def parallel_rm(xxx_todo_changeme ):
(plate,mjd,fiberid) = xxx_todo_changeme
specs = spec.Spec(plate=plate, mjd=mjd, fiberid=fiberid)
zssp = zfinder.ZFinder(fname='ndArch-ssp_em_galaxy-v000.fits', npoly=4, zmin=-0.01, zmax=1.2)
zssp.zchi2(specs.flux, specs.loglambda, specs.ivar)
# Write chi2 file with zbase
prihdu = fits.PrimaryHDU(zssp.zchi2arr)
col1 = fits.Column(name='ZBASE', format='E', array=zssp.zbase)
cols = fits.ColDefs([col1])
tbhdu = fits.BinTableHDU.from_columns(cols)
thdulist = fits.HDUList([prihdu,tbhdu])
thdulist.writeto('/uufs/astro.utah.edu/common/home/u0814744/scratch/screens/chi2arr-%s-%s.fits' % (plate, zssp.type), overwrite=True)
# ----
zstar = zfinder.ZFinder(fname='ndArch-spEigenStar-55734.fits', npoly=4, zmin=-.005, zmax=.005)
zstar.zchi2(specs.flux, specs.loglambda, specs.ivar)
# Write chi2 file with zbase
prihdu = fits.PrimaryHDU(zstar.zchi2arr)
col1 = fits.Column(name='ZBASE', format='E', array=zstar.zbase)
cols = fits.ColDefs([col1])
tbhdu = fits.BinTableHDU.from_columns(cols)
thdulist = fits.HDUList([prihdu,tbhdu])
thdulist.writeto('/uufs/astro.utah.edu/common/home/u0814744/scratch/screens/chi2arr-%s-%s.fits' % (plate, zstar.type), overwrite=True)
# ----
zfit_ssp = zfitter.ZFitter(zssp.zchi2arr, zssp.zbase)
zfit_ssp.z_refine()
zfit_star = zfitter.ZFitter(zstar.zchi2arr, zstar.zbase)
zfit_star.z_refine()
ssp_flags = misc.comb_flags(specs, zssp, zfit_ssp)
star_flags = misc.comb_flags(specs, zstar, zfit_star)
zpick = zpicker.ZPicker(specs, zssp, zfit_ssp, ssp_flags, zstar, zfit_star, star_flags)
# Write flags file
prihdu = fits.PrimaryHDU(zpick.zwarning)
thdulist = fits.HDUList([prihdu])
thdulist.writeto('/uufs/astro.utah.edu/common/home/u0814744/scratch/screens/flags-%s.fits' % plate, overwrite=True)
output = io.WriteRedmonster(zpick, dest='/uufs/astro.utah.edu/common/home/u0814744/scratch/screens', overwrite=True)
def parallel_rm(xxx_todo_changeme ):
(plate,mjd,fiberid) = xxx_todo_changeme
specs = spec.Spec(plate=plate, mjd=mjd, fiberid=fiberid)
zssp = zfinder.ZFinder(fname='ndArch-ssp_em_galaxy-v000.fits', npoly=4, zmin=-0.01, zmax=1.2)
zssp.zchi2(specs.flux, specs.loglambda, specs.ivar)
# Write chi2 file with zbase
prihdu = fits.PrimaryHDU(zssp.zchi2arr)
col1 = fits.Column(name='ZBASE', format='E', array=zssp.zbase)
cols = fits.ColDefs([col1])
tbhdu = fits.BinTableHDU.from_columns(cols)
thdulist = fits.HDUList([prihdu,tbhdu])
thdulist.writeto('/uufs/astro.utah.edu/common/home/u0814744/scratch/screens/chi2arr-%s-%s.fits' % (plate, zssp.type), clobber=True)
# ----
zstar = zfinder.ZFinder(fname='ndArch-spEigenStar-55734.fits', npoly=4, zmin=-.005, zmax=.005)
zstar.zchi2(specs.flux, specs.loglambda, specs.ivar)
# Write chi2 file with zbase
prihdu = fits.PrimaryHDU(zstar.zchi2arr)
col1 = fits.Column(name='ZBASE', format='E', array=zstar.zbase)
