def grab_meta():
""" Grab UVES Dall'Aglio meta table
Returns
-------
"""
#
uvesdall_meta = Table.read(os.getenv('RAW_IGMSPEC')+'/UVES_Dall/uves_dall_summ.dat', format='ascii')
nspec = len(uvesdall_meta)
# DATE
#datearr = [day.split('/') for day in list(uvesdall_meta['ObsDate'])]
#ndate = ['20'+str(day[2])+'-'+str(day[0])+'-'+str(day[1]) for day in datearr]
t = Time(uvesdall_meta['OBS-DATE'], out_subfmt='date') # Fixes to YYYY-MM-DD
uvesdall_meta.add_column(Column(t.iso, name='DATE-OBS'))
# RA/DEC
coord = SkyCoord(ra=uvesdall_meta['RA'], dec=uvesdall_meta['DEC'], unit=(u.hour,u.deg))
rad = [icoord.ra.value for icoord in coord]
decd = [icoord.dec.value for icoord in coord]
uvesdall_meta.rename_column('RA', 'RA_STR')
uvesdall_meta.rename_column('DEC', 'DEC_STR')
uvesdall_meta['RA_GROUP'] = rad
uvesdall_meta['DEC_GROUP'] = decd
# Add zem
igmsp = IgmSpec()
ztbl = Table(igmsp.hdf['quasars'].value)
zem, zsource = zem_from_radec(rad, decd, ztbl)
badz = np.where(zem < 0.1)[0]
for ibadz in badz:
if uvesdall_meta['NAME'][ibadz] == 'HE2243-6031':
zem[ibadz] = 3.005
zsource[ibadz] = 'FOP13' # Fumagalli+13
elif uvesdall_meta['NAME'][ibadz] == 'HE1341-1020':
zem[ibadz] = 2.137
zsource[ibadz] = 'Dall08' # Dall'Aglio+08
elif uvesdall_meta['NAME'][ibadz] == 'Q0002-422':
zem[ibadz] = 2.769
zsource[ibadz] = 'Dall08' # Dall'Aglio+08
elif uvesdall_meta['NAME'][ibadz] == 'PKS2000-330':
zem[ibadz] = 3.786
zsource[ibadz] = 'Dall08' # Dall'Aglio+08
else:
raise ValueError("Should not be here")
uvesdall_meta['zem_GROUP'] = zem
uvesdall_meta['sig_zem'] = [0.]*nspec
uvesdall_meta['flag_zem'] = zsource
#
uvesdall_meta.add_column(Column([2000.]*nspec, name='EPOCH'))
uvesdall_meta.add_column(Column(['VLT']*nspec, name='TELESCOPE'))
uvesdall_meta.add_column(Column(['UVES']*nspec, name='INSTR'))
uvesdall_meta.add_column(Column(['BOTH']*nspec, name='DISPERSER'))
uvesdall_meta.add_column(Column([45000.]*nspec, name='R'))
uvesdall_meta['STYPE'] = str('QSO')
# Sort
uvesdall_meta.sort('RA_GROUP')
# Check
assert chk_meta(uvesdall_meta, chk_cat_only=True)
return uvesdall_meta
def grab_meta(hdf, old=False):
""" Grab SDSS meta Table
Returns
-------
meta
"""
from specdb.zem.utils import zem_from_radec
#sdss_meta = Table.read(os.getenv('RAW_IGMSPEC')+'/SDSS/SDSS_DR7_qso.fits.gz')
sdss_meta = Table.read(os.getenv('RAW_IGMSPEC') + '/SDSS/dr7qso.fit.gz')
nspec = len(sdss_meta)
# DATE
#t = Time(list(sdss_meta['MJD'].data), format='mjd', out_subfmt='date') # Fixes to YYYY-MM-DD
t = Time(list(sdss_meta['SMJD'].data), format='mjd',
out_subfmt='date') # Fixes to YYYY-MM-DD
sdss_meta.add_column(Column(t.iso, name='DATE-OBS'))
# Add a few columns
sdss_meta.add_column(Column([2000.] * nspec, name='EPOCH'))
sdss_meta.add_column(Column([2000.] * nspec, name='R'))
sdss_meta.add_column(Column(['SDSS'] * nspec, name='INSTR'))
sdss_meta.add_column(Column(['BOTH'] * nspec, name='GRATING'))
sdss_meta.add_column(Column(['SDSS 2.5-M'] * nspec, name='TELESCOPE'))
# Rename
if old:
# Some of these were corrected by QPQ
sdss_meta.rename_column('RAOBJ', 'RA')
sdss_meta.rename_column('DECOBJ', 'DEC')
sdss_meta.rename_column('Z_ERR', 'sig_zem')
pdb.set_trace()
else:
sdss_meta.rename_column('z', 'zem_GROUP')
sdss_meta['sig_zem'] = 0.
