def load_hotgas(self):
""" Load data on hot gas (e.g. OVII, OVIII)
Fang+15
"""
from linetools.lists.linelist import LineList
from linetools.analysis.absline import linear_clm
llist = LineList('EUV',use_ISM_table=False)
ovii = AbsLine('OVII 21', linelist=llist)
# Fang+15 Table 1 [OVII]
self.fang15 = Table.read(pyigm.__path__[0]+'/data/CGM/Galaxy/fang15_table1.dat', format='cds')
print('Loading Fang+15 for OVII')
# Reference
if len(self.refs) > 0:
self.refs += ','
self.refs += 'Fang+15'
# Generate the systems
# # (should check to see if low-ion ones exist already)
for row in self.fang15:
# Coordinates
gc = SkyCoord(l=row['GLON']*u.degree, b=row['GLAT']*u.degree, frame='galactic')
# Limits
# OVII line
aline = ovii.copy()
aline.attrib['coord'] = gc
z = row['Vel']/c_kms
try:
aline.setz(z)
except IOError:
z = 0.
vlim = np.array([-300,300]) * u.km/u.s
aline.attrib['flag_EW'] = 3
aline.attrib['flag_N'] = 0 # Might be able to set an upper limit
aline.attrib['EW'] = row['EW1'] / 1e3 * u.AA
aline.attrib['sig_EW'] = 99. * u.AA
else:
aline.attrib['b'] = row['b'] * u.km / u.s
aline.attrib['flag_EW'] = 1
aline.attrib['EW'] = row['EW1'] / 1e3 * u.AA
aline.attrib['sig_EW'] = row['e_EW1'] / 1e3 * u.AA
vlim = np.array([-1,1]) * (2 * row['b'] + 2 * row['E_b']) * u.km/u.s
# N_OVII
aline.attrib['flag_N'] = 1
aline.attrib['logN'] = row['logNO']
aline.attrib['sig_logN'] = np.array([row['e_logNO'], row['E_logNO']])
# Fill linear
_,_ = linear_clm(aline.attrib)
# OVII
aline.limits.set(vlim)
# Generate component and add
comp = AbsComponent.from_abslines([aline])
comp.synthesize_colm()
# Instantiate
abssys = IGMSystem(gc, z, vlim, name=row['Name']+'_z0', zem=row['z'])
abssys.add_component(comp, chk_sep=False)
# CGM Abs
cgmabs = CGMAbsSys(self.galaxy, abssys, Galactic=True)
# Add to cgm_abs
self.abs.cgm_abs.append(cgmabs)
scoord = self.abs.scoord # Sightline coordiantes
# Savage+03 Table 2 [OVI] -- Thick disk/halo only??
print('Loading Savage+03 for OVI')
self.savage03 = Table.read(pyigm.__path__[0] + '/data/CGM/Galaxy/savage03_table2.fits')
# Reference
if len(self.refs) > 0:
self.refs += ','
self.refs += 'Savage+03'
# Generate the systems
# # (should check to see if low-ion ones exist already)
for row in self.savage03:
# Coordinates
coord = SkyCoord(ra=row['_RA']*u.deg, dec=row['_DE']*u.deg, frame='fk5')
gc = coord.transform_to('galactic')
# Build the component
vlim = np.array([row['V-'],row['V_']])*u.km/u.s
comp = AbsComponent(gc, (8,6), 0., vlim)
# Add attributes
if row['b'] > 0.:
comp.attrib['vcen'] = row['__v_obs']*u.km/u.s
comp.attrib['sig_vcen'] = row['e__v_obs']*u.km/u.s
comp.attrib['b'] = row['b']*u.km/u.s
comp.attrib['sig_b'] = row['e_b']*u.km/u.s
# Column
comp.flag_N = 1
comp.logN = row['logN_OVI_']
comp.sig_logN = np.sqrt(row['e_sc']**2 + row['e_sys']**2)
else: # Upper limit
comp.flag_N = 3
comp.logN = row['logN_OVI_']
comp.sig_logN = 99.
