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

GPy/core/gp.py

@@ -309,11 +309,11 @@ class GP(Model):
 
 
 
-    def getstate(self):
+    def _getstate(self):
         """
         Get the current state of the class, here we return everything that is needed to recompute the model.
         """
-        return Model.getstate(self) + [self.X,
+        return Model._getstate(self) + [self.X,
                 self.num_data,
                 self.input_dim,
                 self.kern,
@@ -323,7 +323,7 @@ class GP(Model):
                 self._Xscale,
                 ]
 
-    def setstate(self, state):
+    def _setstate(self, state):
         self._Xscale = state.pop()
         self._Xoffset = state.pop()
         self.output_dim = state.pop()
@@ -332,6 +332,6 @@ class GP(Model):
         self.input_dim = state.pop()
         self.num_data = state.pop()
         self.X = state.pop()
-        Model.setstate(self, state)
+        Model._setstate(self, state)
 
 

GPy/core/model.py

@@ -40,7 +40,7 @@ class Model(Parameterized):
         return g
         raise NotImplementedError, "this needs to be implemented to use the model class"
 
-    def getstate(self):
+    def _getstate(self):
         """
         Get the current state of the class.
         Inherited from Parameterized, so add those parameters to the state
@@ -48,24 +48,24 @@ class Model(Parameterized):
         :return: list of states from the model.
 
         """
-        return Parameterized.getstate(self) + \
+        return Parameterized._getstate(self) + \
             [self.priors, self.optimization_runs,
              self.sampling_runs, self.preferred_optimizer]
 
-    def setstate(self, state):
+    def _setstate(self, state):
         """
-        set state from previous call to getstate
+        set state from previous call to _getstate
         call Parameterized with the rest of the state
 
         :param state: the state of the model.
-        :type state: list as returned from getstate.
+        :type state: list as returned from _getstate.
 
         """
         self.preferred_optimizer = state.pop()
         self.sampling_runs = state.pop()
         self.optimization_runs = state.pop()
         self.priors = state.pop()
-        Parameterized.setstate(self, state)
+        Parameterized._setstate(self, state)
 
     def set_prior(self, regexp, what):
         """

GPy/core/parameterization/param.py

@@ -403,7 +403,7 @@ class Param(ObservableArray, Constrainable):
                             x=self.name_hirarchical)
         return name + super(Param, self).__repr__(*args,**kwargs)
     def _ties_for(self, rav_index):
-        size = sum(p.size for p in self._tied_to_)
+        #size = sum(p.size for p in self._tied_to_)
         ties = numpy.empty(shape=(len(self._tied_to_), numpy.size(rav_index)), dtype=Param)
         for i, tied_to in enumerate(self._tied_to_):
             for t, ind in tied_to._tied_to_me_.iteritems():

GPy/core/parameterization/parameter_core.py

@@ -21,7 +21,7 @@ class Observable(object):
         [callble(self) for callble in self._observers_.itervalues()]
         
 class Pickleable(object):
-    def getstate(self):
+    def _getstate(self):
         """
         Returns the state of this class in a memento pattern.
         The state must be a list-like structure of all the fields
@@ -30,13 +30,13 @@ class Pickleable(object):
         See python doc "pickling" (`__getstate__` and `__setstate__`) for details.
         """
         raise NotImplementedError, "To be able to use pickling you need to implement this method"
-    def setstate(self, state):
+    def _setstate(self, state):
         """
         Set the state (memento pattern) of this class to the given state.
-        Usually this is just the counterpart to getstate, such that
+        Usually this is just the counterpart to _getstate, such that
         an object is a copy of another when calling
     
-            copy = <classname>.__new__(*args,**kw).setstate(<to_be_copied>.getstate())
+            copy = <classname>.__new__(*args,**kw)._setstate(<to_be_copied>._getstate())
             
         See python doc "pickling" (`__getstate__` and `__setstate__`) for details.
         """
@@ -54,7 +54,7 @@ class Parentable(object):
         self._highest_parent_ = highest_parent
         
     def has_parent(self):
-        return self._direct_parent_ is not None
+        return self._direct_parent_ is not None and self._highest_parent_ is not None
     
 class Nameable(Parentable):
     _name = None
@@ -96,6 +96,7 @@ class Constrainable(Nameable):
                 self._add_constrain(p, transform, warning)
             if update:
                 self.parameters_changed()
+                
     def constrain_positive(self, warning=True):
         """
         :param warning: print a warning if re-constraining parameters.

