def add_planet(self):
"""Add parameters for one more planet to posterior.
"""
current_num_planets = self.post.params.num_planets
fitting_basis = self.post.params.basis.name
param_list = fitting_basis.split()
new_num_planets = current_num_planets + 1
default_pars = utils.initialize_default_pars(
instnames=self.tels, fitting_basis=fitting_basis)
new_params = radvel.Parameters(new_num_planets, basis=fitting_basis)
for planet in np.arange(1, new_num_planets):
for par in param_list:
parkey = par + str(planet)
new_params[parkey] = self.post.params[parkey]
for par in self.post.likelihood.extra_params:
new_params[par] = self.post.params[par] # For gamma and jitter
# Set default parameters for n+1th planet
default_params = utils.initialize_default_pars(
self.tels, fitting_basis=fitting_basis)
for par in param_list:
parkey = par + str(new_num_planets)
onepar = par + '1' # MESSY, FIX THIS 10/22/18
new_params[parkey] = default_params[onepar]
new_params['dvdt'] = self.post.params['dvdt']
new_params['curv'] = self.post.params['curv']
if not self.post.params['dvdt'].vary:
new_params['dvdt'].vary = False
if not self.post.params['curv'].vary:
new_params['curv'].vary = False
new_params['per{}'.format(new_num_planets)].vary = False
if not self.eccentric:
new_params['secosw{}'.format(new_num_planets)].vary = False
new_params['sesinw{}'.format(new_num_planets)].vary = False
new_params.num_planets = new_num_planets
# Respect setup file priors.
if self.setup:
priors = self.priors
else:
priors = []
priors.append(radvel.prior.PositiveKPrior(new_num_planets))
priors.append(radvel.prior.EccentricityPrior(new_num_planets))
new_post = utils.initialize_post(self.data, new_params, priors)
self.post = new_post
def test_priors():
"""
Test basic functionality of all Priors
"""
params = radvel.Parameters(1)
params['per1'] = radvel.Parameter(10.0)
params['tc1'] = radvel.Parameter(0.0)
params['secosw1'] = radvel.Parameter(0.0)
params['sesinw1'] = radvel.Parameter(0.0)
params['logk1'] = radvel.Parameter(1.5)
testTex = 'Delta Function Prior on $\sqrt{e}\cos{\omega}_{b}$'
def userdef_prior_func(inp_list):
if inp_list[0] >= 0. and inp_list[0] < 1.:
return 0.
else:
return -np.inf
prior_tests = {
radvel.prior.EccentricityPrior(1):
1 / .99,
radvel.prior.PositiveKPrior(1):
1.0,
radvel.prior.Gaussian('per1', 9.9, 0.1):
scipy.stats.norm(9.9, 0.1).pdf(10.),
radvel.prior.HardBounds('per1', 1.0, 9.0):
0.,
radvel.prior.HardBounds('per1', 1.0, 11.0):
1. / 10.,
radvel.prior.Jeffreys('per1', 0.1, 100.0):
(1. / 10.) / np.log(100. / 0.1),
radvel.prior.ModifiedJeffreys('per1', 0.1, 100.0, 0.):
(1. / 10.) / np.log(100. / 0.1),
radvel.prior.ModifiedJeffreys('per1', 2., 100.0, 1.):
(1. / 9.) / np.log(99.),
radvel.prior.SecondaryEclipsePrior(1, 5.0, 10.0):
1. / np.sqrt(2. * np.pi),
radvel.prior.NumericalPrior(['sesinw1'], np.random.randn(1, 5000000)):
scipy.stats.norm(0, 1).pdf(0.),
radvel.prior.UserDefinedPrior(['secosw1'], userdef_prior_func, testTex):
1.0
}
for prior, val in prior_tests.items():
print(prior.__repr__())
print(prior.__str__())
tolerance = .01
print(abs(np.exp(prior(params))))
print(val)
assert abs(np.exp(prior(params)) - val) < tolerance, \
"Prior output does not match expectation"
def initialize_model(e):
time_base = 0.0
params = radvel.Parameters(1, basis='per tp e w k')
params['per1'] = radvel.Parameter(value=6)
params['tp1'] = radvel.Parameter(value=2)
params['e1'] = radvel.Parameter(value=e)
params['w1'] = radvel.Parameter(value=0.0)
params['k1'] = radvel.Parameter(value=10.1)
mod = radvel.RVModel(params, time_base=time_base)
mod.params['dvdt'] = radvel.Parameter(value=-0.0)
mod.params['curv'] = radvel.Parameter(value=0.0)
return mod
def initialize_default_pars(instnames=['inst'],
times=None,
linear=True,
fitting_basis='per tc secosw sesinw k'):
"""Set up a default Parameters object.
