"""
Script to determine the sensitivity function for a PypeIt 1D spectrum.
.. include common links, assuming primary doc root is up one directory
.. include:: ../include/links.rst
"""
from IPython import embed
from pypeit.scripts import scriptbase
from pathlib import Path
[docs]
class SensFunc(scriptbase.ScriptBase):
# TODO: Need an option here for multi_spec_det detectors, passed as a list
# of numbers in the SensFunc parset, or as --det 3 7 on the command line
[docs]
@classmethod
def get_parser(cls, width=None):
parser = super().get_parser(description='Compute a sensitivity function', width=width,
formatter=scriptbase.SmartFormatter, default_log_file=True)
parser.add_argument("spec1dfiles", type=str, nargs='+',
help='file(s) of the reduced standard star spectrum. These '
'can be either spec1d*.fits files or the output of '
'`pypeit_coadd_1dspec` (except for cross-dispersed echelle data).'
' Multiple files can be provided, but they are helpful only'
'if they cover different wavelength ranges, since this'
'script will splice (not combine) them together.')
parser.add_argument("--extr", type=str, default=None, choices=['OPT', 'BOX'],
help="R|Override the default extraction method used for computing the sensitivity "
"function. Note that it is not possible to set --extr and "
"simultaneously use a .sens file with the --sens_file option. If "
"you are using a .sens file, set the algorithm there via:\n\n"
"F| [sensfunc]\n"
"F| extr = BOX\n"
"\nThe extraction options are: OPT or BOX")
parser.add_argument("--algorithm", type=str, default=None, choices=['UVIS', 'IR'],
help="R|Override the default algorithm for computing the sensitivity "
"function. Note that it is not possible to set --algorithm and "
"simultaneously use a .sens file with the --sens_file option. If "
"you are using a .sens file, set the algorithm there via:\n\n"
"F| [sensfunc]\n"
"F| algorithm = IR\n"
"\nThe algorithm options are:\n\n"
"UVIS = Should be used for data with lambda < 7000A. No "
"detailed model of telluric absorption but corrects for "
"atmospheric extinction.\n\n"
"IR = Should be used for data with lambbda > 7000A. Performs "
"joint fit for sensitivity function and telluric absorption "
"using HITRAN models.\n\n")
parser.add_argument("--multi", type=str,
help="R|List of detector numbers to splice together for instruments "
"with multiple detectors arranged in the spectral direction, "
"e.g. --multi = '3,7'. Note that it is not possible to set "
"--multi and simultaneously use a .sens file with the "
"--sens_file option. If you are using a .sens file, set the "
"multi_spec_det param there via:\n\n"
"F| [sensfunc]\n"
"F| multi_spec_det = 3,7\n"
"\n")
parser.add_argument("-o", "--outfile", type=str,
help='Output file for sensitivity function. If not specified, the '
'sensitivity function will be written out to a standard filename '
'in the current working directory, i.e. if the standard spec1d '
'file is named spec1d_b24-Feige66_KASTb_foo.fits the sensfunc '
'will be written to sens_b24-Feige66_KASTb_foo.fits. A QA file '
'will also be written as sens_spec1d_b24-Feige66_KASTb_foo_QA.pdf '
'and a file showing throughput plots to '
'sens_spec1d_b24-Feige66_KASTb_foo_throughput.pdf. The same '
'extensions for QA and throughput will be used if outfile is '
'provided but with .fits trimmed off if it is in the filename.')
parser.add_argument("-s", "--sens_file", type=str,
help='Configuration file with sensitivity function parameters')
parser.add_argument("-f", "--use_flat", default=False, action="store_true",
help="R|Use the extracted spectrum of the flatfield calibration to estimate the blaze "
"function when generating the sensitivity function. This is helpful to account for "
"small scale undulations in the sensitivity function. The spec1dfile must contain the "
"extracted flatfield response in order to use this option. This spectrum is extracted "
"by default, unless you did not compute a pixelflat frame. Note that it is not "
"possible to set --use_flat and simultaneously use a .sens file with the --sens_file "
"option. If you are using a .sens file, set the use_flat flag with the argument:\n\n"
"F| [sensfunc]\n"
"F| use_flat = True")
parser.add_argument("--debug", default=False, action="store_true",
help="show debug plots?")
parser.add_argument("--par_outfile", default='sensfunc.par',
help="Name of output file to save the parameters used by the fit")
return parser
[docs]
@classmethod
def main(cls, args):
"""Executes sensitivity function computation."""
