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-rw-r--r--noao/imred/src/doslit/Revisions129
-rw-r--r--noao/imred/src/doslit/apslitproc.par145
-rw-r--r--noao/imred/src/doslit/demologfile1
-rw-r--r--noao/imred/src/doslit/doslit.cl64
-rw-r--r--noao/imred/src/doslit/doslit.par26
-rw-r--r--noao/imred/src/doslit/doslittasks.cl17
-rw-r--r--noao/imred/src/doslit/sarcrefs.cl118
-rw-r--r--noao/imred/src/doslit/sarcrefs.par9
-rw-r--r--noao/imred/src/doslit/sbatch.cl199
-rw-r--r--noao/imred/src/doslit/sbatch.par20
-rw-r--r--noao/imred/src/doslit/sdoarcs.cl101
-rw-r--r--noao/imred/src/doslit/sdoarcs.par7
-rw-r--r--noao/imred/src/doslit/sfluxcal.cl196
-rw-r--r--noao/imred/src/doslit/sfluxcal.par14
-rw-r--r--noao/imred/src/doslit/sgetspec.cl178
-rw-r--r--noao/imred/src/doslit/sgetspec.par11
-rw-r--r--noao/imred/src/doslit/slistonly.cl180
-rw-r--r--noao/imred/src/doslit/slistonly.par12
-rw-r--r--noao/imred/src/doslit/sparams.par65
-rw-r--r--noao/imred/src/doslit/sproc.cl404
-rw-r--r--noao/imred/src/doslit/sproc.par33
21 files changed, 1929 insertions, 0 deletions
diff --git a/noao/imred/src/doslit/Revisions b/noao/imred/src/doslit/Revisions
new file mode 100644
index 00000000..5e219369
--- /dev/null
+++ b/noao/imred/src/doslit/Revisions
@@ -0,0 +1,129 @@
+.help revisions Dec94 noao.imred.src.doslit
+.nf
+
+=======
+V2.12.3
+=======
+
+doslit$sbatch.cl
+doslit$sproc.cl
+ Error messages now hint to check imtype setting.
+ (4/15/05, Valdes)
+
+========
+V2.12.2b
+========
+
+=======
+V2.12.1
+=======
+
+doslit$sproc.cl
+doslit$sbatch.cl
+doslit$sarcrefs.cl
+doslit$sfluxcal.cl
+ Added a flpr after dispcor to workaround a bug with the FITS kernel
+ header caching. (6/24/02, Valdes)
+
+=====
+V2.12
+=====
+
+doslit$sproc.cl
+ Modified code to eliminate goto. This is for use with pyraf.
+ (11/21/00, Valdes)
+
+========
+V2.11.3a
+========
+
+doslit$sarcrefs.cl
+ The test for INDEF values on CRVAL/CDELT did not work correctly.
+ (9/24/99, Valdes)
+
+doslit$doslit.cl
+doslit$doslit.par
+doslit$sarcrefs.cl
+doslit$sarcrefs.par
+doslit$sproc.cl
+doslit$sproc.par
+ No change made though dates were modified. (9/24/99, Valdes)
+
+=======
+V2.11.2
+=======
+
+doslit$sarcrefs.cl
+ The test on CRVAL and CDELT would not work with header keywords.
+ (9/22/98, Valdes)
+
+doslit$sarcrefs.cl
+doslit$sbatch.cl
+doslit$sdoarcs.cl
+doslit$sfluxcal.cl
+doslit$sgetspec.cl
+doslit$slistonly.cl
+doslit$sproc.cl
+ Any additional qualifiers in the imtype string are stripped.
+ (8/14/97, Valdes)
+
+doslit$sgetspec.cl
+ Added the field parameter to the RENAME call. (8/12/97, Valdes)
+
+=========
+V2.11Beta
+=========
+
+doslit$sarcrefs.cl
+ If both crval and cdelt are INDEF then the autoidentify option is not
+ used. (5/2/97, Valdes)
+
+doslit$apslitproc.par
+ Made changes for the new aperture selection option. (9/5/96, Valdes)
+
+doslit.cl
+doslit.par
+sproc.cl
+sproc.par
+sarcrefs.cl
+sarcrefs.par
+sparams.par
+ Modified to use autoidentify. (4/5/96, Valdes)
+
+doslit$sproc.cl
+doslit$sproc.par
+ Added missing parameter declaration. (5/25/95, Valdes)
+
+doslit$sgetspec.cl
+doslit$doslit.cl
+ The arc table will now be checked for arc spectra. (5/1/95, Valdes)
+
+doslit$sparams.par
+doslit$sdoarcs.cl
+doslit$sarcrefs.cl
+ Added "threshold" as a user parameter. (1/16/95, Valdes)
+
+doslit$sproc.cl
+doslit$sbatch.cl
+doslit$sfluxcal.cl
+doslit$sproc.par
+doslit$sbatch.par
+doslit$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)
+
+doslit$sgetspec.cl
+doslit$sgetspec.par
+ Added warning and query for missing CCDPROC keyword. (12/31/94, Valdes)
+
+doslit$sproc.cl
+doslit$sarcrefs.cl
+ 1. If the object apertures used for reference arc contain more than
+ one aperture then after extraction all apertures but the first
+ are removed. This will be one reference arc aperture for the
+ master dispersion solution.
+ 2. Set ignoreaps=yes so that any new apertures added to the objects
+ will inherit the wavelength scale of the reference arc.
