def test_abscomp_H2():
Zion = (-1, -1) # temporary code for molecules
Ntuple = (1, 17, -1) # initial guess for Ntuple (needs to be given for adding lines from linelist)
coord = SkyCoord(0,0, unit='deg')
z = 0.212
vlim = [-100., 100.] * u.km/u.s
comp = AbsComponent(coord, Zion, z, vlim, Ntup=Ntuple)
comp.add_abslines_from_linelist(llist='H2', init_name="B19-0P(1)", wvlim=[1100, 5000]*u.AA)
assert len(comp._abslines) == 7
def test_abscomp_H2():
Zion = (-1, -1) # temporary code for molecules
Ntuple = (
1, 17, -1
) # initial guess for Ntuple (needs to be given for adding lines from linelist)
coord = SkyCoord(0, 0, unit='deg')
z = 0.212
vlim = [-100., 100.] * u.km / u.s
comp = AbsComponent(coord, Zion, z, vlim, Ntup=Ntuple)
comp.add_abslines_from_linelist(llist='H2',
init_name="B19-0P(1)",
wvlim=[1100, 5000] * u.AA)
assert len(comp._abslines) == 7
def stack_plot(self,
to_plot,
pvlim=None,
maxtrans=3,
return_fig=True,
add_missing_lines=False,
spec=None,
**kwargs):
'''Show a stack plot of the CGM absorption system
Parameters
----------
to_plot : List of AbsLines, AbsComponents, tuples, or strs
If AbsLines, pass list on to linetools.analysis.plots.stack_plot()
If not Abslines, will plot up to maxtrans of strongest transitions
covered by spectra for components of some species.
If tuples or strs, should be Zion value or ion name: (8,6) or 'OVI'
pvlim : Quantities, optional
Override system vlim for plotting
maxtrans : int, optional
Maximum number of lines per transition to plot
add_missing_lines : bool, optional
If True, plot transitions that do not have associated AbsLine objects
spec : XSpectrum1D, optional
Spectrum to plot in regions of requested lines; required if assoc.
AbsLine objects do not have their analy['specfile'] attributes set
Returns
-------
fig : matplotlib Figure, optional
Figure instance containing stack plot with subplots, axes, etc.
'''
from linetools.analysis import plots as ltap
from linetools.spectralline import AbsLine
from linetools.isgm.abscomponent import AbsComponent
from linetools.spectra.io import readspec
from linetools.lists.linelist import LineList
from linetools.abund import ions as ltai
from pyigm import utils as pu
ilist = LineList('ISM')
if not isinstance(to_plot[0], AbsLine):
lines2plot = [] # Master list of lines to plot
for i, tp in enumerate(to_plot):
if isinstance(tp, AbsComponent):
comp = to_plot
else: # Pick components in system closest to z_cgm
thesecomps = pu.get_components(self, tp)
if len(thesecomps) == 0:
if add_missing_lines is True:
# Add components
if isinstance(tp, str):
tup = ltai.name_to_ion(tp)
else:
tup = tp
comp = AbsComponent(self.coord,
tup,
zcomp=self.z,
vlim=[-100., 100.] * u.km /
u.s)
comp.add_abslines_from_linelist()
if spec is not None:
for al in comp._abslines:
al.analy['spec'] = spec
else:
raise ValueError('spec must be provided if '
'requesting species without'
' existing components.')
else:
continue
else:
# Find component with redshift closest to systemic
compvels = np.array(
[np.median(tc.vlim.value) for tc in thesecomps])
comp = thesecomps[np.argmin(np.abs(compvels))]
### Get strongest transitions covered
wmins = []
wmaxs = []
for j, al in enumerate(comp._abslines):
# Load spectrum if not already loaded
if al.analy['spec'] is None:
try:
if spec is not None:
al.analy['spec'] = spec
else:
al.analy['spec'] = readspec(
al.analy['spec_file'])
except:
raise LookupError("spec must be defined or "
"analy['specfile'] must be "
"declared for AbsLines")
# Get wavelength limits to know where to look
wmins.append(al.analy['spec'].wvmin.value)
wmaxs.append(al.analy['spec'].wvmax.value)
wlims = (np.min(np.array(wmins)), np.max(
np.array(wmaxs))) * u.Angstrom
# ID the strong transitions
strong = ilist.strongest_transitions(tp,
wvlims=wlims /
(1. + comp.zcomp),
n_max=maxtrans)
if strong is None: # No lines covered in the spectra
warnings.warn(
'No lines for {} are covered by the spectra'
'provided.'.format(tp))
continue
# Grab the AbsLines from this AbsComponent and their names
complines = comp._abslines
complines = np.array(complines) # For the indexing
compnames = np.array([ll.name for ll in complines])
### Add the lines found to the master list
if isinstance(strong, dict): # Only one line covered
lines2plot.append(
complines[compnames == strong['name']][0])
else: # Multiple lines covered
for i, sn in enumerate(strong['name']):
# Handle case where relevant components are defined
if sn in compnames:
tokeep = [complines[compnames == sn][0]]
lines2plot.extend(tokeep)
# Now case where components were not attached to sys
elif add_missing_lines is True:
# Add line to the existing comp to preserve z, etc.
compcopy = comp.copy(
) #Copy to add dummy lines
# Set up observed wavelength range
obswave = strong['wrest'][i] * (1. +
compcopy.zcomp)
wvrange = [obswave - 0.1, obswave + 0.1
] * u.Angstrom
# Add this line to the component
compcopy.add_abslines_from_linelist(
wvlim=wvrange)
al = compcopy._abslines[-1]
# Set the spectrum
if spec is not None:
al.analy['spec'] = spec
else:
al.analy['spec'] = comp._abslines[0].analy[
'spec']
# Add the line
lines2plot.append(al)
else:
warnings.warn(
'{} covered by spectra but not in'
'components list'.format(sn))
else:
lines2plot = to_plot
# Deal with velocity limits
if pvlim is not None:
vlim = pvlim
else:
vlim = self.vlim
### Make the plot!
fig = ltap.stack_plot(lines2plot,
vlim=vlim,
return_fig=return_fig,
zref=self.z,
**kwargs)
fig.subplots_adjust(bottom=0.,
left=0.1,
right=0.95,
hspace=0.,
wspace=0.35)
return fig
