,'slope, one order at a time. Window 1 will contain a plot of the current' print,"order's centerline. Also, the program will print out the current slope" print,'of the extracted centerline. If the extraction slope is correct, then this' print,'slope should be zero. The commands during this step are s, x, y, or q' print,'' print,' s - Compute current slope and set new slope to the new value.' print,' x - Set the x bounds for the extraction in this order.' print,' y - Set the y location for this order.' print,' q - Quit, go on to the next step.' print,'' print,'Normally, you would just use "s" on each order and you would be done.' print,'Occasionally, you may need to tweak the x location. You only need to' print,'tweak the y location if the centerline is not located at all. As long' print,'as you can see the bright star spectrum in this step you are close enough.' print,'' dirtycal=0 for i=0,calib.nor-1 do begin choice='' title='Order '+string(i,form='(i1)') repeat begin getstrip,calib,info.dirroot+'/'+info.root,info.bsrefn,strip setwin,1,xsize=256,ysize=calib.height erase tv,bytscl(strip[calib.o[i,0]:calib.o[i,1],*], $ min=0,max=imx,top=!d.n_colors-1) maxloc,strip[calib.o[i,0]:calib.o[i,1],*],/x,xpos,ypos xpos=xpos+calib.x1[i] coeff=goodpoly(xpos,ypos,1,2.0,yfit,newx,newy) setwin,2,xsize=400,ysize=250 setusym,-1 plot,xpos,ypos,psym=-8,yr=[0,calib.height-1],title=title, $ xtitle='Column number',ytitle='Row number' setusym,1 oplot,newx,newy,psym=8 oplot,xpos,yfit print,title,' slope = ',coeff[1] read,prompt='Action? (s,x,y or q) ',choice case choice of 's': begin calib.slope[i] = calib.slope[i]+coeff[1] dirtycal = 1 endif 'x': begin print,'Current x bounds: ',calib.x1[i],calib.x2[i] newx1=0 newx2=0 read,prompt='New x bounds? ',newx1,newx2 calib.x1[i]=newx1 calib.x2[i]=newx2 dirtycal = 1 endif 'y': begin print,'Current y position: ',calib.y0[i] newy=0.0 read,prompt='New y position? ',newy calib.y0[i] = newy dirtycal = 1 endif else: begin if choice ne 'q' then begin print,'' print,' s - Adjust slope based on fitted line' print,' x - Provide new x boundaries for the order' print,' y - Provide new y position for the order' print,'' print,' q - Quit, no more changes to this order' print,'' endif endif endcase if dirtycal then begin wrcalir,calib,'files.cal' ldcalir,'files.cal',calib,valid,/silent spawn,lscmd+'-l files.cal',result info.caldate=result[0] dirtycal=0 endif endrep until choice eq 'q' endfor endif ; end slope adjustment block ; Set the relative shifts between orders if allcal or relposcal then begin print,'' print,'The next step is to get the relative shifts between the orders set so that' print,'the centerline of the star spectrum is in the same place in all orders' print,'(after extraction). To set the relative location, you will be asked to' print,'pick a reference order. It does not really matter which order you pick if' print,'you have picked a good reference star. After selecting the reference order' print,'the locations of the other orders are shifted to make them all have the same' print,'location as the reference order.' print,'' dirtycal=0 choice='' repeat begin getstrip,calib,info.dirroot+'/'+info.root,info.bsrefn,strip setwin,2,xsize=400,ysize=250 plot,[0],[0],xr=[0,calib.height-1],yr=[-0.1,1.1] backsub,strip,/col,order=1 