From 9867330861c6b515636c9c732771ed34c3ade677 Mon Sep 17 00:00:00 2001
From: James Hensman <james.hensman@gmail.com>
Date: Wed, 26 Feb 2014 14:30:28 +0000
Subject: [PATCH] moved plot functionality from add to kern

---
 GPy/kern/_src/add.py           | 10 +---------
 GPy/kern/_src/coregionalize.py | 11 -----------
 GPy/kern/_src/kern.py          |  8 ++++++++
 GPy/kern/_src/rbf.py           | 12 ++++++++----
 4 files changed, 17 insertions(+), 24 deletions(-)

diff --git a/GPy/kern/_src/add.py b/GPy/kern/_src/add.py
index 1466800c..77fe057d 100644
--- a/GPy/kern/_src/add.py
+++ b/GPy/kern/_src/add.py
@@ -184,20 +184,12 @@ class Add(Kern):
             target_S += b
         return target_mu, target_S
 
-    def plot(self, *args, **kwargs):
-        """
-        See GPy.plotting.matplot_dep.plot
-        """
-        assert "matplotlib" in sys.modules, "matplotlib package has not been imported."
-        from ..plotting.matplot_dep import kernel_plots
-        kernel_plots.plot(self,*args)
-
     def input_sensitivity(self):
         in_sen = np.zeros((self.num_params, self.input_dim))
         for i, [p, i_s] in enumerate(zip(self._parameters_, self.input_slices)):
             in_sen[i, i_s] = p.input_sensitivity()
         return in_sen
-    
+
     def _getstate(self):
         """
         Get the current state of the class,
diff --git a/GPy/kern/_src/coregionalize.py b/GPy/kern/_src/coregionalize.py
index cafdd5ee..6679eba4 100644
--- a/GPy/kern/_src/coregionalize.py
+++ b/GPy/kern/_src/coregionalize.py
@@ -60,17 +60,6 @@ class Coregionalize(Kern):
     def K(self, X, X2=None):
         index = np.asarray(X, dtype=np.int)
 
-        #here's the old code (numpy)
-        #if index2 is None:
-            #index2 = index
-        #else:
-            #index2 = np.asarray(index2, dtype=np.int)
-        #false_target = target.copy()
-        #ii, jj = np.meshgrid(index, index2)
-        #ii, jj = ii.T, jj.T
-        #false_target += self.B[ii, jj]
-
-
         if X2 is None:
             target = np.empty((X.shape[0], X.shape[0]), dtype=np.float64)
             code="""
diff --git a/GPy/kern/_src/kern.py b/GPy/kern/_src/kern.py
index d7d8f9ca..eb3291e0 100644
--- a/GPy/kern/_src/kern.py
+++ b/GPy/kern/_src/kern.py
@@ -68,6 +68,14 @@ class Kern(Parameterized):
         """
         raise NotImplementedError
 
+    def plot(self, *args, **kwargs):
+        """
+        See GPy.plotting.matplot_dep.plot
+        """
+        assert "matplotlib" in sys.modules, "matplotlib package has not been imported."
+        from ..plotting.matplot_dep import kernel_plots
+        kernel_plots.plot(self,*args)
+
     def plot_ARD(self, *args, **kw):
         """
         See :class:`~GPy.plotting.matplot_dep.kernel_plots`
diff --git a/GPy/kern/_src/rbf.py b/GPy/kern/_src/rbf.py
index 666a79f4..f5bafb48 100644
--- a/GPy/kern/_src/rbf.py
+++ b/GPy/kern/_src/rbf.py
@@ -178,6 +178,11 @@ class RBF(Stationary):
         return denom, dist, dist_sq, psi1
 
 
+    #@cache_this(ignore_args=(1,))
+    def _Z_distances(self, Z):
+        Zhat = 0.5 * (Z[:, None, :] + Z[None, :, :]) # M,M,Q
+        Zdist = 0.5 * (Z[:, None, :] - Z[None, :, :]) # M,M,Q
+        return Zhat, Zdist
 
     #@cache_this TODO
     def _psi2computations(self, Z, vp):
@@ -187,8 +192,7 @@ class RBF(Stationary):
         M = Z.shape[0]
 
         #compute required distances
-        Zhat = 0.5 * (Z[:, None, :] + Z[None, :, :]) # M,M,Q
-        Zdist = 0.5 * (Z[:, None, :] - Z[None, :, :]) # M,M,Q
+        Zhat, Zdist = self._Z_distances(Z)
         Zdist_sq = np.square(Zdist / self.lengthscale) # M,M,Q
 
         #allocate memory for the things we want to compute
@@ -201,7 +205,7 @@ class RBF(Stationary):
         denom = (2.*S[:,None,None,:] / l2) + 1. # N,Q
         half_log_denom = 0.5 * np.log(denom[:,0,0,:])
         denom_l2 = denom[:,0,0,:]*l2
-        
+
         variance_sq = float(np.square(self.variance))
         code = """
         double tmp, exponent_tmp;
@@ -237,7 +241,7 @@ class RBF(Stationary):
             }
         }
         """
-        
+
         support_code = """
         #include <omp.h>
         #include <math.h>