def meiring06():
'''Meiring et al. 2006, MNRAS, 370, 43
Q1107+0003
Taken from Table 4 by JXP
NHI from RTN06 (damping wings)
RA/DEC from STIS header
'''
# Setup
lls = LLSSystem(name='SDSSJ1107+0003_z0.954',
RA=166.90273 * u.deg,
Dec=0.05795000 * u.deg,
zem=1.726,
zabs=0.9542,
vlim=[-300., 300.] * u.km / u.s,
NHI=20.26,
sigNHI=np.array([0.14, 0.09]))
# Meiring06, Table 4
ion_dict = {}
ion_dict['Zn II'] = dict(clm=12.08, sig_clm=0., flg_clm=3, Z=30, ion=2)
ion_dict['Ti II'] = dict(clm=13.01, sig_clm=0., flg_clm=3, Z=22, ion=2)
ion_dict['Cr II'] = dict(clm=12.76, sig_clm=0., flg_clm=3, Z=24, ion=2)
# Finish
lls._ionclms = IonClms(idict=ion_dict)
lls.Refs.append('Mei06')
return lls
def kacprzak12():
'''Kacprzak, G. et al. 2012, MNRAS, 427, 3029-3043
TON 153
Taken from Table 1 by JXP
NHI from Churchill+2007
RA/DEC from Simbad
'''
# Setup
radec = xor.stod1('J131956.2209+272808.271')
lls = LLSSystem(name='TON153_z1.002',
RA=radec[0],
Dec=radec[1],
zem=0.6610,
zabs=1.0023,
vlim=[-250., 200.] * u.km / u.s,
NHI=18.30,
sigNHI=np.array([0.30, 0.30]))
# Table 1 (total)
ion_dict = {}
ion_dict['Mg II'] = dict(clm=13.11, sig_clm=0.07, flg_clm=1, Z=12, ion=2)
ion_dict['Mg I'] = dict(clm=11.54, sig_clm=0.06, flg_clm=1, Z=12, ion=1)
ion_dict['Si I'] = dict(clm=11.8, sig_clm=0.00, flg_clm=3, Z=14, ion=1)
ion_dict['Si II'] = dict(clm=13.16, sig_clm=0.11, flg_clm=1, Z=14, ion=2)
ion_dict['Si IV'] = dict(clm=12.4, sig_clm=0.0, flg_clm=3, Z=14, ion=4)
ion_dict['C II'] = dict(clm=13.39, sig_clm=0.0, flg_clm=2, Z=6, ion=2)
ion_dict['C III'] = dict(clm=14.20, sig_clm=0.05, flg_clm=1, Z=6, ion=3)
ion_dict['C III'] = dict(clm=14.41, sig_clm=0.05, flg_clm=1, Z=6, ion=4)
ion_dict['O VI'] = dict(clm=14.49, sig_clm=0.05, flg_clm=1, Z=8, ion=6)
# Finish
lls._ionclms = IonClms(idict=ion_dict)
lls.Refs.append('Kcz12')
return lls
def zonak2004():
'''Zoank, S. et al. 2004, ApJ, 2004, 606, 196
PG1634+706
HST+Keck spectra
MgII, SiIV, SiIII from Table 2. Summing Subsystems A (Model 2) and B
Errors estimated by JXP (not reported)
SiIII in A may be a model
SiIV in B may be a model
Total NHI from LL. Taken from Fig 3 caption.
Error estimated by JXP
Not all EWs in Table 1 included
Adopting their M/H
'''
# Setup
radec = xor.stod1('J163428.9897+703132.422') # SIMBAD
lls = LLSSystem(name='PG1634+706_z1.041',
RA=radec[0],
Dec=radec[1],
zem=1.337,
zabs=1.0414,
vlim=[-200., 30.] * u.km / u.s,
NHI=17.23,
MH=-1.4,
sigNHI=np.array([0.15, 0.15]))
# SubSystems
lls.mk_subsys(2)
# Abundances
adict = dict(MgII={
'clm': log_sum([11.45, 11.90, 12.02, 11.68]),
'sig_clm': 0.05,
'flg_clm': 1
},
SiIII={
'clm': log_sum([12.5, 12.5, 12.8, 12.7]),
'sig_clm': 0.25,
'flg_clm': 1
},
SiIV={
'clm': log_sum([10.9, 10.8, 11.2, 11.1]),
'sig_clm': 0.15,
'flg_clm': 1
})
lls.subsys['A']._ionclms = IonClms(idict=adict)
bdict = dict(SiIII={
'clm': log_sum([11.8, 12.8, 12.4]),
'sig_clm': 0.15,
'flg_clm': 1
},
SiIV={
'clm': log_sum([11.2, 12.2, 11.8]),
'sig_clm': 0.15,
'flg_clm': 1
})
lls.subsys['B']._ionclms = IonClms(idict=bdict)
# Total
lls._ionclms = lls.subsys['A']._ionclms.sum(lls.subsys['B']._ionclms)
lls.Refs.append('Zon04')
# Return
return lls
def test_parse_ion():
# JXP .ion file
if os.getenv('LLSTREE') is None:
assert True
# Read
datfil = 'Data/UM184.z2929.dat'
lls = LLSSystem(dat_file=datfil, tree=os.getenv('LLSTREE'))
#
lls.get_ions()
assert len(lls.lines) == 24
def test_parse_ion():
# JXP .ion file
if os.getenv('LLSTREE') is None:
