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

Merging new devel

.travis.yml

@@ -20,33 +20,17 @@ env:
   - PYTHON_VERSION=3.5
 
 before_install:
-  - export CONDA_CACHED=1
+- wget https://github.com/mzwiessele/travis_scripts/raw/master/download_miniconda.sh
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; 
+- wget https://github.com/mzwiessele/travis_scripts/raw/master/install_retry.sh
-      then export OS=Linux; 
+- source download_miniconda.sh
-    elif [[ "$TRAVIS_OS_NAME" == "osx" ]]; 
+- echo $PATH
-      then export OS=MacOSX;
-      brew install pandoc; 
-    else 
-      echo "OS not supported yet"; 
-      exit 1; fi;
-  - if [[ $PYTHON_VERSION == "2.7" ]]; 
-      then export MINICONDA=Miniconda; 
-    elif [[ $PYTHON_VERSION == 3* ]]; 
-      then export MINICONDA=Miniconda3; 
-    else echo "Could not find python version";exit 1; fi;
-  - if [ ! -d $HOME/download/ ]; then mkdir $HOME/download/; fi;
-  - if [ ! -d $HOME/install/ ]; then mkdir $HOME/install/; fi;
-  - export MINICONDA_FILE=$MINICONDA-latest-$OS-x86_64-$PYTHON_VERSION
-  - export MINCONDA_CACHE_FILE=$HOME/download/$MINICONDA_FILE.sh
-  - export MINICONDA_INSTALL=$HOME/install/$MINICONDA_FILE
-  - if [ ! -f $MINCONDA_CACHE_FILE ]; then export CONDA_CACHED=0; wget http://repo.continuum.io/miniconda/$MINICONDA-latest-$OS-x86_64.sh -O $MINCONDA_CACHE_FILE; bash $MINCONDA_CACHE_FILE -b -p $MINICONDA_INSTALL; fi;
-  - export PATH="$MINICONDA_INSTALL/bin:$PATH";
 
 install:
-  - conda install --yes python=$PYTHON_VERSION numpy=1.9 scipy=0.16 nose pip six matplotlib sphinx;
+- echo $PATH
-  - pip install codecov
+- source install_retry.sh
-  - pip install pypandoc
+- pip install codecov
-  - python setup.py develop
+- pip install pypandoc
+- python setup.py develop
 
 script:
   - coverage run travis_tests.py
@@ -60,16 +44,16 @@ before_deploy:
   - sphinx-apidoc -o source/ ../GPy
   - make html
   - cd ../
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; 
+  - if [[ "$TRAVIS_OS_NAME" == "linux" ]];
       then export DIST='sdist';
-    elif [[ "$TRAVIS_OS_NAME" == "osx" ]]; 
+    elif [[ "$TRAVIS_OS_NAME" == "osx" ]];
       then export DIST='bdist_wheel';
     fi;
 
 deploy:
   provider: pypi
   user: maxz
-  password: 
+  password:
     secure: "vMEOlP7DQhFJ7hQAKtKC5hrJXFl5BkUt4nXdosWWiw//Kg8E+PPLg88XPI2gqIosir9wwgtbSBBbbwCxkM6uxRNMpoNR8Ixyv9fmSXp4rLl7bbBY768W7IRXKIBjpuEy2brQjoT+CwDDSzUkckHvuUjJDNRvUv8ab4P/qYO1LG4="
   on:
     tags: false

GPy/__version__.py

@@ -1 +1 @@
-__version__ = "0.9.4"
+__version__ = "0.9.7"

GPy/core/gp.py

@@ -181,7 +181,7 @@ class GP(Model):
     def parameters_changed(self):
         """
         Method that is called upon any changes to :class:`~GPy.core.parameterization.param.Param` variables within the model.
-        In particular in the GP class this method reperforms inference, recalculating the posterior and log marginal likelihood and gradients of the model
+        In particular in the GP class this method re-performs inference, recalculating the posterior and log marginal likelihood and gradients of the model
 
         .. warning::
             This method is not designed to be called manually, the framework is set up to automatically call this method upon changes to parameters, if you call
@@ -365,13 +365,14 @@ class GP(Model):
             mean_jac[:,:,i] = kern.gradients_X(self.posterior.woodbury_vector[:,i:i+1].T, Xnew, self._predictive_variable)
 
         dK_dXnew_full = np.empty((self._predictive_variable.shape[0], Xnew.shape[0], Xnew.shape[1]))
+        one = np.ones((1,1))
         for i in range(self._predictive_variable.shape[0]):
-            dK_dXnew_full[i] = kern.gradients_X([[1.]], Xnew, self._predictive_variable[[i]])
+            dK_dXnew_full[i] = kern.gradients_X(one, Xnew, self._predictive_variable[[i]])
 
         if full_cov:
-            dK2_dXdX = kern.gradients_XX([[1.]], Xnew)
+            dK2_dXdX = kern.gradients_XX(one, Xnew)
         else:
-            dK2_dXdX = kern.gradients_XX_diag([[1.]], Xnew)
+            dK2_dXdX = kern.gradients_XX_diag(one, Xnew)
 
         def compute_cov_inner(wi):
             if full_cov:
@@ -458,7 +459,7 @@ class GP(Model):
         m, v = self._raw_predict(X,  full_cov=full_cov, **predict_kwargs)
         if self.normalizer is not None:
             m, v = self.normalizer.inverse_mean(m), self.normalizer.inverse_variance(v)
-        
+
         def sim_one_dim(m, v):
             if not full_cov:
                 return np.random.multivariate_normal(m.flatten(), np.diag(v.flatten()), size).T

GPy/core/svgp.py

@@ -89,7 +89,7 @@ class SVGP(SparseGP):
         """
         Return a new batch of X and Y by taking a chunk of data from the complete X and Y
         """
-        i = self.slicer.next()
+        i = next(self.slicer)
         return self.X_all[i], self.Y_all[i]
 
     def stochastic_grad(self, parameters):

GPy/examples/dimensionality_reduction.py

@@ -459,7 +459,7 @@ def mrd_simulation(optimize=True, verbose=True, plot=True, plot_sim=True, **kw):
     D1, D2, D3, N, num_inducing, Q = 60, 20, 36, 60, 6, 5
     _, _, Ylist = _simulate_sincos(D1, D2, D3, N, num_inducing, plot_sim)
 
-    k = kern.Linear(Q) + kern.White(Q, variance=1e-4)
+    k = kern.Linear(Q, ARD=True) + kern.White(Q, variance=1e-4)
     m = MRD(Ylist, input_dim=Q, num_inducing=num_inducing, kernel=k, initx="PCA_concat", initz='permute', **kw)
 
     m['.*noise'] = [Y.var() / 40. for Y in Ylist]
@@ -479,7 +479,7 @@ def mrd_simulation_missing_data(optimize=True, verbose=True, plot=True, plot_sim
     D1, D2, D3, N, num_inducing, Q = 60, 20, 36, 60, 6, 5
     _, _, Ylist = _simulate_matern(D1, D2, D3, N, num_inducing, plot_sim)
 
-    k = kern.Linear(Q) + kern.White(Q, variance=1e-4)
+    k = kern.Linear(Q, ARD=True) + kern.White(Q, variance=1e-4)
     inanlist = []
 
     for Y in Ylist:

GPy/inference/latent_function_inference/var_dtc.py

@@ -190,8 +190,8 @@ class VarDTC(LatentFunctionInference):
             tmp, _ = dtrtrs(Lm, psi1V, lower=1, trans=0)
             tmp, _ = dpotrs(LB, tmp, lower=1)
             woodbury_vector, _ = dtrtrs(Lm, tmp, lower=1, trans=1)
-        Bi, _ = dpotri(LB, lower=1)
+        #Bi, _ = dpotri(LB, lower=1)
-        symmetrify(Bi)
+        #symmetrify(Bi)
         Bi = -dpotri(LB, lower=1)[0]
         diag.add(Bi, 1)
 

GPy/inference/latent_function_inference/var_dtc_parallel.py

@@ -28,7 +28,7 @@ class VarDTC_minibatch(LatentFunctionInference):
         self.limit = limit
 
         # Cache functions
-        from ...util.caching import Cacher
+        from paramz.caching import Cacher
         self.get_trYYT = Cacher(self._get_trYYT, limit)
         self.get_YYTfactor = Cacher(self._get_YYTfactor, limit)
 
@@ -46,7 +46,7 @@ class VarDTC_minibatch(LatentFunctionInference):
         self.mpi_comm = None
         self.midRes = {}
         self.batch_pos = 0
-        from ...util.caching import Cacher
+        from paramz.caching import Cacher
         self.get_trYYT = Cacher(self._get_trYYT, self.limit)
         self.get_YYTfactor = Cacher(self._get_YYTfactor, self.limit)
 

GPy/installation.cfg

@@ -15,4 +15,4 @@
 
 
 # [plotting]
-# library = matplotlib # plotly
+# library = matplotlib # plotly, none

GPy/kern/__init__.py

@@ -28,4 +28,4 @@ from .src.trunclinear import TruncLinear,TruncLinear_inf
 from .src.splitKern import SplitKern,DEtime
 from .src.splitKern import DEtime as DiffGenomeKern
 from .src.spline import Spline
-from .src.basis_funcs import LinearSlopeBasisFuncKernel, BasisFuncKernel, ChangePointBasisFuncKernel, DomainKernel
+from .src.basis_funcs import LogisticBasisFuncKernel, LinearSlopeBasisFuncKernel, BasisFuncKernel, ChangePointBasisFuncKernel, DomainKernel

GPy/kern/src/ODE_UYC.py

@@ -18,7 +18,7 @@ class ODE_UYC(Kern):
         self.lengthscale_U = Param('lengthscale_U', lengthscale_U, Logexp())
         self.ubias = Param('ubias', ubias, Logexp())
 
-        self.add_parameters(self.variance_Y, self.variance_U, self.lengthscale_Y, self.lengthscale_U, self.ubias)
+        self.link_parameters(self.variance_Y, self.variance_U, self.lengthscale_Y, self.lengthscale_U, self.ubias)
 
     def K(self, X, X2=None):
         # model :   a * dy/dt + b * y = U

GPy/kern/src/ODE_st.py

@@ -38,7 +38,7 @@ class ODE_st(Kern):
         self.b = Param('b', b, Logexp())
         self.c = Param('c', c, Logexp())
 
-        self.add_parameters(self.a, self.b, self.c, self.variance_Yt, self.variance_Yx, self.lengthscale_Yt,self.lengthscale_Yx)
+        self.link_parameters(self.a, self.b, self.c, self.variance_Yt, self.variance_Yx, self.lengthscale_Yt,self.lengthscale_Yx)
 
 
     def K(self, X, X2=None):        

GPy/kern/src/ODE_t.py

@@ -17,7 +17,7 @@ class ODE_t(Kern):
                 self.a= Param('a', a, Logexp())
                 self.c = Param('c', c, Logexp())
                 self.ubias = Param('ubias', ubias, Logexp())
-                self.add_parameters(self.a, self.c, self.variance_Yt, self.lengthscale_Yt,self.ubias)
+                self.link_parameters(self.a, self.c, self.variance_Yt, self.lengthscale_Yt,self.ubias)
 
         def K(self, X, X2=None):
                 """Compute the covariance matrix between X and X2."""        

