def test_complist_from_table_and_table_from_complist():
tab = Table()
tab['ion_name'] = ['HI', 'HI', 'CIV', 'SiII', 'OVI']
tab['z_comp'] = [0.05, 0.0999, 0.1, 0.1001, 0.6]
tab['RA'] = [100.0] * len(tab) * u.deg
tab['DEC'] = [-0.8] * len(tab) * u.deg
tab['vmin'] = [-50.] * len(tab) * u.km / u.s
tab['vmax'] = [100.] * len(tab) * u.km / u.s
tab['reliability'] = ['a', 'b', 'b', 'none', 'a']
complist = ltiu.complist_from_table(tab)
assert np.sum(complist[0].vlim == [-50., 100.] * u.km / u.s) == 2
tab2 = ltiu.table_from_complist(complist)
np.testing.assert_allclose(tab['z_comp'], tab2['z_comp'])
# test other columns
tab['logN'] = 13.7
tab['sig_logN'] = 0.1
tab['flag_logN'] = 1
complist = ltiu.complist_from_table(tab)
tab2 = ltiu.table_from_complist(complist)
np.testing.assert_allclose(tab['logN'], tab2['logN'])
comp = complist[0]
# comment now
tab['comment'] = [
'good', 'good', 'bad', 'bad',
'This is a longer comment with symbols &*^%$'
]
complist = ltiu.complist_from_table(tab)
tab2 = ltiu.table_from_complist(complist)
comp = complist[-1]
assert comp.comment == 'This is a longer comment with symbols &*^%$'
assert tab2['comment'][-1] == comp.comment
assert tab2['reliability'][-1] == comp.reliability
# other naming
tab['name'] = tab['ion_name']
complist = ltiu.complist_from_table(tab)
tab2 = ltiu.table_from_complist(complist)
comp = complist[-1]
assert comp.name == 'OVI'
# other attributes
tab['b'] = [10, 10, 20, 10, 60] * u.km / u.s
complist = ltiu.complist_from_table(tab)
tab2 = ltiu.table_from_complist(complist)
comp = complist[-1]
assert comp.attrib['b'] == 60 * u.km / u.s
# test errors
tab['sig_b'] = [1, 2, 3, 4, 5] * u.AA
with pytest.raises(IOError):
complist = ltiu.complist_from_table(tab) # bad units for sig_b
tab = Table()
tab['ion_name'] = ['HI', 'HI', 'CIV', 'SiII', 'OVI']
tab['z_comp'] = [0.05, 0.0999, 0.1, 0.1001, 0.6]
with pytest.raises(IOError):
complist = ltiu.complist_from_table(
tab) # not enough mandatory columns
def test_get_components_at_z():
tab = mk_comptable()
complist = ltiu.complist_from_table(tab)
z01_comps = ltiu.get_components_at_z(complist, 0.1, [-1000,1000]*u.km/u.s)
assert len(z01_comps) == 3
# check expected errors
with pytest.raises(IOError):
ltiu.get_components_at_z([1,2,3], 0.1, [-1000,1000]*u.km/u.s) # wrong complist
with pytest.raises(IOError):
ltiu.get_components_at_z(complist, 0.1, [-1000,1000, 1000]*u.km/u.s) # wrong vlims size
with pytest.raises(IOError):
ltiu.get_components_at_z(complist, 0.1, [-1000,1000]*u.km) # wrong vlims units
def test_complist_from_table_and_table_from_complist():
tab = Table()
tab['ion_name'] = ['HI', 'HI', 'CIV', 'SiII', 'OVI']
tab['z_comp'] = [0.05, 0.0999, 0.1, 0.1001, 0.6]
tab['RA'] = [100.0]*len(tab) * u.deg
tab['DEC'] = [-0.8]*len(tab) * u.deg
