def calibrate(spec_in, spec_out, data_path='.', sens_prefix='sens', params={}):
"""
Run iraf calibrate to flux calibrate input spectrum.
Parameters
----------
spec_in : str
Input spectrum file name.
spec_out : str
Output spectrum file name.
data_path : str
Directory that contains the data.
sens_prefix : str
Sensitivity correction file name prefix.
params : dict
Iraf calibrate parameters.
"""
_check_working_dir(data_path)
logger.info('running iraf calibrate')
iraf.calibrate.unlearn()
iraf.calibrate.extinct = params.pop('extinct', 'no')
iraf.calibrate.flux = params.pop('flux', 'yes')
iraf.calibrate.extinction = params.pop('extinction', '')
iraf.calibrate.ignoreaps = params.pop('ignoreaps', 'yes')
iraf.calibrate.sensitivity = params.pop('sensitivity', sens_prefix)
iraf.calibrate.fnu = params.pop('fnu', 'no')
iraf.calibrate(input=spec_in, output=spec_out)
def calibrate(namelst):
iraf.noao()
iraf.twodspec()
iraf.longslit(dispaxis=2,
nsum=1,
observatory='ca',
extinction=extpath,
caldir=stdpath)
for fitname in namelst:
outname = 'mark_' + fitname
if os.path.isfile(outname):
print('remove file ' + outname)
os.remove(outname)
iraf.calibrate(input=fitname,
output=outname,
extinct='yes',
flux='yes',
extinction=extpath,
ignoreaps='yes',
sensitivity='Sens',
fnu='no')
iraf.splot(images=outname)
iraf.flpr()
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$kpnoextinct.dat',
observatory='Lick', sensitivity=sens, airmass='',
exptime='')
return
def blue_science(image, spath, object=None, flat='Flat-Blue.fits',
arc='Arc-Blue.fits', smooth='BD284211.smooth.fits',
sens='BD284211.sens', biassec1=BLUEBIAS1, trimsec1=BLUETRIM1,
biassec2=BLUEBIAS2, trimsec2=BLUETRIM2, gain=BLUEGAIN,
rdnoise=BLUERDNOISE):
'''Full reduction of KAST science spectra on blue CCD'''
# Bias subtract everything first
bluebias(image, biassec1=biassec1, trimsec1=trimsec1, biassec2=biassec2,
trimsec2=trimsec2)
# Apply flat-field
shutil.copy('%s/%s' % (spath, flat), '.')
iraf.ccdproc('j%s' % image[0], ccdtype='', noproc=no, fixpix=no,
overscan=no, trim=no, zerocor=no, darkcor=no, flatcor=yes,
illumcor=no, fringecor=no, readcor=no, scancor=no,
flat=flat)
# Cosmic ray rejection
#iraf.lacos_spec('j%s' % image[0], 'cj%s' % image[0], 'cmj%s' % image[0],
# gain=gain, readn=rdnoise, xorder=9, yorder=3,
# sigclip=4.5, sigfrac=0.5, objlim=1.0, niter=3)
# Extract spectrum
if object==None:
object=get_head(image, 'OBJECT')
iraf.apall('j%s' % image[0], output=object, references='',
interactive=yes, find=yes, recenter=yes, resize=yes, edit=yes,
trace=yes, fittrace=yes, extract=yes, extras=yes, review=no,
background='fit', weights='variance', pfit='fit1d',
readnoise=rdnoise, gain=gain)
# Apply wavelength solution to standard
shutil.copy('%s/%s' % (spath, arc), '.')
shutil.copy('%s/database/id%s' % (spath, arc.rstrip('.fits')), 'database')
iraf.refspec(object, references=arc, sort="", group="", override=yes,
confirm=no, assign=yes)
iraf.dispcor(object, '%s.w' % object, confirm=no, listonly=no)
# Smooth
shutil.copy('%s/%s' % (spath, smooth), '.')
iraf.sarith('%s.w' % object, '/', smooth, '%s.s' % object)
# Flux calibration
shutil.copy('%s/%s.0001.fits' % (spath, sens), '.')
