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rbf kern chaching bug fixed

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This commit is contained in:
Max Zwiessele 2013-07-18 16:42:17 +01:00
parent cdf7735176
commit 0eac358f46
3 changed files with 16 additions and 11 deletions
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14
GPy/examples/dimensionality_reduction.py
View file

@ -24,7 +24,7 @@ def BGPLVM(seed=default_seed):
Y = np.random.multivariate_normal(np.zeros(N), K, Q).T
lik = Gaussian(Y, normalize=True)
k = GPy.kern.rbf_inv(Q, ARD=True) + GPy.kern.bias(Q) + GPy.kern.white(Q)
k = GPy.kern.rbf(Q, ARD=True) + GPy.kern.bias(Q) + GPy.kern.white(Q)
# k = GPy.kern.rbf(Q) + GPy.kern.bias(Q) + GPy.kern.white(Q, 0.00001)
# k = GPy.kern.rbf(Q, ARD = False) + GPy.kern.white(Q, 0.00001)
@ -144,7 +144,7 @@ def BGPLVM_oil(optimize=True, N=200, Q=10, num_inducing=15, max_iters=150, plot=
data = GPy.util.datasets.oil()
# create simple GP model
kernel = GPy.kern.rbf_inv(Q, ARD=True) + GPy.kern.bias(Q, np.exp(-2)) + GPy.kern.white(Q, np.exp(-2))
kernel = GPy.kern.rbf(Q, ARD=True) + GPy.kern.bias(Q, np.exp(-2)) + GPy.kern.white(Q, np.exp(-2))
Y = data['X'][:N]
Yn = Y - Y.mean(0)
@ -160,9 +160,9 @@ def BGPLVM_oil(optimize=True, N=200, Q=10, num_inducing=15, max_iters=150, plot=
# optimize
if optimize:
m.constrain_fixed('noise')
m.optimize('scg', messages=1, max_iters=200, gtol=.05)
m.constrain_positive('noise')
# m.constrain_fixed('noise')
# m.optimize('scg', messages=1, max_iters=200, gtol=.05)
# m.constrain_positive('noise')
m.optimize('scg', messages=1, max_iters=max_iters, gtol=.05)
if plot:
@ -377,10 +377,10 @@ def stick_bgplvm(model=None):
data = GPy.util.datasets.stick()
Q = 6
kernel = GPy.kern.rbf(Q, ARD=True) + GPy.kern.bias(Q, np.exp(-2)) + GPy.kern.white(Q, np.exp(-2))
m = BayesianGPLVM(data['Y'], Q, init="PCA", num_inducing=20,kernel=kernel)
m = BayesianGPLVM(data['Y'], Q, init="PCA", num_inducing=20, kernel=kernel)
# optimize
m.ensure_default_constraints()
m.optimize(messages=1, max_iters=3000,xtol=1e-300,ftol=1e-300)
m.optimize(messages=1, max_iters=3000, xtol=1e-300, ftol=1e-300)
m._set_params(m._get_params())
plt.clf, (latent_axes, sense_axes) = plt.subplots(1, 2)
plt.sca(latent_axes)

6
GPy/kern/kern.py
View file

@ -104,6 +104,8 @@ class kern(Parameterized):
x = np.arange(x0)
transOffset = offset_copy(ax.transData, fig=fig,
x=0., y= -2., units='points')
transOffsetUp = offset_copy(ax.transData, fig=fig,
x=0., y=2., units='points')
for bar in bars:
for patch, num in zip(bar.patches, np.arange(len(bar.patches))):
height = patch.get_height()
@ -111,10 +113,12 @@ class kern(Parameterized):
va = 'top'
c = 'w'
t = TextPath((0, 0), "${xi}$".format(xi=xi), rotation=0, usetex=True, ha='center')
transform = transOffset
if patch.get_extents().height <= t.get_extents().height + 2:
va = 'bottom'
c = 'k'
ax.text(xi, height, "${xi}$".format(xi=int(num)), color=c, rotation=0, ha='center', va=va, transform=transOffset)
transform = transOffsetUp
ax.text(xi, height, "${xi}$".format(xi=int(num)), color=c, rotation=0, ha='center', va=va, transform=transform)
# for xi, t in zip(x, xticklabels):
# ax.text(xi, maxi / 2, t, rotation=90, ha='center', va='center')
# ax.set_xticklabels(xticklabels, rotation=17)

7
GPy/kern/parts/rbf.py
View file

@ -221,9 +221,10 @@ class RBF(Kernpart):
#---------------------------------------#
def _K_computations(self, X, X2):
if not (fast_array_equal(X, self._X) and fast_array_equal(X2, self._X2) and fast_array_equal(self._params , self._get_params())):
params = self._get_params()
if not (fast_array_equal(X, self._X) and fast_array_equal(X2, self._X2) and fast_array_equal(self._params , params)):
self._X = X.copy()
self._params = self._get_params().copy()
self._params = params.copy()
if X2 is None:
self._X2 = None
X = X / self.lengthscale
@ -244,7 +245,7 @@ class RBF(Kernpart):
self._psi2_Zdist = 0.5 * (Z[:, None, :] - Z[None, :, :]) # M,M,Q
self._psi2_Zdist_sq = np.square(self._psi2_Zdist / self.lengthscale) # M,M,Q
if not (fast_array_equal(Z, self._Z) and fast_array_equal(mu, self._mu) and fast_array_equal(S, self._S)):
if not fast_array_equal(Z, self._Z) or not fast_array_equal(mu, self._mu) or not fast_array_equal(S, self._S):
# something's changed. recompute EVERYTHING
# psi1