"""
Script for fluxing PYPEIT 1d spectra
.. include common links, assuming primary doc root is up one directory
.. include:: ../include/links.rst
"""
from IPython import embed
from astropy.io import fits
from pypeit import msgs
from pypeit import inputfiles
from pypeit.spectrographs.util import load_spectrograph
from pypeit import fluxcalibrate
from pypeit.par import pypeitpar
from pypeit.scripts import scriptbase
from pypeit.sensfilearchive import SensFileArchive
[docs]class FluxCalib(scriptbase.ScriptBase):
[docs] @classmethod
def get_parser(cls, width=None):
parser = super().get_parser(description='Flux calibrate 1D spectra produced by PypeIt',
width=width, formatter=scriptbase.SmartFormatter)
parser.add_argument("flux_file", type=str,
help="R|File to guide fluxing process. This file must have the "
"following format: \n\n"
"F|flux read\n"
"F| filename | sensfile\n"
"F| spec1dfile1 | sensfile1\n"
"F| spec1dfile2 | \n"
"F| ... \n"
"F|flux end\n"
"\nOR\n\n"
"F|flux read\n"
"F| filename | sensfile\n"
"F| spec1dfile1 | sensfile1\n"
"F| spec1dfile2 | sensfile2\n"
"F| spec1dfile3 | sensfile3\n"
"F| ... \n"
"F|flux end\n"
"\nOR\n\n"
"F|[fluxcalib]\n"
"F| use_archived_sens = True\n"
"F|flux read\n"
"F| filename\n"
"F| spec1dfile1\n"
"F| spec1dfile2\n"
"F| spec1dfile3\n"
"F| ... \n"
"F|flux end\n"
"\n"
"That is, you must specify either a sensfile for all spec1dfiles "
"on the first line, specify one sensfile for each spec1dfile, or "
"specify no sensfiles and use an archived one.\n"
"Archived sensfiles are available for the following spectrographs: "
+ ",".join(SensFileArchive.supported_spectrographs()) + "\n\n")
# parser.add_argument("--debug", default=False, action="store_true",
# help="show debug plots?")
parser.add_argument("--par_outfile", default='fluxing.par', action="store_true",
help="Output to save the parameters")
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 flux_calib_YYYYMMDD-HHMM.log')
# parser.add_argument("--plot", default=False, action="store_true",
# help="Show the sensitivity function?")
parser.add_argument('--try_old', default=False, action='store_true',
help='Attempt to load old datamodel versions. A crash may ensue..')
return parser
[docs] @staticmethod
def main(args):
""" Runs fluxing steps
"""
chk_version = not args.try_old
# Set the verbosity, and create a logfile if verbosity == 2
msgs.set_logfile_and_verbosity('flux_calib', args.verbosity)
# Load the file
fluxFile = inputfiles.FluxFile.from_file(args.flux_file)
# Read in spectrograph from spec1dfile header
header = fits.getheader(fluxFile.filenames[0])
spectrograph = load_spectrograph(header['PYP_SPEC'])
# Parameters
spectrograph_def_par = spectrograph.default_pypeit_par()
par = pypeitpar.PypeItPar.from_cfg_lines(cfg_lines=spectrograph_def_par.to_config(),
merge_with=(fluxFile.cfg_lines,))
# Write the par to disk
print("Writing the parameters to {}".format(args.par_outfile))
par.to_config(args.par_outfile)
# Chck the sizes of the inputs
nspec = len(fluxFile.filenames)
# Archived solution?
if len(fluxFile.sensfiles) > 0:
sensfiles = fluxFile.sensfiles
elif len(fluxFile.sensfiles) == 0 and par['fluxcalib']['use_archived_sens'] == True:
# No sensfile specified, but an archived sensfunc can be used.
sf_archive = SensFileArchive.get_instance(spectrograph.name)
sensfiles = nspec*[sf_archive.get_archived_sensfile(fluxFile.filenames[0])]
else:
msgs.error('Invalid format for .flux file.' + msgs.newline() +
'You must specify a single sensfile on the first line of the flux block,' + msgs.newline() +
'or specify a sensfile for every spec1dfile in the flux block,' + msgs.newline() +
'or specify "use_archived_sens = True" to use an archived sensfile.' + msgs.newline() +
'Run pypeit_flux_calib --help for information on the format')
# Instantiate
fluxcalibrate.flux_calibrate(fluxFile.filenames, sensfiles, par=par['fluxcalib'],
chk_version=chk_version)
msgs.info('Flux calibration complete')
return 0