def test_sumlogn_limit():
obj1 = dict(flag_N=3, logN=15., sig_logN=99.)
obj2 = dict(flag_N=1, logN=14., sig_logN=0.3)
flag_N, logN, sig_logN = sum_logN(obj1, obj2)
# Test
assert flag_N == 1
np.testing.assert_allclose((logN, sig_logN), (obj2['logN'], obj2['sig_logN']))
def synthesize_components(components, zcomp=None, vbuff=0 * u.km / u.s):
"""Synthesize a list of components into one
Requires consistent RA/DEC, Zion, Ej, (A; future)
Is agnostic about z+vlim
Melds column densities
Melds velocities with an optional buffer
Note: Could make this a way to instantiate AbsComponent
Parameters
----------
components : list
list of AbsComponent objects
zcomp : float, optional
Input z to reference the synthesized component
If not input, the mean of the input components is used
vbuff : Quantity, optional
Buffer for synthesizing velocities. Deals with round off, c, etc.
"""
# Checks
assert chk_components(components, chk_A_none=True, chk_match=True)
# Meld column densities
obj = dict(flag_N=components[0].flag_N,
logN=components[0].logN,
sig_logN=components[0].sig_logN)
for comp in components[1:]:
if comp.flag_N != 0:
obj['flag_N'], obj['logN'], obj['sig_logN'] = ltaa.sum_logN(
obj, comp)
# zcomp
if zcomp is None:
zcomp = np.mean([comp.zcomp for comp in components])
# Set vlim by min/max [Using non-relativistic + buffer]
vmin = u.Quantity([
(comp.zcomp - zcomp) / (1 + zcomp) * const.c.to('km/s') + comp.vlim[0]
for comp in components
])
vmax = u.Quantity([
(comp.zcomp - zcomp) / (1 + zcomp) * const.c.to('km/s') + comp.vlim[1]
for comp in components
])
vlim = u.Quantity([np.min(vmin) - vbuff, np.max(vmax) + vbuff])
# Init final component
synth_comp = AbsComponent(
components[0].coord,
components[0].Zion,
zcomp,
vlim,
Ej=components[0].Ej,
stars=components[0].stars,
Ntup=(obj['flag_N'], obj['logN'],
obj['sig_logN'])) # Should probably set attrib instead
# Return
return synth_comp
def test_sumlogn_limit():
obj1 = dict(flag_N=3, logN=15., sig_logN=99.)
obj2 = dict(flag_N=1, logN=14., sig_logN=0.3)
flag_N, logN, sig_logN = sum_logN(obj1, obj2)
# Test
assert flag_N == 1
np.testing.assert_allclose((logN, sig_logN),
(obj2['logN'], obj2['sig_logN']))
def sum_ionN(tbl1, tbl2):
""" Sum two ion column density tables
Parameters
----------
tbl1 : Table
tbl2 : Table
Returns
-------
sum_tbl : Table
"""
# Instantiate and use data form original as starting point
sum_tbl = tbl1.copy()
# Loop through other
for row2 in tbl2:
