- `distance` : distance from the central source
'''
import os
import glob
import traceback
import warnings
import ChiantiPy.tools.io as chio
try:
xuvtop = os.environ['XUVTOP']
Defaults = chio.defaultsRead()
Ip = chio.ipRead()
MasterList = chio.masterListRead()
IoneqAll = chio.ioneqRead(ioneqname=Defaults['ioneqfile'])
ChiantiVersion = chio.versionRead()
keywordArgs = [
'temperature', 'eDensity', 'hDensity', 'pDensity', 'radTemperature',
'rStar', 'distance'
]
AbundanceDefault = chio.abundanceRead(abundancename=Defaults['abundfile'])
AbundanceList = []
for fname in glob.glob(os.path.join(xuvtop, 'abundance', '*.abund')):
AbundanceList.append(os.path.splitext(os.path.basename(fname))[0])
Abundance = {
abundance: chio.abundanceRead(abundancename=abundance)
for abundance in AbundanceList
}
except (KeyError, IOError) as e:
print(traceback.format_exc())
vFile.close()
return versionStr.strip()
import chianti.core as ch
logger = logging.getLogger(__name__)
masterlist_ions_path = os.path.join(os.getenv('XUVTOP'), "masterlist",
"masterlist_ions.pkl")
masterlist_ions_file = open(masterlist_ions_path, 'rb')
masterlist_ions = pickle.load(masterlist_ions_file).keys()
# Exclude the "d" ions for now
masterlist_ions = [_ for _ in masterlist_ions if re.match("^[a-z]+_\d+$", _)]
masterlist_version = versionRead()
class ChiantiIonReaderError(Exception):
pass
class ChiantiIonReader(object):
"""
Class for reading ion data from the CHIANTI database
Attributes
----------
ion: chianti.core.ion instance
Methods
def _get_levels_lines(self, get_collisions=False):
"""Generates `levels`, `lines` and `collisions` DataFrames.
Parameters
----------
get_collisions : bool, optional
Grab collisional data, by default False.
"""
lvl_list = []
lns_list = []
col_list = []
for ion in self.ions:
ch_ion = convert_species_tuple2chianti_str(ion)
reader = ChiantiIonReader(ch_ion)
# Do not keep levels if lines are not available.
try:
lvl = reader.levels
lns = reader.lines
except ChiantiIonReaderError:
logger.info(f'Missing levels/lines data for `{ch_ion}`.')
continue
lvl['atomic_number'] = ion[0]
lvl['ion_charge'] = ion[1]
# Indexes must start from zero
lvl.index = range(0, len(lvl))
lvl.index.name = 'level_index'
lvl_list.append(reader.levels)
lns['atomic_number'] = ion[0]
lns['ion_charge'] = ion[1]
lns_list.append(lns)
if get_collisions:
try:
col = reader.collisions
col['atomic_number'] = ion[0]
col['ion_charge'] = ion[1]
col_list.append(col)
except ChiantiIonReaderError:
logger.info(f'Missing collisional data for `{ch_ion}`.')
levels = pd.concat(lvl_list, sort=True)
levels = levels.rename(columns={'J': 'j'})
levels['method'] = None
levels['priority'] = self.priority
levels = levels.reset_index()
levels = levels.set_index(
['atomic_number', 'ion_charge', 'level_index'])
levels = levels[['energy', 'j', 'label', 'method', 'priority']]
lines = pd.concat(lns_list, sort=True)
lines = lines.reset_index()
lines = lines.rename(
columns={
'lower_level_index': 'level_index_lower',
'upper_level_index': 'level_index_upper',
'gf_value': 'gf'
})
# Kurucz levels starts from zero, Chianti from 1.
lines['level_index_lower'] = lines['level_index_lower'] - 1
lines['level_index_upper'] = lines['level_index_upper'] - 1
lines = lines.set_index([
'atomic_number', 'ion_charge', 'level_index_lower',
'level_index_upper'
])
lines['energy_upper'] = None
lines['energy_lower'] = None
lines['j_upper'] = None
lines['j_lower'] = None
lines = lines[[
'energy_upper', 'j_upper', 'energy_lower', 'j_lower', 'wavelength',
'gf'
]]
lines['wavelength'] = u.Quantity(lines['wavelength'],
u.AA).to('nm').value
col_columns = [
'temperatures', 'collision_strengths', 'gf', 'energy', 'ttype',
'cups'
]
if get_collisions:
collisions = pd.concat(col_list, sort=True)
collisions = collisions.reset_index()
collisions = collisions.rename(
columns={
'lower_level_index': 'level_index_lower',
'upper_level_index': 'level_index_upper',
'gf_value': 'gf',
})
collisions['level_index_lower'] -= 1
collisions['level_index_upper'] -= 1
collisions = collisions.set_index([
'atomic_number', 'ion_charge', 'level_index_lower',
'level_index_upper'
])
collisions = collisions[col_columns]
self.collisions = collisions
else:
self.collisions = pd.DataFrame(columns=[col_columns])
self.levels = levels
self.lines = lines
self.version = versionRead()
- `distance` : distance from the central source
'''
import os
import glob
import traceback
import warnings
import ChiantiPy.tools.io as chio
try:
xuvtop = os.environ['XUVTOP']
Defaults = chio.defaultsRead()
Ip = chio.ipRead()
MasterList = chio.masterListRead()
IoneqAll = chio.ioneqRead(ioneqname=Defaults['ioneqfile'])
ChiantiVersion = chio.versionRead()
keywordArgs = ['temperature', 'eDensity', 'hDensity', 'pDensity', 'radTemperature',
'rStar', 'distance']
AbundanceDefault = chio.abundanceRead(abundancename=Defaults['abundfile'])
AbundanceList = []
for fname in glob.glob(os.path.join(xuvtop, 'abundance', '*.abund')):
AbundanceList.append(os.path.splitext(os.path.basename(fname))[0])
Abundance = {abundance: chio.abundanceRead(abundancename=abundance)
for abundance in AbundanceList}
except (KeyError, IOError) as e:
print(traceback.format_exc())
if isinstance(e, KeyError):
warnings.warn(
'XUVTOP environment variable not set. You will not be able to access any data from the CHIANTI database.')
else: