def test_convert_qdict():
vlim = dict(unit='km/s', value=50.)
time = dict(unit='s', value=100.)
mass = dict(unit='g', value=10.)
idict = dict(vlim=vlim, nest=dict(time=time, mass=mass))
newdict = ltu.convert_quantity_in_dict(idict)
assert newdict['nest']['mass'] == 10 * u.g
# Simple one
obj = ltu.convert_quantity_in_dict(vlim)
assert obj.unit == u.km / u.s
def test_convert_qdict():
vlim = dict(unit='km/s', value=50.)
time = dict(unit='s', value=100.)
mass = dict(unit='g', value=10.)
idict = dict(vlim=vlim, nest=dict(time=time, mass=mass))
newdict = ltu.convert_quantity_in_dict(idict)
assert newdict['nest']['mass'] == 10 * u.g
# Simple one
obj = ltu.convert_quantity_in_dict(vlim)
assert obj.unit == u.km / u.s
def from_dict(cls, idict, **kwargs):
"""
Instantiate from a dict
Args:
idict (dict):
**kwargs: Passed to the __init__ call
Returns:
"""
# Init
coord = SkyCoord(ra=idict['ra'], dec=idict['dec'], unit='deg')
DM = units.Quantity(idict['DM']['value'], unit=idict['DM']['unit'])
slf = cls(idict['FRB'], coord, DM, **kwargs)
for key in ['ra', 'dec', 'DM']:
idict.pop(key)
for key in [
'DM_err', 'DMISM', 'DMISM_err', 'RM', 'RM_err', 'fluence',
'fluence_err'
]:
if key in idict.keys():
setattr(
slf, key,
units.Quantity(idict[key]['value'],
unit=idict[key]['unit']))
idict.pop(key)
# Cosmology
if slf.cosmo.name != idict['cosmo']:
raise AssertionError(
f"Your cosmology does not match the expected for {idict['FRB']}. Gotta deal.."
)
idict.pop('cosmo')
# dicts
for ndict in slf.main_dict:
if ndict in idict.keys():
for key, value in idict[ndict].items():
if isinstance(value, dict):
newvalue = ltu.convert_quantity_in_dict(value)
else:
newvalue = value
idict[ndict][key] = newvalue
setattr(slf, ndict, idict[ndict])
# Deal with quantities
idict.pop(ndict)
# Remainder
for key in idict.keys():
setattr(slf, key, idict[key])
# Return
return slf
def from_dict(cls, idict):
""" Generate a LineLimits class from an input dict
keys -- wrest, z, zlim -- are required
Parameters
----------
idict
Returns
-------
"""
wrest = ltu.convert_quantity_in_dict(idict['wrest'])
slf = cls(wrest, idict['z'], idict['zlim'])
# Return
return slf
def add_other_from_dict(slf, idict):
""" Add other attributes to a system from a dict
Useful for handling various AbsSystem types
Parameters
----------
slf : AbsSystem
idict : dict
"""
# Other
if 'kin' in idict.keys():
slf.kin = ltu.convert_quantity_in_dict(idict['kin'])
if 'Refs' in idict.keys():
slf.Refs = idict['Refs']
if 'ZH' in idict.keys():
slf.ZH = idict['ZH']
slf.sig_ZH = idict['sig_ZH']
def add_other_from_dict(slf, idict):
""" Add other attributes to a system from a dict
Useful for handling various AbsSystem types
Parameters
----------
slf : AbsSystem
idict : dict
"""
# Other
if 'kin' in idict.keys():
slf.kin = ltu.convert_quantity_in_dict(idict['kin'])
if 'Refs' in idict.keys():
slf.Refs = idict['Refs']
if 'ZH' in idict.keys():
slf.ZH = idict['ZH']
slf.sig_ZH = idict['sig_ZH']
def from_dict(cls, idict):
""" Generate a LineLimits class from an input dict
keys -- wrest, z, zlim -- are required
Parameters
----------
idict
Returns
-------
"""
try:
wrest = ltu.convert_quantity_in_dict(idict['wrest'])
except KeyError:
wrest = None
slf = cls(idict['z'], idict['zlim'], wrest=wrest)
# Return
return slf
def from_dict(cls, idict):
""" Generate a LineLimits class from an input dict
keys -- wrest, z, zlim -- are required
Parameters
----------
idict
Returns
-------
"""
try:
wrest = ltu.convert_quantity_in_dict(idict['wrest'])
except KeyError:
wrest = None
slf = cls(idict['z'], idict['zlim'], wrest=wrest)
# Return
return slf
def from_dict(cls, idict, skip_components=False, use_coord=False, **kwargs):
""" Instantiate from a dict. Usually read from the hard-drive
Parameters
----------
idict : dict
skip_components : bool, optional
If True, absorption components (if any exist) are not loaded from the input dict.
