Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel

GPy/core/parameterization/index_operations.py

@@ -5,7 +5,7 @@ import numpy
 from numpy.lib.function_base import vectorize
 from .lists_and_dicts import IntArrayDict
 from functools import reduce
-from transformations import Transformation
+from .transformations import Transformation
 
 def extract_properties_to_index(index, props):
     prop_index = dict()

GPy/core/parameterization/parameter_core.py

@@ -440,7 +440,7 @@ class Indexable(Nameable, Updateable):
         log_j = 0.
         priored_indexes = np.hstack([i for p, i in self.priors.items()])
         for c,j in self.constraints.items():
-            if c is 'fixed':continue
+            if not isinstance(c, Transformation):continue
             for jj in j:
                 if jj in priored_indexes:
                     log_j += c.log_jacobian(x[jj])
@@ -457,6 +457,7 @@ class Indexable(Nameable, Updateable):
         #add in jacobian derivatives if transformed
         priored_indexes = np.hstack([i for p, i in self.priors.items()])
         for c,j in self.constraints.items():
+            if not isinstance(c, Transformation):continue
             for jj in j:
                 if jj in priored_indexes:
                     ret[jj] += c.log_jacobian_grad(x[jj])

GPy/core/parameterization/parameterized.py

@@ -6,10 +6,10 @@ import numpy; np = numpy
 import itertools
 from re import compile, _pattern_type
 from .param import ParamConcatenation
-from parameter_core import HierarchyError, Parameterizable, adjust_name_for_printing
+from .parameter_core import HierarchyError, Parameterizable, adjust_name_for_printing
 
 import logging
-from index_operations import ParameterIndexOperationsView
+from .index_operations import ParameterIndexOperationsView
 logger = logging.getLogger("parameters changed meta")
 
 class ParametersChangedMeta(type):

GPy/inference/latent_function_inference/inferenceX.py

@@ -45,16 +45,22 @@ class InferenceX(Model):
         super(InferenceX, self).__init__(name)
         self.likelihood = model.likelihood.copy()
         self.kern = model.kern.copy()
-        if model.kern.useGPU:
-            from ...models import SSGPLVM
-            if isinstance(model, SSGPLVM):
-                self.kern.GPU_SSRBF(True)
-            else:
-                self.kern.GPU(True)
+#         if model.kern.useGPU:
+#             from ...models import SSGPLVM
+#             if isinstance(model, SSGPLVM):
+#                 self.kern.GPU_SSRBF(True)
+#             else:
+#                 self.kern.GPU(True)
         from copy import deepcopy
         self.posterior = deepcopy(model.posterior)
         if hasattr(model, 'variational_prior'):
             self.uncertain_input = True
+            from ...models.ss_gplvm import IBPPrior
+            from ...models.ss_mrd import IBPPrior_SSMRD
+            if isinstance(model.variational_prior, IBPPrior) or isinstance(model.variational_prior, IBPPrior_SSMRD):
+                from ...core.parameterization.variational import SpikeAndSlabPrior
+                self.variational_prior = SpikeAndSlabPrior(pi=05,learnPi=False, group_spike=False)
+            else:
                 self.variational_prior = model.variational_prior.copy()
         else:
             self.uncertain_input = False
@@ -147,9 +153,9 @@ class InferenceX(Model):
             from ...core.parameterization.variational import SpikeAndSlabPrior
             if isinstance(self.variational_prior, SpikeAndSlabPrior):
                 # Update Log-likelihood
-                KL_div = self.variational_prior.KL_divergence(self.X, N=self.Y.shape[0])
+                KL_div = self.variational_prior.KL_divergence(self.X)
                 # update for the KL divergence
-                self.variational_prior.update_gradients_KL(self.X, N=self.Y.shape[0])
+                self.variational_prior.update_gradients_KL(self.X)
             else:
                 # Update Log-likelihood
                 KL_div = self.variational_prior.KL_divergence(self.X)

GPy/inference/optimization/optimization.py

@@ -142,7 +142,7 @@ class opt_lbfgsb(Optimizer):
 
