manual merging

GPy/core/parameterization/array_core.py

@@ -30,12 +30,16 @@ class ObservableArray(np.ndarray, Observable):
     def __new__(cls, input_array):
         obj = np.atleast_1d(input_array).view(cls)
         cls.__name__ = "ObservableArray\n     "
-        obj._observer_callables_ = []
         return obj
+    
+    def __init__(self, *a, **kw):
+        super(ObservableArray, self).__init__(*a, **kw)
+    
     def __array_finalize__(self, obj):
         # see InfoArray.__array_finalize__ for comments
         if obj is None: return
         self._observer_callables_ = getattr(obj, '_observer_callables_', None)
+        
     def __array_wrap__(self, out_arr, context=None):
         return out_arr.view(np.ndarray)
 

GPy/core/parameterization/param.py

@@ -15,7 +15,7 @@ __precision__ = numpy.get_printoptions()['precision'] # numpy printing precision
 __print_threshold__ = 5
 ######
 
-class Param(ObservableArray, Constrainable, Gradcheckable, Indexable, Parentable):
+class Param(Constrainable, ObservableArray, Gradcheckable, Indexable):
     """
     Parameter object for GPy models.
 
@@ -57,8 +57,8 @@ class Param(ObservableArray, Constrainable, Gradcheckable, Indexable, Parentable
         obj._gradient_ = None
         return obj
 
-    def __init__(self, name, input_array, default_constraint=None):
-        super(Param, self).__init__(name=name, default_constraint=default_constraint)
+    def __init__(self, name, input_array, default_constraint=None, *a, **kw):
+        super(Param, self).__init__(name=name, default_constraint=default_constraint, *a, **kw)
 
     def __array_finalize__(self, obj):
         # see InfoArray.__array_finalize__ for comments
@@ -146,6 +146,9 @@ class Param(ObservableArray, Constrainable, Gradcheckable, Indexable, Parentable
     def _collect_gradient(self, target):
         target += self.gradient.flat
 
+    def _set_gradient(self, g):
+        self.gradient = g
+
     #===========================================================================
     # Array operations -> done
     #===========================================================================

GPy/core/parameterization/parameter_core.py

@@ -7,18 +7,23 @@ __updated__ = '2013-12-16'
 
 def adjust_name_for_printing(name):
     if name is not None:
-        return name.replace(" ", "_").replace(".", "_").replace("-","").replace("+","").replace("!","").replace("*","").replace("/","")
+        return name.replace(" ", "_").replace(".", "_").replace("-", "").replace("+", "").replace("!", "").replace("*", "").replace("/", "")
     return ''
 
 class Observable(object):
-    _observer_callables_ = []
-    def add_observer(self, callble):
-        self._observer_callables_.append(callble)
-        #callble(self)
-    def remove_observer(self, callble):
-        del self._observer_callables_[callble]
+    def __init__(self, *args, **kwargs):
+        from collections import defaultdict
+        self._observer_callables_ = defaultdict(list)
+
+    def add_observer(self, observer, callble):
+        self._observer_callables_[observer].append(callble)
+
+    def remove_observer(self, observer, callble):
+        del self._observer_callables_[observer][callble]
+
     def _notify_observers(self):
-        [callble(self) for callble in self._observer_callables_]
+        [[callble(self) for callble in callables]
+         for callables in self._observer_callables_.itervalues()]
 
 class Pickleable(object):
     def _getstate(self):
@@ -47,10 +52,8 @@ class Pickleable(object):
 #===============================================================================
 
 class Parentable(object):
-    def __init__(self, direct_parent=None, parent_index=None):
-        super(Parentable,self).__init__()
-        self._direct_parent_ = direct_parent
-        self._parent_index_ = parent_index
+    _direct_parent_ = None
+    _parent_index_ = None
         
     def has_parent(self):
         return self._direct_parent_ is not None
@@ -73,9 +76,8 @@ class Parentable(object):
             self._direct_parent_._notify_parameters_changed()
 
 class Nameable(Parentable):
-    _name = None
-    def __init__(self, name, direct_parent=None, parent_index=None):
-        super(Nameable,self).__init__(direct_parent, parent_index)
+    def __init__(self, name, *a, **kw):
+        super(Nameable, self).__init__(*a, **kw)
         self._name = name or self.__class__.__name__
 
