def telluric(iname, oname, cal, dscale=0.0):
"""
call iraf command telluric.
if output file already exist, this function will delete the old one.
iname : input file name
type : string
oname : output file name
type : string
cal : calibration file name
type : string
"""
if os.path.isfile(oname):
print('remove file ' + oname)
os.remove(oname)
iraf.telluric(input=iname,
output=oname,
cal=cal,
ignoreaps='Yes',
xcorr='Yes',
tweakrms='Yes',
interactive='Yes',
sample='*',
threshold=0.0,
lag=10,
shift=0.0,
scale=1.0,
dshift=1.0,
dscale=dscale,
offset=1.0,
smooth=1,
cursor='',
airmass='',
answer='yes')
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 vega(spectrum, band, path, hlineinter, telluric_shift_scale_record, log, over, airmass=1.0):
"""
Use iraf.telluric to remove H lines from standard star, then remove
normalization added by telluric with iraf.imarith.
The extension for vega_ext.fits is specified from band (from header of
telluricfile.fits).
Args:
spectrum (string): filename from 'telluricfile'.
band: from telluricfile .fits header. Eg 'K', 'H', 'J'.
path: usually top directory with Nifty scripts.
hlineinter (boolean): Interactive H line fitting. Specified with -i at
command line. Default False.
airmass: from telluricfile .fits header.
telluric_shift_scale_record: "pointer" to telluric_hlines.txt.
log: path to logfile.
over (boolean): overwrite old files. Specified at command line.
"""
if band=='K':
ext = '1'
sample = "21537:21778"
scale = 0.8
if band=='H':
ext = '2'
sample = "16537:17259"
scale = 0.7
if band=='J':
ext = '3'
sample = "11508:13492"
scale = 0.885
if band=='Z':
ext = '4'
sample = "*"
scale = 0.8
if os.path.exists("tell_nolines.fits"):
if over:
os.remove("tell_nolines.fits")
tell_info = iraf.telluric(input=spectrum+"[1]", output='tell_nolines', cal= RUNTIME_DATA_PATH+'vega_ext.fits['+ext+']', xcorr='yes', tweakrms='yes', airmass=airmass, inter=hlineinter, sample=sample, threshold=0.1, lag=3, shift=0., dshift=0.05, scale=scale, dscale=0.05, offset=0., smooth=1, cursor='', mode='al', Stdout=1)
else:
logging.info("Output file exists and -over not set - skipping H line correction")
else:
tell_info = iraf.telluric(input=spectrum+"[1]", output='tell_nolines', cal= RUNTIME_DATA_PATH+'vega_ext.fits['+ext+']', xcorr='yes', tweakrms='yes', inter=hlineinter, airmass=airmass, sample=sample, threshold=0.1, lag=3, shift=0., dshift=0.05, scale=scale, dscale=0.05, offset=0., smooth=1, cursor='', mode='al', Stdout=1)
# need this loop to identify telluric output containing warning about pix outside calibration limits (different formatting)
if "limits" in tell_info[-1].split()[-1]:
norm=tell_info[-2].split()[-1]
else:
norm=tell_info[-1].split()[-1]
if os.path.exists("final_tel_no_hlines_no_norm.fits"):
if over:
os.remove("final_tel_no_hlines_no_norm.fits")
iraf.imarith(operand1='tell_nolines', op='/', operand2=norm, result='final_tel_no_hlines_no_norm', title='', divzero=0.0, hparams='', pixtype='', calctype='', verbose='yes', noact='no', mode='al')
else:
logging.info("Output file exists and -over not set - skipping H line normalization")
else:
iraf.imarith(operand1='tell_nolines', op='/', operand2=norm, result='final_tel_no_hlines_no_norm', title='', divzero=0.0, hparams='', pixtype='', calctype='', verbose='yes', noact='no', mode='al')
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 tell_corr(imgID):
#tell_rootname = '%s%04d' % (side, telluric_cal_id)
#tell_rootname = 'norm_red.std.fits'
#if not os.path.exists('norm_red.std.fits'):
#iraf.splot('red')
iraf.unlearn('telluric')
rootname = 'red%04d' % (imgID)
iraf.telluric.input = rootname + '_flux.spec.fits'
iraf.telluric.output = rootname + '_flux_cor.spec.fits'
iraf.telluric.sample = "6277:6288,6860:7000,7584:7678,9252:9842"
iraf.telluric.interactive = "yes"
iraf.telluric.cal = 'norm_red.std.fits'
iraf.telluric.ignoreaps = 'yes'
iraf.telluric.xcorr = 'yes'
iraf.telluric.tweakrms = 'yes'
iraf.telluric.threshold = 0.01
iraf.telluric()
def vega(rawFrame, grating, hLineInter, log, over):
"""
Use iraf.telluric to remove H lines from standard star, then remove
normalization added by telluric with iraf.imarith.