         #a more helpful error message is available in opt_result in the Error case
         if opt_result[2]['warnflag']==2:
-            self.status = 'Error' + opt_result[2]['task']
+            self.status = 'Error' + str(opt_result[2]['task'])
 
 class opt_simplex(Optimizer):
     def __init__(self, *args, **kwargs):

GPy/kern/__init__.py

@@ -19,5 +19,5 @@ from ._src.splitKern import SplitKern,DEtime
 from ._src.splitKern import DEtime as DiffGenomeKern
 
 
-from _src.basis_funcs import LinearSlopeBasisFuncKernel, BasisFuncKernel, ChangePointBasisFuncKernel, DomainKernel
+from ._src.basis_funcs import LinearSlopeBasisFuncKernel, BasisFuncKernel, ChangePointBasisFuncKernel, DomainKernel
 

GPy/kern/_src/coregionalize.py

@@ -6,7 +6,7 @@ import numpy as np
 from ...core.parameterization import Param
 from ...core.parameterization.transformations import Logexp
 from ...util.config import config # for assesing whether to use cython
-import coregionalize_cython
+from . import coregionalize_cython
 
 class Coregionalize(Kern):
     """

GPy/kern/_src/independent_outputs.py

@@ -105,7 +105,7 @@ class IndependentOutputs(CombinationKernel):
         if X2 is None:
             # TODO: make use of index_to_slices
             # FIXME: Broken as X is already sliced out
-            print "Warning, gradients_X may not be working, I believe X has already been sliced out by the slicer!"
+            print("Warning, gradients_X may not be working, I believe X has already been sliced out by the slicer!")
             values = np.unique(X[:,self.index_dim])
             slices = [X[:,self.index_dim]==i for i in values]
             [target.__setitem__(s, kern.gradients_X(dL_dK[s,s],X[s],None))

GPy/kern/_src/rbf.py

@@ -20,7 +20,6 @@ class RBF(Stationary):
     _support_GPU = True
     def __init__(self, input_dim, variance=1., lengthscale=None, ARD=False, active_dims=None, name='rbf', useGPU=False):
         super(RBF, self).__init__(input_dim, variance, lengthscale, ARD, active_dims, name, useGPU=useGPU)
-        self.psicomp = PSICOMP_RBF()
         if self.useGPU:
             self.psicomp = PSICOMP_RBF_GPU()
         else:
@@ -36,6 +35,7 @@ class RBF(Stationary):
         dc = super(RBF, self).__getstate__()
         if self.useGPU:
             dc['psicomp'] = PSICOMP_RBF()
+            dc['useGPU'] = False
         return dc
 
     def __setstate__(self, state):

GPy/kern/_src/stationary.py

@@ -13,7 +13,7 @@ from ...util.config import config # for assesing whether to use cython
 from ...util.caching import Cache_this
 
 try:
-    import stationary_cython
+    from . import stationary_cython
 except ImportError:
     print('warning in sationary: failed to import cython module: falling back to numpy')
     config.set('cython', 'working', 'false')

GPy/likelihoods/likelihood.py

@@ -266,8 +266,8 @@ class Likelihood(Parameterized):
             stop
 
         if self.size:
-            dF_dtheta = self.dlogpdf_dtheta(X, Y[:,None]) # Ntheta x (orig size) x N_{quad_points}
-            dF_dtheta = np.dot(dF_dtheta, gh_w)
+            dF_dtheta = self.dlogpdf_dtheta(X, Y[:,None], Y_metadata=Y_metadata) # Ntheta x (orig size) x N_{quad_points}
+            dF_dtheta = np.dot(dF_dtheta, gh_w)/np.sqrt(np.pi)
             dF_dtheta = dF_dtheta.reshape(self.size, shape[0], shape[1])
         else:
             dF_dtheta = None # Not yet implemented

GPy/models/bayesian_gplvm_minibatch.py

@@ -64,9 +64,6 @@ class BayesianGPLVMMiniBatch(SparseGPMiniBatch):
             self.logger.debug("creating inference_method var_dtc")
             inference_method = VarDTC(limit=1 if not missing_data else Y.shape[1])
 