assert True
# Read
datfil = 'Data/UM184.z2929.dat'
lls = LLSSystem(dat_file=datfil, tree=os.getenv('LLSTREE'))
#
lls.get_ions()
assert len(lls.lines) == 24
def add_LLS(self,z,NHI=17.3,bval=20.*u.km/u.s):
'''Generate a new LLS
'''
#
new_sys = LLSSystem(NHI=NHI)
new_sys.zabs = z
new_sys.fill_lls_lines(bval=bval)
# Name
self.count_lls += 1
new_sys.label = 'LLS_Sys_{:d}'.format(self.count_lls)
# Add
self.abssys_widg.add_fil(new_sys.label)
self.abssys_widg.all_abssys.append(new_sys)
self.abssys_widg.abslist_widget.item(
len(self.abssys_widg.all_abssys)).setSelected(True)
def test_dat_init():
# JXP .dat files
if os.getenv('LLSTREE') is None:
assert True
# Read
datfil = 'Data/UM184.z2929.dat'
lls = LLSSystem(dat_file=datfil, tree=os.getenv('LLSTREE'))
#
np.testing.assert_allclose(lls.zabs, 2.93012)
def nestor08():
'''Nestor, D. et al. 2008, MNRAS, 390, 1670-1682
Q2149+212
Taken from Table 1 by JXP
NHI from RTN06 (damping wings)
RA/DEC from STIS header
'''
# Setup
lls = LLSSystem(name='SDSSJ2151+2130_z1.002',
RA=327.94096 * u.deg,
Dec=21.503750 * u.deg,
zem=1.534,
zabs=1.0023,
vlim=[-300., 300.] * u.km / u.s,
NHI=19.30,
sigNHI=np.array([0.10, 0.10]))
# Meiring06, Table 4
ion_dict = {}
ion_dict['Zn II'] = dict(clm=12.13, sig_clm=0., flg_clm=3, Z=30, ion=2)
ion_dict['Cr II'] = dict(clm=12.59, sig_clm=0., flg_clm=3, Z=24, ion=2)
# Finish
lls._ionclms = IonClms(idict=ion_dict)
lls.Refs.append('Nes08')
return lls
def add_LLS(self, z, NHI=17.3, bval=20. * u.km / u.s, comment='None'):
'''Generate a new LLS
'''
#
new_sys = LLSSystem(NHI=NHI)
new_sys.zabs = z
new_sys.bval = bval # This is not standard, but for convenience
new_sys.comment = comment
new_sys.fill_lls_lines(bval=bval)
# Name
self.count_lls += 1
new_sys.label = 'LLS_Sys_{:d}'.format(self.count_lls)
# Add
self.abssys_widg.add_fil(new_sys.label)
self.abssys_widg.all_abssys.append(new_sys)
self.abssys_widg.abslist_widget.item(len(
self.abssys_widg.all_abssys)).setSelected(True)
def add_LLS(self, z, NHI=17.3, bval=20.0 * u.km / u.s, comment="None"):
"""Generate a new LLS
"""
#
new_sys = LLSSystem(NHI=NHI)
new_sys.zabs = z
new_sys.bval = bval # This is not standard, but for convenience
new_sys.comment = comment
new_sys.fill_lls_lines(bval=bval)
# Name
self.count_lls += 1
new_sys.label = "LLS_Sys_{:d}".format(self.count_lls)
# Add
self.abssys_widg.add_fil(new_sys.label)
self.abssys_widg.all_abssys.append(new_sys)
self.abssys_widg.abslist_widget.item(len(self.abssys_widg.all_abssys)).setSelected(True)
def add_LLS(self, z, NHI=17.3, bval=20. * u.km / u.s):
'''Generate a new LLS
'''
#
new_sys = LLSSystem(NHI=NHI)
new_sys.zabs = z
new_sys.fill_lls_lines(bval=bval)
# Name
self.count_lls += 1
new_sys.label = 'LLS_Sys_{:d}'.format(self.count_lls)
# Add
self.abssys_widg.add_fil(new_sys.label)
self.abssys_widg.all_abssys.append(new_sys)
self.abssys_widg.abslist_widget.item(len(
self.abssys_widg.all_abssys)).setSelected(True)
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 peroux06a():
'''Peroux, C. et al. 2006a, MNRAS, 372, 369
SDSS J0134+0051
One of her sample
Metal columns taken by JXP from Table 2 (no online data)
Total NHI from damping wings
'''
# Setup
radec = xor.stod1('J013405.75+005109.4') # SDSS Name
lls = LLSSystem(name='SDSSJ0134+0051_z0.842',
RA=radec[0],
Dec=radec[1],
zem=1.522,
zabs=0.842,
vlim=[-150., 150.] * u.km / u.s,
NHI=19.93,
sigNHI=np.array([0.15, 0.15]))
# Table 2
ion_dict = {}
