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 load_data(self, **kwargs):
#
if self.from_dict:
q5file = self.data_file
qpq5dict = CGMAbsSurvey.from_json(q5file)
ism = LineList('ISM')
qpq5dict.build_systems_from_dict(llist=ism)
self.survey_data = qpq5dict
#self.cgm_abs = qpq5dict.cgm_abs
else:
qpqdata = load_qpq(5)
nmax = len(qpqdata) # max number of QSOs
for i in range(nmax):
# Instantiate the galaxy
gal = Galaxy((qpqdata['RAD'][i], qpqdata['DECD'][i]),
z=qpqdata['Z_FG'][i])
gal.L_BOL = qpqdata['L_BOL'][i]
gal.L_912 = qpqdata['L_912'][i]
gal.G_UV = qpqdata['G_UV'][i]
gal.flg_BOSS = qpqdata['FLG_BOSS'][i]
gal.zsig = qpqdata['Z_FSIG'][i] * u.km / u.s
# Instantiate the IGM System
igm_sys = IGMSystem(
(qpqdata['RAD_BG'][i], qpqdata['DECD_BG'][i]),
qpqdata['Z_FG'][i], [-5500, 5500.] * u.km / u.s,
abs_type='CGM')
igm_sys.zem = qpqdata['Z_BG'][i]
igm_sys.NHI = qpqdata['NHI'][i]
igm_sys.sig_NHI = qpqdata['SIG_NHI'][i]
igm_sys.flag_NHI = qpqdata['FLG_NHI'][i]
igm_sys.s2n_lya = qpqdata['S2N_LYA'][i]
igm_sys.flg_othick = qpqdata['FLG_OTHICK'][i]
igm_sys.z_lya = qpqdata['Z_LYA'][i]
iname = qpqdata['QSO'][i]
# Instantiate
rho = qpqdata['R_PHYS'][i] * u.kpc
cgabs = CGMAbsSys(gal, igm_sys, name=iname, rho=rho, **kwargs)
aline = AbsLine(1215.67 * u.AA,
closest=True,
z=igm_sys.zabs,
linelist=ism)
aline.attrib['EW'] = qpqdata['EWLYA'][i] * u.AA # Rest EW
aline.attrib['sig_EW'] = qpqdata['SIG_EWLYA'][i] * u.AA
if aline.attrib['EW'] > 3. * aline.attrib['sig_EW']:
aline.attrib['flag_EW'] = 1
else:
aline.attrib['flag_EW'] = 3
aline.attrib['coord'] = igm_sys.coord
#aline.limits._wvlim = qpqdata['WVMNX'][i]*u.AA ## (no data in QPQ7 file)
#dv = ltu.rel_vel(aline.limits._wvlim, aline.wrest * (1 + qpqdata['Z_FG'][i]))
#aline.limits._vlim = dv
abslines = []
abslines.append(aline)
comp = AbsComponent.from_abslines(abslines, chk_vel=False)
cgabs.igm_sys.add_component(comp)
# add metal lines
for j in range(100):
if qpqdata[i]['FLG_METAL_EW'][j] > 0:
wave0 = qpqdata[i]['METAL_WREST'][j]
iline = AbsLine(wave0 * u.AA,
closest=True,
z=igm_sys.zabs,
linelist=ism)
iline.attrib[
'EW'] = qpqdata['METAL_EW'][i][j] * u.AA # Rest EW
iline.attrib[
'sig_EW'] = qpqdata['METAL_SIGEW'][i][j] * u.AA
iline.attrib['flag_EW'] = qpqdata['FLG_METAL_EW'][i][j]
iline.analy['flg_eye'] = qpqdata['FLG_METAL_EYE'][i][j]
iline.attrib['coord'] = igm_sys.coord
abslines = []
abslines.append(iline)
comp = AbsComponent.from_abslines(abslines,
chk_vel=False)
cgabs.igm_sys.add_component(comp)
