def test_name_to_ion():
Zion = ions.name_ion('Si II')
assert Zion == (14,2)
# bad input
with pytest.raises(ValueError):
aux = ions.name_ion(4) # not a string
# Deuterium
aux = ions.name_ion('DI')
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 = '132323.78-002155.2' # SDSS Name
lls = LLSSystem(name='SDSSJ1323-0021_z0.716', radec=radec, zem=1.390,
zabs=0.716, vlim=[-200., 200.]*u.km/u.s, NHI=20.21,
sig_NHI=np.array([0.20,0.20]))
# Parse table file
tab_fil = pyigm_path+"/data/LLS/Literature/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 = ltai.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._ionN = pyiau.dict_to_ions(ion_dict)
lls.Refs.append('Prx06b')
return lls
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 = '132323.78-002155.2' # SDSS Name
lls = LLSSystem(name='SDSSJ1323-0021_z0.716', radec=radec, zem=1.390,
zabs=0.716, vlim=[-200., 200.]*u.km/u.s, NHI=20.21,
sig_NHI=np.array([0.20,0.20]))
# Parse table file
tab_fil = pyigm_path+"/data/LLS/Literature/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 = ltai.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._ionN = pyiau.dict_to_ions(ion_dict)
lls.Refs.append('Prx06b')
return lls
def main(args=None):
pargs = parser(options=args)
if pargs.inp is None and pargs.all is False:
print("No option selected. Use -h for Help")
return
# Setup
from astropy import units as u
from astropy.table import Column
from linetools.lists.linelist import LineList
from linetools.abund import ions as ltai
import numpy as np
cols = ['name', 'wrest', 'f', 'A']
# LineList
llist = LineList(pargs.llist)
# Redshift?
if float(pargs.redshift) != 0.:
z = llist._data['wrest']*(1+float(pargs.redshift))
llist._data.add_column(Column(z, name='z'))
cols += ['z']
# All?
if pargs.all:
llist._data[cols].pprint(99999)
return
# Grab line(s)
if ustr(pargs.inp[0]).isdecimal(): # Input rest wavelength
wrest = float(pargs.inp)*u.AA
mtch = np.abs(wrest-llist.wrest) < pargs.toler*u.AA
llist._data[cols][mtch].pprint(99999)
else: # Either ion or transition
istrans = False
for jj,char in enumerate(pargs.inp):
if char.isdigit():
istrans = True
i0 = jj
break
if istrans:
trans = pargs.inp[0:i0]+' '+pargs.inp[i0:]
tdict = llist[trans]
for key,value in tdict.items():
if key in cols:
print('{:s}: {}'.format(key,value))
else: # Ion
Zion = ltai.name_ion(pargs.inp)
mtion = (llist.Z == Zion[0]) & (llist.ion == Zion[1])
llist._data[cols][mtion].pprint(99999)
def dict_to_ions(idict):
""" Manipulate dict into an ion astropy Table
Will likely be deprecated
Parameters
----------
idict : dict
Returns
-------
table : astropy.Table
"""
# Could probably use add_row or dict instantiation
table = None
for ion in idict.keys():
Zion = ltai.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]
tkeys = idict[ion].keys()
if 'Z' not in tkeys:
tdict['Z'] = Zion[0]
tdict['ion'] = Zion[1]
# Add
table.add_row(tdict)
# Finish
try: # Historical keys
table.rename_column('clm', 'logN')
except:
pass
else:
table.rename_column('sig_clm', 'sig_logN')
table.rename_column('flg_clm', 'flag_N')
# Return
return table
def dict_to_ions(idict):
""" Manipulate dict into an ion astropy Table
Will likely be deprecated
Parameters
----------
idict : dict
Returns
-------
table : astropy.Table
"""
# Could probably use add_row or dict instantiation
table = None
for ion in idict.keys():
Zion = ltai.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]
tkeys = idict[ion].keys()
if 'Z' not in tkeys:
tdict['Z'] = Zion[0]
tdict['ion'] = Zion[1]
# Add
table.add_row(tdict)
# Finish
try: # Historical keys
table.rename_column('clm', 'logN')
except:
pass
else:
table.rename_column('sig_clm', 'sig_logN')
table.rename_column('flg_clm', 'flag_N')
# Return
return 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 = 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 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 = pyigm_path+"/data/LLS/Literature/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 = '215501.5152-092224.688' # SIMBAD
lls = LLSSystem(name='PHL1811_z0.081', radec=radec, zem=0.192,
zabs=0.080923, vlim=[-100., 100.]*u.km/u.s, NHI=17.98, ZH=-0.19,
sig_NHI=np.array([0.05,0.05]))
lls.lines = [] # Probably not used
# 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 = ltai.name_ion(ionc)
except KeyError:
pdb.set_trace()
# Generate the Line
try:
newline = AbsLine(float(isplit[2+ioff])*u.AA,linelist=ism, closest=True)
except ValueError:
pdb.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:
pdb.set_trace()
newline.attrib['EW'] = float(EWvals[0])*u.AA/1e3
newline.attrib['sig_EW'] = float(EWvals[2])*u.AA/1e3
newline.attrib['flag_EW'] = 1
if len(isplit) < (5+ioff+1):
