def __getitem__(self, ion):
'''Passback a dict of measured data on a given ion
Parameters:
-----------
ion: tuple or str
tuple: (Z,ion_state) e.g. (14,2)
str: Name, e.g. 'SiII'
Returns:
----------
Dict (from row in the data table)
'''
if isinstance(ion, tuple):
mt = np.where((self._data['Z'] == ion[0])
& (self._data['ion'] == ion[1]))[0]
elif isinstance(ion, basestring):
# Convert to tuple
return self.__getitem__(xai.name_ion(ion))
else:
raise ValueError('Not prepared for this type')
if len(mt) == 0:
raise KeyError
else:
return dict(zip(self._data.dtype.names, self._data[mt][0]))
def __getitem__(self, k):
'''Passback list of lines with this input
See also grab_line method for quries on individual lines
Parameters:
-----------
k: Quantity, tuple, or str
float -- Rest wavelength, e.g. 1215.6701*u.AA
tuple -- Zion, e.g. (14,2)
str -- Name of the ion, e.g. 'SiII'
Returns:
----------
float: List of all matching absorption lines
str: Dict of info on that ion and wavelengths of matching lines
'''
if isinstance(k,Quantity): # List of AbsLines
return [ilin for ilin in self.lines if np.abs(ilin.wrest-k)<1e-4*u.AA]
elif isinstance(k,(basestring,tuple)): #
# Column densities
idict = self._ionclms[k]
# Matching Absorption lines matching
if isinstance(k,basestring):
Zion = xai.name_ion(k)
else:
Zion = k
idict[str('lines')] = [ilin.wrest for ilin in self.lines if (
(ilin.data['Z']==Zion[0]) & (ilin.data['ion']==Zion[1]))]
return idict
#lines = [ilin for ilin in self.lines if ilin.trans==k]
else:
raise ValueError('Not prepared for this type')
def __getitem__(self, ion):
'''Passback a dict of measured data on a given ion
Parameters:
-----------
ion: tuple or str
tuple: (Z,ion_state) e.g. (14,2)
str: Name, e.g. 'SiII'
Returns:
----------
Dict (from row in the data table)
'''
if isinstance(ion,tuple):
mt = np.where((self._data['Z'] == ion[0]) & (self._data['ion'] == ion[1]))[0]
elif isinstance(ion,basestring):
# Convert to tuple
return self.__getitem__(xai.name_ion(ion))
else:
raise ValueError('Not prepared for this type')
if len(mt) == 0:
raise KeyError
else:
return dict(zip(self._data.dtype.names,self._data[mt][0]))
def __getitem__(self, k):
'''Passback list of lines with this input
See also grab_line method for quries on individual lines
Parameters:
-----------
k: Quantity, tuple, or str
float -- Rest wavelength, e.g. 1215.6701*u.AA
tuple -- Zion, e.g. (14,2)
str -- Name of the ion, e.g. 'SiII'
Returns:
----------
float: List of all matching absorption lines
str: Dict of info on that ion and wavelengths of matching lines
'''
if isinstance(k,Quantity): # List of AbsLines
return [ilin for ilin in self.lines if np.abs(ilin.wrest-k)<1e-4*u.AA]
elif isinstance(k,(basestring,tuple)): #
# Column densities
idict = self._ionclms[k]
# Matching Absorption lines matching
if isinstance(k,basestring):
Zion = xai.name_ion(k)
else:
Zion = k
idict[str('lines')] = [ilin.wrest for ilin in self.lines if (
(ilin.data['Z']==Zion[0]) & (ilin.data['ion']==Zion[1]))]
return idict
#lines = [ilin for ilin in self.lines if ilin.trans==k]
else:
raise ValueError('Not prepared for this type')
def from_dict(self, idict, verbose=False):
# Manipulate for astropy Table
table = None
for ion in idict.keys():
Zion = xai.name_ion(ion)
if table is None:
