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[stick] bgplvm example now working

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mzwiessele 2014-05-13 09:03:57 +01:00
parent 4b1577178c
commit 53ff580a6e
1 changed files with 5 additions and 8 deletions
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13
GPy/examples/dimensionality_reduction.py
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@ -480,18 +480,14 @@ def stick_bgplvm(model=None, optimize=True, verbose=True, plot=True):
data = GPy.util.datasets.osu_run1() data = GPy.util.datasets.osu_run1()
Q = 6 Q = 6
kernel = GPy.kern.RBF(Q, lengthscale=np.repeat(.5, Q), ARD=True) + GPy.kern.Bias(Q, _np.exp(-2)) kernel = GPy.kern.RBF(Q, lengthscale=np.repeat(.5, Q), ARD=True)
m = BayesianGPLVM(data['Y'], Q, init="PCA", num_inducing=20, kernel=kernel) m = BayesianGPLVM(data['Y'], Q, init="PCA", num_inducing=20, kernel=kernel)
m.data = data m.data = data
m.X.mean -= m.X.mean.mean(0); m.X.mean /= m.X.mean.var(0)
m.X.variance /= 100
m.likelihood.variance = 0.001 m.likelihood.variance = 0.001
m.Z.randomize()
# optimize # optimize
if optimize: m.optimize('bfgs', messages=verbose, max_iters=1500, xtol=1e-300, ftol=1e-300) if optimize: m.optimize('bfgs', messages=verbose, max_iters=800, xtol=1e-300, ftol=1e-300)
if plot: if plot:
plt.clf, (latent_axes, sense_axes) = plt.subplots(1, 2) plt.clf, (latent_axes, sense_axes) = plt.subplots(1, 2)
plt.sca(latent_axes) plt.sca(latent_axes)
@ -499,7 +495,8 @@ def stick_bgplvm(model=None, optimize=True, verbose=True, plot=True):
y = m.Y[:1, :].copy() y = m.Y[:1, :].copy()
data_show = GPy.plotting.matplot_dep.visualize.stick_show(y, connect=data['connect']) data_show = GPy.plotting.matplot_dep.visualize.stick_show(y, connect=data['connect'])
GPy.plotting.matplot_dep.visualize.lvm_dimselect(m.X.mean[:1, :].copy(), m, data_show, latent_axes=latent_axes, sense_axes=sense_axes) GPy.plotting.matplot_dep.visualize.lvm_dimselect(m.X.mean[:1, :].copy(), m, data_show, latent_axes=latent_axes, sense_axes=sense_axes)
raw_input('Press enter to finish') plt.draw()
#raw_input('Press enter to finish')
return m return m
@ -516,7 +513,7 @@ def cmu_mocap(subject='35', motion=['01'], in_place=True, optimize=True, verbose
if optimize: m.optimize(messages=verbose, max_f_eval=10000) if optimize: m.optimize(messages=verbose, max_f_eval=10000)
if plot: if plot:
ax = m.plot_latent() ax = m.plot_latent()
y = m.likelihood.Y[0, :] y = m.Y[0, :]
data_show = GPy.plotting.matplot_dep.visualize.skeleton_show(y[None, :], data['skel']) data_show = GPy.plotting.matplot_dep.visualize.skeleton_show(y[None, :], data['skel'])
lvm_visualizer = GPy.plotting.matplot_dep.visualize.lvm(m.X[0, :].copy(), m, data_show, ax) lvm_visualizer = GPy.plotting.matplot_dep.visualize.lvm(m.X[0, :].copy(), m, data_show, ax)
raw_input('Press enter to finish') raw_input('Press enter to finish')