# CL extract by spectra and wavelength calibrate x-disp OSIRIS data 
# by Richard Elston, 8/18/93
#

procedure mkxsky(inimage, outpref, inflat)

string inimage {prompt="Input sky spectra"}
string outpref {prompt="output spectra prefix"}
string inflat  {prompt="Input flat field prefix"}

begin

#
# flatten and make subimages of the input sky spectra
#
	xdispflatten (inimage, inflat, outpref)

#
# extract spectra and then combine
#

	imdel("xyzskyref*.imh")
	imcopy (outpref//".hsub.imh", "xyzskyref.imh")

	apall ("xyzskyref.imh", 
1, output="", format="onedspec", references="", profiles="", interactive=yes,
find=no, recenter=no, resize=no, edit=yes, trace=no, fittrace=yes,
extract=yes, extras=no, review=no, line=INDEF, nsum=10, 
lower=-1.5, upper=1.5, apidtable="", b_function="chebyshev", b_order=1,
b_sample="-10:-6,6:10", b_naverage=-3, b_niterate=0, b_low_reject=3.,
b_high_rejec=3., b_grow=0., width=5., radius=10., threshold=0., minsep=5.,
maxsep=1000., order="increasing", apertures="", npeaks=INDEF, shift=yes,
llimit=INDEF, ulimit=INDEF, ylevel=0.1, peak=yes, bkg=yes, r_grow=0.,
avglimits=no, t_nsum=1, t_step=1, t_nlost=3, t_function="legendre", t_order=3,
t_sample="*", t_naverage=1, t_niterate=0, t_low_reject=3., t_high_rejec=3.,
t_grow=0., background="none", skybox=1, weights="variance", pfit="fit1d",
clean=no, saturation=INDEF, readnoise="0.", gain="1.", lsigma=4., usigma=4.,
nsubaps=1)

	apall (outpref//".ksub", 
1, output="", format="onedspec", references="xyzskyref.imh", 
profiles="", interactive=no,
find=no, recenter=no, resize=no, edit=no, trace=no, fittrace=no,
extract=yes, extras=no, review=no, line=INDEF, nsum=10,
lower=-1.5, upper=1.5, apidtable="", b_function="chebyshev", b_order=1,
b_sample="-10:-6,6:10", b_naverage=-3, b_niterate=0, b_low_reject=3.,
b_high_rejec=3., b_grow=0., width=5., radius=10., threshold=0., minsep=5.,
maxsep=1000., order="increasing", apertures="", npeaks=INDEF, shift=yes,
llimit=INDEF, ulimit=INDEF, ylevel=0.1, peak=yes, bkg=yes, r_grow=0.,
avglimits=no, t_nsum=1, t_step=1, t_nlost=3, t_function="legendre", t_order=3,
t_sample="*", t_naverage=1, t_niterate=0, t_low_reject=3., t_high_rejec=3.,
t_grow=0., background="none", skybox=1, weights="variance", pfit="fit1d",
clean=no, saturation=INDEF, readnoise="0.", gain="1.", lsigma=4., usigma=4.,
nsubaps=1)

	apall (outpref//".jsub", 
1, output="", format="onedspec", references="xyzskyref.imh", 
profiles="", interactive=no,
find=no, recenter=no, resize=no, edit=no, trace=no, fittrace=no,
extract=yes, extras=no, review=no, line=INDEF, nsum=10, 
lower=-1.5, upper=1.5, apidtable="", b_function="chebyshev", b_order=1,
b_sample="-10:-6,6:10", b_naverage=-3, b_niterate=0, b_low_reject=3.,
b_high_rejec=3., b_grow=0., width=5., radius=10., threshold=0., minsep=5.,
maxsep=1000., order="increasing", apertures="", npeaks=INDEF, shift=yes,
llimit=INDEF, ulimit=INDEF, ylevel=0.1, peak=yes, bkg=yes, r_grow=0.,
avglimits=no, t_nsum=1, t_step=1, t_nlost=3, t_function="legendre", t_order=3,
t_sample="*", t_naverage=1, t_niterate=0, t_low_reject=3., t_high_rejec=3.,
t_grow=0., background="none", skybox=1, weights="variance", pfit="fit1d",
clean=no, saturation=INDEF, readnoise="0.", gain="1.", lsigma=4., usigma=4.,
nsubaps=1)

	apall (outpref//".isub", 
1, output="", format="onedspec", references="xyzskyref.imh", 
profiles="", interactive=no,
find=no, recenter=no, resize=no, edit=no, trace=no, fittrace=no,
extract=yes, extras=no, review=no, line=INDEF, nsum=10, 
lower=-1.5, upper=1.5, apidtable="", b_function="chebyshev", b_order=1,
b_sample="-10:-6,6:10", b_naverage=-3, b_niterate=0, b_low_reject=3.,
b_high_rejec=3., b_grow=0., width=5., radius=10., threshold=0., minsep=5.,
maxsep=1000., order="increasing", apertures="", npeaks=INDEF, shift=yes,
llimit=INDEF, ulimit=INDEF, ylevel=0.1, peak=yes, bkg=yes, r_grow=0.,
avglimits=no, t_nsum=1, t_step=1, t_nlost=3, t_function="legendre", t_order=3,
t_sample="*", t_naverage=1, t_niterate=0, t_low_reject=3., t_high_rejec=3.,
t_grow=0., background="none", skybox=1, weights="variance", pfit="fit1d",
clean=no, saturation=INDEF, readnoise="0.", gain="1.", lsigma=4., usigma=4.,
nsubaps=1)