diff=strip idx=findgen(calib.height) avgcol=fltarr(calib.height) for i=0,calib.npts-1 do begin diff[i,*]=diff[i,*]/max(diff[i,*]) endfor yloc=fltarr(calib.nor) for i=0,calib.nor-1 do begin for j=0,calib.height-1 do begin robomean,diff[calib.o[i,0]:calib.o[i,1],j],3,.5,avg avgcol[j]=avg endfor yfit=gaussfit(idx,avgcol,a) yloc[i] = a[1] if i eq 0 then begin aref=a[1] print,'order ',i,a[1] endif else begin print,'order ',i,a[1],calib.y0[i]+a[1]-aref endelse oplot,idx,avgcol,psym=-8,symsize=0.5,color=!d.n_colors-1-i*20 z=where(avgcol eq max(avgcol)) xyouts,idx[z],avgcol[z],string(i,format='(i1)'),align=0.5 endfor ;Just look and make sure object spectrum lines up between orders. setwin,1,xsize=calib.npts,ysize=calib.height tv,bytscl(strip,min=-20,max=70,top=!d.n_colors-1) read,prompt='Reference order for shift? (or q to quit) ',choice case choice of '0': begin oref = fix(choice) dirtycal = 1 endif '1': begin oref = fix(choice) dirtycal = 1 endif '2': begin oref = fix(choice) dirtycal = 1 endif '3': begin oref = fix(choice) dirtycal = 1 endif else: begin endif endcase if dirtycal then begin if oref lt calib.nor then begin calib.y0=calib.y0+(yloc-yloc[oref]) wrcalir,calib,'files.cal' ldcalir,'files.cal',calib,valid,/silent spawn,lscmd+'-l files.cal',result info.caldate=result[0] endif dirtycal=0 endif endrep until choice eq 'q' endif ; end relative shift block ; Set the absolute positions of all orders (together) if allcal or absposcal then begin print,'' print,'The final location step is the set the absolute location of the slit on' print,'the image. To do this you are shown a plot of some random columns in the' print,'image as traces across the raw flat field image. You want to set the' print,'slit location such that you are seeing just those pixels illuminated by' print,'the spectrograph. Each shift value you give is relative to the current' print,'location so you can move things around by successively smaller amounts' print,'until the extraction parameters look right.' print,'' choice='' dirtycal=0 repeat begin setwin,1,xsize=calib.npts,ysize=calib.height getpair,calib,info.dirroot+info.root,info.flaton, $ info.flatoff,strip,/raw erase tvscl,strip,0 setwin,2,xsize=400,ysize=250 plot,strip[100,*]/max(strip[100,*]),yr=[0.,1.] oplot,strip[101,*]/max(strip[101,*]) oplot,strip[102,*]/max(strip[102,*]) oplot,strip[250,*]/max(strip[250,*]),color=100 oplot,strip[251,*]/max(strip[251,*]),color=100 oplot,strip[252,*]/max(strip[252,*]),color=100 oplot,strip[480,*]/max(strip[480,*]),color=80 oplot,strip[481,*]/max(strip[481,*]),color=80 oplot,strip[482,*]/max(strip[482,*]),color=80 oplot,strip[680,*]/max(strip[680,*]),color=60 oplot,strip[681,*]/max(strip[681,*]),color=60 oplot,strip[682,*]/max(strip[682,*]),color=60 read,prompt='Shift amount (or q to quit) ',choice if choice ne 'q' then begin calib.y0=calib.y0+float(choice) wrcalir,calib,'files.cal' ldcalir,'files.cal',calib,valid,/silent spawn,lscmd+'-l files.cal',result info.caldate=result[0] endif endrep until choice eq 'q' endif ; end absolute position block ; Construct flat field if calib.flatname eq '[none]' then begin print,'' print,'The final step in the creation of the flat field is its normalization.' print,'You should select an intensity level from the plot in window 2 that' print,'roughly corresponds to the average peak signal.' print,'' getpair,calib,info.dirroot+info.root,info.flaton, $ info.flatoff,strip,/raw setwin,2,xsize=400,ysize=250 plot,strip[*,calib.height/2],yr=[0,max(strip[*,calib.height/2])] for i=0,calib.height-1 do oplot,strip[*,i] ; Get normalization constant print,'Click on window 2 at the normalization level' cursor,x,ynorm,3,/data ; Normalize and clip very low values. setwin,1,xsize=calib.npts,ysize=calib.height*3 erase tvscl,strip,0 flat = strip/ynorm mflat=median(flat,7) z=where(mflat lt 0.005,count) if count ne 0 then mflat[z]=0.005 tvscl,mflat,1 z=where(abs(flat/mflat - 1.0) gt 0.2 or (flat lt 0.005),count) if count ne 0 then flat[z]=mflat[z] tvscl,flat,2 ; Plot the normalized flat field. setwin,3,xsize=400,ysize=250 plot,flat[*,calib.height/2],yr=[0.,max(flat)] for i=0,calib.height-1 do oplot,flat[*,i] setwin,4,xsize=400,ysize=250 plot,[0],[1],/nodata,xr=[0,calib.npts-1],yr=[0,max(flat/mflat)] for i=0,calib.height-1 do oplot,flat[*,i]/mflat[*,i] ; Save data to FITS file. calib.flatname = '+'+info.root+'.flat' writefits,info.root+'.flat',flat print,'New flat field saved to ',info.root+'.flat' wrcalir,calib,'files.cal' ldcalir,'files.cal',calib,valid,/silent spawn,lscmd+'-l files.cal',result info.caldate=result[0] endif ; Wavelength calibration if allcal or wavecal then begin if not exists('sky.spec') then begin print,'' print,'Determining the wavelength calibration requires the generation of a sky' print,'spectrum. This is best done from a set of images on an object that is' print,'faint and thus has a considerable sky signal in the data. Just select' print,'an appropriate object the program will automatically construct a sky' print,'spectrum from the block of observations you selected.' print,'' retry_sky: ; Pick an object that has lots of sky signal. frlist=strarr(tbl.nobs) for i=0,tbl.nobs-1 do frlist[i] = tbl.fn[i] + ' ' + tbl.objnam[i] skys=picker(frlist,title='Select frame for sky',index=ski,ysize=40) if skys eq '[[[CANCEL]]]' then return ; Scan to find range of contiguous frames for this object i10=ski i20=ski repeat i10=i10-1 until tbl.objnam[i10] ne tbl.objnam[ski] or i10 eq 0 repeat i20=i20+1 until tbl.objnam[i20] ne tbl.objnam[ski] or i20 eq tbl.nobs-1 if i10 ne 0 then i10=i10+1 if i20 ne tbl.nobs-1 then i20=i20-1 words=str_sep(tbl.fn[i10],'.') i1=fix(words[1]) words=str_sep(tbl.fn[i20],'.') i2=fix(words[1]) ; Check for any excluded frames zg=where(tbl.imflag[i10:i20] eq '-',countzg) if zg[0] eq -1 then begin print,'All frames for this object set are excluded, try another object set.' goto,retry_sky endif zidx=indgen(i20-i10+1)+i10 ; Read in entire stack of frames stack=fltarr(calib.npts,calib.height,countzg,/nozero) print,' ---> Loading frames ',i1,i2 j=i10 k=0 for i=i1,i2 do begin if tbl.imflag[j] eq '-' then begin getstrip,calib,info.dirroot+info.root,i,strip stack[*,*,k] = strip k=k+1 endif j=j+1 endfor ; Combine stack into a single frame. print,' ---> Averaging stack of frames ' avgclip,stack,avg,/silent setwin,1,xsize=calib.npts,ysize=calib.height*3 tvscl,avg,0 ; Get an averaged sky signal nonsky=avg backsub,nonsky,/col tvscl,nonsky,1 sky=avg-nonsky tvscl,sky,2 skyspec=sky[*,15] print,' ---> Saving sky spectrum to sky.spec ' writefits,'sky.spec',skyspec endif ; end sky spectrum creation block sky=readfits('sky.spec',/silent) gotlines=0 if exists('/opt/local/iraf/iraf/noao/lib/linelists/ohlines.dat') then begin readcol,'/opt/local/iraf/iraf/noao/lib/linelists/ohlines.dat', $ ohlam,flux,/silent gotlines=1 endif if exists('/usr/local/iraf/noao/lib/linelists/ohlines.dat') then begin readcol,'/usr/local/iraf/noao/lib/linelists/ohlines.dat', $ ohlam,flux,/silent gotlines=1 endif if not gotlines then begin print,'FATAL ERROR! Unable to find the IRAF ohlines.dat file.' return endif ohlam=ohlam/10000.0 dd=[-2,-1,0,1,2] ; centroiding aperture dirtycal=0 print,'' print,'You need to calibrate the wavelength scale for each order. You will be' print,'shown the measured sky spectrum (on top in white) and a synthetic OH line' print,'spectrum (on the bottom in orange). You will identify corresponding lines' print,'in each spectrum. As the number of lines identified increases, the' print,'wavelength calibration is recomputed and replotted accordingly. During this' print,'step the mouse buttons have the following functions:' print,'' print,' (1st:sky spectrum) (2nd:synthetic)' print,' left measure nearest line grab nearest strong line' print,' middle delete nearest point nothing' print,' right done abort this line' print,'' for i=0,calib.nor-1 do begin ordfile='order'+string(i,format='(i1)')+'.dat' title='Order '+string(i,form='(i1)') ;Extract working copy for this order and sort by increasing wavelength osky=sky[calib.o[i,0]:calib.o[i,1]] wsky=calib.w[calib.o[i,0]:calib.o[i,1]] n = calib.x2[i] - calib.x1[i] + 1 xsky=indgen(n) idx=sort(wsky) wsky=wsky[idx] osky=osky[idx] xsky=xsky[idx] ; Find local minima to define a spline-based continuum and remove. zcont=lclxtrem(osky,5,/point_order) tmpval=spl_init(wsky[zcont],osky[zcont]) cont=spl_interp(wsky[zcont],osky[zcont],tmpval,wsky) osky=osky-cont ; Find all local maxima, most will be sky lines. zsky=lclxtrem(osky,5,/max,/point_order) yr=[-max(osky)/2.0,max(osky)] done=0 if exists(ordfile) then begin readcol,ordfile,xloc,wloc,fwhm,fwhs,bad,format='f,f,f,f,i',/silent nmeas=n_elements(xloc) endif else begin nmeas=0 endelse repeat begin ; do as much as possible given what is known from current ; line assignments if nmeas eq 1 then begin xa = poly(xloc[0],calib.cof[i,*]) calib.cof[i,0] = calib.cof[i,0]-xa+wloc[0] endif else if nmeas eq 2 then begin calib.cof[i,2:*] = 0.0 calib.cof[i,1] = (wloc[1]-wloc[0])/(xloc[1]-xloc[0]) xa = poly(xloc[0],calib.cof[i,*]) calib.cof[i,0] = calib.cof[i,0]-xa+wloc[0] endif else if nmeas eq 3 then begin por=min([2,calib.por]) calib.cof[i,0:por]=goodpoly(xloc,wloc,por,2.0,yfit,newx,newy) endif else if nmeas ge 4 then begin por=min([3,calib.por]) calib.cof[i,0:por]=goodpoly(xloc,wloc,por,2.0,yfit,newx,newy) endif else begin endelse ; Update the wavelength segment in the calibration info for the ; current provisional coefficients. wsky=poly(findgen(n),calib.cof[i,*]) calib.w[calib.o[i,0]:calib.o[i,1]]=wsky wsky=wsky[idx] ; Create synthetic spectrum from OH line list. disp = abs( (calib.w[calib.o[i,1]]-calib.w[calib.o[i,0]]) / $ (calib.o[i,1]-calib.o[i,0]) ) npts = calib.o[i,1]-calib.o[i,0]+1+20 lam0 = min(calib.w[calib.o[i,0]:calib.o[i,1]])-abs(disp)*10 ohl = findgen(npts)*disp + lam0 