[parameterized] handle updates inside init

GPy/core/parameterization/index_operations.py

@@ -26,39 +26,39 @@ class ParameterIndexOperations(object):
     This object wraps a dictionary, whos keys are _operations_ that we'd like
     to apply to a parameter array, and whose values are np integer arrays which
     index the parameter array appropriately.
-    
+
     A model instance will contain one instance of this class for each thing
     that needs indexing (i.e. constraints, ties and priors). Parameters within
     the model constain instances of the ParameterIndexOperationsView class,
     which can map from a 'local' index (starting 0) to this global index.
-    
+
     Here's an illustration:
-    
+
     #=======================================================================
     model : 0 1 2 3 4 5 6 7 8 9
     key1: 4 5
     key2: 7 8
-    
+
     param1: 0 1 2 3 4 5
     key1: 2 3
     key2: 5
-    
+
     param2: 0 1 2 3 4
     key1: 0
     key2: 2 3
     #=======================================================================
-    
+
     The views of this global index have a subset of the keys in this global
     (model) index.
-    
+
     Adding a new key (e.g. a constraint) to a view will cause the view to pass
     the new key to the global index, along with the local index and an offset.
     This global index then stores the key and the appropriate global index
     (which can be seen by the view).
-    
+
     See also:
     ParameterIndexOperationsView
-    
+
     """
     _offset = 0
     def __init__(self, constraints=None):
@@ -221,8 +221,6 @@ class ParameterIndexOperationsView(object):
 
     def shift_left(self, start, size):
         self._param_index_ops.shift_left(start+self._offset, size)
-        self._offset -= size
-        self._size -= size
 
     def clear(self):
         for i, ind in self.items():

GPy/core/parameterization/parameter_core.py

@@ -18,7 +18,7 @@ import numpy as np
 import re
 import logging
 
-__updated__ = '2014-10-28'
+__updated__ = '2014-11-03'
 
 class HierarchyError(Exception):
     """
@@ -924,7 +924,7 @@ class Parameterizable(OptimizationHandlable):
         !WARNING!: setting the parameter array MUST always be done in memory:
         m.param_array[:] = m_copy.param_array
         """
-        if self.__dict__.get('_param_array_', None) is None:
+        if (self.__dict__.get('_param_array_', None) is None) or (self._param_array_.size != self.size):
             self._param_array_ = np.empty(self.size, dtype=np.float64)
         return self._param_array_
 
@@ -1002,7 +1002,7 @@ class Parameterizable(OptimizationHandlable):
     #=========================================================================
     @property
     def gradient(self):
-        if self.__dict__.get('_gradient_array_', None) is None:
+        if (self.__dict__.get('_gradient_array_', None) is None) or self._gradient_array_.size != self.size:
             self._gradient_array_ = np.empty(self.size, dtype=np.float64)
         return self._gradient_array_
 

GPy/core/parameterization/parameterized.py

@@ -9,6 +9,7 @@ from param import ParamConcatenation
 from parameter_core import HierarchyError, Parameterizable, adjust_name_for_printing
 
 import logging
+from GPy.core.parameterization.index_operations import ParameterIndexOperationsView
 logger = logging.getLogger("parameters changed meta")
 
 class ParametersChangedMeta(type):
@@ -20,7 +21,7 @@ class ParametersChangedMeta(type):
         self._in_init_ = False
         logger.debug("connecting parameters")
         self._highest_parent_._connect_parameters()
-        self._highest_parent_._notify_parent_change()
+        #self._highest_parent_._notify_parent_change()
         self._highest_parent_._connect_fixes()
         logger.debug("calling parameters changed")
         self.parameters_changed()
@@ -140,6 +141,8 @@ class Parameterized(Parameterizable):
                 self.priors.shift_right(start, param.size)
                 self.constraints.update(param.constraints, self.size)
                 self.priors.update(param.priors, self.size)
+                param._parent_ = self
+                param._parent_index_ = len(self.parameters)
                 self.parameters.append(param)
             else:
                 start = sum(p.size for p in self.parameters[:index])
@@ -147,19 +150,23 @@ class Parameterized(Parameterizable):
                 self.priors.shift_right(start, param.size)
                 self.constraints.update(param.constraints, start)
                 self.priors.update(param.priors, start)
+                param._parent_ = self
+                param._parent_index_ = index if index>=0 else len(self.parameters[:index])
+                for p in self.parameters[index:]:
+                    p._parent_index_ += 1
                 self.parameters.insert(index, param)
 
-            self._notify_parent_change()
             param.add_observer(self, self._pass_through_notify_observers, -np.inf)
 
             parent = self
             while parent is not None:
                 parent.size += param.size
                 parent = parent._parent_
+            self._notify_parent_change()
 
             if not self._in_init_:
-                self._connect_parameters()
+                #self._connect_parameters()
-                self._notify_parent_change()
+                #self._notify_parent_change()
 
                 self._highest_parent_._connect_parameters(ignore_added_names=_ignore_added_names)
                 self._highest_parent_._notify_parent_change()