-        if kernel.useGPU and isinstance(inference_method, VarDTC_GPU):
-            kernel.psicomp.GPU_direct = True
-
         super(BayesianGPLVMMiniBatch,self).__init__(X, Y, Z, kernel, likelihood=likelihood,
                                            name=name, inference_method=inference_method,
                                            normalizer=normalizer,

GPy/models/dpgplvm.py

@@ -3,7 +3,7 @@
 
 import numpy as np
 from .. import kern
-from bayesian_gplvm import BayesianGPLVM
+from .bayesian_gplvm import BayesianGPLVM
 from ..core.parameterization.variational import NormalPosterior, NormalPrior
 
 class DPBayesianGPLVM(BayesianGPLVM):

GPy/models/gp_regression.py

@@ -16,6 +16,7 @@ class GPRegression(GP):
     :param Y: observed values
     :param kernel: a GPy kernel, defaults to rbf
     :param Norm normalizer: [False]
+    :param noise_var: the noise variance for Gaussian likelhood, defaults to 1.
 
         Normalize Y with the norm given.
         If normalizer is False, no normalization will be done
@@ -25,12 +26,12 @@ class GPRegression(GP):
 
     """
 
-    def __init__(self, X, Y, kernel=None, Y_metadata=None, normalizer=None):
+    def __init__(self, X, Y, kernel=None, Y_metadata=None, normalizer=None, noise_var=1.):
 
         if kernel is None:
             kernel = kern.RBF(X.shape[1])
 	
-        likelihood = likelihoods.Gaussian()
+        likelihood = likelihoods.Gaussian(variance=noise_var)
 
         super(GPRegression, self).__init__(X, Y, kernel, likelihood, name='GP regression', Y_metadata=Y_metadata, normalizer=normalizer)
 

GPy/models/gradient_checker.py

@@ -228,14 +228,14 @@ class HessianChecker(GradientChecker):
 
         if verbose:
             if block_indices:
-                print "\nBlock {}".format(block_indices)
+                print("\nBlock {}".format(block_indices))
             else:
-                print "\nAll blocks"
+                print("\nAll blocks")
 
             header = ['Checked', 'Max-Ratio', 'Min-Ratio', 'Min-Difference', 'Max-Difference']
             header_string = map(lambda x: ' | '.join(header), [header])
             separator = '-' * len(header_string[0])
-            print '\n'.join([header_string[0], separator])
+            print('\n'.join([header_string[0], separator]))
             min_r = '%.6f' % float(numpy.min(ratio))
             max_r = '%.6f' % float(numpy.max(ratio))
             max_d = '%.6f' % float(numpy.max(difference))
@@ -248,7 +248,7 @@ class HessianChecker(GradientChecker):
                 checked = "\033[91m  False \033[0m"
 
             grad_string = "{} | {}  | {} |    {}    |   {} ".format(checked, cols[0], cols[1], cols[2], cols[3])
-            print grad_string
+            print(grad_string)
 
             if plot:
                 import pylab as pb
@@ -348,7 +348,7 @@ class SkewChecker(HessianChecker):
             numeric_hess_partial = nd.Jacobian(self._df, vectorized=True)
             numeric_hess = numeric_hess_partial(x)
 
-            print "Done making numerical hessian"
+            print("Done making numerical hessian")
             if analytic_hess.dtype is np.dtype('object'):
                 #Blockify numeric_hess aswell
                 blocksizes, pagesizes = get_block_shapes_3d(analytic_hess)
@@ -365,7 +365,7 @@ class SkewChecker(HessianChecker):
                 #Unless super_plot is set, just plot the first one
                 p = True if (plot and block_ind == numeric_hess.shape[2]-1) or super_plot else False
                 if verbose:
-                    print "Checking derivative of hessian wrt parameter number {}".format(block_ind)
+                    print("Checking derivative of hessian wrt parameter number {}".format(block_ind))
                 check_passed[block_ind] = self.checkgrad_block(analytic_hess[:,:,block_ind], numeric_hess[:,:,block_ind], verbose=verbose, step=step, tolerance=tolerance, block_indices=block_indices, plot=p)
 
             current_index += current_size

GPy/plotting/matplot_dep/visualize.py

@@ -451,7 +451,7 @@ class mocap_data_show(matplotlib_show):
         self.initialize_axes_modify()
         self.draw_vertices()
         self.initialize_axes()
-        self.finalize_axes_modify()
+        #self.finalize_axes_modify()
         self.draw_edges()
         self.axes.figure.canvas.draw()
 