ohs = fltarr(npts) ohp=fix((ohlam - lam0)/disp + 0.5) z=where(ohp ge 0 and ohp lt npts) ohs[ohp[z]]=flux[z] gauss2d,11,11,5,5,2.0,arr kern=arr[*,5] kern=kern/total(kern) sohs=convol(ohs,kern) sohs=sohs/max(sohs)*max(osky) zsyn=lclxtrem(sohs,5,/max,/point_order) sohss=sohs-max(osky)/2.0 ; plot dispersion fit (if enough points). if nmeas ge 3 then begin setwin,5,xsize=500,ysize=250 setusym,-1 plot,wloc,(wloc-poly(xloc,calib.cof[i,*]))/calib.cof[i,1], $ xtitle='Wavelength (microns)',ytitle='Residuals (pixels)', $ title=title,psym=8 setusym,1 oplot,newy,(newy-poly(newx,calib.cof[i,*]))/calib.cof[i,1],psym=8 endif ; plot spectrum with overlain synthetic spectrum setwin,4,xsize=1000,ysize=600 plot,wsky,osky,yr=yr, $ xtitle='Wavelength (microns)',ytitle='Signal',title=title oplot,ohl,sohss,color=80 if nmeas ne 0 then begin xa = poly(xloc,calib.cof[i,*]) if nmeas ge 3 then begin oplot,xa,replicate(0.,nmeas),psym=5,color=55 oplot,wloc,replicate(yr[0],nmeas),psym=5,color=55 xa = poly(newx,calib.cof[i,*]) oplot,xa,replicate(0.,nmeas),psym=5 oplot,newy,replicate(yr[0],nmeas),psym=5,color=80 endif else begin oplot,xa,replicate(0.,nmeas),psym=5 oplot,wloc,replicate(yr[0],nmeas),psym=5,color=80 endelse endif print,'Click on line in sky spectrum (white)' cursor,x,y,3,/data if !mouse.button eq 1 then begin dirtycal=1 z=where(abs(x-wsky[zsky]) eq min(abs(x-wsky[zsky]))) z=z[0] oplot,[wsky[zsky[z]]],[osky[zsky[z]]],psym=4 xloc0 = total(xsky[zsky[z]+dd]*osky[zsky[z]+dd]) / $ total(osky[zsky[z]+dd]) fwhm0 = total(osky[zsky[z]+dd])/max(osky[zsky[z]+dd]) print,'Click on line in synthetic spectrum (orange)' cursor,x,y,3,/data if !mouse.button eq 1 then begin ; based on centroiding synthetic spectrum z=where(abs(x-ohl[zsyn]) eq min(abs(x-ohl[zsyn]))) z=z[0] ;wloc0 = total(ohl[zsyn[z]+dd]*sohs[zsyn[z]+dd]) / $ ; total(sohs[zsyn[z]+dd]) fwhs0 = total(sohs[zsyn[z]+dd])/max(sohs[zsyn[z]+dd]) ; based on nearest bright line. z=where(abs(x-ohlam) lt 2.0*abs(calib.cof[i,1])) zz=where(flux[z] eq max(flux[z])) wloc0 = ohlam[z[zz]] if nmeas eq 0 then begin xloc = [xloc0] wloc = [wloc0] fwhm = [fwhm0] fwhs = [fwhs0] bad = 0 nmeas = 1 endif else begin xloc = [xloc,xloc0] wloc = [wloc,wloc0] fwhm = [fwhm,fwhm0] fwhs = [fwhs,fwhs0] bad = [bad,0] nmeas = nmeas+1 endelse print,nmeas,xloc0,wloc0,fwhm0,fwhs0 endif endif else if !mouse.button eq 2 then begin if nmeas eq 1 then begin dirtycal=1 nmeas=0 endif else begin dirtycal=1 z=where(abs(x-wloc) ne min(abs(x-wloc))) xloc = xloc[z] wloc = wloc[z] fwhm = fwhm[z] fwhs = fwhs[z] bad = bad[z] nmeas = nmeas - 1 endelse endif else begin if nmeas ne 0 and dirtycal then begin openw,lun,ordfile,/get_lun for j=0,nmeas-1 do $ printf,lun,xloc[j],wloc[j],fwhm[j],fwhs[j],bad[j] free_lun,lun endif done=1 endelse endrep until done endfor if dirtycal then begin print,' ---> Updating files.cal with new dispersion correction' wrcalir,calib,'files.cal' ldcalir,'files.cal',calib,valid,/silent spawn,lscmd+'-l files.cal',result info.caldate=result[0] dirtycal=0 endif endif ; end wavelength calibration block ;========================= ; Begin section on spectral extraction if not nospec then begin tblparse,tbl,oblist,badset ng=n_elements(oblist)/3 if badset then begin print,'' print,'OSIRIS data cannot be properly reduced with