GPy/core/parameterization/parameterized.py

@@ -218,7 +218,7 @@ class Parameterized(Constrainable, Pickleable, Observable):
             p._direct_parent_ = self
             p._parent_index_ = i
             i += 1
-            for pi in p.flattened_parameters:
+            for pi in p._parameters_:
                 pi._highest_parent_ = self
             not_unique = []
             sizes.append(p.size+sizes[-1])
@@ -233,6 +233,7 @@ class Parameterized(Constrainable, Pickleable, Observable):
             elif not (pname in not_unique):
                 self.__dict__[pname] = p
                 self._added_names_.add(pname)
+            
     #===========================================================================
     # Pickling operations
     #===========================================================================
@@ -253,24 +254,24 @@ class Parameterized(Constrainable, Pickleable, Observable):
         return copy.deepcopy(self)
     def __getstate__(self):
         if self._has_get_set_state():
-            return self.getstate()
+            return self._getstate()
         return self.__dict__
     def __setstate__(self, state):
         if self._has_get_set_state():
-            self.setstate(state) # set state
+            self._setstate(state) # set state
             #self._set_params(self._get_params()) # restore all values
             return
         self.__dict__ = state
     def _has_get_set_state(self):
-        return 'getstate' in vars(self.__class__) and 'setstate' in vars(self.__class__)
+        return '_getstate' in vars(self.__class__) and '_setstate' in vars(self.__class__)
-    def getstate(self):
+    def _getstate(self):
         """
         Get the current state of the class,
         here just all the indices, rest can get recomputed
         For inheriting from Parameterized:
 
         Allways append the state of the inherited object
-        and call down to the inherited object in setstate!!
+        and call down to the inherited object in _setstate!!
         """
         return [
                 self._fixes_,
@@ -280,7 +281,7 @@ class Parameterized(Constrainable, Pickleable, Observable):
                 self._added_names_,
                 ]
 
-    def setstate(self, state):
+    def _setstate(self, state):
         self._added_names_ = state.pop()
         self._name = state.pop()
         self._parameters_ = state.pop()

GPy/core/sparse_gp.py

@@ -183,20 +183,20 @@ class SparseGP(GP):
         else:
             raise NotImplementedError, "Cannot define a frame with more than two input dimensions"
 
-    def getstate(self):
+    def _getstate(self):
         """
         Get the current state of the class,
         here just all the indices, rest can get recomputed
         """
-        return GP.getstate(self) + [self.Z,
+        return GP._getstate(self) + [self.Z,
                 self.num_inducing,
                 self.has_uncertain_inputs,
                 self.X_variance]
 
-    def setstate(self, state):
+    def _setstate(self, state):
         self.X_variance = state.pop()
         self.has_uncertain_inputs = state.pop()
         self.num_inducing = state.pop()
         self.Z = state.pop()
-        GP.setstate(self, state)
+        GP._setstate(self, state)
 

GPy/core/svigp.py

@@ -90,9 +90,9 @@ class SVIGP(GP):
         self._param_steplength_trace = []
         self._vb_steplength_trace = []
 
-    def getstate(self):
+    def _getstate(self):
         steplength_params = [self.hbar_t, self.tau_t, self.gbar_t, self.gbar_t1, self.gbar_t2, self.hbar_tp, self.tau_tp, self.gbar_tp, self.adapt_param_steplength, self.adapt_vb_steplength, self.vb_steplength, self.param_steplength]
-        return GP.getstate(self) + \
+        return GP._getstate(self) + \
             [self.get_vb_param(),
              self.Z,
              self.num_inducing,
@@ -116,7 +116,7 @@ class SVIGP(GP):
              self.iterations
             ]
 
-    def setstate(self, state):
+    def _setstate(self, state):
         self.iterations = state.pop()
         self._permutation = state.pop()
         self.Y = state.pop()
@@ -139,7 +139,7 @@ class SVIGP(GP):
         self.num_inducing = state.pop()
         self.Z = state.pop()
         vb_param = state.pop()
-        GP.setstate(self, state)
+        GP._setstate(self, state)
         self.set_vb_param(vb_param)
 
     def _compute_kernel_matrices(self):

GPy/kern/kern.py

@@ -50,25 +50,25 @@ class kern(Parameterized):
     def connect_input(self, Xparam):
         [p.connect_input(Xparam) for p in self._parameters_]
 
-    def getstate(self):
+    def _getstate(self):
         """
         Get the current state of the class,
         here just all the indices, rest can get recomputed
         """
-        return Parameterized.getstate(self) + [#self._parameters_,
+        return Parameterized._getstate(self) + [#self._parameters_,
                 #self.num_params,
                 self.input_dim,
                 self.input_slices,
                 self._param_slices_
                 ]
 
-    def setstate(self, state):
+    def _setstate(self, state):
         self._param_slices_ = state.pop()
         self.input_slices = state.pop()
         self.input_dim = state.pop()
         #self.num_params = state.pop()
         #self._parameters_ = state.pop()
-        Parameterized.setstate(self, state)
+        Parameterized._setstate(self, state)
 
 
     def plot_ARD(self, fignum=None, ax=None, title='', legend=False):

GPy/models/bayesian_gplvm.py

@@ -51,17 +51,17 @@ class BayesianGPLVM(SparseGP, GPLVM):
         self.add_parameter(self.q, gradient=self._dbound_dmuS, index=0)
         self.ensure_default_constraints()
 
-    def getstate(self):
+    def _getstate(self):
         """
         Get the current state of the class,
         here just all the indices, rest can get recomputed
         """
-        return SparseGP.getstate(self) + [self.init]
+        return SparseGP._getstate(self) + [self.init]
 
-    def setstate(self, state):
+    def _setstate(self, state):
         self._const_jitter = None
         self.init = state.pop()
-        SparseGP.setstate(self, state)
+        SparseGP._setstate(self, state)
 