     @property
@@ -95,108 +97,10 @@ class Nameable(Parentable):
             return self._direct_parent_.hirarchy_name() + "." + adjust(self.name)
         return adjust(self.name)
 
-class Parameterizable(Parentable):
-    def __init__(self, *args, **kwargs):
-        super(Parameterizable, self).__init__(*args, **kwargs)
-        from GPy.core.parameterization.array_core import ParamList
-        _parameters_ = ParamList()
-        self._added_names_ = set()
-    
-    def parameter_names(self, add_self=False, adjust_for_printing=False, recursive=True):
-        if adjust_for_printing: adjust = lambda x: adjust_name_for_printing(x)
-        else: adjust = lambda x: x
-        if recursive: names = [xi for x in self._parameters_ for xi in x.parameter_names(add_self=True, adjust_for_printing=adjust_for_printing)]
-        else: names = [adjust(x.name) for x in self._parameters_]
-        if add_self: names = map(lambda x: adjust(self.name) + "." + x, names)
-        return names
-    
-    def _add_parameter_name(self, param):
-        pname = adjust_name_for_printing(param.name)
-        # and makes sure to not delete programmatically added parameters
-        if pname in self.__dict__:
-            if not (param is self.__dict__[pname]):
-                if pname in self._added_names_:
-                    del self.__dict__[pname]
-                    self._add_parameter_name(param)
-        else:
-            self.__dict__[pname] = param
-            self._added_names_.add(pname)
-            
-    def _remove_parameter_name(self, param=None, pname=None):
-        assert param is None or pname is None, "can only delete either param by name, or the name of a param"
-        pname = adjust_name_for_printing(pname) or adjust_name_for_printing(param.name)
-        if pname in self._added_names_:
-            del self.__dict__[pname]
-            self._added_names_.remove(pname)
-        self._connect_parameters()
-
-    def _name_changed(self, param, old_name):
-        self._remove_parameter_name(None, old_name)
-        self._add_parameter_name(param)
-            
-    def _collect_gradient(self, target):
-        import itertools
-        [p._collect_gradient(target[s]) for p, s in itertools.izip(self._parameters_, self._param_slices_)]
-
-    def _get_params(self):
-        import numpy as np
-        # don't overwrite this anymore!
-        if not self.size:
-            return np.empty(shape=(0,), dtype=np.float64)
-        return np.hstack([x._get_params() for x in self._parameters_ if x.size > 0])
-
-    def _set_params(self, params, update=True):
-        # don't overwrite this anymore!
-        import itertools
-        [p._set_params(params[s], update=update) for p, s in itertools.izip(self._parameters_, self._param_slices_)]
-        self.parameters_changed()
-
-    def copy(self):
-        """Returns a (deep) copy of the current model"""
-        import copy
-        from .index_operations import ParameterIndexOperations, ParameterIndexOperationsView
-        from .array_core import ParamList
-        dc = dict()
-        for k, v in self.__dict__.iteritems():
-            if k not in ['_direct_parent_', '_parameters_', '_parent_index_'] + self.parameter_names():
-                if isinstance(v, (Constrainable, ParameterIndexOperations, ParameterIndexOperationsView)):
-                    dc[k] = v.copy()
-                else:
-                    dc[k] = copy.deepcopy(v)
-            if k == '_parameters_':
-                params = [p.copy() for p in v]
-        #dc = copy.deepcopy(self.__dict__)
-        dc['_direct_parent_'] = None
-        dc['_parent_index_'] = None
-        dc['_parameters_'] = ParamList()
-        s = self.__new__(self.__class__)
-        s.__dict__ = dc
-        #import ipdb;ipdb.set_trace()
-        for p in params:
-            s.add_parameter(p)
-        #dc._notify_parent_change()
-        return s
-        #return copy.deepcopy(self)
-
-    def _notify_parameters_changed(self):
-        self.parameters_changed()
-        if self.has_parent():
-            self._direct_parent_._notify_parameters_changed()
-
-    def parameters_changed(self):
-        """
-        This method gets called when parameters have changed.
-        Another way of listening to param changes is to
-        add self as a listener to the param, such that
-        updates get passed through. See :py:function:``GPy.core.param.Observable.add_observer``
-        """
-        pass
-
 
