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-rw-r--r--noao/imred/src/doecslit/Revisions93
-rw-r--r--noao/imred/src/doecslit/apslitproc.par145
-rw-r--r--noao/imred/src/doecslit/doecslit.cl106
-rw-r--r--noao/imred/src/doecslit/doecslit.par28
-rw-r--r--noao/imred/src/doecslit/sarcrefs.cl77
-rw-r--r--noao/imred/src/doecslit/sarcrefs.par6
-rw-r--r--noao/imred/src/doecslit/sbatch.cl216
-rw-r--r--noao/imred/src/doecslit/sbatch.par24
-rw-r--r--noao/imred/src/doecslit/sdoarcs.cl102
-rw-r--r--noao/imred/src/doecslit/sdoarcs.par8
-rw-r--r--noao/imred/src/doecslit/sfluxcal.cl214
-rw-r--r--noao/imred/src/doecslit/sfluxcal.par16
-rw-r--r--noao/imred/src/doecslit/sgetspec.cl177
-rw-r--r--noao/imred/src/doecslit/sgetspec.par11
-rw-r--r--noao/imred/src/doecslit/slistonly.cl241
-rw-r--r--noao/imred/src/doecslit/slistonly.par13
-rw-r--r--noao/imred/src/doecslit/slittasks.cl19
-rw-r--r--noao/imred/src/doecslit/sparams.par65
-rw-r--r--noao/imred/src/doecslit/sproc.cl490
-rw-r--r--noao/imred/src/doecslit/sproc.par35
20 files changed, 2086 insertions, 0 deletions
diff --git a/noao/imred/src/doecslit/Revisions b/noao/imred/src/doecslit/Revisions
new file mode 100644
index 00000000..c4e6ee16
--- /dev/null
+++ b/noao/imred/src/doecslit/Revisions
@@ -0,0 +1,93 @@
+.help revisions Dec94 noao.imred.src.doecslit
+.nf
+
+=======
+V2.12.3
+=======
+
+doecslit$sdoarcs.cl
+ The sparams.refit parameter was being ignored and the ecreidentify
+ step has refit=yes hardwired. The parameter reference is now used.
+ (11/14/05, Valdes)
+
+doecslit$sbatch.cl
+doecslit$sproc.cl
+doecslit$fibresponse.cl
+ Error messages now hint to check imtype setting.
+ (4/15/05, Valdes)
+
+========
+V2.12.2b
+========
+
+doecslit$sproc.cl
+ Modified code to eliminate goto. This is for use with pyraf.
+ (11/21/00, Valdes)
+
+========
+V2.11.3a
+========
+
+doecslit$sproc.cl
+ The arcref and arcrefs variables were not initialized if dispcor=no
+ and if the user goes directly to batch mode there is an undefined
+ local variable error. Added initialization. (1/27/98, Valdes)
+
+=======
+V2.11.1
+=======
+
+doecslit$sarcrefs.cl
+doecslit$sbatch.cl
+doecslit$sfluxcal.cl
+doecslit$sgetspec.cl
+doecslit$slistonly.cl
+doecslit$sproc.cl
+doecslit$sdoarcs.cl
+ Any additional qualifiers in the imtype string are stripped.
+ (8/14/97, Valdes)
+
+doecslit$sgetspec.cl
+ Added the field parameter to the RENAME call. (8/12/97, Valdes)
+
+=========
+V2.11Beta
+=========
+
+doecslit$sbatch.cl
+ Fixed typo bugs in this script. (10/3/96, Valdes)
+
+doecslit$apslitproc.par
+ Made changes for the new aperture selection option. (9/5/96, Valdes)
+
+=======
+V2.10.4
+=======
+
+doecslit$sgetspec.cl
+doecslit$doecslit.cl
+ The arc table will now be checked for arc spectra. (5/1/95, Valdes)
+
+doecslit$sparams.par
+doecslit$sdoarcs.cl
+doecslit$sarcrefs.cl
+ Added "threshold" as a user parameter. (1/16/95, Valdes)
+
+doecslit$sproc.cl
+doecslit$sbatch.cl
+doecslit$sfluxcal.cl
+doecslit$sproc.par
+doecslit$sbatch.par
+doecslit$sfluxcal.par
+ SETAIRMASS and SETJD are only called if the required keywords are
+ present. Errors from missing airmass or JD are then reported from
+ the task that actually uses them. (12/31/94, Valdes)
+
+doecslit$sgetspec.cl
+doecslit$sgetspec.par
+ Added warning and query for missing CCDPROC keyword. (12/31/94, Valdes)
+
+=======
+V2.10.3
+=======
+.endhelp
diff --git a/noao/imred/src/doecslit/apslitproc.par b/noao/imred/src/doecslit/apslitproc.par
new file mode 100644
index 00000000..3233960a
--- /dev/null
+++ b/noao/imred/src/doecslit/apslitproc.par
@@ -0,0 +1,145 @@
+# APSCRIPT
+
+input,s,a,,,,List of input images
+output,s,h,"",,,List of output spectra
+apertures,s,h,"",,,Apertures
+scatter,s,h,"",,,List of scattered light images (optional)
+references,s,h,"",,,List of aperture reference images
+profiles,s,h,"",,,"List of aperture profile images
+"
+interactive,b,h,yes,,,Run task interactively?
+find,b,h,yes,,,Find apertures?
+recenter,b,h,yes,,,Recenter apertures?
+resize,b,h,yes,,,Resize apertures?
+edit,b,h,yes,,,Edit apertures?
+trace,b,h,yes,,,Trace apertures?
+fittrace,b,h,yes,,,Fit the traced points interactively?
+extract,b,h,yes,,,Extract spectra?
+review,b,h,yes,,,Review extractions?
+subtract,b,h,yes,,,Subtract scattered light?
+smooth,b,h,yes,,,Smooth scattered light along the dispersion?
+fitscatter,b,h,yes,,,Fit scattered light interactively?
+fitsmooth,b,h,yes,,,"Smooth the scattered light interactively?
+"
+line,i,h,)sparams.line,,,>sparams.line
+nsum,i,h,)sparams.nsum,,,>sparams.nsum
+buffer,r,h,)sparams.buffer,,,">sparams.buffer
+
+# OUTPUT PARAMETERS
+"
+format,s,h,"echelle",,,Extracted spectra format
+extras,b,h,)sparams.extras,,,"Extract sky, sigma, etc.?"
+dbwrite,s,h,"YES",,,Write to database?
+initialize,b,h,no,,,Initialize answers?
+verbose,b,h,)_.verbose,,,"Verbose output?
+
+# DEFAULT APERTURE PARAMETERS
+"
+lower,r,h,,,,Lower aperture limit relative to center
+upper,r,h,,,,Upper aperture limit relative to center
+apidtable,s,h,"",,,"Aperture ID table (optional)
+
+# DEFAULT BACKGROUND PARAMETERS
+"
+b_function,s,h,)sparams.b_function,,,>sparams.b_function
+b_order,i,h,)sparams.b_order,,,>sparams.b_order
+b_sample,s,h,)sparams.b_sample,,,>sparams.b_sample
+b_naverage,i,h,)sparams.b_naverage,,,>sparams.b_naverage
+b_niterate,i,h,)sparams.b_niterate,,,>sparams.b_niterate
+b_low_reject,r,h,)sparams.b_low,,,>sparams.b_low
+b_high_reject,r,h,)sparams.b_high,,,>sparams.b_high
+b_grow,r,h,0.,0.,,"Background rejection growing radius
+
+# APERTURE CENTERING PARAMETERS
+"
+width,r,h,,,,Profile centering width
+radius,r,h,,,,Profile centering radius
+threshold,r,h,10.,0.,,"Detection threshold for profile centering
+
+# AUTOMATIC FINDING AND ORDERING PARAMETERS
+"
+nfind,i,h,,,,Number of apertures to be found automatically
+minsep,r,h,,,,Minimum separation between spectra
+maxsep,r,h,100000.,,,Maximum separation between spectra
+order,s,h,"increasing",,,"Order of apertures
+
+# RECENTERING PARAMETERS
+"
+aprecenter,s,h,"",,,Apertures for recentering calculation
+npeaks,r,h,INDEF,,,Select brightest peaks
+shift,b,h,yes,,,"Use average shift instead of recentering?
+
+# RESIZING PARAMETERS
+"
+llimit,r,h,INDEF,,,Lower aperture limit relative to center
+ulimit,r,h,INDEF,,,Upper aperture limit relative to center
+ylevel,r,h,)sparams.ylevel,,,>sparams.ylevel
+peak,b,h,yes,,,Is ylevel a fraction of the peak?
+bkg,b,h,yes,,,Subtract background in automatic width?
+r_grow,r,h,0.,,,Grow limits by this factor
+avglimits,b,h,no,,,"Average limits over all apertures?
+
+# EDITING PARAMETERS
+"
+e_output,s,q,,,,Output spectra rootname
+e_profiles,s,q,,,,"Profile reference image
+
+# TRACING PARAMETERS
+"
+t_nsum,i,h,)sparams.nsum,,,>sparams.nsum
+t_step,i,h,)sparams.t_step,,,>sparams.t_step
+t_nlost,i,h,3,1,,Number of consecutive times profile is lost before quitting
+t_width,r,h,)sparams.width,,,>sparams.width
+t_function,s,h,)sparams.t_function,,,>sparams.t_function
+t_sample,s,h,"*",,,Trace sample regions
+t_order,i,h,)sparams.t_order,,,>sparams.t_order
+t_naverage,i,h,1,,,Trace average or median
+t_niterate,i,h,)sparams.t_niterate,,,>sparams.t_niterate
+t_low_reject,r,h,)sparams.t_low,,,>sparams.t_low
+t_high_reject,r,h,)sparams.t_high,,,>sparams.t_high
+t_grow,r,h,0.,0.,,"Trace rejection growing radius
+
+# EXTRACTION PARAMETERS
+"
+background,s,h,,,,Background to subtract
+skybox,i,h,1,,,Box car smoothing length for sky
+weights,s,h,)sparams.weights,,,>sparams.weights
+pfit,s,h,)sparams.pfit,,,>sparams.pfit
+clean,b,h,no,,,Detect and replace bad pixels?
