Repatch (from linux) of OSX IRAF

14 files changed, 417 insertions, 0 deletions

diff --git a/noao/imred/irs/Revisions b/noao/imred/irs/Revisions
new file mode 100644
index 00000000..ac156735
--- /dev/null
+++ b/noao/imred/irs/Revisions
@@ -0,0 +1,111 @@
+.help revisions Jun88 noao.imred.irs
+.nf
+
+=====
+V2.12
+=====
+
+imred$irs/standard.par
+    Added blackbody query parameters.  (5/2/02, Valdes)
+
+========
+V2.11.3b
+========
+
+imred$irs/identify.par
+    Added new units parameters.  (3/11/97, Valdes)
+
+=========
+V2.10.4p2
+=========
+
+imred$irs/
+   Updated to new version of ONEDSPEC (7/11/91, Valdes)
+
+================
+
+imred$irs/standard.par
+   Removed ennumerated list.  (4/10/89, Valdes)
+
+imred$irs/irs.cl
+imred$irs/irs.men
+specplot.par+
+	Task SPECPLOT added.  (4/3/89 ShJ)
+
+imred$irs/batchred.cl
+imred$irs/batchred.par
+imred$irs/irs.cl
+imred$irs/irs.men
+   1. New BATCHRED script. (4/27/88 Valdes)
+   2. Eliminated EXTINCT. (4/27/88 Valdes)
+
+imred$irs/sensfunc.par
+    Added aperture selection and query parameters.  (4/15/88 Valdes)
+
+imred$irs/irs.cl
+imred$irs/refspectra.par +
+    Refer to new ONEDSPEC executable and tasks.  (4/7/88 Valdes)
+
+noao$imred/irs/reidentify.par
+    Valdes, Jan 4, 1988
+    Updated parameter file for new REIDENTIFY parameter.
+
+noao$imred/irs/dispcor.par
+    Valdes, March 5, 1987
+    1.  The DISPCOR default parameter file has been updated because of
+	changes to the task; most notable being that wstart and wpc are
+	list structured.
+
+noao$imred/irs/flatdiv.par
+noao$imred/irs/flatfit.par
+    Valdes, December, 2, 1986
+    1.  New parameter "power" added to these tasks.
+
+noao$imred/irs/coincor.par
+    Valdes, October 20, 1986
+    1.  New parameter "checkdone" added to COINCOR to allow overriding
+	coincidence correction checking.
+
+noao$imred/irs/irs.par
+noao$imred/irs/coincor.par
+noao$imred/irs/irs.men
+    Valdes, October 13, 1986
+    1.  Added new COINCOR parameter "power".
+
+noao$imred/irs/irs.cl
+noao$imred/irs/irs.men
+noao$imred/irs/shedit.par +
+    Valdes, October 6, 1986
+    1.  Added new task SHEDIT.
+
+noao$imred/irs/identify.par
+    Valdes, October 3, 1986
+    1.  Added new IDENTIFY parameter "threshold".
+
+irs:  Valdes, July 3, 1986:
+    1.  New coordlist name in IDENTIFY parameter file.
+    2.  New calibration file name in package parameter file.
+
+=====================================
+STScI Pre-release and SUN 2.3 Release
+=====================================
+
+irs$bswitch.par:  Valdes, May 19, 1986
+    1.  The parameter "add_const" in BSWITCH is directed to the parameter
+	in SENSFUNC of the same name.
+
+irs:  Valdes, May 12, 1986:
+    1.  SPLOT updated.  New parameters XMIN, XMAX, YMIN, YMAX.
+
+irs:  Valdes, April 7, 1986:
+    1.  Package parameter file changed to delete latitude.
+    2.  DISPCOR, BSWITCH, and STANDARD latitude parameter now obtained from
+	OBSERVATORY.
+
+irs:  Valdes, March 27, 1986:
+    1.  New task SETDISP added.
+
+===========
+Release 2.2
+===========
+.endhelp
diff --git a/noao/imred/irs/calibrate.par b/noao/imred/irs/calibrate.par
new file mode 100644
index 00000000..795965b7
--- /dev/null
+++ b/noao/imred/irs/calibrate.par
@@ -0,0 +1,14 @@
+# CALIBRATE parameter file
+
+input,s,a,,,,Input spectra to calibrate
+output,s,a,,,,Output calibrated spectra
+records,s,a,,,,Record number extensions
+extinct,b,h,yes,,,Apply extinction correction?
+flux,b,h,yes,,,Apply flux calibration?
