def main() :
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--infile', type = str, default = None, required=True,
help = 'path of DESI exposure frame fits file')
parser.add_argument('--fiberflat', type = str, default = None,
help = 'path of DESI fiberflat fits file')
parser.add_argument('--sky', type = str, default = None,
help = 'path of DESI sky fits file')
parser.add_argument('--calib', type = str, default = None,
help = 'path of DESI calibration fits file')
parser.add_argument('--outfile', type = str, default = None, required=True,
help = 'path of DESI sky fits file')
# add calibration here when exists
args = parser.parse_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)
if args.fiberflat!=None :
log.info("apply fiberflat")
# read fiberflat
fiberflat = read_fiberflat(args.fiberflat)
# apply fiberflat to sky fibers
apply_fiberflat(frame, fiberflat)
if args.sky!=None :
log.info("subtract sky")
# read sky
skymodel=read_sky(args.sky)
# subtract sky
subtract_sky(frame, skymodel)
if args.calib!=None :
log.info("calibrate")
# read calibration
fluxcalib=read_flux_calibration(args.calib)
# apply calibration
apply_flux_calibration(frame, fluxcalib)
# save output
write_frame(args.outfile, frame)
log.info("successfully wrote %s"%args.outfile)
def test_apply_fluxcalibration(self):
#get frame_data
wave = np.arange(5000, 6000)
nwave = len(wave)
nspec = 3
flux = np.random.uniform(0.9, 1.0, size=(nspec, nwave))
ivar = np.ones_like(flux)
origframe = Frame(wave, flux, ivar, spectrograph=0)
#define fluxcalib object
calib = np.ones_like(origframe.flux)
mask = np.zeros(origframe.flux.shape, dtype=np.uint32)
calib[0] *= 0.5
calib[1] *= 1.5
# fc with essentially no error
fcivar = 1e20 * np.ones_like(origframe.flux)
fc = FluxCalib(origframe.wave, calib, fcivar,mask)
frame = copy.deepcopy(origframe)
apply_flux_calibration(frame, fc)
self.assertTrue(np.allclose(frame.ivar, calib**2))
# origframe.flux=0 should result in frame.flux=0
fcivar = np.ones_like(origframe.flux)
calib = np.ones_like(origframe.flux)
fc = FluxCalib(origframe.wave, calib, fcivar, mask)
frame = copy.deepcopy(origframe)
frame.flux[0,0:10]=0.0
apply_flux_calibration(frame, fc)
self.assertTrue(np.all(frame.flux[0, 0:10] == 0.0))
#fcivar=0 should result in frame.ivar=0
fcivar=np.ones_like(origframe.flux)
calib=np.ones_like(origframe.flux)
fcivar[0,0:10]=0.0
fc=FluxCalib(origframe.wave,calib,fcivar,mask)
frame=copy.deepcopy(origframe)
apply_flux_calibration(frame,fc)
self.assertTrue(np.all(frame.ivar[0,0:10]==0.0))
# should also work even the calib =0 ??
#fcivar=np.ones_like(origframe.flux)
#calib=np.ones_like(origframe.flux)
#fcivar[0,0:10]=0.0
#calib[0,0:10]=0.0
#fc=FluxCalib(origframe.wave,calib,fcivar,mask)
#frame=copy.deepcopy(origframe)
#apply_flux_calibration(frame,fc)
#self.assertTrue(np.all(frame.ivar[0,0:10]==0.0))
# test different wavelength bins
frame=copy.deepcopy(origframe)
calib = np.ones_like(frame.flux)
fcivar=np.ones_like(frame.ivar)
mask=np.zeros(origframe.flux.shape, dtype=np.uint32)
fc=FluxCalib(origframe.wave+0.01,calib,fcivar,mask)
with self.assertRaises(SystemExit): #should be ValueError instead?