sdss_meta['flag_zem'] = str(' ')
# Fix zem
zem, zsource = zem_from_radec(sdss_meta['RA'],
sdss_meta['DEC'],
hdf['quasars'].value,
toler=1.0 * u.arcsec)
gdz = zem > 0.
sdss_meta['zem_GROUP'][gdz] = zem[gdz]
sdss_meta['flag_zem'] = zsource
sdss_meta['flag_zem'][~gdz] = str('SDSS-DR7')
# Sort
sdss_meta.sort('RA')
# Rename
sdss_meta.rename_column('RA', 'RA_GROUP')
sdss_meta.rename_column('DEC', 'DEC_GROUP')
# Add
sdss_meta['STYPE'] = [str('QSO')] * nspec
# Check
assert chk_meta(sdss_meta, chk_cat_only=True)
# Return
return sdss_meta
def grab_meta(hdf, old=False):
""" Grab SDSS meta Table
Returns
-------
meta
"""
from specdb.zem.utils import zem_from_radec
#sdss_meta = Table.read(os.getenv('RAW_IGMSPEC')+'/SDSS/SDSS_DR7_qso.fits.gz')
sdss_meta = Table.read(os.getenv('RAW_IGMSPEC')+'/SDSS/dr7qso.fit.gz')
nspec = len(sdss_meta)
# DATE
#t = Time(list(sdss_meta['MJD'].data), format='mjd', out_subfmt='date') # Fixes to YYYY-MM-DD
t = Time(list(sdss_meta['SMJD'].data), format='mjd', out_subfmt='date') # Fixes to YYYY-MM-DD
sdss_meta.add_column(Column(t.iso, name='DATE-OBS'))
# Add a few columns
sdss_meta.add_column(Column([2000.]*nspec, name='EPOCH'))
sdss_meta.add_column(Column([2000.]*nspec, name='R'))
sdss_meta.add_column(Column(['SDSS']*nspec, name='INSTR'))
sdss_meta.add_column(Column(['BOTH']*nspec, name='GRATING'))
sdss_meta.add_column(Column(['SDSS 2.5-M']*nspec, name='TELESCOPE'))
# Rename
if old:
# Some of these were corrected by QPQ
sdss_meta.rename_column('RAOBJ', 'RA')
sdss_meta.rename_column('DECOBJ', 'DEC')
sdss_meta.rename_column('Z_ERR', 'sig_zem')
pdb.set_trace()
else:
sdss_meta.rename_column('z', 'zem_GROUP')
sdss_meta['sig_zem'] = 0.
sdss_meta['flag_zem'] = str(' ')
# Fix zem
zem, zsource = zem_from_radec(sdss_meta['RA'], sdss_meta['DEC'], hdf['quasars'].value, toler=1.0*u.arcsec)
gdz = zem > 0.
