def from_dict(cls, idict, use_angrho=False, **kwargs):
""" Generate a CGMAbsSys object from a dict
Parameters
----------
idict : dict
use_angrho : bool, optional
Use ang_sep and rho if in idict and cosmo is too
"""
# Galaxy object
galaxy = Galaxy.from_dict(idict['galaxy'])
# IGM system
igm_sys = IGMSystem.from_dict(idict['igm_sys'], **kwargs)
# Keywords
kwargs2 = kwargs.copy()
kwargs2['name'] = idict['Name']
if 'cosmo' in idict.keys():
kwargs2['cosmo'] = getattr(cosmology, idict['cosmo'])
if use_angrho:
kwargs2['ang_sep'] = idict['ang_sep']*u.arcsec
kwargs2['rho'] = idict['rho']*u.kpc
# Instantiate
slf = cls(galaxy, igm_sys, **kwargs2)
# Return
return slf
def test_init_cgm():
# Simple properties
radec = SkyCoord(ra=123.1143 * u.deg, dec=-12.4321 * u.deg)
gal = Galaxy(radec, z=0.3)
cgm = CGM(gal)
# Test
np.testing.assert_allclose(cgm.galaxy.z, 0.3)
def from_dict(cls, idict, use_angrho=False, **kwargs):
""" Generate a CGMAbsSys object from a dict
Parameters
----------
idict : dict
use_angrho : bool, optional
Use ang_sep and rho if in idict and cosmo is too
"""
# Galaxy object
galaxy = Galaxy.from_dict(idict['galaxy'])
# IGM system
igm_sys = IGMSystem.from_dict(idict['igm_sys'], **kwargs)
# Keywords
kwargs2 = kwargs.copy()
kwargs2['name'] = idict['Name']
if 'cosmo' in idict.keys():
kwargs2['cosmo'] = getattr(cosmology, idict['cosmo'])
if use_angrho:
kwargs2['ang_sep'] = idict['ang_sep'] * u.arcsec
kwargs2['rho'] = idict['rho'] * u.kpc
# Instantiate
slf = cls(galaxy, igm_sys, **kwargs2)
# Extras
for key in ['ebv']:
if key in idict.keys():
setattr(slf, key, idict[key])
# Return
return slf
def test_calcrho():
# Dummy
galaxy = Galaxy((100., 50.), 0.2)
igmsys = IGMSystem((100., 50.001), 1.2, None)
# Calc
rho, angle = calc_cgm_rho(galaxy, igmsys, cosmo)
# Test
assert np.isclose(rho.value, 12.2587523534)
assert rho.unit == astropy.units.kpc
assert isinstance(angle, astropy.coordinates.Angle)
def __init__(self, load=True, **kwargs):
# Generate the Milky Way
milkyway = Galaxy((0.,0.), z=0.)
CGM.__init__(self, milkyway)
self.refs = ''
# Absorption
self.abs = CGMAbsSurvey(survey='Galaxy')
# Hot gas
if load:
self.load_hotgas()
def test_calcrho():
# Dummy
galaxy = Galaxy((100., 50.), 0.2)
igmsys = IGMSystem((100., 50.001), 1.2, None)
# Calc
rho, angle = calc_rho(galaxy, igmsys, cosmo)
# Test
assert np.isclose(rho.value, 12.2587523534)
assert rho.unit == astropy.units.kpc
assert isinstance(angle, astropy.coordinates.Angle)
# Galactic
milkyway = Galaxy((0., 0.), 0.)
igmsys.coord = SkyCoord(l=0. * u.deg, b=0. * u.deg, frame='galactic')
rho2, angle2 = calc_rho(galaxy, igmsys, None, Galactic=True)
assert np.isclose(rho2.value, 0.)
assert np.isclose(angle2.value, 0.)
