def test_roman():
# out of limits
with pytest.raises(OutOfRangeError):
s = roman.toRoman(6000)
# not integer
with pytest.raises(NotIntegerError):
s = roman.toRoman(1.5)
# no input
with pytest.raises(InvalidRomanNumeralError):
s = roman.fromRoman(None)
# bad pattern
with pytest.raises(InvalidRomanNumeralError):
s = roman.fromRoman('YT')
def test_roman():
# out of limits
with pytest.raises(OutOfRangeError):
s = roman.toRoman(6000)
# not integer
with pytest.raises(NotIntegerError):
s = roman.toRoman(1.5)
# no input
with pytest.raises(InvalidRomanNumeralError):
s = roman.fromRoman(None)
# bad pattern
with pytest.raises(InvalidRomanNumeralError):
s = roman.fromRoman('YT')
def name_ion(ion):
""" Convert string into ion tuple
Parameters
----------
ion : str
Name of the ion, e.g. 'SiII' or 'Si II'
Returns
-------
ion_tup : tuple
Z, ion -- e.g. (14,2)
"""
if isinstance(ion,basestring):
pass
else:
raise ValueError('ionization.name_ion: Not ready for this input yet.')
ion = ion.strip('*') # e.g. CII*
if ion[1] in ['I','V', 'X', ' ']:
iion = 1
else:
iion = 2
# Element
elm = ion[0:iion]
if elm == 'D': # Deuterium
Z = 1
else:
Z = ELEMENTS[ion[0:iion]].number
# Ion
ion_state = roman.fromRoman(ion[iion:].strip())
return Z, ion_state
def name_to_ion(ion):
""" Convert string into ion tuple
Parameters
----------
ion : str
Name of the ion, e.g. 'SiII' or 'Si II'
Returns
-------
ion_tup : tuple
Z, ion -- e.g. (14,2)
"""
if isinstance(ion,basestring):
pass
else:
raise ValueError('ionization.name_ion: Not ready for this input yet.')
ion = ion.strip('*') # e.g. CII*
if ion[1] in ['I','V', 'X', ' ']:
iion = 1
else:
iion = 2
# Element
elm = ion[0:iion]
if elm == 'D': # Deuterium
Z = 1
else:
Z = ELEMENTS[ion[0:iion]].number
# Ion
ion_state = roman.fromRoman(ion[iion:].strip())
return Z, ion_state
def parse_morton03(orig=False, tab_fil=None, HIcombine=True):
"""Parse tables from Morton 2003, ApJS, 149, 205
Parameters
----------
orig : bool, optional
Use original code to parse the ASCII file
tab_fil : str, optional
Filename to use. Default = /data/lines/morton03_table2.dat
HIcombine : bool, optional
Combine doublet for HI [True]
Returns
-------
data : Table
Atomic data
"""
# Look for FITS
fitsf = lt_path + '/data/lines/morton03_table2.fits.gz'
morton03_tab2 = glob.glob(fitsf)
if (len(morton03_tab2) > 0) & (not orig):
print('linetools.lists.parse: Reading linelist --- \n {:s}'.format(
morton03_tab2[0]))
data = Table(Table.read(morton03_tab2[0]), masked=True)
else:
## Read Table 2
if tab_fil is None:
morton03_tab2 = lt_path + '/data/lines/morton03_table2.dat'
else:
morton03_tab2 = tab_fil
print(
'linetools.lists.parse: Reading linelist --- \n {:s}'.format(
morton03_tab2))
f = open(morton03_tab2, 'r', encoding="ISO-8859-1")
lines = f.readlines()
f.close()
## Find Elements and Ions
elmi = []
elmZ = []
elmc = []
ioni = []
isoi = []
ionv = []
for kk,line in enumerate(lines):
#print('kk = {:d}'.format(kk))
try: # Deals with bad Byte in Morton00
tmp = ('Z = ' in line) & ('A =' in line)
except UnicodeDecodeError:
tmp = False
if tmp:
# Grab Z
ipos = line.find('Z = ')
elmZ.append(int(line[ipos+4:ipos+7]))
ipos2 = line.find('= ')
elmc.append(line[ipos2+2:ipos].strip())
#xdb.set_trace()
# Line index
elmi.append(kk)
# Kludge!!
if 'HOLMIUM' in line:
elmc[-1] = 'Ho'
# ISOTOPE and ION
try: # Deals with bad Byte in Morton00
tmp2 = ( (('I ' in line[0:13]) | ('V ' in line[0:13]))
& (line[0:3] not in ['IOD','VAN']) & (line[0:2] != 'I ') )
except UnicodeDecodeError:
tmp2 = False
if tmp2:
# Grab ion
ipos = line[0:10].find(' ')
if ipos > 4:
ipos3 = line[0:10].find('I')
iionv = line[ipos3:ipos]
else:
iionv = line[ipos:6].strip()
if (len(iionv) == 0) | (iionv == '5s') | (iionv == 'B I'):
pdb.set_trace()
ionv.append(iionv)
if iionv == 'Z =':
pdb.set_trace()
# Line index
ioni.append(kk)
# Deal with Isotope
if line[0] in ['0','1','2','3','4','5','6','7','8','9']:
