def reduceIm(self, inIm, **kwargs):
print "\nREDUCING", inIm
# remove previously reduced exposures
inPref = inIm[:inIm.find(".") - 14]
if inPref == "":
outPref = "g"
images = outPref + inIm
outPref = "r" + outPref
images += "," + outPref + inIm
else:
outPref = ""
images = ""
if "fl_gscrrej" in kwargs.keys() and kwargs["fl_gscrrej"] == "yes":
outPref = "x" + outPref
images += "," + outPref + inIm
else:
pass
if "fl_scatsub" in kwargs.keys() and kwargs["fl_scatsub"] == "yes":
outPref = "b" + outPref
images += "," + outPref + inIm
else:
pass
if "fl_qecorr" in kwargs.keys() and kwargs["fl_qecorr"] == "yes":
outPref = "q" + outPref
images += "," + outPref + inIm
else:
pass
if "fl_extract" in kwargs.keys() and kwargs["fl_extract"] == "no":
pass
else:
outPref = "e" + outPref
images += "," + outPref + inIm
iraf.imdelete(images)
# reduce the image
iraf.gfreduce(inIm, **kwargs)
return
iraf.unlearn('gfscatsub')
# ---------- Pre-processing of the science frames ---------- #
# MDF, bias, and overscan
iraf.imdelete('g@' + ic.lst_std)
iraf.imdelete('rg@' + ic.lst_std)
iraf.gfreduce('@' + ic.lst_std,
rawpath=ic.rawdir,
fl_extract='no',
bias=ic.caldir + ic.procbias,
fl_over='yes',
fl_trim='yes',
mdffile=ic.nmdf,
mdfdir='./',
slits=ic.cslit,
line=pk_line,
fl_fluxcal='no',
fl_gscrrej='no',
fl_wavtran='no',
fl_skysub='no',
fl_vardq='yes',
fl_inter='no')
# Scattered light
blkmsk = np.loadtxt("blkmask_name.txt", dtype=str).item(0)
blkmsk0 = blkmsk
iraf.imdelete('brg@' + ic.lst_std)
std = np.loadtxt(ic.lst_std, dtype=str)
def reduce_science(rawdir, rundir, flat, arc, twilight, twilight_flat, sciimg,
starimg, bias, overscan, vardq, observatory, lacos,
apply_lacos, lacos_xorder, lacos_yorder, lacos_sigclip,
lacos_objlim, bpm, instrument, slits, fl_gscrrej,
wltrim_frac, grow_gap, cube_bit_mask):
"""
Reduction pipeline for standard star.
Parameters
----------
rawdir: string
Directory containing raw images.
rundir: string
Directory where processed files are saved.
flat: string
Names of the files containing flat field images.
arc: string
Arc images.
twilight: string
Twilight flat images.
twilight_flat: string
Flat field for twilight image.
starimg: string
Name of the file containing the image to be reduced.
bias: string
Bias images.
grow_gap: number
Number of pixels by which to grow the bad pixel mask around
the chip gaps.