+extinction,s,h,)_.extinction,,,Extinction file
+observatory,s,h,)_.observatory,,,Observatory of observation
+ignoreaps,b,h,no,,,Ignore aperture numbers in flux calibration?
+sensitivity,s,h,"sens",,,Image root name for sensitivity spectra
+fnu,b,h,no,,,Create spectra having units of FNU?
+airmass,r,q,,1.,,Airmass
+exptime,r,q,,,,Exposure time (seconds)
diff --git a/noao/imred/irs/dispcor.par b/noao/imred/irs/dispcor.par
new file mode 100644
index 00000000..90257214
--- /dev/null
+++ b/noao/imred/irs/dispcor.par
@@ -0,0 +1,19 @@
+input,s,a,,,,List of input spectra
+output,s,a,,,,List of output spectra
+records,s,a,,,,Record number extensions
+linearize,b,h,yes,,,Linearize (interpolate) spectra?
+database,s,h,"database",,,Dispersion solution database
+table,s,h,"",,,Wavelength table for apertures
+w1,r,h,INDEF,,,Starting wavelength
+w2,r,h,INDEF,,,Ending wavelength
+dw,r,h,INDEF,,,Wavelength interval per pixel
+nw,i,h,1024,,,Number of output pixels
+log,b,h,no,,,Logarithmic wavelength scale?
+flux,b,h,yes,,,Conserve total flux?
+samedisp,b,h,yes,,,Same dispersion in all apertures?
+global,b,h,yes,,,Apply global defaults?
+ignoreaps,b,h,no,,,Ignore apertures?
+confirm,b,h,yes,,,Confirm dispersion coordinates?
+listonly,b,h,no,,,List the dispersion coordinates only?
+verbose,b,h,yes,,,Print linear dispersion assignments?
+logfile,s,h,"logfile",,,Log file
diff --git a/noao/imred/irs/flatfit.par b/noao/imred/irs/flatfit.par
new file mode 100644
index 00000000..bd693aed
--- /dev/null
+++ b/noao/imred/irs/flatfit.par
@@ -0,0 +1,24 @@
+# FLATFIT parameter file
+
+input,s,a,,,,Input image root file name
+records,s,a,,,,Range of spectral records
+output,s,a,,,,Output file root name for new spectra
+function,s,h,"chebyshev",,,Function to fit (chebyshev|legendre|spline3|spline1)
+order,i,h,1,1,,Fitting order (number of terms)
+niter,i,h,1,1,,Number of rejection iterations
+lower,r,h,100.,0,,Lower rejection criterion in sigmas
+upper,r,h,100.,0,,Upper rejection criterion in sigmas
+ngrow,i,h,0,,,Growing region
+div_min,r,h,1.0,,,Value to use if division by zero occurs
+interact,b,h,yes,,,Interact with the first accumulation?
+all_interact,b,h,no,,,Interact with all accumulations?
+coincor,b,h,)_.coincor,,,Apply coincidence correction to flats
+ccmode,s,h,)_.ccmode,,,Correction mode (photo|iids)
+deadtime,r,h,)_.deadtime,,,Deadtime in seconds
+power,r,h,)_.power,,,IIDS power law coefficient
+new_order,i,a,4,1,,enter order
+new_lower,r,a,,,,enter nr sigma
+new_upper,r,a,,,,enter nr sigma
+new_niter,i,a,,,,enter nr of iterations
+confirm,b,a,,,,Exit and save solution?
+cursor,*gcur,h,"",,,Graphics cursor input
diff --git a/noao/imred/irs/identify.par b/noao/imred/irs/identify.par
new file mode 100644
index 00000000..d42065e1
--- /dev/null
+++ b/noao/imred/irs/identify.par
@@ -0,0 +1,33 @@
+# Parameters for identify task.