cols = fits.ColDefs([col1])
tbhdu = fits.BinTableHDU.from_columns(cols)
thdulist = fits.HDUList([prihdu,tbhdu])
thdulist.writeto('/uufs/astro.utah.edu/common/home/u0814744/scratch/screens/chi2arr-%s-%s.fits' % (plate, zstar.type), clobber=True)
# ----
zfit_ssp = zfitter.ZFitter(zssp.zchi2arr, zssp.zbase)
zfit_ssp.z_refine()
zfit_star = zfitter.ZFitter(zstar.zchi2arr, zstar.zbase)
zfit_star.z_refine()
ssp_flags = misc.comb_flags(specs, zssp, zfit_ssp)
star_flags = misc.comb_flags(specs, zstar, zfit_star)
zpick = zpicker.ZPicker(specs, zssp, zfit_ssp, ssp_flags, zstar, zfit_star, star_flags)
# Write flags file
prihdu = fits.PrimaryHDU(zpick.zwarning)
thdulist = fits.HDUList([prihdu])
thdulist.writeto('/uufs/astro.utah.edu/common/home/u0814744/scratch/screens/flags-%s.fits' % plate, clobber=True)
output = io.WriteRedmonster(zpick, dest='/uufs/astro.utah.edu/common/home/u0814744/scratch/screens', clobber=True)
def reduce_gen(self, filepath=None, data_range=None, chi2file=False):
self.chi2file = False
if filepath is None: print("Invalid file path.")
else:
specs = io2.SpecGen(filepath=filepath)
zfindobjs = []
zfitobjs = []
if (self.zmin is not None) & (self.zmax is not None):
for i in range(len(self.templates)):
zfindobjs.append( zfinder.ZFinder(fname=self.templates[i],
group=self.group[i],
npoly=self.npoly[i],
zmin=self.zmin[i],
zmax=self.zmax[i],
nproc=self.nproc) )
zfindobjs[i].zchi2(specs.flux, specs.loglambda, specs.ivar,
npixstep=self.npixstep[i],
chi2file=self.chi2file)
zfitobjs.append( zfitter.ZFitter(zfindobjs[i].zchi2arr,
zfindobjs[i].zbase) )
zfitobjs[i].z_refine2()
else:
for i in range(len(self.templates)):
zfindobjs.append( zfinder.ZFinder(fname=self.templates[i],
group=self.group[i],
npoly=self.npoly[i],
npixstep=self.npixstep[i],
nproc=self.nproc) )
zfindobjs[i].zchi2( specs.flux, specs.loglambda, specs.ivar,
npixstep=self.npixstep[i],
chi2file=self.chi2file )
zfitobjs.append( zfitter.ZFitter(zfindobjs[i].zchi2arr,
zfindobjs[i].zbase) )
zfitobjs[i].z_refine2()
# Flags
flags = []
for i in range(len(zfindobjs)):
flags.append( misc.comb_flags(specs, zfindobjs[i], zfitobjs[i]))
# ZPicker
zpick = zpicker2.ZPicker(specs, zfindobjs, zfitobjs, flags)
output = None
# Write output
if self.dest is None:
output = io2.WriteRedmonster(zpick, dest=filepath, overwrite=True)
if output:
output.write_gen()
def reduce_plate_mjd(self, plate, mjd, fiberid=None, chi2file=False):
self.chi2file = chi2file
# Check types and try to convert to proper types if necessary
if fiberid is None: fiberid = [i for i in range(1000)]
else:
if type(fiberid) is not list:
try:
fiberid = [fiberid]
fiberid = list(map(int, fiberid))
except:
try:
fiberid = fiberid.tolist()
fiberid = list(map(int, fiberid))
except:
print('fiberid not set properly - running full plate!')