tkeys = idict[ion].keys()
lst = [[idict[ion][tkey]] for tkey in tkeys]
table = Table(lst, names=tkeys)
# Extra columns
if 'Z' not in tkeys:
table.add_column(Column([Zion[0]], name='Z'))
table.add_column(Column([Zion[1]], name='ion'))
else:
tdict = idict[ion]
if 'Z' not in tkeys:
tdict['Z'] = Zion[0]
tdict['ion'] = Zion[1]
# Add
table.add_row(tdict)
# Finish
self._data = table
def from_dict(self,idict,verbose=False):
# Manipulate for astropy Table
table = None
for ion in idict.keys():
Zion = xai.name_ion(ion)
if table is None:
tkeys = idict[ion].keys()
lst = [[idict[ion][tkey]] for tkey in tkeys]
table = Table(lst, names=tkeys)
# Extra columns
if 'Z' not in tkeys:
table.add_column(Column([Zion[0]],name='Z'))
table.add_column(Column([Zion[1]],name='ion'))
else:
tdict = idict[ion]
if 'Z' not in tkeys:
tdict['Z'] = Zion[0]
tdict['ion'] = Zion[1]
# Add
table.add_row(tdict)
# Finish
self._data = table
def tumlinson11():
'''Tumlinson, J. et al. 2011, ApJ, 733, 111
J1009+0713
HST/COS
Metal columns parsed from Table 1
NHI from LL+Lyman series (uncertain)
'''
# Grab ASCII file from ApJ
tab_fil = xa_path + "/data/LLS/tumlinson11.tb1.ascii"
url = 'http://iopscience.iop.org/0004-637X/733/2/111/suppdata/apj388927t1_ascii.txt'
chk_fil = glob.glob(tab_fil)
if len(chk_fil) > 0:
tab_fil = chk_fil[0]
else:
print('LLSSurvey: Grabbing table file from {:s}'.format(url))
f = urllib2.urlopen(url)
with open(tab_fil, "wb") as code:
code.write(f.read())
# Setup
radec = xor.stod1('J100902.06+071343.8') # From paper
lls = LLSSystem(name='J1009+0713_z0.356',
RA=radec[0],
Dec=radec[1],
zem=0.456,
zabs=0.3558,
vlim=[-200., 250.] * u.km / u.s,
NHI=18.4,
sigNHI=np.array([0.41, 0.41]))
#lls.mk_subsys(2)
# Columns
# Start with Table 3 (VPFIT)
with open(tab_fil, 'r') as f:
flines1 = f.readlines()
# Trim
flines1 = flines1[18:]
#
ion_dict = {}
line_dict = dict(OI='1302',
OVI='1038',
MgII='2803^b',
SiII='1190',
CaII='3934',
FeII='2586')
ion = None
for iline in flines1:
isplit = iline.split('\t')
if ion == 'FeIII': # Last line
break
# Ion
is2 = isplit[0].split(' ')
ion = is2[0] + is2[1]
try:
gdl = line_dict[ion]
except:
pass
#print('Taking {:s}'.format(isplit[0]))
else:
if is2[2] != gdl:
continue
Zion = xai.name_ion(ion)
ion_dict[ion] = dict(clm=0.,
sig_clm=0.,
flg_clm=0,
Z=Zion[0],
ion=Zion[1])
# Combine components [could replace with SubSystems some day]
for iis in isplit[1:-1]:
# Upper limit
if (iis.strip()[0] == '<') & (ion_dict[ion]['flg_clm'] == 0):
ion_dict[ion]['flg_clm'] = 3
ion_dict[ion]['clm'] = float(iis[1:])
elif (iis.strip()[0] == '>'): # Saturated
ion_dict[ion]['flg_clm'] = 2
ion_dict[ion]['clm'] = log_sum(
[ion_dict[ion]['clm'],
float(iis[1:5])])
elif iis.strip()[0] in ['.', '<']:
pass
else:
if ion_dict[ion]['flg_clm'] == 2: # Add to saturated
ion_dict[ion]['clm'] = log_sum(
[ion_dict[ion]['clm'],
float(iis[0:4])])
else:
ion_dict[ion]['flg_clm'] = 1
obj = dict(clm=float(iis[0:4]), sig_clm=float(iis[-4:]))
# Add
N, sig = xiai.sum_logN(ion_dict[ion], obj)
ion_dict[ion]['clm'] = N
ion_dict[ion]['sig_clm'] = sig
# Finish
lls._ionclms = IonClms(idict=ion_dict)
lls.Refs.append('Tum11')
return lls
def dessauges09():
'''Dessauges-Zavadsky et al. 2009, MNRAS, 396, L96
SLLS with UVES
Zn,Fe abundances from Table 1 from astro-ph (LateX) by JXP [AODM]
