def main(args=None):
from linetools.scripts.utils import coord_arg_to_coord
from linetools import utils as ltu
from astropy.io import fits, ascii
from astropy.coordinates import SkyCoord
import astropy.units as u
from pyntejos.catalogs import add_radec_deg_columns
pargs = parser(options=args)
# RA,DEC
icoord = coord_arg_to_coord(pargs.radec)
coord = ltu.radec_to_coord(icoord)
# define catalog
print('Reading {} catalog'.format(pargs.catalog))
if pargs.catalog == 'QSO':
# read qsos from MILLIQUAS catalog
col_names = [
'ra_d', 'dec_d', 'name', 'description', 'rmag', 'bmag', 'comment',
'psf_r', 'psf_b', 'z', 'cite', 'zcite', 'qso_prob', 'Xname',
'Rname', 'Lobe1', 'Lobe2'
]
cat = ascii.read(
'/media/ntejos/disk1/catalogs/qsos/milliquas/milliquas.txt',
format='fixed_width',
names=col_names)
elif pargs.catalog == 'GC':
# read MW globular cluster catalog
cat = ascii.read(
'/media/ntejos/disk1/catalogs/globular_clusters/mwgc10_1.dat',
format='fixed_width')
# add ra_d, dec_d columns
cat = add_radec_deg_columns(cat)
else:
print(' Not implemented for such catalog.')
return
# cross-match
print('Cross-matching...')
cat_coords = SkyCoord(cat['ra_d'], cat['dec_d'], unit='deg')
seplim = pargs.angsep * u.arcmin
sep2d = coord.separation(cat_coords)
cond = sep2d <= seplim
cat = cat[cond]
if len(cat) < 1:
print("No matches found.")
else:
cat['sep2d'] = sep2d[cond]
if pargs.redshift is not None:
from astropy.cosmology import Planck15 as cosmo
import pdb
pdb.set_trace()
sep = (cosmo.kpc_comoving_per_arcmin(float(pargs.redshift)) *
cat['sep2d']).to('Mpc')
cat['sep_mpc'] = sep.value
cat.sort('sep2d')
print(cat)
def query_Simbad_NED(objname, z=np.nan):
'''
Make use to astroquery to extract basic coordiantes/redshift information
z: redshift. Normally NED query would give an answer. Provide z if NED answer is not satifying
return: astropy SkyCoord object
'''
import numpy as np
from astroquery.simbad import Simbad
from astroquery.ned import Ned
from astropy.coordinates import SkyCoord
import astropy.units as u
from astropy.cosmology import Planck15 as cosmo
sim = Simbad.query_object(objname)
try:
test1 = sim['RA']
except:
print('Danger: %s cannot be recognized by Simbad, try other names.' %
(objname))
return False
try:
ned = Ned.query_object(objname)
except:
print('Danger: %s cannot be recognized by NED, try other names.' %
(objname))
return False
galcoord = SkyCoord(ra=sim['RA'],
dec=sim['DEC'],
unit=(u.hour, u.deg),
frame='icrs')
if np.isfinite(z):
gz = z
else:
gz = ned['Redshift'][0]
scale_kpc_arcmin = cosmo.kpc_comoving_per_arcmin(gz)
scale_pc_arcsec = scale_kpc_arcmin.to(u.pc / u.arcsec)
print('Simbad: RA = %.4f deg ' % (galcoord.icrs.ra.deg), galcoord.icrs.ra)
print('Simbad: DEC = %.4f deg ' % (galcoord.icrs.dec.deg),
galcoord.icrs.dec)
print('Simbad: l = %.4f deg, b = %.4f deg' %
(galcoord.galactic.l.deg, galcoord.galactic.b.deg))
print('NED: z = %.4f; Input z = %.4f' % (ned['Redshift'], z))
print('Scale at z = %.4f: %.1f kpc/arcmin, %.1f pc/arcsec' %
(gz, abs(scale_kpc_arcmin.value), abs(scale_pc_arcsec.value)))
print('Returning astropy SkyCoord object...')
