def build_sys_from_dict(self, sys_name, llist=None, **kwargs):
""" Build CGMAbsSys from the internal dict
Parameters
----------
sys_name : str
Name of the system
llist : LineList, optional
kwargs : passed to CGMAbsSys.from_dict
Returns
-------
CGMAbsSys
"""
tdict = self._dict[sys_name]
cgmsys = CGMAbsSys.from_dict(tdict,
chk_vel=False,
chk_sep=False,
chk_data=False,
use_coord=True,
use_angrho=True,
linelist=llist,
**kwargs)
# Return
return cgmsys
def cgm_from_galaxy_igmsystems(galaxy,
igmsystems,
R_max=300 * u.kpc,
dv_max=400 * u.km / u.s,
cosmo=None,
**kwargs):
""" Generate a list of CGMAbsSys objects given an input galaxy and a list of IGMSystems
Parameters
----------
galaxy : Galaxy
igmsystems : list
list of IGMSystems
R_max : Quantity
Maximum projected separation from sightline to galaxy
dv_max
Maximum velocity offset between system and galaxy
Returns
-------
cgm_list : list
list of CGM objects generated
"""
from pyigm.cgm.cgm import CGMAbsSys
# Cosmology
if cosmo is None:
cosmo = cosmology.Planck15
# R
rho, angles = calc_rho(galaxy, igmsystems, cosmo)
# 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 < R_max) & (np.abs(dv) < dv_max))[0]
if len(match) == 0:
print("No CGM objects match your rules")
return []
else:
# Loop to generate
cgm_list = []
for imatch in match:
cgm = CGMAbsSys(galaxy, igmsystems[imatch], cosmo=cosmo, **kwargs)
cgm_list.append(cgm)
# Return
return cgm_list
def from_tarball(cls, tfile, debug=False, **kwargs):
""" Load the COS-Halos survey from a tarball of JSON files
Parameters
----------
tfile : str
Returns
-------
"""
import tarfile
import json
from linetools.lists.linelist import LineList
llist = LineList('ISM')
slf = cls(**kwargs)
# Load
tar = tarfile.open(tfile)
for kk, member in enumerate(tar.getmembers()):
if '.' not in member.name:
print('Skipping a likely folder: {:s}'.format(member.name))
continue
# Debug
if debug and (kk == 5):
break
# Extract
f = tar.extractfile(member)
tdict = json.load(f)
# Generate
cgmsys = CGMAbsSys.from_dict(tdict,
chk_vel=False,
chk_sep=False,
chk_data=False,
use_coord=True,
use_angrho=True,
linelist=llist,
**kwargs)
slf.cgm_abs.append(cgmsys)
tar.close()
# Return
return slf
def from_tarball(cls, tfile, debug=False, **kwargs):
""" Load the COS-Halos survey from a tarball of JSON files
Parameters
----------
tfile : str
Returns
-------
"""
import tarfile
import json
from linetools.lists.linelist import LineList
llist = LineList('ISM')
slf = cls(**kwargs)
# Load
tar = tarfile.open(tfile)
for kk, member in enumerate(tar.getmembers()):
if '.' not in member.name:
print('Skipping a likely folder: {:s}'.format(member.name))
continue
# Debug
if debug and (kk == 5):
break
# Extract
f = tar.extractfile(member)
tdict = json.load(f)
# Generate
cgmsys = CGMAbsSys.from_dict(tdict, chk_vel=False, chk_sep=False, chk_data=False,
use_coord=True, use_angrho=True,
linelist=llist, **kwargs)
slf.cgm_abs.append(cgmsys)
tar.close()
# Return
return slf
def p11():
""" Ingest Prochaska et al. 2011 CGM survey
"""
# Low z OVI summary
ovi_file = pyigm.__path__[0] + '/data/CGM/P11/lowovidat.fits'
ovidat = Table.read(ovi_file)
qso_radec = SkyCoord(ra=ovidat['QSO_RA'],
dec=ovidat['QSO_DEC'],
unit=(u.hourangle, u.deg))
qso_nms = np.array([row['QSO'].strip() for row in ovidat])
# CGM Survey
p11 = CGMAbsSurvey(survey='P11', ref='Prochaska+11')
# Dwarfs
cgm_dwarf_file = pyigm.__path__[0] + '/data/CGM/P11/dwarf_galabs_strct.fits'
cgm_dwarfs = Table.read(cgm_dwarf_file)
# sub L*
cgm_subls_file = pyigm.__path__[0] + '/data/CGM/P11/subls_galabs_strct.fits'
cgm_subls = Table.read(cgm_subls_file)
# L*
cgm_lstar_file = pyigm.__path__[0] + '/data/CGM/P11/lstar_galabs_strct.fits'