continue
# Colm?
#xdb.set_trace()
newline.attrib['sig_logN'] = 0.
if (len(isplit[5+ioff].strip()) > 0) & (isplit[5+ioff].strip() != '\\ldots'):
if isplit[5+ioff][0] == '\\':
ipos = isplit[5+ioff].find(' ')
newline.attrib['logN'] = float(isplit[5+ioff][ipos+1:])
newline.attrib['flag_N'] = 2
elif isplit[5+ioff][0] == '<':
ipos = 0
newline.attrib['logN'] = float(isplit[5+ioff][ipos+1:])
newline.attrib['flag_N'] = 3
elif isplit[5+ioff][0] == '1':
try:
newline.attrib['logN'] = float(isplit[5+ioff][0:5])
except ValueError:
pdb.set_trace()
newline.attrib['flag_N'] = 1
try:
newline.attrib['sig_logN'] = 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['logN'], sig_clm=newline.attrib['sig_logN'],
flg_clm=newline.attrib['flag_N'], 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._ionN = pyiau.dict_to_ions(ion_dict)
lls.Refs.append('Jen05')
# Return
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 = pyigm_path+"/data/LLS/Literature/dessauges09.tb1.ascii"
with open(tab_fil,'r') as f:
flines1 = f.readlines()
# Trim the first few lines
flines1 = flines1[3:]
for iline in flines1:
# Parse
isplit = iline.split('&')
# QSO
if iline[0:2] == 'QS':
# QSO, RA/DEC, zem
qso = isplit[0][4:].strip()
radec = isplit[1].strip()[1:].replace('$','')
zem = float(isplit[3].strip())
# NHI, zabs
zabs = float(isplit[4].strip())
is2 = isplit[6].strip()
NHI = float(is2[1:6])
sigNHI = np.array([float(is2[10:14])]*2)
# name
name = qso+'z_{:.3f}'.format(zabs)
lls = LLSSystem(name=name, radec=radec, vlim=[-500,500]*u.km/u.s,
zem=zem, zabs=zabs, NHI=NHI, sig_NHI=sigNHI)
# ADOM Columns
ion_dict = {}
for kk,ion in enumerate(['Fe II','Zn II']):
Zion = ltai.name_ion(ion)
is2 = isplit[7+kk].strip()
if is2[0:2] == '$>':
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] == '$<':
ion_dict[ion] = dict(sig_clm=0.,flg_clm=3,Z=Zion[0],ion=Zion[1])
ion_dict[ion]['clm'] = float(is2[2:7]) + NHI - 12 + sol[kk]
elif is2[0:2] == '..':
pass
else:
ion_dict[ion] = dict(flg_clm=1,Z=Zion[0],ion=Zion[1])
ion_dict[ion]['clm'] = float(is2[1:6]) + NHI - 12 + sol[kk]
ion_dict[ion]['sig_clm'] = float(is2[10:14])
#xdb.set_trace()
# Finish
lls._ionN = pyiau.dict_to_ions(ion_dict)
lls.Refs.append('DZ09')
all_lls.append(lls)
# Return SLLS only
fin_slls = [ills for ills in all_lls if ills.NHI < 20.3]
return fin_slls
def meiring09():
'''Meiring et al. 2009, MNRAS, 393, 1513
SLLS with Magellan
Abundances from Table 3 from astro-ph (LateX) by JXP [AODM]
RA/DEC from Table 1
'''
all_lls = []
# Table 1
tab_fil = pyigm_path+"/data/LLS/Literature/meiring09.tb1.ascii"
with open(tab_fil,'r') as f:
flines1 = f.readlines()