GPy/kern/src/add.py

@@ -181,6 +181,8 @@ class Add(CombinationKernel):
         return psi2
 
     def update_gradients_expectations(self, dL_dpsi0, dL_dpsi1, dL_dpsi2, Z, variational_posterior):
+        tmp = dL_dpsi2.sum(0)+ dL_dpsi2.sum(1) if len(dL_dpsi2.shape)==2 else dL_dpsi2.sum(2)+ dL_dpsi2.sum(1)
+        
         if not self._exact_psicomp: return Kern.update_gradients_expectations(self, dL_dpsi0, dL_dpsi1, dL_dpsi2, Z, variational_posterior)
         from .static import White, Bias
         for p1 in self.parts:
@@ -192,12 +194,13 @@ class Add(CombinationKernel):
                 if isinstance(p2, White):
                     continue
                 elif isinstance(p2, Bias):
-                    eff_dL_dpsi1 += dL_dpsi2.sum(1) * p2.variance * 2.
+                    eff_dL_dpsi1 += tmp * p2.variance 
                 else:# np.setdiff1d(p1._all_dims_active, ar2, assume_unique): # TODO: Careful, not correct for overlapping _all_dims_active
-                    eff_dL_dpsi1 += dL_dpsi2.sum(1) * p2.psi1(Z, variational_posterior) * 2.
+                    eff_dL_dpsi1 += tmp * p2.psi1(Z, variational_posterior) 
             p1.update_gradients_expectations(dL_dpsi0, eff_dL_dpsi1, dL_dpsi2, Z, variational_posterior)
 
     def gradients_Z_expectations(self, dL_psi0, dL_dpsi1, dL_dpsi2, Z, variational_posterior):
+        tmp = dL_dpsi2.sum(0)+ dL_dpsi2.sum(1) if len(dL_dpsi2.shape)==2 else dL_dpsi2.sum(2)+ dL_dpsi2.sum(1)
         if not self._exact_psicomp: return Kern.gradients_Z_expectations(self, dL_psi0, dL_dpsi1, dL_dpsi2, Z, variational_posterior)
         from .static import White, Bias
         target = np.zeros(Z.shape)
@@ -210,13 +213,15 @@ class Add(CombinationKernel):
                 if isinstance(p2, White):
                     continue
                 elif isinstance(p2, Bias):
-                    eff_dL_dpsi1 += dL_dpsi2.sum(1) * p2.variance * 2.
+                    eff_dL_dpsi1 += tmp * p2.variance 
                 else:
-                    eff_dL_dpsi1 += dL_dpsi2.sum(1) * p2.psi1(Z, variational_posterior) * 2.
+                    eff_dL_dpsi1 += tmp * p2.psi1(Z, variational_posterior)
             target += p1.gradients_Z_expectations(dL_psi0, eff_dL_dpsi1, dL_dpsi2, Z, variational_posterior)
         return target
 
     def gradients_qX_expectations(self, dL_dpsi0, dL_dpsi1, dL_dpsi2, Z, variational_posterior):
+        tmp = dL_dpsi2.sum(0)+ dL_dpsi2.sum(1) if len(dL_dpsi2.shape)==2 else dL_dpsi2.sum(2)+ dL_dpsi2.sum(1)
+        
         if not self._exact_psicomp: return Kern.gradients_qX_expectations(self, dL_dpsi0, dL_dpsi1, dL_dpsi2, Z, variational_posterior)
         from .static import White, Bias
         target_grads = [np.zeros(v.shape) for v in variational_posterior.parameters]
@@ -229,9 +234,9 @@ class Add(CombinationKernel):
                 if isinstance(p2, White):
                     continue
                 elif isinstance(p2, Bias):
-                    eff_dL_dpsi1 += dL_dpsi2.sum(1) * p2.variance * 2.
+                    eff_dL_dpsi1 += tmp * p2.variance 
                 else:
-                    eff_dL_dpsi1 += dL_dpsi2.sum(1) * p2.psi1(Z, variational_posterior) * 2.
+                    eff_dL_dpsi1 += tmp * p2.psi1(Z, variational_posterior) 
             grads = p1.gradients_qX_expectations(dL_dpsi0, eff_dL_dpsi1, dL_dpsi2, Z, variational_posterior)
             [np.add(target_grads[i],grads[i],target_grads[i]) for i in range(len(grads))]
         return target_grads

GPy/kern/src/kern.py

@@ -61,12 +61,12 @@ class Kern(Parameterized):
         self.psicomp = PSICOMP_GH()
 
     def __setstate__(self, state):
-        self._all_dims_active = range(0, max(state['active_dims'])+1)
+        self._all_dims_active = np.arange(0, max(state['active_dims'])+1)
         super(Kern, self).__setstate__(state)
 
     @property
     def _effective_input_dim(self):
-        return self._all_dims_active.size
+        return np.size(self._all_dims_active)
 
     @Cache_this(limit=20)
     def _slice_X(self, X):

GPy/kern/src/linear.py

@@ -73,14 +73,15 @@ class Linear(Kern):
         return np.sum(self.variances * np.square(X), -1)
 
     def update_gradients_full(self, dL_dK, X, X2=None):
+        if X2 is None: dL_dK = (dL_dK+dL_dK.T)/2
         if self.ARD:
             if X2 is None:
                 #self.variances.gradient = np.array([np.sum(dL_dK * tdot(X[:, i:i + 1])) for i in range(self.input_dim)])
-                self.variances.gradient = np.einsum('ij,iq,jq->q', dL_dK, X, X)
+                self.variances.gradient = (dL_dK.dot(X)*X).sum(0) #np.einsum('ij,iq,jq->q', dL_dK, X, X)
             else:
                 #product = X[:, None, :] * X2[None, :, :]
                 #self.variances.gradient = (dL_dK[:, :, None] * product).sum(0).sum(0)
-                self.variances.gradient = np.einsum('ij,iq,jq->q', dL_dK, X, X2)
+                self.variances.gradient = (dL_dK.dot(X2)*X).sum(0)  #np.einsum('ij,iq,jq->q', dL_dK, X, X2)
         else:
             self.variances.gradient = np.sum(self._dot_product(X, X2) * dL_dK)
 
@@ -93,13 +94,15 @@ class Linear(Kern):
 
 
     def gradients_X(self, dL_dK, X, X2=None):
+        if X2 is None: dL_dK = (dL_dK+dL_dK.T)/2
         if X2 is None:
-            return np.einsum('jq,q,ij->iq', X, 2*self.variances, dL_dK)
+            return dL_dK.dot(X)*(2*self.variances) #np.einsum('jq,q,ij->iq', X, 2*self.variances, dL_dK)
         else:
             #return (((X2[None,:, :] * self.variances)) * dL_dK[:, :, None]).sum(1)
-            return np.einsum('jq,q,ij->iq', X2, self.variances, dL_dK)
+            return dL_dK.dot(X2)*self.variances #np.einsum('jq,q,ij->iq', X2, self.variances, dL_dK)
 
     def gradients_XX(self, dL_dK, X, X2=None):
+        if X2 is None: dL_dK = (dL_dK+dL_dK.T)/2
         if X2 is None:
             return 2*np.ones(X.shape)*self.variances
         else:
@@ -162,6 +165,7 @@ class LinearFull(Kern):
         return np.einsum('ij,jk,lk->il', X, P, X if X2 is None else X2)
 
     def update_gradients_full(self, dL_dK, X, X2=None):
+        if X2 is None: dL_dK = (dL_dK+dL_dK.T)/2
         self.kappa.gradient = np.einsum('ij,ik,kj->j', X, dL_dK, X if X2 is None else X2)
         self.W.gradient = np.einsum('ij,kl,ik,lm->jm', X, X if X2 is None else X2, dL_dK, self.W)
         self.W.gradient += np.einsum('ij,kl,ik,jm->lm', X, X if X2 is None else X2, dL_dK, self.W)
@@ -175,6 +179,7 @@ class LinearFull(Kern):
         self.W.gradient = 2.*np.einsum('ij,ik,jl,i->kl', X, X, self.W, dL_dKdiag)
 
     def gradients_X(self, dL_dK, X, X2=None):
+        if X2 is None: dL_dK = (dL_dK+dL_dK.T)/2
         P = np.dot(self.W, self.W.T) + np.diag(self.kappa)
         if X2 is None:
             return 2.*np.einsum('ij,jk,kl->il', dL_dK, X, P)

GPy/kern/src/poly.py

@@ -5,32 +5,49 @@ import numpy as np
 from .kern import Kern
 from ...core.parameterization import Param
 from paramz.transformations import Logexp
+from paramz.caching import Cache_this
 
 class Poly(Kern):
     """
     Polynomial kernel
     """
 
-    def __init__(self, input_dim, variance=1., order=3., active_dims=None, name='poly'):
+    def __init__(self, input_dim, variance=1., scale=1., bias=1., order=3., active_dims=None, name='poly'):
         super(Poly, self).__init__(input_dim, active_dims, name)
         self.variance = Param('variance', variance, Logexp())
-        self.link_parameter(self.variance)
+        self.scale = Param('scale', scale, Logexp())
+        self.bias = Param('bias', bias, Logexp())
+
+        self.link_parameters(self.variance, self.scale, self.bias)
+        assert order >= 1, 'The order of the polynomial has to be at least 1.'
         self.order=order
 
-    def K(self, X, X2=None):
-        return (self._dot_product(X, X2) + 1.)**self.order * self.variance
 
-    def _dot_product(self, X, X2=None):
+    def K(self, X, X2=None):
+        _, _, B = self._AB(X, X2)
+        return B * self.variance
+
+    @Cache_this(limit=2)
+    def _AB(self, X, X2=None):
         if X2 is None:
-            return np.dot(X, X.T)
+            dot_prod = np.dot(X, X.T)
         else:
-            return np.dot(X, X2.T)
+            dot_prod = np.dot(X, X2.T)
+        A = (self.scale * dot_prod) + self.bias
+        B = A ** self.order
+        return dot_prod, A, B
 
     def Kdiag(self, X):
-        return self.variance*(np.square(X).sum(1) + 1.)**self.order
+        return self.K(X).diagonal()#self.variance*(np.square(X).sum(1) + 1.)**self.order
 
     def update_gradients_full(self, dL_dK, X, X2=None):
-        self.variance.gradient = np.sum(dL_dK * (self._dot_product(X, X2) + 1.)**self.order)
+        dot_prod, A, B = self._AB(X, X2)
+        dK_dA = self.variance * self.order * A ** (self.order-1.)
+        dL_dA = dL_dK * (dK_dA)
+        self.scale.gradient = (dL_dA * dot_prod).sum()
+        self.bias.gradient = dL_dA.sum()
+        self.variance.gradient = np.sum(dL_dK * B)
+        #import ipdb;ipdb.set_trace()
 
     def update_gradients_diag(self, dL_dKdiag, X):
         raise NotImplementedError

GPy/kern/src/psi_comp/gaussherm.py

@@ -16,7 +16,7 @@ from . import PSICOMP
 
 class PSICOMP_GH(PSICOMP):
     
-    def __init__(self, degree=5, cache_K=True):
+    def __init__(self, degree=11, cache_K=True):
         self.degree = degree
         self.cache_K = cache_K
         self.locs, self.weights = np.polynomial.hermite.hermgauss(degree)

GPy/kern/src/psi_comp/rbf_psi_comp.py

@@ -106,6 +106,8 @@ def _psi2compDer(dL_dpsi2, variance, lengthscale, Z, mu, S):
     denom = 1./(2*S+lengthscale2)
     denom2 = np.square(denom)
 
+    if len(dL_dpsi2.shape)==2: dL_dpsi2 = (dL_dpsi2+dL_dpsi2.T)/2
+    else: dL_dpsi2  = (dL_dpsi2+ np.swapaxes(dL_dpsi2, 1,2))/2
     _psi2 = _psi2computations(variance, lengthscale, Z, mu, S) # NxMxM
     Lpsi2 = dL_dpsi2*_psi2 # dL_dpsi2 is MxM, using broadcast to multiply N out
     Lpsi2sum = Lpsi2.reshape(N,M*M).sum(1) #N

GPy/kern/src/psi_comp/rbf_psi_gpucomp.py

@@ -360,7 +360,10 @@ class PSICOMP_RBF_GPU(PSICOMP_RBF):
         if self.GPU_direct:
             return psi0, psi1_gpu, psi2_gpu
         else:
-            return psi0, psi1_gpu.get(), psi2_gpu.get()
+            if return_psi2_n:
+                return psi0, psi1_gpu.get(), psi2n_gpu.get()
+            else:
+                return psi0, psi1_gpu.get(), psi2_gpu.get()
         
     def psiDerivativecomputations(self, kern, dL_dpsi0, dL_dpsi1, dL_dpsi2, Z, variational_posterior):
         try:
@@ -370,6 +373,10 @@ class PSICOMP_RBF_GPU(PSICOMP_RBF):
 
     @Cache_this(limit=10, ignore_args=(0,2,3,4))
     def _psiDerivativecomputations(self, kern, dL_dpsi0, dL_dpsi1, dL_dpsi2, Z, variational_posterior):
+        # resolve the requirement of dL_dpsi2 to be symmetric
+        if len(dL_dpsi2.shape)==2: dL_dpsi2 = (dL_dpsi2+dL_dpsi2.T)/2
+        else: dL_dpsi2  = (dL_dpsi2+ np.swapaxes(dL_dpsi2, 1,2))/2
+    
         variance, lengthscale = kern.variance, kern.lengthscale
         from ....util.linalg_gpu import sum_axis
         ARD = (len(lengthscale)!=1)

GPy/kern/src/stationary.py

@@ -97,7 +97,7 @@ class Stationary(Kern):
         r = self._scaled_dist(X, X2)
         return self.K_of_r(r)
 
-    @Cache_this(limit=20, ignore_args=())
+    @Cache_this(limit=3, ignore_args=())
     def dK_dr_via_X(self, X, X2):
         #a convenience function, so we can cache dK_dr
         return self.dK_dr(self._scaled_dist(X, X2))
@@ -127,7 +127,7 @@ class Stationary(Kern):
             r2 = np.clip(r2, 0, np.inf)
             return np.sqrt(r2)
 
-    @Cache_this(limit=20, ignore_args=())
+    @Cache_this(limit=3, ignore_args=())
     def _scaled_dist(self, X, X2=None):
         """
         Efficiently compute the scaled distance, r.

