def add_ssa(hdf, dset):
""" Add SSA info to meta dataset
Parameters
----------
hdf
dset : str
"""
from specdb.ssa import default_fields
Title = '{:s}: Quasar Spectra from the COS-Halos Survey'.format(dset)
ssa_dict = default_fields(Title, flux='flambda', fxcalib='ABSOLUTE')
hdf[dset]['meta'].attrs['SSA_COS'] = json.dumps(ltu.jsonify(ssa_dict))
# HIRES
ssa_dict = default_fields(Title, flux='normalized')
hdf[dset]['meta'].attrs['SSA_HIRES'] = json.dumps(ltu.jsonify(ssa_dict))
def add_ssa(hdf, dset):
""" Add SSA info to meta dataset
Parameters
----------
hdf
dset : str
"""
from specdb.ssa import default_fields
Title = '{:s}: Quasar Spectra from the COS-Halos Survey'.format(dset)
ssa_dict = default_fields(Title, flux='flambda', fxcalib='ABSOLUTE')
hdf[dset]['meta'].attrs['SSA_COS'] = json.dumps(ltu.jsonify(ssa_dict))
# HIRES
ssa_dict = default_fields(Title, flux='normalized')
hdf[dset]['meta'].attrs['SSA_HIRES'] = json.dumps(ltu.jsonify(ssa_dict))
def test_default_fields():
title = 'BOSS: DR12 Quasars'
ssa_dict = spdb_ssa.default_fields(title)
assert ssa_dict['FluxUcd'] == 'arith.ratio;phot.flux.density'
assert ssa_dict['FluxUnit'] == ''
assert ssa_dict['SpecUcd'] == 'em.wl'
assert ssa_dict['SpecUnit'] == 'Angstrom'
# flambda
ssa_dict = spdb_ssa.default_fields(title, flux='flambda')
assert ssa_dict['FluxUcd'] == 'phot.fluDens;em.wl'
# calib
ssa_dict = spdb_ssa.default_fields(title,
flux='flambda',
fxcalib='ABSOLUTE')
assert ssa_dict['FluxCalib'] == 'ABSOLUTE'
def add_ssa(hdf, dset):
""" Add SSA info to meta dataset
Parameters
----------
hdf
dset : str
"""
from specdb.ssa import default_fields
Title = '{:s}: Dall''Aglio et al. (2008) compilation of VLT/UVES spectra'.format(dset)
ssa_dict = default_fields(Title, flux='flambda')
hdf[dset]['meta'].attrs['SSA'] = json.dumps(ltu.jsonify(ssa_dict))
def add_ssa(hdf, dset):
""" Add SSA info to meta dataset
Parameters
----------
hdf
dset : str
"""
from specdb.ssa import default_fields
Title = '{:s}: HST UV spectra for surveying LLS and DLAs'.format(dset)
ssa_dict = default_fields(Title, flux='flambda', fxcalib='ABSOLUTE')
hdf[dset]['meta'].attrs['SSA'] = json.dumps(ltu.jsonify(ssa_dict))
def add_ssa(hdf, dset):
""" Add SSA info to meta dataset
Parameters
----------
hdf
dset : str
"""
from specdb.ssa import default_fields
Title = '{:s}: SDSS DR7 Quasars'.format(dset)
ssa_dict = default_fields(Title, flux='flambda', fxcalib='ABSOLUTE')
hdf[dset]['meta'].attrs['SSA'] = json.dumps(ltu.jsonify(ssa_dict))
def add_ssa(hdf, dset):
""" Add SSA info to meta dataset
Parameters
----------
hdf
dset : str
"""
from specdb.ssa import default_fields
Title = '{:s}: Keck/HIRES KODIAQ DR1'.format(dset)
ssa_dict = default_fields(Title, flux='normalized')
hdf[dset]['meta'].attrs['SSA'] = json.dumps(ltu.jsonify(ssa_dict))
def add_ssa(hdf, dset):
""" Add SSA info to meta dataset
Parameters
----------
hdf
dset : str
"""
from specdb.ssa import default_fields
Title = '{:s}: Dall' 'Aglio et al. (2008) compilation of VLT/UVES spectra'.format(
dset)
ssa_dict = default_fields(Title, flux='flambda')
hdf[dset]['meta'].attrs['SSA'] = json.dumps(ltu.jsonify(ssa_dict))
def add_ssa(hdf, dset):
""" Add SSA info to meta dataset
Parameters
----------
hdf
dset : str
"""
from specdb.ssa import default_fields
Title = '{:s}: The XQ-100 Survey of 100 z>3 quasars with VLT/XShooter'.format(dset)
ssa_dict = default_fields(Title, flux='flambda')
hdf[dset]['meta'].attrs['SSA'] = json.dumps(ltu.jsonify(ssa_dict))
def add_ssa(hdf, dset):
""" Add SSA info to meta dataset
Parameters
----------
hdf
dset : str
"""
from specdb.ssa import default_fields
Title = '{:s}: The Keck/ESI Survey for high-z DLAs'.format(dset)
ssa_dict = default_fields(Title, flux='flambda')
hdf[dset]['meta'].attrs['SSA'] = json.dumps(ltu.jsonify(ssa_dict))
def add_ssa(hdf, dset):
""" Add SSA info to meta dataset
Parameters
----------
hdf
dset : str
"""
from specdb.ssa import default_fields
Title = '{:s}: The Keck/ESI Survey for high-z DLAs'.format(dset)
ssa_dict = default_fields(Title, flux='flambda')
hdf[dset]['meta'].attrs['SSA'] = json.dumps(ltu.jsonify(ssa_dict))
def add_ssa(hdf, dset):
""" Add SSA info to meta dataset
Parameters
----------
hdf
dset : str
"""
from specdb.ssa import default_fields
Title = '{:s}: Giant Gemini GMOS Survey of z>4 quasars'.format(dset)
ssa_dict = default_fields(Title, flux='flambda')
hdf[dset]['meta'].attrs['SSA'] = json.dumps(ltu.jsonify(ssa_dict))
def add_ssa(hdf, dset):
""" Add SSA info to meta dataset
Parameters
----------
hdf
dset : str
"""
from specdb.ssa import default_fields
Title = '{:s}: HST and FUSE spectra of AGN and Quasars by Cooksey et al. (2010)'.format(
dset)
ssa_dict = default_fields(Title, flux='flambda')
hdf[dset]['meta'].attrs['SSA'] = json.dumps(ltu.jsonify(ssa_dict))
def add_ssa(hdf, dset):
""" Add SSA info to meta dataset
Parameters
----------
hdf
dset : str
"""
from specdb.ssa import default_fields
Title = '{:s}: The Magellan uniform survey of damped Lya systems'.format(
dset)
ssa_dict = default_fields(Title, flux='normalized')
hdf[dset]['meta'].attrs['SSA'] = json.dumps(ltu.jsonify(ssa_dict))
def add_ssa(hdf, dset):
""" Add SSA info to meta dataset
Parameters
----------
hdf
dset : str
"""
from specdb.ssa import default_fields
Title = '{:s}: Giant Gemini GMOS Survey of z>4 quasars'.format(dset)
ssa_dict = default_fields(Title, flux='flambda')
hdf[dset]['meta'].attrs['SSA'] = json.dumps(ltu.jsonify(ssa_dict))
def add_ssa(hdf, dset):
""" Add SSA info to meta dataset
Parameters
----------
hdf
dset : str
"""
from specdb.ssa import default_fields
Title = '{:s}: The XQ-100 Survey of 100 z>3 quasars with VLT/XShooter'.format(
dset)
ssa_dict = default_fields(Title, flux='flambda')
hdf[dset]['meta'].attrs['SSA'] = json.dumps(ltu.jsonify(ssa_dict))
def mk_db(dbname, tree, outfil, iztbl, version='v00', id_key='PRIV_ID',
publisher='Unknown', **kwargs):
""" Generate the DB
Parameters
----------
dbname : str
Name for the database
tree : str
Path to top level of the tree of FITS files
Typically, each branch in the tree corresponds to a single instrument
outfil : str
Output file name for the hdf5 file
iztbl : Table or str
If Table, see meta() docs for details on its format
If str, it must be 'igmspec' and the user must have that DB downloaded
version : str, optional
Version code
Returns
-------
"""
from specdb import defs
# ztbl
if isinstance(iztbl, str):
if iztbl == 'igmspec':
from specdb.specdb import IgmSpec
igmsp = IgmSpec()
ztbl = Table(igmsp.idb.hdf['quasars'][...])
elif isinstance(iztbl, Table):
ztbl = iztbl
else:
raise IOError("Bad type for ztbl")
# Find the branches
branches = glob.glob(tree+'/*')
branches.sort()
# HDF5 file
hdf = h5py.File(outfil,'w')
# Defs
zpri = defs.z_priority()
gdict = {}
# Main DB Table
maindb, tkeys = spbu.start_maindb(id_key)
# MAIN LOOP
for ss,branch in enumerate(branches):
# Skip files
if not os.path.isdir(branch):
continue
print('Working on branch: {:s}'.format(branch))
# Files
fits_files, out_tup = grab_files(branch)
meta_file, mtbl_file, ssa_file = out_tup
# Meta
maxpix, phead, mdict, stype = 10000, None, None, 'QSO'
if meta_file is not None:
# Load
meta_dict = ltu.loadjson(meta_file)
# Maxpix
if 'maxpix' in meta_dict.keys():
maxpix = meta_dict['maxpix']
# STYPE
if 'stype' in meta_dict.keys():
stype = meta_dict['stype']
# Parse header
if 'parse_head' in meta_dict.keys():
phead = meta_dict['parse_head']
if 'meta_dict' in meta_dict.keys():
mdict = meta_dict['meta_dict']
full_meta = mk_meta(fits_files, ztbl, mtbl_file=mtbl_file,
parse_head=phead, mdict=mdict, **kwargs)
# Update group dict
group_name = branch.split('/')[-1]
flag_g = spbu.add_to_group_dict(group_name, gdict)
# IDs
maindb = add_ids(maindb, full_meta, flag_g, tkeys, 'PRIV_ID', first=(flag_g==1))
# Ingest
ingest_spectra(hdf, group_name, full_meta, max_npix=maxpix, **kwargs)
# SSA
if ssa_file is not None:
user_ssa = ltu.loadjson(ssa_file)
ssa_dict = default_fields(user_ssa['Title'], flux=user_ssa['flux'], fxcalib=user_ssa['fxcalib'])
hdf[group_name]['meta'].attrs['SSA'] = json.dumps(ltu.jsonify(ssa_dict))
# Check stacking
if not spbu.chk_vstack(hdf):
print("Meta data will not stack using specdb.utils.clean_vstack")
print("Proceed to write at your own risk..")
pdb.set_trace()
# Write
write_hdf(hdf, str(dbname), maindb, zpri, gdict, version,
Publisher=publisher)
print("Wrote {:s} DB file".format(outfil))