Taken from the Zn/H and Fe/H assuming *no* ionization corrections
RA/DEC from the 'other' name
'''
# Solar abundances
eZn = 4.63
eFe = 7.45
sol = [eFe, eZn]
#
all_lls = []
# Table 1
tab_fil = xa_path + "/data/LLS/dessauges09.tb1.ascii"
with open(tab_fil, 'r') as f:
flines1 = f.readlines()
# Trim the first few lines
flines1 = flines1[3:]
ion_dict = {}
for iline in flines1:
# Parse
isplit = iline.split('&')
# QSO
if iline[0:2] == 'QS':
# QSO, RA/DEC, zem
qso = isplit[0][4:].strip()
radec = xor.stod1(isplit[1].strip().replace('$', ''))
zem = float(isplit[3].strip())
# NHI, zabs
zabs = float(isplit[4].strip())
is2 = isplit[6].strip()
NHI = float(is2[1:6])
sigNHI = np.array([float(is2[10:14])] * 2)
# name
name = qso + 'z_{:.3f}'.format(zabs)
lls = LLSSystem(name=name,
RA=radec[0],
Dec=radec[1],
zem=zem,
zabs=zabs,
NHI=NHI,
sigNHI=sigNHI)
# ADOM Columns
ion_dict = {}
for kk, ion in enumerate(['Fe II', 'Zn II']):
Zion = xai.name_ion(ion)
is2 = isplit[7 + kk].strip()
if is2[0:2] == '$>':
ion_dict[ion] = dict(sig_clm=0.,
flg_clm=2,
Z=Zion[0],
ion=Zion[1])
ion_dict[ion]['clm'] = float(is2[2:7]) + NHI - 12 + sol[kk]
elif is2[0:2] == '$<':
ion_dict[ion] = dict(sig_clm=0.,
flg_clm=3,
Z=Zion[0],
ion=Zion[1])
ion_dict[ion]['clm'] = float(is2[2:7]) + NHI - 12 + sol[kk]
elif is2[0:2] == '..':
pass
else:
ion_dict[ion] = dict(flg_clm=1, Z=Zion[0], ion=Zion[1])
ion_dict[ion]['clm'] = float(is2[1:6]) + NHI - 12 + sol[kk]
ion_dict[ion]['sig_clm'] = float(is2[10:14])
#xdb.set_trace()
# Finish
lls._ionclms = IonClms(idict=ion_dict)
lls.Refs.append('DZ09')
all_lls.append(lls)
# Return SLLS only
fin_slls = [ills for ills in all_lls if ills.NHI < 20.3]
return fin_slls
def meiring09():
'''Meiring et al. 2009, MNRAS, 393, 1513
SLLS with Magellan
Abundances from Table 3 from astro-ph (LateX) by JXP [AODM]
RA/DEC from Table 1
'''
all_lls = []
# Table 1
tab_fil = xa_path + "/data/LLS/meiring09.tb1.ascii"
with open(tab_fil, 'r') as f:
flines1 = f.readlines()
# Grab RA/DEC
qso_dict = {}
for iline in flines1:
if iline[0:3] in [' QS', '\hl', '$\\c', ' J2', ' ']:
continue
# Parse
isplit = iline.split('&')
#xdb.set_trace()
if '$' in isplit[3].strip():
isplit[3] = '-' + (isplit[3].strip())[3:]
radec = xor.stod1((isplit[2], isplit[3]))
# zem
zem = float(isplit[5].strip())
# Save
qso_dict[isplit[0].strip()] = dict(RA=radec[0], Dec=radec[1], zem=zem)
# Abundances (AODM)
# Table 3
tab_fil = xa_path + "/data/LLS/meiring09.tb3.ascii"
with open(tab_fil, 'r') as f:
flines3 = f.readlines()
#
ion_dict = {}
for iline in flines3:
if iline[0:2] in ['\h', ' ']:
continue
# Parse
isplit = iline.split('&')
# Ions
if iline[0:2] == 'QS':
ioncs = []
Zions = []
for iis in isplit[3:-1]: # Skipping HI
# Parse
#is2 = iis.split('\\')
#ip2 = is2[2].find('}')
ionc = iis.strip()
# Zion
Zion = xai.name_ion(ionc)
# Append
ioncs.append(ionc)
Zions.append(Zion)
continue
if iline[0] == 'Q':
# QSO
qso = isplit[0].strip()
if qso[-1] in ['A', 'B', 'C']:
qso = qso[0:-1]
# zabs and name
zabs = float(isplit[1].strip())
qso_dict[qso]['name'] = qso + 'z_{:.3f}'.format(zabs)
qso_dict[qso]['zabs'] = zabs
# NHI
is2 = isplit[2].strip()
if is2[0] == '$':
qso_dict[qso]['NHI'] = 99.99 # THROW OUT Q1436-0051B
qso_dict[qso]['sigNHI'] = np.array([0., 0.])