GPy/models/mrd.py

@@ -5,14 +5,14 @@ import numpy as np
 import itertools, logging
 
 from ..kern import Kern
-from GPy.core.parameterization.variational import NormalPrior
+from ..core.parameterization.variational import NormalPrior
 from ..core.parameterization import Param
 from paramz import ObsAr
 from ..inference.latent_function_inference.var_dtc import VarDTC
 from ..inference.latent_function_inference import InferenceMethodList
 from ..likelihoods import Gaussian
 from ..util.initialization import initialize_latent
-from GPy.models.bayesian_gplvm_minibatch import BayesianGPLVMMiniBatch
+from ..models.bayesian_gplvm_minibatch import BayesianGPLVMMiniBatch
 
 class MRD(BayesianGPLVMMiniBatch):
     """
@@ -215,40 +215,6 @@ class MRD(BayesianGPLVMMiniBatch):
             Z = np.random.randn(self.num_inducing, self.input_dim) * X.var()
         return Z
 
-    def _handle_plotting(self, fignum, axes, plotf, sharex=False, sharey=False):
-        import matplotlib.pyplot as plt
-        if axes is None:
-            fig = plt.figure(num=fignum)
-        sharex_ax = None
-        sharey_ax = None
-        plots = []
-        for i, g in enumerate(self.bgplvms):
-            try:
-                if sharex:
-                    sharex_ax = ax # @UndefinedVariable
-                    sharex = False # dont set twice
-                if sharey:
-                    sharey_ax = ax # @UndefinedVariable
-                    sharey = False # dont set twice
-            except:
-                pass
-            if axes is None:
-                ax = fig.add_subplot(1, len(self.bgplvms), i + 1, sharex=sharex_ax, sharey=sharey_ax)
-            elif isinstance(axes, (tuple, list, np.ndarray)):
-                ax = axes[i]
-            else:
-                raise ValueError("Need one axes per latent dimension input_dim")
-            plots.append(plotf(i, g, ax))
-            if sharey_ax is not None:
-                plt.setp(ax.get_yticklabels(), visible=False)
-        plt.draw()
-        if axes is None:
-            try:
-                fig.tight_layout()
-            except:
-                pass
-        return plots
-
     def predict(self, Xnew, full_cov=False, Y_metadata=None, kern=None, Yindex=0):
         """
         Prediction for data set Yindex[default=0].
@@ -270,59 +236,53 @@ class MRD(BayesianGPLVMMiniBatch):
     #                                     sharex=sharex, sharey=sharey)
     #         return fig
 
-    def plot_scales(self, fignum=None, ax=None, titles=None, sharex=False, sharey=True, *args, **kwargs):
+    def plot_scales(self, titles=None, fig_kwargs=dict(figsize=None, tight_layout=True), **kwargs):
         """
-
+        Plot input sensitivity for all datasets, to see which input dimensions are
-        TODO: Explain other parameters
+        significant for which dataset.
 
         :param titles: titles for axes of datasets
 
+        kwargs go into plot_ARD for each kernel.
         """
+        from ..plotting import plotting_library as pl
+
         if titles is None:
             titles = [r'${}$'.format(name) for name in self.names]
-        ymax = reduce(max, [np.ceil(max(g.kern.input_sensitivity())) for g in self.bgplvms])
+
-        def plotf(i, g, ax):
+        M = len(self.bgplvms)
-            #ax.set_ylim([0,ymax])
+        fig = pl().figure(rows=1, cols=M, **fig_kwargs)
-            return g.kern.plot_ARD(ax=ax, title=titles[i], *args, **kwargs)
+        plots = {}
-        fig = self._handle_plotting(fignum, ax, plotf, sharex=sharex, sharey=sharey)
+        for c in range(M):
-        return fig
+            canvas = self.bgplvms[c].kern.plot_ARD(title=titles[c], figure=fig, col=c+1, **kwargs)
+            plots[titles[c]] = canvas
+        pl().show_canvas(canvas)
+        return plots
 
     def plot_latent(self, labels=None, which_indices=None,
-                resolution=50, ax=None, marker='o', s=40,
+                resolution=60, legend=True,
-                fignum=None, plot_inducing=True, legend=True,
                 plot_limits=None,
-                aspect='auto', updates=False, predict_kwargs={}, imshow_kwargs={}):
+                updates=False,
+                kern=None, marker='<>^vsd',
+                num_samples=1000, projection='2d',
+                predict_kwargs={},
+                scatter_kwargs=None, **imshow_kwargs):
         """
         see plotting.matplot_dep.dim_reduction_plots.plot_latent
         if predict_kwargs is None, will plot latent spaces for 0th dataset (and kernel), otherwise give
         predict_kwargs=dict(Yindex='index') for plotting only the latent space of dataset with 'index'.
         """
-        import sys
+        from ..plotting.gpy_plot.latent_plots import plot_latent
-        assert "matplotlib" in sys.modules, "matplotlib package has not been imported."
+
-        from matplotlib import pyplot as plt
-        from ..plotting.matplot_dep import dim_reduction_plots
         if "Yindex" not in predict_kwargs:
             predict_kwargs['Yindex'] = 0
 
         Yindex = predict_kwargs['Yindex']
-        if ax is None:
+
-            fig = plt.figure(num=fignum)
-            ax = fig.add_subplot(111)
-        else:
-            fig = ax.figure
         self.kern = self.bgplvms[Yindex].kern
         self.likelihood = self.bgplvms[Yindex].likelihood
-        plot = dim_reduction_plots.plot_latent(self, labels, which_indices,
-                                        resolution, ax, marker, s,
-                                        fignum, plot_inducing, legend,
-                                        plot_limits, aspect, updates, predict_kwargs, imshow_kwargs)
-        ax.set_title(self.bgplvms[Yindex].name)
-        try:
-            fig.tight_layout()
-        except:
-            pass
 
-        return plot
+        return plot_latent(self, labels, which_indices, resolution, legend, plot_limits, updates, kern, marker, num_samples, projection, scatter_kwargs)
 
     def __getstate__(self):
         state = super(MRD, self).__getstate__()

GPy/models/ss_gplvm.py

@@ -190,4 +190,38 @@ class SSGPLVM(SparseGP_MPI):
         if self.kern.ARD:
             return self.kern.input_sensitivity()
         else:
-            return self.variational_prior.pi
+            return self.variational_prior.pi
+        
+    def sample_W(self, nSamples, raw_samples=False):
+        """
+        Sample the loading matrix if the kernel is linear.
+        """
+        assert isinstance(self.kern, kern.Linear)
+        from ..util.linalg import pdinv
+        N, D = self.Y.shape
+        Q = self.X.shape[1]
+        noise_var = self.likelihood.variance.values
+        
+        # Draw samples for X
+        Xs = np.random.randn(*((nSamples,)+self.X.shape))*np.sqrt(self.X.variance.values)+self.X.mean.values
+        b = np.random.rand(*((nSamples,)+self.X.shape))
+        Xs[b>self.X.gamma.values] = 0
+        
+        invcov = (Xs[:,:,:,None]*Xs[:,:,None,:]).sum(1)/noise_var+np.eye(Q)
+        cov = np.array([pdinv(invcov[s_idx])[0] for s_idx in xrange(invcov.shape[0])])
+        Ws = np.empty((nSamples, Q, D))
+        tmp = (np.transpose(Xs, (0,2,1)).reshape(nSamples*Q,N).dot(self.Y)).reshape(nSamples,Q,D)
+        mean = (cov[:,:,:,None]*tmp[:,None,:,:]).sum(2)/noise_var
+        zeros = np.zeros((Q,))
+        for s_idx in xrange(Xs.shape[0]):
+            Ws[s_idx] = (np.random.multivariate_normal(mean=zeros,cov=cov[s_idx],size=(D,))).T+mean[s_idx]
+        
+        if raw_samples:
+            return Ws
+        else:
+            return Ws.mean(0), Ws.std(0)
+
+        
+        
+
+        

GPy/plotting/__init__.py

@@ -25,18 +25,66 @@ def change_plotting_library(lib):
             current_lib[0] = PlotlyPlots()
         if lib == 'none':
             current_lib[0] = None
+        inject_plotting()
         #===========================================================================
     except (ImportError, NameError):
         config.set('plotting', 'library', 'none')
+        raise
         import warnings
         warnings.warn(ImportWarning("You spevified {} in your configuration, but is not available. Install newest version of {} for plotting".format(lib, lib)))
 
-from ..util.config import config, NoOptionError
+def inject_plotting():
-try:
+    if current_lib[0] is not None:
-    lib = config.get('plotting', 'library')
+        # Inject the plots into classes here:
-    change_plotting_library(lib)
+
-except NoOptionError:
+        # Already converted to new style:
-    print("No plotting library was specified in config file. \n{}".format(error_suggestion))
+        from . import gpy_plot
+
+        from ..core import GP
+        GP.plot_data = gpy_plot.data_plots.plot_data
+        GP.plot_data_error = gpy_plot.data_plots.plot_data_error
+        GP.plot_errorbars_trainset = gpy_plot.data_plots.plot_errorbars_trainset
+        GP.plot_mean = gpy_plot.gp_plots.plot_mean
+        GP.plot_confidence = gpy_plot.gp_plots.plot_confidence
+        GP.plot_density = gpy_plot.gp_plots.plot_density
+        GP.plot_samples = gpy_plot.gp_plots.plot_samples
+        GP.plot = gpy_plot.gp_plots.plot
+        GP.plot_f = gpy_plot.gp_plots.plot_f
+        GP.plot_magnification = gpy_plot.latent_plots.plot_magnification
+
+        from ..core import SparseGP
+        SparseGP.plot_inducing = gpy_plot.data_plots.plot_inducing
+
+        from ..models import GPLVM, BayesianGPLVM, bayesian_gplvm_minibatch, SSGPLVM, SSMRD
+        GPLVM.plot_latent = gpy_plot.latent_plots.plot_latent
+        GPLVM.plot_scatter = gpy_plot.latent_plots.plot_latent_scatter
+        GPLVM.plot_inducing = gpy_plot.latent_plots.plot_latent_inducing
+        GPLVM.plot_steepest_gradient_map = gpy_plot.latent_plots.plot_steepest_gradient_map
+        BayesianGPLVM.plot_latent = gpy_plot.latent_plots.plot_latent
+        BayesianGPLVM.plot_scatter = gpy_plot.latent_plots.plot_latent_scatter
+        BayesianGPLVM.plot_inducing = gpy_plot.latent_plots.plot_latent_inducing
+        BayesianGPLVM.plot_steepest_gradient_map = gpy_plot.latent_plots.plot_steepest_gradient_map
+        bayesian_gplvm_minibatch.BayesianGPLVMMiniBatch.plot_latent = gpy_plot.latent_plots.plot_latent
+        bayesian_gplvm_minibatch.BayesianGPLVMMiniBatch.plot_scatter = gpy_plot.latent_plots.plot_latent_scatter
+        bayesian_gplvm_minibatch.BayesianGPLVMMiniBatch.plot_inducing = gpy_plot.latent_plots.plot_latent_inducing
+        bayesian_gplvm_minibatch.BayesianGPLVMMiniBatch.plot_steepest_gradient_map = gpy_plot.latent_plots.plot_steepest_gradient_map
+        SSGPLVM.plot_latent = gpy_plot.latent_plots.plot_latent
+        SSGPLVM.plot_scatter = gpy_plot.latent_plots.plot_latent_scatter
+        SSGPLVM.plot_inducing = gpy_plot.latent_plots.plot_latent_inducing
+        SSGPLVM.plot_steepest_gradient_map = gpy_plot.latent_plots.plot_steepest_gradient_map
+
+        from ..kern import Kern
+        Kern.plot_covariance = gpy_plot.kernel_plots.plot_covariance
+        def deprecate_plot(self, *args, **kwargs):
+            import warnings
+            warnings.warn(DeprecationWarning('Kern.plot is being deprecated and will not be available in the 1.0 release. Use Kern.plot_covariance instead'))
+            return self.plot_covariance(*args, **kwargs)
+        Kern.plot = deprecate_plot
+        Kern.plot_ARD = gpy_plot.kernel_plots.plot_ARD
+
+        from ..inference.optimization import Optimizer
+        Optimizer.plot = gpy_plot.inference_plots.plot_optimizer
+        # Variational plot!
 
 def plotting_library():
     if current_lib[0] is None:
@@ -53,54 +101,10 @@ def show(figure, **kwargs):
     """
     return plotting_library().show_canvas(figure, **kwargs)
 
-if config.get('plotting', 'library') is not 'none':
-    # Inject the plots into classes here:
 
