def main(args) :
log=get_logger()
log.info("starting at {}".format(time.asctime()))
# Process
frame = read_frame(args.infile)
if args.cosmics_nsig>0 : # Reject cosmics
reject_cosmic_rays_1d(frame,args.cosmics_nsig)
fiberflat = compute_fiberflat(frame,nsig_clipping=args.nsig,accuracy=args.acc,smoothing_res=args.smoothing_resolution)
# QA
if (args.qafile is not None):
log.info("performing fiberflat QA")
# Load
qaframe = load_qa_frame(args.qafile, frame, flavor=frame.meta['FLAVOR'])
# Run
qaframe.run_qa('FIBERFLAT', (frame, fiberflat))
# Write
if args.qafile is not None:
write_qa_frame(args.qafile, qaframe)
log.info("successfully wrote {:s}".format(args.qafile))
# Figure(s)
if args.qafig is not None:
qa_plots.frame_fiberflat(args.qafig, qaframe, frame, fiberflat)
# Write
write_fiberflat(args.outfile, fiberflat, frame.meta)
log.info("successfully wrote %s"%args.outfile)
log.info("done at {}".format(time.asctime()))
def main(args) :
log=get_logger()
log.info("starting")
# read exposure to load data and get range of spectra
frame = read_frame(args.infile)
specmin, specmax = np.min(frame.fibers), np.max(frame.fibers)
if args.cosmics_nsig>0 : # Reject cosmics
reject_cosmic_rays_1d(frame,args.cosmics_nsig)
# read fiberflat
fiberflat = read_fiberflat(args.fiberflat)
# apply fiberflat to sky fibers
apply_fiberflat(frame, fiberflat)
# compute sky model
skymodel = compute_sky(frame,add_variance=(not args.no_extra_variance),\
angular_variation_deg=args.angular_variation_deg,\
chromatic_variation_deg=args.chromatic_variation_deg,\
adjust_wavelength=args.adjust_wavelength,\
adjust_lsf=args.adjust_lsf)
# QA
if (args.qafile is not None) or (args.qafig is not None):
log.info("performing skysub QA")
# Load
qaframe = load_qa_frame(args.qafile, frame_meta=frame.meta, flavor=frame.meta['FLAVOR'])
# Run
qaframe.run_qa('SKYSUB', (frame, skymodel))
# Write
if args.qafile is not None:
write_qa_frame(args.qafile, qaframe)
log.info("successfully wrote {:s}".format(args.qafile))
# Figure(s)
if args.qafig is not None:
qa_plots.frame_skyres(args.qafig, frame, skymodel, qaframe)
# record inputs
frame.meta['IN_FRAME'] = shorten_filename(args.infile)
frame.meta['FIBERFLT'] = shorten_filename(args.fiberflat)
# write result
write_sky(args.outfile, skymodel, frame.meta)
log.info("successfully wrote %s"%args.outfile)
def main(args):
log = get_logger()
if (args.fiberflat is None) and (args.sky is None) and (args.calib is None):
log.critical('no --fiberflat, --sky, or --calib; nothing to do ?!?')
sys.exit(12)
frame = read_frame(args.infile)
#- Raw scores already added in extraction, but just in case they weren't
#- it is harmless to rerun to make sure we have them.
