def main(pargs):
""" Run
"""
import json
from linetools import utils as ltu
from linetools.scripts.utils import coord_arg_to_coord
from frb.galaxies import nebular
from frb import mw
from frb.surveys import survey_utils
# Deal with coord
icoord = ltu.radec_to_coord(coord_arg_to_coord(pargs.coord))
# EBV
EBV = nebular.get_ebv(icoord)['meanValue'] #
AV = EBV * 3.1 # RV
print("AV = {}".format(AV))
# NE 2001
DM_ISM = mw.ismDM(icoord)
print(f"NE2001 = {DM_ISM}")
# Surveys
print("Checking the imaging surveys...")
inside = survey_utils.in_which_survey(icoord)
print(inside)
def main(args, unit_test=False, **kwargs):
""" Run
"""
import numpy as np
from astropy import units as u
from specdb.utils import load_db
from specdb import group_utils
from linetools.scripts.utils import coord_arg_to_coord
# init
Specdb = load_db(args.dbase, db_file=args.db_file, **kwargs)
# Grab
icoord = coord_arg_to_coord(args.coord)
if args.group is not None:
groups=[args.group]
else:
groups = None
meta = Specdb.meta_from_position(icoord, args.tol*u.arcsec, groups=groups)
if unit_test:
return meta
# Outcome
if meta is None:
print("No source found within the data groups, try another location or a larger tolerance.")
return
else:
group_utils.show_group_meta(meta, idkey=Specdb.idkey, show_all_keys=False)
def main(args, unit_test=False, **kwargs):
""" Run
"""
import numpy as np
from astropy import units as u
from specdb.utils import load_db
from linetools.scripts.utils import coord_arg_to_coord
# init
Specdb = load_db(args.dbase, db_file=args.db_file, **kwargs)
# Grab
icoord = coord_arg_to_coord(args.coord)
if args.group is not None:
groups = [args.group]
else:
groups = None
spec, meta = Specdb.spectra_from_coord(icoord,
tol=args.tol * u.arcsec,
groups=groups)
# Outcome
if meta is None:
print("No source found, try another location or a larger tolerance.")
return
elif len(meta) == 1: # One group hit
print("Source located in group: {:s}".format(meta['GROUP'][0]))
else: # More than 1 spectrum
print(
"More than 1 spectrum found for input source. Here is a summary:")
#meta = all_meta[idx]
#groups = [meta.meta['group'] for meta in all_meta]
#print("Using group {:s}. You can choose from this list {}".format(groups[idx], groups))
indices = np.arange(len(meta)).astype(int)
meta['INDEX'] = indices
print(meta[[
'INDEX', 'GROUP', 'RA_GROUP', 'DEC_GROUP', Specdb.idkey, 'INSTR',
'DISPERSER', 'GROUP_ID'
]])
idx = args.select
print(
"Plotting index={:d} which you can specify with --select".format(idx))
#if args.meta:
# group_utils.show_group_meta(meta)
# Load spectra
spec.select = args.select
if unit_test:
return
# Add labels
lbls = []
for imeta in meta:
lbls.append('{:d}_{:s}'.format(imeta['INDEX'], imeta['GROUP']))
spec.labels = lbls
# Show
if args.mplot:
spec.plot()
else:
spec.plot(xspec=True)
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 main(pargs):
""" Run
"""
import numpy as np
from linetools import utils as ltu
from linetools.scripts.utils import coord_arg_to_coord
from frb import mw
from frb.dm import prob_dmz
# Deal with coord
icoord = ltu.radec_to_coord(coord_arg_to_coord(pargs.coord))
# NE 2001
DM_ISM = mw.ismDM(icoord)
print("")
print("-----------------------------------------------------")
print(f"NE2001 = {DM_ISM:.2f}")
# DM Cosmic
DM_cosmic = pargs.DM_FRB - DM_ISM.value - pargs.dm_hostmw
# Redshift estimates
# Load
sdict = prob_dmz.grab_repo_grid()
PDM_z = sdict['PDM_z']
z = sdict['z']
DM = sdict['DM']
# Do it
iDM = np.argmin(np.abs(DM - DM_cosmic))
PzDM = PDM_z[iDM, :] / np.sum(PDM_z[iDM, :])
cum_sum = np.cumsum(PzDM)
limits = pargs.cl
z_min = z[np.argmin(np.abs(cum_sum - limits[0] / 100.))]
z_max = z[np.argmin(np.abs(cum_sum - limits[1] / 100.))]
# Finish
print("")
print(f"The redshift range for your confidence interval {pargs.cl} is:")
print(f"z = [{z_min:.3f}, {z_max:.3f}]")
return z_min, z_max
def main(pargs):
""" Run
"""
import warnings
import numpy as np
from matplotlib import pyplot as plt
from astropy.io import fits
from astropy import units
from frb import frb
from frb.figures import galaxies as ffgal
from frb.figures import utils as ffutils
from linetools.scripts.utils import coord_arg_to_coord
# Load up
hdu = fits.open(pargs.fits_file)
icoord = coord_arg_to_coord(pargs.frb_coord)
# Parse
if pargs.vmnx is not None:
tstr = pargs.vmnx.split(',')
vmnx = (float(tstr[0]), float(tstr[1]))
else:
vmnx = (None, None)
# Dummy FRB object
FRB = frb.FRB('TMP', icoord, 0.)
