def Fit0_Jitter(x, y, yerr = None, verbose = True, doPlot = False, \
xpred = None):
k = terms.Matern32Term(log_sigma=0.0, log_rho=0.0)
if yerr is None:
wn = np.median(abs(np.diff(y)))
else:
wn = np.median(yerr)
k += terms.JitterTerm(log_sigma=np.log(wn))
gp = GP(k, mean=1.0)
gp.compute(x)
HP_init = gp.get_parameter_vector()
soln = minimize(NLL0, gp.get_parameter_vector(), jac=True, args=(gp, y))
gp.set_parameter_vector(soln.x)
if verbose:
print 'Initial pars:', HP_init
print 'Fitted pars:', soln.x
if xpred is None:
return soln.x
mu, var = gp.predict(y, xpred, return_var=True)
std = np.sqrt(var)
if doPlot:
plt.errorbar(x, y, yerr=yerr, fmt=".k", capsize=0)
plt.plot(xpred, mu, 'C0')
plt.fill_between(xpred,
mu + std,
mu - std,
color='C0',
alpha=0.4,
lw=0)
return soln.x, mu, std
def test_log_likelihood(method, seed=42):
np.random.seed(seed)
x = np.sort(np.random.rand(10))
yerr = np.random.uniform(0.1, 0.5, len(x))
y = np.sin(x)
kernel = terms.RealTerm(0.1, 0.5)
gp = GP(kernel, method=method)
with pytest.raises(RuntimeError):
gp.log_likelihood(y)
for term in [(0.6, 0.7, 1.0)]:
kernel += terms.ComplexTerm(*term)
gp = GP(kernel, method=method)
assert gp.computed is False
with pytest.raises(ValueError):
gp.compute(np.random.rand(len(x)), yerr)
gp.compute(x, yerr)
assert gp.computed is True
assert gp.dirty is False
ll = gp.log_likelihood(y)
K = gp.get_matrix(include_diagonal=True)
ll0 = -0.5 * np.dot(y, np.linalg.solve(K, y))
ll0 -= 0.5 * np.linalg.slogdet(K)[1]
ll0 -= 0.5 * len(x) * np.log(2*np.pi)
assert np.allclose(ll, ll0)
# Check that changing the parameters "un-computes" the likelihood.
gp.set_parameter_vector(gp.get_parameter_vector())
assert gp.dirty is True
assert gp.computed is False
# Check that changing the parameters changes the likelihood.
gp.compute(x, yerr)
ll1 = gp.log_likelihood(y)
params = gp.get_parameter_vector()
params[0] += 0.1
gp.set_parameter_vector(params)
gp.compute(x, yerr)
ll2 = gp.log_likelihood(y)
assert not np.allclose(ll1, ll2)
gp[1] += 0.1
assert gp.dirty is True
gp.compute(x, yerr)
ll3 = gp.log_likelihood(y)
assert not np.allclose(ll2, ll3)
def test_grad_log_likelihood(kernel, seed=42, eps=1.34e-7):
np.random.seed(seed)
x = np.sort(np.random.rand(100))
yerr = np.random.uniform(0.1, 0.5, len(x))
y = np.sin(x)
if not terms.HAS_AUTOGRAD:
gp = GP(kernel)
gp.compute(x, yerr)
with pytest.raises(ImportError):
_, grad = gp.grad_log_likelihood(y)
return
for fit_mean in [True, False]:
gp = GP(kernel, fit_mean=fit_mean)
gp.compute(x, yerr)
_, grad = gp.grad_log_likelihood(y)
grad0 = np.empty_like(grad)
v = gp.get_parameter_vector()
for i, pval in enumerate(v):
v[i] = pval + eps
gp.set_parameter_vector(v)
ll = gp.log_likelihood(y)
v[i] = pval - eps
gp.set_parameter_vector(v)
ll -= gp.log_likelihood(y)
grad0[i] = 0.5 * ll / eps
v[i] = pval