The extension for vega_ext.fits is specified from grating (from header of
telluricfile.fits).
Args:
"""
if grating == 'K':
ext = '1'
sample = "21537:21778"
scale = 0.8
elif grating == 'H':
ext = '2'
sample = "16537:17259"
scale = 0.7
elif grating == 'J':
ext = '3'
sample = "11508:13492"
scale = 0.885
elif grating == 'Z':
ext = '4'
sample = "*"
scale = 0.8
else:
logging.info(
"\nWARNING: invalid standard star band. Exiting this correction.")
return
if os.path.exists("1_htel" + rawFrame + ".fits"):
if over:
os.remove("1_htel" + rawFrame + ".fits")
iraf.chdir(os.getcwd())
tell_info = iraf.telluric(input="0_tel" + rawFrame + ".fits[1]",
output="1_htel" + rawFrame,
cal=RUNTIME_DATA_PATH +
'vega_ext.fits[' + ext + ']',
xcorr='yes',
tweakrms='yes',
airmass=1.0,
inter=hLineInter,
sample=sample,
threshold=0.1,
lag=3,
shift=0.,
dshift=0.05,
scale=scale,
dscale=0.05,
offset=0.,
smooth=1,
cursor='',
mode='al',
Stdout=1)
else:
logging.info(
"Output file exists and -over not set - skipping H line correction"
)
return
else:
iraf.chdir(os.getcwd())
tell_info = iraf.telluric(input="0_tel" + rawFrame + ".fits[1]",
output="1_htel" + rawFrame,
cal=RUNTIME_DATA_PATH + 'vega_ext.fits[' +
ext + ']',
xcorr='yes',
tweakrms='yes',
airmass=1.0,
inter=hLineInter,
sample=sample,
threshold=0.1,
lag=3,
shift=0.,
dshift=0.05,
scale=scale,
dscale=0.05,
offset=0.,
smooth=1,
cursor='',
mode='al',
Stdout=1)
# need this loop to identify telluric output containing warning about pix outside calibration limits (different formatting)
if "limits" in tell_info[-1].split()[-1]:
norm = tell_info[-2].split()[-1]
else:
norm = tell_info[-1].split()[-1]
if os.path.exists("final_tel_no_hLines_no_norm.fits"):
if over:
# Subtle bugs in iraf mean imarith doesn't work. So we use an astropy/numpy solution.
# Open the image and the scalar we will be dividing it by.
operand1 = astropy.io.fits.open("1_htel" + rawFrame +
'.fits')[0].data
operand2 = float(norm)
# Create a new data array
multiplied = np.array(operand1, copy=True)
# Don't forget to include the original header! If you don't later IRAF tasks get confused.
header = astropy.io.fits.open("1_htel" + rawFrame +
'.fits')[0].header
for i in range(len(multiplied)):
if operand2 != 0:
multiplied[i] = operand1[i] / operand2
else:
multiplied[i] = 1
# Set the data and header of the in-memory image
hdu = astropy.io.fits.PrimaryHDU(multiplied)
hdu.header = header
# Finally, write the new image to a new .fits file. It only has one extension; zero, with a header and data.
hdu.writeto('final_tel_no_hLines_no_norm.fits')
#iraf.imarith(operand1="1_htel" + rawFrame, op='/', operand2=norm, result='final_tel_no_hLines_no_norm', title='', divzero=0.0, hparams='', pixtype='', calctype='', verbose='yes', noact='no', mode='al')
else:
logging.info(
"Output file exists and -over not set - skipping H line normalization correction"
)
else:
#iraf.imarith(operand1="1_htel" + rawFrame, op='/', operand2=norm, result='final_tel_no_hLines_no_norm', title='', divzero=0.0, hparams='', pixtype='', calctype='', verbose='yes', noact='no', mode='al')
operand1 = astropy.io.fits.open("1_htel" + rawFrame + '.fits')[0].data
operand2 = float(norm)
multiplied = np.array(operand1, copy=True)
header = astropy.io.fits.open("1_htel" + rawFrame + '.fits')[0].header
for i in range(len(multiplied)):
if operand2 != 0:
multiplied[i] = operand1[i] / operand2
else:
multiplied[i] = 1
hdu = astropy.io.fits.PrimaryHDU(multiplied)
hdu.header = header
hdu.writeto('final_tel_no_hLines_no_norm.fits')
if os.path.exists('final_tel_no_hLines_no_norm.fits'):
os.remove("1_htel" + rawFrame + ".fits")
shutil.move('final_tel_no_hLines_no_norm.fits',
"1_htel" + rawFrame + ".fits")
def getShiftScale(rawFrame, telluricInter, log, over):
"""
Use iraf.telluric() to get the best shift and scale of a telluric correction spectrum.