# Grab RA/DEC
qso_dict = {}
for iline in flines1:
if iline[0:3] in [' QS','\hl','$\\c', ' J2', ' ']:
continue
# Parse
isplit = iline.split('&')
#xdb.set_trace()
if '$' in isplit[3].strip():
isplit[3] = '-'+(isplit[3].strip())[3:]
radec = isplit[2].strip()+isplit[3].strip()
radec = radec.replace(':','')
# zem
zem = float(isplit[5].strip())
# Save
qso_dict[isplit[0].strip()] = dict(radec=radec,zem=zem,
vlim=[-500,500.]*u.km/u.s)
# Abundances (AODM)
# Table 3
tab_fil = pyigm_path+"/data/LLS/Literature/meiring09.tb3.ascii"
with open(tab_fil,'r') as f:
flines3 = f.readlines()
#
for iline in flines3:
if iline[0:2] in ['\h',' ']:
continue
# Parse
isplit = iline.split('&')
# Ions
if iline[0:2] == 'QS':
ioncs = []
Zions = []
for iis in isplit[3:-1]: # Skipping HI
# Parse
#is2 = iis.split('\\')
#ip2 = is2[2].find('}')
ionc = iis.strip()
# Zion
Zion = ltai.name_ion(ionc)
# Append
ioncs.append(ionc)
Zions.append(Zion)
continue
if iline[0] == 'Q':
# QSO
qso = isplit[0].strip()
if qso[-1] in ['A','B','C']:
qso = qso[0:-1]
# zabs and name
zabs = float(isplit[1].strip())
qso_dict[qso]['name']=qso+'z_{:.3f}'.format(zabs)
qso_dict[qso]['zabs']=zabs
# NHI
is2 = isplit[2].strip()
if is2[0] == '$':
qso_dict[qso]['NHI'] = 99.99 # THROW OUT Q1436-0051B
qso_dict[qso]['sig_NHI'] = np.array([0.,0.])
else:
qso_dict[qso]['NHI'] = float(is2[0:5])
qso_dict[qso]['sig_NHI'] = 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._ionN = pyiau.dict_to_ions(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 meiring07():
"""Meiring et al. 2007, MNRAS, 376, 557
SLLS with Magellan
Abundances from Table 11 from astro-ph (LateX) by JXP [AODM]
RA/DEC from Table 1
"""
all_lls = []
# Table 1
tab_fil = pyigm_path+"/data/LLS/Literature/meiring07.tb1.ascii"
with open(tab_fil,'r') as f:
flines1 = f.readlines()
# Grab RA/DEC
qso_dict = {}
for iline in flines1:
if iline[0:2] in ['QS','\h','$\\', 'J2']:
continue
# Parse
isplit = iline.split('&')
if '-' not in isplit[3]:
sgn = '+'
else:
sgn = ''
radec = isplit[2].strip()+sgn+isplit[3].strip()
radec = radec.replace(':','')
# zem
if isplit[0].strip() != 'Q0826-2230':
zem = float(isplit[5].strip())
else:
zem = 0.911
# Save
qso_dict[isplit[0].strip()] = dict(radec=radec, zem=zem,
vlim=[-500.,500]*u.km/u.s)
# Abundances (AODM)
# Table 11
tab_fil = pyigm_path+"/data/LLS/Literature/meiring07.tb11.ascii"
with open(tab_fil,'r') as f:
flines11 = f.readlines()
#
for iline in flines11:
if iline[0:2] in ['\h',' ']:
continue
# Parse
isplit = iline.split('&')
# Ions
if iline[0:2] == 'QS':
ioncs = []
Zions = []
for iis in isplit[3:-1]: # Skipping HI
# Parse
is2 = iis.split('\\')
