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calib_mus.cl
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#
#Version: 0.1 Modified by D. Moser in 2015-01-12
#
procedure calib_mus
bool biascomb = yes {prompt="Combine bias (filenames '*bias*.fits')?"}
bool flatccd = no {prompt="Use CCD flat only ('*flat*.fits')? Suffixes ignored"}
string flatpfx1 = "_a1" {prompt="Suffix 1 of lamp files to be combined (WITHOUT '_') at end"}
string flatpfx2 = "_v1" {prompt="Suffix 2 of lamp files to be combined (WITHOUT '_') at end"}
string flatpfx3 = "_a2" {prompt="Suffix 3 of lamp files to be combined (WITHOUT '_') at end"}
string flatpfx4 = "_v2" {prompt="Suffix 4 of lamp files to be combined (WITHOUT '_') at end"}
bool timgs = yes {prompt="Trim the images?"}
string trimsec= "[1:2048,49:2000]" {prompt="[1:2048,49:2000]](Ikon)"}
real rdnoise = 0.9 {prompt="ReadNoise (e-) to be used"}
real gain = 6.66 {prompt="Gain to be used"}
bool verify = yes {prompt="* Stop script if no bias images are found?",mode="q"}
struct *fstruct, fstruct2
begin
string ftemp, fname, fname2, lixo, refflat
bool flatcor
#~ if (verify) {
#~ print('# blah!')
#~ }
if(flatpfx1==" " || flatpfx1==" ")
flatpfx1=""
if(flatpfx2==" " || flatpfx2==" ")
flatpfx2=""
if(flatpfx3==" " || flatpfx3==" ")
flatpfx3=""
if(flatpfx4==" " || flatpfx4==" ")
flatpfx4=""
#Clean the routines parameters
unlearn flatcombine
unlearn ccdproc
unlearn apflatten
unlearn aptrace
unlearn apdefault
unlearn ecidentify
ccdproc.ccdtype = ""
ccdproc.fixpix = no
ccdproc.overscan = no
ccdproc.trim = no
ccdproc.flatcor = no
ccdproc.darkcor = no
ccdproc.zero = "avg_bias"
#Combine bias images
if (biascomb) {
print("# Bias correction enabled ...")
ftemp = mktemp("ftemp")
files("bias*.fits", > ftemp)
fstruct = ftemp
if (fscan(fstruct, fname) != EOF) {
del ("avg_bias.fits", verify=no, >& "dev$null")
print("# Combining bias images...")
unlearn zerocombine
zerocombine ("@"//ftemp, output="avg_bias", ccdtype="")
}
else {
print ("# NO BIAS IMAGES FOUND!")
if (verify) {
delete (ftemp, ver-, >& "dev$null")
fstruct = ""
}
}
if(timgs){
imcopy("avg_bias", "avg_bias.ori")
ccdproc.flat=""
ccdproc("avg_bias", ccdtype="", fixpix=no, overscan=no, trim=timgs, zerocor=no, darkcor=no, flatcor=no, trimsec=trimsec, zero="")
}
}
else {
ccdproc.zerocor = no
print ("# NO BIAS IMAGES FOUND!")
if (verify) {
delete (ftemp, ver-, >& "dev$null")
fstruct = ""
}
}
apflatten.functio="spline3"
apflatten.order=5
aptrace.order=4
apdefault.b_sampl="-15:-11,11:15"
apdefault.b_order=2
apall.b_order=2
apfit.backgro="fit"
apsum.backgro="fit"
imcombine.rdnoise=rdnoise
imcombine.gain=gain
#imcombine.reject="avsigclip"
ecidentify.xorder=2
ecidentify.yorder=2
#Combine flat 1 images
if (flatccd) {
flatcor = no
ftemp = mktemp("ftemp")
files("*flat*.fits", > ftemp)
fstruct = ftemp
if (fscan(fstruct, fname) != EOF) {
flatcor = yes
print("# Combining flat images...")