+nclean,r,h,0.5,,,Maximum number of pixels to clean
+niterate,i,h,5,0,,Number of profile fitting iterations
+saturation,r,h,INDEF,,,Saturation level
+readnoise,s,h,,,,Read out noise sigma (photons)
+gain,s,h,,,,Photon gain (photons/data number)
+lsigma,r,h,)sparams.lsigma,,,>sparams.lsigma
+usigma,r,h,)sparams.usigma,,,>sparams.usigma
+polysep,r,h,0.95,0.1,0.95,Marsh algorithm polynomial spacing
+polyorder,i,h,10,1,,Marsh algorithm polynomial order
+nsubaps,i,h,1,1,,"Number of subapertures per aperture
+
+# ANSWER PARAMETERS
+"
+ansclobber,s,h,"NO",,," "
+ansclobber1,s,h,"NO",,," "
+ansdbwrite,s,h,"YES",,," "
+ansdbwrite1,s,h,"NO",,," "
+ansedit,s,h,"NO",,," "
+ansextract,s,h,"NO",,," "
+ansfind,s,h,"NO",,," "
+ansfit,s,h,"NO",,," "
+ansfitscatter,s,h,"NO",,," "
+ansfitsmooth,s,h,"NO",,," "
+ansfitspec,s,h,"NO",,," "
+ansfitspec1,s,h,"NO",,," "
+ansfittrace,s,h,"NO",,," "
+ansfittrace1,s,h,"NO",,," "
+ansflat,s,h,"NO",,," "
+ansnorm,s,h,"NO",,," "
+ansrecenter,s,h,"NO",,," "
+ansresize,s,h,"NO",,," "
+ansreview,s,h,"NO",,," "
+ansreview1,s,h,"NO",,," "
+ansscat,s,h,"NO",,," "
+ansskyextract,s,h,"NO",,," "
+anssmooth,s,h,"NO",,," "
+anstrace,s,h,"NO",,," "
diff --git a/noao/imred/src/doecslit/doecslit.cl b/noao/imred/src/doecslit/doecslit.cl
new file mode 100644
index 00000000..a3675416
--- /dev/null
+++ b/noao/imred/src/doecslit/doecslit.cl
@@ -0,0 +1,106 @@
+# DOECSLIT -- Process Echelle slit spectra from 2D to wavelength calibrated
+# and flux calibrated 1D spectra.
+#
+# The task PROC does all of the interactive work and BATCH does the
+# background work. This procedure is organized this way to minimize the
+# dictionary space when the background task is submitted.
+
+procedure doecslit (objects)
+
+string objects = "" {prompt="List of object spectra"}
+
+file apref = "" {prompt="Aperture reference spectrum"}
+string arcs = "" {prompt="List of arc spectra"}
+file arctable = "" {prompt="Arc assignment table (optional)"}
+string standards = "" {prompt="List of standard star spectra\n"}
+
+string readnoise = "0." {prompt="Read out noise sigma (photons)"}
+string gain = "1." {prompt="Photon gain (photons/data number)"}
+real datamax = INDEF {prompt="Max data value / cosmic ray threshold"}
+int norders = 10 {prompt="Number of orders"}
+real width = 5. {prompt="Width of profiles (pixels)\n"}
+
+bool dispcor = yes {prompt="Dispersion correct spectra?"}
+bool extcor = no {prompt="Extinction correct spectra?"}
+bool fluxcal = no {prompt="Flux calibrate spectra?"}
+bool resize = no {prompt="Resize object apertures?"}
+bool clean = no {prompt="Detect and replace bad pixels?"}
+bool trace = yes {prompt="Trace object spectra?"}
+string background = "none" {prompt="Background to subtract",
+ enum="none|scattered|average|median|minimum|fit"}
+bool splot = no {prompt="Plot the final spectra?"}
+bool redo = no {prompt="Redo operations if previously done?"}
+bool update = no {prompt="Update spectra if cal data changes?"}
+bool quicklook = no {prompt="Approximate quicklook reductions?"}
+bool batch = no {prompt="Extract objects in batch?"}
+bool listonly = no {prompt="List steps but don't process?\n"}
+
+pset sparams = "" {prompt="Algorithm parameters"}
+
+begin
+ bool recenter, arcap, tr, scat
+
+ int i, j
+ file obj, arc, std
+
+ # Expand image lists
+ obj = mktemp ("tmp$iraf")
+ arc = mktemp ("tmp$iraf")
+ std = mktemp ("tmp$iraf")
+ sgetspec (objects, arcs, arctable, standards, obj, arc, std)
+
+ # Remove any leading whitespace from parameters that might be null.
+ if (logfile != "") {
+ j = strlen (logfile)
+ for (i=1; i<=j && substr(logfile,i,i)==" "; i+=1);
+ logfile = substr (logfile, i, j)
+ }
+ if (arctable != "") {
+ j = strlen (arctable)
+ for (i=1; i<=j && substr(arctable,i,i)==" "; i+=1);
+ arctable = substr (arctable, i, j)
+ }
+
+ apslitproc.readnoise = readnoise
+ apslitproc.gain = gain
+ apslitproc.nfind = norders
+ apslitproc.width = width
+ apslitproc.lower = -width / 2.
+ apslitproc.upper = width / 2.
+ apslitproc.b_sample = \
+ str(-2*width)//":"//str(-width)//","//str(width)//":"//str(2*width)
+ apslitproc.t_width = width
+ apslitproc.radius = width
+ apslitproc.minsep = width
+ apslitproc.clean = clean
+ if (background == "scattered") {
+ scat = yes
+ apslitproc.background = "none"
+ } else {
+ scat = no
+ apslitproc.background = background
+ }
+ sproc.datamax = datamax
+
+ recenter = yes
+ tr = trace
+ arcap = yes
+ if (quicklook) {
+ tr = no
+ scat = no
+ arcap = no
+ }
+
+ sproc (obj, apref, arc, arctable, std, recenter,
+ resize, quicklook, tr, scat, arcap, dispcor,
+ extcor, fluxcal, splot, redo, update, batch, listonly)
+ delete (std, verify=no)
+
+ if (sproc.dobatch) {
+ print ("-- Do remaining spectra as a batch job --")
+ print ("sbatch&batch") | cl
+ } else {
+ delete (obj, verify=no)
+ delete (arc, verify=no)
+ }
+end
diff --git a/noao/imred/src/doecslit/doecslit.par b/noao/imred/src/doecslit/doecslit.par
new file mode 100644
index 00000000..1d68f729
--- /dev/null
+++ b/noao/imred/src/doecslit/doecslit.par
@@ -0,0 +1,28 @@
+objects,s,a,"",,,"List of object spectra"
+apref,f,h,"",,,"Aperture reference spectrum"
+arcs,s,h,"",,,"List of arc spectra"
+arctable,f,h,"",,,"Arc assignment table (optional)"
+standards,s,h,"",,,"List of standard star spectra
+"
+readnoise,s,h,"0.",,,"Read out noise sigma (photons)"
+gain,s,h,"1.",,,"Photon gain (photons/data number)"
+datamax,r,h,INDEF,,,"Max data value / cosmic ray threshold"
+norders,i,h,10,,,"Number of orders"
+width,r,h,5.,,,"Width of profiles (pixels)
+"
+dispcor,b,h,yes,,,"Dispersion correct spectra?"
+extcor,b,h,no,,,"Extinction correct spectra?"
+fluxcal,b,h,no,,,"Flux calibrate spectra?"
+resize,b,h,no,,,"Resize object apertures?"
+clean,b,h,no,,,"Detect and replace bad pixels?"
+trace,b,h,yes,,,"Trace object spectra?"
+background,s,h,"none",none|scattered|average|median|minimum|fit,,"Background to subtract"
+splot,b,h,no,,,"Plot the final spectra?"
+redo,b,h,no,,,"Redo operations if previously done?"
+update,b,h,no,,,"Update spectra if cal data changes?"
+quicklook,b,h,no,,,"Approximate quicklook reductions?"
+batch,b,h,no,,,"Extract objects in batch?"
+listonly,b,h,no,,,"List steps but don\'t process?
+"
+sparams,pset,h,"",,,"Algorithm parameters"
+mode,s,h,"ql",,,
diff --git a/noao/imred/src/doecslit/sarcrefs.cl b/noao/imred/src/doecslit/sarcrefs.cl
new file mode 100644
index 00000000..907b446f
--- /dev/null
+++ b/noao/imred/src/doecslit/sarcrefs.cl
@@ -0,0 +1,77 @@
+# SARCREFS -- Determine dispersion relation for reference arc.
+
+procedure sarcrefs (arcref, done, log1, log2)
+
+file arcref
+file done
+file log1
+file log2
+
+struct *fd
+
+begin
+ string arcrefec, arcec, temp
+ int i, dc
+ bool log
+
+ temp = mktemp ("tmp$iraf")
+
+ # Extract the primary arc reference spectrum. Determine the
+ # dispersion function with IDENTIFY/REIDENTIFY. Set the wavelength
+ # parameters with ECDISPCOR.
+
+ arcrefec = arcref // ".ec." // envget ("imtype")
+ i = stridx (",", arcrefec)
+ if (i > 0)
+ arcrefec = substr (arcrefec, 1, i-1)
+ if (!access (arcrefec)) {
+ print ("Extract arc reference image ", arcref) | tee (log1)
+ apslitproc (arcref, background="none", clean=no, weights="none")
+ }
+
+ # Get the dispersion parameters from the header. These are
+ # used for all further spectra and also flag whether this
+ # spectrum has been processed. If the parameters are missing
+ # the spectrum needs to have the dispersion function and
+ # wavelength scale determined. The HEDIT is needed because
+ # in some cases the user may exit ECIDENTIFY without updating
+ # the database (if the image was deleted but the database
+ # entry was not).
+
+ hselect (arcrefec, "dc-flag", yes, > temp)
+ fd = temp
+ dc = -1
+ i = fscan (fd, dc)
+ fd = ""; delete (temp, verify=no)
+ if (i < 1) {
+ print ("Determine dispersion solution for ", arcref) | tee (log1)
+ #delete (database//"/ec"//arcref//".ec*", verify=no)
+ ecidentify (arcrefec, database=database,
+ coordlist=sparams.coordlist, match=sparams.match,
+ maxfeatures=100, zwidth=10., ftype="emission",
+ fwidth=sparams.fwidth, cradius=sparams.cradius,
+ threshold=sparams.threshold, minsep=2.,
+ function=sparams.i_function, xorder=sparams.i_xorder,
+ yorder=sparams.i_yorder, niterate=sparams.i_niterate,
+ lowreject=sparams.i_low, highreject=sparams.i_high,
+ autowrite=yes)
+ hedit (arcrefec, "refspec1", arcref // ".ec", add=yes,
+ show=no, verify=no, update=yes)
+ }
+
+ # Dispersion correct the reference arc. This step is required to
+ # to set the wavelength scale for all further spectra.