iraf.calibrate('%s.s' % object, '%s.f' % object, extinct=yes, flux=yes,
extinction='onedstds$kpnoextinct.dat',
observatory='Lick', sensitivity=sens, airmass='',
exptime='')
return
def calibrate():
scilist = glob.glob('AGN*LF.fits')
for f in scilist:
os.remove(f)
scired = glob.glob('AGN*EL.fits')
extinct = 'extinction_lasilla.dat'
observ = 'paranal'
for spec in scired:
hdo = pyfits.getheader(spec)
_airmass = np.average([hdo['HIERARCH ESO TEL AIRM START'],hdo['HIERARCH ESO TEL AIRM END']])
_exptime = hdo['EXPTIME']
name = spec.rsplit('_EL',1)[0]+'_LF'
iraf.calibrate(spec,name,extinction=extinct,observatory=observ,airmass=_airmass,exptime=_exptime)
def calibrate_err(mefile):
'''Apply a sensitivity function to a linearized multispectrum file.
The error is propagated simply by dividing it by the sensitivity
function. This makes the assumption that there is no error in the
sensitivity function itself.
'''
outputname = mefile.replace('me_', 'me_rf_')
iraf.calibrate(mefile,
outputname,
extinct=False,
flux=True,
ignoreap=True,
sensiti='sens',
fnu=False)
return outputname
def calibrate_err(mefile):
'''Apply a sensitivity function to a linearized multispectrum file.
The error is propagated simply by dividing it by the sensitivity
function. This makes the assumption that there is no error in the
sensitivity function itself.
'''
outputname = mefile.replace('me_','me_rf_')
iraf.calibrate(mefile,
outputname,
extinct=False,
flux=True,
ignoreap=True,
sensiti='sens',
fnu=False)
return outputname
def calibrate():
namelst = [i.split('\n')[0] for i in file(targetoutput)]
for i in namelst:
iraf.twodspec()
iraf.longslit(dispaxis=2,
nsum=1,
observatory='Lijiang',
extinction='onedstds$LJextinct.dat',
caldir='onedstds$ctiocal/')
iraf.calibrate(input=i,
output=i.split('.')[0] + 'f.fits',
extinct='yes',
flux='yes',
extinction='onedstds$LJextinct.dat',
ignoreaps='yes',
sensitivity='sens',
fnu='no')
def calibrate(lstfile):
stdpath = os.path.split(os.path.realpath(__file__))[0] + os.sep + 'standarddir' + os.sep
extpath = os.path.split(os.path.realpath(__file__))[0] + os.sep + 'LJextinct.dat'
iraf.noao()
iraf.twodspec()
iraf.longslit(dispaxis = 2, nsum = 1, observatory = 'Lijiang',
extinction = extpath, caldir = stdpath)
f = open(lstfile)
l = f.readlines()
f.close()
l = [tmp.split('\n')[0] for tmp in l]
for fitname in l:
stdobjname = select_std(fitname)
stdfitname = 'sensawftbo' + stdgroup[stdobjname][0]
iraf.calibrate(input = 'awftbo'+ fitname, output = 'mark_awftbo' + fitname,
extinct = 'yes', flux = 'yes', extinction = extpath,
ignoreaps = 'yes', sensitivity = stdfitname, fnu = 'no')
iraf.splot(images = 'mark_awftbo' + fitname)
def iraf_standard(directory, objecto, sensfile):
'''
Do the flux calibration on the targets in the directory using the
sensfile
Parameters
-------------
directory: Directory where all the science files are located.
i.e. Objectname/Science
objecto: Name of the object in the directory to flux calibrate
sensfile: Full name of the sensfile to calibrate the data
Output
-------------
Flux calibrated data
'''
# Check that the files don't exist
if check_existence("%s/%s*OutWaveStd.fits" % (directory, objecto),
'iraf_standard'):
return
# Create file suffix
suffix = sensfile[5:-5]
# For each of the science targets, correct the flux
list_of_objects = glob.glob('%s/%s*BiasFlatSkyOutWave.fits' %
(directory, objecto))
for file_name in list_of_objects:
calibrate(
input=file_name, # Input spectra to calibrate
output=file_name[:-5] +
"Std_%s.fits" % suffix, # Output calibrated spectra
extinct='no', # Apply extinction correction
flux='yes', # Apply flux calibration
extinction='', # Extinction file
observatory=')_.observatory', # Observatory for data
ignoreaps='yes', # Ignore aperture numbers in flux calibration
sensitivity=sensfile, # Image root name for sensitivity spectra.
fnu='no', # Create spectra having units of FNU?