+
+images,s,a,,,,Images containing features to be identified
+section,s,h,"middle line",,,Section to apply to two dimensional images
+database,f,h,database,,,Database in which to record feature data
+coordlist,f,h,linelists$henear.dat,,,User coordinate list
+units,s,h,"",,,Coordinate units
+nsum,s,h,"10",,,Number of lines/columns/bands to sum in 2D images
+match,r,h,50.,,,Coordinate list matching limit
+maxfeatures,i,h,50,,,Maximum number of features for automatic identification
+zwidth,r,h,100.,,,Zoom graph width in user units
+
+ftype,s,h,"emission","emission|absorption",,Feature type
+fwidth,r,h,4.,,,Feature width in pixels
+cradius,r,h,5.,,,Centering radius in pixels
+threshold,r,h,10.,0.,,Feature threshold for centering
+minsep,r,h,2.,0.,,Minimum pixel separation
+
+function,s,h,"chebyshev","legendre|chebyshev|spline1|spline3",,Coordinate function
+order,i,h,8,1,,Order of coordinate function
+sample,s,h,"*",,,Coordinate sample regions
+niterate,i,h,0,0,,Rejection iterations
+low_reject,r,h,3.,0.,,Lower rejection sigma
+high_reject,r,h,3.,0.,,Upper rejection sigma
+grow,r,h,0.,0.,,Rejection growing radius
+
+autowrite,b,h,no,,,"Automatically write to database"
+graphics,s,h,"stdgraph",,,Graphics output device
+cursor,*gcur,h,"",,,Graphics cursor input
+
+crval,s,q,,,,"Approximate coordinate (at reference pixel)"
+cdelt,s,q,,,,"Approximate dispersion"
+aidpars,pset,h,,,,"Automatic identification algorithm parameters"
diff --git a/noao/imred/irs/irs.cl b/noao/imred/irs/irs.cl
new file mode 100644
index 00000000..6814185f
--- /dev/null
+++ b/noao/imred/irs/irs.cl
@@ -0,0 +1,64 @@
+#{ IRS -- KPNO IRS Spectral Reduction Package
+
+# Load necessary packages
+
+lists		# List package for table
+
+# Define necessary paths
+
+set	irscal		= "onedstds$irscal/"
+set	irsiids		= "onedspec$irsiids/"
+
+package irs
+
+# Standard ONEDSPEC tasks
+task	autoidentify,
+	continuum,
+	deredden,
+	dopcor,
+	mkspec,
+	names,
+	sarith,
+	sflip,
+	sinterp,
+	splot,
+	specplot,
+	specshift	= onedspec$x_onedspec.e
+task	scombine	= "onedspec$scombine/x_scombine.e"
+task	aidpars		= "onedspec$aidpars.par"
+task	dispcor1	= onedspec$dispcor1.par
+task	scopy		= onedspec$scopy.cl
+hidetask dispcor1
+
+# Special  IRS/IIDS tasks
+task	addsets,
+	bswitch,
+	coefs,
+	flatdiv,
+	slist1d,
+	subsets,
+	sums		= irsiids$x_onedspec.e
+task	batchred	= irsiids$batchred.cl
+task	bplot		= irsiids$bplot.cl
+task	extinct		= irsiids$extinct.cl
+
+# Different default parameters
+task	calibrate,
+	dispcor,
+	flatfit,
+	identify,
+	lcalib,
+	reidentify,
+	refspectra,
+	sensfunc,
+	standard	= irs$x_onedspec.e
+
+# Astutil tasks
+task	setairmass,
+	setjd		= "astutil$x_astutil.e"
+
+# Define a task living in the users directory - it is created by BATCHRED
+
+task	$process	= process.cl
+
+clbye()
diff --git a/noao/imred/irs/irs.hd b/noao/imred/irs/irs.hd
new file mode 100644
index 00000000..e5125e4f
--- /dev/null
+++ b/noao/imred/irs/irs.hd
@@ -0,0 +1 @@
+# Help directory for the KPNOSLIT package.
diff --git a/noao/imred/irs/irs.men b/noao/imred/irs/irs.men
new file mode 100644
index 00000000..60e4a37d
--- /dev/null
+++ b/noao/imred/irs/irs.men
@@ -0,0 +1,35 @@
+	addsets - Add subsets of strings of spectra
+       batchred - Batch processing of IIDS/IRS spectra
+          bplot - Batch plots of spectra
+	bswitch - Beam-switch strings of spectra to make obj-sky pairs
+      calibrate - Apply sensitivity correction to spectra
+          coefs - Extract mtn reduced coefficients from henear scans
+      continuum - Fit the continuum in spectra
+       deredden - Apply interstellar extinction corrections
+	dispcor - Dispersion correct spectra
+	 dopcor - Doppler correct spectra
+	extinct - Use BSWITCH for extinction correction
+	flatdiv - Divide spectra by flat field
+	flatfit - Sum and normalize flat field spectra
+       identify - Identify features in spectrum for dispersion solution
+         lcalib - List calibration file data
+         mkspec - Generate an artificial spectrum
+          names - Generate a list of image names from a string