object sets that are' print,'not homogeneous. You must locate the oddball frames and marked them' print,'to be skipped. The second column in file ',info.root,'.tbl should be' print,'changed from - to x to mark it as a frame to skip. You must fix this' print,'problem before this program will proceed to extract spectra from this' print,'nights data. Edit the file and try again.' print,'' goto,exitproc endif ; Find images mates for those that need it. if max(oblist[2,*]) ne 0 then print,' ---> Scanning for image mates.' for i=0,ng-1 do begin if oblist[2,i] eq 1 then begin i1=oblist[0,i] i2=oblist[1,i] zg=where(tbl.imflag[i1:i2] ne 'x',countzg) idx=indgen(i2-i1+1)+i1 idx=idx[zg] if i1 eq i2 then begin tbl.imtype[i1]='t' print,'Warning, ',tbl.fn[i1],' is a solitary frame and' print,'cannot be reduced. It has now been marked as such and will' print,'be skipped in future processing.' oblist[0,i]=-1 endif else begin print,tbl.objnam[i1]+blanks,tbl.imnum[i1], $ tbl.imnum[i2],format='(a16,1x,"frames",2x,i3," to ",i3)' zx=where(tbl.imflag[i1:i2] eq 'x',countzx) zidx=indgen(i2-i1+1)+i1 if countzx ne 0 then begin imnum=tbl.imnum[i1:i2] excl=imnum[zx] tbl.mate[zidx[zx]]=-1 endif else begin excl=-1 endelse clscan,calib,info.root,tbl.imnum[oblist[0,i]], $ tbl.imnum[oblist[1,i]],frno,mate,EXCLUDE=excl, $ xrange=[250,450],path=info.dirroot tbl.mate[idx]=mate ; for j=oblist[0,i],oblist[1,i] do begin ; outprof='Spec/'+info.root+'p.'+string(tbl.imnum[j],format='(i3.3)') ; outspec='Spec/'+info.root+'s.'+string(tbl.imnum[j],format='(i3.3)') ; outbadp='Spec/'+info.root+'b.'+string(tbl.imnum[j],format='(i3.3)') ; outmask='mask.'+string(tbl.imnum[j],format='(i3.3)') ; kill=0 ; if exists(outprof) then kill=1 ; if not kill then if exists(outspec) then kill=1 ; if not kill then if exists(outbadp) then kill=1 ; if kill then spawn,'rm '+outprof+' '+outspec+' '+ $ ; outbadp+' '+outmask+' >& /dev/null' ; endfor endelse tbl.dirty=1 endif endfor if max(oblist[2,*]) ne 0 then print,'' maskname = info.root+'.mask' ; If on a final pass, build the mask image if not already done. if not exists(maskname) and final then begin bildmask,maskname spawn,rmcmd+' mask.*' spawn,rmcmd+' Spec/'+info.root+'b.* >& /dev/null' endif ; Set conditions for bad pixel mask if exists(maskname) then begin fmask=readfits(maskname,/silent) mask = fix(fmask / maskthresh) < 1 findbad=0 endif else begin findbad=1 endelse ; Extract spectra if not exists('Spec') then spawn,'mkdir Spec' for i=0,tbl.nobs-1 do begin if tbl.imtype[i] eq 'o' and tbl.imflag[i] eq '-' then begin outspec='Spec/'+info.root+'s.'+string(tbl.imnum[i],format='(i3.3)') outprof='Spec/'+info.root+'p.'+string(tbl.imnum[i],format='(i3.3)') ; Check to see if existing frame is consistent with frame mates. if exists(outspec) then begin chkhdr=headfits(outspec) frammate=sxpar(chkhdr,'FRAMMATE') if frammate ne tbl.mate[i] then begin print,'Mate changed for frame ',tbl.fn[i],', recomputing.' outbadp='Spec/'+info.root+'b.'+string(tbl.imnum[i],format='(i3.3)') outmask='mask.'