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Merge branch 'cython2' into devel

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James Hensman 2015-04-28 16:05:37 +01:00
commit 44fbcb4914
23 changed files with 25833 additions and 377 deletions
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57
GPy/testing/cython_tests.py Normal file
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@ -0,0 +1,57 @@
import numpy as np
import scipy as sp
from GPy.util import choleskies
import GPy
"""
These tests make sure that the opure python and cython codes work the same
"""
class CythonTestChols(np.testing.TestCase):
def setUp(self):
self.flat = np.random.randn(45, 5)
self.triang = np.dstack([np.eye(20)[:,:,None] for i in range(3)])
def test_flat_to_triang(self):
L1 = choleskies._flat_to_triang_pure(self.flat)
L2 = choleskies._flat_to_triang_cython(self.flat)
np.testing.assert_allclose(L1, L2)
def test_triang_to_flat(self):
A1 = choleskies._triang_to_flat_pure(self.triang)
A2 = choleskies._triang_to_flat_cython(self.triang)
np.testing.assert_allclose(A1, A2)
class test_stationary(np.testing.TestCase):
def setUp(self):
self.k = GPy.kern.RBF(10)
self.X = np.random.randn(300,10)
self.Z = np.random.randn(20,10)
self.dKxx = np.random.randn(300,300)
self.dKzz = np.random.randn(20,20)
self.dKxz = np.random.randn(300,20)
def test_square_gradX(self):
g1 = self.k._gradients_X_cython(self.dKxx, self.X)
g2 = self.k._gradients_X_pure(self.dKxx, self.X)
np.testing.assert_allclose(g1, g2)
def test_rect_gradx(self):
g1 = self.k._gradients_X_cython(self.dKxz, self.X, self.Z)
g2 = self.k._gradients_X_pure(self.dKxz, self.X, self.Z)
np.testing.assert_allclose(g1, g2)
def test_square_lengthscales(self):
g1 = self.k._lengthscale_grads_pure(self.dKxx, self.X, self.X)
g2 = self.k._lengthscale_grads_cython(self.dKxx, self.X, self.X)
np.testing.assert_allclose(g1, g2)
def test_rect_lengthscales(self):
g1 = self.k._lengthscale_grads_pure(self.dKxz, self.X, self.Z)
g2 = self.k._lengthscale_grads_cython(self.dKxz, self.X, self.Z)
np.testing.assert_allclose(g1, g2)

38
GPy/testing/kernel_tests.py
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@ -366,9 +366,9 @@ class KernelTestsNonContinuous(unittest.TestCase):
X2 = self.X2[self.X2[:,-1]!=2]
self.assertTrue(check_kernel_gradient_functions(kern, X=X, X2=X2, verbose=verbose, fixed_X_dims=-1))
class Coregionalize_weave_test(unittest.TestCase):
class Coregionalize_cython_test(unittest.TestCase):
"""
Make sure that the coregionalize kernel work with and without weave enabled
Make sure that the coregionalize kernel work with and without cython enabled
"""
def setUp(self):
self.k = GPy.kern.Coregionalize(1, output_dim=12)
@ -378,36 +378,42 @@ class Coregionalize_weave_test(unittest.TestCase):
def test_sym(self):
dL_dK = np.random.randn(self.N1, self.N1)
GPy.util.config.config.set('weave', 'working', 'True')
K_weave = self.k.K(self.X)
GPy.util.config.config.set('cython', 'working', 'True')
K_cython = self.k.K(self.X)
self.k.update_gradients_full(dL_dK, self.X)
grads_weave = self.k.gradient.copy()
grads_cython = self.k.gradient.copy()
GPy.util.config.config.set('weave', 'working', 'False')
GPy.util.config.config.set('cython', 'working', 'False')
K_numpy = self.k.K(self.X)
self.k.update_gradients_full(dL_dK, self.X)
grads_numpy = self.k.gradient.copy()
self.assertTrue(np.allclose(K_numpy, K_weave))
self.assertTrue(np.allclose(grads_numpy, grads_weave))
self.assertTrue(np.allclose(K_numpy, K_cython))
self.assertTrue(np.allclose(grads_numpy, grads_cython))
#reset the cython state for any other tests
GPy.util.config.config.set('cython', 'working', 'true')
def test_nonsym(self):
dL_dK = np.random.randn(self.N1, self.N2)
GPy.util.config.config.set('weave', 'working', 'True')
K_weave = self.k.K(self.X, self.X2)
GPy.util.config.config.set('cython', 'working', 'True')
K_cython = self.k.K(self.X, self.X2)
self.k.gradient = 0.
self.k.update_gradients_full(dL_dK, self.X, self.X2)
grads_weave = self.k.gradient.copy()
grads_cython = self.k.gradient.copy()
GPy.util.config.config.set('weave', 'working', 'False')
GPy.util.config.config.set('cython', 'working', 'False')
K_numpy = self.k.K(self.X, self.X2)
self.k.gradient = 0.
self.k.update_gradients_full(dL_dK, self.X, self.X2)
grads_numpy = self.k.gradient.copy()
self.assertTrue(np.allclose(K_numpy, K_weave))
self.assertTrue(np.allclose(grads_numpy, grads_weave))
self.assertTrue(np.allclose(K_numpy, K_cython))
self.assertTrue(np.allclose(grads_numpy, grads_cython))
#reset the cython state for any other tests
GPy.util.config.config.set('cython', 'working', 'true')
#reset the weave state for any other tests
GPy.util.config.config.set('weave', 'working', 'False')
class KernelTestsProductWithZeroValues(unittest.TestCase):