Examples for the LLSSystem Class (v1.1.1)¶
%matplotlib inline
# imports
try:
import seaborn as sns; sns.set_style("white")
except:
pass
from linetools.spectra.xspectrum1d import XSpectrum1D
from pyigm.abssys import utils as igmau
from pyigm.abssys.lls import LLSSystem
Simple Instantiate¶
lls = LLSSystem((0.*u.deg, 0.*u.deg), 2.5, None, NHI=17.9)
lls
[LLSSystem: 00:00:00 +00:00:00, zabs=2.5, logNHI=17.9, tau_LL=5.03537, [Z/H]=0 dex]
Generate/plot a model¶
# Fill HI lines
lls.fill_lls_lines()
WARNING: UnitsWarning: The unit 'Angstrom' has been deprecated in the FITS standard. Suggested: 10**-1 nm. [astropy.units.format.utils]
WARNING:astropy:UnitsWarning: The unit 'Angstrom' has been deprecated in the FITS standard. Suggested: 10**-1 nm.
linetools.lists.parse: Reading linelist ---
/Users/xavier/local/Python/linetools/linetools/data/lines/morton03_table2.fits.gz
read_sets: Using set file --
/Users/xavier/local/Python/linetools/linetools/lists/sets/llist_v0.4.ascii
# Generate a spectrum
wave = np.arange(3000., 6500)
npix = len(wave)
spec = XSpectrum1D.from_tuple((wave*u.AA,np.ones(npix)))
# Model
model = lls.flux_model(spec)
model.plot()
/Users/xavier/local/Python/linetools/linetools/analysis/voigt.py:177: UserWarning: Using a sub-grid wavelength array because the input array is too coarse.
warnings.warn('Using a sub-grid wavelength array because the input array is too coarse.')
/Users/xavier/local/Python/linetools/linetools/analysis/voigt.py:178: UserWarning: Will return values rebinned to the input array.
warnings.warn('Will return values rebinned to the input array.')
/Users/xavier/local/Python/linetools/linetools/analysis/voigt.py:213: UserWarning: Rebinned tau back to your input array. Reconsider input
warnings.warn('Rebinned tau back to your input array. Reconsider input')
From a JXP .dat file¶
(use of these .dat files is no longer recommended)
datfil = 'Data/UM184.z2929.dat'
lls = LLSSystem.from_datfile(dat_file=datfil, tree=os.getenv('LLSTREE'))
lls
[LLSSystem: 23:50:57.87 -00:52:09.9, zabs=2.93012, logNHI=18.5, tau_LL=20.0462, [Z/H]=0 dex]
print(lls.nsub)
lls.subsys['A']._datdict
1
{u'Fe_H': 0.0,
u'NH': 0.0,
u'NHI': 18.5,
u'NHIsig': array([ 1.1, 0.4]),
u'NHsig': array([ 0., 0.]),
u'U': 0.0,
u'Usig': array([ 0., 0.]),
u'VPFIT_file': u'',
u'alpha_H': 0.0,
u'bsig': 0.0,
u'bval': 0.0,
u'clm_file': u'Abund/UM184.z2929_MAGE.clm',
u'flg_Fe': 0,
u'flg_alpha': 0,
u'flg_low': 0,
u'logx': 0.0,
u'sig_Fe_H': 0.0,
u'sig_a_H': 0.0,
u'sigx': array([ 0., 0.]),
u'zabs': 2.93}
lls._datdict
OrderedDict([(u'QSO name', u'UM184'),
(u'RA (2000)', u'23:50:57.87'),
(u'DEC (2000)', u'-00:52:09.9'),
(u'QSO zem', u'3.021000'),
(u'flg_QSOmag', u'0'),
(u'QSO Mag', u'0.000000'),
(u'QSO Survey', u'0'),
(u'Survey', u'0.00000'),
(u'Referenc', u''),
(u'SDSS plt,fib,mjd', u'0 0 0'),
(u'zabs', u'2.93012'),
(u'NHI tot', u'18.5000'),
(u'NHI sig', u'1.1000 0.4000'),
(u'NH tot', u'0.0000'),
(u'NH sig', u'0.0000 0.0000'),
(u'vmn,vmx (2f7)', u'0.0 0.0'),