-    # Already converted to new style:
+from ..util.config import config, NoOptionError
-    from . import gpy_plot
+try:
-
+    lib = config.get('plotting', 'library')
-    from ..core import GP
+    change_plotting_library(lib)
-    GP.plot_data = gpy_plot.data_plots.plot_data
+except NoOptionError:
-    GP.plot_data_error = gpy_plot.data_plots.plot_data_error
+    print("No plotting library was specified in config file. \n{}".format(error_suggestion))
-    GP.plot_errorbars_trainset = gpy_plot.data_plots.plot_errorbars_trainset
-    GP.plot_mean = gpy_plot.gp_plots.plot_mean
-    GP.plot_confidence = gpy_plot.gp_plots.plot_confidence
-    GP.plot_density = gpy_plot.gp_plots.plot_density
-    GP.plot_samples = gpy_plot.gp_plots.plot_samples
-    GP.plot = gpy_plot.gp_plots.plot
-    GP.plot_f = gpy_plot.gp_plots.plot_f
-    GP.plot_magnification = gpy_plot.latent_plots.plot_magnification
-
-    from ..core import SparseGP
-    SparseGP.plot_inducing = gpy_plot.data_plots.plot_inducing
-
-    from ..models import GPLVM, BayesianGPLVM, bayesian_gplvm_minibatch, SSGPLVM, SSMRD
-    GPLVM.plot_latent = gpy_plot.latent_plots.plot_latent
-    GPLVM.plot_scatter = gpy_plot.latent_plots.plot_latent_scatter
-    GPLVM.plot_inducing = gpy_plot.latent_plots.plot_latent_inducing
-    GPLVM.plot_steepest_gradient_map = gpy_plot.latent_plots.plot_steepest_gradient_map
-    BayesianGPLVM.plot_latent = gpy_plot.latent_plots.plot_latent
-    BayesianGPLVM.plot_scatter = gpy_plot.latent_plots.plot_latent_scatter
-    BayesianGPLVM.plot_inducing = gpy_plot.latent_plots.plot_latent_inducing
-    BayesianGPLVM.plot_steepest_gradient_map = gpy_plot.latent_plots.plot_steepest_gradient_map
-    bayesian_gplvm_minibatch.BayesianGPLVMMiniBatch.plot_latent = gpy_plot.latent_plots.plot_latent
-    bayesian_gplvm_minibatch.BayesianGPLVMMiniBatch.plot_scatter = gpy_plot.latent_plots.plot_latent_scatter
-    bayesian_gplvm_minibatch.BayesianGPLVMMiniBatch.plot_inducing = gpy_plot.latent_plots.plot_latent_inducing
-    bayesian_gplvm_minibatch.BayesianGPLVMMiniBatch.plot_steepest_gradient_map = gpy_plot.latent_plots.plot_steepest_gradient_map
-    SSGPLVM.plot_latent = gpy_plot.latent_plots.plot_latent
-    SSGPLVM.plot_scatter = gpy_plot.latent_plots.plot_latent_scatter
-    SSGPLVM.plot_inducing = gpy_plot.latent_plots.plot_latent_inducing
-    SSGPLVM.plot_steepest_gradient_map = gpy_plot.latent_plots.plot_steepest_gradient_map
-
-    from ..kern import Kern
-    Kern.plot_covariance = gpy_plot.kernel_plots.plot_covariance
-    def deprecate_plot(self, *args, **kwargs):
-        import warnings
-        warnings.warn(DeprecationWarning('Kern.plot is being deprecated and will not be available in the 1.0 release. Use Kern.plot_covariance instead'))
-        return self.plot_covariance(*args, **kwargs)
-    Kern.plot = deprecate_plot
-    Kern.plot_ARD = gpy_plot.kernel_plots.plot_ARD
-
-    from ..inference.optimization import Optimizer
-    Optimizer.plot = gpy_plot.inference_plots.plot_optimizer
-    # Variational plot!

GPy/plotting/gpy_plot/gp_plots.py

@@ -46,7 +46,7 @@ def plot_mean(self, plot_limits=None, fixed_inputs=None,
     """
     Plot the mean of the GP.
 
-    You can deactivate the legend for this one plot by supplying None to label. 
+    You can deactivate the legend for this one plot by supplying None to label.
 
     Give the Y_metadata in the predict_kw if you need it.
 
@@ -91,7 +91,7 @@ def _plot_mean(self, canvas, helper_data, helper_prediction,
             if projection == '2d':
                 update_not_existing_kwargs(kwargs, pl().defaults.meanplot_2d)  # @UndefinedVariable
                 plots = dict(gpmean=[pl().contour(canvas, x[:,0], y[0,:],
-                                               mu.reshape(resolution, resolution),
+                                               mu.reshape(resolution, resolution).T,
                                                levels=levels, label=label, **kwargs)])
             elif projection == '3d':
                 update_not_existing_kwargs(kwargs, pl().defaults.meanplot_3d)  # @UndefinedVariable
@@ -116,7 +116,7 @@ def plot_confidence(self, lower=2.5, upper=97.5, plot_limits=None, fixed_inputs=
     E.g. the 95% confidence interval is $2.5, 97.5$.
     Note: Only implemented for one dimension!
 
-    You can deactivate the legend for this one plot by supplying None to label. 
+    You can deactivate the legend for this one plot by supplying None to label.
 
     Give the Y_metadata in the predict_kw if you need it.
 
@@ -170,7 +170,7 @@ def plot_samples(self, plot_limits=None, fixed_inputs=None,
     """
     Plot the mean of the GP.
 
-    You can deactivate the legend for this one plot by supplying None to label. 
+    You can deactivate the legend for this one plot by supplying None to label.
 
     Give the Y_metadata in the predict_kw if you need it.
 
@@ -231,7 +231,7 @@ def plot_density(self, plot_limits=None, fixed_inputs=None,
     E.g. the 95% confidence interval is $2.5, 97.5$.
     Note: Only implemented for one dimension!
 
-    You can deactivate the legend for this one plot by supplying None to label. 
+    You can deactivate the legend for this one plot by supplying None to label.
 
     Give the Y_metadata in the predict_kw if you need it.
 
@@ -288,7 +288,7 @@ def plot(self, plot_limits=None, fixed_inputs=None,
     """
     Convenience function for plotting the fit of a GP.
 
-    You can deactivate the legend for this one plot by supplying None to label. 
+    You can deactivate the legend for this one plot by supplying None to label.
 
     Give the Y_metadata in the predict_kw if you need it.
 
@@ -319,9 +319,17 @@ def plot(self, plot_limits=None, fixed_inputs=None,
     :param {2d|3d} projection: plot in 2d or 3d?
     :param bool legend: convenience, whether to put a legend on the plot or not.
     """
-    canvas, _ = pl().new_canvas(projection=projection, **kwargs)
     X = get_x_y_var(self)[0]
     helper_data = helper_for_plot_data(self, X, plot_limits, visible_dims, fixed_inputs, resolution)
+    xmin, xmax = helper_data[5:7]
+    free_dims = helper_data[1]
+
+    if not 'xlim' in kwargs:
+        kwargs['xlim'] = (xmin[0], xmax[0])
+    if not 'ylim' in kwargs and len(free_dims) == 2:
+        kwargs['ylim'] = (xmin[1], xmax[1])
+
+    canvas, _ = pl().new_canvas(projection=projection, **kwargs)
     helper_prediction = helper_predict_with_model(self, helper_data[2], plot_raw,
                                           apply_link, np.linspace(2.5, 97.5, levels*2) if plot_density else (lower,upper),
                                           get_which_data_ycols(self, which_data_ycols),
@@ -330,9 +338,11 @@ def plot(self, plot_limits=None, fixed_inputs=None,
         # It does not make sense to plot the data (which lives not in the latent function space) into latent function space.
         plot_data = False
     plots = {}
+    if hasattr(self, 'Z') and plot_inducing:
+        plots.update(_plot_inducing(self, canvas, visible_dims, projection, 'Inducing'))
     if plot_data:
-        plots.update(_plot_data(self, canvas, which_data_rows, which_data_ycols, visible_dims, projection, "Data"))
+        plots.update(_plot_data(self, canvas, which_data_rows, which_data_ycols, free_dims, projection, "Data"))
-        plots.update(_plot_data_error(self, canvas, which_data_rows, which_data_ycols, visible_dims, projection, "Data Error"))
+        plots.update(_plot_data_error(self, canvas, which_data_rows, which_data_ycols, free_dims, projection, "Data Error"))
     plots.update(_plot(self, canvas, plots, helper_data, helper_prediction, levels, plot_inducing, plot_density, projection))
     if plot_raw and (samples_likelihood > 0):
         helper_prediction = helper_predict_with_model(self, helper_data[2], False,
@@ -340,8 +350,6 @@ def plot(self, plot_limits=None, fixed_inputs=None,
                                       get_which_data_ycols(self, which_data_ycols),
                                       predict_kw, samples_likelihood)
         plots.update(_plot_samples(canvas, helper_data, helper_prediction, projection, "Lik Samples"))
-    if hasattr(self, 'Z') and plot_inducing:
-        plots.update(_plot_inducing(self, canvas, visible_dims, projection, 'Inducing'))
     return pl().add_to_canvas(canvas, plots, legend=legend)
 
 
@@ -362,7 +370,7 @@ def plot_f(self, plot_limits=None, fixed_inputs=None,
 
     If you want fine graned control use the specific plotting functions supplied in the model.
 
-    You can deactivate the legend for this one plot by supplying None to label. 
+    You can deactivate the legend for this one plot by supplying None to label.
 
     Give the Y_metadata in the predict_kw if you need it.
 
@@ -389,7 +397,7 @@ def plot_f(self, plot_limits=None, fixed_inputs=None,
     :param dict error_kwargs: kwargs for the error plot for the plotting library you are using
     :param kwargs plot_kwargs: kwargs for the data plot for the plotting library you are using
     """
-    plot(self, plot_limits, fixed_inputs, resolution, True,
+    return plot(self, plot_limits, fixed_inputs, resolution, True,
          apply_link, which_data_ycols, which_data_rows,
          visible_dims, levels, samples, 0,
          lower, upper, plot_data, plot_inducing,

GPy/plotting/gpy_plot/kernel_plots.py

@@ -33,7 +33,7 @@ from .. import Tango
 from .plot_util import update_not_existing_kwargs, helper_for_plot_data
 from ...kern.src.kern import Kern, CombinationKernel
 
-def plot_ARD(kernel, filtering=None, legend=False, **kwargs):
+def plot_ARD(kernel, filtering=None, legend=False, canvas=None, **kwargs):
     """
     If an ARD kernel is present, plot a bar representation using matplotlib
 
@@ -62,7 +62,11 @@ def plot_ARD(kernel, filtering=None, legend=False, **kwargs):
 
     bars = []
     kwargs = update_not_existing_kwargs(kwargs, pl().defaults.ard)
-    canvas, kwargs = pl().new_canvas(xlim=(-.5, kernel._effective_input_dim-.5), xlabel='input dimension', ylabel='sensitivity', **kwargs)
+
+
+    if canvas is None:
+        canvas, kwargs = pl().new_canvas(xlim=(-.5, kernel._effective_input_dim-.5), xlabel='input dimension', ylabel='sensitivity', **kwargs)
+
     for i in range(ard_params.shape[0]):
         if parts[i].name in filtering:
             c = Tango.nextMedium()
@@ -96,7 +100,7 @@ def plot_covariance(kernel, x=None, label=None,
     """
     X = np.ones((2, kernel._effective_input_dim)) * [[-3], [3]]
     _, free_dims, Xgrid, xx, yy, _, _, resolution = helper_for_plot_data(kernel, X, plot_limits, visible_dims, None, resolution)
-    
+
     from numbers import Number
     if x is None:
         from ...kern.src.stationary import Stationary
@@ -104,7 +108,7 @@ def plot_covariance(kernel, x=None, label=None,
     elif isinstance(x, Number):
         x = np.ones((1, kernel._effective_input_dim))*x
     K = kernel.K(Xgrid, x)
-    
+
     if projection == '3d':
         xlabel = 'X[:,0]'
         ylabel = 'X[:,1]'

GPy/plotting/gpy_plot/latent_plots.py

@@ -50,6 +50,17 @@ def _wait_for_updates(view, updates):
             # No updateable view:
             pass
 
+def _new_canvas(self, projection, kwargs, which_indices):
+    input_1, input_2, input_3 = sig_dims = self.get_most_significant_input_dimensions(which_indices)
+
+    if input_3 is None:
+        zlabel = None
+    else:
+        zlabel = 'latent dimension %i' % input_3
+    canvas, kwargs = pl().new_canvas(projection=projection, xlabel='latent dimension %i' % input_1,
+        ylabel='latent dimension %i' % input_2,
+        zlabel=zlabel, **kwargs)
+    return canvas, projection, kwargs, sig_dims
 
 def _plot_latent_scatter(canvas, X, visible_dims, labels, marker, num_samples, projection='2d', **kwargs):
     from .. import Tango
@@ -85,12 +96,8 @@ def plot_latent_scatter(self, labels=None,
     :param str marker: markers to use - cycle if more labels then markers are given
     :param kwargs: the kwargs for the scatter plots
     """
-    input_1, input_2, input_3 = sig_dims = self.get_most_significant_input_dimensions(which_indices)
+    canvas, projection, kwargs, sig_dims = _new_canvas(self, projection, kwargs, which_indices)
 
-    canvas, kwargs = pl().new_canvas(projection=projection,
-                              xlabel='latent dimension %i' % input_1,
-                              ylabel='latent dimension %i' % input_2,
-                              zlabel='latent dimension %i' % input_3, **kwargs)
     X, _, _ = get_x_y_var(self)
     if labels is None:
         labels = np.ones(self.num_data)
@@ -101,8 +108,6 @@ def plot_latent_scatter(self, labels=None,
     return pl().add_to_canvas(canvas, dict(scatter=scatters), legend=legend)
 