+string(tbl.imnum[i],format='(i3.3)') spawn,rmcmd+' '+outprof+' '+outspec+' '+ $ outbadp+' '+outmask+' >& /dev/null' endif endif if not exists(outspec) or not exists(outprof) or allspec or final then begin if findbad then begin optspec,calib,info.root,tbl.imnum[i],tbl.mate[i],/save, $ path=info.dirroot,findbad=findbad, $ outpath='Spec',gausscor=gausscor,final=final,plots=plots endif else begin optspec,calib,info.root,tbl.imnum[i],tbl.mate[i],/save, $ path=info.dirroot,mask=mask, $ outpath='Spec',gausscor=gausscor,/final,plots=plots endelse endif endif endfor ; Within groups, generate final average spectra if not exists('Final') then spawn,'mkdir Final' for i=0,ng-1 do begin if oblist[0,i] ne -1 and oblist[0,i] ne oblist[1,i] then begin root = 'Final/' + info.root + '.' + string(i,format='(i2.2)') suff = strlowcase(tbl.objnam[oblist[0,i]]) outname= root + '.' + suff i1=oblist[0,i] i2=oblist[1,i] zg=where(tbl.imflag[i1:i2] eq '-',countzg) idx=indgen(i2-i1+1)+i1 idx=idx[zg] if not exists(outname) or allspec or final or avgspec or $ min(tbl.relsig[idx]) lt 0.0 then begin print,tbl.objnam[i1]+blanks,tbl.imnum[i1],tbl.imnum[i2],outname, $ format='(a16,1x,"frames",2x,i3," to ",i3," saving avg to ",a)' zx=where(tbl.imflag[i1:i2] ne '-',countzx) if countzx ne 0 then begin imnum=tbl.imnum[i1:i2] excl=imnum[zx] endif else begin excl=-1 endelse nframes = countzg jd=total(tbl.jd[idx])/double(nframes) airmas=mean(tbl.airmas[idx]) avgspec,'Spec/'+info.root+'s',suff,tbl.imnum[i1],EXCLUDE=excl, $ tbl.imnum[i2],OUTROOT=root,JD=jd,AIRMASS=airmas, $ OBJECT=tbl.objnam[i1],scfactor=sf,/WEIGHTED tbl.relsig[idx]=sf tbl.dirty=1 endif endif endfor endif ;========================= ; End spectral extraction section if min(groupcheck) ge 0 then begin dname=!d.name set_plot,'PS' setpage,/portrait,xsize=18.0,ysize=24.0 device,/Helvetica page=0 plot=0 gap=0.03 nplots=8 ; 5 x1=0.05 x2=0.95 cs=0.5 dx=0.05 dl=0.009 blankt=replicate(' ',30) dy = (1.0-(nplots-1)*gap)/float(nplots) for i=groupcheck[0],groupcheck[1] do begin z=where(tbl.imnum eq i and tbl.imtype eq 'o' and tbl.imflag ne 'x') z=z[0] if z ne -1 then begin if plot eq 0 then noerase=0 else noerase=1 y2 = 1.0 - (gap+dy)*plot y1 = y2 - dy specname='Spec/'+info.root+'s.'+string(tbl.imnum[z],format='(i3.3)') profname='Spec/'+info.root+'p.'+string(tbl.imnum[z],format='(i3.3)') print,'plot',page,plot,specname,format='(a,1x,i2,1x,i2,1x,a)' spec=readfits(specname,hdr,/silent) readcol,profname,colno,avgcol,tag,lowband,hiband, $ format='i,f,a,f,f',/silent idx=reverse(sort(spec)) yr=[0.,mean(spec[idx[20:30]])] plotspec,calib,spec,yr=yr,position=[x1,y1,x2-dx,y2],noerase=noerase, $ charsize=cs xyouts,x2,y2-dl*0.5,tbl.objnam[z],align=0.5,charsize=cs,/normal jdstr,tbl.jd[z],0,jds xyouts,x2,y2-dl*2.0,strmid(jds,0,10),align=0.5,charsize=cs,/normal xyouts,x2,y2-dl*3.0,strmid(jds,11,20),align=0.5,charsize=cs,/normal if tbl.avego[z] eq 1 then begin str=strcompress(string(tbl.exptim[z],format='(f10.1)'),/remove_all)+" sec" endif else begin str=strcompress(string(tbl.avego[z],tbl.exptim[z], $ format='(i10,"x",f10.1)'),/remove_all)+" sec" endelse xyouts,x2,y2-dl*4.0,str,align=0.5,charsize=cs,/normal str=strcompress(string(tbl.airmas[z],format='("Airmass=",f5.2)'),/remove_all) xyouts,x2,y2-dl*5.0,str,align=0.5,charsize=cs,/normal str=tbl.fn[z]+'-'+string(tbl.mate[z],format='(i3.3)') xyouts,x2,y2-dl*6.5,str,align=0.5,charsize=cs,/normal str=strcompress(string(tbl.relsig[z],format='("RelSig=",f10.3)'),/remove_all) xyouts,x2,y2-dl*7.5,str,align=0.5,charsize=cs,/normal plot = plot + 1 if plot eq nplots then begin plot = 0 page = page + 1 endif endif endfor device,/close if page gt 0 or plot gt 0 and queue ne '[none]' then begin spawn,'lp -c -d '+queue+' idl.ps' spawn,rmcmd+' idl.ps' endif set_plot,dname !p.font=-1 !p.multi=0 endif ; Optional summary plots if min(plotrange) ge 0 then begin dname=!d.name set_plot,'PS' setpage,/portrait,xsize=18.0,ysize=24.0 device,/Helvetica page=0 plot=0 gap=0.03 nplots=8 ; 5 x1=0.05 x2=0.725 x3=1.0 cs=0.5 dx=0.05 dl=0.009 blankt=replicate(' ',30) dy = (1.0-(nplots-1)*gap)/float(nplots) for i=plotrange[0],plotrange[1] do begin z=where(tbl.imnum eq i and tbl.imtype eq 'o' and tbl.imflag eq '-') z=z[0] if z ne -1 then begin if plot eq 0 then noerase=0 else noerase=1 y2 = 1.0 - (gap+dy)*plot y1 = y2 - dy specname='Spec/'+info.root+'s.'+string(tbl.imnum[z],format='(i3.3)') profname='Spec/'+info.root+'p.'+string(tbl.imnum[z],format='(i3.3)') print,'plot',page,plot,specname,format='(a,1x,i2,1x,i2,1x,a)' spec=readfits(specname,hdr,/silent) readcol,profname,colno,avgcol,tag,lowband,hiband, $ format='i,f,a,f,f',/silent idx=reverse(sort(spec)) yr=[0.,mean(spec[idx[20:30]])] plotspec,calib,spec,yr=yr,position=[x1,y1,x2-dx,y2],noerase=noerase, $ charsize=cs yr=[min([-1.0,min(avgcol)]),max([1.0,max(avgcol)])] plot,colno,avgcol,xtitle='Row number',position=[x2+dx,y1,x3,y2], $ ytitle='Relative signal strength',/noerase,yr=yr, $ xstyle=7,ystyle=7 oplot,colno,lowband,linestyle=1 oplot,colno,hiband,linestyle=1 zp=where(tag eq 'p') zn=where(tag eq 'n') zs=where(tag eq 's') oplot,colno[zp],avgcol[zp],psym=5,symsize=0.5 oplot,colno[zn],avgcol[zn],psym=2,symsize=0.5 oplot,colno[zs],avgcol[zs],psym=8,symsize=0.2 axis,xaxis=0,charsize=cs,xtitle='Row number' axis,xaxis=1,xtickname=blankt axis,yaxis=0,ytickname=blankt axis,yaxis=1,charsize=cs,ytitle='Relative signal strength' xyouts,x2,y2-dl*0.5,tbl.objnam[z],align=0.5,charsize=cs,/normal jdstr,tbl.jd[z],0,jds xyouts,x2,y2-dl*2.0,strmid(jds,0,10),align=0.5,charsize=cs,/normal xyouts,x2,y2-dl*3.0,strmid(jds,11,20),align=0.5,charsize=cs,/normal if tbl.avego[z] eq 1 then begin str=strcompress(string(tbl.exptim[z],format='(f10.1)'),/remove_all)+" sec" endif else begin str=strcompress(string(tbl.avego[z],tbl.exptim[z], $ format='(i10,"x",f10.1)'),/remove_all)+" sec" endelse xyouts,x2,y2-dl*4.0,str,align=0.5,charsize=cs,/normal str=strcompress(string(tbl.airmas[z],format='("Airmass=",f5.2)'),/remove_all) xyouts,x2,y2-dl*5.0,str,align=0.5,charsize=cs,/normal str=tbl.fn[z]+'-'+string(tbl.mate[z],format='(i3.3)') xyouts,x2,y2-dl*6.5,str,align=0.5,charsize=cs,/normal str=strcompress(string(tbl.relsig[z],format='("RelSig=",f10.3)'),/remove_all) xyouts,x2,y2-dl*7.5,str,align=0.5,charsize=cs,/normal plot = plot + 1 if plot eq nplots then begin plot = 0 page = page + 1 endif endif endfor device,/close if page gt 0 or plot gt 0 and queue ne '[none]' then begin spawn,'lp -c -d '+queue+' idl.ps' spawn,rmcmd+' idl.ps' endif set_plot,dname !p.font=-1 !p.multi=0 endif ;========================= ; Exit processing exitproc: ; If information table has been changed, regenerate output file. if tbl.dirty then begin print,' ---> updating information table.' wrtbl,tablname,tbl spawn,lscmd+'-l '+tablname,result info.tbldate = result[0] tbl.dirty = 0 endif end