def test_add_component():
radec = SkyCoord(ra=123.1143*u.deg, dec=-12.4321*u.deg)
# HI Lya, Lyb
lya = AbsLine(1215.670*u.AA)
lya.analy['vlim'] = [-300.,300.]*u.km/u.s
lya.attrib['z'] = 2.92939
lya.attrib['N'] = 1e17 / u.cm**2
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])
abscomp.coord = radec
# Instantiate
abssys = GenericAbsSystem.from_components([abscomp])
# New component
oi = AbsLine('OI 1302')
oi.analy['vlim'] = [-300.,300.]*u.km/u.s
oi.attrib['z'] = lya.attrib['z']
abscomp2 = AbsComponent.from_abslines([oi])
abscomp2.coord = radec
# Standard
assert abssys.add_component(abscomp2)
# Fail
abssys = GenericAbsSystem.from_components([abscomp])
abscomp2.vlim = [-400.,300.]*u.km/u.s
assert not abssys.add_component(abscomp2)
# Overlap
assert abssys.add_component(abscomp2, overlap_only=True)
def read_ion_file(self,ion_fil,zabs=0.,RA=0.*u.deg, Dec=0.*u.deg):
"""Read in JXP-style .ion file in an appropriate manner
NOTE: If program breaks in this function, check the all file
to see if it is properly formatted.
"""
# Read
names=('wrest', 'clm', 'sig_clm', 'flg_clm', 'flg_inst')
table = ascii.read(ion_fil, format='no_header', names=names)
if self.linelist is None:
self.linelist = LineList('ISM')
# Generate AbsLine's
for row in table:
# Generate the line
aline = AbsLine(row['wrest']*u.AA, linelist=self.linelist, closest=True)
# Set z, RA, DEC, etc.
aline.attrib['z'] = self.zabs
aline.attrib['RA'] = self.coord.ra
aline.attrib['Dec'] = self.coord.dec
# Check against existing lines
mt = [kk for kk,oline in enumerate(self.lines) if oline.ismatch(aline)]
if len(mt) > 0:
mt.reverse()
for imt in mt:
print('read_ion_file: Removing line {:g}'.format(self.lines[imt].wrest))
self.lines.pop(imt)
# Append
self.lines.append(aline)
def add_DLA(self,z, NHI=20.3,bval=30.*u.km/u.s, comment='None', model=True):
"""Generate a new DLA
"""
# Lya, Lyb
dla_lines = [] # For convenience
for trans in ['HI 1025', 'HI 1215']:
iline = AbsLine(trans)
iline.attrib['z'] = z
iline.attrib['N'] = 10**NHI / u.cm**2
iline.attrib['b'] = bval
iline.attrib['coord'] = SkyCoord(ra=0*u.deg,dec=0*u.deg)
dla_lines.append(iline)
# Generate system
new_sys = DLASystem.from_abslines(dla_lines) #(0*u.deg,0*u.deg),z,None,NHI)
new_sys.bval = bval # This is not standard, but for convenience
new_sys.comment = comment
new_sys.dla_lines = dla_lines # Also for convenience
# Name
self.count_dla += 1
new_sys.label = 'DLA_Sys_{:d}'.format(self.count_dla)
# Add
self.abssys_widg.add_fil(new_sys.label)
self.abssys_widg.all_abssys.append(new_sys)
self.abssys_widg.abslist_widget.item(
len(self.abssys_widg.all_abssys)).setSelected(True)
# Update
self.llist['Plot'] = False # Turn off metal-lines
if model: # For dealing with initialization
self.update_model()
def stack_plot(self, inp, use_lines=None, ymnx=None, add_lines=None, **kwargs):
""" Generate a stack plot of the key lines for a given COS-Halos system
Parameters
----------
inp : int or tuple
int -- Index of the cgm_abs list
tuple -- (field,gal_id)
add_lines : list, optional
List of additional lines to plot
"""
# Init
from linetools.analysis import plots as ltap
if ymnx is None:
ymnx=(-0.1,1.2)
cgm_abs = self[inp]
abs_lines = []
# Setup the lines (defaults to a key seto)
if use_lines is None:
use_lines = [1215.6700, 1025.7223, 1334.5323, 977.020, 1031.9261, 1037.6167,
1260.4221, 1206.500, 1393.7550, 2796.352]*u.AA
if add_lines is not None:
use_lines = list(use_lines.value) + add_lines
use_lines.sort()
use_lines = use_lines*u.AA
for iline in use_lines:
spec = self.load_bg_cos_spec(inp, iline)
if spec is None:
print('Skipping {:g}. Assuming no coverage'.format(iline))
aline = AbsLine(iline, closest=True)
aline.analy['spec'] = spec
aline.attrib['z'] = cgm_abs.galaxy.z
abs_lines.append(aline)
# Execute
ltap.stack_plot(abs_lines, vlim=[-400., 400]*u.km/u.s, ymnx=ymnx, **kwargs)
def read_ion_file(self,ion_fil,zabs=0.,RA=0.*u.deg, Dec=0.*u.deg):
"""Read in JXP-style .ion file in an appropriate manner
NOTE: If program breaks in this function, check the all file
to see if it is properly formatted.
"""
# Read
names=('wrest', 'clm', 'sig_clm', 'flg_clm', 'flg_inst')
table = ascii.read(ion_fil, format='no_header', names=names)
if self.linelist is None:
self.linelist = LineList('ISM')
# Generate AbsLine's
for row in table:
# Generate the line
aline = AbsLine(row['wrest']*u.AA, linelist=self.linelist, closest=True)
# Set z, RA, DEC, etc.
aline.attrib['z'] = self.zabs
aline.attrib['RA'] = self.coord.ra
aline.attrib['Dec'] = self.coord.dec
# Check against existing lines
mt = [kk for kk,oline in enumerate(self.lines) if oline.ismatch(aline)]
if len(mt) > 0:
mt.reverse()
for imt in mt:
print('read_ion_file: Removing line {:g}'.format(self.lines[imt].wrest))
self.lines.pop(imt)
# Append
self.lines.append(aline)
def test_coincident_line():
# Init AbsLines
line1 = AbsLine(1215.6700*u.AA)
line2 = AbsLine('CII 1334')
# expected errors
# no limits set
try:
answer = line1.coincident_line(line2)
except ValueError:
pass
# limit only for l1
line1.limits.set((1500,1510)*u.AA)
try:
answer = line1.coincident_line(line2)
except ValueError:
pass
# now limit for l2
line2.limits.set((1509,1520)*u.AA)
# expected overlap
assert line1.coincident_line(line2)
assert line2.coincident_line(line1)
# not expected overlap
line2.limits.set((1510.1,1520)*u.AA)
assert not line1.coincident_line(line2)
assert not line2.coincident_line(line1)
def test_molecules():
h2 = LineList('H2')
#
for kk, name in enumerate(h2.name):
lyi = AbsLine(name, linelist=h2)
# gamma values
h2_B3_0R0 = AbsLine('B3-0R(0)', linelist=h2)
assert h2_B3_0R0.data['gamma'].value > 0.