igmsys.coord = SkyCoord(l=45. * u.deg, b=45. * u.deg, frame='galactic')
rho3, angle3 = calc_rho(galaxy, igmsys, None, Galactic=True)
assert np.isclose(rho3.value, 6.928203230275509)
def simple_cgmabssys():
radec = (125.0 * u.deg, 45.2 * u.deg)
gal = Galaxy(radec, z=0.3)
radec_qso = (125.0 * u.deg, 45.203 * u.deg)
igmsys = IGMSystem(radec_qso,
gal.z, [-500, 500] * u.km / u.s,
abs_type='CGM')
# Instantiate
cgmabs = CGMAbsSys(gal, igmsys, cosmo=cosmo)
return cgmabs
def test_init_cgmabssys():
radec = (125 * u.deg, 45.2 * u.deg)
gal = Galaxy(radec, z=0.3)
radec_qso = (125 * u.deg, 45.203 * u.deg)
igmsys = IGMSystem(radec_qso,
gal.z, [-500, 500] * u.km / u.s,
abs_type='CGM')
# Instantiate
cgmabs = CGMAbsSys(gal, igmsys)
# Test
np.testing.assert_allclose(cgmabs.rho.value, 48.72077748027017)
def test_cgm_from_igmsystems_lowz():
# Load sightlines
sl_file = pyigm.__path__[
0] + '/data/sightlines/Blind_CIV/J115120.46+543733.08.json'
igmsl = IGMSightline.from_json(sl_file)
igmsys = igmsl.make_igmsystems(vsys=400 * u.km / u.s)
# Galaxy
galaxy = Galaxy((178.84787, 54.65734), z=0.00283)
# Go
cgm_list = cgm_from_galaxy_igmsystems(galaxy, igmsys, correct_lowz=True)
assert len(cgm_list) == 1
np.testing.assert_allclose(cgm_list[0].rho.value, 189.01377)
def test_to_dict():
from linetools import utils as ltu
radec = (125 * u.deg, 45.2 * u.deg)
gal = Galaxy(radec, z=0.3)
radec_qso = (125 * u.deg, 45.203 * u.deg)
igmsys = IGMSystem(radec_qso,
gal.z, [-500, 500] * u.km / u.s,
abs_type='CGM')
# Instantiate
cgmabs = CGMAbsSys(gal, igmsys)
# Test
cdict = cgmabs.to_dict()
ltu.savejson('tmp.json', cdict, overwrite=True)
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 test_to_dict():
radec = (125 * u.deg, 45.2 * u.deg)
gal = Galaxy(radec, z=0.3)
radec_qso = (125 * u.deg, 45.203 * u.deg)
igmsys = IGMSystem(radec_qso,
gal.z, [-500, 500] * u.km / u.s,
abs_type='CGM')
# Instantiate
cgmabs = CGMAbsSys(gal, igmsys)
# Test
cdict = cgmabs.to_dict()
with io.open('tmp.json', 'w', encoding='utf-8') as f:
f.write(
unicode(
json.dumps(cdict,
sort_keys=True,
indent=4,
separators=(',', ': '))))
def calc_rho(coords1,
coords2,
z2,
cosmo,
ang_sep=None,
correct_lowz=True,
z_low=0.05,
comoving=False,
**kwargs):
""" Calculate the impact parameter between coordinates at a redshift (or redshifts)
Parameters
----------
coords1 : SkyCoord (one or more)
If more than one, size must match coords2
coords2 : SkyCoord (one or more)
z2 : float or ndarray
Redshifts of sources at coords2
cosmo : astropy.cosmology
z_low : float, optional
Redshift below which corrections for the local universe would be applied
correct_lowz : bool, optional
Apply corrections for the local universe, as desired
Only those with z < z_low
Follows Mould et al. 2000
ang_sep : Angle or Quantity
Input angular separation
May speed up calculation
comoving : bool, optional
If True then comoving, else physical
Returns
-------
rho : Quantity
impact parameter(s) in physical kpc
ang_sep : Angle
separation in arcsec
"""
# Handle inputs
if isinstance(z2, float): # recast as arrays
z2 = np.array([z2])
coords2 = SkyCoord([coords2])
if not (coords2.size == z2.size):
raise IOError("Length of z2 must match coords2")
if coords1.size > 1:
if coords2.size != coords1.size:
raise IOError("Length of coords1 must match coords2")
# ang_sep
if ang_sep is None:
ang_sep = coords1.separation(coords2).to('arcsec')
# Init rho
rho = np.zeros_like(z2, dtype=np.float64) * u.kpc
# Handle cases where object's distance needs correction from peculiar velocities
# This is especially important at very low redshifts
lowz = z2 < z_low
if correct_lowz and np.any(lowz):
# Ugly for loop for now
for idx in np.where(lowz)[0]:
# Call Mould correction
velcorrdict = velcorr_mould(Galaxy(coords2[idx], z=z2[idx]),
cosmo=cosmo)
kpc_amin = velcorrdict['scale'].to(u.kpc / u.arcmin)
rho[idx] = ang_sep.to('arcmin')[idx] * kpc_amin
# Higher z
highz = ~lowz
else:
highz = np.array([True] * len(z2))
if np.any(highz):
if comoving:
kpc_amin = cosmo.kpc_comoving_per_arcmin(
z2[highz]) # kpc per arcmin
else:
kpc_amin = cosmo.kpc_proper_per_arcmin(z2[highz])