"""
iraf.set(stdimage='imtgmos')
iraf.gemini()
iraf.unlearn('gemini')
iraf.gmos()
iraf.unlearn('gmos')
iraf.gemtools()
iraf.unlearn('gemtools')
# os.path.isfile('arquivo')
iraf.unlearn('gemini')
iraf.unlearn('gmos')
iraf.task(lacos_spec=lacos)
# set directories
iraf.set(caldir=rawdir) #
iraf.set(rawdir=rawdir) # raw files
iraf.set(procdir=rundir) # processed files
iraf.gmos.logfile = 'logfile.log'
iraf.gfextract.verbose = 'no'
iraf.cd('procdir')
flat = flat.replace('.fits', '')
twilight = twilight.replace('.fits', '')
twilight_flat = twilight_flat.replace('.fits', '')
arc = arc.replace('.fits', '')
starimg = starimg.replace('.fits', '')
sciimg = sciimg.replace('.fits', '')
mdffile = 'mdf' + flat + '.fits'
iraf.gfreduce.bias = 'caldir$' + bias
iraf.gfreduce.fl_fulldq = 'yes'
iraf.gfreduce.fl_fixgaps = 'yes'
iraf.gfreduce.grow = grow_gap
iraf.gireduce.bpm = 'rawdir$' + bpm
iraf.gfextract.verbose = 'no'
cal_reduction(rawdir=rawdir,
rundir=rundir,
flat=flat,
arc=arc,
twilight=twilight,
bias=bias,
bpm=bpm,
overscan=overscan,
vardq=vardq,
instrument=instrument,
slits=slits,
twilight_flat=twilight_flat,
grow_gap=grow_gap)
#
# Actually reduce science
#
image_name = 'rg' + sciimg + '.fits'
if os.path.isfile(image_name):
pipe.skipwarn(image_name)
else:
iraf.gfreduce(sciimg,
slits='header',
rawpath='rawdir$',
fl_inter='no',
fl_addmdf='yes',
key_mdf='MDF',
mdffile=mdffile,
weights='no',
fl_over=overscan,
fl_trim='yes',
fl_bias='yes',
trace='no',
recenter='no',
fl_fulldq='yes',
fl_flux='no',
fl_gscrrej='no',
fl_extract='no',
fl_gsappwave='no',
fl_wavtran='no',
fl_novl='yes',
fl_skysub='no',
fl_vardq=vardq,
mdfdir='procdir$')
prefix = 'rg'
# Gemfix
image_name = 'p' + prefix + sciimg + '.fits'
if os.path.isfile(image_name):
pipe.skipwarn(image_name)
else:
iraf.gemfix(prefix + sciimg,
out='p' + prefix + sciimg,
method='fit1d',
bitmask=65535,
axis=1)
prefix = 'p' + prefix
# LA Cosmic - cosmic ray removal
if apply_lacos:
image_name = 'l' + prefix + sciimg + '.fits'
if os.path.isfile(image_name):
pipe.skipwarn(image_name)
else:
iraf.gemcrspec(prefix + sciimg,
out='l' + prefix + sciimg,
sigfrac=0.5,
niter=4,
fl_vardq=vardq,
xorder=lacos_xorder,
yorder=lacos_yorder,
sigclip=lacos_sigclip,
objlim=lacos_objlim)
prefix = 'l' + prefix
if fl_gscrrej:
image_name = 'ex' + prefix + sciimg + '.fits'
else:
image_name = 'e' + prefix + sciimg + '.fits'
if os.path.isfile(image_name):
pipe.skipwarn(image_name)
else:
iraf.gfreduce(prefix + sciimg,
slits='header',
rawpath='./',
fl_inter='no',
fl_addmdf='no',
key_mdf='MDF',
mdffile=mdffile,
fl_over='no',
fl_trim='no',
fl_bias='no',
trace='no',
recenter='no',
fl_flux='no',
fl_gscrrej=fl_gscrrej,
fl_extract='yes',
fl_gsappwave='yes',
fl_wavtran='no',
fl_novl='no',
fl_skysub='no',
grow=grow_gap,
reference='eprg' + flat,
weights='no',
wavtraname='eprg' + arc,
response='eprg' + flat + '_response.fits',
fl_vardq=vardq,
fl_fulldq='yes',
fl_fixgaps='yes')
if fl_gscrrej:
prefix = 'ex' + prefix
else:
prefix = 'e' + prefix
# if wl2 > 7550.0:
# wl2 = 7550.0
#
# Apply wavelength transformation
#
wl1, wl2 = wl_lims(prefix + sciimg + '.fits', wltrim_frac)
image_name = 't' + prefix + sciimg + '.fits'