cgm_lstar = Table.read(cgm_lstar_file)
# Loop on subsets
for subset in [cgm_dwarfs, cgm_subls, cgm_lstar]:
for row in subset:
# RA, DEC
# Galaxy
gal = Galaxy((row['RA'], row['DEC']), z=row['Z'])
gal.Lstar = row['DDEC']
gal.type = row['GAL_TYPE']
# IGMSys
mtqso = np.where(qso_nms == row['FIELD'].strip())[0]
if len(mtqso) != 1:
pdb.set_trace()
raise ValueError("No Field match")
igmsys = IGMSystem(qso_radec[mtqso[0]], row['Z'],
(-400., 400.) * u.km / u.s)
# HI
if row['MAG'][2] > 0.:
# Lya
lya = AbsLine(1215.67 * u.AA, z=float(row['MAG'][3]))
lya.attrib['EW'] = row['MAG'][4] / 1e3 * u.AA
if row['MAG'][5] >= 99.:
lya.attrib['flag_EW'] = 3
else:
lya.attrib['flag_EW'] = 1
lya.attrib['sig_EW'] = row['MAG'][5] / 1e3 * u.AA
# Ref
lya.attrib['Ref'] = int(row['MAG'][2])
# HI component
if row['MAG'][9] <= 0.:
flagN = 3
elif row['MAG'][9] > 9.:
flagN = 2
else:
flagN = 1
HIcomp = AbsComponent(qso_radec[mtqso[0]], (1, 1),
float(row['MAG'][3]),
(-400, 400) * u.km / u.s,
Ntup=(flagN, row['MAG'][8],
row['MAG'][9]))
HIcomp._abslines.append(lya)
igmsys._components.append(HIcomp)
# NHI
igmsys.NHI = HIcomp.logN
igmsys.flag_NHI = HIcomp.flag_N
igmsys.sig_NHI = HIcomp.sig_N
# OVI
if row['MAGERR'][2] > 0.:
# OVI 1031
ovi1031 = None
if row['MAGERR'][4] > 0.:
ovi1031 = AbsLine(1031.9261 * u.AA,
z=float(row['MAGERR'][3]))
if row['MAGERR'][5] >= 99.:
ovi1031.attrib['flag_EW'] = 3
else:
ovi1031.attrib['flag_EW'] = 1
ovi1031.attrib['EW'] = row['MAGERR'][4] / 1e3 * u.AA
ovi1031.attrib['sig_EW'] = row['MAGERR'][5] / 1e3 * u.AA
# OVI component
if row['MAGERR'][9] <= 0.:
flagN = 3
elif row['MAGERR'][9] > 9.:
flagN = 2
else:
flagN = 1
OVIcomp = AbsComponent(qso_radec[mtqso[0]], (8, 6),
float(row['MAGERR'][3]),
(-400, 400) * u.km / u.s,
Ntup=(flagN, row['MAGERR'][8],
row['MAGERR'][9]))
if ovi1031 is not None:
OVIcomp._abslines.append(ovi1031)
# Ref
OVIcomp.Ref = int(row['MAG'][2])
igmsys._components.append(OVIcomp)
# CGM
cgmabs = CGMAbsSys(gal, igmsys, chk_lowz=False)
p11.cgm_abs.append(cgmabs)
# Write tarball
out_file = pyigm.__path__[0] + '/data/CGM/P11/P11_sys.tar'
p11.to_json_tarball(out_file)
def ingest_johnson15():
""" Ingest Johnson+15
"""
# Dict for QSO coords
qsos = {}
qsos['1ES1028+511'] = ltu.radec_to_coord('J103118.52517+505335.8193')
qsos['FBQS1010+3003'] = ltu.radec_to_coord((152.5029167, 30.056111))
qsos['HE0226-4110'] = ltu.radec_to_coord('J022815.252-405714.62')
qsos['HS1102+3441'] = ltu.radec_to_coord('J110539.8189+342534.672')
qsos['LBQS1435-0134'] = ltu.radec_to_coord((219.451183, -1.786328))
qsos['PG0832+251'] = ltu.radec_to_coord('J083535.8048+245940.146')
qsos['PG1522+101'] = ltu.radec_to_coord((231.1023075, 9.9749372))
qsos['PKS0405-123'] = ltu.radec_to_coord('J040748.4376-121136.662')
qsos['SBS1108+560'] = ltu.radec_to_coord((167.8841667, 55.790556))
qsos['SBS1122+594'] = ltu.radec_to_coord((171.4741250, 59.172667))
qsos['Ton236'] = ltu.radec_to_coord((232.1691746, 28.424928))
# Virial matching
j15_file = resource_filename('pyigm',
'data/CGM/z0/johnson2015_table1.fits')
j15_tbl = Table.read(j15_file)
# Clip COS-Halos
keep = j15_tbl['Survey'] != 'COS-Halos'
j15_tbl = j15_tbl[keep]
# CGM Survey
j15 = CGMAbsSurvey(survey='J15', ref='Johnson+15')
# Linelist
llist = LineList('ISM')
for row in j15_tbl:
# RA, DEC
# Galaxy
gal = Galaxy((row['RAJ2000'], row['DEJ2000']), z=float(row['zgal']))
gal.Class = row['Class']
gal.Mstar = row['logM_']
gal.field = row['Name']
gal.Env = row['Env']
gal.d_Rh = row['d_Rh']
#
igmsys = IGMSystem(qsos[row['Name']], float(row['zgal']),
(-400., 400.) * u.km / u.s)
# HI
if np.isnan(row['logNHI']):
pass
else:
# HI component
if row['l_logNHI'] == '<':
flagN = 3
sigNHI = 99.
