def telluric_correct(coadd: str,
output_path: str,
spectrograph: str,
user_config_lines: List[str],
debug: bool = False,
plot: bool = False):
"""
method to telluric correct one coadded file
"""
coadd_path = os.path.join(output_path, 'Science', coadd)
spectrograph = load_spectrograph(spectrograph)
par = spectrograph.default_pypeit_par()
par['telluric']['objmodel'] = 'poly'
par['telluric']['fit_wv_min_max'] = [5500, 11000]
# maybe somehow choose between poly and exp??????? look at median
par['telluric']['model'] = 'exp'
par['telluric']['polyorder'] = 8
if par['telluric']['telgridfile'] is None:
if par['sensfunc']['IR']['telgridfile'] is not None:
par['telluric']['telgridfile'] = par['sensfunc']['IR'][
'telgridfile']
par = pypeitpar.PypeItPar.from_cfg_lines(cfg_lines=par.to_config(),
merge_with=user_config_lines)
# Parse the output filename
outfile = os.path.join(output_path, 'Science',
os.path.splitext(coadd)[0] + '_tellcorr.fits')
modelfile = os.path.join(output_path, 'Science',
os.path.splitext(coadd)[0] + '_tellmodel.fits')
try:
TelPoly = telluric.poly_telluric(
coadd_path,
par['telluric']['telgridfile'],
modelfile,
outfile,
z_obj=par['telluric']['redshift'],
func=par['telluric']['func'],
model=par['telluric']['model'],
polyorder=par['telluric']['polyorder'],
fit_wv_min_max=par['telluric']['fit_wv_min_max'],
mask_lyman_a=par['telluric']['mask_lyman_a'],
delta_coeff_bounds=par['telluric']['delta_coeff_bounds'],
minmax_coeff_bounds=par['telluric']['minmax_coeff_bounds'],
only_orders=par['telluric']['only_orders'],
debug_init=debug,
disp=debug,
debug=debug,
show=plot)
except ValueError:
print(f"ERROR!! Telluric correction of {coadd} FAILED!")
def apply_tell_from_file(z_obj,
stackfilename,
tell_method='qso',
instrument='NIRES',
telgridfile=None,
polyorder=3,
fit_region_min=[9200.0],
fit_region_max=[9700.0],
mask_lyman_a=True,
show=True,
debug=False):
# output names
if tell_method == 'poly':
telloutfile = stackfilename.replace('.fits', '_polytellmodel.fits')
outfile = stackfilename.replace('.fits', '_polytellcorr.fits')
else:
telloutfile = stackfilename.replace('.fits', '_tellmodel.fits')
outfile = stackfilename.replace('.fits', '_tellcorr.fits')
if tell_method == 'qso':
pca_file = os.path.join(basedir,
'Dropbox/PypeIt_Redux/qso_pca_1200_3100.pckl')
# run telluric.qso_telluric to get the final results
# TODO: add other modes here
TelQSO = telluric.qso_telluric(stackfilename,
telgridfile,
pca_file,
z_obj,
telloutfile,
outfile,
create_bal_mask=None,
disp=disp,
debug=debug,
show=show)
elif tell_method == 'poly':
TelPoly = telluric.poly_telluric(stackfilename,
telgridfile,
telloutfile,
outfile,
z_obj=z_obj,
polyorder=polyorder,
fit_region_min=fit_region_min,
fit_region_max=fit_region_max,
func='legendre',
model='exp',
mask_lyman_a=mask_lyman_a,
debug_init=debug,
debug=debug,
show=show)
def main(args):
"""
Executes telluric correction.
"""
import os
from astropy.io import fits
from pypeit import msgs
from pypeit import io
from pypeit.par import pypeitpar
from pypeit.spectrographs.util import load_spectrograph
from pypeit.core import telluric
# Determine the spectrograph
header = fits.getheader(args.spec1dfile)
spectrograph = load_spectrograph(header['PYP_SPEC'])
spectrograph_def_par = spectrograph.default_pypeit_par()
# If the .tell file was passed in read it and overwrite default parameters
par = spectrograph_def_par if args.tell_file is None else \
pypeitpar.PypeItPar.from_cfg_lines(cfg_lines=spectrograph_def_par.to_config(),
merge_with=io.read_tellfile(args.tell_file))
# If args was provided override defaults. Note this does undo .tell file
if args.objmodel is not None:
par['telluric']['objmodel'] = args.objmodel
if args.pca_file is not None:
par['telluric']['pca_file'] = args.pca_file
if args.redshift is not None:
par['telluric']['redshift'] = args.redshift
if args.tell_grid is not None:
par['telluric']['telgridfile'] = args.tell_grid
if par['telluric']['telgridfile'] is None:
if par['sensfunc']['IR']['telgridfile'] is not None:
par['telluric']['telgridfile'] = par['sensfunc']['IR'][
'telgridfile']
else:
par['telluric'][
'telgridfile'] = 'TelFit_MaunaKea_3100_26100_R20000.fits'
msgs.warn(
f"No telluric grid file given. Using {par['telluric']['telgridfile']}."