@@ -470,10 +470,18 @@ class mocap_data_show(matplotlib_show):
         self.line_handle[0].remove()
 
     def finalize_axes(self):
-        self.axes.set_xlim(self.x_lim)
-        self.axes.set_ylim(self.y_lim)
-        self.axes.set_zlim(self.z_lim)
-        self.axes.auto_scale_xyz([-1., 1.], [-1., 1.], [-1., 1.])
+#         self.axes.set_xlim(self.x_lim)
+#         self.axes.set_ylim(self.y_lim)
+#         self.axes.set_zlim(self.z_lim)
+#         self.axes.auto_scale_xyz([-1., 1.], [-1., 1.], [-1., 1.])
+
+        extents = np.array([getattr(self.axes, 'get_{}lim'.format(dim))() for dim in 'xyz'])
+        sz = extents[:,1] - extents[:,0]
+        centers = np.mean(extents, axis=1)
+        maxsize = max(abs(sz))
+        r = maxsize/2
+        for ctr, dim in zip(centers, 'xyz'):
+            getattr(self.axes, 'set_{}lim'.format(dim))(ctr - r, ctr + r)
         
 #         self.axes.set_aspect('equal')
 #         self.axes.autoscale(enable=False)

GPy/testing/link_function_tests.py

@@ -49,7 +49,7 @@ class LinkFunctionTests(np.testing.TestCase):
         self.assertTrue(grad3.checkgrad(verbose=True))
 
         if test_lim:
-            print "Testing limits"
+            print("Testing limits")
             #Remove some otherwise we are too close to the limit for gradcheck to work effectively
             lim_of_inf = lim_of_inf - 1e-4
             grad = GradientChecker(link_func.transf, link_func.dtransf_df, x0=lim_of_inf)

GPy/util/block_matrices.py

@@ -100,10 +100,10 @@ def block_dot(A, B, diagonal=False):
         Dshape = D.shape
         if diagonal and (len(Cshape) == 1 or len(Dshape) == 1\
                 or C.shape[0] != C.shape[1] or D.shape[0] != D.shape[1]):
-            print "Broadcasting, C: {} D:{}".format(C.shape, D.shape)
+            print("Broadcasting, C: {} D:{}".format(C.shape, D.shape))
             return C*D
         else:
-            print "Dotting, C: {} C:{}".format(C.shape, D.shape)
+            print("Dotting, C: {} C:{}".format(C.shape, D.shape))
             return np.dot(C,D)
     dot = np.vectorize(f, otypes = [np.object])
     return dot(A,B)

GPy/util/choleskies.py

@@ -5,7 +5,7 @@ import numpy as np
 from . import linalg
 from .config import config
 
-import choleskies_cython
+from . import choleskies_cython
 
 def safe_root(N):
     i = np.sqrt(N)
@@ -59,12 +59,12 @@ def _backprop_gradient_pure(dL, L):
     """
     dL_dK = np.tril(dL).copy()
     N = L.shape[0]
-    for k in xrange(N - 1, -1, -1):
-        for j in xrange(k + 1, N):
-            for i in xrange(j, N):
+    for k in range(N - 1, -1, -1):
+        for j in range(k + 1, N):
+            for i in range(j, N):
                 dL_dK[i, k] -= dL_dK[i, j] * L[j, k]
                 dL_dK[j, k] -= dL_dK[i, j] * L[i, k]
-        for j in xrange(k + 1, N):
+        for j in range(k + 1, N):
             dL_dK[j, k] /= L[k, k]
             dL_dK[k, k] -= L[j, k] * dL_dK[j, k]
         dL_dK[k, k] /= (2 * L[k, k])
@@ -100,7 +100,7 @@ def indexes_to_fix_for_low_rank(rank, size):
 if config.getboolean('cython', 'working'):
     triang_to_flat = _triang_to_flat_cython
     flat_to_triang = _flat_to_triang_cython
-    backprop_gradient = choleskies_cython.backprop_gradient
+    backprop_gradient = choleskies_cython.backprop_gradient_par_c
 else:
     backprop_gradient = _backprop_gradient_pure
     triang_to_flat =  _triang_to_flat_pure

