def lris_standard(standards, xcorr=yes):
'''Extract standard stars and calculate sensitivity functions.'''
for ofile, nstd in standards:
shutil.copy(ofile, "%s.fits" % nstd)
# Extract standard
if get_head("%s.fits" % nstd, "SKYSUB"):
iraf.apall(nstd, output="", inter=yes, find=yes, recenter=yes, resize=yes,
edit=yes, trace=yes, fittrace=yes, extract=yes, extras=yes,
review=no, background="none")
else:
iraf.apall(nstd, output="", inter=yes, find=yes, recenter=yes, resize=yes,
edit=yes, trace=yes, fittrace=yes, extract=yes, extras=yes,
review=no, background="fit")
if xcorr:
# Cross correlate to tweak wavelength
iraf.xcsao("%s.ms" % nstd, templates=XCTEMPLATE,
correlate="wavelength", logfiles="%s.xcsao" % ofile)
# If a solution was found, apply shift
try:
xcsaof = open("%s.xcsao" % ofile)
shift = float(xcsaof.readlines()[6].split()[14])
except:
shift = 0.0
iraf.specshift("%s.ms" % nstd, -shift)
# Create telluric
iraf.splot("%s.ms" % nstd) # Remove telluric and absorption, save as a%s.ms
iraf.sarith("%s.ms" % nstd, "/", "a%s.ms" % nstd, "telluric.%s.fits" % nstd)
iraf.imreplace("telluric.%s.fits" % nstd, 1.0, lower=0.0, upper=0.0)
iraf.splot("telluric.%s.fits" % nstd) # Remove stellar features and resave
# Create smoothed standard
iraf.gauss("a%s.ms[*,1,1]" % nstd, "s%s.ms" % nstd, 5.0)
iraf.sarith("%s.ms" % nstd, "/", "s%s.ms" % nstd, "ds%s.ms" % nstd)
# Apply telluric correction
iraf.telluric("ds%s.ms" % nstd, "tds%s.ms" % nstd, "telluric.%s.fits" % nstd,
xcorr=no, tweakrms=no, interactive=no,
sample='4000:4010,6850:6975,7150:7350,7575:7725,8050:8400,8900:9725')
# Define bandpasses for standard star calculation
obj=get_head("%s.fits" % nstd, "OBJECT")
iraf.standard("tds%s.ms" % nstd, "%s.std" % nstd,
extinction='home$extinct/maunakeaextinct.dat',
caldir='home$standards/', observatory='Keck', interac=yes,
star_name=obj, airmass='', exptime='')
# Determine sensitivity function
iraf.sensfunc('%s.std' % nstd, '%s.sens' % nstd,
extinction='home$extinct/maunakeaextinct.dat',
newextinction='extinct.dat', observatory='Keck',
function='legendre', order=4, interactive=yes)
return
def red_science(image, flats, spath, object=None, arc='Arc-Red.fits',
smooth='BD284211.smooth.fits', telluric='telluric.fits',
sens='BD284211.sens', biassec=REDBIAS, trimsec=REDTRIM,
outflat='Flat-Red.fits', gain=REDGAIN, rdnoise=REDRDNOISE):
'''Full reduction of KAST science spectra on red CCD'''
# Bias subtract everything first
redbias(image, biassec=biassec, trimsec=trimsec)
redbias(flats, biassec=biassec, trimsec=trimsec)
# Create and apply flat-field
make_flat(flats, outflat, gain=gain, rdnoise=rdnoise)
iraf.ccdproc(image[0], ccdtype='', noproc=no, fixpix=no, overscan=no,
trim=no, zerocor=no, darkcor=no, flatcor=yes, illumcor=no,
fringecor=no, readcor=no, scancor=no, flat=outflat)
# Cosmic ray rejection
#iraf.lacos_spec(image[0], 'c%s' % image[0], 'cm%s' % image[0],
# gain=gain, readn=rdnoise, xorder=9, yorder=3,
# sigclip=4.5, sigfrac=0.5, objlim=1.0, niter=3)
# Extract spectrum
if object==None:
object=get_head(image, 'OBJECT')
iraf.apall('%s' % image[0], output=object, references='', interactive=yes,
find=yes, recenter=yes, resize=yes, edit=yes, trace=yes,
fittrace=yes, extract=yes, extras=yes, review=no,
background='fit', weights='variance', pfit='fit1d',
readnoise=rdnoise, gain=gain)
# Apply wavelength solution to standard
shutil.copy('%s/%s' % (spath, arc), '.')
shutil.copy('%s/database/id%s' % (spath, arc.rstrip('.fits')), 'database')
iraf.refspec(object, references=arc, sort="", group="", override=yes,
confirm=no, assign=yes)
iraf.dispcor(object, '%s.w' % object, confirm=no, listonly=no)
# Smooth
shutil.copy('%s/%s' % (spath, smooth), '.')
iraf.sarith('%s.w' % object, '/', smooth, '%s.s' % object)
# Create and apply telluric correction
shutil.copy('%s/%s' % (spath, telluric), '.')
iraf.telluric('%s.s' % object, '%s.t' % object, telluric, xcorr=yes,
tweakrms=yes, interactive=yes, sample='6850:6950,7575:7700')
# Flux calibration
shutil.copy('%s/%s.0001.fits' % (spath, sens), '.')
iraf.calibrate('%s.t' % object, '%s.f' % object, extinct=yes, flux=yes,
extinction='onedstds$kpnoextinct.dat',
observatory='Lick', sensitivity=sens, airmass='',
exptime='')
return
def SarithTask(self, Input1, Input2, operation, OutputFile, FitsFolder, Suffix = 'tell'):
if OutputFile == None:
OutputFile = self.outputNameGenerator(Input1, Suffix)
self.deleteIrafFiles(FitsFolder + OutputFile)
sarith_conf = self.SarithAttributes(InputFile1 = Input1, InputFile2 = Input2, OuputFile = OutputFile, Fits_Folder = FitsFolder, operation = operation)
iraf.sarith(**sarith_conf)
return OutputFile
def blue_science(image, spath, object=None, flat='Flat-Blue.fits',
arc='Arc-Blue.fits', smooth='BD284211.smooth.fits',
sens='BD284211.sens', biassec1=BLUEBIAS1, trimsec1=BLUETRIM1,
biassec2=BLUEBIAS2, trimsec2=BLUETRIM2, gain=BLUEGAIN,
rdnoise=BLUERDNOISE):
'''Full reduction of KAST science spectra on blue CCD'''
# Bias subtract everything first
bluebias(image, biassec1=biassec1, trimsec1=trimsec1, biassec2=biassec2,
trimsec2=trimsec2)
# Apply flat-field
shutil.copy('%s/%s' % (spath, flat), '.')
iraf.ccdproc('j%s' % image[0], ccdtype='', noproc=no, fixpix=no,
overscan=no, trim=no, zerocor=no, darkcor=no, flatcor=yes,
illumcor=no, fringecor=no, readcor=no, scancor=no,
flat=flat)
# Cosmic ray rejection
#iraf.lacos_spec('j%s' % image[0], 'cj%s' % image[0], 'cmj%s' % image[0],
# gain=gain, readn=rdnoise, xorder=9, yorder=3,
# sigclip=4.5, sigfrac=0.5, objlim=1.0, niter=3)
# Extract spectrum
if object==None:
object=get_head(image, 'OBJECT')
iraf.apall('j%s' % image[0], output=object, references='',
interactive=yes, find=yes, recenter=yes, resize=yes, edit=yes,
trace=yes, fittrace=yes, extract=yes, extras=yes, review=no,
background='fit', weights='variance', pfit='fit1d',
readnoise=rdnoise, gain=gain)
# Apply wavelength solution to standard
shutil.copy('%s/%s' % (spath, arc), '.')
shutil.copy('%s/database/id%s' % (spath, arc.rstrip('.fits')), 'database')
iraf.refspec(object, references=arc, sort="", group="", override=yes,
confirm=no, assign=yes)
iraf.dispcor(object, '%s.w' % object, confirm=no, listonly=no)
# Smooth
shutil.copy('%s/%s' % (spath, smooth), '.')
iraf.sarith('%s.w' % object, '/', smooth, '%s.s' % object)
# Flux calibration
shutil.copy('%s/%s.0001.fits' % (spath, sens), '.')