return galcoord
def main(args=None):
from linetools.scripts.utils import coord_arg_to_coord
from linetools import utils as ltu
from astropy.io import fits, ascii
from astropy.coordinates import SkyCoord
import astropy.units as u
from pyntejos.catalogs import add_radec_deg_columns
pargs = parser(options=args)
# RA,DEC
icoord = coord_arg_to_coord(pargs.radec)
coord = ltu.radec_to_coord(icoord)
# define catalog
print('Reading {} catalog'.format(pargs.catalog))
if pargs.catalog == 'QSO':
# read qsos from MILLIQUAS catalog
col_names = ['ra_d', 'dec_d', 'name', 'description', 'rmag', 'bmag', 'comment', 'psf_r', 'psf_b', 'z', 'cite', 'zcite', 'qso_prob', 'Xname', 'Rname', 'Lobe1', 'Lobe2']
cat = ascii.read('/media/ntejos/disk1/catalogs/qsos/milliquas/milliquas.txt', format='fixed_width', names=col_names)
elif pargs.catalog == 'GC':
# read MW globular cluster catalog
cat = ascii.read('/media/ntejos/disk1/catalogs/globular_clusters/mwgc10_1.dat', format='fixed_width')
# add ra_d, dec_d columns
cat = add_radec_deg_columns(cat)
else:
print(' Not implemented for such catalog.')
return
# cross-match
print('Cross-matching...')
cat_coords = SkyCoord(cat['ra_d'], cat['dec_d'], unit='deg')
seplim = pargs.angsep * u.arcmin
sep2d = coord.separation(cat_coords)
cond = sep2d <= seplim
cat = cat[cond]
if len(cat) < 1:
print("No matches found.")
else:
cat['sep2d'] = sep2d[cond]
if pargs.redshift is not None:
from astropy.cosmology import Planck15 as cosmo
import pdb; pdb.set_trace()
sep = (cosmo.kpc_comoving_per_arcmin(float(pargs.redshift)) * cat['sep2d']).to('Mpc')
cat['sep_mpc'] = sep.value
cat.sort('sep2d')
print(cat)
def stack_spec(spec_file, dv=100 * u.km / u.s, cut_on_rho=4.):
# Load
xspec, tpe, spec_tbl = load_spec(spec_file)
# Cut on separation (should do this much earlier in the process)
if cut_on_rho is not None:
warnings.warn("Cutting on rho in stack. Should do this earlier")
b_coords = SkyCoord(ra=tpe['BG_RA'], dec=tpe['BG_DEC'], unit='deg')
f_coords = SkyCoord(ra=tpe['FG_RA'], dec=tpe['FG_DEC'], unit='deg')
kpc_amin = cosmo.kpc_comoving_per_arcmin(tpe['FG_Z']) # kpc per arcmin
ang_seps = b_coords.separation(f_coords)
rho = ang_seps.to('arcmin') * kpc_amin / (1 + tpe['FG_Z'])
cut_rho = rho.to('Mpc').value < cut_on_rho
print("We have {:d} spectra after the cut.".format(np.sum(cut_rho)))
xspec = xspec[cut_rho]
tpe = tpe[cut_rho]
spec_tbl = spec_tbl[cut_rho]
# Remove those without continua
has_co = spec_tbl['HAS_CO'].data
co_spec = xspec[has_co]
co_spec.normed = True # Apply continuum
# May also wish to isolate in wavelength to avoid rejected pixels
for ii in range(co_spec.nspec):
co_spec.select = ii
co = co_spec.co.value
sig = co_spec.sig.value
bad_pix = np.any([(co == 0.), (co == 1.), (sig <= 0.)], axis=0)
co_spec.add_to_mask(bad_pix, compressed=True)
# Rebin to rest
zarr = tpe['FG_Z'][has_co]
rebin_spec = lspu.rebin_to_rest(co_spec, zarr, dv)
# Stack
stack = lspu.smash_spectra(rebin_spec)
# Plot
tpep.plot_stack(stack, 'all_stack.pdf')
tpep.plot_spec_img(rebin_spec, 'spec_img.pdf')