ip2 = is2[2].find('}')
ionc = is2[1][2:].strip()+' '+is2[2][0:ip2].strip()
# Zion
Zion = ltai.name_ion(ionc)
# Append
ioncs.append(ionc)
Zions.append(Zion)
continue
if iline[0] == 'Q':
# QSO
qso = isplit[0].strip()
# zabs and name
zabs = float(isplit[1].strip())
qso_dict[qso]['name']=qso+'z_{:.3f}'.format(zabs)
qso_dict[qso]['zabs']=zabs
# NHI
is2 = isplit[2].strip()
qso_dict[qso]['NHI'] = float(is2[0:5])
#if qso_dict[qso]['NHI'] >= 20.3:
# print('Uh oh. DLA')
qso_dict[qso]['sig_NHI'] = np.array([float(is2[10:])]*2)
# Generate LLS
lls = LLSSystem(**qso_dict[qso])
continue
else:
# ADOM Columns
ion_dict = {}
for kk,iis in enumerate(isplit[3:-1]):
is2 = iis.strip()
if is2[0:3] == '$>$':
ion_dict[ioncs[kk]] = dict(sig_clm=0.,flg_clm=2,Z=Zions[kk][0],ion=Zions[kk][1])
ion_dict[ioncs[kk]]['clm'] = float(is2[3:])
elif is2[0:3] == '$<$':
ion_dict[ioncs[kk]] = dict(sig_clm=0.,flg_clm=3,Z=Zions[kk][0],ion=Zions[kk][1])
ion_dict[ioncs[kk]]['clm'] = float(is2[3:])
elif len(is2) == 0:
pass
else:
ion_dict[ioncs[kk]] = dict(flg_clm=1,Z=Zions[kk][0],ion=Zions[kk][1])
ion_dict[ioncs[kk]]['clm'] = float(is2[0:5])
ion_dict[ioncs[kk]]['sig_clm'] = float(is2[10:])
# Finish
lls._ionN = pyiau.dict_to_ions(ion_dict)
lls.Refs.append('Mei07')
all_lls.append(lls)
# Return SLLS only
fin_slls = [ills for ills in all_lls if ills.NHI < 20.3]
return fin_slls
def fig_sngl_cldy_model(sys, dpath=os.getenv('COSHALOS_DATA')+'/Cloudy/', ax=None, outfil=None,
lsz=15., show_sys=False):
""" Compare columns between model and data
"""
# Read
fh5 = h5py.File(dpath+sys+'_emcee.hd5', 'r')
ions = fh5['inputs']['ions'].value
data = fh5['inputs']['data'].value
fit = fh5['outputs']['best_fit'].value
fh5.close()
# IP values
IPs = np.zeros(len(ions))
for ii,ion in enumerate(ions):
Zion = lai.name_ion(ion)
elm = ELEMENTS[Zion[0]]
IPs[ii] = elm.ionenergy[Zion[1]-1]
#xdb.set_trace()
resid = data[:,1].astype(float) - fit
# Start the plot
if outfil is not None:
pp = PdfPages(outfil)
plt.figure(figsize=(7, 7))
plt.clf()
gs = gridspec.GridSpec(1, 1)
ax = plt.subplot(gs[0])
# Axes
#wvmnx = awvmnx[iuvq['instr']]
#ax.yaxis.set_major_locator(plt.MultipleLocator(1.))
ax.minorticks_on()
xlim = (5., np.max(IPs)+4)
ax.set_xlim(xlim)
ylim = (-1., 1.)
ax.set_ylim(ylim)
# Labels
ax.set_xlabel('IP (eV)', size=lsz)
ax.set_ylabel(r'$\Delta \, \log \, N$', size=lsz)
ax.xaxis.set_major_locator(plt.MultipleLocator(10.))
# Values
gdv = np.where(data[:,3].astype(int) == 0)[0]
if len(gdv) > 0:
ax.errorbar(IPs[gdv],resid[gdv], xerr=0, linestyle='None',
yerr=data[:,2].astype(float)[gdv], color='blue', marker='o')
# Limits
limsz = 50.