if os.path.isfile(image_name):
pipe.skipwarn(image_name)
else:
iraf.gftransform(
prefix + sciimg,
wavtraname='eprg' + arc,
fl_vardq=vardq,
w1=wl1,
w2=wl2,
)
prefix = 't' + prefix
#
# Sky subtraction
#
image_name = 's' + prefix + sciimg + '.fits'
if os.path.isfile(image_name):
pipe.skipwarn(image_name)
else:
iraf.gfskysub(
prefix + sciimg,
expr='default',
combine='median',
reject='avsigclip',
scale='none',
zero='none',
weight='none',
sepslits='yes',
fl_inter='no',
lsigma=1,
hsigma=1,
)
prefix = 's' + prefix
#
# Apply flux calibration to galaxy
#
image_name = 'c' + prefix + sciimg + '.fits'
if os.path.isfile(image_name):
pipe.skipwarn(image_name)
else:
iraf.gscalibrate(prefix + sciimg,
sfuncti=starimg,
extinct='onedstds$ctioextinct.dat',
observatory=observatory,
fluxsca=1,
fl_vardq=vardq)
prefix = 'c' + prefix
#
# Remove spurious data with PCA
#
image_name = 'x' + prefix + sciimg + '.fits'
print(os.getcwd())
print(image_name)
if os.path.isfile(image_name):
pipe.skipwarn(image_name)
else:
t = pca.Tomography(prefix + sciimg + '.fits')
t.decompose()
t.remove_cosmic_rays(sigma_threshold=10.0)
t.write(image_name)
prefix = 'x' + prefix
#
# Create data cubes
#
image_name = 'd' + prefix + sciimg + '.fits'
if os.path.isfile(image_name):
pipe.skipwarn(image_name)
else:
data_cube = CubeBuilder(prefix + sciimg + '.fits')
data_cube.build_cube()
data_cube.fit_refraction_function()
data_cube.fix_atmospheric_refraction()
data_cube.write(image_name)
# ---------- Trace reference ---------- #
iraf.imdelete('g@' + ic.lst_flat)
iraf.imdelete('rg@' + ic.lst_flat)
iraf.imdelete('erg@' + ic.lst_flat)
for flat in iraf.type(ic.lst_flat, Stdout=1):
flat = flat.strip()
iraf.gfreduce(flat,
rawpath=ic.rawdir,
fl_extract='yes',
bias=ic.bias,
fl_over='yes',
fl_trim='yes',
mdffile=ic.nmdf,
mdfdir='./',
slits='both',
line=1400,
fl_fluxcal='no',
fl_gscrrej='no',
fl_wavtran='no',
fl_skysub='no',
fl_inter='no',
fl_vardq='yes')
os.system('ds9 &')
iraf.sleep(5.0)
for flat in iraf.type(ic.lst_flat, Stdout=1):
flat = flat.strip()
iraf.gfdisplay('erg' + flat, 1)
# Printing the running time
def reduce_stdstar(rawdir,
rundir,
caldir,
starobj,
stdstar,
flat,
arc,
twilight,
twilight_flat,
starimg,
bias,
overscan,
vardq,
lacos,
observatory,
apply_lacos,
lacos_xorder,
lacos_yorder,
lacos_objlim,
lacos_sigclip,
bpm,
instrument,
slits,
fl_gscrrej,
wltrim_frac=0.03,
sens_order=6,
sens_function='spline3',
apsum_radius=1):
"""
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.task(lacos_spec=lacos)
iraf.gemini()
iraf.unlearn('gemini')
iraf.gmos()
iraf.unlearn('gmos')
iraf.gemtools()
iraf.unlearn('gemtools')
iraf.gmos.logfile = 'logfile.log'
iraf.gemtools.gloginit.logfile = 'logfile.log'
iraf.gfextract.verbose = 'no'
# set directories
iraf.set(caldir=rawdir) #
iraf.set(rawdir=rawdir) # raw files
iraf.set(procdir=rundir) # processed files
# os.path.isfile('arquivo')
iraf.cd('procdir')
flat = flat.strip('.fits')
twilight = twilight.strip('.fits')
twilight_flat = twilight_flat.strip('.fits')
arc = arc.strip('.fits')
starimg = starimg.strip('.fits')
mdffile = 'mdf' + flat + '.fits'
iraf.gfreduce.bias = 'rawdir$' + bias
iraf.gfreduce.fl_fulldq = 'yes'
iraf.gfreduce.fl_fixgaps = 'yes'
iraf.gireduce.bpm = 'rawdir$' + bpm
cal_reduction(rawdir=rawdir,
rundir=rundir,
flat=flat,
arc=arc,
twilight=twilight,
bias=bias,
bpm=bpm,
overscan=overscan,
vardq=vardq,
instrument=instrument,
slits=slits,
twilight_flat=twilight_flat)
#
# Actually reduce star
#
imageName = 'rg' + starimg + '.fits'
if os.path.isfile(imageName):
skipwarn(imageName)
else:
imageName = 'g' + starimg + '.fits'
if os.path.isfile(imageName):
iraf.printlog(
'GIREDS: WARNING: Removing file {:s}'.format(imageName),
'logfile.log', 'yes')
iraf.delete(imageName)
iraf.gfreduce(starimg,
slits='header',
rawpath='rawdir$',
fl_inter='no',
fl_addmdf='yes',
key_mdf='MDF',
mdffile=mdffile,
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,
mdfdir='procdir$')
prefix = 'rg'
#
# Gemfix
#
imageName = 'p' + prefix + starimg + '.fits'
if os.path.isfile(imageName):
skipwarn(imageName)
else:
iraf.gemfix(prefix + starimg,
out='p' + prefix + starimg,
method='fit1d',
bitmask=1,
axis=1)
prefix = 'p' + prefix
#
# LA Cosmic
#
if apply_lacos:
imageName = 'l' + prefix + starimg + '.fits'
if os.path.isfile(imageName):
skipwarn(imageName)
else:
if apply_lacos:
iraf.gemcrspec(prefix + starimg,
out='l' + prefix + starimg,
sigfrac=0.32,
niter=4,
fl_vardq=vardq,
xorder=lacos_xorder,
yorder=lacos_yorder,
objlim=lacos_objlim,
sigclip=lacos_sigclip)
prefix = 'l' + prefix
#
# Extraction and Gemini's comsmic ray rejection
#
if fl_gscrrej:
imageName = 'x' + prefix + starimg + '.fits'
if os.path.isfile(imageName):
skipwarn(imageName)
fl_gscrrej = False
else:
imageName = 'ex' + prefix + starimg + '.fits'
if os.path.isfile(imageName):
skipwarn(imageName)
else:
iraf.gfreduce(prefix + starimg,
slits='header',
rawpath='./',
fl_inter='no',
fl_addmdf='no',
key_mdf='MDF',
mdffile=mdffile,
fl_over='no',
fl_trim='no',
fl_bias='no',
trace='no',
recenter='no',
fl_flux='no',
fl_gscrrej=fl_gscrrej,
fl_extract='yes',
fl_gsappwave='yes',
fl_wavtran='no',
fl_novl='no',
fl_skysub='no',
reference='eprg' + flat,
weights='no',
wavtraname='eprg' + arc,
response='eprg' + flat + '_response.fits',
fl_vardq=vardq)
prefix = 'ex' + prefix
else:
imageName = 'e' + prefix + starimg + '.fits'
if os.path.isfile(imageName):
skipwarn(imageName)
else:
iraf.gfreduce(prefix + starimg,
slits='header',
rawpath='./',
fl_inter='no',
fl_addmdf='no',
key_mdf='MDF',
mdffile=mdffile,
fl_over='no',
fl_trim='no',
fl_bias='no',
trace='no',
recenter='no',
fl_flux='no',
fl_gscrrej=fl_gscrrej,
fl_extract='yes',
fl_gsappwave='yes',
fl_wavtran='no',
fl_novl='no',
fl_skysub='no',
reference='eprg' + flat,
weights='no',
wavtraname='eprg' + arc,
response='eprg' + flat + '_response.fits',
fl_vardq=vardq)
prefix = 'e' + prefix
#
# Wavelength transform
#
wl1, wl2 = wl_lims(prefix + starimg + '.fits', wltrim_frac)
imageName = 't' + prefix + starimg + '.fits'
if os.path.isfile(imageName):
skipwarn(imageName)
else:
iraf.gfreduce(prefix + starimg,
slits='header',
rawpath='./',
fl_inter='no',
fl_addmdf='no',
key_mdf='MDF',
mdffile=mdffile,
fl_over='no',
fl_trim='no',
fl_bias='no',
trace='no',
recenter='no',
fl_flux='no',
fl_gscrrej='no',
fl_extract='no',