# Skip ArI !
if 'Ar I' in line:
pass
else:
isoi.append(kk)
# Deuterium
if line[0] == 'D':
Dline = kk
#pdb.set_trace()
## Initialize table
ldict, tbl = line_data(nrows=len(lines))
## Parse lines with UV rest wavelength
count = 0
for kk,line in enumerate(lines):
try:
tmp = line[23] == '.'
except IndexError:
pass
else:
if tmp: # UV wavelength?
# Parse
# Ion/Isotope
if kk > np.max(ioni):
gdi = len(ioni)-1
else:
gdi = np.where( (kk > np.array(ioni)) & (kk < np.roll(np.array(ioni),-1)))[0]
if len(gdi) != 1:
pdb.set_trace()
raise ValueError('Uh oh ion')
else:
gdi = gdi[0]
if ioni[gdi] in isoi: # Isotope
continue
# Ion
tbl[count]['ion'] = roman.fromRoman(ionv[gdi])
# Wavelength
tbl[count]['wrest'] = float(line[19:28]) #* u.AA
# Z
gdZ = np.where( (kk > np.array(elmi)) & (kk < np.roll(np.array(elmi),-1)))[0]
if len(gdZ) != 1:
if kk > np.max(elmi):
gdZ = len(elmi)-1
else:
#xdb.set_trace()
raise ValueError('Uh oh elm')
else:
gdZ = gdZ[0]
tbl[count]['Z'] = elmZ[gdZ]
# Name
try:
tbl[count]['name'] = elmc[gdZ]+ionv[gdi]+' {:d}'.format(
int(tbl['wrest'][count]))
except UnicodeEncodeError:
pdb.set_trace()
# Isotope (Atomic number)
if ioni[gdi] == Dline:
tbl[count]['Am'] = 2
tbl[count]['name'] = 'D'+ionv[gdi]+' {:d}'.format(
int(tbl[count]['wrest']))
# f
try:
tbl[count]['f'] = float(line[79:89])
except ValueError:
continue # Skip ones without f-value
# Ej, Ek
tbl[count]['Ej'] = float(line[29:38]) #/ u.cm
tbl[count]['Ek'] = float(line[40:50]) #/ u.cm
# A
try:
tbl[count]['A'] = float(line[59:68]) #/ u.s
except ValueError:
pass
# gamma
try:
tbl[count]['gamma'] = float(line[69:79]) #/ u.s
except ValueError:
pass
# gl, gu
tbl[count]['gj'] = int(line[52:54])
tbl[count]['gk'] = int(line[56:58])
# Only use combined HI lines
if HIcombine:
if ((tbl[count]['Z'] == 1) & (tbl[count]['ion']==1)
& (tbl[count]['gk'] != 6)):
#print('Skipping HI line {:g}'.format(tbl[count]['wrest']))
continue
# Ex
#all_dict[count]['Ex'] = 0. # Zero out units (for Table)
# Increment
count += 1
# Trim
data = tbl[0:count]
# Last
data['group'] = 1
data['Ref'] = 'Morton2003'
data['mol'] = ''
# Return
#pdb.set_trace()
return data
def parse_morton03(orig=False, tab_fil=None, HIcombine=True):
"""Parse tables from Morton 2003, ApJS, 149, 205
Parameters
----------
orig : bool, optional
Use original code to parse the ASCII file
tab_fil : str, optional
Filename to use. Default = /data/lines/morton03_table2.dat
HIcombine : bool, optional
Combine doublet for HI [True]
Returns
-------
data : Table
Atomic data
"""
# Look for FITS
fitsf = lt_path + '/data/lines/morton03_table2.fits.gz'
morton03_tab2 = glob.glob(fitsf)
if (len(morton03_tab2) > 0) & (not orig):
print('linetools.lists.parse: Reading linelist --- \n {:s}'.format(
morton03_tab2[0]))
data = Table(Table.read(morton03_tab2[0]), masked=True)
else:
## Read Table 2
if tab_fil is None:
morton03_tab2 = lt_path + '/data/lines/morton03_table2.dat'
else:
morton03_tab2 = tab_fil
print('linetools.lists.parse: Reading linelist --- \n {:s}'.format(
morton03_tab2))
f = open(morton03_tab2, 'r', encoding="ISO-8859-1")
lines = f.readlines()
f.close()
## Find Elements and Ions
elmi = []
elmZ = []
elmc = []
ioni = []
isoi = []
ionv = []
for kk, line in enumerate(lines):
#print('kk = {:d}'.format(kk))
try: # Deals with bad Byte in Morton00
tmp = ('Z = ' in line) & ('A =' in line)
except UnicodeDecodeError:
tmp = False
if tmp:
# Grab Z
ipos = line.find('Z = ')
elmZ.append(int(line[ipos + 4:ipos + 7]))
ipos2 = line.find('= ')
elmc.append(line[ipos2 + 2:ipos].strip())
#xdb.set_trace()
# Line index
elmi.append(kk)