tab['vmin'] = [-50.] *len(tab) * u.km / u.s
tab['vmax'] = [100.] *len(tab) * u.km / u.s
complist = ltiu.complist_from_table(tab)
assert np.sum(complist[0].vlim == [ -50., 100.] * u.km / u.s) == 2
tab2 = ltiu.table_from_complist(complist)
np.testing.assert_allclose(tab['z_comp'], tab2['z_comp'])
# test other columns
tab['logN'] = 13.7
tab['sig_logN'] = 0.1
tab['flag_logN'] = 1
complist = ltiu.complist_from_table(tab)
tab2 = ltiu.table_from_complist(complist)
np.testing.assert_allclose(tab['logN'], tab2['logN'])
comp = complist[0]
# comment now
tab['comment'] = ['good', 'good', 'bad', 'bad', 'This is a longer comment with symbols &*^%$']
complist = ltiu.complist_from_table(tab)
tab2 = ltiu.table_from_complist(complist)
comp = complist[-1]
assert comp.comment == 'This is a longer comment with symbols &*^%$'
assert tab2['comment'][-1] == comp.comment
# other naming
tab['name'] = tab['ion_name']
complist = ltiu.complist_from_table(tab)
tab2 = ltiu.table_from_complist(complist)
comp = complist[-1]
assert comp.name == 'OVI'
# other attributes
tab['b'] = [10, 10, 20, 10, 60] * u.km / u.s
complist = ltiu.complist_from_table(tab)
tab2 = ltiu.table_from_complist(complist)
comp = complist[-1]
assert comp.attrib['b'] == 60*u.km/u.s
# test errors
tab['sig_b'] = [1,2,3,4,5] * u.AA
with pytest.raises(IOError):
complist = ltiu.complist_from_table(tab) # bad units for sig_b
tab = Table()
tab['ion_name'] = ['HI', 'HI', 'CIV', 'SiII', 'OVI']
tab['z_comp'] = [0.05, 0.0999, 0.1, 0.1001, 0.6]
with pytest.raises(IOError):
complist = ltiu.complist_from_table(tab) # not enough mandatory columns
def test_get_components_at_z():
tab = mk_comptable()
complist = ltiu.complist_from_table(tab)
z01_comps = ltiu.get_components_at_z(complist, 0.1,
[-1000, 1000] * u.km / u.s)
assert len(z01_comps) == 3
# check expected errors
with pytest.raises(IOError):
ltiu.get_components_at_z([1, 2, 3], 0.1,
[-1000, 1000] * u.km / u.s) # wrong complist
with pytest.raises(IOError):
ltiu.get_components_at_z(complist, 0.1, [-1000, 1000, 1000] * u.km /
u.s) # wrong vlims size
with pytest.raises(IOError):
ltiu.get_components_at_z(complist, 0.1,
[-1000, 1000] * u.km) # wrong vlims units
def test_complist_from_table_and_table_from_complist():
# Setup
tab = Table()
tab['ion_name'] = ['HI', 'HI', 'CIV', 'SiII', 'OVI']
tab['Z'] = [1, 1, 4, 14, 8]
tab['ion'] = [1, 1, 4, 2, 6]
tab['z_comp'] = [0.05, 0.0999, 0.1, 0.1001, 0.6]
tab['RA'] = [100.0] * len(tab) * u.deg
tab['DEC'] = [-0.8] * len(tab) * u.deg
tab['vmin'] = [-50.] * len(tab) * u.km / u.s
tab['vmax'] = [100.] * len(tab) * u.km / u.s
tab['Ej'] = [0.] * len(tab) / u.cm
tab['reliability'] = ['a', 'b', 'b', 'none', 'a']
complist = ltiu.complist_from_table(tab)
tmp = [-50., 100.] * u.km / u.s