assert np.allclose(grad, grad0)
def test_build_gp(method, seed=42):
kernel = terms.RealTerm(0.5, 0.1)
kernel += terms.ComplexTerm(0.6, 0.7, 1.0)
gp = GP(kernel, method=method)
assert gp.vector_size == 5
p = gp.get_parameter_vector()
assert np.allclose(p, [0.5, 0.1, 0.6, 0.7, 1.0])
gp.set_parameter_vector([0.5, 0.8, 0.6, 0.7, 2.0])
p = gp.get_parameter_vector()
assert np.allclose(p, [0.5, 0.8, 0.6, 0.7, 2.0])
with pytest.raises(ValueError):
gp.set_parameter_vector([0.5, 0.8, -0.6])
with pytest.raises(ValueError):
gp.set_parameter_vector("face1")
def test_grad_log_likelihood(kernel, with_general, seed=42, eps=1.34e-7):
np.random.seed(seed)
x = np.sort(np.random.rand(100))
yerr = np.random.uniform(0.1, 0.5, len(x))
y = np.sin(x)
if with_general:
U = np.vander(x - np.mean(x), 4).T
V = U * np.random.rand(4)[:, None]
A = np.sum(U * V, axis=0) + 1e-8
else:
A = np.empty(0)
U = np.empty((0, 0))
V = np.empty((0, 0))
if not terms.HAS_AUTOGRAD:
gp = GP(kernel)
gp.compute(x, yerr, A=A, U=U, V=V)
with pytest.raises(ImportError):
_, grad = gp.grad_log_likelihood(y)
return
for fit_mean in [True, False]:
gp = GP(kernel, fit_mean=fit_mean)
gp.compute(x, yerr, A=A, U=U, V=V)
_, grad = gp.grad_log_likelihood(y)
grad0 = np.empty_like(grad)
v = gp.get_parameter_vector()
for i, pval in enumerate(v):
v[i] = pval + eps
gp.set_parameter_vector(v)
ll = gp.log_likelihood(y)
v[i] = pval - eps
gp.set_parameter_vector(v)
ll -= gp.log_likelihood(y)
grad0[i] = 0.5 * ll / eps
v[i] = pval
assert np.allclose(grad, grad0)
def __call__(self, period: Optional[float] = None):
logger.info("Running Celerite")
assert hasattr(
self.ts, 'ls'), "Celerite step requires a prior Lomb-Scargle step"
self.period = period if period is not None else self.ts.ls.period
gp = GP(SHOTerm(log(self.ts.flux.var()), log(10),
log(2 * pi / self.period)),
mean=1.)
gp.freeze_parameter('kernel:log_omega0')
gp.compute(self.ts.time, yerr=self.ts.ferr)
def minfun(pv):
gp.set_parameter_vector(pv)
gp.compute(self.ts.time, yerr=self.ts.ferr)
return -gp.log_likelihood(self.ts.flux)
res = minimize(minfun,
gp.get_parameter_vector(),
jac=False,
method='powell')
self.result = res
self.parameters = res.x
self.prediction = gp.predict(self.ts.flux, return_cov=False)
class LineFitter(object):
def __init__(self,
x,
flux,
ivar=None,
absorp_emiss=None,
n_bg_coef=2,
target_x=None):
"""
Parameters
----------
x : array_like
Dispersion parameter. Usually either pixel or wavelength.
flux : array_like
Flux array.
ivar : array_like
Inverse-variance array.
absorp_emiss : numeric [-1, 1] (optional)
If -1, absorption line. If +1, emission line. If not specified,
will try to guess.
n_bg_coef : int (optional)
The order of the polynomial used to fit the background.
1 = constant, 2 = linear, 3 = quadratic, etc.
target_x : numeric (optional)
Where we think the line of interest is.