rho[highz] = ang_sep.to('arcmin')[highz] * kpc_amin
# Recast as float?
if coords2.size == 1:
rho = rho[0]
ang_sep = ang_sep[0]
# Return
return rho, ang_sep
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 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 cgmabssys_from_sightline_field(field,
sightline,
rho_max=300. * u.kpc,
minz=0.001,
maxz=None,
dv_max=400. * u.km / u.s,
embuffer=None,
dummysys=True,
dummyspec=None,
linelist=None,
debug=False,
**kwargs):
"""Instantiate list of CgmAbsSys objects from IgmgGalaxyField and IGMSightline.
Parameters
----------
field : IgmGalaxyField
sightline : IGMSightline
rho_max : Quantity, optional
Maximum impact parameter for associated galaxies
minz : float, optional
Minimum redshift for galaxy/absorber search
maxz : float, optional
Maximum redshift for galaxy/absorber search
dv_max : Quantity, optional
Maximum galaxy-absorber velocity separation
embuffer : Quantity, optional
Velocity buffer between background source (e.g., QSO) and CGMAbsSys
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.
dummyspec : XSpectrum1D, optional
Spectrum object to attach to dummy AbsLine/AbsComponent objects when
adding IGMSystems if dummysys is True
linelist : LineList, optional
ListList from which to add dummy line in case of no IGMSystem match
Returns
-------
cgmabslist : list
List of CgmAbsSys objects
"""
if dummyspec is None:
dummyspec = sightline._abssystems[0]._components[0]._abslines[0].analy[
'spec']
if linelist is None:
from linetools.spectralline import AbsLine
linelist = LineList('ISM')
if embuffer is not None:
try:
bufmax = ltu.z_from_dv(-embuffer, field.zem)
if maxz is not None:
zmax = np.max(bufmax, maxz)
else:
zmax = bufmax
except:
zmax = maxz
else:
zmax = maxz
closegals = get_close_galaxies(field, rho_max, minz, zmax)
if debug:
closegals = closegals[0:10]
cgmabslist = []
for i, gal in enumerate(closegals):
#print('i={:d}'.format(i))
galobj = Galaxy((gal['RA'], gal['DEC']), z=gal['Z'])
cgmobj = cgm_from_galaxy_igmsystems(galobj,
sightline._abssystems,
dv_max=dv_max,
dummysys=dummysys,
dummyspec=dummyspec,
rho_max=rho_max,
linelist=linelist,
**kwargs)
cgmabslist.extend(cgmobj)
return cgmabslist
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):
#
#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)
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 load_single_fits(self, inp, skip_ions=False, verbose=True, **kwargs):
""" Load a single COS-Halos sightline
Appends to cgm_abs list
Parameters
----------
inp : tuple or str
if tuple -- (field,gal_id)
field: str
Name of field (e.g. 'J0226+0015')
gal_id: str
Name of galaxy (e.g. '268_22')
skip_ions : bool, optional
Avoid loading the ions (not recommended)
verbose : bool, optional
"""
# Parse input
if isinstance(inp, basestring):
fil = inp
