if do_sens:
if std1dfile is None:
msgs.error('You need either give a std1dfile to derive sensfunc')
else:
# run telluric.sensfunc_telluric to get the sensfile
TelSens = telluric.sensfunc_telluric(std1dfile,
telgridfile,
sensfile,
mask_abs_lines=True,
debug=debug)
## Apply the sensfunc to all spectra (only sensfunc but not tellluric)
# TODO: change show=False to show=show
apply_sensfunc(fnames,
sensfile,
extinct_correct=False,
tell_correct=False,
debug=debug,
show=show)
fnames_flux = [f.replace('.fits', '_flux.fits') for f in fnames]
## Let's coadd all the fluxed spectra
# you should get a coadded spectrum named as 'spec1d_stack_{:}.fits'.format(qsoname)
# a straight merge of individual order stacked spectra named as 'spec1d_merge_{:}.fits'.format(qsoname)
# a individual order stacked spectra (multi-extension) named as 'spec1d_order_{:}.fits'.format(qsoname)
# TODO: change the outfile to work with datapath. It's a hard coding on these names in coadd1d
wave_stack, flux_stack, ivar_stack, mask_stack = coadd1d.ech_combspec(
fnames_flux,
objids,
sensfile=sensfile,
ex_value='OPT',
def flux_coadd_telluric(spec1dfiles,
sensfile,
tell_function,
telloutfile,
outfile,
objids=None,
z_qso=None,
ex_value='OPT',
polyorder=3,
fit_region_min=[9200.0],
fit_region_max=[9700.0],
scale_method=None,
hand_scale=None,
const_weights=False,
wave_grid_min=None,
wave_grid_max=None,
mask_lyman_a=True,
do_flux=False,
do_stack=False,
do_tell=False,
use_exist_sens=True,
show=False,
debug=False):
nfiles = len(spec1dfiles)
if objids is None:
objids = ['OBJ0001'] * nfiles
elif len(objids) != nfiles:
msgs.error(
'The length of objids should be exactly the same as the number of spec1d files.'
)
#fnames = np.sort(fnames)
### Apply the sensfunc to all spectra (only sensfunc but not tellluric)
if do_flux:
apply_sensfunc(spec1dfiles,
sensfile,
extinct_correct=False,
tell_correct=False,
debug=debug,
show=show)
# fnames_flux = [f.replace('.fits', '_flux.fits') for f in fnames]
else:
msgs.warn(
'You skiped the fluxing step, make sure you have applied sensfunction to your 1D spectra.'
)
# The name of the final stacked 1d spectrum
if len(outroot.split('.')) == 1:
outroot = outroot + '.fits'
elif outroot.split('.')[-1] != 'fits':
outroot = outroot + '.fits'
stackfile = os.path.join(sci_path, outroot)
if do_stack:
## Let's coadd all the fluxed spectra
# you should get a coadded spectrum named as '{:}_stack.fits'.format(qsoname)
# a straight merge of individual order stacked spectra named as '{:}_merge.fits'.format(qsoname)
# a individual order stacked spectra (multi-extension) named as '{:}_order.fits'.format(qsoname)
if pypeline == 'Echelle':
wave_stack, flux_stack, ivar_stack, mask_stack = coadd1d.ech_combspec(
fnames,
objids,
show=show,
sensfile=sensfile,
ex_value=ex_value,
outfile=stackfile,
scale_method=scale_method,
hand_scale=hand_scale,
wave_grid_min=wave_grid_min,
wave_grid_max=wave_grid_max,
const_weights=const_weights,
debug=debug)
else:
wave_stack, flux_stack, ivar_stack, mask_stack = coadd1d.multi_combspec(
fnames,
objids,
show=show,
ex_value=ex_value,
outfile=stackfile,
wave_grid_min=wave_grid_min,
wave_grid_max=wave_grid_max,
scale_method=scale_method,
hand_scale=hand_scale,
const_weights=const_weights,
debug=debug,
debug_scale=debug)
elif os.path.exists(stackfile):
msgs.info('Loading stacked 1d spectrum {:}'.format(stackfile))
else:
msgs.warn(
'No stacked 1d spectrum was found. Please set do_stack=True!')