"""
self.x = np.array(x)
self.flux = np.array(flux)
if ivar is not None:
self.ivar = np.array(ivar)
self._err = 1 / np.sqrt(self.ivar)
else:
self.ivar = np.ones_like(flux)
self._err = None
if absorp_emiss is None:
raise NotImplementedError(
"You must supply an absorp_emiss for now")
self.absorp_emiss = float(absorp_emiss)
self.target_x = target_x
self.n_bg_coef = int(n_bg_coef)
# result of fitting
self.gp = None
self.success = None
@classmethod
def transform_pars(cls, p):
new_p = OrderedDict()
for k, v in p.items():
if k in cls._log_pars:
k = 'ln_{0}'.format(k)
v = np.log(v)
new_p[k] = v
return new_p
def get_init_generic(self, amp=None, x0=None, bg=None, bg_buffer=None):
"""
Get initial guesses for the generic line parameters.
Parameters
----------
amp : numeric
Line amplitude. This should be strictly positive; the
``absorp_emiss`` parameter controls whether it is absorption or
emission.
x0 : numeric
Line centroid.
bg : iterable
Background polynomial coefficients.
bg_buffer : int
The number of values to use on either end of the flux array to
estimate the background parameters.
"""
target_x = self.target_x
if x0 is None: # estimate the initial guess for the centroid
relmins = argrelmin(-self.absorp_emiss * self.flux)[0]
if len(relmins) > 1 and target_x is None:
logger.log(
0, "no target_x specified - taking largest line "
"in spec region")
target_x = self.x[np.argmin(-self.absorp_emiss * self.flux)]
if len(relmins) == 1:
x0 = self.x[relmins[0]]
else:
x0_idx = relmins[np.abs(self.x[relmins] - target_x).argmin()]
x0 = self.x[x0_idx]
# shift x array so that line is approximately at 0
_x = np.array(self.x, copy=True)
x = np.array(_x) - x0
# background polynomial parameters
if bg_buffer is None:
bg_buffer = len(x) // 4
bg_buffer = max(1, bg_buffer)
if bg is None:
if self.n_bg_coef < 2:
bg = np.array([0.])
bg[0] = np.median(self.flux)
else:
# estimate linear background model
bg = np.array([0.] * self.n_bg_coef)
i1 = argmedian(self.flux[:bg_buffer])
i2 = argmedian(self.flux[-bg_buffer:])
f1 = self.flux[:bg_buffer][i1]
f2 = self.flux[-bg_buffer:][i2]
x1 = x[:bg_buffer][i1]
x2 = x[-bg_buffer:][i2]
bg[1] = (f2 - f1) / (x2 - x1) # slope
bg[0] = f2 - bg[1] * x2 # estimate constant term
else:
if len(bg) != self.n_bg_coef:
raise ValueError('Number of bg polynomial coefficients does '
'not match n_bg_coef specified when fitter '
'was created.')
if amp is None: # then estimate the initial guess for amplitude
_i = np.argmin(np.abs(x))
if len(bg) > 1:
_bg = bg[0] + bg[1] * x[_i]
else:
_bg = bg[0]
# amp = np.sqrt(2*np.pi) * (flux[_i] - bg)
amp = self.flux[_i] - _bg
p0 = OrderedDict()
p0['amp'] = np.abs(amp)
p0['x0'] = x0
p0['bg_coef'] = bg
return p0
def get_init_gp(self, log_sigma=None, log_rho=None, x0=None):
"""
Set up the GP kernel parameters.
"""
if log_sigma is None:
if x0 is not None:
# better initial guess for GP parameters
mask = np.abs(self.x - x0) > 2.
y_MAD = np.median(
np.abs(self.flux[mask] - np.median(self.flux[mask])))
else:
y_MAD = np.median(np.abs(self.flux - np.median(self.flux)))
log_sigma = np.log(3 * y_MAD)
if log_rho is None:
log_rho = np.log(5.)