fl_gsappwave='no',
fl_wavtran='yes',
fl_novl='no',
fl_skysub='no',
reference='eprg' + flat,
weights='no',
wavtraname='eprg' + arc,
response='eprg' + flat + '_response.fits',
fl_vardq=vardq,
w1=wl1,
w2=wl2)
prefix = 't' + prefix
#
# Sky subtraction
#
imageName = 's' + prefix + starimg + '.fits'
if os.path.isfile(imageName):
skipwarn(imageName)
else:
iraf.gfreduce(prefix + starimg,
slits='header',
rawpath='./',
fl_inter='no',
fl_addmdf='no',
key_mdf='MDF',
mdffile=mdffile,
fl_over='no',
fl_trim='no',
fl_bias='no',
trace='no',
recenter='no',
fl_flux='no',
fl_gscrrej='no',
fl_extract='no',
fl_gsappwave='no',
fl_wavtran='no',
fl_novl='no',
fl_skysub='yes',
reference='eprg' + flat,
weights='no',
wavtraname='eprg' + arc,
response='eprg' + flat + '_response.fits',
fl_vardq=vardq,
w1=wl1,
w2=wl2)
prefix = 's' + prefix
#
# Apsumming the stellar spectra
#
xinst = pf.getdata(prefix + starimg + '.fits', ext=1)['XINST']
if instrument == 'GMOS-N':
x0 = np.average(xinst[xinst < 10])
elif instrument == 'GMOS-S':
x0 = np.average(xinst[xinst > 10])
ap_expression = '((XINST-{:.2f})**2 + '\
'(YINST-2.45)**2)**0.5 < {:.2f}'.format(x0, apsum_radius)
imageName = 'a' + prefix + starimg + '.fits'
if os.path.isfile(imageName):
skipwarn(imageName)
else:
iraf.gfapsum(prefix + starimg,
fl_inter='no',
lthreshold='INDEF',
hthreshold='INDEF',
reject='avsigclip',
expr=ap_expression)
#
# Building sensibility function
#
if os.path.isfile('std' + starimg)\
and os.path.isfile('sens' + starimg + '.fits'):
skipwarn('std{0:s} and sens{0:s}.fits'.format(starimg))
else:
imageName = 'std' + starimg
if os.path.isfile(imageName):
iraf.printlog(
'GIREDS: WARNING: Removing file {:s}'.format(imageName),
'logfile.log', 'yes')
iraf.delete(imageName)
imageName = 'sens' + starimg + '.fits'
if os.path.isfile(imageName):
iraf.printlog(
'GIREDS: WARNING: Removing file {:s}'.format(imageName),
'logfile.log', 'yes')
iraf.delete(imageName)
iraf.gsstandard('a' + prefix + starimg,
starname=stdstar,
observatory=observatory,
sfile='std' + starimg,
sfunction='sens' + starimg,
caldir=caldir,
order=sens_order,
function=sens_function)
#
# Apply flux calibration to star
#
imageName = 'c' + prefix + starimg + '.fits'
if os.path.isfile(imageName):
skipwarn(imageName)
else:
iraf.gscalibrate(prefix + starimg,
sfuncti='sens' + starimg,
extinct='onedstds$ctioextinct.dat',
observatory=observatory,
fluxsca=1,
fl_vardq=vardq)
#
# Create data cubes
#
imageName = 'dc' + prefix + starimg + '.fits'
if os.path.isfile(imageName):
skipwarn(imageName)
else:
data_cube = CubeBuilder('c' + prefix + starimg + '.fits')
data_cube.build_cube()
data_cube.fit_refraction_function()
data_cube.fix_atmospheric_refraction()
data_cube.write(imageName)
#
# Test calibration
#
iraf.cd(caldir)
caldata = np.loadtxt(stdstar + '.dat', unpack=True)
iraf.cd('procdir')
calflux = mag2flux(caldata[0], caldata[1])
imageName = 'ca' + prefix + starimg + '.fits'
if os.path.isfile(imageName):
skipwarn(imageName)
else:
iraf.gscalibrate('a' + prefix + starimg,
sfuncti='sens' + starimg,
extinct='onedstds$ctioextinct.dat',
observatory=observatory,
fluxsca=1)
sumflux = pf.getdata('ca' + prefix + starimg + '.fits', ext=2)
