def __init__(self, cdir=None, fits_path=None, load=True, **kwargs):
CGMAbsSurvey.__init__(self)
self.survey = 'COS-Halos'
self.ref = 'Tumlinson+11; Werk+12; Tumlinson+13; Werk+13; Werk+14'
#
if cdir is None:
self.cdir = pyigm.__path__[0] + '/data/CGM/COS_Halos/'
else:
self.cdir = cdir
# Spectra dir
self.data_dir = os.getenv('COSHALOS_DATA')
# Summary Tables
if fits_path is None:
self.fits_path = self.cdir + '/Summary/'
else:
self.fits_path = fits_path
try:
self.werk14_cldy = Table.read(self.fits_path +
'coshaloscloudysol_newphi.fits')
except IOError:
self.werk14_cldy = None
# Kinematics
self.kin_init_file = self.cdir + '/Kin/coshalo_kin_driver.dat'
# Init?
if load:
self.load_sys(**kwargs)
# Metallicity flag
self.flag_mtlpdf = False
def __init__(self,
cdir=None,
nmax=None,
load=True,
from_dict=True,
**kwargs):
CGMAbsSurvey.__init__(self)
self.survey = 'QPQ7'
self.ref = 'Prochaska+14'
#
if cdir is None:
self.cdir = pyigm.__path__[0] + '/data/CGM/QPQ/'
else:
self.cdir = cdir
#self.data_file = pyigm.__path__[0] + '/data/CGM/QPQ/'+'qpq7_pairs.fits.gz'
if from_dict:
self.data_file = self.cdir + 'jsons/qpq7.json'
else:
self.data_file = self.cdir + 'qpq7_pairs.fits.gz'
self.nmax = nmax
self.from_dict = from_dict
# Init?
if load:
self.load_data(**kwargs)
def __init__(self,
tree=None,
fits_path=None,
kin_init_file=None,
cdir=None):
# Generate with type
CGMAbsSurvey.__init__(self)
self.survey = 'COS-Dwarfs'
self.ref = 'Bordoloi+14'
if cdir is None:
self.cdir = os.environ.get('COSHALOS_DATA')
#self.cdir = os.environ.get('DROPBOX_DIR')+'/COS-Dwarfs/'
else:
self.cdir = cdir ### need to define cdir
if fits_path is None:
self.fits_path = os.path.abspath(
os.environ.get('DROPBOX_DIR') + '/COS-Dwarfs/Targets/FITS')
else:
self.fits_path = fits_path
# Kinematics
if kin_init_file is None:
#self.kin_init_file = os.path.abspath(os.environ.get('DROPBOX_DIR')+'/COS-Dwarfs/Kin/cosdwarfs_kin_driver.dat')
self.kin_init_file = self.cdir + '/Kin/cosdwarfs_kin_driver.dat'
else:
self.kin_init_file = kin_init_file
# Load
self.load_sys()
def __init__(self, cdir=None, fits_path=None, load=True, **kwargs):
CGMAbsSurvey.__init__(self)
self.survey = 'COS-Halos'
self.ref = 'Tumlinson+11; Werk+12; Tumlinson+13; Werk+13; Werk+14'
#
if cdir is None:
if os.environ.get('COSHALOS_DATA') is None:
raise ValueError("Need to set COSHALOS_DATA variable")
self.cdir = os.environ.get('COSHALOS_DATA')
else:
self.cdir = cdir
# Summary Tables
if fits_path is None:
self.fits_path = self.cdir+'/Summary/'
else:
self.fits_path = fits_path
try:
self.werk14_cldy = Table.read(self.fits_path+'coshaloscloudysol_newphi.fits')
except IOError:
self.werk14_cldy = None
# Kinematics
self.kin_init_file = self.cdir+'/Kin/coshalo_kin_driver.dat'
