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authorJoseph Hunkeler <jhunkeler@gmail.com>2015-07-08 20:46:52 -0400
committerJoseph Hunkeler <jhunkeler@gmail.com>2015-07-08 20:46:52 -0400
commitfa080de7afc95aa1c19a6e6fc0e0708ced2eadc4 (patch)
treebdda434976bc09c864f2e4fa6f16ba1952b1e555 /noao/imred/src/dofoe/proc.cl
downloadiraf-linux-fa080de7afc95aa1c19a6e6fc0e0708ced2eadc4.tar.gz
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+# PROC -- Process echelle fiber spectra
+# This program combines the operations of extraction, flat fielding, and
+# dispersion correction in as simple and noninteractive way as possible.
+# It supports a second simultaneous arc fiber. The data must all share
+# the same position on the 2D image and the same dispersion solution
+# apart from small instrumental changes which can be tracked
+# automatically. The apertures must be identified sequentially and must
+# be properly paired if a arc fiber is used.
+#
+# If every needed on could add sky subtraction (with a sky fiber) and
+# fluxing following the model of the multifiber packages.
+
+procedure proc (objects, apref, flat, arcs, arctable, naps, objaps, arcaps,
+ objbeams, arcbeams, fitflat, recenter, scattered, edit, trace, arcap,
+ clean, dispcor, splot, redo, update, batch, listonly)
+
+string objects {prompt="List of object spectra"}
+
+file apref {prompt="Aperture reference spectrum"}
+file flat {prompt="Flat field spectrum"}
+string arcs {prompt="List of arc spectra"}
+file arctable {prompt="Arc assignment table (optional)\n"}
+
+int naps {prompt="Number of apertures"}
+string objaps {prompt="Object apertures"}
+string arcaps {prompt="Arc apertures"}
+string objbeams {prompt="Object beam numbers"}
+string arcbeams {prompt="Arc beam numbers\n"}
+
+bool fitflat {prompt="Fit and ratio flat field spectrum?"}
+bool recenter {prompt="Recenter object apertures?"}
+bool scattered {prompt="Subtract scattered light?"}
+bool edit {prompt="Edit/review object apertures?"}
+bool trace {prompt="Trace object spectra?"}
+bool arcap {prompt="Use object apertures for arcs?"}
+bool clean {prompt="Detect and replace bad pixels?"}
+bool dispcor {prompt="Dispersion correct spectra?"}
+bool splot {prompt="Plot the final spectrum?"}
+bool redo {prompt="Redo operations if previously done?"}
+bool update {prompt="Update spectra if cal data changes?"}
+bool batch {prompt="Extract objects in batch?"}
+bool listonly {prompt="List steps but don't process?\n"}
+
+real datamax = INDEF {prompt="Max data value / cosmic ray threshold"}
+
+bool newaps, newresp, newdisp, newarcs, dobatch
+
+string anssplot = "yes" {prompt="Splot spectrum?", mode="q",
+ enum="no|yes|NO|YES"}
+
+struct *fd1, *fd2
+
+begin
+ string imtype, ectype
+ string arcref, spec, arc
+ string arcrefec, specec, arcec, response
+ string temp1, temp2, done
+ string str1, objs, arcrefs, log1, log2
+ bool reextract, extract, scat, disp, disperr, log
+ bool splot1, splot2
+ int i, j, n, nspec
+ struct err
+
+ # Call a separate task to do the listing to minimize the size of
+ # this script and improve it's readability.
+
+ dobatch = no
+ if (listonly) {
+ listonly (objects, apref, flat, arcs, scattered, dispcor,
+ redo, update)
+ bye
+ }
+
+ imtype = "." // envget ("imtype")
+ i = stridx (",", imtype)
+ if (i > 0)
+ imtype = substr (imtype, 1, i-1)
+ ectype = ".ec" // imtype
+ n = strlen (imtype)
+
+ # Get query parameter.
+ objs = objects
+ if (arctable == "")
+ arcrefs = arcs
+ else
+ arcrefs = arctable
+ arcref = ""
+
+ # Temporary files used repeatedly in this script. Under some
+ # abort circumstances these files may be left behind.
+
+ temp1 = mktemp ("tmp$iraf")
+ temp2 = mktemp ("tmp$iraf")
+ done = mktemp ("tmp$iraf")
+
+ # Rather than always have switches on the logfile and verbose flags
+ # we use TEE and set a file to "dev$null" if output is not desired.