# New?
Zion = (row2['Z'], row2['ion'])
try:
row1 = sum_tbl[(sum_tbl['Z'] == Zion[0])
& (sum_tbl['ion'] == Zion[1])]
except KeyError:
# Add in the new row
sum_tbl.add_row(row2)
else:
idx = np.where((sum_tbl['Z'] == Zion[0])
& (sum_tbl['ion'] == Zion[1]))[0][0]
# Clm
flagN, logN, siglogN = ltaa.sum_logN(row1, row2)
sum_tbl['logN'][idx] = logN
# Error
sum_tbl['sig_logN'][idx] = siglogN
# Flag
flags = [row1['flag_N'], row2['flag_N']]
if 2 in flags: # At least one saturated
flag = 2
elif 1 in flags: # None saturated; at least one detection
flag = 1
else: # Both upper limits
flag = 3
sum_tbl['flag_N'][idx] = flag
# Instrument (assuming binary flag)
if 'flg_inst' in row1.keys():
binflg = [0] * 10
for jj in range(10):
if (row2['flg_inst'] % 2**(jj + 1)) >= 2**jj:
binflg[jj] = 1
if (row1['flg_inst'] % 2**(jj + 1)) >= 2**jj:
binflg[jj] = 1
sum_tbl['flg_inst'][idx] = int(
np.sum([
2**kk for kk, ibinf in enumerate(binflg) if ibinf == 1
]))
# Return
return sum_tbl
def add_ion_to_data(self, inp_ion):
""" Add columns for ion info (column density)
to the Table
Parameters
----------
inp_ion
Returns
-------
"""
from linetools.analysis import absline as ltaa
ion = inp_ion.replace(' ', '')
# Check for previous
if 'flag_N_{:s}'.format(ion) in self._data.keys():
print("Ion data is already in the _data table")
return
# Loop on the systems
flagNs, Ns, sigNs = [], [], []
for key in self._dict.keys():
igm_comp = self._dict[key]['igm_sys']['components']
comps = [] # Allow for more than one
for comp in igm_comp.keys():
sion = comp.split('_')[0]
if sion == ion:
if 'attrib' in igm_comp[comp].keys():
attrib = igm_comp[comp]['attrib']
attrib['sig_logN'] = np.array(attrib['sig_logN'])
comps.append(attrib.copy())
else: # Deprecated
comps.append(
dict(logN=igm_comp[comp]['logN'],
flag_N=igm_comp[comp]['flag_N'],
sig_logN=np.array(
[igm_comp[comp]['sig_logN']] * 2)))
# Now sum em up
if len(comps) == 0:
flagNs.append(0)
Ns.append(0.)
sigNs.append(np.array([0.] * 2))
continue
obj = dict(flag_N=comps[0]['flag_N'],
logN=comps[0]['logN'],
sig_logN=comps[0]['sig_logN'])
for comp in comps[1:]:
if comp['flag_N'] != 0:
obj['flag_N'], obj['logN'], obj[
'sig_logN'] = ltaa.sum_logN(obj, comp)
# Save
flagNs.append(obj['flag_N'])
Ns.append(obj['logN'])
sigNs.append(obj['sig_logN'])
# Add to Table
self._data.add_column(Column(flagNs, name='flag_N_{:s}'.format(ion)))
self._data.add_column(Column(Ns, name='logN_{:s}'.format(ion)))
self._data.add_column(Column(sigNs, name='sig_logN_{:s}'.format(ion)))
def sum(self,other):
'''Sum two IonClms classes
Parameters:
----------
other: IonClms Class
Another one
Returns:
--------
A new instance of IonClms with the column densities summed
'''
# Instantiate and use data form original as starting point
newIC = IonClms()
newIC._data = copy.deepcopy(self._data)
# Loop through other
for row in other._data:
# New?
Zion = (row['Z'], row['ion'])
try:
sdict = newIC[Zion]
except KeyError:
# Add in the new row
newIC._data.add_row(row)
else:
idx = np.where((newIC.Z==Zion[0]) & (newIC.ion==Zion[1]))[0][0]
# Clm
logN, siglogN = ltaa.sum_logN(sdict,row)
newIC._data['logN'][idx] = logN
# Error
newIC._data['sig_logN'][idx] = siglogN
'''
np.sqrt(
np.sum([(sdict['sig_clm']*(10.**sdict['clm']))**2,
(row['sig_clm']*(10.**row['clm']))**2]))/(10.**newIC._data['clm'][idx])
'''
# Flag
flags = [sdict['flg_clm'], row['flg_clm']]
if 2 in flags: # At least one saturated
flag = 2
elif 1 in flags: # None saturated; at least one detection
flag = 1
else: # Both upper limits
flag = 3
newIC._data['flg_clm'][idx] = flag
# Instrument (assuming binary flag)
if 'flg_inst' in sdict.keys():
binflg = [0]*10
for jj in range(10):
if (row['flg_inst'] % 2**(jj+1)) >= 2**jj:
binflg[jj] = 1
if (sdict['flg_inst'] % 2**(jj+1)) >= 2**jj:
binflg[jj] = 1
newIC._data['flg_inst'][idx] = int(np.sum(
[2**kk for kk,ibinf in enumerate(binflg) if ibinf==1]))
# Return
return newIC
def sum_ionN(tbl1, tbl2):
""" Sum two ion column density tables
Parameters
----------
tbl1 : Table
tbl2 : Table
Returns
-------
sum_tbl : Table
"""
# Instantiate and use data form original as starting point
sum_tbl = tbl1.copy()
# Loop through other
for row2 in tbl2:
# New?
Zion = (row2['Z'], row2['ion'])
try:
row1 = sum_tbl[(sum_tbl['Z'] == Zion[0])&(sum_tbl['ion'] == Zion[1])]
except KeyError:
# Add in the new row
sum_tbl.add_row(row2)
else:
idx = np.where((sum_tbl['Z'] == Zion[0]) &
(sum_tbl['ion'] == Zion[1]))[0][0]
# Clm
flagN, logN, siglogN = ltaa.sum_logN(row1, row2)
sum_tbl['logN'][idx] = logN
# Error
sum_tbl['sig_logN'][idx] = siglogN
# Flag
flags = [row1['flag_N'], row2['flag_N']]
if 2 in flags: # At least one saturated
flag = 2
elif 1 in flags: # None saturated; at least one detection
flag = 1
else: # Both upper limits
flag = 3
sum_tbl['flag_N'][idx] = flag
# Instrument (assuming binary flag)
if 'flg_inst' in row1.keys():
binflg = [0]*10
for jj in range(10):
if (row2['flg_inst'] % 2**(jj+1)) >= 2**jj:
binflg[jj] = 1
if (row1['flg_inst'] % 2**(jj+1)) >= 2**jj:
binflg[jj] = 1
sum_tbl['flg_inst'][idx] = int(np.sum(
[2**kk for kk, ibinf in enumerate(binflg) if ibinf==1]))
# Return
return sum_tbl
def synthesize_components(components, zcomp=None, vbuff=0*u.km/u.s):
"""Synthesize a list of components into one
Requires consistent RA/DEC, Zion, Ej, (A; future)
Is agnostic about z+vlim
Melds column densities
Melds velocities with an optional buffer
Note: Could make this a way to instantiate AbsComponent
Parameters
----------
components : list
list of AbsComponent objects
zcomp : float, optional
Input z to reference the synthesized component
If not input, the mean of the input components is used
vbuff : Quantity, optional
Buffer for synthesizing velocities. Deals with round off, c, etc.
"""
# Checks
assert chk_components(components, chk_A_none=True, chk_match=True)
# Meld column densities
obj = dict(flag_N=components[0].flag_N, logN=components[0].logN,
sig_logN=components[0].sig_logN)
for comp in components[1:]:
if comp.flag_N != 0:
obj['flag_N'], obj['logN'], obj['sig_logN'] = ltaa.sum_logN(obj, comp)
# zcomp
if zcomp is None:
zcomp = np.mean([comp.zcomp for comp in components])
# Set vlim by min/max [Using non-relativistic + buffer]
vmin = u.Quantity([(comp.zcomp-zcomp)/(1+zcomp)*const.c.to('km/s')+comp.vlim[0] for comp in components])
vmax = u.Quantity([(comp.zcomp-zcomp)/(1+zcomp)*const.c.to('km/s')+comp.vlim[1] for comp in components])
vlim = u.Quantity([np.min(vmin)-vbuff, np.max(vmax)+vbuff])
# Init final component
synth_comp = AbsComponent(components[0].coord, components[0].Zion, zcomp,
vlim, Ej=components[0].Ej, stars=components[0].stars,
Ntup=(obj['flag_N'], obj['logN'], obj['sig_logN'])) # Should probably set attrib instead
# Return
return synth_comp
def synthesize_components(components, zcomp=None, vbuff=0 * u.km / u.s):
"""Synthesize a list of components into one
Requires consistent RA/DEC, Zion, Ej, (A; future)
Is agnostic about z+vlim
Melds column densities
Melds velocities with a small buffer (10 km/s)
Note: Could make this a way to instantiate AbsComponent
Parameters
----------
components : list
list of AbsComponent objects
zcomp : float, optional
Input z to reference the synthesized component
If not input, the mean of the input components is used
vbuff : Quantity, optional
Buffer for synthesizing velocities. Deals with round off, c, etc.