compute_and_append_frame_scores(frame,suffix="RAW")
if args.cosmics_nsig>0 and args.sky==None : # Reject cosmics (otherwise do it after sky subtraction)
log.info("cosmics ray 1D rejection")
reject_cosmic_rays_1d(frame,args.cosmics_nsig)
if args.fiberflat!=None :
log.info("apply fiberflat")
# read fiberflat
fiberflat = read_fiberflat(args.fiberflat)
# apply fiberflat to all fibers
apply_fiberflat(frame, fiberflat)
compute_and_append_frame_scores(frame,suffix="FFLAT")
if args.sky!=None :
# read sky
skymodel=read_sky(args.sky)
if args.cosmics_nsig>0 :
# use a copy the frame (not elegant but robust)
copied_frame = copy.deepcopy(frame)
# first subtract sky without throughput correction
subtract_sky(copied_frame, skymodel, apply_throughput_correction = False)
# then find cosmics
log.info("cosmics ray 1D rejection after sky subtraction")
reject_cosmic_rays_1d(copied_frame,args.cosmics_nsig)
# copy mask
frame.mask = copied_frame.mask
# and (re-)subtract sky, but just the correction term
subtract_sky(frame, skymodel, apply_throughput_correction = (not args.no_sky_throughput_correction) )
else :
# subtract sky
subtract_sky(frame, skymodel, apply_throughput_correction = (not args.no_sky_throughput_correction) )
compute_and_append_frame_scores(frame,suffix="SKYSUB")
if args.calib!=None :
log.info("calibrate")
# read calibration
fluxcalib=read_flux_calibration(args.calib)
# apply calibration
apply_flux_calibration(frame, fluxcalib)
# Ensure that ivars are set to 0 for all values if any designated
# fibermask bit is set. Also flips a bits for each frame.mask value using specmask.BADFIBER
frame = get_fiberbitmasked_frame(frame,bitmask="flux",ivar_framemask=True)
compute_and_append_frame_scores(frame,suffix="CALIB")
# save output
write_frame(args.outfile, frame, units='10**-17 erg/(s cm2 Angstrom)')
log.info("successfully wrote %s"%args.outfile)
def main(args):
log = get_logger()
if (args.fiberflat is None) and (args.sky is None) and (args.calib is
None):
log.critical('no --fiberflat, --sky, or --calib; nothing to do ?!?')
sys.exit(12)
frame = read_frame(args.infile)
#- Raw scores already added in extraction, but just in case they weren't
#- it is harmless to rerun to make sure we have them.
compute_and_append_frame_scores(frame, suffix="RAW")
if args.cosmics_nsig > 0 and args.sky == None: # Reject cosmics (otherwise do it after sky subtraction)
log.info("cosmics ray 1D rejection")
reject_cosmic_rays_1d(frame, args.cosmics_nsig)
if args.fiberflat != None:
log.info("apply fiberflat")
# read fiberflat
fiberflat = read_fiberflat(args.fiberflat)
# apply fiberflat to all fibers
apply_fiberflat(frame, fiberflat)
compute_and_append_frame_scores(frame, suffix="FFLAT")
if args.sky != None:
# read sky
skymodel = read_sky(args.sky)
if args.cosmics_nsig > 0:
# first subtract sky without throughput correction
subtract_sky(frame, skymodel, throughput_correction=False)
# then find cosmics
log.info("cosmics ray 1D rejection after sky subtraction")
reject_cosmic_rays_1d(frame, args.cosmics_nsig)
if args.sky_throughput_correction:
# and (re-)subtract sky, but just the correction term
subtract_sky(frame,
skymodel,
throughput_correction=True,
default_throughput_correction=0.)
else:
# subtract sky
subtract_sky(frame,
skymodel,
throughput_correction=args.sky_throughput_correction)
compute_and_append_frame_scores(frame, suffix="SKYSUB")
if args.calib != None:
log.info("calibrate")
# read calibration
fluxcalib = read_flux_calibration(args.calib)
# apply calibration
apply_flux_calibration(frame, fluxcalib)
compute_and_append_frame_scores(frame, suffix="CALIB")
# save output
write_frame(args.outfile, frame, units='1e-17 erg/(s cm2 Angstrom)')
log.info("successfully wrote %s" % args.outfile)
def main(args):
log = get_logger()
if (args.fiberflat is None) and (args.sky is None) and (args.calib is
None):
log.critical('no --fiberflat, --sky, or --calib; nothing to do ?!?')