+ (10/12/94, Valdes)
+.endhelp
diff --git a/noao/imred/src/doslit/apslitproc.par b/noao/imred/src/doslit/apslitproc.par
new file mode 100644
index 00000000..bab5b58e
--- /dev/null
+++ b/noao/imred/src/doslit/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,"multispec",,,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,)sparams.lower,,,>sparams.lower
+upper,r,h,)sparams.upper,,,>sparams.upper
+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,1,,,Number of apertures to be found automatically
+minsep,r,h,1.,,,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,)sparams.background,,,>sparams.background
+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/doslit/demologfile b/noao/imred/src/doslit/demologfile
new file mode 100644
index 00000000..a5a245c2
--- /dev/null
+++ b/noao/imred/src/doslit/demologfile
@@ -0,0 +1 @@
+Define object apertures
diff --git a/noao/imred/src/doslit/doslit.cl b/noao/imred/src/doslit/doslit.cl
new file mode 100644
index 00000000..56458435
--- /dev/null
+++ b/noao/imred/src/doslit/doslit.cl
@@ -0,0 +1,64 @@
+# DOSLIT -- Process slit spectra from 2D to wavelength calibrated 1D.
+#
+# The task SPROC does all of the interactive work and SBATCH does the
+# background work. This procedure is organized this way to minimize the
+# dictionary space when the background task is submitted.
+
+procedure doslit (objects)
+
+string objects = "" {prompt="List of object spectra"}
+
+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 = "rdnoise" {prompt="Read out noise sigma (photons)"}
+string gain = "gain" {prompt="Photon gain (photons/data number)"}
+real datamax = INDEF {prompt="Max data value / cosmic ray threshold"}
+real width = 5. {prompt="Width of profiles (pixels)"}
+string crval = "INDEF" {prompt="Approximate wavelength"}
+string cdelt = "INDEF" {prompt="Approximate dispersion\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="Automatically resize apertures?"}
+bool clean = no {prompt="Detect and replace bad pixels?"}
+bool splot = no {prompt="Plot the final spectrum?"}
+bool redo = no {prompt="Redo operations if previously done?"}
+bool update = no {prompt="Update spectra if cal data changes?"}
+bool quicklook = no {prompt="Minimally interactive quick-look?"}
+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
+ 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)
+
+ apslitproc.readnoise = readnoise
+ apslitproc.gain = gain
+ apslitproc.width = width
+ apslitproc.t_width = width
+ apslitproc.radius = width
+ apslitproc.clean = clean
+ sproc.datamax = datamax
+
+ sproc (obj, arc, arctable, std, crval, cdelt, dispcor, extcor, fluxcal,
+ resize, clean, splot, redo, update, quicklook, 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/doslit/doslit.par b/noao/imred/src/doslit/doslit.par
new file mode 100644
index 00000000..6e4119f6
--- /dev/null
+++ b/noao/imred/src/doslit/doslit.par
@@ -0,0 +1,26 @@
+objects,s,a,"",,,"List of object spectra"
+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,"rdnoise",,,"Read out noise sigma (photons)"
+gain,s,h,"gain",,,"Photon gain (photons/data number)"
+datamax,r,h,INDEF,,,"Max data value / cosmic ray threshold"
+width,r,h,5.,,,"Width of profiles (pixels)"
+crval,s,h,"INDEF",,,"Approximate wavelength"
+cdelt,s,h,"INDEF",,,"Approximate dispersion
+"
+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,,,"Automatically resize apertures?"
+clean,b,h,no,,,"Detect and replace bad pixels?"
+splot,b,h,no,,,"Plot the final spectrum?"
+redo,b,h,no,,,"Redo operations if previously done?"
+update,b,h,no,,,"Update spectra if cal data changes?"
+quicklook,b,h,no,,,"Minimally interactive quick-look?"
+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/doslit/doslittasks.cl b/noao/imred/src/doslit/doslittasks.cl
new file mode 100644
index 00000000..a7b635a9
--- /dev/null
+++ b/noao/imred/src/doslit/doslittasks.cl
@@ -0,0 +1,17 @@
+#{ SLITPROC tasks
+
+task doslit = "doslit$doslit.cl"
+task sproc = "doslit$sproc.cl"
+task sarcrefs = "doslit$sarcrefs.cl"
+task sdoarcs = "doslit$sdoarcs.cl"
+task sfluxcal = "doslit$sfluxcal.cl"
+task sbatch = "doslit$sbatch.cl"
+task slistonly = "doslit$slistonly.cl"
+task sgetspec = "doslit$sgetspec.cl"
+
+task apslitproc = "doslit$x_apextract.e"
+
+hidetask sproc, sbatch, sarcrefs, sdoarcs, sfluxcal, slistonly, sgetspec
+hidetask apslitproc
+
+keep
diff --git a/noao/imred/src/doslit/sarcrefs.cl b/noao/imred/src/doslit/sarcrefs.cl
new file mode 100644
index 00000000..304983f1
--- /dev/null
+++ b/noao/imred/src/doslit/sarcrefs.cl
@@ -0,0 +1,118 @@
+# SARCREFS -- Determine dispersion relation for reference arcs.
+
+procedure sarcrefs (arcref1, crval, cdelt, done, log1, log2)
+
+file arcref1
+string crval = "INDEF"
+string cdelt = "INDEF"
+file done
+file log1
+file log2
+bool newdisp = no
+
+struct *fd
+
+begin
+ string arcref, arcrefms, arc, arcms, temp, str1, str2
+ int i, dc, nspec
+ bool log
+ struct str3
+
+ temp = mktemp ("tmp$iraf")
+
+ # Extract the primary arc reference spectrum. Determine the
+ # dispersion function with IDENTIFY/REIDENTIFY. Set the wavelength
+ # parameters with MSDISPCOR.