FRB.set_ee(1.0, 1.0, 0., 95.)
fig = plt.figure(figsize=(7, 7))
ffutils.set_mplrc()
ffgal.sub_image(fig,
hdu,
FRB,
vmnx=vmnx,
cmap='gist_heat',
frb_clr='white',
imsize=pargs.imsize) #img_center=HG190608.coord,
# Layout and save
plt.tight_layout(pad=0.2, h_pad=0.1, w_pad=0.1)
plt.savefig(pargs.outfile, dpi=300)
plt.close()
print('Wrote {:s}'.format(pargs.outfile))
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 main(args, unit_test=False, **kwargs):
""" Run
"""
import numpy as np
from astropy import units as u
from specdb.utils import load_db
from specdb import group_utils
from linetools.scripts.utils import coord_arg_to_coord
# init
Specdb = load_db(args.dbase, db_file=args.db_file, **kwargs)
# Grab
icoord = coord_arg_to_coord(args.coord)
# Cut down using source catalog
matches, sub_cat, IDs = Specdb.qcat.query_position(icoord,
args.tol * u.arcsec)
print(sub_cat['RA', 'DEC', 'zem', 'flag_group', 'STYPE'])
def main(pargs):
""" Run
"""
import json
import os
import numpy as np
from pkg_resources import resource_filename
from linetools import utils as ltu
from linetools.scripts.utils import coord_arg_to_coord
from frb.galaxies import nebular
from frb.galaxies import photom
from frb.galaxies import utils as frb_gal_u
from frb import mw
from frb.dm import prob_dmz
# Deal with coord
icoord = ltu.radec_to_coord(coord_arg_to_coord(pargs.coord))
# EBV
EBV = nebular.get_ebv(icoord)['meanValue'] #
print(f"EBV = {EBV}")
# NE 2001
DM_ISM = mw.ismDM(icoord)
print(f"NE2001 = {DM_ISM}")
# DM Cosmic
DM_cosmic = pargs.DM_FRB - DM_ISM.value - pargs.dm_hostmw
# Redshift estimates
# Load
sdict = prob_dmz.grab_repo_grid()
PDM_z = sdict['PDM_z']
z = sdict['z']
DM = sdict['DM']
# Do it
iDM = np.argmin(np.abs(DM - DM_cosmic))
PzDM = PDM_z[iDM, :] / np.sum(PDM_z[iDM, :])
cum_sum = np.cumsum(PzDM)
limits = [10, 90]
z_min = z[np.argmin(np.abs(cum_sum - limits[0] / 100.))]
z_max = z[np.argmin(np.abs(cum_sum - limits[1] / 100.))]
# Setup Luminosity
# Extinction correct
dust_correct = photom.extinction_correction(pargs.filter, EBV)
mag_dust = 2.5 * np.log10(1. / dust_correct)
mag_corr = pargs.mag_limit + mag_dust
# ##########################3
# Convert to L
# Load f_mL
f_mL = frb_gal_u.load_f_mL()
# m_r(L*)
m_r_Lstar_min = float(f_mL(z_min))
m_r_Lstar_max = float(f_mL(z_max))
frac_Lstar_min = 10**(-0.4 * (mag_corr - m_r_Lstar_min))
frac_Lstar_max = 10**(-0.4 * (mag_corr - m_r_Lstar_max))
# Finish
print("-----------------------------------------------------")
print(
f"For z_{limits[0]}={z_min:.2f}, the limiting magnitude corresponds to L={frac_Lstar_min:.5f}L*"
)
print(
f"For z_{limits[1]}={z_max:.2f}, the limiting magnitude corresponds to L={frac_Lstar_max:.5f}L*"
)
return frac_Lstar_min, frac_Lstar_max
def main(pargs):
""" Run
"""
import warnings
import numpy as np
from astropy import units
from frb import frb
from frb.galaxies import utils as gutils
from linetools.scripts.utils import coord_arg_to_coord
try:
from specdb import group_utils
except ImportError:
print("You need to first install specdb")
return
# Load it up
specDB = gutils.load_specdb(specdb_file=pargs.specdb)
if specDB is None:
return
if pargs.coord[0:3].upper() == 'FRB':
frb = frb.FRB.by_name(pargs.coord.upper())
icoord = frb.coord.ra.value, frb.coord.dec.value
else:
icoord = coord_arg_to_coord(pargs.coord)
# Meta?
if pargs.cat:
if pargs.ang_offset is not None:
_, cat, _ = specDB.qcat.query_position(
icoord, pargs.ang_offset * units.arcsec)
else:
_, cat, _ = specDB.qcat.query_position(icoord,
pargs.rho * units.kpc)
# Show
ckeys = ['RA', 'DEC', 'zem', 'ZQ']
group_utils.show_group_meta(cat, show_all_keys=False, meta_keys=ckeys)
else: # Meta
if pargs.ang_offset is not None:
meta = specDB.meta_from_position(icoord,
pargs.ang_offset * units.arcsec)
else:
meta = specDB.meta_from_position(icoord, pargs.rho * units.kpc)
# Keys
mkeys = ['GROUP', 'RA_GROUP', 'DEC_GROUP', 'zem_GROUP', 'ZQ', 'Ref']
# Show
if meta is None:
print(
"No source found, try another location or a larger tolerance.")
return
else:
group_utils.show_group_meta(
meta, show_all_keys=False,
meta_keys=mkeys) #, max_lines=10000000)
# Plot
if pargs.plot:
if pargs.cat:
print("Cannot mix --plot with --cat. Try again!")
return
plot_spec(specDB, meta, frb=frb)