None of the basis values are free params, for the initial 0-planet fit.
Remember to reset .vary to True for all relevant params.
Args:
instnames (list): codes of instruments used
times (array): optional, timestamps of observations.
linear (bool): Determine whether to optimize gammas linearly.
fitting_basis: optional
Returns:
Parameters object
"""
anybasis_params = radvel.Parameters(num_planets=1, basis='per tc e w k')
if times is None:
anybasis_params['tc1'] = radvel.Parameter(value=2455200.0)
else:
anybasis_params['tc1'] = radvel.Parameter(value=np.median(times))
anybasis_params['w1'] = radvel.Parameter(value=np.pi / 2.)
anybasis_params['k1'] = radvel.Parameter(value=0.0)
anybasis_params['e1'] = radvel.Parameter(value=0.0)
anybasis_params['per1'] = radvel.Parameter(value=100.0)
anybasis_params['dvdt'] = radvel.Parameter(value=0.0)
anybasis_params['curv'] = radvel.Parameter(value=0.0)
for inst in instnames:
if linear:
anybasis_params['gamma_' + inst] = radvel.Parameter(value=0.0,
linear=True,
vary=False)
else:
anybasis_params['gamma_' + inst] = radvel.Parameter(value=0.0)
anybasis_params['jit_' + inst] = radvel.Parameter(value=2.0)
params = anybasis_params.basis.to_any_basis(anybasis_params, fitting_basis)
params['secosw1'].vary = False
params['sesinw1'].vary = False
params['per1'].vary = False
params['dvdt'].vary = False
params['curv'].vary = False
return params
def initialize_params():
params = radvel.Parameters(1, basis='per tp e w k')
params['per1'] = radvel.Parameter(value=12525.0)
params['tp1'] = radvel.Parameter(value=2450593.5)
params['k1'] = radvel.Parameter(value=725.3)
params['e1'] = radvel.Parameter(value=0.74)
params['w1'] = radvel.Parameter(value=4.6967)
params['dvdt'] = radvel.Parameter(value=0, vary=vary_dvdt)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params, fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(1, basis='per tc e w k')
params['per1'] = radvel.Parameter(value=26905)
params['tc1'] = radvel.Parameter(value=7604.22 + bjd0)
params['k1'] = radvel.Parameter(value=711.0)
params['e1'] = radvel.Parameter(value=0.637)
params['w1'] = radvel.Parameter(value=2.358)
params['dvdt'] = radvel.Parameter(value=0, vary=vary_dvdt)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params, fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(1, basis='per tc e w k')
params['per1'] = radvel.Parameter(value=323.33)
params['tc1'] = radvel.Parameter(value=2450305.3)
params['k1'] = radvel.Parameter(value=27019.0)
params['e1'] = radvel.Parameter(value=0.832)
params['w1'] = radvel.Parameter(value=2.2)
params['dvdt'] = radvel.Parameter(value=4.07, vary=vary_dvdt)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params, fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(1, basis='per tc secosw sesinw k')
params['per1'] = radvel.Parameter(value=30477.33)
params['tc1'] = radvel.Parameter(value=2451703.3)
params['k1'] = radvel.Parameter(value=4252.6)
params['secosw1'] = radvel.Parameter(value=0.23)
params['sesinw1'] = radvel.Parameter(value=0.65)
params['dvdt'] = radvel.Parameter(value=0, vary=vary_dvdt)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params, fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(1, basis='per tc e w k')
params['per1'] = radvel.Parameter(value=4433.0)
params['tc1'] = radvel.Parameter(value=2451281.0)
params['k1'] = radvel.Parameter(value=612.2)
params['e1'] = radvel.Parameter(value=0.34)
params['w1'] = radvel.Parameter(value=-2.36)
params['dvdt'] = radvel.Parameter(value=0, vary=vary_dvdt)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params, fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(1,basis='per tc e w k')
params['per1'] = radvel.Parameter(value=44495.8)
params['tc1'] = radvel.Parameter(value=2441100.06)
params['k1'] = radvel.Parameter(value=578.2)
params['e1'] = radvel.Parameter(value=0.63)
params['w1'] = radvel.Parameter(value=-1.85)
params['dvdt'] = radvel.Parameter(value=0, vary=vary_dvdt)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params,fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(1, basis='per tc e w k')
params['per1'] = radvel.Parameter(value=6829)
params['tc1'] = radvel.Parameter(value=2458538.0)
params['k1'] = radvel.Parameter(value=3530)
params['e1'] = radvel.Parameter(value=0.87)
params['w1'] = radvel.Parameter(value=2.97)
params['dvdt'] = radvel.Parameter(value=0, vary=vary_dvdt)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params, fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(1, basis='per tp e w k')
params['per1'] = radvel.Parameter(value=25962.)
