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

GPy/core/parameterization/index_operations.py

@@ -77,6 +77,12 @@ class ParameterIndexOperations(object):
     def iter_properties(self):
         return self._properties.iterkeys()
     
+    def shift(self, start, size):
+        for ind in self.iterindices():
+            toshift = ind>=start
+            if len(toshift) > 0:
+                ind[toshift] += size
+    
     def clear(self):
         self._properties.clear()
     

GPy/core/parameterization/parameterized.py

@@ -154,6 +154,8 @@ class Parameterized(Constrainable, Pickleable, Observable, Gradcheckable):
                 elif param._has_fixes(): self._fixes_ = np.r_[np.ones(self.size, dtype=bool), fixes_param]
 
             else:
+                start = sum(p.size for p in self._parameters_[:index])
+                self.constraints.shift(start, param.size)
                 self._parameters_.insert(index, param)
 
                 # make sure fixes and constraints are indexed right
@@ -165,10 +167,13 @@ class Parameterized(Constrainable, Pickleable, Observable, Gradcheckable):
                     self._fixes_ = np.ones(self.size+param.size, dtype=bool)
                     self._fixes_[ins:ins+param.size] = fixes_param
             self.size += param.size
+        else:
+            raise RuntimeError, """Parameter exists already added and no copy made"""
         self._connect_parameters()
         # make sure the constraints are pulled over:
         if hasattr(param, "_constraints_") and param._constraints_ is not None:
             for t, ind in param._constraints_.iteritems():
+                
                 self.constraints.add(t, ind+self._offset_for(param))
             param._constraints_.clear()
         if param._default_constraint_ is not None:

GPy/core/parameterization/variational.py

@@ -5,6 +5,7 @@ Created on 6 Nov 2013
 '''
 from parameterized import Parameterized
 from param import Param
+from transformations import Logexp
 
 class Normal(Parameterized):
     '''
@@ -15,7 +16,7 @@ class Normal(Parameterized):
     def __init__(self, means, variances, name='latent space'):
         Parameterized.__init__(self, name=name)
         self.means = Param("mean", means)
-        self.variances = Param('variance', variances)
+        self.variances = Param('variance', variances, Logexp())
         self.add_parameters(self.means, self.variances)
 
     def plot(self, *args):