def test_use():
# Init
llim = zLimits(1., (0.999, 1.001), wrest=1215.67 * u.AA)
# Use
np.testing.assert_allclose(llim.zlim, (0.999, 1.001))
np.testing.assert_allclose(llim.wvlim.value, [2430.12433, 2432.55567])
np.testing.assert_allclose(llim.vlim.value, [-149.93370, 149.858755])
assert llim.vlim.unit == u.km / u.s
# Print
print(llim)
def test_set():
# Init
zlim = (0.999, 1.001)
llim = zLimits(1., zlim, wrest=1215.67 * u.AA)
# Set
llim.set(zlim)
np.testing.assert_allclose(llim.wvlim.value, [2430.12433, 2432.55567])
llim.set([2430., 2433.] * u.AA)
np.testing.assert_allclose(llim.vlim.value, [-165.27207033, 204.61374917])
llim.set([-160., 200] * u.km / u.s)
def test_init():
# Init
zlim = (0.999, 1.001)
llim = zLimits(1., zlim)
# Init
zlim = (0.999, 1.001)
llim = zLimits(1., zlim, wrest=1215.67 * u.AA)
# Test
with pytest.raises(AttributeError):
llim.zlim = 3
# AbsLine
lya = AbsLine('HI 1215')
z = 1.
zlim = (0.999, 1.001)
llim = zLimits.from_specline(lya, z, zlim)
# Bad zlim
with pytest.raises(IOError):
llim = zLimits(1., (1.1, 1.2), wrest=1215.67 * u.AA, chk_z=True)
# Null zlim
llim = zLimits(1., (1., 1), wrest=1215.67 * u.AA)
assert llim.is_set() is False
def update_component_vel(self):
"""Change the velocities of each component to rest frame of zsys
"""
from linetools.analysis.zlimits import zLimits
for i, comp in enumerate(self._components):
dv = ltu.dv_from_z(comp.zcomp, self.zabs)
zmin = ltu.z_from_dv(comp.limits.vlim[0] + dv, self.zabs)
zmax = ltu.z_from_dv(comp.limits.vlim[1] + dv, self.zabs)
newzlim = zLimits(self.zabs, (zmin, zmax))
comp.limits = newzlim
comp.attrib['vel'] = comp.attrib['vel'] + dv
def __init__(self,
radec,
Zion,
zcomp,
vlim,
Ej=0. / u.cm,
A=None,
Ntup=None,
comment='',
name=None,
stars=None,
reliability='none'):
""" Initiator
Parameters
----------
radec : tuple or SkyCoord
(RA,DEC) in deg or astropy.coordinate.SkyCoord
Zion : tuple
Atomic number, ion -- (int,int)
e.g. (8,1) for OI
Note: (-1, -1) is special and is meant for moleculer (e.g. H2)
This notation will most likely change in the future.
zcomp : float
Absorption component redshift
vlim : Quantity array
Velocity limits of the component w/r to `z`
e.g. [-300,300]*u.km/u.s
A : int, optional
Atomic mass -- used to distinguish isotopes
Ntup : tuple
(int,float,two-element list,tuple or array)
(flag_N, logN, sig_logN)
flag_N : Flag describing N measurement (0: no info; 1: detection; 2: saturated; 3: non-detection)
logN : log10 N column density
sig_logN : Error in log10 N. Two elements are expected but not required
Ej : Quantity, optional
Energy of lower level (1/cm)
stars : str, optional
asterisks to add to name, e.g. '**' for CI**
Required if name=None and Ej>0.
reliability : str, optional
Reliability of AbsComponent
'a' - reliable
'b' - possible
'c' - uncertain
'none' - not defined (default)
comment : str, optional
A comment, default is ``
"""
# Required
self.coord = ltu.radec_to_coord(radec)
self.Zion = Zion
# Limits
zlim = ltu.z_from_dv(vlim, zcomp)
self.limits = zLimits(zcomp, zlim.tolist())
# Attributes
self.attrib = init_attrib.copy()
# Optional
self.A = A
self.Ej = Ej
self.stars = stars
self.comment = comment
if Ntup is not None:
self.attrib['flag_N'] = Ntup[0]
self.attrib['logN'] = Ntup[1]
if isiterable(Ntup[2]):
self.attrib['sig_logN'] = np.array(Ntup[2])
else:
self.attrib['sig_logN'] = np.array([Ntup[2]] * 2)
_, _ = ltaa.linear_clm(self.attrib) # Set linear quantities
# Name
if (name is None) and (self.Zion != (-1, -1)):
iname = ions.ion_to_name(self.Zion, nspace=0)
if self.Ej.value > 0: # Need to put *'s in name
if stars is not None:
iname += stars
else:
warnings.warn(
"No stars provided. Adding one because Ej > 0.")