params['tp1'] = radvel.Parameter(value=18134.)
params['e1'] = radvel.Parameter(value=0.84)
params['w1'] = radvel.Parameter(value=-0.26)
params['k1'] = radvel.Parameter(value=38.)
params['dvdt'] = radvel.Parameter(value=0, vary=vary_dvdt)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params, fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(1, basis='per tc e w k')
params['per1'] = radvel.Parameter(value=10084.5)
params['tc1'] = radvel.Parameter(value=2455548.8)
params['k1'] = radvel.Parameter(value=900.3)
params['e1'] = radvel.Parameter(value=0.52)
params['w1'] = radvel.Parameter(value=-0.83)
params['dvdt'] = radvel.Parameter(value=0, vary=vary_dvdt)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params, fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(1, basis='per tc e w k')
params['per1'] = radvel.Parameter(value=8443.5) #8585.24)
params['tc1'] = radvel.Parameter(value=2458314.1) #8341.5)
params['k1'] = radvel.Parameter(value=2908.0) #2958.5)
params['e1'] = radvel.Parameter(value=0.678) #0.685)
params['w1'] = radvel.Parameter(value=1.129) #1.134)
params['dvdt'] = radvel.Parameter(value=0, vary=False)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params, fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(1,basis='per tc e w k')
params['per1'] = radvel.Parameter(value=16469.7)
params['tc1'] = radvel.Parameter(value=2457211.2)
params['k1'] = radvel.Parameter(value=786.5)
params['e1'] = radvel.Parameter(value=0.645)
params['w1'] = radvel.Parameter(value=-2.48)
params['dvdt'] = radvel.Parameter(value=0, vary=vary_dvdt)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params,fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(1, basis='per tp e w k')
params['per1'] = radvel.Parameter(value=71.4808)
params['tp1'] = radvel.Parameter(value=2450300.608)
params['k1'] = radvel.Parameter(value=343.232)
params['e1'] = radvel.Parameter(value=0.11316)
params['w1'] = radvel.Parameter(value=2.89598)
params['dvdt'] = radvel.Parameter(value=0, vary=False)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params, fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(1, basis='per tc e w k')
params['per1'] = radvel.Parameter(value=709.54)
params['tc1'] = radvel.Parameter(value=2457758.54) #2454920.0)
params['k1'] = radvel.Parameter(value=5672.0)
params['e1'] = radvel.Parameter(value=0.32)
params['w1'] = radvel.Parameter(value=1.11)
params['dvdt'] = radvel.Parameter(value=0, vary=vary_dvdt)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params, fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(1,basis='per tc e w k')
params['per1'] = radvel.Parameter(value=80686)
params['tc1'] = radvel.Parameter(value=2455110.7)
params['k1'] = radvel.Parameter(value=2730.3)
params['e1'] = radvel.Parameter(value=0.66)
params['w1'] = radvel.Parameter(value=0.76)
params['dvdt'] = radvel.Parameter(value=0, vary=vary_dvdt)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params,fitting_basis)
return params
def __init__(self,j,k,acr_curves_fn,time_base=0):
self.j = j
self.k = k
self._acr_curves_fn = acr_curves_fn
params = radvel.Parameters(1,basis ='per tc secosw sesinw k')
params.pop('secosw1')
params.pop('sesinw1')
alpha = ((j-k)/j)**(2/3.)
params['jres']=radvel.Parameter(j,vary=False)
params['kres']=radvel.Parameter(k,vary=False)
params['m2_by_m1']=radvel.Parameter(1,vary=True)
params['stcosw']=radvel.Parameter(0,vary=True)
params['stsinw']=radvel.Parameter(0,vary=True)
params['angle_n']=radvel.Parameter(0,vary=False)
super(ACRModel,self).__init__(params,acr_forward_model,time_base)
def initialize_params():
params = radvel.Parameters(1, basis='per tc e w k')
#From Halbwachs et al. 2018
params['per1'] = radvel.Parameter(value=5554.71)
params['tc1'] = radvel.Parameter(value=2453540.68) #2448024.2)
params['k1'] = radvel.Parameter(value=2812.17)
params['e1'] = radvel.Parameter(value=0.656)
params['w1'] = radvel.Parameter(value=1.987)
params['dvdt'] = radvel.Parameter(value=0, vary=vary_dvdt)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params, fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(nplanets, basis='per tp e w k')
params['per1'] = radvel.Parameter(value=7832.52)
params['tp1'] = radvel.Parameter(value=2460992.28) #2453159.76)
params['k1'] = radvel.Parameter(value=2041.37)
params['e1'] = radvel.Parameter(value=0.357)
params['w1'] = radvel.Parameter(value=-2.176)
params['dvdt'] = radvel.Parameter(value=0, vary=False)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params, fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(nplanets, basis='per tp e w k')
params['per1'] = radvel.Parameter(value=18882.) #8729.5)
params['tp1'] = radvel.Parameter(value=2457296.2) #2457218.85)
params['k1'] = radvel.Parameter(value=5481.5) #4756.)