pdb.set_trace()
# Return
return
def grab_sdss_spectra(radec,
radius=0.1 * u.deg,
outfil=None,
debug=False,
maxsep=None,
timeout=600.,
zmin=None):
""" Grab SDSS spectra
Parameters
----------
radec : tuple
RA, DEC in deg
radius : float, optional (0.1*u.deg)
Search radius -- Astroquery actually makes a box, not a circle
timeout : float, optional
Timeout limit for connection with SDSS
outfil : str ('tmp.fits')
Name of output file for FITS table
maxsep : float (None) :: Mpc
Maximum separation to include
zmin : float (None)
Minimum redshift to include
Returns
-------
tbl : Table
"""
cC = coords.SkyCoord(ra=radec[0], dec=radec[1])
# Query
photoobj_fs = ['ra', 'dec', 'objid', 'run', 'rerun', 'camcol', 'field']
mags = [
'petroMag_u', 'petroMag_g', 'petroMag_r', 'petroMag_i', 'petroMag_z'
]
magsErr = [
'petroMagErr_u', 'petroMagErr_g', 'petroMagErr_r', 'petroMagErr_i',
'petroMagErr_z'
]
phot_catalog = SDSS.query_region(cC,
spectro=True,
radius=radius,
timeout=timeout,
photoobj_fields=photoobj_fs + mags +
magsErr) # Unique
spec_catalog = SDSS.query_region(cC,
spectro=True,
radius=radius,
timeout=timeout) # Duplicates exist
nobj = len(phot_catalog)
#
print('grab_sdss_spectra: Found {:d} sources in the search box.'.format(
nobj))
# Coordinates
cgal = SkyCoord(ra=phot_catalog['ra'] * u.degree,
dec=phot_catalog['dec'] * u.degree)
sgal = SkyCoord(ra=spec_catalog['ra'] * u.degree,
dec=spec_catalog['dec'] * u.degree)
sepgal = cgal.separation(cC) #in degrees
# Check for problems and parse z
zobj = np.zeros(nobj)
idx, d2d, d3d = coords.match_coordinates_sky(cgal, sgal, nthneighbor=1)
if np.max(d2d) > 1. * u.arcsec:
print('No spectral match!')
xdb.set_trace()
else:
zobj = spec_catalog['z'][idx]
idx, d2d, d3d = coords.match_coordinates_sky(cgal, cgal, nthneighbor=2)
if np.min(d2d.to('arcsec')) < 1. * u.arcsec:
print('Two photometric sources with same RA/DEC')
xdb.set_trace()
#xdb.set_trace()
# Cut on Separation
if not maxsep is None:
print('grab_sdss_spectra: Restricting to {:g} Mpc separation.'.format(
maxsep))
sepgal_kpc = cosmo.kpc_comoving_per_arcmin(zobj) * sepgal.to('arcmin')
sepgal_mpc = sepgal_kpc.to('Mpc')
gdg = np.where(sepgal_mpc < (maxsep * u.Unit('Mpc')))[0]
phot_catalog = phot_catalog[gdg]
#xdb.set_trace()
nobj = len(phot_catalog)
print('grab_sdss_spectra: Grabbing data for {:d} sources.'.format(nobj))
# Grab Spectra from SDSS
# Generate output table
attribs = galaxy_attrib()
npix = 5000 #len( spec_hdus[0][1].data.flux )
spec_attrib = [(str('FLUX'), np.float32, (npix, )),
(str('SIG'), np.float32, (npix, )),
(str('WAVE'), np.float64, (npix, ))]
tbl = np.recarray((nobj, ), dtype=attribs + spec_attrib)
tbl['RA'] = phot_catalog['ra']
tbl['DEC'] = phot_catalog['dec']
tbl['TELESCOPE'] = str('SDSS 2.5-M')
# Deal with spectra separately (for now)
npix = 5000 #len( spec_hdus[0][1].data.flux )
for idx, obj in enumerate(phot_catalog):
#print('idx = {:d}'.format(idx))
# Grab spectra (there may be duplicates)
mt = np.where(
sgal.separation(cgal[idx]).to('arcsec') < 1. * u.Unit('arcsec'))[0]
if len(mt) > 1:
# Use BOSS if you have it
mmt = np.where(spec_catalog[mt]['instrument'] == 'BOSS')[0]
if len(mmt) > 0:
mt = mt[mmt[0]]
else:
mt = mt[0]
elif len(mt) == 0:
xdb.set_trace()
else:
mt = mt[0]
# Grab spectra
spec_hdus = SDSS.get_spectra(matches=Table(spec_catalog[mt]))
tbl[idx]['INSTRUMENT'] = spec_catalog[mt]['instrument']
spec = spec_hdus[0][1].data
npp = len(spec.flux)
tbl[idx]['FLUX'][0:npp] = spec.flux
sig = np.zeros(npp)
gdi = np.where(spec.ivar > 0.)[0]
if len(gdi) > 0:
sig[gdi] = np.sqrt(1. / spec.ivar[gdi])
tbl[idx]['SIG'][0:npp] = sig
tbl[idx]['WAVE'][0:npp] = 10.**spec.loglam
# Redshifts
meta = spec_hdus[0][2].data
for attrib in ['Z', 'Z_ERR']:
tbl[idx][attrib] = meta[attrib]
if debug:
sep_to_qso = cgal[idx].separation(cC).to('arcmin')
print('z = {:g}, Separation = {:g}'.format(tbl[idx].Z, sep_to_qso))
xdb.set_trace()
# Fill in rest
tbl[idx].SDSS_MAG = np.array([obj[phot] for phot in mags])
tbl[idx].SDSS_MAGERR = np.array([obj[phot] for phot in magsErr])
# Clip on redshift to excise stars/quasars
if zmin is not None:
gd = np.where(tbl['Z'] > zmin)[0]
tbl = tbl[gd]
# Write to FITS file
if outfil is not None:
prihdr = fits.Header()
prihdr['COMMENT'] = 'SDSS Spectra'
prihdu = fits.PrimaryHDU(header=prihdr)
tbhdu = fits.BinTableHDU(tbl)
thdulist = fits.HDUList([prihdu, tbhdu])
thdulist.writeto(outfil, clobber=True)
print('Wrote SDSS table to {:s}'.format(outfil))
return tbl
def grab_sdss_spectra(radec, radius=0.1*u.deg, outfil=None,
debug=False, maxsep=None, timeout=600., zmin=None):
""" Grab SDSS spectra
Parameters
----------
radec : tuple
RA, DEC in deg
radius : float, optional (0.1*u.deg)
Search radius -- Astroquery actually makes a box, not a circle
timeout : float, optional
Timeout limit for connection with SDSS
outfil : str ('tmp.fits')
Name of output file for FITS table
maxsep : float (None) :: Mpc
Maximum separation to include
zmin : float (None)
Minimum redshift to include
Returns
-------
tbl : Table
"""
cC = coords.SkyCoord(ra=radec[0], dec=radec[1])
# Query
photoobj_fs = ['ra', 'dec', 'objid', 'run', 'rerun', 'camcol', 'field']
mags = ['petroMag_u', 'petroMag_g', 'petroMag_r', 'petroMag_i', 'petroMag_z']
magsErr = ['petroMagErr_u', 'petroMagErr_g', 'petroMagErr_r', 'petroMagErr_i', 'petroMagErr_z']
phot_catalog = SDSS.query_region(cC,spectro=True,radius=radius, timeout=timeout,
photoobj_fields=photoobj_fs+mags+magsErr) # Unique
spec_catalog = SDSS.query_region(cC,spectro=True, radius=radius, timeout=timeout) # Duplicates exist
nobj = len(phot_catalog)
#
print('grab_sdss_spectra: Found {:d} sources in the search box.'.format(nobj))
# Coordinates
cgal = SkyCoord(ra=phot_catalog['ra']*u.degree, dec=phot_catalog['dec']*u.degree)
sgal = SkyCoord(ra=spec_catalog['ra']*u.degree, dec=spec_catalog['dec']*u.degree)
sepgal = cgal.separation(cC) #in degrees
# Check for problems and parse z
zobj = np.zeros(nobj)
idx, d2d, d3d = coords.match_coordinates_sky(cgal, sgal, nthneighbor=1)
if np.max(d2d) > 1.*u.arcsec:
print('No spectral match!')