 
-
-
 def plot_latent_inducing(self,
                         which_indices=None,
                         legend=False,
@@ -122,17 +127,8 @@ def plot_latent_inducing(self,
     :param str marker: markers to use - cycle if more labels then markers are given
     :param kwargs: the kwargs for the scatter plots
     """
-    input_1, input_2, input_3 = sig_dims = self.get_most_significant_input_dimensions(which_indices)
+    canvas, projection, kwargs, sig_dims = _new_canvas(self, projection, kwargs, which_indices)
-    if input_3 is None: zlabel=None
-    else: zlabel = 'latent dimension %i' % input_3
-        
 
-    if 'color' not in kwargs:
-        kwargs['color'] = 'white'
-    canvas, kwargs = pl().new_canvas(projection=projection,
-                              xlabel='latent dimension %i' % input_1,
-                              ylabel='latent dimension %i' % input_2,
-                              zlabel=zlabel, **kwargs)
     Z = self.Z.values
     labels = np.array(['inducing'] * Z.shape[0])
     scatters = _plot_latent_scatter(canvas, Z, sig_dims, labels, marker, num_samples, projection=projection, **kwargs)
@@ -167,7 +163,8 @@ def plot_magnification(self, labels=None, which_indices=None,
                 updates=False,
                 mean=True, covariance=True,
                 kern=None, num_samples=1000,
-                scatter_kwargs=None, **imshow_kwargs):
+                scatter_kwargs=None, plot_scatter=True,
+                **imshow_kwargs):
     """
     Plot the magnification factor of the GP on the inputs. This is the
     density of the GP as a gray scale.
@@ -192,17 +189,20 @@ def plot_magnification(self, labels=None, which_indices=None,
     _, _, Xgrid, _, _, xmin, xmax, resolution = helper_for_plot_data(self, X, plot_limits, which_indices, None, resolution)
     canvas, imshow_kwargs = pl().new_canvas(xlim=(xmin[0], xmax[0]), ylim=(xmin[1], xmax[1]),
                            xlabel='latent dimension %i' % input_1, ylabel='latent dimension %i' % input_2, **imshow_kwargs)
-    if (labels is not None):
+    plots = {}
-        legend = find_best_layout_for_subplots(len(np.unique(labels)))[1]
+    if legend and plot_scatter:
-    else:
+        if (labels is not None):
-        labels = np.ones(self.num_data)
+            legend = find_best_layout_for_subplots(len(np.unique(labels)))[1]
-        legend = False
+        else:
-    scatters = _plot_latent_scatter(canvas, X, which_indices, labels, marker, num_samples, projection='2d', **scatter_kwargs or {})
+            labels = np.ones(self.num_data)
-    view = _plot_magnification(self, canvas, which_indices, Xgrid, xmin, xmax, resolution, updates, mean, covariance, kern, **imshow_kwargs)
+            legend = False
-    retval = pl().add_to_canvas(canvas, dict(scatter=scatters, imshow=view),
+    if plot_scatter:
+        plots['scatters'] = _plot_latent_scatter(canvas, X, which_indices, labels, marker, num_samples, projection='2d', **scatter_kwargs or {})
+    plots['view'] = _plot_magnification(self, canvas, which_indices, Xgrid, xmin, xmax, resolution, updates, mean, covariance, kern, **imshow_kwargs)
+    retval = pl().add_to_canvas(canvas, plots,
                            legend=legend,
                            )
-    _wait_for_updates(view, updates)
+    _wait_for_updates(plots['view'], updates)
     return retval
 
 
@@ -231,7 +231,7 @@ def plot_latent(self, labels=None, which_indices=None,
                 plot_limits=None,
                 updates=False,
                 kern=None, marker='<>^vsd',
-                num_samples=1000,
+                num_samples=1000, projection='2d',
                 scatter_kwargs=None, **imshow_kwargs):
     """
     Plot the latent space of the GP on the inputs. This is the
@@ -251,16 +251,19 @@ def plot_latent(self, labels=None, which_indices=None,
     :param imshow_kwargs: the kwargs for the imshow (magnification factor)
     :param scatter_kwargs: the kwargs for the scatter plots
     """
+    if projection != '2d':
+        raise ValueError('Cannot plot latent in other then 2 dimensions, consider plot_scatter')
     input_1, input_2 = which_indices = self.get_most_significant_input_dimensions(which_indices)[:2]
     X = get_x_y_var(self)[0]
     _, _, Xgrid, _, _, xmin, xmax, resolution = helper_for_plot_data(self, X, plot_limits, which_indices, None, resolution)
     canvas, imshow_kwargs = pl().new_canvas(xlim=(xmin[0], xmax[0]), ylim=(xmin[1], xmax[1]),
                            xlabel='latent dimension %i' % input_1, ylabel='latent dimension %i' % input_2, **imshow_kwargs)
-    if (labels is not None):
+    if legend:
-        legend = find_best_layout_for_subplots(len(np.unique(labels)))[1]
+        if (labels is not None):
-    else:
+            legend = find_best_layout_for_subplots(len(np.unique(labels)))[1]
-        labels = np.ones(self.num_data)
+        else:
-        legend = False
+            labels = np.ones(self.num_data)
+            legend = False
     scatters = _plot_latent_scatter(canvas, X, which_indices, labels, marker, num_samples, projection='2d', **scatter_kwargs or {})
     view = _plot_latent(self, canvas, which_indices, Xgrid, xmin, xmax, resolution, updates, kern, **imshow_kwargs)
     retval = pl().add_to_canvas(canvas, dict(scatter=scatters, imshow=view), legend=legend)

GPy/plotting/gpy_plot/plot_util.py

@@ -203,7 +203,7 @@ def subsample_X(X, labels, num_samples=1000):
     num_samples and the returned subsampled X.
     """
     if X.shape[0] > num_samples:
-        print("Warning: subsampling X, as it has more samples then 1000. X.shape={!s}".format(X.shape))
+        print("Warning: subsampling X, as it has more samples then {}. X.shape={!s}".format(int(num_samples), X.shape))
         if labels is not None:
             subsample = []
             for _, _, _, _, index, _ in scatter_label_generator(labels, X, (0, None, None)):
@@ -289,7 +289,10 @@ def get_x_y_var(model):
         X = model.X.mean.values
         X_variance = model.X.variance.values
     else:
-        X = model.X.values
+        try:
+            X = model.X.values
+        except AttributeError:
+            X = model.X
         X_variance = None
     try:
         Y = model.Y.values
@@ -352,7 +355,7 @@ def x_frame1D(X,plot_limits=None,resolution=None):
             xmin,xmax = X.min(0),X.max(0)
         xmin, xmax = xmin-0.25*(xmax-xmin), xmax+0.25*(xmax-xmin)
     elif len(plot_limits) == 2:
-        xmin, xmax = plot_limits
+        xmin, xmax = map(np.atleast_1d, plot_limits)
     else:
         raise ValueError("Bad limits for plotting")
 

GPy/plotting/matplot_dep/__init__.py

@@ -18,4 +18,4 @@
 
 
 from .util import align_subplot_array, align_subplots, fewerXticks, removeRightTicks, removeUpperTicks
-from . import controllers
+from . import controllers, base_plots

GPy/plotting/matplot_dep/base_plots.py

@@ -0,0 +1,265 @@
+# #Copyright (c) 2012, GPy authors (see AUTHORS.txt).
+# Licensed under the BSD 3-clause license (see LICENSE.txt)
+from matplotlib import pyplot as plt
+import numpy as np
+
+def ax_default(fignum, ax):
+    if ax is None:
+        fig = plt.figure(fignum)
+        ax = fig.add_subplot(111)
+    else:
+        fig = ax.figure
+    return fig, ax
+
+def meanplot(x, mu, color='#3300FF', ax=None, fignum=None, linewidth=2,**kw):
+    _, axes = ax_default(fignum, ax)
+    return axes.plot(x,mu,color=color,linewidth=linewidth,**kw)
+
+def gpplot(x, mu, lower, upper, edgecol='#3300FF', fillcol='#33CCFF', ax=None, fignum=None, **kwargs):
+    _, axes = ax_default(fignum, ax)
+
+    mu = mu.flatten()
+    x = x.flatten()
+    lower = lower.flatten()
+    upper = upper.flatten()
+
+    plots = []
+
+    #here's the mean
+    plots.append(meanplot(x, mu, edgecol, axes))
+
+    #here's the box
+    kwargs['linewidth']=0.5
+    if not 'alpha' in kwargs.keys():
+        kwargs['alpha'] = 0.3
+    plots.append(axes.fill(np.hstack((x,x[::-1])),np.hstack((upper,lower[::-1])),color=fillcol,**kwargs))
+
+    #this is the edge:
+    plots.append(meanplot(x, upper,color=edgecol, linewidth=0.2, ax=axes))
+    plots.append(meanplot(x, lower,color=edgecol, linewidth=0.2, ax=axes))
+
+    return plots
+
+def gradient_fill(x, percentiles, ax=None, fignum=None, **kwargs):
+    _, ax = ax_default(fignum, ax)
+
+    plots = []
+
+    #here's the box
+    if 'linewidth' not in kwargs:
+        kwargs['linewidth'] = 0.5
+    if not 'alpha' in kwargs.keys():
+        kwargs['alpha'] = 1./(len(percentiles))
+    
+    # pop where from kwargs
+    where = kwargs.pop('where') if 'where' in kwargs else None
+    # pop interpolate, which we actually do not do here!
+    if 'interpolate' in kwargs: kwargs.pop('interpolate')
+    
+    def pairwise(inlist):
+        l = len(inlist)
+        for i in range(int(np.ceil(l/2.))):
+            yield inlist[:][i], inlist[:][(l-1)-i]
+    
+    polycol = []
+    for y1, y2 in pairwise(percentiles):
+        import matplotlib.mlab as mlab
+        # Handle united data, such as dates
+        ax._process_unit_info(xdata=x, ydata=y1)
+        ax._process_unit_info(ydata=y2)
+    
+        # Convert the arrays so we can work with them
+        from numpy import ma
+        x = ma.masked_invalid(ax.convert_xunits(x))
+        y1 = ma.masked_invalid(ax.convert_yunits(y1))
+        y2 = ma.masked_invalid(ax.convert_yunits(y2))
+    
+        if y1.ndim == 0:
+            y1 = np.ones_like(x) * y1
+        if y2.ndim == 0:
+            y2 = np.ones_like(x) * y2
+    
+        if where is None:
+            where = np.ones(len(x), np.bool)
+        else:
+            where = np.asarray(where, np.bool)
+    
+        if not (x.shape == y1.shape == y2.shape == where.shape):
+            raise ValueError("Argument dimensions are incompatible")
+    
+        mask = reduce(ma.mask_or, [ma.getmask(a) for a in (x, y1, y2)])
+        if mask is not ma.nomask:
+            where &= ~mask
+        
+        polys = []
+        for ind0, ind1 in mlab.contiguous_regions(where):
+            xslice = x[ind0:ind1]
+            y1slice = y1[ind0:ind1]
+            y2slice = y2[ind0:ind1]
+    
+            if not len(xslice):
+                continue
+    
+            N = len(xslice)
+            X = np.zeros((2 * N + 2, 2), np.float)
+    
+            # the purpose of the next two lines is for when y2 is a
+            # scalar like 0 and we want the fill to go all the way
+            # down to 0 even if none of the y1 sample points do
+            start = xslice[0], y2slice[0]
+            end = xslice[-1], y2slice[-1]
+    
+            X[0] = start
+            X[N + 1] = end
+    
+            X[1:N + 1, 0] = xslice
+            X[1:N + 1, 1] = y1slice
+            X[N + 2:, 0] = xslice[::-1]
+            X[N + 2:, 1] = y2slice[::-1]
+    
+            polys.append(X)
+        polycol.extend(polys)
+    from matplotlib.collections import PolyCollection
+    plots.append(PolyCollection(polycol, **kwargs))
+    ax.add_collection(plots[-1], autolim=True)
+    ax.autoscale_view()
+    return plots
+
+def gperrors(x, mu, lower, upper, edgecol=None, ax=None, fignum=None, **kwargs):
+    _, axes = ax_default(fignum, ax)
+
+    mu = mu.flatten()
+    x = x.flatten()
+    lower = lower.flatten()
+    upper = upper.flatten()
+
+    plots = []
+
+    if edgecol is None:
+        edgecol='#3300FF'
+
+    if not 'alpha' in kwargs.keys():
+        kwargs['alpha'] = 1.
+
+
+    if not 'lw' in kwargs.keys():
+        kwargs['lw'] = 1.
+
+
+    plots.append(axes.errorbar(x,mu,yerr=np.vstack([mu-lower,upper-mu]),color=edgecol,**kwargs))
+    plots[-1][0].remove()
+    return plots
+
+
+def removeRightTicks(ax=None):
+    ax = ax or plt.gca()
+    for i, line in enumerate(ax.get_yticklines()):
+        if i%2 == 1:   # odd indices
+            line.set_visible(False)
+
+def removeUpperTicks(ax=None):
+    ax = ax or plt.gca()
+    for i, line in enumerate(ax.get_xticklines()):
+        if i%2 == 1:   # odd indices
+            line.set_visible(False)
+
+def fewerXticks(ax=None,divideby=2):
+    ax = ax or plt.gca()
+    ax.set_xticks(ax.get_xticks()[::divideby])
+
+def align_subplots(N,M,xlim=None, ylim=None):
+    """make all of the subplots have the same limits, turn off unnecessary ticks"""
+    #find sensible xlim,ylim
+    if xlim is None:
+        xlim = [np.inf,-np.inf]
+        for i in range(N*M):
+            plt.subplot(N,M,i+1)
+            xlim[0] = min(xlim[0],plt.xlim()[0])
+            xlim[1] = max(xlim[1],plt.xlim()[1])
+    if ylim is None:
+        ylim = [np.inf,-np.inf]
+        for i in range(N*M):
+            plt.subplot(N,M,i+1)
+            ylim[0] = min(ylim[0],plt.ylim()[0])
+            ylim[1] = max(ylim[1],plt.ylim()[1])
+
+    for i in range(N*M):
+        plt.subplot(N,M,i+1)
+        plt.xlim(xlim)
+        plt.ylim(ylim)
+        if (i)%M:
+            plt.yticks([])
+        else:
+            removeRightTicks()
+        if i<(M*(N-1)):
+            plt.xticks([])
+        else:
+            removeUpperTicks()
+
+def align_subplot_array(axes,xlim=None, ylim=None):
+    """
+    Make all of the axes in the array hae the same limits, turn off unnecessary ticks
+    use plt.subplots() to get an array of axes
+    """
+    #find sensible xlim,ylim
+    if xlim is None:
+        xlim = [np.inf,-np.inf]
+        for ax in axes.flatten():
+            xlim[0] = min(xlim[0],ax.get_xlim()[0])
+            xlim[1] = max(xlim[1],ax.get_xlim()[1])
+    if ylim is None:
+        ylim = [np.inf,-np.inf]
+        for ax in axes.flatten():
+            ylim[0] = min(ylim[0],ax.get_ylim()[0])
+            ylim[1] = max(ylim[1],ax.get_ylim()[1])
+
+    N,M = axes.shape
+    for i,ax in enumerate(axes.flatten()):
+        ax.set_xlim(xlim)
+        ax.set_ylim(ylim)
+        if (i)%M:
+            ax.set_yticks([])
+        else:
+            removeRightTicks(ax)
+        if i<(M*(N-1)):
+            ax.set_xticks([])
+        else:
+            removeUpperTicks(ax)
+
+def x_frame1D(X,plot_limits=None,resolution=None):
+    """
+    Internal helper function for making plots, returns a set of input values to plot as well as lower and upper limits
+    """
+    assert X.shape[1] ==1, "x_frame1D is defined for one-dimensional inputs"
+    if plot_limits is None:
+        from ...core.parameterization.variational import VariationalPosterior
+        if isinstance(X, VariationalPosterior):
+            xmin,xmax = X.mean.min(0),X.mean.max(0)
+        else:
+            xmin,xmax = X.min(0),X.max(0)
+        xmin, xmax = xmin-0.2*(xmax-xmin), xmax+0.2*(xmax-xmin)
+    elif len(plot_limits)==2:
+        xmin, xmax = plot_limits
+    else:
+        raise ValueError("Bad limits for plotting")
+
+    Xnew = np.linspace(xmin,xmax,resolution or 200)[:,None]
+    return Xnew, xmin, xmax
+
+def x_frame2D(X,plot_limits=None,resolution=None):
+    """
+    Internal helper function for making plots, returns a set of input values to plot as well as lower and upper limits
+    """
+    assert X.shape[1] ==2, "x_frame2D is defined for two-dimensional inputs"
+    if plot_limits is None:
+        xmin,xmax = X.min(0),X.max(0)
+        xmin, xmax = xmin-0.2*(xmax-xmin), xmax+0.2*(xmax-xmin)
+    elif len(plot_limits)==2:
+        xmin, xmax = plot_limits
+    else:
+        raise ValueError("Bad limits for plotting")
+
+    resolution = resolution or 50
+    xx,yy = np.mgrid[xmin[0]:xmax[0]:1j*resolution,xmin[1]:xmax[1]:1j*resolution]
+    Xnew = np.vstack((xx.flatten(),yy.flatten())).T
+    return Xnew, xx, yy, xmin, xmax

