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Fixed deprecated warning and sense_axes bug

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Teo de Campos 2013-05-08 18:16:43 +01:00
parent e60eb4e236
commit d209b963f2
2 changed files with 7 additions and 7 deletions
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4
GPy/examples/dimensionality_reduction.py
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@ -82,7 +82,7 @@ def BGPLVM_oil(optimize=True, N=100, Q=10, M=15, max_f_eval=300):
m.ensure_default_constraints() m.ensure_default_constraints()
y = m.likelihood.Y[0, :] y = m.likelihood.Y[0, :]
fig, (latent_axes, hist_axes) = plt.subplots(1, 2) fig, (latent_axes, sense_axes) = plt.subplots(1, 2)
plt.sca(latent_axes) plt.sca(latent_axes)
m.plot_latent() m.plot_latent()
data_show = GPy.util.visualize.vector_show(y) data_show = GPy.util.visualize.vector_show(y)
@ -362,7 +362,7 @@ def brendan_faces():
# optimize # optimize
m.ensure_default_constraints() m.ensure_default_constraints()
m.optimize(messages=1, max_f_eval=10000) # m.optimize(messages=1, max_f_eval=10000)
ax = m.plot_latent() ax = m.plot_latent()
y = m.likelihood.Y[0, :] y = m.likelihood.Y[0, :]

10
GPy/util/linalg.py
View file

@ -16,7 +16,7 @@ import cPickle
import types import types
import ctypes import ctypes
from ctypes import byref, c_char, c_int, c_double # TODO from ctypes import byref, c_char, c_int, c_double # TODO
#import scipy.lib.lapack.flapack #import scipy.lib.lapack
import scipy as sp import scipy as sp
try: try:
@ -63,7 +63,7 @@ def _mdot_r(a,b):
def jitchol(A,maxtries=5): def jitchol(A,maxtries=5):
A = np.asfortranarray(A) A = np.asfortranarray(A)
L,info = linalg.lapack.flapack.dpotrf(A,lower=1) L,info = linalg.lapack.dpotrf(A,lower=1)
if info ==0: if info ==0:
return L return L
else: else:
@ -124,7 +124,7 @@ def pdinv(A, *args):
L = jitchol(A, *args) L = jitchol(A, *args)
logdet = 2.*np.sum(np.log(np.diag(L))) logdet = 2.*np.sum(np.log(np.diag(L)))
Li = chol_inv(L) Li = chol_inv(L)
Ai = linalg.lapack.flapack.dpotri(L)[0] Ai = linalg.lapack.dpotri(L)[0]
Ai = np.tril(Ai) + np.tril(Ai,-1).T Ai = np.tril(Ai) + np.tril(Ai,-1).T
return Ai, L, Li, logdet return Ai, L, Li, logdet
@ -139,7 +139,7 @@ def chol_inv(L):
""" """
return linalg.lapack.flapack.dtrtri(L, lower = True)[0] return linalg.lapack.dtrtri(L, lower = True)[0]
def multiple_pdinv(A): def multiple_pdinv(A):
@ -156,7 +156,7 @@ def multiple_pdinv(A):
N = A.shape[-1] N = A.shape[-1]
chols = [jitchol(A[:,:,i]) for i in range(N)] chols = [jitchol(A[:,:,i]) for i in range(N)]
halflogdets = [np.sum(np.log(np.diag(L[0]))) for L in chols] halflogdets = [np.sum(np.log(np.diag(L[0]))) for L in chols]
invs = [linalg.lapack.flapack.dpotri(L[0],True)[0] for L in chols] invs = [linalg.lapack.dpotri(L[0],True)[0] for L in chols]
invs = [np.triu(I)+np.triu(I,1).T for I in invs] invs = [np.triu(I)+np.triu(I,1).T for I in invs]
return np.dstack(invs),np.array(halflogdets) return np.dstack(invs),np.array(halflogdets)