+
+ if (i < 1) {
+ dispcor (arcrefec, "", linearize=sparams.linearize,
+ database=database, table="", w1=INDEF, w2=INDEF, dw=INDEF,
+ nw=INDEF, log=sparams.log, flux=sparams.flux, samedisp=no,
+ global=no, ignoreaps=no, confirm=no, listonly=no, verbose=yes,
+ logfile=log1, > log2)
+ hedit (arcrefec, "dc-flag", 0, add=yes, show=no,
+ verify=no, update=yes)
+ sproc.newdisp = yes
+ }
+
+ print (arcref, >> done)
+end
diff --git a/noao/imred/src/doecslit/sarcrefs.par b/noao/imred/src/doecslit/sarcrefs.par
new file mode 100644
index 00000000..38b81646
--- /dev/null
+++ b/noao/imred/src/doecslit/sarcrefs.par
@@ -0,0 +1,6 @@
+arcref,f,a,"",,,
+done,f,a,"",,,
+log1,f,a,"",,,
+log2,f,a,"",,,
+fd,*struct,h,"",,,
+mode,s,h,"q",,,
diff --git a/noao/imred/src/doecslit/sbatch.cl b/noao/imred/src/doecslit/sbatch.cl
new file mode 100644
index 00000000..062ac3e5
--- /dev/null
+++ b/noao/imred/src/doecslit/sbatch.cl
@@ -0,0 +1,216 @@
+# SBATCH -- 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 sbatch ()
+
+file objects {prompt="Object spectra"}
+real datamax {prompt="Max data value / cosmic ray threshold"}
+
+file arcs {prompt="List of arc spectra"}
+file arcref {prompt="Arc reference for dispersion solution"}
+string arcrefs {prompt="Arc references\n"}
+
+file done {prompt="File of spectra already done"}
+file logfile {prompt="Logfile"}
+bool redo {prompt="Redo operations?"}
+bool update {prompt="Update spectra?\n"}
+
+bool scattered {prompt="Subtract scattered light?"}
+bool arcap {prompt="Use object apertures for arcs?"}
+bool dispcor {prompt="Dispersion correct spectra?"}
+bool extcor {prompt="Extinction correct spectra?"}
+bool fluxcal1 {prompt="Flux calibrate spectra?"}
+
+bool newaps, newdisp, newsens, newarcs
+
+struct *fd1, *fd2, *fd3
+
+begin
+ file temp, spec, specec, arc
+ bool reextract, extract, scat, disp, ext, flux, log, disperr
+ string imtype, ectype, str1, str2, str3, str4
+ int i
+ str1 = ""
+
+ imtype = "." // envget ("imtype")
+ i = stridx (",", imtype)
+ if (i > 0)
+ imtype = substr (imtype, 1, i-1)
+ ectype = ".ec" // imtype
+
+ temp = mktemp ("tmp$iraf")
+
+ reextract = redo || (update && (newaps || newdisp))
+
+ fd1 = objects
+ while (fscan (fd1, spec) != EOF) {
+ if (access (done)) {
+ fd2 = done
+ while (fscan (fd2, specec) != EOF)
+ if (spec == specec)
+ break
+ if (spec == specec)
+ next
+ fd2 = ""
+ }
+ if (!access (spec // imtype)) {
+ print ("Object spectrum not found - " // spec // imtype,
+ >> logfile)
+ print ("Check setting of imtype", >> logfile)
+ next
+ }
+ specec = spec // ectype
+
+ scat = no
+ extract = no
+ disp = no
+ ext = no
+ flux = no
+ if (scattered) {
+ hselect (spec, "apscatte", yes, > temp)
+ fd2 = temp
+ if (fscan (fd2, str1) < 1)
+ scat = yes
+ fd2 = ""; delete (temp, verify=no)
+ }
+ if (reextract || !access (specec) || (update && scat))
+ extract = yes
+ else {
+ hselect (specec, "dc-flag", yes, > temp)
+ hselect (specec, "ex-flag", yes, >> temp)
+ hselect (specec, "ca-flag", yes, >> temp)
+ fd2 = temp
+ 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
+ if (fscan (fd2, str1) == 1)
+ extract = update && !extcor
+ else
+ ext = extcor
+ if (fscan (fd2, str1) == 1)
+ extract = update && (!fluxcal1 || newsens)
+ else
+ flux = fluxcal1
+ fd2 = ""; delete (temp, verify=no)
+ }
+
+ if (extract) {
+ disp = dispcor
+ ext = extcor
+ flux = fluxcal1
+ }
+
+ if (extract) {
+ if (access (specec))
+ imdelete (specec, verify=no)
+
+ if (scat) {
+ print ("Subtract scattered light in ", spec, >> logfile)
+ apslitproc (spec, ansextract="NO", ansscat="YES")
+ }
+
+ print ("Extract object spectrum ", spec, >> logfile)
+ hselect (spec, "date-obs,ut,exptime", yes, > temp)
+ hselect (spec, "ra,dec,epoch,st", yes, >> temp)
+ fd3 = temp
+ if (fscan (fd3, str1, 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, str1, str2, str3, str4) == 4)
+ setairmass (spec, intype="beginning",
+ outtype="effective", exposure="exptime",
+ observatory=observatory, show=no, update=yes,
+ override=yes, >> logfile)
+ }
+ fd3 = ""; delete (temp, verify=no)
+ apslitproc (spec, saturation=datamax, verbose=no)
+ }
+
+ disperr = no
+ if (disp) {
+ # Fix arc headers if necessary.
+ if (newarcs) {
+ fd2 = arcs
+ while (fscan (fd2, arc) != EOF) {
+ hselect (arc, "date-obs,ut,exptime", yes, > temp)
+ hselect (arc, "ra,dec,epoch,st", yes, >> temp)
+ fd3 = temp
+ if (fscan (fd3, str1, 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, str1, str2, str3, str4) == 4)
+ setairmass (arc, intype="beginning",
+ outtype="effective", exposure="exptime",
+ observatory=observatory, show=no,
+ update=yes, override=yes, >> logfile)
+ }
+ fd3 = ""; delete (temp, verify=no)
+ hedit (arc, "refspec1", arc, add=yes, verify=no,
+ show=no, update=yes)
+ }
+ fd2 = ""
+ newarcs = no
+ }
+
+ print ("Assign arc spectra for ", spec, >> logfile)
+ refspectra (spec, references=arcrefs,
+ apertures="", refaps="", ignoreaps=no,
+ select=sparams.select, sort=sparams.sort,
+ group=sparams.group, time=sparams.time,
+ timewrap=sparams.timewrap, override=yes, confirm=no,
+ assign=yes, logfiles="STDOUT", verbose=no,
+ >> logfile)
+
+ sdoarcs (spec, arcref, reextract, arcap, logfile, yes)
+
+ hselect (specec, "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)
+ disperr = yes
+ } else {
+ print ("Dispersion correct ", spec, >> logfile)
+ dispcor (specec, "", linearize=sparams.linearize,
+ database=database, table=arcref//ectype,
+ w1=INDEF, w2=INDEF, dw=INDEF, nw=INDEF,
+ log=sparams.log, flux=sparams.flux, samedisp=no,
+ global=no, ignoreaps=no, confirm=no, listonly=no,
+ logfile=logfile, > "dev$null")
+ hedit (specec, "dc-flag", 0, add=yes, show=no,
+ verify=no, update=yes)
+ }
+ }
+
+ if (!disperr && (extract || disp)) {
+ if (ext)
+ print ("Extinction correct ", spec, >> logfile)
+ if (flux)
+ print ("Flux calibrate ", spec, >> logfile)
+ if (flux || ext)
+ calibrate (specec, "", extinct=extcor, flux=fluxcal1,
+ extinction=extinction, observatory=observatory,
+ ignoreaps=no, sensitivity="sens", fnu=sparams.fnu,
+ >> logfile)
+ }
+ }
+ fd1 = ""
+ delete (objects, verify=no)
+ delete (arcs, verify=no)
+
+ if (access (done))
+ delete (done, verify=no)
+
+ flprcache (0)
+end
diff --git a/noao/imred/src/doecslit/sbatch.par b/noao/imred/src/doecslit/sbatch.par
new file mode 100644
index 00000000..9bb5239d
--- /dev/null
+++ b/noao/imred/src/doecslit/sbatch.par
@@ -0,0 +1,24 @@
+objects,f,h,"",,,"Object spectra"
+datamax,r,h,,,,"Max data value / cosmic ray threshold"
+arcs,f,h,"",,,"List of arc spectra"
+arcref,f,h,"",,,"Arc reference for dispersion solution"
+arcrefs,s,h,,,,"Arc references
+"
+done,f,h,"",,,"File of spectra already done"
+logfile,f,h,"",,,"Logfile"
+redo,b,h,,,,"Redo operations?"
+update,b,h,,,,"Update spectra?
+"
+scattered,b,h,,,,"Subtract scattered light?"
+arcap,b,h,,,,"Use object apertures for arcs?"
+dispcor,b,h,,,,"Dispersion correct spectra?"
+extcor,b,h,,,,"Extinction correct spectra?"
+fluxcal1,b,h,,,,"Flux calibrate spectra?"
+newaps,b,h,,,,
+newdisp,b,h,,,,
+newsens,b,h,,,,
+newarcs,b,h,,,,
+fd1,*struct,h,"",,,
+fd2,*struct,h,"",,,
+fd3,*struct,h,"",,,
+mode,s,h,"ql",,,
diff --git a/noao/imred/src/doecslit/sdoarcs.cl b/noao/imred/src/doecslit/sdoarcs.cl
new file mode 100644
index 00000000..76ccaab8
--- /dev/null
+++ b/noao/imred/src/doecslit/sdoarcs.cl
@@ -0,0 +1,102 @@
+# SDOARCS -- Determine dispersion relation for spectrum based on reference arcs.