+
+ newdisp = no
+ arcref = arcref1
+ arcrefms = arcref1 // ".ms." // envget ("imtype")
+ i = stridx (",", arcrefms)
+ if (i > 0)
+ arcrefms = substr (arcrefms, 1, i-1)
+ if (!access (arcrefms)) {
+ print ("Extract arc reference image ", arcref) | tee (log1)
+ if (apslitproc.reference == "") {
+ delete (database//"/ap"//arcref, verify=no, >& "dev$null")
+ apslitproc (arcref, nfind=-1, ansfind="YES",
+ background="none", clean=no, weights="none")
+ } else
+ apslitproc (arcref, background="none", clean=no, weights="none")
+
+ nspec = 1
+ hselect (arcrefms, "naxis2", yes) | scan (nspec)
+ if (nspec > 1)
+ scopy (arcrefms//"[*,1]", arcrefms, w1=INDEF, w2=INDEF,
+ apertures="", bands="", beams="", apmodulus=0,
+ format="multispec", renumber=no, offset=0, clobber=yes,
+ merge=no, rebin=yes, verbose=no)
+ }
+
+ # Check for dispersion correction. If missing determine the
+ # dispersion function and dispersion correct. Dispersion
+ # correction is required to define the dispersion parameters
+ # for the objects.
+
+ hselect (arcrefms, "dispcor", yes, > temp)
+ fd = temp
+ dc = -1
+ i = fscan (fd, dc)
+ fd = ""; delete (temp, verify=no)
+ if (i < 1 || dc == -1) {
+ print ("Determine dispersion solution for ", arcref) | tee (log1)
+ #delete (database//"/id"//arcref//".ms*", verify=no)
+ printf ("%s %s\n", crval, cdelt) | scan (str3)
+ if (str3 == "INDEF INDEF")
+ identify (arcrefms, section="middle line", database=database,
+ coordlist=sparams.coordlist, nsum=1, match=sparams.match,
+ maxfeatures=50, zwidth=100., ftype="emission",
+ fwidth=sparams.fwidth, cradius=sparams.cradius,
+ threshold=sparams.threshold, minsep=2.,
+ function=sparams.i_function, order=sparams.i_order,
+ sample="*", niterate=sparams.i_niterate,
+ low_reject=sparams.i_low, high_reject=sparams.i_high,
+ grow=0., autowrite=yes)
+ else
+ autoidentify (arcrefms, crval, cdelt,
+ coordlist=sparams.coordlist,
+ interactive="YES", section="middle line", nsum="1",
+ ftype="emission", fwidth=sparams.fwidth,
+ cradius=sparams.cradius, threshold=sparams.threshold,
+ minsep=2., match=sparams.match, function=sparams.i_function,
+ order=sparams.i_order, sample="*",
+ niterate=sparams.i_niterate, low_reject=sparams.i_low,
+ high_reject=sparams.i_high, grow=0., dbwrite="YES",
+ overwrite=yes, database="database", verbose=yes,
+ logfile=logfile, plotfile=plotfile,
+ reflist="", refspec="", crpix="INDEF", cddir="unknown",
+ crsearch="-0.5", cdsearch="INDEF", aidpars="")
+
+ hedit (arcrefms, "refspec1", arcref // ".ms", add=yes,
+ show=no, verify=no)
+
+ dispcor (arcrefms, "", linearize=sparams.linearize,
+ database=database, table="", w1=INDEF, w2=INDEF, dw=INDEF,
+ nw=INDEF, log=sparams.log, flux=sparams.flux, samedisp=yes,
+ global=no, ignoreaps=yes, confirm=yes, verbose=no, listonly=no,
+ logfile=logfile)
+ flpr
+
+ hedit (arcrefms, "dispcor", 0, add=yes, verify=no,
+ show=no, update=yes)
+ newdisp = yes
+
+# if (sproc.splot1) {
+# print (arcrefms, ":")
+# 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 (arcrefms)
+ }
+ print (arcref, >> done)
+end
diff --git a/noao/imred/src/doslit/sarcrefs.par b/noao/imred/src/doslit/sarcrefs.par
new file mode 100644
index 00000000..012dcaf7
--- /dev/null
+++ b/noao/imred/src/doslit/sarcrefs.par
@@ -0,0 +1,9 @@
+arcref1,f,a,"",,,
+crval,s,a,"INDEF",,,
+cdelt,s,a,"INDEF",,,
+done,f,a,"",,,
+log1,f,a,"",,,
+log2,f,a,"",,,
+newdisp,b,h,no,,,
+fd,*struct,h,"",,,
+mode,s,h,"ql",,,
diff --git a/noao/imred/src/doslit/sbatch.cl b/noao/imred/src/doslit/sbatch.cl
new file mode 100644
index 00000000..8e01b09e
--- /dev/null
+++ b/noao/imred/src/doslit/sbatch.cl
@@ -0,0 +1,199 @@
+# 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="List of object spectra"}
+real datamax {prompt="Max data value / cosmic ray threshold"}
+file arcs1 {prompt="List of arc spectra"}
+file arcref1 {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?"}
+bool dispcor {prompt="Dispersion correct spectra?"}
+bool extcor {prompt="Extinction correct spectra?"}
+bool fluxcal1 {prompt="Flux calibrate spectra?"}
+
+bool newdisp, newsens, newarcs
+
+struct *fd1, *fd2, *fd3
+
+begin
+ file temp, spec, specms, arc, arcms
+ bool reextract, extract, disp, ext, flux, log
+ string imtype, mstype, str1, str2, str3, str4
+ int i
+ struct err
+
+ imtype = "." // envget ("imtype")
+ i = stridx (",", imtype)
+ if (i > 0)
+ imtype = substr (imtype, 1, i-1)
+ mstype = ".ms" // imtype
+ temp = mktemp ("tmp$iraf")
+
+ reextract = redo || (update && newdisp)
+
+ fd1 = objects
+ 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\n",
+ spec, imtype) | scan (err)
+ print (err, >> logfile)
+ print ("Check setting of imtype", >> logfile)
+ next
+ }
+ specms = spec // mstype
+
+ extract = no
+ disp = no
+ ext = no
+ flux = no
+ if (reextract || !access (specms))
+ extract = yes
+ else {
+ hselect (specms, "dispcor", yes, > temp)
+ hselect (specms, "ex-flag", yes, >> temp)
+ hselect (specms, "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 (specms))
+ imdelete (specms, verify=no)
+ print ("Extract object spectrum ", spec, >> logfile)
+ 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,
+ >> logfile)
+ if (fscan (fd2, str1, str2, str3, str4) == 4)
+ setairmass (spec, intype="beginning",
+ outtype="effective", exposure="exptime",
+ observatory=observatory, show=no, update=yes,
+ override=yes, >> logfile)
+ }
+ fd2 = ""; delete (temp, verify=no)
+ apslitproc (spec, saturation=datamax, verbose=no)
+ }
+
+ if (disp) {
+ # Fix arc headers if necessary.