 class Gradcheckable(Parentable):
-    #===========================================================================
-    # Gradchecking
-    #===========================================================================
+    def __init__(self, *a, **kw):
+        super(Gradcheckable, self).__init__(*a, **kw)
     def checkgrad(self, verbose=0, step=1e-6, tolerance=1e-3):
         if self.has_parent():
             return self._highest_parent_._checkgrad(self, verbose=verbose, step=step, tolerance=tolerance)
@@ -204,6 +108,7 @@ class Gradcheckable(Parentable):
     def _checkgrad(self, param):
         raise NotImplementedError, "Need log likelihood to check gradient against"
 
+
 class Indexable(object):
     def _raveled_index(self):
         raise NotImplementedError, "Need to be able to get the raveled Index"
@@ -222,9 +127,10 @@ class Indexable(object):
         """
         raise NotImplementedError, "shouldnt happen, raveld index transformation required from non parameterization object?"        
         
-class Constrainable(Nameable, Indexable, Parentable):
-    def __init__(self, name, default_constraint=None):
-        super(Constrainable,self).__init__(name)
+
+class Constrainable(Nameable, Indexable):
+    def __init__(self, name, default_constraint=None, *a, **kw):
+        super(Constrainable, self).__init__(name=name, *a, **kw)
         self._default_constraint_ = default_constraint
         from index_operations import ParameterIndexOperations
         self.constraints = ParameterIndexOperations()
@@ -275,7 +181,7 @@ class Constrainable(Nameable, Indexable, Parentable):
     def _set_unfixed(self, index):
         import numpy as np
         if not self._has_fixes(): self._fixes_ = np.ones(self.size, dtype=bool)
-        #rav_i = self._raveled_index_for(param)[index]
+        # rav_i = self._raveled_index_for(param)[index]
         self._fixes_[index] = UNFIXED
         if np.all(self._fixes_): self._fixes_ = None  # ==UNFIXED
 
@@ -305,7 +211,7 @@ class Constrainable(Nameable, Indexable, Parentable):
         """evaluate the prior"""
         if self.priors.size > 0:
             x = self._get_params()
-            return reduce(lambda a,b: a+b, [p.lnpdf(x[ind]).sum() for p, ind in self.priors.iteritems()], 0)
+            return reduce(lambda a, b: a + b, [p.lnpdf(x[ind]).sum() for p, ind in self.priors.iteritems()], 0)
         return 0.
     
     def _log_prior_gradients(self):
@@ -409,7 +315,7 @@ class Constrainable(Nameable, Indexable, Parentable):
         if len(transforms) == 0:
             transforms = which.properties()
         import numpy as np
-        removed = np.empty((0, ), dtype=int)
+        removed = np.empty((0,), dtype=int)
         for t in transforms:
             unconstrained = which.remove(t, self._raveled_index())
             removed = np.union1d(removed, unconstrained)
@@ -419,5 +325,104 @@ class Constrainable(Nameable, Indexable, Parentable):
         return removed
 
 
+class Parameterizable(Constrainable):
+    def __init__(self, *args, **kwargs):
+        super(Parameterizable, self).__init__(*args, **kwargs)
+        from GPy.core.parameterization.array_core import ParamList
+        _parameters_ = ParamList()
+        self._added_names_ = set()
     
