def reduce_stdstar(rawdir, rundir, caldir, starobj, stdstar, flat,
arc, twilight, starimg, bias, overscan, vardq):
"""
Reduction pipeline for standard star.
Parameters
----------
rawdir: string
Directory containing raw images.
rundi: string
Directory where processed files are saved.
caldir: string
Directory containing standard star calibration files.
starobj: string
Object keyword for the star image.
stdstar: string
Star name in calibration file.
flat: list
Names of the files containing flat field images.
arc: list
Arc images.
twilight: list
Twilight flat images.
starimg: string
Name of the file containing the image to be reduced.
bias: list
Bias images.
"""
iraf.set(stdimage='imtgmos')
iraf.gemini()
iraf.gemtools()
iraf.gmos()
#iraf.unlearn('gemini')
#iraf.unlearn('gmos')
iraf.task(lacos_spec='/storage/work/gemini_pairs/lacos_spec.cl')
tstart = time.time()
#set directories
iraf.set(caldir=rawdir) #
iraf.set(rawdir=rawdir) # raw files
iraf.set(procdir=rundir) # processed files
iraf.gmos.logfile='logfile.log'
iraf.cd('procdir')
# building lists
def range_string(l):
return (len(l)*'{:4s},').format(*[i[-9:-5] for i in l])
iraf.gemlist(range=range_string(flat), root=flat[0][:-9],
Stdout='flat.list')
iraf.gemlist(range=range_string(arc), root=arc[0][:-9],
Stdout='arc.list')
#iraf.gemlist(range=range_string(star), root=star[0][:-4],
# Stdout='star.list')
iraf.gemlist(range=range_string(twilight),
root=twilight[0][:-9], Stdout='twilight.list')
iraf.gfreduce.bias = 'caldir$'+bias[0]
#######################################################################
#######################################################################
### Star reduction #
#######################################################################
#######################################################################
#
# Flat reduction
#
iraf.gfreduce(
'@flat.list', slits='header', rawpath='rawdir$', fl_inter='no',
fl_addmdf='yes', key_mdf='MDF', mdffile='default', weights='no',
fl_over=overscan, fl_trim='yes', fl_bias='yes', trace='yes', t_order=4,
fl_flux='no', fl_gscrrej='no', fl_extract='yes', fl_gsappwave='no',
fl_wavtran='no', fl_novl='no', fl_skysub='no', reference='',
recenter='yes', fl_vardq=vardq)
iraf.gfreduce('@twilight.list', slits='header', rawpath='rawdir$',
fl_inter='no', fl_addmdf='yes', key_mdf='MDF',
mdffile='default', weights='no',
fl_over=overscan, fl_trim='yes', fl_bias='yes', trace='yes',
recenter='no',
fl_flux='no', fl_gscrrej='no', fl_extract='yes', fl_gsappwave='no',
fl_wavtran='no', fl_novl='no', fl_skysub='no',
reference='erg'+flat[0], fl_vardq=vardq)
#
# Response function
#
for i, j in enumerate(flat):
j = j[:-5]
iraf.imdelete(j+'_response')
iraf.gfresponse('erg'+j+'.fits', out='erg'+j+'_response',
skyimage='erg'+twilight[i], order=95, fl_inter='no',
func='spline3',
sample='*', verbose='yes')
# Arc reduction
#
iraf.gfreduce(
'@arc.list', slits='header', rawpath='rawdir$', fl_inter='no',
fl_addmdf='yes', key_mdf='MDF', mdffile='default', weights='no',
fl_over=overscan, fl_trim='yes', fl_bias='yes', trace='no',
recenter='no',
fl_flux='no', fl_gscrrej='no', fl_extract='yes', fl_gsappwave='no',
fl_wavtran='no', fl_novl='no', fl_skysub='no', reference='erg'+flat[0],
fl_vardq=vardq)
# Finding wavelength solution
# Note: the automatic identification is very good
#
for i in arc:
iraf.gswavelength('erg'+i, function='chebyshev', nsum=15, order=4,
fl_inter='no', nlost=5, ntarget=20, aiddebug='s', threshold=5,
section='middle line')
#
# Apply wavelength solution to the lamp 2D spectra
#
iraf.gftransform('erg'+i, wavtran='erg'+i, outpref='t', fl_vardq=vardq)
##
## Actually reduce star
##
iraf.gfreduce(
starimg, slits='header', rawpath='rawdir$', fl_inter='no',
fl_addmdf='yes', key_mdf='MDF', mdffile='default', weights='no',
fl_over=overscan, fl_trim='yes', fl_bias='yes', trace='no',
recenter='no',
fl_flux='no', fl_gscrrej='no', fl_extract='no', fl_gsappwave='no',
fl_wavtran='no', fl_novl='yes', fl_skysub='no', fl_vardq=vardq)
iraf.gemcrspec('rg{:s}'.format(starimg), out='lrg'+starimg, sigfrac=0.32,
niter=4, fl_vardq=vardq)
iraf.gfreduce(
'lrg'+starimg, slits='header', rawpath='./', fl_inter='no',
fl_addmdf='no', key_mdf='MDF', mdffile='default',
fl_over='no', fl_trim='no', fl_bias='no', trace='no',
recenter='no',
fl_flux='no', fl_gscrrej='no', fl_extract='yes',
fl_gsappwave='yes',
fl_wavtran='yes', fl_novl='no', fl_skysub='yes',
reference='erg'+flat[0][:-5], weights='no',
wavtraname='erg'+arc[0][:-5],
response='erg'+flat[0][:-5]+'_response.fits',
fl_vardq=vardq)
#
# Apsumming the stellar spectra
#
iraf.gfapsum(
'stexlrg'+starimg, fl_inter='no', lthreshold=400.,
reject='avsigclip')
#
# Building sensibility function
#
iraf.gsstandard(
('astexlrg{:s}').format(starimg), starname=stdstar,
observatory='Gemini-South', sfile='std', sfunction='sens',
caldir=caldir)
#
# Apply flux calibration to galaxy
#
#
##iraf.imdelete('*****@*****.**')
#
##iraf.gscalibrate('*****@*****.**',sfunction='sens.fits',fl_ext='yes',extinct='onedstds$ctioextinct.dat',observatory='Gemini-South',fluxsca=1)
#
##
## Create data cubes
##
#
#
##for i in objs:
## iraf.imdelete('d0.1cstexlrg'+i+'.fits')
## iraf.gfcube('cstexlrg'+i+'.fits',outpref='d0.1',ssample=0.1,fl_atmd='yes',fl_flux='yes')
#
##
## Combine cubes
##
#
#
##iraf.imdelete('am2306-721r4_wcsoffsets.fits')
##iraf.imcombine('d0.1cstexlrgS20141113S00??.fits[1]',output='am2306-721r4_wcsoffsets.fits',combine='average',reject='sigclip',masktype='badvalue',lsigma=2,hsigma=2,offset='wcs',outlimits='2 67 2 48 100 1795')
#
tend = time.time()
print('Elapsed time in reduction: {:.2f}'.format(tend - tstart))
caldir = [starinfo[i]['caldir'] for i in starinfo_idx]
starflux = [[starinfo[i]['flux'] for i in starinfo_idx]]
iraf.cd('procdir')
# remove previous lists
# no need
# building lists
def range_string(l):
return (len(l)*'{:4s},').format(*[i[-4:] for i in l])
for j in range(len(star)):
iraf.gemlist(range=range_string(flat[j]), root=flat[j][0][:-4],
Stdout='flat'+str(j)+'.list')
iraf.gemlist(range=range_string(arc[j]), root=arc[j][0][:-4],
Stdout='arc'+str(j)+'.list')
iraf.gemlist(range=range_string([star[j]]), root=[star[j]][0][:-4],
Stdout='star'+str(j)+'.list')
iraf.gemlist(range=range_string(twilight[j]),
root=twilight[j][0][:-4], Stdout='twilight'+str(j)+'.list')
#######################################################################
#######################################################################
### Star reduction #
#######################################################################
#######################################################################
#
