def test_get_spectra():
"""
Check grabbing spectra from the specDB
Note: This requires that specdb be installed..
"""
try:
import specdb
except ImportError:
assert True
return
# Check for specDB file
if utils.load_specdb() is None:
assert True
return
# Do it!
host180924 = frbgalaxy.FRBHost.by_name('180924')
meta, xspec = host180924.get_metaspec()
# Test
assert isinstance(meta, Table)
assert isinstance(xspec, xspectrum1d.XSpectrum1D)
assert xspec.nspec == 1
#
meta, xspec = host180924.get_metaspec(instr='MUSE')
# Test
assert isinstance(xspec, xspectrum1d.XSpectrum1D)
assert xspec.nspec == 1
#
meta, xspecs = host180924.get_metaspec(return_all=True)
assert xspecs.nspec == 2
def get_metaspec(self, instr=None, return_all=False, specdb_file=None):
"""
Return the meta data and spectra for this FRBGalaxy
from the specDB
If there is more than one spectrum, the code returns the first
unless return_all=True
Args:
instr (str, optional):
Restrict to the input Instrument
return_all (bool, optional):
Return all of the meta, spectra
specdb_file (str, optional):
Path+name of the specDB file to use (over-ride the default)
Returns:
astropy.table.Table, linetools.spectra.XSpectrum1D: meta data, spectra
"""
specDB = gutils.load_specdb(specdb_file=specdb_file)
if specDB is None:
print(f"{specdb_file} yielded nothing. Returning None")
return
# Grab the spectra
xspec, meta = specDB.spectra_from_coord(
self.coord) # Tolerance is 0.5''
# Return all?
if return_all:
return meta, xspec
# Cut down
if instr is None:
if len(meta) > 1:
warnings.warn(
"Multiple spectra returned for this galaxy. Taking the first, but you may wish to specify your instrument"
)
xspec = xspec[0]
meta = meta[0:1]
else:
idx = meta['GROUP'] == instr
if np.sum(idx) == 0:
warnings.warn("No spectrum with instrument = {}".format(instr))
return
elif np.sum(idx) > 1:
warnings.warn(
"Multiple spectra returned for this galaxy. Taking the first, but you may wish to specify your instrument"
)
xspec = xspec[np.where(idx)[0][0]]
meta = meta[np.where(idx)[0][0]]
# Return
return meta, xspec
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)