def get_ions(self,
use_Nfile=False,
idict=None,
update_zvlim=True,
linelist=None,
verbose=True):
"""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)
NOTE: This ignores velocity constraints on components (i.e. skip_vel=True)
update_zvlim : bool, optional
Update zvlim from lines in .clm (as applicable)
linelist : LineList
"""
if use_Nfile:
clm_fil = self.tree + self._datdict['Abund file']
# Read
self._clmdict = igmau.read_clmfile(clm_fil, linelist=linelist)
#pdb.set_trace()
# Build components
components = ltiu.build_components_from_dict(self._clmdict,
coord=self.coord,
chk_vel=False)
# Read .ion file and fill in components
ion_fil = self.tree + self._clmdict['ion_fil']
self._indiv_ionclms = igmau.read_ion_file(ion_fil, components)
# Parse .all file
all_file = ion_fil.split('.ion')[0] + '.all'
self.all_file = all_file #MF: useful
_ = igmau.read_all_file(all_file, components=components)
# Build table
self._ionN = ltiu.iontable_from_components(components,
ztbl=self.zabs)
# Add to AbsSystem
for comp in components:
self.add_component(comp)
elif idict is not None:
table = dict_to_ions(idict)
self._ionN = table
else:
raise IOError("Not ready for this")
def get_ions(self, use_Nfile=False, idict=None, update_zvlim=True,
linelist=None, verbose=True):
"""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)
NOTE: This ignores velocity constraints on components (i.e. skip_vel=True)
update_zvlim : bool, optional
Update zvlim from lines in .clm (as applicable)
linelist : LineList
"""
if use_Nfile:
clm_fil = self.tree+self._datdict['Abund file']
# Read
self._clmdict = igmau.read_clmfile(clm_fil, linelist=linelist)
#pdb.set_trace()
# Build components
components = ltiu.build_components_from_dict(self._clmdict,
coord=self.coord,
chk_vel=False)
# Read .ion file and fill in components
ion_fil = self.tree+self._clmdict['ion_fil']
self._indiv_ionclms = igmau.read_ion_file(ion_fil, components)
# Parse .all file
all_file = ion_fil.split('.ion')[0]+'.all'
self.all_file=all_file #MF: useful to have
_ = igmau.read_all_file(all_file, components=components)
# Build table
self._ionN = ltiu.iontable_from_components(components, ztbl=self.zabs)
# Add to AbsSystem
for comp in components:
self.add_component(comp)
elif idict is not None:
table = dict_to_ions(idict)
self._ionN = table
else:
raise IOError("Not ready for this")
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)
NOTE: This ignores velocity constraints on components (i.e. skip_vel=True)
update_zvlim : bool, optional
Update zvlim from lines in .clm (as applicable)
linelist : LineList
"""
if idict is not None:
table = dict_to_ions(idict)
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 = ltiu.build_components_from_dict(self.subsys[lbl]._clmdict,
coord=self.coord, skip_vel=True)
self.subsys[lbl]._components = components
# Update z, vlim
if update_zvlim:
self.update_vlim(sub_system=lbl)
self.subsys[lbl].zabs = self.subsys[lbl]._clmdict['zsys']
# 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 = ltiu.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")
def get_ions(self,
use_Nfile=False,
idict=None,
update_zvlim=True,
linelist=None,
verbose=True):
"""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)
NOTE: This ignores velocity constraints on components (i.e. chk_vel=False)
update_zvlim : bool, optional
Update zvlim from lines in .clm (as applicable)
linelist : LineList
"""
if idict is not None:
table = dict_to_ions(idict)
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 = ltiu.build_components_from_dict(
self.subsys[lbl]._clmdict, coord=self.coord, chk_vel=False)
self.subsys[lbl]._components = components
# Update z, vlim
if update_zvlim:
self.update_vlim(sub_system=lbl)
self.subsys[lbl].zabs = self.subsys[lbl]._clmdict['zsys']
# 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 = ltiu.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")
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")