Initial commit

1 files changed, 297 insertions, 0 deletions

diff --git a/noao/imred/src/fibers/batch.cl b/noao/imred/src/fibers/batch.cl
new file mode 100644
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+++ b/noao/imred/src/fibers/batch.cl
@@ -0,0 +1,297 @@
+# BATCH -- Process spectra in batch.
+# This task is called in batch mode.  It only processes objects
+# not previously processed unless the update or redo flags are set.
+
+procedure batch ()
+
+string	objects		{prompt="Object spectra"}
+real	datamax		{prompt="Max data value / cosmic ray threshold"}
+
+file	response	{prompt="Response spectrum"}
+string	arcs1		{prompt="List of arc spectra"}
+string	arcs2		{prompt="List of shift arc spectra"}
+file	arcref1		{prompt="Arc reference for dispersion solution"}
+file	arcref2		{prompt="Arc reference for dispersion solution"}
+file	arcreplace	{prompt="Special aperture replacements"}
+string	arcrefs		{prompt="Arc references"}
+string	extn		{prompt="Extraction extension"}
+
+file	apidtable	{prompt="Aperture identifications"}
+string	objaps		{prompt="Object apertures"}
+string	skyaps		{prompt="Sky apertures"}
+string	arcaps		{prompt="Arc apertures"}
+string	objbeams	{prompt="Object beam numbers"}
+string	skybeams	{prompt="Sky beam numbers"}
+string	arcbeams	{prompt="Arc beam numbers\n"}
+
+file	done		{prompt="File of spectra already done"}
+file	logfile		{prompt="Logfile"}
+
+bool	redo		{prompt="Redo operations?"}
+bool	update		{prompt="Update spectra?"}
+bool	scattered	{prompt="Subtracted scattered light?"}
+bool	arcap		{prompt="Use object apertures for arcs?"}
+bool	dispcor		{prompt="Dispersion correct spectra?"}
+bool	savearcs	{prompt="Save internal arcs?"}
+bool	skyalign	{prompt="Align sky lines?"}
+bool	skysubtract	{prompt="Subtract sky?"}
+bool	saveskys	{prompt="Save sky spectra?\n"}
+
+bool	newaps, newresp, newdisp, newarcs
+
+struct	*fd1, *fd2, *fd3
+
+begin
+	file	objs, temp, temp1, spec, specms, arc
+	bool	reextract, extract, scat, disp, sky, log
+	string	imtype, mstype, str, str2, str3, str4
+	int	i
+
+	imtype = "." // envget ("imtype")
+	i = stridx (",", imtype)
+	if (i > 0)
+	    imtype = substr (imtype, 1, i-1)
+	mstype = ".ms" // imtype
+
+	objs = mktemp ("tmp$iraf")
+	temp = mktemp ("tmp$iraf")
+	temp1 = mktemp ("tmp$iraf")
+
+	# Initialize extraction to be noninteractive.
+	if (apscript.ansrecenter == "yes")
+	    apscript.ansrecenter = "YES"
+	else if (apscript.ansrecenter == "no")
+	    apscript.ansrecenter = "NO"
+	apscript.ansedit = "NO"
+	if (apscript.anstrace == "yes") {
+	    apscript.anstrace = "YES"
+	    apscript.ansfittrace = "NO"
+	} else if (apscript.anstrace == "no")
+	    apscript.anstrace = "NO"
+
+	reextract = redo || (update && (newaps || newresp || newdisp))
+
+	getspec (objects, objs)
+	fd1 = objs
+	while (fscan (fd1, spec) != EOF) {
+	    if (access (done)) {
+	        fd2 = done
+	        while (fscan (fd2, specms) != EOF)
+		    if (spec == specms)
+		        break
+	        if (spec == specms)
+		    next
+	        fd2 = ""
+	    }
+	    if (!access (spec // imtype)) {
+		printf ("Object spectrum not found - %s%s\nCheck setting of imtype\n", spec, imtype, >> logfile)
+		next
+	    }
+	    specms = spec // mstype
+
+	    scat = no
+	    extract = no
+	    disp = no
+	    sky = no
+	    if (scattered) {
+		if (redo && access (spec//"noscat"//imtype)) {
+		    imdelete (spec, verify=no)
+		    imrename (spec//"noscat", spec)
+		}
+		hselect (spec, "apscatte", yes) | scan (str)
+		if (nscan() == 0)
+		    scat = yes
+	    }
+	    if (reextract || !access (specms) || (update && scat))
+		extract = yes
+	    else {
+		hselect (specms, "dclog1", yes) | scan (str)
+		if (nscan () == 1) {
+		    extract = update && newdisp
+		    if (update && !newdisp)
+		        # We really should check if REFSPEC will assign
+			# different reference spectra.
+			;
+		} else
+		    disp = dispcor
+
+		hselect (specms, "skysub", yes) | scan (str)
+		if (nscan() == 0)
+		    sky = skysubtract
+	    }
+		
+	    if (extract) {
+		disp = dispcor
+		sky = skysubtract
+	    }
+
+	    if (extract) {
+		if (access (specms))
+		    imdelete (specms, verify=no)
+		if (scat) {
+		    print ("Subtract scattered light from ", spec, >> logfile)
+		    imrename (spec, spec//"noscat")
+		    apscript (spec//"noscat", output=spec, ansextract="NO",
+			ansscat="YES", anssmooth="YES", verbose=no)
+		}
+		print ("Extract object spectrum ", spec, >> logfile)
+		hselect (spec, "date-obs,ut,exptime", yes, > temp1)
+		hselect (spec, "ra,dec,epoch,st", yes, >> temp1)
+		fd3 = temp1
+		if (fscan (fd3, str, str2, str3) == 3) {
+		    setjd (spec, observatory=observatory, date="date-obs",
+			time="ut", exposure="exptime", jd="jd", hjd="",
+			ljd="ljd", utdate=yes, uttime=yes, listonly=no,
+			>> logfile)
+		    if (fscan (fd3, str, str2, str3, str4) == 4)
+			setairmass (spec, intype="beginning",
+			    outtype="effective", exposure="exptime",
+			    observatory=observatory, show=no, update=yes,
+			    override=yes, >> logfile)
+		}
+		fd3 = ""; delete (temp1, verify=no)
+		apscript (spec, nsubaps=params.nsubaps, saturation=datamax,
+		    verbose=no)
+		sapertures (specms, apertures="", apidtable=apidtable,
+		    wcsreset=no, verbose=no, beam=INDEF, dtype=INDEF, w1=INDEF,
+		    dw=INDEF, z=INDEF, aplow=INDEF, aphigh=INDEF, title=INDEF)
+		if (response != "") {
+		    if (params.nsubaps == 1)
+			sarith (specms, "/", response, specms, w1=INDEF,
+			    w2=INDEF, apertures="", bands="", beams="",
+			    apmodulus=0, reverse=no, ignoreaps=no,
+			    format="multispec", renumber=no, offset=0,
+			    clobber=yes, merge=no, errval=0, verbose=no)
+		    else {
+			blkrep (response, temp, 1, params.nsubaps)
+			sarith (specms, "/", temp, specms, w1=INDEF,
+			    w2=INDEF, apertures="", bands="", beams="",
+			    apmodulus=0, reverse=no, ignoreaps=yes,
+			    format="multispec", renumber=no, offset=0,
+			    clobber=yes, merge=no, errval=0, verbose=no)
+			imdelete (temp, verify=no)
+		    }
+		}
+	    }
+
+	    if (disp) {
+		# Fix arc headers if necessary.
