def main(args=None):
log = get_logger()
if args is None:
args = parse()
if args.lin_step is not None and args.log10_step is not None:
print(
"cannot have both linear and logarthmic bins :-), choose either --lin-step or --log10-step"
)
return 12
if args.coadd_cameras and (args.lin_step is not None
or args.log10_step is not None):
print(
"cannot specify a new wavelength binning along with --coadd-cameras option"
)
return 12
log.info("reading spectra ...")
spectra = read_spectra(args.infile)
if args.coadd_cameras:
log.info("coadding cameras ...")
spectra = coadd_cameras(spectra, cosmics_nsig=args.nsig)
else:
log.info("coadding ...")
coadd(spectra, cosmics_nsig=args.nsig)
if args.lin_step is not None:
log.info("resampling ...")
spectra = resample_spectra_lin_or_log(spectra,
linear_step=args.lin_step,
wave_min=args.wave_min,
wave_max=args.wave_max,
fast=args.fast,
nproc=args.nproc)
if args.log10_step is not None:
log.info("resampling ...")
spectra = resample_spectra_lin_or_log(spectra,
log10_step=args.log10_step,
wave_min=args.wave_min,
wave_max=args.wave_max,
fast=args.fast,
nproc=args.nproc)
log.info("writing {} ...".format(args.outfile))
write_spectra(args.outfile, spectra)
log.info("done")
def test_fiberstatus(self):
"""Test that FIBERSTATUS=0 isn't included in coadd"""
def _makespec(nspec, nwave):
s1 = self._random_spectra(nspec, nwave)
s1.flux['x'][:,:] = 1.0
s1.ivar['x'][:,:] = 1.0
return s1
#- Nothing masked
nspec, nwave = 4,10
s1 = _makespec(nspec, nwave)
expt = 33 # random number
s1.fibermap['EXPTIME'][:]=expt
self.assertEqual(len(s1.fibermap), nspec)
coadd(s1)
self.assertEqual(len(s1.fibermap), 1)
self.assertEqual(s1.fibermap['COADD_NUMEXP'][0], nspec)
self.assertEqual(s1.fibermap['COADD_EXPTIME'][0], expt*nspec)
self.assertEqual(s1.fibermap['FIBERSTATUS'][0], 0)
self.assertTrue(np.all(s1.flux['x'] == 1.0))
self.assertTrue(np.allclose(s1.ivar['x'], 1.0*nspec))
#- Two spectra masked
nspec, nwave = 5,10
s1 = _makespec(nspec, nwave)
self.assertEqual(len(s1.fibermap), nspec)
s1.fibermap['FIBERSTATUS'][0] = fibermask.BROKENFIBER
s1.fibermap['FIBERSTATUS'][1] = fibermask.BADFIBER
coadd(s1)
self.assertEqual(len(s1.fibermap), 1)
self.assertEqual(s1.fibermap['COADD_NUMEXP'][0], nspec-2)
self.assertEqual(s1.fibermap['FIBERSTATUS'][0], 0)
self.assertTrue(np.all(s1.flux['x'] == 1.0))
self.assertTrue(np.allclose(s1.ivar['x'], 1.0*(nspec-2)))
#- All spectra masked
nspec, nwave = 5,10
s1 = _makespec(nspec, nwave)
self.assertEqual(len(s1.fibermap), nspec)
s1.fibermap['FIBERSTATUS'] = fibermask.BROKENFIBER
coadd(s1)
self.assertEqual(len(s1.fibermap), 1)
self.assertEqual(s1.fibermap['COADD_NUMEXP'][0], 0)
self.assertEqual(s1.fibermap['FIBERSTATUS'][0], fibermask.BROKENFIBER)
self.assertTrue(np.all(s1.flux['x'] == 0.0))
self.assertTrue(np.all(s1.ivar['x'] == 0.0))
def test_coadd(self):
"""Test coaddition"""
s1 = self._random_spectra(3, 10)
coadd(s1)
def main(args=None):
log = get_logger()
if args is None:
args = parse()
if args.lin_step is not None and args.log10_step is not None:
log.critical(
"cannot have both linear and logarthmic bins :-), choose either --lin-step or --log10-step"
)
return 12
if args.coadd_cameras and (args.lin_step is not None
or args.log10_step is not None):
log.critical(
"cannot specify a new wavelength binning along with --coadd-cameras option"
)
return 12
if len(args.infile) == 0:
log.critical("You must specify input files")
return 12
log.info("reading input ...")
