def test_cgmsurvey_from_fields_sightlines():
# Instantiate fields and add galaxies
field1 = ('PG1407+265', 212.349634 * u.deg, 26.3058650 * u.deg)
fieldobj1 = IgmGalaxyField((field1[1], field1[2]),
name=field1[0],
verbose=False)
field2 = ('PG1148+549', 177.83526042 * u.deg, 54.625855 * u.deg)
fieldobj2 = IgmGalaxyField((field2[1], field2[2]),
name=field2[0],
verbose=False)
f1ras = [212.33310891, 212.329875] * u.deg
f1decs = [26.3722716934, 26.3084391667] * u.deg
f1zs = [0.974413514137, 0.22016787529]
f1gals = Table([f1ras, f1decs, f1zs], names=['RA', 'DEC', 'Z'])
f2ras = [177.835229336, 178.536958333] * u.deg
f2decs = [54.625851084, 54.6176108333] * u.deg
f2zs = [0.0595485754311, 0.00385531364009]
f2gals = Table([f2ras, f2decs, f2zs], names=['RA', 'DEC', 'Z'])
fieldobj1.galaxies = f1gals
fieldobj2.galaxies = f2gals
fields = [fieldobj1, fieldobj2]
# Instantiate sightlines
sl1coord = SkyCoord(field1[1], field1[2], unit='deg')
sl2coord = SkyCoord(field2[1], field2[2], unit='deg')
comp11 = AbsComponent(sl1coord, (8, 6), 0.9743, [-200, 200] * u.km / u.s)
comp12 = AbsComponent(sl1coord, (1, 1), 0.9743, [-200, 200] * u.km / u.s)
al11 = AbsLine('OVI 1031')
al11.attrib['coord'] = sl1coord
al11.analy['spec'] = 'files/J0042-1037.358_9.fits.gz'
al12 = AbsLine('HI 1215')
al12.attrib['coord'] = sl1coord
al12.analy['spec'] = 'files/J0042-1037.358_9.fits.gz'
comp11.add_absline(al11, chk_sep=False, chk_vel=False)
comp12.add_absline(al12, chk_sep=False, chk_vel=False)
sys1 = IGMSystem.from_components([comp11, comp12])
sl1 = IGMSightline.from_systems([sys1])
comp21 = AbsComponent(sl2coord, (6, 4), 0.0037, [-200, 200] * u.km / u.s)
comp22 = AbsComponent(sl2coord, (1, 1), 0.0037, [-200, 200] * u.km / u.s)
al21 = AbsLine('CIV 1548')
al21.attrib['coord'] = sl1coord
al21.analy['spec'] = 'files/J0042-1037.358_9.fits.gz'
al22 = AbsLine('HI 1215')
al22.attrib['coord'] = sl1coord
al22.analy['spec'] = 'files/J0042-1037.358_9.fits.gz'
comp21.add_absline(al21, chk_sep=False, chk_vel=False)
comp22.add_absline(al22, chk_sep=False, chk_vel=False)
sys2 = IGMSystem.from_components([comp21, comp22])
sl2 = IGMSightline.from_systems([sys2])
sightlines = [sl1, sl2]
# Run function
csurvey = cgmsurvey_from_sightlines_fields(fields, sightlines)
assert isinstance(csurvey, CGMAbsSurvey)
def load_coolgas(self):
""" Load data on cool gas (CII, CIV, SiII, SiIII)
Richter+17
"""
llist = LineList('ISM')
# Ricther+17
print('Loading Richter+17 for CII, CIV, SiII, SiIII')
r17_a1_file = resource_filename('pyigm',
'/data/CGM/Galaxy/richter17_A1.fits')
r17_a1 = Table.read(r17_a1_file)
r17_a2_file = resource_filename('pyigm',
'/data/CGM/Galaxy/richter17_A2.fits')
r17_a2 = Table.read(r17_a2_file)
# Coords
coords = SkyCoord(ra=r17_a1['_RAJ2000'],
dec=r17_a1['_DEJ2000'],
unit='deg')
gc = coords.transform_to('galactic')
ra = np.zeros((len(r17_a2)))
dec = np.zeros((len(r17_a2)))
# Loop on Sightlines
for kk, row in enumerate(r17_a1):
if self.debug and (kk == 5):
break
a2_idx = np.where(r17_a2['Name'] == row['Name'])[0]
if len(a2_idx) == 0:
continue
ra[a2_idx] = row['_RAJ2000']
dec[a2_idx] = row['_DEJ2000']
# Generate the components
icoord = gc[kk]
alines = []
for jj, idx in enumerate(a2_idx):
# Transition
trans = '{:s} {:d}'.format(r17_a2['Ion'][idx].strip(),
int(r17_a2['lambda0'][idx]))
try:
aline = AbsLine(trans, linelist=llist)
except ValueError:
pdb.set_trace()
aline.attrib['coord'] = icoord
# Skip EW=0 lines
if r17_a2['e_W'][idx] == 0:
continue
# Velocity
z = 0.
aline.setz(z)
vlim = np.array([r17_a2['vmin'][idx], r17_a2['vmax'][idx]
]) * u.km / u.s
aline.limits.set(vlim) # These are v_LSR
# EW
aline.attrib['flag_EW'] = 1
aline.attrib['EW'] = r17_a2['W'][idx] / 1e3 * u.AA
aline.attrib['sig_EW'] = r17_a2['e_W'][idx] / 1e3 * u.AA
# Column
if np.isnan(
r17_a2['logN']
[idx]): # Odd that some lines had an error but no value
aline.attrib['flag_N'] = 0
elif r17_a2['l_logN'][idx] == '>':
aline.attrib['flag_N'] = 2
aline.attrib['sig_logN'] = 99.99
else:
aline.attrib['flag_N'] = 1
aline.attrib['sig_logN'] = r17_a2['e_logN'][idx]
aline.attrib['logN'] = r17_a2['logN'][idx]
# Fill linear
_, _ = linear_clm(aline.attrib)
alines.append(aline)
# Generate components from abslines
comps = ltiu.build_components_from_abslines(alines,
chk_sep=False,
chk_vel=False)
# Limits
vmin = np.min([icomp.limits.vmin.value for icomp in comps])
vmax = np.max([icomp.limits.vmax.value for icomp in comps])
# Instantiate
s_kwargs = dict(name=row['Name'] + '_z0')
c_kwargs = dict(chk_sep=False, chk_z=False)
abssys = IGMSystem.from_components(comps,
vlim=[vmin, vmax] * u.km / u.s,
s_kwargs=s_kwargs,
c_kwargs=c_kwargs)
# CGM Abs
rho, ang_sep = calc_Galactic_rho(abssys.coord)
cgmabs = CGMAbsSys(self.galaxy,
abssys,
rho=rho,
ang_sep=ang_sep,
cosmo=self.cosmo)
# Add to cgm_abs
self.abs.cgm_abs.append(cgmabs)
# Finish
r17_a2['RA'] = ra
r17_a2['DEC'] = dec
self.richter17 = r17_a2
# Reference
if len(self.refs) > 0:
self.refs += ','
self.refs += 'Richter+17'