def test_init_single_absline():
# Single AbsLine
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])
# Test
assert abscomp.Zion[0] == 1
np.testing.assert_allclose(abscomp.zcomp,2.92939)
def dla_vary_NHI(outfil='Figures/dla_vary_NHI.pdf'):
""" DLA profiles with NHI varying
"""
# Wavelength array for my 'perfect' instrument
wave = np.linspace(1160., 1270., 20000) * u.AA
vel = (wave-1215.67*u.AA)/(1215.67*u.AA) * const.c.to('km/s')
# Lya line
lya = AbsLine(1215.6700*u.AA)
#lya.attrib['N'] = 10.**(13.6)/u.cm**2
lya.attrib['b'] = 30 * u.km/u.s
lya.attrib['z'] = 0.
aNHI = [20.3, 21., 21.5, 22.]
# Start the plot
xmnx = (-10000, 10000)
ymnx = (0., 1.0)
pp = PdfPages(outfil)
fig = plt.figure(figsize=(8.0, 5.0))
plt.clf()
gs = gridspec.GridSpec(1,1)
# Lya line
ax = plt.subplot(gs[0])
#ax.xaxis.set_minor_locator(plt.MultipleLocator(0.5))
#ax.xaxis.set_major_locator(plt.MultipleLocator(20.))
#ax.yaxis.set_minor_locator(plt.MultipleLocator(0.1))
#ax.yaxis.set_major_locator(plt.MultipleLocator(0.2))
ax.set_xlim(xmnx)
ax.set_ylim(ymnx)
ax.set_ylabel('Normalized Flux')
ax.set_xlabel('Relative Velocity (km/s)')
lw = 1.5
# Data
for NHI in aNHI:
lyai = copy.deepcopy(lya)
lyai.attrib['N'] = 10**NHI / u.cm**2
f_obsi = ltav.voigt_from_abslines(wave, [lyai])
ax.plot(vel, f_obsi.flux, linewidth=lw,
label=r'$\log N_{\rm HI} = $'+'{:0.2f}'.format(NHI))
# Legend
legend = plt.legend(loc='lower left', scatterpoints=1, borderpad=0.3,
handletextpad=0.3, fontsize='large', numpoints=1)
xputils.set_fontsize(ax, 17.)
# Layout and save
print('Writing {:s}'.format(outfil))
plt.tight_layout(pad=0.2,h_pad=0.0,w_pad=0.4)
plt.subplots_adjust(hspace=0)
pp.savefig(bbox_inches='tight')
plt.close()
# Finish
pp.close()
def test_ismatch():
# Test Simple kinematics
abslin1 = AbsLine('NiII 1741', z=1.)
abslin2 = AbsLine('NiII 1741', z=1.)
# Run
answer = abslin1.ismatch(abslin2)
assert answer
# Tuple too
answer2 = abslin1.ismatch((1., abslin1.wrest))
assert answer2
def test_ismatch():
# Test Simple kinematics
abslin1 = AbsLine('NiII 1741', z=1.)
abslin2 = AbsLine('NiII 1741', z=1.)
# Run
answer = abslin1.ismatch(abslin2)
assert answer
# Tuple too
answer2 = abslin1.ismatch((1., abslin1.wrest))
assert answer2
def test_add_absline():
abscomp,_ = mk_comp('HI', zcomp=0.)
abscomp.add_absline(AbsLine('HI 972'), chk_sep=False, chk_vel=False)
with pytest.raises(ValueError):
abscomp.add_absline(AbsLine('HI 949'), vtoler=-10)
# failed addition
bad_absline = AbsLine('CIV 1550')
bad_absline.limits.set([500, 1000]*u.km/u.s)
bad_absline.attrib['coord'] = SkyCoord(20,20, unit='deg')
abscomp.add_absline(bad_absline)
def test_add_absline():
abscomp, _ = mk_comp('HI', zcomp=0.)