ulim = np.where(data[:,3].astype(int) == -1)[0]
ax.scatter(IPs[ulim],resid[ulim], color='red', marker='v', s=limsz)
llim = np.where(data[:,3].astype(int) == -2)[0]
ax.scatter(IPs[llim],resid[llim], color='green', marker='^', s=limsz)
# Label
for kk,ion in enumerate(ions):
if (resid[kk] < ylim[1]) & (resid[kk] > ylim[0]):
ax.text(IPs[kk]+1, resid[kk], ion, color='k', size=lsz) # Only if on page
if show_sys:
ax.text(0.04, 0.04, sys, transform=ax.transAxes, size=lsz-1, ha='left')
#bbox={'facecolor':'white'})
#legend = plt.legend(loc='upper right', scatterpoints=1, borderpad=0.3,
# handletextpad=0.3, fontsize='small', numpoints=1)
ax.plot(xlim, [0.,0.], 'g:')
# End
xputils.set_fontsize(ax,lsz)
if outfil is not None:
print('Writing {:s}'.format(outfil))
plt.tight_layout(pad=0.2,h_pad=0.,w_pad=0.1)
pp.savefig()
pp.close()
plt.close()
def fig_sngl_cldy_model(sys,
dpath=os.getenv('COSHALOS_DATA') + '/Cloudy/',
ax=None,
outfil=None,
lsz=15.,
show_sys=False):
""" Compare columns between model and data
"""
# Read
fh5 = h5py.File(dpath + sys + '_emcee.hd5', 'r')
ions = fh5['inputs']['ions'].value
data = fh5['inputs']['data'].value
fit = fh5['outputs']['best_fit'].value
fh5.close()
# IP values
IPs = np.zeros(len(ions))
for ii, ion in enumerate(ions):
Zion = lai.name_ion(ion)
elm = ELEMENTS[Zion[0]]
IPs[ii] = elm.ionenergy[Zion[1] - 1]
#xdb.set_trace()
resid = data[:, 1].astype(float) - fit
# Start the plot
if outfil is not None:
pp = PdfPages(outfil)
plt.figure(figsize=(7, 7))
plt.clf()
gs = gridspec.GridSpec(1, 1)
ax = plt.subplot(gs[0])
# Axes
#wvmnx = awvmnx[iuvq['instr']]
#ax.yaxis.set_major_locator(plt.MultipleLocator(1.))
ax.minorticks_on()
xlim = (5., np.max(IPs) + 4)
ax.set_xlim(xlim)
ylim = (-1., 1.)
ax.set_ylim(ylim)
# Labels
ax.set_xlabel('IP (eV)', size=lsz)
ax.set_ylabel(r'$\Delta \, \log \, N$', size=lsz)
ax.xaxis.set_major_locator(plt.MultipleLocator(10.))
# Values
gdv = np.where(data[:, 3].astype(int) == 0)[0]
if len(gdv) > 0:
ax.errorbar(IPs[gdv],
resid[gdv],
xerr=0,
linestyle='None',
yerr=data[:, 2].astype(float)[gdv],
color='blue',
marker='o')
# Limits
limsz = 50.
ulim = np.where(data[:, 3].astype(int) == -1)[0]
ax.scatter(IPs[ulim], resid[ulim], color='red', marker='v', s=limsz)
llim = np.where(data[:, 3].astype(int) == -2)[0]
ax.scatter(IPs[llim], resid[llim], color='green', marker='^', s=limsz)
# Label
for kk, ion in enumerate(ions):
if (resid[kk] < ylim[1]) & (resid[kk] > ylim[0]):
ax.text(IPs[kk] + 1, resid[kk], ion, color='k',
size=lsz) # Only if on page
if show_sys:
ax.text(0.04,
0.04,
sys,
transform=ax.transAxes,
size=lsz - 1,
ha='left')
#bbox={'facecolor':'white'})
#legend = plt.legend(loc='upper right', scatterpoints=1, borderpad=0.3,
# handletextpad=0.3, fontsize='small', numpoints=1)
ax.plot(xlim, [0., 0.], 'g:')
# End
xputils.set_fontsize(ax, lsz)
if outfil is not None:
print('Writing {:s}'.format(outfil))
plt.tight_layout(pad=0.2, h_pad=0., w_pad=0.1)
pp.savefig()
pp.close()
plt.close()
def complist_from_table(table):
"""
Returns a list of AbsComponents from an input astropy.Table.
Parameters
----------
table : Table
Table with component information (each row must correspond
to a component). Each column is expecting a unit when
appropriate.
Returns
-------
complist : list
List of AbsComponents defined from the input table.
Notes
-----
Mandatory column names: 'RA', 'DEC', 'ion_name', 'z_comp', 'vmin', 'vmax'
These column are required.