# Check for existing system
minsep = np.min(comp.coord.separation(scoord).to('arcsec'))
if minsep < 30*u.arcsec:
idx = np.argmin(comp.coord.separation(scoord).to('arcsec'))
self.abs.cgm_abs[idx].igm_sys.add_component(comp, chk_sep=False, debug=True)
else: # New
if row['RV'] > 0:
zem = row['RV']/c_kms
else:
zem = row['z']
abssys = IGMSystem(gc, comp.zcomp, vlim, name=row['Name']+'_z0', zem=zem)
abssys.add_component(comp, chk_sep=False, debug=True)
# CGM Abs
cgmabs = CGMAbsSys(self.galaxy, abssys, Galactic=True)
# Add to cgm_abs
self.abs.cgm_abs.append(cgmabs)
def cgm_from_galaxy_igmsystems(galaxy,
igmsystems,
rho_max=300 * u.kpc,
dv_max=400 * u.km / u.s,
cosmo=None,
dummysys=False,
dummyspec=None,
verbose=True,
**kwargs):
""" Generate a list of CGMAbsSys objects given an input galaxy and a list of IGMSystems
Parameters
----------
galaxy : Galaxy
igmsystems : list
list of IGMSystems
rho_max : Quantity
Maximum projected separation from sightline to galaxy
dv_max
Maximum velocity offset between system and galaxy
dummysys: bool, optional
If True, instantiate CGMAbsSys even if no match is found in igmsystems
dummyspec : XSpectrum1D, optional
Spectrum object to attach to dummy AbsLine/AbsComponent objects when
adding IGMSystems if dummysys is True.
Returns
-------
cgm_list : list
list of CGM objects generated
"""
from pyigm.cgm.cgm import CGMAbsSys
# Cosmology
if cosmo is None:
cosmo = cosmology.Planck15
if dummysys is True:
if dummyspec is None:
dummyspec = igmsystems[0]._components[0]._abslines[0].analy['spec']
dummycoords = igmsystems[0].coord
# R -- speed things up
rho, angles = calc_cgm_rho(galaxy, igmsystems, cosmo, **kwargs)
if len(igmsystems) == 1: # Kludge
rho = u.Quantity([rho])
angles = u.Quantity([angles])
# dv
igm_z = np.array([igmsystem.zabs for igmsystem in igmsystems])
dv = ltu.dv_from_z(igm_z, galaxy.z)
# Rules
match = np.where((rho < rho_max) & (np.abs(dv) < dv_max))[0]
### If none, see if some system has a component that's actually within dv_max
if (len(match) == 0) & (rho[0] < rho_max):
zcomps = []
sysidxs = []
for i, csys in enumerate(igmsystems):
thesezs = [comp.zcomp for comp in csys._components]
sysidxs.extend([i] * len(thesezs))
zcomps.extend(thesezs)
zcomps = np.array(zcomps)
sysidxs = np.array(sysidxs)
dv_comps = ltu.dv_from_z(zcomps, galaxy.z)
match = np.unique(sysidxs[np.where(np.abs(dv_comps) < dv_max)[0]])
if len(match) == 0:
if dummysys is False:
print(
"No IGMSystem paired to this galaxy. CGM object not created.")
return []
else:
if verbose:
print("No IGMSystem match found. Attaching dummy IGMSystem.")
dummysystem = IGMSystem(dummycoords, galaxy.z, vlim=None)
dummycomp = AbsComponent(dummycoords, (1, 1), galaxy.z,
[-100., 100.] * u.km / u.s)
dummycomp.flag_N = 3
dummyline = AbsLine(
'HI 1215',
**kwargs) # Need an actual transition for comp check
dummyline.analy['spec'] = dummyspec
dummyline.attrib['coord'] = dummycoords
dummycomp.add_absline(dummyline, chk_vel=False, chk_sep=False)
dummysystem.add_component(dummycomp, chk_vel=False, chk_sep=False)
cgm = CGMAbsSys(galaxy, dummysystem, cosmo=cosmo, **kwargs)
cgm_list = [cgm]
else:
# Loop to generate
cgm_list = []
for imatch in match:
# Instantiate new IGMSystem
# Otherwise, updates to the IGMSystem cross-pollinate other CGMs
sysmatch = igmsystems[imatch]
newisys = sysmatch.copy()
# Handle z limits
zlim = ltu.z_from_dv((-dv_max.value, dv_max.value) * u.km / u.s,
galaxy.z)
newlims = zLimits(galaxy.z, zlim.tolist())
newisys.limits = newlims
# Allow for components extending beyond dv_max
newisys.update_vlim()
newisys.update_component_vel()
# Finish
cgm = CGMAbsSys(galaxy,
newisys,
cosmo=cosmo,
rho=rho[imatch],
ang_sep=angles[imatch],
**kwargs)
cgm_list.append(cgm)
# Return
return cgm_list
def load_hotgas(self):
""" Load data on hot gas (e.g. OVII, OVIII)
Fang+15
"""
# Init
llist = LineList('EUV')
ovii = AbsLine('OVII 21', linelist=llist)
scoord = self.abs.scoord # Sightline coordiantes
# Fang+15 Table 1 [OVII]
fang15_file = resource_filename('pyigm',
'/data/CGM/Galaxy/fang15_table1.dat')
self.fang15 = Table.read(fang15_file, format='cds')
print('Loading Fang+15 for OVII')
# Reference
if len(self.refs) > 0:
self.refs += ','
self.refs += 'Fang+15'
# Generate the systems
# # (should check to see if low-ion ones exist already)
for row in self.fang15:
# Coordinates
gc = SkyCoord(l=row['GLON'] * u.degree,
b=row['GLAT'] * u.degree,
frame='galactic')
# Limits
# OVII line
aline = ovii.copy()
aline.attrib['coord'] = gc
z = row['Vel'] / c_kms
try:
aline.setz(z)
except IOError:
z = 0.