abscomp.add_absline(AbsLine('HI 972'), chk_sep=False, chk_vel=False)
with pytest.raises(ValueError):
abscomp.add_absline(AbsLine('HI 949'), vtoler=-10)
# failed addition
bad_absline = AbsLine('CIV 1550')
bad_absline.limits.set([500, 1000] * u.km / u.s)
bad_absline.attrib['coord'] = SkyCoord(20, 20, unit='deg')
abscomp.add_absline(bad_absline)
def test_transtabl():
# Init AbsLines
abslines = [AbsLine(1215.6700*u.AA), AbsLine('CII 1334')]
#
tbl = ltlu.transtable_from_speclines(abslines)
assert len(tbl) == 2
assert 'logN' in tbl.keys()
# add keys
tbl = ltlu.transtable_from_speclines(abslines, add_keys=['A', 'log(w*f)'])
assert 'A' in tbl.keys()
def test_multi_components():
radec = SkyCoord(ra=123.1143*u.deg, dec=-12.4321*u.deg)
# HI Lya, Lyb
lya = AbsLine(1215.670*u.AA)
lya.analy['vlim'] = [-300.,300.]*u.km/u.s
lya.attrib['z'] = 2.92939
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])
abscomp.coord = radec
# SiII
SiIItrans = ['SiII 1260', 'SiII 1304', 'SiII 1526', 'SiII 1808']
abslines = []
for trans in SiIItrans:
iline = AbsLine(trans)
iline.attrib['z'] = 2.92939
iline.analy['vlim'] = [-250.,80.]*u.km/u.s
abslines.append(iline)
#
SiII_comp = AbsComponent.from_abslines(abslines)
SiII_comp.coord = radec
# Instantiate
LLSsys = GenericAbsSystem.from_components([abscomp,SiII_comp])
# Test
assert len(LLSsys._components) == 2
def test_aodm_absline():
# Init CIV 1548
abslin = AbsLine('CIV 1548', z=2.9304)
# Set spectrum
abslin.analy['spec'] = lsio.readspec(
data_path('UM184_nF.fits')) # Fumagalli+13 MagE spectrum
abslin.limits.set([6080.78, 6087.82] * u.AA)
#abslin.analy['wvlim'] = [6080.78, 6087.82]*u.AA
#
abslin.measure_aodm()
N, sig_N, flgN = [abslin.attrib[key] for key in ['N', 'sig_N', 'flag_N']]
np.testing.assert_allclose(N.value, 76369981945649.38)
assert N.unit == 1 / u.cm**2
assert flgN == 1
# Now velocity limits
abslin.setz(2.92929)
abslin.limits.set((-150., 150.) * u.km / u.s)
#
abslin.measure_aodm()
N, sig_N, flgN = [abslin.attrib[key] for key in ['N', 'sig_N', 'flag_N']]
np.testing.assert_allclose(N.value, 80410608889125.64)
return
def test_list_of_abslines():
radec = SkyCoord(ra=123.1143*u.deg, dec=-12.4321*u.deg)
# HI Lya, Lyb
lya = AbsLine(1215.670*u.AA)
lya.analy['vlim'] = [-300.,300.]*u.km/u.s
lya.attrib['z'] = 2.92939
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])
abscomp.coord = radec
# SiII
SiIItrans = ['SiII 1260', 'SiII 1304', 'SiII 1526', 'SiII 1808']
abslines = []
for trans in SiIItrans:
iline = AbsLine(trans)
iline.attrib['z'] = 2.92939
iline.analy['vlim'] = [-250.,80.]*u.km/u.s
abslines.append(iline)
#
SiII_comp = AbsComponent.from_abslines(abslines)
SiII_comp.coord = radec
# Instantiate
gensys = GenericAbsSystem.from_components([abscomp,SiII_comp])
# Now the list
abslines = gensys.list_of_abslines()
# Test
assert len(abslines) == 6
# Grab one line
lyb = gensys.get_absline('HI 1025')
np.testing.assert_allclose(lyb.wrest.value, 1025.7222)
lyb = gensys.get_absline(1025.72*u.AA)
np.testing.assert_allclose(lyb.wrest.value, 1025.7222)
def test_voigt_sngl_line():
# Wavelength array
wave = np.linspace(3644, 3650, 100) * u.AA
imn = np.argmin(np.abs(wave.value - 3647))
# HI line
abslin = AbsLine(1215.670 * u.AA, z=2.)
abslin.attrib['N'] = 10**14. / u.cm**2
abslin.attrib['b'] = 25. * u.km / u.s
# Voigt
vmodel = abslin.generate_voigt(wave=wave)
np.testing.assert_allclose(vmodel.flux[imn].value, 0.05145500775919881)
def test_voigt_sngl_tau():
# Wavelength array
wave = np.linspace(3644, 3650, 100)*u.AA
imn = np.argmin(np.abs(wave.value-3647))
# HI line
abslin = AbsLine(1215.670*u.AA, z=2.)
abslin.attrib['N'] = 10**14./u.cm**2
abslin.attrib['b'] = 25.*u.km/u.s
# Tau
tau = lav.voigt_from_abslines(wave,abslin,ret='tau')
np.testing.assert_allclose(tau[imn], 2.9681283001576779)
def test_voigt_sngl_tau():
# Wavelength array
wave = np.linspace(3644, 3650, 100) * u.AA
imn = np.argmin(np.abs(wave.value - 3647))
# HI line
abslin = AbsLine(1215.670 * u.AA, z=2.)
abslin.attrib['N'] = 10**14. / u.cm**2
abslin.attrib['b'] = 25. * u.km / u.s
# Tau
tau = lav.voigt_from_abslines(wave, abslin, ret='tau')
np.testing.assert_allclose(tau[imn], 2.9681283001576779)
def test_voigt_sngl_line():
# Wavelength array
wave = np.linspace(3644, 3650, 100)*u.AA
imn = np.argmin(np.abs(wave.value-3647))
# HI line
abslin = AbsLine(1215.670*u.AA, z=2.)
abslin.attrib['N'] = 10**14./u.cm**2
abslin.attrib['b'] = 25.*u.km/u.s
# Voigt
vmodel = abslin.generate_voigt(wave=wave)
np.testing.assert_allclose(vmodel.flux[imn].value,0.05145500775919881)
def test_measurekin_absline():
# Test Simple kinematics
abslin = AbsLine('NiII 1741',z=2.307922)
# Set spectrum
abslin.analy['spec'] = lsio.readspec(data_path('PH957_f.fits'))
abslin.limits.set([-70., 70.]*u.km/u.s)
# Measure Kin
abslin.measure_kin()
np.testing.assert_allclose(abslin.attrib['kin']['Dv'].value, 75.)
np.testing.assert_allclose(abslin.attrib['kin']['fedg'], 0.20005782376000183)
def test_failed_init():
with pytest.raises(ValueError):
abslin = AbsLine(1215.700 * u.AA)
with pytest.raises(ValueError):
abslin = AbsLine('HI Ly99')
with pytest.raises(ValueError):
sline = SpectralLine.from_dict(dict(ltype='wrong ltype'))
with pytest.raises(ValueError):
sline = SpectralLine('wrong ltype', 1215.67 * u.AA)
with pytest.raises(ValueError):
sline = SpectralLine('Abs',
dict(bad_trans='because I am dict, right?'))
def test_measurekin_absline():
# Test Simple kinematics
abslin = AbsLine('NiII 1741',z=2.307922)
# Set spectrum
abslin.analy['spec'] = lsio.readspec(data_path('PH957_f.fits'))
abslin.limits.set([-70., 70.]*u.km/u.s)
# Measure Kin
abslin.measure_kin()
np.testing.assert_allclose(abslin.attrib['kin']['Dv'].value, 75.)