iname += '*'
self.name = '{:s}_z{:0.5f}'.format(iname, self.zcomp)
elif (name is None) and (self.Zion == (-1, -1)):
self.name = 'mol_z{:0.5f}'.format(self.zcomp)
else:
self.name = name
# reliability
if reliability not in ['a', 'b', 'c', 'none']:
raise ValueError(
"Input reliability `{}` not valid.".format(reliability))
self.reliability = reliability
# AbsLines
self._abslines = []
def test_to_dict():
# Init
llim = zLimits(1., (0.999, 1.001), wrest=1215.67 * u.AA)
ldict = llim.to_dict()
for key in ['vlim', 'wrest', 'wvlim', 'z', 'zlim']:
assert key in ldict.keys()
def from_dict(cls, idict, coord=None, warn_only=False, chk_data=True, **kwargs):
""" Initialize from a dict (usually read from disk)
Parameters
----------
idict : dict
dict with the Line parameters
chk_data : bool, optional
Check atomic data in dict against current values in LineList
warn_only : bool, optional
If the chk_data is performed and the values do not match, only
throw a Warning as opposed to crashing
Returns
-------
sline : SpectralLine
SpectralLine of the proper type
"""
# Init
if idict['ltype'] == 'Abs':
# TODO: remove this try/except eventually
try:
sline = AbsLine(idict['name'], **kwargs)
except KeyError: # This is to be compatible JSON files already written with old notation (e.g. DLA H100)
sline = AbsLine(idict['trans'], **kwargs)
elif idict['ltype'] == 'Em':
sline = EmLine(idict['name'], **kwargs)
else:
raise ValueError("Not prepared for type {:s}.".format(idict['ltype']))
# Check data
if chk_data:
#for key in idict['data']:
for key in sline.data.keys():
if key not in idict['data'].keys():
warnings.warn("Key {:s} not in your input dict".format(key))
continue
if isinstance(idict['data'][key], dict): # Assume Quantity
val = idict['data'][key]['value']
else:
val = idict['data'][key]
try:
assert sline.data[key] == val
except AssertionError:
if warn_only:
warnings.warn("Different data value for {:s}: {}, {}".format(key,sline.data[key],val))
# Set analy
for key in idict['analy'].keys():
if isinstance(idict['analy'][key], dict): # Assume Quantity
#sline.analy[key] = Quantity(idict['analy'][key]['value'],
# unit=idict['analy'][key]['unit'])
#pdb.set_trace()
sline.analy[key] = ltu.convert_quantity_in_dict(idict['analy'][key])
elif key == 'spec_file':
# spec_file is intended to be the name of the spectrum file
# spec is intended to hold an XSpectrum1D object
#warnings.warn("You will need to load {:s} into analy['spec'] yourself".format(
# idict['analy'][key]))
sline.analy[key] = idict['analy'][key]
else:
sline.analy[key] = idict['analy'][key]
# Set attrib
for key in idict['attrib'].keys():
if isinstance(idict['attrib'][key], dict):
sline.attrib[key] = ltu.convert_quantity_in_dict(idict['attrib'][key])
elif key in ['RA','DEC']:
if coord is None:
sline.attrib['coord'] = SkyCoord(ra=idict['attrib']['RA']*u.deg,
dec=idict['attrib']['DEC']*u.deg)
else:
sline.attrib['coord'] = coord
else:
sline.attrib[key] = idict['attrib'][key]
# Set z and limits
if 'z' in sline.attrib.keys(): # Backwards compatability
z = sline.attrib.pop('z')
else:
z = 0.