Use when you are only interested in the global properties of an AbsSystem
use_coord : bool, optinal
Use coordinates from the AbsSystem to build the components (and lines)
Speeds up performance, but you should know things are OK before using this
Returns
-------
AbsSystem
"""
if 'NHI' in idict.keys():
ckwargs = dict(NHI=idict['NHI'], sig_NHI=idict['sig_NHI'], flag_NHI=idict['flag_NHI'])
slf = cls(SkyCoord(ra=idict['RA']*u.deg, dec=idict['DEC']*u.deg),
idict['zabs'], idict['vlim']*u.km/u.s, zem=idict['zem'],
name=idict['Name'], **ckwargs)
# Other
if 'kin' in idict.keys():
slf.kin = ltu.convert_quantity_in_dict(idict['kin'])
if 'Refs' in idict.keys():
slf.Refs = idict['Refs']
# Components
if not skip_components:
# Components
if use_coord: # Speed up performance
coord = slf.coord
else:
coord = None
components = ltiu.build_components_from_dict(idict, coord=coord, **kwargs)
for component in components:
# This is to insure the components follow the rules
slf.add_component(component, **kwargs)
# Return
return slf
def from_dict(cls, idict, coord=None, skip_abslines=False, **kwargs):
""" Instantiate from a dict
Parameters
----------
idict : dict
skip_abslines : bool, optional
Skip loading up the AbsLine objects.
Speeds up performance when one only needs the component object
Returns
-------
AbsComponent
"""
if coord is not None:
radec = coord
else:
radec = SkyCoord(ra=idict['RA'], dec=idict['DEC'], unit='deg')
# Init
# slf = cls(radec, tuple(idict['Zion']), idict['zcomp'], Quantity(idict['vlim'], unit='km/s'),
# For IGMGuesses
for key in ['reliability', 'Reliability']:
if key in idict.keys():
reliability = idict[key]
break
else:
reliability = 'none'
# Deprecated column density attributes
if 'logN' in idict.keys():
warnings.warn('Column density attributes are now Deprecated',
DeprecationWarning)
#print("We will use yours for now..")
Ntup = tuple(
[idict[key] for key in ['flag_N', 'logN', 'sig_logN']])
else:
Ntup = None
# Instantiate
slf = cls(radec,
tuple(idict['Zion']),
idict['zcomp'],
idict['vlim'] * u.km / u.s,
Ej=idict['Ej'] / u.cm,
A=idict['A'],
Ntup=Ntup,
comment=idict['comment'],
name=idict['Name'],
reliability=reliability)
# Attributes
if 'attrib' in idict.keys():
attrkeys = idict['attrib'].keys()
for ak in attrkeys:
if isinstance(idict['attrib'][ak], dict):
slf.attrib[ak] = ltu.convert_quantity_in_dict(
idict['attrib'][ak])
else:
slf.attrib[ak] = idict['attrib'][ak]
# Insist that error values are 2-elements :: Mainly for older saved files
if ak == 'sig_N':
if slf.attrib[ak].size == 1:
slf.attrib[ak] = Quantity(
[slf.attrib[ak].value] * 2) * slf.attrib[ak].unit
if ak == 'sig_logN':
if isinstance(slf.attrib[ak], (float, int)):
slf.attrib[ak] = np.array([slf.attrib[ak]] * 2)
elif isinstance(slf.attrib[ak], (list)):
slf.attrib[ak] = np.array(slf.attrib[ak])
# Deprecated column (again)
if Ntup is not None:
warnings.warn(
'Overwriting column density attributes (if they existed).',
DeprecationWarning)
slf.attrib['flag_N'] = Ntup[0]
slf.attrib['logN'] = Ntup[1]
if isiterable(Ntup[2]):
slf.attrib['sig_logN'] = np.array(Ntup[2])
else:
slf.attrib['sig_logN'] = np.array([Ntup[2]] * 2)
_, _ = ltaa.linear_clm(slf.attrib) # Set linear quantities
# Add AbsLine objects
if not skip_abslines:
for key in idict['lines'].keys():
iline = AbsLine.from_dict(idict['lines'][key],