np.testing.assert_allclose(abslin.attrib['kin']['fedg'], 0.20005782376000183)
def test_mk_absline():
# Init HI Lya
abslin = AbsLine(1215.6700 * u.AA)
np.testing.assert_allclose(abslin.data['f'], 0.4164)
# Init CII 1334 with LineList
abslin2 = AbsLine(1334.5323 * u.AA, linelist='Strong', use_CACHE=True)
np.testing.assert_allclose(abslin2.data['Ek'], 74932.62 / u.cm)
# Init CII 1334 by name
abslin3 = AbsLine('CII 1334')
np.testing.assert_allclose(abslin3.data['wrest'], 1334.5323 * u.AA)
def test_init_multi_absline():
# AbsLine(s)
lya = AbsLine(1215.670*u.AA, z=2.92939)
lya.limits.set([-300.,300.]*u.km/u.s)
lyb = AbsLine(1025.7222*u.AA)
lyb.setz(lya.z)
lyb.limits.set([-300.,300.]*u.km/u.s)
# Instantiate
abscomp = AbsComponent.from_abslines([lya,lyb])
# Test
assert len(abscomp._abslines) == 2
np.testing.assert_allclose(abscomp.zcomp,2.92939)
def test_init_multi_absline():
# AbsLine(s)
lya = AbsLine(1215.670 * u.AA, z=2.92939)
lya.limits.set([-300., 300.] * u.km / u.s)
lyb = AbsLine(1025.7222 * u.AA)
lyb.setz(lya.z)
lyb.limits.set([-300., 300.] * u.km / u.s)
# Instantiate
abscomp = AbsComponent.from_abslines([lya, lyb])
# Test
assert len(abscomp._abslines) == 2
np.testing.assert_allclose(abscomp.zcomp, 2.92939)
def test_dicts():
# Init HI Lya
abslin = AbsLine(1215.6700*u.AA)
adict = abslin.to_dict()
assert isinstance(adict, dict)
# Write
#pdb.set_trace()
ltu.savejson('tmp.json', adict, overwrite=True)
# Read
newdict = ltu.loadjson('tmp.json')
newlin = SpectralLine.from_dict(newdict)
assert newlin.name == 'HI 1215'
def si2_comp(radec):
# SiII
SiIItrans = ['SiII 1260', 'SiII 1304', 'SiII 1526', 'SiII 1808']
abslines = []
for trans in SiIItrans:
iline = AbsLine(trans)
iline.attrib['z'] = 2.92939
iline.analy['vlim'] = [-250.,80.]*u.km/u.s
abslines.append(iline)
#
SiII_comp = AbsComponent.from_abslines(abslines)
SiII_comp.coord = radec
#
return SiII_comp
def test_todict_withjson():
radec = SkyCoord(ra=123.1143 * u.deg, dec=-12.4321 * u.deg)
# HI Lya, Lyb
lya = AbsLine(1215.670 * u.AA)
lya.limits.set([-300., 300.] * u.km / u.s)
lya.attrib['z'] = 2.92939
lya.attrib['coord'] = radec
lyb = AbsLine(1025.7222 * u.AA)
lyb.limits.set([-300., 300.] * u.km / u.s)
lyb.attrib['z'] = lya.attrib['z']
lyb.attrib['coord'] = radec
abscomp = AbsComponent.from_abslines([lya, lyb])
# Instantiate
HIsys = LymanAbsSystem.from_components([abscomp])
# Dict
adict = HIsys.to_dict()
assert isinstance(adict, dict)
# Verify it is JSON compatible (failing in Python 3)
import io, json
with io.open('tmp.json', 'w', encoding='utf-8') as f:
f.write(
unicode(
json.dumps(adict,
sort_keys=True,
indent=4,
separators=(',', ': '))))
def test_copy():
# Single AbsLine
lya = AbsLine(1215.670*u.AA, z=2.92939)
lya.analy['vlim'] = [-300.,300.]*u.km/u.s
abscomp = AbsComponent.from_abslines([lya])
# Copy
abscomp2 = abscomp.copy()
# Checks
attrs = vars(abscomp).keys()
attrs2 = vars(abscomp2).keys()
for attr in attrs:
assert attr in attrs2
np.testing.assert_allclose(abscomp._abslines[0].z,
abscomp2._abslines[0].z)
def mk_comp(ctype,vlim=[-300.,300]*u.km/u.s,add_spec=False, use_rand=True,
add_trans=False, zcomp=2.92939):
# Read a spectrum Spec
if add_spec:
xspec = lsio.readspec(lt_path+'/spectra/tests/files/UM184_nF.fits')
else:
xspec = None
# AbsLines
if ctype == 'HI':
all_trans = ['HI 1215', 'HI 1025']
elif ctype == 'SiII':
all_trans = ['SiII 1260', 'SiII 1304', 'SiII 1526', 'SiII 1808']
if add_trans:
all_trans += ['SiII 1193']
abslines = []
for trans in all_trans:
iline = AbsLine(trans)
iline.attrib['z'] = zcomp
if use_rand:
rnd = np.random.rand()
else:
rnd = 0.
iline.attrib['logN'] = 13.3 + rnd
iline.attrib['sig_logN'] = 0.15
iline.attrib['flag_N'] = 1
iline.analy['spec'] = xspec
iline.analy['vlim'] = vlim
iline.analy['wvlim'] = iline.wrest * (1 + zcomp + ltu.give_dz(vlim, zcomp))
_,_ = ltaa.linear_clm(iline.attrib) # Loads N, sig_N
abslines.append(iline)
# Component
abscomp = AbsComponent.from_abslines(abslines)
return abscomp, abslines
def fill_lls_lines(self, bval=20. * u.km / u.s, do_analysis=1):
"""
Generate an HI line list for an LLS.
Goes into self.lls_lines
Now generates a component too.
Should have it check for an existing HI component..