# if (access ("combflatobj.fits"))
# imdel ("combflatobj.fits", verify=no)
flatcombine ("@"//ftemp, output="avg_flat", ccdtype="", subsets=no, scale="mean")
#~ boxcar ("avg"//flatpfx1, "norm"//flatpfx1, 10, 10, boundary="nearest", constant=0.)
#~ imarith ("avg"//flatpfx1,"/","norm"//flatpfx1, "norm"//flatpfx1, title="", divzero=0.,hparams="",pixtype="", calctype="", verbose=no, noact=no)
ccdproc.flat=""
ccdproc("avg_flat", ccdtype="", fixpix=no, overscan=no, trim=timgs, zerocor=yes, darkcor=no, flatcor=no, trimsec=trimsec, zero="avg_bias")
apflatten("avg_flat", "norm_flat")
}
else{
print("# No flat images found !!!")
}
delete (ftemp, ver-, >& "dev$null")
}
else{
if (flatpfx1 != "") {
flatcor = no
ftemp = mktemp("ftemp")
files("flat"//flatpfx1//"_*.fits", > ftemp)
fstruct = ftemp
if (fscan(fstruct, fname) != EOF) {
flatcor = yes
print("# Combining flat"//flatpfx1//"_* images...")
ccdproc (fname, output="cp_"//fname, ccdtype="", flatcor=no, zero="avg_bias", trim=timgs, trimsec=trimsec)
if (access ("cp_"//fname)==no) {
imcopy(fname, "cp_"//fname)
}
while (fscan(fstruct, fname) != EOF) {
ccdproc (fname, output="cp_"//fname, ccdtype="", flatcor=no, zero="avg_bias", trim=timgs, trimsec=trimsec)
if (access("cp_"//fname)==no) {
imcopy(fname, "cp_"//fname)
}
}
lixo = mktemp("ftemp2")
files("cp_flat"//flatpfx1//"_*.fits", > lixo)
# if (access ("combflatobj.fits"))
# imdel ("combflatobj.fits", verify=no)
flatcombine ("@"//lixo, output="avg_flat"//flatpfx1, ccdtype="", subsets = no, scale="mean")
#~ boxcar ("avg"//flatpfx1, "norm"//flatpfx1, 10, 10, boundary="nearest", constant=0.)
#~ imarith ("avg"//flatpfx1,"/","norm"//flatpfx1, "norm"//flatpfx1, title="", divzero=0.,hparams="",pixtype="", calctype="", verbose=no, noact=no)
apflatten("avg_flat"//flatpfx1, "norm_flat"//flatpfx1)
delete (lixo, ver-, >& "dev$null")
}
else{
print("# No flat images found !!!")
}
delete (ftemp, ver-, >& "dev$null")
}
if (flatpfx2 != "") {
flatcor = no
ftemp = mktemp("ftemp")
files("flat"//flatpfx2//"_*.fits", > ftemp)
fstruct = ftemp
if (fscan(fstruct, fname) != EOF) {
flatcor = yes
print("# Combining flat"//flatpfx2//"_* images...")
ccdproc (fname, output="cp_"//fname, ccdtype="", flatcor=no, zero="avg_bias", trim=timgs, trimsec=trimsec)
if (access ("cp_"//fname)==no) {
imcopy(fname, "cp_"//fname)
}
while (fscan(fstruct, fname) != EOF) {
ccdproc (fname, output="cp_"//fname, ccdtype="", flatcor=no, zero="avg_bias", trim=timgs, trimsec=trimsec)
if (access("cp_"//fname)==no) {
imcopy(fname, "cp_"//fname)
}
}
lixo = mktemp("ftemp2")
files("cp_flat"//flatpfx2//"_*.fits", > lixo)
# if (access ("combflatobj.fits"))
# imdel ("combflatobj.fits", verify=no)
flatcombine ("@"//lixo, output="avg_flat"//flatpfx2, ccdtype="", subsets = no, scale="mean")
#~ boxcar ("avg"//flatpfx2, "norm"//flatpfx2, 10, 10, boundary="nearest", constant=0.)