params['e1'] = radvel.Parameter(value=0.66) #0.54)
params['w1'] = radvel.Parameter(value=-2.59) #-2.628)
params['dvdt'] = radvel.Parameter(value=0, vary=False)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params, fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(nplanets, basis='per tp e w k')
params['per1'] = radvel.Parameter(value=31168.7)
params['tp1'] = radvel.Parameter(value=2454063.2)
params['k1'] = radvel.Parameter(value=8619.68)
params['e1'] = radvel.Parameter(value=0.9776)
params['w1'] = radvel.Parameter(value=1.4421)
params['dvdt'] = radvel.Parameter(value=0, vary=False)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params, fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(nplanets, basis='per tp e w k')
params['per1'] = radvel.Parameter(value=494.62)
params['tp1'] = radvel.Parameter(value=2458002.08) #2457507.46)
params['k1'] = radvel.Parameter(value=69.9)
params['e1'] = radvel.Parameter(value=0.741)
params['w1'] = radvel.Parameter(value=1.774)
params['dvdt'] = radvel.Parameter(value=0, vary=False)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params, fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(1,basis='per tc e w k')
params['per1'] = radvel.Parameter(value=14.8386, vary=True)
params['tc1'] = radvel.Parameter(value=2450770.578)
params['k1'] = radvel.Parameter(value=10713.9)
params['e1'] = radvel.Parameter(value=0.206929)
params['w1'] = radvel.Parameter(value=0.179116)
params['dvdt'] = radvel.Parameter(value=0, vary=vary_dvdt)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params,fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(nplanets, basis='per tp e w k')
params['per1'] = radvel.Parameter(value=694.29)
params['tp1'] = radvel.Parameter(value=2456800)
params['k1'] = radvel.Parameter(value=8239.)
params['e1'] = radvel.Parameter(value=0.84)
params['w1'] = radvel.Parameter(value=-2.6)
params['dvdt'] = radvel.Parameter(value=0, vary=False)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params, fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(nplanets, basis='per tp e w k')
params['per1'] = radvel.Parameter(value=13296.1)
params['tp1'] = radvel.Parameter(value=2454937)
params['k1'] = radvel.Parameter(value=2619)
params['e1'] = radvel.Parameter(value=0.06)
params['w1'] = radvel.Parameter(value=-1.047)
params['dvdt'] = radvel.Parameter(value=0, vary=False)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params, fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(nplanets, basis='per tp e w k')
params['per1'] = radvel.Parameter(value=25884.52)
params['tp1'] = radvel.Parameter(value=2453958.17)
params['k1'] = radvel.Parameter(value=1755.8)
params['e1'] = radvel.Parameter(value=0.59)
params['w1'] = radvel.Parameter(value=-0.87)
params['dvdt'] = radvel.Parameter(value=0, vary=False)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params,fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(nplanets, basis='per tp e w k')
params['per1'] = radvel.Parameter(value=4401.43)
params['tp1'] = radvel.Parameter(value=2456550.94)
params['k1'] = radvel.Parameter(value=4000.)
params['e1'] = radvel.Parameter(value=0.62)
params['w1'] = radvel.Parameter(value=0.39)
params['dvdt'] = radvel.Parameter(value=0, vary=False)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params,fitting_basis)
return params
def initialize_params():
params = radvel.Parameters(nplanets, basis='per tp e w k')
params['per1'] = radvel.Parameter(value=3759.22)
params['tp1'] = radvel.Parameter(value=2457360.69)
params['k1'] = radvel.Parameter(value=1336.42)
params['e1'] = radvel.Parameter(value=0.60)
params['w1'] = radvel.Parameter(value=0.94)
params['dvdt'] = radvel.Parameter(value=0, vary=False)
params['curv'] = radvel.Parameter(value=0, vary=False)
# Convert input orbital parameters into the fitting basis
params = params.basis.to_any_basis(params,fitting_basis)
return params