)
# Checks
if par['telluric']['telgridfile'] is None:
msgs.error('A file with the telluric grid must be provided.')
elif not os.path.isfile(
os.path.join(data.Paths.telgrid,
par['telluric']['telgridfile'])):
msgs.error(
f"{par['telluric']['telgridfile']} does not exist. Check your "
f"installation.")
# Write the par to disk
# TODO: Make it optional to write this file? Is the relevant metadata
# saved to the main output file?
msgs.info(
f'Writing the telluric fitting parameters to {args.par_outfile}')
par['telluric'].to_config(args.par_outfile,
section_name='telluric',
include_descr=False)
# Parse the output filename
outfile = (os.path.basename(args.spec1dfile)).replace(
'.fits', '_tellcorr.fits')
modelfile = (os.path.basename(args.spec1dfile)).replace(
'.fits', '_tellmodel.fits')
msgs.info(f'Telluric-corrected spectrum will be saved to: {outfile}.')
msgs.info(f'Best-fit telluric model will be saved to: {modelfile}.')
# Run the telluric fitting procedure.
if par['telluric']['objmodel'] == 'qso':
# run telluric.qso_telluric to get the final results
TelQSO = telluric.qso_telluric(
args.spec1dfile,
par['telluric']['telgridfile'],
par['telluric']['pca_file'],
par['telluric']['redshift'],
modelfile,
outfile,
npca=par['telluric']['npca'],
pca_lower=par['telluric']['pca_lower'],
pca_upper=par['telluric']['pca_upper'],
bounds_norm=par['telluric']['bounds_norm'],
tell_norm_thresh=par['telluric']['tell_norm_thresh'],
only_orders=par['telluric']['only_orders'],
bal_wv_min_max=par['telluric']['bal_wv_min_max'],
maxiter=par['telluric']['maxiter'],
debug_init=args.debug,
disp=args.debug,
debug=args.debug,
show=args.plot)
elif par['telluric']['objmodel'] == 'star':
TelStar = telluric.star_telluric(
args.spec1dfile,
par['telluric']['telgridfile'],
modelfile,
outfile,
star_type=par['telluric']['star_type'],
star_mag=par['telluric']['star_mag'],
star_ra=par['telluric']['star_ra'],
star_dec=par['telluric']['star_dec'],
func=par['telluric']['func'],
model=par['telluric']['model'],
polyorder=par['telluric']['polyorder'],
only_orders=par['telluric']['only_orders'],
mask_abs_lines=par['telluric']['mask_abs_lines'],
delta_coeff_bounds=par['telluric']['delta_coeff_bounds'],
minmax_coeff_bounds=par['telluric']['minmax_coeff_bounds'],
maxiter=par['telluric']['maxiter'],
debug_init=args.debug,
disp=args.debug,
debug=args.debug,
show=args.plot)
elif par['telluric']['objmodel'] == 'poly':
TelPoly = telluric.poly_telluric(
args.spec1dfile,
par['telluric']['telgridfile'],
modelfile,
outfile,
z_obj=par['telluric']['redshift'],
func=par['telluric']['func'],
model=par['telluric']['model'],
polyorder=par['telluric']['polyorder'],
fit_wv_min_max=par['telluric']['fit_wv_min_max'],
mask_lyman_a=par['telluric']['mask_lyman_a'],
delta_coeff_bounds=par['telluric']['delta_coeff_bounds'],
minmax_coeff_bounds=par['telluric']['minmax_coeff_bounds'],
only_orders=par['telluric']['only_orders'],
maxiter=par['telluric']['maxiter'],
debug_init=args.debug,
disp=args.debug,
debug=args.debug,
show=args.plot)
else:
msgs.error(
"Object model is not supported yet. Must be 'qso', 'star', or 'poly'."
)
def main(args):
"""
Executes telluric correction.