+		if (newarcs) {
+		    getspec (arcs1, temp)
+	    	    fd2 = temp
+	    	    while (fscan (fd2, arc) != EOF) {
+			hselect (arc, "date-obs,ut,exptime", yes, > temp1)
+			hselect (arc, "ra,dec,epoch,st", yes, >> temp1)
+			fd3 = temp1
+			if (fscan (fd3, str, str2, str3) == 3) {
+			    setjd (arc, observatory=observatory, date="date-obs",
+				time="ut", exposure="exptime", jd="jd", hjd="",
+				ljd="ljd", utdate=yes, uttime=yes, listonly=no,
+				>> logfile)
+			    if (fscan (fd3, str, str2, str3, str4) == 4)
+				setairmass (arc, intype="beginning",
+				    outtype="effective", exposure="exptime",
+				    observatory=observatory, show=no, update=yes,
+				    override=yes, >> logfile)
+			}
+			fd3 = ""; delete (temp1, verify=no)
+	        	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 (temp, verify=no)
+		    getspec (arcs2, temp)
+	    	    fd2 = temp
+	    	    while (fscan (fd2, arc) != EOF) {
+			hselect (arc, "date-obs,ut,exptime", yes, > temp1)
+			hselect (arc, "ra,dec,epoch,st", yes, >> temp1)
+			fd3 = temp1
+			if (fscan (fd3, str, str2, str3) == 3) {
+			    setjd (arc, observatory=observatory,
+				date="date-obs", time="ut", exposure="exptime",
+				jd="jd", hjd="", ljd="ljd", utdate=yes,
+				uttime=yes, listonly=no, >> logfile)
+			    if (fscan (fd3, str, str2, str3, str4) == 4)
+				setairmass (arc, intype="beginning",
+				    outtype="effective", exposure="exptime",
+				    observatory=observatory, show=no,
+				    update=yes, override=yes, >> logfile)
+
+			}
+			fd3 = ""; delete (temp1, verify=no)
+	        	hedit (arc, "refspec1", arc, add=yes, verify=no,
+		    	    show=no, update=yes)
+	        	hedit (arc, "arctype", "shift", add=yes, verify=no,
+		    	    show=no, update=yes)
+	    	    }
+	    	    fd2 = ""; delete (temp, verify=no)
+		    newarcs = no
+		}
+
+		print ("Assign arc spectra for ", spec, >> logfile)
+		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,
+		    >> logfile)
+
+		doarcs (spec, response, arcref1, arcref2, extn, arcreplace,
+		    apidtable, arcaps, arcbeams, savearcs, reextract, arcap,
+		    logfile, yes, done)
+
+	        hselect (specms, "refspec1", yes, > temp)
+	        fd2 = temp
+	        i = fscan (fd2, arc)
+	        fd2 = ""; delete (temp, verify=no)
+		if (i < 1)
+		    print ("No arc reference assigned for ", spec, >> logfile)
+		else {
+		    if (skyalign)
+			doalign (spec, specms, "align"//extn//imtype,
+			    arcref1//extn, logfile, yes)
+	            print ("Dispersion correct ", spec, >> logfile)
+		    dispcor (specms, "", linearize=params.linearize,
+			database=database, table=arcref1//extn, w1=INDEF,
+			w2=INDEF, dw=INDEF, nw=INDEF, log=params.log,
+			flux=params.flux, samedisp=no, global=no,
+			ignoreaps=no, confirm=no, listonly=no, verbose=no,
+			logfile=logfile)
+		    if (params.nsubaps > 1) {
+			imrename (specms, temp, verbose=no)
+			scopy (temp, specms, w1=INDEF, w2=INDEF,
+			    apertures="1-999", bands="", beams="", apmodulus=0,
+			    offset=0, format="multispec", clobber=no, merge=no,
+			    renumber=no, verbose=no)
+			blkavg (temp, temp, 1, params.nsubaps, option="sum")
+			imcopy (temp, specms//"[*,*]", verbose=no)
+			imdelete (temp, verify=no)
+		    }
+		    disp = no
+		}
+	    }
+
+	    if (sky && !disp) {
+		str = ""
+		if (skyaps != "")
+		    str = "skyaps=" // skyaps
+		if (skybeams != "")
+		    str = str // " skybeams=" // skybeams
+	        print ("Sky subtract ", spec, ": ", str, >> logfile)
+		skysub (specms, output="", objaps=objaps, skyaps=skyaps,
+		    objbeams=objbeams, skybeams=skybeams, skyedit=no,
+		    combine=params.combine, reject=params.reject,
+		    scale=params.scale, saveskys=saveskys, logfile=logfile)
+	        hedit (specms, "skysub", str, add=yes, show=no, verify=no,
+		    update=yes)
+	    }
+	}
+	fd1 = ""; delete (objs, verify=no)
+
+	if (access (done))
+	    delete (done, verify=no)
+
+	flprcache (0)
+end