+ # We must check for the null string to signify no logfile.
+
+ tee.append = yes
+ if (logfile == "")
+ log1 = "dev$null"
+ else
+ log1 = logfile
+ if (verbose)
+ log2 = "STDOUT"
+ else
+ log2 = "dev$null"
+
+ # If the update switch is used changes in the calibration data
+ # can cause images to be reprocessed (if they are in the object
+ # list). Possible changes are in the aperture definitions,
+ # response function, dispersion solution, and sensitivity
+ # function. The newarcs flag is used to only go through the arc
+ # image headers once setting the reference spectrum, airmass, and
+ # UT.
+
+ newaps = no
+ newresp = no
+ newdisp = no
+ newarcs = yes
+
+ # Check if there are aperture definitions in the database and
+ # define them if needed. This is usually somewhat interactive.
+ # Delete the database entry to start fresh if we enter this
+ # because of a redo. Set the newaps flag in case an update is
+ # desired.
+
+ i = strlen (apref)
+ if (i > n && substr (apref, i-n+1, i) == imtype)
+ apref = substr (apref, 1, i-n)
+
+ # Initialize
+ apscript.saturation = INDEF
+ apscript.references = apref
+ apscript.profiles = ""
+ apscript.nfind = naps
+ apscript.clean = clean
+ if (splot) {
+ splot1 = yes
+ splot2 = yes
+ } else {
+ splot1 = no
+ splot2 = no
+ }
+
+ reextract = redo
+ if (reextract || !access (database // "/ap" // apref)) {
+ if (!access (apref // imtype)) {
+ printf ("Aperture reference spectrum not found - %s%s\n",
+ apref, imtype) | scan (err)
+ error (1, err // "\nCheck setting of imtype")
+ }
+ print ("Set reference apertures for ", apref) | tee (log1)
+ if (access (database // "/ap" // apref))
+ delete (database // "/ap" // apref, verify=no)
+ apscript.ansresize = "yes"
+ apscript.ansedit = "YES"
+ apscript.ansfittrace = "yes"
+ apscript (apref, references="", ansfind="YES", ansrecenter="NO",
+ anstrace="YES", ansextract="NO")
+ newaps = yes
+ }
+
+ if (recenter)
+ apscript.ansrecenter = "YES"
+ else
+ apscript.ansrecenter = "NO"
+ apscript.ansresize = "NO"
+ if (edit)
+ apscript.ansedit = "yes"
+ else
+ apscript.ansedit = "NO"
+ if (trace)
+ apscript.anstrace = "YES"
+ else
+ apscript.anstrace = "NO"
+ apscript.ansfittrace = "NO"
+ apscript.ansextract = "YES"
+ apscript.ansreview = "NO"
+
+ # The next step is to setup the scattered light correction if needed.
+ # We use the flat field image for the interactive setting unless
+ # one is not used an then we use the aperture reference.
+ # If these images have been scattered light corrected we assume the
+ # scattered light functions parameters are correctly set.
+
+ i = strlen (flat)
+ if (i > n && substr (flat, i-n+1, i) == imtype)
+ flat = substr (flat, 1, i-n)
+
+ if (flat != "")
+ spec = flat
+ else
+ spec = apref
+
+ scat = no
+ if (scattered) {
+ hselect (spec, "apscatte", yes, > temp1)
+ fd1 = temp1
+ if (fscan (fd1, str1) < 1)
+ scat = yes
+ fd1 = ""; delete (temp1, verify=no)
+ }
+ if (scat) {
+ print ("Subtract scattered light in ", spec) | tee (log1)
+ apscript.ansfitscatter = "yes"
+ apscript.ansfitsmooth = "yes"
+ apscript (spec, output="", ansextract="NO", ansscat="YES",
+ anssmooth="YES")
+ apscript.ansfitscatter = "NO"
+ apscript.ansfitsmooth = "NO"
+ }
+
+ response = ""
+ if (flat != "") {
+ response = flat // "norm.ec"
+ reextract = redo || (update && newaps)
+ if (reextract || !access (response // imtype) || (update && scat)) {
+ print ("Create response function ", response) | tee (log1)
+
+ if (access (response // imtype))
+ imdelete (response, verify=no)
+ if (access (flat //ectype))
+ imdelete (flat//ectype, verify=no)
+
+ response (flat, apref, response, recenter=recenter,
+ edit=edit, trace=trace, clean=clean, fitflat=fitflat,
+ interactive=params.f_interactive,
+ function=params.f_function, order=params.f_order)
+
+ newresp = yes
+ }
+ }
+
+ # If not dispersion correcting we can go directly to extracting
+ # the object spectra. The reference arcs are the first on
+ # the arc lists. The processing of the reference arcs is done
+ # by the task ARCREFS.
+
+ if (dispcor) {
+ hselect (arcs, "$I", yes, >temp1)
+ fd1 = temp1
+ i = fscan (fd1, arcref)
+ if (i < 1)
+ error (1, "No reference arcs")
+ fd1 = ""; delete (temp1, verify=no)
+ i = strlen (arcref)
+ if (i > n && substr (arcref, i-n+1, i) == imtype)
+ arcref = substr (arcref, 1, i-n)
+ if (!access (arcref // imtype)) {
+ printf ("Arc reference spectrum not found - %s%s\n",
+ arcref, imtype) | scan (err)
+ error (1, err // "\nCheck setting of imtype")
+ }
+ arcrefec = arcref // ectype
+ reextract = redo || (update && newaps)
+ if (reextract && access (arcrefec))
+ imdelete (arcrefec, verify=no)
+
+ arcrefs (arcref, arcaps, arcbeams, response, done, log1, log2)
+ }
+
+ # Now we are ready to process the object spectra.
+
+ reextract = redo || (update && (newaps || newresp || newdisp))
+ hselect (objs, "$I", yes, > temp1)
+ fd1 = temp1
+ while (fscan (fd1, spec) != EOF) {
+ i = strlen (spec)
+ if (i > n && substr (spec, i-n+1, i) == imtype)
+ spec = substr (spec, 1, i-n)
+
+ # Check if previously done; i.e. arc.
+ if (access (done)) {
+ fd2 = done
+ while (fscan (fd2, specec) != EOF)
+ if (spec == specec)
+ break
+ if (spec == specec)
+ next
+ fd2 = ""
+ }
+ if (!access (spec // imtype)) {
+ printf ("Object spectrum not found - %s%s\n",
+ spec, imtype) | scan (err)
+ print (err) | tee (log1)
+ print ("Check setting of imtype")
+ next
+ }
+ specec = spec // ectype
+
+ # Determine required operations from the flags and image header.
+ scat = no
+ extract = no
+ disp = no
+ if (scattered) {
+ hselect (spec, "apscatte", yes, > temp2)
+ fd2 = temp2
+ if (fscan (fd2, str1) < 1)
+ scat = yes
+ fd2 = ""; delete (temp2, verify=no)
+ }
+ if (reextract || !access (specec) || (update && scat))
+ extract = yes
+ else {
+ hselect (specec, "dc-flag", yes, > temp2)
+ fd2 = temp2
+ if (fscan (fd2, str1) == 1) {
+ extract = update && newdisp
+ if (update && !newdisp)
+ # We really should check if REFSPEC will assign
+ # different reference spectra.
+ ;
+ } else
+ disp = dispcor
+
+ fd2 = ""; delete (temp2, verify=no)
+ }
+
+ if (extract)
+ disp = dispcor
+
+ # If fully processed go to the next object.
+ if (!extract && !disp)
+ next
+
+ # If not interactive and the batch flag is set submit rest to batch.
+ if (batch && !splot1 && !splot2 && apscript.ansedit == "NO") {
+ fd1 = ""; delete (temp1, verify=no)
+ flprcache
+ batch.objects = objs
+ batch.datamax = datamax
+ batch.response = response
+ batch.arcs = arcs
+ batch.arcref = arcref
+ batch.arcrefs = arcrefs
+ batch.objaps = objaps
+ batch.arcaps = arcaps
+ batch.objbeams = objbeams
+ batch.arcbeams = arcbeams
+ batch.done = done
+ batch.logfile = log1
+ batch.redo = reextract
+ batch.update = update
+ batch.scattered = scattered
+ batch.arcap = arcap
+ batch.dispcor = dispcor
+ batch.newaps = newaps
+ batch.newresp = newresp
+ batch.newdisp = newdisp
+ batch.newarcs = newarcs
+ dobatch = yes
+ return
+ }
+
+ # Process the spectrum in foreground.