+
+procedure sdoarcs (spec, arcref, reextract, arcap, logfile, batch)
+
+file spec
+file arcref
+bool reextract
+bool arcap
+file logfile
+bool batch
+
+struct *fd
+
+begin
+ string imtype, ectype
+ int i, j, k, n
+ file temp, arc1, arc2, str1, str2, arctype, apref, arc, arcec, logs
+ file specec, specarc
+ bool verbose1
+
+ imtype = "." // envget ("imtype")
+ i = stridx (",", imtype)
+ if (i > 0)
+ imtype = substr (imtype, 1, i-1)
+ ectype = ".ec" // imtype
+ n = strlen (imtype)
+
+ temp = mktemp ("tmp$iraf")
+
+ if (batch)
+ verbose1 = no
+ else
+ verbose1 = verbose
+ if (verbose1)
+ logs = logfile//",STDOUT"
+ else
+ logs = logfile
+
+ for (j=1; j<=2; j+=1) {
+ # The reference spectra refer initially to the 2D image. At the
+ # end we will reset them to refer to the 1D spectra.
+
+ hselect (spec, "refspec"//j, yes, > temp)
+ fd = temp
+ k = fscan (fd, arc1, str1)
+ fd = ""; delete (temp, verify=no)
+ if (k < 1)
+ break
+
+ # Strip possible image extension.
+ i = strlen (arc1)
+ if (i > n && substr (arc1, i-n+1, i) == imtype)
+ arc1 = substr (arc1, 1, i-n)
+
+ # Set extraction output and aperture reference depending on whether
+ # the arcs are to be rextracted using recentered or retraced object
+ # apertures.
+
+ if (arcap) {
+ arc2 = spec // arc1
+ apref = spec
+ if (access (arc2//ectype))
+ imdelete (arc2//ectype, verify=no)
+ delete (database//"/ec"//arc2//".ec*", verify = no)
+ } else {
+ arc2 = arc1
+ apref = apslitproc.references
+ if (reextract && access (arc2//ectype)) {
+ if (arc2 != arcref)
+ imdelete (arc2//ectype, verify=no)
+ }
+ }
+
+ # Extract and determine dispersion function if necessary.
+ if (!access (arc2//ectype)) {
+ delete (database//"/ec"//arc2//".ec*", verify = no)
+ if (!batch)
+ print ("Extract and reidentify arc spectrum ", arc1)
+ print ("Extract and reidentify arc spectrum ", arc1, >> logfile)
+ apslitproc (arc1, output=arc2//".ec", references=apref,
+ background="none", clean=no, weights="none",
+ verbose=verbose1)
+ ecreidentify (arc2//".ec", arcref//".ec", shift=0.,
+ cradius=sparams.cradius, threshold=sparams.threshold,
+ refit=sparams.refit, database=database, logfiles=logs)
+
+ # If not reextracting arcs based on object apertures
+ # then save the extracted arc to avoid doing it again.
+
+ if (arc1 != arc2)
+ imdelete (arc2//".ec", verify=no)
+ }
+
+ # Set the REFSPEC parameters for echelle spectrum.
+ if (k == 1)
+ hedit (spec//".ec", "refspec"//j, arc2//".ec", add=yes,
+ verify=no, show=no, update=yes)
+ else
+ hedit (spec//".ec", "refspec"//j, arc2//".ec "//str1, add=yes,
+ verify=no, show=no, update=yes)
+ }
+end
diff --git a/noao/imred/src/doecslit/sdoarcs.par b/noao/imred/src/doecslit/sdoarcs.par
new file mode 100644
index 00000000..648bacaf
--- /dev/null
+++ b/noao/imred/src/doecslit/sdoarcs.par
@@ -0,0 +1,8 @@
+spec,f,a,"",,,
+arcref,f,a,"",,,
+reextract,b,a,,,,
+arcap,b,a,,,,
+logfile,f,a,"",,,
+batch,b,a,,,,
+fd,*struct,h,"",,,
+mode,s,h,"q",,,
diff --git a/noao/imred/src/doecslit/sfluxcal.cl b/noao/imred/src/doecslit/sfluxcal.cl
new file mode 100644
index 00000000..b8b7fd80
--- /dev/null
+++ b/noao/imred/src/doecslit/sfluxcal.cl
@@ -0,0 +1,214 @@
+# SFLUXCAL -- Extract standard stars and determine sensitivity function.
+# If flux calibrating, extract and dispersion correct the standard star
+# spectra. Compile the standard star fluxes from the calibration
+# directory. The user is queried for the star name but the band passes
+# are not allow to change interactively. Next compute the sensitivity
+# function using SENSFUNC. This is interactive. Once the sensitivity
+# function images are created, flux and extinction calibrate the standard
+# stars. This is done in such a way that if new standard stars are added
+# in a later execution only the new stars are added and then a new
+# sensitivity function is computed. If the update flag is set all
+# spectra which are specified are reprocessed if they were previously
+# processed. In a redo the "std" file is deleted, otherwise additions
+# are appended to this file.
+
+procedure sfluxcal (stds, arcs, arcref, arcrefs, redo, update,
+ scattered, arcap, extcor, done, log1, log2)
+
+file stds
+file arcs
+file arcref
+string arcrefs
+bool redo
+bool update
+bool scattered
+bool arcap
+bool extcor
+file done
+file log1
+file log2
+
+struct *fd1, *fd2, *fd3
+
+begin
+ string imtype, ectype
+ string spec, specec, arc, str1, str2, str3, str4
+ file temp1, temp2
+ int i, j
+ bool reextract, log, scat
+ str1 = ""
+ str2 = ""
+
+ imtype = "." // envget ("imtype")
+ i = stridx (",", imtype)
+ if (i > 0)
+ imtype = substr (imtype, 1, i-1)
+ ectype = ".ec" // imtype
+
+ temp1 = mktemp ("tmp$iraf")
+ temp2 = mktemp ("tmp$iraf")
+
+ reextract = redo || (update && (sproc.newaps || sproc.newdisp))
+ sproc.newsens = no
+
+ if (redo && access ("std"))
+ delete ("std", verify=no)
+
+ fd1 = stds
+ while (fscan (fd1, spec) != EOF) {
+ specec = spec // ectype
+
+ scat = no
+ if (scattered) {
+ hselect (spec, "apscatte", yes, > temp1)
+ fd2 = temp1
+ if (fscan (fd2, str1) < 1)
+ scat = yes
+ fd2 = ""; delete (temp1, verify=no)
+ }
+ if (reextract || !access (specec) || (update && scat)) {
+ if (access (specec))
+ imdelete (specec, verify=no)
+
+ if (scat) {
+ print ("Subtract scattered light in ", spec) | tee (log1)
+ apslitproc (spec, ansextract="NO", ansscat="YES")
+ }
+
+ print ("Extract standard star spectrum ", spec) | tee (log1)
+ hselect (spec, "date-obs,ut,exptime", yes, > temp1)
+ hselect (spec, "ra,dec,epoch,st", yes, >> temp1)
+ fd2 = temp1
+ if (fscan (fd2, str1, 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,
+ >> log1)
+ if (fscan (fd2, str1, str2, str3, str4) == 4)
+ setairmass (spec, intype="beginning",
+ outtype="effective", exposure="exptime",
+ observatory=observatory, show=no, update=yes,
+ override=yes, >> log1)
+ }
+ fd2 = ""; delete (temp1, verify=no)
+ apslitproc (spec)
+ }
+
+ hselect (specec, "dc-flag,std-flag", yes, > temp1)
+ fd2 = temp1
+ j = fscan (fd2, str1, str2)
+ fd2 = ""; delete (temp1, verify=no)
+ if (j < 1) {
+ # Fix arc headers if necessary.
+ if (sproc.newarcs) {
+ fd2 = arcs
+ 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, str1, 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, >> log1)
+ if (fscan (fd3, str1, str2, str3, str4) == 4)
+ setairmass (arc, intype="beginning",
+ outtype="effective", exposure="exptime",
+ observatory=observatory, show=no,
+ update=yes, override=yes, >> log1)
+ }
+ fd3 = ""; delete (temp1, verify=no)
+ hedit (arc, "refspec1", arc, add=yes, verify=no,
+ show=no, update=yes)
+ }
+ fd2 = ""
+ sproc.newarcs = no
+ }
+
+ print ("Assign arc spectra for ", spec) | tee (log1)
+ refspectra (spec, references=arcrefs,
+ apertures="", refaps="", ignoreaps=no,
+ select=sparams.select, sort=sparams.sort,
+ group=sparams.group, time=sparams.time,
+ timewrap=sparams.timewrap, override=yes, confirm=no,
+ assign=yes, logfiles="STDOUT", verbose=no) |
+ tee (log1, > log2)
+
+ sdoarcs (spec, arcref, reextract, arcap, log1, no)
+
+ hselect (specec, "refspec1", yes, > temp1)
+ fd2 = temp1
+ i = fscan (fd2, arc)
+ fd2 = ""; delete (temp1, verify=no)
+ if (i < 1) {
+ print ("No arc reference assigned for ", spec) | tee (log1)
+ next
+ } else {
+ print ("Dispersion correct ", spec) | tee (log1)
+ dispcor (specec, "", linearize=sparams.linearize,
+ database=database, table=arcref//ectype,
+ w1=INDEF, w2=INDEF, dw=INDEF, nw=INDEF, log=sparams.log,
+ flux=sparams.flux, global=no, ignoreaps=no, confirm=no,
+ listonly=no, logfile=logfile)
+ hedit (specec, "dc-flag", 0, add=yes, show=no,
+ verify=no, update=yes)
+ }
+ }
+
+ if (j < 2 || !access ("std")) {
+ print ("Compile standard star fluxes for ", spec) | tee (log1)
+ standard (specec, output="std", samestar=yes, beam_switch=no,
+ apertures="", bandwidth=sparams.bandwidth,
+ bandsep=sparams.bandsep, fnuzero=3.68E-20,
+ extinction=extinction, caldir=caldir,
+ observatory=observatory, interact=sparams.s_interact)
+ hedit (specec, "std-flag", "yes", add=yes, verify=no,
+ show=no, update=yes)
+ print (specec, >> temp2)
+ sproc.newsens = yes
+ }
+ }
+ fd1 = ""
+
+ sections ("sens.????"//imtype, option="nolist")
+ if (sproc.newsens || sections.nimages == 0) {
+ if (!access ("std")) {
+ print ("No standard star data") | tee (log1)
+ sproc.fluxcal1 = no
+ } else {
+ imdelete ("sens.????"//imtype, verify=no)
+ print ("Compute sensitivity function") | tee (log1)
+ sensfunc ("std", "sens", apertures="", ignoreaps=no,
+ logfile=logfile, extinction=extinction,
+ newextinction="extinct.dat", observatory=observatory,
+ function=sparams.s_function, order=sparams.s_order,
+ interactive=yes, graphs="sr", marks="plus cross box")
+ sproc.newsens = yes
+ }
+ }
+
+ # Note that if new standard stars are added the old standard
+ # stars are not recalibrated unless the redo flag is used.
+
+ if (sproc.fluxcal1 && sproc.newsens) {
+ print ("Flux and/or extinction calibrate standard stars") |
+ tee (log1)
+ calibrate ("@"//temp2, "", extinct=extcor, flux=sproc.fluxcal1,
+ extinction=extinction, observatory=observatory, ignoreaps=no,
+ sensitivity="sens", fnu=sparams.fnu) | tee (log1, > log2)
+ if (sproc.splot1) {
+ print ("Standard stars:")
+ str1 = sproc.anssplot
+ if (str1 == "NO" || str1 == "YES")
+ sproc.splot1 = no
+ if (str1 == "no" || str1 == "NO")
+ sproc.splot2 = no
+ else
+ sproc.splot2 = yes
+ }
+ if (sproc.splot2)
+ splot ("@"//temp2)
+ sections (temp2, option="fullname", >> done)
+ delete (temp2, verify=no)
+ }
+end
diff --git a/noao/imred/src/doecslit/sfluxcal.par b/noao/imred/src/doecslit/sfluxcal.par
new file mode 100644
index 00000000..b750d265
--- /dev/null
+++ b/noao/imred/src/doecslit/sfluxcal.par
@@ -0,0 +1,16 @@
+stds,s,a,,,,
+arcs,s,a,,,,
+arcref,f,a,"",,,
+arcrefs,s,a,,,,
+redo,b,a,,,,
+update,b,a,,,,
+scattered,b,a,,,,
+arcap,b,a,,,,
+extcor,b,a,,,,
+done,f,a,"",,,
+log1,f,a,"",,,
+log2,f,a,"",,,
+fd1,*struct,h,"",,,
+fd2,*struct,h,"",,,
+fd3,*struct,h,"",,,
+mode,s,h,"q",,,
diff --git a/noao/imred/src/doecslit/sgetspec.cl b/noao/imred/src/doecslit/sgetspec.cl
new file mode 100644
index 00000000..7038dcb2
--- /dev/null
+++ b/noao/imred/src/doecslit/sgetspec.cl
@@ -0,0 +1,177 @@
+# SGETSPEC -- Get spectra which are CCD processed and not extracted.
+# This task also recognizes the arc spectra in the object list and arc table.
+# This task also strips the image type extension.
+
+procedure sgetspec (objects, arcs, arctable, standards, obj, arc, std)
+
+string objects {prompt="List of object images"}
+string arcs {prompt="List of arc images"}
+file arctable {prompt="Arc table"}
+string standards {prompt="List of standard images"}
+file obj {prompt="File of object images"}
+file arc {prompt="File of arc images"}
+file std {prompt="File of standard images"}
+bool ccdproc {prompt="Add CCDPROC keyword and continue?",
+ mode="q"}
+struct *fd1, *fd2
+
+begin
+ string imtype, temp, image, itype
+ int n, n1, narcs
+
+ imtype = "." // envget ("imtype")
+ n = stridx (",", imtype)
+ if (n > 0)
+ imtype = substr (imtype, 1, n-1)
+ n1 = strlen (imtype)
+
+ temp = mktemp ("tmp$iraf")
+
+ # Initialize files
+ set clobber=yes
+ sleep (> obj)
+ sleep (> arc)
+ sleep (> std)
+ set clobber=no
+
+ # Do arcs
+ narcs = 0
+ sections (arcs, option="fullname", > temp)
+ fd1 = temp
+ while (fscan (fd1, image) != EOF) {
+ hselect (image, "ccdproc", yes) | scan (itype)
+ if (nscan() == 0) {
+ printf ("%s: CCDPROC keyword not found.\n", image)
+ printf (" Either run CCDPROC or add CCDPROC keyword with HEDIT.\n")
+ if (!ccdproc)
+ error (1, "Exit")
+ hedit (image, "ccdproc", "DOSLIT", add=yes, update=yes,
+ verify=no, show=no)
+ }
+ hselect (image, "wat0_001", yes) | scanf ("system=%s", itype)
+ if (itype == "equispec" || itype == "multispec")
+ next
+ hselect (image, "imagetyp", yes) | scan (itype)
+ if (nscan() == 0)
+ itype = "comp"
+ if (itype != "comp" && itype != "COMPARISON" &&
+ itype != "comparison" && itype != "COMP")
+ next
+ n = strlen (image)
+ if (n > n1 && substr (image, n-n1+1, n) == imtype)
+ image = substr (image, 1, n-n1)
+ narcs = narcs + 1
+ printf ("%s %02d\n", image, narcs, >> arc)
+ }
+ fd1 = ""; delete (temp, verify=no)
+
+ # Do arc table.
+ if (arctable != "") {
+ fd2 = arctable
+ while (fscan (fd2, image, image) != EOF) {
+ if (nscan() != 2)
+ next
+ sections (image, option="fullname", > temp)
+ fd1 = temp
+ while (fscan (fd1, image) != EOF) {
+ hselect (image, "ccdproc", yes) | scan (itype)
+ if (nscan() == 0) {
+ printf ("%s: CCDPROC keyword not found.\n", image)
+ printf (" Either run CCDPROC or add CCDPROC keyword with HEDIT.\n")
+ if (!ccdproc)
+ error (1, "Exit")
+ hedit (image, "ccdproc", "DOSLIT", add=yes, update=yes,
+ verify=no, show=no)
+ }
+ hselect (image, "wat0_001", yes) | scanf ("system=%s", itype)
+ if (itype == "equispec" || itype == "multispec")
+ next
+ hselect (image, "imagetyp", yes) | scan (itype)
+ if (nscan() == 0)
+ itype = "comp"
+ if (itype != "comp" && itype != "COMPARISON" &&
+ itype != "comparison" && itype != "COMP")
+ next
+ n = strlen (image)
+ if (n > n1 && substr (image, n-n1+1, n) == imtype)
+ image = substr (image, 1, n-n1)
+ narcs = narcs + 1
+ printf ("%s %02d\n", image, narcs, >> arc)
+ }
+ fd1 = ""; delete (temp, verify=no)
+ }
+ }
+
+ # Do standards
+ sections (standards, option="fullname", > temp)
+ fd1 = temp
+ while (fscan (fd1, image) != EOF) {
+ hselect (image, "ccdproc", yes) | scan (itype)
+ if (nscan() == 0) {
+ printf ("%s: CCDPROC keyword not found.\n", image)
+ printf (" Either run CCDPROC or add CCDPROC keyword with HEDIT.\n")
+ if (!ccdproc)
+ error (1, "Exit")
+ hedit (image, "ccdproc", "DOSLIT", add=yes, update=yes,
+ verify=no, show=no)
+ }
+ hselect (image, "wat0_001", yes) | scanf ("system=%s", itype)
+ if (itype == "equispec" || itype == "multispec")
+ next
+ n = strlen (image)
+ if (n > n1 && substr (image, n-n1+1, n) == imtype)
+ image = substr (image, 1, n-n1)
+ print (image, >> std)
+ }
+ fd1 = ""; delete (temp, verify=no)
+
+ # Do objects
+ sections (objects, option="fullname", > temp)
+ fd1 = temp
+ while (fscan (fd1, image) != EOF) {
+ hselect (image, "ccdproc", yes) | scan (itype)
+ if (nscan() == 0) {
+ printf ("%s: CCDPROC keyword not found.\n", image)
+ printf (" Either run CCDPROC or add CCDPROC keyword with HEDIT.\n")
+ if (!ccdproc)
+ error (1, "Exit")
+ hedit (image, "ccdproc", "DOSLIT", add=yes, update=yes,
+ verify=no, show=no)
+ }
+ hselect (image, "wat0_001", yes) | scanf ("system=%s", itype)
+ if (itype == "equispec" || itype == "multispec")
+ next
+ hselect (image, "imagetyp", yes) | scan (itype)
+ if (nscan() == 0)
+ itype = "object"
+
+ n = strlen (image)
+ if (n > n1 && substr (image, n-n1+1, n) == imtype)
+ image = substr (image, 1, n-n1)
+ if (itype == "object" || itype == "OBJECT")
+ print (image, >> obj)
+ else if (itype == "comp" || itype == "COMPARISON" ||
+ itype == "comparison" || itype == "COMP") {
+ narcs = narcs + 1
+ printf ("%s %02d\n", image, narcs, >> arc)
+ }
+ }
+ fd1 = ""; delete (temp, verify=no)
+
+ if (narcs > 0) {
+ sort (arc, column=0, ignore=yes, numeric=no, reverse=no, > temp)
+ delete (arc, verify=no)
+ rename (temp, arc, field="all")
+ itype = ""
+ fd1 = arc
+ while (fscan (fd1, image, narcs) != EOF) {
+ if (image != itype)
+ printf ("%s %02d\n", image, narcs, >> temp)
+ itype = image
+ }
+ delete (arc, verify=no)
+ sort (temp, column=2, ignore=yes, numeric=yes, reverse=no) |
+ fields ("STDIN", "1", lines="1-99", > arc)
+ delete (temp, verify=no)
+ }
+end
diff --git a/noao/imred/src/doecslit/sgetspec.par b/noao/imred/src/doecslit/sgetspec.par
new file mode 100644
index 00000000..1f5387cc
--- /dev/null
+++ b/noao/imred/src/doecslit/sgetspec.par
@@ -0,0 +1,11 @@
+objects,s,a,,,,"List of object images"
+arcs,s,a,,,,"List of arc images"
+arctable,f,a,"",,,"Arc table"
+standards,s,a,,,,"List of standard images"
+obj,f,a,"",,,"File of object images"
+arc,f,a,"",,,"File of arc images"
+std,f,a,"",,,"File of standard images"
+ccdproc,b,q,,,,"Add CCDPROC keyword and continue?"