"""
# Checks
assert chk_components(components, chk_A_none=True, chk_match=True)
# Init final component
synth_comp = AbsComponent.from_component(
components[0], Ntup=(components[0].flag_N, components[0].logN, components[0].sig_logN)
)
# Meld column densities
for comp in components[1:]:
synth_comp.flag_N, synth_comp.logN, synth_comp.sig_logN = ltaa.sum_logN(synth_comp, comp)
# Meld z, vlim
# zcomp
if zcomp is None:
zcomp = np.mean([comp.zcomp for comp in components])
synth_comp.zcomp = zcomp
# Set vlim by min/max [Using non-relativistic + buffer]
vmin = u.Quantity([(comp.zcomp - zcomp) / (1 + zcomp) * const.c.to("km/s") + comp.vlim[0] for comp in components])
vmax = u.Quantity([(comp.zcomp - zcomp) / (1 + zcomp) * const.c.to("km/s") + comp.vlim[1] for comp in components])
synth_comp.vlim = u.Quantity([np.min(vmin) - vbuff, np.max(vmax) + vbuff])
# Return
return synth_comp
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 = pyigm_path + "/data/LLS/Literature/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 = urlopen(url)
with open(tab_fil, "wb") as code:
code.write(f.read())
# Setup
radec = '100902.06+071343.8' # From paper
lls = LLSSystem(name='J1009+0713_z0.356',
radec=radec,
zem=0.456,
zabs=0.3558,
vlim=[-200., 250.] * u.km / u.s,
NHI=18.4,
sig_NHI=np.array([0.41, 0.41]))
# 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 = ltai.name_ion(ion)
ion_dict[ion] = dict(logN=0.,
sig_logN=0.,
flag_N=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]['flag_N'] == 0):
ion_dict[ion]['flag_N'] = 3
ion_dict[ion]['logN'] = float(iis[1:])
elif (iis.strip()[0] == '>'): # Saturated
ion_dict[ion]['flag_N'] = 2
ion_dict[ion]['logN'] = log_sum(
[ion_dict[ion]['logN'],
float(iis[1:5])])
elif iis.strip()[0] in ['.', '<']:
pass
else:
if ion_dict[ion]['flag_N'] == 2: # Add to saturated
ion_dict[ion]['logN'] = log_sum(
[ion_dict[ion]['logN'],
float(iis[0:4])])
else:
ion_dict[ion]['flag_N'] = 1
obj = dict(logN=float(iis[0:4]),
sig_logN=float(iis[-4:]),
flag_N=1)
# Add
flag, N, sig = ltaa.sum_logN(ion_dict[ion], obj)
ion_dict[ion]['logN'] = N
ion_dict[ion]['sig_logN'] = sig
# Finish
lls._ionN = pyiau.dict_to_ions(ion_dict)
lls.Refs.append('Tum11')
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 = [
pyigm_path + "/data/LLS/tripp2005.tb3.ascii",
pyigm_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 = urlopen(url)
with open(tab_fil, "wb") as code:
code.write(f.read())
# Setup
radec = '121920.9320+063838.476' # SIMBAD
lls = LLSSystem(name='PG1216+069_z0.006',
radec=radec,
zem=0.3313,
zabs=0.00632,
vlim=[-100., 100.] * u.km / u.s,
NHI=19.32,
ZH=-1.6,
sig_NHI=np.array([0.03, 0.03]))
# 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 = ltai.name_ion(ionc)
except KeyError:
pdb.set_trace()
flg = 1
# Column
csplit = isplit[3].split(' ')
clm = float(csplit[0])
sig = float(csplit[2])
if flg == 1:
ion_dict[ionc] = dict(logN=clm,
sig_logN=sig,
flag_N=1,
Z=Zion[0],
ion=Zion[1])
else: # Add it in
tmp_dict = dict(logN=clm,
sig_logN=sig,
flag_N=1,
Z=Zion[0],
ion=Zion[1])
flagN, logN, siglogN = ltaa.sum_logN(ion_dict[ionc], tmp_dict)
ion_dict[ionc]['logN'] = logN
ion_dict[ionc]['sig_logN'] = 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 = ltai.name_ion(ionc)
ion_dict[ionc] = dict(Z=Zion[0], ion=Zion[1], sig_logN=0.)