+ if (extract) {
+ if (access (specec))
+ imdelete (specec, verify=no)
+
+ if (scat) {
+ print ("Subtract scattered light in ", spec) | tee (log1)
+ apscript (spec, output="", ansextract="NO",
+ ansscat="YES", anssmooth="YES")
+ }
+
+ print ("Extract object spectrum ", spec) | tee (log1)
+ setjd (spec, observatory=observatory, date="date-obs",
+ time="ut", exposure="exptime", jd="jd", hjd="",
+ ljd="ljd", utdate=yes, uttime=yes, listonly=no,
+ >> log1)
+ setairmass (spec, intype="beginning",
+ outtype="effective", exposure="exptime",
+ observatory=observatory, show=no, update=yes,
+ override=yes, >> log1)
+ apscript (spec, saturation=datamax)
+ if (response != "")
+ imarith (specec, "/", response, specec)
+ }
+
+ disperr = no
+ if (disp) {
+ # Fix arc headers if necessary.
+ if (newarcs) {
+ sections (arcs, option="fullname", >temp2)
+ setjd ("@"//temp2, observatory=observatory, date="date-obs",
+ time="ut", exposure="exptime", jd="jd", hjd="",
+ ljd="ljd", utdate=yes, uttime=yes, listonly=no,
+ >> log1)
+ setairmass ("@"//temp2, intype="beginning",
+ outtype="effective", exposure="exptime",
+ observatory=observatory, show=no, update=yes,
+ override=yes, >> log1)
+ delete (temp2, verify=no)
+ hselect (arcs, "$I", yes, >temp2)
+ fd2 = temp2
+ while (fscan (fd2, arc) != EOF) {
+ i = strlen (arc)
+ if (i > n && substr (arc, i-n+1, i) == imtype)
+ arc = substr (arc, 1, i-n)
+ hedit (arc, "refspec1", arc, add=yes, verify=no,
+ show=no, update=yes)
+ hedit (arc, "arctype", "henear", add=yes, verify=no,
+ show=no, update=yes)
+ }
+ fd2 = ""; delete (temp2, verify=no)
+ newarcs = no
+ }
+
+ print ("Assign arc spectra for ", spec) | tee (log1)
+ refspectra (spec, references=arcrefs,
+ apertures="", refaps="", ignoreaps=no,
+ select=params.select, sort=params.sort,
+ group=params.group, time=params.time,
+ timewrap=params.timewrap, override=yes, confirm=no,
+ assign=yes, logfiles="STDOUT", verbose=no) |
+ tee (log1, > log2)
+
+ doarcs (spec, response, arcref, arcaps, arcbeams, reextract,
+ arcap, log1, no)
+
+ hselect (specec, "refspec1", yes, > temp2)
+ fd2 = temp2
+ i = fscan (fd2, arc)
+ fd2 = ""; delete (temp2, verify=no)
+ if (i < 1) {
+ print ("No arc reference assigned for ", spec) | tee (log1)
+ disperr = yes
+ } else {
+ print ("Dispersion correct ", spec) | tee (log1)
+ dispcor (specec, "", linearize=params.linearize,
+ database=database, table=arcref//ectype,
+ w1=INDEF, w2=INDEF, dw=INDEF, nw=INDEF,
+ log=params.log, samedisp=no, flux=params.flux,
+ global=no, ignoreaps=no, confirm=no, listonly=no,
+ verbose=verbose, logfile=logfile)
+ hedit (specec, "dc-flag", 0, add=yes, verify=no,
+ show=no, update=yes)
+ }
+ }
+
+ if (!disperr && (extract || disp)) {
+ if (splot1) {
+ print (specec, ":")
+ str1 = anssplot
+ if (str1 == "NO" || str1 == "YES")
+ splot1 = no
+ if (str1 == "no" || str1 == "NO")
+ splot2 = no
+ else
+ splot2 = yes
+ }
+ if (splot2)
+ splot (specec)
+ }
+
+ print (spec, >> done)
+ }
+ fd1 = ""; delete (temp1, verify=no)
+
+ if (access (done))
+ delete (done, verify=no)
+end