if 'limits' in idict.keys():
if 'wrest' not in idict['limits'].keys(): # compatibility with IGMGuesses
# import pdb; pdb.set_trace()
idict['limits']['wrest'] = ltu.jsonify(sline.wrest)
idict['limits']['z'] = z
sline.limits = zLimits.from_dict(idict['limits'])
else:
sline.limits = zLimits(z, [z,z], wrest=sline.wrest)
if 'vlim' in sline.analy.keys(): # Backwards compatability
if sline.analy['vlim'][1] > sline.analy['vlim'][0]:
sline.limits.set(sline.analy['vlim'])
elif 'wvlim' in sline.analy.keys(): # Backwards compatability
if sline.analy['wvlim'][1] > sline.analy['wvlim'][0]:
sline.limits.set(sline.analy['wvlim'])
return sline
def cgm_from_galaxy_igmsystems(galaxy,
igmsystems,
rho_max=300 * u.kpc,
dv_max=400 * u.km / u.s,
cosmo=None,
dummysys=False,
dummyspec=None,
verbose=True,
**kwargs):
""" Generate a list of CGMAbsSys objects given an input galaxy and a list of IGMSystems
Parameters
----------
galaxy : Galaxy
igmsystems : list
list of IGMSystems
rho_max : Quantity
Maximum projected separation from sightline to galaxy
dv_max
Maximum velocity offset between system and galaxy
dummysys: bool, optional
If True, instantiate CGMAbsSys even if no match is found in igmsystems
dummyspec : XSpectrum1D, optional
Spectrum object to attach to dummy AbsLine/AbsComponent objects when
adding IGMSystems if dummysys is True.
Returns
-------
cgm_list : list
list of CGM objects generated
"""
from pyigm.cgm.cgm import CGMAbsSys
# Cosmology
if cosmo is None:
cosmo = cosmology.Planck15
if dummysys is True:
if dummyspec is None:
dummyspec = igmsystems[0]._components[0]._abslines[0].analy['spec']
dummycoords = igmsystems[0].coord
# R -- speed things up
rho, angles = calc_cgm_rho(galaxy, igmsystems, cosmo, **kwargs)
if len(igmsystems) == 1: # Kludge
rho = u.Quantity([rho])
angles = u.Quantity([angles])
# dv
igm_z = np.array([igmsystem.zabs for igmsystem in igmsystems])
dv = ltu.dv_from_z(igm_z, galaxy.z)
# Rules
match = np.where((rho < rho_max) & (np.abs(dv) < dv_max))[0]
### If none, see if some system has a component that's actually within dv_max
if (len(match) == 0) & (rho[0] < rho_max):
zcomps = []
sysidxs = []
for i, csys in enumerate(igmsystems):
thesezs = [comp.zcomp for comp in csys._components]
sysidxs.extend([i] * len(thesezs))
zcomps.extend(thesezs)
zcomps = np.array(zcomps)
sysidxs = np.array(sysidxs)
dv_comps = ltu.dv_from_z(zcomps, galaxy.z)
match = np.unique(sysidxs[np.where(np.abs(dv_comps) < dv_max)[0]])
if len(match) == 0:
if dummysys is False:
print(
"No IGMSystem paired to this galaxy. CGM object not created.")
return []
else:
if verbose:
print("No IGMSystem match found. Attaching dummy IGMSystem.")