Special column names: 'name', 'comment', 'logN', 'sig_logN', 'flag_logN'
These columns will fill internal attributes when corresponding.
In order to fill in the Ntuple attribute all three 'logN', 'sig_logN', 'flag_logN'
must be present. For convenience 'logN' and 'sig_logN' are expected to be floats
corresponding to their values in np.log10(1/cm^2).
Other columns: 'any_column_name'
These will be added as attributes within the AbsComponent.attrib dictionary,
with their respective units if given.
"""
# Convert to QTable to handle units in individual entries more easily
table = QTable(table)
# mandatory and optional columns
min_columns = ['RA', 'DEC', 'ion_name', 'z_comp', 'vmin', 'vmax']
special_columns = ['name', 'comment', 'logN', 'sig_logN', 'flag_logN']
for colname in min_columns:
if colname not in table.keys():
raise IOError(
'{} is a mandatory column. Please make sure your input table has it.'
.format(colname))
#loop over rows
complist = []
for row in table:
# mandatory
coord = SkyCoord(row['RA'].to('deg').value,
row['DEC'].to('deg').value,
unit='deg') # RA y DEC must both come with units
Zion = name_ion(row['ion_name'])
zcomp = row['z_comp']
vlim = [row['vmin'].to('km/s').value, row['vmax'].to('km/s').value
] * u.km / u.s # units are expected here too
# special columns
try:
Ntuple = (row['flag_logN'], row['logN'], row['sig_logN']
) # no units expected
except KeyError:
Ntuple = None
try:
comment = row['comment']
except KeyError:
comment = ''
try:
name = row['name']
except KeyError:
name = None
# define the component
comp = AbsComponent(coord,
Zion,
zcomp,
vlim,
Ntup=Ntuple,
comment=comment,
name=name)
# other columns will be filled in comp.attrib dict
for colname in table.keys():
if (colname not in special_columns) and (colname
not in min_columns):
kms_cols = ['b', 'sig_b']
if colname in kms_cols: # check units for parameters expected in velocity units
try:
val_aux = row[colname].to('km/s').value * u.km / u.s
except u.UnitConversionError:
raise IOError(
'If `{}` column is present, it must have velocity units.'
.format(colname))
comp.attrib[colname] = val_aux
# parameters we do not care about units much
else:
comp.attrib[colname] = row[colname]
# append
complist += [comp]
return complist
def test_name_to_ion():
Zion = ions.name_ion('Si II')
assert Zion == (14,2)
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 = [pyigm_path+"/data/LLS/Literature/battisti12.tb1.ascii",
pyigm_path+"/data/LLS/Literature/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 = name[1:]
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,radec=radec,zem=zem,
zabs=zabs,NHI=NHI,sig_NHI=sigNHI, vlim=[-500,500]*u.km/u.s)
#
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 = ltai.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._ionN = pyiau.dict_to_ions(all_idict[kk])
except ValueError:
pdb.set_trace()
lls.Refs.append('Bat12')
fin_slls = [ills for ills in all_lls if ills.NHI < 20.3]
return fin_slls
def complist_from_table(table):
"""
Returns a list of AbsComponents from an input Table.
Parameters
----------
table : QTable
Table with component information (each row must correspond
to a component). Each column is expecting a unit when
appropriate.
Returns
-------
complist : list
List of AbsComponents defined from the input table.
Notes
-----
Mandatory column names: 'RA', 'DEC', 'ion_name', 'z_comp', 'vmin', 'vmax'
These column are required.
Special column names: 'name', 'comment', 'logN', 'sig_logN', 'flag_logN'
These columns will fill internal attributes when corresponding.
In order to fill in the Ntuple attribute all three 'logN', 'sig_logN', 'flag_logN'
must be present. For convenience 'logN' and 'sig_logN' are expected to be floats
corresponding to their values in np.log10(1/cm^2).
Other columns: 'any_column_name'
These will be added as attributes within the AbsComponent.attrib dictionary,
with their respective units if given.