+fd1,*struct,h,"",,,
+fd2,*struct,h,"",,,
+mode,s,h,"ql",,,
diff --git a/noao/imred/src/doecslit/slistonly.cl b/noao/imred/src/doecslit/slistonly.cl
new file mode 100644
index 00000000..f765af36
--- /dev/null
+++ b/noao/imred/src/doecslit/slistonly.cl
@@ -0,0 +1,241 @@
+# SLISTONLY -- List processing to be done.
+#
+# This follows pretty much the same logic as the full procedure but doesn't
+# do anything but list the operations.
+
+procedure slistonly (objects, apref, arcs, standards, scattered, dispcor,
+ extcor, fluxcal, redo, update)
+
+string objects
+file apref
+string arcs
+string standards
+
+bool scattered
+bool dispcor
+bool extcor
+bool fluxcal
+bool redo
+bool update
+
+struct *fd1
+struct *fd2
+
+begin
+ string imtype, ectype
+ string spec, arcref
+ string specec, arcrefec
+ string temp1, temp2, done, str
+ bool newaps, newdisp, newsens
+ bool extract, disp, ext, flux, scat, reextract, fluxcal1, stdfile
+ int i, j, n
+
+ imtype = "." // envget ("imtype")
+ i = stridx (",", imtype)
+ if (i > 0)
+ imtype = substr (imtype, 1, i-1)
+ ectype = ".ec" // imtype
+ n = strlen (imtype)
+
+ temp1 = mktemp ("tmp$iraf")
+ temp2 = mktemp ("tmp$iraf")
+ done = mktemp ("tmp$iraf")
+
+ newaps = no
+ newdisp = no
+ newsens = no
+ fluxcal1 = fluxcal
+
+ i = strlen (apref)
+ if (i > n && substr (apref, i-n+1, i) == imtype)
+ apref = substr (apref, 1, i-n)
+
+ reextract = redo
+ if (reextract || !access (database // "/ap" // apref)) {
+ print ("Set reference aperture for ", apref)
+ newaps = yes
+ }
+
+ scat = no
+ if (scattered) {
+ hselect (apref, "apscatte", yes, > temp1)
+ fd1 = temp1
+ if (fscan (fd1, str1) < 1)
+ scat = yes
+ fd1 = ""; delete (temp1, verify=no)
+ }
+ if (scat)
+ print ("Subtract scattered light in ", apref) | tee (log1)
+
+ if (dispcor) {
+ hselect (arcs, "$I,wat0_001", yes, > temp1)
+ fd1 = temp1; s1 = ""
+ i = fscanf (fd1, "%s\tsystem=%s", arcref, s1)
+ if (i < 1 || (i == 2 && (s1 == "equispec" || s1 == "multispec")))
+ error (1, "No reference arcs")
+ fd1 = ""; delete (temp1, verify=no)
+ i = strlen (arcref)
+ if (i > n && substr (arcref, i-n+1, i) == imtype)
+ arcref = substr (arcref, 1, i-n)
+ arcrefec = arcref // ectype
+
+ reextract = redo || (update && newaps)
+ if (reextract || !access (arcrefec)) {
+ print ("Extract arc reference image ", arcref)
+ print ("Determine dispersion solution for ", arcref)
+ newdisp = yes
+ } else {
+ hselect (arcrefec, "refspec1,dc-flag", yes, > temp1)
+ fd1 = temp1
+ i = fscan (fd1, str, j)
+ fd1 = ""; delete (temp1, verify=no)
+ if (i < 1) {
+ print ("Determine dispersion solution for ", arcref)
+ newdisp = yes
+ }
+ }
+ print (arcref, > done)
+
+ if (fluxcal1) {
+ stdfile = access ("std")
+ if (redo && stdfile)
+ stdfile = no
+
+ reextract = redo || (update && (newaps || newdisp))
+ hselect (standards, "$I,ctype1", yes, >temp1)
+ fd1 = temp1
+ while (fscan (fd1, spec, s1) != EOF) {
+ if (nscan() == 2 && s1 == "MULTISPE")
+ next
+ i = strlen (spec)
+ if (i > n && substr (spec, i-n+1, i) == imtype)
+ spec = substr (spec, 1, i-n)
+ specec = spec // ectype
+
+ scat = no
+ if (scattered) {
+ hselect (spec, "apscatte", yes, > temp2)
+ fd2 = temp2
+ if (fscan (fd2, str) < 1)
+ scat = yes
+ fd2 = ""; delete (temp2, verify=no)
+ }
+ if (reextract || !access (specec) || (update && scat)) {
+ if (scat)
+ print ("Subtract scattered light from ", spec)
+ print ("Extract standard star spectrum ", spec)
+ print ("Dispersion correct ", spec)
+ print ("Compile standard star fluxes for ", spec)
+ stdfile = yes
+ newsens = yes
+ } else {
+ hselect (specec, "dc-flag,std-flag", yes, > temp2)
+ fd2 = temp2
+ i = fscan (fd2, str1, str2)
+ fd2 = ""; delete (temp2, verify=no)
+ if (i < 1)
+ print ("Dispersion correct ", spec)
+ if (i < 2) {
+ print ("Compile standard star fluxes for ", spec)
+ stdfile = yes
+ newsens = yes
+ }
+ }
+ print (spec, >> done)
+ }
+ fd1 = ""; delete (temp1, verify=no)
+
+ sections ("sens.????"//imtype, option="nolist")
+ if (newsens || sections.nimages == 0) {
+ if (!stdfile) {
+ print ("No standard stars")
+ fluxcal1 = no
+ } else {
+ print ("Compute sensitivity function")
+ newsens = yes
+ }
+ }
+
+ if (fluxcal1 && newsens)
+ print ("Flux and/or extinction calibrate standard stars")
+ }
+ }
+
+ reextract = redo || (update && (newaps || newdisp))
+ hselect (objects, "$I,ctype1", yes, > temp1)
+ fd1 = temp1
+ while (fscan (fd1, spec, s1) != EOF) {
+ if (nscan() == 2 && s1 == "MULTISPE")
+ next
+ if (i > n && substr (spec, i-n+1, i) == imtype)
+ spec = substr (spec, 1, i-n)
+
+ if (access (done)) {
+ fd2 = done
+ while (fscan (fd2, specec) != EOF)
+ if (spec == specec)
+ break
+ if (spec == specec)
+ next
+ fd2 = ""
+ }
+
+ specec = spec // ectype
+
+ scat = no
+ extract = no
+ disp = no
+ ext = no
+ flux = no
+ if (scattered) {
+ hselect (spec, "apscatte", yes, > temp2)
+ fd2 = temp2
+ if (fscan (fd2, str) < 1)
+ scat = yes
+ fd2 = ""; delete (temp2, verify=no)
+ }
+ if (reextract || !access (specec) || (update && scat)) {
+ extract = yes
+ } else {
+ hselect (specec, "dc-flag", yes, > temp2)
+ hselect (specec, "ex-flag", yes, >> temp2)
+ hselect (specec, "ca-flag", yes, >> temp2)
+ fd2 = temp2
+ extract = update && newaps
+ if (fscan (fd2, str1) == 1)
+ extract = update && newdisp
+ else
+ disp = yes
+ if (fscan (fd2, str1) == 1)
+ extract = update && !extcor
+ else
+ ext = extcor
+ if (fscan (fd2, str1) == 1)
+ extract = update && (!fluxcal1 || newsens)
+ else
+ flux = fluxcal1
+ fd2 = ""; delete (temp2, verify=no)
+ }
+
+ if (extract) {
+ disp = dispcor
+ ext = extcor
+ flux = fluxcal1
+ }
+
+ if (scat)
+ print ("Subtract scattered light from ", spec)
+ if (extract)
+ print ("Extract object spectrum ", spec)
+ if (disp)
+ print ("Dispersion correct ", spec)
+ if (ext)
+ print ("Extinction correct ", spec)
+ if (flux)
+ print ("Flux calibrate ", spec)
+ }
+ fd1 = ""; delete (temp1, verify=no)
+
+ if (access (done))
+ delete (done, verify=no)
+end
diff --git a/noao/imred/src/doecslit/slistonly.par b/noao/imred/src/doecslit/slistonly.par
new file mode 100644
index 00000000..f0986d61
--- /dev/null
+++ b/noao/imred/src/doecslit/slistonly.par
@@ -0,0 +1,13 @@
+objects,s,a,,,,
+apref,f,a,"",,,
+arcs,s,a,,,,
+standards,s,a,,,,
+scattered,b,a,,,,
+dispcor,b,a,,,,
+extcor,b,a,,,,
+fluxcal,b,a,,,,
+redo,b,a,,,,
+update,b,a,,,,
+fd1,*struct,h,"",,,
+fd2,*struct,h,"",,,
+mode,s,h,"q",,,
diff --git a/noao/imred/src/doecslit/slittasks.cl b/noao/imred/src/doecslit/slittasks.cl
new file mode 100644
index 00000000..ada92452
--- /dev/null
+++ b/noao/imred/src/doecslit/slittasks.cl
@@ -0,0 +1,19 @@
+#{ ECSLITPROC tasks
+
+task doecslit = "doecslit$doecslit.cl"
+task sproc = "doecslit$sproc.cl"
+task sarcrefs = "doecslit$sarcrefs.cl"
+task sdoarcs = "doecslit$sdoarcs.cl"
+task sfluxcal = "doecslit$sfluxcal.cl"
+task sbatch = "doecslit$sbatch.cl"
+task slistonly = "doecslit$slistonly.cl"
+task sgetspec = "doecslit$sgetspec.cl"
+
+task sparams = "doecslit$sparams.par"
+
+task apslitproc = "doecslit$x_apextract.e"
+
+hidetask sproc, sbatch, sarcrefs, sdoarcs, sfluxcal, slistonly, sgetspec
+hidetask sparams, apslitproc
+
+keep
diff --git a/noao/imred/src/doecslit/sparams.par b/noao/imred/src/doecslit/sparams.par
new file mode 100644
index 00000000..62868ed8
--- /dev/null
+++ b/noao/imred/src/doecslit/sparams.par
@@ -0,0 +1,65 @@
+line,i,h,INDEF,,,"Default dispersion line"
+nsum,i,h,10,,,"Number of dispersion lines to sum or median"
+extras,b,h,no,,,"Extract sky, sigma, etc.?
+
+-- AUTOMATIC APERTURE RESIZING PARAMETERS --"
+ylevel,r,h,0.05,,,"Fraction of peak or intensity for resizing
+
+-- TRACE PARAMETERS --"
+t_step,i,h,10,,,"Tracing step"
+t_function,s,h,"spline3","chebyshev|legendre|spline1|spline3",,"Trace fitting function"
+t_order,i,h,2,,,"Trace fitting function order"
+t_niterate,i,h,1,0,,"Trace rejection iterations"
+t_low,r,h,3.,0.,,"Trace lower rejection sigma"
+t_high,r,h,3.,0.,,"Trace upper rejection sigma
+
+-- BACKGROUND AND SCATTERED LIGHT PARAMETERS --"
+b_function,s,h,"legendre","chebyshev|legendre|spline1|spline3",,Background function
+b_order,i,h,1,,,Background function order
+b_naverage,i,h,-100,,,Background average or median
+b_niterate,i,h,0,0,,Background rejection iterations
+b_low,r,h,3.,0.,,Background lower rejection sigma
+b_high,r,h,3.,0.,,Background upper rejection sigma
+buffer,r,h,1.,0.,,Buffer distance from apertures
+apscat1,pset,h,"",,,Fitting parameters across the dispersion
+apscat2,pset,h,"",,,"Fitting parameters along the dispersion
+
+-- APERTURE EXTRACTION PARAMETERS --"
+weights,s,h,"none","none|variance",,Extraction weights (none|variance)
+pfit,s,h,"fit1d","fit1d|fit2d",,Profile fitting algorithm (fit1d|fit2d)
+lsigma,r,h,3.,,,Lower rejection threshold
+usigma,r,h,3.,,,"Upper rejection threshold
+
+-- ARC DISPERSION FUNCTION PARAMETERS --"
+threshold,r,h,10.,0.,,"Minimum line contrast threshold"
+coordlist,f,h,linelists$thar.dat,,,"Line list"
+match,r,h,1.,,,"Line list matching limit in Angstroms"
+fwidth,r,h,4,,,"Arc line widths in pixels"
+cradius,r,h,10.,,,"Centering radius in pixels"
+i_function,s,h,"legendre","legendre|chebyshev",,"Echelle coordinate function"
+i_xorder,i,h,3,1,,Order of coordinate function along dispersion
+i_yorder,i,h,3,1,,Order of coordinate function across dispersion
+i_niterate,i,h,3,0,,"Rejection iterations"
+i_low,r,h,3.,0.,,"Lower rejection sigma"
+i_high,r,h,3.,0.,,"Upper rejection sigma"
+refit,b,h,yes,,,"Refit coordinate function when reidentifying
+
+-- AUTOMATIC ARC ASSIGNMENT PARAMETERS --"
+select,s,h,"interp",,,"Selection method for reference spectra"
+sort,s,h,"jd",,,"Sort key"
+group,s,h,"ljd",,,"Group key"
+time,b,h,no,,,"Is sort key a time?"
+timewrap,r,h,17.,0.,24.,"Time wrap point for time sorting
+
+-- DISPERSION CORRECTION PARAMETERS --"
+linearize,b,h,yes,,,Linearize (interpolate) spectra?
+log,b,h,no,,,"Logarithmic wavelength scale?"
+flux,b,h,yes,,,"Conserve flux?
+
+-- SENSITIVITY CALIBRATION PARAMETERS --"
+bandwidth,r,h,10.,,,Bandpass widths
+bandsep,r,h,10.,,,Bandpass separation
+s_interact,b,h,yes,,,Graphic interaction to examine/define bandpasses
+s_function,s,h,"spline3","chebyshev|legendre|spline3|spline1",,"Fitting function"
+s_order,i,h,1,1,,"Order of sensitivity function"
+fnu,b,h,no,,,"Create spectra having units of FNU?"
diff --git a/noao/imred/src/doecslit/sproc.cl b/noao/imred/src/doecslit/sproc.cl
new file mode 100644
index 00000000..8caeadd9
--- /dev/null
+++ b/noao/imred/src/doecslit/sproc.cl
@@ -0,0 +1,490 @@
+# SPROC -- Process echelle slit spectra
+# This program combines all the operations of scattered light
+# subtraction, extraction, dispersion correction, extinction correction,
+# and flux calibration in as simple and noninteractive manner as
+# possible. 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 followed automatically.
+
+procedure sproc (objects, apref, arcs, arctable, standards, recenter,
+ resize, quicklook, trace, scattered, arcap, dispcor, extcor,
+ fluxcal, splot, redo, update, batch, listonly)
+
+file objects {prompt="List of object spectra"}
+
+file apref {prompt="Aperture reference spectrum"}
+file arcs {prompt="List of arc spectra"}
+file arctable {prompt="Arc assignment table (optional)"}
+file standards {prompt="List of standard star spectra\n"}
+
+bool recenter {prompt="Recenter object apertures?"}
+bool resize {prompt="Resize object apertures?"}
+bool quicklook {prompt="Edit/review object apertures?"}
+bool trace {prompt="Trace object spectra?"}
+bool scattered {prompt="Subtract scattered light?"}
+bool arcap {prompt="Use object apertures for arcs?"}
+bool dispcor {prompt="Dispersion correct spectra?"}
+bool extcor {prompt="Extinction correct spectra?"}
+bool fluxcal {prompt="Flux calibrate 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"}
+
+string anssplot = "yes" {prompt="Splot spectrum?", mode="q",
+ enum="no|yes|NO|YES"}
+bool newaps, newdisp, newsens, newarcs
+bool fluxcal1, splot1, splot2
+bool dobatch
+
+struct *fd1, *fd2, *fd3
+
+begin
+ string imtype, ectype
+ string arcref, spec, arc
+ string arcrefec, specec, arcec
+ string temp, done
+ string str1, str2, str3, str4, arcrefs, log1, log2
+ bool reextract, extract, scat, disp, ext, flux, log, disperr
+ int i, j, n
+ struct err
+ str1 = ""
+
+ # Call a separate task to do the listing to minimize the size of
+ # this script and improve it's readability.
+
+ dobatch = no
+ if (listonly) {
+ slistonly (objects, apref, arcs, standards, scattered,
+ dispcor, extcor, fluxcal, redo, update)
+ bye
+ }
+
+ imtype = "." // envget ("imtype")
+ i = stridx (",", imtype)
+ if (i > 0)
+ imtype = substr (imtype, 1, i-1)
+ ectype = ".ec" // imtype
+ n = strlen (imtype)
+
+ # Temporary files used repeatedly in this script. Under some
+ # abort circumstances these files may be left behind.
+
+ temp = 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$null"
+
+ # If the update switch is used changes in the calibration data
+ # can cause images to be reprocessed (if they are in the object
+ # list). Possible changes are in the aperture definitions,
+ # dispersion solution, and sensitivity function. The newarcs
+ # flag is used to only go through the arc image headers once
+ # setting the reference spectrum, airmass, and UT.
+
+ newaps = no
+ newdisp = no
+ newsens = no
+ newarcs = yes
+ fluxcal1 = fluxcal
+
+ # Check if there are aperture definitions in the database and
+ # define them if needed. This is usually somewhat interactive.
+ # Set the newaps flag in case an update is desired.
+
+ # Initialize APSCRIPT for aperture reference.
+ apslitproc.saturation = INDEF
+ apslitproc.references = ""
+ apslitproc.ansfind = "YES"
+ if (recenter)
+ apslitproc.ansrecenter = "YES"
+ else
+ apslitproc.ansrecenter = "NO"
+ if (resize)
+ apslitproc.ansresize = "YES"
+ else
+ apslitproc.ansresize = "NO"
+ apslitproc.ansedit = "yes"
+ apslitproc.anstrace = "YES"
+ apslitproc.ansfittrace = "yes"
+ apslitproc.ansextract = "NO"
+
+ i = strlen (apref)
+ if (i > n && substr (apref, i-n+1, i) == imtype)
+ apref = substr (apref, 1, i-n)
+
+ reextract = redo
+ if (reextract || !access (database // "/ap" // apref)) {
+ if (!access (apref // imtype)) {
+ printf ("Aperture reference spectrum not found - %s%s\n",
+ apref, imtype) | scan (err)
+ error (1, err // "\nCheck setting of imtype")
+ }
+ scat = no
+ if (scattered) {
+ hselect (apref, "apscatte", yes, > temp)
+ fd1 = temp
+ if (fscan (fd1, str1) < 1)
+ scat = yes
+ fd1 = ""; delete (temp, verify=no)
+ }
+
+ print ("Set reference aperture for ", apref) | tee (log1)
+ delete (database//"/ap"//apref, verify=no, >& "dev$null")
+ apslitproc (apref)
+ newaps = yes
+ }
+
+ # Initialize APSCRIPT for aperture definitions.
+ if (quicklook) {
+ apslitproc.ansedit = "NO"
+ apslitproc.ansfittrace = "NO"
+ }
+ if (trace) {
+ apslitproc.anstrace = "yes"
+ } else {
+ apslitproc.anstrace = "NO"
+ }
+ apslitproc.ansextract = "NO"
+ apslitproc.ansscat = "NO"
+
+ print ("Define object apertures", >> log1)
+ if (redo)
+ apslitproc ("@"//objects, references=apref)
+ else
+ apslitproc ("@"//objects, references="NEW"//apref)
+ if (dispcor && fluxcal1) {
+ if (redo)
+ apslitproc ("@"//standards, references=apref)
+ else
+ apslitproc ("@"//standards, references="NEW"//apref)
+ }
+
+ # Initialize APSCRIPT for extraction and SPLOT.
+ apslitproc.ansrecenter = "NO"
+ apslitproc.ansresize = "NO"
+ apslitproc.ansedit = "NO"
+ apslitproc.anstrace = "NO"
+ apslitproc.ansextract = "YES"
+ apslitproc.ansreview = "NO"
+ apslitproc.ansscat = "NO"
+ apslitproc.anssmooth = "YES"
+
+ if (splot && !quicklook) {
+ splot1 = yes
+ splot2 = yes
+ } else {
+ splot1 = no
+ splot2 = no
+ }
+
+ # The next step is to setup the scattered light correction if needed.