Parameters
----------
bval : float, optional
Doppler parameter in km/s
do_analysis : int, optional
flag for analysis
"""
from linetools.lists import linelist as lll
# May be replaced by component class (as NT desires)
HIlines = lll.LineList('HI')
self.lls_lines = []
Nval = 10**self.NHI / u.cm**2
for wrest in u.Quantity(HIlines._data['wrest']):
aline = AbsLine(wrest, linelist=HIlines)
# Attributes
aline.attrib['N'] = Nval
aline.attrib['b'] = bval
aline.setz(self.zabs)
aline.limits.set(self.vlim)
aline.analy['do_analysis'] = do_analysis
aline.attrib['coord'] = self.coord
self.lls_lines.append(aline)
# Generate a component (should remove any previous HI)
self.add_component(AbsComponent.from_abslines(self.lls_lines))
def test_init_single_absline():
# Single AbsLine
lya = AbsLine(1215.670 * u.AA, z=2.92939)
lya.limits.set([-300., 300.] * u.km / u.s)
lya.attrib['N'] = 1e12 / u.cm**2
lya.attrib['sig_N'] = [1e11] * 2 / u.cm**2
lya.attrib['flag_N'] = 1
abscomp = AbsComponent.from_abslines([lya])
# Test
assert abscomp.Zion[0] == 1
assert len(abscomp.sig_N) == 2
assert np.isclose(abscomp.sig_logN[0], 0.04342945)
assert isinstance(abscomp.sig_logN, np.ndarray)
np.testing.assert_allclose(abscomp.zcomp, 2.92939)
def measure_sodium_EW(filename):
from linetools.lists.linelist import LineList
from astropy import units as u
from linetools.spectralline import AbsLine
from linetools.spectra.xspectrum1d import XSpectrum1D
import matplotlib.pyplot as plt
sp = XSpectrum1D.from_file('RF_' + filename)
sp.normalize(co=sp.co)
wvlim = [5880, 6030] * u.AA
strong = LineList('Strong')
transitions = strong.available_transitions(wvlim,
n_max_tuple=None,
min_strength=0.0)
line1 = transitions['wrest'][0]
line2 = transitions['wrest'][1]
avg_line = (line1 + line2) / 2.0
# Plot the spectrum to get limits for EW
fig = plt.figure()
plt.axvline(x=line1, color='k', linestyle='--')
plt.axhline(y=1.0, color='r', linestyle='--')
plt.axvline(x=line2, color='k', linestyle='--')
sp.plot(xlim=(avg_line - 30, avg_line + 30))
S1 = AbsLine(transitions['wrest'][0] * u.AA, z=0.0)
S1.analy['spec'] = sp
S2 = AbsLine(transitions['wrest'][1] * u.AA, z=0.0)
S2.analy['spec'] = sp
#x = float(input("Enter a lower lim: "))
#y = float(input("Enter a higher lim: "))
x = 5888
y = 5896
S1.limits.set([x, y] * u.AA)
S1.measure_ew(flg=1) # Measure the EW of the first line
EW1 = S1.attrib['EW'], S1.attrib['sig_EW']
#x = float(input("Enter a lower lim: "))
#y = float(input("Enter a higher lim: "))
x = 5895
y = 5905
S2.limits.set([x, y] * u.AA)
S2.measure_ew() # Measure the EW of the second line
EW2 = S2.attrib['EW'], S2.attrib['sig_EW']
return EW1, EW2
def test_voigt_model():
from astropy.modeling import fitting
# Wavelength array
wave = np.linspace(3644, 3650, 100) * u.AA
# HI line
abslin = AbsLine(1215.670 * u.AA, z=2.)
abslin.attrib['N'] = 10**14. / u.cm**2
abslin.attrib['b'] = 25. * u.km / u.s
# Voigt
vmodel = abslin.generate_voigt(wave=wave)
vmodel.sig = 0.1
# Voigt fit
abslin.analy['spec'] = vmodel
abslin.limits.set([-100., 100] * u.km / u.s)
abslin.measure_aodm(normalize=False) # Sets analysis pixels
fitvoigt = lav.single_voigt_model(logN=np.log10(abslin.attrib['N'].value),
b=abslin.attrib['b'].value,
z=2.,
wrest=abslin.wrest.value,
gamma=abslin.data['gamma'].value,
f=abslin.data['f'],
fwhm=3.)
# Restrict parameter space
fitvoigt.logN.min = 12.
fitvoigt.b.min = 10.
fitvoigt.z.min = 2. + -100. * (1 + 2.) / c_kms
fitvoigt.z.max = 2. + 100 * (1 + 2.) / c_kms
# Fit
fitter = fitting.LevMarLSQFitter()
parm = fitter(fitvoigt, vmodel.wavelength[abslin.analy['pix']].value,
vmodel.flux[abslin.analy['pix']].value)
assert np.abs(parm.logN.value - np.log10(abslin.attrib['N'].value)) < 0.1
def plot_absline(iinp,logN,b, show=True):
"""Plot an absorption line with N,b properties
Parameters
----------
iinp : float or str
Rest wavelength (Ang) or name of transition (e.g. CIV1548)
logN : float
Log10 column
b : float
Doppler parameter (km/s)
show : bool
Whether to display the plot (set False for running
tests). Default True.
"""
import numpy as np
from linetools.spectralline import AbsLine
from astropy import units as u
# Search for the closest absline
if isinstance(iinp,basestring):
aline = AbsLine(iinp, closest=True)
else:
aline = AbsLine(iinp*u.AA, closest=True)
wrest = aline.wrest.value
# Generate a fake wavelength array near the line
wvoff = 50. # Ang
dwv = wrest/100000. # Ang (echelle)
wave = np.arange(wrest-wvoff, wrest+wvoff, dwv)
# Generate spectrum with voigt
aline.attrib['N'] = 10**logN * u.cm**-2
aline.attrib['b'] = b * u.km/u.s
xspec = aline.generate_voigt(wave=wave*u.AA)
# get the plotting limits
# remove first and last pixels
fl = xspec.flux.value[1:-2]
ind = np.flatnonzero(fl < 1 - 0.1 * (1 - np.min(fl)))
ind += 1
wmin = xspec.wavelength[max(0, ind[0] - 10)]
wmax = xspec.wavelength[min(len(xspec.flux) - 1, ind[-1] + 10)]
#import pdb; pdb.set_trace()
xspec.constant_sig(0.1) # S/N = 10 per pix
# Calculate EW
aline.analy['spec'] = xspec
aline.analy['wvlim'] = np.array([wrest-15., wrest+15])*u.AA
aline.measure_ew()
print(aline)
print('EW = {:g}'.format(aline.attrib['EW']))
# Plot
xspec.plot(xlim=(wmin.to(u.AA).value, wmax.to(u.AA).value), show=show)
def si2_comp(radec):
# SiII
SiIItrans = ['SiII 1260', 'SiII 1304', 'SiII 1526', 'SiII 1808']
abslines = []
for trans in SiIItrans:
iline = AbsLine(trans, z=2.92939)
iline.attrib['coord'] = radec
iline.limits.set([-250.,80.]*u.km/u.s)
abslines.append(iline)
#
SiII_comp = AbsComponent.from_abslines(abslines)
SiII_comp.logN = 15.