airmass='', #
exptime='', #
mode='ql' # IRAF mode
)
def sens_corr_standard():
"""
Check this has worked by correcting stanard for wavelength-dependent sensitivity
"""
if os.path.exists('cdimcomb.ms.fits'):
os.remove('cdimcomb.ms.fits')
print 'Removing file cdimcomb.ms.fits'
iraf.calibrate.unlearn()
# Input spectra to calibrate. Output should have 'c' prefixed.
iraf.calibrate.setParam('input','dimcomb.ms.fits[1]')
iraf.calibrate.setParam('output','cdimcomb.ms.fits')
# Should be found automatically from header - check this for target spectrum.
iraf.calibrate.setParam('airmass','')
iraf.calibrate.setParam('exptime','')
# Apply extinction correction? Not sure what this does
iraf.calibrate.setParam('extinct','no')
# Apply flux calibration?
iraf.calibrate.setParam('flux','yes')
# Extinction file
iraf.calibrate.setParam('extinction','')
# Ignore aperture numbers in flux calibration? Maybe this should be yes
iraf.calibrate.setParam('ignoreaps','yes')
# Image root name for sensitivity spectra
iraf.calibrate.setParam('sensitivity','sens.fits')
# Create spectra having units of FNU?
iraf.calibrate.setParam('fnu','no')
iraf.calibrate()
return None
def calibrate(imlist_name, obs):
"""
calibrate -- Apply extinction corrections and flux calibrations
calibrate input output [records]
"""
import glob
import os, sys
from pyraf import iraf
iraf.noao()
iraf.onedspec()
imlist = glob.glob(imlist_name)
imlist.sort()
for i in range(len(imlist)):
inim = imlist[i]
#iraf.calibrate(input=inim , output='s'+inim, extinct='/iraf/iraf/noao/lib/onedstds/ctioextinct.dat', flux='yes', observatory=obs)
iraf.calibrate(input=inim,
output='s' + inim,
extinct='yes',
flux='yes',
observatory=obs)
def flux_cal_new(objname, stdobjnames):
print 'run flux_cal...'
iraf.imred()
iraf.kpnoslit()
stdname, stdmag, stdmagband = get_std_name(stdobjnames[0])
print 'the standard star is ' + stdname
stdmag = float(stdmag)
stdairmass, stdexptime = get_fits_airmass_exptime(stdobjnames[0])
scripath = sys.argv[0]
tempindex = scripath.rfind(os.sep)
scripath = scripath[:tempindex]
extpath = scripath + os.sep + 'LJextinct.dat'
calpath = scripath + os.sep + 'standarddir' + os.sep
outname1 = 'std' + stdobjnames[0]
stdobjname = ''
for tempstdname in stdobjnames:
stdobjname = stdobjname + tempstdname + ','
stdobjname = stdobjname[:-1]
if os.path.isfile(outname1):
print 'file %s is already exist' % outname1
else:
print 'run standard...'
print 'make file %s ...' % outname1
iraf.standard(input = stdobjname
, output = outname1, samestar = True, beam_switch = False
, apertures = '', bandwidth = 30.0, bandsep = 20.0
, fnuzero = 3.6800000000000E-20, extinction = extpath
, caldir = calpath, observatory = ')_.observatory'
, interact = True, graphics = 'stdgraph', cursor = ''
, star_name = stdname, airmass = stdairmass, exptime = stdexptime
, mag = stdmag, magband = stdmagband, teff = '', answer = 'yes')
outname2 = 'sens' + stdobjname
if os.path.isfile(outname2):
print 'file %s is already exist' % outname2
else:
print 'run sensfunc...'
print 'make file %s ...' % outname2
iraf.sensfunc(standards = outname1
, sensitivity = outname2, apertures = '', ignoreaps = True
, logfile = 'logfile', extinction = ')_.extinction'
, newextinction = extpath, observatory = 'bao', function = 'spline3'
, order = 6, interactive = True, graphs = 'sr'
, marks = 'plus cross box', colors = '2 1 3 4', cursor =''
, device = 'stdgraph', answer = 'yes')
outname3 = 'c' + objname
if os.path.isfile(outname3):
print 'file %s is already exist' % outname3
else:
print 'run calibrate...'
