def test_dz_from_dv():
dz = ltu.dz_from_dv(1000. * u.km / u.s, 2.)
np.testing.assert_allclose(dz, 0.0100236684175417)
dz1 = ltu.dz_from_dv([1000., 1000., 1000.] * u.km / u.s,
np.array([2., 2., 2.]))
dz2 = ltu.dz_from_dv([1000., 1000., 1000.] * u.km / u.s, [2., 2., 2.])
np.testing.assert_allclose(dz1, [0.0100236684175417] * 3)
np.testing.assert_allclose(dz2, [0.0100236684175417] * 3)
# non-relativistic
dz = ltu.dz_from_dv(1000. * u.km / u.s, 2., rel=False)
np.testing.assert_allclose(dz, 0.010006922855944561)
# test expected errors
with pytest.raises(IOError):
ltu.dz_from_dv('dv_not_a_quantity', 2.)
with pytest.raises(IOError):
ltu.dz_from_dv(1000. * u.km / u.s, 'zref_not_a_float_nor_array')
with pytest.raises(IOError):
ltu.dz_from_dv([1000., 1000., 1000.] * u.km / u.s,
np.array([2., 2.])) # wrong shape for zref
with pytest.raises(IOError):
ltu.dz_from_dv([1000., 1000., 1000.] * u.km, 1.) # wrong dv units
def give_dz(dv, zref, **kwargs):
"""Wrapper for convinience"""
print(
"This function is now in linetools.utils.dz_from_dv(), please avoid using this one."
)
return ltu.dz_from_dv(dv, zref, **kwargs)
def test_dz_from_dv():
dz = ltu.dz_from_dv(1000. * u.km / u.s, 2.)
np.testing.assert_allclose(dz, 0.0100236684175417)
dz1 = ltu.dz_from_dv([1000., 1000., 1000.] * u.km / u.s, np.array([2., 2., 2.]))
dz2 = ltu.dz_from_dv([1000., 1000., 1000.] * u.km / u.s, [2., 2., 2.])
np.testing.assert_allclose(dz1, [0.0100236684175417] * 3)
np.testing.assert_allclose(dz2, [0.0100236684175417] * 3)
# non-relativistic
dz = ltu.dz_from_dv(1000. * u.km / u.s, 2., rel=False)
np.testing.assert_allclose(dz, 0.010006922855944561)
# test expected errors
with pytest.raises(IOError):
ltu.dz_from_dv('dv_not_a_quantity', 2.)
with pytest.raises(IOError):
ltu.dz_from_dv(1000. * u.km / u.s, 'zref_not_a_float_nor_array')
with pytest.raises(IOError):
ltu.dz_from_dv([1000., 1000., 1000.] * u.km / u.s, np.array([2., 2.])) # wrong shape for zref
with pytest.raises(IOError):
ltu.dz_from_dv([1000., 1000., 1000.] * u.km, 1.) # wrong dv units
def read_joebvp_to_components(filename,
coord,
llist=None,
specfile=None,
chk_vel=False):
""" Generate a list of AbsComponent objects from a JoeB VP output file
Parameters
----------
filename : str
joeB VP filename
coord : SkyCoord
QSO sightline
llist : LineList, optional
Used to construct AbsLine objects
specfile : str, optional
chk_vel : bool, optional
Demand that the velocities of a given ion all be the same
Returns
-------
comps : list
list of AbsComponent objects
"""
# init
if llist is None:
llist = LineList('ISM')
comps = []
# Read
vp_data = Table.read(filename, format='ascii')
# Subset by zsys + trans
lbls = []
for izsys, itrans in zip(vp_data['zsys'], vp_data['trans']):
lbls.append('{:.6f}_{:s}'.format(izsys, itrans))
lbls = np.array(lbls)
ulbls = np.unique(lbls)
# Subset by nflag; Build components
for lbl in ulbls:
mt_lines = np.where(lbls == lbl)[0]
if chk_vel:
if len(np.unique(vp_data['vel'][mt_lines])) != 1:
pdb.set_trace()
z_fit = ltu.z_from_dv(vp_data['vel'][mt_lines[0]] * u.km / u.s,
vp_data['zsys'][mt_lines[0]])
# Loop on abs lines
alines = []
for idx in mt_lines:
zlim = [
vp_data['zsys'][idx] + vp_data[vkey][idx] *
(1 + vp_data['zsys'][idx]) / ckms
for vkey in ['vlim1', 'vlim2']
]
absline = AbsLine(vp_data['restwave'][idx] * u.AA,
z=z_fit,
zlim=zlim,
linelist=llist)
# Add measurements [JB -- Want to capture anything else??]
absline.attrib['coord'] = coord
absline.attrib['flag_N'] = 1
absline.attrib['logN'] = vp_data['col'][idx]
absline.attrib['sig_logN'] = vp_data['sigcol'][idx]
absline.attrib['b'] = vp_data['bval'][idx]
absline.attrib['sig_b'] = vp_data['sigbval'][idx]
absline.attrib['z'] = z_fit
absline.attrib['sig_z'] = ltu.dz_from_dv(
vp_data['sigvel'][idx] * u.km / u.s, vp_data['z_comp'][idx])
if specfile is None:
absline.attrib['specfile'] = vp_data['specfile'][idx]
else:
absline.attrib['specfile'] = specfile
# Fill N, sig_N
_, _, = linear_clm(absline.attrib)
alines.append(absline)
# AbsComponent
stars = '*' * alines[0].ion_name.count('*')
if 'comment' in vp_data.keys():
comment = vp_data['comment'][mt_lines[0]]
else:
comment = ''
if 'rely' in vp_data.keys():
reliability = vp_data['rely'][mt_lines[0]]
else:
reliability = 'none'
abscomp = AbsComponent.from_abslines(alines,
stars=stars,
comment=comment,
reliability=reliability)
# Add measurements [JB -- Want to capture anything else??]
abscomp.attrib = alines[0].attrib.copy()
# Remove undesired keys
for key in ['EW', 'sig_EW', 'flag_EW', 'N', 'sig_N']:
abscomp.attrib.pop(key)
# And more required
for key in ['flag_N', 'logN', 'sig_logN']:
setattr(abscomp, key, abscomp.attrib[key])
# Errors must be in first line!
assert abscomp.sig_logN > 0.
comps.append(abscomp)
# Finish
return comps
def give_dz(dv, zref, **kwargs):
"""Wrapper for convinience"""
print("This function is now in linetools.utils.dz_from_dv(), please avoid using this one.")
return ltu.dz_from_dv(dv, zref, **kwargs)