+ if (newarcs) {
+ fd2 = arcs1
+ 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, arcref1, reextract, logfile, yes)
+
+ 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 {
+ print ("Dispersion correct ", spec, >> logfile)
+ dispcor (specms, "", linearize=sparams.linearize,
+ database=database, table=arcref1//mstype,
+ 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=no, logfile=logfile)
+ flpr
+ hedit (specms, "dispcor", 0, add=yes, verify=no,
+ show=no, update=yes)
+ disp = no
+ }
+ }
+
+ if (!disp) {
+ if (ext)
+ print ("Extinction correct ", spec, >> logfile)
+ if (flux)
+ print ("Flux calibrate ", spec, >> logfile)
+ if (flux || ext)
+ calibrate (specms, "", extinct=extcor, flux=fluxcal1,
+ extinction=extinction, observatory=observatory,
+ ignoreaps=yes, sensitivity="sens", fnu=sparams.fnu,
+ >> logfile)
+ }
+ }
+ fd1 = ""
+ delete (objects, verify=no)
+ delete (arcs1, verify=no)
+
+ if (access (done))
+ delete (done, verify=no)
+
+ flprcache (0)
+end
diff --git a/noao/imred/src/doslit/sbatch.par b/noao/imred/src/doslit/sbatch.par
new file mode 100644
index 00000000..582bdf03
--- /dev/null
+++ b/noao/imred/src/doslit/sbatch.par
@@ -0,0 +1,20 @@
+objects,f,h,"",,,"List of object spectra"
+datamax,r,h,,,,"Max data value / cosmic ray threshold"
+arcs1,f,h,"",,,"List of arc spectra"
+arcref1,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?"
+dispcor,b,h,,,,"Dispersion correct spectra?"
+extcor,b,h,,,,"Extinction correct spectra?"
+fluxcal1,b,h,,,,"Flux calibrate spectra?"
+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/doslit/sdoarcs.cl b/noao/imred/src/doslit/sdoarcs.cl
new file mode 100644
index 00000000..19b8f3af
--- /dev/null
+++ b/noao/imred/src/doslit/sdoarcs.cl
@@ -0,0 +1,101 @@
+# SDOARCS -- Determine dispersion relation for spectrum based on refernece arcs.
+
+procedure sdoarcs (spec, arcref1, reextract, logfile, batch)
+
+file spec
+file arcref1
+bool reextract
+file logfile
+bool batch
+
+struct *fd
+
+begin
+ file temp, arc1, arc2, str1
+ string imtype, mstype, reid
+ bool verbose1
+ int i, n
+
+ imtype = "." // envget ("imtype")
+ i = stridx (",", imtype)
+ if (i > 0)
+ imtype = substr (imtype, 1, i-1)
+ mstype = ".ms" // imtype
+ n = strlen (imtype)
+
+ temp = mktemp ("tmp$iraf")
+
+ for (j=1; j<=2; j+=1) {
+
+ # Setup interactive/batch parameters
+ if (batch) {
+ verbose1 = no
+ reid = "no"
+ } else {
+ verbose1 = verbose
+ reidentify.answer.p_mode = "h"
+ reid = reidentify.answer
+ reidentify.answer.p_mode = "q"
+ if (reid == "no")
+ reid = "yes"
+ }
+
+ # 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
+ i = fscan (fd, arc1, str1)
+ fd = ""; delete (temp, verify=no)
+ if (nscan() < 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.
+
+ arc2 = spec // arc1
+ if (access (arc2//mstype))
+ imdelete (arc2//mstype, verify=no)
+ delete (database//"/id"//arc2//".ms*", verify = no, >& "dev$null")
+
+ # Extract and determine dispersion function if necessary.
+ if (!access (arc2//mstype)) {
+ if (!batch)
+ print ("Extract and reidentify arc spectrum ", arc1)
+ print ("Extract and reidentify arc spectrum ", arc1, >> logfile)
+ apslitproc (arc1, output=arc2//".ms", references=spec,
+ background="none", clean=no, weights="none",
+ verbose=verbose1)
+ delete (database//"/id"//arc2//".ms*", verify = no,
+ >& "dev$null")
+ reidentify (arcref1//".ms", arc2//".ms", interactive=reid,
+ section="middle line", shift=0., step=1, nsum=1,
+ cradius=sparams.cradius, threshold=sparams.threshold,
+ nlost=100, refit=sparams.refit, trace=no, override=no,
+ newaps=yes, addfeatures=sparams.addfeatures,
+ coordlist=sparams.coordlist, match=sparams.match,
+ maxfeatures=50, minsep=2., database=database,
+ plotfile=plotfile, logfiles=logfile, verbose=verbose1)
+
+ # If not reextracting arcs based on object apertures
+ # then save the extracted arc to avoid doing it again.