apply_flux_calibration(frame,fc)
def test_apply_fluxcalibration(self):
#get frame_data
wave = np.arange(5000, 6000)
nwave = len(wave)
nspec = 3
flux = np.random.uniform(0.9, 1.0, size=(nspec, nwave))
ivar = np.ones_like(flux)
origframe = Frame(wave, flux, ivar, spectrograph=0)
#define fluxcalib object
calib = np.ones_like(origframe.flux)
mask = np.zeros(origframe.flux.shape, dtype=np.uint32)
calib[0] *= 0.5
calib[1] *= 1.5
# fc with essentially no error
fcivar = 1e20 * np.ones_like(origframe.flux)
fc = FluxCalib(origframe.wave, calib, fcivar,mask)
frame = copy.deepcopy(origframe)
apply_flux_calibration(frame, fc)
self.assertTrue(np.allclose(frame.ivar, calib**2))
# origframe.flux=0 should result in frame.flux=0
fcivar = np.ones_like(origframe.flux)
calib = np.ones_like(origframe.flux)
fc = FluxCalib(origframe.wave, calib, fcivar, mask)
frame = copy.deepcopy(origframe)
frame.flux[0,0:10]=0.0
apply_flux_calibration(frame, fc)
self.assertTrue(np.all(frame.flux[0, 0:10] == 0.0))
#fcivar=0 should result in frame.ivar=0
fcivar=np.ones_like(origframe.flux)
calib=np.ones_like(origframe.flux)
fcivar[0,0:10]=0.0
fc=FluxCalib(origframe.wave,calib,fcivar,mask)
frame=copy.deepcopy(origframe)
apply_flux_calibration(frame,fc)
self.assertTrue(np.all(frame.ivar[0,0:10]==0.0))
# should also work even the calib =0 ??
#fcivar=np.ones_like(origframe.flux)
#calib=np.ones_like(origframe.flux)
#fcivar[0,0:10]=0.0
#calib[0,0:10]=0.0
#fc=FluxCalib(origframe.wave,calib,fcivar,mask)
#frame=copy.deepcopy(origframe)
#apply_flux_calibration(frame,fc)
#self.assertTrue(np.all(frame.ivar[0,0:10]==0.0))
# test different wavelength bins
frame=copy.deepcopy(origframe)
calib = np.ones_like(frame.flux)
fcivar=np.ones_like(frame.ivar)
mask=np.zeros(origframe.flux.shape, dtype=np.uint32)
fc=FluxCalib(origframe.wave+0.01,calib,fcivar,mask)
with self.assertRaises(SystemExit): #should be ValueError instead?
apply_flux_calibration(frame,fc)
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)
if args.fiberflat!=None :
log.info("apply fiberflat")
# read fiberflat
fiberflat = read_fiberflat(args.fiberflat)
# apply fiberflat to sky fibers
apply_fiberflat(frame, fiberflat)
if args.sky!=None :
log.info("subtract sky")
# read sky
skymodel=read_sky(args.sky)
# subtract sky
subtract_sky(frame, skymodel)
if args.calib!=None :
log.info("calibrate")
# read calibration
fluxcalib=read_flux_calibration(args.calib)
# apply calibration
apply_flux_calibration(frame, fluxcalib)
# save output
write_frame(args.outfile, frame, units='1e-17 erg/(s cm2 A)')
log.info("successfully wrote %s"%args.outfile)
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--infile',
type=str,
default=None,
required=True,
help='path of DESI exposure frame fits file')
parser.add_argument('--fiberflat',
type=str,
default=None,
help='path of DESI fiberflat fits file')
parser.add_argument('--sky',
type=str,
default=None,
help='path of DESI sky fits file')
parser.add_argument('--calib',
type=str,
default=None,
help='path of DESI calibration fits file')
parser.add_argument('--outfile',
type=str,
default=None,
required=True,
help='path of DESI sky fits file')
# add calibration here when exists
args = parser.parse_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)
if args.fiberflat != None:
log.info("apply fiberflat")
# read fiberflat
fiberflat = read_fiberflat(args.fiberflat)
# apply fiberflat to sky fibers
apply_fiberflat(frame, fiberflat)
if args.sky != None:
log.info("subtract sky")
# read sky
skymodel = read_sky(args.sky)
# subtract sky
subtract_sky(frame, skymodel)
if args.calib != None:
log.info("calibrate")
# read calibration
fluxcalib = read_flux_calibration(args.calib)
# apply calibration
apply_flux_calibration(frame, fluxcalib)
# save output
write_frame(args.outfile, frame)
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)
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)
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)