vlim = np.array([-300, 300]) * u.km / u.s
aline.attrib['flag_EW'] = 3
aline.attrib['EW'] = row['EW1'] / 1e3 * u.AA
aline.attrib['sig_EW'] = 99. * u.AA
#
aline.attrib[
'flag_N'] = 0 # Might be able to set an upper limit
else:
aline.attrib['b'] = row['b'] * u.km / u.s
aline.attrib['flag_EW'] = 1
aline.attrib['EW'] = row['EW1'] / 1e3 * u.AA
aline.attrib['sig_EW'] = row['e_EW1'] / 1e3 * u.AA
vlim = np.array(
[-1, 1]) * (2 * row['b'] + 2 * row['E_b']) * u.km / u.s
# N_OVII
aline.attrib['flag_N'] = 1
aline.attrib['logN'] = row['logNO']
aline.attrib['sig_logN'] = np.array(
[row['e_logNO'], row['E_logNO']])
# Fill linear
_, _ = linear_clm(aline.attrib)
# OVII
aline.limits.set(vlim)
# Generate component and add
comp = AbsComponent.from_abslines([aline])
if aline.attrib['flag_N'] == 0: # Hack to merge later
comp.attrib['sig_logN'] = np.array([0., 0.])
else:
pass
# Check for existing system
minsep = np.min(comp.coord.separation(scoord).to('arcsec'))
if minsep < 30 * u.arcsec: # Add component to existing system
idx = np.argmin(comp.coord.separation(scoord).to('arcsec'))
if self.verbose:
print("Adding OVII system to {}".format(
self.abs.cgm_abs[idx].igm_sys))
self.abs.cgm_abs[idx].igm_sys.add_component(comp,
chk_sep=False,
debug=True)
else: # Instantiate
abssys = IGMSystem(gc,
z,
vlim,
name=row['Name'] + '_z0',
zem=row['z'])
abssys.add_component(comp, chk_sep=False)
# 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)
scoord = self.abs.scoord # Sightline coordiantes
# Savage+03 Table 2 [OVI] -- Thick disk/halo only??
print('Loading Savage+03 for OVI')
savage03_file = resource_filename(
'pyigm', '/data/CGM/Galaxy/savage03_table2.fits')
self.savage03 = Table.read(savage03_file)
# Reference
if len(self.refs) > 0:
self.refs += ','
self.refs += 'Savage+03'
# Generate the systems
# # (should check to see if low-ion ones exist already)
for row in self.savage03:
# Coordinates
coord = SkyCoord(ra=row['_RA'] * u.deg,
dec=row['_DE'] * u.deg,
frame='icrs')
gc = coord.transform_to('galactic')
# Build the component
vlim = np.array([row['V-'], row['V_']]) * u.km / u.s
comp = AbsComponent(gc, (8, 6), 0., vlim)
# Add attributes
if row['b'] > 0.:
comp.attrib['vcen'] = row['__v_obs'] * u.km / u.s
comp.attrib['sig_vcen'] = row['e__v_obs'] * u.km / u.s
comp.attrib['b'] = row['b'] * u.km / u.s
comp.attrib['sig_b'] = row['e_b'] * u.km / u.s
# Column
comp.attrib['flag_N'] = 1
comp.attrib['logN'] = row['logN_OVI_']
comp.attrib['sig_logN'] = np.array(
[np.sqrt(row['e_sc']**2 + row['e_sys']**2)] * 2)
else: # Upper limit
comp.attrib['flag_N'] = 3
comp.attrib['logN'] = row['logN_OVI_']
comp.attrib['sig_logN'] = np.array([99.] * 2)
# Set linear quantities
_, _ = linear_clm(comp.attrib)
# Check for existing system
minsep = np.min(comp.coord.separation(scoord).to('arcsec'))
if minsep < 30 * u.arcsec:
idx = np.argmin(comp.coord.separation(scoord).to('arcsec'))
self.abs.cgm_abs[idx].igm_sys.add_component(comp,
chk_sep=False,
debug=True,
update_vlim=True)
else: # New
if row['RV'] > 0:
zem = row['RV'] / c_kms
else:
zem = row['z']
abssys = IGMSystem(gc,
comp.zcomp,
vlim,
name=row['Name'] + '_z0',
zem=zem)
abssys.add_component(comp, chk_sep=False, debug=True)
# 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)