elif np.isnan(row['e_logNHI']):
flagN = 2
sigNHI = 99.
else:
flagN = 1
sigNHI = row['e_logNHI']
HIcomp = AbsComponent(qsos[row['Name']], (1, 1),
float(row['zgal']), (-400, 400) * u.km / u.s,
Ntup=(flagN, row['logNHI'], sigNHI))
igmsys._components.append(HIcomp)
# NHI
igmsys.NHI = HIcomp.logN
igmsys.flag_NHI = HIcomp.flag_N
igmsys.sig_NHI = HIcomp.sig_N
# OVI
if np.isnan(row['logNHOVI']):
pass
else:
# OVI component
if row['l_logNHOVI'] == '<':
flagN = 3
sigNHOVI = 99.
elif np.isnan(row['e_logNHOVI']):
flagN = 2
sigNHOVI = 99.
else:
flagN = 1
sigNHOVI = row['e_logNHOVI']
OVIcomp = AbsComponent(qsos[row['Name']], (8, 6),
float(row['zgal']),
(-400, 400) * u.km / u.s,
Ntup=(flagN, row['logNHOVI'], sigNHOVI))
igmsys._components.append(OVIcomp)
# CGM
cgmabs = CGMAbsSys(gal, igmsys, chk_lowz=False)
j15.cgm_abs.append(cgmabs)
# Write tarball
out_file = resource_filename('pyigm', '/data/CGM/z0/J15_sys.tar')
j15.to_json_tarball(out_file)
def ingest_burchett16(smthd='vir'):
""" Ingest Burchett+16
"""
# Virial matching
if smthd == 'vir':
b16_file = resource_filename(
'pyigm', 'data/CGM/z0/Burchett2016_CIV_HI_virselect.fits')
else:
b16_file = resource_filename(
'pyigm', 'data/CGM/z0/Burchett2016_CIV_HI_kpcselect.fits')
b16_tbl = Table.read(b16_file)
# CGM Survey
b16 = CGMAbsSurvey(survey='B16', ref='Burchett+16')
# Linelist
llist = LineList('ISM')
for row in b16_tbl:
# RA, DEC
# Galaxy
gal = Galaxy((row['ra_gal'], row['dec_gal']), z=row['zgal'])
gal.SFR = row['SFR']
gal.sig_SFR = row['SFR_err']
gal.Mstar = row['mstars']
gal.field = row['field']
gal.RRvir = row['rrvir']
gal.NSAidx = row['NSAidx']
#
igmsys = IGMSystem((row['ra_qso'], row['dec_qso']), row['zgal'],
(-400., 400.) * u.km / u.s)
# HI
if row['flag_h1'] > 0:
# Lya
lya = AbsLine(1215.67 * u.AA, z=row['zgal'], linelist=llist)
lya.attrib['EW'] = row['EW_h1'] * u.AA
lya.attrib['logN'] = row['col_h1']
lya.attrib['N'] = 10**row['col_h1'] * u.cm**-2
if row['flag_h1'] == 3:
lya.attrib['flag_EW'] = 3
lya.attrib['flag_N'] = 3
lya.attrib['sig_N'] = (10**(row['col_h1'])) / 3. * u.cm**-2
elif row['flag_h1'] == 2:
lya.attrib['flag_EW'] = 1
lya.attrib['flag_N'] = 2
else:
lya.attrib['flag_EW'] = 1
lya.attrib['flag_N'] = 1
lya.attrib['sig_N'] = (10**(row['col_h1'] + row['colsig_h1']) -
10**row['col_h1']) * u.cm**-2
lya.attrib['sig_EW'] = row['EWsig_h1'] * u.AA
# Ref
lya.attrib['Ref'] = 'Burchett+16'
# HI component
if row['colsig_h1'] >= 99.:
flagN = 2
elif row['colsig_h1'] <= 0.:
flagN = 3
else:
flagN = 1
HIcomp = AbsComponent(
(row['ra_qso'], row['dec_qso']), (1, 1),
row['zgal'], (-400, 400) * u.km / u.s,
Ntup=(flagN, row['col_h1'], row['colsig_h1']))
HIcomp._abslines.append(lya)
igmsys._components.append(HIcomp)
# NHI
igmsys.NHI = HIcomp.logN
igmsys.flag_NHI = HIcomp.flag_N
igmsys.sig_NHI = HIcomp.sig_N