else:
qso_dict[qso]['NHI'] = float(is2[0:5])
qso_dict[qso]['sigNHI'] = np.array([float(is2[10:])] * 2)
#if qso_dict[qso]['NHI'] >= 20.3:
# print('Uh oh. DLA')
# Generate LLS
lls = LLSSystem(**qso_dict[qso])
continue
else:
# ADOM Columns
ion_dict = {}
for kk, iis in enumerate(isplit[3:-1]):
is2 = iis.strip()
if is2[0:3] == '$>$':
ion_dict[ioncs[kk]] = dict(sig_clm=0.,
flg_clm=2,
Z=Zions[kk][0],
ion=Zions[kk][1])
ion_dict[ioncs[kk]]['clm'] = float(is2[3:])
elif is2[0:3] == '$<$':
ion_dict[ioncs[kk]] = dict(sig_clm=0.,
flg_clm=3,
Z=Zions[kk][0],
ion=Zions[kk][1])
ion_dict[ioncs[kk]]['clm'] = float(is2[3:])
elif len(is2) == 0:
pass
else:
ion_dict[ioncs[kk]] = dict(flg_clm=1,
Z=Zions[kk][0],
ion=Zions[kk][1])
ion_dict[ioncs[kk]]['clm'] = float(is2[0:5])
ion_dict[ioncs[kk]]['sig_clm'] = float(is2[10:])
# Finish
lls._ionclms = IonClms(idict=ion_dict)
lls.Refs.append('Mei09')
all_lls.append(lls)
# Return SLLS only
fin_slls = [ills for ills in all_lls if ills.NHI < 20.3]
return fin_slls
def peroux06b():
'''Peroux, C. et al. 2006b, A&A, 450, 53
SDSS J1323-0021
Metal rich
Metal columns copied by JXP from Table 1
Total NHI from damping wings
'''
# Setup
radec = xor.stod1('J132323.78-002155.2') # SDSS Name
lls = LLSSystem(name='SDSSJ1323-0021_z0.716',
RA=radec[0],
Dec=radec[1],
zem=1.390,
zabs=0.716,
vlim=[-200., 200.] * u.km / u.s,
NHI=20.21,
sigNHI=np.array([0.20, 0.20]))
# Parse table file
tab_fil = xa_path + "/data/LLS/peroux06b.tb1.ascii"
with open(tab_fil, 'r') as f:
flines = f.readlines()
ion_dict = {}
for iline in flines:
isplit = iline.split('\t')
if len(isplit[0]) == 0:
# Grab ions and init
ions = isplit[3:10]
for ion in ions:
Zion = xai.name_ion(ion)
ion_dict[ion] = dict(clm=0.,
sig_clm=0.,
flg_clm=1,
Z=Zion[0],
ion=Zion[1])
continue
# Column or sigma?
if isplit[0][0] == 'N': # Column
for kk, iis in enumerate(isplit[3:10]):
ion = ions[kk]
if iis[0] == '>':
ion_dict[ion]['flg_clm'] = 2
ion_dict[ion]['clm'] += float(iis[1:])
elif iis[0] == '<':
pass
elif iis[0] == '.':
pass
else:
ion_dict[ion]['clm'] += float(iis)
else: # Sigma
for kk, iis in enumerate(isplit[3:10]):
ion = ions[kk]
if iis[0] == '.':
pass
else:
ion_dict[ion]['sig_clm'] += float(iis)**2
# Convert to log
for ion in ions:
N = ion_dict[ion]['clm']
sig = np.sqrt(ion_dict[ion]['sig_clm'])
#
ion_dict[ion]['clm'] = np.log10(N)
if ion_dict[ion]['flg_clm'] == 2:
ion_dict[ion]['sig_clm'] = 0.
else:
ion_dict[ion]['sig_clm'] = sig / N / np.log(10)
# Finish
lls._ionclms = IonClms(idict=ion_dict)
lls.Refs.append('Prx06b')
return lls
def tripp2005():
'''Tripp, T. et al. 2005, ApJ, 2005, 619, 714
PG 1216+069 (LLS in Virgo)
HST/STIS, FUSE
Metal columns parsed from Tables 2 and 3
Total NHI from damping wings
M/H from O/H
'''
# Grab ASCII files from ApJ
tab_fils = [
xa_path + "/data/LLS/tripp2005.tb3.ascii",
xa_path + "/data/LLS/tripp2005.tb2.ascii"
]
urls = [
'http://iopscience.iop.org/0004-637X/619/2/714/fulltext/60797.tb3.txt',
'http://iopscience.iop.org/0004-637X/619/2/714/fulltext/60797.tb2.txt'
]
for jj, tab_fil in enumerate(tab_fils):
chk_fil = glob.glob(tab_fil)
if len(chk_fil) > 0:
tab_fil = chk_fil[0]
else:
url = urls[jj]
print('LLSSurvey: Grabbing table file from {:s}'.format(url))
f = urllib2.urlopen(url)
with open(tab_fil, "wb") as code:
code.write(f.read())
# Setup
radec = xor.stod1('J121920.9320+063838.476') # SIMBAD
lls = LLSSystem(name='PG1216+069_z0.006',
RA=radec[0],
Dec=radec[1],
zem=0.3313,
zabs=0.00632,
vlim=[-100., 100.] * u.km / u.s,
NHI=19.32,
MH=-1.6,
sigNHI=np.array([0.03, 0.03]))
#lls.mk_subsys(2)
# Columns
# Start with Table 3 (VPFIT)
with open(tab_fils[0], 'r') as f:
flines3 = f.readlines()
ion_dict = {}
for iline in flines3:
if (len(iline.strip()) == 0):
continue
isplit = iline.split('\t')
# Ion
flg = 2
if (len(isplit[0].strip()) > 0): # & (isplit[0][0] not in ['1','2']):
ipos = isplit[0].find('1')
ionc = isplit[0][0:ipos - 1].strip()
try:
Zion = xai.name_ion(ionc)
except KeyError:
xdb.set_trace()
flg = 1
# Column
csplit = isplit[3].split(' ')
clm = float(csplit[0])
sig = float(csplit[2])
if flg == 1:
ion_dict[ionc] = dict(clm=clm,
sig_clm=sig,
flg_clm=1,
Z=Zion[0],
ion=Zion[1])
else: # Add it in
tmp_dict = dict(clm=clm,
sig_clm=sig,
flg_clm=1,
Z=Zion[0],
ion=Zion[1])
logN, siglogN = xiai.sum_logN(ion_dict[ionc], tmp_dict)
ion_dict[ionc]['clm'] = logN
ion_dict[ionc]['sig_clm'] = siglogN
ions = ion_dict.keys()
# Now Table 2 for the extras
with open(tab_fils[1], 'r') as f:
flines2 = f.readlines()
# Trim the first 10 lines
flines2 = flines2[10:]
# Loop
for iline in flines2:
isplit = iline.split('\t')
#
ionc = isplit[0].strip()
if (len(ionc) == 0) or (ionc in ions):
continue
#
Zion = xai.name_ion(ionc)
ion_dict[ionc] = dict(Z=Zion[0], ion=Zion[1], sig_clm=0.)