+
+ if (arc1 != arc2)
+ imdelete (arc2//".ms", verify=no)
+ }
+
+ # Set the REFSPEC parameters for multispec spectrum.
+ if (nscan() == 1)
+ hedit (spec//".ms", "refspec"//j, arc2//".ms", add=yes,
+ verify=no, show=no, update=yes)
+ else
+ hedit (spec//".ms", "refspec"//j, arc2//".ms "//str1,
+ add=yes, verify=no, show=no, update=yes)
+ }
+end
diff --git a/noao/imred/src/doslit/sdoarcs.par b/noao/imred/src/doslit/sdoarcs.par
new file mode 100644
index 00000000..cea554c2
--- /dev/null
+++ b/noao/imred/src/doslit/sdoarcs.par
@@ -0,0 +1,7 @@
+spec,f,a,"",,,
+arcref1,f,a,"",,,
+reextract,b,a,,,,
+logfile,f,a,"",,,
+batch,b,a,,,,
+fd,*struct,h,"",,,
+mode,s,h,"ql",,,
diff --git a/noao/imred/src/doslit/sfluxcal.cl b/noao/imred/src/doslit/sfluxcal.cl
new file mode 100644
index 00000000..e9399ac3
--- /dev/null
+++ b/noao/imred/src/doslit/sfluxcal.cl
@@ -0,0 +1,196 @@
+# 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, arcs1, arcref1, arcrefs, redo, update, extcor,
+ done, log1, log2)
+
+file stds
+file arcs1
+file arcref1
+string arcrefs
+bool redo
+bool update
+bool extcor
+file done
+file log1
+file log2
+
+struct *fd1, *fd2, *fd3
+
+begin
+ string imtype, mstype
+ string spec, specms, arc, str1, str2, str3, str4
+ file temp1, temp2
+ int i, j
+ bool reextract, log
+
+ imtype = "." // envget ("imtype")
+ i = stridx (",", imtype)
+ if (i > 0)
+ imtype = substr (imtype, 1, i-1)
+ mstype = ".ms" // imtype
+
+ temp1 = mktemp ("tmp$iraf")
+ temp2 = mktemp ("tmp$iraf")
+
+ reextract = redo || (update && sproc.newdisp)
+ sproc.newsens = no
+
+ if (redo && access ("std"))
+ delete ("std", verify=no)
+
+ fd1 = stds
+ while (fscan (fd1, spec) != EOF) {
+ specms = spec // mstype
+
+ if (reextract && access (specms))
+ imdelete (specms, verify=no)
+ if (!access (specms)) {
+ 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 (specms, "dispcor,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 = arcs1
+ 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, arcref1, reextract, log1, no)
+
+ hselect (specms, "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 (specms, "", linearize=sparams.linearize,
+ database=database, table=arcref1//mstype,
+ 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, > log2)
+ flpr
+ hedit (specms, "dispcor", 0, add=yes, verify=no,
+ show=no, update=yes)
+ }
+ }
+
+ if (j < 2 || !access ("std")) {
+ print ("Compile standard star fluxes for ", spec) | tee (log1)
+ standard (specms, output="std", samestar=no, beam_switch=no,
+ apertures="", bandwidth=INDEF, bandsep=INDEF,
+ fnuzero=3.68E-20, extinction=extinction, caldir=caldir,
+ observatory=observatory, interact=no)
+ hedit (specms, "std-flag", "yes", add=yes, verify=no,
+ show=no, update=yes)
+ print (specms, >> temp2)
+ sproc.newsens = yes
+ }
+ }
+ fd1 = ""
+
+ if (sproc.newsens || !access ("sens"//imtype)) {
+ if (!access ("std")) {
+ print ("No standard star data") | tee (log1)
+ sproc.fluxcal1 = no
+ } else {
+ imdelete ("sens"//imtype, verify=no, >& "dev$null")
+ print ("Compute sensitivity function") | tee (log1)
+ sensfunc ("std", "sens", apertures="", ignoreaps=yes,
+ 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 && access (temp2)) {
+ print ("Flux and/or extinction calibrate standard stars") |
+ tee (log1)
+ calibrate ("@"//temp2, "", extinct=extcor, flux=sproc.fluxcal1,
+ extinction=extinction, observatory=observatory, ignoreaps=yes,
+ 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/doslit/sfluxcal.par b/noao/imred/src/doslit/sfluxcal.par
new file mode 100644
index 00000000..44474335
--- /dev/null
+++ b/noao/imred/src/doslit/sfluxcal.par
@@ -0,0 +1,14 @@
+stds,f,a,,,,
+arcs1,f,a,,,,
+arcref1,f,a,"",,,
+arcrefs,s,a,,,,
+redo,b,a,,,,
+update,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,"ql",,,
diff --git a/noao/imred/src/doslit/sgetspec.cl b/noao/imred/src/doslit/sgetspec.cl
new file mode 100644
index 00000000..1140e610
--- /dev/null
+++ b/noao/imred/src/doslit/sgetspec.cl
@@ -0,0 +1,178 @@
+# 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
+ itype = ""
+ 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/doslit/sgetspec.par b/noao/imred/src/doslit/sgetspec.par
new file mode 100644
index 00000000..1f5387cc
--- /dev/null
+++ b/noao/imred/src/doslit/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/doslit/slistonly.cl b/noao/imred/src/doslit/slistonly.cl
new file mode 100644
index 00000000..71ee3b40
--- /dev/null
+++ b/noao/imred/src/doslit/slistonly.cl
@@ -0,0 +1,180 @@
+# 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, arcs1, standards, dispcor, extcor, fluxcal,
+ redo, update)
+
+file objects
+file arcs1
+file standards
+
+bool dispcor
+bool extcor
+bool fluxcal
+bool redo
+bool update
+
+struct *fd1
+struct *fd2
+
+begin
+ string imtype, mstype
+ string spec, arcref1
+ string specms, arcref1ms
+ string temp, done, str1, str2
+ bool reextract, fluxcal1, stdfile
+ bool newdisp, newsens, extract, disp, ext, flux
+ int i, dc, sf
+
+ imtype = "." // envget ("imtype")
+ i = stridx (",", imtype)
+ if (i > 0)
+ imtype = substr (imtype, 1, i-1)
+ mstype = ".ms" // imtype
+ temp = mktemp ("tmp$iraf")
+ done = mktemp ("tmp$iraf")
+
+ newdisp = no
+ newsens = no
+ fluxcal1 = fluxcal
+
+ print ("Check and set new object aperture definitions")
+
+ if (dispcor) {
+ fd1 = arcs1
+ if (fscan (fd1, arcref1) == EOF)
+ error (1, "No reference arcs")
+ fd1 = ""
+ arcref1ms = arcref1 // mstype
+
+ if (redo || !access (arcref1ms)) {
+ print ("Extract arc reference image ", arcref1)
+ print ("Determine dispersion solution for ", arcref1)
+ newdisp = yes
+ } else {
+ hselect (arcref1ms, "dispcor", yes, > temp)
+ fd1 = temp
+ dc = -1
+ i = fscan (fd1, dc)
+ fd1 = ""; delete (temp, verify=no)
+ if (i < 1) {
+ print ("Determine dispersion solution for ", arcref1)
+ newdisp = yes
+ }
+ }
+ print (arcref1, > done)
+
+ if (fluxcal1) {
+ stdfile = access ("std")
+ if (redo && stdfile)
+ stdfile = no
+
+ reextract = redo || (update && newdisp)
+ fd1 = standards
+ while (fscan (fd1, spec) != EOF) {
+ specms = spec // mstype
+ if (reextract || !access (specms)) {
+ print ("Extract standard star spectrum ", spec)
+ print ("Dispersion correct ", spec)
+ print ("Compile standard star fluxes for ", spec)
+ stdfile = yes
+ newsens = yes
+ } else {
+ hselect (specms, "dispcor,std-flag", yes, > temp)
+ fd2 = temp
+ dc = -1
+ sf = -1
+ i = fscan (fd2, dc, sf)
+ fd2 = ""; delete (temp, 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 = ""
+
+ 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 && newdisp)
+ fd1 = objects
+ while (fscan (fd1, spec) != EOF) {
+ if (access (done)) {
+ fd2 = done
+ while (fscan (fd2, specms) != EOF)
+ if (spec == specms)
+ break
+ if (spec == specms)
+ next
+ fd2 = ""
+ }
+
+ specms = spec // mstype
+
+ extract = no
+ disp = no
+ ext = no
+ flux = no
+ if (reextract || !access (specms))
+ extract = yes
+ else {
+ hselect (specms, "dispcor", yes, > temp)
+ hselect (specms, "ex-flag", yes, >> temp)
+ hselect (specms, "ca-flag", yes, >> temp)
+ fd2 = temp
+ extract = update
+ 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 (temp, verify=no)
+ }
+
+ if (extract) {
+ disp = dispcor
+ ext = extcor
+ flux = fluxcal1
+ }
+
+ 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 = ""
+
+ if (access (done))
+ delete (done, verify=no)
+end
diff --git a/noao/imred/src/doslit/slistonly.par b/noao/imred/src/doslit/slistonly.par
new file mode 100644
index 00000000..08d4e016
--- /dev/null
+++ b/noao/imred/src/doslit/slistonly.par
@@ -0,0 +1,12 @@
+objects,f,a,,,,
+arcs1,f,a,,,,
+standards,f,a,,,,
+dispcor,b,a,,,,
+extcor,b,a,,,,
+fluxcal,b,a,,,,
+redo,b,a,,,,
+update,b,a,,,,
+fd1,*struct,h,"",,,
+fd2,*struct,h,"",,,
+fd3,*struct,h,"",,,
+mode,s,h,"ql",,,
diff --git a/noao/imred/src/doslit/sparams.par b/noao/imred/src/doslit/sparams.par
new file mode 100644
index 00000000..1cc001d8
--- /dev/null
+++ b/noao/imred/src/doslit/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.?
+
+-- DEFAULT APERTURE PARAMETERS -- "
+lower,r,h,-3.,,,Lower aperture limit relative to center
+upper,r,h,3.,,,"Upper aperture limit relative to center
+
+-- 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,1,,,"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
+
+-- APERTURE EXTRACTION PARAMETERS --"
+weights,s,h,"none",,,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
+
+-- BACKGROUND SUBTRACTION PARAMETERS --"
+background,s,h,"fit","none|average|median|minimum|fit",,Background to subtract
+b_function,s,h,"legendre","chebyshev|legendre|spline1|spline3",,"Background function"
+b_order,i,h,1,,,"Background function order"
+b_sample,s,h,"-10:-6,6:10",,,"Background sample regions"
+b_naverage,i,h,-100,,,"Background average or median"
+b_niterate,i,h,1,0,,"Background rejection iterations"
+b_low,r,h,3.,0.,,"Background lower rejection sigma"
+b_high,r,h,3.,0.,,"Background upper rejection sigma
+
+-- ARC DISPERSION FUNCTION PARAMETERS --"
+threshold,r,h,10.,0.,,"Minimum line contrast threshold"
+coordlist,f,h,linelists$idhenear.dat,,,"Line list"
+match,r,h,-3.,,,"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,"spline3","legendre|chebyshev|spline1|spline3",,"Coordinate function"
+i_order,i,h,1,1,,"Order of dispersion function"
+i_niterate,i,h,1,0,,"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?"