+	process - A task generated by BATCHRED
+     refspectra - Assign reference spectra to object spectra
+     reidentify - Automatically identify features in spectra
+         sarith - Spectrum arithmetic
+       scombine - Combine spectra having different wavelength ranges
+          scopy - Select and copy apertures in different spectral formats
+       sensfunc - Create sensitivity function
+     setairmass - Compute effective airmass and middle UT for an exposure
+          setjd - Compute and set Julian dates in images
+	  sflip - Flip data and/or dispersion coordinates in spectra
+        sinterp - Interpolate a table of x,y pairs to create a spectrum
+	slist1d - List spectral header elements
+       specplot - Stack and plot multiple spectra
+      specshift - Shift spectral dispersion coordinate systems
+	  splot - Preliminary spectral plot/analysis
+       standard - Identify standard stars to be used in sensitivity calc
+	subsets - Subtract pairs in strings of spectra
+           sums - Generate sums of object and sky spectra by aperture
diff --git a/noao/imred/irs/irs.par b/noao/imred/irs/irs.par
new file mode 100644
index 00000000..1a59fd5e
--- /dev/null
+++ b/noao/imred/irs/irs.par
@@ -0,0 +1,17 @@
+# PARAMETERS FOR KPNO IRS SPECTRAL REDUCTION PACKAGE
+
+observatory,s,h,"kpno",,,Observatory for data
+interp,s,h,"poly5","nearest|linear|poly3|poly5|spline3|sinc",,Interpolation type
+extinction,s,h,"onedstds$kpnoextinct.dat",,,Extinction file
+caldir,s,h,"irscal$",,,Directory containing calibration data
+coincor,b,h,no,,,Apply coincidence correction to flats
+ccmode,s,h,"",,,Correction mode (photo|iids|power)
+deadtime,r,h,,0,,Deadtime in seconds
+power,r,h,,,,IIDS power law coefficient
+
+dispaxis,i,h,1,1,3,Image axis for 2D/3D images
+nsum,s,h,"1",,,Number of lines/columns/bands to sum for 2D/3D images
+
+next_rec,i,h,1,,,"Next output record"
+
+version,s,h,"IRS V3: July 1991"
diff --git a/noao/imred/irs/lcalib.par b/noao/imred/irs/lcalib.par
new file mode 100644
index 00000000..30436625
--- /dev/null
+++ b/noao/imred/irs/lcalib.par
@@ -0,0 +1,7 @@
+# CALIBLIST parameter file
+
+option,s,a,,,,"List option (bands, ext, mags, fnu, flam, stars)"
+star_name,s,a,,,,Star name in calibration list
+extinction,s,h,,,,Extinction file
+caldir,s,h,)_.caldir,,,Directory containing calibration data
+fnuzero,r,h,3.68e-20,,,Absolute flux zero point
diff --git a/noao/imred/irs/refspectra.par b/noao/imred/irs/refspectra.par
new file mode 100644
index 00000000..47cd54f9
--- /dev/null
+++ b/noao/imred/irs/refspectra.par
@@ -0,0 +1,17 @@
+input,s,a,,,,"List of input spectra"
+records,s,a,,,,Record number extensions
+references,s,h,"*.imh",,,"List of reference spectra"
+apertures,s,h,"",,,"Input aperture selection list"
+refaps,s,h,"",,,"Reference aperture selection list"
+ignoreaps,b,h,no,,,Ignore input and reference apertures?
+select,s,h,"interp","match|nearest|preceding|following|interp|average",,"Selection method for reference spectra"
+sort,s,h,"ut",,,"Sort key"
+group,s,h,"none",,,"Group key"
+time,b,h,yes,,,"Is sort key a time?"
+timewrap,r,h,17.,0.,24.,"Time wrap point for time sorting"
+override,b,h,no,,,"Override previous assignments?"
+confirm,b,h,yes,,,"Confirm reference spectrum assignments?"
+assign,b,h,yes,,,"Assign the reference spectra to the input spectrum?"
+logfiles,s,h,"STDOUT,logfile",,,"List of logfiles"
+verbose,b,h,no,,,"Verbose log output?"
+answer,s,q,,"no|yes|YES",,"Accept assignment?"
diff --git a/noao/imred/irs/reidentify.par b/noao/imred/irs/reidentify.par
new file mode 100644
index 00000000..13b21740
--- /dev/null
+++ b/noao/imred/irs/reidentify.par
@@ -0,0 +1,36 @@
+# Parameters for reidentify task.
+
+reference,s,a,,,,Reference image
+images,s,a,,,,Images to be reidentified
+interactive,s,h,"no","no|yes|NO|YES",,Interactive fitting?
+section,s,h,"middle line",,,Section to apply to two dimensional images
+newaps,b,h,yes,,,Reidentify apertures in images not in reference?
+override,b,h,no,,,Override previous solutions?
+refit,b,h,yes,,,"Refit coordinate function?