p0 = OrderedDict()
p0['log_sigma'] = log_sigma
p0['log_rho'] = log_rho
return p0
def init_gp(self,
log_sigma=None,
log_rho=None,
amp=None,
x0=None,
bg=None,
bg_buffer=None,
**kwargs):
"""
**kwargs:
"""
# Call the different get_init methods with the correct kwargs passed
sig = inspect.signature(self.get_init)
kw = OrderedDict()
for k in list(sig.parameters.keys()):
kw[k] = kwargs.pop(k, None)
p0 = self.get_init(**kw)
# Call the generic init method - all line models must have these params
p0_generic = self.get_init_generic(amp=amp,
x0=x0,
bg=bg,
bg_buffer=bg_buffer)
for k, v in p0_generic.items():
p0[k] = v
# expand bg parameters
bgs = p0.pop('bg_coef')
for i in range(self.n_bg_coef):
p0['bg{}'.format(i)] = bgs[i]
# transform
p0 = self.transform_pars(p0)
# initialize model
mean_model = self.MeanModel(n_bg_coef=self.n_bg_coef,
absorp_emiss=self.absorp_emiss,
**p0)
p0_gp = self.get_init_gp(log_sigma=log_sigma, log_rho=log_rho)
kernel = terms.Matern32Term(log_sigma=p0_gp['log_sigma'],
log_rho=p0_gp['log_rho'])
# set up the gp model
self.gp = GP(kernel, mean=mean_model, fit_mean=True)
if self._err is not None:
self.gp.compute(self.x, self._err)
else:
self.gp.compute(self.x)
init_params = self.gp.get_parameter_vector()
init_ll = self.gp.log_likelihood(self.flux)
logger.log(0, "Initial log-likelihood: {0}".format(init_ll))
return init_params
def get_gp_mean_pars(self):
"""
Return a parameter dictionary for the mean model parameters only.
"""
fit_pars = OrderedDict()
for k, v in self.gp.get_parameter_dict().items():
if 'mean' not in k:
continue
k = k[5:] # remove 'mean:'
if k.startswith('ln'):
if 'amp' in k:
fit_pars[k[3:]] = self.absorp_emiss * np.exp(v)
else:
fit_pars[k[3:]] = np.exp(v)
elif k.startswith('bg'):
if 'bg_coef' not in fit_pars:
fit_pars['bg_coef'] = []
fit_pars['bg_coef'].append(v)
else:
fit_pars[k] = v
return fit_pars
def _neg_log_like(self, params):
self.gp.set_parameter_vector(params)
try:
ll = self.gp.log_likelihood(self.flux)
except (RuntimeError, LinAlgError):
return np.inf
if np.isnan(ll):
return np.inf
return -ll
def fit(self, bounds=None, **kwargs):
"""
"""
init_params = self.init_gp()
if bounds is None:
bounds = OrderedDict()
# default bounds for mean model parameters
i = self.gp.models['mean'].get_parameter_names().index('x0')
mean_bounds = self.gp.models['mean'].get_parameter_bounds()
if mean_bounds[i][0] is None and mean_bounds[i][1] is None:
mean_bounds[i] = (min(self.x), max(self.x))
for i, k in enumerate(self.gp.models['mean'].parameter_names):
mean_bounds[i] = bounds.get(k, mean_bounds[i])
self.gp.models['mean'].parameter_bounds = mean_bounds
# HACK: default bounds for kernel parameters
self.gp.models['kernel'].parameter_bounds = [(None, None),
(np.log(0.5), None)]
soln = minimize(self._neg_log_like,
init_params,
method="L-BFGS-B",
bounds=self.gp.get_parameter_bounds())
self.success = soln.success
self.gp.set_parameter_vector(soln.x)
if self.success:
logger.debug("Success: {0}, Final log-likelihood: {1}".format(
soln.success, -soln.fun))
else:
logger.warning("Fit failed! Final log-likelihood: {0}, "
"Final parameters: {1}".format(-soln.fun, soln.x))
return self
def plot_fit(self, axes=None, fit_alpha=0.5):
unbinned_color = '#3182bd'
binned_color = '#2ca25f'
gp_color = '#ff7f0e'
noise_color = '#de2d26'
if self.gp is None:
raise ValueError("You must run .fit() first!")