# Kludge!!
if 'HOLMIUM' in line:
elmc[-1] = 'Ho'
# ISOTOPE and ION
try: # Deals with bad Byte in Morton00
tmp2 = ((('I ' in line[0:13]) | ('V ' in line[0:13]))
& (line[0:3] not in ['IOD', 'VAN']) &
(line[0:2] != 'I '))
except UnicodeDecodeError:
tmp2 = False
if tmp2:
# Grab ion
ipos = line[0:10].find(' ')
if ipos > 4:
ipos3 = line[0:10].find('I')
iionv = line[ipos3:ipos]
else:
iionv = line[ipos:6].strip()
if (len(iionv) == 0) | (iionv == '5s') | (iionv == 'B I'):
pdb.set_trace()
ionv.append(iionv)
if iionv == 'Z =':
pdb.set_trace()
# Line index
ioni.append(kk)
# Deal with Isotope
if line[0] in [
'0', '1', '2', '3', '4', '5', '6', '7', '8', '9'
]:
# Skip ArI !
if 'Ar I' in line:
pass
else:
isoi.append(kk)
# Deuterium
if line[0] == 'D':
Dline = kk
#pdb.set_trace()
## Initialize table
ldict, tbl = line_data(nrows=len(lines))
## Parse lines with UV rest wavelength
count = 0
for kk, line in enumerate(lines):
try:
tmp = line[23] == '.'
except IndexError:
pass
else:
if tmp: # UV wavelength?
# Parse
# Ion/Isotope
if kk > np.max(ioni):
gdi = len(ioni) - 1
else:
gdi = np.where((kk > np.array(ioni))
& (kk < np.roll(np.array(ioni), -1)))[0]
if len(gdi) != 1:
pdb.set_trace()
raise ValueError('Uh oh ion')
else:
gdi = gdi[0]
if ioni[gdi] in isoi: # Isotope
continue
# Ion
tbl[count]['ion'] = roman.fromRoman(ionv[gdi])
# Wavelength
tbl[count]['wrest'] = float(line[19:28]) #* u.AA
# Z
gdZ = np.where((kk > np.array(elmi))
& (kk < np.roll(np.array(elmi), -1)))[0]
if len(gdZ) != 1:
if kk > np.max(elmi):
gdZ = len(elmi) - 1
else:
#xdb.set_trace()
raise ValueError('Uh oh elm')
else:
gdZ = gdZ[0]
tbl[count]['Z'] = elmZ[gdZ]
# Name
try:
tbl[count][
'name'] = elmc[gdZ] + ionv[gdi] + ' {:d}'.format(
int(tbl['wrest'][count]))
except UnicodeEncodeError:
pdb.set_trace()
# Isotope (Atomic number)
if ioni[gdi] == Dline:
tbl[count]['Am'] = 2
tbl[count]['name'] = 'D' + ionv[gdi] + ' {:d}'.format(
int(tbl[count]['wrest']))
# f
try:
tbl[count]['f'] = float(line[79:89])
except ValueError:
continue # Skip ones without f-value
# Ej, Ek
tbl[count]['Ej'] = float(line[29:38]) #/ u.cm
tbl[count]['Ek'] = float(line[40:50]) #/ u.cm
# A
try:
tbl[count]['A'] = float(line[59:68]) #/ u.s
except ValueError:
pass
# gamma
try:
tbl[count]['gamma'] = float(line[69:79]) #/ u.s
except ValueError:
pass
# gl, gu
tbl[count]['gj'] = int(line[52:54])
tbl[count]['gk'] = int(line[56:58])
# Only use combined HI lines
if HIcombine:
if ((tbl[count]['Z'] == 1) & (tbl[count]['ion'] == 1)
& (tbl[count]['gk'] != 6)):
#print('Skipping HI line {:g}'.format(tbl[count]['wrest']))
continue
# Ex
#all_dict[count]['Ex'] = 0. # Zero out units (for Table)
# Increment
count += 1
# Trim
data = tbl[0:count]
# Last
data['group'] = 1
data['Ref'] = 'Morton2003'
data['mol'] = ''
# Return
#pdb.set_trace()
return data