if isplit[4][0] == '<':
ion_dict[ionc]['clm'] = float(isplit[4][1:])
ion_dict[ionc]['flg_clm'] = 3
else:
raise ValueError('Should not get here')
# Finish
lls._ionclms = IonClms(idict=ion_dict)
lls.Refs.append('Tri05')
return lls
def battisti12():
'''Battisti, A. et al. 2012, ApJ, 744, 93
HST/COS
QSO info from Table 1
Metal columns parsed from Table 3
NHI from Lya
'''
all_lls = []
# Grab ASCII files from ApJ
tab_fils = [
xa_path + "/data/LLS/battisti12.tb1.ascii",
xa_path + "/data/LLS/battisti12.tb3.ascii"
]
urls = [
'http://iopscience.iop.org/0004-637X/744/2/93/suppdata/apj413924t1_ascii.txt',
'http://iopscience.iop.org/0004-637X/744/2/93/suppdata/apj413924t3_ascii.txt'
]
for jj, tab_fil in enumerate(tab_fils):
chk_fil = glob.glob(tab_fil)
if len(chk_fil) > 0:
tab_fil = chk_fil[0]
else:
url = urls[jj]
print('LLSSurvey: Grabbing table file from {:s}'.format(url))
f = urllib2.urlopen(url)
with open(tab_fil, "wb") as code:
code.write(f.read())
# QSO info
with open(tab_fils[0], 'r') as f:
flines1 = f.readlines()
# Grab RA/DEC
all_idict = []
for iline in flines1:
if iline[0:2] != 'SD':
continue
# Parse
isplit = iline.split('\t')
name = isplit[0].split(' ')[1]
radec = xor.stod1(name)
zem = float(isplit[1].strip())
zabs = float(isplit[2].strip())
NHI = float(isplit[3].strip()[0:4])
sigNHI = np.array([float(isplit[3].strip()[11:])] * 2)
# Save
lls = LLSSystem(name=name,
RA=radec[0],
Dec=radec[1],
zem=zem,
zabs=zabs,
NHI=NHI,
sigNHI=sigNHI)
#
all_lls.append(lls)
all_idict.append({})
# Abundances
with open(tab_fils[1], 'r') as f:
flines3 = f.readlines()
flines3 = flines3[5:]
ion = None
for iline in flines3:
if ion == 'Ni II':
break
isplit = iline.split('\t')
if isplit[0] == 'C II*': # Skipping CII*
continue
# ion
ipos = -1
while (isplit[0][ipos] not in ['I', 'V']):
ipos -= 1
ion = isplit[0][0:ipos + 1 + len(isplit[0])]
Zion = xai.name_ion(ion)
# Loop on systems
for kk, iis in enumerate(isplit[1:-1]):
if iis.strip()[0] == '.':
continue
all_idict[kk][ion] = dict(Z=Zion[0], ion=Zion[1], sig_clm=0.)
if iis[0] == '>':
all_idict[kk][ion]['flg_clm'] = 2
all_idict[kk][ion]['clm'] = float(iis[1:6])
elif iis[0] == '<':
all_idict[kk][ion]['flg_clm'] = 3
all_idict[kk][ion]['clm'] = float(iis[1:])
else:
all_idict[kk][ion]['flg_clm'] = 1
all_idict[kk][ion]['clm'] = float(iis[0:5])
all_idict[kk][ion]['sig_clm'] = float(iis[-4:])
# Return SLLS only
for kk, lls in enumerate(all_lls):
try:
lls._ionclms = IonClms(idict=all_idict[kk])
except ValueError:
xdb.set_trace()
lls.Refs.append('Bat12')
fin_slls = [ills for ills in all_lls if ills.NHI < 20.3]
return fin_slls
def jenkins2005():
'''Jenkins, E. et al. 2005, ApJ, 2005, 623, 767
PHL 1811
HST/STIS, FUSE
Metals parsed from Table 1
OI taken from text
Had to input error on columns by hand (JXP)
Total NHI from Lyman series. see Fig 3
M/H from O/H
'''
# Grab ASCII file from ApJ
tab_fil = xa_path + "/data/LLS/jenkins2005.tb1.ascii"
