def test_stau():
# Generate stau
_, velo, fx, sig = dummy_spec()
stau = generate_stau(velo, fx, sig)
np.testing.assert_allclose(stau[1000], 0.27800134641010432)
# Different binning now
stau2 = generate_stau(velo, fx, sig, kbin=35*u.km/u.s)
np.testing.assert_allclose(stau2[1000], 0.17871515126363854)
def test_pw97():
# Generate stau
_, velo, fx, sig = dummy_spec()
stau = generate_stau(velo, fx, sig)
# pw97
kin_data = pw97_kin(velo, stau)
np.testing.assert_allclose(kin_data['Dv'].value, 20.)
np.testing.assert_allclose(kin_data['fedg'], 0.37035142148289424)
def measure_kin(self, **kwargs):
""" Measure Kinematics
"""
from linetools.analysis import abskin
fx, sig, cdict = self.cut_spec()
stau = abskin.generate_stau(cdict['velo'], fx, sig, **kwargs)
# Measure
kin_data = abskin.pw97_kin(cdict['velo'], stau, **kwargs)
# Save
self.attrib['kin'] = kin_data
def measure_kin(self, **kwargs):
""" Measure Kinematics
"""
from linetools.analysis import abskin
fx, sig, cdict = self.cut_spec()
stau = abskin.generate_stau(cdict['velo'], fx, sig, **kwargs)
# Measure
kin_data = abskin.pw97_kin(cdict['velo'], stau, **kwargs)
# Save
self.attrib['kin'] = kin_data
def test_cgmkin():
# Grab spectrum
wave, velo, fx, sig = dummy_spec()
# stau
stau = generate_stau(velo, fx, sig)
# CGM
kin_data = cgm_kin(velo, stau)
for tst in [u'zero_pk', u'delta_v', u'X_fcover', u'JF_fcover', u'v_peak']:
assert tst in kin_data.keys()
np.testing.assert_allclose(kin_data['delta_v'].value, -164.9989, rtol=1e-5)
"""
def load_abskin(self, flg=1, kin_file=None, kin_init_file=None):
""" Load the absorption-line kinematic data for COS-Halos (or COS-Dwarfs)
Calculate from scratch if needed
Parameters
----------
flg: int, optional
Flag indicating how to load the data
0 = Load from file
1 = Generate
kin_init_file: str
Name of kinematics driver file
kin_file: str
Name of kinematics output file [First made for John Forbes]
"""
if flg == 0: # Load
if kin_file is None:
kin_file = os.path.abspath(
os.environ.get('DROPBOX_DIR') + '/COS-Halos/Kin/' +
'COS-Halos_kin.fits')
hdu = fits.open(kin_file)
# Metals
metals = Table(hdu[1].data)
for row in metals:
mt = np.where((row['field'] == self.field)
& (row['gal_id'] == self.gal_id))[0]
pdb.set_trace()
elif flg == 1: # Generate
# Read init file
if kin_init_file is None:
kin_init_file = self.kin_init_file
kin_init = ascii.read(kin_init_file, guess=False)
# Loop to my loop
fgal = zip(self.field, self.gal_id)
for qq, cgm_abs in enumerate(self.cgm_abs):
# Match to kin_init
mt = np.where((kin_init['QSO'] == cgm_abs.field)
& (kin_init['Galaxy'] == cgm_abs.gal_id))[0]
if len(mt) == 0:
warnings.warn(
'load_kin: No kinematics for {:s}, {:s}'.format(
cgm_abs.field, cgm_abs.gal_id))
continue
mt = mt[0]
# Metals
if kin_init['flgL'][mt] > 0:
wrest = kin_init['mtl_wr'][mt] * u.AA
if wrest.value <= 1:
pdb.set_trace()
spec = self.load_bg_cos_spec(qq, wrest)
vmnx = (kin_init['L_vmn'][mt],
kin_init['L_vmx'][mt]) * u.km / u.s
# Process
aline = AbsLine(wrest)
aline.analy['spec'] = spec
aline.analy['vlim'] = vmnx
aline.attrib['z'] = cgm_abs.igm_sys.zabs
fx, sig, cdict = aline.cut_spec()
# Kin
stau = laak.generate_stau(cdict['velo'], fx, sig)
cgm_abs.igm_sys.kin['Metal'] = laak.pw97_kin(cdict['velo'],
stau,
per=0.07)
cgm_abs.igm_sys.kin['Metal'].update(
laak.cgm_kin(cdict['velo'], stau, per=0.07))
# Save spec
#cgm_abs.igm_sys.kin['Metal']['spec'] = spec
