def name_ion(ion, flg=0, nspace=None):
""" Convert string into ion tuple
JXP on 28 June 2015
Parameters
----------
ion: str
Name of the ion, e.g. 'SiII' or 'Si II'
Returns
-------
ion_tup : tuple
e.g. (14,2)
"""
if isinstance(ion, basestring):
pass
else:
raise ValueError('ionization.name_ion: Not ready for this input yet.')
if ion[1] in ['I', 'V', 'X', ' ']:
iion = 1
else:
iion = 2
# Element
Z = ELEMENTS[ion[0:iion]].number
# Ion
ion_state = roman.fromRoman(ion[iion:].strip())
return (Z, ion_state)
def name_ion(ion, flg=0, nspace=None):
""" Convert string into ion tuple
JXP on 28 June 2015
Parameters
----------
ion: str
Name of the ion, e.g. 'SiII' or 'Si II'
Returns
-------
ion_tup : tuple
e.g. (14,2)
"""
if isinstance(ion, basestring):
pass
else:
raise ValueError("ionization.name_ion: Not ready for this input yet.")
if ion[1] in ["I", "V", "X", " "]:
iion = 1
else:
iion = 2
# Element
Z = ELEMENTS[ion[0:iion]].number
# Ion
ion_state = roman.fromRoman(ion[iion:].strip())
return (Z, ion_state)
def mk_line_list_fits_table(outfil=None,XIDL=False):
from barak import absorb as ba
if XIDL is True:
lindat = os.getenv('XIDL_DIR')+'/Spec/Lines/Lists/grb.lst'
finedat = os.getenv('XIDL_DIR')+'/Spec/Lines/Lists/fine_strct.lst'
else:
lindat = 'grb.lst' # This pulls from xastropy/data/spec_lines first
finedat = os.getenv('XIDL_DIR')+'/Spec/Lines/Lists/fine_strct.lst'
# Read XIDL line list
llist = Abs_Line_List(lindat)
ndata = len(llist.data)
# Add columns
from astropy.table import Column
gamma = Column(np.zeros(ndata),name='gamma')
A = Column(np.zeros(ndata),name='A') # Einstein coefficient
j = Column(np.zeros(ndata),name='j') # Tot ang mom (z projection)
Ex = Column(np.zeros(ndata),name='Ex') # Excitation energy (cm^-1)
Elow = Column(np.zeros(ndata),name='Elow') # Energy of lower level
Eup = Column(np.zeros(ndata),name='Eup') # Energy of upper level
Z = Column(np.zeros(ndata,dtype='int'),name='Z') # Atomic number
ion = Column(np.zeros(ndata,dtype='int'),name='ion') # Ionic state
llist.data.add_columns([gamma,A,j,Ex,Elow,Eup,Z,ion])
# Z,ion
for ii in range(ndata):
nm = llist.data['name'][ii]
# Z
if nm[1] == 'I' or nm[1] == 'V':
ielm = 1
else:
ielm = 2
elm = nm[:ielm]
try:
Zv = ELEMENTS[elm].number
except KeyError:
if elm in ['CO','CC','HH']: # Molecules
Zv = 999
elif elm in ['D']: # Deuterium
Zv = 1
else:
xdb.set_trace()
llist.data['Z'][ii] = Zv
# ion
ispc = nm.find(' ')
cion = nm[ielm:ispc].strip('*')
if len(cion) == 0:
ionv =0
else:
ionv = roman.fromRoman(cion)
llist.data['ion'][ii] = ionv
# #######
# Fill in matches
# Read atom.dat using barak
atom, atomflat = ba.readatom(flat=True)
#pdb.set_trace()
llist.sources.append('atom.dat') # I wish I could pull this from ba.readatom
# Fine structure
fdata = ascii.read(finedat)
llist.sources.append(finedat)
# Loop
for ii in range(ndata):
# Atom.dat
mt = np.where(np.fabs(llist.data['wrest'][ii]-atomflat['wa']) < 1e-3)[0]
if len(mt) > 0: llist.data['gamma'][ii] = atomflat['gam'][mt[0]] # Takes the first match
# Fine structure
mt = np.where(np.fabs(llist.data['wrest'][ii]-fdata['wrest']) < 1e-3)[0]
if len(mt) > 0:
llist.data['A'][ii] = fdata['A'][mt[0]] # Takes the first match