iraf.calibrate('%s.s' % object, '%s.f' % object, extinct=yes, flux=yes,
extinction='onedstds$kpnoextinct.dat',
observatory='Lick', sensitivity=sens, airmass='',
exptime='')
return
def divide_smooth(input_file):
os.system("rm smoothdiv*_"+input_file)
print wave_w1,wave_w2
iraf.sarith(
input1 = "spec_" + input_file,\
op = "/",\
input2 = "master_smooth.fits",\
output = "smoothdivtemp_"+input_file,\
w1 = wave_w1,\
w2 = wave_w2,\
apertures = "*",\
bands = "",\
beams = "",\
apmodulus = 0,\
reverse = 0,\
ignoreaps = 1,\
format = "multispec",\
renumber = 1,\
offset = 0,\
clobber = 1,\
merge = 0,\
rebin = 1,\
errval = 0.0,\
verbose = 1)
### Apply continuum to remove artifacts from the division
iraf.continuum(
input = "smoothdivtemp_" + input_file,\
output = "smoothdiv_" + input_file,\
ask = "no",\
lines = "*",\
bands = "1",\
type = "data",\
replace = 1,\
wavescale = 1,\
logscale = 0,\
override = 1,\
listonly = 0,\
logfiles = "logfile",\
interactive = 0,\
sample = "*",\
naverage = 1,\
function = "spline3",\
order = 10,\
low_reject = 30.0,\
high_reject = 30.0,\
niterate = 1,\
grow = 5.0)
def trim(fs=None):
iraf.cd('work')
if fs is None:
fs=glob('flx/sci*c?.fits')
if not os.path.exists('trm'):
os.mkdir('trm')
for i,f in enumerate(fs):
outfile=f.replace('flx','trm')
w=WCS(f)
hdu= pyfits.open(f)
npix=hdu[0].data.shape[2]
W1=int(w.wcs_pix2world(2,0,0,0)[0])
W2=int(w.wcs_pix2world(npix-2,0,0,0)[0])
iraf.sarith(input1=f,op='copy',output=outfile,w1=W1,w2=W2
,clobber='yes')
iraf.cd('..')
def combine_normalize_images(WORK_DIR, combine=False):
if combine:
print '\n + Combine images\n'
try:
os.remove('combined_sum.fits')
except: pass
iraf.scombine(input=','.join([obj+'.ec.vh' for obj in observations[WORK_DIR]['objects']]), output='combined_sum', group='apertures', combine='sum', reject='none', Stdout="/dev/null")
# normalize spectra
# This step will require you to manually normalize all the spectra.
print '\n + Normalize spectra\n'
if combine:
try:
os.remove('combined_sum_cone_rv_echellet.fits')
except: pass
iraf.continuum(input='combined_sum', output='combined_sum_cont', type='fit', replace='no', listonly='no', functio='cheb', order=13, low_rej=2, high_rej=3, naverag=-3, niter=9, interac='no', markrej='no')
else:
for obj in observations[WORK_DIR]['objects']:
try:
os.remove(obj+'_cont.fits')
os.remove(obj+'_vh_norm.fits')
except: pass
iraf.continuum(input=obj+'.ec.vh', output=obj+'_cont', type='fit', replace='no', listonly='no', functio='cheb', order=13, low_rej=2, high_rej=3, naverag=-3, niter=9, interac='no', markrej='no', ask='yes')
iraf.sarith(input1=obj+'.ec.vh', op='/', input2=obj+'_cont', output=obj+'_vh_norm', format='multispec', Stdout="/dev/null")
#combine apertures
print '\n + Combine apertures\n'
if combine:
try:
os.remove('combined_sum_data.fits')
os.remove('combined_sum_norm.fits')
os.remove('combined_final.0001.fits')
except: pass
iraf.scombine(input='combined_sum', output='combined_sum_data', group='all', combine='sum', reject='none', Stdout="/dev/null")
iraf.scombine(input='combined_sum_cont', output='combined_sum_norm', group='all', combine='sum', reject='none', Stdout="/dev/null")
iraf.sarith(input1='combined_sum_data', op='/', input2='combined_sum_norm', output='combined_final', format='onedspec', Stdout="/dev/null")
else:
for obj in observations[WORK_DIR]['objects']:
try:
os.remove(obj+'_data1D.fits')
os.remove(obj+'_cont1D.fits')
os.remove(obj+'_1D_vh_norm.0001.fits')
os.remove(obj+'_1D_vh_norm.fits')
except: pass
iraf.scombine(input=obj+'.ec.vh', output=obj+'_data1D', group='all', combine='sum', reject='none', Stdout="/dev/null")
iraf.scombine(input=obj+'_cont', output=obj+'_cont1D', group='all', combine='sum', reject='none', Stdout="/dev/null")
iraf.sarith(input1=obj+'_data1D', op='/', input2=obj+'_cont1D', output=obj+'_1D_vh_norm', format='onedspec', Stdout="/dev/null")
def normalize_and_merge(reduced_science_files):
current_directory = os.getcwd()
for k in range(len(reduced_science_files)):
remove_file(current_directory, "norm.dummyI.fits")
remove_file(current_directory, "norm.dummyIa.fits")
remove_file(current_directory, "norm.dummyII.fits")
remove_file(current_directory, "norm.dummyIIa.fits")
remove_file(current_directory, "norm.dummyIII.fits")
remove_file(current_directory, "norm.dummyIV.fits")
remove_file(current_directory, "norm.dummyV.fits")
remove_file(current_directory, "norm.dummy1.fits")
remove_file(current_directory, "norm.dummy2.fits")
remove_file(current_directory, "norm.dummy3.fits")
remove_file(current_directory, "norm.dummy4.fits")
remove_file(current_directory, "norm.dummy5.fits")
remove_file(current_directory, "norm.dummy6.fits")
remove_file(current_directory, "norm.dummy7.fits")
remove_file(current_directory, "norm.dummy8.fits")
ranges = np.loadtxt("ranges.lis", delimiter=",")
aperturlist = open("test.norm.apertures.lis", "w")
merge = reduced_science_files[k].replace(".extracted.fits",
".norm.fits")
iraf.scopy(reduced_science_files[k],
place_here("norm.dummyI.fits"),
apertures="5:14",
format="multispec")
iraf.scopy(reduced_science_files[k],
place_here("norm.dummyII.fits"),
apertures="35:42",
format="multispec")
iraf.fit1d(place_here("norm.dummyI.fits"),
place_here("norm.dummyIa.fits"),
naverage=1,
axis=2,
type="fit",
low_rej=1.0,
high_rej=2.0,
order=2,
niterate=2,
func="spline3",
sample="*")
iraf.fit1d(place_here("norm.dummyII.fits"),
place_here("norm.dummyIIa.fits"),
naverage=1,
axis=2,
type="fit",
low_rej=1.0,
high_rej=2.0,
order=2,
niterate=2,
func="spline3",
sample="*")
iraf.scopy(reduced_science_files[k],
place_here("norm.dummy1.fits"),
apertures="1",
format="multispec",
w1="4544")
iraf.scopy(reduced_science_files[k],
place_here("norm.dummy2.fits"),
apertures="2",
format="multispec",
w1="4569")
iraf.scopy(reduced_science_files[k],
place_here("norm.dummy3.fits"),
apertures="3:7",
format="multispec")
iraf.scopy(place_here("norm.dummyIa.fits"),
place_here("norm.dummy4.fits"),
apertures="8:10",
format="multispec")
iraf.scopy(reduced_science_files[k],
place_here("norm.dummy5.fits"),
apertures="11:37",
format="multispec")
iraf.scopy(place_here("norm.dummyIIa.fits"),
place_here("norm.dummy6.fits"),
apertures="38:40",
format="multispec")
iraf.scopy(reduced_science_files[k],
place_here("norm.dummy7.fits"),
apertures="41:50",
format="multispec")
iraf.scopy(reduced_science_files[k],
place_here("norm.dummy8.fits"),
apertures="51",
format="multispec",
w2="7591")
iraf.scombine("@normalization.list.lis",
place_here("norm.dummyIII.fits"),
group='apertures')
iraf.fit1d(place_here("norm.dummyIII.fits"),
place_here("norm.dummyIV.fits"),
naverage=1,
axis=1,
type="fit",
low_rej=0.8,
high_rej=2.0,
order=7,
niterate=4,
func="spline3",
sample="*")
iraf.sarith(reduced_science_files[k], "/",
place_here("norm.dummyIV.fits"),
place_here("norm.dummyV.fits"))
iraf.fit1d(place_here("norm.dummyV.fits"),
merge,
naverage=1,
axis=1,
type="ratio",
low_rej=0.2,
high_rej=2.0,
order=1,
niterate=4,
func="chebyshev",
sample="*")
iraf.hedit(merge, "INSTRUME", 'TLS-echelle')
for i in range(len(ranges)):
apertures = int(ranges[i][0])
new_name = merge.replace(".fits", "." + str(apertures) + ".fits")
input1 = os.path.join(current_directory, merge)
output = os.path.join(current_directory, new_name)
iraf.scopy(input1,
output,
w1=ranges[i][1],
w2=ranges[i][2],
apertur=apertures,
format="multispec")
aperturlist.write(new_name + "\n")
aperturlist.close()
new_name_merged = reduced_science_files[k].replace(
".extracted.fits", ".merged.fits")
iraf.scombine("@test.norm.apertures.lis", new_name_merged, group='all')
cut_for_ston = new_name_merged.replace("merged", "cut")
iraf.scopy(new_name_merged,
cut_for_ston,
w1=5603,
w2=5612,
format="multispec",
apertures="")
stddev = iraf.imstat(cut_for_ston,
Stdout=1,
fields="stddev",
format="no")
ston = 1 / float(stddev[0])
iraf.hedit(new_name, "STON", ston)
for i in range(len(ranges)):
apertures = int(ranges[i][0])
os.remove(
os.path.join(
merge.replace(".fits", "." + str(apertures) + ".fits")))
os.remove(os.path.join(current_directory, "test.norm.apertures.lis"))
remove_file(current_directory, "norm.dummyI.fits")
remove_file(current_directory, "norm.dummyIa.fits")
remove_file(current_directory, "norm.dummyII.fits")
remove_file(current_directory, "norm.dummyIIa.fits")
remove_file(current_directory, "norm.dummyIII.fits")
remove_file(current_directory, "norm.dummyIV.fits")
remove_file(current_directory, "norm.dummyV.fits")
remove_file(current_directory, "norm.dummy1.fits")
remove_file(current_directory, "norm.dummy2.fits")
remove_file(current_directory, "norm.dummy3.fits")
remove_file(current_directory, "norm.dummy4.fits")
remove_file(current_directory, "norm.dummy5.fits")
remove_file(current_directory, "norm.dummy6.fits")
remove_file(current_directory, "norm.dummy7.fits")
remove_file(current_directory, "norm.dummy8.fits")
print("Success! Produced files *merged.fits, *norm.fits")
def deimos_standard(standard):
'''Extract standard star and calculate sensitivit function.'''