# CIV
if row['flag_c4'] > 0:
# CIV 1548
civ1548 = AbsLine(1548.195 * u.AA, z=row['zgal'], linelist=llist)
civ1548.attrib['EW'] = row['EW_c4'] * u.AA
civ1548.attrib['logN'] = row['col_c4']
civ1548.attrib['N'] = 10**row['col_c4'] * u.cm**-2
if row['flag_c4'] == 3:
civ1548.attrib['flag_EW'] = 3
civ1548.attrib['flag_N'] = 3
civ1548.attrib['sig_N'] = (10**(row['col_c4'])) / 3. * u.cm**-2
elif row['flag_c4'] == 2:
civ1548.attrib['flag_EW'] = 1
civ1548.attrib['flag_N'] = 2
else:
civ1548.attrib['flag_EW'] = 1
civ1548.attrib['flag_N'] = 1
civ1548.attrib['sig_N'] = (10**
(row['col_c4'] + row['colsig_c4']) -
10**row['col_c4']) * u.cm**-2
civ1548.attrib['sig_EW'] = row['EWsig_c4'] * u.AA
# Ref
civ1548.attrib['Ref'] = 'Burchett+16'
# CIV component
if row['colsig_c4'] >= 99.:
flagN = 2
elif row['colsig_c4'] <= 0.:
flagN = 3
else:
flagN = 1
CIVcomp = AbsComponent(
(row['ra_qso'], row['dec_qso']), (6, 4),
row['zgal'], (-400, 400) * u.km / u.s,
Ntup=(flagN, row['col_c4'], row['colsig_c4']))
CIVcomp._abslines.append(civ1548)
igmsys._components.append(CIVcomp)
# CGM
cgmabs = CGMAbsSys(gal, igmsys, correct_lowz=False)
b16.cgm_abs.append(cgmabs)
# Write tarball
if smthd == 'vir':
out_file = resource_filename('pyigm', '/data/CGM/z0/B16_vir_sys.tar')
else:
out_file = resource_filename('pyigm', '/data/CGM/z0/B16_kpc_sys.tar')
b16.to_json_tarball(out_file)
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_tarball(self,
tfile,
build_data=True,
build_sys=False,
llist=None,
verbose=True,
**kwargs):
"""
Parameters
----------
tfile
build_data
build_sys
llist
kwargs
Returns
-------
"""
import tarfile
# Load
tar = tarfile.open(tfile)
for kk, member in enumerate(tar.getmembers()):
if '.json' not in member.name:
print('Skipping a likely folder: {:s}'.format(member.name))
continue
# Extract
f = tar.extractfile(member)
try:
tdict = json.load(f)
except:
if verbose:
print('Unable to load {}'.format(member))
continue
# Build dict
self._dict[tdict['Name']] = tdict
# Generate
if build_sys:
cgmsys = CGMAbsSys.from_dict(tdict,
chk_vel=False,
chk_sep=False,
chk_data=False,
use_coord=True,
use_angrho=True,
linelist=llist,
**kwargs)
self.cgm_abs.append(cgmsys)
tar.close()
# Galaxy coords
ras = [self._dict[key]['RA'] for key in self._dict.keys()]
decs = [self._dict[key]['DEC'] for key in self._dict.keys()]
self.coords = SkyCoord(ra=ras, dec=decs, unit='deg')
# Sightline coords
ras = [self._dict[key]['igm_sys']['RA'] for key in self._dict.keys()]
decs = [self._dict[key]['igm_sys']['DEC'] for key in self._dict.keys()]
self.scoords = SkyCoord(ra=ras, dec=decs, unit='deg')
# Data table
if build_data:
self.build_data_from_dict()
# Return
return
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'
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)