+addfeatures,b,h,no,,,"Add features 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 --"
+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/doslit/sproc.cl b/noao/imred/src/doslit/sproc.cl
new file mode 100644
index 00000000..0b13d71a
--- /dev/null
+++ b/noao/imred/src/doslit/sproc.cl
@@ -0,0 +1,404 @@
+# SPROC -- Process spectra from 2D to 1D
+#
+# This program combines all the operations of extraction, dispersion
+# correction, extinction correction, and flux calibration in as simple
+# and noninteractive manner as possible.
+
+procedure sproc (objects, arcs1, arctable, standards, crval, cdelt, dispcor,
+ extcor, fluxcal, resize, clean, splot, redo, update, quicklook, batch,
+ listonly)
+
+file objects = "" {prompt="List of object spectra"}
+
+file arcs1 = "" {prompt="List of arc spectra"}
+file arctable = "" {prompt="Arc assignment table (optional)"}
+file standards = "" {prompt="List of standard star spectra\n"}
+
+string crval = "INDEF" {prompt="Approximate wavelength"}
+string cdelt = "INDEF" {prompt="Approximate dispersion\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="Automatically resize apertures?"}
+bool clean = no {prompt="Detect and replace bad pixels?"}
+bool splot = no {prompt="Plot the final spectrum?"}
+bool redo = no {prompt="Redo operations if previously done?"}
+bool update = no {prompt="Update spectra if cal data changes?"}
+bool quicklook = no {prompt="Minimally interactive quick-look?"}
+bool batch = no {prompt="Extract objects in batch?"}
+bool listonly = no {prompt="List steps but don't process?\n"}
+
+real datamax = INDEF {prompt="Max data value / cosmic ray threshold"}
+
+string anssplot {prompt="Splot spectrum?", mode="q",
+ enum="no|yes|NO|YES"}
+bool newdisp, newsens, newarcs
+bool fluxcal1, splot1, splot2
+bool dobatch
+
+struct *fd1, *fd2, *fd3
+
+begin
+ file arcref1, spec, arc
+ file arcref1ms, specms, arcms
+ file temp, done
+ string imtype, mstype
+ string str1, str2, str3, str4, arcrefs, log1, log2
+ bool reextract, extract, disp, ext, flux, log
+ 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) {
+ slistonly (objects, arcs1, standards, dispcor, extcor,
+ fluxcal, redo, update)
+ bye
+ }
+
+ imtype = "." // envget ("imtype")
+ i = stridx (",", imtype)
+ if (i > 0)
+ imtype = substr (imtype, 1, i-1)
+ mstype = ".ms" // 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$iraf")
+
+ # Get query parameters
+ if (arctable == "")
+ arcrefs = "@"//arcs1
+ else
+ arcrefs = arctable
+ arcref1 = ""
+
+ # Rather than always have switches on the logfile and verbose flags
+ # we use TEE and set a file to "dev$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 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.
+
+ newdisp = no
+ newsens = no
+ newarcs = yes
+ fluxcal1 = fluxcal
+
+ # Check if there are aperture definitions in the database and
+ # define them if needed. This is interactive.
+
+ print ("Define object apertures", >> log1)
+ if (resize)
+ apslitproc.ansresize = "YES"
+ else
+ apslitproc.ansresize = "NO"
+ if (quicklook) {
+ apslitproc.ansedit = "NO"
+ apslitproc.ansfittrace = "NO"
+ } else {
+ apslitproc.ansedit = "yes"
+ apslitproc.ansfittrace = "yes"
+ }
+ if (redo) {
+ delete (database//"/ap//@"//objects, verify=no, >& "dev$null")
+ apslitproc ("@"//objects, references="", ansfind="YES",
+ ansrecenter="NO", anstrace="YES", ansextract="NO")
+ } else
+ apslitproc ("@"//objects, references="NEW", ansfind="YES",
+ ansrecenter="NO", anstrace="YES", ansextract="NO")
+ if (dispcor && fluxcal1) {
+ if (redo) {
+ delete (database//"/ap//@"//standards, verify=no, >& "dev$null")
+ apslitproc ("@"//standards, references="", ansfind="YES",
+ ansrecenter="NO", anstrace="YES", ansextract="NO")
+ } else
+ apslitproc ("@"//standards, references="NEW", ansfind="YES",
+ ansrecenter="NO", anstrace="YES", ansextract="NO")
+ }
+
+ # Initialize APSLITPROC.
+ apslitproc.saturation = INDEF
+ apslitproc.references = ""
+ apslitproc.profiles = ""
+ apslitproc.ansrecenter = "NO"
+ apslitproc.ansresize = "NO"
+ apslitproc.ansedit = "NO"
+ apslitproc.anstrace = "NO"
+ apslitproc.ansfittrace = "NO"
+ apslitproc.ansextract = "YES"
+ apslitproc.ansreview = "NO"
+
+ # Initialize REIDENTIFY
+ if (quicklook)
+ reidentify.answer = "NO"
+ else
+ reidentify.answer = "yes"
+
+ if (splot && !quicklook) {
+ splot1 = yes
+ splot2 = yes
+ } else {
+ splot1 = no
+ splot2 = 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 SARCREFS.