bstd = "%s_01_B" % standard; rstd = "%s_01_R" % standard
# Extract standard
if get_head("%s.fits" % bstd, "SKYSUB"):
iraf.apall(bstd, output="", inter=yes, find=yes, recenter=yes, resize=yes,
edit=yes, trace=yes, fittrace=yes, extract=yes, extras=yes,
review=no, background="none")
iraf.apall(rstd, output="", inter=yes, find=yes, recenter=yes, resize=yes,
edit=yes, trace=yes, fittrace=yes, extract=yes, extras=yes,
review=no, background="none")
else:
iraf.apall(bstd, output="", inter=yes, find=yes, recenter=yes, resize=yes,
edit=yes, trace=yes, fittrace=yes, extract=yes, extras=yes,
review=no, background="fit")
iraf.apall(rstd, output="", inter=yes, find=yes, recenter=yes, resize=yes,
edit=yes, trace=yes, fittrace=yes, extract=yes, extras=yes,
review=no, background="fit")
# Fit the continuum
#iraf.continuum("%s.ms" % bstd, output="s%s.ms" % bstd, lines=1, bands=1,
# type="fit", sample="*", naverage=1, function="chebyshev",
# order=15, low_reject=3.0, high_reject=5.0, niterate=10, grow=1.0,
# interac=yes)
#iraf.continuum("%s.ms" % rstd, output="s%s.ms" % rstd, lines=1, bands=1,
# type="fit", sample="*", naverage=1, function="chebyshev",
# order=15, low_reject=3.0, high_reject=5.0, niterate=10, grow=1.0,
# interac=yes)
# Create telluric
iraf.splot("%s.ms" % bstd) # Remove telluric and absorption, save as a%s.ms
iraf.sarith("%s.ms" % bstd, "/", "a%s.ms" % bstd, "telluric.B.%s.fits" % bstd)
iraf.imreplace("telluric.B.%s.fits" % bstd, 1.0, lower=0.0, upper=0.0)
iraf.splot("telluric.B.%s.fits" % bstd) # Remove stellar features and resave
iraf.splot("%s.ms" % rstd) # Remove telluric and absorption, save as a%s.ms
iraf.sarith("%s.ms" % rstd, "/", "a%s.ms" % rstd, "telluric.R.%s.fits" % rstd)
iraf.imreplace("telluric.R.%s.fits" % rstd, 1.0, lower=0.0, upper=0.0)
iraf.splot("telluric.R.%s.fits" % rstd) # Remove stellar features and resave
# Create smoothed standard
iraf.gauss("a%s.ms[*,1,1]" % bstd, "s%s.ms" % bstd, 5.0)
iraf.sarith("%s.ms" % bstd, "/", "s%s.ms" % bstd, "ds%s.ms" % bstd)
iraf.gauss("a%s.ms[*,1,1]" % rstd, "s%s.ms" % rstd, 5.0)
iraf.sarith("%s.ms" % rstd, "/", "s%s.ms" % rstd, "ds%s.ms" % rstd)
# Divide through by smoothed standard
#iraf.sarith("%s.ms" % bstd, "/", "s%s.ms" % bstd, "ds%s.ms" % bstd)
#iraf.sarith("%s.ms" % rstd, "/", "s%s.ms" % rstd, "ds%s.ms" % rstd)
# Create and apply telluric correction
#iraf.splot("%s.ms" % bstd) # Remove telluric, save as a%s.ms
#iraf.splot("%s.ms" % rstd) # Remove telluric, save as a%s.ms
#iraf.sarith("%s.ms" % bstd, "/", "a%s.ms" % bstd, "telluric.B.fits")
#iraf.sarith("%s.ms" % rstd, "/", "a%s.ms" % rstd, "telluric.R.fits")
#iraf.imreplace("telluric.B.fits", 1.0, lower=0.0, upper=0.0)
#iraf.imreplace("telluric.R.fits", 1.0, lower=0.0, upper=0.0)
iraf.telluric("ds%s.ms" % bstd, "tds%s.ms" % bstd, "telluric.B.%s.fits" % bstd,
xcorr=no, tweakrms=no, interactive=no, sample='6850:6950,7575:7700')
iraf.telluric("ds%s.ms" % rstd, "tds%s.ms" % rstd, "telluric.R.%s.fits" % rstd,
xcorr=no, tweakrms=no, interactive=no, sample='6850:6950,7575:7700')
# Define bandpasses for standard star calculation
iraf.standard("tds%s.ms" % bstd, "%s.B.std" % standard,
extinction='home$extinct/maunakeaextinct.dat',
caldir='home$standards/', observatory='Keck', interac=yes,
star_name=standard, airmass='', exptime='')
iraf.standard("tds%s.ms" % rstd, "%s.R.std" % standard,
extinction='home$extinct/maunakeaextinct.dat',
caldir='home$standards/', observatory='Keck', interac=yes,
star_name=standard, airmass='', exptime='')
# Determine sensitivity function
iraf.sensfunc('%s.B.std' % standard, '%s.B.sens' % standard,
extinction='home$extinct/maunakeaextinct.dat',
newextinction='extinct.dat', observatory='Keck',
function='legendre', order=4, interactive=yes)
iraf.sensfunc('%s.R.std' % standard, '%s.R.sens' % standard,
extinction='home$extinct/maunakeaextinct.dat',
newextinction='extinct.dat', observatory='Keck',
function='legendre', order=4, interactive=yes)
return
def deimos_extract(science, standard, dostandard=yes):
'''Extract and flux calibrate DEIMOS spectra (assuming they have been
processed into 2D images using deimos_pipe above).'''
if dostandard:
deimos_standard(standard)
for source in science:
images = iraffiles("%s_??_B.fits" % source)
joinstr = ""
for image in images:
bimage = image.split(".")[0]; rimage = bimage[:-1] + "R"
update_head(bimage, "FLUX_OBJ", standard)
update_head(rimage, "FLUX_OBJ", standard)
# Extract 1D spectra
if get_head("%s.fits" % bimage, "SKYSUB"):
iraf.apall(bimage, output="", inter=yes, find=yes, recenter=yes,
resize=yes, edit=yes, trace=yes, fittrace=yes, extract=yes,
extras=yes, review=no, background="none",
reference="%s_01_B" % standard)
iraf.apall(rimage, output="", inter=yes, find=yes, recenter=yes,
resize=yes, edit=yes, trace=yes, fittrace=yes, extract=yes,
extras=yes, review=no, background="none",
reference="%s_01_R" % standard)
else:
iraf.apall(bimage, output="", inter=yes, find=yes, recenter=yes,
resize=yes, edit=yes, trace=yes, fittrace=yes, extract=yes,
extras=yes, review=no, background="fit",
reference="%s_01_B" % standard)
iraf.apall(rimage, output="", inter=yes, find=yes, recenter=yes,
resize=yes, edit=yes, trace=yes, fittrace=yes, extract=yes,
extras=yes, review=no, background="fit",
reference="%s_01_R" % standard)
# Normalize by the standard continuua
iraf.sarith("%s.ms" % bimage, "/", "s%s_01_B.ms.fits" % standard,
"s%s.ms" % bimage)
iraf.sarith("%s.ms" % rimage, "/", "s%s_01_R.ms.fits" % standard,
"s%s.ms" % rimage)
# Telluric correct
bstd = "%s_01_B" % standard; rstd = "%s_01_R" % standard
iraf.telluric("s%s.ms" % bimage, "ts%s.ms" % bimage,
"telluric.B.%s.fits" % bstd, tweakrms=yes,
interactive=yes, sample='6850:6950,7575:7700')
iraf.telluric("s%s.ms" % rimage, "ts%s.ms" % rimage,
"telluric.R.%s.fits" % rstd, tweakrms=yes,
interactive=yes, sample='6850:6950,7575:7700')
# Flux calibration
iraf.calibrate("ts%s.ms" % bimage, "fts%s.ms" % bimage, extinct=yes,
flux=yes, extinction="home$extinct/maunakeaextinct.dat",
observatory="Keck", sensitivity="%s.B.sens" % standard,
airmass='', exptime='')
iraf.calibrate("ts%s.ms" % rimage, "fts%s.ms" % rimage, extinct=yes,
flux=yes, extinction="home$extinct/maunakeaextinct.dat",
observatory="Keck", sensitivity="%s.R.sens" % standard,
airmass='', exptime='')
joinstr += "fts%s.ms,fts%s.ms," % (bimage, rimage)
# Combine
iraf.scombine(joinstr[:-1], "%s.ms.fits" % source, combine="average",
reject="avsigclip", w1=INDEF, w2=INDEF, dw=INDEF, nw=INDEF,
scale="none", zero="none", weight="none", lsigma=3.0,
hsigma=3.0, gain=CCDGAIN, rdnoise=CCDRNOISE)
# Plot to enable final tweaks
iraf.splot("%s.ms.fits" % source)
return
def lris_standard(standards, xcorr=yes):
'''Extract standard stars and calculate sensitivity functions.'''
