def update_hdr_config(self):
self.survey = self.survey_widget.value.lower()
self.hetdex_api_config = HDRconfig( survey=self.survey)
self.FibIndex = FiberIndex(self.survey)
self.ampflag_table = Table.read(self.hetdex_api_config.badamp)
# update survey class and shot list
self.survey_class = Survey(self.survey)
if shotid in badshot:
print("Shot is in badshot list. Making mask zero everywhere")
badshot = True
else:
badshot = False
# also check if shot is in bad throughput list
# and set mask to zero everywhere
badtpshots = np.loadtxt(config.lowtpshots, dtype=int)
if shotid in badtpshots:
badshot = True
print("Shot has bad throughput. Setting flux limit mask to 0")
bad_amps = Table.read(config.badamp)
FibIndex = FiberIndex()
try:
hdf_filename = return_sensitivity_hdf_path(datevshot,
release=LATEST_HDR_NAME)
except NoFluxLimsAvailable:
sys.exit("No flux limit file found for " + datevshot)
flimhdf = SensitivityCubeHDF5Container(
filename=hdf_filename, aper_corr=1.0, flim_model="hdr2pt1"
)
hdf_outfilename = datevshot + "_mask.h5"
fileh = tb.open_file(hdf_outfilename, "w")
def get_source_spectra_mp(source_dict, shotid, manager, args):
E = Extract()
FibIndex = FiberIndex(args.survey)
if args.survey == "hdr1":
source_num_switch = 20
else:
source_num_switch = 0
if len(args.matched_sources[shotid]) > 0:
args.log.info("Working on shot: %s" % shotid)
if args.survey == "hdr1":
fwhm = args.survey_class.fwhm_moffat[args.survey_class.shotid ==
shotid][0]
else:
fwhm = args.survey_class.fwhm_virus[args.survey_class.shotid ==
shotid][0]
moffat = E.moffat_psf(fwhm, 10.5, 0.25)
if len(args.matched_sources[shotid]) > source_num_switch:
E.load_shot(shotid, fibers=True, survey=args.survey)
else:
E.load_shot(shotid, fibers=False, survey=args.survey)
for ind in args.matched_sources[shotid]:
try:
info_result = E.get_fiberinfo_for_coord(
args.coords[ind],
radius=args.rad,
ffsky=args.ffsky,
return_fiber_info=True,
)
except TypeError:
info_result = E.get_fiberinfo_for_coord(
args.coords,
radius=args.rad,
ffsky=args.ffsky,
return_fiber_info=True,
)
if info_result is not None:
if np.size(args.ID) > 1:
args.log.info("Extracting %s" % args.ID[ind])
else:
args.log.info("Extracting %s" % args.ID)
ifux, ifuy, xc, yc, ra, dec, data, error, mask, fiberid, \
multiframe = info_result
weights = E.build_weights(xc, yc, ifux, ifuy, moffat)
# added by EMC 20210609
norm = np.sum(weights, axis=0)
weights = weights / norm[np.newaxis, :]
result = E.get_spectrum(data,
error,
mask,
weights,
remove_low_weights=False)
spectrum_aper, spectrum_aper_error = [res for res in result]
# apply aperture correction
spectrum_aper /= norm
spectrum_aper_error /= norm
weights *= norm[np.newaxis, :]
#add in the total weight of each fiber (as the sum of its weight per wavebin)
if args.fiberweights:
try:
fiber_weights = np.array([
x for x in zip(ra, dec,
np.sum(weights * mask, axis=1))
])
except:
fiber_weights = []
else:
fiber_weights = []
# get fiber info no matter what so we can flag
try:
fiber_info = np.array([
x for x in zip(fiberid, multiframe, ra, dec,
np.sum(weights * mask, axis=1))
])
except:
args.log.warning(
'Could not get fiber info, no flagging created')
fiber_info = []
if len(fiber_info) > 0:
try:
flags = FibIndex.get_fiber_flags(
coord=args.coords[ind], shotid=shotid)
except:
flags = FibIndex.get_fiber_flags(coord=args.coords,
shotid=shotid)
else:
flags = None
if np.size(args.ID) > 1:
if args.ID[ind] in source_dict:
source_dict[args.ID[ind]][shotid] = [
spectrum_aper,
spectrum_aper_error,
weights.sum(axis=0),
fiber_weights,
fiber_info,
flags,
]
else:
source_dict[args.ID[ind]] = manager.dict()
source_dict[args.ID[ind]][shotid] = [
spectrum_aper,
spectrum_aper_error,
weights.sum(axis=0),
fiber_weights,
fiber_info,
flags,
]
else:
if args.ID in source_dict:
source_dict[args.ID][shotid] = [
spectrum_aper,
spectrum_aper_error,
weights.sum(axis=0),
fiber_weights,
fiber_info,
flags,
]
else:
source_dict[args.ID] = manager.dict()
source_dict[args.ID][shotid] = [
spectrum_aper,
spectrum_aper_error,
weights.sum(axis=0),
fiber_weights,
fiber_info,
flags,
]
E.shoth5.close()
FibIndex.close()
return source_dict