# inspect headers
input_is_frames = False
input_is_spectra = False
for filename in args.infile:
ifile = fitsio.FITS(filename)
head = ifile[0].read_header()
identified = False
if "EXTNAME" in head and head["EXTNAME"] == "FLUX":
print(filename, "is a frame")
input_is_frames = True
identified = True
ifile.close()
continue
for hdu in ifile:
head = hdu.read_header()
if "EXTNAME" in head and head["EXTNAME"].find("_FLUX") >= 0:
print(filename, "is a spectra")
input_is_spectra = True
identified = True
break
ifile.close()
if not identified:
log.error(
"{} not identified as frame of spectra file".format(filename))
sys.exit(1)
if input_is_frames and input_is_spectra:
log.error("cannot combine input spectra and frames")
sys.exit(1)
if input_is_spectra:
spectra = read_spectra(args.infile[0])
for filename in args.infile[1:]:
log.info("append {}".format(filename))
spectra.update(read_spectra(filename))
else: # frames
frames = dict()
cameras = {}
for filename in args.infile:
frame = read_frame(filename)
night = frame.meta['NIGHT']
expid = frame.meta['EXPID']
camera = frame.meta['CAMERA']
frames[(night, expid, camera)] = frame
if args.coadd_cameras:
cam, spec = camera[0], camera[1]
# Keep a list of cameras (b,r,z) for each exposure + spec
if (night, expid) not in cameras.keys():
cameras[(night, expid)] = {spec: [cam]}
elif spec not in cameras[(night, expid)].keys():
cameras[(night, expid)][spec] = [cam]
else:
cameras[(night, expid)][spec].append(cam)
if args.coadd_cameras:
# If not all 3 cameras are available, remove the incomplete sets
for (night, expid), camdict in cameras.items():
for spec, camlist in camdict.items():
log.info("Found {} for SP{} on NIGHT {} EXP {}".format(
camlist, spec, night, expid))
if len(camlist) != 3 or np.any(
np.sort(camlist) != np.array(['b', 'r', 'z'])):
for cam in camlist:
frames.pop((night, expid, cam + spec))
log.warning(
"Removing {}{} from Night {} EXP {}".format(
cam, spec, night, expid))
#import pdb
#pdb.set_trace()
spectra = frames2spectra(frames)
#- hacks to make SpectraLite like a Spectra
spectra.fibermap = Table(spectra.fibermap)
del frames #- maybe free some memory
if args.coadd_cameras:
log.info("coadding cameras ...")
spectra = coadd_cameras(spectra, cosmics_nsig=args.nsig)
else:
log.info("coadding ...")
coadd(spectra, cosmics_nsig=args.nsig)
if args.lin_step is not None:
log.info("resampling ...")
spectra = resample_spectra_lin_or_log(spectra,
linear_step=args.lin_step,
wave_min=args.wave_min,
wave_max=args.wave_max,
fast=args.fast,
nproc=args.nproc)
if args.log10_step is not None:
log.info("resampling ...")
spectra = resample_spectra_lin_or_log(spectra,
log10_step=args.log10_step,
wave_min=args.wave_min,
wave_max=args.wave_max,
fast=args.fast,
nproc=args.nproc)
#- Add input files to header
if spectra.meta is None:
spectra.meta = dict()
for i, filename in enumerate(args.infile):
spectra.meta['INFIL{:03d}'.format(i)] = os.path.basename(filename)
log.info("writing {} ...".format(args.outfile))
write_spectra(args.outfile, spectra)
log.info("done")