# Module for flux calibrating spectra
import numpy as np
import os
import matplotlib.pyplot as plt
from astropy.io import fits
from pypeit import msgs
from pypeit.spectrographs.util import load_spectrograph
from pypeit import specobjs
from pypeit import sensfunc
from pypeit.history import History
from astropy import table
from IPython import embed
[docs]def flux_calibrate(spec1dfiles, sensfiles, par=None, outfiles=None, chk_version=True):
"""
Function for flux calibrating spectra.
Args:
spec1dfiles (list):
List of PypeIt spec1d files that you want to flux calibrate
sensfiles (list):
List of sensitivity function files to use to flux calibrate the spec1d files. This list and the sensfiles
list need to have the same length and be aligned
par (:class:`~pypeit.par.pypeitpar.FluxCalibratePar`, optional):
Parset object containing parameters governing the flux calibration.
outfiles (list, optional):
Names of the output files. If None, this is set to spec1dfiles and those are overwritten
chk_version (bool, optional):
Whether to check of the data model versions of spec1d and sens files. Defaults to True.
"""
# Output file names
outfiles = spec1dfiles if outfiles is None else outfiles
# Load the spectrograph
header = fits.getheader(spec1dfiles[0])
spectrograph = load_spectrograph(header['PYP_SPEC'])
par = spectrograph.default_pypeit_par()['fluxcalib'] if par is None else par
sensf_last = None
for spec1, sensf, outfile in zip(spec1dfiles, sensfiles, outfiles):
# Read in the data
sobjs = specobjs.SpecObjs.from_fitsfile(spec1, chk_version=chk_version)
history = History(sobjs.header)
if sensf != sensf_last:
sens = sensfunc.SensFunc.from_file(sensf, chk_version=chk_version)
sensf_last = sensf
history.append(f'PypeIt Flux calibration "{sensf}"')
sobjs.apply_flux_calib(par, spectrograph, sens)
sobjs.write_to_fits(sobjs.header, outfile, history=history, overwrite=True)