elif isinstance(inp, tuple):
field, gal_id = inp
tmp = self.fits_path+'/'+field+'.'+gal_id+'.fits.gz'
fils = glob.glob(tmp)
if len(fils) != 1:
raise IOError('Bad field, gal_id: {:s}'.format(tmp))
fil = fils[0]
else:
raise IOError('Bad input to load_single')
# Read COS-Halos file
if verbose:
print('cos_halos: Reading {:s}'.format(fil))
hdu = fits.open(fil)
summ = Table(hdu[1].data)
galx = Table(hdu[2].data)
# Instantiate the galaxy
gal = Galaxy((galx['RA'][0], galx['DEC'][0]), z=summ['ZFINAL'][0])
gal.field = galx['FIELD'][0]
gal.gal_id = galx['GALID'][0]
# Galaxy properties
gal.halo_mass = summ['LOGMHALO'][0]
gal.stellar_mass = summ['LOGMFINAL'][0]
gal.rvir = galx['RVIR'][0]
gal.MH = galx['ABUN'][0]
gal.flag_MH = galx['ABUN_FLAG'][0]
gal.sdss_phot = [galx[key][0] for key in ['SDSSU','SDSSG','SDSSR','SDSSI','SDSSZ']]
gal.sdss_phot_sig = [galx[key][0] for key in ['SDSSU_ERR','SDSSG_ERR','SDSSR_ERR','SDSSI_ERR','SDSSZ_ERR']]
gal.sfr = (galx['SFR_UPLIM'][0], galx['SFR'][0],
galx['SFR_FLAG'][0]) # FLAG actually gives method used
gal.ssfr = galx['SSFR'][0]
# Instantiate the IGM System
igm_sys = IGMSystem((galx['QSORA'][0], galx['QSODEC'][0]),
summ['ZFINAL'][0], [-600, 600.]*u.km/u.s,
abs_type='CGM')
igm_sys.zqso = galx['ZQSO'][0]
# Instantiate
cgabs = CGMAbsSys(gal, igm_sys, name=gal.field+'_'+gal.gal_id, **kwargs)
# EBV
cgabs.ebv = galx['EBV'][0]
# Ions
if skip_ions is True:
# NHI
dat_tab = Table(hdu[3].data)
#if dat_tab['Z'] != 1:
# raise ValueError("Uh oh")
cgabs.igm_sys.NHI = dat_tab['CLM'][0]
cgabs.igm_sys.sig_NHI = dat_tab['SIG_CLM'][0]
cgabs.igm_sys.flag_NHI = dat_tab['FLG_CLM'][0]
self.cgm_abs.append(cgabs)
return
all_Z = []
all_ion = []
for jj in range(summ['NION'][0]):
iont = hdu[3+jj].data
if jj == 0: # Generate new Table
dat_tab = Table(iont)
else:
try:
dat_tab.add_row(Table(iont)[0])
except:
pdb.set_trace()
all_Z.append(iont['ZION'][0][0])
all_ion.append(iont['ZION'][0][1])
# AbsLines
abslines = []
ntrans = len(np.where(iont['LAMBDA'][0] > 1.)[0])
for kk in range(ntrans):
flg = iont['FLG'][0][kk]
# Fill in
aline = AbsLine(iont['LAMBDA'][0][kk]*u.AA, closest=True)
aline.attrib['flag_origCH'] = int(flg)
aline.attrib['EW'] = iont['WOBS'][0][kk]*u.AA/1e3 # Observed
aline.attrib['sig_EW'] = iont['SIGWOBS'][0][kk]*u.AA/1e3
if aline.attrib['EW'] > 3.*aline.attrib['sig_EW']:
aline.attrib['flag_EW'] = 1
else:
aline.attrib['flag_EW'] = 3
# Force an upper limit (i.e. from a blend)
if (flg == 2) or (flg == 4) or (flg == 6):
aline.attrib['flag_EW'] = 3
#
aline.analy['vlim'] = [iont['VMIN'][0][kk],iont['VMAX'][0][kk]]*u.km/u.s
aline.attrib['z'] = igm_sys.zabs
aline.attrib['coord'] = igm_sys.coord
# Check f
if (np.abs(aline.data['f']-iont['FVAL'][0][kk])/aline.data['f']) > 0.001:
Nscl = iont['FVAL'][0][kk] / aline.data['f']
flag_f = True
else:
Nscl = 1.