xdb.set_trace()
else:
zobj = spec_catalog['z'][idx]
idx, d2d, d3d = coords.match_coordinates_sky(cgal, cgal, nthneighbor=2)
if np.min(d2d.to('arcsec')) < 1.*u.arcsec:
print('Two photometric sources with same RA/DEC')
xdb.set_trace()
#xdb.set_trace()
# Cut on Separation
if not maxsep is None:
print('grab_sdss_spectra: Restricting to {:g} Mpc separation.'.format(maxsep))
sepgal_kpc = cosmo.kpc_comoving_per_arcmin(zobj) * sepgal.to('arcmin')
sepgal_mpc = sepgal_kpc.to('Mpc')
gdg = np.where( sepgal_mpc < (maxsep * u.Unit('Mpc')))[0]
phot_catalog = phot_catalog[gdg]
#xdb.set_trace()
nobj = len(phot_catalog)
print('grab_sdss_spectra: Grabbing data for {:d} sources.'.format(nobj))
# Grab Spectra from SDSS
# Generate output table
attribs = galaxy_attrib()
npix = 5000 #len( spec_hdus[0][1].data.flux )
spec_attrib = [(str('FLUX'), np.float32, (npix,)),
(str('SIG'), np.float32, (npix,)),
(str('WAVE'), np.float64, (npix,))]
tbl = np.recarray( (nobj,), dtype=attribs+spec_attrib)
tbl['RA'] = phot_catalog['ra']
tbl['DEC'] = phot_catalog['dec']
tbl['TELESCOPE'] = str('SDSS 2.5-M')
# Deal with spectra separately (for now)
npix = 5000 #len( spec_hdus[0][1].data.flux )
for idx,obj in enumerate(phot_catalog):
#print('idx = {:d}'.format(idx))
# Grab spectra (there may be duplicates)
mt = np.where( sgal.separation(cgal[idx]).to('arcsec') < 1.*u.Unit('arcsec'))[0]
if len(mt) > 1:
# Use BOSS if you have it
mmt = np.where( spec_catalog[mt]['instrument'] == 'BOSS')[0]
if len(mmt) > 0:
mt = mt[mmt[0]]
else:
mt = mt[0]
elif len(mt) == 0:
xdb.set_trace()
else:
mt = mt[0]
# Grab spectra
spec_hdus = SDSS.get_spectra(matches=Table(spec_catalog[mt]))
tbl[idx]['INSTRUMENT'] = spec_catalog[mt]['instrument']
spec = spec_hdus[0][1].data
npp = len(spec.flux)
tbl[idx]['FLUX'][0:npp] = spec.flux
sig = np.zeros(npp)
gdi = np.where(spec.ivar > 0.)[0]
if len(gdi) > 0:
sig[gdi] = np.sqrt( 1./spec.ivar[gdi] )
tbl[idx]['SIG'][0:npp] = sig
tbl[idx]['WAVE'][0:npp] = 10.**spec.loglam
# Redshifts
meta = spec_hdus[0][2].data
for attrib in ['Z','Z_ERR']:
tbl[idx][attrib] = meta[attrib]
if debug:
sep_to_qso = cgal[idx].separation(cC).to('arcmin')
print('z = {:g}, Separation = {:g}'.format(tbl[idx].Z, sep_to_qso))
xdb.set_trace()
# Fill in rest
tbl[idx].SDSS_MAG = np.array( [obj[phot] for phot in mags])
tbl[idx].SDSS_MAGERR = np.array( [obj[phot] for phot in magsErr])
# Clip on redshift to excise stars/quasars
if zmin is not None:
gd = np.where(tbl['Z'] > zmin)[0]
tbl = tbl[gd]
# Write to FITS file
if outfil is not None:
prihdr = fits.Header()