print 'make file %s ...' % outname3
iraf.calibrate(input = objname
, output = outname3, extinct = True, flux = True
, extinction = extpath, observatory = 'bao', ignoreaps = True
, sensitivity = outname2, fnu = False)
final_outname = 'mark_' + objname
if os.path.isfile(final_outname):
print 'file %s is already exist'
else:
print 'run scopy'
print 'make file %s ...' % final_outname
iraf.scopy(input = outname3
, output = final_outname, w1 = 'INDEF', w2 = 'INDEF'
, apertures = '', bands = 1, beams = '', apmodulus = 0
, format = 'multispec', renumber = False, offset = 0
, clobber = False, merge = False, rebin = True, verbose = False)
print 'splot %s' % final_outname
iraf.splot(images = final_outname)
return final_outname
mode = "al")
### Apply calibration to file_name
hdulist = pyfits.open("smoothdiv_" + file_name)
air_mass = hdulist[0].header['AIRMASS']
exposure_time = hdulist[0].header['EXPTIME']
os.system("rm fluxcal_" + file_name )
iraf.calibrate(
input = "smoothdiv_" + file_name,\
output = "fluxcal_" + file_name,\
airmass = air_mass,\
exptime = exposure_time,\
extinct = 1,\
flux = 1,\
extinction = program_dir + "flux_data/extinsso.tab",\
observatory = "SSO",\
ignoreaps = 1,\
sensitivity = "sens",\
fnu = 0,\
mode = "al")
### Apply high/low rejection again to remove cosmic rays
os.system("rm temp.fits")
iraf.continuum(
input = "fluxcal_"+ file_name,\
output = "temp.fits",\
ask = "no",\
lines = "*",\
bands = "*",\
iraf.sensfunc(standard="std",
sensitiv="sens",
apertures="",
ignoreaps="no",
logfile="logfile",
extinction="/home/aries/Music/Atsoa2018/iao_extinction.dat",
newextinctio="extinct.dat",
observatory=" ",
function="spline3",
order=6,
interactive="yes",
graphs="sr",
marks="plus cross box",
colors="2 1 3 4",
cursor="",
device="stdgraph",
answer="yes")
iraf.calibrate(
input="J105829_250_3500_4_Grism_7_2015_06_17_yf170018apbfcw.fits",
output="J105829_250_3500_4_Grism_7_2015_06_17_yf170018apbfcwf.fits",
extinct="yes",
flux="yes",
extinction="/home/aries/Music/Atsoa2018/iao_extinction.dat",
observatory=" ",
ignoreaps="yes",
sensitivity="sens",
fnu="no",
airmass=2.3,
exptime=2700)
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_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$extinct/maunakeaextinct.dat",
observatory="Keck", sensitivity="%s.R.sens" % standard,
airmass='', exptime='')
joinstr += "fts%s.ms,fts%s.ms," % (bimage, rimage)
# Combine
iraf.scombine(joinstr[:-1], "%s.ms.fits" % source, combine="average",
reject="avsigclip", w1=INDEF, w2=INDEF, dw=INDEF, nw=INDEF,
scale="none", zero="none", weight="none", lsigma=3.0,
hsigma=3.0, gain=CCDGAIN, rdnoise=CCDRNOISE)
# Plot to enable final tweaks
iraf.splot("%s.ms.fits" % source)
return
def lris_extract(science, standards, dostandard=yes):
'''Extract and flux calibrate LRIS spectra (assuming they have been
processed into 2D images using LRIS_pipe above).'''