# Init?
if load:
self.load_sys(**kwargs)
def __init__(self,
cdir=None,
nmax=None,
load=True,
from_dict=True,
**kwargs):
CGMAbsSurvey.__init__(self)
self.survey = 'QPQ6'
self.ref = 'Prochaska+13'
#
if cdir is None:
self.cdir = pyigm.__path__[0] + '/data/CGM/QPQ/'
else:
self.cdir = cdir
if from_dict:
self.data_file = self.cdir + 'jsons/qpq6.json'
else:
self.data_file = self.cdir + 'qpq6_final_cut_2015nov16.fits'
self.nmax = nmax
self.from_dict = from_dict
# Init?
if load:
self.load_data(**kwargs)
def __init__(self,
cdir=None,
nmax=None,
load=True,
from_dict=True,
**kwargs):
CGMAbsSurvey.__init__(self)
self.survey = 'QPQ8'
self.ref = 'Lau+16'
#
if cdir is None:
self.cdir = pyigm.__path__[0] + '/data/CGM/QPQ/'
else:
self.cdir = cdir
#self.data_file = pyigm.__path__[0] + '/data/CGM/QPQ/'+'qpq8_pairs.fits'
if from_dict:
self.data_file = self.cdir + 'jsons/qpq8.json'
else:
self.data_file = self.cdir + 'qpq8_all_measured.dat'
self.nmax = nmax
self.from_dict = from_dict
# Init?
if load:
self.load_data(**kwargs)
def test_from_json():
# Without building systems
cos_halos = CGMAbsSurvey.from_json(data_path('cos_halos.json'))
assert len(cos_halos.cgm_abs) == 0
# Build the systems too
cos_halos2 = CGMAbsSurvey.from_json(data_path('cos_halos.json'),
build_sys=True)
assert len(cos_halos2.cgm_abs) == 44
def cgmsurvey_from_sightlines_fields(fields,
sightlines,
rho_max=300 * u.kpc,
name=None,
dummysys=True,
embuffer=None,
**kwargs):
"""Instantiate CGMAbsSurvey object from lists fo IgmGalaxyFields and IGMSightlines
Parameters
----------
fields: list of IgmGalaxyFields
sightlines : list of IGMSightlines
name : str, optional
Name for the survey
dummysys : bool, optional
Passed on to 'cgm_from_galaxy_igmsystems()'. If True, create CGMAbsSys
even if no matching IGMSystem is found in any sightline for some galaxy
embuffer : Quantity, optional
Velocity buffer between background source (e.g., QSO) and CGMAbsSys
Returns
-------
cgmsurvey: CGMAbsSurvey
"""
if ((not isinstance(fields, list)) | (not isinstance(sightlines, list)) |
(len(fields) != len(sightlines))):
raise IOError(
"Inputs fields and sightlines must lists of the same length")
if dummysys is True:
from linetools.spectralline import AbsLine
ismlist = LineList('ISM')
from pyigm.cgm.cgmsurvey import CGMAbsSurvey
cgmsys = []
for i, ff in enumerate(fields):
print(ff.name)
thiscgmlist = cgmabssys_from_sightline_field(ff,
sightlines[i],
rho_max=rho_max,
dummysys=dummysys,
linelist=ismlist,
embuffer=embuffer,
**kwargs)
cgmsys.extend(thiscgmlist)
if name is not None:
cgmsurvey = CGMAbsSurvey.from_cgmabssys(cgmsys, survey=name)
else:
cgmsurvey = CGMAbsSurvey.from_cgmabssys(cgmsys)
return cgmsurvey
def __init__(self, tree=None, fits_path=None, kin_init_file=None, cdir=None):
# Generate with type
CGMAbsSurvey.__init__(self)
self.survey = 'COS-Dwarfs'
self.ref = 'Bordoloi+14'
if cdir is None:
self.cdir = os.environ.get('DROPBOX_DIR')+'/COS-Dwarfs/'
if fits_path is None:
self.fits_path = os.path.abspath(os.environ.get('DROPBOX_DIR')+'/COS-Dwarfs/Targets/FITS')
else:
self.fits_path = fits_path
# Kinematics
if kin_init_file is None:
self.kin_init_file = os.path.abspath(os.environ.get('DROPBOX_DIR')+'/COS-Dwarfs/Kin/cosdwarfs_kin_driver.dat')
else:
self.kin_init_file = kin_init_file
def __init__(self, load=True, from_dict=True, **kwargs):
CGMAbsSurvey.__init__(self)
self.survey = 'QPQ7'
self.ref = 'Prochaska+13'
#
self.cdir = pyigm.__path__[0] + '/data/CGM/QPQ/'
if from_dict:
self.data_file = self.cdir + 'jsons/qpq5.json'
else:
self.data_file = self.cdir + 'qpq7_pairs.fits.gz'