flag_f = False
# Colm
if ((flg % 2) == 0) or (flg == 15) or (flg == 13):
flgN = 0
print('Skipping column contribution from {:g} as NG for a line; flg={:d}'.format(iont['LAMBDA'][0][kk],flg))
elif (flg == 1) or (flg == 3):
flgN = 1
elif (flg == 5) or (flg == 7):
flgN = 3
elif (flg == 9) or (flg == 11):
flgN = 2
else:
pdb.set_trace()
raise ValueError("Bad flag!")
if flgN == 3:
aline.attrib['logN'] = iont['LOGN2SIG'][0][kk] + np.log10(Nscl)
aline.attrib['sig_logN'] = 9.
elif flgN == 0: # Not for N measurement
pass
else:
aline.attrib['logN'] = iont['LOGN'][0][kk] + np.log10(Nscl)
aline.attrib['sig_logN'] = iont['SIGLOGN'][0][kk]
aline.attrib['flag_N'] = int(flgN)
#pdb.set_trace()
if flgN != 0:
_,_ = ltaa.linear_clm(aline.attrib)
# Append
abslines.append(aline)
# Component
if len(abslines) == 0:
comp = AbsComponent(cgabs.igm_sys.coord,
(iont['ZION'][0][0],iont['ZION'][0][1]),
igm_sys.zabs, igm_sys.vlim)
else:
comp = AbsComponent.from_abslines(abslines, chk_vel=False)
if comp.Zion != (1,1):
comp.synthesize_colm() # Combine the abs lines
if np.abs(comp.logN - float(iont['CLM'][0])) > 0.15:
print("New colm for ({:d},{:d}) and sys {:s} is {:g} different from old".format(
comp.Zion[0], comp.Zion[1], cgabs.name, comp.logN - float(iont['CLM'][0])))
if comp.flag_N != iont['FLG_CLM'][0]:
if comp.flag_N == 0:
pass
else:
print("New flag for ({:d},{:d}) and sys {:s} is different from old".format(
comp.Zion[0], comp.Zion[1], cgabs.name))
pdb.set_trace()
#_,_ = ltaa.linear_clm(comp)
cgabs.igm_sys.add_component(comp)
self.cgm_abs.append(cgabs)
# Add Z,ion
dat_tab.add_column(Column(all_Z,name='Z'))
dat_tab.add_column(Column(all_ion,name='ion'))
# Rename
dat_tab.rename_column('LOGN','indiv_logN')
dat_tab.rename_column('SIGLOGN','indiv_sig_logN')
dat_tab.rename_column('CLM','logN')
dat_tab.rename_column('SIG_CLM','sig_logN')
dat_tab.rename_column('FLG_CLM','flag_N')
# Set
self.cgm_abs[-1].igm_sys._ionN = dat_tab
# NHI
HI = (dat_tab['Z'] == 1) & (dat_tab['ion'] == 1)
if np.sum(HI) > 0:
self.cgm_abs[-1].igm_sys.NHI = dat_tab[HI]['logN'][0]
self.cgm_abs[-1].igm_sys.sig_NHI = dat_tab[HI]['sig_logN'][0]
self.cgm_abs[-1].igm_sys.flag_NHI = dat_tab[HI]['flag_N'][0]
else:
warnings.warn("No HI measurement for {}".format(self.cgm_abs[-1]))
self.cgm_abs[-1].igm_sys.flag_NHI = 0
def load_single_fits(self, inp, skip_ions=False, verbose=True, **kwargs):
""" Load a single COS-Halos sightline
Appends to cgm_abs list
Parameters
----------
inp : tuple or str
if tuple -- (field,gal_id)
field: str
Name of field (e.g. 'J0226+0015')
gal_id: str
Name of galaxy (e.g. '268_22')
skip_ions : bool, optional
Avoid loading the ions (not recommended)
verbose : bool, optional
"""
# Parse input
if isinstance(inp, basestring):
fil = inp
elif isinstance(inp, tuple):
field, gal_id = inp