# ----------------------------------------------------------------------
# Plot the maximum likelihood model
if axes is None:
fig, axes = plt.subplots(1, 3, figsize=(15, 5), sharex=True)
# data
for ax in axes[:2]:
ax.plot(self.x,
self.flux,
drawstyle='steps-mid',
marker='',
color='#777777',
zorder=2)
if self._err is not None:
ax.errorbar(self.x,
self.flux,
self._err,
marker='',
ls='none',
ecolor='#666666',
zorder=1)
# mean model
wave_grid = np.linspace(self.x.min(), self.x.max(), 256)
mu, var = self.gp.predict(self.flux, self.x, return_var=True)
std = np.sqrt(var)
axes[0].plot(wave_grid,
self.gp.mean.get_unbinned_value(wave_grid),
marker='',
alpha=fit_alpha,
zorder=10,
color=unbinned_color)
axes[0].plot(self.x,
self.gp.mean.get_value(self.x),
marker='',
alpha=fit_alpha,
zorder=10,
drawstyle='steps-mid',
color=binned_color)
# full GP model
axes[1].plot(self.x,
mu,
color=gp_color,
drawstyle='steps-mid',
marker='',
alpha=fit_alpha,
zorder=10)
axes[1].fill_between(self.x,
mu + std,
mu - std,
color=gp_color,
alpha=fit_alpha / 10.,
edgecolor="none",
step='mid')
# just GP noise component
mean_model = self.gp.mean.get_value(self.x)
axes[2].plot(self.x,
mu - mean_model,
marker='',
alpha=fit_alpha,
zorder=10,
drawstyle='steps-mid',
color=noise_color)
axes[2].plot(self.x,
self.flux - mean_model,
drawstyle='steps-mid',
marker='',
color='#777777',
zorder=2)
if self._err is not None:
axes[2].errorbar(self.x,
self.flux - mean_model,
self._err,
marker='',
ls='none',
ecolor='#666666',
zorder=1)
axes[0].set_ylabel('flux')
axes[0].set_xlim(self.x.min(), self.x.max())
axes[0].set_title('Line model')
axes[1].set_title('Line + noise model')
axes[2].set_title('Noise model')
fig = axes[0].figure
fig.tight_layout()
return fig
def drw_fit(lc_df, de=True, debug=False, plot=False, bounds=None):
best_fit = np.zeros((2, 6))
# fail_num = 0
lc_df = lc_df.copy()
std = np.std(lc_df.flux.values)
if bounds is not None:
first_bounds = bounds
else:
first_bounds = [(-4, np.log(4 * std)), (-4, 10)]
# loop through lc in each passband
for band in range(6):
try:
lc_band = lc_df[lc_df.passband == band].copy()
t = lc_band.mjd.values - lc_band.mjd.min()
y = lc_band.flux.values
yerr = lc_band.flux_err.values
rerun = True # dynamic control of bounds
counter = 0
bounds = first_bounds
jac_log_rec = 10
# initialize parameter and kernel
kernel = DRW_term(*drw_log_param_init(std))
gp = GP(kernel, mean=np.mean(y))
gp.compute(t, yerr)
if de:
# set bound based on LC std for amp
while rerun and (counter < 5):
counter += 1
r = differential_evolution(neg_ll,
bounds=bounds,
args=(y, yerr, gp),
maxiter=200)
if r.success:
best_fit[:, band] = np.exp(r.x)
if "jac" not in r.keys():
rerun = False
else:
jac_log = np.log10(np.dot(r.jac, r.jac) + 1e-8)
# if positive jac, then increase bounds
if jac_log > 0:
bounds = [(x[0] - 1, x[1] + 1) for x in bounds]
else:
rerun = False
# update best-fit if smaller jac found
if jac_log < jac_log_rec:
jac_log_rec = jac_log
best_fit[:, band] = np.exp(r.x)
else:
bounds = [(x[0] - 1, x[1] + 1) for x in bounds]
gp.set_parameter_vector(drw_log_param_init(std))