GPy/plotting/matplot_dep/plot_definitions.py

@@ -1,21 +1,21 @@
 #===============================================================================
 # Copyright (c) 2015, Max Zwiessele
 # All rights reserved.
-# 
+#
 # Redistribution and use in source and binary forms, with or without
 # modification, are permitted provided that the following conditions are met:
-# 
+#
 # * Redistributions of source code must retain the above copyright notice, this
 #   list of conditions and the following disclaimer.
-# 
+#
 # * Redistributions in binary form must reproduce the above copyright notice,
 #   this list of conditions and the following disclaimer in the documentation
 #   and/or other materials provided with the distribution.
-# 
+#
 # * Neither the name of GPy.plotting.matplot_dep.plot_definitions nor the names of its
 #   contributors may be used to endorse or promote products derived from
 #   this software without specific prior written permission.
-# 
+#
 # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
@@ -41,14 +41,15 @@ class MatplotlibPlots(AbstractPlottingLibrary):
     def __init__(self):
         super(MatplotlibPlots, self).__init__()
         self._defaults = defaults.__dict__
-    
+
-    def figure(self, rows=1, cols=1, **kwargs):
+    def figure(self, rows=1, cols=1, gridspec_kwargs={}, tight_layout=True, **kwargs):
-        fig = plt.figure(**kwargs)
+        fig = plt.figure(tight_layout=tight_layout, **kwargs)
         fig.rows = rows
         fig.cols = cols
+        fig.gridspec = plt.GridSpec(rows, cols, **gridspec_kwargs)
         return fig
-    
+
-    def new_canvas(self, figure=None, col=1, row=1, projection='2d', xlabel=None, ylabel=None, zlabel=None, title=None, xlim=None, ylim=None, zlim=None, **kwargs):
+    def new_canvas(self, figure=None, row=1, col=1, projection='2d', xlabel=None, ylabel=None, zlabel=None, title=None, xlim=None, ylim=None, zlim=None, **kwargs):
         if projection == '3d':
             from mpl_toolkits.mplot3d import Axes3D
         elif projection == '2d':
@@ -56,7 +57,9 @@ class MatplotlibPlots(AbstractPlottingLibrary):
         if 'ax' in kwargs:
             ax = kwargs.pop('ax')
         else:
-            if 'num' in kwargs and 'figsize' in kwargs:
+            if figure is not None:
+                fig = figure
+            elif 'num' in kwargs and 'figsize' in kwargs:
                 fig = self.figure(num=kwargs.pop('num'), figsize=kwargs.pop('figsize'))
             elif 'num' in kwargs:
                 fig = self.figure(num=kwargs.pop('num'))
@@ -64,10 +67,10 @@ class MatplotlibPlots(AbstractPlottingLibrary):
                 fig = self.figure(figsize=kwargs.pop('figsize'))
             else:
                 fig = self.figure()
-        
+
             #if hasattr(fig, 'rows') and hasattr(fig, 'cols'):
-            ax = fig.add_subplot(fig.rows, fig.cols, (col,row), projection=projection)
+            ax = fig.add_subplot(fig.gridspec[row-1, col-1], projection=projection)
-            
+
         if xlim is not None: ax.set_xlim(xlim)
         if ylim is not None: ax.set_ylim(ylim)
         if xlabel is not None: ax.set_xlabel(xlabel)
@@ -77,9 +80,9 @@ class MatplotlibPlots(AbstractPlottingLibrary):
             if zlim is not None: ax.set_zlim(zlim)
             if zlabel is not None: ax.set_zlabel(zlabel)
         return ax, kwargs
-    
+
     def add_to_canvas(self, ax, plots, legend=False, title=None, **kwargs):
-        ax.autoscale_view()
+        #ax.autoscale_view()
         fontdict=dict(family='sans-serif', weight='light', size=9)
         if legend is True:
             ax.legend(*ax.get_legend_handles_labels())
@@ -88,18 +91,16 @@ class MatplotlibPlots(AbstractPlottingLibrary):
             legend_ontop(ax, ncol=legend, fontdict=fontdict)
         if title is not None: ax.figure.suptitle(title)
         return ax
-    
+
-    def show_canvas(self, ax, tight_layout=False, **kwargs):
+    def show_canvas(self, ax):
-        if tight_layout:
-            ax.figure.tight_layout()
         ax.figure.canvas.draw()
         return ax.figure
-    
+
     def scatter(self, ax, X, Y, Z=None, color=Tango.colorsHex['mediumBlue'], label=None, marker='o', **kwargs):
         if Z is not None:
             return ax.scatter(X, Y, c=color, zs=Z, label=label, marker=marker, **kwargs)
         return ax.scatter(X, Y, c=color, label=label, marker=marker, **kwargs)
-    
+
     def plot(self, ax, X, Y, Z=None, color=None, label=None, **kwargs):
         if Z is not None:
             return ax.plot(X, Y, color=color, zs=Z, label=label, **kwargs)
@@ -122,23 +123,23 @@ class MatplotlibPlots(AbstractPlottingLibrary):
         if 'align' not in kwargs:
             kwargs['align'] = 'center'
         return ax.bar(left=x, height=height, width=width,
-               bottom=bottom, label=label, color=color,  
+               bottom=bottom, label=label, color=color,
                **kwargs)
-        
+
     def xerrorbar(self, ax, X, Y, error, color=Tango.colorsHex['mediumBlue'], label=None, **kwargs):
         if not('linestyle' in kwargs or 'ls' in kwargs):
             kwargs['ls'] = 'none'
         #if Z is not None:
         #    return ax.errorbar(X, Y, Z, xerr=error, ecolor=color, label=label, **kwargs)
         return ax.errorbar(X, Y, xerr=error, ecolor=color, label=label, **kwargs)
-    
+
     def yerrorbar(self, ax, X, Y, error, color=Tango.colorsHex['mediumBlue'], label=None, **kwargs):
         if not('linestyle' in kwargs or 'ls' in kwargs):
             kwargs['ls'] = 'none'
         #if Z is not None:
         #    return ax.errorbar(X, Y, Z, yerr=error, ecolor=color, label=label, **kwargs)
         return ax.errorbar(X, Y, yerr=error, ecolor=color, label=label, **kwargs)
-    
+
     def imshow(self, ax, X, extent=None, label=None, vmin=None, vmax=None, **imshow_kwargs):
         if 'origin' not in imshow_kwargs:
             imshow_kwargs['origin'] = 'lower'
@@ -178,7 +179,7 @@ class MatplotlibPlots(AbstractPlottingLibrary):
         if 'origin' not in imshow_kwargs:
             imshow_kwargs['origin'] = 'lower'
         return ImAnnotateController(ax, plot_function, extent, resolution=resolution, imshow_kwargs=imshow_kwargs or {}, **annotation_kwargs)
-    
+
     def contour(self, ax, X, Y, C, levels=20, label=None, **kwargs):
         return ax.contour(X, Y, C, levels=np.linspace(C.min(), C.max(), levels), label=label, **kwargs)
 
@@ -191,13 +192,13 @@ class MatplotlibPlots(AbstractPlottingLibrary):
     def fill_gradient(self, canvas, X, percentiles, color=Tango.colorsHex['mediumBlue'], label=None, **kwargs):
         ax = canvas
         plots = []
-        
+
         if 'edgecolors' not in kwargs:
             kwargs['edgecolors'] = 'none'
-        
+
         if 'facecolors' in kwargs:
             color = kwargs.pop('facecolors')
-            
+
         if 'array' in kwargs:
             array = kwargs.pop('array')
         else:
@@ -231,8 +232,8 @@ class MatplotlibPlots(AbstractPlottingLibrary):
             #    pass
             a, b = tee(iterable)
             next(b, None)
-            return zip(a, b)            
+            return zip(a, b)
-            
+
         polycol = []
         for y1, y2 in pairwise(percentiles):
             import matplotlib.mlab as mlab
@@ -244,51 +245,51 @@ class MatplotlibPlots(AbstractPlottingLibrary):
             x = ma.masked_invalid(ax.convert_xunits(X))
             y1 = ma.masked_invalid(ax.convert_yunits(y1))
             y2 = ma.masked_invalid(ax.convert_yunits(y2))
-        
+
             if y1.ndim == 0:
                 y1 = np.ones_like(x) * y1
             if y2.ndim == 0:
                 y2 = np.ones_like(x) * y2
-        
+
             if where is None:
                 where = np.ones(len(x), np.bool)
             else:
                 where = np.asarray(where, np.bool)
-        
+
             if not (x.shape == y1.shape == y2.shape == where.shape):
                 raise ValueError("Argument dimensions are incompatible")
-        
+
             from functools import reduce
             mask = reduce(ma.mask_or, [ma.getmask(a) for a in (x, y1, y2)])
             if mask is not ma.nomask:
                 where &= ~mask
-            
+
             polys = []
             for ind0, ind1 in mlab.contiguous_regions(where):
                 xslice = x[ind0:ind1]
                 y1slice = y1[ind0:ind1]
                 y2slice = y2[ind0:ind1]
-        
+
                 if not len(xslice):
                     continue
-        
+
                 N = len(xslice)
                 p = np.zeros((2 * N + 2, 2), np.float)
-        
+
                 # the purpose of the next two lines is for when y2 is a
                 # scalar like 0 and we want the fill to go all the way
                 # down to 0 even if none of the y1 sample points do
                 start = xslice[0], y2slice[0]
                 end = xslice[-1], y2slice[-1]
-        
+
                 p[0] = start
                 p[N + 1] = end
-        
+
                 p[1:N + 1, 0] = xslice
                 p[1:N + 1, 1] = y1slice
                 p[N + 2:, 0] = xslice[::-1]
                 p[N + 2:, 1] = y2slice[::-1]
-        
+
                 polys.append(p)
             polycol.extend(polys)
         from matplotlib.collections import PolyCollection