Writes:
"6_shiftScale"+rawFrame+".txt" :
"""
if os.path.exists('5_oneDCorrected' + rawFrame +
'.fits') and os.path.exists("6_shiftScale" + rawFrame +
".txt"):
if over:
os.remove('5_oneDCorrected' + rawFrame + '.fits')
# TODO(nat): implement logging for this
iraf.chdir(os.getcwd())
tell_info = iraf.telluric(
input='4_cubeslice' + rawFrame + '.fits[0]',
output='5_oneDCorrected' + rawFrame + '.fits',
cal="3_chtel" + rawFrame + '.fits[0]',
airmass=1.0,
answer='yes',
ignoreaps='yes',
xcorr='yes',
tweakrms='yes',
inter=telluricInter,
sample="*",
threshold=0.1,
lag=3,
shift=0.,
dshift=0.1,
scale=1.0,
dscale=0.1,
offset=1,
smooth=1,
cursor='',
mode='al',
Stdout=1)
else:
logging.info(
"\nOutput exists and -over not set - skipping get shift scale of telluric correction and fit"
)
return
else:
iraf.chdir(os.getcwd())
tell_info = iraf.telluric(input='4_cubeslice' + rawFrame + '.fits[0]',
output='5_oneDCorrected' + rawFrame +
'.fits',
cal="3_chtel" + rawFrame + '.fits[0]',
airmass=1.0,
answer='yes',
ignoreaps='yes',
xcorr='yes',
tweakrms='yes',
inter=telluricInter,
sample="*",
threshold=0.1,
lag=3,
shift=0.,
dshift=0.1,
scale=1.0,
dscale=0.1,
offset=1,
smooth=1,
cursor='',
mode='al',
Stdout=1)
# Get shift and scale from the list of values iraf.telluric() returns.
# Sample tell_info:
# ['cubeslice.fits[0]: norm.fits[1]: cubeslice.fits[0]: dshift 5.', 'window:again:window:window:again:window:window:again:window:TELLURIC:',
# ' Output: vtella - HE1353-1917', ' Input: cubeslice.fits[0] - HE1353-1917', '
# Calibration: norm.fits[1] - Hip70765', ' Tweak: shift = 59.12, scale = 1.323,
# normalization = 0.9041', ' WARNING: 3 pixels outside of calibration limits']
tellshift = 0.
scale = 1.0
for i in range(len(tell_info)):
# Now string looks like ' Tweak: shift = 59.12, scale = 1.323, normalization = 0.9041'
if "Tweak" in tell_info[i]:
# Remove the first 9 characters,
temp = tell_info[i][9:]
# Split into a list; now it looks like '['shift', '=', '59.12,', 'scale', '=', '1.323,', 'normalization', '=', '0.9041']'
temp = temp.split()
# Index two is the shift value with a trailing comma, index 5 is the scale value with a trailing comma.
# Remove trailing comma.
tellshift = temp[2].replace(',', '')
# Turn it into a float.
tellshift = float(tellshift) # Convert to a clean float
# Do the same for the scale.
scale = temp[5].replace(',', '')
scale = float(scale)
with open("6_shiftScale" + rawFrame + ".txt", "w") as text_file:
text_file.write("Shift: {} Scale: {} \n".format(tellshift, scale))
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 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 telluric_correct_standard():
"""
Now do telluric correction on sensitivity corrected telluric spectrum,
as a check.