else:
initial_params = gp.get_parameter_vector()
while rerun and (counter < 5):
counter += 1
r = minimize(
neg_ll,
initial_params,
method="L-BFGS-B",
bounds=bounds,
args=(y, yerr, gp),
)
if r.success:
best_fit[:, band] = np.exp(r.x)
if "jac" not in r.keys():
rerun = False
else:
jac_log = np.log10(np.dot(r.jac, r.jac) + 1e-8)
# if positive jac, then increase bounds
if jac_log > 0:
bounds = [(x[0] - 1, x[1] + 1) for x in bounds]
else:
rerun = False
# update best-fit if smaller jac found
if jac_log < jac_log_rec:
jac_log_rec = jac_log
best_fit[:, band] = np.exp(r.x)
else:
bounds = [(x[0] - 1, x[1] + 1) for x in bounds]
gp.set_parameter_vector(drw_log_param_init(std))
if not r.success:
best_fit[:, band] = np.nan
except Exception as e:
print(r)
print(e)
print(
f"Exception at object_id: {lc_df.object_id.values[0]}, passband: {band}"
)
best_fit[:, band] = np.nan
# fail_num += 1
# Below code is used to visualize if stuck in local minima
if debug:
print(r)
if plot:
plot_drw_ll(t, y, yerr, np.exp(r.x), gp, vec_neg_ll)
return np.concatenate([[lc_df.object_id.values[0]], best_fit.flatten()])
def carma_fit(lc_df, p, q, de=True, debug=False, plot=False, bounds=None):
best_fit = np.zeros((int(p + q + 1), 6))
lc_df = lc_df.copy()
if bounds is not None:
first_bounds = bounds
else:
first_bounds = [(-10, 5)] * int(p + q + 1)
# loop through lc in each passband
for band in range(6):
try:
lc_band = lc_df[lc_df.passband == band].copy()
t = lc_band.mjd.values - lc_band.mjd.min()
y = lc_band.flux.values
yerr = lc_band.flux_err.values
rerun = True # dynamic control of bounds
compute = True # handle can't factorize in gp.compute()
succeded = False # ever succeded
compute_ct = 0
counter = 0
bounds = first_bounds
jac_log_rec = 10
# initialize parameter, kernel and GP
log_params = carma_param_init(int(p + q + 1))
kernel = CARMA_term(log_params[:p], log_params[p:])
gp = GP(kernel, mean=np.mean(y))
# compute can't factorize, try 4 more times
while compute & (compute_ct < 5):
compute_ct += 1
try:
gp.compute(t, yerr)
compute = False
except celerite.solver.LinAlgError:
gp.set_parameter_vector(carma_param_init(int(p + q + 1)))
if de:
# set bound based on LC std for amp
while rerun and (counter < 5):
counter += 1
r = differential_evolution(neg_ll,
bounds=bounds,
args=(y, yerr, gp),
maxiter=200)
if r.success:
succeded = True
best_fit[:, band] = np.exp(r.x)
if "jac" not in r.keys():
rerun = False
else:
jac_log = np.log10(np.dot(r.jac, r.jac) + 1e-8)
# if positive jac, then increase bounds
if jac_log > 0:
bounds = [(x[0] - 1, x[1] + 1) for x in bounds]
else:
rerun = False
# update best-fit if smaller jac found
if jac_log < jac_log_rec:
jac_log_rec = jac_log
best_fit[:, band] = np.exp(r.x)
else:
bounds = [(x[0] - 1, x[1] + 1) for x in bounds]
gp.set_parameter_vector(
carma_param_init(int(p + q + 1)))
else:
initial_params = gp.get_parameter_vector()
while rerun and (counter < 5):
counter += 1
r = minimize(
neg_ll,
initial_params,
method="L-BFGS-B",
bounds=bounds,
args=(y, yerr, gp),
)
if r.success:
succeded = True
best_fit[:, band] = np.exp(r.x)