+
+ if (dispcor) {
+ fd1 = arcs1
+ fd2 = objects
+ if (fscan (fd1, arcref1) == EOF)
+ error (1, "No reference arcs")
+ fd1 = ""
+ if (fscan (fd2, spec) == EOF)
+ error (1, "No object spectra for arc reference")
+ fd2 = ""
+ i = strlen (arcref1)
+ if (!access (arcref1 // imtype)) {
+ printf ("Arc reference spectrum not found - %s%s\n",
+ arcref1, imtype) | scan (err)
+ error (1, err // "\nCheck setting of imtype")
+ }
+ arcref1ms = arcref1 // mstype
+ if (redo && access (arcref1ms))
+ imdelete (arcref1ms, verify=no)
+ apslitproc.references = spec
+ sarcrefs (arcref1, crval, cdelt, done, log1, log2)
+ apslitproc.references = ""
+
+ if (fluxcal1)
+ sfluxcal (standards, arcs1, arcref1, arcrefs,
+ redo, update, extcor, done, log1, log2)
+ }
+
+ # Now we are ready to process the object spectra.
+
+ reextract = redo || (update && newdisp)
+ fd1 = objects
+ 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, specms) != EOF)
+ if (spec == specms)
+ break
+ if (spec == specms)
+ next
+ fd2 = ""
+ }
+ if (!access (spec // imtype)) {
+ print ("Object spectrum not found - " // spec // imtype) |
+ tee (log1)
+ print ("Check setting of imtype")
+ next
+ }
+ specms = spec // mstype
+
+ # Determine required operations from the flags and image header.
+ extract = no
+ disp = no
+ ext = no
+ flux = no
+ if (reextract || !access (specms))
+ extract = yes
+ else {
+ hselect (specms, "dispcor", yes, > temp)
+ hselect (specms, "ex-flag", yes, >> temp)
+ hselect (specms, "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.arcs1 = arcs1
+ sbatch.arcref1 = arcref1
+ sbatch.arcrefs = arcrefs
+ sbatch.done = done
+ sbatch.logfile = log1
+ sbatch.redo = reextract
+ sbatch.update = update
+ sbatch.dispcor = dispcor
+ sbatch.fluxcal1 = fluxcal1
+ sbatch.extcor = extcor
+ sbatch.newdisp = newdisp
+ sbatch.newsens = newsens
+ sbatch.newarcs = newarcs
+ dobatch = yes
+ return
+ }
+
+ # Process the spectrum in foreground.
+ if (extract) {
+ if (access (specms))
+ imdelete (specms, verify=no)
+ 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)
+ }
+
+ if (disp) {
+ # Fix arc headers if necessary.
+ if (newarcs) {
+ fd2 = arcs1
+ 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, arcref1, reextract, log1, no)
+
+ 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) | tee (log1)
+ else {
+ print ("Dispersion correct ", spec) | tee (log1)
+ dispcor (specms, "", linearize=sparams.linearize,
+ database=database, table=arcref1//mstype,
+ w1=INDEF, w2=INDEF, dw=INDEF, nw=INDEF,
+ log=sparams.log, flux=sparams.flux, samedisp=no,
+ global=no, ignoreaps=yes, confirm=no, listonly=no,
+ verbose=verbose, logfile=logfile)
+ flpr
+ hedit (specms, "dispcor", 0, add=yes, verify=no,
+ show=no, update=yes)
+ disp = no
+ }
+ }
+
+ if (!disp) {
+ if (ext)
+ print ("Extinction correct ", spec) | tee (log1)
+ if (flux)
+ print ("Flux calibrate ", spec) | tee (log1)
+ if (flux || ext)
+ calibrate (specms, "", extinct=extcor, flux=fluxcal1,
+ extinction=extinction, observatory=observatory,
+ ignoreaps=yes, sensitivity="sens", fnu=sparams.fnu) |
+ tee (log1, > log2)
+ }
+ if (extract || disp || ext || flux) {
+ if (splot1) {
+ print (specms, ":")
+ str1 = anssplot
+ if (str1 == "NO" || str1 == "YES")
+ splot1 = no
+ if (str1 == "no" || str1 == "NO")
+ splot2 = no
+ else
+ splot2 = yes
+ }
+ if (splot2)
+ splot (specms)
+ else if (splot && quicklook)
+ bplot (specms, apertures="1", band=1, graphics="stdgraph",
+ cursor="onedspec$gcurval")
+ }
+ print (spec, >> done)
+ }
+ fd1 = ""
+
+ if (access (done))
+ delete (done, verify=no)
+end
diff --git a/noao/imred/src/doslit/sproc.par b/noao/imred/src/doslit/sproc.par
new file mode 100644
index 00000000..536e05e4
--- /dev/null
+++ b/noao/imred/src/doslit/sproc.par
@@ -0,0 +1,33 @@
+objects,f,a,"",,,"List of object spectra"
+arcs1,f,a,"",,,"List of arc spectra"
+arctable,f,a,"",,,"Arc assignment table (optional)"
+standards,f,a,"",,,"List of standard star spectra
+"
+crval,s,a,"INDEF",,,"Approximate wavelength"
+cdelt,s,a,"INDEF",,,"Approximate dispersion
+"
+dispcor,b,a,yes,,,"Dispersion correct spectra?"
+extcor,b,a,no,,,"Extinction correct spectra?"
+fluxcal,b,a,no,,,"Flux calibrate spectra?"
+resize,b,a,no,,,"Automatically resize apertures?"
+clean,b,a,no,,,"Detect and replace bad pixels?"
+splot,b,a,no,,,"Plot the final spectrum?"
+redo,b,a,no,,,"Redo operations if previously done?"
+update,b,a,no,,,"Update spectra if cal data changes?"
+quicklook,b,a,no,,,"Minimally interactive quick-look?"
+batch,b,a,no,,,"Extract objects in batch?"
+listonly,b,a,no,,,"List steps but don\'t process?
+"
+datamax,r,h,INDEF,,,"Max data value / cosmic ray threshold"
+anssplot,s,q,,no|yes|NO|YES,,"Splot spectrum?"
+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 07:12:52 -0400