for ofile, nstd in standards:
shutil.copy(ofile, "%s.fits" % nstd)
# Extract standard
if get_head("%s.fits" % nstd, "SKYSUB"):
iraf.apall(nstd,
output="",
inter=yes,
find=yes,
recenter=yes,
resize=yes,
edit=yes,
trace=yes,
fittrace=yes,
extract=yes,
extras=yes,
review=no,
background="none")
else:
iraf.apall(nstd,
output="",
inter=yes,
find=yes,
recenter=yes,
resize=yes,
edit=yes,
trace=yes,
fittrace=yes,
extract=yes,
extras=yes,
review=no,
background="fit")
if xcorr:
# Cross correlate to tweak wavelength
iraf.xcsao("%s.ms" % nstd,
templates=XCTEMPLATE,
correlate="wavelength",
logfiles="%s.xcsao" % ofile)
# If a solution was found, apply shift
try:
xcsaof = open("%s.xcsao" % ofile)
shift = float(xcsaof.readlines()[6].split()[14])
except:
shift = 0.0
iraf.specshift("%s.ms" % nstd, -shift)
# Create telluric
iraf.splot("%s.ms" %
nstd) # Remove telluric and absorption, save as a%s.ms
iraf.sarith("%s.ms" % nstd, "/", "a%s.ms" % nstd,
"telluric.%s.fits" % nstd)
iraf.imreplace("telluric.%s.fits" % nstd, 1.0, lower=0.0, upper=0.0)
iraf.splot("telluric.%s.fits" %
nstd) # Remove stellar features and resave
# Create smoothed standard
iraf.gauss("a%s.ms[*,1,1]" % nstd, "s%s.ms" % nstd, 5.0)
iraf.sarith("%s.ms" % nstd, "/", "s%s.ms" % nstd, "ds%s.ms" % nstd)
# Apply telluric correction
iraf.telluric(
"ds%s.ms" % nstd,
"tds%s.ms" % nstd,
"telluric.%s.fits" % nstd,
xcorr=no,
tweakrms=no,
interactive=no,
sample='4000:4010,6850:6975,7150:7350,7575:7725,8050:8400,8900:9725'
)
# Define bandpasses for standard star calculation
obj = get_head("%s.fits" % nstd, "OBJECT")
iraf.standard("tds%s.ms" % nstd,
"%s.std" % nstd,
extinction='home$extinct/maunakeaextinct.dat',
caldir='home$standards/',
observatory='Keck',
interac=yes,
star_name=obj,
airmass='',
exptime='')
# Determine sensitivity function
iraf.sensfunc('%s.std' % nstd,
'%s.sens' % nstd,
extinction='home$extinct/maunakeaextinct.dat',
newextinction='extinct.dat',
observatory='Keck',
function='legendre',
order=4,
interactive=yes)
return
def lris_extract(science, standards, dostandard=yes):
'''Extract and flux calibrate LRIS spectra (assuming they have been
processed into 2D images using LRIS_pipe above).'''
if dostandard:
lris_standard(standards)
for src in science:
bimages = iraffiles("%s_??_B.fits" % src)
rimages = iraffiles("%s_??_R.fits" % src)
joinstr = ""
for bimage in bimages:
bimage = bimage.split(".")[0]
# Find appropriate standard for this image
bstd = get_head("%s.fits" % bimage, "STDNAME")
# Extract 1D spectra
if get_head("%s.fits" % bimage, "SKYSUB"):
iraf.apall(bimage,
output="",
inter=yes,
find=yes,
recenter=yes,
resize=yes,
edit=yes,
trace=yes,
fittrace=yes,
extract=yes,
extras=yes,
review=no,
background="none",
reference=bstd)
else:
iraf.apall(bimage,
output="",
inter=yes,
find=yes,
recenter=yes,
resize=yes,
edit=yes,
trace=yes,
fittrace=yes,
extract=yes,
extras=yes,
review=no,
background="fit",
reference=bstd)
# Normalize by the standard continuua
iraf.sarith("%s.ms" % bimage,
"/",
"../standards/s%s.ms.fits" % bstd,
"s%s.ms" % bimage,
w1=INDEF,
w2=INDEF)
# Telluric correct
iraf.telluric("s%s.ms" % bimage,
"ts%s.ms" % bimage,
"../standards/telluric.%s.fits" % bstd,
tweakrms=yes,
interactive=yes,
sample='6850:6950,7575:7700,8750:9925')
# Flux calibration
iraf.calibrate("ts%s.ms" % bimage,
"fts%s.ms" % bimage,
extinct=yes,
flux=yes,
extinction="home$extinct/maunakeaextinct.dat",
observatory="Keck",
sens="../standards/%s.sens" % bstd,
airmass='',
exptime='')
joinstr += "fts%s.ms," % bimage
for rimage in rimages:
rimage = rimage.split(".")[0]
# Find appropriate standard for this image
rstd = get_head("%s.fits" % rimage, "STDNAME")
# Extract 1D spectra
if get_head("%s.fits" % rimage, "SKYSUB"):
iraf.apall(rimage,
output="",
inter=yes,
find=yes,
recenter=yes,
resize=yes,
edit=yes,
trace=yes,
fittrace=yes,
extract=yes,
extras=yes,
review=no,
background="none",
reference=rstd)
else:
iraf.apall(rimage,
output="",
inter=yes,
find=yes,
recenter=yes,
resize=yes,
edit=yes,
trace=yes,
fittrace=yes,
extract=yes,
extras=yes,
review=no,
background="fit",
reference=rstd)
# Normalize by the standard continuua
iraf.sarith("%s.ms" % rimage,
"/",
"../standards/s%s.ms.fits" % rstd,
"s%s.ms" % rimage,
w1=5500,
w2=INDEF)
# Telluric correct
iraf.telluric("s%s.ms" % rimage,
"ts%s.ms" % rimage,
"../standards/telluric.%s.fits" % rstd,
tweakrms=yes,
interactive=yes,
sample='6850:6950,7575:7700')
# Flux calibration
iraf.calibrate("ts%s.ms" % rimage,
"fts%s.ms" % rimage,
extinct=yes,
flux=yes,
extinction="home$extinct/maunakeaextinct.dat",
observatory="Keck",
sens="../standards/%s.sens" % rstd,
airmass='',
exptime='')
joinstr += "fts%s.ms," % rimage
# Combine
iraf.scombine(joinstr[:-1],
"%s.ms.fits" % src,
combine="average",
reject="avsigclip",
w1=INDEF,
w2=INDEF,
dw=INDEF,
nw=INDEF,
scale="median",
zero="none",
weight="none",
sample="5450:5600",
lsigma=3.0,
hsigma=3.0,
gain=RCCDGAIN,
rdnoise=RCCDRNOISE)
# Plot to enable final tweaks
iraf.splot("%s.ms.fits" % src)
return
iraf.imdelete('flat_fid_mag.ec.fits', verify=no)
# The extraction of the flat ends up with some negative values, which
# skews the fit in the following steps, so I added a small bias level
# equal to the minimum value in the
minval = iraf.imstat('nonorm_flat_fid_mag.ec.fits', fields='min', Stdout=1)[-1]
minval = float(minval)
if minval < 0:
iraf.imcopy('nonorm_flat_fid_mag.ec.fits',
'nonorm_flat_fid_mag_bias.ec.fits')
iraf.imdelete('nonorm_flat_fid_mag.ec.fits', verify=no)
print 'adding an offset to avoid negative'
iraf.sarith('nonorm_flat_fid_mag_bias.ec.fits',
'-',
minval - .02,
'nonorm_flat_fid_mag.ec.fits',
verbose=yes)
iraf.sfit(input='nonorm_flat_fid_mag.ec.fits',
output='flat_fid_mag.ec.fits',
type='ratio',
replace=no,
wavesca=no,
logscal=no,
override=yes,
listonly=no,
interac=no,
sample='*',
naverage=-5,
function='spline3',
def red_science(image,
flats,
spath,
object=None,
arc='Arc-Red.fits',
smooth='BD284211.smooth.fits',
telluric='telluric.fits',
sens='BD284211.sens',
biassec=REDBIAS,
trimsec=REDTRIM,
outflat='Flat-Red.fits',
gain=REDGAIN,
rdnoise=REDRDNOISE):
'''Full reduction of KAST science spectra on red CCD'''
# Bias subtract everything first
redbias(image, biassec=biassec, trimsec=trimsec)
redbias(flats, biassec=biassec, trimsec=trimsec)
# Create and apply flat-field
make_flat(flats, outflat, gain=gain, rdnoise=rdnoise)
iraf.ccdproc(image[0],
ccdtype='',
noproc=no,
fixpix=no,
overscan=no,
trim=no,
zerocor=no,
darkcor=no,
flatcor=yes,
illumcor=no,
fringecor=no,
readcor=no,
scancor=no,
flat=outflat)
# Cosmic ray rejection
#iraf.lacos_spec(image[0], 'c%s' % image[0], 'cm%s' % image[0],
# gain=gain, readn=rdnoise, xorder=9, yorder=3,
# sigclip=4.5, sigfrac=0.5, objlim=1.0, niter=3)
# Extract spectrum
if object == None:
object = get_head(image, 'OBJECT')
iraf.apall('%s' % image[0],
output=object,
references='',
interactive=yes,
find=yes,
recenter=yes,
resize=yes,
edit=yes,
trace=yes,
fittrace=yes,
extract=yes,
extras=yes,
review=no,
background='fit',
weights='variance',
pfit='fit1d',
readnoise=rdnoise,
gain=gain)
# Apply wavelength solution to standard
shutil.copy('%s/%s' % (spath, arc), '.')
