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 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)
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)