"""
# mandatory and optional columns
min_columns = ['RA', 'DEC', 'ion_name', 'z_comp', 'vmin', 'vmax']
special_columns = ['name', 'comment', 'logN', 'sig_logN', 'flag_logN']
for colname in min_columns:
if colname not in table.keys():
raise IOError('{} is a mandatory column. Please make sure your input table has it.'.format(colname))
#loop over rows
complist = []
for row in table:
# mandatory
coord = SkyCoord(row['RA'].to('deg').value, row['DEC'].to('deg').value, unit='deg') # RA y DEC must both come with units
Zion = name_ion(row['ion_name'])
zcomp = row['z_comp']
vlim =[row['vmin'].to('km/s').value, row['vmax'].to('km/s').value] * u.km / u.s # units are expected here too
# special columns
try:
Ntuple = (row['flag_logN'], row['logN'], row['sig_logN']) # no units expected
except KeyError:
Ntuple = None
try:
comment = row['comment']
except KeyError:
comment = ''
try:
name = row['name']
except KeyError:
name = None
# define the component
comp = AbsComponent(coord, Zion, zcomp, vlim, Ntup=Ntuple, comment=comment, name=name)
# other columns will be filled in comp.attrib dict
for colname in table.keys():
if (colname not in special_columns) and (colname not in min_columns):
kms_cols = ['b', 'sig_b']
if colname in kms_cols: # check units for parameters expected in velocity units
try:
val_aux = row[colname].to('km/s').value * u.km / u.s
except u.UnitConversionError:
raise IOError('If `{}` column is present, it must have velocity units.'.format(colname))
comp.attrib[colname] = val_aux
# parameters we do not care about units much
else:
comp.attrib[colname] = row[colname]
# append
complist += [comp]
return complist
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
def available_transitions(self, wvlims, n_max=None, n_max_tuple=None, min_strength=1.):
""" Find the strongest transitions in a wavelength interval.
For a given wavelength range, wvlims = (wv_min, wv_max), this
function retrieves the n_max_tuple strongest transitions per
each ion species in the LineList available at such a
wavelength range and having strength larger than min_strength.
Strength is defined as log10(wrest * fosc * abundance). The output
is sorted by strength of the strongest available transition
per ion species.
Parameters
----------
wvlims : tuple of Quantity
Wavelength range, e.g. wvlims = (1100 * u.AA, 3200 * u.AA)
n_max : int, optional
Maximum number of transitions retrieved when given,
otherwise recover all of them
n_max_tuple : int, optional
Maximum number of transitions in a given ion species to
retrieve. e.g., if Lyman series are all available, it will
retrieve only up to Lyman gamma if
n_max_tuple = 3. Otherwise it returns all of them
min_strength : float, optional
Minimum strength calculated from log10(wrest * fosc *
abundance) In this way HI 1215 has 14.7 by definition.
Returns
-------
dict (if only 1 transition found) or QTable (if > 1
transitions are found) or None (if no transition is found)
"""
# Init
from linetools.abund.solar import SolarAbund
from linetools.abund import ions as laions
solar = SolarAbund()
if all((isinstance(n, int) or (n is None)) for n in [n_max, n_max_tuple]):
if (n_max is not None) and (n_max < 1):
return None
else:
raise SyntaxError(
'Both n_max and n_max_tuple must be integers when given!')