"""
if os.path.exists('tcdimcomb.ms.fits'):
os.remove('tcdimcomb.ms.fits')
print 'Removing file tcdimcomb.ms.fits'
# List of input spectra to correct
iraf.telluric.setParam('input', 'cdimcomb.ms.fits')
# List of output corrected spectra
iraf.telluric.setParam('output', 'tcdimcomb.ms.fits')
# List of telluric calibration spectra
iraf.telluric.setParam('cal', 'model_tell_spec.fits')
# Airmass - of telluric spectrum I think, in this case the same as cdimcomb.ms.fits
# should now read from header.
# hdulist = fits.open('cdimcomb.ms.fits')
# hdr = hdulist[0].header
# airmass = hdr['airmass']
# iraf.telluric.setParam('airmass', airmass)
# Search interactively?
iraf.telluric.setParam('answer', 'yes')
# Ignore aperture numbers in calibration spectra?
iraf.telluric.setParam('ignoreaps', 'yes')
# Cross correlate for shift?
iraf.telluric.setParam('xcorr', 'yes')
# Tweak to minimize RMS?
iraf.telluric.setParam('tweakrms', 'yes')
# Interactive tweaking?
iraf.telluric.setParam('interactive', 'yes')
# Sample ranges
# Don't fit bit between H and K
iraf.telluric.setParam('sample', '15000:18000,19700:23800')
# Threshold for calibration
iraf.telluric.setParam('threshold', 0.)
# Cross correlation lag (pixels)
iraf.telluric.setParam('lag', 10)
# Initial shift of calibration spectrum (pixels)
iraf.telluric.setParam('shift', 0.)
# Initial scale factor multiplying airmass ratio
iraf.telluric.setParam('scale', 1.)
# Initial shift search step
iraf.telluric.setParam('dshift', 5.)
# Initial scale factor search step
iraf.telluric.setParam('dscale', 0.2)
# Initial offset for graphs
iraf.telluric.setParam('offset', 1.)
# Smoothing box for graphs
iraf.telluric.setParam('smooth', 3)
iraf.telluric()
return None
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$extinct/maunakeaextinct.dat",
observatory="Keck",
sensitivity="%s.R.sens" % standard,
airmass='',
exptime='')
joinstr += "fts%s.ms,fts%s.ms," % (bimage, rimage)
# Combine
iraf.scombine(joinstr[:-1],
"%s.ms.fits" % source,
combine="average",
reject="avsigclip",
w1=INDEF,
w2=INDEF,
dw=INDEF,
nw=INDEF,
scale="none",
zero="none",
weight="none",
lsigma=3.0,
hsigma=3.0,
gain=CCDGAIN,
rdnoise=CCDRNOISE)
# Plot to enable final tweaks
iraf.splot("%s.ms.fits" % source)
return
def red_standard(image, arcs, flats, object=None, biassec=REDBIAS,
trimsec=REDTRIM, outflat='Flat-Red.fits', gain=REDGAIN,
rdnoise=REDRDNOISE, arc='Arc-Red.fits',
caldir='home$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 vega(spectrum, band, path, hlineinter, airmass, t1, log, over):
# Use "telluric" to remove H lines from standard star, then remove normalization added by telluric
# specify the extension for vega_ext.fits from the band
if band == 'K':
ext = '1'
if band == 'H':
ext = '2'
if band == 'J':
ext = '3'
if band == 'Z':
ext = '4'
if os.path.exists("tell_nolines" + band + ".fits"):
if over:
os.remove("tell_nolines" + band + ".fits")
tell_info = iraf.telluric(input=spectrum + "[1]",
output='tell_nolines' + band,
cal=sys.prefix + '/vega_ext.fits[' +
ext + ']',
answer='yes',
ignoreaps='yes',
xcorr='yes',
airmass=airmass,
tweakrms='yes',
inter=hlineinter,
threshold=0.1,
lag=3,
shift=0.,
dshift=0.05,
scale=.75,
dscale=0.05,
offset=0.,
smooth=1,
cursor='',
mode='al',
Stdout=1)
else:
print "Output file exists and -over not set - skipping H line correction"
else:
tell_info = iraf.telluric(input=spectrum + "[1]",
output='tell_nolines' + band,
cal=sys.prefix + '/vega_ext.fits[' + ext +
']',
answer='yes',
ignoreaps='yes',
xcorr='yes',
airmass=airmass,
tweakrms='yes',
inter=hlineinter,
threshold=0.1,
lag=3,
shift=0.,
dshift=0.05,
scale=1.,
dscale=0.05,
offset=0,
smooth=1,
cursor='',
mode='al',
Stdout=1)
# record shift and scale info for future reference
t1.write(str(tell_info) + '\n')
# need this loop to identify telluric output containing warning about pix outside calibration limits (different formatting)
if "limits" in tell_info[-1].split()[-1]:
norm = tell_info[-2].split()[-1]
else:
norm = tell_info[-1].split()[-1]
if os.path.exists("ftell_nolines" + band + ".fits"):
if over:
os.remove("ftell_nolines" + band + ".fits")
iraf.imarith(operand1='tell_nolines' + band,
op='/',
operand2=norm,
result='ftell_nolines' + band,
title='',
divzero=0.0,
hparams='',
pixtype='',
calctype='',
verbose='yes',
noact='no',
mode='al')
else:
print "Output file exists and -over not set - skipping H line normalization"
else:
iraf.imarith(operand1='tell_nolines' + band,
op='/',
operand2=norm,
result='ftell_nolines' + band,
title='',
divzero=0.0,
hparams='',
pixtype='',
calctype='',
verbose='yes',
noact='no',
mode='al')
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 telluric_corr_target():
"""
Remove telluric lines (badly!)