(u'fdelv', u'0.00'),
(u'fmm', u'0.00'),
(u'fedg', u'0.00'),
(u'ftpk', u'0.00'),
(u'flg_M/H', u'0'),
(u'[M/H] ave', u'0.00'),
(u'sig[M/H]', u'0.00'),
(u'flg_D/H', u'0'),
(u'[D/H]', u'0.000000'),
(u'N subsys', u'1'),
(u'Cloudy Grid File', u'dum.fil'),
(u'System A', u'A'),
(u'A zabs', u'2.930000'),
(u'A NHI', u'18.5000'),
(u'A NHIsig', u'1.1000 0.4000'),
(u'A NH', u'0.0000'),
(u'A NHsig', u'0.0000 0.0000'),
(u'A log x', u'0.0000'),
(u'A sigx', u'0.0000 0.0000'),
(u'A b', u'0.0000'),
(u'A bsig', u'0.0000'),
(u'A Abund file', u'Abund/UM184.z2929_MAGE.clm'),
(u'A U', u'0.00'),
(u'A Usig', u'0.0000 0.0000'),
(u'A flg_low', u'0'),
(u'A flg_alpha', u'0'),
(u'A [alpha/H]', u'0.000000'),
(u'A sig[a/H]', u'0.000000'),
(u'A flg_Fe', u'0'),
(u'A [Fe/H]', u'0.000000'),
(u'A sig[Fe/H]', u'0.000000'),
(u'A VPFIT file', u'')])
Load up ions¶
lls.get_ions(use_Nfile=True)
linetools.lists.parse: Reading linelist ---
/Users/xavier/local/Python/linetools/linetools/data/lines/morton03_table2.fits.gz
linetools.lists.parse: Reading linelist ---
/Users/xavier/local/Python/linetools/linetools/data/lines/morton00_table2.fits.gz
linetools.lists.parse: Reading linelist ---
/Users/xavier/local/Python/linetools/linetools/data/lines/verner94_tab6.fits
WARNING: UnitsWarning: '0.1nm' did not parse as fits unit: Numeric factor not supported by FITS [astropy.units.core]
WARNING:astropy:UnitsWarning: '0.1nm' did not parse as fits unit: Numeric factor not supported by FITS
linetools.lists.parse: Reading linelist ---
/Users/xavier/local/Python/linetools/linetools/data/lines/EUV_lines.ascii
read_sets: Using set file --
/Users/xavier/local/Python/linetools/linetools/lists/sets/llist_v0.4.ascii
WARNING: Using 1250.5780 Angstrom for your input 1250.5840 Angstrom
WARNING: Using 1253.8050 Angstrom for your input 1253.8110 Angstrom
WARNING: Using 2056.2569 Angstrom for your input 2056.2539 Angstrom
lls._ionN
| Z | ion | A | Ej | z | vmin | vmax | flag_N | logN | sig_logN |
|---|---|---|---|---|---|---|---|---|---|
| km / s | km / s | ||||||||
| int64 | int64 | int64 | float64 | float64 | float64 | float64 | int64 | float64 | float64 |
| 6 | 1 | 0 | 0.0 | 2.93 | -204.0 | 60.0 | 3 | 13.091 | 0.0 |
| 6 | 2 | 0 | 0.0 | 2.93 | -204.0 | 60.0 | 1 | 14.004 | 0.038 |
| 6 | 4 | 0 | 0.0 | 2.93 | -204.0 | 191.0 | 1 | 13.9 | 0.019 |
| 8 | 1 | 0 | 0.0 | 2.93 | -204.0 | 60.0 | 1 | 14.162 | 0.059 |
| 13 | 2 | 0 | 0.0 | 2.93 | -204.0 | 60.0 | 1 | 12.591 | 0.06 |
| 13 | 3 | 0 | 0.0 | 2.93 | -204.0 | 60.0 | 3 | 12.752 | 0.0 |
| 14 | 2 | 0 | 0.0 | 2.93 | -204.0 | 60.0 | 1 | 13.7 | 0.046 |
| 14 | 4 | 0 | 0.0 | 2.93 | -243.0 | 101.0 | 1 | 13.517 | 0.03 |
| 16 | 2 | 0 | 0.0 | 2.93 | -204.0 | 60.0 | 3 | 14.411 | 0.0 |
| 24 | 2 | 0 | 0.0 | 2.93 | -204.0 | 60.0 | 3 | 13.366 | 0.0 |
| 26 | 2 | 0 | 0.0 | 2.93 | -204.0 | 60.0 | 3 | 13.512 | 0.0 |
| 28 | 2 | 0 | 0.0 | 2.93 | -204.0 | 60.0 | 3 | 13.632 | 0.0 |
| 30 | 2 | 0 | 0.0 | 2.93 | -204.0 | 60.0 | 3 | 12.601 | 0.0 |