def load_specdb(specdb_file=None):
"""
Automatically load the specDB file from $SPECDB/FRB_specDB.hdf5
Args:
specdb_file (str, optional):
Over-ride the default file
Returns:
specdb.specdb.SpecDB:
"""
if not flg_specdb:
raise IOError("You must install the specdb package first!")
return
if specdb_file is None:
if os.getenv('SPECDB') is None:
raise IOError("You must set the SPECDB environmental variable")
specdb_files = glob.glob(
os.path.join(os.getenv('SPECDB'), 'FRB_specDB_*.hdf5'))
if len(specdb_files) > 0:
specdb_file = specdb_files[0]
print("Loading spectra from {:s}".format(specdb_file))
else:
raise IOError(
"There are no FRB_specdb.hdf5 files in your SPECDB folder")
# Load it up
specDB = SpecDB(db_file=specdb_file)
# Return
return specDB
def load_db(db_type, **kwargs):
"""
Parameters
----------
db_type : str
Type of database
Current allowed entries are [igmspec]
Returns
-------
dbobj : SpecDB object
Generally a child
"""
if db_type == 'igmspec':
from specdb.specdb import IgmSpec
Specdb = IgmSpec(**kwargs)
elif db_type == 'uvqs':
from specdb.specdb import UVQS
Specdb = UVQS(**kwargs)
elif db_type == 'priv': # Private
from specdb.specdb import SpecDB
Specdb = SpecDB(**kwargs)
else:
raise IOError("Not ready for this dbase value: {:s}".format(db_type))
# Return
return Specdb
def test_load_group():
db_file = data_path('IGMspec_DB_{:s}_debug.hdf5'.format(version))
# Instantiate
sdb = SpecDB(db_file=db_file)
# Load a DB
sdb['BOSS_DR12']
assert 'BOSS_DR12' in sdb._gdict.keys()
# Try meta
assert isinstance(sdb['BOSS_DR12'].meta, Table)
def load_specb(specdb_file):
"""
Load a specdb_file
Parameters
----------
specdb_file: str
Full path to the specdb file
Returns
-------
spdb: SpecDB or None
Returns None if specdb cannot be imported
"""
# Required import?
if not flg_specdb:
return None
#
spdb = SpecDB(db_file=specdb_file)
return spdb
def main(*args, **kwargs):
""" Runs the XAbsSysGui on input files
"""
import argparse
parser = argparse.ArgumentParser(description='Parse for XAbsSys')
parser.add_argument("spec_file", type=str, help="Spectral file")
parser.add_argument("abssys_file", type=str, help="AbsSys file (JSON)")
parser.add_argument("-outfile", type=str, help="Output filename")
parser.add_argument("-llist", type=str, help="Name of LineList")
#parser.add_argument("-exten", type=int, help="FITS extension")
parser.add_argument("--specdb",
help="Spectral file is a SPECDB database",
action="store_true")
parser.add_argument("--group", type=str, help="SPECDB group name")
parser.add_argument("--un_norm",
help="Spectrum is NOT normalized",
action="store_true")
parser.add_argument(
"--chk_z",
help="Check the z limits of your components? [default=False]",
action="store_true")
pargs = parser.parse_args()
from PyQt5.QtWidgets import QApplication
from linetools.guis.xabssysgui import XAbsSysGui
from linetools.isgm.io import abssys_from_json
from IPython import embed
# Normalized?
norm = True
if pargs.un_norm:
norm = False
# Extension
#exten = (pargs.exten if hasattr(pargs, 'exten') else 0)
# Read spec keywords
rsp_kwargs = {}
# Line list
if pargs.llist is not None:
from linetools.lists.linelist import LineList
llist = LineList(pargs.llist)
else:
llist = None
# Read AbsSystem
from linetools.isgm.abssystem import GenericAbsSystem
abs_sys = GenericAbsSystem.from_json(pargs.abssys_file) #, chk_vel=False)
if not pargs.chk_z:
warnings.warn(
"Not checking your system's velocity limits. This is the Default but be so warned."
)
abs_sys = GenericAbsSystem.from_json(pargs.abssys_file, chk_z=pargs.chk_z)
if len(abs_sys.list_of_abslines()) == 0:
warnings.warn(
"No absorption lines given. I hope you intended that to be the case!"
)
app = QApplication(sys.argv)
# Load spectrum using specdb?
if pargs.specdb:
# Instantiate
from specdb.specdb import SpecDB
from specdb import group_utils
sdb = SpecDB(db_file=pargs.spec_file)
# Grab spectrum
if pargs.group is not None:
groups = [pargs.group]
else:
groups = None
spec, meta = sdb.spectra_from_coord(abs_sys.coord, groups=groups)
if spec.nspec > 1:
group_utils.show_group_meta(meta,
idkey=sdb.idkey,
show_all_keys=False)
raise ValueError(
"Retreived more than 1 spectrum. Choose your GROUP with --group="
)
spec_file = pargs.spec_file + '_{:s}'.format(meta['GROUP'][0])
else:
spec = pargs.spec_file
spec_file = pargs.spec_file
# Save spectrum filename to AbsSystem
abs_sys.spec_file = spec_file
# Run
gui = XAbsSysGui(spec,
abs_sys,
norm=norm,
llist=llist,
outfil=pargs.outfile)
gui.show()
app.exec_()
def test_init():
db_file = data_path('IGMspec_DB_{:s}_debug.hdf5'.format(version))
# Instantiate
sdb = SpecDB(db_file=db_file)
assert 'BOSS_DR12' in sdb.groups