#~ imarith ("avg"//flatpfx2,"/","norm"//flatpfx2, "norm"//flatpfx2, title="", divzero=0.,hparams="",pixtype="", calctype="", verbose=no, noact=no)
apflatten("avg_flat"//flatpfx2, "norm_flat"//flatpfx2)
delete (lixo, ver-, >& "dev$null")
}
else{
print("# No flat images found !!!")
}
delete (ftemp, ver-, >& "dev$null")
}
if (flatpfx3 != "") {
flatcor = no
ftemp = mktemp("ftemp")
files("flat"//flatpfx3//"_*.fits", > ftemp)
fstruct = ftemp
if (fscan(fstruct, fname) != EOF) {
flatcor = yes
print("# Combining flat"//flatpfx3//"_* images...")
ccdproc (fname, output="cp_"//fname, ccdtype="", flatcor=no, zero="avg_bias", trim=timgs, trimsec=trimsec)
if (access ("cp_"//fname)==no) {
imcopy(fname, "cp_"//fname)
}
while (fscan(fstruct, fname) != EOF) {
ccdproc (fname, output="cp_"//fname, ccdtype="", flatcor=no, zero="avg_bias", trim=timgs, trimsec=trimsec)
if (access("cp_"//fname)==no) {
imcopy(fname, "cp_"//fname)
}
}
lixo = mktemp("ftemp2")
files("cp_flat"//flatpfx3//"_*.fits", > lixo)
# if (access ("combflatobj.fits"))
# imdel ("combflatobj.fits", verify=no)
flatcombine ("@"//lixo, output="avg_flat"//flatpfx3, ccdtype="", subsets = no, scale="mean")
#~ boxcar ("avg"//flatpfx3, "norm"//flatpfx3, 10, 10, boundary="nearest", constant=0.)
#~ imarith ("avg"//flatpfx3,"/","norm"//flatpfx3, "norm"//flatpfx3, title="", divzero=0.,hparams="",pixtype="", calctype="", verbose=no, noact=no)
apflatten("avg_flat"//flatpfx3, "norm_flat"//flatpfx3)
delete (lixo, ver-, >& "dev$null")
}
else{
print("# No flat images found !!!")
}
delete (ftemp, ver-, >& "dev$null")
}
if (flatpfx4 != "") {
flatcor = no
ftemp = mktemp("ftemp")
files("flat"//flatpfx4//"_*.fits", > ftemp)
fstruct = ftemp
if (fscan(fstruct, fname) != EOF) {
flatcor = yes
print("# Combining flat"//flatpfx4//"_* images...")
ccdproc (fname, output="cp_"//fname, ccdtype="", flatcor=no, zero="avg_bias", trim=timgs, trimsec=trimsec)
if (access ("cp_"//fname)==no) {
imcopy(fname, "cp_"//fname)
}
while (fscan(fstruct, fname) != EOF) {
ccdproc (fname, output="cp_"//fname, ccdtype="", flatcor=no, zero="avg_bias", trim=timgs, trimsec=trimsec)
if (access("cp_"//fname)==no) {
imcopy(fname, "cp_"//fname)
}
}
lixo = mktemp("ftemp2")
files("cp_flat"//flatpfx4//"_*.fits", > lixo)
# if (access ("combflatobj.fits"))
# imdel ("combflatobj.fits", verify=no)
flatcombine ("@"//lixo, output="avg_flat"//flatpfx4, ccdtype="", subsets = no, scale="mean")
#~ boxcar ("avg"//flatpfx4, "norm"//flatpfx4, 10, 10, boundary="nearest", constant=0.)
#~ imarith ("avg"//flatpfx4,"/","norm"//flatpfx4, "norm"//flatpfx4, title="", divzero=0.,hparams="",pixtype="", calctype="", verbose=no, noact=no)
apflatten("avg_flat"//flatpfx4, "norm_flat"//flatpfx4)
delete (lixo, ver-, >& "dev$null")
}
else{
print("# No flat images found !!!")
