diff --git a/GPy/examples/dimensionality_reduction.py b/GPy/examples/dimensionality_reduction.py index f1fdaaf1..61a4abd8 100644 --- a/GPy/examples/dimensionality_reduction.py +++ b/GPy/examples/dimensionality_reduction.py @@ -133,32 +133,3 @@ def stick(): plt.close('all') return m - - -def BGPLVM_oil(): - data = GPy.util.datasets.oil() - Y, X = data['Y'], data['X'] - X -= X.mean(axis=0) - X /= X.std(axis=0) - - Q = 10 - M = 30 - - kernel = GPy.kern.rbf(Q, ARD = True) + GPy.kern.bias(Q) + GPy.kern.white(Q) - m = GPy.models.Bayesian_GPLVM(X, Q, kernel=kernel, M=M) - # m.scale_factor = 100.0 - m.constrain_positive('(white|noise|bias|X_variance|rbf_variance|rbf_length)') - from sklearn import cluster - km = cluster.KMeans(M, verbose=10) - Z = km.fit(m.X).cluster_centers_ - # Z = GPy.util.misc.kmm_init(m.X, M) - m.set('iip', Z) - m.set('bias', 1e-4) - # optimize - # m.ensure_default_constraints() - - import pdb; pdb.set_trace() - m.optimize('tnc', messages=1) - print m - m.plot_latent(labels=data['Y'].argmax(axis=1)) - return m diff --git a/GPy/models/GPLVM.py b/GPy/models/GPLVM.py index 470aff96..2ce55dda 100644 --- a/GPy/models/GPLVM.py +++ b/GPy/models/GPLVM.py @@ -89,7 +89,7 @@ class GPLVM(GP): Xtest_full = np.zeros((Xtest.shape[0], self.X.shape[1])) Xtest_full[:, :2] = Xtest mu, var, low, up = self.predict(Xtest_full) - var = var[:, :1] # FIXME: this was a :2 + var = var[:, :1] pb.imshow(var.reshape(resolution,resolution).T[::-1,:], extent=[xmin[0], xmax[0], xmin[1], xmax[1]], cmap=pb.cm.binary,interpolation='bilinear') @@ -119,5 +119,6 @@ class GPLVM(GP): pb.xlim(xmin[0],xmax[0]) pb.ylim(xmin[1],xmax[1]) pb.grid(b=False) # remove the grid if present, it doesn't look good + ax = pb.gca() ax.set_aspect('auto') # set a nice aspect ratio - return pb.gca() #input_1, input_2 temporary removal, to return axes. + return ax