if isplit[4][0] == '<':
ion_dict[ionc]['logN'] = float(isplit[4][1:])
ion_dict[ionc]['flag_N'] = 3
else:
raise ValueError('Should not get here')
# Finish
lls._ionN = pyiau.dict_to_ions(ion_dict)
lls.Refs.append('Tri05')
return lls
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 = pyigm_path+"/data/LLS/Literature/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 = '100902.06+071343.8' # From paper
lls = LLSSystem(name='J1009+0713_z0.356', radec=radec, zem=0.456,
zabs=0.3558, vlim=[-200., 250.]*u.km/u.s, NHI=18.4,
sig_NHI=np.array([0.41,0.41]))
# 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 = ltai.name_ion(ion)
ion_dict[ion] = dict(logN=0., sig_logN=0., flag_N=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]['flag_N']==0):
ion_dict[ion]['flag_N']=3
ion_dict[ion]['logN']=float(iis[1:])
elif (iis.strip()[0] == '>'): # Saturated
ion_dict[ion]['flag_N']=2
ion_dict[ion]['logN']=log_sum([ion_dict[ion]['logN'],float(iis[1:5])])
elif iis.strip()[0] in ['.','<']:
pass
else:
if ion_dict[ion]['flag_N']==2: # Add to saturated
ion_dict[ion]['logN']=log_sum([ion_dict[ion]['logN'],float(iis[0:4])])
else:
ion_dict[ion]['flag_N']=1
obj = dict(logN=float(iis[0:4]),sig_logN=float(iis[-4:]),
flag_N=1)
# Add
flag,N,sig = ltaa.sum_logN(ion_dict[ion],obj)
ion_dict[ion]['logN']=N
ion_dict[ion]['sig_logN']=sig
# Finish
lls._ionN = pyiau.dict_to_ions(ion_dict)
lls.Refs.append('Tum11')
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 = [pyigm_path+"/data/LLS/tripp2005.tb3.ascii",
pyigm_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 = '121920.9320+063838.476' # SIMBAD
lls = LLSSystem(name='PG1216+069_z0.006', radec=radec, zem=0.3313,
zabs=0.00632, vlim=[-100., 100.]*u.km/u.s, NHI=19.32, ZH=-1.6,
sig_NHI=np.array([0.03, 0.03]))
# 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 = ltai.name_ion(ionc)
except KeyError:
pdb.set_trace()
flg = 1
# Column
csplit = isplit[3].split(' ')
clm = float(csplit[0])
sig = float(csplit[2])
if flg == 1:
ion_dict[ionc] = dict(logN=clm, sig_logN=sig, flag_N=1,
Z=Zion[0], ion=Zion[1])
else: # Add it in
tmp_dict = dict(logN=clm, sig_logN=sig, flag_N=1, Z=Zion[0],
ion=Zion[1])
flagN, logN, siglogN = ltaa.sum_logN(ion_dict[ionc], tmp_dict)
ion_dict[ionc]['logN'] = logN
ion_dict[ionc]['sig_logN'] = 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 = ltai.name_ion(ionc)
ion_dict[ionc] = dict(Z=Zion[0], ion=Zion[1], sig_logN=0.)
if isplit[4][0] == '<':
ion_dict[ionc]['logN'] = float(isplit[4][1:])
ion_dict[ionc]['flag_N'] = 3
else:
raise ValueError('Should not get here')
# Finish
lls._ionN = pyiau.dict_to_ions(ion_dict)
lls.Refs.append('Tri05')
return lls