}
delete (ftemp, ver-, >& "dev$null")
}
}
#LAMP process...
if (flatpfx1 != "") {
ftemp = mktemp("ftemp")
files("lamp*"//flatpfx1//"_*.fits", > ftemp)
fstruct = ftemp
if (flatccd) {
ccdproc.flat="norm_flat"
refflat="avg_flat"
}
else {
ccdproc.flat="norm_flat"//flatpfx1
refflat="avg_flat"//flatpfx1
}
while (fscan(fstruct, fname) != EOF) {
ccdproc (fname, output="cp_"//fname, ccdtype="", flatcor=flatcor, zero="avg_bias", trim=timgs, trimsec=trimsec)
}
delete (ftemp, ver-, >& "dev$null")
ftemp = mktemp("ftemp")
files("cp_*lamp*"//flatpfx1//"*.fits", > ftemp)
imcombine("@"//ftemp, output="avg_lamp"//flatpfx1)
imdel ("cp*", verify-)
delete (ftemp, ver-, >& "dev$null")
#
apall ("avg_lamp"//flatpfx1, 50, output="avg_lamp"//flatpfx1//".ms", apertures="", format="multispec", references=refflat, profiles="", interactive=no, find=no, recenter=no, resize=no, edit=no, trace=no, fittrace=no, extract=yes, extras=no, review=no, line=INDEF, nsum=20, lower=-5., upper=5., apidtable="", b_function="chebyshev", b_order=2, b_sample="-15:-11,11:15", 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", aprecenter="", npeaks=INDEF, shift=yes, llimit=INDEF, ulimit=INDEF,ylevel=0.1, peak=yes, bkg=yes, r_grow=0., avglimits=no, t_nsum=10, t_step=10, t_nlost=3, t_function="legendre", t_order=4, 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=yes, saturation=INDEF, readnoise=rdnoise, gain=gain, lsigma=4., usigma=4., nsubaps=1)
ecidentify ("avg_lamp"//flatpfx1//".ms")
}
if (flatpfx2 != "") {
ftemp = mktemp("ftemp")
files("lamp*"//flatpfx2//"_*.fits", > ftemp)
fstruct = ftemp
if (flatccd) {
ccdproc.flat="norm_flat"
refflat="avg_flat"
}
else {
ccdproc.flat="norm_flat"//flatpfx2
refflat="avg_flat"//flatpfx2
}
while (fscan(fstruct, fname) != EOF) {
ccdproc (fname, output="cp_"//fname, ccdtype="", flatcor=flatcor, zero="avg_bias", trim=timgs, trimsec=trimsec)
}
delete (ftemp, ver-, >& "dev$null")
ftemp = mktemp("ftemp")
files("cp_*lamp*"//flatpfx2//"*.fits", > ftemp)
imcombine("@"//ftemp, output="avg_lamp"//flatpfx2)
imdel ("cp*", verify-)
delete (ftemp, ver-, >& "dev$null")
#
apall ("avg_lamp"//flatpfx2, 50, output="avg_lamp"//flatpfx2//".ms", apertures="", format="multispec", references=refflat, profiles="", interactive=no, find=no, recenter=no, resize=no, edit=no, trace=no, fittrace=no, extract=yes, extras=no, review=no, line=INDEF, nsum=20, lower=-5., upper=5., apidtable="", b_function="chebyshev", b_order=2, b_sample="-15:-11,11:15", 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", aprecenter="", npeaks=INDEF, shift=yes, llimit=INDEF, ulimit=INDEF,ylevel=0.1, peak=yes, bkg=yes, r_grow=0., avglimits=no, t_nsum=10, t_step=10, t_nlost=3, t_function="legendre", t_order=4, 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=yes, saturation=INDEF, readnoise=rdnoise, gain=gain, lsigma=4., usigma=4., nsubaps=1)
