Examples for the AbsComponent Class (v0.3)

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%matplotlib inline

# suppress warnings for these examples
import warnings
warnings.filterwarnings('ignore')

# import
try:
    import seaborn as sns; sns.set_style("white")
except:
    pass

import astropy.units as u
from linetools.spectralline import AbsLine
from linetools.isgm import utils as ltiu
from linetools.analysis import absline as laa
from linetools.spectra import io as lsio
from linetools.isgm.abscomponent import AbsComponent

import imp
lt_path = imp.find_module('linetools')[1]

Instantiate

Standard

abscomp = AbsComponent((10.0*u.deg, 45*u.deg), (14,2), 1.0, [-300,300]*u.km/u.s)
abscomp

<AbsComponent: 00:40:00 +45:00:00, Name=SiII_z1.00000, Zion=(14,2), Ej=0 1 / cm, z=1, vlim=-300 km / s,300 km / s>

From AbsLines

From one line

lya = AbsLine(1215.670*u.AA)
lya.analy['vlim'] = [-300.,300.]*u.km/u.s
lya.attrib['z'] = 2.92939

abscomp = AbsComponent.from_abslines([lya])
print(abscomp)
abscomp._abslines

<AbsComponent: 00:00:00 +00:00:00, Name=HI_z2.92939, Zion=(1,1), Ej=0 1 / cm, z=2.92939, vlim=-300 km / s,300 km / s>

[<AbsLine: HI 1215, wrest=1215.6700 Angstrom>]

From multiple

lyb = AbsLine(1025.7222*u.AA)
lyb.analy['vlim'] = [-300.,300.]*u.km/u.s
lyb.attrib['z'] = lya.attrib['z']

abscomp = AbsComponent.from_abslines([lya,lyb])
print(abscomp)
abscomp._abslines

<AbsComponent: 00:00:00 +00:00:00, Name=HI_z2.92939, Zion=(1,1), Ej=0 1 / cm, z=2.92939, vlim=-300 km / s,300 km / s>

[<AbsLine: HI 1215, wrest=1215.6700 Angstrom>,
 <AbsLine: HI 1025, wrest=1025.7222 Angstrom>]

Methods

Generate a Component Table

lya.attrib['logN'] = 14.1
lya.attrib['sig_logN'] = 0.15
lya.attrib['flag_N'] = 1
laa.linear_clm(lya.attrib)
lyb.attrib['logN'] = 14.15
lyb.attrib['sig_logN'] = 0.19
lyb.attrib['flag_N'] = 1
laa.linear_clm(lyb.attrib)

(<Quantity 141253754462275.53 1 / cm2>, <Quantity 61797269977312.6 1 / cm2>)

abscomp = AbsComponent.from_abslines([lya,lyb])
comp_tbl = abscomp.build_table()
comp_tbl

<QTable length=2>

wrest	z	flag_N	logN	sig_logN
Angstrom
float64	float64	int64	float64	float64
1215.67	2.92939	1	14.1	0.15
1025.7222	2.92939	1	14.15	0.19

Synthesize multiple components

SiIItrans = ['SiII 1260', 'SiII 1304', 'SiII 1526']
SiIIlines = []
for trans in SiIItrans:
    iline = AbsLine(trans)
    iline.attrib['logN'] = 12.8 + np.random.rand()
    iline.attrib['sig_logN'] = 0.15
    iline.attrib['flag_N'] = 1
    iline.attrib['z'] = 2.92939
    iline.analy['vlim'] = [-300.,50.]*u.km/u.s
    _,_ = laa.linear_clm(iline.attrib)
    SiIIlines.append(iline)
SiIIcomp = AbsComponent.from_abslines(SiIIlines)
SiIIcomp.synthesize_colm()

SiIIlines2 = []
for trans in SiIItrans:
    iline = AbsLine(trans)
    iline.attrib['logN'] = 13.3 + np.random.rand()
    iline.attrib['sig_logN'] = 0.15
    iline.attrib['flag_N'] = 1
    iline.attrib['z'] = 2.92939
    iline.analy['vlim'] = [50.,300.]*u.km/u.s
    _,_ = laa.linear_clm(iline.attrib)
    SiIIlines2.append(iline)
SiIIcomp2 = AbsComponent.from_abslines(SiIIlines2)
SiIIcomp2.synthesize_colm()

abscomp.synthesize_colm()
[abscomp,SiIIcomp,SiIIcomp2]

[<AbsComponent: 00:00:00 +00:00:00, Name=HI_z2.92939, Zion=(1,1), Ej=0 1 / cm, z=2.92939, vlim=-300 km / s,300 km / s, logN=14.1172, sig_N=0.117912, flag_N=1>,
 <AbsComponent: 00:00:00 +00:00:00, Name=SiII_z2.92939, Zion=(14,2), Ej=0 1 / cm, z=2.92939, vlim=-300 km / s,50 km / s, logN=12.9226, sig_N=0.112727, flag_N=1>,
 <AbsComponent: 00:00:00 +00:00:00, Name=SiII_z2.92939, Zion=(14,2), Ej=0 1 / cm, z=2.92939, vlim=50 km / s,300 km / s, logN=13.8523, sig_N=0.0897197, flag_N=1>]

synth_SiII = ltiu.synthesize_components([SiIIcomp,SiIIcomp2])
synth_SiII

<AbsComponent: 00:00:00 +00:00:00, Name=SiII_z2.92939, Zion=(14,2), Ej=0 1 / cm, z=2.92939, vlim=-300 km / s,300 km / s, logN=13.9006, sig_N=0.0811523, flag_N=1>

Generate multiple components from abslines

comps = ltiu.build_components_from_abslines([lya,lyb,SiIIlines[0],SiIIlines[1]])
comps

[<AbsComponent: 00:00:00 +00:00:00, Name=HI_z2.92939, Zion=(1,1), Ej=0 1 / cm, z=2.92939, vlim=-300 km / s,300 km / s>,
 <AbsComponent: 00:00:00 +00:00:00, Name=SiII_z2.92939, Zion=(14,2), Ej=0 1 / cm, z=2.92939, vlim=-300 km / s,50 km / s>]

Generate an Ion Table

tbl = ltiu.iontable_from_components([abscomp,SiIIcomp,SiIIcomp2])
tbl

<QTable length=2>

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
1	1	0	0.0	2.92939	-300.0	300.0	1	14.1172024817	0.117911610801
14	2	0	0.0	2.92939	-300.0	300.0	1	13.9006157733	0.0811522506077

Stack plot

Load a spectrum

xspec = lsio.readspec(lt_path+'/spectra/tests/files/UM184_nF.fits')
lya.analy['spec'] = xspec
lyb.analy['spec'] = xspec

Show

abscomp = AbsComponent.from_abslines([lya,lyb])
abscomp.stack_plot()