shutil.copy('%s/database/id%s' % (spath, arc.rstrip('.fits')), 'database')
iraf.refspec(object,
references=arc,
sort="",
group="",
override=yes,
confirm=no,
assign=yes)
iraf.dispcor(object, '%s.w' % object, confirm=no, listonly=no)
# Smooth
shutil.copy('%s/%s' % (spath, smooth), '.')
iraf.sarith('%s.w' % object, '/', smooth, '%s.s' % object)
# Create and apply telluric correction
shutil.copy('%s/%s' % (spath, telluric), '.')
iraf.telluric('%s.s' % object,
'%s.t' % object,
telluric,
xcorr=yes,
tweakrms=yes,
interactive=yes,
sample='6850:6950,7575:7700')
# Flux calibration
shutil.copy('%s/%s.0001.fits' % (spath, sens), '.')
iraf.calibrate('%s.t' % object,
'%s.f' % object,
extinct=yes,
flux=yes,
extinction='onedstds$kpnoextinct.dat',
observatory='Lick',
sensitivity=sens,
airmass='',
exptime='')
return
def red_standard(image,
arcs,
flats,
object=None,
biassec=REDBIAS,
trimsec=REDTRIM,
outflat='Flat-Red.fits',
gain=REDGAIN,
rdnoise=REDRDNOISE,
arc='Arc-Red.fits',
caldir='home$standards/'):
'''Reduce and calibrate standard star observation with red CCD'''
# Bias subtract everything first
redbias(image, biassec=biassec, trimsec=trimsec)
redbias(arcs, biassec=biassec, trimsec=trimsec)
redbias(flats, biassec=biassec, trimsec=trimsec)
# Create and apply flat-field
make_flat(flats, outflat, gain=gain, rdnoise=rdnoise)
iraf.ccdproc(image[0],
ccdtype='',
noproc=no,
fixpix=no,
overscan=no,
trim=no,
zerocor=no,
darkcor=no,
flatcor=yes,
illumcor=no,
fringecor=no,
readcor=no,
scancor=no,
flat=outflat)
arcimages = ','.join(arcs)
iraf.ccdproc(arcs,
ccdtype='',
noproc=no,
fixpix=no,
overscan=no,
trim=no,
zerocor=no,
darkcor=no,
flatcor=yes,
illumcor=no,
fringecor=no,
readcor=no,
scancor=no,
flat=outflat)
# Extract spectrum of standard
if object == None:
object = get_head(image, 'OBJECT')
iraf.apall(image[0],
output=object,
references='',
interactive=yes,
find=yes,
recenter=yes,
resize=yes,
edit=yes,
trace=yes,
fittrace=yes,
extract=yes,
extras=yes,
review=no,
background='fit',
weights='variance',
pfit='fit1d',
readnoise=rdnoise,
gain=gain)
# Extract arc and fit wavelength solution
iraf.imarith(arcs[0], '+', arcs[1], 'Arc-Sum.fits')
reference_arc('Arc-Sum.fits', arc, image[0])
# Apply wavelength solution to standard
iraf.refspec(object,
references=arc,
sort="",
group="",
override=yes,
confirm=no,
assign=yes)
iraf.dispcor(object, '%s.w' % object, confirm=no, listonly=no)
# Remove absorption features and smooth
iraf.splot('%s.w' % object, 1, 1)
iraf.gauss('temp1[*,1,1]', '%s.smooth' % object, 3.0)
iraf.sarith('%s.w' % object, '/', '%s.smooth' % object, '%s.s' % object)
# Create and apply telluric correction
iraf.sarith('%s.w' % object, '/', 'temp1', 'telluric')
iraf.splot('telluric', 1, 1)
iraf.telluric('%s.s' % object,
'%s.t' % object,
'telluric',
xcorr=no,
tweakrms=no,
interactive=no,
sample='6850:6950,7575:7700')
# Define bandpasses for standard star calculation
iraf.standard('%s.t' % object,
'%s.std' % object,
extinction='onedstds$kpnoextinct.dat',
caldir=caldir,
observatory='Lick',
interact=yes,
star_name=object,
airmass='',
exptime='')
# Determine sensitivity function
iraf.sensfunc('%s.std' % object,
'%s.sens' % object,
extinction='onedstds$kpnoextinct.dat',
newextinction='extinct.dat',
observatory='Lick',
function='legendre',
order=3,
interactive=yes)
return
def blue_standard(image,
arcs,
flats,
object=None,
biassec1=BLUEBIAS1,
trimsec1=BLUETRIM1,
biassec2=BLUEBIAS2,
trimsec2=BLUETRIM2,
outflat='Flat-Blue.fits',
gain=BLUEGAIN,
rdnoise=BLUERDNOISE,
arc='Arc-Blue.fits',
caldir='home$standards/'):
'''Reduce and calibrate standard star observation with blue CCD'''
# Bias subtract everything first
bluebias(image,
biassec1=biassec1,
trimsec1=trimsec1,
biassec2=biassec2,
trimsec2=trimsec2)
bluebias(arcs,
biassec1=biassec1,
trimsec1=trimsec1,
biassec2=biassec2,
trimsec2=trimsec2)
bluebias(flats,
biassec1=biassec1,
trimsec1=trimsec1,
biassec2=biassec2,
trimsec2=trimsec2)
# Create and apply flat-field
for i in range(len(flats)):
flats[i] = 'j%s' % flats[i]
make_flat(flats, outflat, gain=gain, rdnoise=rdnoise)
iraf.ccdproc('j%s' % image[0],
ccdtype='',
noproc=no,
fixpix=no,
overscan=no,
trim=no,
zerocor=no,
darkcor=no,
flatcor=yes,
illumcor=no,
fringecor=no,
readcor=no,
scancor=no,
flat=outflat)
iraf.ccdproc('j%s' % arcs[0],
ccdtype='',
noproc=no,
fixpix=no,
overscan=no,
trim=no,
zerocor=no,
darkcor=no,
flatcor=yes,
illumcor=no,
fringecor=no,
readcor=no,
scancor=no,
flat=outflat)
# Extract spectrum of standard
if object == None:
object = get_head(image, 'OBJECT')
iraf.apall('j%s' % image[0],
output=object,
references='',
interactive=yes,
find=yes,
recenter=yes,
resize=yes,
edit=yes,
trace=yes,
fittrace=yes,
extract=yes,
extras=yes,
review=no,
background='fit',
weights='variance',
pfit='fit1d',
readnoise=rdnoise,
gain=gain)
# Extract arc and fit wavelength solution
reference_arc('j%s' % arcs[0], arc, 'j%s' % image[0])
# Apply wavelength solution to standard
iraf.refspec(object,
references=arc,
sort="",
group="",
override=yes,
confirm=no,
assign=yes)
iraf.dispcor(object, '%s.w' % object, confirm=no, listonly=no)
# Remove absorption features and smooth
iraf.splot('%s.w' % object, 1, 1)
iraf.gauss('temp1[*,1,1]', '%s.smooth' % object, 3.0)
iraf.sarith('%s.w' % object, '/', '%s.smooth' % object, '%s.s' % object)
# Define bandpasses for standard star calculation
iraf.standard('%s.s' % object,
'%s.std' % object,
extinction='onedstds$kpnoextinct.dat',
