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 run_redmonster(this_thresh):
#global completeness
#global purity
global nfib
completeness = []
purity = []
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)
zstar = zfinder.ZFinder(fname='ndArch-spEigenStar-55734.fits', npoly=4, zmin=-.005, zmax=.005)
zstar.zchi2(specs.flux, specs.loglambda, specs.ivar)
zfit_ssp = zfitter.ZFitter(zssp.zchi2arr, zssp.zbase)
zfit_ssp.z_refine(threshold=this_thresh)
zfit_star = zfitter.ZFitter(zstar.zchi2arr, zstar.zbase)
zfit_star.z_refine(threshold=this_thresh)
zpick = zpicker.ZPicker(specs, zssp, zfit_ssp, zstar, zfit_star)
ssp_flags = n.zeros(len(fiberid))
star_flags = n.zeros(len(fiberid))
for ifiber in range(len(fiberid)):
ssp_flags[ifiber] = (int(specs.zwarning[ifiber]) | int(zssp.zwarning[ifiber])) | int(zfit_ssp.zwarning[ifiber])
star_flags[ifiber] = (int(specs.zwarning[ifiber]) | int(zstar.zwarning[ifiber])) | int(zfit_star.zwarning[ifiber])
#purity.append( (len(n.where(ssp_flags == 0)))/float(nfib) )
#completeness.append( (len(n.where(abs(zpick.z[:,0]-zperson) <= .0001)))/float(nfib) )
purity = (len(n.where(ssp_flags == 0)))/float(nfib)
completeness = (len(n.where(abs(zpick.z[:,0]-zperson) <= .0001)))/float(nfib)
return completeness, purity
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('chi2arr-%s-%s.fits' % (plate, zssp.type), overwrite=True)
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()
#specs.flux = specs.flux[skyfibers]
#specs.ivar = specs.ivar[skyfibers]
#specs.dof = specs.dof[skyfibers]
''' Instantiate zfinder object that will do z-finding for the entire
plate using a single template. Here, fname is the template filename,
assumed to be in $REDMONSTER_DIR/templates/ . npoly specifies number
of polynomial terms to be used in finding, zmin and zmax are upper
and lower bounds of the redshift range to be explored. Optionally,
npixstep can specify the width of pixel steps in doing the
cross-correlation. If left blank, it defaults to 1.
'''
#zssp1 = zfinder.ZFinder(fname='ndArch-ssp_galaxy_cont-v002.fits',
#npoly=4, zmin=-0.01, zmax=1.2)
zssp1 = zfinder.ZFinder(fname='ndArch-ssp_galaxy_noemit-v000.fits',
npoly=4, zmin=-0.01, zmax=1.2)
''' Run actual fitting routine on the object created above. zssp.zchi2arr
is array of of minimum chi^2 values of shape [nfibers, ndim_1,
ndim_2, ..., ndim_N, nredshifts], where ndim_i is the i'th dimension
of the template file. Input flux need not be SDSS data - any
spectra binned in constant log(lambda) will work.
'''
zssp1.zchi2(specs.flux, specs.loglambda, specs.ivar, npixstep=2)
''' New objects and fitting for different templates.'''
#zssp2 = zfinder.ZFinder(fname='ndArch-ssp_galaxy_emit-v002.fits',
#npoly=4, zmin=-0.01, zmax=1.2)
#zssp2.zchi2(specs.flux, specs.loglambda, specs.ivar, npixstep=2)
plate = 3686
mjd = 55268
completeness = []
purity = []
#-------------------------------------------------------------------------------------------------------
# Loop over various dchi2 thresholds
for inc in range(2):
this_thresh = 41 + inc
threshold_vals.append(this_thresh)
specs = spec.Spec(plate=plate, mjd=mjd, fiberid=fiberid)
zssp = zfinder.ZFinder(fname='ndArch-ssp_em_galaxy-v000.fits', type='GALAXY', npoly=4, zmin=-0.01, zmax=1.2)
zssp.zchi2(specs.flux, specs.loglambda, specs.ivar)
zstar = zfinder.ZFinder(fname='ndArch-spEigenStar-55734.fits', type='STAR', npoly=4, zmin=-.005, zmax=.005)
zstar.zchi2(specs.flux, specs.loglambda, specs.ivar)
zfit_ssp = zfitter.ZFitter(zssp.zchi2arr, zssp.zbase)
zfit_ssp.z_refine(threshold=this_thresh)
zfit_star = zfitter.ZFitter(zstar.zchi2arr, zstar.zbase)
zfit_star.z_refine(threshold=this_thresh)
zpick = zpicker.ZPicker(specs, zssp, zfit_ssp, zstar, zfit_star)
ssp_flags = n.zeros(len(fiberid))
star_flags = n.zeros(len(fiberid))
for ifiber in range(len(fiberid)):
ssp_flags[ifiber] = (int(specs.zwarning[ifiber]) | int(zssp.zwarning[ifiber])) | int(zfit_ssp.zwarning[ifiber])
star_flags[ifiber] = (int(specs.zwarning[ifiber]) | int(zstar.zwarning[ifiber])) | int(zfit_star.zwarning[ifiber])
purity.append( (len(n.where(ssp_flags == 0)))/float(nfib) )
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()
from redmonster.datamgr import spec, io
from redmonster.physics import zfinder, zfitter, zpicker
from redmonster.sandbox import yanny as y
from redmonster.physics import misc
from redmonster.physics.misc import poly_array
plate = 3686 # Set plate, mjd, and fiberid here
mjd = 55268
fiberid = [89, 100, 102] #935, 937
specs = spec.Spec(plate=plate, mjd=mjd, fiberid=fiberid)
# Use Charlie's SSPs
ztemp = zfinder.ZFinder(fname='ndArch-ssp_em_galaxy-v000.fits',
npoly=4,
zmin=-0.01,
zmax=1.2)
# Use Carlos' stellar templates
#ztemp = zfinder.ZFinder(fname='ndArch-all-CAP-grids.fits', npoly=4,
#zmin=-.005, zmax=.005)
# Use spEigenstars from IDL pipeline
#ztemp = zfinder.ZFinder(fname='ndArch-spEigenStar-55734.fits', npoly=4,
#zmin=-.005, zmax=.005)
# Use Nao's quasars
#ztemp = zfinder.ZFinder(fname='ndArch-QSO-V003.fits', npoly=4, zmin=.4,
#zmax=3.5)
ztemp.zchi2(specs.flux, specs.loglambda, specs.ivar, npixstep=1)
zfit_temp = zfitter.ZFitter(ztemp.zchi2arr, ztemp.zbase)
zfit_temp.z_refine()
#temp_flags = misc.comb_flags(specs, ztemp, zfit_temp)