def __call__(self, params, vector):
def _getpar(key):
return synth_params[vector.indices['{}{}'.format(key, self.planet_num)]][0]
synth_params = vector.params.basis.v_to_synth(vector)
tp = synth_params[-4+(5*self.planet_num)][0]
per = synth_params[-5+(5*self.planet_num)][0]
ecc = synth_params[-3+(5*self.planet_num)][0]
omega = synth_params[-2+(5*self.planet_num)][0]
ts = orbit.timeperi_to_timetrans(tp, per, ecc, omega, secondary=True)
ts_phase = utils.t_to_phase_vector(vector, ts, self.planet_num)
pts = utils.t_to_phase_vector(vector, self.ts, self.planet_num)
epts = self.ts_err / per
penalty = -0.5 * ((ts_phase - pts) / epts)**2 - 0.5*np.log((epts**2)*2.*np.pi)
return penalty
def __call__(self, params):
def _getpar(key):
return synth_params['{}{}'.format(key, self.planet_num)].value
synth_params = params.basis.to_synth(params)
tp = _getpar('tp')
per = _getpar('per')
ecc = _getpar('e')
omega = _getpar('w')
ts = orbit.timeperi_to_timetrans(tp, per, ecc, omega, secondary=True)
ts_phase = utils.t_to_phase(synth_params, ts, self.planet_num)
pts = utils.t_to_phase(synth_params, self.ts, self.planet_num)
epts = self.ts_err / per
penalty = -0.5 * ((ts_phase - pts) / epts)**2
return penalty
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_from_synth(self, params_in, newbasis):
if isinstance(params_in, radvel.Vector):
vector = params_in.vector
else:
vector = params_in
vector2 = vector.copy()
def setvary(indices):
for i in indices:
vector2[i][1] = True
vector2[i][2] = None
for num_planet in range(self.num_planets):
if newbasis == 'per tc e w k':
vector2[1+(5*num_planet)][0] = timeperi_to_timetrans(vector[1+(5*num_planet)][0],
vector[(5*num_planet)][0],
vector[2+(5*num_planet)][0],
vector[3+(5*num_planet)][0])
setvary([3+(5*num_planet)])
if newbasis == 'per tc se w k':
vector2[1 + (5 * num_planet)][0] = timeperi_to_timetrans(vector[1 + (5 * num_planet)][0],
vector[(5 * num_planet)][0],
vector[2 + (5 * num_planet)][0],
vector[3 + (5 * num_planet)][0])
vector2[2+(5*num_planet)][0] = np.sqrt(vector[2+(5*num_planet)][0])
setvary([1 + (5 * num_planet),2+(5*num_planet)])
if newbasis == 'per tc secosw sesinw logk':
vector2[1 + (5 * num_planet)][0] = timeperi_to_timetrans(vector[1 + (5 * num_planet)][0],
vector[(5 * num_planet)][0],
vector[2 + (5 * num_planet)][0],
vector[3 + (5 * num_planet)][0])
vector2[2+(5*num_planet)][0] = np.sqrt(vector[2+(5*num_planet)][0])*np.cos(vector[3+(5*num_planet)][0])
vector2[3+(5 * num_planet)][0] = np.sqrt(vector[2+(5 * num_planet)][0]) * np.sin(vector[3 + (5 * num_planet)][0])
vector2[4+(5*num_planet)][0] = np.log(vector[4+(5*num_planet)][0])
setvary([1 + (5 * num_planet),2+(5*num_planet),3+(5 * num_planet),4+(5*num_planet)])
if newbasis == 'per tc secosw sesinw k':
vector2[1 + (5 * num_planet)][0] = timeperi_to_timetrans(vector[1 + (5 * num_planet)][0],
vector[(5 * num_planet)][0],
vector[2 + (5 * num_planet)][0],
vector[3 + (5 * num_planet)][0])
vector2[2 + (5 * num_planet)][0] = np.sqrt(vector[2 + (5 * num_planet)][0]) * np.cos(vector[3 + (5 * num_planet)][0])
vector2[3 + (5 * num_planet)][0] = np.sqrt(vector[2 + (5 * num_planet)][0]) * np.sin(vector[3 + (5 * num_planet)][0])
setvary([1 + (5 * num_planet), 2+(5 * num_planet), 3 + (5 * num_planet)])
if newbasis == 'logper tc secosw sesinw k':
vector2[1 + (5 * num_planet)][0] = timeperi_to_timetrans(vector[1 + (5 * num_planet)][0],
vector[(5 * num_planet)][0],
vector[2 + (5 * num_planet)][0],
vector[3 + (5 * num_planet)][0])
vector2[2 + (5 * num_planet)][0] = np.sqrt(vector[2 + (5 * num_planet)][0]) * np.cos(vector[3 + (5 * num_planet)][0])
vector2[3 + (5 * num_planet)][0] = np.sqrt(vector[2 + (5 * num_planet)][0]) * np.sin(vector[3 + (5 * num_planet)][0])
vector2[(5*num_planet)][0] = np.log(vector[(5*num_planet)][0])
setvary([1 + (5 * num_planet), 2+(5 * num_planet),3 + (5 * num_planet),(5*num_planet)])
if newbasis == 'logper tc secosw sesinw logk':
vector2[1 + (5 * num_planet)][0] = timeperi_to_timetrans(vector[1 + (5 * num_planet)][0],
vector[(5 * num_planet)][0],
vector[2 + (5 * num_planet)][0],
vector[3 + (5 * num_planet)][0])
vector2[2 + (5 * num_planet)][0] = np.sqrt(vector[2 + (5 * num_planet)][0]) * np.cos(vector[3 + (5 * num_planet)][0])
vector2[3 + (5 * num_planet)][0] = np.sqrt(vector[2 + (5 * num_planet)][0]) * np.sin(vector[3 + (5 * num_planet)][0])
vector2[(5 * num_planet)][0] = np.log(vector[(5 * num_planet)][0])
vector2[4+(5*num_planet)][0] = np.log(vector[4+(5*num_planet)][0])
setvary([1 + (5 * num_planet), 2+(5 * num_planet), 3+ (5 * num_planet), (5 * num_planet),4+(5*num_planet)])
if newbasis == 'per tc ecosw esinw k':
vector2[1 + (5 * num_planet)][0] = timeperi_to_timetrans(vector[1 + (5 * num_planet)][0],
vector[(5 * num_planet)][0],
vector[2 + (5 * num_planet)][0],
vector[3 + (5 * num_planet)][0])
vector2[2+(5*num_planet)][0] = vector[2+(5*num_planet)][0]*np.cos(vector[3+(5*num_planet)][0])
vector2[3+(5 * num_planet)][0] = vector[2+(5 * num_planet)][0] * np.sin(vector[3 + (5 * num_planet)][0])
setvary([1 + (5 * num_planet),2+(5*num_planet),3+(5 * num_planet)])
if newbasis == 'logper tp e w logk':
vector2[(5 * num_planet)][0] = np.log(vector[(5 * num_planet)][0])
vector2[4 + (5 * num_planet)][0] = np.log(vector[4 + (5 * num_planet)][0])
setvary([(5 * num_planet),4 + (5 * num_planet)])
return vector2