fiberid = [i for i in range(1000)]
else:
fiberid = list(map(int, fiberid))
# Spec
specs = spec.Spec(plate=plate, mjd=mjd, fiberid=fiberid)
# ZFinder, ZFitter
zfindobjs = []
zfitobjs = []
if (self.zmin is not None) & (self.zmax is not None):
for i in range(len(self.templates)):
zfindobjs.append(
zfinder.ZFinder(fname=self.templates[i],
npoly=self.npoly[i],
zmin=self.zmin[i],
zmax=self.zmax[i]))
zfindobjs[i].zchi2(specs.flux,
specs.loglambda,
specs.ivar,
npixstep=self.npixstep[i],
plate=plate,
mjd=mjd,
fiberid=fiberid[0],
chi2file=self.chi2file)
zfitobjs.append(
zfitter.ZFitter(zfindobjs[i].zchi2arr, zfindobjs[i].zbase))
zfitobjs[i].z_refine()
else:
for i in range(len(self.templates)):
zfindobjs.append(
zfinder.ZFinder(fname=self.templates[i],
npoly=self.npoly[i],
npixstep=self.npixstep[i]))
zfindobjs[i].zchi2(specs.flux,
specs.loglambda,
specs.ivar,
npixstep=self.npixstep[i],
plate=plate,
mjd=mjd,
fiberid=fiberid[0],
chi2file=self.chi2file)
zfitobjs.append(
zfitter.ZFitter(zfindobjs[i].zchi2arr, zfindobjs[i].zbase))
zfitobjs[i].z_refine()
# Flags
flags = []
for i in range(len(zfindobjs)):
flags.append(misc.comb_flags(specs, zfindobjs[i], zfitobjs[i]))
# ZPicker
if len(self.templates) == 1:
zpick = zpicker.ZPicker(specs, zfindobjs[0], zfitobjs[0], flags[0])
elif len(self.templates) == 2:
zpick = zpicker.ZPicker(specs, zfindobjs[0], zfitobjs[0], flags[0],
zfindobjs[1], zfitobjs[1], flags[1])
elif len(self.templates) == 3:
zpick = zpicker.ZPicker(specs, zfindobjs[0], zfitobjs[0], flags[0],
zfindobjs[1], zfitobjs[1], flags[1],
zfindobjs[2], zfitobjs[2], flags[2])
elif len(self.templates) == 4:
zpick = zpicker.ZPicker(specs, zfindobjs[0], zfitobjs[0], flags[0],
zfindobjs[1], zfitobjs[1], flags[1],
zfindobjs[2], zfitobjs[2], flags[2],
zfindobjs[3], zfitobjs[3], flags[3])
elif len(self.templates) == 5:
zpick = zpicker.ZPicker(specs, zfindobjs[0], zfitobjs[0], flags[0],
zfindobjs[1], zfitobjs[1], flags[1],
zfindobjs[2], zfitobjs[2], flags[2],
zfindobjs[3], zfitobjs[3], flags[3],
zfindobjs[4], zfitobjs[4], flags[4])
output = None
# Write output
if self.dest is None:
output = io.WriteRedmonster(zpick, overwrite=self.overwrite)
else:
if type(self.dest) is str:
output = io.WriteRedmonster(zpick,
dest=self.dest,
overwrite=self.overwrite)
else:
try:
self.dest = str(self.dest)
output = io.WriteRedmonster(zpick,
dest=self.dest,
overwrite=self.overwrite)
except:
print(
'Could not convert dest to string - writing to default directory and NOT clobbering old files!'
)
output = io.WriteRedmonster(zpick, overwrite=True)
if output:
if len(zpick.fiberid) == 1: output.write_fiberid()
else: output.write_plate()
def reduce_plate_mjd(self, plate, mjd, fiberid=None, chi2file=False):
self.chi2file = chi2file
# Check types and try to convert to proper types if necessary
if fiberid is None: fiberid = [i for i in range(1000)]
else:
if type(fiberid) is not list:
try:
fiberid = [fiberid]
fiberid = list(map(int, fiberid))
except:
try:
fiberid = fiberid.tolist()
fiberid = list(map(int, fiberid))
except:
print('fiberid not set properly - running full plate!')