tmp = self.fits_path + '/' + field + '.' + gal_id + '.fits.gz'
fils = glob.glob(tmp)
if len(fils) != 1:
raise IOError('Bad field, gal_id: {:s}'.format(tmp))
fil = fils[0]
else:
raise IOError('Bad input to load_single')
# Read COS-Halos file
if verbose:
print('cos_halos: Reading {:s}'.format(fil))
hdu = fits.open(fil)
summ = Table(hdu[1].data)
galx = Table(hdu[2].data)
# Instantiate the galaxy
gal = Galaxy((galx['RA'][0], galx['DEC'][0]), z=summ['ZFINAL'][0])
gal.field = galx['FIELD'][0]
gal.gal_id = galx['GALID'][0]
# Galaxy properties
gal.halo_mass = summ['LOGMHALO'][0]
gal.stellar_mass = summ['LOGMFINAL'][0]
gal.rvir = galx['RVIR'][0]
gal.MH = galx['ABUN'][0]
gal.flag_MH = galx['ABUN_FLAG'][0]
gal.sdss_phot = [
galx[key][0]
for key in ['SDSSU', 'SDSSG', 'SDSSR', 'SDSSI', 'SDSSZ']
]
gal.sdss_phot_sig = [
galx[key][0] for key in
['SDSSU_ERR', 'SDSSG_ERR', 'SDSSR_ERR', 'SDSSI_ERR', 'SDSSZ_ERR']
]
gal.sfr = (galx['SFR_UPLIM'][0], galx['SFR'][0], galx['SFR_FLAG'][0]
) # FLAG actually gives method used
gal.ssfr = galx['SSFR'][0]
# Instantiate the IGM System
igm_sys = IGMSystem((galx['QSORA'][0], galx['QSODEC'][0]),
summ['ZFINAL'][0], [-600, 600.] * u.km / u.s,
abs_type='CGM')
igm_sys.zqso = galx['ZQSO'][0]
# Instantiate
cgabs = CGMAbsSys(gal,
igm_sys,
name=gal.field + '_' + gal.gal_id,
**kwargs)
# EBV
cgabs.ebv = galx['EBV'][0]
# Ions
if skip_ions is True:
# NHI
dat_tab = Table(hdu[3].data)
#if dat_tab['Z'] != 1:
# raise ValueError("Uh oh")
cgabs.igm_sys.NHI = dat_tab['CLM'][0]
cgabs.igm_sys.sig_NHI = dat_tab['SIG_CLM'][0]
cgabs.igm_sys.flag_NHI = dat_tab['FLG_CLM'][0]
self.cgm_abs.append(cgabs)
return
all_Z = []
all_ion = []
for jj in range(summ['NION'][0]):
iont = hdu[3 + jj].data
if jj == 0: # Generate new Table
dat_tab = Table(iont)
else:
try:
dat_tab.add_row(Table(iont)[0])
except:
pdb.set_trace()
all_Z.append(iont['ZION'][0][0])
all_ion.append(iont['ZION'][0][1])
# AbsLines
abslines = []
ntrans = len(np.where(iont['LAMBDA'][0] > 1.)[0])
for kk in range(ntrans):
flg = iont['FLG'][0][kk]
# Fill in
aline = AbsLine(iont['LAMBDA'][0][kk] * u.AA, closest=True)
aline.attrib['flag_origCH'] = int(flg)
aline.attrib[
'EW'] = iont['WOBS'][0][kk] * u.AA / 1e3 # Observed
aline.attrib['sig_EW'] = iont['SIGWOBS'][0][kk] * u.AA / 1e3
if aline.attrib['EW'] > 3. * aline.attrib['sig_EW']:
aline.attrib['flag_EW'] = 1
else:
aline.attrib['flag_EW'] = 3
# Force an upper limit (i.e. from a blend)
if (flg == 2) or (flg == 4) or (flg == 6):
aline.attrib['flag_EW'] = 3
#
aline.analy['vlim'] = [
iont['VMIN'][0][kk], iont['VMAX'][0][kk]
] * u.km / u.s
aline.attrib['z'] = igm_sys.zabs
aline.attrib['coord'] = igm_sys.coord
# Check f
if (np.abs(aline.data['f'] - iont['FVAL'][0][kk]) /
aline.data['f']) > 0.001:
Nscl = iont['FVAL'][0][kk] / aline.data['f']
flag_f = True
else:
Nscl = 1.