dummysystem = IGMSystem(dummycoords, galaxy.z, vlim=None)
dummycomp = AbsComponent(dummycoords, (1, 1), galaxy.z,
[-100., 100.] * u.km / u.s)
dummycomp.flag_N = 3
dummyline = AbsLine(
'HI 1215',
**kwargs) # Need an actual transition for comp check
dummyline.analy['spec'] = dummyspec
dummyline.attrib['coord'] = dummycoords
dummycomp.add_absline(dummyline, chk_vel=False, chk_sep=False)
dummysystem.add_component(dummycomp, chk_vel=False, chk_sep=False)
cgm = CGMAbsSys(galaxy, dummysystem, cosmo=cosmo, **kwargs)
cgm_list = [cgm]
else:
# Loop to generate
cgm_list = []
for imatch in match:
# Instantiate new IGMSystem
# Otherwise, updates to the IGMSystem cross-pollinate other CGMs
sysmatch = igmsystems[imatch]
newisys = sysmatch.copy()
# Handle z limits
zlim = ltu.z_from_dv((-dv_max.value, dv_max.value) * u.km / u.s,
galaxy.z)
newlims = zLimits(galaxy.z, zlim.tolist())
newisys.limits = newlims
# Allow for components extending beyond dv_max
newisys.update_vlim()
newisys.update_component_vel()
# Finish
cgm = CGMAbsSys(galaxy,
newisys,
cosmo=cosmo,
rho=rho[imatch],
ang_sep=angles[imatch],
**kwargs)
cgm_list.append(cgm)
# Return
return cgm_list
def from_dict(cls,
idict,
coord=None,
warn_only=False,
chk_data=True,
**kwargs):
""" Initialize from a dict (usually read from disk)
Parameters
----------
idict : dict
dict with the Line parameters
chk_data : bool, optional
Check atomic data in dict against current values in LineList
warn_only : bool, optional
If the chk_data is performed and the values do not match, only
throw a Warning as opposed to crashing
Returns
-------
sline : SpectralLine
SpectralLine of the proper type
"""
# Init
if idict['ltype'] == 'Abs':
# TODO: remove this try/except eventually
try:
sline = AbsLine(idict['name'], **kwargs)
except KeyError: # This is to be compatible JSON files already written with old notation (e.g. DLA H100)
sline = AbsLine(idict['trans'], **kwargs)
elif idict['ltype'] == 'Em':
sline = EmLine(idict['name'], **kwargs)
else:
raise ValueError("Not prepared for type {:s}.".format(
idict['ltype']))
# Check data
if chk_data:
#for key in idict['data']:
for key in sline.data.keys():
if key not in idict['data'].keys():
warnings.warn(
"Key {:s} not in your input dict".format(key))
continue
if isinstance(idict['data'][key], dict): # Assume Quantity
val = idict['data'][key]['value']
else:
val = idict['data'][key]
try:
assert sline.data[key] == val
except AssertionError:
if warn_only:
warnings.warn(
"Different data value for {:s}: {}, {}".format(
key, sline.data[key], val))
# Set analy
for key in idict['analy'].keys():
if isinstance(idict['analy'][key], dict): # Assume Quantity
#sline.analy[key] = Quantity(idict['analy'][key]['value'],
# unit=idict['analy'][key]['unit'])
#pdb.set_trace()
sline.analy[key] = ltu.convert_quantity_in_dict(
idict['analy'][key])
elif key == 'spec_file':
# spec_file is intended to be the name of the spectrum file
# spec is intendended to hold an XSpectrum1D object
warnings.warn(
"You will need to load {:s} into analy['spec'] yourself".
format(idict['analy'][key]))
sline.analy[key] = idict['analy'][key]
else:
sline.analy[key] = idict['analy'][key]
# Set attrib
for key in idict['attrib'].keys():
if isinstance(idict['attrib'][key], dict):
sline.attrib[key] = ltu.convert_quantity_in_dict(
idict['attrib'][key])
elif key in ['RA', 'DEC']:
if coord is None:
sline.attrib['coord'] = SkyCoord(
ra=idict['attrib']['RA'] * u.deg,
dec=idict['attrib']['DEC'] * u.deg)
else:
sline.attrib['coord'] = coord
else:
sline.attrib[key] = idict['attrib'][key]
# Set z and limits
if 'z' in sline.attrib.keys(): # Backwards compatability
z = sline.attrib.pop('z')
else:
z = 0.