assert np.all(np.isclose(complist[0].vlim.value, tmp.value))
tab2 = ltiu.table_from_complist(complist)
np.testing.assert_allclose(tab['z_comp'], tab2['z_comp'])
# Without units
tab = Table()
tab['ion_name'] = ['HI', 'HI', 'CIV', 'SiII', 'OVI']
tab['Z'] = [1, 1, 4, 14, 8]
tab['ion'] = [1, 1, 4, 2, 6]
tab['z_comp'] = [0.05, 0.0999, 0.1, 0.1001, 0.6]
tab['RA'] = [100.0] * len(tab) * u.deg
tab['DEC'] = [-0.8] * len(tab) * u.deg
tab['vmin'] = [-50.] * len(tab)
tab['vmax'] = [100.] * len(tab)
tab['Ej'] = [0.] * len(tab)
tab['reliability'] = ['a', 'b', 'b', 'none', 'a']
complist = ltiu.complist_from_table(tab)
assert np.all(np.isclose(complist[0].vlim.value, tmp.value))
assert complist[0].Ej.unit == 1 / u.cm
# test other columns
tab['logN'] = 13.7
tab['sig_logN'] = 0.1 * np.ones((len(tab), 2))
tab['flag_logN'] = 1
complist = ltiu.complist_from_table(tab)
tab2 = ltiu.table_from_complist(complist)
np.testing.assert_allclose(tab['logN'], tab2['logN'])
# NHI obj
SiIIcomp1, _ = mk_comp('SiII',
vlim=[-300., 50.] * u.km / u.s,
add_spec=True)
SiIIIcomp1, _ = mk_comp('SiIII',
vlim=[-300., 50.] * u.km / u.s,
add_spec=True)
NHI_obj = DummyObj()
NHI_obj.NHI = 21.0
NHI_obj.sig_NHI = np.array([0.1, 0.1])
NHI_obj.flag_NHI = 1
tab2b = ltiu.table_from_complist([SiIIcomp1, SiIIIcomp1], NHI_obj=NHI_obj)
assert tab2b['Z'][-1] == 1
assert tab2b['ion_name'][-1] == 'HI'
# comment now
tab['comment'] = [
'good', 'good', 'bad', 'bad',
'This is a longer comment with symbols &*^%$'
]
complist = ltiu.complist_from_table(tab)
tab2 = ltiu.table_from_complist(complist)
comp = complist[-1]
assert comp.comment == 'This is a longer comment with symbols &*^%$'
assert tab2['comment'][-1] == comp.comment
assert tab2['reliability'][-1] == comp.reliability
# other naming
tab['name'] = tab['ion_name']
complist = ltiu.complist_from_table(tab)
tab2 = ltiu.table_from_complist(complist)
comp = complist[-1]
assert comp.name == 'OVI'
# other attributes
tab['b'] = [10, 10, 20, 10, 60] * u.km / u.s
complist = ltiu.complist_from_table(tab)
tab2 = ltiu.table_from_complist(complist)
comp = complist[-1]
assert comp.attrib['b'] == 60 * u.km / u.s
# test errors
#tab['sig_b'] = [1,2,3,4,5] * u.AA
#with pytest.raises(IOError):
# complist = ltiu.complist_from_table(tab) # bad units for sig_b
tab = Table()
tab['ion_name'] = ['HI', 'HI', 'CIV', 'SiII', 'OVI']
tab['z_comp'] = [0.05, 0.0999, 0.1, 0.1001, 0.6]
with pytest.raises(IOError):
complist = ltiu.complist_from_table(
tab) # not enough mandatory columns
def test_complist_from_table_and_table_from_complist():
# Setup
tab = Table()
tab['ion_name'] = ['HI', 'HI', 'CIV', 'SiII', 'OVI']
tab['Z'] = [1,1,4,14,8]
tab['ion'] = [1,1,4,2,6]
tab['z_comp'] = [0.05, 0.0999, 0.1, 0.1001, 0.6]