# Output file
if outfil is None:
outfil = xa_path+'/data/atomic/spec_atomic_lines.fits'
# Header
'''
prihdr = fits.Header()
prihdr['COMMENT'] = "Above are the data sources"
for ii in range(len(llist.sources)):
card = 'SOURCE'+str(ii+1)
prihdr[card] = llist.sources[ii]
prihdu = fits.PrimaryHDU(header=prihdr)
# Table
table_hdu = fits.BinTableHDU.from_columns(np.array(llist.data.filled()))
'''
# Write
llist.data.write(outfil, overwrite=True, format='fits')
print('mk_line_list: Wrote {:s}'.format(outfil))
def mk_line_list_fits_table(outfil=None,XIDL=False):
from barak import absorb as ba
if XIDL is True:
lindat = os.getenv('XIDL_DIR')+'/Spec/Lines/Lists/grb.lst'
finedat = os.getenv('XIDL_DIR')+'/Spec/Lines/Lists/fine_strct.lst'
else:
lindat = 'grb.lst' # This pulls from xastropy/data/spec_lines first
finedat = os.getenv('XIDL_DIR')+'/Spec/Lines/Lists/fine_strct.lst'
# Read XIDL line list
llist = Abs_Line_List(lindat)
ndata = len(llist.data)
# Add columns
from astropy.table import Column
gamma = Column(np.zeros(ndata),name='gamma')
A = Column(np.zeros(ndata),name='A') # Einstein coefficient
j = Column(np.zeros(ndata),name='j') # Tot ang mom (z projection)
Ex = Column(np.zeros(ndata),name='Ex') # Excitation energy (cm^-1)
Elow = Column(np.zeros(ndata),name='Elow') # Energy of lower level
Eup = Column(np.zeros(ndata),name='Eup') # Energy of upper level
Z = Column(np.zeros(ndata,dtype='int'),name='Z') # Atomic number
ion = Column(np.zeros(ndata,dtype='int'),name='ion') # Ionic state
llist.data.add_columns([gamma,A,j,Ex,Elow,Eup,Z,ion])
# Z,ion
for ii in range(ndata):
nm = llist.data['name'][ii]
# Z
if nm[1] == 'I' or nm[1] == 'V':
ielm = 1
else:
ielm = 2
elm = nm[:ielm]
try:
Zv = ELEMENTS[elm].number
except KeyError:
if elm in ['CO','CC','HH']: # Molecules
Zv = 999
elif elm in ['D']: # Deuterium
Zv = 1
else:
xdb.set_trace()
llist.data['Z'][ii] = Zv
# ion
ispc = nm.find(' ')
cion = nm[ielm:ispc].strip('*')
if len(cion) == 0:
ionv =0
else:
ionv = roman.fromRoman(cion)
llist.data['ion'][ii] = ionv
# #######
# Fill in matches
# Read atom.dat using barak
atom, atomflat = ba.readatom(flat=True)
#pdb.set_trace()
llist.sources.append('atom.dat') # I wish I could pull this from ba.readatom
# Fine structure
fdata = ascii.read(finedat)
llist.sources.append(finedat)
# Loop
for ii in range(ndata):
# Atom.dat
mt = np.where(np.fabs(llist.data['wrest'][ii]-atomflat['wa']) < 1e-3)[0]
if len(mt) > 0: llist.data['gamma'][ii] = atomflat['gam'][mt[0]] # Takes the first match
# Fine structure
mt = np.where(np.fabs(llist.data['wrest'][ii]-fdata['wrest']) < 1e-3)[0]
if len(mt) > 0:
llist.data['A'][ii] = fdata['A'][mt[0]] # Takes the first match
# Output file
if outfil is None:
outfil = xa_path+'/data/atomic/spec_atomic_lines.fits'
# Header
'''
prihdr = fits.Header()
prihdr['COMMENT'] = "Above are the data sources"
for ii in range(len(llist.sources)):
card = 'SOURCE'+str(ii+1)
prihdr[card] = llist.sources[ii]
prihdu = fits.PrimaryHDU(header=prihdr)
# Table
table_hdu = fits.BinTableHDU.from_columns(np.array(llist.data.filled()))
'''
# Write
llist.data.write(outfil, overwrite=True, format='fits')
print('mk_line_list: Wrote {:s}'.format(outfil))
