def to_synth(self, params_in, **kwargs):
"""Convert to synth basis
Convert Parameters object with parameters of a given basis into the
synth basis
Args:
params_in (radvel.Parameters or pandas.DataFrame): radvel.Parameters object or pandas.Dataframe containing
orbital parameters expressed in current basis
noVary (Optional[bool]): if True, set the 'vary' attribute of the returned Parameter objects
to '' (used for displaying best fit parameters)
Returns:
Parameters or DataFrame: parameters expressed in the synth basis
"""
basis_name = kwargs.setdefault('basis_name', self.name)
if isinstance(params_in, pd.core.frame.DataFrame):
# Output by emcee
params_out = params_in.copy()
else:
params_out = _copy_params(params_in)
for num_planet in range(1, 1 + self.num_planets):
def _getpar(key):
if isinstance(params_in, pd.core.frame.DataFrame):
return params_in['{}{}'.format(key, num_planet)]
else:
return params_in['{}{}'.format(key, num_planet)].value
def _setpar(key, new_value):
key_name = '{}{}'.format(key, num_planet)
if isinstance(params_in, pd.core.frame.DataFrame):
params_out[key_name] = new_value
else:
if key_name in params_in:
local_vary = params_in[key_name].vary
local_mcmcscale = params_in[key_name].mcmcscale
elif kwargs.get('noVary', True):
local_vary = ''
local_mcmcscale = None
else:
local_vary = True
local_mcmcscale = None
params_out[key_name] = radvel.model.Parameter(
value=new_value,
vary=local_vary,
mcmcscale=local_mcmcscale)
# transform into synth basis
if basis_name == 'per tp e w k':
# already in the synth basis
per = _getpar('per')
tp = _getpar('tp')
e = _getpar('e')
w = _getpar('w')
k = _getpar('k')
if basis_name == 'per tc e w k':
per = _getpar('per')
tc = _getpar('tc')
e = _getpar('e')
w = _getpar('w')
k = _getpar('k')
tp = timetrans_to_timeperi(tc, per, e, w)
if basis_name == 'per tc secosw sesinw logk':
# pull out parameters
per = _getpar('per')
tc = _getpar('tc')
secosw = _getpar('secosw')
sesinw = _getpar('sesinw')
logk = _getpar('logk')
k = np.exp(logk)
e = secosw**2 + sesinw**2
w = np.arctan2(sesinw, secosw)
tp = timetrans_to_timeperi(tc, per, e, w)
if basis_name == 'per tc secosw sesinw k':
# pull out parameters
per = _getpar('per')
tc = _getpar('tc')
secosw = _getpar('secosw')
sesinw = _getpar('sesinw')
k = _getpar('k')
# transform into synth basis
e = secosw**2 + sesinw**2
w = np.arctan2(sesinw, secosw)
tp = timetrans_to_timeperi(tc, per, e, w)
if basis_name == 'logper tc secosw sesinw k':
# pull out parameters
logper = _getpar('logper')
tc = _getpar('tc')
secosw = _getpar('secosw')
sesinw = _getpar('sesinw')
k = _getpar('k')
# transform into synth basis
per = np.exp(logper)
e = secosw**2 + sesinw**2
w = np.arctan2(sesinw, secosw)
tp = timetrans_to_timeperi(tc, per, e, w)
if basis_name == 'logper tc secosw sesinw logk':
# pull out parameters
logper = _getpar('logper')
tc = _getpar('tc')
secosw = _getpar('secosw')
sesinw = _getpar('sesinw')
k = _getpar('logk')
# transform into synth basis
per = np.exp(logper)
e = secosw**2 + sesinw**2
k = np.exp(k)
w = np.arctan2(sesinw, secosw)
tp = timetrans_to_timeperi(tc, per, e, w)
if basis_name == 'per tc ecosw esinw k':
# pull out parameters
per = _getpar('per')
tc = _getpar('tc')
ecosw = _getpar('ecosw')
esinw = _getpar('esinw')
k = _getpar('k')
# transform into synth basis
e = np.sqrt(ecosw**2 + esinw**2)
w = np.arctan2(esinw, ecosw)
tp = timetrans_to_timeperi(tc, per, e, w)
# shoves synth parameters from namespace into param_out
_setpar('per', per)
_setpar('tp', tp)
_setpar('e', e)
_setpar('w', w)
_setpar('k', k)
if isinstance(params_out, radvel.model.Parameters):
params_out.basis = Basis('per tp e w k', self.num_planets)
return params_out
def process_acr_posterior_dataframe(acr_df,
acrlike,
Mstar=1,
meters_per_second=True):
"""
Process a Pandas dataframe containing the posterior samples from a radvel MCMC fit with
an ACR model. Columns for orbital parameters and planet masses are are added to the dataframe.
Arguments
---------
acr_df : pandas.Dataframe
Dataframe containing posterior samples
acrlike : radvel likelihood
The likelihood object used to compute the ACR model posterior sample.
Mstar : float (optional)
Host star mass in solar masses.
Used for converting semi-amplitudes and periods to planet masses.
Default value is 1
meters_per_second : bool (optional)
Whether semi-amplitude values are reported in meters per second or km/s.
True (default) if values are given in m/s.
"""
acr_df['timebase'] = acrlike.model.time_base
acr_df['t'] = acr_df.stcosw**2 + acr_df.stsinw**2
acr_df['Mstar'] = Mstar
acrfn = acrlike.model._acr_curves_fn
# Planet 1
acr_df['pomega1'] = np.arctan2(acr_df.stsinw, acr_df.stcosw)
acr_df['e1'] = acrfn.e1_rbs(acr_df.m2_by_m1, acr_df.t, grid=False)
acr_df['tp1'] = timetrans_to_timeperi(acr_df.tc1, acr_df.per1, acr_df.e1,
acr_df.pomega1)
acr_df['M1'] = 2 * np.pi * (acr_df.timebase - acr_df.tp1) / acr_df.per1
acr_df['l1'] = np.mod(acr_df.M1 + acr_df.pomega1, 2 * np.pi)
k1 = acr_df['k1'].values
if not meters_per_second:
acr_df['m1'] = np.vectorize(get_planet_mass_from_mstar_K_P_e)(
acr_df['Mstar'].values, 1e3 * k1, acr_df['per1'].values,
acr_df['e1'].values)
else:
acr_df['m1'] = np.vectorize(get_planet_mass_from_mstar_K_P_e)(
acr_df['Mstar'].values, k1, acr_df['per1'].values,
acr_df['e1'].values)
# Resonance-related variables
acr_df['jres'] = acrlike.params['jres'].value
acr_df['kres'] = acrlike.params['kres'].value
acr_df['angle_n'] = acrlike.params['angle_n'].value
# Planet 2
acr_df['m2'] = acr_df.m1 * acr_df.m2_by_m1
acr_df['e2'] = acrfn.e2_rbs(acr_df.m2_by_m1, acr_df.t, grid=False)
acr_df['pomega2'] = np.mod(acr_df['pomega1'] + np.pi, 2 * np.pi)
j, k = acr_df['jres'].values, acr_df['kres'].values
acr_df['per2'] = j * acr_df.per1 / (j - k)
M1 = acr_df['M1']
angle_n = acr_df['angle_n']
acr_df['M2'] = (1 - k / j) * acr_df.M1 + (
(1 - j + k + 2 * acr_df.angle_n) / j) * np.pi
acr_df['tp2'] = acr_df.timebase - acr_df.per2 * acr_df.M2 / 2 / np.pi
for i in range(1, 3):
rt_e = acr_df['e{}'.format(i)].apply(np.sqrt)
pmg = acr_df['pomega{}'.format(i)]
acr_df['secosw{}'.format(i)] = rt_e * np.cos(pmg)
acr_df['sesinw{}'.format(i)] = rt_e * np.sin(pmg)
def from_synth(self, params_in, newbasis, **kwargs):
"""Convert from synth basis into another basis
Convert instance of Parameters with parameters of a given basis into the synth basis
Args:
params_in (radvel.Parameters or pandas.DataFrame): radvel.Parameters object or pandas.Dataframe containing
orbital parameters expressed in current basis
newbasis (string): string corresponding to basis to switch into
keep (Optional[bool]): keep the parameters expressed in
the old basis, else remove them from the output
dictionary/DataFrame
Returns:
dict or dataframe with the parameters converted into the new basis
"""
if newbasis not in BASIS_NAMES:
print("{} not valid basis".format(newbasis))
_print_valid_basis()
return None
if isinstance(params_in, pd.core.frame.DataFrame):
# Output by emcee
params_out = params_in.copy()
else:
params_out = _copy_params(params_in)
for num_planet in range(1, 1 + self.num_planets):
def _getpar(key):
if isinstance(params_in, pd.core.frame.DataFrame):
return params_in['{}{}'.format(key, num_planet)]
else:
return params_in['{}{}'.format(key, num_planet)].value
def _setpar(key, new_value):
key_name = '{}{}'.format(key, num_planet)
if isinstance(params_in, pd.core.frame.DataFrame):
params_out[key_name] = new_value
else:
if key_name in params_in:
local_vary = params_in[key_name].vary
local_mcmcscale = params_in[key_name].mcmcscale
else:
local_vary = True
local_mcmcscale = None
params_out[key_name] = radvel.model.Parameter(
value=new_value,
vary=local_vary,
mcmcscale=local_mcmcscale)
def _delpar(key):
if isinstance(params_in, OrderedDict):
del params_out['{}{}'.format(key, num_planet)]
elif isinstance(params_in, pd.core.frame.DataFrame):
params_out.drop('{}{}'.format(key, num_planet))
if newbasis == 'per tc e w k':
per = _getpar('per')
e = _getpar('e')
w = _getpar('w')
tp = _getpar('tp')
_setpar('tc', timeperi_to_timetrans(tp, per, e, w))
_setpar('w', w)
if not kwargs.get('keep', True):
_delpar('tp')
if newbasis == 'per tc secosw sesinw logk':
per = _getpar('per')
e = _getpar('e')
w = _getpar('w')
k = _getpar('k')
try:
tp = _getpar('tp')
except KeyError:
tc = _getpar('tc')
tp = timetrans_to_timeperi(tc, per, e, w)
_setpar('tp', tp)
_setpar('secosw', np.sqrt(e) * np.cos(w))
_setpar('sesinw', np.sqrt(e) * np.sin(w))
_setpar('logk', np.log(k))
_setpar('tc', timeperi_to_timetrans(tp, per, e, w))
if not kwargs.get('keep', True):
_delpar('tp')
_delpar('e')
_delpar('w')
_delpar('k')
# basis_name = newbasis
self.params = newbasis.split()
if newbasis == 'per tc secosw sesinw k':
per = _getpar('per')
e = _getpar('e')
w = _getpar('w')
k = _getpar('k')
try:
tp = _getpar('tp')
except KeyError:
tp = timetrans_to_timeperi(_getpar('tc'), per, e, w)
_setpar('tp', tp)
_setpar('secosw', np.sqrt(e) * np.cos(w))
_setpar('sesinw', np.sqrt(e) * np.sin(w))
_setpar('k', k)
_setpar('tc', timeperi_to_timetrans(tp, per, e, w))
if not kwargs.get('keep', True):
_delpar('tp')
_delpar('e')
_delpar('w')
self.name = newbasis
self.params = newbasis.split()
if newbasis == 'logper tc secosw sesinw k':
per = _getpar('per')
e = _getpar('e')
w = _getpar('w')
k = _getpar('k')
try:
tp = _getpar('tp')
except KeyError:
tp = timetrans_to_timeperi(_getpar('tc'), per, e, w)
_setpar('tp', tp)
_setpar('logper', np.log(per))
_setpar('secosw', np.sqrt(e) * np.cos(w))
_setpar('sesinw', np.sqrt(e) * np.sin(w))
_setpar('k', k)
_setpar('tc', timeperi_to_timetrans(tp, per, e, w))
if not kwargs.get('keep', True):
_delpar('per')
_delpar('tp')
_delpar('e')
_delpar('w')
self.name = newbasis
self.params = newbasis.split()
if newbasis == 'logper tc secosw sesinw logk':
per = _getpar('per')
e = _getpar('e')
w = _getpar('w')
k = _getpar('k')
try:
tp = _getpar('tp')
except KeyError:
tp = timetrans_to_timeperi(_getpar('tc'), per, e, w)
_setpar('tp', tp)
_setpar('logper', np.log(per))
_setpar('secosw', np.sqrt(e) * np.cos(w))
_setpar('sesinw', np.sqrt(e) * np.sin(w))
_setpar('logk', np.log(k))
_setpar('tc', timeperi_to_timetrans(tp, per, e, w))
if not kwargs.get('keep', True):
_delpar('per')
_delpar('tp')
_delpar('e')
_delpar('w')
_delpar('k')
self.name = newbasis
self.params = newbasis.split()
if newbasis == 'per tc ecosw esinw k':
per = _getpar('per')
e = _getpar('e')
w = _getpar('w')
k = _getpar('k')
try:
tp = _getpar('tp')
except KeyError:
tp = timetrans_to_timeperi(_getpar('tc'), per, e, w)
_setpar('tp', tp)
_setpar('ecosw', e * np.cos(w))
_setpar('esinw', e * np.sin(w))
_setpar('k', k)
_setpar('tc', timeperi_to_timetrans(tp, per, e, w))
if not kwargs.get('keep', True):
_delpar('tp')
_delpar('e')
_delpar('w')
self.name = newbasis
self.params = newbasis.split()
params_out.basis = Basis(newbasis, self.num_planets)
return params_out
def v_to_synth(self, params_in, **kwargs):
basis_name = kwargs.setdefault('basis_name', self.name)
if isinstance(params_in, radvel.Vector):
vector = params_in.vector
else:
vector = params_in
vector2 = vector.copy()
def setvary(indices):
if kwargs.get('noVary', True):
for i in indices:
vector2[i][1] = False
vector2[i][2] = None
else:
for i in indices:
vector2[i][1] = True
vector2[i][2] = None
for num_planet in range(self.num_planets):
#per: (5*num_planet)
#tp: 1 + (5*num_planet)
#e: 2 + (5*num_planet)
#w: 3 + (5*num_planet)
#k: 4 + (5*num_planet)
if basis_name == 'per tp e w k':
return vector2
if basis_name == 'per tc e w k':
vector2[1+(5*num_planet)][0] = timetrans_to_timeperi(vector[1+(5*num_planet)][0],
vector[(5*num_planet)][0],
vector[2+(5*num_planet)][0],
vector[3+(5*num_planet)][0])
setvary([1+(5*num_planet)])
if basis_name == 'per tc se w k':
vector2[2+(5 * num_planet)][0] = vector[2+(5 * num_planet)][0] ** 2
vector2[1+(5*num_planet)][0] = timetrans_to_timeperi(vector[1+(5*num_planet)][0],
vector[(5*num_planet)][0],
vector2[2+(5*num_planet)][0],
vector[3+(5*num_planet)][0])
setvary([2+(5*num_planet), 1+(5*num_planet)])
if basis_name == 'per tc secosw sesinw logk':
vector2[4+(5*num_planet)][0] = np.exp(vector[4+(5*num_planet)][0])
vector2[2+(5*num_planet)][0] = vector[2+(5*num_planet)][0]**2 + vector[3+(5*num_planet)][0]**2
vector2[3+(5 * num_planet)][0] = np.arctan2(vector[3+(5 * num_planet)][0], vector[2+(5 * num_planet)][0])
vector2[1+(5*num_planet)][0] = timetrans_to_timeperi(vector[1+(5*num_planet)][0],
vector[(5*num_planet)][0],
vector2[2+(5*num_planet)][0],
vector2[3+(5*num_planet)][0])
setvary([4+(5*num_planet),2+(5 * num_planet),3+(5 * num_planet),1+(5 * num_planet)])
if basis_name == 'per tc secosw sesinw k':
vector2[2 + (5 * num_planet)][0] = vector[2+(5 * num_planet)][0] ** 2 + vector[3+(5 * num_planet)][0] ** 2
vector2[3 + (5 * num_planet)][0] = np.arctan2(vector[3+(5 * num_planet)][0], vector[2+(5 * num_planet)][0])
vector2[1 + (5 * num_planet)][0] = timetrans_to_timeperi(vector[1+(5 * num_planet)][0],
vector[(5 * num_planet)][0],
vector2[2+(5 * num_planet)][0],
vector2[3+(5 * num_planet)][0])
setvary([2+(5 * num_planet),3+(5 * num_planet),1+(5 * num_planet)])
if basis_name == 'logper tc secosw sesinw k':
vector2[2+(5 * num_planet)][0] = vector[2+(5 * num_planet)][0] ** 2 + vector[3+(5 * num_planet)][0] ** 2
vector2[3+(5 * num_planet)][0] = np.arctan2(vector[3+(5 * num_planet)][0], vector[2+(5 * num_planet)][0])
vector2[(5 * num_planet)][0] = np.exp(vector[(5 * num_planet)][0])
vector2[1 + (5 * num_planet)][0] = timetrans_to_timeperi(vector[1 + (5 * num_planet)][0],
vector2[(5 * num_planet)][0],
vector2[2+(5 * num_planet)][0],
vector2[3 + (5 * num_planet)][0])
setvary([2+(5 * num_planet),3+(5 * num_planet),(5 * num_planet),1 + (5 * num_planet)])
if basis_name == 'logper tc secosw sesinw logk':
vector2[2+(5 * num_planet)][0] = vector[2+(5 * num_planet)][0] ** 2 + vector[3+(5 * num_planet)][0] ** 2
vector2[3+(5 * num_planet)][0] = np.arctan2(vector[3+(5 * num_planet)][0], vector[2+(5 * num_planet)][0])
vector2[(5 * num_planet)][0] = np.exp(vector[(5 * num_planet)][0])
vector2[4 + (5 * num_planet)][0] = np.exp(vector[4 + (5 * num_planet)][0])
vector2[1 + (5 * num_planet)][0] = timetrans_to_timeperi(vector[1 + (5 * num_planet)][0],
vector2[(5 * num_planet)][0],
vector2[2+(5 * num_planet)][0],
vector2[3+(5 * num_planet)][0])
setvary([2+(5 * num_planet),3 + (5 * num_planet),(5 * num_planet),4 + (5 * num_planet),1 + (5 * num_planet)])
if basis_name == 'per tc ecosw esinw k':
vector2[2 + (5 * num_planet)][0] = np.sqrt(vector[2 + (5 * num_planet)][0] ** 2 + vector[3 + (5 * num_planet)][0] ** 2)
vector2[3+(5 * num_planet)][0] = np.arctan2(vector[3+(5 * num_planet)][0], vector[2+(5 * num_planet)][0])
vector2[1 + (5 * num_planet)][0] = timetrans_to_timeperi(vector[1 + (5 * num_planet)][0],
vector[(5 * num_planet)][0],
vector2[2+(5 * num_planet)][0],
vector2[3+(5 * num_planet)][0])
setvary([3+(5 * num_planet),2+(5 * num_planet),1 + (5 * num_planet)])
if basis_name == 'logper tp e w logk':
vector2[4 + (5 * num_planet)][0] = np.exp(vector[4 + (5 * num_planet)][0])
vector2[(5 * num_planet)][0] = np.exp(vector[(5 * num_planet)][0])
setvary([4+(5 * num_planet),(5 * num_planet)])
return vector2