N = np.sum(np.array([5.56, 12.6, 13.7, 23.5, 61.4, 39.8, 6, 9.14]) * 1e10)
sig = np.sqrt(
np.sum((np.array([2.32, 3.1, 3.68, 4.13, 8.02, 6.65, 3.37, 2.82]) *
1e10)**2))
ion_dict['Mg I'] = dict(clm=np.log10(N),
sig_clm=sig / N / np.log(10),
flg_clm=1,
Z=12,
ion=1)
ion_dict['Mg II'] = dict(clm=np.log10(5e13),
sig_clm=0.,
flg_clm=2,
Z=12,
ion=2)
N = np.sum(
np.array([8.17, 4.28, 32.1, 125, 710, 301, 893, 600, 263, 65.7]) *
1e11)
sig = np.sqrt(
np.sum((np.array(
[2.63, 1.40, 2.37, 8.6, 53.2, 28.4, 73.5, 61.7, 14.0, 2.95]) *
1e11)**2))
ion_dict['Fe II'] = dict(clm=np.log10(N),
sig_clm=sig / N / np.log(10),
flg_clm=1,
Z=26,
ion=2)
sig = np.sqrt(np.sum((np.array([3.72, 1.84, 2.36, 3.83]) * 1e11)**2))
ion_dict['Zn II'] = dict(clm=np.log10(2 * sig),
sig_clm=0.,
flg_clm=3,
Z=30,
ion=2)
sig = np.sqrt(np.sum((np.array([19.4, 9.79]) * 1e11)**2))
ion_dict['Cr II'] = dict(clm=np.log10(2 * sig),
sig_clm=0.,
flg_clm=3,
Z=24,
ion=2)
# Not including MnII. Appears as a detection but also given as a limit..
# Finish
lls._ionclms = IonClms(idict=ion_dict)
lls.Refs.append('Prx06a')
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 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 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
def xq100_plls_ex(outfil='fig_xq100_plls_ex.pdf'):
# Load spectrum
spec_fil = os.getenv('DROPBOX_DIR') + '/XQ-100/data/J0030-5159_uvb.fits'
spec = load_spectrum(spec_fil)
# Generate model
model_file = os.getenv(
'DROPBOX_DIR') + '/XQ-100/LLS/convg_J0030-5159_llsfit.json'
with open(model_file) as data_file:
lls_dict = json.load(data_file)
# Continuum
basec = Quantity(lls_dict['conti'])
telfer_spec = XSpectrum1D.from_tuple((spec.dispersion.value, basec.value))
# Start the plot
if outfil is not None:
pp = PdfPages(outfil)
plt.figure(figsize=(8, 4))
plt.clf()
gs = gridspec.GridSpec(1, 1)
fsz = 17.
# Read and plot full spectrum
ax_full = plt.subplot(gs[0])
# Limits
wvmnx = [3600., 5000.]
gdpix = np.where(spec.dispersion < wvmnx[1] * u.AA)[0]
perc = xsb.perc(spec.flux[gdpix])
ax_full.set_xlim(wvmnx)
#ax_full.set_ylim(-0.05*perc[1], 1.1*perc[1])
ax_full.set_ylim(-1e-18, 4e-17)
# Plot
ax_full.plot(spec.dispersion, spec.flux, color='black', lw=1.0)
ax_full.plot(wvmnx, [0., 0.], '--', color='green')
# Label
ax_full.set_xlabel('Wavelength')
ax_full.set_ylabel('Relative Flux')
ax_full.text(0.05,
0.9,
'XQ100 J0030-5159',
transform=ax_full.transAxes,
color='black',
size='x-large',
ha='left',
va='center',
bbox={'facecolor': 'white'})
all_ills = []
all_lls = []
all_zlls = []
for key in lls_dict['LLS'].keys():
new_sys = LLSSystem(NHI=lls_dict['LLS'][key]['NHI'])
new_sys.zabs = lls_dict['LLS'][key]['z']
new_sys.fill_lls_lines(bval=lls_dict['LLS'][key]['bval'] * u.km / u.s)
#
all_ills.append(new_sys)
all_lls.append(new_sys)
all_zlls.append(new_sys.zabs)
# Model
norm_flux = lls_model(spec.dispersion, all_ills, smooth=lls_dict['smooth'])
continuum = telfer_spec.flux * lls_dict['conti_model']['Norm'] * (
spec.dispersion.value /
lls_dict['conti_model']['piv_wv'])**lls_dict['conti_model']['tilt']
# Model
ax_full.plot(spec.dispersion, continuum * norm_flux)
# Font size
xputils.set_fontsize(ax_full, fsz)
# Finish page
plt.tight_layout(pad=0.2, h_pad=0.3, w_pad=0.0)
pp.savefig()
plt.close()
print('Wrote: {:s}'.format(outfil))
# Finish
pp.close()
def test_simple_init():
# Init
lls = LLSSystem(NHI=17.9)
#
np.testing.assert_allclose(lls.NHI, 17.9)
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