sdss_meta['zem_GROUP'][gdz] = zem[gdz]
sdss_meta['flag_zem'] = zsource
sdss_meta['flag_zem'][~gdz] = str('SDSS-DR7')
# Sort
sdss_meta.sort('RA')
# Rename
sdss_meta.rename_column('RA', 'RA_GROUP')
sdss_meta.rename_column('DEC', 'DEC_GROUP')
# Add
sdss_meta['STYPE'] = [str('QSO')]*nspec
# Check
assert chk_meta(sdss_meta, chk_cat_only=True)
# Return
return sdss_meta
def grab_meta():
""" Grab COS-Halos meta table
Returns
-------
"""
from time import strptime
from specdb.zem.utils import zem_from_radec
from specdb.specdb import IgmSpec
from specdb.defs import get_res_dicts
Rdicts = get_res_dicts()
igmsp = IgmSpec(db_file=os.getenv('SPECDB')+'/IGMspec_DB_v01.hdf5', skip_test=True)
summ_file = os.getenv('RAW_IGMSPEC')+'/COS-Halos/cos_halos_obs.ascii'
chalos_meta = Table.read(summ_file, format='ascii')
# RA/DEC, DATE
# Visits from this page: http://www.stsci.edu/cgi-bin/get-visit-status?id=11598&markupFormat=html
visit_file = os.getenv('RAW_IGMSPEC')+'/COS-Halos/cos_halos_visits.ascii'
ch_visits = Table.read(visit_file,format='ascii')
ra = []
dec = []
datet = []
for row in chalos_meta:
coord = ltu.radec_to_coord(row['QSO'])
ra.append(coord.ra.value)
dec.append(coord.dec.value)
#
visit = row['Visit']
mtv = np.where(ch_visits['Visit'] == visit)[0]
if len(mtv) != 1:
pdb.set_trace()
else:
chv = ch_visits['Start_UT'][mtv].data[0]
icmma = chv.find(',')
datet.append('{:s}-{:02d}-{:02d}'.format(
chv[icmma+1:icmma+5], strptime(chv[:3],'%b').tm_mon,
int(chv[3:icmma])))
chalos_meta.add_column(Column(ra, name='RA'))
chalos_meta.add_column(Column(dec, name='DEC'))
chalos_meta.add_column(Column(datet, name='DATE-OBS'))
# Others
chalos_meta.add_column(Column([' ']*len(chalos_meta), name='TELESCOPE')) # Padding
chalos_meta.add_column(Column([' ']*len(chalos_meta), name='INSTR')) # Padding for HIRES
chalos_meta.add_column(Column(['G130M/G160M']*len(chalos_meta), name='DISPERSER'))
chalos_meta.add_column(Column([20000.]*len(chalos_meta), name='R'))
chalos_meta.add_column(Column([2000.]*len(chalos_meta), name='EPOCH'))
chalos_meta['INSTR'] = 'COS' # Deals with padding
chalos_meta['TELESCOPE'] = 'HST'
# Myers for zem
zem, zsource = zem_from_radec(chalos_meta['RA'], chalos_meta['DEC'], Table(igmsp.hdf['quasars'].value))
badz = zem <= 0.
if np.sum(badz) > 0:
raise ValueError("Bad zem in COS-Halos")
chalos_meta['zem'] = zem
chalos_meta['sig_zem'] = 0. # Need to add
chalos_meta['flag_zem'] = zsource
# HIRES
hires_files = glob.glob(os.getenv('RAW_IGMSPEC')+'/COS-Halos/HIRES/J*f.fits.gz')
hires_tab = chalos_meta[0:0]
subnm = np.array([row['QSO'][4:9] for row in chalos_meta])
signs = np.array([row['QSO'][14] for row in chalos_meta])
for ifile in hires_files:
print(ifile)
fname = ifile.split('/')[-1]
mt = np.where((subnm == fname[0:5]) & (signs == fname[5]))[0]
if len(mt) != 1:
pdb.set_trace()
# Add row
hires_tab.add_row(chalos_meta[mt[0]])
hires_tab[-1]['INSTR'] = 'HIRES'
hires_tab[-1]['TELESCOPE'] = 'Keck I'
hires_tab[-1]['DISPERSER'] = 'Red'
hires_tab[-1]['R'] = Rdicts['HIRES']['C1']
# Combine
chalos_meta = vstack([chalos_meta, hires_tab])
chalos_meta['STYPE'] = str('QSO')
# Rename
chalos_meta.rename_column('RA', 'RA_GROUP')
chalos_meta.rename_column('DEC', 'DEC_GROUP')
chalos_meta.rename_column('zem', 'zem_GROUP')
# Check
assert chk_meta(chalos_meta, chk_cat_only=True)
# Done
return chalos_meta
def mk_meta(files, ztbl, fname=False, stype='QSO', skip_badz=False,
mdict=None, parse_head=None, debug=False, chkz=False,
mtbl_file=None,
verbose=False, specdb=None, sdb_key=None, **kwargs):
""" Generate a meta Table from an input list of files
Parameters
----------
files : list
List of FITS files