+    def parameter_names(self, add_self=False, adjust_for_printing=False, recursive=True):
+        if adjust_for_printing: adjust = lambda x: adjust_name_for_printing(x)
+        else: adjust = lambda x: x
+        if recursive: names = [xi for x in self._parameters_ for xi in x.parameter_names(add_self=True, adjust_for_printing=adjust_for_printing)]
+        else: names = [adjust(x.name) for x in self._parameters_]
+        if add_self: names = map(lambda x: adjust(self.name) + "." + x, names)
+        return names
+    
+    def _add_parameter_name(self, param):
+        pname = adjust_name_for_printing(param.name)
+        # and makes sure to not delete programmatically added parameters
+        if pname in self.__dict__:
+            if not (param is self.__dict__[pname]):
+                if pname in self._added_names_:
+                    del self.__dict__[pname]
+                    self._add_parameter_name(param)
+        else:
+            self.__dict__[pname] = param
+            self._added_names_.add(pname)
+            
+    def _remove_parameter_name(self, param=None, pname=None):
+        assert param is None or pname is None, "can only delete either param by name, or the name of a param"
+        pname = adjust_name_for_printing(pname) or adjust_name_for_printing(param.name)
+        if pname in self._added_names_:
+            del self.__dict__[pname]
+            self._added_names_.remove(pname)
+        self._connect_parameters()
+
+    def _name_changed(self, param, old_name):
+        self._remove_parameter_name(None, old_name)
+        self._add_parameter_name(param)
+            
+    def _collect_gradient(self, target):
+        import itertools
+        [p._collect_gradient(target[s]) for p, s in itertools.izip(self._parameters_, self._param_slices_)]
+
+    def _set_gradient(self, g):
+        import itertools
+        [p._set_gradient(g[s]) for p, s in itertools.izip(self._parameters_, self._param_slices_)]
+
+    def _get_params(self):
+        import numpy as np
+        # don't overwrite this anymore!
+        if not self.size:
+            return np.empty(shape=(0,), dtype=np.float64)
+        return np.hstack([x._get_params() for x in self._parameters_ if x.size > 0])
+
+    def _set_params(self, params, update=True):
+        # don't overwrite this anymore!
+        import itertools
+        [p._set_params(params[s], update=update) for p, s in itertools.izip(self._parameters_, self._param_slices_)]
+        self.parameters_changed()
+
+    def copy(self):
+        """Returns a (deep) copy of the current model"""
+        import copy
+        from .index_operations import ParameterIndexOperations, ParameterIndexOperationsView
+        from .array_core import ParamList
+        dc = dict()
+        for k, v in self.__dict__.iteritems():
+            if k not in ['_direct_parent_', '_parameters_', '_parent_index_'] + self.parameter_names():
+                if isinstance(v, (Constrainable, ParameterIndexOperations, ParameterIndexOperationsView)):
+                    dc[k] = v.copy()
+                else:
+                    dc[k] = copy.deepcopy(v)
+            if k == '_parameters_':
+                params = [p.copy() for p in v]
+        # dc = copy.deepcopy(self.__dict__)
+        dc['_direct_parent_'] = None
+        dc['_parent_index_'] = None
+        dc['_parameters_'] = ParamList()
+        s = self.__new__(self.__class__)
+        s.__dict__ = dc
+        # import ipdb;ipdb.set_trace()
+        for p in params:
+            s.add_parameter(p)
+        # dc._notify_parent_change()
+        return s
+        # return copy.deepcopy(self)
+
+    def _notify_parameters_changed(self):
+        self.parameters_changed()
+        if self.has_parent():
+            self._direct_parent_._notify_parameters_changed()
+
+    def parameters_changed(self):
+        """
+        This method gets called when parameters have changed.
+        Another way of listening to param changes is to
+        add self as a listener to the param, such that
+        updates get passed through. See :py:function:``GPy.core.param.Observable.add_observer``
+        """
+        pass
 

GPy/core/parameterization/parameterized.py

@@ -7,11 +7,11 @@ import cPickle
 import itertools
 from re import compile, _pattern_type
 from param import ParamConcatenation
-from parameter_core import Constrainable, Pickleable, Observable, Parameterizable, Parentable, adjust_name_for_printing, Gradcheckable
+from parameter_core import Constrainable, Pickleable, Parentable, Observable, Parameterizable, adjust_name_for_printing, Gradcheckable
 from transformations import __fixed__
 from array_core import ParamList
 