### Telluric correction
if do_tell:
apply_tell_from_file(z_qso,
stackfile,
tell_method=tell_method,
instrument=instrument,
telgridfile=telgridfile,
polyorder=polyorder,
fit_region_min=fit_region_min,
fit_region_max=fit_region_max,
mask_lyman_a=mask_lyman_a,
show=show,
debug=debug)
def flux_tell(sci_path,
stdfile,
spec1dfiles=None,
std_path=None,
fileroot=None,
outroot=None,
z_qso=None,
tell_method='qso',
instrument=None,
star_type=None,
star_mag=None,
star_ra=None,
star_dec=None,
mask_abs_lines=True,
sens_polyorder=8,
objids=None,
ex_value='OPT',
polyorder=3,
fit_region_min=[9200.0],
fit_region_max=[9700.0],
scale_method=None,
hand_scale=None,
const_weights=False,
wave_grid_min=None,
wave_grid_max=None,
mask_lyman_a=True,
do_sens=False,
do_flux=False,
do_stack=False,
do_tell=False,
use_exist_sens=True,
show=False,
debug=False):
if std_path is None:
std_path = sci_path
if fileroot is None:
fileroot = 'spec1d_flux_tell.fits'
if outroot is None:
outroot = fileroot
std1dfile = os.path.join(std_path, stdfile)
header = fits.getheader(std1dfile, 0)
pypeline = header['PYPELINE']
if spec1dfiles is None:
scifiles_all = os.listdir(sci_path)
spec1dfiles = []
for i in range(len(scifiles_all)):
if ('spec1d' in scifiles_all[i]) and (fileroot in scifiles_all[i]):
spec1dfiles.append(scifiles_all[i])
nfiles = len(spec1dfiles)
fnames = []
for ifile in range(nfiles):
fnames.append(os.path.join(sci_path, spec1dfiles[ifile]))
if objids is None:
objids = ['OBJ0001'] * nfiles
elif len(objids) != nfiles:
msgs.error(
'The length of objids should be exactly the same with the number of spec1d files.'
)
#fnames = np.sort(fnames)
### get sensfunc
if (star_ra is None) and (star_dec is None) and (star_mag is None) and (
star_type is None):
star_ra, star_dec = header['RA'], header['DEC']
if '.sens.fits' not in stdfile:
sensfile = std1dfile.replace('.fits', '_sens.fits')
telgridfile = None # value it to None
if do_sens:
if os.path.exists(sensfile) and (use_exist_sens):
msgs.warn(
'{:} is already exists. Skip doing sensfunc.'.format(sensfile))
else:
sensfile, telgridfile = get_sens_from_file(
std1dfile=std1dfile,
instrument=instrument,
star_type=star_type,
star_mag=star_mag,
star_ra=star_ra,
star_dec=star_dec,
sens_polyorder=sens_polyorder,
mask_abs_lines=mask_abs_lines,
show=show,
debug=debug)
if telgridfile is None:
msgs.info('Loading sensfile {:}'.format(sensfile))
if (instrument == 'GNIRS') or (instrument == 'NIRES'):
telgridfile = os.path.join(
basedir,
'Dropbox/PypeIt_Redux/TelFit_MaunaKea_3100_26100_R20000.fits')
elif (instrument == 'XSHOOTER_VIS') or (instrument == 'GMOS-S'):
telgridfile = os.path.join(
basedir,
'Dropbox/PypeIt_Redux/XSHOOTER/TelFit_Paranal_VIS_4900_11100_R25000.fits'
)
elif instrument == 'XSHOOTER_NIR':
telgridfile = os.path.join(
basedir,
'Dropbox/PypeIt_Redux/XSHOOTER/TelFit_Paranal_NIR_9800_25000_R25000.fits'
)
else:
telgridfile = os.path.join(
basedir,
'Dropbox/PypeIt_Redux/TelFit_MaunaKea_3100_26100_R20000.fits')
msgs.warn('No telluric grid is found. Using MaunaKea!')