+ # We use the aperture reference image for the interactive setting.
+ # If this image has been scattered light corrected we assume the
+ # scattered light functions parameters are correctly set.
+
+ scat = no
+ if (scattered) {
+ hselect (apref, "apscatte", yes, > temp)
+ fd1 = temp
+ if (fscan (fd1, str1) < 1)
+ scat = yes
+ fd1 = ""; delete (temp, verify=no)
+ }
+ if (scat) {
+ print ("Setup and do scattered light subtraction in ", apref) |
+ tee (log1)
+ apslitproc.ansfitscatter = "yes"
+ apslitproc.ansfitsmooth = "yes"
+ apslitproc (apref, ansextract="NO", ansscat="YES")
+ apslitproc.ansfitscatter = "NO"
+ apslitproc.ansfitsmooth = "NO"
+ }
+
+ # 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.
+
+ arcref = ""
+ arcrefs = ""
+ if (dispcor) {
+ if (arctable == "")
+ arcrefs = "@"//arcs
+ else
+ arcrefs = arctable
+
+ fd1 = arcs
+ if (fscan (fd1, arcref) == EOF)
+ error (1, "No reference arcs")
+ fd1 = ""
+ 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)
+
+ apslitproc.references = apref
+ sarcrefs (arcref, done, log1, log2)
+ apslitproc.references = ""
+
+ if (fluxcal1)
+ sfluxcal (standards, arcs, arcref, arcrefs, redo, update,
+ scattered, arcap, extcor, done, log1, log2)
+ }
+
+ # Now we are ready to process the object spectra.
+
+ reextract = redo || (update && (newaps || newdisp))
+ fd1 = objects
+ while (fscan (fd1, spec) != EOF) {
+ # 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
+ ext = no
+ flux = no
+ if (scattered) {
+ hselect (spec, "apscatte", yes, > temp)
+ fd2 = temp
+ if (fscan (fd2, str1) < 1)
+ scat = yes
+ fd2 = ""; delete (temp, verify=no)
+ }
+ if (reextract || !access (specec) || (update && scat))
+ extract = yes
+ else {
+ hselect (specec, "dc-flag", yes, > temp)
+ hselect (specec, "ex-flag", yes, >> temp)
+ hselect (specec, "ca-flag", yes, >> temp)
+ fd2 = temp
+ 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
+ if (fscan (fd2, str1) == 1)
+ extract = update && !extcor
+ else
+ ext = extcor
+ if (fscan (fd2, str1) == 1)
+ extract = update && (!fluxcal1 || newsens)
+ else
+ flux = fluxcal1
+ fd2 = ""; delete (temp, verify=no)
+ }
+
+ if (extract) {
+ disp = dispcor
+ ext = extcor
+ flux = fluxcal1
+ }
+
+ # If fully processed go to the next object.
+ if (!extract && !disp && !extcor && !flux)
+ next
+
+ # If not interactive and the batch flag is set submit rest to batch.
+ if (batch && !splot1 && !splot2) {
+ fd1 = ""
+ flprcache
+ sbatch.objects = objects
+ sbatch.datamax = datamax
+ sbatch.arcs = arcs
+ sbatch.arcref = arcref
+ sbatch.arcrefs = arcrefs
+ sbatch.done = done
+ sbatch.logfile = log1
+ sbatch.redo = reextract
+ sbatch.update = update
+ sbatch.scattered = scattered
+ sbatch.arcap = arcap
+ sbatch.dispcor = dispcor
+ sbatch.fluxcal1 = fluxcal1
+ sbatch.extcor = extcor
+ sbatch.newaps = newaps
+ sbatch.newdisp = newdisp
+ sbatch.newsens = newsens
+ sbatch.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)
+ apslitproc (spec, ansextract="NO", ansscat="YES")
+ }
+
+ print ("Extract object spectrum ", spec) | tee (log1)
+ hselect (spec, "date-obs,ut,exptime", yes, > temp)
+ hselect (spec, "ra,dec,epoch,st", yes, >> temp)
+ fd2 = temp
+ if (fscan (fd2, str1, 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,
+ >> log1)
+ if (fscan (fd2, str1, str2, str3, str4) == 4)
+ setairmass (spec, intype="beginning",
+ outtype="effective", exposure="exptime",
+ observatory=observatory, show=no, update=yes,
+ override=yes, >> log1)
+ }
+ fd2 = ""; delete (temp, verify=no)
+ apslitproc (spec, saturation=datamax)
+ }
+
+ disperr = no
+ if (disp) {
+ # Fix arc headers if necessary.
+ if (newarcs) {
+ fd2 = arcs
+ while (fscan (fd2, arc) != EOF) {
+ hselect (arc, "date-obs,ut,exptime", yes, > temp)
+ hselect (arc, "ra,dec,epoch,st", yes, >> temp)
+ fd3 = temp
+ if (fscan (fd3, str1, 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, >> log1)
+ if (fscan (fd3, str1, str2, str3, str4) == 4)
+ setairmass (arc, intype="beginning",
+ outtype="effective", exposure="exptime",
+ observatory=observatory, show=no,
+ update=yes, override=yes, >> log1)
+ }
+ fd3 = ""; delete (temp, verify=no)
+ hedit (arc, "refspec1", arc, add=yes, verify=no,
+ show=no, update=yes)
+ }
+ fd2 = ""
+ newarcs = no
+ }
+
+ print ("Assign arc spectra for ", spec) | tee (log1)
+ refspectra (spec, references=arcrefs,
+ apertures="", refaps="", ignoreaps=no,
+ select=sparams.select, sort=sparams.sort,
+ group=sparams.group, time=sparams.time,
+ timewrap=sparams.timewrap, override=yes, confirm=no,
+ assign=yes, logfiles="STDOUT", verbose=no) |
+ tee (log1, > log2)
+
+ sdoarcs (spec, arcref, reextract, arcap, log1, no)
+
+ hselect (specec, "refspec1", yes, > temp)
+ fd2 = temp
+ i = fscan (fd2, arc)
+ fd2 = ""; delete (temp, 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=sparams.linearize,
+ database=database, table=arcref//ectype,
+ w1=INDEF, w2=INDEF, dw=INDEF, nw=INDEF,
+ log=sparams.log, flux=sparams.flux, samedisp=no,
+ global=no, confirm=no, ignoreaps=no, listonly=no,
+ logfile=logfile)
+ hedit (specec, "dc-flag", 0, add=yes, show=no,
+ verify=no, update=yes)
+ }
+ }
+
+ if (!disperr && (extract || disp)) {
+ if (ext)
+ print ("Extinction correct ", spec) | tee (log1)
+ if (flux)
+ print ("Flux calibrate ", spec) | tee (log1)
+ if (flux || ext)
+ calibrate (specec, "", extinct=extcor, flux=fluxcal1,
+ extinction=extinction, observatory=observatory,
+ ignoreaps=no, sensitivity="sens", fnu=sparams.fnu) |
+ tee (log1, > log2)
+ }
+ if (extract || disp || ext || flux) {
+ 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)
+ else if (splot && quicklook) {
+ if (disp) {
+ print ("q") |
+ specplot (specec, apertures="", autolayout=no,
+ scale=1., offset=0., step=0., sysid=yes,
+ yscale=yes, xmin=INDEF, xmax=INDEF, ymin=INDEF,
+ ymax=INDEF, logfile="", graphics="stdgraph",
+ cursor="STDIN")
+ } else {
+ print ("q") |
+ specplot (specec, apertures="", autolayout=yes,
+ autoscale=no, scale=1., offset=0., step=0.,
+ sysid=yes, yscale=no, xmin=INDEF, xmax=INDEF,
+ ymin=INDEF, ymax=INDEF, logfile="",
+ graphics="stdgraph", cursor="STDIN")
+ }
+ }
+ }
+ print (spec, >> done)
+ }
+ fd1 = ""
+
+ if (access (done))
+ delete (done, verify=no)
+end
diff --git a/noao/imred/src/doecslit/sproc.par b/noao/imred/src/doecslit/sproc.par
new file mode 100644
index 00000000..a0ecbd0c
--- /dev/null
+++ b/noao/imred/src/doecslit/sproc.par
@@ -0,0 +1,35 @@
+objects,f,a,"",,,"List of object spectra"
+apref,f,a,"",,,"Aperture reference spectrum"
+arcs,f,a,"",,,"List of arc spectra"
+arctable,f,a,"",,,"Arc assignment table (optional)"
+standards,f,a,"",,,"List of standard star spectra
+"
+recenter,b,a,,,,"Recenter object apertures?"
+resize,b,a,,,,"Resize object apertures?"
+quicklook,b,a,,,,"Edit/review object apertures?"
+trace,b,a,,,,"Trace object spectra?"
+scattered,b,a,,,,"Subtract scattered light?"
+arcap,b,a,,,,"Use object apertures for arcs?"
+dispcor,b,a,,,,"Dispersion correct spectra?"
+extcor,b,a,,,,"Extinction correct spectra?"
+fluxcal,b,a,,,,"Flux calibrate spectra?"
+splot,b,a,,,,"Plot the final spectrum?"
+redo,b,a,,,,"Redo operations if previously done?"
+update,b,a,,,,"Update spectra if cal data changes?"
+batch,b,a,,,,"Extract objects in batch?"
+listonly,b,a,,,,"List steps but don\'t process?
+"
+datamax,r,h,INDEF,,,"Max data value / cosmic ray threshold"
+anssplot,s,q,"yes",no|yes|NO|YES,,"Splot spectrum?"
+newaps,b,h,,,,
+newdisp,b,h,,,,
+newsens,b,h,,,,
+newarcs,b,h,,,,
+fluxcal1,b,h,,,,
+splot1,b,h,,,,
+splot2,b,h,,,,
+dobatch,b,h,,,,
+fd1,*struct,h,"",,,
+fd2,*struct,h,"",,,
+fd3,*struct,h,"",,,
+mode,s,h,"ql",,,
generated by cgit (git 2.34.1) at 2025-09-20 13:22:12 -0400