"""
Fit telluric absorption to observed spectra
.. include common links, assuming primary doc root is up one directory
.. include:: ../include/links.rst
"""
from IPython import embed
from pypeit.scripts import scriptbase
[docs]class TellFit(scriptbase.ScriptBase):
[docs] @classmethod
def get_parser(cls, width=None):
parser = super().get_parser(description='Telluric correct a spectrum',
width=width, formatter=scriptbase.SmartFormatter)
parser.add_argument("spec1dfile", type=str,
help="spec1d or coadd file that will be used for telluric correction.")
parser.add_argument("--objmodel", type=str, default=None, choices=['qso', 'star', 'poly'],
help='R|science object model used in the fitting. The options are:\n'
'\n'
'qso = For quasars. You might need to set redshift, '
'bal_wv_min_max in the tell file.\n'
'\n'
'star = For stars. You need to set star_type, star_ra, star_dec, '
'and star_mag in the tell_file.\n'
'\n'
'poly = For other type object, You might need to set '
'fit_wv_min_max, and norder in the tell_file.\n'
'\n')
parser.add_argument("-r", "--redshift", type=float, default=None,
help="Specify redshift. Used with the --objmodel qso option above.")
parser.add_argument("-g", "--tell_grid", type=str,
help='Telluric grid. You should download the giant grid file to the '
'pypeit/data/telluric folder. It should only be passed if you '
'want to overwrite the default tell_grid that is set via each '
'spectrograph file.')
parser.add_argument("-p", "--pca_file", type=str,
help='Quasar PCA fits file with full path. The default file '
'(qso_pca_1200_3100.fits) is stored in the pypeit/data/telluric '
'folder. If you change the fits file, make sure to set the '
'pca_lower and pca_upper in the tell_file to specify the '
'wavelength coverage of your model. The defaults are '
'pca_lower=1220. and pca_upper=3100.')
parser.add_argument("-t", "--tell_file", type=str,
help='R|Configuration file to change default telluric parameters. '
'Note that the parameters in this file will be overwritten if '
'you set argument in your terminal. The --tell_file option '
'requires a .tell file with the following format:\n\n'
'F| [telluric]\n'
'F| objmodel = qso\n'
'F| redshift = 7.6\n'
'F| bal_wv_min_max = 10825,12060\n'
'OR\n'
'F| [telluric]\n'
'F| objmodel = star\n'
'F| star_type = A0\n'
'F| star_mag = 8.\n'
'OR\n'
'F| [telluric]\n'
'F| objmodel = poly\n'
'F| polyorder = 3\n'
'F| fit_wv_min_max = 9000.,9500.\n'
'\n')
parser.add_argument("--debug", default=False, action="store_true",
help="show debug plots?")
parser.add_argument("--plot", default=False, action="store_true",
help="Show the telluric corrected spectrum")
parser.add_argument("--par_outfile", default='telluric.par',
help="Name of output file to save the parameters used by the fit")
parser.add_argument('-v', '--verbosity', type=int, default=1,
help='Verbosity level between 0 [none] and 2 [all]. Default: 1. '
'Level 2 writes a log with filename tellfit_YYYYMMDD-HHMM.log')
parser.add_argument('--chk_version', default=False, action='store_true',
help='Ensure the datamodels are from the current PypeIt version. '
'By default (consistent with previous functionality) this is '
'not enforced and crashes may ensue ...')
return parser
[docs] @staticmethod
def main(args):
"""
Executes telluric correction.
"""
import os
from astropy.io import fits
from pypeit import msgs
from pypeit import data
from pypeit.par import pypeitpar
from pypeit.spectrographs.util import load_spectrograph
from pypeit.core import telluric
from pypeit import inputfiles
# Set the verbosity, and create a logfile if verbosity == 2
msgs.set_logfile_and_verbosity('tellfit', args.verbosity)
# Determine the spectrograph
header = fits.getheader(args.spec1dfile)
spectrograph = load_spectrograph(header['PYP_SPEC'])
spectrograph_def_par = spectrograph.default_pypeit_par()
# Load tell file if provided
if args.tell_file is not None:
tellFile = inputfiles.TelluricFile.from_file(args.tell_file)
tcfg_lines = tellFile.cfg_lines
else:
tcfg_lines = []
# 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=(tcfg_lines,))
# 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'] = 'TellPCA_3000_26000_R10000.fits'
msgs.warn(f"No telluric file given. Using PCA method with {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(data.get_telgrid_filepath(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'],
teltype=par['telluric']['teltype'], tell_npca=par['telluric']['tell_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'],
pix_shift_bounds=par['telluric']['pix_shift_bounds'],
maxiter=par['telluric']['maxiter'],
popsize=par['telluric']['popsize'],
tol=par['telluric']['tol'],
debug_init=args.debug, disp=args.debug,
debug=args.debug, show=args.plot,
chk_version=args.chk_version)
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'],
teltype=par['telluric']['teltype'], tell_npca=par['telluric']['tell_npca'],
mask_hydrogen_lines=par['sensfunc']['mask_hydrogen_lines'],
mask_helium_lines=par['sensfunc']['mask_helium_lines'],
hydrogen_mask_wid=par['sensfunc']['hydrogen_mask_wid'],
delta_coeff_bounds=par['telluric']['delta_coeff_bounds'],
minmax_coeff_bounds=par['telluric']['minmax_coeff_bounds'],
pix_shift_bounds=par['telluric']['pix_shift_bounds'],
maxiter=par['telluric']['maxiter'],
popsize=par['telluric']['popsize'],
tol=par['telluric']['tol'],
debug_init=args.debug, disp=args.debug,
debug=args.debug, show=args.plot,
chk_version=args.chk_version)
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'],
teltype=par['telluric']['teltype'], tell_npca=par['telluric']['tell_npca'],
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'],
pix_shift_bounds=par['telluric']['pix_shift_bounds'],
maxiter=par['telluric']['maxiter'],
popsize=par['telluric']['popsize'],
tol=par['telluric']['tol'],
debug_init=args.debug, disp=args.debug,
debug=args.debug, show=args.plot,
chk_version=args.chk_version)
else:
msgs.error("Object model is not supported yet. Must be 'qso', 'star', or 'poly'.")