GPy/plotting/matplot_dep/ssgplvm.py

@@ -13,16 +13,16 @@ class SSGPLVM_plot(object):
         self.model = model
         self.imgsize= imgsize
         assert model.Y.shape[1] == imgsize[0]*imgsize[1]
-        
+
     def plot_inducing(self):
         fig1 = pylab.figure()
         mean = self.model.posterior.mean
         arr = mean.reshape(*(mean.shape[0],self.imgsize[1],self.imgsize[0]))
         plot_2D_images(fig1, arr)
         fig1.gca().set_title('The mean of inducing points')
-        
+
         fig2 = pylab.figure()
         covar = self.model.posterior.covariance
         plot_2D_images(fig2, covar)
         fig2.gca().set_title('The variance of inducing points')
-        
+

GPy/plotting/plotly_dep/defaults.py

@@ -72,5 +72,5 @@ ard = dict(linewidth=1.2, barmode='stack')
 latent = dict(colorscale='Greys', reversescale=True, zsmooth='best')
 gradient = dict(colorscale='RdBu', opacity=.7)
 magnification = dict(colorscale='Greys', zsmooth='best', reversescale=True)
-latent_scatter = dict(marker_kwargs=dict(size='15', opacity=.7))
+latent_scatter = dict(marker_kwargs=dict(size='5', opacity=.7))
 # annotation = dict(fontdict=dict(family='sans-serif', weight='light', fontsize=9), zorder=.3, alpha=.7)

GPy/plotting/plotly_dep/plot_definitions.py

@@ -130,14 +130,15 @@ class PlotlyPlots(AbstractPlottingLibrary):
         except:
             #not matplotlib marker
             pass
+        marker_kwargs = marker_kwargs or {}
         marker_kwargs.setdefault('symbol', marker)
         if Z is not None:
-            return Scatter3d(x=X, y=Y, z=Z, mode='markers', 
+            return Scatter3d(x=X, y=Y, z=Z, mode='markers',
-                             showlegend=label is not None, 
+                             showlegend=label is not None,
-                             marker=Marker(color=color, colorscale=cmap, **marker_kwargs or {}), 
+                             marker=Marker(color=color, colorscale=cmap, **marker_kwargs),
                              name=label, **kwargs)
-        return Scatter(x=X, y=Y, mode='markers', showlegend=label is not None, 
+        return Scatter(x=X, y=Y, mode='markers', showlegend=label is not None,
-                       marker=Marker(color=color, colorscale=cmap, **marker_kwargs or {}), 
+                       marker=Marker(color=color, colorscale=cmap, **marker_kwargs or {}),
                        name=label, **kwargs)
 
     def plot(self, ax, X, Y, Z=None, color=None, label=None, line_kwargs=None, **kwargs):
@@ -169,10 +170,10 @@ class PlotlyPlots(AbstractPlottingLibrary):
         elif X.shape[1] == 2:
             marker_kwargs.setdefault('symbol', 'diamond')
             opacity = kwargs.pop('opacity', .8)
-            return Scatter3d(x=X[:, 0], y=X[:, 1], z=np.zeros(X.shape[0]), 
+            return Scatter3d(x=X[:, 0], y=X[:, 1], z=np.zeros(X.shape[0]),
                              mode='markers',
-                             projection=dict(z=dict(show=True, opacity=opacity)), 
+                             projection=dict(z=dict(show=True, opacity=opacity)),
-                             marker=Marker(color=color, **marker_kwargs or {}), 
+                             marker=Marker(color=color, **marker_kwargs or {}),
                              opacity=0,
                              name=label,
                              showlegend=label is not None, **kwargs)
@@ -284,11 +285,11 @@ class PlotlyPlots(AbstractPlottingLibrary):
         if color.startswith('#'):
             colarray = Tango.hex2rgb(color)
             opacity = .9
-        else: 
+        else:
             colarray = map(float(color.strip(')').split('(')[1]))
             if len(colarray) == 4:
                 colarray, opacity = colarray[:3] ,colarray[3]
-        
+
         alpha = opacity*(1.-np.abs(np.linspace(-1,1,len(percentiles)-1)))
 
         def pairwise(iterable):
@@ -302,11 +303,11 @@ class PlotlyPlots(AbstractPlottingLibrary):
         for i, y1, a in zip(range(len(percentiles)), percentiles, alpha):
             fcolor = 'rgba({}, {}, {}, {alpha})'.format(*colarray, alpha=a)
             if i ==  len(percentiles)/2:
-                polycol.append(Scatter(x=X, y=y1, fillcolor=fcolor, showlegend=True, 
+                polycol.append(Scatter(x=X, y=y1, fillcolor=fcolor, showlegend=True,
-                                       name=label, line=Line(width=0, smoothing=0), mode='none', fill='tonextx', 
+                                       name=label, line=Line(width=0, smoothing=0), mode='none', fill='tonextx',
                                        legendgroup='density', hoverinfo='none', **kwargs))
             else:
-                polycol.append(Scatter(x=X, y=y1, fillcolor=fcolor, showlegend=False, 
+                polycol.append(Scatter(x=X, y=y1, fillcolor=fcolor, showlegend=False,
-                                       name=None, line=Line(width=1, smoothing=0, color=fcolor), mode='none', fill='tonextx', 
+                                       name=None, line=Line(width=1, smoothing=0, color=fcolor), mode='none', fill='tonextx',
                                        legendgroup='density', hoverinfo='none', **kwargs))
         return polycol

GPy/testing/__init__.py

@@ -1,14 +1,9 @@
-# Copyright (c) 2014, Max Zwiessele
+# Copyright (c) 2014, Max Zwiessele, GPy Authors
 # Licensed under the BSD 3-clause license (see LICENSE.txt)
-"""
-
-MaxZ
-
-"""
 import unittest
 import sys
 
 def deepTest(reason):
     if reason:
         return lambda x:x
-    return unittest.skip("Not deep scanning, enable deepscan by adding 'deep' argument")
+    return unittest.skip("Not deep scanning, enable deepscan by adding 'deep' argument to unittest call")

GPy/testing/inference_tests.py

@@ -51,5 +51,20 @@ class InferenceXTestCase(unittest.TestCase):
         np.testing.assert_array_almost_equal(m.X, mi.X, decimal=2)
 
 
+class HMCSamplerTest(unittest.TestCase):
+
+    def test_sampling(self):
+        np.random.seed(1)
+        x = np.linspace(0.,2*np.pi,100)[:,None]
+        y = -np.cos(x)+np.random.randn(*x.shape)*0.3+1
+
+        m = GPy.models.GPRegression(x,y)
+        m.kern.lengthscale.set_prior(GPy.priors.Gamma.from_EV(1.,10.))
+        m.kern.variance.set_prior(GPy.priors.Gamma.from_EV(1.,10.))
+        m.likelihood.variance.set_prior(GPy.priors.Gamma.from_EV(1.,10.))
+
+        hmc = GPy.inference.mcmc.HMC(m,stepsize=1e-2)
+        s = hmc.sample(num_samples=3)
+
 if __name__ == "__main__":
     unittest.main()

GPy/testing/kernel_tests.py

@@ -31,9 +31,9 @@ class Kern_check_model(GPy.core.Model):
             X = np.random.randn(20, kernel.input_dim)
         if dL_dK is None:
             if X2 is None:
-                dL_dK = np.ones((X.shape[0], X.shape[0]))
+                dL_dK = np.random.rand(X.shape[0], X.shape[0])
             else:
-                dL_dK = np.ones((X.shape[0], X2.shape[0]))
+                dL_dK = np.random.rand(X.shape[0], X2.shape[0])
 
         self.kernel = kernel
         self.X = X
@@ -310,7 +310,7 @@ class KernelGradientTestsContinuous(unittest.TestCase):
         self.assertTrue(check_kernel_gradient_functions(k, X=self.X, X2=self.X2, verbose=verbose))
 
     def test_RBF(self):
-        k = GPy.kern.RBF(self.D)
+        k = GPy.kern.RBF(self.D, ARD=True)
         k.randomize()
         self.assertTrue(check_kernel_gradient_functions(k, X=self.X, X2=self.X2, verbose=verbose))
 
@@ -324,6 +324,11 @@ class KernelGradientTestsContinuous(unittest.TestCase):
         k.randomize()
         self.assertTrue(check_kernel_gradient_functions(k, X=self.X, X2=self.X2, verbose=verbose))
 
+    def test_Poly(self):
+        k = GPy.kern.Poly(self.D, order=5)
+        k.randomize()
+        self.assertTrue(check_kernel_gradient_functions(k, X=self.X, X2=self.X2, verbose=verbose))
+
     def test_standard_periodic(self):
         k = GPy.kern.StdPeriodic(self.D, self.D-1)
         k.randomize()
@@ -366,6 +371,7 @@ class KernelTestsNonContinuous(unittest.TestCase):
         self.X2[:(N0*2), -1] = 0
         self.X2[(N0*2):, -1] = 1
 
+    @unittest.expectedFailure
     def test_IndependentOutputs(self):
         k = GPy.kern.RBF(self.D, active_dims=range(self.D))
         kern = GPy.kern.IndependentOutputs(k, -1, 'ind_single')
@@ -374,6 +380,7 @@ class KernelTestsNonContinuous(unittest.TestCase):
         kern = GPy.kern.IndependentOutputs(k, -1, name='ind_split')
         self.assertTrue(check_kernel_gradient_functions(kern, X=self.X, X2=self.X2, verbose=verbose, fixed_X_dims=-1))
 
+    @unittest.expectedFailure
     def test_Hierarchical(self):
         k = [GPy.kern.RBF(2, active_dims=[0,2], name='rbf1'), GPy.kern.RBF(2, active_dims=[0,2], name='rbf2')]
         kern = GPy.kern.IndependentOutputs(k, -1, name='ind_split')
@@ -467,7 +474,7 @@ class Kernel_Psi_statistics_GradientTests(unittest.TestCase):
         self.w1 = np.random.randn(N)
         self.w2 = np.random.randn(N,M)
         self.w3 = np.random.randn(M,M)
-        self.w3 = self.w3+self.w3.T
+        self.w3 = self.w3#+self.w3.T
         self.w3n = np.random.randn(N,M,M)
         self.w3n = self.w3n+np.swapaxes(self.w3n, 1,2)
 
@@ -475,7 +482,7 @@ class Kernel_Psi_statistics_GradientTests(unittest.TestCase):
         from GPy.kern import RBF,Linear,MLP,Bias,White
         Q = self.Z.shape[1]
         kernels = [RBF(Q,ARD=True), Linear(Q,ARD=True),MLP(Q,ARD=True), RBF(Q,ARD=True)+Linear(Q,ARD=True)+Bias(Q)+White(Q)
-                   ,RBF(Q,ARD=True)+Bias(Q)+White(Q),  Linear(Q,ARD=True)+Bias(Q)+White(Q)]
+                  ,RBF(Q,ARD=True)+Bias(Q)+White(Q),  Linear(Q,ARD=True)+Bias(Q)+White(Q)]
 
         for k in kernels:
             k.randomize()

GPy/testing/plotting_tests.py

@@ -27,21 +27,29 @@
 # OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #===============================================================================
+
+
+#===============================================================================
+# SKIPPING PLOTTING BECAUSE IT BEHAVES DIFFERENTLY ON DIFFERENT
+# SYSTEMS, AND WILL MISBEHAVE
+from nose import SkipTest
+raise SkipTest("Skipping Matplotlib testing")
+#===============================================================================
+
 import matplotlib
 from unittest.case import TestCase
 matplotlib.use('agg')
 
 import numpy as np
 import GPy, os
-from nose import SkipTest
 
-from ..util.config import config
+from GPy.util.config import config
-from ..plotting import change_plotting_library, plotting_library
+from GPy.plotting import change_plotting_library, plotting_library
 
 class ConfigTest(TestCase):
     def tearDown(self):
         change_plotting_library('matplotlib')
-        
+
     def test_change_plotting(self):
         self.assertRaises(ValueError, change_plotting_library, 'not+in9names')
         change_plotting_library('none')
@@ -69,8 +77,8 @@ def _image_directories():
     #module_name = __init__.__module__
     #mods = module_name.split('.')
     #basedir = os.path.join(*mods)
-    result_dir = os.path.join(basedir, 'testresult')
+    result_dir = os.path.join(basedir, 'testresult','.')
-    baseline_dir = os.path.join(basedir, 'baseline')
+    baseline_dir = os.path.join(basedir, 'baseline','.')
     if not os.path.exists(result_dir):
         cbook.mkdirs(result_dir)
     return baseline_dir, result_dir
@@ -115,12 +123,12 @@ def test_figure():
     import warnings
     with warnings.catch_warnings():
         warnings.simplefilter("ignore")
-    
+
         ax, _ = pl().new_canvas(num=1)
         def test_func(x):
             return x[:, 0].reshape(3,3)
         pl().imshow_interact(ax, test_func, extent=(-1,1,-1,1), resolution=3)
-    
+
         ax, _ = pl().new_canvas()
         def test_func_2(x):
             y = x[:, 0].reshape(3,3)
@@ -129,21 +137,21 @@ def test_figure():
 
         pl().annotation_heatmap_interact(ax, test_func_2, extent=(-1,1,-1,1), resolution=3)
         pl().annotation_heatmap_interact(ax, test_func_2, extent=(-1,1,-1,1), resolution=3, imshow_kwargs=dict(interpolation='nearest'))
-    
+
         ax, _ = pl().new_canvas(figsize=(4,3))
         x = np.linspace(0,1,100)
         y = [0,1,2]
         array = np.array([.4,.5])
         cmap = matplotlib.colors.LinearSegmentedColormap.from_list('WhToColor', ('r', 'b'), N=array.size)
 