"""
# Determine the spectrograph
header = fits.getheader(args.spec1dfile)
spectrograph = load_spectrograph(header['PYP_SPEC'])
spectrograph_def_par = spectrograph.default_pypeit_par()
# If the .tell file was passed in read it and overwrite default parameters
if args.tell_file is not None:
cfg_lines = read_tellfile(args.tell_file)
par = pypeitpar.PypeItPar.from_cfg_lines(
cfg_lines=spectrograph_def_par.to_config(), merge_with=cfg_lines)
else:
par = spectrograph_def_par
# If args was provided override defaults. Note this does undo .tell file
if args.objmodel is not None:
par['tellfit']['objmodel'] = args.objmodel
if args.pca_file is not None:
par['tellfit']['pca_file'] = args.pca_file
if args.redshift is not None:
par['tellfit']['redshift'] = args.redshift
if args.tell_grid is not None:
par['tellfit']['tell_grid'] = args.tell_grid
elif par['sensfunc']['IR']['telgridfile'] is not None:
par['tellfit']['tell_grid'] = par['sensfunc']['IR']['telgridfile']
else:
msgs.warn('No telluric grid file given. Using {:}'.format(
'TelFit_MaunaKea_3100_26100_R20000.fits'))
par['tellfit']['tell_grid'] = resource_filename(
'pypeit', '/data/telluric/TelFit_MaunaKea_3100_26100_R20000.fits')
# Write the par to disk
print("Writing the parameters to {}".format(args.par_outfile))
par['tellfit'].to_config('telluric.par',
section_name='tellfit',
include_descr=False)
# Parse the output filename
outfile = (os.path.basename(args.spec1dfile)).replace(
'.fits', '_tellcorr.fits')
modelfile = (os.path.basename(args.spec1dfile)).replace(
'.fits', '_tellmodel.fits')
# Run the telluric fitting procedure.
if par['tellfit']['objmodel'] == 'qso':
# run telluric.qso_telluric to get the final results
TelQSO = telluric.qso_telluric(
args.spec1dfile,
par['tellfit']['tell_grid'],
par['tellfit']['pca_file'],
par['tellfit']['redshift'],
modelfile,
outfile,
npca=par['tellfit']['npca'],
pca_lower=par['tellfit']['pca_lower'],
pca_upper=par['tellfit']['pca_upper'],
bounds_norm=par['tellfit']['bounds_norm'],
tell_norm_thresh=par['tellfit']['tell_norm_thresh'],
only_orders=par['tellfit']['only_orders'],
bal_wv_min_max=par['tellfit']['bal_wv_min_max'],
debug_init=args.debug,
disp=args.debug,
debug=args.debug,
show=args.plot)
elif par['tellfit']['objmodel'] == 'star':
TelStar = telluric.star_telluric(
args.spec1dfile,
par['tellfit']['tell_grid'],
modelfile,
outfile,
star_type=par['tellfit']['star_type'],
star_mag=par['tellfit']['star_mag'],
star_ra=par['tellfit']['star_ra'],
star_dec=par['tellfit']['star_dec'],
func=par['tellfit']['func'],
model=par['tellfit']['model'],
polyorder=par['tellfit']['polyorder'],
only_orders=par['tellfit']['only_orders'],
mask_abs_lines=par['tellfit']['mask_abs_lines'],
delta_coeff_bounds=par['tellfit']['delta_coeff_bounds'],
minmax_coeff_bounds=par['tellfit']['minmax_coeff_bounds'],
debug_init=args.debug,
disp=args.debug,
debug=args.debug,
show=args.plot)
elif par['tellfit']['objmodel'] == 'poly':
TelPoly = telluric.poly_telluric(
args.spec1dfile,
par['tellfit']['tell_grid'],
modelfile,
outfile,
z_obj=par['tellfit']['redshift'],
func=par['tellfit']['func'],
model=par['tellfit']['model'],
polyorder=par['tellfit']['polyorder'],
fit_wv_min_max=par['tellfit']['fit_wv_min_max'],
mask_lyman_a=par['tellfit']['mask_lyman_a'],
delta_coeff_bounds=par['tellfit']['delta_coeff_bounds'],
minmax_coeff_bounds=par['tellfit']['minmax_coeff_bounds'],
only_orders=par['tellfit']['only_orders'],
debug_init=args.debug,
disp=args.debug,
debug=args.debug,
show=args.plot)
else:
msgs.error(
"Object model is not supported yet. Please choose one of 'qso', 'star', 'poly'."
)