fiberid = [i for i in range(1000)]
else: fiberid = list(map(int, fiberid))
# Spec
specs = spec.Spec(plate=plate, mjd=mjd, fiberid=fiberid)
# ZFinder, ZFitter
zfindobjs = []
zfitobjs = []
if (self.zmin is not None) & (self.zmax is not None):
for i in range(len(self.templates)):
zfindobjs.append( zfinder.ZFinder(fname=self.templates[i],
npoly=self.npoly[i],
zmin=self.zmin[i],
zmax=self.zmax[i]) )
zfindobjs[i].zchi2( specs.flux, specs.loglambda, specs.ivar,
npixstep=self.npixstep[i], plate=plate,
mjd=mjd, fiberid=fiberid[0],
chi2file=self.chi2file )
zfitobjs.append( zfitter.ZFitter(zfindobjs[i].zchi2arr,
zfindobjs[i].zbase) )
zfitobjs[i].z_refine()
else:
for i in range(len(self.templates)):
zfindobjs.append( zfinder.ZFinder(fname=self.templates[i],
npoly=self.npoly[i],
npixstep=self.npixstep[i]) )
zfindobjs[i].zchi2( specs.flux, specs.loglambda, specs.ivar,
npixstep=self.npixstep[i], plate=plate,
mjd=mjd, fiberid=fiberid[0],
chi2file=self.chi2file )
zfitobjs.append( zfitter.ZFitter(zfindobjs[i].zchi2arr,
zfindobjs[i].zbase) )
zfitobjs[i].z_refine()
# Flags
flags = []
for i in range(len(zfindobjs)):
flags.append( misc.comb_flags(specs, zfindobjs[i], zfitobjs[i]) )
# ZPicker
if len(self.templates) == 1:
zpick = zpicker.ZPicker(specs, zfindobjs[0], zfitobjs[0], flags[0])
elif len(self.templates) == 2: zpick = zpicker.ZPicker(specs, zfindobjs[0], zfitobjs[0], flags[0], zfindobjs[1], zfitobjs[1], flags[1])
elif len(self.templates) == 3: zpick = zpicker.ZPicker(specs, zfindobjs[0], zfitobjs[0], flags[0], zfindobjs[1], zfitobjs[1], flags[1],
zfindobjs[2], zfitobjs[2], flags[2])
elif len(self.templates) == 4: zpick = zpicker.ZPicker(specs, zfindobjs[0], zfitobjs[0], flags[0], zfindobjs[1], zfitobjs[1], flags[1],
zfindobjs[2], zfitobjs[2], flags[2], zfindobjs[3], zfitobjs[3], flags[3])
elif len(self.templates) == 5: zpick = zpicker.ZPicker(specs, zfindobjs[0], zfitobjs[0], flags[0], zfindobjs[1], zfitobjs[1], flags[1],
zfindobjs[2], zfitobjs[2], flags[2], zfindobjs[3], zfitobjs[3], flags[3],
zfindobjs[4], zfitobjs[4], flags[4])
output = None
# Write output
if self.dest is None:
output = io.WriteRedmonster(zpick, clobber=self.clobber)
else:
if type(self.dest) is str:
output = io.WriteRedmonster(zpick, dest=self.dest, clobber=self.clobber)
else:
try:
self.dest = str(self.dest)
output = io.WriteRedmonster(zpick, dest=self.dest, clobber=self.clobber)
except:
print('Could not convert dest to string - writing to default directory and NOT clobbering old files!')
output = io.WriteRedmonster(zpick, clobber=True)
if output:
if len(zpick.fiberid) == 1: output.write_fiberid()
else: output.write_plate()
''' Same as above for second template.'''
#zfit_ssp2 = zfitter.ZFitter(zssp2.zchi2arr, zssp2.zbase)
#zfit_ssp2.z_refine2()
zfit_star = zfitter.ZFitter(zstar.zchi2arr, zstar.zbase)
zfit_star.z_refine2()
zfit_qso = zfitter.ZFitter(zqso.zchi2arr, zqso.zbase)
zfit_qso.z_refine2()
''' Flagging throughout redmonster is done individually by the classes
responsible for handling the relevant computations. To have an
'overall' flag for each fiber, the individual flags need to be
combined.
'''
ssp1_flags = misc.comb_flags(specs, zssp1, zfit_ssp1)
#ssp2_flags = misc.comb_flags(specs, zssp2, zfit_ssp2)
star_flags = misc.comb_flags(specs, zstar, zfit_star)
qso_flags = misc.comb_flags(specs, zqso, zfit_qso)
''' Compare chi2 surfaces from each template and classify each object
accordingly. Arguments are data object (in a format identical to
that created by Spec), followed by each object created by ZFinder,
ZFitter, and flags, in that order. This function can currently
handle up to five objects from five separate templates. If specs
is a user created data object rather than one created by
redmonster.datamgr.spec, it must contain specs.npix, the number of
pixels in a single spectrum.