-        pl().fill_gradient(ax, x, y, facecolors=['r', 'g'], array=array, cmap=cmap)    
+        pl().fill_gradient(ax, x, y, facecolors=['r', 'g'], array=array, cmap=cmap)
-    
+
         ax, _ = pl().new_canvas(num=4, figsize=(4,3), projection='3d', xlabel='x', ylabel='y', zlabel='z', title='awsome title', xlim=(-1,1), ylim=(-1,1), zlim=(-3,3))
         z = 2-np.abs(np.linspace(-2,2,(100)))+1
         x, y = z*np.sin(np.linspace(-2*np.pi,2*np.pi,(100))), z*np.cos(np.linspace(-np.pi,np.pi,(100)))
-        
+
         pl().plot(ax, x, y, z, linewidth=2)
-    
+
         for do_test in _image_comparison(
                 baseline_images=['coverage_{}'.format(sub) for sub in ["imshow_interact",'annotation_interact','gradient','3d_plot',]],
                 extensions=extensions):
@@ -194,9 +202,9 @@ def test_plot():
         m.plot_errorbars_trainset()
         m.plot_samples()
         m.plot_data_error()
-    for do_test in _image_comparison(baseline_images=['gp_{}'.format(sub) for sub in ["data", "mean", 'conf', 
+    for do_test in _image_comparison(baseline_images=['gp_{}'.format(sub) for sub in ["data", "mean", 'conf',
-                                                                                      'density', 
+                                                                                      'density',
-                                                                                      'out_error', 
+                                                                                      'out_error',
                                                                                       'samples', 'in_error']], extensions=extensions):
         yield (do_test, )
 
@@ -216,9 +224,9 @@ def test_twod():
     m.plot_inducing()
     #m.plot_errorbars_trainset()
     m.plot_data_error()
-    for do_test in _image_comparison(baseline_images=['gp_2d_{}'.format(sub) for sub in ["data", "mean", 
+    for do_test in _image_comparison(baseline_images=['gp_2d_{}'.format(sub) for sub in ["data", "mean",
-                                                                                         'inducing', 
+                                                                                         'inducing',
-                                                                                         #'out_error', 
+                                                                                         #'out_error',
                                                                                          'in_error',
                                                                                          ]], extensions=extensions):
         yield (do_test, )
@@ -242,7 +250,7 @@ def test_threed():
     m.plot_mean(projection='3d')
     m.plot_inducing(projection='3d')
     #m.plot_errorbars_trainset(projection='3d')
-    for do_test in _image_comparison(baseline_images=['gp_3d_{}'.format(sub) for sub in ["data", "mean", 'inducing', 
+    for do_test in _image_comparison(baseline_images=['gp_3d_{}'.format(sub) for sub in ["data", "mean", 'inducing',
                                                                                          #'error',
                                                                                           #"samples", "samples_lik"
                                                                                           ]], extensions=extensions):
@@ -316,7 +324,7 @@ def test_gplvm():
     matplotlib.rcParams[u'figure.figsize'] = (4,3)
     matplotlib.rcParams[u'text.usetex'] = False
     Q = 3
-    # Define dataset 
+    # Define dataset
     N = 10
     k1 = GPy.kern.RBF(5, variance=1, lengthscale=1./np.random.dirichlet(np.r_[10,10,10,0.1,0.1]), ARD=True)
     k2 = GPy.kern.RBF(5, variance=1, lengthscale=1./np.random.dirichlet(np.r_[10,0.1,10,0.1,10]), ARD=True)
@@ -325,10 +333,10 @@ def test_gplvm():
     A = np.random.multivariate_normal(np.zeros(N), k1.K(X), Q).T
     B = np.random.multivariate_normal(np.zeros(N), k2.K(X), Q).T
     C = np.random.multivariate_normal(np.zeros(N), k3.K(X), Q).T
-    
+
     Y = np.vstack((A,B,C))
     labels = np.hstack((np.zeros(A.shape[0]), np.ones(B.shape[0]), np.ones(C.shape[0])*2))
-    
+
     k = RBF(Q, ARD=True, lengthscale=2)  # + kern.white(Q, _np.exp(-2)) # + kern.bias(Q)
     m = GPLVM(Y, Q, init="PCA", kernel=k)
     m.kern.lengthscale[:] = [1./.3, 1./.1, 1./.7]
@@ -341,7 +349,7 @@ def test_gplvm():
     np.random.seed(111)
     m.plot_magnification(labels=labels)
     m.plot_steepest_gradient_map(resolution=10, data_labels=labels)
-    for do_test in _image_comparison(baseline_images=['gplvm_{}'.format(sub) for sub in ["latent", "latent_3d", "magnification", 'gradient']], 
+    for do_test in _image_comparison(baseline_images=['gplvm_{}'.format(sub) for sub in ["latent", "latent_3d", "magnification", 'gradient']],
                                      extensions=extensions,
                                      tol=12):
         yield (do_test, )
@@ -355,7 +363,7 @@ def test_bayesian_gplvm():
     matplotlib.rcParams[u'figure.figsize'] = (4,3)
     matplotlib.rcParams[u'text.usetex'] = False
     Q = 3
-    # Define dataset 
+    # Define dataset
     N = 10
     k1 = GPy.kern.RBF(5, variance=1, lengthscale=1./np.random.dirichlet(np.r_[10,10,10,0.1,0.1]), ARD=True)
     k2 = GPy.kern.RBF(5, variance=1, lengthscale=1./np.random.dirichlet(np.r_[10,0.1,10,0.1,10]), ARD=True)
@@ -364,10 +372,10 @@ def test_bayesian_gplvm():
     A = np.random.multivariate_normal(np.zeros(N), k1.K(X), Q).T
     B = np.random.multivariate_normal(np.zeros(N), k2.K(X), Q).T
     C = np.random.multivariate_normal(np.zeros(N), k3.K(X), Q).T
-    
+
     Y = np.vstack((A,B,C))
     labels = np.hstack((np.zeros(A.shape[0]), np.ones(B.shape[0]), np.ones(C.shape[0])*2))
-    
+
     k = RBF(Q, ARD=True, lengthscale=2)  # + kern.white(Q, _np.exp(-2)) # + kern.bias(Q)
     m = BayesianGPLVM(Y, Q, init="PCA", kernel=k)
     m.kern.lengthscale[:] = [1./.3, 1./.1, 1./.7]

GPy/util/mocap.py

@@ -304,6 +304,11 @@ class acclaim_skeleton(skeleton):
         channels = self.read_channels(fid)
         fid.close()
         return channels
+    
+    def save_channels(self, file_name, channels):
+        with open(file_name,'w') as fid:
+            self.writ_channels(fid, channels)
+            fid.close()
 
     def load_skel(self, file_name):
 
@@ -469,6 +474,18 @@ class acclaim_skeleton(skeleton):
         self.smooth_angle_channels(channels)
         return channels
 
+    def writ_channels(self, fid, channels):
+        fid.write('#!OML:ASF \n')
+        fid.write(':FULLY-SPECIFIED\n')
+        fid.write(':DEGREES\n')
+        num_frames = channels.shape[0]
+        for i_frame in range(num_frames):
+            fid.write(str(i_frame+1)+'\n')
+            offset = 0
+            for vertex in self.vertices:
+                fid.write(vertex.name+' '+ ' '.join([str(v) for v in channels[i_frame,offset:offset+len(vertex.meta['channels'])]])+'\n')
+                offset += len(vertex.meta['channels'])
+        
 
     def read_documentation(self, fid):
         """Read documentation from an acclaim skeleton file stream."""

GPy/util/parallel.py

@@ -29,14 +29,14 @@ def divide_data(datanum, rank, size):
         offset = size*rank+residue
     return offset, offset+size, datanum_list
 
-def optimize_parallel(model, optimizer=None, messages=True, max_iters=1000, outpath='.', interval=100, name=None):
+def optimize_parallel(model, optimizer=None, messages=True, max_iters=1000, outpath='.', interval=100, name=None, **kwargs):
     from math import ceil
     from datetime import datetime
     import os
     if name is None: name = model.name
     stop = 0
     for iter in range(int(ceil(float(max_iters)/interval))):
-        model.optimize(optimizer=optimizer, messages= True if messages and model.mpi_comm.rank==model.mpi_root else False, max_iters=interval)
+        model.optimize(optimizer=optimizer, messages= True if messages and model.mpi_comm.rank==model.mpi_root else False, max_iters=interval, **kwargs)
         if model.mpi_comm.rank==model.mpi_root:
             timenow = datetime.now()
             timestr = timenow.strftime('%Y:%m:%d_%H:%M:%S')

doc/source/conf.py

@@ -24,6 +24,32 @@ import shlex
 sys.path.insert(0, os.path.abspath('../../'))
 sys.path.insert(0, os.path.abspath('../../GPy/'))
 
+on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
+
+#on_rtd = True
+if on_rtd:
+    # sys.path.append(os.path.abspath('../GPy'))
+
+    import subprocess
+
+    proc = subprocess.Popen("pwd", stdout=subprocess.PIPE, shell=True)
+    (out, err) = proc.communicate()
+    print "program output:", out
+    proc = subprocess.Popen("ls ../../", stdout=subprocess.PIPE, shell=True)
+    (out, err) = proc.communicate()
+    print "program output:", out
+    #Lets regenerate our rst files from the source, -P adds private modules (i.e kern._src)
+    proc = subprocess.Popen("sphinx-apidoc -P -f -o . ../../GPy", stdout=subprocess.PIPE, shell=True)
+    (out, err) = proc.communicate()
+    print "program output:", out
+    #proc = subprocess.Popen("whereis numpy", stdout=subprocess.PIPE, shell=True)
+    #(out, err) = proc.communicate()
+    #print "program output:", out
+    #proc = subprocess.Popen("whereis matplotlib", stdout=subprocess.PIPE, shell=True)
+    #(out, err) = proc.communicate()
+    #print "program output:", out
+
+
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -51,10 +77,10 @@ extensions = [
 #    def __getattr__(cls, name):
 #            return Mock()
 #
-MOCK_MODULES = ['scipy.linalg.blas', 'blas', 'scipy.optimize', 'scipy.optimize.linesearch', 'scipy.linalg', 
+MOCK_MODULES = ['scipy.linalg.blas', 'blas', 'scipy.optimize', 'scipy.optimize.linesearch', 'scipy.linalg',
                 'scipy', 'scipy.special', 'scipy.integrate', 'scipy.io', 'scipy.stats',
-                'sympy', 'sympy.utilities.iterables', 'sympy.utilities.lambdify', 
+                'sympy', 'sympy.utilities.iterables', 'sympy.utilities.lambdify',
-                'sympy.utilities', 'sympy.utilities.codegen', 'sympy.core.cache', 
+                'sympy.utilities', 'sympy.utilities.codegen', 'sympy.core.cache',
                 'sympy.core', 'sympy.parsing', 'sympy.parsing.sympy_parser',
                 'nose', 'nose.tools']
 
@@ -94,7 +120,7 @@ master_doc = 'index'
 # General information about the project.
 project = u'GPy'
 #author = u'`Humans <https://github.com/SheffieldML/GPy/graphs/contributors>`_'
-author = 'GPy Authors, see https://github.com/SheffieldML/GPy/graphs/contributors' 
+author = 'GPy Authors, see https://github.com/SheffieldML/GPy/graphs/contributors'
 copyright = u'2015, '+author
 
 # The version info for the project you're documenting, acts as replacement for

doc/source/index.rst~

@@ -1,22 +0,0 @@
-.. GPy documentation master file, created by
-   sphinx-quickstart on Fri Sep 18 18:16:28 2015.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome to GPy's documentation!
-===============================
-
-Contents:
-
-.. toctree::
-   :maxdepth: 2
-
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-

doc/source/requirements.txt

@@ -0,0 +1 @@
+paramz

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.9.4
+current_version = 0.9.7
 tag = True
 commit = True