sumhead = pf.getheader('ca' + prefix + starimg + '.fits', ext=2)
sumwl = sumhead['crval1'] + np.arange(
sumhead['naxis1']) * sumhead['cdelt1']
plt.close('all')
plt.plot(sumwl, sumflux, 'b', lw=.5)
plt.plot(caldata[0], calflux, 'r', lw=1.5)
plt.xlim(sumwl[0] * .99, sumwl[-1] * 1.01)
plt.ylim(min(calflux) * .8, max(calflux) * 1.2)
plt.savefig('calib' + starimg + '.eps')
cross='yes', fl_inter='no')
# os.system('ds9 &')
# iraf.sleep(5.0)
# for flat in iraf.type(ic.lst_flat, Stdout=1):
# flat = flat.strip()
# for i in np.arange(12):
# iraf.imexamine('brg'+flat+'[sci,'+str(i+1)+']', 1)
# QE correction and extract
iraf.imdelete('qbrg@'+ic.lst_flat)
iraf.imdelete('eqbrg@'+ic.lst_flat)
iraf.gfreduce('brg@'+ic.lst_flat, recenter='no', reference='erg'+flat0,
fl_extract='yes', fl_qecorr='yes', qe_refim='erg'+arc0,
fl_addmdf='no', fl_bias='no', fl_over='no', fl_trim='no',
mdffile=ic.nmdf, mdfdir='./',
slits=ic.cslit, line=pk_line, fl_fluxcal='no', fl_gscrrej='no',
fl_wavtran='no', fl_skysub='no', fl_inter='no', fl_vardq='yes')
if (ic.nslit == 1):
vkw = '1'
if (ic.nslit == 2):
vkw = '*'
os.system('ds9 &')
iraf.sleep(5.0)
iraf.gfdisplay('eqbrg'+flat0, 1, version=vkw)
# ---------- Response function ---------- #
iraf.imdelete(flat0+'_resp')
iraf.gfresponse('eqbrg'+flat0, outimage=flat0+'_resp', sky='',
# ---------- Wavelength solution ---------- #
# Extract the arc
flatref = iraf.type(ic.lst_flat, Stdout=1)[0].strip()
iraf.imdelete('g@'+ic.lst_arc)
iraf.imdelete('rg@'+ic.lst_arc)
iraf.imdelete('erg@'+ic.lst_arc)
for arc in iraf.type(ic.lst_arc, Stdout=1):
arc = arc.strip()
iraf.gfreduce(arc, rawpath=ic.rawdir, fl_extract='yes', recenter='no',
trace='no', reference='erg'+flatref, fl_bias='no',
fl_over='yes', fl_trim='yes', mdffile=ic.nmdf, mdfdir='./',
slits='both', fl_fluxcal='no', fl_gscrrej='no',
fl_wavtran='no', fl_skysub='no', fl_inter='no')
iraf.sleep(10.0)
# ----- Measure the wavelength solution ----- #
for arc in iraf.type(ic.lst_arc, Stdout=1):
arc = arc.strip()
iraf.gswavelength('erg'+arc, fl_inter='yes',
nlost=20, ntarget=15, threshold=25,
coordlis='gmos$data/GCALcuar.dat')
# Printing the running time
print('--- %s seconds ---' %(time.time()-start_time))
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))
#######################################################################
#
# Flat reduction
#
for m in range(len(star)):
for i in ['g', 'rg', 'erg']:
iraf.imdelete(i+'@flat'+str(m)+'.list')
# (B) - 'fl_over=no';
iraf.gfreduce('@flat'+str(m)+'.list', slits='header',
rawpath='rawdir$', fl_inter='no',
fl_addmdf='yes', key_mdf='MDF', mdffile='default', weights='no',
fl_over='no', fl_trim='yes', fl_bias='yes', trace='yes', t_order=4,
fl_flux='no', fl_gscrrej='no', fl_extract='yes', fl_gsappwave='no',
fl_wavtran='no', fl_novl='no', fl_skysub='no', reference='',
recenter='yes', fl_vardq='yes', bias='caldir$'+bias[m][0])
#
# Twilight reduction
#
for m in range(len(star)):
for i in ['g', 'rg', 'erg']:
iraf.imdelete(i+'@twilight'+str(m)+'.list')
# (B) - 'fl_over=no';
iraf.gfreduce('@twilight'+str(m)+'.list', slits='header', rawpath='rawdir$',
fl_inter='no', fl_addmdf='yes', key_mdf='MDF',