'''
#zpick = zpicker.ZPicker(specs, zssp, zfit_ssp, ssp_flags, zstar, zfit_star,
def reduce_gen(self, filepath=None, data_range=None, chi2file=False):
self.chi2file = False
if filepath is None: print("Invalid file path.")
else:
specs = io2.SpecGen(filepath=filepath)
zfindobjs = []
zfitobjs = []
if (self.zmin is not None) & (self.zmax is not None):
for i in range(len(self.templates)):
zfindobjs.append(
zfinder.ZFinder(fname=self.templates[i],
group=self.group[i],
npoly=self.npoly[i],
zmin=self.zmin[i],
zmax=self.zmax[i],
nproc=self.nproc))
zfindobjs[i].zchi2(specs.flux,
specs.loglambda,
specs.ivar,
npixstep=self.npixstep[i],
chi2file=self.chi2file)
zfitobjs.append(
zfitter.ZFitter(zfindobjs[i].zchi2arr,
zfindobjs[i].zbase))
zfitobjs[i].z_refine2()
else:
for i in range(len(self.templates)):
zfindobjs.append(
zfinder.ZFinder(fname=self.templates[i],
group=self.group[i],
npoly=self.npoly[i],
npixstep=self.npixstep[i],
nproc=self.nproc))
zfindobjs[i].zchi2(specs.flux,
specs.loglambda,
specs.ivar,
npixstep=self.npixstep[i],
chi2file=self.chi2file)
zfitobjs.append(
zfitter.ZFitter(zfindobjs[i].zchi2arr,
zfindobjs[i].zbase))
zfitobjs[i].z_refine2()
# Flags
flags = []
for i in range(len(zfindobjs)):
flags.append(misc.comb_flags(specs, zfindobjs[i], zfitobjs[i]))
# ZPicker
zpick = zpicker2.ZPicker(specs, zfindobjs, zfitobjs, flags)
output = None
# Write output
if self.dest is None:
output = io2.WriteRedmonster(zpick,
dest=filepath,
overwrite=True)
if output:
output.write_gen()
def reduce_plate_mjd(self,
plate=None,
mjd=None,
fiberid=None,
data_range=None,
chi2file=False,
platepath=None):
print "\nPlate %s MJD %s Fiber %s" % (plate, mjd, fiberid)
self.chi2file = chi2file
# Check types and try to convert to proper types if necessary
if fiberid is not None:
if type(fiberid) is not list:
try:
fiberid = [fiberid]
fiberid = list(map(int, fiberid))
except ValueError:
try:
fiberid = fiberid.tolist()
fiberid = list(map(int, fiberid))
except ValueError:
print('fiberid not set properly - running full plate!')
else:
fiberid = list(map(int, fiberid))
# Spec
specs = spec.Spec(plate=plate,
mjd=mjd,
fiberid=fiberid,
platepath=platepath)
fiberid = specs.fiberid
# ZFinder, ZFitter
zfindobjs = []
zfitobjs = []
if (self.zmin is not None) & (self.zmax is not None):
for i in range(len(self.templates)):
zfindobjs.append(
zfinder.ZFinder(fname=self.templates[i],
group=self.group[i],
npoly=self.npoly[i],
zmin=self.zmin[i],
zmax=self.zmax[i],
nproc=self.nproc))
if self.mask:
zfindobjs[i].zchi2(specs.flux,
specs.loglambda,
specs.ivar,
npixstep=self.npixstep[i],
plate=plate,
mjd=mjd,
fiberid=fiberid[0],
chi2file=self.chi2file,
linelist=__linelist__)
else:
zfindobjs[i].zchi2(specs.flux,
specs.loglambda,
specs.ivar,
npixstep=self.npixstep[i],
plate=plate,
mjd=mjd,
fiberid=fiberid[0],
chi2file=self.chi2file)
zfitobjs.append(
zfitter.ZFitter(zfindobjs[i].zchi2arr, zfindobjs[i].zbase))
zfitobjs[i].z_refine2()
else:
for i in range(len(self.templates)):
zfindobjs.append(
zfinder.ZFinder(fname=self.templates[i],
group=self.group[i],
npoly=self.npoly[i],
npixstep=self.npixstep[i],
nproc=self.nproc))
if mask:
zfindobjs[i].zchi2(specs.flux,
specs.loglambda,
specs.ivar,
npixstep=self.npixstep[i],
plate=plate,
mjd=mjd,
fiberid=fiberid[0],
chi2file=self.chi2file,
linelist=__linelist__)
else:
zfindobjs[i].zchi2(specs.flux,
specs.loglambda,
specs.ivar,
npixstep=self.npixstep[i],
plate=plate,
mjd=mjd,
fiberid=fiberid[0],
chi2file=self.chi2file)
zfitobjs.append(
zfitter.ZFitter(zfindobjs[i].zchi2arr, zfindobjs[i].zbase))
zfitobjs[i].z_refine2()
# Flags
flags = []
for i in range(len(zfindobjs)):
flags.append(misc.comb_flags(specs, zfindobjs[i], zfitobjs[i]))
# ZPicker
zpick = zpicker2.ZPicker(specs, zfindobjs, zfitobjs, flags)
output = None
# Write output
if self.dest is None:
output = io2.WriteRedmonster(zpick, overwrite=True)
else:
if type(self.dest) is str:
output = io2.WriteRedmonster(zpick,
dest=self.dest,
overwrite=True)
else:
try:
self.dest = str(self.dest)
output = io2.WriteRedmonster(zpick,
dest=self.dest,
overwrite=True)
except Exception as e:
print(
'Could not convert dest to string - writing to \
default directory and NOT clobbering old files! \
Exception: %r' % e)
output = io2.WriteRedmonster(zpick, overwrite=True)
if output:
if len(zpick.fiberid) == 1: output.write_fiber()
else: output.write_plate()
def reduce_plate_mjd(self, plate=None, mjd=None, fiberid=None, data_range=None, chi2file=False, platepath=None):
self.chi2file = chi2file
# Check types and try to convert to proper types if necessary
if fiberid is not None:
if type(fiberid) is not list:
try:
fiberid = [fiberid]
fiberid = map(int, fiberid)
except ValueError:
try:
fiberid = fiberid.tolist()
fiberid = map(int, fiberid)
except ValueError:
print "fiberid not set properly - running full plate!"
else:
fiberid = map(int, fiberid)
# Spec
specs = spec.Spec(plate=plate, mjd=mjd, fiberid=fiberid, platepath=platepath)
fiberid = specs.fiberid
# ZFinder, ZFitter
zfindobjs = []
zfitobjs = []
if (self.zmin is not None) & (self.zmax is not None):
for i in xrange(len(self.templates)):
zfindobjs.append(
zfinder.ZFinder(fname=self.templates[i], npoly=self.npoly[i], zmin=self.zmin[i], zmax=self.zmax[i])
)
zfindobjs[i].zchi2(
specs.flux,
specs.loglambda,
specs.ivar,
npixstep=self.npixstep[i],
plate=plate,
mjd=mjd,
fiberid=fiberid[0],
chi2file=self.chi2file,
)
zfitobjs.append(zfitter.ZFitter(zfindobjs[i].zchi2arr, zfindobjs[i].zbase))
zfitobjs[i].z_refine2()
else:
for i in xrange(len(self.templates)):
zfindobjs.append(
zfinder.ZFinder(fname=self.templates[i], npoly=self.npoly[i], npixstep=self.npixstep[i])
)
zfindobjs[i].zchi2(
specs.flux,
specs.loglambda,
specs.ivar,
npixstep=self.npixstep[i],
plate=plate,
mjd=mjd,
fiberid=fiberid[0],
chi2file=self.chi2file,
)
zfitobjs.append(zfitter.ZFitter(zfindobjs[i].zchi2arr, zfindobjs[i].zbase))
zfitobjs[i].z_refine2()
# Flags
flags = []
for i in xrange(len(zfindobjs)):
flags.append(misc.comb_flags(specs, zfindobjs[i], zfitobjs[i]))
# ZPicker
zpick = zpicker2.ZPicker(specs, zfindobjs, zfitobjs, flags)
output = None
# Write output
if self.dest is None:
output = io2.WriteRedmonster(zpick, clobber=True)
else:
if type(self.dest) is str:
output = io2.WriteRedmonster(zpick, dest=self.dest, clobber=True)
else:
try:
self.dest = str(self.dest)
output = io2.WriteRedmonster(zpick, dest=self.dest, clobber=True)
except Exception as e:
print "Could not convert dest to string - writing to \
default directory and NOT clobbering old files! \
Exception: %r" % e
output = io2.WriteRedmonster(zpick, clobber=True)
if output:
if len(zpick.fiberid) == 1:
output.write_fiber()
else:
output.write_plate()