ztbl : Table
Table of redshifts. Must include RA, DEC, ZEM, ZEM_SOURCE
Used for RA/DEC if fname=False; then requires SPEC_FILE too
fname : bool, optional
Attempt to parse RA/DEC from the file name
Format must be
SDSSJ######(.##)+/-######(.#)[x]
where x cannot be a #. or +/-
stype : str, optional
Description of object type (e.g. 'QSO', 'Galaxy', 'SN')
specdb : SpecDB, optional
Database object to grab ID values from
Requires sdb_key
sdb_key : str, optional
ID key in SpecDB object
skip_badz : bool, optional
Skip spectra without a parseable redshift (using the Myers catalog)
parse_head : dict, optional
Parse header for meta info with this dict
mdict : dict, optional
Input meta data in dict form e.g. mdict=dict(INSTR='ESI')
chkz : bool, optional
If any sources have no parseable redshift, hit a set_trace
mtbl_file : str
Filename of input meta table. Current allowed extensions are _meta.ascii or _meta.fits
and they must be readable by Table.read(). The values in this table will overwrite
any others generated. Table must include a SPEC_FILE column to link meta data
Returns
-------
meta : Table
Meta table
"""
if specdb is not None:
if sdb_key is None:
raise IOError("Must specify sdb_key if you are passing in specdb")
#
coordlist = []
snames = []
for ifile in files:
sname = ifile.split('/')[-1]
snames.append(sname)
if fname:
# Starting index
if 'SDSSJ' in ifile:
i0 = ifile.find('SDSSJ')+4
else:
i0 = ifile.rfind('J')+1
# Find end (ugly)
for ii in range(i0+1,99999):
if ifile[ii] in ('0','1','2','3','4','5','6','7','8','9',
'.','+','-'):
continue
else:
i1 = ii
break
# Deal with .fits
if ifile[i1-1] == '.':
i1 -= 1
# Get coord
try:
coord = ltu.radec_to_coord(ifile[i0:i1])
except (UnboundLocalError, ValueError):
pdb.set_trace()
else:
mt = np.where(ztbl['SPEC_FILE'] == sname)[0]
if len(mt) != 1:
raise IndexError("NO MATCH FOR {:s}".format(sname))
coord = ltu.radec_to_coord((ztbl['RA'][mt],
ztbl['DEC'][mt]))[0]
coordlist.append(coord)
ras = np.array([coord.ra.degree for coord in coordlist])
decs= np.array([coord.dec.degree for coord in coordlist])
coords = SkyCoord(ra=ras, dec=decs, unit='deg')
# Generate maindb Table
#maindb, tkeys = spbu.start_maindb(private=True)
# Fill
meta = Table()
meta['RA_GROUP'] = coords.ra.deg
meta['DEC_GROUP'] = coords.dec.deg
meta['STYPE'] = [str(stype)]*len(meta)
zem, zsource, ZQ = spzu.zem_from_radec(meta['RA_GROUP'], meta['DEC_GROUP'],
ztbl, **kwargs)
badz = zem <= 0.
if np.sum(badz) > 0:
if skip_badz:
warnings.warn("Skipping {:d} entries without a parseable redshift".format(
np.sum(badz)))
badz[:] = False # Risky!
else:
if chkz: # Turn this on to hit a stop instead of an Exception
pdb.set_trace()
else:
raise ValueError("{:d} entries without a parseable redshift".format(
np.sum(badz)))
meta['zem_GROUP'] = zem
meta['sig_zem'] = 0. # Need to add
meta['flag_zem'] = zsource
if ZQ is not None:
meta['ZQ'] = ZQ
# Cut?
meta = meta[~badz]
# specdb IDs
if sdb_key is not None:
meta[sdb_key] = [-9999]*len(meta)
if sdb_key not in meta.keys():
meta[sdb_key] = [-9999]*len(meta)
c_igmsp = SkyCoord(ra=specdb.qcat.cat['RA'], dec=specdb.qcat.cat['DEC'], unit='deg')
c_new = SkyCoord(ra=meta['RA_GROUP'], dec=meta['DEC_GROUP'], unit='deg')
# Find new sources
idx, d2d, d3d = match_coordinates_sky(c_new, c_igmsp, nthneighbor=1)
cdict = defs.get_cat_dict()
mtch = d2d < cdict['match_toler']
meta[sdb_key][mtch] = specdb.qcat.cat[sdb_key][idx[mtch]]
# Stack (primarily as a test)
'''
try:
maindb = vstack([maindb,meta], join_type='exact')
except:
pdb.set_trace()
'''
# SPEC_FILE
meta['SPEC_FILE'] = np.array(files)[~badz]
root_names = np.array(snames)[~badz]
