Exemple #1
0
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)
Exemple #2
0
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)
Exemple #3
0
    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()
Exemple #4
0
    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()
Exemple #5
0
    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()
Exemple #6
0
''' 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,
Exemple #7
0
    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()
Exemple #8
0
    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()
Exemple #9
0
    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()