ecidentify ("avg_lamp"//flatpfx2//".ms")
}
if (flatpfx3 != "") {
ftemp = mktemp("ftemp")
files("lamp*"//flatpfx3//"_*.fits", > ftemp)
fstruct = ftemp
if (flatccd) {
ccdproc.flat="norm_flat"
refflat="avg_flat"
}
else {
ccdproc.flat="norm_flat"//flatpfx3
refflat="avg_flat"//flatpfx3
}
while (fscan(fstruct, fname) != EOF) {
ccdproc (fname, output="cp_"//fname, ccdtype="", flatcor=flatcor, zero="avg_bias", trim=timgs, trimsec=trimsec)
}
delete (ftemp, ver-, >& "dev$null")
ftemp = mktemp("ftemp")
files("cp_*lamp*"//flatpfx3//"*.fits", > ftemp)
imcombine("@"//ftemp, output="avg_lamp"//flatpfx3)
imdel ("cp*", verify-)
delete (ftemp, ver-, >& "dev$null")
#
apall ("avg_lamp"//flatpfx3, 50, apertures="", format="multispec", references=refflat, profiles="", interactive=no, find=no, recenter=no, resize=no, edit=no, trace=no, fittrace=no, extract=yes, extras=no, review=no, line=INDEF, nsum=20, lower=-5., upper=5., apidtable="", b_function="chebyshev", b_order=2, b_sample="-15:-11,11:15", 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", aprecenter="", npeaks=INDEF, shift=yes, llimit=INDEF, ulimit=INDEF,ylevel=0.1, peak=yes, bkg=yes, r_grow=0., avglimits=no, t_nsum=10, t_step=10, t_nlost=3, t_function="legendre", t_order=4, 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=yes, saturation=INDEF, readnoise=rdnoise, gain=gain, lsigma=4., usigma=4., nsubaps=1)
ecidentify ("avg_lamp"//flatpfx3//".ms")
}
if (flatpfx4 != "") {
ftemp = mktemp("ftemp")
files("lamp*"//flatpfx4//"_*.fits", > ftemp)
fstruct = ftemp
if (flatccd) {
ccdproc.flat="norm_flat"
refflat="avg_flat"
}
else {
ccdproc.flat="norm_flat"//flatpfx4
refflat="avg_flat"//flatpfx4
}
while (fscan(fstruct, fname) != EOF) {
ccdproc (fname, output="cp_"//fname, ccdtype="", flatcor=flatcor, zero="avg_bias", trim=timgs, trimsec=trimsec)
}
delete (ftemp, ver-, >& "dev$null")
ftemp = mktemp("ftemp")
files("cp_*lamp*"//flatpfx4//"*.fits", > ftemp)
imcombine("@"//ftemp, output="avg_lamp"//flatpfx4)
imdel ("cp*", verify-)
delete (ftemp, ver-, >& "dev$null")
#
apall ("avg_lamp"//flatpfx4, 50, apertures="", format="multispec", references=refflat, profiles="", interactive=no, find=no, recenter=no, resize=no, edit=no, trace=no, fittrace=no, extract=yes, extras=no, review=no, line=INDEF, nsum=20, lower=-5., upper=5., apidtable="", b_function="chebyshev", b_order=2, b_sample="-15:-11,11:15", 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", aprecenter="", npeaks=INDEF, shift=yes, llimit=INDEF, ulimit=INDEF,ylevel=0.1, peak=yes, bkg=yes, r_grow=0., avglimits=no, t_nsum=10, t_step=10, t_nlost=3, t_function="legendre", t_order=4, 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=yes, saturation=INDEF, readnoise=rdnoise, gain=gain, lsigma=4., usigma=4., nsubaps=1)
ecidentify ("avg_lamp"//flatpfx4//".ms")
}
fstruct = ""
delete (ftemp, ver-, >& "dev$null")
end