caldir=caldir,
observatory='Lick',
interact=yes,
star_name=object,
airmass='',
exptime='')
# Determine sensitivity function
iraf.sensfunc('%s.std' % object,
'%s.sens' % object,
extinction='onedstds$kpnoextinct.dat',
newextinction='extinct.dat',
observatory='Lick',
function='legendre',
order=3,
interactive=yes)
return
def blue_standard(image, arcs, flats, object=None, biassec1=BLUEBIAS1,
trimsec1=BLUETRIM1, biassec2=BLUEBIAS2,
trimsec2=BLUETRIM2, outflat='Flat-Blue.fits', gain=BLUEGAIN,
rdnoise=BLUERDNOISE, arc='Arc-Blue.fits',
caldir='home$standards/'):
'''Reduce and calibrate standard star observation with blue CCD'''
# Bias subtract everything first
bluebias(image, biassec1=biassec1, trimsec1=trimsec1, biassec2=biassec2,
trimsec2=trimsec2)
bluebias(arcs, biassec1=biassec1, trimsec1=trimsec1, biassec2=biassec2,
trimsec2=trimsec2)
bluebias(flats, biassec1=biassec1, trimsec1=trimsec1, biassec2=biassec2,
trimsec2=trimsec2)
# Create and apply flat-field
for i in range(len(flats)):
flats[i]='j%s' % flats[i]
make_flat(flats, outflat, gain=gain, rdnoise=rdnoise)
iraf.ccdproc('j%s' % image[0], ccdtype='', noproc=no, fixpix=no,
overscan=no, trim=no, zerocor=no, darkcor=no, flatcor=yes,
illumcor=no, fringecor=no, readcor=no, scancor=no,
flat=outflat)
iraf.ccdproc('j%s' % arcs[0], ccdtype='', noproc=no, fixpix=no,
overscan=no, trim=no, zerocor=no, darkcor=no, flatcor=yes,
illumcor=no, fringecor=no, readcor=no, scancor=no,
flat=outflat)
# Extract spectrum of standard
if object==None:
object=get_head(image, 'OBJECT')
iraf.apall('j%s' % image[0], output=object, references='', interactive=yes,
find=yes, recenter=yes, resize=yes, edit=yes, trace=yes,
fittrace=yes, extract=yes, extras=yes, review=no,
background='fit', weights='variance', pfit='fit1d',
readnoise=rdnoise, gain=gain)
# Extract arc and fit wavelength solution
reference_arc('j%s' % arcs[0], arc, 'j%s' % image[0])
# Apply wavelength solution to standard
iraf.refspec(object, references=arc, sort="", group="", override=yes,
confirm=no, assign=yes)
iraf.dispcor(object, '%s.w' % object, confirm=no, listonly=no)
# Remove absorption features and smooth
iraf.splot('%s.w' % object, 1, 1)
iraf.gauss('temp1[*,1,1]', '%s.smooth' % object, 3.0)
iraf.sarith('%s.w' % object, '/', '%s.smooth' % object, '%s.s' % object)
# Define bandpasses for standard star calculation
iraf.standard('%s.s' % object, '%s.std' % object,
extinction='onedstds$kpnoextinct.dat', caldir=caldir,
observatory='Lick', interact=yes, star_name=object,
airmass='', exptime='')
# Determine sensitivity function
iraf.sensfunc('%s.std' % object, '%s.sens' % object,
extinction='onedstds$kpnoextinct.dat',
newextinction='extinct.dat', observatory='Lick',
function='legendre', order=3, interactive=yes)
return
def red_standard(image, arcs, flats, object=None, biassec=REDBIAS,
trimsec=REDTRIM, outflat='Flat-Red.fits', gain=REDGAIN,
rdnoise=REDRDNOISE, arc='Arc-Red.fits',
caldir='home$standards/'):
'''Reduce and calibrate standard star observation with red CCD'''
# Bias subtract everything first
redbias(image, biassec=biassec, trimsec=trimsec)
redbias(arcs, biassec=biassec, trimsec=trimsec)
redbias(flats, biassec=biassec, trimsec=trimsec)
# Create and apply flat-field
make_flat(flats, outflat, gain=gain, rdnoise=rdnoise)
iraf.ccdproc(image[0], ccdtype='', noproc=no, fixpix=no, overscan=no,
trim=no, zerocor=no, darkcor=no, flatcor=yes, illumcor=no,
fringecor=no, readcor=no, scancor=no, flat=outflat)
arcimages=','.join(arcs)
iraf.ccdproc(arcs, ccdtype='', noproc=no, fixpix=no, overscan=no,
trim=no, zerocor=no, darkcor=no, flatcor=yes, illumcor=no,
fringecor=no, readcor=no, scancor=no, flat=outflat)
# Extract spectrum of standard
if object==None:
object=get_head(image, 'OBJECT')
iraf.apall(image[0], output=object, references='', interactive=yes,
find=yes, recenter=yes, resize=yes, edit=yes, trace=yes,
fittrace=yes, extract=yes, extras=yes, review=no,
background='fit', weights='variance', pfit='fit1d',
readnoise=rdnoise, gain=gain)
# Extract arc and fit wavelength solution
iraf.imarith(arcs[0], '+', arcs[1], 'Arc-Sum.fits')
reference_arc('Arc-Sum.fits', arc, image[0])
# Apply wavelength solution to standard
iraf.refspec(object, references=arc, sort="", group="", override=yes,
confirm=no, assign=yes)
iraf.dispcor(object, '%s.w' % object, confirm=no, listonly=no)
# Remove absorption features and smooth
iraf.splot('%s.w' % object, 1, 1)
iraf.gauss('temp1[*,1,1]', '%s.smooth' % object, 3.0)
iraf.sarith('%s.w' % object, '/', '%s.smooth' % object, '%s.s' % object)
# Create and apply telluric correction
iraf.sarith('%s.w' % object, '/', 'temp1', 'telluric')
iraf.splot('telluric', 1, 1)
iraf.telluric('%s.s' % object, '%s.t' % object, 'telluric', xcorr=no,
tweakrms=no, interactive=no, sample='6850:6950,7575:7700')
# Define bandpasses for standard star calculation
iraf.standard('%s.t' % object, '%s.std' % object,
extinction='onedstds$kpnoextinct.dat', caldir=caldir,
observatory='Lick', interact=yes, star_name=object,
airmass='', exptime='')
# Determine sensitivity function
iraf.sensfunc('%s.std' % object, '%s.sens' % object,
extinction='onedstds$kpnoextinct.dat',
newextinction='extinct.dat', observatory='Lick',
function='legendre', order=3, interactive=yes)
return
def lris_extract(science, standards, dostandard=yes):
'''Extract and flux calibrate LRIS spectra (assuming they have been
processed into 2D images using LRIS_pipe above).'''