jac_log = np.log10(np.dot(r.jac, r.jac) + 1e-8)
# if positive jac, then increase bounds
if jac_log > 0:
bounds = [(x[0] - 1, x[1] + 1) for x in bounds]
else:
rerun = False
# update best-fit if smaller jac found
if jac_log < jac_log_rec:
jac_log_rec = jac_log
best_fit[:, band] = np.exp(r.x)
else:
bounds = [(x[0] - 1, x[1] + 1) for x in bounds]
gp.set_parameter_vector(
carma_param_init(int(p + q + 1)))
if not succeded:
best_fit[:, band] = np.nan
except Exception as e:
print(e)
print(
f"Exception at object_id: {lc_df.object_id.values[0]}, passband: {band}"
)
best_fit[:, band] = np.nan
# Below code is used to visualize if stuck in local minima
if debug:
print(r)
# if plot:
# plot_dho_ll(t, y, yerr, np.exp(r.x), gp, vec_neg_ll)
return np.concatenate([[lc_df.object_id.values[0]], best_fit.flatten()])
def test_log_likelihood(seed=42):
np.random.seed(seed)
x = np.sort(np.random.rand(10))
yerr = np.random.uniform(0.1, 0.5, len(x))
y = np.sin(x)
kernel = terms.RealTerm(0.1, 0.5)
gp = GP(kernel)
with pytest.raises(RuntimeError):
gp.log_likelihood(y)
termlist = [(0.1 + 10./j, 0.5 + 10./j) for j in range(1, 4)]
termlist += [(1.0 + 10./j, 0.01 + 10./j, 0.5, 0.01) for j in range(1, 10)]
termlist += [(0.6, 0.7, 1.0), (0.3, 0.05, 0.5, 0.6)]
for term in termlist:
if len(term) > 2:
kernel += terms.ComplexTerm(*term)
else:
kernel += terms.RealTerm(*term)
gp = GP(kernel)
assert gp.computed is False
with pytest.raises(ValueError):
gp.compute(np.random.rand(len(x)), yerr)
gp.compute(x, yerr)
assert gp.computed is True
assert gp.dirty is False
ll = gp.log_likelihood(y)
K = gp.get_matrix(include_diagonal=True)
ll0 = -0.5 * np.dot(y, np.linalg.solve(K, y))
ll0 -= 0.5 * np.linalg.slogdet(K)[1]
ll0 -= 0.5 * len(x) * np.log(2*np.pi)
assert np.allclose(ll, ll0)
# Check that changing the parameters "un-computes" the likelihood.
gp.set_parameter_vector(gp.get_parameter_vector())
assert gp.dirty is True
assert gp.computed is False
# Check that changing the parameters changes the likelihood.
gp.compute(x, yerr)
ll1 = gp.log_likelihood(y)
params = gp.get_parameter_vector()
params[0] += 10.0
gp.set_parameter_vector(params)
gp.compute(x, yerr)
ll2 = gp.log_likelihood(y)
assert not np.allclose(ll1, ll2)
gp[1] += 10.0
assert gp.dirty is True
gp.compute(x, yerr)
ll3 = gp.log_likelihood(y)
assert not np.allclose(ll2, ll3)
# Test zero delta t
ind = len(x) // 2
x = np.concatenate((x[:ind], [x[ind]], x[ind:]))
y = np.concatenate((y[:ind], [y[ind]], y[ind:]))
yerr = np.concatenate((yerr[:ind], [yerr[ind]], yerr[ind:]))
gp.compute(x, yerr)
ll = gp.log_likelihood(y)
K = gp.get_matrix(include_diagonal=True)
ll0 = -0.5 * np.dot(y, np.linalg.solve(K, y))
ll0 -= 0.5 * np.linalg.slogdet(K)[1]
ll0 -= 0.5 * len(x) * np.log(2*np.pi)
assert np.allclose(ll, ll0), "face"
def test_log_likelihood(with_general, seed=42):
np.random.seed(seed)
x = np.sort(np.random.rand(10))
yerr = np.random.uniform(0.1, 0.5, len(x))
y = np.sin(x)
if with_general:
U = np.vander(x - np.mean(x), 4).T
V = U * np.random.rand(4)[:, None]
A = np.sum(U * V, axis=0) + 1e-8
else:
A = np.empty(0)
U = np.empty((0, 0))
V = np.empty((0, 0))