tab['RA'] = [100.0]*len(tab) * u.deg
tab['DEC'] = [-0.8]*len(tab) * u.deg
tab['vmin'] = [-50.] *len(tab) * u.km / u.s
tab['vmax'] = [100.] *len(tab) * u.km / u.s
tab['Ej'] = [0.] *len(tab) / u.cm
tab['reliability'] = ['a', 'b', 'b', 'none', 'a']
complist = ltiu.complist_from_table(tab)
tmp = [-50.,100.]*u.km/u.s
assert np.all(np.isclose(complist[0].vlim.value, tmp.value))
tab2 = ltiu.table_from_complist(complist)
np.testing.assert_allclose(tab['z_comp'], tab2['z_comp'])
# Without units
tab = Table()
tab['ion_name'] = ['HI', 'HI', 'CIV', 'SiII', 'OVI']
tab['Z'] = [1,1,4,14,8]
tab['ion'] = [1,1,4,2,6]
tab['z_comp'] = [0.05, 0.0999, 0.1, 0.1001, 0.6]
tab['RA'] = [100.0]*len(tab) * u.deg
tab['DEC'] = [-0.8]*len(tab) * u.deg
tab['vmin'] = [-50.] *len(tab)
tab['vmax'] = [100.] *len(tab)
tab['Ej'] = [0.] *len(tab)
tab['reliability'] = ['a', 'b', 'b', 'none', 'a']
complist = ltiu.complist_from_table(tab)
assert np.all(np.isclose(complist[0].vlim.value, tmp.value))
assert complist[0].Ej.unit == 1/u.cm
# test other columns
tab['logN'] = 13.7
tab['sig_logN'] = 0.1*np.ones((len(tab),2))
tab['flag_logN'] = 1
complist = ltiu.complist_from_table(tab)
tab2 = ltiu.table_from_complist(complist)
np.testing.assert_allclose(tab['logN'], tab2['logN'])
# NHI obj
SiIIcomp1,_ = mk_comp('SiII',vlim=[-300.,50.]*u.km/u.s, add_spec=True)
SiIIIcomp1,_ = mk_comp('SiIII',vlim=[-300.,50.]*u.km/u.s, add_spec=True)
NHI_obj = DummyObj()
NHI_obj.NHI = 21.0
NHI_obj.sig_NHI = np.array([0.1,0.1])
NHI_obj.flag_NHI = 1
tab2b = ltiu.table_from_complist([SiIIcomp1, SiIIIcomp1], NHI_obj=NHI_obj)
assert tab2b['Z'][-1] == 1
assert tab2b['ion_name'][-1] == 'HI'
# comment now
tab['comment'] = ['good', 'good', 'bad', 'bad', 'This is a longer comment with symbols &*^%$']
complist = ltiu.complist_from_table(tab)
tab2 = ltiu.table_from_complist(complist)
comp = complist[-1]
assert comp.comment == 'This is a longer comment with symbols &*^%$'
assert tab2['comment'][-1] == comp.comment
assert tab2['reliability'][-1] == comp.reliability
# other naming
tab['name'] = tab['ion_name']
complist = ltiu.complist_from_table(tab)
tab2 = ltiu.table_from_complist(complist)
comp = complist[-1]
assert comp.name == 'OVI'
# other attributes
tab['b'] = [10, 10, 20, 10, 60] * u.km / u.s
complist = ltiu.complist_from_table(tab)
tab2 = ltiu.table_from_complist(complist)
comp = complist[-1]
assert comp.attrib['b'] == 60*u.km/u.s
# test errors
#tab['sig_b'] = [1,2,3,4,5] * u.AA
#with pytest.raises(IOError):
# complist = ltiu.complist_from_table(tab) # bad units for sig_b
tab = Table()
tab['ion_name'] = ['HI', 'HI', 'CIV', 'SiII', 'OVI']
tab['z_comp'] = [0.05, 0.0999, 0.1, 0.1001, 0.6]
with pytest.raises(IOError):
complist = ltiu.complist_from_table(tab) # not enough mandatory columns