def from_dict(cls, idict):
""" Generate an LLSSystem from a dict
Parameters
----------
idict : dict
Usually read from the hard-drive
"""
kwargs = dict(zem=idict['zem'], NHI=idict['NHI'],
sig_NHI=idict['sig_NHI'], name=idict['Name'])
slf = cls(SkyCoord(ra=idict['RA']*u.deg, dec=idict['DEC']*u.deg),
idict['zabs'], idict['vlim']*u.km/u.s, **kwargs)
# Components
components = ltiu.build_components_from_dict(idict)
for component in components:
# This is to insure the components follow the rules
slf.add_component(component)
# Subsystems
if 'A' in idict.keys():
lbls= map(chr, range(65, 91))
for lbl in lbls:
if lbl in idict.keys():
# Generate
subsys = AbsSubSystem.from_dict(slf, idict[lbl], lbl)
slf.subsys[lbl] = subsys
else:
pass
# Total them
slf.nsub = len(slf.subsys.keys())
# Return
return slf
def from_dict(cls, idict, **kwargs):
""" Generate an LLSSystem from a dict
Parameters
----------
idict : dict
Usually read from the hard-drive
"""
from linetools.isgm.abssystem import add_comps_from_dict, add_other_from_dict
kwargs = dict(zem=idict['zem'], NHI=idict['NHI'],
sig_NHI=idict['sig_NHI'], name=idict['Name'])
slf = cls(SkyCoord(ra=idict['RA']*u.deg, dec=idict['DEC']*u.deg),
idict['zabs'], idict['vlim']*u.km/u.s, **kwargs)
#
add_other_from_dict(slf, idict)
add_comps_from_dict(slf, idict, **kwargs)
# Subsystems
if 'A' in idict.keys():
lbls= map(chr, range(65, 91))
for lbl in lbls:
if lbl in idict.keys():
# Generate
subsys = AbsSubSystem.from_dict(slf, idict[lbl], lbl)
slf.subsys[lbl] = subsys
else:
pass
# Total them
slf.nsub = len(slf.subsys.keys())
# Return
return slf
def parse_dat_file(self, vlim=[-300.,300]*u.km/u.s):
""" Parse the datdict read from the .dat file
Parameters
----------
vlim : Quantity array (2), optional
Velocity limits of the subsystems
Should be pulled from the .clm files
"""
# LLS keys
self.bgsrc = self._datdict['QSO name']
self.zem = float(self._datdict['QSO zem']) # Was zqso
self.ZH = float(self._datdict['[M/H] ave'])
self.nsub = int(self._datdict['N subsys'])
self.cldyfil = self._datdict['Cloudy Grid File']
# LLS Subsystems
if self.nsub > 0:
lbls= map(chr, range(65, 91))
# Dict
keys = (['zabs','NHI','NHIsig','NH','NHsig','log x','sigx','b','bsig','Abund file',
'U','Usig','flg_low','flg_alpha','[alpha/H]','sig[a/H]',
'flg_Fe','[Fe/H]','sig[Fe/H]','VPFIT file'])
att = (['zabs','NHI','NHIsig','NH','NHsig','logx','sigx','bval','bsig','clm_file',
'U','Usig','flg_low','flg_alpha','alpha_H','sig_a_H',
'flg_Fe','Fe_H','sig_Fe_H','VPFIT_file'])
values = ([0., 0., np.zeros(2), 0., np.zeros(2), 0., np.zeros(2), 0., 0.,
'', 0., np.zeros(2), 0, 0, 0., 0., 0, 0., 0., ''])
null_dict = dict(zip(keys,values))
# Loop on subsystems
for i in range(self.nsub):
# Generate
zabs = float(self._datdict[lbls[i] + ' zabs'])
self.subsys[lbls[i]] = AbsSubSystem(self, zabs, vlim, lbls[i])
self.subsys[lbls[i]]._datdict = {}
# Fill in dict
for ii, key in enumerate(keys):
try:
tmpc = self._datdict[lbls[i]+' '+key]
except:
raise ValueError('lls_utils: Key "{:s}" not found in {:s}'
.format(lbls[i]+key,self.dat_file))
else: # Convert
val = null_dict[key]
if val.__class__ == np.ndarray:
self.subsys[lbls[i]]._datdict[att[ii]] = np.array(map(float,tmpc.split()))
else: # Single value
self.subsys[lbls[i]]._datdict[att[ii]] = (map(type(val),[tmpc]))[0]
# Set a few special ones as attributes
self.subsys[lbls[i]].NHI = self.subsys[lbls[i]]._datdict['NHI']
self.subsys[lbls[i]].sig_NHI = self.subsys[lbls[i]]._datdict['NHIsig']
def zonak2004():
"""Zonak, 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 = '163428.9897+703132.422' # SIMBAD
lls = LLSSystem(name='PG1634+706_z1.041', radec=radec, zem=1.337,
zabs=1.0414, vlim=[-250., 100.]*u.km/u.s, NHI=17.23, ZH=-1.4,
sig_NHI=np.array([0.15,0.15]))
# SubSystems
lls.nsub = 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'] = AbsSubSystem(lls, 1.0414, [-80, 100]*u.km/u.s, 'A')
lls.subsys['A']._ionN = pyiau.dict_to_ions(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'] = AbsSubSystem(lls, 1.0414, [-240, -80]*u.km/u.s, 'B')
lls.subsys['B']._ionN = pyiau.dict_to_ions(bdict)
# Total
lls._ionN = pyiau.sum_ionN(lls.subsys['A']._ionN, lls.subsys['B']._ionN)
lls.Refs.append('Zon04')
# Return
return lls
def load_components(self, inp):
""" Load components for subsystems from an input object
May also update/create subsystems
Parameters
----------
inp : dict or ??
Input object for loading the components
"""
if isinstance(inp, dict):
lbls = map(chr, range(65, 91))
# Subsystems?
if 'A' in inp.keys():
for lbl in lbls:
if lbl in inp.keys():
if lbl not in self.subsys.keys():
self.subsys[lbl] = AbsSubSystem(
self, inp[lbl]['zsys'],
[-300., 300] * u.km / u.s, lbl)
# Fill/update
self.subsys[lbl]._clmdict = inp[
lbl] # Not so necessary
components = ltiu.build_components_from_dict(
self.subsys[lbl]._clmdict,
coord=self.coord,
chk_vel=True)
self.subsys[lbl]._components = components
# Update vlim
self.update_vlim(sub_system=lbl)
else:
pass
self.nsub = len(self.subsys.keys())
else:
raise ValueError("Not sure what to do here")
else:
raise NotImplementedError("Not ready for this input")