if dostandard:
lris_standard(standards)
for src in science:
bimages = iraffiles("%s_??_B.fits" % src)
rimages = iraffiles("%s_??_R.fits" % src)
joinstr = ""
for bimage in bimages:
bimage = bimage.split(".")[0]
# Find appropriate standard for this image
bstd = get_head("%s.fits" % bimage, "STDNAME")
# Extract 1D spectra
if get_head("%s.fits" % bimage, "SKYSUB"):
iraf.apall(bimage,
output="",
inter=yes,
find=yes,
recenter=yes,
resize=yes,
edit=yes,
trace=yes,
fittrace=yes,
extract=yes,
extras=yes,
review=no,
background="none",
reference=bstd)
else:
iraf.apall(bimage,
output="",
inter=yes,
find=yes,
recenter=yes,
resize=yes,
edit=yes,
trace=yes,
fittrace=yes,
extract=yes,
extras=yes,
review=no,
background="fit",
reference=bstd)
# Normalize by the standard continuua
iraf.sarith("%s.ms" % bimage,
"/",
"../standards/s%s.ms.fits" % bstd,
"s%s.ms" % bimage,
w1=INDEF,
w2=INDEF)
# Telluric correct
iraf.telluric("s%s.ms" % bimage,
"ts%s.ms" % bimage,
"../standards/telluric.%s.fits" % bstd,
tweakrms=yes,
interactive=yes,
sample='6850:6950,7575:7700,8750:9925')
# Flux calibration
iraf.calibrate("ts%s.ms" % bimage,
"fts%s.ms" % bimage,
extinct=yes,
flux=yes,
extinction="home$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 sens_corr_target():
"""
Take out wavelength-dependent sensitivity
"""
if not os.path.exists('sens.fits'):
print 'need file sens.fits'
if not os.path.exists('model_tell_spec.fits'):
print 'need file model_tell_spec.fits'
if os.path.exists('cdimcomb.ms.fits'):
os.remove('cdimcomb.ms.fits')
print 'Removing file cdimcomb.ms.fits'
"""
for some reason dimcomb+bkgd doesn't have much in its fits header,
so we need to add these keys words
"""
# hdulist = fits.open('dimcomb.ms.fits')
# airmass = hdulist[0].header['airmass']
# exptime = float(hdulist[0].header['ncombine']) * 60.0
# hdulist = fits.open('dimcomb.ms.fits', mode='update')
# hdulist[0].header['airmass'] = airmass
# hdulist[0].header['exptime'] = exptime
# hdulist.flush()
iraf.calibrate.unlearn()
# Input spectra to calibrate. Output should have 'c' prefixed.
iraf.calibrate.setParam('input','dimcomb.ms.fits') # might need to specify extension.
iraf.calibrate.setParam('output','cdimcomb.ms.fits')
# Should be found automatically from header - check this for target spectrum.
iraf.calibrate.setParam('airmass','')
iraf.calibrate.setParam('exptime','')
# Apply extinction correction? Not sure what this does
iraf.calibrate.setParam('extinct','no')
# Apply flux calibration?
iraf.calibrate.setParam('flux','yes')
# Extinction file
iraf.calibrate.setParam('extinction','')
# Ignore aperture numbers in flux calibration? Maybe this should be yes
iraf.calibrate.setParam('ignoreaps','yes')
# Image root name for sensitivity spectra
iraf.calibrate.setParam('sensitivity','sens.fits')
# Create spectra having units of FNU?
iraf.calibrate.setParam('fnu','no')
iraf.calibrate()
return None
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
print('\n' + 'Combining spectra...')
iraf.scombine(input='@speclist',
output='allspec',
group='all',
combine='median',
gain=2.45,
reject='crreject',
lthresh=1e-30,
hthresh=hthresh2)
print('\n' + 'Applying flux calibration to sensitivity function...')
iraf.calibrate(
'@speclist',
'allspeccal',
obs='lapalma',
sens=sensfile,
extinct='no',
ignoreaps='yes'
) ## If extinct='yes', try extinction ='onedstds$ctioextinct.dat'
print('\n' +
'Extracting the 1D spectra from the calibrated multispec file...')
iraf.scopy('allspeccal[0]',
'allspeccal2',
format='onedspec',
w1=4000,
w2=8000,
rebin='no')
print('\n' + '1D spectrum output...')
iraf.wspectext('allspeccal2.0001', obj + '_' + date + '.txt', header='no')
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
iraf.hedit(file,fields="REFSPEC1",value="arc1.ms",add='yes',ver='no',show='yes')
#wavelength calinration
for file in os.listdir(os.getcwd()):
if file.endswith('ms.fits'):
iraf.dispcor(file, 'd'+file)
#flux calibration
shutil.copy('./stds/sens.0001.fits','.')
shutil.copy('./stds/lapalmaextinct.dat','.')
for file in os.listdir(os.getcwd()):
if file.startswith('dspec'):
iraf.calibrate(file, 'f'+file)
#combine spectra
finalcomb = []
for file in os.listdir(os.getcwd()):
if file.startswith('fds'):
finalcomb.append(file)
file1 = open('listascombine', 'w')
file1.writelines(["%s\n" % item for item in finalcomb])
file1.close()
iraf.scombine('@listascombine', 'temp_quick.fits')
iraf.scopy('temp_quick.fits',target+'_quick.fits',w1='4000',w2='9000')
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