# Check quiet argument with a non-positive definite kernel.
class NPDTerm(terms.Term):
parameter_names = ("par1", )
def get_real_coefficients(self, params): # NOQA
return [params[0]], [0.1]
gp = GP(NPDTerm(-1.0))
with pytest.raises(celerite.solver.LinAlgError):
gp.compute(x, 0.0)
with pytest.raises(celerite.solver.LinAlgError):
gp.log_likelihood(y)
assert np.isinf(gp.log_likelihood(y, quiet=True))
if terms.HAS_AUTOGRAD:
assert np.isinf(gp.grad_log_likelihood(y, quiet=True)[0])
kernel = terms.RealTerm(0.1, 0.5)
gp = GP(kernel)
with pytest.raises(RuntimeError):
gp.log_likelihood(y)
termlist = [(0.1 + 10. / j, 0.5 + 10. / j) for j in range(1, 4)]
termlist += [(1.0 + 10. / j, 0.01 + 10. / j, 0.5, 0.01)
for j in range(1, 10)]
termlist += [(0.6, 0.7, 1.0), (0.3, 0.05, 0.5, 0.6)]
for term in termlist:
if len(term) > 2:
kernel += terms.ComplexTerm(*term)
else:
kernel += terms.RealTerm(*term)
gp = GP(kernel)
assert gp.computed is False
with pytest.raises(ValueError):
gp.compute(np.random.rand(len(x)), yerr)
gp.compute(x, yerr, A=A, U=U, V=V)
assert gp.computed is True
assert gp.dirty is False
ll = gp.log_likelihood(y)
K = gp.get_matrix(include_diagonal=True)
ll0 = -0.5 * np.dot(y, np.linalg.solve(K, y))
ll0 -= 0.5 * np.linalg.slogdet(K)[1]
ll0 -= 0.5 * len(x) * np.log(2 * np.pi)
assert np.allclose(ll, ll0)
# Check that changing the parameters "un-computes" the likelihood.
gp.set_parameter_vector(gp.get_parameter_vector())
assert gp.dirty is True
assert gp.computed is False
# Check that changing the parameters changes the likelihood.
gp.compute(x, yerr, A=A, U=U, V=V)
ll1 = gp.log_likelihood(y)
params = gp.get_parameter_vector()
params[0] += 10.0
gp.set_parameter_vector(params)
gp.compute(x, yerr, A=A, U=U, V=V)
ll2 = gp.log_likelihood(y)
assert not np.allclose(ll1, ll2)
gp[1] += 10.0
assert gp.dirty is True
gp.compute(x, yerr, A=A, U=U, V=V)
ll3 = gp.log_likelihood(y)
assert not np.allclose(ll2, ll3)
# Test zero delta t
ind = len(x) // 2
x = np.concatenate((x[:ind], [x[ind]], x[ind:]))
y = np.concatenate((y[:ind], [y[ind]], y[ind:]))
yerr = np.concatenate((yerr[:ind], [yerr[ind]], yerr[ind:]))
gp.compute(x, yerr)
ll = gp.log_likelihood(y)
K = gp.get_matrix(include_diagonal=True)
ll0 = -0.5 * np.dot(y, np.linalg.solve(K, y))
ll0 -= 0.5 * np.linalg.slogdet(K)[1]
ll0 -= 0.5 * len(x) * np.log(2 * np.pi)
assert np.allclose(ll, ll0)