#
# combine the spectra into one
#


	 imcomb ("xyzskyref.00??.imh", outpref//".hsky",
plfile="", sigma="", logfile="STDOUT", combine="median",
reject="pclip", project=no, outtype="real", offsets="none", masktype="none",
maskvalue=0., blank=0., scale="med", zero="none", weight="none", statsec="",
expname="", lthreshold=INDEF, hthreshold=INDEF, nlow=1, nhigh=1, nkeep=1,
mclip=yes, lsigma=3., hsigma=3., rdnoise="0.", gain="1.", snoise="0.",
sigscale=0.1, pclip=-0.5, grow=0)
	
	imdel("xyzskyref*.imh")
	imdel(outpref//".hsub*.imh")

	 imcomb (outpref//".ksub.00??.imh", outpref//".ksky",
plfile="", sigma="", logfile="STDOUT", combine="median",
reject="pclip", project=no, outtype="real", offsets="none", masktype="none",
maskvalue=0., blank=0., scale="med", zero="none", weight="none", statsec="",
expname="", lthreshold=INDEF, hthreshold=INDEF, nlow=1, nhigh=1, nkeep=1,
mclip=yes, lsigma=3., hsigma=3., rdnoise="0.", gain="1.", snoise="0.",
sigscale=0.1, pclip=-0.5, grow=0)

	imdel(outpref//".ksub*.imh")
	

	 imcomb (outpref//".jsub.00??.imh", outpref//".jsky",
plfile="", sigma="", logfile="STDOUT", combine="median",
reject="pclip", project=no, outtype="real", offsets="none", masktype="none",
maskvalue=0., blank=0., scale="med", zero="none", weight="none", statsec="",
expname="", lthreshold=INDEF, hthreshold=INDEF, nlow=1, nhigh=1, nkeep=1,
mclip=yes, lsigma=3., hsigma=3., rdnoise="0.", gain="1.", snoise="0.",
sigscale=0.1, pclip=-0.5, grow=0)

	imdel(outpref//".jsub*.imh")
	

	 imcomb (outpref//".isub.00??.imh", outpref//".isky",
plfile="", sigma="", logfile="STDOUT", combine="median",
reject="pclip", project=no, outtype="real", offsets="none", masktype="none",
maskvalue=0., blank=0., scale="med", zero="none", weight="none", statsec="",
expname="", lthreshold=INDEF, hthreshold=INDEF, nlow=1, nhigh=1, nkeep=1,
mclip=yes, lsigma=3., hsigma=3., rdnoise="0.", gain="1.", snoise="0.",
sigscale=0.1, pclip=-0.5, grow=0)

	imdel(outpref//".isub*.imh")

#
# identify the spectra
#

	identify (outpref//".ksky.imh",
section="middle line", database="database", coordlist="argon.list    ",
nsum=10, match=10., maxfeatures=50, zwidth=100., ftype="emission", fwidth=4.,
cradius=5., threshold=10., minsep=2., function="legendre", order=3,
sample="*", niterate=4, low_reject=3., high_reject=3., grow=0., autowrite=no,
graphics="stdgraph", cursor="")

	identify (outpref//".hsky.imh",
section="middle line", database="database", coordlist="argon.list    ",
nsum=10, match=10., maxfeatures=50, zwidth=100., ftype="emission", fwidth=4.,
cradius=5., threshold=10., minsep=2., function="legendre", order=3,
sample="*", niterate=4, low_reject=3., high_reject=3., grow=0., autowrite=no,
graphics="stdgraph", cursor="")

	identify (outpref//".jsky.imh",
section="middle line", database="database", coordlist="argon.list    ",
nsum=10, match=10., maxfeatures=50, zwidth=100., ftype="emission", fwidth=4.,
cradius=5., threshold=10., minsep=2., function="legendre", order=3,
sample="*", niterate=4, low_reject=3., high_reject=3., grow=0., autowrite=no,
graphics="stdgraph", cursor="")

	identify (outpref//".isky.imh",
section="middle line", database="database", coordlist="argon.list    ",
nsum=10, match=10., maxfeatures=50, zwidth=100., ftype="emission", fwidth=4.,
cradius=5., threshold=10., minsep=2., function="legendre", order=2,
sample="*", niterate=4, low_reject=3., high_reject=3., grow=0., autowrite=no,
graphics="stdgraph", cursor="")

end