if isinstance(min_strength, (float,int)):
pass
else:
raise SyntaxError('min_strength must be a float value')
# Identify unique ion_names (e.g. HI, CIV, CIII)
# unique_ion_names = list(set([name.split(' ')[0] for name in self._data['name']]))
# unique_ion_names = np.array(unique_ion_names)
unique_ion_names = np.unique(
[name.split(' ')[0] for name in self._data['name']])
# obtain the strongest transition of a given unique ion species
ion_name = []
strength = []
for ion in unique_ion_names: # This loop is necessary to have a non trivial but convinient order in the final output
# Abundance
Zion = laions.name_ion(ion)
if ion == 'DI':
abundance = 12. - 4.8 # Approximate for Deuterium
else:
abundance = solar[Zion[0]]
aux = self.strongest_transitions(
ion, wvlims, n_max=1) # only the strongest
if aux is not None:
if isinstance(aux, dict): # this should always be True given n_max=1
name = aux['name']
else:
name = aux['name'][0]
ion_name += [name]
strength += [np.log10(aux['wrest'].value *
aux['f']) + abundance]
if len(ion_name) == 0:
# no matches
return None
# create Table
unique = Table()
unique.add_column(Column(data=ion_name, name='name'))
unique.add_column(Column(data=strength, name='strength'))
# get rid of those below the min_strength threshold
cond = unique['strength'] >= min_strength
unique = unique[cond]
if len(unique) < 1:
return None
# sort by strength
unique.sort(['strength'])
unique.reverse() # Table unique is now sorted by strength, with only
# 1 entry per ion species
# Create output data adding up to n_max_tuple per ion species
for i, row in enumerate(unique):
name = row['name']
aux = self.strongest_transitions(name, wvlims, n_max=n_max_tuple)
# need to deal with dict vs QTable format now
if isinstance(aux, dict):
aux = self.from_dict_to_qtable(aux)
if i == 0:
# convert to Table because QTable does not like vstack
output = Table(aux)
else:
# vstack is only supported for Table()
output = vstack([output, Table(aux)])
# if len==1 return dict
if len(output) == 1:
name = output['name'][0]
return self.__getitem__(name)
else: # n_max>1
if n_max > 1:
output = output[:n_max]
if len(output) == 1: # return dictionary
name = output['name'][0]
return self.__getitem__(name)
else:
return QTable(output)
def get_ions(self, use_Nfile=False, idict=None, update_zvlim=True, linelist=None):
"""Parse the ions for each Subsystem
And put them together for the full system
Fills ._ionN with a QTable
Parameters
----------
idict : dict, optional
dict containing the IonClms info
use_Nfile : bool, optional
Parse ions from a .clm file (JXP historical)
update_zvlim : bool, optional
Update zvlim from lines in .clm (as applicable)
linelist : LineList
"""
if idict is not None:
# Manipulate for astropy Table
# Could probably use add_row or dict instantiation
table = None
for ion in idict.keys():
Zion = ltai.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]
tkeys = idict[ion].keys()
if 'Z' not in tkeys:
tdict['Z'] = Zion[0]
tdict['ion'] = Zion[1]
# Add
table.add_row(tdict)
# Finish
try: # Historical keys
table.rename_column('clm', 'logN')
except:
pass
else:
table.rename_column('sig_clm', 'sig_logN')
table.rename_column('flg_clm', 'flag_N')
self._ionN = table
elif use_Nfile:
# Subsystems
if self.nsub > 0: # This speeds things up (but is rarely used)
linelist = LineList('ISM')
for lbl in self.subsys.keys():
clm_fil = self.tree+self.subsys[lbl]._datdict['clm_file']
# Parse .clm file
self.subsys[lbl]._clmdict = igmau.read_clmfile(clm_fil, linelist=linelist)
# Build components from lines
components = igmau.build_components_from_abslines([], clmdict=self.subsys[lbl]._clmdict, coord=self.coord)
# Update z, vlim
if update_zvlim:
vmin,vmax = 9999., -9999.
for component in components:
vmin = min(vmin, component.vlim[0].value)
vmax = max(vmax, component.vlim[1].value)
self.subsys[lbl].zabs = self.subsys[lbl]._clmdict['zsys']
self.subsys[lbl].vlim = [vmin, vmax]*u.km/u.s
# Read .ion file and fill in components
ion_fil = self.tree+self.subsys[lbl]._clmdict['ion_fil']
self.subsys[lbl]._indiv_ionclms = igmau.read_ion_file(ion_fil, components)
# Parse .all file
all_file = ion_fil.split('.ion')[0]+'.all'
self.subsys[lbl].all_file=all_file #MF: useful to have
_ = igmau.read_all_file(all_file, components=components)
# Build table
self.subsys[lbl]._ionN = igmau.iontable_from_components(components,ztbl=self.subsys[lbl].zabs)
# Add to IGMSystem
for comp in components:
self.add_component(comp)
# Combine
if self.nsub == 1:
self._ionN = self.subsys['A']._ionN
self._clmdict = self.subsys['A']._clmdict
#xdb.set_trace()
elif self.nsub == 0:
raise ValueError('lls_utils.get_ions: Cannot have 0 subsystems..')
else:
self._ionN = self.subsys['A']._ionN
self._clmdict = self.subsys['A']._clmdict
warnings.warn('lls_utils.get_ions: Need to update multiple subsystems!! Taking A.')
else:
raise ValueError("Need an option in get_ions")