"""
if os.path.exists('tcdimcomb.ms.fits'):
os.remove('tcdimcomb.ms.fits')
print 'Removing file tcdimcomb.ms.fits'
# List of input spectra to correct
iraf.telluric.setParam('input', 'cdimcomb.ms.fits')
# List of output corrected spectra
iraf.telluric.setParam('output', 'tcdimcomb.ms.fits')
# List of telluric calibration spectra
iraf.telluric.setParam('cal', 'model_tell_spec.fits')
# Airmass - of telluric spectrum I think, should read from header of model_tell_spec.fits
# iraf.telluric.setParam('airmass', airmass)
# Search interactively?
iraf.telluric.setParam('answer', 'yes')
# Ignore aperture numbers in calibration spectra?
iraf.telluric.setParam('ignoreaps', 'yes')
# Cross correlate for shift?
iraf.telluric.setParam('xcorr', 'yes')
# Tweak to minimize RMS?
iraf.telluric.setParam('tweakrms', 'yes')
# Interactive tweaking?
iraf.telluric.setParam('interactive', 'yes')
# Sample ranges
# Don't fit bit between H and K
iraf.telluric.setParam('sample', '15000:18000,19700:23800')
# Threshold for calibration
iraf.telluric.setParam('threshold', 0.)
# Cross correlation lag (pixels)
iraf.telluric.setParam('lag', 10)
# Initial shift of calibration spectrum (pixels)
iraf.telluric.setParam('shift', 0.)
# Initial scale factor multiplying airmass ratio
iraf.telluric.setParam('scale', 1.)
# Initial shift search step
iraf.telluric.setParam('dshift', 5.)
# Initial scale factor search step
iraf.telluric.setParam('dscale', 0.2)
# Initial offset for graphs
iraf.telluric.setParam('offset', 1.)
# Smoothing box for graphs
iraf.telluric.setParam('smooth', 3)
iraf.telluric()
return None
def telluric_correction(targetdir,telluricdir,stype):
"""
Removes telluric lines from 1D spectrum
Assumes both science and telluric spectrum have been extracted and
wavelength calibrated, i.e. file dimcomb.ms.fits exists in telluric
directory.
"""
print 'Target directory is ' + targetdir
if os.path.exists( os.path.join(targetdir,'dimcomb.ms.fits') ):
print "Wavelength calibrated target spectrum 'dimcomb.ms.fits' exists"
print 'Telluric directory is ' + telluricdir
if os.path.exists( os.path.join(telluricdir,'dimcomb.ms.fits') ):
print "Wavelength calibrated telluric spectrum 'dimcomb.ms.fits' exists"
print 'Generating black-body spectrum...'
print 'Telluric star type ' + stype
# from this site http://www.gemini.edu/sciops/instruments/nir/photometry/temps_colors.txt
if stype == 'A0V': bbtemp = 9480.0
if stype == 'A1V': bbtemp = 9230.0
if stype == 'A2V': bbtemp = 8810.0
if stype == 'A3V': bbtemp = 8270.0
if stype == 'A4V': bbtemp = 8200.0
if stype == 'A5V': bbtemp = 8160.0
print 'Fitting with blackbody, temperature = ' + str(bbtemp) + 'K'
iraf.noao(_doprint=0)
iraf.artdata (_doprint=0)
if os.path.exists( os.path.join(telluricdir,'blackbody.fits') ):
os.remove( os.path.join(telluricdir,'blackbody.fits') )
iraf.mk1dspec.setParam('input', os.path.join(telluricdir,'blackbody.fits') )
iraf.mk1dspec.setParam('title','blackbody')
iraf.mk1dspec.setParam('ncols',1024)
iraf.mk1dspec.setParam('wstart',13900)
iraf.mk1dspec.setParam('wend',24000)
iraf.mk1dspec.setParam('temperature',bbtemp)
iraf.mk1dspec()
print 'Generated blackbody spectrum'
# Divide telluric star spectrum by black-body
if os.path.exists( os.path.join(telluricdir,'tdimcomb.ms.fits') ):
os.remove( os.path.join(telluricdir,'tdimcomb.ms.fits') )
iraf.onedspec(_doprint=0)
"""
To divide by blackbody I want to turn off the cross-correlation - which I
think would only work if both spectra had similar features. I don't want to scale
the spectrum - which scales the airmass using Beer's Law - or shift it. If the temperature
is correct I should be able to simply divide. If not then I should change
the temperature
"""
iraf.telluric.setParam('input',os.path.join(telluricdir,'dimcomb.ms.fits') ) # List of input spectra to correct
iraf.telluric.setParam('output',os.path.join(telluricdir,'tdimcomb.ms.fits') ) # List of output corrected spectra
iraf.telluric.setParam('cal',os.path.join(telluricdir,'blackbody.fits') ) # List of telluric calibration spectra
iraf.telluric.setParam('answer','yes') # Search interactively?
iraf.telluric.setParam('xcorr', 'no') # Cross correlate for shift?
iraf.telluric.setParam('tweakrms', 'no') # Twak to minise rms?
iraf.telluric.setParam('interactive', 'yes') # Interactive?
iraf.telluric.setParam('threshold',0.0) # Threshold for calibration
iraf.telluric.setParam('offset',1) # Displayed offset between spectra
iraf.telluric.setParam('sample','15000:18000,19700:23800')
iraf.telluric.setParam('dshift',5.0)
iraf.telluric.setParam('smooth',3.0)
iraf.telluric()
"""
When your calibration spectrum has zero or negative intensity values,
you have to set the "threshold" parameter accordingly. As explained in
the help page for the TELLURIC task, you can think of the "threshold"
value as the minimum intensity value TELLURIC will accept from your
calibration spectra. Any intensity value lower than the threshold value
will be replaced by the threshold.
"""
"""
I've turned cross-correlation off, since I don't really understand it.
Tweak is on, but doesn't seem to do that much. Still not sure if it's understanding
the airmass
"""
print 'Now correcting target spectrum...'
if os.path.exists( os.path.join(targetdir,'tdimcomb+bkgd.ms.fits') ):
os.remove( os.path.join(targetdir,'tdimcomb+bkgd.ms.fits') )
iraf.telluric.setParam('input',os.path.join(targetdir,'dimcomb+bkgd.ms.fits') ) # List of input spectra to correct
iraf.telluric.setParam('output',os.path.join(targetdir,'tdimcomb+bkgd.ms.fits') ) # List of output corrected spectra
iraf.telluric.setParam('cal',os.path.join(telluricdir,'tdimcomb.ms.fits') ) # List of telluric calibration spectra
iraf.telluric.setParam('answer','yes') # Search interactively?
iraf.telluric.setParam('threshold',0.0)
iraf.telluric.setParam('xcorr', 'no') # Cross correlate for shift?
iraf.telluric.setParam('tweakrms', 'yes') # Tweak to minise rms?
iraf.telluric.setParam('interactive', 'yes') # Interactive?
iraf.telluric.setParam('offset',6) # Displayed offset between spectra
hdulist = fits.open(os.path.join(targetdir,'imcomb.ms.fits'))
hdr = hdulist[0].header
hdulist.close()
iraf.telluric.setParam('airmass',hdr['AIRMASS'])
iraf.telluric()
return None
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 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$extinct/maunakeaextinct.dat',
newextinction='extinct.dat',
observatory='Keck',
function='legendre',
order=4,
interactive=yes)
return
def red_standard(image,
arcs,
flats,
object=None,
biassec=REDBIAS,
trimsec=REDTRIM,
outflat='Flat-Red.fits',
gain=REDGAIN,
rdnoise=REDRDNOISE,
arc='Arc-Red.fits',
caldir='home$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