prihdr['COMMENT'] = 'SDSS Spectra'
prihdu = fits.PrimaryHDU(header=prihdr)
tbhdu = fits.BinTableHDU(tbl)
thdulist = fits.HDUList([prihdu, tbhdu])
thdulist.writeto(outfil,clobber=True)
print('Wrote SDSS table to {:s}'.format(outfil))
return tbl
def tpe_stack_lris(dv=100 * u.km / u.s):
""" Testing stacks with LRIS
"""
# Load sample
ipos = this_file.rfind('/')
if ipos == -1:
path = './'
else:
path = this_file[0:ipos]
tpe = Table.read(path + '/../TPE_DR12_31.2_spec.fits')
# Load spectra
# Coordiantes
b_coords = SkyCoord(ra=tpe['BG_RA'], dec=tpe['BG_DEC'], unit='deg')
f_coords = SkyCoord(ra=tpe['FG_RA'], dec=tpe['FG_DEC'], unit='deg')
# Cut on impact parameter and BOSS
kpc_amin = cosmo.kpc_comoving_per_arcmin(tpe['FG_Z']) # kpc per arcmin
ang_seps = b_coords.separation(f_coords)
rho = ang_seps.to('arcmin') * kpc_amin / (1 + tpe['FG_Z'])
cut_Rlris = (rho.to('Mpc').value < 4) & (tpe['BG_LYA_INSTRUMENT'] == 'LRIS'
) # & (
#tpe['FG_Z'] > 2.) # Some of these have too low z (just barely)
# Cut
gd_b_coords = b_coords[cut_Rlris]
gd_tpe = tpe[cut_Rlris]
# Grab these spectra from QPQ
# For boss, we are ok taking the first entry of each
# The returned set is aligned with the input coords
qpq = IgmSpec(db_file=qpq_file, skip_test=True)
IDs = qpq.qcat.match_coord(gd_b_coords, group='LRIS')
meta = qpq['LRIS'].meta
gcut = meta['GRATING'] == '1200/3400' # There is one with B400
B1200 = np.in1d(IDs, meta['PRIV_ID'][gcut])
print("There are {:d} sources without B1200".format(np.sum(~B1200)))
# Cut again
gd_b_coords = gd_b_coords[B1200]
gd_tpe = gd_tpe[B1200]
gd_IDs = IDs[B1200]
# Find the rows
idx = cat_utils.match_ids(gd_IDs, meta['PRIV_ID'])
rows = meta['GROUP_ID'][idx]
pdb.set_trace()
spec, meta = qpq.coords_to_spectra(gd_b_coords, 'LRIS', all_spec=False)
# Check for continua
has_co = np.array([True] * spec.nspec)
for ii in range(spec.nspec):
# Select
spec.select = ii
# Match to lya
lya = (1 + gd_tpe['FG_Z'][ii]) * 1215.67 * u.AA
iwave = np.argmin(np.abs(spec.wavelength - lya))
# Check for co
#coval = spec.co[iwave]
#print('spec: {:d} with co={:g}'.format(ii, coval))
if np.isclose(spec.co[iwave], 0.) or np.isclose(spec.co[iwave], 1.):
has_co[ii] = False
# Slice to good co
print("{:d} BOSS spectra with a continuum".format(np.sum(has_co)))
co_spec = spec[has_co]
co_spec.normed = True # Apply continuum
# NEED TO ZERO OUT REGIONS WITHOUT CONTINUUM
# May also wish to isolate in wavelength to avoid rejected pixels
for ii in range(co_spec.nspec):
co_spec.select = ii
co = co_spec.co.value
bad_pix = np.any([(co == 0.), (co == 1.)], axis=0)
co_spec.add_to_mask(bad_pix, compressed=True)
# Rebin to rest
zarr = gd_tpe['FG_Z'][has_co]
rebin_spec = lspu.rebin_to_rest(co_spec, zarr, dv)
# Stack
stack = lspu.smash_spectra(rebin_spec)
# Plot
plot_stack(stack, 'LRIS_stack.pdf')
return stack
def tpe_stack_boss(dv=100 * u.km / u.s):
""" Testing stacks with BOSS
"""
# Load sample
ipos = this_file.rfind('/')
if ipos == -1:
path = './'
else:
path = this_file[0:ipos]
tpe = Table.read(path + '/../TPE_DR12_31.2_spec.fits')
# Load spectra
igmsp = IgmSpec()
# Coordiantes
b_coords = SkyCoord(ra=tpe['BG_RA'], dec=tpe['BG_DEC'], unit='deg')
f_coords = SkyCoord(ra=tpe['FG_RA'], dec=tpe['FG_DEC'], unit='deg')
# Cut on impact parameter and BOSS
kpc_amin = cosmo.kpc_comoving_per_arcmin(tpe['FG_Z']) # kpc per arcmin
ang_seps = b_coords.separation(f_coords)
rho = ang_seps.to('arcmin') * kpc_amin / (1 + tpe['FG_Z'])
cut_Rboss = (rho.to('Mpc').value < 4) & (
tpe['BG_LYA_INSTRUMENT'] == 'BOSS') & (
tpe['FG_Z'] > 2.) # Some of these have too low z (just barely)
# Cut
gd_b_coords = b_coords[cut_Rboss]
gd_f_coords = f_coords[cut_Rboss]
gd_tpe = tpe[cut_Rboss]
# Grab these spectra from igmsp
# For boss, we are ok taking the first entry of each
# The returned set is aligned with the input coords
spec, meta = igmsp.coords_to_spectra(gd_b_coords,
'BOSS_DR12',
all_spec=False)
# Check for continua
has_co = np.array([True] * spec.nspec)
for ii in range(spec.nspec):
# Select
spec.select = ii
# Match to lya
lya = (1 + gd_tpe['FG_Z'][ii]) * 1215.67 * u.AA
iwave = np.argmin(np.abs(spec.wavelength - lya))
# Check for co
#coval = spec.co[iwave]
#print('spec: {:d} with co={:g}'.format(ii, coval))
if np.isclose(spec.co[iwave], 0.) or np.isclose(spec.co[iwave], 1.):
has_co[ii] = False
# Slice to good co
print("{:d} BOSS spectra with a continuum".format(np.sum(has_co)))
co_spec = spec[has_co]
co_spec.normed = True # Apply continuum
# NEED TO ZERO OUT REGIONS WITHOUT CONTINUUM
# May also wish to isolate in wavelength to avoid rejected pixels
for ii in range(co_spec.nspec):
co_spec.select = ii
co = co_spec.co.value
bad_pix = np.any([(co == 0.), (co == 1.)], axis=0)
co_spec.add_to_mask(bad_pix, compressed=True)
# Rebin to rest
zarr = gd_tpe['FG_Z'][has_co]
rebin_spec = lspu.rebin_to_rest(co_spec, zarr, dv)
# Check 2D
check_td = True
if check_td:
fx = rebin_spec.data['flux']
sig = rebin_spec.data['sig']
gds = sig > 0.
fx[~gds] = 0.
xdb.set_trace() # xdb.ximshow(fx)
# Stack
stack = lspu.smash_spectra(rebin_spec)
# Plot
plot_stack(stack, 'BOSS_stack.pdf')
print('Wrote')
return stack