if dostandard:
lris_standard(standards)
for src in science:
bimages = iraffiles("%s_??_B.fits" % src)
rimages = iraffiles("%s_??_R.fits" % src)
joinstr = ""
for bimage in bimages:
bimage = bimage.split(".")[0]
# Find appropriate standard for this image
bstd = get_head("%s.fits" % bimage, "STDNAME")
# Extract 1D spectra
if get_head("%s.fits" % bimage, "SKYSUB"):
iraf.apall(bimage, output="", inter=yes, find=yes, recenter=yes,
resize=yes, edit=yes, trace=yes, fittrace=yes, extract=yes,
extras=yes, review=no, background="none",
reference=bstd)
else:
iraf.apall(bimage, output="", inter=yes, find=yes, recenter=yes,
resize=yes, edit=yes, trace=yes, fittrace=yes, extract=yes,
extras=yes, review=no, background="fit",
reference=bstd)
# Normalize by the standard continuua
iraf.sarith("%s.ms" % bimage, "/", "../standards/s%s.ms.fits" % bstd,
"s%s.ms" % bimage, w1=INDEF, w2=INDEF)
# Telluric correct
iraf.telluric("s%s.ms" % bimage, "ts%s.ms" % bimage,
"../standards/telluric.%s.fits" % bstd, tweakrms=yes,
interactive=yes, sample='6850:6950,7575:7700,8750:9925')
# Flux calibration
iraf.calibrate("ts%s.ms" % bimage, "fts%s.ms" % bimage, extinct=yes,
flux=yes, extinction="home$extinct/maunakeaextinct.dat",
observatory="Keck", sens="../standards/%s.sens" % bstd,
airmass='', exptime='')
joinstr += "fts%s.ms," % bimage
for rimage in rimages:
rimage = rimage.split(".")[0]
# Find appropriate standard for this image
rstd = get_head("%s.fits" % rimage, "STDNAME")
# Extract 1D spectra
if get_head("%s.fits" % rimage, "SKYSUB"):
iraf.apall(rimage, output="", inter=yes, find=yes, recenter=yes,
resize=yes, edit=yes, trace=yes, fittrace=yes, extract=yes,
extras=yes, review=no, background="none",
reference=rstd)
else:
iraf.apall(rimage, output="", inter=yes, find=yes, recenter=yes,
resize=yes, edit=yes, trace=yes, fittrace=yes, extract=yes,
extras=yes, review=no, background="fit",
reference=rstd)
# Normalize by the standard continuua
iraf.sarith("%s.ms" % rimage, "/", "../standards/s%s.ms.fits" % rstd,
"s%s.ms" % rimage, w1=5500, w2=INDEF)
# Telluric correct
iraf.telluric("s%s.ms" % rimage, "ts%s.ms" % rimage,
"../standards/telluric.%s.fits" % rstd, tweakrms=yes,
interactive=yes, sample='6850:6950,7575:7700')
# Flux calibration
iraf.calibrate("ts%s.ms" % rimage, "fts%s.ms" % rimage, extinct=yes,
flux=yes, extinction="home$extinct/maunakeaextinct.dat",
observatory="Keck", sens="../standards/%s.sens" % rstd,
airmass='', exptime='')
joinstr += "fts%s.ms," % rimage
# Combine
iraf.scombine(joinstr[:-1], "%s.ms.fits" % src, combine="average",
reject="avsigclip", w1=INDEF, w2=INDEF, dw=INDEF, nw=INDEF,
scale="median", zero="none", weight="none", sample="5450:5600",
lsigma=3.0, hsigma=3.0, gain=RCCDGAIN, rdnoise=RCCDRNOISE)
# Plot to enable final tweaks
iraf.splot("%s.ms.fits" % src)
return
def deimos_standard(standard):
'''Extract standard star and calculate sensitivit function.'''
bstd = "%s_01_B" % standard
rstd = "%s_01_R" % standard
# Extract standard
if get_head("%s.fits" % bstd, "SKYSUB"):
iraf.apall(bstd,
output="",
inter=yes,
find=yes,
recenter=yes,
resize=yes,
edit=yes,
trace=yes,
fittrace=yes,
extract=yes,
extras=yes,
review=no,
background="none")
iraf.apall(rstd,
output="",
inter=yes,
find=yes,
recenter=yes,
resize=yes,
edit=yes,
trace=yes,
fittrace=yes,
extract=yes,
extras=yes,
review=no,
background="none")
else:
iraf.apall(bstd,
output="",
inter=yes,
find=yes,
recenter=yes,
resize=yes,
edit=yes,
trace=yes,
fittrace=yes,
extract=yes,
extras=yes,
review=no,
background="fit")
iraf.apall(rstd,
output="",
inter=yes,
find=yes,
recenter=yes,
resize=yes,
edit=yes,
trace=yes,
fittrace=yes,
extract=yes,
extras=yes,
review=no,
background="fit")
# Fit the continuum
#iraf.continuum("%s.ms" % bstd, output="s%s.ms" % bstd, lines=1, bands=1,
# type="fit", sample="*", naverage=1, function="chebyshev",
# order=15, low_reject=3.0, high_reject=5.0, niterate=10, grow=1.0,
# interac=yes)
#iraf.continuum("%s.ms" % rstd, output="s%s.ms" % rstd, lines=1, bands=1,
# type="fit", sample="*", naverage=1, function="chebyshev",
# order=15, low_reject=3.0, high_reject=5.0, niterate=10, grow=1.0,
# interac=yes)
# Create telluric
iraf.splot("%s.ms" %
bstd) # Remove telluric and absorption, save as a%s.ms
iraf.sarith("%s.ms" % bstd, "/", "a%s.ms" % bstd,
"telluric.B.%s.fits" % bstd)
iraf.imreplace("telluric.B.%s.fits" % bstd, 1.0, lower=0.0, upper=0.0)
iraf.splot("telluric.B.%s.fits" %
bstd) # Remove stellar features and resave
iraf.splot("%s.ms" %
rstd) # Remove telluric and absorption, save as a%s.ms
iraf.sarith("%s.ms" % rstd, "/", "a%s.ms" % rstd,
"telluric.R.%s.fits" % rstd)
iraf.imreplace("telluric.R.%s.fits" % rstd, 1.0, lower=0.0, upper=0.0)
iraf.splot("telluric.R.%s.fits" %
rstd) # Remove stellar features and resave
# Create smoothed standard
iraf.gauss("a%s.ms[*,1,1]" % bstd, "s%s.ms" % bstd, 5.0)
iraf.sarith("%s.ms" % bstd, "/", "s%s.ms" % bstd, "ds%s.ms" % bstd)
iraf.gauss("a%s.ms[*,1,1]" % rstd, "s%s.ms" % rstd, 5.0)
iraf.sarith("%s.ms" % rstd, "/", "s%s.ms" % rstd, "ds%s.ms" % rstd)
# Divide through by smoothed standard
#iraf.sarith("%s.ms" % bstd, "/", "s%s.ms" % bstd, "ds%s.ms" % bstd)
#iraf.sarith("%s.ms" % rstd, "/", "s%s.ms" % rstd, "ds%s.ms" % rstd)
# Create and apply telluric correction
#iraf.splot("%s.ms" % bstd) # Remove telluric, save as a%s.ms
#iraf.splot("%s.ms" % rstd) # Remove telluric, save as a%s.ms
#iraf.sarith("%s.ms" % bstd, "/", "a%s.ms" % bstd, "telluric.B.fits")
#iraf.sarith("%s.ms" % rstd, "/", "a%s.ms" % rstd, "telluric.R.fits")
#iraf.imreplace("telluric.B.fits", 1.0, lower=0.0, upper=0.0)
#iraf.imreplace("telluric.R.fits", 1.0, lower=0.0, upper=0.0)
iraf.telluric("ds%s.ms" % bstd,
"tds%s.ms" % bstd,
"telluric.B.%s.fits" % bstd,
xcorr=no,
tweakrms=no,
interactive=no,
sample='6850:6950,7575:7700')
iraf.telluric("ds%s.ms" % rstd,
"tds%s.ms" % rstd,
"telluric.R.%s.fits" % rstd,
xcorr=no,
tweakrms=no,
interactive=no,
sample='6850:6950,7575:7700')
# Define bandpasses for standard star calculation
iraf.standard("tds%s.ms" % bstd,
"%s.B.std" % standard,
extinction='home$extinct/maunakeaextinct.dat',
caldir='home$standards/',
observatory='Keck',
interac=yes,
star_name=standard,
airmass='',
exptime='')
iraf.standard("tds%s.ms" % rstd,
"%s.R.std" % standard,
extinction='home$extinct/maunakeaextinct.dat',
caldir='home$standards/',
observatory='Keck',
interac=yes,
star_name=standard,
airmass='',
exptime='')
# Determine sensitivity function
iraf.sensfunc('%s.B.std' % standard,
'%s.B.sens' % standard,
extinction='home$extinct/maunakeaextinct.dat',
newextinction='extinct.dat',
observatory='Keck',
function='legendre',
order=4,
interactive=yes)
iraf.sensfunc('%s.R.std' % standard,
'%s.R.sens' % standard,
extinction='home$extinct/maunakeaextinct.dat',
newextinction='extinct.dat',
observatory='Keck',
function='legendre',
order=4,
interactive=yes)
return
def blue_science(image,
spath,
object=None,
flat='Flat-Blue.fits',
arc='Arc-Blue.fits',
smooth='BD284211.smooth.fits',
sens='BD284211.sens',
biassec1=BLUEBIAS1,
trimsec1=BLUETRIM1,
biassec2=BLUEBIAS2,
trimsec2=BLUETRIM2,
gain=BLUEGAIN,
rdnoise=BLUERDNOISE):
'''Full reduction of KAST science spectra on blue CCD'''
# Bias subtract everything first
bluebias(image,
biassec1=biassec1,
trimsec1=trimsec1,
biassec2=biassec2,
trimsec2=trimsec2)
# Apply flat-field
shutil.copy('%s/%s' % (spath, flat), '.')