 #     def _get_param_names(self):
 #         X_names = sum([['X_%i_%i' % (n, q) for q in range(self.input_dim)] for n in range(self.num_data)], [])

GPy/models/gp_regression.py

@@ -29,8 +29,8 @@ class GPRegression(GP):
 
         super(GPRegression, self).__init__(X, Y, kernel, likelihood, name='GP regression')
 
-    def getstate(self):
+    def _getstate(self):
-        return GP.getstate(self)
+        return GP._getstate(self)
 
-    def setstate(self, state):
+    def _setstate(self, state):
-        return GP.setstate(self, state)
+        return GP._setstate(self, state)

GPy/models/gplvm.py

@@ -41,11 +41,11 @@ class GPLVM(GP):
             Xr[:PC.shape[0], :PC.shape[1]] = PC
         return Xr
 
-    def getstate(self):
+    def _getstate(self):
-        return GP.getstate(self)
+        return GP._getstate(self)
 
-    def setstate(self, state):
+    def _setstate(self, state):
-        GP.setstate(self, state)
+        GP._setstate(self, state)
 
 #     def _get_param_names(self):
 #         return sum([['X_%i_%i' % (n, q) for q in range(self.input_dim)] for n in range(self.num_data)], []) + GP._get_param_names(self)

GPy/models/mrd.py

@@ -79,8 +79,8 @@ class MRD(Model):
         Model.__init__(self)
         self.ensure_default_constraints()
 
-    def getstate(self):
+    def _getstate(self):
-        return Model.getstate(self) + [self.names,
+        return Model._getstate(self) + [self.names,
                 self.bgplvms,
                 self.gref,
                 self.nparams,
@@ -90,7 +90,7 @@ class MRD(Model):
                 self.NQ,
                 self.MQ]
 
-    def setstate(self, state):
+    def _setstate(self, state):
         self.MQ = state.pop()
         self.NQ = state.pop()
         self.num_data = state.pop()
@@ -100,7 +100,7 @@ class MRD(Model):
         self.gref = state.pop()
         self.bgplvms = state.pop()
         self.names = state.pop()
-        Model.setstate(self, state)
+        Model._setstate(self, state)
 
     @property
     def X(self):

GPy/models/sparse_gp_classification.py

@@ -46,11 +46,11 @@ class SparseGPClassification(SparseGP):
         SparseGP.__init__(self, X, likelihood, kernel, Z=Z, normalize_X=normalize_X)
         self.ensure_default_constraints()
 
-    def getstate(self):
+    def _getstate(self):
-        return SparseGP.getstate(self)
+        return SparseGP._getstate(self)
 
 
-    def setstate(self, state):
+    def _setstate(self, state):
-        return SparseGP.setstate(self, state)
+        return SparseGP._setstate(self, state)
 
     pass

GPy/models/sparse_gp_regression.py

@@ -49,11 +49,11 @@ class SparseGPRegression(SparseGP):
         self.ensure_default_constraints()
         pass
 
-    def getstate(self):
+    def _getstate(self):
-        return SparseGP.getstate(self)
+        return SparseGP._getstate(self)
 
 
-    def setstate(self, state):
+    def _setstate(self, state):
-        return SparseGP.setstate(self, state)
+        return SparseGP._setstate(self, state)
 
     pass

GPy/models/sparse_gplvm.py

@@ -28,12 +28,12 @@ class SparseGPLVM(SparseGPRegression, GPLVM):
         SparseGPRegression.__init__(self, X, Y, kernel=kernel, num_inducing=num_inducing)
         self.ensure_default_constraints()
 
-    def getstate(self):
+    def _getstate(self):
-        return SparseGPRegression.getstate(self)
+        return SparseGPRegression._getstate(self)
 
 
-    def setstate(self, state):
+    def _setstate(self, state):
-        return SparseGPRegression.setstate(self, state)
+        return SparseGPRegression._setstate(self, state)
 
 
     def _get_param_names(self):

GPy/models/svigp_regression.py

@@ -43,10 +43,10 @@ class SVIGPRegression(SVIGP):
         SVIGP.__init__(self, X, likelihood, kernel, Z, q_u=q_u, batchsize=batchsize)
         self.load_batch()
 
-    def getstate(self):
+    def _getstate(self):
-        return GPBase.getstate(self)
+        return GPBase._getstate(self)
 
 
-    def setstate(self, state):
+    def _setstate(self, state):
-        return GPBase.setstate(self, state)
+        return GPBase._setstate(self, state)
 

GPy/models/warped_gp.py

@@ -30,12 +30,12 @@ class WarpedGP(GP):
         GP.__init__(self, X, likelihood, kernel, normalize_X=normalize_X)
         self._set_params(self._get_params())
 
-    def getstate(self):
+    def _getstate(self):
-        return GP.getstate(self)
+        return GP._getstate(self)
 
 
-    def setstate(self, state):
+    def _setstate(self, state):
-        return GP.setstate(self, state)
+        return GP._setstate(self, state)
 
 
     def _scale_data(self, Y):