if 'limits' in idict.keys():
if 'wrest' not in idict['limits'].keys(
): # compatibility with IGMGuesses
# import pdb; pdb.set_trace()
idict['limits']['wrest'] = ltu.jsonify(sline.wrest)
idict['limits']['z'] = z
sline.limits = zLimits.from_dict(idict['limits'])
else:
sline.limits = zLimits(z, [z, z], wrest=sline.wrest)
if 'vlim' in sline.analy.keys(): # Backwards compatability
if sline.analy['vlim'][1] > sline.analy['vlim'][0]:
sline.limits.set(sline.analy['vlim'])
elif 'wvlim' in sline.analy.keys(): # Backwards compatability
if sline.analy['wvlim'][1] > sline.analy['wvlim'][0]:
sline.limits.set(sline.analy['wvlim'])
return sline
def __init__(self,
radec,
zabs,
vlim,
zem=0.,
abs_type=None,
NHI=0.,
sig_NHI=np.zeros(2),
flag_NHI=None,
name=None,
**kwargs):
self.zem = zem
# Limits
zlim = ltu.z_from_dv(vlim, zabs)
self.limits = zLimits(zabs, zlim.tolist())
# NHI
self.NHI = NHI
self.sig_NHI = sig_NHI
# Special handling for the flag as this is often not input with NHI
if flag_NHI is None:
if NHI > 0.:
self.flag_NHI = 1
else:
self.flag_NHI = 0
else:
self.flag_NHI = flag_NHI
self.coord = ltu.radec_to_coord(radec)
if name is None:
self.name = 'J{:s}{:s}_z{:.6f}'.format( # Should be unique
self.coord.icrs.ra.to_string(unit=u.hour, sep='', pad=True),
self.coord.icrs.dec.to_string(sep='',
pad=True,
alwayssign=True), self.zabs)
else:
self.name = name
# Abs type
if abs_type is None:
self.abs_type = 'NONE'
else:
self.abs_type = abs_type
# Components
self._components = [] # List of AbsComponent objects
# Kinematics
self.kin = {}
# Metallicity
self.ZH = 0.
self.sig_ZH = 0.
self.flag_ZH = 0
# Abundances and Tables
self._EW = Table()
self._ionN = None # Needs to be None for fill_ion
self._trans = Table()
self._ionstate = {}
self._abund = Table()
# Refs (list of references)
self.Refs = []
def __init__(self, radec, Zion, zcomp, vlim, Ej=0./u.cm, A=None,
Ntup=None, comment='', name=None, stars=None, reliability='none'):
""" Initiator
Parameters
----------
radec : tuple or SkyCoord
(RA,DEC) in deg or astropy.coordinate.SkyCoord
Zion : tuple
Atomic number, ion -- (int,int)
e.g. (8,1) for OI
Note: (-1, -1) is special and is meant for moleculer (e.g. H2)
This notation will most likely change in the future.
zcomp : float
Absorption component redshift
vlim : Quantity array
Velocity limits of the component w/r to `z`
e.g. [-300,300]*u.km/u.s
A : int, optional
Atomic mass -- used to distinguish isotopes
Ntup : tuple
(int,float,two-element list,tuple or array)
(flag_N, logN, sig_logN)
flag_N : Flag describing N measurement (0: no info; 1: detection; 2: saturated; 3: non-detection)
logN : log10 N column density
sig_logN : Error in log10 N. Two elements are expected but not required
Ej : Quantity, optional
Energy of lower level (1/cm)
stars : str, optional
asterisks to add to name, e.g. '**' for CI**
Required if name=None and Ej>0.
reliability : str, optional
Reliability of AbsComponent
'a' - reliable
'b' - possible
'c' - uncertain
'none' - not defined (default)
comment : str, optional
A comment, default is ``
"""
# Required
self.coord = ltu.radec_to_coord(radec)
self.Zion = Zion
# Limits
zlim = ltu.z_from_dv(vlim, zcomp)
self.limits = zLimits(zcomp, zlim.tolist())
# Attributes
self.attrib = init_attrib.copy()
# Optional
self.A = A
self.Ej = Ej
self.stars = stars
self.comment = comment
if Ntup is not None:
self.attrib['flag_N'] = Ntup[0]
self.attrib['logN'] = Ntup[1]
if isiterable(Ntup[2]):
self.attrib['sig_logN'] = np.array(Ntup[2])
else:
self.attrib['sig_logN'] = np.array([Ntup[2]]*2)
_, _ = ltaa.linear_clm(self.attrib) # Set linear quantities
# Name
if (name is None) and (self.Zion != (-1, -1)):
iname = ions.ion_to_name(self.Zion, nspace=0)
if self.Ej.value > 0: # Need to put *'s in name
if stars is not None:
iname += stars
else:
warnings.warn("No stars provided. Adding one because Ej > 0.")
iname += '*'
self.name = '{:s}_z{:0.5f}'.format(iname, self.zcomp)
elif (name is None) and (self.Zion == (-1, -1)):
self.name = 'mol_z{:0.5f}'.format(self.zcomp)
else:
self.name = name
# reliability
if reliability not in ['a', 'b', 'c', 'none']:
raise ValueError("Input reliability `{}` not valid.".format(reliability))
self.reliability = reliability
# AbsLines
self._abslines = []