self.from_dict = from_dict
# Init?
if load:
self.load_data(**kwargs)
def __init__(self, load=True, verbose=False, debug=False, **kwargs):
# Init
self.verbose = verbose
self.debug = debug
# Generate the Milky Way
milkyway = Galaxy((0., 0.), z=0.)
self.galaxy = milkyway
CGM.__init__(self, milkyway)
self.refs = ''
# Absorption
self.abs = CGMAbsSurvey(survey='Galaxy')
# Load Data
if load:
print("Loading data. This takes ~20s to build it all...")
self.load_coolgas() # This needs to be first!
self.load_hotgas()
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 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_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)
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"], (-400.0, 400.0) * u.km / u.s)
# HI
if row["MAG"][2] > 0.0:
# 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] >= 99.0:
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] <= 0.0:
flagN = 3
elif row["MAG"][9] > 9.0:
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)
# OVI
if row["MAGERR"][2] > 0.0:
# OVI 1031
ovi1031 = None
if row["MAGERR"][4] > 0.0:
ovi1031 = AbsLine(1031.9261 * u.AA, z=float(row["MAGERR"][3]))
if row["MAGERR"][5] >= 99.0:
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] <= 0.0:
flagN = 3
elif row["MAGERR"][9] > 9.0:
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 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 load_data(self, **kwargs):
#
#q8file = resource_filename('pyigm', 'data/CGM/QPQ/qpq8_all_measured.dat')
q8file = self.data_file
if self.from_dict:
q8file = self.data_file
qpq8dict = CGMAbsSurvey.from_json(q8file)
ism = LineList('ISM')
qpq8dict.build_systems_from_dict(llist=ism)
self.survey_data = qpq8dict
#self.cgm_abs = qpq8dict.cgm_abs
else:
qpqdata = Table.read(q8file, format='ascii')
#nmax = len(qpqdata) # max number of QSOs
q8filecoord = resource_filename('pyigm',
'data/CGM/QPQ/qpq8_pairs.fits')
qpqdatacoord = Table.read(q8filecoord)
if self.nmax is not None:
nmax = self.nmax
else:
nmax = len(qpqdatacoord) #(qpqdata)
# match names with qpqdatacoord
qnames = []
for i in range(len(qpqdatacoord)):
qname = qpqdatacoord['QSO'][i].strip()
qnames.append(qname[-10:])
qnames2 = []
for i in range(len(qpqdata)):
qname = qpqdata['Pair'][i]
qnames2.append(qname)
for j in range(nmax): # i,j
# match names with qpqdatacoord
i = np.where(np.asarray(qnames2) == qnames[j])[0]
# Instantiate the galaxy
gal = Galaxy((qpqdatacoord['RAD'][j], qpqdatacoord['DECD'][j]),
z=qpqdatacoord['Z_FG'][j])
gal.L_BOL = qpqdatacoord['L_BOL'][j]
gal.L_912 = qpqdatacoord['L_912'][j]
gal.G_UV = qpqdatacoord['G_UV'][j]
gal.zsig = qpqdatacoord['Z_FSIG'][j] * u.km / u.s
# Instantiate the IGM System
igm_sys = IGMSystem(
(qpqdatacoord['RAD_BG'][j], qpqdatacoord['DECD_BG'][j]),