chk_fil = glob.glob(tab_fil)
if len(chk_fil) > 0:
tab_fil = chk_fil[0]
else:
url = 'http://iopscience.iop.org/0004-637X/623/2/767/fulltext/61520.tb1.txt'
print('LLSSurvey: Grabbing table file from {:s}'.format(url))
f = urllib2.urlopen(url)
with open(tab_fil, "wb") as code:
code.write(f.read())
# Setup
radec = xor.stod1('J215501.5152-092224.688') # SIMBAD
lls = LLSSystem(name='PHL1811_z0.081',
RA=radec[0],
Dec=radec[1],
zem=0.192,
zabs=0.080923,
vlim=[-100., 100.] * u.km / u.s,
NHI=17.98,
MH=-0.19,
sigNHI=np.array([0.05, 0.05]))
# AbsLines
ism = LineList('ISM')
Nsig = {
'C IV': 0.4,
'N II': 0.4,
'Si II': 0.05,
'Si IV': 0.25,
'S II': 0.2,
'Fe II': 0.12,
'H I': 0.05,
'S III': 0.06
}
# Parse Table
with open(tab_fil, 'r') as f:
flines = f.readlines()
ion_dict = {}
for iline in flines:
iline = iline.strip()
if (len(iline) == 0):
continue
# Split on tabs
isplit = iline.split('\t')
# Offset?
ioff = 0
if isplit[0][0] in ['1', '2']:
ioff = -1
# Catch bad lines
if (isplit[1 + ioff][0:6]
in ['1442.0', '1443.7',
'1120.9']): # Skip goofy CII line and CII*
continue
if len(isplit[2 + ioff]) == 0:
continue
# Ion
if (len(isplit[0].strip()) > 0) & (isplit[0][0] not in ['1', '2']):
ionc = isplit[0].strip()
try:
Zion = xai.name_ion(ionc)
except KeyError:
xdb.set_trace()
# Generate the Line
try:
newline = AbsLine(float(isplit[2 + ioff]) * u.AA,
linelist=ism,
closest=True)
except ValueError:
xdb.set_trace()
newline.attrib['z'] = lls.zabs
# Spectrum
newline.analy['datafile'] = 'STIS' if 'S' in isplit[1] else 'FUSE'
# EW
try:
EWvals = isplit[4 + ioff].split(' ')
except IndexError:
xdb.set_trace()
newline.attrib['EW'] = float(EWvals[0]) * u.AA / 1e3
newline.attrib['EWsig'] = float(EWvals[2]) * u.AA / 1e3
newline.attrib['flgEW'] = 1
if len(isplit) < (5 + ioff + 1):
continue
# Colm?
#xdb.set_trace()
if (len(isplit[5 + ioff].strip()) > 0) & (isplit[5 + ioff].strip() !=
'\\ldots'):
if isplit[5 + ioff][0] == '\\':
ipos = isplit[5 + ioff].find(' ')
newline.attrib['N'] = float(isplit[5 + ioff][ipos + 1:])
newline.attrib['flagN'] = 2
elif isplit[5 + ioff][0] == '<':
ipos = 0
newline.attrib['N'] = float(isplit[5 + ioff][ipos + 1:])
newline.attrib['flagN'] = 3
elif isplit[5 + ioff][0] == '1':
try:
newline.attrib['N'] = float(isplit[5 + ioff][0:5])
except ValueError:
xdb.set_trace()
newline.attrib['flagN'] = 1
try:
newline.attrib['Nsig'] = Nsig[ionc]
except KeyError:
print('No error for {:s}'.format(ionc))
else:
raise ValueError('Bad character')
# ion_dict
ion_dict[ionc] = dict(clm=newline.attrib['N'],
sig_clm=newline.attrib['Nsig'],
flg_clm=newline.attrib['flagN'],
Z=Zion[0],
ion=Zion[1])
# Append
lls.lines.append(newline)
# Fix NI, OI
ion_dict['O I']['clm'] = 14.47
ion_dict['O I']['sig_clm'] = 0.05
ion_dict['N I']['flg_clm'] = 3
lls._ionclms = IonClms(idict=ion_dict)
lls.Refs.append('Jen05')
# Return
return lls