flag_f = False
# Colm
if ((flg % 2) == 0) or (flg == 15) or (flg == 13):
flgN = 0
print(
'Skipping column contribution from {:g} as NG for a line; flg={:d}'
.format(iont['LAMBDA'][0][kk], flg))
elif (flg == 1) or (flg == 3):
flgN = 1
elif (flg == 5) or (flg == 7):
flgN = 3
elif (flg == 9) or (flg == 11):
flgN = 2
else:
pdb.set_trace()
raise ValueError("Bad flag!")
if flgN == 3:
aline.attrib['logN'] = iont['LOGN2SIG'][0][kk] + np.log10(
Nscl)
aline.attrib['sig_logN'] = 9.
elif flgN == 0: # Not for N measurement
pass
else:
aline.attrib['logN'] = iont['LOGN'][0][kk] + np.log10(Nscl)
aline.attrib['sig_logN'] = iont['SIGLOGN'][0][kk]
aline.attrib['flag_N'] = int(flgN)
#pdb.set_trace()
if flgN != 0:
_, _ = ltaa.linear_clm(aline.attrib)
# Append
abslines.append(aline)
# Component
if len(abslines) == 0:
comp = AbsComponent(cgabs.igm_sys.coord,
(iont['ZION'][0][0], iont['ZION'][0][1]),
igm_sys.zabs, igm_sys.vlim)
else:
comp = AbsComponent.from_abslines(abslines, chk_vel=False)
if comp.Zion != (1, 1):
comp.synthesize_colm() # Combine the abs lines
if np.abs(comp.logN - float(iont['CLM'][0])) > 0.15:
print(
"New colm for ({:d},{:d}) and sys {:s} is {:g} different from old"
.format(comp.Zion[0], comp.Zion[1], cgabs.name,
comp.logN - float(iont['CLM'][0])))
if comp.flag_N != iont['FLG_CLM'][0]:
if comp.flag_N == 0:
pass
else:
print(
"New flag for ({:d},{:d}) and sys {:s} is different from old"
.format(comp.Zion[0], comp.Zion[1],
cgabs.name))
pdb.set_trace()
#_,_ = ltaa.linear_clm(comp)
cgabs.igm_sys.add_component(comp)
self.cgm_abs.append(cgabs)
# Add Z,ion
dat_tab.add_column(Column(all_Z, name='Z'))
dat_tab.add_column(Column(all_ion, name='ion'))
# Rename
dat_tab.rename_column('LOGN', 'indiv_logN')
dat_tab.rename_column('SIGLOGN', 'indiv_sig_logN')
dat_tab.rename_column('CLM', 'logN')
dat_tab.rename_column('SIG_CLM', 'sig_logN')
dat_tab.rename_column('FLG_CLM', 'flag_N')
# Set
self.cgm_abs[-1].igm_sys._ionN = dat_tab
# NHI
HI = (dat_tab['Z'] == 1) & (dat_tab['ion'] == 1)
if np.sum(HI) > 0:
self.cgm_abs[-1].igm_sys.NHI = dat_tab[HI]['logN'][0]
self.cgm_abs[-1].igm_sys.sig_NHI = dat_tab[HI]['sig_logN'][0]
self.cgm_abs[-1].igm_sys.flag_NHI = dat_tab[HI]['flag_N'][0]
else:
warnings.warn("No HI measurement for {}".format(self.cgm_abs[-1]))
self.cgm_abs[-1].igm_sys.flag_NHI = 0