else:
cgm_abs.igm_sys.kin['Metal'] = {}
# HI
if kin_init['flgH'][mt] > 0:
wrest = kin_init['HI_wrest'][mt] * u.AA
if wrest.value <= 1:
pdb.set_trace()
spec = self.load_bg_cos_spec(qq, wrest)
if spec is None:
pdb.set_trace()
vmnx = (kin_init['HIvmn'][mt],
kin_init['HIvmx'][mt]) * u.km / u.s
# Process
aline = AbsLine(wrest)
aline.analy['spec'] = spec
aline.analy['vlim'] = vmnx
aline.attrib['z'] = cgm_abs.igm_sys.zabs
fx, sig, cdict = aline.cut_spec()
# Kin
stau = laak.generate_stau(cdict['velo'], fx, sig)
cgm_abs.igm_sys.kin['HI'] = laak.pw97_kin(cdict['velo'],
stau,
per=0.07)
cgm_abs.igm_sys.kin['HI'].update(
laak.cgm_kin(cdict['velo'], stau, per=0.07))
else:
# Fill with zeros (for the keys)
cgm_abs.igm_sys.kin['HI'] = {}
def load_abskin(self, flg=1, kin_file=None, kin_init_file=None):
""" Load the absorption-line kinematic data for COS-Halos (or COS-Dwarfs)
Calculate from scratch if needed
Parameters
----------
flg: int, optional
Flag indicating how to load the data
0 = Load from file
1 = Generate
kin_init_file: str
Name of kinematics driver file
kin_file: str
Name of kinematics output file [First made for John Forbes]
"""
if flg == 0: # Load
if kin_file is None:
kin_file = os.path.abspath(os.environ.get('DROPBOX_DIR')+'/COS-Halos/Kin/'+
'COS-Halos_kin.fits')
hdu = fits.open(kin_file)
# Metals
metals = Table(hdu[1].data)
for row in metals:
mt = np.where( (row['field']==self.field) &
(row['gal_id']==self.gal_id))[0]
pdb.set_trace()
elif flg == 1: # Generate
# Read init file
if kin_init_file is None:
kin_init_file = self.kin_init_file
kin_init = ascii.read(kin_init_file,guess=False)
# Loop to my loop
fgal = zip(self.field, self.gal_id)
for qq,cgm_abs in enumerate(self.cgm_abs):
# Match to kin_init
mt = np.where((kin_init['QSO'] == cgm_abs.field) &
(kin_init['Galaxy'] == cgm_abs.gal_id))[0]
if len(mt) == 0:
warnings.warn('load_kin: No kinematics for {:s}, {:s}'.format(cgm_abs.field,
cgm_abs.gal_id))
continue
mt = mt[0]
# Metals
if kin_init['flgL'][mt] > 0:
wrest = kin_init['mtl_wr'][mt]*u.AA
if wrest.value <= 1:
pdb.set_trace()
spec = self.load_bg_cos_spec(qq, wrest)
vmnx = (kin_init['L_vmn'][mt], kin_init['L_vmx'][mt])*u.km/u.s
# Process
aline = AbsLine(wrest)
aline.analy['spec'] = spec
aline.analy['vlim'] = vmnx
aline.attrib['z'] = cgm_abs.igm_sys.zabs
fx, sig, cdict = aline.cut_spec()
# Kin
stau = laak.generate_stau(cdict['velo'], fx, sig)
cgm_abs.igm_sys.kin['Metal'] = laak.pw97_kin(cdict['velo'], stau, per=0.07)
cgm_abs.igm_sys.kin['Metal'].update(laak.cgm_kin(cdict['velo'], stau, per=0.07))
# Save spec
#cgm_abs.igm_sys.kin['Metal']['spec'] = spec
else:
cgm_abs.igm_sys.kin['Metal'] = {}
# HI
if kin_init['flgH'][mt] > 0:
wrest = kin_init['HI_wrest'][mt]*u.AA
if wrest.value <= 1:
pdb.set_trace()
spec = self.load_bg_cos_spec( qq, wrest )
if spec is None:
pdb.set_trace()
vmnx = (kin_init['HIvmn'][mt], kin_init['HIvmx'][mt])*u.km/u.s
# Process
aline = AbsLine(wrest)
aline.analy['spec'] = spec
aline.analy['vlim'] = vmnx
aline.attrib['z'] = cgm_abs.igm_sys.zabs
fx, sig, cdict = aline.cut_spec()
# Kin
stau = laak.generate_stau(cdict['velo'], fx, sig)
cgm_abs.igm_sys.kin['HI'] = laak.pw97_kin(cdict['velo'], stau, per=0.07)
cgm_abs.igm_sys.kin['HI'].update(laak.cgm_kin(cdict['velo'], stau, per=0.07))
else:
# Fill with zeros (for the keys)
cgm_abs.igm_sys.kin['HI'] = {}