SiII_comp.flag_N = 1
#
return SiII_comp
def oi_comp(radec, vlim=[-250., 80.] * u.km / u.s, z=2.92939):
# SiII
OItrans = ['OI 1302']
abslines = []
for trans in OItrans:
iline = AbsLine(trans, z=z, linelist=ism)
iline.attrib['coord'] = radec
iline.limits.set(vlim)
abslines.append(iline)
#
OI_comp = AbsComponent.from_abslines(abslines, skip_synth=True)
OI_comp.logN = 15.
OI_comp.flag_N = 1
#
return OI_comp
def test_parse_abslines():
# Init AbsLines
abslines = [AbsLine(1215.6700*u.AA), AbsLine('CII 1334')]
# wrest
wrest_values = ltlu.parse_speclines(abslines, 'wrest')
np.testing.assert_allclose(wrest_values[1], 1334.5323*u.AA)
# EW
EW_values = ltlu.parse_speclines(abslines, 'EW')
np.testing.assert_allclose(EW_values[1].value, 0.)
# data
A_values = ltlu.parse_speclines(abslines, 'A')
np.testing.assert_allclose(A_values[0].value, 626500000.0)
# append None
aux = ltlu.parse_speclines(abslines, 'wrong_attribute')
assert aux[0] is None
def oi_comp(radec, vlim=[-250.,80.]*u.km/u.s, z=2.92939):
# SiII
OItrans = ['OI 1302']
abslines = []
for trans in OItrans:
iline = AbsLine(trans, z=z, linelist=ism)
iline.attrib['coord'] = radec
iline.limits.set(vlim)
abslines.append(iline)
#
OI_comp = AbsComponent.from_abslines(abslines, skip_synth=True)
OI_comp.logN = 15.
OI_comp.flag_N = 1
#
return OI_comp
def si2_comp(radec):
# SiII
SiIItrans = ['SiII 1260', 'SiII 1304', 'SiII 1526', 'SiII 1808']
abslines = []
for trans in SiIItrans:
iline = AbsLine(trans, z=2.92939)
iline.attrib['coord'] = radec
iline.limits.set([-250., 80.] * u.km / u.s)
abslines.append(iline)
#
SiII_comp = AbsComponent.from_abslines(abslines)
SiII_comp.logN = 15.
SiII_comp.flag_N = 1
#
return SiII_comp
def test_rest_limits():
SiIItrans = ['SiII 1260', 'SiII 1304']
radec = SkyCoord(ra=1., dec=1., unit='deg')
abslines = []
for kk, trans in enumerate(SiIItrans):
iline = AbsLine(trans, z=1., linelist=ism)
iline.attrib['coord'] = radec
if kk == 0:
iline.limits.set([-250., 80.] * u.km / u.s)
else:
iline.limits.set([-50., 180.] * u.km / u.s)
abslines.append(iline)
#
comp = AbsComponent.from_abslines(abslines, chk_vel=False)
comp.reset_limits_from_abslines()
assert np.isclose(comp.vlim[1].value, 180.)
def setatomicdata(lines, precise=True, linelist=ilist):
lam = np.zeros(len(lines))
fosc = np.zeros(len(lines))
gam = np.zeros(len(lines))
for i, ll in enumerate(lines):
try:
al = AbsLine(ll * u.AA, closest=True, linelist=linelist)
lam[i] = al.data['wrest'].value
fosc[i] = al.data['f']
gam[i] = al.data['gamma'].value
except:
idx = jbg.closest(adata['wrest'], ll)
lam[i] = adata['wrest'][idx]
fosc[i] = adata['f'][idx]
gam[i] = adata['gamma'][idx]
if ((abs(lam[i] - ll) > 0.01) & (precise == True)):
idx = jbg.closest(vdata['wrest'], ll)
try:
lam[i] = vdata['wrest'][idx].value
fosc[i] = vdata['f'][idx]
gam[i] = vdata['gamma'][idx].value
except:
lam[i] = vdata['wrest'][idx]
fosc[i] = vdata['f'][idx]
gam[i] = vdata['gamma'][idx]
return lam, fosc, gam
def test_stack_plot(show=False):
abslin1 = AbsLine(1548.204 * u.AA)
abslin2 = AbsLine('CIV 1550')
# no spectrum first
ltap.stack_plot([abslin1], show=show)
# Set spectrum
spec = ltsio.readspec(data_path('UM184_nF.fits')) # already normalized
abslin1.analy['spec'] = spec
abslin1.analy['wvlim'] = [6079.78, 6168.82] * u.AA
abslin1.attrib['z'] = 2.92929
ltap.stack_plot([abslin1], show=show)
# second line
abslin2.analy['spec'] = spec
abslin2.analy['wvlim'] = [6079.78, 6168.82] * u.AA
abslin2.attrib['z'] = 2.92929
ltap.stack_plot([abslin1, abslin2], show=show)
def test_rest_limits():
SiIItrans = ['SiII 1260', 'SiII 1304']
radec = SkyCoord(ra=1., dec=1., unit='deg')
abslines = []
for kk,trans in enumerate(SiIItrans):
iline = AbsLine(trans, z=1., linelist=ism)
iline.attrib['coord'] = radec
if kk == 0:
iline.limits.set([-250.,80.]*u.km/u.s)
else:
iline.limits.set([-50.,180.]*u.km/u.s)
abslines.append(iline)
#
comp = AbsComponent.from_abslines(abslines, chk_vel=False)
comp.reset_limits_from_abslines()
assert np.isclose(comp.vlim[1].value, 180.)
def add_forest(self,inp,z):
"""Add a Lya/Lyb forest line
"""
forest = []
# NHI
NHI_dict = {'6':12.,'7':13.,'8':14.,'9':15.}
forest_NHI=NHI_dict[inp]
# Lines
for name in ['HI 1215','HI 1025', 'HI 972']:
aline = AbsLine(name, linelist=self.llist[self.llist['List']], z=z)
# Attributes
aline.attrib['N'] = 10**forest_NHI * u.cm**-2
aline.attrib['b'] = 20.*u.km/u.s
# Append
forest.append(aline)
# Append to forest lines
self.all_forest.append(forest)
def fill_lls_lines(self, bval=20.*u.km/u.s, do_analysis=1):
"""
Generate an HI line list for an LLS.
