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_chk_spec(tpe_file):
""" Check spectrum exists and then look for continuum
Parameters
----------
tpe_file
Returns
-------
"""
from astropy import units as u
# Load spectral datasets
igmsp = IgmSpec()
qpq_file = os.getenv('DROPBOX_DIR')+'/QSOPairs/spectra/qpq_oir_spec.hdf5'
qpq = IgmSpec(db_file=qpq_file, skip_test=True)
# Load TPE table
tpe = Table.read(tpe_file)
b_coords = SkyCoord(ra=tpe['BG_RA'], dec=tpe['BG_DEC'], unit='deg')
uni_instr = np.unique(tpe['BG_LYA_INSTRUMENT'])
# Instrument dict
inst_dict = {}
for instr in uni_instr:
inst_dict[instr] = {}
inst_dict[instr]['NO_CO'] = 0
inst_dict['LRIS']['GRATING'] = '1200/3400'
inst_dict['BOSS']['GROUP'] = 'BOSS_DR12'
inst_dict['SDSS']['GROUP'] = 'SDSS_DR7'
# Standard process
# -- Find all b/g spectra covering Lya (igmspec, QPQ): Generate list (INSTR,GRATING)
# -- Order by: UVES/HIRES/MIKE,
# MagE/ESI/XShooter,
# LRIS+B1200, B600?, B400?
# MODS?/GMOS+B600?
# BOSS/SDSS
# Query catalogs
igm_cat = igmsp.qcat.query_coords(b_coords)
# Scan
for instr in uni_instr:
# Parse
idx = np.where(tpe['BG_LYA_INSTRUMENT'] == instr)[0]
inst_dict[instr]['NSPEC'] = len(idx)
gd_b_coords = b_coords[idx]
# Load
if instr in ['BOSS', 'SDSS']:
spec, meta = igmsp.coords_to_spectra(gd_b_coords, inst_dict[instr]['GROUP'], all_spec=False)
else:
continue
# Checks
for ii,iidx in enumerate(idx):
lya = (1+tpe['FG_Z'][iidx]) * 1215.67 * u.AA
spec.select = ii
iwave = np.argmin(np.abs(spec.wavelength-lya))
if np.isclose(spec.co[iwave], 0.) or np.isclose(spec.co[iwave],1.):
print("BG source {} at z={} has no continuum at Lya".format(b_coords[iidx],
tpe['FG_Z'][iidx]))
inst_dict[instr]['NO_CO'] += 1
pdb.set_trace()
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