GPy/util/choleskies_cython.pyx

@@ -5,6 +5,7 @@
 # Copyright James Hensman and Alan Saul 2015
 
 import numpy as np
+from cython.parallel import prange, parallel
 cimport numpy as np
 
 def flat_to_triang(np.ndarray[double, ndim=2] flat, int M):
@@ -57,3 +58,50 @@ def backprop_gradient(np.ndarray[double, ndim=2] dL, np.ndarray[double, ndim=2]
             dL_dK[k, k] -= L[j, k] * dL_dK[j, k]
         dL_dK[k, k] /= (2. * L[k, k])
     return dL_dK
+
+def backprop_gradient_par(double[:,:] dL, double[:,:] L):
+    cdef double[:,:] dL_dK = np.tril(dL).copy()
+    cdef int N = L.shape[0]
+    cdef int k, j, i
+    for k in range(N - 1, -1, -1):
+        with nogil, parallel():
+            for i in prange(k + 1, N):
+                for j in range(k+1, i+1):
+                    dL_dK[i, k] -= dL_dK[i, j] * L[j, k]
+                for j in range(i, N):
+                    dL_dK[i, k] -= dL_dK[j, i] * L[j, k]
+        for j in range(k + 1, N):
+            dL_dK[j, k] /= L[k, k]
+            dL_dK[k, k] -= L[j, k] * dL_dK[j, k]
+        dL_dK[k, k] /= (2. * L[k, k])
+    return dL_dK
+
+#here's a pure C version...
+cdef extern from "cholesky_backprop.h" nogil:
+    void chol_backprop(int N, double* dL, double* L)
+
+def backprop_gradient_par_c(np.ndarray[double, ndim=2] dL, np.ndarray[double, ndim=2] L):
+    cdef np.ndarray[double, ndim=2] dL_dK = np.tril(dL) # makes a copy, c-contig
+    cdef int N = L.shape[0]
+    with nogil:
+        chol_backprop(N, <double*> dL_dK.data, <double*> L.data)
+    return dL_dK
+
+cdef extern from "cholesky_backprop.h" nogil:
+    void old_chol_backprop(int N, double* dL, double* L)
+
+def backprop_gradient_par_c_old(np.ndarray[double, ndim=2] dL, np.ndarray[double, ndim=2] L):
+    cdef np.ndarray[double, ndim=2] dL_dK = np.tril(dL) # makes a copy, c-contig
+    cdef int N = L.shape[0]
+    with nogil:
+        old_chol_backprop(N, <double*> dL_dK.data, <double*> L.data)
+    return dL_dK
+
+
+
+
+
+
+
+
+