### Apply the sensfunc to all spectra (only sensfunc but not tellluric)
if do_flux:
apply_sensfunc(fnames,
sensfile,
extinct_correct=False,
tell_correct=False,
debug=debug,
show=show)
# fnames_flux = [f.replace('.fits', '_flux.fits') for f in fnames]
else:
msgs.warn(
'You skiped the fluxing step, make sure you have applied sensfunction to your 1D spectra.'
)
# The name of the final stacked 1d spectrum
if len(outroot.split('.')) == 1:
outroot = outroot + '.fits'
elif outroot.split('.')[-1] != 'fits':
outroot = outroot + '.fits'
stackfile = os.path.join(sci_path, outroot)
if do_stack:
## Let's coadd all the fluxed spectra
# you should get a coadded spectrum named as '{:}_stack.fits'.format(qsoname)
# a straight merge of individual order stacked spectra named as '{:}_merge.fits'.format(qsoname)
# a individual order stacked spectra (multi-extension) named as '{:}_order.fits'.format(qsoname)
if pypeline == 'Echelle':
wave_stack, flux_stack, ivar_stack, mask_stack = coadd1d.ech_combspec(
fnames,
objids,
show=show,
sensfile=sensfile,
ex_value=ex_value,
outfile=stackfile,
scale_method=scale_method,
hand_scale=hand_scale,
wave_grid_min=wave_grid_min,
wave_grid_max=wave_grid_max,
const_weights=const_weights,
debug=debug)
else:
wave_stack, flux_stack, ivar_stack, mask_stack = coadd1d.multi_combspec(
fnames,
objids,
show=show,
ex_value=ex_value,
outfile=stackfile,
wave_grid_min=wave_grid_min,
wave_grid_max=wave_grid_max,
scale_method=scale_method,
hand_scale=hand_scale,
const_weights=const_weights,
debug=debug,
debug_scale=debug)
elif os.path.exists(stackfile):
msgs.info('Loading stacked 1d spectrum {:}'.format(stackfile))
else:
msgs.warn(
'No stacked 1d spectrum was found. Please set do_stack=True!')
### Telluric correction
if do_tell:
apply_tell_from_file(z_qso,
stackfile,
tell_method=tell_method,
instrument=instrument,
telgridfile=telgridfile,
polyorder=polyorder,
fit_region_min=fit_region_min,
fit_region_max=fit_region_max,
mask_lyman_a=mask_lyman_a,
show=show,
debug=debug)
if not os.path.exists(sensfile) or clobber:
# Run sensfun_teluric to get the sensitivity function
TelSens = telluric.sensfunc_telluric(std1dfile,
telgridfile,
sensfile,
star_type=star_type,
star_mag=Vmag,
mask_abs_lines=True,
debug=True)
## Apply the sensfunc to all spectra. This is flux calibration only, but not telluric correction.
spec1dfiles_flux = [f.replace('.fits', '_flux.fits') for f in spec1dfiles]
if not os.path.exists(spec1dfiles_flux[0]):
apply_sensfunc(spec1dfiles,
sensfile,
extinct_correct=False,
tell_correct=False,
debug=False,
show=False)
# Now let's coadd the spectrum
spec1dfluxfile = os.path.join(mpia_path,
'spec1d_coadd_{:}.fits'.format(qsoname))
wave_stack, flux_stack, ivar_stack, mask_stack = coadd1d.ech_combspec(
spec1dfiles_flux,
objids,
show=show,
show_exp=True,
sensfile=sensfile,
ex_value='OPT',
outfile=spec1dfluxfile,
debug=debug)