# Try Header?
if parse_head is not None:
# Setup to store
plist = {}
for key in parse_head.keys():
plist[key] = []
# Loop on files
for count, sfile in enumerate(meta['SPEC_FILE']):
if verbose:
print('Parsing {:s}'.format(sfile))
try:
head = fits.open(sfile)[0].header
except FileNotFoundError: # Try for compressed
head = fits.open(sfile+'.gz')[0].header
# Call it
_ = spbu.parse_header(parse_head, head, mdict=mdict,
plist=plist, count=count)
'''
for key,item in parse_head.items():
# R
if key == 'R':
if parse_head[key] is True:
try:
plist[key].append(spbu.set_resolution(head))
except ValueError:
if mdict is not None:
try:
plist[key].append(mdict['R'])
except KeyError:
print("Key error!")
pdb.set_trace()
else:
print('Bad inputs to set_resolution()')
pdb.set_trace()
plist[key].append(0.)
else:
raise ValueError("Set something else for R")
elif key == 'DATE-OBS':
if 'MJD' in item:
tval = Time(head[item], format='mjd')
tval.format = 'iso'
else:
tval = Time(head[item].replace('/','-'), format='iso')
tval.out_submfit = 'date'
plist[key].append(tval.iso)
else:
plist[key].append(head[item])
# INSTRUMENT SPECIFIC
try:
instr = head['INSTRUME']
except KeyError:
instr = 'none'
# LRIS
if 'LRIS' in instr:
# Init
for skey in ['DISPERSER', 'INSTR', 'R']:
if skey not in plist.keys():
plist[skey] = []
# Figure out detector
try:
det = head['DETECTOR']
except KeyError:
if 'BLUE' in instr:
det = 'LRIS-B'
else:
if head['OUTFILE'] == 'lred':
det = 'LRIS-R'
else:
det = 'LRIS-B'
# Add
if 'LRIS-R' in det:
if len(plist['DISPERSER']) == count:
plist['DISPERSER'].append(head['GRANAME'])
if len(plist['INSTR']) == count:
plist['INSTR'].append('LRISr')
else:
plist['INSTR'][-1] = 'LRISr'
else:
if len(plist['DISPERSER']) == count:
plist['DISPERSER'].append(head['GRISNAME'])
if len(plist['INSTR']) == count:
plist['INSTR'].append('LRISb')
else:
plist['INSTR'][-1] = 'LRISb'
# Resolution
res = Rdicts[plist['INSTR'][-1]][plist['DISPERSER'][-1]]
try:
sname = head['SLITNAME']
except KeyError:
swidth = 1.
else:
swidth = defs.slit_width(sname, LRIS=True)
plist['R'].append(res/swidth)
'''
# Finish
for key in plist.keys():
try:
meta[key] = plist[key]
except:
embed(header='338 of private')
# mdict
if mdict is not None:
for key,item in mdict.items():
meta[key] = [item]*len(meta)
# EPOCH
if 'EPOCH' not in meta.keys():
warnings.warn("EPOCH not defined. Filling with 2000.")
meta['EPOCH'] = 2000.
# GROUP ID
meta['GROUP_ID'] = np.arange(len(meta)).astype(int)
# Fill in empty columns with warning
mkeys = meta.keys()
req_clms = defs.get_req_clms(sdb_key=sdb_key)
for clm in req_clms:
if clm not in mkeys:
if clm not in ['NPIX','WV_MIN','WV_MAX']: # File in ingest_spec
warnings.warn("Meta Column {:s} not defined. Filling with DUMMY".format(clm))
if clm == 'DATE-OBS':
meta[clm] = ['9999-1-1']*len(meta)
else:
meta[clm] = ['DUMMY']*len(meta)
# Input meta table
if mtbl_file is not None:
# Read
if '_meta.ascii' in mtbl_file:
imtbl = Table.read(mtbl_file, format='ascii')
elif '_meta.fits' in mtbl_file:
imtbl = Table.read(mtbl_file)
else:
raise IOError("Input meta table must have either an ascii or fits extension")
# Check length
if len(imtbl) != len(meta):
raise IOError("Input meta table must have same length as self-generated one")
# Check for SPEC_FILE
if 'SPEC_FILE' not in imtbl.keys():
raise ValueError("Input meta table must include SPEC_FILE column")
# Loop to get indices
idx = []
for row in imtbl:
imt = np.where(root_names == row['SPEC_FILE'])[0]
if len(imt) == 0:
print("No match to spec file {:s}. Will ignore".format(row['SPEC_FILE']))
elif len(imt) == 1:
idx.append(imt[0])
else:
raise ValueError("Two entries with the same SPEC_FILE. Something went wrong..")