sys.exit(12)
if (not args.no_tsnr) and (args.calib is None):
log.critical(
'need --fiberflat --sky and --calib to compute template SNR')
sys.exit(12)
frame = read_frame(args.infile)
if not args.no_tsnr:
# tsnr alpha calc. requires uncalibrated + no substraction rame.
uncalibrated_frame = copy.deepcopy(frame)
#- Raw scores already added in extraction, but just in case they weren't
#- it is harmless to rerun to make sure we have them.
compute_and_append_frame_scores(frame, suffix="RAW")
if args.cosmics_nsig > 0 and args.sky == None: # Reject cosmics (otherwise do it after sky subtraction)
log.info("cosmics ray 1D rejection")
reject_cosmic_rays_1d(frame, args.cosmics_nsig)
if args.fiberflat != None:
log.info("apply fiberflat")
# read fiberflat
fiberflat = read_fiberflat(args.fiberflat)
# apply fiberflat to all fibers
apply_fiberflat(frame, fiberflat)
compute_and_append_frame_scores(frame, suffix="FFLAT")
else:
fiberflat = None
if args.no_xtalk:
zero_ivar = (not args.no_zero_ivar)
else:
zero_ivar = False
if args.sky != None:
# read sky
skymodel = read_sky(args.sky)
if args.cosmics_nsig > 0:
# use a copy the frame (not elegant but robust)
copied_frame = copy.deepcopy(frame)
# first subtract sky without throughput correction
subtract_sky(copied_frame,
skymodel,
apply_throughput_correction=False,
zero_ivar=zero_ivar)
# then find cosmics
log.info("cosmics ray 1D rejection after sky subtraction")
reject_cosmic_rays_1d(copied_frame, args.cosmics_nsig)
# copy mask
frame.mask = copied_frame.mask
# and (re-)subtract sky, but just the correction term
subtract_sky(frame,
skymodel,
apply_throughput_correction=(
not args.no_sky_throughput_correction),
zero_ivar=zero_ivar)
else:
# subtract sky
subtract_sky(frame,
skymodel,
apply_throughput_correction=(
not args.no_sky_throughput_correction),
zero_ivar=zero_ivar)
compute_and_append_frame_scores(frame, suffix="SKYSUB")
if not args.no_xtalk:
log.info("fiber crosstalk correction")
correct_fiber_crosstalk(frame, fiberflat)
if not args.no_zero_ivar:
frame.ivar *= (frame.mask == 0)
if args.calib != None:
log.info("calibrate")
# read calibration
fluxcalib = read_flux_calibration(args.calib)
# apply calibration
apply_flux_calibration(frame, fluxcalib)
# Ensure that ivars are set to 0 for all values if any designated
# fibermask bit is set. Also flips a bits for each frame.mask value using specmask.BADFIBER
frame = get_fiberbitmasked_frame(
frame, bitmask="flux", ivar_framemask=(not args.no_zero_ivar))
compute_and_append_frame_scores(frame, suffix="CALIB")
if not args.no_tsnr:
log.info("calculating tsnr")
results, alpha = calc_tsnr2(uncalibrated_frame,
fiberflat=fiberflat,
skymodel=skymodel,
fluxcalib=fluxcalib,
alpha_only=args.alpha_only)
frame.meta['TSNRALPH'] = alpha
comments = {k: "from calc_frame_tsnr" for k in results.keys()}
append_frame_scores(frame, results, comments, overwrite=True)
# record inputs
frame.meta['IN_FRAME'] = shorten_filename(args.infile)
frame.meta['FIBERFLT'] = shorten_filename(args.fiberflat)
frame.meta['IN_SKY'] = shorten_filename(args.sky)
frame.meta['IN_CALIB'] = shorten_filename(args.calib)
# save output
write_frame(args.outfile, frame, units='10**-17 erg/(s cm2 Angstrom)')
log.info("successfully wrote %s" % args.outfile)