qpqdatacoord['Z_FG'][j], [-5500, 5500.] * u.km / u.s,
abs_type='CGM')
# Redshifts: QSO emission redshifts
igm_sys.zem = qpqdatacoord['Z_BG'][j]
igm_sys.NHI = qpqdata['HIcol'][i]
igm_sys.sig_NHI = [
qpqdata['HIcolhierr'][i], qpqdata['HIcolloerr'][i]
]
igm_sys.s2n_lya = qpqdatacoord['S2N_LYA'][j]
iname = qpqdata['Pair'][i][0] #+'_'+qpqdata['subsys'][i]
# Instantiate
rho = qpqdatacoord['R_PHYS'][j] * u.kpc
cgabs = CGMAbsSys(gal, igm_sys, name=iname, rho=rho, **kwargs)
### add metal lines
### not included CII*, SiII*
lines = [
['CII 1334'], ## ['CII* 1335'],
['CIV 1548', 'CIV 1550'],
['NI 1134', 'NI 1199'],
['NII 1083'],
['NV 1238', 'NV 1242'],
['OI 1302'],
['OVI 1037'],
['MgI 2852'],
['MgII 2796', 'MgII 2803'],
['AlII 1670'],
['AlIII 1854', 'AlIII 1862'],
[
'SiII 1190', 'SiII 1193', 'SiII 1304', 'SiII 1260',
'SiII 1526', 'SiII 1808'
], ## ['SiII* 1264'],
['SiIII 1206'],
['SiIV 1393', 'SiIV 1402'],
[
'FeII 1608', 'FeII 2344', 'FeII 2374', 'FeII 2382',
'FeII 2586', 'FeII 2600'
],
['FeIII 1122']
]
for kk in i:
for icmp in range(len(lines)):
abslines = []
for ii in range(len(lines[icmp])):
wave0 = float(lines[icmp][ii].split(' ')[1])
ewstr = str(lines[icmp][ii].split(' ')[1]) + 'EW'
ewerrstr = str(
lines[icmp][ii].split(' ')[1]) + 'EWerr'
if ewstr == '1808EW':
ewstr = '1808E'
if ewerrstr == '1122EWerr':
ewerrstr = '122EWerr'
if qpqdata[ewstr][kk] != '/':
# find z
v0 = 0.5 * (
qpqdata['v_lobound'][kk] +
qpqdata['v_upbound'][kk]) * u.km / u.s
dv = v0
zref = igm_sys.zabs
z_cmp = ltu.z_from_dv(dv, zref)
## vlim
v1 = qpqdata['v_lobound'][kk] * u.km / u.s
z1 = ltu.z_from_dv(v1, zref)
v1_cmp = ltu.dv_from_z(z1, z_cmp)
v2 = qpqdata['v_upbound'][kk] * u.km / u.s
z2 = ltu.z_from_dv(v2, zref)
v2_cmp = ltu.dv_from_z(z2, z_cmp)
# iline
iline = AbsLine(wave0 * u.AA,
closest=True,
z=z_cmp)
iline.attrib['coord'] = igm_sys.coord
## EW
iline.attrib['EW'] = float(
qpqdata[ewstr][kk]) * u.AA # Rest EW
iline.attrib['sig_EW'] = float(
qpqdata[ewerrstr][kk]) * u.AA
flgew = 1
if iline.attrib[
'EW'] < 3. * iline.attrib['sig_EW']:
flgew = 3
iline.attrib['flag_EW'] = flgew
## column densities
colstr = str(
lines[icmp][ii].split(' ')[0]) + 'col'
colerrstr = str(
lines[icmp][ii].split(' ')[0]) + 'colerr'
iline.attrib['logN'] = qpqdata[colstr][kk]
iline.attrib['sig_logN'] = qpqdata[colerrstr][
kk]
abslines.append(iline)
if len(abslines) > 0:
comp = AbsComponent.from_abslines(abslines,
chk_vel=False)
comp.limits._vlim = [v1_cmp.value, v2_cmp.value
] * u.km / u.s
cgabs.igm_sys.add_component(comp)
# add ang_sep
qsocoord = SkyCoord(ra=qpqdatacoord['RAD'][j],
dec=qpqdatacoord['DECD'][j],
unit='deg')
bgcoord = SkyCoord(ra=qpqdatacoord['RAD_BG'][j],
dec=qpqdatacoord['DECD_BG'][j],
unit='deg')
cgabs.ang_sep = qsocoord.separation(bgcoord).to('arcsec')
self.cgm_abs.append(cgabs)