iraf.ccdproc('j%s' % image[0],
ccdtype='',
noproc=no,
fixpix=no,
overscan=no,
trim=no,
zerocor=no,
darkcor=no,
flatcor=yes,
illumcor=no,
fringecor=no,
readcor=no,
scancor=no,
flat=flat)
# Cosmic ray rejection
#iraf.lacos_spec('j%s' % image[0], 'cj%s' % image[0], 'cmj%s' % image[0],
# gain=gain, readn=rdnoise, xorder=9, yorder=3,
# sigclip=4.5, sigfrac=0.5, objlim=1.0, niter=3)
# Extract spectrum
if object == None:
object = get_head(image, 'OBJECT')
iraf.apall('j%s' % image[0],
output=object,
references='',
interactive=yes,
find=yes,
recenter=yes,
resize=yes,
edit=yes,
trace=yes,
fittrace=yes,
extract=yes,
extras=yes,
review=no,
background='fit',
weights='variance',
pfit='fit1d',
readnoise=rdnoise,
gain=gain)
# Apply wavelength solution to standard
shutil.copy('%s/%s' % (spath, arc), '.')
shutil.copy('%s/database/id%s' % (spath, arc.rstrip('.fits')), 'database')
iraf.refspec(object,
references=arc,
sort="",
group="",
override=yes,
confirm=no,
assign=yes)
iraf.dispcor(object, '%s.w' % object, confirm=no, listonly=no)
# Smooth
shutil.copy('%s/%s' % (spath, smooth), '.')
iraf.sarith('%s.w' % object, '/', smooth, '%s.s' % object)
# Flux calibration
shutil.copy('%s/%s.0001.fits' % (spath, sens), '.')
iraf.calibrate('%s.s' % object,
'%s.f' % object,
extinct=yes,
flux=yes,
extinction='onedstds$kpnoextinct.dat',
observatory='Lick',
sensitivity=sens,
airmass='',
exptime='')
return
def deimos_extract(science, standard, dostandard=yes):
'''Extract and flux calibrate DEIMOS spectra (assuming they have been
processed into 2D images using deimos_pipe above).'''
if dostandard:
deimos_standard(standard)
for source in science:
images = iraffiles("%s_??_B.fits" % source)
joinstr = ""
for image in images:
bimage = image.split(".")[0]
rimage = bimage[:-1] + "R"
update_head(bimage, "FLUX_OBJ", standard)
update_head(rimage, "FLUX_OBJ", standard)
# Extract 1D spectra
if get_head("%s.fits" % bimage, "SKYSUB"):
iraf.apall(bimage,
output="",
inter=yes,
find=yes,
recenter=yes,
resize=yes,
edit=yes,
trace=yes,
fittrace=yes,
extract=yes,
extras=yes,
review=no,
background="none",
reference="%s_01_B" % standard)
iraf.apall(rimage,
output="",
inter=yes,
find=yes,
recenter=yes,
resize=yes,
edit=yes,
trace=yes,
fittrace=yes,
extract=yes,
extras=yes,
review=no,
background="none",
reference="%s_01_R" % standard)
else:
iraf.apall(bimage,
output="",
inter=yes,
find=yes,
recenter=yes,
resize=yes,
edit=yes,
trace=yes,
fittrace=yes,
extract=yes,
extras=yes,
review=no,
background="fit",
reference="%s_01_B" % standard)
iraf.apall(rimage,
output="",
inter=yes,
find=yes,
recenter=yes,
resize=yes,
edit=yes,
trace=yes,
fittrace=yes,
extract=yes,
extras=yes,
review=no,
background="fit",
reference="%s_01_R" % standard)
# Normalize by the standard continuua
iraf.sarith("%s.ms" % bimage, "/", "s%s_01_B.ms.fits" % standard,
"s%s.ms" % bimage)
iraf.sarith("%s.ms" % rimage, "/", "s%s_01_R.ms.fits" % standard,
"s%s.ms" % rimage)
# Telluric correct
bstd = "%s_01_B" % standard
rstd = "%s_01_R" % standard
iraf.telluric("s%s.ms" % bimage,
"ts%s.ms" % bimage,
"telluric.B.%s.fits" % bstd,
tweakrms=yes,
interactive=yes,
sample='6850:6950,7575:7700')
iraf.telluric("s%s.ms" % rimage,
"ts%s.ms" % rimage,
"telluric.R.%s.fits" % rstd,
tweakrms=yes,
interactive=yes,
sample='6850:6950,7575:7700')
# Flux calibration
iraf.calibrate("ts%s.ms" % bimage,
"fts%s.ms" % bimage,
extinct=yes,
flux=yes,
extinction="home$extinct/maunakeaextinct.dat",
observatory="Keck",
sensitivity="%s.B.sens" % standard,
airmass='',
exptime='')
iraf.calibrate("ts%s.ms" % rimage,
"fts%s.ms" % rimage,
extinct=yes,
flux=yes,
extinction="home$extinct/maunakeaextinct.dat",
observatory="Keck",
sensitivity="%s.R.sens" % standard,
airmass='',
exptime='')
joinstr += "fts%s.ms,fts%s.ms," % (bimage, rimage)
# Combine
iraf.scombine(joinstr[:-1],
"%s.ms.fits" % source,
combine="average",
reject="avsigclip",
w1=INDEF,
w2=INDEF,
dw=INDEF,
nw=INDEF,
scale="none",
zero="none",
weight="none",
lsigma=3.0,
hsigma=3.0,
gain=CCDGAIN,
rdnoise=CCDRNOISE)
# Plot to enable final tweaks
iraf.splot("%s.ms.fits" % source)
return
def iterate():
os.system("rm temp_norm.dat")
iraf.wspectext(
input = "temp_norm.fits",\
output = "temp_norm.dat",\
header = 0)
data_spec = transpose(loadtxt("temp_norm.dat"))
wave = arange(min(data_spec[0]),max(data_spec[0]),1)
data_flux = interpolate.splrep(data_spec[0],data_spec[1])
data_flux = interpolate.splev(wave,data_flux)
telluric_spec = transpose(loadtxt("telluric.dat"))
telluric_flux = interpolate.splrep(telluric_spec[0],telluric_spec[1])
telluric_flux = interpolate.splev(wave,telluric_flux)
### Loop through telluric scaling
telluric_scaling = []
rms_list = []
maxscale = 1.08
for scale in arange(0.0,maxscale,0.01):
scatter_list = []
for region in telluric_region_list:
temp_flux = []
temp_tel = []
for i in range(len(wave)):
if wave[i] > region[0] and wave[i] < region[1]:
temp_flux.append(data_flux[i])
temp_tel.append(telluric_flux[i])
if wave[i] > region[1]:
break
temp_flux = array(temp_flux)
temp_tel = array(temp_tel)
scatter = temp_flux / (temp_tel * scale + (1-scale))
# plt.plot(scatter)
# plt.show()
scatter_list.append(std(scatter))
telluric_scaling.append(scale)
rms_list.append(average(scatter_list))
telluric_scaling,rms_list = array(telluric_scaling),array(rms_list)
best_scale = find_min(telluric_scaling,rms_list)
if best_scale > maxscale:
best_scale = maxscale
if best_scale < 0:
best_scale = 0
print "scaling telluric by",best_scale
# plt.plot(telluric_scaling,rms_list)
# plt.show()
os.system("cp telluric.fits telluric_temp.fits")
iraf.sarith(
input1 = "telluric_temp.fits",\
op = "*",\
input2 = best_scale,\
output = "telluric_temp.fits",\
w1 = "INDEF",\
w2 = "INDEF",\
apertures = "",\
bands = "",\
beams = "",\
apmodulus = 0,\
reverse = 0,\
ignoreaps = 1,\
format = "multispec",\
renumber = 0,\
offset = 0,\
clobber = 1,\
merge = 0,\
rebin = 0,\
verbose = 0)
iraf.sarith(
input1 = "telluric_temp.fits",\
op = "+",\
input2 = 1-best_scale,\
output = "telluric_temp.fits",\
w1 = "INDEF",\
w2 = "INDEF",\
apertures = "",\
bands = "",\
beams = "",\
apmodulus = 0,\
reverse = 0,\
ignoreaps = 1,\
format = "multispec",\
renumber = 0,\
offset = 0,\
clobber = 1,\
merge = 0,\
rebin = 0,\
verbose = 0)
iraf.sarith(
input1 = "temp_spec.fits",\
op = "/",\
input2 = "telluric_temp.fits",\
output = "temp_spec",\
w1 = "INDEF",\
w2 = "INDEF",\
apertures = "",\
bands = "",\
beams = "",\
apmodulus = 0,\
reverse = 0,\
ignoreaps = 1,\
format = "multispec",\
renumber = 0,\
offset = 0,\
clobber = 1,\
merge = 0,\
rebin = 0,\
verbose = 0)
iraf.sarith(
input1 = "temp_norm.fits",\
op = "/",\
input2 = "telluric_temp.fits",\
output = "temp_norm",\
w1 = "INDEF",\
w2 = "INDEF",\
apertures = "",\
bands = "",\
beams = "",\
apmodulus = 0,\
reverse = 0,\
ignoreaps = 1,\
format = "multispec",\
renumber = 0,\
offset = 0,\
clobber = 1,\
merge = 0,\
rebin = 0,\
verbose = 0)
return best_scale