+"
+trace,b,h,no,,,Trace reference image?
+step,s,h,"10",,,Step in lines/columns/bands for tracing an image
+nsum,s,h,"10",,,Number of lines/columns/bands to sum
+shift,s,h,"0.",,,Shift to add to reference features (INDEF to search)
+search,r,h,0.,,,Search radius
+nlost,i,h,0,0,,"Maximum number of features which may be lost
+"
+cradius,r,h,5.,,,Centering radius
+threshold,r,h,10.,0.,,Feature threshold for centering
+addfeatures,b,h,no,,,Add features from a line list?
+coordlist,f,h,linelists$henear.dat,,,User coordinate list
+match,r,h,10.,,,Coordinate list matching limit
+maxfeatures,i,h,50,,,Maximum number of features for automatic identification
+minsep,r,h,2.,0.,,"Minimum pixel separation
+"
+database,f,h,database,,,Database
+logfiles,s,h,"logfile",,,List of log files
+plotfile,s,h,"",,,Plot file for residuals
+verbose,b,h,no,,,Verbose output?
+graphics,s,h,"stdgraph",,,Graphics output device
+cursor,*gcur,h,"",,,"Graphics cursor input
+"
+answer,s,q,"yes","no|yes|NO|YES",,Fit dispersion function interactively?
+crval,s,q,,,,"Approximate coordinate (at reference pixel)"
+cdelt,s,q,,,,"Approximate dispersion"
+aidpars,pset,h,,,,"Automatic identification algorithm parameters"
diff --git a/noao/imred/irs/sensfunc.par b/noao/imred/irs/sensfunc.par
new file mode 100644
index 00000000..022190a4
--- /dev/null
+++ b/noao/imred/irs/sensfunc.par
@@ -0,0 +1,17 @@
+standards,s,a,std,,,Input standard star data file (from STANDARD)
+sensitivity,s,a,"sens",,,Output root sensitivity function imagename
+apertures,s,h,"",,,Aperture selection list
+ignoreaps,b,h,no,,,Ignore apertures and make one sensitivity function?
+logfile,f,h,"logfile",,,Output log for statistics information
+extinction,f,h,")_.extinction",,,Extinction file
+newextinction,f,h,"extinct.dat",,,Output revised extinction file
+observatory,s,h,)_.observatory,,,Observatory of data
+function,s,h,"spline3","chebyshev|legendre|spline3|spline1",,Fitting function
+order,i,h,6,1,,Order of fit
+interactive,b,h,yes,,,Determine sensitivity function interactively?
+graphs,s,h,"sr",,,Graphs per frame
+marks,s,h,"plus cross box",,,Data mark types (marks deleted added)
+colors,s,h,"2 1 3 4",,,Colors (lines marks deleted added)
+cursor,*gcur,h,"",,,Graphics cursor input
+device,s,h,"stdgraph",,,Graphics output device
+answer,s,q, yes,"no|yes|NO|YES",,"(no|yes|NO|YES)"
diff --git a/noao/imred/irs/standard.par b/noao/imred/irs/standard.par
new file mode 100644
index 00000000..3abf645a
--- /dev/null
+++ b/noao/imred/irs/standard.par
@@ -0,0 +1,22 @@
+input,f,a,,,,Input image file root name
+records,s,a,,,,Spectral records
+output,s,a,std,,,Output flux file (used by SENSFUNC)
+samestar,b,h,yes,,,Same star in all apertures?
+beam_switch,b,h,yes,,,Beam switch spectra?
+apertures,s,h,"",,,Aperture selection list
+bandwidth,r,h,INDEF,,,Bandpass widths
+bandsep,r,h,INDEF,,,Bandpass separation
+fnuzero,r,h,3.68e-20,,,Absolute flux zero point
+extinction,s,h,)_.extinction,,,Extinction file
+caldir,s,h,)_.caldir,,,Directory containing calibration data
+observatory,s,h,)_.observatory,,,Observatory for data
+interact,b,h,yes,,,Graphic interaction to define new bandpasses
+graphics,s,h,"stdgraph",,,Graphics output device
+cursor,*gcur,h,"",,,Graphics cursor input
+star_name,s,q,,,,Star name in calibration list
+airmass,r,q,,1.,,Airmass
+exptime,r,q,,,,Exposure time (seconds)
+mag,r,q,,,,Magnitude of star
+magband,s,q,,"U|B|V|R|I|J|H|K|L|Lprime|M",,"Magnitude type"
+teff,s,q,,,,Effective temperature or spectral type
+answer,s,q,no,,,"(no|yes|NO|YES|NO!|YES!)"