GPy/util/cholesky_backprop.c

@@ -0,0 +1,51 @@
+#include <cblas.h>
+void chol_backprop(int N, double* dL, double* L){
+    //at the input to this fn, dL is df_dL. after this fn is complet, dL is df_dK
+    int i,k;
+
+    dL[N*N - 1] /= (2. * L[N*N - 1]);
+    for(k=N-2;k>(-1);k--){
+        cblas_dsymv(CblasRowMajor, CblasLower,
+	            N-k-1, -1,
+		    &dL[(N*(k+1) + k+1)],N,
+		    &L[k*N+k+1],1,
+		    1, &dL[N*(k+1)+k], N);
+        for(i=0;i<(N-k-1); i++){
+		dL[N*(k+1+i)+k] -= dL[N*(k+1)+k+i*(N+1)+1] * L[k*N+k+1+i];
+	}
+
+	cblas_dscal(N-k-1, 1.0/L[k*N+k], &dL[(k+1)*N+k], N);
+        dL[k*N + k] -= cblas_ddot(N-k-1, &dL[(k+1)*N+k], N, &L[k*N+k+1], 1);
+        dL[k*N + k] /= (2.0 * L[k*N + k]);
+    }
+}
+
+double mydot(int n, double* a,  int stride_a, double* b, int stride_b){
+    double ret = 0;	
+    for(int i=0; i<n; i++){
+	ret += a[i*stride_a]*b[i*stride_b];
+    }
+    return ret;
+}
+void old_chol_backprop(int N, double* dL, double* U){
+    //at the input to this fn, dL is df_dL. after this fn is complet, dL is df_dK
+    int iN, kN,i,j,k;
+    dL[N*N-1] /= (2. * U[N*N-1]);
+    for(k=N-2;k>(-1);k--){
+	kN = k*N;
+        #pragma omp parallel for private(i,iN)
+        for(i=k+1; i<N; i++){
+	    iN = i*N;
+	    dL[iN+k] -= mydot(i-k, &dL[iN+k+1], 1, &U[kN+k+1], 1);
+	    dL[iN+k] -= mydot(N-i, &dL[iN+i], N, &U[kN+i],  1);
+
+	}
+        for(i=(k + 1); i<N; i++){
+	    iN = i*N;
+            dL[iN + k] /= U[kN + k];
+            dL[kN + k] -= U[kN + i] * dL[iN + k];
+	}
+        dL[kN + k] /= (2. * U[kN + k]);
+    }
+}
+

GPy/util/cholesky_backprop.h

@@ -0,0 +1,5 @@
+#include <cblas.h>
+
+void dsymv(int N, double*A, double*b, double*y);
+double mydot(int n, double* a,  int stride_a, double* b, int stride_b);
+void chol_backprop(int N, double* dL, double* L);

GPy/util/linalg.py

@@ -15,7 +15,7 @@ import warnings
 import os
 from .config import config
 import logging
-import linalg_cython
+from . import linalg_cython
 
 
 _scipyversion = np.float64((scipy.__version__).split('.')[:2])

README.md

@@ -13,7 +13,6 @@ Continuous integration status: ![CI status](https://travis-ci.org/SheffieldML/GP
 ### Python 3 Compatibility
 Work is underway to make GPy run on Python 3.
 
-* Python 2.x compatibility is currently broken in this fork
 * All tests in the testsuite now run on Python3. 
 
 To see this for yourself, in Ubuntu 14.04, you can do
@@ -21,12 +20,17 @@ To see this for yourself, in Ubuntu 14.04, you can do
     git clone https://github.com/mikecroucher/GPy.git
     cd GPy
     git checkout devel
+    python3 setup.py build_ext --inplace
     nosetests3 GPy/testing
 
 nosetests3 is Ubuntu's way of reffering to the Python 3 version of nosetests. You install it with 
 
     sudo apt-get install python3-nose
 
+The command `python3 setup.py build_ext --inplace` builds the Cython extensions. IF it doesn't work, you may need to install this:
+
+    sudo apt-get install python3-dev
+
 * Test coverage is less than 100% so it is expected that there is still more work to be done. We need more tests and examples to try out.
 * All weave functions not covered by the test suite are *simply commented out*. Can add equivalents later as test functions become available
 * A set of benchmarks would be useful! 

setup.py

@@ -20,9 +20,10 @@ ext_mods = [Extension(name='GPy.kern._src.stationary_cython',
                       extra_compile_args=compile_flags,
                       extra_link_args = ['-lgomp']),
             Extension(name='GPy.util.choleskies_cython',
-                      sources=['GPy/util/choleskies_cython.c'],
+                      sources=['GPy/util/choleskies_cython.c', 'GPy/util/cholesky_backprop.c'],
                       include_dirs=[np.get_include()],
-                      extra_compile_args=compile_flags),
+                      extra_link_args = ['-lgomp', '-lblas'],
+                      extra_compile_args=compile_flags+['-std=c99']),
             Extension(name='GPy.util.linalg_cython',
                       sources=['GPy/util/linalg_cython.c'],
                       include_dirs=[np.get_include()],