-class Parameterized(Constrainable, Pickleable, Observable, Gradcheckable, Parameterizable, Parentable):
+class Parameterized(Parameterizable, Pickleable, Observable, Gradcheckable):
     """
     Parameterized class
 
@@ -53,8 +53,8 @@ class Parameterized(Constrainable, Pickleable, Observable, Gradcheckable, Parame
         If you want to operate on all parameters use m[''] to wildcard select all paramters
         and concatenate them. Printing m[''] will result in printing of all parameters in detail.
     """
-    def __init__(self, name=None):
-        super(Parameterized, self).__init__(name=name)
+    def __init__(self, name=None, *a, **kw):
+        super(Parameterized, self).__init__(name=name, parent=None, parent_index=None, *a, **kw)
         self._in_init_ = True
         self._parameters_ = ParamList()
         self.size = sum(p.size for p in self._parameters_)

GPy/kern/_src/kern.py

@@ -9,7 +9,7 @@ from ...core.parameterization.param import Param
 
 
 class Kern(Parameterized):
-    def __init__(self, input_dim, name):
+    def __init__(self, input_dim, name, *a, **kw):
         """
         The base class for a kernel: a positive definite function
         which forms of a covariance function (kernel).
@@ -19,7 +19,7 @@ class Kern(Parameterized):
 
         Do not instantiate.
         """
-        super(Kern, self).__init__(name)
+        super(Kern, self).__init__(name=name, *a, **kw)
         self.input_dim = input_dim
 
     def K(self, X, X2):

GPy/kern/_src/linear.py

@@ -9,7 +9,7 @@ from ...util.linalg import tdot
 from ...util.misc import fast_array_equal, param_to_array
 from ...core.parameterization import Param
 from ...core.parameterization.transformations import Logexp
-from ...util.caching import Cacher, cache_this
+from ...util.caching import cache_this
 
 class Linear(Kern):
     """

GPy/models/bayesian_gplvm.py

@@ -36,7 +36,7 @@ class BayesianGPLVM(SparseGP, GPLVM):
         assert Z.shape[1] == X.shape[1]
 
         if kernel is None:
-            kernel = kern.rbf(input_dim) # + kern.white(input_dim)
+            kernel = kern.RBF(input_dim) # + kern.white(input_dim)
         
         if likelihood is None:
             likelihood = Gaussian()

GPy/util/caching.py

@@ -12,7 +12,7 @@ class Cacher(object):
     def __call__(self, *args):
         if self._reset_on_first:
             assert isinstance(args[0], Observable)
-            args[0].add_observer(self.reset)
+            args[0].add_observer(self, self.reset)
             cached_args = args
         else:
             cached_args = args[1:]
@@ -29,21 +29,21 @@ class Cacher(object):
         else:
             if len(self.cached_inputs) == self.limit:
                 args_ = self.cached_inputs.pop(0)
-                [a.remove_observer(self.on_cache_changed) for a in args_]
+                [a.remove_observer(self, self.on_cache_changed) for a in args_]
                 self.inputs_changed.pop(0)
                 self.cached_outputs.pop(0)
 
             self.cached_inputs.append(cached_args)
             self.cached_outputs.append(self.operation(*args))
             self.inputs_changed.append(False)
-            [a.add_observer(self.on_cache_changed) for a in args]
+            [a.add_observer(self, self.on_cache_changed) for a in args]
             return self.cached_outputs[-1]
 
     def on_cache_changed(self, arg):
         self.inputs_changed = [any([a is arg for a in args]) or old_ic for args, old_ic in zip(self.cached_inputs, self.inputs_changed)]
 
     def reset(self, obj):
-        [[a.remove_observer(self.reset) for a in args] for args in self.cached_inputs]
+        [[a.remove_observer(self, self.reset) for a in args] for args in self.cached_inputs]
         self.cached_inputs = []
         self.cached_outputs = []
         self.inputs_changed = []