idx = np.array(idx)
# Loop on keys
for key in imtbl.keys():
# Skip?
if key in ['SPEC_FILE']:
continue
if key in meta.keys():
pdb.set_trace()
else:
# Add Column
meta.add_column(imtbl[key][idx])
# Return
if debug:
meta[['RA_GROUP', 'DEC_GROUP', 'SPEC_FILE']].pprint(max_width=120)
pdb.set_trace()
return meta
def grab_meta():
""" Grab COS-Halos meta table
Returns
-------
"""
from time import strptime
from specdb.zem.utils import zem_from_radec
from specdb.specdb import IgmSpec
from specdb.defs import get_res_dicts
Rdicts = get_res_dicts()
igmsp = IgmSpec(db_file=os.getenv('SPECDB') + '/IGMspec_DB_v01.hdf5',
skip_test=True)
summ_file = os.getenv('RAW_IGMSPEC') + '/COS-Halos/cos_halos_obs.ascii'
chalos_meta = Table.read(summ_file, format='ascii')
# RA/DEC, DATE
# Visits from this page: http://www.stsci.edu/cgi-bin/get-visit-status?id=11598&markupFormat=html
visit_file = os.getenv('RAW_IGMSPEC') + '/COS-Halos/cos_halos_visits.ascii'
ch_visits = Table.read(visit_file, format='ascii')
ra = []
dec = []
datet = []
for row in chalos_meta:
coord = ltu.radec_to_coord(row['QSO'])
ra.append(coord.ra.value)
dec.append(coord.dec.value)
#
visit = row['Visit']
mtv = np.where(ch_visits['Visit'] == visit)[0]
if len(mtv) != 1:
pdb.set_trace()
else:
chv = ch_visits['Start_UT'][mtv].data[0]
icmma = chv.find(',')
datet.append('{:s}-{:02d}-{:02d}'.format(
chv[icmma + 1:icmma + 5],
strptime(chv[:3], '%b').tm_mon, int(chv[3:icmma])))
chalos_meta.add_column(Column(ra, name='RA'))
chalos_meta.add_column(Column(dec, name='DEC'))
chalos_meta.add_column(Column(datet, name='DATE-OBS'))
# Others
chalos_meta.add_column(
Column([' '] * len(chalos_meta), name='TELESCOPE')) # Padding
chalos_meta.add_column(Column([' '] * len(chalos_meta),
name='INSTR')) # Padding for HIRES
chalos_meta.add_column(
Column(['G130M/G160M'] * len(chalos_meta), name='DISPERSER'))
chalos_meta.add_column(Column([20000.] * len(chalos_meta), name='R'))
chalos_meta.add_column(Column([2000.] * len(chalos_meta), name='EPOCH'))
chalos_meta['INSTR'] = 'COS' # Deals with padding
chalos_meta['TELESCOPE'] = 'HST'
# Myers for zem
zem, zsource = zem_from_radec(chalos_meta['RA'], chalos_meta['DEC'],
Table(igmsp.hdf['quasars'].value))
badz = zem <= 0.