Goes into self.lls_lines
Now generates a component too.
Should have it check for an existing HI component..
Parameters
----------
bval : float, optional
Doppler parameter in km/s
do_analysis : int, optional
flag for analysis
"""
from linetools.lists import linelist as lll
# May be replaced by component class (as NT desires)
HIlines = lll.LineList('HI')
self.lls_lines = []
Nval = 10**self.NHI / u.cm**2
for lline in HIlines._data:
aline = AbsLine(lline['wrest'], linelist=HIlines)
# Attributes
aline.attrib['N'] = Nval
aline.attrib['b'] = bval
aline.attrib['z'] = self.zabs
aline.analy['vlim'] = self.vlim
aline.analy['do_analysis'] = do_analysis
aline.attrib['coord'] = self.coord
self.lls_lines.append(aline)
# Generate a component (should remove any previous HI)
self.add_component(AbsComponent.from_abslines(self.lls_lines))
def test_voigt_model():
from astropy.modeling import fitting
# Wavelength array
wave = np.linspace(3644, 3650, 100)*u.AA
# HI line
abslin = AbsLine(1215.670*u.AA, z=2.)
abslin.attrib['N'] = 10**14./u.cm**2
abslin.attrib['b'] = 25.*u.km/u.s
# Voigt
vmodel = abslin.generate_voigt(wave=wave)
vmodel.sig = 0.1
# Voigt fit
abslin.analy['spec'] = vmodel
abslin.limits.set([-100.,100]*u.km/u.s)
abslin.measure_aodm(normalize=False) # Sets analysis pixels
fitvoigt = lav.single_voigt_model(logN=np.log10(abslin.attrib['N'].value),
b=abslin.attrib['b'].value, z=2., wrest=abslin.wrest.value,
gamma=abslin.data['gamma'].value,
f=abslin.data['f'], fwhm=3.)
# Restrict parameter space
fitvoigt.logN.min = 12.
fitvoigt.b.min = 10.
fitvoigt.z.min = 2. + -100. * (1 + 2.) / c_kms
fitvoigt.z.max = 2. + 100 * (1 + 2.) / c_kms
# Fit
fitter = fitting.LevMarLSQFitter()
parm = fitter(fitvoigt,vmodel.wavelength[abslin.analy['pix']].value,
vmodel.flux[abslin.analy['pix']].value)
assert np.abs(parm.logN.value-np.log10(abslin.attrib['N'].value)) < 0.1
def fill_lls_lines(self, bval=20. * u.km / u.s):
"""
Generate an HI line list for an LLS.
Goes into self.lls_lines
Parameters
----------
bval : float (20.) Doppler parameter in km/s
"""
from linetools.lists import linelist as lll
from linetools.spectralline import AbsLine
# May be replaced by component class (as NT desires)
HIlines = lll.LineList('HI')
self.lls_lines = []
for lline in HIlines._data:
aline = AbsLine(lline['wrest'], linelist=HIlines)
# Attributes
aline.attrib['N'] = self.NHI
aline.attrib['b'] = bval
aline.attrib['z'] = self.zabs
# Could set RA and DEC too
aline.attrib['RA'] = self.coord.ra
aline.attrib['DEC'] = self.coord.dec
self.lls_lines.append(aline)
def test_init_single_absline():
# Single AbsLine
lya = AbsLine(1215.670 * u.AA, z=2.92939)
lya.limits.set([-300., 300.] * u.km / u.s)
abscomp = AbsComponent.from_abslines([lya])
# Test
assert abscomp.Zion[0] == 1
np.testing.assert_allclose(abscomp.zcomp, 2.92939)
print(abscomp)
def test_stack_plot(show=False):
abslin1 = AbsLine(1548.204*u.AA)
abslin2 = AbsLine('CIV 1550')
# no spectrum first
ltap.stack_plot([abslin1], show=show)
# Set spectrum
spec = ltsio.readspec(data_path('UM184_nF.fits')) # already normalized
abslin1.analy['spec'] = spec
abslin1.analy['wvlim'] = [6079.78, 6168.82]*u.AA
abslin1.setz(2.92929)
ltap.stack_plot([abslin1], show=show)
# second line
abslin2.analy['spec'] = spec
abslin2.analy['wvlim'] = [6079.78, 6168.82]*u.AA
abslin2.setz(2.92929)
ltap.stack_plot([abslin1, abslin2], show=show)
# now with a zref
ltap.stack_plot([abslin1, abslin2], show=show, zref=2.928)
def test_synthesize_colm():
# Read a spectrum Spec
xspec = lsio.readspec(lt_path+'/spectra/tests/files/UM184_nF.fits')
# AbsLines
SiIItrans = ['SiII 1260', 'SiII 1304', 'SiII 1526', 'SiII 1808']
abslines = []
for trans in SiIItrans:
iline = AbsLine(trans)
iline.attrib['z'] = 2.92939
iline.analy['vlim'] = [-250.,80.]*u.km/u.s
iline.analy['spec'] = xspec
abslines.append(iline)
# Component
abscomp = AbsComponent.from_abslines(abslines)
# Column
abscomp.synthesize_colm(redo_aodm=True)
# Test
np.testing.assert_allclose(abscomp.logN,13.594447075294818)
def stack_plot(self,
inp,
use_lines=None,
ymnx=None,
add_lines=None,
**kwargs):
""" Generate a stack plot of the key lines for a given COS-Halos system
Parameters
----------
inp : int or tuple
int -- Index of the cgm_abs list
tuple -- (field,gal_id)
add_lines : list, optional
List of additional lines to plot
"""
# Init
from linetools.analysis import plots as ltap
if ymnx is None:
ymnx = (-0.1, 1.2)
