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
os.system("rm "+extracted_filename+" "+calibrated_filename)
# Run the spectral extraction program.
iraf.apextract.setParam("dispaxis", "1")
iraf.apall(input=filename, find="No", recenter="No", resize="No",interactive="Yes")
# Make sure that the dispersion axis is in the header.
iraf.hedit(images=[filename], fields=["DISPAXIS"], value=["1"], add="Yes")
iraf.identify(filename[:-5], coordli=home+"/Downloads/HgNe(1).dat",
section="line 105 125",
crval=crval,
cdelt=dispersion,
fwidth=5)
# Tell the extracted spectrum what the wavelength solutions are.
iraf.hedit(images=[extracted_filename],
fields=["REFSPEC1"], \
value=[filename], add="Yes")
iraf.refspec(input = extracted_filename,referen=filename[:-5],sort='',group='',confirm='no')
iraf.dispcor(input=extracted_filename,
output=calibrated_filename)
# Plot the extracted spectrum?
iraf.splot(calibrated_filename)
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
iraf.apall(input=filename,
find="No",
recenter="No",
resize="No",
interactive="Yes")
# Make sure that the dispersion axis is in the header.
iraf.hedit(images=[filename], fields=["DISPAXIS"], value=["1"], add="Yes")
iraf.identify(filename[:-5],
coordli=home + "/Downloads/HgNe(1).dat",
section="line 105 125",
crval=crval,
cdelt=dispersion,
fwidth=5)
# Tell the extracted spectrum what the wavelength solutions are.
iraf.hedit(images=[extracted_filename],
fields=["REFSPEC1"], \
value=[filename], add="Yes")
iraf.refspec(input=extracted_filename,
referen=filename[:-5],
sort='',
group='',
confirm='no')
iraf.dispcor(input=extracted_filename, output=calibrated_filename)
# Plot the extracted spectrum?
iraf.splot(calibrated_filename)
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 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_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