import os
from pypeit import log
from pypeit import PypeItError
from pypeit import inputfiles
from pypeit import io
from pypeit.par import pypeitpar
from pypeit import sensfunc
from pypeit.spectrographs.util import load_spectrograph
# Initialize the log
cls.init_log(args)
# Check parameter inputs
if args.algorithm is not None and args.sens_file is not None:
raise PypeItError("It is not possible to set --algorithm and simultaneously use a .sens "
"file via the --sens_file option. If you are using a .sens file set the "
"algorithm there via:\n"
"\n"
" [sensfunc]\n"
" algorithm = IR\n"
"\n")
if args.use_flat and args.sens_file is not None:
raise PypeItError("It is not possible to set --use_flat and simultaneously use a .sens "
"file via the --sens_file option. If you are using a .sens file set the "
"use_flat flag in your .sens file using the argument:\n"
"\n"
" [sensfunc]\n"
" use_flat = True\n"
"\n")
if args.multi is not None and args.sens_file is not None:
raise PypeItError("It is not possible to set --multi and simultaneously use a .sens file via "
"the --sens_file option. If you are using a .sens file set the detectors "
"there via:\n"
"\n"
" [sensfunc]\n"
" multi_spec_det = 3,7\n"
"\n")
if args.extr is not None and args.sens_file is not None:
raise PypeItError("It is not possible to set --extr and simultaneously use a .sens file via "
"the --sens_file option. If you are using a .sens file set the extraction "
"method there via:\n"
"\n"
" [sensfunc]\n"
" extr = BOX\n"
"\n")
# Determine the spectrograph and generate the primary FITS header
with io.fits_open(args.spec1dfiles[0]) as hdul:
spectrograph = load_spectrograph(hdul[0].header['PYP_SPEC'], pypeit_fits=True)
spectrograph_config_par = spectrograph.config_specific_par(hdul)
# Construct a primary FITS header that includes the spectrograph's
# config keys for inclusion in the output sensfunc file
primary_hdr = io.initialize_header()
add_keys = (
['PYP_SPEC', 'DATE-OBS', 'TELESCOP', 'INSTRUME', 'DETECTOR']
+ spectrograph.configuration_keys() + spectrograph.raw_header_cards()
)
for key in add_keys:
if key.upper() in hdul[0].header.keys():
primary_hdr[key.upper()] = hdul[0].header[key.upper()]
# If the .sens file was passed in read it and overwrite default parameters
if args.sens_file is not None:
sensFile = inputfiles.SensFile.from_file(args.sens_file)
# Read sens file
par = pypeitpar.PypeItPar.from_cfg_lines(
cfg_lines=spectrograph_config_par.to_config(),
merge_with=(sensFile.cfg_lines,))
else:
par = pypeitpar.PypeItPar.from_cfg_lines(cfg_lines=spectrograph_config_par.to_config())
# If algorithm was provided override defaults. Note this does undo .sens
# file since they cannot both be passed
if args.algorithm is not None:
par['sensfunc']['algorithm'] = args.algorithm
# If use_flat was flagged in the input, set use_flat to True. Note this does undo .sens
# file since they cannot both be passed
if args.use_flat:
par['sensfunc']['use_flat'] = True
# If multi was set override defaults. Note this does undo .sens file
# since they cannot both be passed
if args.multi is not None:
# parse
multi_spec_det = [int(item) for item in args.multi.split(',')]
par['sensfunc']['multi_spec_det'] = multi_spec_det
# If extr was provided override defaults. Note this does undo .sens
# file since they cannot both be passed
if args.extr is not None:
par['sensfunc']['extr'] = args.extr
# TODO Add parsing of detectors here. If detectors passed from the
# command line, overwrite the parset values read in from the .sens file
# Write the par to disk
log.info(f'Writing the parameters to {args.par_outfile}')
par['sensfunc'].to_config(args.par_outfile, section_name='sensfunc', include_descr=False)
# TODO JFH I would like to be able to run only
# par['sensfunc'].to_config('sensfunc.par') but this crashes.
# TODO: KBW - You can do that if you override the
# pypeit.par.parset.ParSet.to_config method in the
# pypeit.par.pypeitpar.SensFuncPar class.
# Parse the output filename
if args.outfile is not None:
outfile = args.outfile
else:
# read the filenames and parse
_names = [Path(f).name for f in args.spec1dfiles]
# if spec1d_ in the filename, remove it
_names = [n.split('spec1d_')[-1] if n.startswith('spec1d') else n for n in _names]
spec1dname = _names[0] if len(_names) == 1 else f"{_names[0].split('.fits')[0]}-{_names[-1]}"
outfile = 'sens_' + spec1dname
# Instantiate the relevant class for the requested algorithm
sensobj = sensfunc.SensFunc.get_instance(args.spec1dfiles, outfile, par['sensfunc'],
par_fluxcalib=par['fluxcalib'], debug=args.debug,
chk_version=par['rdx']['chk_version'])
# Generate the sensfunc
sensobj.run()
# Write it out to a file, including the new primary FITS header
sensobj.to_file(outfile, primary_hdr=primary_hdr, overwrite=True)
#TODO JFH Add a show_sensfunc option here and to the sensfunc classes.