cgm_abs = self[inp]
abs_lines = []
# Setup the lines (defaults to a key seto)
if use_lines is None:
use_lines = [
1215.6700, 1025.7223, 1334.5323, 977.020, 1031.9261, 1037.6167,
1260.4221, 1206.500, 1393.7550, 2796.352
] * u.AA
if add_lines is not None:
use_lines = list(use_lines.value) + add_lines
use_lines.sort()
use_lines = use_lines * u.AA
for iline in use_lines:
spec = self.load_bg_cos_spec(inp, iline)
if spec is None:
print('Skipping {:g}. Assuming no coverage'.format(iline))
aline = AbsLine(iline, closest=True)
aline.analy['spec'] = spec
aline.attrib['z'] = cgm_abs.galaxy.z
abs_lines.append(aline)
# Execute
ltap.stack_plot(abs_lines,
vlim=[-400., 400] * u.km / u.s,
ymnx=ymnx,
**kwargs)
def equiv_width_map(cube, varcube, measure_range, contwave1=None, contwave2=None,
transition='MgII 2796', zsys=0.6942,normalize_continuum=True):
"""Calculate the equivalent width over some wavelength range
"""
from linetools.spectralline import AbsLine
if normalize_continuum:
normcube,signormcube = continuum_subtract(cube,varcube,contwave1,contwave2,
normalize=True)
else:
normcube = cube
signormcube = varcube
al = AbsLine(transition,z = zsys)
try:
if measure_range[0].unit == u.AA:
#import pdb; pdb.set_trace()
al.limits.set(((measure_range[0]/al.wrest-1.).value,(measure_range[1]/al.wrest-1.).value))
elif measure_range.unit == (u.km/u.s):
al.limits.set(measure_range)
except:
raise ValueError("measure_range should be a quantity with velocity or wavelength units")
cubedims = np.shape(cube.data)
ys = np.arange(cubedims[2])
xs = np.arange(cubedims[1])
grdTarr = np.array(np.meshgrid(xs, ys)).T
rows = np.shape(grdTarr)[0] * np.shape(grdTarr)[1]
spcoords = grdTarr.reshape(rows, 2)
ewarr = np.zeros((cubedims[1],cubedims[2]))
sigewarr = np.zeros((cubedims[1],cubedims[2]))
for i,cc in enumerate(spcoords):
spec = extract_spectrum(cube,cc)
sigspec = extract_spectrum(varcube,cc)
spec.sig = sigspec.flux
al.analy['spec'] = spec
al.measure_restew()
ewarr[cc[0],cc[1]] = al.attrib['EW'].value
sigewarr[cc[0],cc[1]] = al.attrib['sig_EW'].value
return ewarr, sigewarr
def add_forest(self, inp, z):
'''Add a Lya/Lyb forest line
'''
from xastropy.igm.abs_sys.abssys_utils import GenericAbsSystem
forest = GenericAbsSystem(zabs=z)
# NHI
NHI_dict = {'6': 12., '7': 13., '8': 14., '9': 15.}
forest.NHI = NHI_dict[inp]
# Lines
for name in ['HI 1215', 'HI 1025', 'HI 972']:
aline = AbsLine(name, linelist=self.llist[self.llist['List']])
# Attributes
aline.attrib['N'] = forest.NHI
aline.attrib['b'] = 20. * u.km / u.s
aline.attrib['z'] = forest.zabs
# Append
forest.lines.append(aline)
# Append to forest lines
self.all_forest.append(forest)
def test_cog():
# Read a spectrum Spec
xspec = lsio.readspec(lt_path+'/spectra/tests/files/UM184_nF.fits')
# AbsLines
SiIItrans = ['SiII 1260', 'SiII 1304', 'SiII 1526', 'SiII 1808']
abslines = []
for trans in SiIItrans:
iline = AbsLine(trans)
iline.attrib['z'] = 2.92939
iline.analy['vlim'] = [-250.,80.]*u.km/u.s
iline.analy['spec'] = xspec
abslines.append(iline)
# Component
abscomp = AbsComponent.from_abslines(abslines)
# COG
COG_dict = abscomp.cog(redo_EW=True)
# Test
np.testing.assert_allclose(COG_dict['logN'],13.693355878125537)
np.testing.assert_allclose(COG_dict['sig_logN'],0.054323725737309987)
def test_dicts():
# Init HI Lya
abslin = AbsLine(1215.6700*u.AA)
abslin.analy['spec'] = 'tmp.fits'
adict = abslin.to_dict()
assert isinstance(adict, dict)
# Write
#pdb.set_trace()
ltu.savejson('tmp.json', adict, overwrite=True)
# Read
newdict = ltu.loadjson('tmp.json')
newlin = SpectralLine.from_dict(newdict)
assert newlin.name == 'HI 1215'
# Old dict for compatability
newdict.pop('limits')
newdict['analy']['vlim'] = [-150,150]*u.km/u.s
newdict['attrib']['z'] = 0.5
tmp3 = SpectralLine.from_dict(newdict)
assert newlin.name == 'HI 1215'
def add_forest(self,inp,z):
'''Add a Lya/Lyb forest line
'''
from xastropy.igm.abs_sys.abssys_utils import GenericAbsSystem
forest = GenericAbsSystem((0.*u.deg,0.*u.deg), z, [-300.,300.]*u.km/u.s)
# NHI
NHI_dict = {'6':12.,'7':13.,'8':14.,'9':15.}
forest.NHI=NHI_dict[inp]
# Lines
for name in ['HI 1215','HI 1025', 'HI 972']:
aline = AbsLine(name,
linelist=self.llist[self.llist['List']])
# Attributes
aline.attrib['N'] = 10**forest.NHI * u.cm**-2
aline.attrib['b'] = 20.*u.km/u.s
aline.attrib['z'] = forest.zabs
# Append
forest.lines.append(aline)
# Append to forest lines
self.all_forest.append(forest)