if np.sum(badz) > 0:
raise ValueError("Bad zem in COS-Halos")
chalos_meta['zem'] = zem
chalos_meta['sig_zem'] = 0. # Need to add
chalos_meta['flag_zem'] = zsource
# HIRES
hires_files = glob.glob(
os.getenv('RAW_IGMSPEC') + '/COS-Halos/HIRES/J*f.fits.gz')
hires_tab = chalos_meta[0:0]
subnm = np.array([row['QSO'][4:9] for row in chalos_meta])
signs = np.array([row['QSO'][14] for row in chalos_meta])
for ifile in hires_files:
print(ifile)
fname = ifile.split('/')[-1]
mt = np.where((subnm == fname[0:5]) & (signs == fname[5]))[0]
if len(mt) != 1:
pdb.set_trace()
# Add row
hires_tab.add_row(chalos_meta[mt[0]])
hires_tab[-1]['INSTR'] = 'HIRES'
hires_tab[-1]['TELESCOPE'] = 'Keck I'
hires_tab[-1]['DISPERSER'] = 'Red'
hires_tab[-1]['R'] = Rdicts['HIRES']['C1']
# Combine
chalos_meta = vstack([chalos_meta, hires_tab])
chalos_meta['STYPE'] = str('QSO')
# Rename
chalos_meta.rename_column('RA', 'RA_GROUP')
chalos_meta.rename_column('DEC', 'DEC_GROUP')
chalos_meta.rename_column('zem', 'zem_GROUP')
# Check
assert chk_meta(chalos_meta, chk_cat_only=True)
# Done
return chalos_meta
def grab_meta():
""" Grab UVES Dall'Aglio meta table
Returns
-------
"""
#
uvesdall_meta = Table.read(os.getenv('RAW_IGMSPEC') +
'/UVES_Dall/uves_dall_summ.dat',
format='ascii')
nspec = len(uvesdall_meta)
# DATE
#datearr = [day.split('/') for day in list(uvesdall_meta['ObsDate'])]
#ndate = ['20'+str(day[2])+'-'+str(day[0])+'-'+str(day[1]) for day in datearr]
t = Time(uvesdall_meta['OBS-DATE'],
out_subfmt='date') # Fixes to YYYY-MM-DD
uvesdall_meta.add_column(Column(t.iso, name='DATE-OBS'))
# RA/DEC
coord = SkyCoord(ra=uvesdall_meta['RA'],
dec=uvesdall_meta['DEC'],
unit=(u.hour, u.deg))
rad = [icoord.ra.value for icoord in coord]
decd = [icoord.dec.value for icoord in coord]
uvesdall_meta.rename_column('RA', 'RA_STR')
uvesdall_meta.rename_column('DEC', 'DEC_STR')
uvesdall_meta['RA_GROUP'] = rad
uvesdall_meta['DEC_GROUP'] = decd
# Add zem
igmsp = IgmSpec()
ztbl = Table(igmsp.hdf['quasars'].value)
zem, zsource = zem_from_radec(rad, decd, ztbl)
badz = np.where(zem < 0.1)[0]
for ibadz in badz:
if uvesdall_meta['NAME'][ibadz] == 'HE2243-6031':
zem[ibadz] = 3.005
zsource[ibadz] = 'FOP13' # Fumagalli+13
elif uvesdall_meta['NAME'][ibadz] == 'HE1341-1020':
zem[ibadz] = 2.137
zsource[ibadz] = 'Dall08' # Dall'Aglio+08
elif uvesdall_meta['NAME'][ibadz] == 'Q0002-422':
zem[ibadz] = 2.769
zsource[ibadz] = 'Dall08' # Dall'Aglio+08
elif uvesdall_meta['NAME'][ibadz] == 'PKS2000-330':
zem[ibadz] = 3.786
zsource[ibadz] = 'Dall08' # Dall'Aglio+08
else:
raise ValueError("Should not be here")
uvesdall_meta['zem_GROUP'] = zem
uvesdall_meta['sig_zem'] = [0.] * nspec
uvesdall_meta['flag_zem'] = zsource
#
uvesdall_meta.add_column(Column([2000.] * nspec, name='EPOCH'))
uvesdall_meta.add_column(Column(['VLT'] * nspec, name='TELESCOPE'))
uvesdall_meta.add_column(Column(['UVES'] * nspec, name='INSTR'))
uvesdall_meta.add_column(Column(['BOTH'] * nspec, name='DISPERSER'))
uvesdall_meta.add_column(Column([45000.] * nspec, name='R'))
uvesdall_meta['STYPE'] = str('QSO')
# Sort
uvesdall_meta.sort('RA_GROUP')
# Check
assert chk_meta(uvesdall_meta, chk_cat_only=True)
return uvesdall_meta