# add ang_sep
qsocoord = SkyCoord(ra=qpqdata['RAD'][i],
dec=qpqdata['DECD'][i],
unit='deg')
bgcoord = SkyCoord(ra=qpqdata['RAD_BG'][i],
dec=qpqdata['DECD_BG'][i],
unit='deg')
cgabs.ang_sep = qsocoord.separation(bgcoord).to('arcsec')
self.cgm_abs.append(cgabs)
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 load_data(self, **kwargs):
#
q6file = self.data_file
if self.from_dict:
qpq6dict = CGMAbsSurvey.from_json(q6file)
ism = LineList('ISM')
qpq6dict.build_systems_from_dict(llist=ism)
self.survey_data = qpq6dict
#self.cgm_abs = qpq6dict.cgm_abs
else:
qpqdata = Table.read(q6file)
if self.nmax is not None:
nmax = self.nmax
else:
nmax = len(qpqdata)
for i in range(nmax):
# Instantiate the galaxy
gal = Galaxy((qpqdata['RAD'][i], qpqdata['DECD'][i]),
z=qpqdata['Z_FG'][i])
gal.L_BOL = qpqdata['L_BOL'][i]
gal.L_912 = qpqdata['L_912'][i]
gal.G_UV = qpqdata['G_UV'][i]
gal.flg_BOSS = qpqdata['FLG_BOSS'][i]
gal.zsig = qpqdata['Z_FSIG'][i] * u.km / u.s
# Instantiate the IGM System
igm_sys = IGMSystem(
(qpqdata['RAD_BG'][i], qpqdata['DECD_BG'][i]),
qpqdata['Z_FG'][i], [-5500, 5500.] * u.km / u.s,
abs_type='CGM'
) ## if velocity range lower - does not load all abslines
igm_sys.zem = qpqdata['Z_BG'][i]
igm_sys.NHI = qpqdata['NHI'][i]
igm_sys.sig_NHI = qpqdata['SIG_NHI'][i]
igm_sys.flag_NHI = qpqdata['FLG_NHI'][i]
igm_sys.s2n_lya = qpqdata['S2N_LYA'][i]
igm_sys.flg_othick = qpqdata['FLG_OTHICK'][i]
igm_sys.z_lya = qpqdata['Z_LYA'][i]
iname = qpqdata['QSO'][i]
# Instantiate
rho = qpqdata['R_PHYS'][i] * u.kpc
cgabs = CGMAbsSys(gal, igm_sys, name=iname, rho=rho, **kwargs)
aline = AbsLine(1215.67 * u.AA, closest=True, z=igm_sys.zabs)
aline.attrib['EW'] = qpqdata['EWLYA'][i] * u.AA # Rest EW
aline.attrib['sig_EW'] = qpqdata['SIG_EWLYA'][i] * u.AA
if aline.attrib['EW'] > 3. * aline.attrib['sig_EW']:
aline.attrib['flag_EW'] = 1
else:
aline.attrib['flag_EW'] = 3
aline.attrib['coord'] = igm_sys.coord
aline.limits._wvlim = qpqdata['WVMNX'][i] * u.AA
dv = ltu.rel_vel(aline.limits._wvlim,
aline.wrest * (1 + qpqdata['Z_FG'][i]))
aline.limits._vlim = dv
abslines = []
abslines.append(aline)
###
comp = AbsComponent.from_abslines(abslines, chk_vel=False)
# add ang_sep
qsocoord = SkyCoord(ra=qpqdata['RAD'][i],
dec=qpqdata['DECD'][i],
unit='deg')
bgcoord = SkyCoord(ra=qpqdata['RAD_BG'][i],
dec=qpqdata['DECD_BG'][i],
unit='deg')
cgabs.ang_sep = qsocoord.separation(bgcoord).to('arcsec')
cgabs.igm_sys.add_component(comp)
self.cgm_abs.append(cgabs)