coord=coord,
**kwargs)
slf.add_absline(iline, **kwargs)
# Return
return slf
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 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']:
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 = LineLimits.from_dict(idict['limits'])
else:
sline.limits = LineLimits(sline.wrest, z, [z, z])
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 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)
else:
raise ValueError("Not prepared for type {:s}.".format(idict['ltype']))
# Check data
if chk_data:
for key in idict['data']:
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']:
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':
warnings.warn("You will need to load {:s} into attrib['spec'] yourself".format(
idict['analy'][key]))
else:
sline.analy[key] = idict['analy'][key]
# Set attrib
for key in idict['attrib']:
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]
return sline
def from_dict(cls, idict, coord=None, skip_abslines=False, **kwargs):
""" Instantiate from a dict
Parameters
----------
idict : dict
skip_abslines : bool, optional
Skip loading up the AbsLine objects.
Speeds up performance when one only needs the component object
Returns
-------
AbsComponent
"""
if coord is not None:
radec = coord
else:
radec = SkyCoord(ra=idict['RA'], dec=idict['DEC'], unit='deg')
# Init
# slf = cls(radec, tuple(idict['Zion']), idict['zcomp'], Quantity(idict['vlim'], unit='km/s'),
# For IGMGuesses
for key in ['reliability', 'Reliability']:
if key in idict.keys():
reliability = idict[key]
break
else:
reliability = 'none'
# Deprecated column density attributes
if 'logN' in idict.keys():
warnings.warn('Column density attributes are now Deprecated', DeprecationWarning)
#print("We will use yours for now..")
Ntup = tuple([idict[key] for key in ['flag_N', 'logN', 'sig_logN']])
else:
Ntup = None
# Instantiate
slf = cls(radec, tuple(idict['Zion']), idict['zcomp'], idict['vlim']*u.km/u.s,
Ej=idict['Ej']/u.cm, A=idict['A'], Ntup=Ntup,
comment=idict['comment'], name=idict['Name'], reliability=reliability)
# Attributes
if 'attrib' in idict.keys():
attrkeys = idict['attrib'].keys()
for ak in attrkeys:
if isinstance(idict['attrib'][ak],dict):
slf.attrib[ak] = ltu.convert_quantity_in_dict(idict['attrib'][ak])
else:
slf.attrib[ak] = idict['attrib'][ak]
# Insist that error values are 2-elements :: Mainly for older saved files
if ak == 'sig_N':
if slf.attrib[ak].size == 1:
slf.attrib[ak] = Quantity([slf.attrib[ak].value]*2) * slf.attrib[ak].unit
if ak == 'sig_logN':
if isinstance(slf.attrib[ak], (float,int)):
slf.attrib[ak] = np.array([slf.attrib[ak]]*2)
elif isinstance(slf.attrib[ak], (list)):
slf.attrib[ak] = np.array(slf.attrib[ak])
# Deprecated column (again)
if Ntup is not None:
warnings.warn('Overwriting column density attributes (if they existed).', DeprecationWarning)
slf.attrib['flag_N'] = Ntup[0]
slf.attrib['logN'] = Ntup[1]
if isiterable(Ntup[2]):
slf.attrib['sig_logN'] = np.array(Ntup[2])
else:
slf.attrib['sig_logN'] = np.array([Ntup[2]]*2)
_, _ = ltaa.linear_clm(slf.attrib) # Set linear quantities
# Add AbsLine objects
if not skip_abslines:
for key in idict['lines'].keys():
iline = AbsLine.from_dict(idict['lines'][key], coord=coord, **kwargs)
slf.add_absline(iline, **kwargs)
# Return
return slf