def read_spectra(spplate_name, targetids=None, use_frames=False,
fiberid=None, coadd=False):
"""Read targets from a list of spectra files
Args:
spplate_name (str): input spPlate file
targetids (list): restrict targets to this subset.
use_frames (bool): if True, use frames.
fiberid (int): Use this fiber ID.
coadd (bool): if True, compute and use the coadds.
Returns:
tuple: (targets, meta) where targets is a list of Target objects and
meta is a Table of metadata (currently only BRICKNAME).
"""
## read spplate
spplate = fitsio.FITS(spplate_name)
plate = spplate[0].read_header()["PLATEID"]
mjd = spplate[0].read_header()["MJD"]
if not use_frames:
infiles = [spplate_name]
if use_frames:
path = os.path.dirname(spplate_name)
cameras = ['b1','r1','b2','r2']
infiles = []
nexp_tot=0
for c in cameras:
try:
nexp = spplate[0].read_header()["NEXP_{}".format(c.upper())]
except ValueError:
print("DEBUG: spplate {} has no exposures in camera {} ".format(spplate_name,c))
continue
for i in range(1,nexp+1):
nexp_tot += 1
expid = str(nexp_tot)
if nexp_tot<10:
expid = '0'+expid
exp = path+"/spCFrame-"+spplate[0].read_header()["EXPID"+expid][:11]+".fits"
infiles.append(exp)
spplate.close()
bricknames={}
dic_spectra = {}
for infile in infiles:
h = fitsio.FITS(infile)
assert plate == h[0].read_header()["PLATEID"]
fs = h[5]["FIBERID"][:]
if fiberid is not None:
w = np.in1d(fs,fiberid)
fs = fs[w]
fl = h[0].read()
iv = h[1].read()*(h[2].read()==0)
wd = h[4].read()
## crop to lmin, lmax
lmin = 3500.
lmax = 10000.
if use_frames:
la = 10**h[3].read()
if h[0].read_header()["CAMERAS"][0]=="b":
lmax = 6000.
else:
lmin = 5500.
else:
coeff0 = h[0].read_header()["COEFF0"]
coeff1 = h[0].read_header()["COEFF1"]
la = 10**(coeff0 + coeff1*np.arange(fl.shape[1]))
la = np.broadcast_to(la,fl.shape)
imin = abs(la-lmin).min(axis=0).argmin()
imax = abs(la-lmax).min(axis=0).argmin()
la = la[:,imin:imax]
fl = fl[:,imin:imax]
iv = iv[:,imin:imax]
wd = wd[:,imin:imax]
w = wd<1e-5
wd[w]=2.
ii = np.arange(la.shape[1])
di = ii-ii[:,None]
di2 = di**2
ndiag = int(4*np.ceil(wd.max())+1)
nbins = wd.shape[1]
for f in fs:
i = (f-1)
if use_frames:
i = i%500
if np.all(iv[i]==0):
print("DEBUG: skipping plate,fid = {},{} (no data)".format(plate,f))
continue
t = platemjdfiber2targetid(plate, mjd, f)
if t not in dic_spectra:
dic_spectra[t]=[]
brickname = '{}-{}'.format(plate,mjd)
bricknames[t] = brickname
## build resolution from wdisp
reso = np.zeros([ndiag,nbins])
for idiag in range(ndiag):
offset = ndiag//2-idiag
d = np.diagonal(di2,offset=offset)
if offset<0:
reso[idiag,:len(d)] = np.exp(-d/2/wd[i,:len(d)]**2)
else:
reso[idiag,nbins-len(d):nbins]=np.exp(-d/2/wd[i,nbins-len(d):nbins]**2)
R = Resolution(reso)
ccd = sparse.spdiags(1./R.sum(axis=1).T, 0, *R.shape)
R = (ccd*R).todia()
dic_spectra[t].append(Spectrum(la[i], fl[i], iv[i], R, R.tocsr()))
h.close()
print("DEBUG: read {} ".format(infile))
if targetids == None:
targetids = sorted(list(dic_spectra.keys()))
targets = []
for targetid in targetids:
spectra = dic_spectra[targetid]
# Add the brickname to the meta dictionary. The keys of this dictionary
# will end up as extra columns in the output ZBEST HDU.
tmeta = dict()
tmeta["BRICKNAME"] = bricknames[targetid]
tmeta["BRICKNAME_datatype"] = "S8"
if len(spectra) > 0:
targets.append(Target(targetid, spectra, coadd=coadd, meta=tmeta))
else:
print('ERROR: Target {} on {} has no good spectra'.format(targetid, os.path.basename(brickfiles[0])))
#- Create a metadata table in case we might want to add other columns
#- in the future
assert len(bricknames.keys()) == len(targets)
metatable = Table(names=("TARGETID", "BRICKNAME"), dtype=("i8", "S8",))
for t in targetids:
metatable.add_row( (t, bricknames[t]) )
return targets, metatable
